Hypothesis driven single nucleotide polymorphism search (HyDn-SNP-S)

The advent of complete-genome genotyping across phenotype cohorts has provided a rich source of information for bioinformaticians. However the search for SNPs from this data is generally performed on a study-by-study case without any specific hypothesis of the location for SNPs that are predictive for the phenotype. We have designed a method whereby very large SNP lists (several gigabytes in size), combining several genotyping studies at once, can be sorted and traced back to their ultimate consequence in protein structure. Given a working hypothesis, researchers are able to easily search whole genome genotyping data for SNPs that link genetic locations to phenotypes. This allows a targeted search for cor- relations between phenotypes and potentially relevant systems, rather than utilizing statistical methods only. HyDn-SNP-S returns results that are less data dense, allowing more thorough analysis, including haplotype analysis. We have applied our method to correlate DNA polymerases to cancer phenotypes using four of the available cancer databases in dbGaP. Logistic regression and derived haplotype analysis indicates that ∼80 SNPs, previously overlooked, are statistically significant. Derived haplotypes from this work link POLL to breast cancer and POLG to prostate cancer with an increase in incidence of 3.01- and 9.6-fold, respectively. Molecular dynamics simulations on wild-type and one of the SNP mutants from the haplotype of POLL provide insights at the atomic level on the functional impact of this cancer related SNP. Furthermore, HyDn-SNP-S has been designed to allow application to any system. The program is available upon request from the authors

Thermoelectric Limitations of Graphene Nanodevices at Ultrahigh Current Densities.

Graphene is atomically thin, possesses excellent thermal conductivity, and is able to withstand high current densities, making it attractive for many nanoscale applications such as field-effect transistors, interconnects, and thermal management layers. Enabling integration of graphene into such devices requires nanostructuring, which can have a drastic impact on the self-heating properties, in particular at high current densities. Here, we use a combination of scanning thermal microscopy, finite element thermal analysis, and operando scanning transmission electron microscopy techniques to observe prototype graphene devices in operation and gain a deeper understanding of the role of geometry and interfaces during high current density operation. We find that Peltier effects significantly influence the operational limit due to local electrical and thermal interfacial effects, causing asymmetric temperature distribution in the device. Thus, our results indicate that a proper understanding and design of graphene devices must include consideration of the surrounding materials, interfaces, and geometry. Leveraging these aspects provides opportunities for engineered extreme operation devices

Comparison of Echocardiographic Measures in a Hispanic/Latino Population With the 2005 and 2015 American Society of Echocardiography Reference Limits (The Echocardiographic Study of Latinos)CLINICAL PERSPECTIVE

BACKGROUND: Reference limits for echocardiographic quantification of cardiac chambers in Hispanics are not well studied. METHODS AND RESULTS: We examined the reference values of left atrium and left ventricle (LV) structure in a large ethnically diverse Hispanic cohort. Two-dimensional transthoracic echocardiography was performed in 1818 participants of the Echocardiographic Study of Latinos (ECHO-SOL). Individuals with body mass index ≥30 kg/m(2), hypertension, diabetes mellitus, coronary artery disease, and atrial fibrillation were excluded leaving 525 participants defined as healthy reference cohort. We estimated 95th weighted percentiles of LV end systolic volume, LV end diastolic volume, relative wall and septal thickness, LV mass, and left atrial volume. We then used upper reference limits of the 2005 and 2015 American Society of Echocardiography (ASE) and 95th percentile of reference cohort to classify the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) target population into abnormal and normal. Reference limits were also calculated for each of 6 Hispanic origins. Using ASE 2015 defined reference values, we categorized 7%, 21%, 57%, and 17% of men and 18%, 29%, 60%, and 26% of women as having abnormal LV mass index, relative, septal, and posterior wall thickness, respectively. Conversely, 10% and 11% of men and 4% and 2% of women were classified as having abnormal end-diastolic volume and internal diameter by ASE 2015 cutoffs, respectively. Similar differences were found when we used 2005 ASE cutoffs. Several differences were noted in distribution of cardiac structure and volumes among various Hispanic/Latino origins. Cubans had highest values of echocardiographic measures, and Central Americans had the lowest. CONCLUSIONS: This is the first large study that provides normal reference values for cardiac structure. It further demonstrates that a considerable segment of Hispanic/Latinos residing in the United States may be classified as having abnormal measures of cardiac chambers when 2015 and 2005 ASE reference cutoffs are used

Bone Marrow Stromal Cells Modulate Mouse ENT1 Activity and Protect Leukemia Cells from Cytarabine Induced Apoptosis

BACKGROUND: Despite a high response rate to chemotherapy, the majority of patients with acute myeloid leukemia (AML) are destined to relapse due to residual disease in the bone marrow (BM). The tumor microenvironment is increasingly being recognized as a critical factor in mediating cancer cell survival and drug resistance. In this study, we propose to identify mechanisms involved in the chemoprotection conferred by the BM stroma to leukemia cells. METHODS: Using a leukemia mouse model and a human leukemia cell line, we studied the interaction of leukemia cells with the BM microenvironment. We evaluated in vivo and in vitro leukemia cell chemoprotection to different cytotoxic agents mediated by the BM stroma. Leukemia cell apoptosis was assessed by flow cytometry and western blotting. The activity of the equilibrative nucleoside transporter 1 (ENT1), responsible for cytarabine cell incorporation, was investigated by measuring transport and intracellular accumulation of (3)H-adenosine. RESULTS: Leukemia cell mobilization from the bone marrow into peripheral blood in vivo using a CXCR4 inhibitor induced chemo-sensitization of leukemia cells to cytarabine, which translated into a prolonged survival advantage in our mouse leukemia model. In vitro, the BM stromal cells secreted a soluble factor that mediated significant chemoprotection to leukemia cells from cytarabine induced apoptosis. Furthermore, the BM stromal cell supernatant induced a 50% reduction of the ENT1 activity in leukemia cells, reducing the incorporation of cytarabine. No protection was observed when radiation or other cytotoxic agents such as etoposide, cisplatin and 5-fluorouracil were used. CONCLUSION: The BM stroma secretes a soluble factor that significantly protects leukemia cells from cytarabine-induced apoptosis and blocks ENT1 activity. Strategies that modify the chemo-protective effects mediated by the BM microenvironment may enhance the benefit of conventional chemotherapy for patients with AML

Short-term prediction of threatening and violent behaviour in an Acute Psychiatric Intensive Care Unit based on patient and environment characteristics

<p>Abstract</p> <p>Background</p> <p>The aims of the present study were to investigate clinically relevant patient and environment-related predictive factors for threats and violent incidents the first three days in a PICU population based on evaluations done at admittance.</p> <p>Methods</p> <p>In 2000 and 2001 all 118 consecutive patients were assessed at admittance to a Psychiatric Intensive Care Unit (PICU). Patient-related conditions as actuarial data from present admission, global clinical evaluations by physician at admittance and clinical nurses first day, a single rating with an observer rated scale scoring behaviours that predict short-term violence in psychiatric inpatients (The Brøset Violence Checklist (BVC)) at admittance, and environment-related conditions as use of segregation or not were related to the outcome measure Staff Observation Aggression Scale-Revised (SOAS-R). A multiple logistic regression analysis with SOAS-R as outcome variable was performed.</p> <p>Results</p> <p>The global clinical evaluations and the BVC were effective and more suitable than actuarial data in predicting short-term aggression. The use of segregation reduced the number of SOAS-R incidents.</p> <p>Conclusions</p> <p>In a naturalistic group of patients in a PICU segregation of patients lowers the number of aggressive and threatening incidents. Prediction should be based on clinical global judgment, and instruments designed to predict short-term aggression in psychiatric inpatients.</p> <p>Trial registrations</p> <p><a href="http://www.clinicaltrials.gov/ct2/show/NCT00184119">NCT00184119</a>/<a href="http://www.clinicaltrials.gov/ct2/show/NCT00184132">NCT00184132</a></p

Phylogenomic analysis of a 55.1 kb 19-gene dataset resolves a monophyletic Fusarium that includes the Fusarium solani Species Complex

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user¿s needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option availabl

Pulmonary vascular research institute GoDeep: a meta-registry merging deep phenotyping datafrom international PH reference centers

The Pulmonary Vascular Research Institute GoDeep meta-registry is a collaboration of pulmonary hypertension (PH) reference centers across the globe. Merging worldwide PH data in a central meta-registry to allow advanced analysis of the heterogeneity of PH and its groups/subgroups on a worldwide geographical, ethnical, and etiological landscape (ClinTrial. gov NCT05329714). Retrospective and prospective PH patient data (diagnosis based on catheterization; individuals with exclusion of PH are included as a comparator group) are mapped to a common clinical parameter set of more than 350 items, anonymized and electronically exported to a central server. Use and access is decided by the GoDeep steering board, where each center has one vote. As of April 2022, GoDeep comprised 15,742 individuals with 1.9 million data points from eight PH centers. Geographic distribution comprises 3990 enrollees (25%) from America and 11,752 (75%) from Europe. Eighty-nine perecent were diagnosed with PH and 11% were classified as not PH and provided a comparator group. The retrospective observation period is an average of 3.5 years (standard error of the mean 0.04), with 1159 PH patients followed for over 10 years. Pulmonary arterial hypertension represents the largest PH group (42.6%), followed by Group 2 (21.7%), Group 3 (17.3%), Group 4 (15.2%), and Group 5 (3.3%). The age distribution spans several decades, with patients 60 years or older comprising 60%. The majority of patients met an intermediate risk profile upon diagnosis. Data entry from a further six centers is ongoing, and negotiations with >10 centers worldwide have commenced. Using electronic interface-based automated retrospective and prospective data transfer, GoDeep aims to provide in-depth epidemiological and etiological understanding of PH and its various groups/subgroups on a global scale, offering insights for improved management