bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three-dimensional scan of the uterine cavity of infertile women before assisted reproductive technology use
Authors: Pleş Liana , Alexandrescu Cătălina , Ionescu Cringu Antoniu , Arvătescu Cristian Andrei , Vladareanu Simona , Moga Marius Alexandru 
Published: October 2018

Abstract
The primary objective was to assess the utility of routine 3-dimensional (3D) ultrasound in the evaluation of infertile women and to estimate the prevalence of uterine anomalies before the use of assisted reproductive technology (ART), using the European Society of Human Reproduction and Embryology and the European Society for Gynaecological Endoscopy classification system. A second objective was to assess the effect of uterine anomalies on the pregnancy rate in patients who underwent assisted reproductive techniques.
We retrospectively studied 668 patients treated in the Department Obstetrics Gynecology and Neonatology “Sf Ioan” Clinical Emergency Hospital and in the Department of Medical and Surgical Specialties, Faculty of Medicine “’Transilvania” University of Brasov between July 2016 and February 2017 for subfertility. Patients were examined using 2-dimensional (2D) and 3-dimensional (3D) transvaginal ultrasound. Müllerian duct anomalies were present in 6.13% of patients, with the most common anomaly being a dysmorphic uterus (class U1c in 42.68% of patients), 17 patients (20.73%) with incompletely septate uterus (class U2a), 12 patients (14.63%) with a completely septate uterus (classU2b), 8 patients (9.75%) with a partly bicorporeal uterus (classU3a), and 6 patients (7.31%) with a completely bicorporeal uterus (class U3b). Only 1 (1.21%) patient had an aplastic uterus without a rudimentary cavity (class U5b). The pregnancy rate in the presence of uterine anomalies was 55% and the pregnancy rate in control group patients was 39.8%. The incidence of pregnancy in the group with uterine anomalies was statistically similar with the control group of normal uterus (P < .11). For ongoing pregnancy rate and live birth rate, our data indicated a slightly elevated rate for both of those indexes in the anomalies group. The incidence of miscarriage in the presence of uterine anomalies was 24% and 6.7% in the control group, which is statistically significant (P = .05).
3D ultrasound evaluation of the uterus should be considered before ART in order to make an accurate diagnosis of the uterine congenital anomaly and improve ART results.
The use of SAPS 3, SOFA, and Glasgow Coma Scale to predict mortality in patients with subarachnoid hemorrhage
Authors: Basile-Filho Anibal , Lago Alessandra Fabiane , Menegueti Mayra Gonçalves , Nicolini Edson Antonio , Nunes Roosevelt Santos , Lima Silas Lucena de , Ferreira João Paulo Uvera , Feres Marcus Antonio 
Published: October 2018

Abstract
Guidelines for patients with subarachnoid hemorrhage (SAH) management and several grading systems or prognostic indices have been used not only to improve the quality of care but to predict also the outcome of these patients. Among them, the gold standards Fisher radiological grading scale, Hunt-Hess and the World Federation of Neurological Surgeons (WFNS) are the most employed. The objective of this study is to compare the predictive values of simplified acute physiology score (SAPS) 3, sequential organ failure assessment (SOFA), and Glasgow Coma Scale (GCS) in the outcome of patients with aneurysmal SAH.
Fifty-one SAH patients (33% males and 67% females; mean age of 54.1 ± 10.3 years) admitted to the intensive care units (ICU) in the post-operative phase were retrospectively studied. The patients were divided into survivors (n=37) and nonsurvivors (n = 14). SAPS 3, Fischer scale, WFNS, SOFA, and GCS were recorded on ICU admission (day 1 – D1), and 72-hours (day 3 – D3) SOFA, and GCS. The capability of each index SAPS 3, SOFA, and GCS (D1 and D3) to predict mortality was analyzed by receiver operating characteristic (ROC) curves. The area under the ROC curve (AUC) and the respective confidence interval (CI) were used to measure the index accuracy. The level of significance was set at P < .05.
The mean SAPS 3, SOFA, and GCS on D1 were 13.5 ± 12.7, 3.1 ± 2.4, and 13.7 ± 2.8 for survivors and 32.5 ± 28.0, 5.6 ± 4.9, and 13.5 ± 1.9 for nonsurvivors, respectively. The AUC and 95% CI for SAPS 3, SOFA, and GCS on D1 were 0.735 (0.592–0.848), 0.623 (0.476–0.754), 0.565 (0.419–0.703), respectively. The AUC and 95% CI for SOFA and GCS on D3 were 0.768 (0.629–0.875) and 0.708 (0.563–0.826), respectively. The overall mortality was 37.8%.
Even though SAPS 3 and Fischer scale predicted mortality better on admission (D1), both indices SOFA and GCS performed similarly to predict outcome in SAH patients on D3.
The association between IUGR and maternal inherited thrombophilias
Authors: Dugalić Stefan , Petronijevic Milos , Stefanovic Aleksandar , Jeremic Katarina , Petronijevic Svetlana Vrzic , Soldatovic Ivan , Pantic Igor , Djunic Irena , Jokic Zoran , Djokovic Filip , Dotlic Jelena , Zaric Milica , Todorovic Jovana 
Published: October 2018

Abstract
One of the risk factors for vascular obstetric complications, such as intrauterine growth restriction (IUGR), is inherited thrombophilias. Nevertheless, routine screening for thrombophilias is not endorsed in pregnant women due to their low prevalence and conflicting results of published studies regarding the usefulness of screening in these patients. The cause of IUGR remains unknown in almost 1 quarter of cases. There are no published studies evaluating the association of inherited thrombophilias and IUGR in patients with IUGR of unknown origin. Understanding and preventing IUGR is an important public health concern, as IUGR has been associated with fetal mortality and neonatal morbidity, as well as adverse long-standing consequences. This study aimed to evaluate the prevalence of inherited thrombophilias in IUGR of unknown cause and to test the association between the inherited thrombophilias and IUGR of unknown cause.
This study included 33 cases of IUGR of unknown cause tested for inherited thrombophilias and 66 controls individually matched for age, ethnicity, and smoking status.
Patients with plasminogen activator inhibitor 1 (PAI-1) and methylenetetrahydrofolate reductase (MTHFR) had significantly higher odds for IUGR of unknown cause (P < .001 and P = .002, respectively) with OR 13.546 (CI 95% 3.79–48.37) and 8.139 (CI 95% 2.20–30.10), respectively. A positive association between other inherited thrombophilias (homozygous 20210 prothrombin gene mutation and homozygous factor V Leiden) and IUGR of unknown cause was also found, P = .096, OR 6.106 (CI 95% 0.72–51.30), although it was not statistically significant (P = .096, OR = 6.106, CI 95% 0.72–51.30).
Our results indicate that PAI-1 and MTHFR thrombophilias represent risk factors for IUGR of otherwise unidentified cause.
Blunt traumatic diaphragmatic rupture
Authors: Lim Kyoung Hoon , Park Jinyoung 
Published: October 2018

Abstract
Blunt traumatic diaphragmatic rupture (BTDR) is uncommon, but is associated with high rates of morbidity and mortality. The purpose of this study was to present our experience with management of this injury. Medical records of 38 patients with BTDR who were treated in our hospital from January 2001 to June 2016 were analyzed retrospectively. The sex, age, cause of injury, location of rupture, mode of diagnosis, time to diagnosis, the presence of herniation and bowel perforation, the presence of preoperative shock and intubation, Injury Severity Score (ISS), associated injuries, comorbidity, the operative procedure, morbidity and mortality, and the predictive factors affecting the outcome of BTDR were evaluated. There were 32 men (84.2%) and 6 women (15.8%) with a mean age of 51.2 years (range 18–84 years). The diagnosis could be preoperatively established in 28 patients (73.7%) with a plain chest X-ray or computed tomography scan. Rupture of diaphragm was left-sided in 31 patients (81.6%), right-sided in 6 (15.8%), and bilateral in 1 (2.6%). Sixteen patients had preoperative shock (systolic blood pressure <90 mm Hg, heart rate >120/min). Initial operative approaches were laparotomy in 22 patients (57.9%) and thoracotomy in 16 (42.1%). Eleven required additional exploration. The rate of additional exploration was higher in patients who initially underwent thoracotomy than laparotomy (56.2% vs 9.1%, P = .003). Patients who underwent additional exploration had a significantly longer operation time (330 minutes vs 237.5 minutes, P = .012), and a significantly higher morbidity rate (72.7% vs 22.2%, P =.008). Overall mortality was observed in 6 patients (15.8%). The mortality was associated with right-sided TDR (P = .042) and preoperative shock (P = .003). Neither ISS nor delay in diagnosis posed a statistically significant risk to the outcome of patients. Intra-abdominal organ injuries are more common than intrathoracic injuries in patients with BTDR, indicating that laparotomy should be the initial approach in these patients. Preoperative shock and right-sided TDR are predictive of mortality after BTDR.
Imaging and Cytopathological Criteria Indicating Malignancy in Mucin-Producing Pancreatic Neoplasms
Authors: Salla Charitini , Karvouni Eleni , Nikas Ilias , Ikonomakis Aristidis , Konstantinou Panagiotis , Karoumpalis Ioannis , Sepsa Athanasia , Papaparaskeva Kleio , Tsopanomichalou Maria , Georgiadou Despoina , Kostopoulou Akrivi , Tsiotos Gregory , Theocharis Stamatios , Sergentanis Theodoros N. , Politi Ekaterini 
Published: October 2018

Objectives
This study aims to evaluate the performance of clinical, imaging, and cytopathological criteria in the identification of high-grade dysplasia/carcinoma (HGD/Ca) in pancreatic mucin-producing cystic neoplasms.

Methods
Sixty-eight consecutive, histopathologically confirmed mucin-producing cystic neoplasms, evaluated by endoscopic ultrasound-guided fine-needle aspiration, were enrolled; specifically, 39 branch duct intraductal papillary mucinous neoplasms (BD-IPMNs), 21 main duct IPMNs, and 8 mucinous cystic neoplasms. The associations between HGD/Ca in histopathology and findings of endoscopic ultrasound and cytology, demographic, lifestyle, and clinical parameters were evaluated, separately in IPMNs and mucinous cystic neoplasms.

Results
Age 65 years or more was associated with HGD/Ca in IPMNs. In BD-IPMNs, cyst diameter 3 cm or greater (sensitivity, 68.8%; specificity, 65.2%), a mural nodule (sensitivity, 56.3%; specificity, 78.3%), main pancreatic duct diameter 5 to 9 mm (sensitivity, 50.0%; specificity, 87.0%), and suspicious cytology (sensitivity, 81.3%; specificity, 100%) signaled the presence of HGD/Ca. Similarly, in main duct IPMNs, suspicious cytology predicted HGD/Ca with high sensitivity (88.9%) and excellent specificity (100%). Regarding cytopathological criteria, in BD-IPMNs, HGD/Ca was associated with a high nuclear/cytoplasmic ratio, background necrosis, presence of papillary structures, hypochromatic nuclei, hyperchromatic nuclei, and major nuclear membrane irregularities (thickening and/or indentations).

Conclusions
Clinical, imaging, and cytopathological criteria are useful in the identification of HGD/Ca in IPMNs.
Prelicensure Nursing Students' Attitudes and Perceptions of End-of-Life Care
Authors: Smothers Angel , Young Stephanie , Dai Zheng 
Published: October 2018

Background
It is important that education on palliative care begin early in prelicensure nursing education because of the complex care needs of patients requiring end-of-life care.

Problem
Nursing students often lack confidence and skills in providing quality care for these patients.

Approach
Nursing students’ attitudes on end-of-life care were assessed using the Frommelt Attitudes Toward Care of the Dying scale. Students were tested as sophomores, then again as seniors, in a nursing program where the End-of-Life Nursing Education Consortium (ELNEC) curriculum had previously been integrated.

Outcomes
Seniors reported improved comfort levels providing end-of-life care.

Conclusion
Assessing for improved comfort levels among nursing students who receive ELNEC training could help support ongoing efforts to integrate this education in all nursing programs. Students who had formal education in end-of-life care were more comfortable caring for patients at end of life and had a better understanding of their role.
Preoperative Biliary Stenting and Major Morbidity After Pancreatoduodenectomy: Does Elapsed Time Matter?
Authors: Sandini Marta , Honselmann Kim C. , Birnbaum David J. , Gavazzi Francesca , Chirica Mircea , Wellner Ulrich , Guilbaud Théophile , Bolm Louisa , Angrisani Marco , Moutardier Vincent , Cereda Marco , Girard Édouard , Montorsi Marco , Keck Tobias , Zerbi Alessandro , Gianotti Luca 
Published: October 2018

Objective:
To analyze possible associations between the duration of stent placement before surgery and the occurrence and severity of postoperative complications after pancreatoduodenectomy (PD).

Background:
The effect of preoperative stent duration on postoperative outcomes after PD has not been investigated.

Methods:
From 2013 to 2016, patients who underwent PD for any reasons after biliary stent placement at 5 European academic centers were analyzed from prospectively maintained databases. The primary aim was to investigate the association between the duration of preoperative biliary stenting and postoperative morbidity. Patients were stratified by stent duration into 3 groups: short (<4 weeks), intermediate (4–8 weeks), and long (≥8 weeks).

Results:
In all, 312 patients were analyzed. The median time from stent placement to surgery was 37 days (2–559 days), and most operations were performed for pancreatic cancer (67.6%). Morbidity and mortality rates were 56.0% and 2.6%, respectively. Patients in the short group (n = 106) experienced a higher rate of major morbidity (43.4% vs 20.0% vs 24.2%; P < 0.001), biliary fistulae (13.2% vs 4.3% vs 5.5%; P = 0.031), and length of hospital stay [16 (10–52) days vs 12 (8–35) days vs 12 (8–43) days; P = 0.025]. A multivariate adjusted model identified the short stent duration as an independent risk factor for major complications (odds ratio 2.64, 95% confidence interval 1.23–5.67, P = 0.013).

Conclusions:
When jaundice treatment cannot be avoided, delaying surgery up to 1 month after biliary stenting may reduce major morbidity, procedure-related complications, and length of hospital stay.
Mutations of RAS/RAF Proto-oncogenes Impair Survival After Cytoreductive Surgery and HIPEC for Peritoneal Metastasis of Colorectal Origin
Authors: Schneider Marcel André , Eden Janina , Pache Basile , Laminger Felix , Lopez-Lopez Victor , Steffen Thomas , Hübner Martin , Kober Friedrich , Roka Sebastian , Campos Pedro Cascales , Roth Lilian , Gupta Anurag , Siebenhüner Alexander , Kepenekian Vahan , Passot Guillaume , Gertsch Philippe , Glehen Olivier , Lehmann Kuno 
Published: October 2018

Background:
Adequate selection of patients with peritoneal metastasis (PM) for cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) remains critical for successful long-term outcomes. Factors reflecting tumor biology are currently poorly represented in the selection process. The prognostic relevance of RAS/RAF mutations in patients with PM remains unclear.

Methods:
Survival data of patients with colorectal PM operated in 6 European tertiary centers were retrospectively collected and predictive factors for survival identified by Cox regression analyses. A simple point-based risk score was developed to allow patient selection and outcome prediction.

Results:
Data of 524 patients with a median age of 59 years and a median peritoneal cancer index of 7 (interquartile range: 3–12) were collected. A complete resection was possible in 505 patients; overall morbidity and 90-day mortality were 50.9% and 2.1%, respectively. PCI [hazard ratio (HR): 1.08], N1 stage (HR: 2.15), N2 stage (HR: 2.57), G3 stage (HR: 1.80) as well as KRAS (HR: 1.46) and BRAF (HR: 3.97) mutations were found to significantly impair survival after CRS/HIPEC on multivariate analyses. Mutations of RAS/RAF impaired survival independently of targeted treatment against EGFR. Consequently, a simple point-based risk score termed BIOSCOPE (BIOlogical Score of COlorectal PEritoneal metastasis) based on PCI, N-, G-, and RAS/RAF status was developed, which showed good discrimination [development area under the curve (AUC) = 0.72, validation AUC = 0.70], calibration (P = 0.401) and allowed categorization of patients into 4 groups with strongly divergent survival outcomes.

Conclusion:

RAS/RAF mutations impair survival after CRS/HIPEC. The novel BIOSCOPE score reflects tumor biology, adequately stratifies long-term outcomes, and improves patient assessment and selection.
DIAlignR provides precise retention time alignment across distant runs in DIA and targeted proteomics
Authors: Gupta Shubham , Ahadi Sara , Zhou Wenyu , Röst Hannes 
Published: October 2018

AbstractSWATH-MS has been widely used for proteomics analysis given its high-throughput and reproducibility but ensuring consistent quantification of analytes across large-scale studies of heterogeneous samples such as human-plasma remains challenging. Heterogeneity in large-scale studies can be caused by large time intervals between data-acquisition, acquisition by different operators or instruments, intermittent repair or replacement of parts, such as the liquid chromatography column, all of which affect retention time (RT) reproducibility and successively performance of SWATH-MS data analysis. Here, we present a novel algorithm for retention time alignment of SWATH-MS data based on direct alignment of raw MS2 chromatograms using a hybrid dynamic programming approach. The algorithm does not impose a chronological order of elution and allows for alignment of elution-order swapped peaks. Furthermore, allowing RT-mapping in a certain window around coarse global fit makes it robust against noise. On a manually validated dataset, this strategy outperforms the current state-of-the-art approaches. In addition, on a real-world clinical data, our approach outperforms global alignment methods by mapping 98% of peaks compared to 67% cumulatively and DIAlignR can reduce alignment error up to 30-fold for extremely distant runs. The robustness of technical parameters used in this pairwise alignment strategy has also been demonstrated. The source code is released under the BSD license at https://github.com/Roestlab/DIAlignR.Abbreviations:AUCArea Under the CurveDIAData-independent acquisitionLCLiquid chromatographyLOESSLocal weighted regressionRSEResidual Standard ErrorRTRetention timeXICExtracted ion chromatogramsData Availability:Raw chromatograms and features extracted by OpenSWATH are available on PeptideAtlas.Servername: ftp.peptideatlas.orgUsername: PASS01280Password: KQ2592b
Modular modeling improves the predictions of genetic variant effects on splicing
Authors: Cheng Jun , Nguyen Thi Yen Duong , Cygan Kamil J , Çelik Muhammed Hasan , Fairbrother William G , Avsec Žiga , Gagneur Julien 
Published: October 2018

AbstractPredicting the effects of genetic variants on splicing is highly relevant for human genetics. We describe the framework MMSplice (modular modeling of splicing) with which we built the winning model of the CAGI 2018 exon skipping prediction challenge. The MMSplice modules are neural networks scoring exon, intron, and splice sites, trained on distinct large-scale genomics datasets. These modules are combined to predict effects of variants on exon skipping, alternative donor and acceptor sites, splicing efficiency, and pathogenicity, with matched or higher performance than state-of-the-art. Our models, available in the repository Kipoi, apply to variants including indels directly from VCF files.
Pupil responses to hidden photoreceptor–specific modulations in movies
Authors: Spitschan Manuel , Gardasevic Marina , Martial Franck P. , Lucas Robert J. , Allen Annette E. 
Published: October 2018

AbstractUnder typical daytime light levels, the human pupillary light response (PLR) is driven by the activity of the L, M, and S cones, and melanopsin expressed in the so-called intrinsically photosensitive retinal ganglion cells (ipRGCs). However, the importance of each of these photoreceptive mechanisms in defining pupil size under real-world viewing conditions remains to be established. To address this question, we embedded photoreceptor-specific modulations in a movie displayed using a novel projector-based five-primary spatial stimulation system, which allowed for the precise control of photoreceptor activations in time and space. We measured the pupillary light response in eleven observers, who viewed short cartoon movies which contained hidden low-frequency (0.25 Hz) silent-substitution modulations of the L, M and S cones (no stimulation of melanopsin), melanopsin (no stimulation of L, M and S cones), both L, M, and S cones and melanopsin or no modulation at all. We find that all photoreceptors active at photopic light levels regulate pupil size under this condition. Our data imply that embedding modulations in photoreceptor contrast could provide a method to manipulate key adaptive aspects of the human visual system in everyday, real-world activities such as watching a movie.
Board nationality and educational background diversity and corporate social performance
Authors: Harjoto Maretno Agus , Laksmana Indrarini , Yang Ya wen 
Published: October 2018

PurposeThis paper aims to examine the relationship between the nationality and educational background diversity of directors serving on corporate boards and the firms’ corporate social performance (CSP).Design/methodology/approachThis study measures nationality diversity by directors’ national citizenship and measures educational background diversity by countries from which they earned their undergraduate and post undergraduate degrees. It measures firms’ CSP using the MSCI ESG ratings. The study uses both univariate and multivariate analyses to empirically test the hypotheses.FindingsUsing a sample of US firms, the authors find that board nationality diversity and educational background diversity are positively associated with CSP. The findings suggest that improving director nationality diversity and educational background diversity could improve firms’ social performance.Originality/valueThis study shows that the increasing trend of foreign nationals in the US boards could shift the focus of US corporations to be more stakeholder-oriented.