Publications by authors named "Michael Bender"

69 Publications

Protein and glycan molecular weight determination of highly glycosylated HIV-1 envelope trimers by HPSEC-MALS.

Vaccine 2021 Jun 28;39(28):3650-3654. Epub 2021 May 28.

Vaccine Production Program Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Disease, United States. Electronic address:

High Performance Size-Exclusion Chromatography coupled with Multi-Angle Light Scattering detection (HPSEC-MALS) is an important tool to provide a reliable molecular weight measurement for a large complex biomolecule. A recent HIV-1 soluble envelope trimer vaccine candidate, BG505 DS-SOSIP.664, is among the most glycosylated proteins to enter a clinical trial to date, and determination of its protein and glycan molecular weight is one of the key attributes in pre-clinical characterization. However, protein and glycans possess disparate dndcvalues making molecular weight measurement inaccurate in conventional SEC-MALS. To overcome these challenges, a simple mathematically guided experiment was explored, and a composite dndcvalue was established by utilizing protein and glycan mass contributions for the HIV-1 envelope trimer. This establishment was further verified by an orthogonal mass spectrometry analysis. This innovative, simple, and quick analytical approach can be applied broadly to measuring the molecular weight of various composite molecular structures, such as complex glycoconjugates.
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http://dx.doi.org/10.1016/j.vaccine.2021.05.048DOI Listing
June 2021

The Occurrence of Ophidiomyces ophiodiicola in Northern Georgia Wild and Captive Snake Populations.

J Wildl Dis 2021 May 12. Epub 2021 May 12.

University of North Georgia, 82 College Circle, Dahlonega, Georgia 30597, USA.

Ophidiomycosis, or snake fungal disease, is an emerging wildlife disease caused by the Ophidiomyces ophiodiicola fungus. The fungus can result in high mortality rates among infected snakes and has been documented across much of the eastern US, including southern Georgia. However, little is known about ophidiomycosis in northern Georgia. We surveyed wild snake populations in five counties of northern Georgia between March 2019 and March 2020 and swabbed captured snakes (n=27) for the presence of O. ophiodiicola DNA. We followed similar sampling protocols with a group of captive snakes (n=6) at the Elachee Nature Center in Hall County, Georgia. Quantitative PCR confirmed the presence of O. ophiodiicola DNA in 33% (11/33) of snakes. Eight of the confirmed positive samples were collected from wild snakes (30%, 8/27) across our sample region, while three were from our captive group (50%, 3/6). Our results indicated that O. ophiodiicola is present in wild snake populations in northern Georgia, and the pathogen is present in seemingly healthy captive snakes. This knowledge is critical for conservation and management efforts, but more research is needed to fully understand ophidiomycosis and its effect on snake populations in the region.
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http://dx.doi.org/10.7589/JWD-D-20-00129DOI Listing
May 2021

Job crafting mediates the relation between creativity, personality, job autonomy and well-being in Lebanese nurses.

J Nurs Manag 2021 May 6. Epub 2021 May 6.

Department of Developmental Psychology, Tilburg University, Tilburg, The Netherlands.

Aim: To better understand the functionality of job crafting and its relationship with personality and job autonomy in the context of non-Western health care as an adaptive problem-solving work behaviour that is related to creativity.

Background: Job crafting could be a strategy nurses use to solve problems as health care organisations become more unpredictable.

Methods: This cross-sectional study sampled 547 nurses from seven hospitals in Lebanon. Data were analysed using structural equation modelling (SEM).

Results: The job crafting dimensions of increasing structural job resources and increasing challenging job demands partially mediated the relationship between creativity and subjective well-being, and they fully mediated the relationship between job autonomy and subjective well-being. Creativity, job autonomy, and agreeableness were related to the approach job crafting dimensions, and two of these job crafting dimensions were in turn related to subjective well-being.

Conclusion: Creative nurses tend to job craft more and this is associated with their subjective well-being. Nurses high on extraversion and emotional stability experienced higher subjective well-being.

Implications For Nursing Management: Nursing administration and leaders may want to create an environment fostering creativity and encouraging approach-oriented job crafting.
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http://dx.doi.org/10.1111/jonm.13357DOI Listing
May 2021

Comparison of Huggins Coefficients and Osmotic Second Virial Coefficients of Buffered Solutions of Monoclonal Antibodies.

Polymers (Basel) 2021 02 17;13(4). Epub 2021 Feb 17.

Materials Science and Engineering Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA.

The Huggins coefficient is a well-known metric for quantifying the increase in solution viscosity arising from intermolecular interactions in relatively dilute macromolecular solutions, and there has been much interest in this solution property in connection with developing improved antibody therapeutics. While numerous measurements have been reported for select monoclonal antibodies (mAbs) solutions, there has been limited study of in terms of the fundamental molecular interactions that determine this property. In this paper, we compare measurements of the osmotic second virial coefficient , a common metric of intermolecular and interparticle interaction strength, to measurements of for model antibody solutions. This comparison is motivated by the seminal work of Russel for hard sphere particles having a short-range "sticky" interparticle interaction, and we also compare our data with known results for uncharged flexible polymers having variable excluded volume interactions because proteins are polypeptide chains. Our observations indicate that neither the adhesive hard sphere model, a common colloidal model of globular proteins, nor the familiar uncharged flexible polymer model, an excellent model of intrinsically disordered proteins, describes the dependence of of these antibodies on . Clearly, an improved understanding of protein and ion solvation by water as well as dipole-dipole and charge-dipole effects is required to understand the significance of from the standpoint of fundamental protein-protein interactions. Despite shortcomings in our theoretical understanding of for antibody solutions, this quantity provides a useful practical measure of the strength of interprotein interactions at elevated protein concentrations that is of direct significance for the development of antibody formulations that minimize the solution viscosity.
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http://dx.doi.org/10.3390/polym13040601DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7922252PMC
February 2021

Registered Report: Testing Ideological Asymmetries in Measurement Invariance.

Assessment 2021 04 29;28(3):687-708. Epub 2021 Jan 29.

Tilburg University, Tilburg, Netherlands.

People with different ideological identities differ in their values, personality, affect, and psychological motivations. These differences are observed on measures of practical and clinical importance and these differences are the central node tying together theories about the psychology of political ideology; however, they rest on a critical untested assumption: The measures are invariant across ideological groups. Here, we test this assumption across 28 constructs in data from the United States and the Netherlands. Measures are not invariant across ideological divisions. At the same time, estimates of ideological similarities and differences are largely similar before and after correcting for measurement noninvariance. This may give us increased confidence in the results from this research area, while simultaneously highlighting that some instance of noninvariance did change conclusions and that individual items are not always comparable across political groups.
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http://dx.doi.org/10.1177/1073191120983891DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7961747PMC
April 2021

Unraveling Two Pathways for Electrochemical Alcohol and Aldehyde Oxidation on NiOOH.

J Am Chem Soc 2020 12 15;142(51):21538-21547. Epub 2020 Dec 15.

Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.

Selective oxidation of alcohols to their corresponding aldehyde or carboxylic acid is one of the most important classes of organic synthesis reactions. In addition, electrochemical alcohol oxidation is considered a viable anode reaction that can be paired with H evolution or other reductive fuel production reactions in electrochemical and photoelectrochemical cells. NiOOH, a material that has been extensively studied as an oxygen evolution catalyst, is among the most promising electrocatalysts for selective alcohol oxidation. Electrochemical alcohol oxidation by NiOOH has been understood since the 1970s to proceed through a hydrogen atom transfer to NiOOH. In this study, we establish that there is a second, more dominant general alcohol oxidation pathway on NiOOH enabled at more positive potentials. Using a three-step electrochemical procedure we developed, we deconvoluted the currents corresponding to these two pathways for various alcohols and aldehydes. The results show that alcohols and aldehydes have a distinct difference in their respective preferences for the two oxidation pathways. Our three-step electrochemical procedure also allowed us to evaluate the Ni valence involved with the different oxidation pathways to elucidate their mechanistic differences. Using these experimental results coupled with a computational investigation, we propose that the new pathway entails hydride transfer from the substrate to Ni sites in NiOOH. This study offers an essential foundation to understand various oxidative electrochemical dehydrogenation reactions on oxide and hydroxide-based catalytic electrodes.
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http://dx.doi.org/10.1021/jacs.0c10924DOI Listing
December 2020

Individual and societal risk factors of attitudes justifying intimate partner violence against women: a multilevel cross-sectional study.

BMJ Open 2020 12 10;10(12):e037993. Epub 2020 Dec 10.

Methodology for Behavioral Sciences, University of Granada, Granada, Spain.

Objectives: Attitudes justifying intimate partner violence against women (IPVAW) can play an essential role in explaining the prevalence of such public health problem. The study aim was to explain attitudes justifying IPVAW identifying individual and societal risk factors.

Design And Setting: A multilevel cross-sectional study of the World Values Survey (WVS) in 54 global countries.

Participants: A representative transnational community-based sample of 81 516 participants (47.8% male, 52.1% female), aged mean of 42.41.

Measures: Attitudes justifying IPVAW, sociodemographic, sexism, self-transcendence and conservation values were measured using questions from WVS. Country and regional gender inequality were assessed by Gender Inequality Index.

Results: Around 16% (intraclass correlation=0.16) of individual differences in attitudes justifying IPVAW are explained by countries. Statistically significant predictors at individual and country level were: sex (B=-0.24, 95% CI -0.27 to -0.22), age (B=-0.08 to -0.25, 95% CI -0.34 to -0.03), marital status (B=0.09 to 0.23, 95% CI 0.002 to 0.33), educational level (B=-0.10 to -0.14, 95% CI -0.20 to -0.04), self-transcendence values (B=-0.10, 95% CI -0.20 to -0.12), sexism (B=0.21, 95% CI 0.15 to 0.28), country (B=2.18, 95% CI 1.09 to 3.26) and regional (B=2.23, 95% CI 1.04 to 3.42) gender inequality. Country gender inequality (B=-0.18, p=0.12) and regional gender inequality (B=-0.21, p=0.10) did not moderate the associations between self-transcendence values and attitudes justifying IPVAW. In the same way for sexism, data did not provide support for a moderating role of country gender inequality (B=0.22, p=0.26) and regional gender inequality (B=0.10, p=0.66).

Conclusions: Individual and country predictors accounted for differences in attitudes justifying IPVAW. However, neither gender inequality of country nor gender inequality of region interacted with sexism and self-transcendence values. Theoretical and methodological implications are discussed.
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http://dx.doi.org/10.1136/bmjopen-2020-037993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7733202PMC
December 2020

Early Serum Biomarkers for Intensive Care Unit Treatment within the First 24 Hours in Patients with Intracerebral Hemorrhage.

J Neurol Surg A Cent Eur Neurosurg 2021 Mar 8;82(2):138-146. Epub 2020 Dec 8.

Department of Neurosurgery, Universitätsklinikum Giessen und Marburg Standort Giessen, Giessen, Germany.

Background:  The prognostic significance of serum biomarkers in patients with intracerebral hemorrhage (ICH) is not well investigated concerning inhospital mortality (IHM) and cardiopulmonary events within the first 24 hours of intensive care unit (ICU) treatment. The influence of troponin I (TNI) value and cortisol value (CV) on cardiopulmonary events within the first 24 hours of ICU treatment was reported in subarachnoid hemorrhage patients, but not in ICH patients up to now. The aim of this study was to investigate the role of early serum biomarkers on IHM and TNI value and CV on cardiopulmonary events within the first 24 hours of ICU treatment.

Patients And Methods:  A total of 329 patients with spontaneous ICH were retrospectively analyzed. Blood samples were taken on admission to measure serum biomarkers. The TNI value and CV were defined as biomarkers for cardiopulmonary stress. Demographic data, cardiopulmonary parameters, including norepinephrine application rate (NAR) in microgram per kilogram per minute and inspiratory oxygen fraction (FiO) within the first 24 hours, and treatment regime were analyzed concerning their impact on ICU treatment and in hospital outcome. Binary logistic analysis was used to identify independent prognostic factors for IHM.

Results:  Patients with initially nonelevated CVs required higher NAR ( = 0.01) and FiO ( = 0.046) within the first 24 hours of ICU treatment. Lower cholinesterase level ( = 0.004), higher NAR ( = 0.002), advanced age ( < 0.0001), larger ICH volume ( < 0.0001), presence of intraventricular hemorrhage ( = 0.007) and hydrocephalus ( = 0.009), raised level of C-reactive protein ( = 0.024), serum lactate ( = 0.003), and blood glucose ( = 0.05) on admission were significantly associated with IHM. In a multivariate model, age (odds ratio [OR]: 1.055; 95% confidence interval [CI]: 1.026-1.085;  < 0.0001), ICH volume (OR: 1.016; CI: 1.008-1.025;  < 0.0001), and Glasgow Coma Scale (GCS) score (OR: 0.680; CI: 0.605-0.764;  < 0.0001) on admission as well as requiring NAR (OR: 1.171; CI: 1.026-1.337;  = 0.02) and FiO (OR: 0.951; CI: 0.921-0.983,  = 0.003) within the first 24 hours were independent predictors of IHM.

Conclusion:  Higher levels of C-reactive protein, serum lactate, blood glucose, and lower cholinesterase level on admission were significantly associated with IHM. Patients with initially nonelevated CVs required higher NAR and FiO within the first 24 hours of ICU treatment. Furthermore, requiring an NAR > 0.5 µg/kg/min or an FiO > 0.21 were identified as additional independent predictors for IHM. These results could be helpful to improve ICU treatment in ICH patients.
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http://dx.doi.org/10.1055/s-0040-1716516DOI Listing
March 2021

Alcohol oxidation as alternative anode reactions paired with (photo)electrochemical fuel production reactions.

Nat Commun 2020 09 14;11(1):4594. Epub 2020 Sep 14.

Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.

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http://dx.doi.org/10.1038/s41467-020-18461-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7490346PMC
September 2020

The Association Between Threat and Politics Depends on the Type of Threat, the Political Domain, and the Country.

Pers Soc Psychol Bull 2021 02 26;47(2):324-343. Epub 2020 Aug 26.

Tilburg University, The Netherlands.

Theories link threat with right-wing political beliefs. We use the World Values Survey (60,378 participants) to explore how six types of threat (e.g., economic, violence, and surveillance) are associated with multiple political beliefs (e.g., cultural, economic, and ideological identification) in 56 countries/territories. Multilevel models with individuals nested in countries revealed that the threat-political belief association depends on the type of threat, the type of political belief, and the country. Economic-related threats tended to be associated with more left-wing economic political beliefs and violence-related threats tended to be associated with more cultural right-wing beliefs, but there were exceptions to this pattern. Additional analyses revealed that the associations between threat and political beliefs were different across countries. However, our analyses identified few country characteristics that could account for these cross-country differences. Our findings revealed that political beliefs and perceptions of threat are linked, but that the relationship is not simple.
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http://dx.doi.org/10.1177/0146167220946187DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7859575PMC
February 2021

The Predictive Value of Transcutaneous Electrical Nerve Stimulation for Patient Selection in Peripheral Nerve Field Stimulation for Chronic Low Back Pain: A Prospective Study.

Neuromodulation 2020 Aug 5. Epub 2020 Aug 5.

Department of Neurosurgery, Justus-Liebig-University Giessen, Giessen, Germany.

Objective: Peripheral nerve field stimulation (PNFS) is an effective alternative treatment for patients with chronic low back pain. Transcutaneous electrical nerve stimulation (TENS) is frequently used in pain therapy. Aim of this prospective study was to examine the predictive value of TENS for later PNFS treatment.

Materials And Methods: Between 2014 and 2019, a prospective cohort study of 41 patients with chronic lumbar pain was conducted. Pain intensity (NRS) was assessed before and after TENS use, preoperatively/postoperatively and in the follow-up after three and six months, SF12v2 questionnaires with physical (PCS) and mental component summary (MCS) scores, and Oswestry disability index (ODI) questionnaire at baseline as well as three and six months after PNFS implantation. Implantation of the PNFS-system with two percutaneous leads was performed after four to seven days of positive testing. Statistical analysis was performed using depending t-test, ANOVA, and Spearman correlation.

Results: The cohort consisted of 41 patients (19 females, 22 males) with a median age of 60.5 years (IQR 52-67). Two patients were lost to follow-up. After positive PNFS testing a pulse generator (IPG) was implanted in 15 patients with positive TENS effect and 15 patients without TENS effect. Leads were explanted in nine patients after negative PNFS trial phase. TENS positive patients showed significant correlation to a positive effect in the PNFS trial phase in NRS reduction (p = 0.042) indicating that TENS responders will also respond to PNFS (94% patients). After three and six months follow-up median NRS and SF12v2 (PCS) improved significantly in both cohorts, SF12v2 (MCS) and ODI only in the TENS positive cohort, respectively.

Conclusion: TENS can be predictive for patient selection in PNFS, as TENS positive patients showed significant correlation with a positive PNFS trial period. Therefore, TENS positive patients might be justifiable to be directly implanted with leads and IPG. TENS positive patients further tend to show a better improvement in the follow-up.
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http://dx.doi.org/10.1111/ner.13244DOI Listing
August 2020

Impact of Early C-Reactive Protein/Albumin Ratio on Intra-Hospital Mortality Among Patients with Spontaneous Intracerebral Hemorrhage.

J Clin Med 2020 Apr 24;9(4). Epub 2020 Apr 24.

Department of Neurosurgery, Justus-Liebig-University Gießen, Klinikstraße 33, 35392 Gießen, Germany.

Objective: The impact of increased C-reactive protein (CRP)/albumin ratio on intra-hospital mortality has been investigated among patients admitted to general intensive care units (ICU). However, it was not investigated among patients with spontaneous intracerebral hemorrhage (ICH). This study aimed to investigate the impact of CRP/albumin ratio on intra-hospital mortality in patients with ICH.

Patients And Methods: This retrospective study was conducted on 379 ICH patients admitted between 02/2008 and 12/2017. Blood samples were drawn upon admission and the patients' demographic, medical, and radiological data were collected. The identification of the independent prognostic factors for intra-hospital mortality was calculated using binary logistic regression and COX regression analysis.

Results: Multivariate regression analysis shows that higher CRP/albumin ratio (odds ratio (OR) = 1.66, 95% confidence interval (CI) = 1.193-2.317, = 0.003) upon admission is an independent predictor of intra-hospital mortality. Multivariate Cox regression analysis indicated that an increase of 1 in the CRP/albumin ratio was associated with a 15.3% increase in the risk of intra-hospital mortality (hazard ratio = 1.153, 95% CI = 1.005-1.322, = 0.42). Furthermore, a CRP/albumin ratio cut-off value greater than 1.22 was associated with increased intra-hospital mortality (Youden's Index = 0.19, sensitivity = 28.8, specificity = 89.9, = 0.007).

Conclusions: A CRP/albumin ratio greater than 1.22 upon admission was significantly associated with intra-hospital mortality in the ICH patients.
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http://dx.doi.org/10.3390/jcm9041236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7230407PMC
April 2020

Transcranial Doppler Sonography Defined Vasospasm, Ischemic Brain Lesions, and Delayed Ischemic Neurological Deficit in Younger and Elderly Patients after Aneurysmal Subarachnoid Hemorrhage.

World Neurosurg 2020 06 17;138:e718-e724. Epub 2020 Mar 17.

Department of Neurosurgery, Justus-Liebig-University Gießen, Gießen, Germany.

Background: Vasospasm, delayed ischemic neurologic deficit (DIND), and ischemic brain lesions after acute subarachnoid hemorrhage (SAH) are associated with increased morbidity and mortality. The purpose of this study was to analyze age cutoffs for vasospasm, DIND, and ischemic brain lesions after SAH.

Methods: This study included 292 aneurysmal SAH patients from January 2005 to December 2015. Patients' data were extracted from a prospective database with measurements of transcranial Doppler sonography. Any vasospasm was defined as a maximum mean flow velocity (MMFV) >120 cm/sec. Severe vasospasms were defined as at least 2 measurements of MMFVs >200 cm/sec or an increase of MMFV >50 cm/sec/24 hours over 2 consecutive days or a new neurologic deficit. All MMFVs >120 cm/sec in absence of severe vasospasm criteria were defined as mild vasospasm. Age-related cutoff values were calculated using receiver operating curve analysis.

Results: Any vasospasms occurred in 142 patients and thereof mild vasospasm in 86/142 (60.6%) patients and severe vasospasm in 56/142 patients (39.4%). Significantly higher incidences of any vasospasm (P = 0.005), severe vasospasm (P = 0.003), DIND (P = 0.031), and ischemic brain lesions (P = 0.04) were observed in patients aged <50 years. According to receiver operating curve analysis, the optimal age cutoff was 50 years for the presence of overall vasospasms, severe vasospasms, DIND, and ischemic brain lesions and 65 years for mild vasospasms.

Conclusions: Higher incidences of any vasospasms, severe vasospasms, DIND, and ischemic brain lesions were observed in younger SAH patients.
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http://dx.doi.org/10.1016/j.wneu.2020.03.051DOI Listing
June 2020

Outcomes of total shoulder arthroplasty for instability arthropathy with a prior coracoid transfer procedure: a retrospective review and matched cohort.

J Shoulder Elbow Surg 2020 Jul 4;29(7):1316-1322. Epub 2020 Mar 4.

Texas Education and Research Foundation for Shoulder and Elbow Surgery, Houston, TX, USA; Texas Orthopedic Hospital, Houston, TX, USA; Fondren Orthopedic Group, Houston, TX, USA.

Background: Many surgeons are concerned about reports of increased complications, worse outcomes, and early failures in patients undergoing anatomic total shoulder arthroplasty after coracoid transfer. The purpose of this study was to evaluate minimum 2-year outcomes following anatomic total shoulder arthroplasty for instability arthropathy with a prior coracoid transfer procedure and compare them with a matched cohort of patients undergoing total shoulder arthroplasty for primary osteoarthritis.

Methods: We identified 11 primary anatomic total shoulder arthroplasties performed by a single surgeon for instability arthropathy with a prior coracoid transfer procedure with a minimum of 2 years' follow-up (mean, 58 ± 35 months). A matched cohort of 33 patients with a total shoulder arthroplasty for primary osteoarthritis served as the control group. The American Shoulder and Elbow Surgeons (ASES) score, Single Assessment Numeric Evaluation (SANE) score, patient satisfaction, complications, and revisions were evaluated in both cohorts.

Results: The coracoid transfer cohort showed no difference in the final ASES score (88 vs. 82, P = .166) or SANE score (85 vs. 67, P = .120) vs. the matched cohort. The postoperative ASES pain score (45 vs. 41, P = .004) was higher in the coracoid transfer cohort, but the mean improvement from preoperative to postoperative values for the ASES score (P = .954), ASES pain score (P = .183), and SANE score (P = .293) was no different between cohorts. Both cohorts had high patient satisfaction without a statistically significant difference (P = .784).

Conclusion: At early- to mid-term follow-up, total shoulder arthroplasty performed after a coracoid transfer demonstrated similar results to total shoulder arthroplasty performed for primary osteoarthritis. Longer follow-up and larger patient cohorts will provide further insights and highlight any potential differences in outcomes or revision rates.
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http://dx.doi.org/10.1016/j.jse.2019.12.009DOI Listing
July 2020

Programmable valve breakage in shunt systems of children with posthemorrhagic hydrocephalus after minor head trauma-a case series.

Childs Nerv Syst 2020 09 20;36(9):2027-2031. Epub 2020 Feb 20.

Department of Neurosurgery, Justus-Liebig-University Giessen, Klinikstrasse 33, 35392, Giessen, Germany.

Purpose: We report five rare cases of programmable valve breakage (Codman Hakim-Medos valve) in shunt systems of children with posthemorrhagic hydrocephalus. Only four similar studies have been published in the current literature.

Methods: Between 2013 and 2018, five children with posthemorrhagic hydrocephalus were admitted to the pediatric department. All patients had a history of slight blows to the head in a minor trauma and follow up MRI scans. After initial clinical examination, cranial computed tomography (CT) and X-ray were conducted.

Results: In all cases, pumping the reservoir resulted in very slow refilling. The cranial CT in one patient showed slit ventricles confirming the suspicion of overdrainage, the other cases a slight enhancement of the hydrocephalus. In lateral X-rays of the skull in comparison to the first X-ray control of the shunt valve, the pressure control chamber could be seen dislocated in the inferior part of the reservoir in all cases. Surgery revealed that the shunt valve was broken. The pressure control chamber had dropped to the bottom of the reservoir. After implantation of a new shunt valve, the symptoms resolved completely in all five children. Overall this complication occurred in 4.3% (5 of 85 implanted Codman Hakim-Medos valve) of all children necessitating ventriculoperitoneal shunt implantation between January 2013 and December 2018.

Conclusion: The well-accepted Codman Hakim-Medos programmable valve is part of a tube-system, which is designed to offer the possibility of a reliable and precise treatment of hydrocephalus. Various mechanical and non-mechanical complications of shunt systems have been reported. Valve breakage is a very rare condition, often missed, and must be kept in mind when trauma and prior MRI scan are reported.
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http://dx.doi.org/10.1007/s00381-020-04541-6DOI Listing
September 2020

Troponin I as an early biomarker of cardiopulmonary parameters during the first 24 h of intensive care unit treatment in isolated traumatic brain injury patients.

Injury 2020 May 7;51(5):1189-1195. Epub 2020 Jan 7.

Department of Neurosurgery, Justus-Liebig-University Giessen, Klinikstrasse 33, Giessen 35392, Germany.

Objective: Cardiopulmonary (CP) complications are well-known phenomena after an isolated traumatic brain injury (iTBI) and they may be associated with an elevated serum troponin I (TnI) value. However, the influence of an elevated TnI level on CP parameters within the first 24 h after an iTBI is still unknown. The current study was conducted to assess the associations between the initial TnI value on admission and CP parameters during the first 24 h of intensive care unit (ICU) treatment in iTBI patients.

Patients And Methods: A total of 288 patients with iTBIs, who were admitted to our emergency department between January 2010 and November 2016 were retrospectively analyzed. Blood samples were taken on admission to determine TnI value. Each patient's demographic data, treatment regime, computed tomography results, and intra-hospital outcomes were evaluated, as well as several CP parameters, within the first 24 h of ICU treatment. The entire study population was stratified into patients with an initial TnI elevation (TnI positive) and without an initial TnI elevation (TnI negative).

Results: Increased TnI values on admission were found in 59 (20.5%) patients. There were significant correlations between an initially elevated TnI value and a lower Glasgow Coma Scale score (p = 0.003), higher head Abbreviated Injury Scale score (p<0.0001), and higher Acute Physiology and Chronic Health Evaluation II score (p = 0.005) on admission, as well as a lower Glasgow Outcome Scale score (p = 0.0002) and higher modified Rankin Scale score (p = 0.0001) at discharge. In addition, a significantly higher norepinephrine application rate (NAR) (p<0.0001) and inspiratory oxygen fraction (FiO2) (p = 0.028) were needed in the TnI positive group.

Conclusion: Patients with elevated TnI values on admission require more circulation support (NAR and FiO2) within the first 24 h of ICU treatment after an iTBI. Therefore, the TnI may be a useful biomarker to improve ICU treatment of these patients.
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http://dx.doi.org/10.1016/j.injury.2020.01.002DOI Listing
May 2020

[National Learning Objectives Catalogue in Surgery - General Part Defining Competences of Medical School Graduates in Surgery].

Zentralbl Chir 2019 Dec 16;144(6):573-579. Epub 2019 Dec 16.

Gründungsdekanat, Medizinische Fakultät der Universität Augsburg, Deutschland.

Competency-based medical education is needed in order to meet the requirements of medical care currently and in the future. The basis of this are activity-based learning objectives that are merged in competency-based catalogues. A basis for a core curriculum of undergraduate medical training is the National Catalogue of Learning Objectives for Undergraduate Medical Education (NKLM). Already in 2013, for surgery, the competencies which medical students should have achieved after completing the practical year (PJ) in relation to surgical diseases were defined in the special part of the National Catalogue of Learning Objectives in Surgery (NKLC). In the now amended general part of the NKLC, interdisciplinary competencies were defined and consented from all surgical disciplines, that are relevant for all surgical disciplines and that all representatives from the different surgical disciplines should incorporate in their surgical training. The complete NKLC is now available for faculties, teachers and students for trial (available online: https://www.dgch.de/index.php?id=190&L=528). The guiding principle for the entire development process was to make sure that students gain all competencies they need when starting to work as a medical doctor and therefor to increase patient safety.
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http://dx.doi.org/10.1055/a-1033-7769DOI Listing
December 2019

Serum Biomarkers for Risk Assessment of Intrahospital Transports in Mechanically Ventilated Neurosurgical Intensive Care Unit Patients.

J Intensive Care Med 2021 Apr 28;36(4):419-427. Epub 2019 Nov 28.

Department of Neurosurgery, 9175Justus-Liebig-University Gießen, Germany.

Objective: Intrahospital transports (IHTs) of neurosurgical intensive care unit (NICU) patients can be hazardous. Increasing intracranial pressure (ICP) and/or decreasing cerebral perfusion pressure (CPP) as well as cardiopulmonary alterations are common complications of an IHTs, which can lead to secondary brain injury. This study was performed to assess several serum biomarkers concerning their potential to improve safety of IHTs in mechanically ventilated NICU patients.

Methods: All IHTs of mechanically ventilated and sedated NICU patients from 03/2017 to 01/2018 were retrospectively analyzed. Intracranial pressure and CPP measurements were performed in all patients. Serum hemoglobin, hematocrit, and serum sodium were defined as serum biomarkers. Demographic data, computed tomography scan on admission, Simplified Acute Physiology Score and Acute Physiology and Chronic Health Evaluation II, modified Rankin Scale, indication and consequence of IHTs were analyzed. Alteration of ICP/CPP, hemodynamic and pulmonary events were defined as complications. The study population was stratified into patients with the occurrence of a complication and absence of a complication.

Results: We analyzed a total number of 184 IHTs in 70 NICU patients with an overall complication rate of 57.6%. Of all, 32.1% IHTs had no direct therapeutic consequence. In patients with higher hemoglobin values prior to IHT less complications occurred, concerning ICP ( = .001), CPP ( = .001), hemodynamic ( = .005), and pulmonary ( < .0001) events. In addition, complications concerning ICP ( = .001), CPP ( = .001), hemodynamic ( = .005), and pulmonary problems ( = .002) were significantly lower in patients with higher hematocrit values before IHT.

Conclusion: Intrahospital transports of mechanically ventilated NICU patients carry a high risk of increased ICP and hemodynamic complications and should be performed restrictively. Higher values of hemoglobin and hematocrit prior to IHT were associated with less complications with regard to ICP, CPP as well as hemodynamic and pulmonary events and could be helpful to assess the potential risk of complications prior to IHTs.
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http://dx.doi.org/10.1177/0885066619891063DOI Listing
April 2021

Two-million-year-old snapshots of atmospheric gases from Antarctic ice.

Nature 2019 10 30;574(7780):663-666. Epub 2019 Oct 30.

Department of Geosciences, Princeton University, Princeton, NJ, USA.

Over the past eight hundred thousand years, glacial-interglacial cycles oscillated with a period of one hundred thousand years ('100k world'). Ice core and ocean sediment data have shown that atmospheric carbon dioxide, Antarctic temperature, deep ocean temperature, and global ice volume correlated strongly with each other in the 100k world. Between about 2.8 and 1.2 million years ago, glacial cycles were smaller in magnitude and shorter in duration ('40k world'). Proxy data from deep-sea sediments suggest that the variability of atmospheric carbon dioxide in the 40k world was also lower than in the 100k world, but we do not have direct observations of atmospheric greenhouse gases from this period. Here we report the recovery of stratigraphically discontinuous ice more than two million years old from the Allan Hills Blue Ice Area, East Antarctica. Concentrations of carbon dioxide and methane in ice core samples older than two million years have been altered by respiration, but some younger samples are pristine. The recovered ice cores extend direct observations of atmospheric carbon dioxide, methane, and Antarctic temperature (based on the deuterium/hydrogen isotope ratio δD, a proxy for regional temperature) into the 40k world. All climate properties before eight hundred thousand years ago fall within the envelope of observations from continuous deep Antarctic ice cores that characterize the 100k world. However, the lowest measured carbon dioxide and methane concentrations and Antarctic temperature in the 40k world are well above glacial values from the past eight hundred thousand years. Our results confirm that the amplitudes of glacial-interglacial variations in atmospheric greenhouse gases and Antarctic climate were reduced in the 40k world, and that the transition from the 40k to the 100k world was accompanied by a decline in minimum carbon dioxide concentrations during glacial maxima.
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http://dx.doi.org/10.1038/s41586-019-1692-3DOI Listing
October 2019

Implementation of Transforaminal Endoscopic Lumbar Sequestrectomy in a German University Hospital Setting: A Long and Rocky Road.

J Neurol Surg A Cent Eur Neurosurg 2020 Jan 29;81(1):17-27. Epub 2019 Aug 29.

Department of Neurosurgery, Universitatsklinikum Giessen und Marburg, Giessen, Germany.

Objective:  Microsurgical diskectomy/sequestrectomy is the standard procedure for the surgical treatment of lumbar disk herniations. The transforaminal endoscopic sequestrectomy technique is a minimally invasive alternative with potential advantages such as minimal blood loss and tissue damage, as well as early mobilization of the patient. We report the implementation of this technique in a German university hospital setting.

Methods:  One single surgeon performed transforaminal endoscopic sequestrectomy from February 2013 to July 2016 for lumbar disk herniation in 44 patients. Demographic as well as perioperative, clinical, and radiologic data were analyzed from electronic records. Furthermore, we investigated complications, intraoperative change of the procedure to microsurgery, and reoperations. The postoperative course was analyzed using the Macnab criteria, supplemented by a questionnaire for follow-up. Pre- and postoperative magnetic resonance imaging volumetric analyses were performed to assess the radiologic efficacy of the technique.

Results:  Our study population had a median age of 52 years. The median follow-up was 15 months, and the median length of hospital stay was 4 days. Median duration of surgery was 100 minutes with a median blood loss of 50 mL. Surgery was most commonly performed at the L4-L5 level (63%) and in caudally migrated disk herniations (44%). In six patients, surgery was performed for recurrent disk herniations. The procedure had to be changed to conventional microsurgery in four patients. We observed no major complications. Minor complications occurred in six patients, and in four patients a reoperation was performed. Furthermore, a significantly lower Oswestry Disability Index score ( = 0.03), a lower Short Form 8 Health Survey (SF-8) score ( = 0.001), a lower visual analog scale (VAS) lower back pain score ( = 0.03) and VAS leg pain score ( = 0.0008) at the 12-month follow-up were observed in comparison with the preoperative examination. In MRI volumetry, we detected a median postoperative volume reduction of the disk herniation of 57.1% ( = 0.02).

Conclusions:  The transforaminal endoscopic sequestrectomy can be safely implemented in a university hospital setting in selected patients with primary and recurrent lumbar disk herniations, and it leads to good clinical and radiologic results. However, learning curve, caseload, and residents' microsurgical training requirements clearly affect the implementation process.
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http://dx.doi.org/10.1055/s-0039-1694040DOI Listing
January 2020

Autobiographical recall of mastery experiences is a mechanism of self-affirming under social identity threat.

J Soc Psychol 2020 17;160(1):39-60. Epub 2019 May 17.

American University of Beirut.

Autobiographical memories are relevant to many areas of psychological functioning. So far, however, there is no evidence whether personal memories can also be instrumental for self-affirmation. We conducted two experiments, varying national identity threat among U.S. Americans recruited through MTurk. In Study 1, participants spontaneously recalled autobiographical memories after being exposed to varying levels of threat. When the threat was identity-relevant, those who spontaneously recalled mastery autobiographical memories had higher collective self-esteem than those who did not. In Study 2, we instructed participants to recall either mastery autobiographical memories or routine memories. When the threat was identity-relevant, collective self-esteem was again higher for mastery recall compared to routine recall, moderated by national identification and self-esteem. We also found a general, self-affirmative effect of autobiographical memories, regardless of threat relevance or recall content. Findings provide a first empirical demonstration that autobiographical recall can enhance self-affirmation in identity threat situations.
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http://dx.doi.org/10.1080/00224545.2019.1606775DOI Listing
October 2020

Serum Cortisol as an Early Biomarker of Cardiopulmonary Parameters Within the First 24 Hours After Aneurysmal Subarachnoid Hemorrhage in Intensive Care Unit Patients.

J Intensive Care Med 2020 Nov 26;35(11):1173-1179. Epub 2019 Mar 26.

Department of Neurosurgery, Bremen-Mitte Hospital, Bremen, Germany.

Objective: Cardiopulmonary complications/stress are well-known phenomena in patients after aneurysmal subarachnoid hemorrhage (aSAH) and might be associated with an elevated serum troponin I (TNI) level. Since the glucocorticoid hormone cortisol is released during stress situations, the present study was conducted to investigate the influence of serum cortisol (SC) on cardiac and pulmonary parameters in patients after aSAH within the first 24 hours of intensive care unit (ICU) treatment.

Patients And Methods: We retrospectively analyzed a cohort of 104 patients with aSAH admitted to our emergency department between January 2008 and April 2017. Blood samples were taken to determine SC and TNI. Demographics, initial Glasgow Coma Scale (GCS) score, World Federation of Neurosurgical Societies (WFNS) score, and Fisher grade were evaluated retrospectively. Mean norepinephrine application rate (NAR) in µg/kg/min and mean inspiratory oxygen fraction (OF) within the first 24 hours were defined as cardiopulmonary parameters.

Results: An elevated SC value was found in 44 (42%) patients, and 27 (26%) patients showed an increased TNI value. In patients with initially increased SC value, a significant higher NAR ( = .04) was needed. Furthermore, patients with initially elevated TNI value had a lower GCS score ( = .0013) and a higher WFNS score ( = .003) on admission and required a higher NAR ( = .02) as well as OF ( = .0008) within the first 24 hours of ICU treatment.

Conclusions: In the current study, initially elevated SC values were associated with a higher need of NAR within the first 24 hours of ICU treatment after aSAH. Moreover, patients with initially elevated TNI values required an increased NAR and a higher OF so that these biomarkers could be useful to improve ICU treatment.
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http://dx.doi.org/10.1177/0885066619837910DOI Listing
November 2020

Placement of External Ventricular Drain: Comparison of Two Methods.

J Neurol Surg A Cent Eur Neurosurg 2019 Mar 1;80(2):116-121. Epub 2019 Feb 1.

Department of Neurosurgery, Bremen-Mitte Hospital, Bremen, Germany.

Background:  Insertion of a frontal external ventricular drain (EVD) is a common emergency procedure in neurosurgery. Malpositioning of the EVD and/or triggering a new intracerebral or intraventricular hemorrhage (nICVH) are typical complications. The standard procedure (SP) uses a tape measure to identify the Kocher's point for placement of a frontal burr hole. A faster alternative to determine the correct position is the freehand technique (FHT). This study compared both techniques with regard to the correct positioning of the EVD tip and the induction catheter-induced nICVH.

Methods:  We performed a retrospective analysis of patients who required an EVD for acute or chronic hydrocephalus between January 2013 and March 2014. The study consisted of two groups. In the first group, EVDs were placed with the FHT. In the second group the SP was used. Postoperative computed tomography scans were analyzed regarding correct positioning of the ventricular catheter, malpositioning of the tip of the EVD using a 4-point-scale, and evidence for catheter-induced nICVH.

Results:  A total of 95 patients could be included. The FHT was performed in 43 cases and the SP in 52 cases. No significant differences between the two groups were found regarding the correct position of the EVD tip ( = 0.38) and nICVH ( = 0.12). There was no significant difference in malpositioning of the EVD tip between the groups ( = 0.34).

Conclusion:  Our results show no significant differences between the two methods with regard to correct position, malpositioning, and nICVH. Thus we conclude that the FHT is a fast, safe, and effective alternative to the SP.
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http://dx.doi.org/10.1055/s-0038-1676576DOI Listing
March 2019

Troponin I as an Early Biomarker of Cardiopulmonary Parameters Within the First 24 Hours After Nontraumatic Subarachnoid Hemorrhage in Intensive Care Unit Patients.

J Intensive Care Med 2020 Dec 8;35(12):1368-1373. Epub 2019 Jan 8.

Department of Neurosurgery, Bremen-Mitte Hospital, Bremen, Germany.

Objective: The elevation of serum cardiac troponin I (TNI) in patients with nontraumatic subarachnoid hemorrhage (ntSAH) is a well-known phenomenon. However, the relation between elevated TNI and different cardiopulmonary parameters (CPs) within the first 24 hours after ntSAH is unknown. The present study was conducted to investigate the association between TNI and different CP in patients with ntSAH within the first 24 hours of intensive care unit (ICU) treatment.

Patients And Methods: We retrospectively analyzed a consecutive group of 117 patients with ntSAH admitted to our emergency department between January 2008 and February 2017. Blood samples were taken to determine TNI values on admission. Demographic data, baseline Glasgow Coma Scale (GCS) score, World Federation of Neurosurgical Societies (WFNS) score, baseline Fisher grade (FG), norepinephrine application rate (NAR) in µg/kg/min, and inspiratory oxygen fraction (OF) were recorded within the first 24 hours.

Results: An increased TNI value was found in 32 (27.4%) of 117 patients. There was a significant correlation between initial elevated TNI and a low WFNS score ( = .007), a low GCS score ( = .003) as well as a high OF ( = <.001). The FG ( = .27) and NAR ( = .08) within the first 24 hours of ICU treatment did not show any significant correlation.

Conclusions: In the present study, an increased TNI value was significantly associated with a low WFNS score and GCS score on admission. The TNI was a predictor of the need for a higher OF within the first 24 hours after ntSAH so that TNI could be an informative biomarker to improve ICU therapy.
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http://dx.doi.org/10.1177/0885066618824568DOI Listing
December 2020

Overcoming the Multiple-Monomeric-Peak Profile of Broadly Neutralizing HIV-1 Antibody 10E8 with a Unique Size-Exclusion-Chromatography Method.

Anal Chem 2018 11 22;90(21):12390-12394. Epub 2018 Oct 22.

Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Gaithersburg , Maryland 20878 , United States.

10E8 is a potent broadly neutralizing antibody (bNAb) that targets the membrane-proximal external region (MPER) of the HIV virus. During early analytical development of this bNAb directed towards clinical evaluation, 10E8 exhibited a multiple-monomeric-peak profile caused by secondary interactions in traditional size-exclusion chromatography (SEC), thereby rendering SEC unfit for the purpose of assessing aggregation, a target critical quality attribute. To overcome this challenge, an innovative and robust SEC method was successfully developed in which the mobile phase was tested for excipients capable of reducing the secondary interactions responsible for the multipeak profile, and an optimal mobile phase composed of 2× PBS and 100 mM arginine at pH 10.55 was established. Application of this optimized mobile phase was shown to allow quantification of the intrinsic level of aggregation of 10E8 without alteration to the SEC matrix itself. Furthermore, the newly developed method was linear, specific, accurate, and precise over an established range. Overall, an SEC method involving optimization of the mobile phase has been successfully developed, which allowed for assessment of antibody aggregation throughout process development, manufacturing, release, and stability testing.
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http://dx.doi.org/10.1021/acs.analchem.8b03594DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7727924PMC
November 2018

Implicit motives and basic psychological needs.

J Pers 2019 02 8;87(1):37-55. Epub 2018 Oct 8.

Department I - Psychology, University of Trier, Trier, Germany.

The present article starts with discussing similarities and differences between conceptualizations of human needs in self-determination theory (SDT; Deci & Ryan [1985], Intrinsic motivation and self-determination in human behavior; Deci & Ryan [2000], Nebraska symposium on motivation: Perspectives on motivation) and motive disposition theory (MDT; McClelland, Human motivation, 1985). The second section focuses on the two-process model of psychological needs (Sheldon [2011], Psychological Review, 118: 552), which aims to integrate the two approaches, whereas the third section highlights some aspects of both theories that are still decoupled or even contradictory, but nevertheless still have a high potential to be linked. These three aspects are (a) the noncorresponding concepts of implicit power motive (MDT) and basic need for autonomy (SDT); (b) the differentiation of needs into hope and fear components, which is theoretically embedded in MDT, but not in SDT; and (c) MDT researchers' differentiation into an implicit and explicit motivational system, which is not included in SDT. Particularly, the last section highlights the potential for areas in which further integration is possible, which provides a foundation for comprehensive and exciting research on human motivation.
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http://dx.doi.org/10.1111/jopy.12431DOI Listing
February 2019

Synthesis, Characterization, and Nanomaterials Generated from 6,6'-(((2-Hydroxyethyl)azanediyl)bis(methylene))bis(2,4-di- tert-butylphenol) Modified Group 4 Metal Alkoxides.

Inorg Chem 2018 Sep 21;57(17):11264-11274. Epub 2018 Aug 21.

Department of Chemistry , College of the Holy Cross , Box C, 1 College Street , Worcester , Massachusetts 01610 , United States.

The impact on the morphology nanoceramic materials generated from group 4 metal alkoxides ([M(OR)]) and the same precursors modified by 6,6'-(((2-hydroxyethyl)azanediyl)bis(methylene))bis(2,4-di- tert-butylphenol) (referred to as H-AM-DBP (1)) was explored. The products isolated from the 1:1 stoichiometric reaction of a series of [M(OR)] where M = Ti, Zr, or Hf; OR = OCH(CH)(OPr ); OC(CH)(OBu ); OCHC(CH)(ONep) with H-AM-DBP proved, by single crystal X-ray diffraction, to be [(ONep)Ti( k( O,O',O'',N)-AM-DBP)] (2), [(OR)M(μ( O)- k( O',O'',N)-AM-DBP)] [M = Zr: OR = OPr , 3·tol; OBu , 4·tol; ONep, 5·tol; M = Hf: OR = OBu , 6·tol; ONep, 7·tol]. The product from each system led to a tetradentate AM-DBP ligand and retention of a parent alkoxide ligand. For the monomeric Ti derivative (2), the metal was solved in a trigonal bipyramidal geometry, whereas for the Zr (3-5) and Hf (6, 7) derivatives a symmetric dinuclear complex was formed where the ethoxide moiety of the AM-DBP ligand bridges to the other metal center, generating an octahedral geometry. High quality density functional theory level gas-phase electronic structure calculations on compounds 2-7 using Gaussian 09 were used for meaningful time dependent density functional theory calculations in the interpretation of the UV-vis absorbance spectral data on 2-7. Nanoparticles generated from the solvothermal treatment of the ONep/AM-DBP modified compounds (2, 5, 7) in comparison to their parent [M(ONep)] were larger and had improved regularity and dispersion of the final ceramic nanomaterials.
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http://dx.doi.org/10.1021/acs.inorgchem.8b01907DOI Listing
September 2018

The immediate and 1-week effects of mid-thoracic thrust manipulation on lower extremity passive range of motion.

Physiother Theory Pract 2020 Jun 17;36(6):720-730. Epub 2018 Jul 17.

Healthcare Partners , Torrance, CA, USA.

Background: Research suggests that spinal manipulation may effect motion. Less clear is whether this effect is limited to localized responses or may involve generalizable changes. : To determine whether Mid-thoracic manipulation (MTM) would result in a significant change in the lower extremity passive straight leg raise (PSLR) range of motion immediately and after 1 week. : Twenty-three healthy subjects were randomly assigned in a double-blinded study. An experimental group received MTM and a control group received a sham intervention. PSLR measurements were taken prior to, immediately after, and one week after the intervention. : Mixed model repeated measure analysis of variance was used to determine that there was a significant interaction between MTM and time ((2, 21) = 3.84,  < 0.05). Post hoc tests revealed a significant difference between the pretest to immediate posttest values ( < 0.05, SE = 1.47). PSLR in the MTM group increased 10.3° while the sham group increased 1.9°. Difference was non-significant between pretest and 1-week follow-up ( = 0.129, SE = 2.46). : MTM may immediately increase lower extremity passive range of motion, but the effect was lost by the 1-week follow-up. This supports evolving research suggesting that spinal manipulation may have a generalized but transient physiological effect.
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http://dx.doi.org/10.1080/09593985.2018.1492056DOI Listing
June 2020

Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index.

Cell Syst 2018 08 20;7(2):201-207.e4. Epub 2018 Jun 20.

Computer Science Department, Stony Brook University, 100 Nicolls Rd, Stony Brook, NY 11794, USA. Electronic address:

Sequence-level searches on large collections of RNA sequencing experiments, such as the NCBI Sequence Read Archive (SRA), would enable one to ask many questions about the expression or variation of a given transcript in a population. Existing approaches, such as the sequence Bloom tree, suffer from fundamental limitations of the Bloom filter, resulting in slow build and query times, less-than-optimal space usage, and potentially large numbers of false-positives. This paper introduces Mantis, a space-efficient system that uses new data structures to index thousands of raw-read experiments and facilitates large-scale sequence searches. In our evaluation, index construction with Mantis is 6× faster and yields a 20% smaller index than the state-of-the-art split sequence Bloom tree (SSBT). For queries, Mantis is 6-108× faster than SSBT and has no false-positives or -negatives. For example, Mantis was able to search for all 200,400 known human transcripts in an index of 2,652 RNA sequencing experiments in 82 min; SSBT took close to 4 days.
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http://dx.doi.org/10.1016/j.cels.2018.05.021DOI Listing
August 2018

Measurement of Gross Photosynthesis, Respiration in the Light, and Mesophyll Conductance Using HO Labeling.

Plant Physiol 2018 05 27;177(1):62-74. Epub 2018 Mar 27.

Department of Geosciences, Princeton University, Princeton, New Jersey 08544.

A fundamental challenge in plant physiology is independently determining the rates of gross O production by photosynthesis and O consumption by respiration, photorespiration, and other processes. Previous studies on isolated chloroplasts or leaves have separately constrained net and gross O production (NOP and GOP, respectively) by labeling ambient O with O while leaf water was unlabeled. Here, we describe a method to accurately measure GOP and NOP of whole detached leaves in a cuvette as a routine gas-exchange measurement. The petiole is immersed in water enriched to a δO of ∼9,000‰, and leaf water is labeled through the transpiration stream. Photosynthesis transfers O from HO to O GOP is calculated from the increase in δO of O as air passes through the cuvette. NOP is determined from the increase in O/N Both terms are measured by isotope ratio mass spectrometry. CO assimilation and other standard gas-exchange parameters also were measured. Reproducible measurements are made on a single leaf for more than 15 h. We used this method to measure the light response curve of NOP and GOP in French bean () at 21% and 2% O We then used these data to examine the O/CO ratio of net photosynthesis, the light response curve of mesophyll conductance, and the apparent inhibition of respiration in the light (Kok effect) at both oxygen levels. The results are discussed in the context of evaluating the technique as a tool to study and understand leaf physiological traits.
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http://dx.doi.org/10.1104/pp.16.00741DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5933133PMC
May 2018