bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geometry and Structure of a Fault‐Bounded Extensional Basin by Integrating Geophysical Surveys and Seismic Anisotropy Across the 30 October 2016 Mw 6.5 Earthquake Fault (Central Italy): The Pian Grande di Castelluccio Basin
Authors: Villani F. , Sapia V. , Baccheschi P. , Civico R. , Di Giulio G. , Vassallo M. , Marchetti M. , Pantosti D. 
Published: November 2018

AbstractThe Pian Grande di Castelluccio (PGC) basin is the main Quaternary depocenter of the Mt. Vettore‐Mt. Bove normal fault system (VBFS), responsible for the 30 October 2016 Mw 6.5 Norcia earthquake (central Italy). Coseismic surface faulting through the basin attests the occurrence of active splays of the seismogenic master fault; thus, we explore the subsurface basin structure to infer the long‐term behavior of the VBFS. We integrate electrical resistivity tomography (ERT), time domain electromagnetic soundings (TDEM), and horizontal‐to‐vertical spectral ratios of ambient seismic vibrations (HVSR) along a transect crossing the surface ruptures. The ERT models provide high‐resolution details of three shallow fault zones. One‐dimensional resistivity models from TDEM and HVSR frequency peaks suggest abrupt steps in the top bedrock caused by previously unknown faults and indicate an infill thickness of up to ~300 m. We also analyze shear wave splitting of S phases (fast direction φ and delay time δt) from local earthquakes recorded during our surveys to better constrain the fracture field and the properties of the inferred fault zones. We relate the retrieved pattern of fault‐parallel φ, and the associated larger δt, to the main and secondary faults in the upper crust and to the cracks or shear fabric in the damage zones of the active splays. The PGC basin is due to the interference of an older N30° striking fault system subsequently crosscut by the N150° striking VBFS, which is currently active, seismogenic, and capable of rupturing the surface during M > 6 earthquakes.
Jets and outflows of massive protostars
Authors: Kölligan A. , Kuiper R. 
Published: November 2018

Context. Massive stars live short but intense lives. While less numerous than low-mass stars, they enormously impact their surroundings by several feedback mechanisms. They form in opaque and far-away regions of the galaxy, such that one of these feedback mechanisms also becomes a record of their evolution: their bright large-scale jets and outflows.
Aims. In a comprehensive convergence study, we investigate the computational conditions necessary to resolve (pseudo-) disk formation and jet-launching processes, and analyze possible caveats. We explore the magneto-hydrodynamic (MHD) processes of the collapse of massive prestellar cores in detail, including an analysis of the forces involved and their temporal evolution for up to two free-fall times.
Methods. We conduct MHD simulations using the state-of-the-art code PLUTO, combining nonideal MHD, self-gravity, and very high resolutions as they have never been achieved before. Our setup includes a 100 M⊙ cloud core that collapses under its own self-gravity to self-consistently form a dense disk structure and launch tightly collimated magneto-centrifugal jets and wide-angle tower flows.
Results. We show a comprehensive evolutionary picture of the collapse of a massive prestellar core with a detailed analysis of the physical processes involved and our high-resolution simulations can resolve a magneto-centrifugal jet and a magnetic pressure-driven outflow, separately. The nature of the outflows depends critically on spatial resolution. Only high-resolution simulations are able to differentiate a magneto-centrifugally launched, highly collimated jet from a slow wide-angle magnetic-pressure-driven tower flow. Of these two outflow components, the tower flow dominates angular-momentum transport. The mass outflow rate is dominated by the entrained material from the interaction of the jet with the stellar environment and only part of the ejected medium is directly launched from the accretion disk. A tower flow can only develop to its full extent when much of the original envelope has already dispersed. Taking into account both the mass launched from the surface of the disk and the entrained material from the envelope, we find an ejection-to-accretion efficiency of 10%. Nonideal MHD is required to form centrifugally supported accretion disks and the disk size is strongly dependent on spatial resolution. A converged result for disk and both outflow components requires a spatial resolution of Δx ≤ 0.17 au at 1 au and sink-cell sizes ≤3.1 au.
Conclusions. Massive stars not only possess slow wide-angle tower flows, but also produce magneto-centrifugal jets, just as their low-mass counterparts. The actual difference between low-mass and high-mass star formation lies in the “embeddedness” of the high-mass star which implies that the jet and tower flow interact with the infalling large-scale stellar environment, potentially resulting in entrainment.
Cancer-specific expression quantitative loci are affected by expression dysregulation
Authors: Sheng Quanhu , Samuels David C , Yu Hui , Ness Scott , Zhao Ying-yong , Guo Yan 
Published: November 2018

Abstract
Expression quantitative trait loci (eQTLs) have been touted as the missing piece that can bridge the gap between genetic variants and phenotypes. Over the past decade, we have witnessed a sharp rise of effort in the identification and application of eQTLs. The successful application of eQTLs relies heavily on their reproducibility. The current eQTL databases such as Genotype-Tissue Expression (GTEx) were populated primarily with eQTLs deriving from germline single nucleotide polymorphisms and normal tissue gene expression. The novel scenarios that employ eQTL models for prediction purposes often involve disease phenotypes characterized by altered gene expressions. To evaluate eQTL reproducibility across diverse data sources and the effect of disease-specific gene expression alteration on eQTL identification, we conducted an eQTL study using 5178 samples from The Cancer Genome Atlas (TCGA). We found that the reproducibility of eQTLs between normal and tumor tissues was low in terms of the number of shared eQTLs. However, among the shared eQTLs, the effect directions were generally concordant. This suggests that the source of the gene expression (normal or tumor tissue) has a strong effect on the detectable eQTLs and the effect direction of the eQTLs. Additional analyses demonstrated good directional concordance of eQTLs between GTEx and TCGA. Furthermore, we found that multi-tissue eQTLs may exert opposite effects across multiple tissue types. In summary, our results suggest that eQTL prediction models need to carefully address tissue and disease dependency of eQTLs. Tissue–disease-specific eQTL databases can afford more accurate prediction models for future studies.
CAARS: comparative assembly and annotation of RNA-Seq data
Authors: Rey Carine , Veber Philippe , Boussau Bastien , Sémon Marie 
Published: November 2018

Abstract

Motivation
RNA sequencing (RNA-Seq) is a widely used approach to obtain transcript sequences in non-model organisms, notably for performing comparative analyses. However, current bioinformatic pipelines do not take full advantage of pre-existing reference data in related species for improving RNA-Seq assembly, annotation and gene family reconstruction.

Results
We built an automated pipeline named CAARS to combine novel data from RNA-Seq experiments with existing multi-species gene family alignments. RNA-Seq reads are assembled into transcripts by both de novo and assisted assemblies. Then, CAARS incorporates transcripts into gene families, builds gene alignments and trees and uses phylogenetic information to classify the genes as orthologs and paralogs of existing genes. We used CAARS to assemble and annotate RNA-Seq data in rodents and fishes using distantly related genomes as reference, a difficult case for this kind of analysis. We showed CAARS assemblies are more complete and accurate than those assembled by a standard pipeline consisting of de novo assembly coupled with annotation by sequence similarity on a guide species. In addition to annotated transcripts, CAARS provides gene family alignments and trees, annotated with orthology relationships, directly usable for downstream comparative analyses.

Availability and implementation
CAARS is implemented in Python and Ocaml and is freely available at https://github.com/carinerey/caars.

Supplementary information
Supplementary data are available at Bioinformatics online.
World Pneumonia Day 2011–2016: Twitter contents and retweets
Authors: Adnan Md Mohiuddin , Yin Jingjing , Jackson Ashley M , Tse Zion Tsz Ho , Liang Hai , Fu King-Wa , Saroha Nitin , Althouse Benjamin M , Fung Isaac Chun-Hai 
Published: November 2018

Abstract

Background
Twitter is used for World Pneumonia Day (WPD; November 12) communication. We evaluate if themes of #pneumonia tweets were associated with retweet frequency.

Methods
A total of 28 181 original #pneumonia tweets were retrieved (21 November 2016), from which six subcorpora, 1 mo before and 1 mo after WPD 2011–2016, were extracted (n=6721). Underlying topics were identified via latent Dirichlet allocation and were manually coded into themes. The association of themes with retweet count was assessed via multivariable hurdle regression.

Results
Compared with personal experience tweets, tweets that both raised awareness and promoted intervention were 2.62 times as likely to be retweeted (adjusted odds ratio [aOR] 2.62 [95% 1.79 to 3.85]) and if retweeted had 37% more retweets (adjusted prevalence ratio [aPR] 1.37 [95% CI 1.06 to 1.78]). Tweets that raised concerns about vaccine price were twice as likely to be retweeted (aOR 2.29 [95% CI 1.36 to 3.84]) and if retweeted, had double the retweet count (aPR 2.05 [95% CI 1.27 to 3.29]) of tweets sharing personal experience.

Conclusions
The #pneumonia tweets that both raised awareness and promoted interventions and those discussing vaccine price were more likely to engage users than tweets about personal experience. These results help health professionals craft WPD messages that will engage the audience.
Hassall’s corpuscles with cellular-senescence features maintain IFNα production through neutrophils and pDC activation in the thymus
Authors: Wang Jianwei , Sekai Miho , Matsui Takeshi , Fujii Yosuke , Matsumoto Mitsuru , Takeuchi Osamu , Minato Nagahiro , Hamazaki Yoko 
Published: November 2018

AbstractHassall’s corpuscles (HCs) are composed of cornifying, terminally differentiated medullary thymic epithelial cells (mTECs) that are developed under the control of Aire. Here, we demonstrated that HC-mTECs show features of cellular senescence and produce inflammatory cytokines and chemokines including CXCL5, thereby recruiting and activating neutrophils to produce IL-23 in the thymic medulla. We further indicated that thymic plasmacytoid dendritic cells (pDCs) expressing IL-23 receptors constitutively produced Ifna, which plays a role in single positive (SP) cell maturation, in an Il23a-dependent manner. Neutrophil depletion with anti-Ly6G antibody injection resulted in a significant decrease of Ifna expression in the thymic pDCs, suggesting that thymic neutrophil activation underlies the Ifna expression in thymic pDCs in steady state conditions. A New Zealand White mouse strain showing HC hyperplasia exhibited greater numbers and activation of thymic neutrophils and pDCs than B6 mice, whereas Aire-deficient B6 mice with defective HC development and SP thymocyte maturation showed significantly compromised numbers and activation of these cells. These results collectively suggested that HC-mTECs with cell-senescence features initiate a unique cell activation cascade including neutrophils and pDCs leading to the constitutive IFNα expression required for SP T-cell maturation in the thymic medulla.
Natural language processing and machine learning to identify alcohol misuse from the electronic health record in trauma patients: development and internal validation
Authors: Afshar Majid , Phillips Andrew , Karnik Niranjan , Mueller Jeanne , To Daniel , Gonzalez Richard , Price Ron , Cooper Richard , Joyce Cara , Dligach Dmitriy 
Published: November 2018

AbstractObjectiveAlcohol misuse is present in over a quarter of trauma patients. Information in the clinical notes of the electronic health record of trauma patients may be used for phenotyping tasks with natural language processing (NLP) and supervised machine learning. The objective of this study is to train and validate an NLP classifier for identifying patients with alcohol misuse.Materials and MethodsAn observational cohort of 1422 adult patients admitted to a trauma center between April 2013 and November 2016. Linguistic processing of clinical notes was performed using the clinical Text Analysis and Knowledge Extraction System. The primary analysis was the binary classification of alcohol misuse. The Alcohol Use Disorders Identification Test served as the reference standard.ResultsThe data corpus comprised 91 045 electronic health record notes and 16 091 features. In the final machine learning classifier, 16 features were selected from the first 24 hours of notes for identifying alcohol misuse. The classifier’s performance in the validation cohort had an area under the receiver-operating characteristic curve of 0.78 (95% confidence interval [CI], 0.72 to 0.85). Sensitivity and specificity were at 56.0% (95% CI, 44.1% to 68.0%) and 88.9% (95% CI, 84.4% to 92.8%). The Hosmer-Lemeshow goodness-of-fit test demonstrates the classifier fits the data well (P = .17). A simpler rule-based keyword approach had a decrease in sensitivity when compared with the NLP classifier from 56.0% to 18.2%.ConclusionsThe NLP classifier has adequate predictive validity for identifying alcohol misuse in trauma centers. External validation is needed before its application to augment screening.
The reception of Greek figurative terracottas in the Age of Enlightenment1
Authors: Uhlenbrock Jaimee P 
Published: November 2018

Abstract
While figurative terracottas from Greco-Roman antiquity were brought to light in considerable numbers from sites on the Italian mainland and in Sicily in the seventeenth century, they were consistently overlooked as important and representative examples of classical art. It was only in the later eighteenth century in Sicily that important collections of Greek figurative terracottas were assembled that began to attract the attention of northern Europeans. A demand for these accessible examples of miniature Greek sculpture arose that ultimately contributed to the formation of some of the most important antiquities collections in Europe.
Detection Rate of Colorectal Cancer or Precancer Adenoma by Colonoscopy After 1, 2, or 3 Positive Results via Fecal Immunochemical Testing
Authors: Hancock Jill A , Palmer Glen A 
Published: November 2018

Abstract

Background
Single-vial fecal immunochemical testing (FIT) is an accepted method of colorectal cancer (CRC) screening. The available 3-vial FIT data set allows for comparison of colonoscopy results using various screening methods.

Objective
To determine the optimal number of vials for a strong FIT-screening program by examining whether using only a single vial impacts the use of colonoscopy for CRC screening.

Methods
Patients were given 3-vial FIT collection kits that were processed with a positive hemoglobin cut-off detection level of 100 ng per mL. If FIT results were positive, colonoscopy testing was performed using standard practices.

Results
Detection of CRC and precursor adenoma was examined in 932 patients, with a positive colonoscopy sensitivity of 56.2% and 3.0% CRC detection after 3-vial FIT; after single-vial screening, those values were 60.9% and 4.7%, respectively.

Conclusions
Prescreening patients with FIT testing before colonoscopy allows colonoscopy testing to be targeted to higher-risk patients. Implementing use of only a single vial from the 3-vial FIT screening kit would reduce the colonoscopy reflex rate, colonoscopy complication numbers, facility costs, and patient distress by more than 40%, compared with 3-vial screening.
A clinical approach to respiratory disease in patients with hematological malignancy, with a focus on respiratory infection
Authors: Periselneris J , Brown J S 
Published: November 2018

AbstractRespiratory complications, in particular infections, are common in the setting of hematological malignancy and after hematopoetic stem cell transplant. The symptoms can be nonspecific; therefore, it can be difficult to identify and treat the cause. However, an understanding of the specific immune defect, clinical parameters such as speed of onset, and radiological findings, allows the logical diagnostic and treatment plan to be made. Radiological findings can include consolidation, nodules, and diffuse changes such as ground glass and tree-in-bud changes. Common infections that induce these symptoms include bacterial pneumonia, invasive fungal disease, Pneumocystis jirovecii and respiratory viruses. These infections must be differentiated from inflammatory complications that often require immune suppressive treatment. The diagnosis can be refined with the aid of investigations such as bronchoscopy, computed tomography (CT) guided lung biopsy, culture, and serological tests. This article gives a schema to approach patients with respiratory symptoms in this patient group; however, in the common scenario of a rapidly deteriorating patient, treatment often has to begin empirically, with the aim to de-escalate treatment subsequently after targeted investigations.
External Validation of the Subarachnoid Hemorrhage International Trialists (SAHIT) Predictive Model Using the Barrow Ruptured Aneurysm Trial (BRAT) Cohort
Authors: Mascitelli Justin R , Cole Tyler , Yoon Seungwon , Nakaji Peter , Albuquerque Felipe C , McDougall Cameron G , Zabramski Joseph M , Lawton Michael T , Spetzler Robert F 
Published: November 2018

Abstract

BACKGROUND
The Subarachnoid Hemorrhage International Trialists (SAHIT) repository is a collection of randomized clinical trials, prospective observational studies, and hospital registries that was used to create a predictive model of unfavorable outcome/mortality following aneurysmal SAH.

OBJECTIVE
To externally validate the SAHIT model using Barrow Ruptured Aneurysm Trial (BRAT) data, which was not included in the SAHIT repository.

METHODS
This is a post hoc analysis of the prospective, randomized BRAT. Three models were created: (1) Core (age, hypertension, World Federation of Neurosurgical Societies grade), (2) neuroimaging (aneurysm size/location, Fisher score), and (3) full model (model 1 and 2 plus treatment type). The performance of the models was evaluated by measures of model discrimination (area under the curve [AUC]) and model calibration (goodness of fit test, calibration in-the-large, calibration slope).

RESULTS
A total of 338 patients (average age 54 years; 67.7% good clinical grade; average aneurysm size 6.7 mm; 84.1% anterior circulation) were included. Due to a large number of crossovers, more aneurysms were clipped than coiled (67.5% vs 32.5%, respectively). A total of 10.1% of the patients died and 29.6% experienced an unfavorable outcome. For unfavorable outcome, the AUCs for the three models were: 0.728, 0.732, and 0.734, respectively. For mortality, the AUCs for the three models were: 0.721, 0.739, and 0.744, respectively. Overall, all models showed good calibration, and the measures of calibration fell within 95% CI of those produced in the SAHIT study.

CONCLUSION
Using the BRAT data, we have externally validated the SAHIT model for predicting unfavorable outcome and mortality after SAH. The model may be used to counsel patients and families on prognosis following aneurysmal SAH.
Three Z Camelopardalis-type dwarf novae exhibiting IW Andromedae-type phenomenon
Authors: Kato Taichi 
Published: November 2018

Abstract
I found that V507 Cyg, IM Eri, and FY Vul are Z Cam-type dwarf novae and they showed sequences of standstill terminated by brightening, in contrast to fading as ordinary Z Cam stars do, followed by damping oscillation. These sequences are characteristic to IW And-type objects (also known as anomalous Z Cam stars). New additions to the IW And-type objects suggest that the IW And-type phenomenon is more prevalent among Z Cam stars. I suspect that the regularity of the pattern of the IW And-type phenomenon suggests a previously unknown type of limit-cycle oscillation, and I suggest that the standstill in these objects is somehow maintained in the inner part of the disk and that the thermal instability starting from the outer part of the disk terminates the standstill to complete the cycle.
Third-nearest WZ Sge-Type dwarf nova candidate ASASSN-14dx classified on the basis of Gaia Data Release 2
Authors: Isogai Keisuke , Kato Taichi , Imada Akira , Ohshima Tomohito , Kojiguchi Naoto , Ohnishi Ryuhei , Hambsch Franz-Josef , Monard Berto , Kiyota Seiichiro , Nishimura Hideo , Nogami Daisaku 
Published: November 2018

Abstract
ASASSN-14dx showed an extraordinary outburst whose features are a small outburst amplitude (∼2.3 mag) and long duration (&gt;4 yr). Because we found a long observational gap of 123 d before the outburst detection, we propose that the main outburst plateau was missed and that this outburst is just a “fading tail” often seen after the WZ Sge-type super-outbursts. In order to distinguish between WZ Sge and SU UMa-type dwarf novae (DNe), we investigated Gaia Data Release 2 (DR2) statistically. We applied a logistic regression model and succeeded in classifying by using absolute Gaia magnitudes MG and Gaia colors GBP–GRP. Our new classifier also suggests that ASASSN-14dx is the best candidate of a WZ Sge-type DN. We estimated distances from the Earth of known WZ Sge stars by using Gaia DR2 parallaxes. The result indicates that ASASSN-14dx is the third-nearest WZ Sge star (next to WZ Sge and V455 And), and hence the object can show the third-brightest WZ Sge-type super-outburst whose maximum is V = 8–9 mag.
The Third American Society of Regional Anesthesia and Pain Medicine Practice Advisory on Local Anesthetic Systemic Toxicity
Authors: Neal J.M. , Barrington M.J. , Fettiplace M.R. , Gitman M. , Memtsoudis S.G. , Mörwald E.E. , Rubin D.S. , Weinberg G. 
Published: November 2018

(Reg Anesth Pain Med. 2018;43:113–123)
Local anesthetic systemic toxicity (LAST) is a rare, adverse event that can occur when local anesthetics are administered despite advances in technique. Patients can experience mild prodromal symptoms to serious events such as seizure, cardiac arrest, and/or death. It is important that all professionals administering local anesthetics be educated and prepared for LAST. This article uses emerging research to update the 2010 advisory from the American Society of Regional Anesthesia and Pain Medicine. This practice advisory provides recommendations from recently published articles.
Delayed Versus Early Umbilical Cord Clamping for Preterm Infants: A Systematic Review and Meta-Analysis
Authors: Fogarty M. , Osborn D.A. , Askie L. , Seidler A.L. , Hunter K. , Lui K. , Simes J. , Tarnow-Mordi W. 
Published: November 2018

(Am J Obstet Gynecol. 2018;218(1):1–18)
Delayed umbilical cord clamping may benefit preterm infants by increasing the volume of blood transferred to the neonate as well as allowing time for physiological transition, which may result in improved outcomes. The effects of delayed cord clamping are still unclear and an updated systematic review was needed. This systematic review included randomized controlled trials (RCTs) though July 31, 2017 in order to evaluate the effects of delayed clamping without cord milking compared to early clamping in reducing mortality in preterm infants.