bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fibrinolytic Activators and Inhibitors in Terminal Renal Insufficiency and in Anephric Patients
Authors: Brommer E J P , Schicht I , Wijngaards G , Verheijen J H , Rijken D C 
Published: July 2018

SummaryFibrinolytic factors were measured before and after DDAVP- infusion in 18 patients on chronic, regular haemodialysis, 11 of whom underwent bilateral nephrectomy, and in 7 patients in whom non-functioning kidneys were still present. Baseline fibrinolytic activity was normal or high in all but two cases. Before haemodialysis, the response to DDAVP-infusion was greatly reduced in the majority of patients as compared with healthy controls, irrespective of the baseline level. This was in accordance with mean t-PA-antigen levels which increased only slightly after DDAVP. When DDAVP was given after haemodialysis, previous non-responders showed a normal increase in fibrinolytic activity. The level of free t-PA-inhibitors was normal in most cases as were levels of α2-antiplasmin. and α2-macroglobulin.
Intra-Operative Activation of Coagulation - A Stimulus to Thrombosis Mediated by Vasopressin?
Authors: Grant P J , Tate G M , Davies J A , Williams N S , Prentice C R M 
Published: July 2018

SummaryVasopressin infusions in normal volunteers that produce concentrations in plasma comparable to those seen during stress, cause an increase in plasma factor VIII and shortening of the euglobulin clot lysis time (ECLT). We have investigated the relationship between endogenous vasopressin (aVP) release and haemostatic function in 7 patients undergoing major abdominal surgery. Blood samples were taken at nine intervals during the operative procedure. Plasma aVP levels peaked at median values of 51 pg/ml during bowel manipulation and remained elevated on the first post-operative day. Following, and in close temporal relationship with the rise in aVP there were increases in factor VIII coagulant activity, the ristocetin co-factor, von Willebrand antigen, plasminogen activator activity (106/ECLT2) and fibrinopeptide A concentrations with shortening of the activated partial thromboplastin time. The relationship was similar to that seen following infusion of a VP in human volunteers. The results are consistent with the hypothesis that aVP is an important mediator of changes in haemostatic function which accompany stress and might contribute to the thrombotic risk associated with surgical operations.
Fibrinogen Milano II: A Congenital Dysfibrinogenaemia Associated with Juvenile Arterial and Venous Thrombosis
Authors: Haverkate F , Koopman J , Kluft C , D’Angelo A , Cattaneo M , Mannucci P M 
Published: July 2018

SummaryA congenitally abnormal fibrinogen was isolated from blood of a young man with deep-vein thrombosis. Two other affected members of his family had three episodes of severe arterial thrombosis. The fibrinogen showed a delayed clotting by thrombin, but a normal clotting by Arvin®, Reptilase®, and prothrom-bin-staphylocoagulase complex. Analysis of the fibrinopeptides A and B by High Performance Liquid Chromatography did not reveal an abnormal peptide structure. The rate of release of A and B peptides by thrombin was strongly delayed, whereas the rate of release of fibrinopeptide A by Arvin® appeared to be normal. The fibrin polymerization rate was normal. Interactions between the abnormal fibrinogen, platelets and the fibrinolytic system were also normal. Evidence is presented that the defective interaction between fibrinogen Milano II and thrombin is associated with a defective binding of thrombin to the fibrin moiety of the abnormal fibrinogen.
Functional Involvement of Thrombospondin in Platelet Aggregation Induced by Low Versus High Concentrations of Thrombin
Authors: Kao K J , Shaut David M , Klein Paul A 
Published: July 2018

SummaryThrombospondin (TSP) is a major platelet secretory glycoprotein. Earlier studies of various investigators demonstrated that TSP is the endogenous platelet lectin and is responsible for the hemagglutinating activity expressed on formaldehyde-fixed thrombin-treated platelets. The direct effect of highly purified TSP on thrombin-induced platelet aggregation was studied. It was observed that aggregation of gel-filtered platelets induced by low concentrations of thrombin (≤0.05 U/ml) was progressively inhibited by increasing concentrations of exogenous TSP (≥60 μg/ml). However, inhibition of platelet aggregation by TSP was not observed when higher than 0.1 U/ml thrombin was used to activate platelets. To exclude the possibility that TSP inhibits platelet aggregation by affecting thrombin activation of platelets, three different approaches were utilized. First, by using a chromogenic substrate assay it was shown that TSP does not inhibit the proteolytic activity of thrombin. Second, thromboxane B2 synthesis by thrombin-stimulated platelets was not affected by exogenous TSP. Finally, electron microscopy of thrombin-induced platelet aggregates showed that platelets were activated by thrombin regardless of the presence or absence of exogenous TSP. The results indicate that high concentrations of exogenous TSP (≥60 μg/ml) directly interfere with interplatelet recognition among thrombin-activated platelets. This inhibitory effect of TSP can be neutralized by anti-TSP Fab. In addition, anti-TSP Fab directly inhibits platelet aggregation induced by a low (0.02 U/ml) but not by a high (0.1 U/ml) concentration of thrombin. In conclusion, our findings demonstrate that TSP is functionally important for platelet aggregation induced by low (≤0.05 U/ml) but not high (≥0.1 U/ml) concentrations of thrombin. High concentrations of exogenous TSP may univalently saturate all its platelet binding sites consequently interfering with TSP-crosslinking of thrombin-activated platelets.
Partial Thromboplastin Time Test - Proposed Performance Guidelines
Authors: Koepke J A 
Published: July 2018

SummaryThe partial thromboplastin time (PTT) test is widely used as a screening test for the detection of hemophilia. It is also used to monitor patients on heparin anticoagulation. This proposal from a ICSH Panel proposes guidelines for the performance of this test, including comparable reference ranges, precision and sensitivity requirements.
Evaluation of Blood Glucose before and after Bariatric Surgery
Authors: Martins Ana , Oliveira Alexandre 
Published: July 2018

Abstract For original articles it must be prepared in a structured form containing a maximum of 250 words. It must contain: Background Specific aim Methods Results and Conclusion. For brief communications case reports and review articles the abstract must be structured and limited to 150 words. Enter the words (or keywords) using the DECS - Descriptors in Health Science Bireme http://decs.bvs.br/ available. Three key-words at least are necessary separated by commas. Do not cite references in the abstract.
Text: Divide the text according to the type of article (see detailed information on the item of Content Items; no punctuation should follow their titles). The Introduction should make a brief review of relevant literature in order to demonstrate the relevance of the study. Methods must be described so that the reader understands how the search has been conducted. In human research, it is mandatory to inform the existence of informed consent and approval by the medical ethics committee. The results should be presented in a consistent manner and linked to the goals and methods described. Discussion should reiterate the main findings of the manuscript the negative aspects discuss and compare the importance and implications of the findings. The conclusion must be made so that the author refrains from interference or not deductions based on the findings of the study. In original articles the process number of the Committee or the Ethics Committee of the Institution should be informed. Any financial support for research should be disclosed.
MendelProb: probability and sample size calculations for Mendelian studies of exome and whole genome sequence data
Authors: He Zongxiao , Wang Lu , DeWan Andrew T , Leal Suzanne M 
Published: July 2018

Abstract

Motivation
For the design of genetic studies, it is necessary to perform power calculations. Although for Mendelian traits the power of detecting linkage for pedigree(s) can be determined, it is also of great interest to determine the probability of identifying multiple pedigrees or unrelated cases with variants in the same gene. For many diseases, due to extreme locus heterogeneity this probability can be small. If only one family is observed segregating a variant classified as likely pathogenic or of unknown significance, the gene cannot be implicated in disease etiology. The probability of identifying several disease families or cases is dependent on the gene-specific disease prevalence and the sample size. The observation of multiple disease families or cases with variants in the same gene as well as evidence of pathogenicity from other sources, e.g. in silico prediction, expression and functional studies, can aid in implicating a gene in disease etiology. MendelProb can determine the probability of detecting a minimum number of families or cases with variants in the same gene. It can also calculate the probability of detecting genes with variants in different data types, e.g. identifying a variant in at least one family that can establish linkage and more the two additional families regardless of their size. Additionally, for a specified probability MendelProb can determine the number of probands which need to be screened to detect a minimum number of individuals with variants within the same gene.

Results
A single Mendelian disease family is not sufficient to implicate a gene in disease etiology. It is necessary to observe multiple families or cases with potentially pathogenic variants in the same gene. MendelProb, an R library, was developed to determine the probability of observing multiple families and cases with variants within a gene and to also establish the numbers of probands to screen to detect multiple observations of variants within a gene.

Availability and implementation
https://github.com/statgenetics/mendelprob
Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations
Authors: Salazar Alex N , Abeel Thomas 
Published: July 2018

Abstract

Motivation
A long-standing limitation in comparative genomic studies is the dependency on a reference genome, which hinders the spectrum of genetic diversity that can be identified across a population of organisms. This is especially true in the microbial world where genome architectures can significantly vary. There is therefore a need for computational methods that can simultaneously analyze the architectures of multiple genomes without introducing bias from a reference.

Results
In this article, we present Ptolemy: a novel method for studying the diversity of genome architectures—such as structural variation and pan-genomes—across a collection of microbial assemblies without the need of a reference. Ptolemy is a ‘top-down’ approach to compare whole genome assemblies. Genomes are represented as labeled multi-directed graphs—known as quivers—which are then merged into a single, canonical quiver by identifying ‘gene anchors’ via synteny analysis. The canonical quiver represents an approximate, structural alignment of all genomes in a given collection encoding structural variation across (sub-) populations within the collection. We highlight various applications of Ptolemy by analyzing structural variation and the pan-genomes of different datasets composing of Mycobacterium, Saccharomyces, Escherichia and Shigella species. Our results show that Ptolemy is flexible and can handle both conserved and highly dynamic genome architectures. Ptolemy is user-friendly—requires only FASTA-formatted assembly along with a corresponding GFF-formatted file—and resource-friendly—can align 24 genomes in ∼10 mins with four CPUs and &lt;2 GB of RAM.

Availability and implementation
Github: https://github.com/AbeelLab/ptolemy

Supplementary information
Supplementary data are available at Bioinformatics online.
MoDentify: phenotype-driven module identification in metabolomics networks at different resolutions
Authors: Do Kieu Trinh , Rasp David J N -P , Kastenmüller Gabi , Suhre Karsten , Krumsiek Jan 
Published: July 2018

Abstract

Summary
Associations of metabolomics data with phenotypic outcomes are expected to span functional modules, which are defined as sets of correlating metabolites that are coordinately regulated. Moreover, these associations occur at different scales, from entire pathways to only a few metabolites; an aspect that has not been addressed by previous methods. Here, we present MoDentify, a free R package to identify regulated modules in metabolomics networks at different layers of resolution. Importantly, MoDentify shows higher statistical power than classical association analysis. Moreover, the package offers direct interactive visualization of the results in Cytoscape. We present an application example using complex, multifluid metabolomics data. Due to its generic character, the method is widely applicable to other types of data.

Availability and implementation
https://github.com/krumsieklab/MoDentify (vignette includes detailed workflow).

Supplementary information
Supplementary data are available at Bioinformatics online.
Quality of reporting and assessment of patient-reported health-related quality of life in patients with brain metastases: a systematic review
Authors: DiRisio Aislyn C , Harary Maya , van Westrhenen Anouk , Nassr Eman , Ermakova Anastasia , Smith Timothy R , Dirven Linda , Taphoorn Martin J B , Mekary Rania A , Broekman Marike L D 
Published: July 2018

Abstract
Brain metastases (BMs) have become increasingly prevalent and present unique considerations for patients, including neurocognitive sequelae and advanced disease burden. Therefore, assessing health-related quality of life (HRQoL) via patient-reported outcome measures (PROMs) is an important element of managing these patients. A systematic review of the literature was conducted with the aims of (1) assessing how PROMS used in BM patients were validated, (2) assessing PROM content, and (3) evaluating quality of PROM-results reporting. PROM validation and quality of reporting were assessed using the COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) grading criteria and International Society of Quality of Life (ISOQOL)-recommended PROM-reporting standards, respectively. Forty-seven studies reporting on 5178 patients with a range of primacy cancer types were included. Eight different PROMs were applied, ranging from general to brain-specific questionnaires. Weaknesses in the validation of these PROMs were assessed by the COSMIN criteria. Many of these PROMs were not developed for BM patients and contained little information on cognitive symptoms. The overall quality of PROM reporting was insufficient based on the ISOQOL scale. Given the unique clinical considerations in BM patients, our results indicate the need for a standardized, validated questionnaire to assess HRQoL in this population. Additionally, there is room for quality improvement with regard to reporting of PROM-related results.
Treatment and survival differences across tumor sites in malignant peripheral nerve sheath tumors: a SEER database analysis and review of the literature
Authors: Martin Enrico , Muskens Ivo S , Coert J H , Smith Timothy R , Broekman Marike L D 
Published: July 2018

AbstractBackgroundCurrently, literature is scarce on differences across all possible tumor sites in malignant peripheral nerve sheath tumors (MPNSTs). To determine differences in treatment and survival across tumor sites and assess possible predictors for survival, we used the Surveillance, Epidemiology, and End Results (SEER) database.MethodsMPNST cases were obtained from the SEER database. Tumor sites were recoded into: intracranial, spinal, head and neck (H&N), limbs, core (thorax/abdomen/pelvis), and unknown site of origin. Patient and tumor characteristics, treatment modalities, and survival were extracted. Overall survival (OS) was assessed using univariable and multivariable Cox regression hazard models. Kaplan-Meier survival curves were constructed per tumor site for OS and disease-specific survival (DSS).ResultsA total of 3267 MPNST patients were registered from 1973 to 2013; 167 intracranial (5.1%), 119 spinal (3.6%), 449 H&N (13.7%), 1022 limb (31.3%), 1307 core (40.0%), and 203 unknown (6.2%). The largest tumors were found in core sites (80.0 mm, interquartile range [IQR]: 60.0-115.0 mm) and the smallest were intracranial (37.4 mm, IQR: 17.3-43.5 mm). Intracranial tumors were least frequently resected (58.1%), whereas spinal tumors were most often resected (83.0%). Radiation was administered in 35.5% to 41.8%. Independent factors associated with decreased survival were: older age, male sex, black race, no surgery, partial resection, large tumor size, high tumor grade, H&N site, and core site (all P < .05). Intracranial and pediatric tumors show superior survival (both P < .05). Intracranial tumors show superior OS and DSS curves, whereas core tumors have the worst (P < .001).ConclusionSuperior survival is seen in intracranial and pediatric MPNSTs. Core and H&N tumors have a worse prognosis.
Increasing Age Has Limited Impact on Risk of Clostridium difficile Infection in an Elderly Population
Authors: Olsen Margaret A , Stwalley Dustin , Demont Clarisse , Dubberke Erik R 
Published: July 2018

Abstract

Background
Numerous studies have found increased risk of Clostridium difficile infection (CDI) with increasing age. We hypothesized that increased CDI risk in an elderly population is due to poorer overall health status with older age.

Methods
A total of 174 903 persons aged 66 years and older coded for CDI in 2011 were identified using Medicare claims data. The comparison population consisted of 1 453 867 uninfected persons. Potential risk factors for CDI were identified in the prior 12 months and organized into categories, including infections, acute noninfectious conditions, chronic comorbidities, frailty indicators, and health care utilization. Multivariable logistic regression models with CDI as the dependent variable were used to determine the categories with the biggest impact on model performance.

Results
Increasing age was associated with progressively increasing risk of CDI in univariate analysis, with 5-fold increased risk of CDI in 94–95-year-old persons compared with those aged 66–67 years. Independent risk factors for CDI with the highest effect sizes included septicemia (odds ratio [OR], 4.1), emergency hospitalization(s) (OR, 3.9), short-term skilled nursing facility stay(s) (OR, 2.7), diverticulitis (OR, 2.2), and pneumonia (OR, 2.1). Exclusion of age from the full model had no impact on model performance. Exclusion of acute noninfectious conditions followed by frailty indicators resulted in lower c-statistics and poor model fit. Further exclusion of health care utilization variables resulted in a large drop in the c-statistic.

Conclusions
Age did not improve CDI risk prediction after controlling for a wide variety of infections, other acute conditions, frailty indicators, and prior health care utilization.
Missed Opportunities for HIV Testing of Patients Tested for Sexually Transmitted Infections at a Large Urban Health Care System From 2010 to 2015
Authors: Kapadia Shashi N , Singh Harjot K , Jones Sian , Merrick Samuel , Vaamonde Carlos M 
Published: July 2018

Abstract

Background
Appropriate testing of people at risk for HIV is an important piece of the HIV care continuum. We analyzed HIV testing patterns of patients tested for gonorrhea and chlamydia (GC/CT) at a large urban health care system in New York City.

Methods
We retrospectively studied HIV and GC/CT testing from 2010 to 2015. Data were collected from a clinical laboratory database and linked to electronic health records. Patients were older than age 13 years, not known to be HIV positive, and had had a GC/CT test. The main outcome was the proportion of patients who had both HIV and GC/CT testing performed at the same encounter.

Results
We analyzed 85 768 patients with 139 404 GC/CT testing encounters. Most of the testing encounters (88% for men and 94% for women) were in the outpatient setting. Same-day HIV testing improved from 59% in 2010 to 70% in 2015 for male patients, and from 41% to 51% for female patients. In multivariate regression, male sex was associated with receipt of an HIV test (odds ratio [OR], 2.49; P &lt; .001). Emergency department (OR, 0.22; P &lt; .0001) and inpatient (OR, 0.10; P &lt; .0001) locations were negatively associated with receipt of HIV testing. Among patients with HIV and GC/CT testing at the same encounter, 37 were HIV positive.

Conclusions
Concurrent HIV testing of patients being evaluated for GC/CT increased from 2010 to 2015. However, many patients failed to receive HIV testing, especially in emergency and inpatient settings. There continue to be missed opportunities for diagnosis of HIV among individuals with ongoing high-risk behavior.
Predictors of Mortality Among a National Cohort of Veterans With Recurrent Clostridium difficile Infection
Authors: Appaneal Haley J , Caffrey Aisling R , Beganovic Maya , Avramovic Sanja , LaPlante Kerry L 
Published: July 2018

AbstractBackgroundThough recurrent Clostridium difficile infection (CDI) is common and poses a major clinical concern, data are lacking regarding mortality among patients who survive their initial CDI and have subsequent recurrences. Risk factors for mortality in patients with recurrent CDI are largely unknown.MethodsVeterans Affairs patients with a first CDI (stool sample with positive C. difficile toxin(s) and ≥2 days CDI treatment) were included (2010–2014). Subsequent recurrences were defined as additional CDI episodes ≥14 days after the stool test date and within 30 days of the end of treatment. A matched (1:4) case–control analysis was conducted using multivariable conditional logistic regression to identify predictors of all-cause mortality within 30 days of the first recurrence.ResultsCrude 30-day all-cause mortality rates were 10.6% for the initial CDI episode, 8.3% for the first recurrence, 4.2% for the second recurrence, and 5.9% for the third recurrence. Among 110 cases and 440 controls, 6 predictors of mortality were identified: use of proton pump inhibitors (PPIs; odds ratio [OR], 3.86; 95% confidence interval [CI], 2.14–6.96), any antibiotic (OR, 3.33; 95% CI, 1.79–6.17), respiratory failure (OR, 8.26; 95% CI, 1.71–39.92), congitive dysfunction (OR, 2.41; 95% CI, 1.02–5.72), nutrition deficiency (OR, 2.91; 95% CI, 1.37–6.21), and age (OR, 1.04; 95% CI, 1.01–1.07).ConclusionsIn our national cohort of Veterans, crude mortality decreased by 44% from the initial episode to the third recurrence. Treatment with antibiotics, use of PPIs, and underlying comorbidities were important predictors of mortality in recurrent CDI. Our study assists health care providers in identifying patients at high risk of death after CDI recurrence.