bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is Overall Mortality the Right Composite Endpoint in Clinical Trials of Acute Respiratory Distress Syndrome?*
Authors: Villar Jesús , Martínez Domingo , Mosteiro Fernando , Ambrós Alfonso , Añón José M. , Ferrando Carlos , Soler Juan A. , Montiel Raquel , Vidal Anxela , Conesa-Cayuela Luís A. , Blanco Jesús , Arrojo Regina , Solano Rosario , Capilla Lucía , del Campo Rafael , Civantos Belén , Fernández María Mar , Aldecoa César , Parra Laura , Gutiérrez Andrea , Martínez-Jiménez Chanel , González-Martín Jesús M. , Fernández Rosa L. , Kacmarek Robert M. 
Published: February 2018

Objectives:
Overall mortality in patients with acute respiratory distress syndrome is a composite endpoint because it includes death from multiple causes. In most acute respiratory distress syndrome trials, it is unknown whether reported deaths are due to acute respiratory distress syndrome or the underlying disease, unrelated to the specific intervention tested. We investigated the causes of death after contracting acute respiratory distress syndrome in a large cohort.

Design:
A secondary analysis from three prospective, multicenter, observational studies.

Setting:
A network of multidisciplinary ICUs.

Patients:
We studied 778 patients with moderate-to-severe acute respiratory distress syndrome treated with lung-protective ventilation.

Interventions:
None.

Measurements and Main Results:
We examined death in the ICU from individual causes. Overall ICU mortality was 38.8% (95% CI, 35.4–42.3). Causes of acute respiratory distress syndrome modified the risk of death. Twenty-three percent of deaths occurred from refractory hypoxemia due to nonresolving acute respiratory distress syndrome. Most patients died from causes unrelated to acute respiratory distress syndrome: 48.7% of nonsurvivors died from multisystem organ failure, and cancer or brain injury was involved in 37.1% of deaths. When quantifying the true burden of acute respiratory distress syndrome outcome, we identified 506 patients (65.0%) with one or more exclusion criteria for enrollment into current interventional trials. Overall ICU mortality of the “trial cohort” (21.3%) was markedly lower than the parent cohort (relative risk, 0.55; 95% CI, 0.43–0.70; p < 0.000001).

Conclusions:
Most deaths in acute respiratory distress syndrome patients are not directly related to lung damage but to extrapulmonary multisystem organ failure. It would be challenging to prove that specific lung-directed therapies have an effect on overall survival.
Elevated Venous Thromboembolism Risk Following Colectomy for IBD Is Equal to Those for Colorectal Cancer for Ninety Days After Surgery
Authors: Ali Fadwa , Al-Kindi Sadeer G. , Blank Jacqueline J. , Peterson Carrie Y. , Ludwig Kirk A. , Ridolfi Timothy J. 
Published: February 2018

BACKGROUND:
The risk of postoperative venous thromboembolism is high in patients with colon cancer and IBD. Although The American Society of Colon and Rectal Surgeons suggests posthospital prophylaxis after surgery in patients with colon cancer, there are no such recommendations for patients with IBD.

OBJECTIVE:
This study aims to analyze the incidence and risk factors for postoperative venous thromboembolism.

DESIGN:
This was a retrospective review using the Explorys platform.

SETTINGS:
Aggregated electronic medical records from 26 major health care systems across the United States from 1999 to 2017 were used for this study.

PATIENTS:
Patients who underwent colon surgery were included.

MAIN OUTCOME MEASURES:
Patients were followed up to 90 days postoperatively for deep vein thrombosis and pulmonary embolism.

RESULTS:
A total of 75,620 patients underwent colon resections, including 32,020 patients with colon cancer, 9850 patients with IBD, and 33,750 patients with diverticulitis. The 30-day incidence of venous thromboembolism was higher in patients with cancer and IBD than in patients with diverticulitis (2.9%, 3.1%, and 2.4%, p < 0.001 for both comparisons). The 30-day incidence of venous thromboembolism in patients with ulcerative colitis is greater than in patients with Crohn’s disease (4.1% vs 2.1%, p < 0.001). The cumulative incidence of venous thromboembolism increased from 1.2% at 7 days after surgery to 4.3% at 90 days after surgery in patients with cancer, and from 1.3% to 4.3% in patients with IBD. In multivariable analysis, increase in the risk of venous thromboembolism was associated with cancer diagnosis, IBD diagnosis, age ≥60, smoking, and obesity.

LIMITATIONS:
This study was limited by its retrospective nature and by the use of the aggregated electronic database, which is based on charted codes and contains only limited collateral clinical data.

CONCLUSIONS:
Because of the elevated and sustained risk of postoperative thromboembolism, patients with IBD, especially ulcerative colitis, might benefit from extended thromboembolism prophylaxis similar to that of patients with colon cancer. See Video Abstract at http://links.lww.com/DCR/A544.
New Human Immunodeficiency Virus Diagnoses Among Men Who Have Sex With Men Attending Sexually Transmitted Disease Clinics, STD Surveillance Network, January 2010 to June 2013
Authors: Llata Eloisa , Braxton Jim , Asbel Lenore , Kerani Roxanne P. , Murphy Ryan , Pugsley River , Pathela Preeti , Schumacher Christina , Tabidze Irina , Weinstock Hillard S. 
Published: February 2018

Objective
To estimate new human immunodeficiency virus (HIV) diagnosis rates among HIV negative men who have sex with men (MSM) who are repeatedly tested for HIV in sexually transmitted disease (STD) clinics and assess the impact of demographic and disease-specific characteristics that are associated with higher HIV diagnosis rates.

Study Design
Retrospective analysis using 2010 to 2013 data from the STD Surveillance Network (SSuN), a sentinel surveillance system comprised of health departments in 12 cities conducting sentinel surveillance in 40 STD clinics. We analyzed data from all MSM repeatedly (≥2 times) tested for HIV, with an initial negative HIV test required for staggered cohort entry. Follow-up time was accrued from the date of the first negative HIV test to the most recent negative test or the first positive HIV test. The STD diagnoses during the follow-up period were reviewed. We estimated HIV diagnoses rates (number of HIV diagnoses/total number of person-years [PY] at risk) by demographic and clinical characteristics with 95% confidence intervals (CI) using an inverse variance weighted random effects model, adjusting for heterogeneity between SSuN jurisdictions.

Results
Overall, 640 HIV diagnoses occurred among 14,824 individuals and 20,951.6 PY of observation, for an adjusted incidence of HIV diagnosis of 3.0 per 100 PY (95% CI, 2.6–3.4). Rates varied across race/ethnicity groups with the highest rate among Blacks (4.7/100 PY; 95% CI, 4.1–5.3) followed by Hispanics, whites, and persons of other races/ethnicities. Men who have sex with men having a diagnosis of primary or secondary (P&S) syphilis on or after the first negative HIV test had a higher new HIV diagnosis rate (7.2/100 PY; 95% CI, 5.8–9.0) compared with MSM who did not have a P&S syphilis diagnosis (2.8/100 PY; 95% CI, 2.6–3.1). Men who have sex with men who tested positive for rectal gonorrhea (6.3/100 PY; 95% CI, 5.7–6.9) or rectal chlamydia (5.6/100 PY; 95% CI, 4.6–6.6) had higher rates of new HIV diagnosis when compared to those with negative test results.

Conclusions
Men who have sex with men attending SSuN STD clinics have high rates of new HIV diagnoses, particularly those with a previous diagnosis of P&S syphilis, rectal chlamydia, and/or gonorrhea. Sexually transmitted disease clinics continue to be important clinical setting for diagnosing HIV among MSM populations.
Preliminary Use of the Physical and Neurological Examination of Subtle Signs for Detecting Subtle Motor Signs in Adolescents With Sport-Related Concussion
Authors: Stephens Jaclyn A. , Denckla Martha B. , McCambridge Teri , Slomine Beth S. , Mahone E. Mark , Suskauer Stacy J. 
Published: February 2018

Abstract
Sensitive examination tools are needed to optimize evaluation after sports-related concussion. The Physical and Neurological Examination of Subtle Signs was preliminarily examined for sensitivity to motor changes in a pilot cohort of adolescents aged 13–17 yrs with sports-related concussion. A total of 15 adolescents (5 female adolescents) with sports-related concussion were evaluated up to three times: within 2 wks of injury, approximately 1 mo later (mean, 35 days between visits), and for those not recovered at the second visit, again after clinical recovery (mean, 70 days between the first and last visits for all participants). Comparison data were acquired from 20 age- and sex-matched healthy control athletes with no history of concussion who were evaluated twice (mean, 32 days apart). Main effects of group, time, and interaction effects were evaluated with an analysis of covariance, which controlled for socioeconomic status, times tested, and days between testing sessions. Adolescents with concussion had poorer Physical and Neurological Examination of Subtle Signs performance than controls did at all time points. Performance improved between visits within the concussion group, with no change within the control group. These findings suggest that the Physical and Neurological Examination of Subtle Signs merits additional study in larger cohorts and in combination with other markers of injury to facilitate an enhanced understanding of sports-related concussion and recovery.
Femoral Artery Bypass Graft Pseudoaneurysm Rupture in a Transfemoral Amputee
Authors: Dallas Jonathan , Block John J. , Bastas Gerasimos 
Published: February 2018

Abstract
The case of a patient with an actively bleeding pseudoaneurysm associated with remnants of a polytetrafluoroethylene femoral bypass graft in his transfemoral residual limb is described. Initial graft placement was due to peripheral arterial disease. During subsequent transfemoral amputation, remnants of the nonpatent graft were retained in the residuum. After 4 yrs of lower limb prosthesis use, a proximal anastomosis pseudoaneurysm developed (with avulsion of graft remnants). The patient presented to clinic with a 5-day history of increased left groin fullness and largely nonradiating pain (rated 10/10). He was diagnosed with a pseudoaneurysm (1.9 cm) originating from the left common femoral artery and an associated hematoma (8 cm) on computed tomography; this required emergent reoperation. This case highlights the importance surrounding the decision to leave or explant neovascularization materials, which may carry significant risk for infection or physical disruption complications in residual limbs.
Improved Detection of Foreign Bodies on Radiographs Using X-ray Dark-Field and Phase-Contrast Imaging
Authors: Hellbach Katharina , Beller Ebba , Schindler Andreas , Schoeppe Franziska , Hesse Nina , Baumann Alena , Schinner Regina , Auweter Sigrid , Hauke Christian , Radicke Marcus , Meinel Felix G. 
Published: February 2018

Purpose
The aim of this study was to investigate whether the detection of foreign bodies can be improved using dark-field and phase-contrast radiography compared with conventional (transmission) radiographs.

Materials and Methods
Experiments were performed using ex vivo pig paws, which were prepared with differently sized foreign bodies of metal, wood, and glass (n = 10 each). Paws without foreign bodies served as controls (n = 30). All images were acquired using an experimental grating-based large object radiography system. Five blinded readers (second- to fourth-year radiology residents) were asked to assess the presence or absence of any foreign body. Sensitivity and specificity for the detection of metal, wood, glass, and any foreign body were calculated and compared using McNemar test and generalized linear mixed models.

Results
Sensitivity for the detection of metal foreign bodies was 100% for all readers and image combinations. The sensitivity for the detection of wooden foreign bodies increased from 2% for transmission images to 78% when dark-field images were added (P < 0.0001). For glass foreign bodies, sensitivity increased from 84% for transmission images to 96% when adding phase-contrast images (P = 0.041). Sensitivity for the detection of any foreign body was 91% when transmission, dark-field, and phase-contrast images were viewed simultaneously, compared with 62% for transmission images alone (P < 0.0001). Specificity was 99% to 100% across all readers and radiography modalities.

Conclusions
Adding dark-field images substantially improves the detection of wooden foreign bodies compared with the analysis of conventional (transmission) radiographs alone. Detection of glass foreign bodies was moderately improved when adding phase-contrast images.
Early Response Assessed by Contrast-Enhanced Ultrasound in Breast Cancer Patients Undergoing Neoadjuvant Chemotherapy
Authors: Dong Ting 
Published: February 2018

Abstract
The study was aimed to investigate the role of contrast-enhanced ultrasound (CEUS) in evaluating the response of patients with breast cancer after receiving neoadjuvant chemotherapy (NAC). A systematic search was conducted in PubMed, Spring, Wanfang, and CNKI databases from 1923 to December 2016. Based on fixed effect model or randomized effects model, standardized mean difference (SMD) with its 95% confidence interval (95% CI) was calculated in accordance with heterogeneity analysis. Cochran Q and I2 tests were used to measure heterogeneity. Sensitivity analysis was performed to evaluate the strength of the meta-analysis. In total, 8 studies were enrolled in the meta-analysis. Tumor size of breast cancer was obviously decreased when evaluated by CEUS (SMD, 0.96; 95% CI, 0.76–1.15) after NAC. After aggregating the data by the fixed effect model, the CEUS time-intensity curve showed a great reduction in the area under the curve of patients receiving NAC (SMD, 0.38; 95% CI, 0.08–0.69). Based on CEUS, tumor size and area under the CEUS time-intensity curve were both reduced. We suggest that the CEUS is a promising tool for evaluating the response of breast cancer after NAC.
Myofibroblastoma of the Breast
Authors: Yilmaz Ravza , Akkavak Gulcin , Ozgur Eren , Onder Semen , Ozkurt Enver , Dursun Memduh 
Published: February 2018

Abstract
Myofibroblastoma (MFB) of the breast is an uncommon benign stromal tumor. Herein, we present histopathologically proven MFB that hyperechoic well-defined breast mass in the ultrasonography and circumscribed high-density mass in mammography. Additionally, internal septations and hyperintense appearance on magnetic resonance imaging are very valuable findings in the differential diagnosis of MFB.
Probing the rate-determining region of the potential energy surface for a prototypical ion–molecule reaction
Authors: Xie Changjian , Liu Xinguo , Sweeny Brendan C. , Miller Thomas M. , Ard Shaun G. , Shuman Nicholas S. , Viggiano Albert A. , Guo Hua 
Published: February 2018

We report a joint experimental–theoretical study of the F
–
+ HCl → HF + Cl
−
reaction kinetics. The experimental measurement of the rate coefficient at several temperatures was made using the selected ion flow tube method. Theoretical rate coefficients are calculated using the quasi-classical trajectory method on a newly developed global potential energy surface, obtained by fitting a large number of high-level
ab initio
points with augmentation of long-range electrostatic terms. In addition to good agreement between experiment and theory, analyses suggest that the ion–molecule reaction rate is significantly affected by shorter-range interactions, in addition to the traditionally recognized ion–dipole and ion–induced dipole terms. Furthermore, the statistical nature of the reaction is assessed by comparing the measured and calculated HF product vibrational state distributions to that predicted by the phase space theory.

This article is part of the theme issue ‘Modern theoretical chemistry’.
2,4-Diaminothieno[3,2-d]pyrimidines, a new class of anthelmintic with activity against adult and egg stages of whipworm
Authors: Partridge Frederick A. , Forman Ruth , Willis Nicky J. , Bataille Carole J.R. , Murphy Emma A. , Brown Anwen E. , Heyer-Chauhan Narinder , Marinič Bruno , Sowood Daniel J.C. , Wynne Graham M. , Else Kathryn J. , Russell Angela J. , Sattelle David B. 
Published: February 2018

AbstractThe human whipworm Trichuris trichiura is a parasite that infects around 500 million people globally, with consequences including damage to physical growth and educational performance. Current drugs such as mebendazole have a notable lack of efficacy against whipworm, compared to other soil-transmitted helminths. Mass drug administration programs are therefore unlikely to achieve eradication and new treatments for trichuriasis are desperately needed. All current drug control strategies focus on post-infection eradication, targeting the parasite in vivo. Here we propose developing novel anthelmintics which target the egg stage of the parasite in the soil as an adjunct environmental strategy. As evidence in support of such an approach we describe the actions of a new class of anthelmintic compounds, the 2,4-diaminothieno[3,2-d]pyrimidines (DATPs). This compound class has found broad utility in medicinal chemistry, but has not previously been described as having anthelmintic activity. Importantly, these compounds show efficacy against not only the adult parasite, but also both the embryonated and unembryonated egg stages and thereby may enable a break in the parasite lifecycle.Author SummaryThe human whipworm, Trichuris trichiura, infects around 500 million people globally, impacting on their physical growth and educational performance. There are currently huge mass drug administration (MDA) programs aiming to control whipworm, along with the other major soil transmitted helminths, Ascaris and hookworm. However single doses of albendazole and mebendazole, which are used in MDA, have particularly poor effectiveness against whipworm, with cure rates less than 40%. This means that MDA may not be able to control and eliminate whipworm infection, and risks the spread of resistance to albendazole and mebendazole in the parasite population.We are attempting to develop new treatments for parasitic worm infection, particularly focused on whipworm. We report the identification of a class of compounds, diaminothienopyrimidines (DATPs), which have not previously been described as anthelmintics. These compounds are effective against adult stages of whipworm, and also block the development of the model nematode C. elegans.Our DATP compounds reduce the ability of treated eggs to successfully establish infection in a mouse model of human whipworm. These results support a potential environmental spray to control whipworm by targeting the infectious egg stage in environmental hotspots.
Proteomics as a metrological tool to evaluate genome annotation accuracy following de novo genome assembly: a case study using the Atlantic bottlenose dolphin (Tursiops truncatus)
Authors: Neely Benjamin A. , Ellisor Debra L. , Davis W. Clay 
Published: February 2018

AbstractBackgroundThe last decade has witnessed dramatic improvements in whole-genome sequencing capabilities coupled to drastically decreased costs, leading to an inundation of high-quality de novo genomes. For this reason, continued development of genome quality metrics is imperative. The current study utilized the recently updated Atlantic bottlenose dolphin (Tursiops truncatus) genome and annotation to evaluate a proteomics-based metric of genome accuracy.ResultsProteomic analysis of six tissues provided experimental confirmation of 10 402 proteins from 4 711 protein groups, almost 1/3 of the possible predicted proteins in the genome. There was an increased median molecular weight and number of identified peptides per protein using the current T. truncatus annotation versus the previous annotation. Identification of larger proteins with more identified peptides implied reduced database fragmentation and improved gene annotation accuracy. A metric is proposed, NP10, that attempts to capture this quality improvement. When using the new T. truncatus genome there was a 21 % improvement in NP10. This metric was further demonstrated by using a publicly available proteomic data set to compare human genome annotations from 2004, 2013 and 2016, which had a 33 % improvement in NP10.ConclusionsThese results demonstrate that new whole-genome sequencing techniques can rapidly generate high quality de novo genome assemblies and emphasizes the speed of advancing bioanalytical measurements in a non-model organism. Moreover, proteomics may be a useful metrological tool to benchmark genome accuracy, though there is a need for reference proteomic datasets to facilitate this utility in new de novo and existing genomes.
Mitigating the lack of knowledge about long noncoding RNA: extracting biological functions
Authors: Adam Yagoub A. I. , Ruiz Evandro Eduardo Seron , Macedo Alessandra Alaniz 
Published: February 2018

AbstractLong non-coding RNAs (lncRNAs) play crucial roles in diverse biological processes. For example, they help to regulate gene expression and to shape the 3D organization of the cellular nucleus. However, their functions in these processes are not well known. Most of the ongoing research efforts regarding lncRNAs have focused on predicting their properties and their functions. Here, we aimed to extract the biological functions of lncRNAs referred in the biomedical literature. To this end, we performed gene enrichment tests for 417 verified gene names extracted from the scientific literature. We also succeeded in extracting biologically significant functions from 2455 single sentences of 2513 scientific abstracts retrieved from the PubMed digital library. These sentences had to be filtered to eliminate those that did not mention a biological function. They were also split into 2-3-grams and the meaningful function annotations based on Gene Ontology terms were extracted. The results provided by the gene enrichment test and the knowledge gained by automatic extraction of information from the scientific literature showed that lncRNAs play a critical role in all biological and cellular processes. Although simple natural language processing techniques fulfilled our purposes of extracting concepts concerning the biological functions of lncRNAs, in the future, we aim to use more sophisticated methods, such as grammatical rules, to extract more functions and to generate a full database for the biological functions related to lncRNAs.