Publications by authors named "Nidhi Shah"

66 Publications

Prevalence of acne vulgaris and its clinico-epidemiological pattern in adult patients: Results of a prospective, observational study.

J Cosmet Dermatol 2021 Mar 2. Epub 2021 Mar 2.

Department of. Dermatology, University Medical Center Mainz, Mainz, Germany.

Background: Acne is a common disorder in adolescents. Prevalence of acne in adults is also increasing. There are only a few Indian studies on prevalence and clinical features of adult acne.

Objective: To evaluate prevalence and possible etiological and aggravating factors of acne in adult population.

Material And Methods: Adult patients more than 25 years of with acne were enrolled and detailed history and examination were recorded. Type of acne, age, gender, area of involvement and associated factors were noted.

Results: Out of 24056 adult patients, 180 had acne, with prevalence of 0.74%. Mean patients of patients with acne was 30.1 years. A total of 81.7% patients with acne were female and 68.3% had persistent type of acne. Inflammatory papular acne (72.8%) was the most common type of acne in our study population. Cheek (85%) was the predominant site of involvement; 62.8% patients developed scarring. Underlying chronic stress was present in 23.9% and family history of acne in 60.6%. A total of 43.5% patients reported aggravation with cosmetics and 42.8% provided history of oily and high glycemic food conduction. Premenstrual flare and hirsutism was seen in 61.9% and 16.3% female patients respectively.

Conclusion: Acne is more common in people with 25-35 years age with female preponderence and a gradual decline in prevalence is seen thereafter. Inflammatory nature is more common with cheeks being commonest site of affection. Facial scarring is more common which emphasizes the importance of early and adequate intervention.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/jocd.14040DOI Listing
March 2021

TIPP2: metagenomic taxonomic profiling using phylogenetic markers.

Bioinformatics 2021 Jan 20. Epub 2021 Jan 20.

Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.

Motivation: Metagenomics has revolutionized microbiome research by enabling researchers to characterize the composition of complex microbial communities. Taxonomic profiling is one of the critical steps in metagenomic analyses. Marker genes, which are single-copy and universally found across Bacteria and Archaea, can provide accurate estimates of taxon abundances in the sample.

Results: We present TIPP2, a marker gene-based abundance profiling method, that combines phylogenetic placement with statistical techniques to control classification precision and recall. TIPP2 includes an updated set of reference packages and several algorithmic improvements over the original TIPP method. We find that TIPP2 provides comparable or better estimates of abundance than other profiling methods (including Bracken, mOTUsv2, and MetaPhlAn2), and strictly dominates other methods when there are under-represented (novel) genomes present in the dataset.

Availability And Implementation: The code for our method is freely available in open source form at https://github.com/smirarab/sepp/blob/tipp2/README.TIPP.mdThe code and procedure to create new reference packages for TIPP2 are available at https://github.com/shahnidhi/TIPP_reference_package.

Supplementary Information: Not available online.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btab023DOI Listing
January 2021

NCBI's Virus Discovery Codeathon: Building "FIVE" -The Federated Index of Viral Experiments API Index.

Viruses 2020 12 10;12(12). Epub 2020 Dec 10.

National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA.

Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources. To this end, during this three-day continuation of the Virus Hunting Toolkit codeathon series (VHT-2), a new integrated and federated viral index was elaborated. This Federated Index of Viral Experiments (FIVE) integrates pre-existing and novel functional and taxonomy annotations and virus-host pairings. Variability in the context of viral genomic diversity is often overlooked in virus databases. As a proof-of-concept, FIVE was the first attempt to include viral genome variation for HIV, the most well-studied human pathogen, through viral genome diversity graphs. As per the publication of this manuscript, FIVE is the first implementation of a virus-specific federated index of such scope. FIVE is coded in BigQuery for optimal access of large quantities of data and is publicly accessible. Many projects of database or index federation fail to provide easier alternatives to access or query information. To this end, a Python API query system was developed to enhance the accessibility of FIVE.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/v12121424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7764237PMC
December 2020

Evaluating the Barriers to Isotretinoin Treatment for Acne Vulgaris in Pediatric Patients.

J Am Acad Dermatol 2020 Nov 28. Epub 2020 Nov 28.

The George Washington University School of Medicine and Health Sciences, Washington, DC 20052; Children's National Hospital, Division of Dermatology, Washington, DC 20010. Electronic address:

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jaad.2020.11.055DOI Listing
November 2020

Exploring competency-based education: New tools in the residency assessment tool belt.

J Am Acad Dermatol 2021 Mar 7;84(3):e179-e180. Epub 2020 Nov 7.

Department of Dermatology, Brigham and Women's Hospital, Boston, Massachusetts. Electronic address:

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jaad.2020.10.088DOI Listing
March 2021

Exploring competency-based education: New tools in the residency assessment tool belt.

J Am Acad Dermatol 2021 Mar 7;84(3):e179-e180. Epub 2020 Nov 7.

Department of Dermatology, Brigham and Women's Hospital, Boston, Massachusetts. Electronic address:

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jaad.2020.10.088DOI Listing
March 2021

Granulomatous Cutaneous Drug Eruptions: A Systematic Review.

Am J Clin Dermatol 2021 Jan;22(1):39-53

Division of Dermatology, Department of Medicine, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.

Background: Granulomatous drug eruptions are rare entities, where granuloma formation occurs as an attempt to contain an exogenous or endogenous inciting agent. Granulomatous drug eruptions may be localized to the skin or may include major systemic involvement, and their characteristics depend both on the properties of the causative irritant and host factors. Because of the overlapping features amongst noninfectious granulomatous diseases, granulomatous drug eruptions are challenging to diagnose and distinguish both histologically and clinically.

Objective: The objective of this article is to provide a review and summary of the current literature on the five major types of cutaneous granulomatous drug eruptions: interstitial granulomatous drug reaction, drug-induced accelerated rheumatoid nodulosis, drug-induced granuloma annulare, drug-induced sarcoidosis, and miscellaneous presentations.

Methods: A systematic review was conducted through PubMed using the search terms "granulomatous drug eruption" and "cutaneous" or "skin". English full-text studies that included human subjects experiencing a cutaneous reaction comprising granulomatous inflammation as the direct result of a drug were included. Of 205 studies identified, 48 articles were selected after a full-text review. Evidence was evaluated using the Tool for evaluating the methodological quality of case reports and case series.

Results: Polypharmacy and a prolonged lag period from drug ingestion to rash onset may create diagnostic challenges. Ruling out tuberculosis is imperative in the endemic setting, particularly where anti-tumor necrosis factor therapy is the presumed cause. Interstitial granulomatous drug reactions and granuloma annulare are often localized to the skin whereas accelerated rheumatoid nodulosis and sarcoidosis may sometimes be associated with systemic features as well. Granulomatous drug eruptions typically resolve on discontinuing the offending medication; however, the decision for drug cessation is dependent on a risk-benefit assessment. In some situations, supplementation of an additional agent to suppress the reaction may resolve symptoms. In some cases, granulomatous drug eruptions may be pivotal in the successful outcome of the drug, as in cases of melanoma treatment. In all situations, the decision to continue or withdraw the drug should be carefully based on the severity of the eruption, necessity of continuing the drug, and availability of a suitable alternative.

Conclusions: Granulomatous drug eruptions should always be considered in the differential diagnosis of noninfectious granulomatous diseases of the skin. Further research examining dose-response relationships and the recurrence of granulomatous drug eruptions on the rechallenge of offending agents is required. Increased awareness of granulomatous drug eruption types is important, especially with continuous development of new anti-cancer agents that may induce these reactions.

Clinical Trial Registration: PROSPERO registration number CRD42020157009.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s40257-020-00566-4DOI Listing
January 2021

Outcomes in COVID-19 Positive Neonates and Possibility of Viral Vertical Transmission: A Narrative Review.

Am J Perinatol 2020 10 31;37(12):1208-1216. Epub 2020 Jul 31.

Division of Neonatology, Department of Pediatrics, The Children's Regional Hospital at Cooper, Cooper Medical School of Rowan University, Camden, New Jersey.

Objective: Novel coronavirus disease 2019 (COVID-19) seems to affect adults and pediatric patients differently. While neonates are a special population, little is known about the neonatal outcomes. This study aimed to investigate the outcomes in COVID-19 positive neonates and incidence of vertical transmission of the virus by reviewing available literature.

Study Design: This study is a narrative review of available literature on "COVID-19 in neonates," for which PubMed and Google Scholar were used to search the published articles.

Results: We summarized the data from 39 published studies that are comprised of 326 COVID-19 positive peripartum mothers with respective neonatal outcomes. Twenty-three neonates have been reported to be COVID-19 positive. Male neonates were affected significantly more (79%) than female neonates. Approximately 3% neonates acquired infection through suspected vertical transmission. Strict infection prevention measures during the perinatal time can significantly reduce the chance of horizontal transmission of the virus. Overall, neonates were asymptomatic or mildly symptomatic regardless of gestational age at birth and required only supportive measures. There was 0% mortality in COVID-19 positive neonates.

Conclusion: From available published data to date, we can conclude that the prognosis of COVID-19 positive neonates is good with no mortality. There appears to be minimal vertical transmission of the infection.

Key Points: · Majority of COVID-19 positive neonates showed mild clinical signs and symptoms with no mortality.. · Most COVID-19 positive neonates require only supportive measures.. · Possibility of viral vertical transmission is very low..
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1055/s-0040-1714719DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7645816PMC
October 2020

Germline Sequencing Identifies Rare Variants in Finnish Subjects with Familial Germ Cell Tumors.

Appl Clin Genet 2020 30;13:127-137. Epub 2020 Jun 30.

Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, St. Louis, MO, USA.

Purpose: Pediatric germ cell tumors are rare, representing about 3% of childhood malignancies in children less than 15 years of age, presenting in neonates or adolescents with a greater incidence noted in older adolescents. Aberrations in primordial germ cell proliferation/differentiation can lead to a variety of neoplasms, including teratomas, embryonal carcinoma, choriocarcinoma, and yolk sac tumors.

Patients And Methods: Three Finnish families with varying familial germ cell tumors were identified, and whole-genome sequencing was performed using an Illumina sequencing platform. In total, 22 unique subjects across the three families were sequenced. Family 1 proband (female) was affected by malignant ovarian teratoma, Family 2 proband (female) was affected by sacrococcygeal teratoma with yolk sac tumor in the setting of Cornelia de Lange syndrome, and Family 3 proband (male) was affected by malignant testicular teratoma. Rare variants were identified using an autosomal recessive or de novo model of inheritance.

Results: For family 1 proband (female), an autosomal recessive or de novo model of inheritance identified variants of interest in the following genes: , and . Family 2 proband (female) analysis identified gene variants of interest in the following genes: . Family 3 proband (male) analysis identified the following potential genes: , and .

Conclusion: Leveraging deep pedigrees and next-generation sequencing, rare germline variants were identified that were enriched in three families from Finland with a history of familial germ cell tumors. The data presented support the importance of germline mutations when analyzing complex cancers with a low somatic mutation landscape.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2147/TACG.S245093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7335280PMC
June 2020

Docosahexaenoic acid and bronchopulmonary dysplasia in preterm infants: a systematic review and meta-analysis.

J Matern Fetal Neonatal Med 2020 May 27:1-9. Epub 2020 May 27.

Department of Pediatrics, Saitama Medical Center, Saitama Medical University, Kawagoe, Japan.

Bronchopulmonary dysplasia (BPD) is a common and serious complication of extremely preterm birth. Given the anti-inflammatory properties, docosahexaenoic acid (DHA) supplementation has been proposed as a strategy for the management of BPD. This study aimed to investigate the effects of DHA supplementation on BPD based on a systematic review. A comprehensive literature search was conducted using ClinicalTrials.Gov, CINAHL, Cochrane Library, EMBASE, MEDLINE, PubMed, and the WHO ICTRP from their respective dates of inception to June 2017. The studies included were randomized controlled trials (RCTs) that enrolled preterm infants <33 weeks of gestational age. Trials were included if DHA supplementation was compared with a control. Four RCTs from five reports (1,966 neonates) met our inclusion criteria. The meta-analysis of these studies showed that DHA supplementation did not decrease the risk of BPD at 36 weeks of postmenstrual age among preterm infants (). DHA supplementation did not significantly reduce the risk of other neonatal morbidities including death (), BPD at 28 days of life (), necrotizing enterocolitis (), intraventricular hemorrhage, severe retinopathy of prematurity, or sepsis. DHA supplementation may not exert significant clinical benefits in the treatment of BPD and other neonatal morbidities.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/14767058.2020.1769590DOI Listing
May 2020

Morphomic calcification score from clinical CT scans: A proxy for coronary artery calcium.

Clin Imaging 2020 Oct 18;66:57-63. Epub 2020 Apr 18.

Morphomic Analysis Group, University of Michigan, Ann Arbor, MI, USA; Department of Surgery, University of Michigan, Ann Arbor, MI, USA. Electronic address:

Background: Screening of cardiovascular risk is essential in preventing cardiac events and quantifying asymptomatic risk. Coronary artery calcium (CAC) scores are a well-established in predicting cardiovascular risk, but require specialized computed tomography (CT) scans. Given the relationship of aortic calcification with cardiovascular risk, we sought to determine whether aortic calcification measures from incidental CT scans may approximate CAC.

Study Design: Retrospective CT scans and corresponding volumetric CAC scores were obtained from patients at the University of Michigan. Aortic calcifications were measured in 166 scans. Correlations between a novel morphomic calcium (MC) percent score and CAC score were evaluated using Kendall's correlation coefficients. Comparison of receiver operating characteristic (ROC) curves based on MC at different vertebral levels showed the highest predictive values for measures taken at L4.

Results: MC at L4 shows promise in predicting CAC (AUC 0.90 in non-contrast scans, 0.70 in post-contrast scans). Proposed MC threshold are (4.21% for best sensitivity, B 12.93% for balance, C = 19.26% for specificity) in scans without contrast enhancement and (D = 7.31 for sensitivity, E 8.06 for specificity) in scans with contrast enhancement.

Conclusion: The MC score demonstrates promising potential in approximating CAC, particularly at the L4 level. The utilization of MC from incidental CT scans may be useful for assessment of cardiovascular risk. The ability to extract MC from contrast scans makes it especially valuable to patients receiving additional medical or surgical care. Recognition of high-risk patients would allow the use of indicated preventative strategies to avoid hard cardiovascular events in at risk patients.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.clinimag.2020.03.017DOI Listing
October 2020

Video capsule endoscopy for upper gastrointestinal hemorrhage in the emergency department: A systematic review and meta-analysis.

Am J Emerg Med 2020 06 12;38(6):1245-1252. Epub 2020 Mar 12.

The George Washington University School of Medicine and Health Sciences, Department of Emergency Medicine, The Department of Emergency Medicine, 2120 L Street NW, Suite 450, Washington, DC 20037, USA. Electronic address:

Objective: The assessment of the severity of upper gastrointestinal hemorrhage in emergency department (ED) patients is difficult to assess with commonly available diagnostic tools. Small studies have shown that video capsule endoscopy (VCE) is a promising risk-stratification method and may be better than current clinical decision rules such as the Rockall score and the Glasgow Blatchford score. This review aims to assess the accuracy of VCE to detect active upper gastrointestinal hemorrhage compared to a reference standard.

Methods: The PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) methodology was used to perform a review of studies that have measured the diagnostic accuracy of VCE. Studies were included if they measured ED use of VCE for upper GI hemorrhage as compared to a reference standard of an esophagogastroduodenoscopy (EGD). A meta-analysis was performed on select patients using a fixed effects and random-effects model to determine the primary outcome of diagnostic test accuracy.

Results: 40 studies were screened for eligibility and five studies representing 193 patients met the inclusion and exclusion criteria. All patients received both a VCE and an EGD. The sensitivity and specificity of VCE were 0.724 and 0.748, respectively. The diagnostic odds ratio was 6.29 (95% CI: 3.23-12.25) and the summary receiver operating characteristic curve was 0.782.

Conclusions: VCE demonstrated high accuracy for detecting upper GI hemorrhage in this meta-analysis of existing studies. In light of the potential advantages of VCE in the ED, further research is warranted to further establish its role.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ajem.2020.03.008DOI Listing
June 2020

Investigation of the quorum-sensing regulon of the biocontrol bacterium Pseudomonas chlororaphis strain PA23.

PLoS One 2020 28;15(2):e0226232. Epub 2020 Feb 28.

Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.

Pseudomonas chlororaphis strain PA23 is a biocontrol agent capable of protecting canola from stem rot disease caused by the fungal pathogen Sclerotinia sclerotiorum. PA23 produces several inhibitory compounds that are under control of a complex regulatory network. Included in this cascade is the PhzRI quorum sensing (QS) system, which plays an essential role in PA23 biocontrol, as well as CsaRI and AurRI, which have not yet been characterized in PA23. The focus of the current study was to employ RNA sequencing to explore the spectrum of PA23 genes under QS control. In this work, we investigated genes under the control of the main QS transcriptional regulator, PhzR, as well as those differentially expressed in an AHL-deficient strain, PA23-6863, which constitutively expresses an AiiA lactonase, rendering the strain QS defective. Transcriptomic profiling revealed 545 differentially expressed genes (365 downregulated; 180 upregulated) in the phzR mutant and 534 genes (382 downregulated; 152 upregulated) in the AHL-deficient PA23-6863. In both strains, decreased expression of phenazine, pyrrolnitrin, and exoprotease biosynthetic genes was observed. We have previously reported that QS activates expression of these genes and their encoded products. In addition, elevated siderophore and decreased chitinase gene expression was observed in the QS-deficient stains, which was confirmed by phenotypic analysis. Inspection of the promoter regions revealed the presence of "phz-box" sequences in only 58 of the 807 differentially expressed genes, suggesting that much of the QS regulon is indirectly regulated. Consistent with this notion, 41 transcriptional regulators displayed altered expression in one or both of the QS-deficient strains. Collectively, our findings indicate that QS governs expression of approximately 13% of the PA23 genome affecting diverse functions ranging from secondary metabolite production to general metabolism.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0226232PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7048289PMC
May 2020

An emerging role for endothelial barrier support therapy for congenital disorders of glycosylation.

J Inherit Metab Dis 2020 07 27;43(4):880-890. Epub 2020 Feb 27.

Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts.

Congenital disorders of glycosylation (CDGs) are clinically heterogeneous disorders defined by a decreased ability to modify biomolecules with oligosaccharides. Critical disruptions in protein recognition, interaction, binding, and anchoring lead to broad physiological effects. Patients present with endocrinopathy, immunodeficiency, hepatopathy, coagulopathy, and neurodevelopmental impairment. Patients may experience mortality/morbidity associated with shock physiology that is frequently culture negative and poorly responsive to standard care. Oedema, pleural and pericardial effusions, ascites, proteinuria, and protein-losing enteropathy are observed with an exaggerated inflammatory response. The negative serum protein steady state results from several mechanisms including reduced hepatic synthesis and secretion, increased consumption, and extravasation. Disruption of the glycocalyx, a layer of glycosylated proteins that lines the endothelium preventing thrombosis and extravasation, is a suspected cause of endothelial dysfunction in CDG patients. We performed a retrospective review of CDG patients admitted to our institution with acute illness over the past 2 years. Longitudinal clinical and laboratory data collected during the sick and well states were assessed for biomarkers of inflammation and efficacy of interventions. Six patients representing 4 CDG subtypes and 14 hospitalisations were identified. Acute D-dimer elevation, proteinuria, decreased serum total protein levels, coagulation proteins, and albumin were observed with acute illness. Infusion of fresh frozen plasma, and in some cases protein C concentrate, was associated with clinical and biomarker improvement. This was notable with intra-patient comparison of treated vs untreated courses. Use of endothelial barrier support therapy may reduce endothelial permeability by restoring both regulatory serum protein homeostasis and supporting the glycocalyx and is likely a critical component of care for this population.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/jimd.12225DOI Listing
July 2020

Relationship between sociodemographic factors and geographic distribution of pharmacies dispensing isotretinoin in Washington, DC.

J Am Acad Dermatol 2020 Sep 13;83(3):930-933. Epub 2020 Feb 13.

School of Medicine and Health Sciences, The George Washington University, Washington, DC; Division of Dermatology, Children's National Hospital, Washington, DC. Electronic address:

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jaad.2020.01.014DOI Listing
September 2020

Gain-of-function pathogenic variants in SMAD4 are associated with neoplasia in Myhre syndrome.

Am J Med Genet A 2020 02 14;182(2):328-337. Epub 2019 Dec 14.

Division of Reproductive and Medical Genetics, Department of Obstetrics & Gynecology and Women's Health, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York.

Myhre syndrome is an increasingly diagnosed rare syndrome that is caused by one of two specific heterozygous gain-of-function pathogenic variants in SMAD4. The phenotype includes short stature, characteristic facial appearance, hearing loss, laryngotracheal stenosis, arthritis, skeletal abnormalities, learning and social challenges, distinctive cardiovascular defects, and a striking fibroproliferative response in the ear canals, airways, and serosal cavities (peritoneum, pleura, pericardium). Confirmation of the clinical diagnosis is usually prompted by the characteristic appearance with developmental delay and autistic-like behavior using targeted gene sequencing or by whole exome sequencing. We describe six patients (two not previously reported) with molecularly confirmed Myhre syndrome and neoplasia. Loss-of-function pathogenic variants in SMAD4 cause juvenile polyposis syndrome and we hypothesize that the gain-of-function pathogenic variants observed in Myhre syndrome may contribute to neoplasia in the patients reported herein. The frequency of neoplasia (9.8%, 6/61) in this series (two new, four reported patients) and endometrial cancer (8.8%, 3/34, mean age 40 years) in patients with Myhre syndrome, raises the possibility of cancer susceptibility in these patients. We alert clinicians to the possibility of detecting this syndrome when cancer screening panels are used. We propose that patients with Myhre syndrome are more susceptible to neoplasia, encourage increased awareness, and suggest enhanced clinical monitoring.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/ajmg.a.61430DOI Listing
February 2020

Management of epidermolysis bullosa simplex in pregnancy: A case report.

Case Rep Womens Health 2019 Oct 5;24:e00140. Epub 2019 Sep 5.

Department of Obstetrics & Gynecology, New York Medical College, Westchester Medical Center, 100, Woods Road, Valhalla, New York 10595, USA.

Epidermolysis bullosa (EB) encompasses a group of diseases characterized by extreme fragility of skin and mucous membranes, resulting in blister formation following minimal injury. There are 4 types of EB, with epidermolysis bullosa simplex (EBS) being the most common. We report our experience with the care of a parturient woman diagnosed with EBS. There is little literature on pregnancy in women with this condition. Special precautions are necessary during diagnostic and therapeutic interventions to avoid bullae formation or exacerbation of existing lesions. Frictional or shearing forces are typically more damaging than compressive forces. Multidisciplinary planning was done for our patient to ensure uneventful labor and delivery. Elective induction of labor was started at 40 weeks of gestation. She eventually underwent a cesarean delivery after failed trial of labor. We present this case to highlight the obstetric and anesthetic implications of caring for a parturient with EBS.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.crwh.2019.e00140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6829095PMC
October 2019

Embracing Ambiguity in the Taxonomic Classification of Microbiome Sequencing Data.

Front Genet 2019 17;10:1022. Epub 2019 Oct 17.

Department of Computer Science, University of Maryland, College Park, College Park, MD, United States.

The advent of high throughput sequencing has enabled in-depth characterization of human and environmental microbiomes. Determining the taxonomic origin of microbial sequences is one of the first, and frequently only, analysis performed on microbiome samples. Substantial research has focused on the development of methods for taxonomic annotation, often making trade-offs in computational efficiency and classification accuracy. A side-effect of these efforts has been a reexamination of the bacterial taxonomy itself. Taxonomies developed prior to the genomic revolution captured complex relationships between organisms that went beyond uniform taxonomic levels such as species, genus, and family. Driven in part by the need to simplify computational workflows, the bacterial taxonomies used most commonly today have been regularized to fit within a standard seven taxonomic levels. Consequently, modern analyses of microbial communities are relatively coarse-grained. Few methods make classifications below the genus level, impacting our ability to capture biologically relevant signals. Here, we present ATLAS, a novel strategy for taxonomic annotation that uses significant outliers within database search results to group sequences in the database into partitions. These partitions capture the extent of taxonomic ambiguity within the classification of a sample. The ATLAS pipeline can be found on GitHub [https://github.com/shahnidhi/outlier_in_BLAST_hits]. We demonstrate that ATLAS provides similar annotations to phylogenetic placement methods, but with higher computational efficiency. When applied to human microbiome data, ATLAS is able to identify previously characterized taxonomic groupings, such as those in the class and the genus . Furthermore, the majority of partitions identified by ATLAS are at the subgenus level, replacing higher-level annotations with specific groups of species. These more precise partitions improve our detection power in determining differential abundance in microbiome association studies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fgene.2019.01022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6811648PMC
October 2019

New Discoveries and Updates on Cutaneous Adverse Drug Reactions Presented at the 24th World Congress of Dermatology, Milan, Italy, 2019.

Drug Saf 2020 02;43(2):179-187

Division of Dermatology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s40264-019-00880-9DOI Listing
February 2020

Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019.

mSystems 2019 Oct 8;4(5). Epub 2019 Oct 8.

Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA

Accurate predictions across multiple fields of microbiome research have far-reaching benefits to society, but there are few widely accepted quantitative tools to make accurate predictions about microbial communities and their functions. More discussion is needed about the current state of microbiome analysis and the tools required to overcome the hurdles preventing development and implementation of predictive analyses. We summarize the ideas generated by participants of the Mid-Atlantic Microbiome Meet-up in January 2019. While it was clear from the presentations that most fields have advanced beyond simple associative and descriptive analyses, most fields lack essential elements needed for the development and application of accurate microbiome predictions. Participants stressed the need for standardization, reproducibility, and accessibility of quantitative tools as key to advancing predictions in microbiome analysis. We highlight hurdles that participants identified and propose directions for future efforts that will advance the use of prediction in microbiome research.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/mSystems.00392-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6787564PMC
October 2019

Hemiarthroplasty versus total hip arthroplasty for femoral neck fractures in patients with chronic obstructive pulmonary disease.

Eur J Trauma Emerg Surg 2019 Sep 25. Epub 2019 Sep 25.

Department of Orthopaedic Surgery, The George Washington University, 2300 M St NW, Washington, DC, 20037, USA.

Purpose: This study sought to delineate whether total hip arthroplasty (THA) or hip hemiarthroplasty (HHA) had more complication rates following the treatment of femoral neck fractures (FNF) in chronic obstructive pulmonary disease (COPD) patients.

Materials And Methods: The ACS-NSQIP database was queried for all patients with a history of COPD who had undergone THA and HHA with FNFs, isolated by CPT codes and ICD-9/ICD-10 codes. Propensity score matching without replacement in a 1:1 manner was done to control for patient demographics/preoperative comorbidities. Multivariate logistic regression models were utilized to assess the independent effect of HHA in comparison to THA.

Results: The propensity-matched (PM) HHA cohort was significantly older (76.14 years vs. 73.33 years, p = 0.001) and had significantly higher rates of pneumonia (p = 0.017), extended length of stay (LOS) (p = 0.017), and mortality (p = 0.002), but lower rates of blood transfusions (p = 0.016) and reoperation (p = 0.020). HHA was independently associated with an increased risk of pneumonia (p = 0.043), extended LOS (p = 0.050), and death (p = 0.044) but a decreased risk for blood transfusions (p = 0.008) and reoperation (p = 0.028) when compared to THA.

Discussion: Patients with more comorbidities are more likely to receive HHA than THA, which may explain some of the increased complications and mortality associated with HHA for FNFs compared to THA. Patients undergoing THA were at increased risk for blood transfusion and reoperation. THA does not appear to result in increased morbidity in this population compared to HHA. While THA should be considered in these patients given improved functional outcomes, further prospective studies are needed to establish superiority.

Level Of Evidence: III.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00068-019-01234-xDOI Listing
September 2019

Morphomic Factors Associated With Complete Response to Neoadjuvant Therapy in Esophageal Carcinoma.

Ann Thorac Surg 2020 01 21;109(1):241-248. Epub 2019 Sep 21.

Section of Thoracic Surgery, University of Michigan Medical Center, Ann Arbor, Michigan. Electronic address:

Background: In patients undergoing neoadjuvant chemoradiotherapy (nCRT) followed by surgery for locally advanced esophageal squamous cell carcinoma (ESCC), patients with a pathologic complete response (pCR) have the greatest benefit. The purpose of this study was to identify morphomic factors obtained from pretreatment computed tomography scans associated with a pCR in ESCC.

Methods: We retrospectively analyzed patients with ESCC treated with nCRT who underwent esophagectomy between 2006 and 2016. Clinical and morphomic characteristics pre-nCRT were analyzed to identify factors associated with pCR using univariate and multivariable analyses.

Results: There were 183 patients with ESCC included in this study, and 45 (24.6%) patients achieved pCR. The overall survival in patients with pCR was better than that in patients without pCR (5.8 years vs 1.2 years; P < .001). On univariate analysis, increased age, radiation dose greater than or equal to 4000 cGy, and larger subcutaneous adipose tissue area were correlated with pCR. On multivariable logistic regression, increased age (odds ratio, 1.53; P = .03), radiation dose greater than or equal to 4000 cGy (odds ratio, 2.19; P = .04), and larger dorsal muscle group normal-density area (odds ratio, 1.59; P = .03) were independently associated with pCR.

Conclusions: Increased age, radiation dose greater than or equal to 4000 cGy, and larger dorsal muscle group normal-density area were significantly associated with pCR. These factors may be useful in determining which patients are most likely to benefit from nCRT followed by esophagectomy.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.athoracsur.2019.08.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7150584PMC
January 2020

Larotrectinib imaging response in low-grade glioma.

Pediatr Blood Cancer 2020 01 22;67(1):e28002. Epub 2019 Sep 22.

Pediatric Hematology/Oncology, Penn State College of Medicine, Hershey, Pennsylvania, USA.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/pbc.28002DOI Listing
January 2020

Palliative Care in the Management of Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome in the Primary Care Setting.

Prim Care 2019 Sep 12;46(3):433-445. Epub 2019 Jun 12.

Department of Family and Social Medicine, Palliative Medicine Program, Montefiore Medical Center, The University Hospital for the Albert Einstein College of Medicine, 3544 Jerome Avenue, Bronx, NY 10467, USA.

Human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) has metamorphosed in the past 40 years since the first cases were diagnosed. The advent of highly active antiretroviral treatment (HAART) transformed the disease trajectory for many patients with HIV/AIDS and transitioned the course from a terminal disease to a chronic disease model. This article reviews the epidemiology of HIV/AIDS, prognostic indicators, frailty, opportunistic infections, specific AIDS-defining malignancies and non-AIDS-defining malignancies, role of palliative care, advance care planning, and the role of HAART in patients dying of late-stage AIDS.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.pop.2019.05.009DOI Listing
September 2019

Prognosis after Stroke #374.

J Palliat Med 2019 May;22(5):593-594

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1089/jpm.2019.0085DOI Listing
May 2019

Polyhydroxyalkanoate (PHA) Polymer Accumulation and Gene Expression in Phenazine (phz⁻) and Pyrrolnitrin (prn⁻) Defective Mutants of PA23.

Polymers (Basel) 2018 Oct 27;10(11). Epub 2018 Oct 27.

Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada.

PA23 was isolated from the rhizosphere of soybeans and identified as a biocontrol bacterium against , a fungal plant pathogen This bacterium produces a number of secondary metabolites, including phenazine-1-carboxylic acid, 2-hydroxyphenazine, pyrrolnitrin (PRN), hydrogen cyanide, proteases, lipases and siderophores. It also synthesizes and accumulates polyhydroxyalkanoate (PHA) polymers as carbon and energy storage compounds under nutrient-limited conditions. Pseudomonads like metabolize glucose via the Entner-Doudoroff and Pentose Phosphate pathways, which provide precursors for phenazine production. Mutants defective in phenazine (PHZ; PA23-63), PRN (PA23-8), or both (PA23-63-1) accumulated higher concentrations of PHAs than the wild-type strain (PA23) when cultured in Ramsay's Minimal Medium with glucose or octanoic acid as the carbon source. Expression levels of six genes, , , , , , and , were compared with wild type PA23 by quantitative real time polymerase chain reaction (qPCR). The qPCR studies indicated that there was no change in levels of transcription of the PHA synthase genes and in the (PA23-63) and (PA23-63-1) mutants in glucose medium. There was a significant increase in expression of in octanoate medium. Transcription of , and increased significantly in the (PA23-63-1) mutant. Mutations in regulatory genes like , , and , which affect PHZ and PRN production, also resulted in altered gene expression. The expression of , , , and genes was down-regulated significantly in and mutants. Thus, it appears that PHZ, PRN, and PHA production is regulated by common mechanisms. Higher PHA production in the (PA23-63), - (PA23-8), and (PA23-63-1) mutants in octanoic medium could be correlated with higher expression of . Further, the greater PHA production observed in the and mutants was not due to increased transcription of PHA synthase genes in glucose medium, but due to more accessibility of carbon substrates and reducing power, which were otherwise used for the synthesis of PHZ and PRN.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/polym10111203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6290614PMC
October 2018

metagenomeFeatures: an R package for working with 16S rRNA reference databases and marker-gene survey feature data.

Bioinformatics 2019 10;35(19):3870-3872

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.

Summary: We developed the metagenomeFeatures R Bioconductor package along with annotation packages for three 16S rRNA databases (Greengenes, RDP and SILVA) to facilitate working with 16S rRNA databases and marker-gene survey feature data. The metagenomeFeatures package defines two classes, MgDb for working with 16S rRNA sequence databases, and mgFeatures for marker-gene survey feature data. The associated annotation packages provide a consistent interface to the different databases facilitating database comparison and exploration. The mgFeatures-class represents a crucial step in the development of a common data structure for working with 16S marker-gene survey data in R.

Availability And Implementation: https://bioconductor.org/packages/release/bioc/html/metagenomeFeatures.html.

Supplementary Information: Supplementary material is available at Bioinformatics online.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btz136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6761971PMC
October 2019

Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.

Microbiome 2018 11 5;6(1):197. Epub 2018 Nov 5.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.

The Mid-Atlantic Microbiome Meet-up (M) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time. However, they also stressed the current limitations of genomic approaches for biodefense, including insufficient sensitivity to detect low-abundance pathogens and the inability to quantify viable organisms. Participants discussed ways in which the community can improve software usability and shared new computational tools for metagenomic processing, assembly, annotation, and visualization. Looking to the future, they identified the need for better bioinformatics toolkits for longitudinal analyses, improved sample processing approaches for characterizing viruses and fungi, and more consistent maintenance of database resources. Finally, they addressed the necessity of improving data standards to incentivize data sharing. Here, we summarize the presentations and discussions from the meeting, identifying the areas where microbiome analyses have improved our ability to detect and manage biological threats and infectious disease, as well as gaps of knowledge in the field that require future funding and focus.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40168-018-0582-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6219074PMC
November 2018

Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows.

Bioinformatics 2019 05;35(9):1613-1614

Department of Computer Science, University of Maryland College Park, MD, USA.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bty833DOI Listing
May 2019