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Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs.

Syst Biol 2021 Jul 10. Epub 2021 Jul 10.

Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA.

Many recent phylogenetic methods have focused on accurately inferring species trees when there is gene tree discordance due to incomplete lineage sorting (ILS). For almost all of these methods, and for phylogenetic methods in general, the data for each locus is assumed to consist of orthologous, single-copy sequences. Loci that are present in more than a single copy in any of the studied genomes are excluded from the data. Read More

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A Digital Gaming Intervention to Improve HIV Testing for Adolescents and Young Adults: Protocol for Development and a Pilot Randomized Controlled Trial.

JMIR Res Protoc 2021 Jun 24;10(6):e29792. Epub 2021 Jun 24.

Media Rez, Washington, DC, United States.

Background: Two strategies of the US Ending the HIV Epidemic initiative are early diagnosis of infections via widespread testing and prevention of new infections using pre-exposure prophylaxis (PrEP). These strategies are particularly important for adolescents and young adults (AYAs) who are disproportionately affected by HIV, particularly if they identify as Black and/or lesbian, gay, bisexual, transgender, queer or questioning, and others (LGBTQ+). This study will develop and test an interactive life-simulation game in which players can enact real-life behaviors and receive their HIV risk profile to improve HIV testing and PrEP access among AYAs aged 13-24 years in Washington, DC. Read More

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A genetically encoded anti-CRISPR protein constrains gene drive spread and prevents population suppression.

Nat Commun 2021 06 25;12(1):3977. Epub 2021 Jun 25.

Department of Life Sciences, Imperial College London, London, UK.

CRISPR-based gene drives offer promising means to reduce the burden of pests and vector-borne diseases. These techniques consist of releasing genetically modified organisms carrying CRISPR-Cas nucleases designed to bias their inheritance and rapidly propagate desired modifications. Gene drives can be intended to reduce reproductive capacity of harmful insects or spread anti-pathogen effectors through wild populations, even when these confer fitness disadvantages. Read More

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Exploring the lubrication mechanisms of synovial fluids for joint longevity - A perspective.

Colloids Surf B Biointerfaces 2021 Jun 16;206:111926. Epub 2021 Jun 16.

Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Santiago, Chile. Electronic address:

Synovial fluids are complex fluids responsible for the exceptional lubrication present in synovial joints. These fluids consist of various constituents, including hyaluronic acid, surface-active proteins (i.e. Read More

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Lampenflora in a Show Cave in the Great Basin Is Distinct from Communities on Naturally Lit Rock Surfaces in Nearby Wild Caves.

Microorganisms 2021 May 31;9(6). Epub 2021 May 31.

Department of Biology & M.L. Bean Museum of Life Science, Brigham Young University, Provo, UT 84602, USA.

In show caves, artificial lighting is intended to illuminate striking cave formations for visitors. However, artificial lighting also promotes the growth of novel and diverse biofilm communities, termed lampenflora, that obtain their energy from these artificial light sources. Lampenflora, which generally consist of cyanobacteria, algae, diatoms, and bryophytes, discolor formations and introduce novel ecological interactions in cave ecosystems. Read More

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Nanostructural Arrangements and Surface Morphology on Ureasil-Polyether Films Loaded with Dexamethasone Acetate.

Nanomaterials (Basel) 2021 May 21;11(6). Epub 2021 May 21.

Department of Applied Mechanics and Project Engineering, University of Castilla-La Mancha, Plaza Manuel Meca 1, 13400 Almadén, Spain.

Ureasil-Poly(ethylene oxide) (ureasil-PEO500) and ureasil-Poly(propylene oxide) (u-PPO400) films, unloaded and loaded with dexamethasone acetate (DMA), have been investigated by carrying out atomic force microscopy (AFM), ultrasonic force microscopy (UFM), contact-angle, and drug release experiments. In addition, X-ray diffraction, small angle X-ray scattering, and infrared spectroscopy have provided essential information to understand the films' structural organization. Our results reveal that while in u-PEO500 DMA occupies sites near the ether oxygen and remains absent from the film surface, in u-PPO400 new crystalline phases are formed when DMA is loaded, which show up as ~30-100 nm in diameter rounded clusters aligned along a well-defined direction, presumably related to the one defined by the characteristic polymer ropes distinguished on the surface of the unloaded u-POP film; occasionally, larger needle-shaped DMA crystals are also observed. Read More

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Management After Windstorm Affects the Composition of Ectomycorrhizal Symbionts of Regenerating Trees but Not Their Mycorrhizal Networks.

Front Plant Sci 2021 14;12:641232. Epub 2021 May 14.

Department of Carbon Storage in the Landscape, Global Change Research Institute of the Czech Academy of Sciences, České Budějovice, Czechia.

Due to ongoing climate change, forests are expected to face significant disturbances more frequently than in the past. Appropriate management is intended to facilitate forest regeneration. Because European temperate forests mostly consist of trees associated with ectomycorrhizal (ECM) fungi, understanding their role in these disturbances is important to develop strategies to minimize their consequences and effectively restore forests. Read More

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[Crisis intervention for serious mental disorders. The example of the First Department of Psychiatry of Athens University].

Psychiatriki 2021 Jul 28;32(2):157-164. Epub 2021 May 28.

First Department of Psychiatry, Medical School, National and Kapodestrian University of Athens, Eginition Hospital, Athens, Greece.

We describe the crisis management and resolution service for serious mental disorders established by the First Department of Psychiatry of the National and Kapodistrian University of Athens. The service is intended to meet patients' needs for adequate management of acute mental crisis without hospitalization, while implementing modern standards in mental care and considering existing restrictions in mental health resources and public expenditure. Last decade we witness an increase in demand for psychiatric beds in Psychiatric clinics of General Hospitals resulting in a drastic increase of auxiliary beds that becomes a serious problem in mental health provision. Read More

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Towards catch-up therapy: evaluation of nucleophilic active pharmaceutical ingredients for the treatment of percutaneous VX poisoning, in-vial and in-vitro studies.

Int J Pharm 2021 Jun 7;603:120689. Epub 2021 May 7.

Department of Organic Chemistry, IIBR - Israel Institute for Biological Research, P.O. Box 19, Ness Ziona 7410001, Israel. Electronic address:

Dermal exposure to low volatility organophosphorus chemical warfare agents (OP CWA) poses a great risk to the exposed person. Due to their lipophilic nature, these compounds rapidly absorb into the skin, leading to the formation of a "dermal reservoir" from which they slowly enter the bloodstream causing prolonged intoxication. Traditionally, strategies to counter the toxicity of such substances consist of chemical decontamination/physical removal of the residual agent from the skin surface (preferably as soon as possible following the exposure) and administration of antidotes in the case of intoxication signs. Read More

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Randomized Controlled Trials 5: Biomarkers and Surrogates/Outcomes.

Methods Mol Biol 2021 ;2249:261-280

Department of Medicine, Faculty of Medicine, Memorial University of Newfoundland, St John's, NL, Canada.

Biomarkers are characteristics that are measured as indicators of normal biological processes, pathogenic processes, or responses to an exposure or intervention, including therapeutic interventions. Biomarkers may serve a number of important uses, particularly in diagnosis and prognosis of disease, and as surrogates for clinical outcomes of disease (i.e. Read More

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Fab-Nanolipoprotein Conjugate Causes Vitreous Opacity and Cataracts Following a Single Intravitreal Administration in New Zealand White Rabbits.

Toxicol Pathol 2021 04 2;49(3):647-655. Epub 2020 Dec 2.

7412Genentech Inc, Protein Chemistry, South San Francisco, CA, USA.

One strategy employed to prolong the ocular half-life of large molecule therapeutics is via covalent attachment to a carrier, resulting in an increase in size thereby slowing their clearance from the eye. Rabbit antigen-binding fragment conjugated to nanolipoprotein (RabFab-NLP) is a novel conjugate intended to prolong ocular half-life through an increase in hydrodynamic radius compared to Fab alone (∼12 vs ∼3 nm). Nanolipoproteins are mimetics of endogenous high-density lipoproteins and consist of lipids and apolipoproteins (ApoE422k), both biologically derived materials. Read More

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Latest advances to enhance the therapeutic potential of mesenchymal stromal cells for the treatment of immune-mediated diseases.

Drug Deliv Transl Res 2021 Apr 25;11(2):498-514. Epub 2021 Feb 25.

NanoBioCel Research Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006, Vitoria-Gasteiz, Spain.

Mesenchymal stromal cells (MSCs) present the capacity to secrete multiple immunomodulatory factors in response to their microenvironment. This property grants them a golden status among the novel alternatives to treat multiple diseases in which there is an unneeded or exaggerated immune response. However, important challenges still make difficult the clinical implementation of MSC-based therapies, being one of the most remarkable the lack of efficacy due to their transient immunomodulatory effects. Read More

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Multidisciplinary discovery of ancient restoration using a rare mud carapace on a mummified individual from late New Kingdom Egypt.

PLoS One 2021 3;16(2):e0245247. Epub 2021 Feb 3.

Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia.

CT scans of an unnamed mummified adult from Egypt, now in the Chau Chak Wing Museum, University of Sydney (NMR.27.3), reveal it to be fully sheathed in a mud shell or carapace, exposing a mortuary treatment not previously documented in the Egyptian archaeological record. Read More

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Trustable Environmental Monitoring by Means of Sensors Networks on Swarming Autonomous Marine Vessels and Distributed Ledger Technology.

Front Robot AI 2020 28;7:70. Epub 2020 May 28.

M2M Economy, Inc. ("Merklebot"), San Francisco, CA, United States.

The article describes a highly trustable environmental monitoring system employing a small scalable swarm of small-sized marine vessels equipped with compact sensors and intended for the monitoring of water resources and infrastructures. The technological foundation of the process which guarantees that any third party can not alter the samples taken by the robot swarm is based on the Robonomics platform. This platform provides encrypted decentralized technologies based on distributed ledger tools, and market mechanisms for organizing the work of heterogeneous multi-vendor cyber-physical systems when automated economical transactions are needed. Read More

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Modelling and efficiency evaluation of the continuous biosorption of Cu(II) and Cr(VI) from water by agricultural waste materials.

J Environ Manage 2021 Mar 5;281:111876. Epub 2021 Jan 5.

University of Novi Sad, Faculty of Technology Novi Sad, Bulevar Cara Lazara 1, 21 000, Novi Sad, Serbia.

As a result of intensive anthropogenic activities, population growth and unplanned urbanization, enormous quantities of organic and inorganic pollutants are discharged into the environment every year. The primary hazardous substances of concern regarding their environmental load and health effects are heavy metals. Heavy metal pollution of aquatic ecosystems, including resources of drinking water and water intended for food processing, has been of increasing interest. Read More

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Relative Efficacy and Safety of Pharmacotherapeutic Interventions for Diabetic Peripheral Neuropathy: A Systematic Review and Bayesian Network Meta-Analysis.

Pain Physician 2021 01;24(1):E1-E14

Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research, SAS Nagar (Mohali).

Background: Diabetic peripheral neuropathy (DPN) is a most common devitalizing complication of diabetes mellitus, which is primarily characterized by sensory loss, paresthesia, prickling, pain, or allodynia.

Objectives: To evaluate the relative efficacy and safety of the interventions used in the DPN pain management and rank their order.

Study Design: A systematic review and Bayesian network meta-analysis (NMA). Read More

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January 2021

Correlation of Pediatric Palliative Screening Scale and Quality of Life in Pediatric Cancer Patients.

Indian J Palliat Care 2020 Jul-Sep;26(3):338-341. Epub 2020 Aug 29.

Pediatric Nurse, Cipto Mangunkusumo Hospital, Jakarta, Indonesia.

Context: Palliative care in children is used to be only intended for those in near end-of-life phase. Ideally, palliative intervention should be given since the first time of cancer diagnosis. Palliative care is introduced from the beginning of the treatment by acknowledging that it helps to ensure an ongoing focus on the quality of life (QOL) so that children still can enjoy their life. Read More

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Effect of PARACT (PARAmedical Interventions on Patient ACTivation) on the Cancer Care Pathway: Protocol for Implementation of the Patient Activation Measure-13 Item (PAM-13) Version.

JMIR Res Protoc 2020 Dec 8;9(12):e17485. Epub 2020 Dec 8.

Centre Hygée, University of Saint-Etienne, University of Lyon, Saint-Priest-en-Jarez, France.

Background: The increase in the number of cancer cases and the evolution of cancer care management have become a significant problem for the French health care system, thereby making patient empowerment as a long sought-after goal in chronic pathologies. The implementation of an activation measure via the Patient Activation Measure-13 item (PAM-13) in the course of cancer care can potentially highlight the patient's needs, with nursing care adapting accordingly.

Objective: The objectives of this PARACT (PARAmedical Interventions on Patient ACTivation) multicentric study were as follows: (1) evaluate the implementation of PAM-13 in oncology nursing practices in 5 comprehensive cancer centers, (2) identify the obstacles and facilitators to the implementation of PAM-13, and (3) produce recommendations for the dissemination of such interventions in other comprehensive cancer centers. Read More

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December 2020

Mites, ticks, anaphylaxis and allergy: The Acari hypothesis.

Med Hypotheses 2020 Nov 10;144:110257. Epub 2020 Sep 10.

Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.

Anaphylaxis is a poorly understood immune process in which a Th2-/IgE-mediated adaptive response commandeers cellular machinery, typically reserved for defense against multicellular ectoparasites, to activate against otherwise benign molecules. Its clinical manifestations consist of rapid pathophysiological reflexes that target epithelial surfaces. The galactose-α-1,3-galactose hypersensitivity response is a compelling model of anaphylaxis for which causation has been demonstrated. Read More

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November 2020

Evaluating chemical similarity as a measure to identify potential substances of very high concern.

Regul Toxicol Pharmacol 2021 Feb 20;119:104834. Epub 2020 Nov 20.

National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720BA, Bilthoven, the Netherlands; Institute of Environmental Sciences (CML), Leiden University, P. O. Box 9518, 2300RA, Leiden, the Netherlands.

Due to the large amount of chemical substances on the market, fast and reproducible screening is essential to prioritize chemicals for further evaluation according to highest concern. We here evaluate the performance of structural similarity models that are developed to identify potential substances of very high concern (SVHC) based on structural similarity to known SVHCs. These models were developed following a systematic analysis of the performance of 112 different similarity measures for varying SVHC-subgroups. Read More

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February 2021

Protocol for a multicentre, prospective cohort study of clinical, proteomic and genomic patterns associated with osteoporosis to develop a multidimensional fracture assessment tool: the PoCOsteo Study.

BMJ Open 2020 09 30;10(9):e035363. Epub 2020 Sep 30.

Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran (the Islamic Republic of)

Introduction: The HORIZON 2020 project PoCOsteo aims (1) to develop a multidimensional fracture risk assessment tool which would take into account all factors known to be related to an individual's fracture risk. The fracture risk model is intended to be developed in two different populations, namely a European and a Middle Eastern one; (2) to develop a medical device, which would measure and/or quantify proteomic as well as genomic factors as present in whole blood samples collected through finger prick; (3) to test the clinical applicability and the validity of prototypes of the to be developed point of care device at both clinical centres.

Methods And Analysis: This article presents the protocol of this prospective cohort that will be carried out independently at two different centres (Division of Endocrinology and Diabetology at the Medical University of Graz (MUG) as a clinic-based cohort, and Endocrinology and Metabolism Research Institute (EMRI) at the Tehran University of Medical Sciences (TUMS) as a population-based cohort). Read More

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September 2020

Advances on the Valorisation and Functionalization of By-Products and Wastes from Cereal-Based Processing Industry.

Foods 2020 Sep 5;9(9). Epub 2020 Sep 5.

REQUIMTE-Chemistry and Technology Network, Green Chemistry Laboratory (LAQV), Department of Chemistry and Biochemistry, Faculty of Sciences-University of Porto (FCUP), Rua do Campo Alegre, s/n., P-4169-007 Porto, Portugal.

Cereals have been one of the major food resources for human diets and animal feed for thousands of years, and a large quantity of by-products is generated throughout the entire processing food chain, from farm to fork. These by-products mostly consist of the germ and outer layers (bran) derived from dry and wet milling of the grains, of the brewers' spent grain generated in the brewing industry, or comprise other types obtained from the breadmaking and starch production industries. Cereal processing by-products are an excellent low-cost source of various compounds such as dietary fibres, proteins, carbohydrates and sugars, minerals and antioxidants (such as polyphenols and vitamins), among others. Read More

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September 2020

CellML 2.0.

J Integr Bioinform 2020 Jul 24;17(2-3). Epub 2020 Jul 24.

University of Auckland, Auckland, New Zealand.

We present here CellML 2.0, an XML-based language for describing and exchanging mathematical models of physiological systems. MathML embedded in CellML documents is used to define the underlying mathematics of models. Read More

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Qualitative and Quantitative Analysis of Definitions of e-Health and m-Health.

Healthc Inform Res 2020 Apr 30;26(2):119-128. Epub 2020 Apr 30.

EitiCol Networks, Jönköping, Sweden.

Objectives: Skills to employ nursing informatics to promote the health of individuals is of such importance that it is considered a core competence. Although investments are made to increase the use of e-health, there is no full understanding of the usability of e-health for healthcare. This paper presents a current picture of how e-health and m-health are defined and used as well as the effects their usage may have on the intended target group. Read More

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Association of rs610604 in TNFAIP3 and rs17728338 in TNIP1 gene polymorphisms with psoriasis susceptibility: a meta-analysis of case-control studies.

BMC Med Genet 2020 05 12;21(1):103. Epub 2020 May 12.

Department of Dermatology, Shanghai Xuhui Central Hospital, Shanghai, 200031, China.

Background: To date, the fundamental pathophysiology underlying the occurrence and progression of psoriasis are still unanswered questions. Genome-wide association surveys have revealed that TNFAIP3 and TNIP1 were key biomarkers for psoriasis. Here, we intended to conduct a survey on the association between TNFAIP3 and TNIP1 gene polymorphisms and psoriasis risk. Read More

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Effects of the ACT OUT! Social Issue Theater Program on Social-Emotional Competence and Bullying in Youth and Adolescents: Protocol for a Cluster Randomized Controlled Trial.

JMIR Res Protoc 2020 Apr 13;9(4):e17900. Epub 2020 Apr 13.

Biostatistics Consulting Center, School of Public Health, Indiana University Bloomington, Bloomington, IN, United States.

Background: Students in the United States spend a meaningful portion of their developmental lives in school. In recent years, researchers and educators have begun to focus explicitly on social and emotional learning (SEL) in the school setting. Initial evidence from meta-analyses suggests that curricula designed to promote SEL likely produce benefits in terms of social-emotional competence (SEC) and numerous related behavioral and affective outcomes. Read More

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Quantification of Residual Perfume by Py-GC-MS in Fragrance Encapsulate Polymeric Materials Intended for Biodegradation Tests.

Molecules 2020 Feb 7;25(3). Epub 2020 Feb 7.

Firmenich SA, Corporate R&D Division, Route des Jeunes 1, 1211 Genève, Switzerland.

Perfume encapsulates are widely used in commercial products to control the kinetic release of odorant molecules, increase storage stability and/or improve deposition on different substrates. In most of the cases, they consist of core-shell polymeric microcapsules that contain fragrance molecules. A current challenge is to design and produce polymeric materials for encapsulation that are both resistant and non-persistent. Read More

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February 2020

A qualitative study of forensic patients' perceptions of quasi-coercive offers of biological treatment.

Behav Sci Law 2020 Mar 6;38(2):135-151. Epub 2020 Feb 6.

Division of Forensic Psychiatry, University of Ottawa, and The Royal's Institute of Mental Health Research, Ottawa, Canada.

At various points in the trajectory through the criminal justice system, a person may be encouraged by the hope of legal benefit to consent to medical treatment. This benefit may consist of diversion from prosecution, a favorable sentence, or parole. This form of legal encouragement has been referred to as legal leverage, quasi-coercive, or quasi-compulsory treatment. Read More

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A management algorithm for adult patients with both brain oxygen and intracranial pressure monitoring: the Seattle International Severe Traumatic Brain Injury Consensus Conference (SIBICC).

Intensive Care Med 2020 05 21;46(5):919-929. Epub 2020 Jan 21.

Department of Neurosurgery, Humanitas University and Research Hospital, Milan, Italy.

Background: Current guidelines for the treatment of adult severe traumatic brain injury (sTBI) consist of high-quality evidence reports, but they are no longer accompanied by management protocols, as these require expert opinion to bridge the gap between published evidence and patient care. We aimed to establish a modern sTBI protocol for adult patients with both intracranial pressure (ICP) and brain oxygen monitors in place.

Methods: Our consensus working group consisted of 42 experienced and actively practicing sTBI opinion leaders from six continents. Read More

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