bluuebunny/crossref_metadata_2025_split huggingface dataset:
Test particles dynamics in the JOREK 3D non-linear MHD code and application to electron transport in a disruption simulation
Authors: Sommariva C. , Nardon E. , Beyer P. , Hoelzl M. , Huijsmans G.T.A. , van Vugt D. 
Published: October 2017

Abstract
In order to contribute to the understanding of runaway electron generation mechanisms during tokamak disruptions, a test particle tracker is introduced in the JOREK 3D non-linear MHD code, able to compute both full and guiding center relativistic orbits. Tests of the module show good conservation of the invariants of motion and consistency between full orbit and guiding center solutions. A first application is presented where test electron confinement properties are investigated in a massive gas injection-triggered disruption simulation in JET-like geometry. It is found that electron populations initialised before the thermal quench (TQ) are typically not fully deconfined in spite of the global stochasticity of the magnetic field during the TQ. The fraction of ‘survivors’ decreases from a few tens down to a few tenths of percent as the electron energy varies from 1 keV to 10 MeV. The underlying mechanism for electron ‘survival’ is the prompt reformation of closed magnetic surfaces at the plasma core and, to a smaller extent, the subsequent reappearance of a magnetic surface at the edge. It is also found that electrons are less deconfined at 10 MeV than at 1 MeV, which appears consistent with a phase averaging effect due to orbit shifts at high energy.
Filling reference gaps via assembling DNA barcodes using high-throughput sequencing—moving toward barcoding the world
Authors: Liu Shanlin , Yang Chentao , Zhou Chengran , Zhou Xin 
Published: October 2017

Abstract
Over the past decade, biodiversity researchers have dedicated tremendous efforts to constructing DNA reference barcodes for rapid species registration and identification. Although analytical cost for standard DNA barcoding has been significantly reduced since early 2000, further dramatic reduction in barcoding costs is unlikely because Sanger sequencing is approaching its limits in throughput and chemistry cost. Constraints in barcoding cost not only led to unbalanced barcoding efforts around the globe, but also prevented high-throughput sequencing (HTS)–based taxonomic identification from applying binomial species names, which provide crucial linkages to biological knowledge. We developed an Illumina-based pipeline, HIFI-Barcode, to produce full-length Cytochrome c oxidase subunit I (COI) barcodes from pooled polymerase chain reaction amplicons generated by individual specimens. The new pipeline generated accurate barcode sequences that were comparable to Sanger standards, even for different haplotypes of the same species that were only a few nucleotides different from each other. Additionally, the new pipeline was much more sensitive in recovering amplicons at low quantity. The HIFI-Barcode pipeline successfully recovered barcodes from more than 78% of the polymerase chain reactions that didn't show clear bands on the electrophoresis gel. Moreover, sequencing results based on the single molecular sequencing platform Pacbio confirmed the accuracy of the HIFI-Barcode results. Altogether, the new pipeline can provide an improved solution to produce full-length reference barcodes at about one-tenth of the current cost, enabling construction of comprehensive barcode libraries for local fauna, leading to a feasible direction for DNA barcoding global biomes.
On the Second Boundary Value Problem for a Class of Fully Nonlinear Flows I
Authors: Huang Rongli , Ye Yunhua 
Published: October 2017

Abstract
In this article, a class of fully nonlinear flows with nonlinear Neumann type boundary condition is considered. This problem was solved partly by the first author under the assumption that the flow is the parabolic type special Lagrangian equation in $\mathbb{R}^{2n}$. We show that the convexity is preserved for solutions of the fully nonlinear parabolic equations and prove the long time existence and convergence of the flow. In particular, we can prescribe the second boundary value problems for a family of special Lagrangian graphs in Euclidean and pseudo-Euclidean space.
Correlation between the variation of the ionizing continuum and broad absorption lines
Authors: Lu Wei-Jian , Lin Ying-Ru , Qin Yi-Ping 
Published: October 2017

Abstract
In this Letter, we present an analysis of the relation between the variability of broad absorption lines (BALs) and that of the continuum. Our sample is multi-epoch observations of 483 quasars by the Sloan Digital Sky Survey-I/II/III (SDSS-I/II/III). We derive the fractional flux variations of the continuum and fractional equivalent width (EW) variations for C iv and Si iv BALs, and explore the correlations between the three. Our results reveal moderate anticorrelations with high significance level between the fractional flux variations of the continuum and fractional EW variations for both C iv and Si iv BALs. We also prove a significant positive correlation between the fractional EW variations for C iv and Si iv BALs, which is in agreement with several previous studies. Our discoveries can serve as evidence for the idea: Change of an ionizing continuum is the primary driver of BAL variability.
The international nucleotide sequence database collaboration
Authors: Karsch-Mizrachi Ilene , Takagi Toshihisa , Cochrane Guy ,   on behalf of the International Nucleotide Sequence Database Collaboration
Published: October 2017

Abstract
For more than 30 years, the International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org/) has been committed to capturing, preserving and providing access to comprehensive public domain nucleotide sequence and associated metadata which enables discovery in biomedicine, biodiversity and biological sciences. Since 1987, the DNA Data Bank of Japan (DDBJ) at the National Institute for Genetics in Mishima, Japan; the European Nucleotide Archive (ENA) at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK; and GenBank at National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health in Bethesda, Maryland, USA have worked collaboratively to enable access to nucleotide sequence data in standardized formats for the worldwide scientific community. In this article, we reiterate the principles of the INSDC collaboration and briefly summarize the trends of the archival content.
Eleonora di Toledo
Authors: Tomas Natalie 
Published: October 2017

Eleonora Álvarez di (of) Toledo (b. 1522–d. 1562) was the second duchess of Florence and married Cosimo I de’ Medici (b. 1519–d. 1574) in 1539. She was born in Léon, Spain, and then moved to Naples in 1534, when her father, Don Pedro Álvarez de Toledo, Duke of Alba and Marquis of Villafranca, became Viceroy of Naples. Her mother, Maria Osorio Pimentel, was connected to the Spanish ruling household, and so Eleonora received a traditional Spanish upbringing. Eleonora had eleven children, including five sons, and contemporaries celebrated her fertility. The marriage between the ducal couple appeared to be a very happy one. Eleonora traveled with her husband frequently to their various palaces and villas across Tuscany, enjoying hunting, fishing, riding horses, and gambling. Apart from the production of children, Eleonora was a wealthy landowner who traded in commodities such as grain. The duchess acted as regent at least four times during her marriage, because of Cosimo I’s absence during war (1541, 1543) or illness (1544–1545). The longest period of Eleonora’s regency was between 1551 and 1554, while Cosimo I was away fighting the War of Siena. Eleonora was duchess of Siena from 1559 and together with her husband made a triumphal entry into Siena in 1560. Eleonora was a great patron of art, employing Agnolo Bronzino to decorate her private chapel and paint a series of portraits of her. She also employed other artists, including the sculptors Baccio Bandinelli and Benvenuto Cellini, the miniaturist Giulio Clovio, and the painter and architect Giorgio Vasari. Eleonora acquired the Palazzo Pitti and began renovations, including the development of the Boboli Gardens. However, she did not live to see the completion of the project. Her court included both Italian and Spanish speakers, and she supported the Jesuits in Florence. Her religious patronage reflected her support for Spanish religious practice. She favored female lyric poets at her court, as well as Spanish poets. Eleonora was often ill with tuberculosis from the 1550s, and she died on 17 December 1562 after contracting a malarial fever along with two of her sons, Giovanni and Garzia, who both had died shortly before her. Eleonora di Toledo is best remembered because of the iconic 1545 state portrait of her with her son Giovanni, painted by Bronzino, which is now in the Uffizi Gallery in Florence.
Recognizing primary effort thrombosis in primary care
Authors: Archambault Mark E. , Chila Allison , Lundin Lauren , Walker Rachel 
Published: October 2017

ABSTRACT
Primary effort thrombosis is a noniatrogenic deep vein thrombosis of the upper extremity. The incidence of this condition is 1 to 2 in 100,000 per year. The risk factors and typical patient population differ from other thrombotic events. Patients with primary effort thrombosis are typically young, athletic, and lack comorbidities. Due to its low incidence and unique risk factors, primary effort thrombosis often is misdiagnosed as a musculoskeletal injury. However, early recognition, initial testing with Doppler ultrasound, and immediate referral to a vascular center is essential to achieve optimal outcomes. This article reviews risk factors, pathogenesis, presentation, diagnosis, and acute management of primary effort thrombosis for primary care providers.
Efficiently finding and using evidence to guide clinical practice and improve care
Authors: Akbashev Mikhail Y. , Pittman J. Richard , Dressler Daniel D. 
Published: October 2017

ABSTRACT
Using evidence to guide patient care improves patient outcomes. However, the volume of clinical and scientific literature and demands on provider time make staying current challenging. Primary literature searching or using public search engines to answer clinical questions often results in low-quality or incorrect answers, potentially yielding suboptimal clinical care. This article describes systematic strategies for primary literature searching that can yield higher-quality results than an unstructured approach.
Medical Education to Enhance Critical Consciousness: Facilitators’ Experiences
Authors: Zaidi Zareen , Vyas Rashmi , Verstegen Danielle , Morahan Page , Dornan Tim 
Published: October 2017

Purpose
To analyze educators’ experiences of facilitating cultural discussions in two global health professions education programs and what these experiences had taught them about critical consciousness.

Method
A multicultural research team conducted in-depth interviews with 16 faculty who had extensive experience facilitating cultural discussions. They analyzed transcripts of the interviews thematically, drawing sensitizing insights from Gramsci’s theory of cultural hegemony. Collaboration and conversation helped the team self-consciously examine their positions toward the data set and be critically reflexive.

Results
Participant faculty used their prior experience facilitating cultural discussions to create a “safe space” in which learners could develop critical consciousness. During multicultural interactions they recognized and explicitly addressed issues related to power differentials, racism, implicit bias, and gender bias. They noted the need to be “facile in attending to pain” as learners brought up traumatic experiences and other sensitive issues including racism and the impact of power dynamics. They built relationships with learners by juxtaposing and exploring the sometimes-conflicting norms of different cultures. Participants were reflective about their own understanding and tendency to be biased. They aimed to break free of such biases while role modeling how to have the courage to speak up.

Conclusions
Experience had given facilitators in multicultural programs an understanding of their responsibility to promote critical consciousness and social justice. How faculty without prior experience or expertise could develop those values and skills is a topic for future research.
Clinical Updates in Women’s Health Care Summary: Ischemic Heart Disease
Authors: Fuller Brittany S. , Carlyle Lynn , Voeltz Michele D. 
Published: October 2017

Abstract
Cardiovascular disease is the leading cause of death among women in the United States. Obstetrician–gynecologists often are the sole health care providers for otherwise healthy women. Therefore, they must be aware of risk factors, signs, and symptoms of cardiovascular disease and be prepared to recognize and treat this condition in patients as well as provide referrals when specialized care is indicated. Women with cardiac problems typically present with chest discomfort; however, they also are more likely than healthy women to present with other common symptoms, such as shortness of breath, back pain, jaw pain, or nausea and vomiting. This monograph, with a primary focus on ischemic heart disease (IHD), discusses the basic anatomy of the heart and coronary arteries; vascular biology; pathogenesis of atherosclerosis; and the screening, prevention, diagnosis, and treatment of IHD as well as the multiple risk factors associated with the development of IHD that contribute to both increased morbidity and mortality.
Prediction Model of In-Hospital Mortality After Hip Fracture Surgery
Authors: Endo Atsushi , Baer Heather J. , Nagao Masashi , Weaver Michael J. 
Published: October 2017

Objectives:Mortality in elderly patients after the surgical treatment of hip fractures remains high. Although individual clinical risk factors have been widely studied, there has been limited research on prediction models in this population. The purpose of this study was to develop a prediction model for in-hospital mortality after hip fracture surgery and to evaluate the performance of this model.Methods:Using the National Inpatient Sample database from 2012 to 2013, we collected data on 535,475 patients older than 50 years who had hip fracture surgery. Patient characteristics, surgery-specific factors, and Elixhauser comorbidities were used as candidate variables. The patients were randomly divided into training and testing cohorts. The Lasso (least absolute shrinkage and selection operator) method was used to select predictor variables, and points were assigned to each variable based on its coefficient.Results:We identified 8 essential predictors (age, timing of surgery, male sex, congestive heart failure, pulmonary circulation disease, renal failure, weight loss, and fluid and electrolyte disorders) for mortality, with a maximum prediction score of 20. The model's area under the curve was 0.74, and the Hosmer–Lemeshow testPvalue was 0.59 on the testing set. With the application of cutoff values (scores 0–5, 6–9, and 10–20), the observed in-hospital postoperative mortality was 0.6%, 2.5%, and 7.5%, respectively.Conclusions:We built a simple prediction model with 8 essential clinical factors that predict in-hospital mortality after hip fracture surgery. This model may assist in counseling patients and families and measuring hospital quality of care.Level of Evidence:Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Revisiting tumor patterns and penetrance in germline TP53 mutation carriers: temporal phases of Li–Fraumeni syndrome
Authors: Amadou Amina , Waddington Achatz Maria I. , Hainaut Pierre 
Published: October 2017

Purpose of review
Germline pathogenic TP53 mutation may predispose to multiple cancers but penetrance and cancer patterns remain incompletely documented. We have analyzed international agency for research on cancer TP53 database to reevaluate age and variant-dependent tumor patterns.

Recent findings
Genome-wide studies suggest that germline variants are more frequent than estimated prevalence of Li–Fraumeni syndrome (LFS), suggesting that many carriers of potentially pathogenic mutations may not develop the syndrome. Carriers of a germline TP53 mutation who are detected in a clinical context have a penetrance of 80% at age 70. Penetrance varies according to age, sex and mutation type. Temporal tumor patterns show distinct phases, with childhood phase (0–15 years, 22% of all cancers) characterized by adrenal cortical carcinoma, choroid plexus carcinoma, rhabdomyosarcoma and medulloblastoma; early adulthood phase (16–50 years, 51%) including breast cancer, osteosarcoma, soft tissue sarcomas, leukemia, astrocytoma and glioblastoma, colorectal and lung cancer; late adulthood phase (51–80 years, 27%) including pancreatic and prostate cancer.

Summary
Germline pathogenic variants in TP53 gene have different consequences according to cell, tissue, context and age. The occurrence of frequent variants in patients with no criteria suggestive of LFS calls for attention in predicting individual risk and highlights the need of additional predictors for assigning carriers to appropriate surveillance programs.
Patient and Oncology Nurse Preferences for the Treatment Options in Advanced Melanoma
Authors: Liu Frank Xiaoqing , Witt Edward A. , Ebbinghaus Scot , DiBonaventura Beyer Grace , Basurto Enrique , Joseph Richard W. 
Published: October 2017

Background
Understanding the perceptions of patients and oncology nurses about the relative importance of benefits and risks associated with newer treatments of advanced melanoma can help to inform clinical decision-making.

Objectives
The aims of this study were to quantify and compare the views of patients and oncology nurses regarding the importance of attributes of treatments of advanced melanoma.

Methods
A discrete choice experiment (DCE) was conducted in US-based oncology nurses and patients diagnosed with advanced melanoma. Patients and nurses were enlisted through online panels. In a series of scenarios, respondents had to choose between 2 hypothetical treatments, each with 7 attributes: mode of administration (MoA), dosing schedule (DS), median duration of therapy (DoT), objective response rate (ORR), progression-free survival (PFS), overall survival (OS), and grade 3 or 4 adverse events (AEs). Hierarchical Bayesian logistic regression models were used to estimate preference weights.

Results
A total of 200 patients with advanced melanoma and 150 oncology nurses participated. The relative importance estimates of attributes by patients and nurses, respectively, were as follows: OS, 33% and 28%; AEs, 29% and 26%; ORR, 25% and 27%; PFS, 12% and 15%; DS, 2% and 3%; DoT, 0% and 0%; and MoA, 0% and 0%.

Conclusion
Both patients and oncology nurses valued OS, ORR, and AEs as the most important treatment attributes for advanced melanoma, followed by PFS, whereas DS, DoT, and MoA were given less value in their treatment decisions.

Implications for Practice
Oncology nurses and patients have similar views on important treatment considerations for advanced melanoma, which can help build trust in shared decision-making.
Blocking Liver Autophagy Accelerates Apoptosis and Mitochondrial Injury in Hepatocytes and Reduces Time to Mortality in a Murine Sepsis Model
Authors: Oami Takehiko , Watanabe Eizo , Hatano Masahiko , Teratake Youichi , Fujimura Lisa , Sakamoto Akemi , Ito Chizuru , Toshimori Kiyotaka , Swanson Paul E. , Oda Shigeto 
Published: October 2017

ABSTRACT
Autophagy plays an important role in cell survival, sequestering, and degrading a wide variety of substrates. Although an increase of autophagosomes in liver has been reported in sepsis patients as well as in septic mice, the influence of autophagy on liver injury, the interaction between autophagy, and other types of cell death in sepsis remain unclear. The aim of this study was to elucidate the contribution of liver autophagy to the pathophysiology of sepsis. We performed a cecal ligation and puncture on liver-specific autophagy-deficient (Alb-CreERT2/Atg5f/f) mice (6–8-week-old male). When compared with controls (C57BL/6), we found a significant accumulation of p62 in the liver and demonstrated a greater number of cleaved caspase-3 immunoreactive hepatocytes in these knockout (KO) mice. Additionally, we confirmed a significant increase in autophagic vacuoles in the control mice relative to KO mice; in contrast, cell shrinkage and nuclear fragmentation (morphological characteristics of apoptosis) were preferentially seen in the KO mice by transmission electron microscopy. Severe mitochondrial damage was also prominent in KO mice, relative to controls, associated with an increase of reactive oxygen species in hepatocytes. Serum aspartate transaminase levels (P = 0.005) and serum interleukin-6 levels (P = 0.020) were significantly increased in the KO mice compared with controls. Deficiency of autophagy in liver significantly decreased survival in the murine sepsis model (P = 0.025). In conclusion, blocking liver autophagy accelerates time to mortality in the murine sepsis model, suggesting that liver autophagy plays a protective role for organ failure through degradation of damaged mitochondria, as well as prevention of apoptosis.
Precise excitation-inhibition balance controls gain and timing in the hippocampus
Authors: Bhatia Aanchal , Moza Sahil , Bhalla Upinder S. 
Published: October 2017

ABSTRACTExcitation-inhibition (EI) balance controls excitability, dynamic range, and input gating in many brain circuits. Subsets of synaptic input can be selected or ‘gated’ by precise modulation of finely tuned EI balance, but assessing the granularity of EI balance requires combinatorial analysis of excitatory and inhibitory inputs. Using patterned optogenetic stimulation of hippocampal CA3 neurons, we show that hundreds of unique CA3 input combinations recruit excitation and inhibition with a nearly identical ratio, demonstrating precise EI balance at the hippocampus. Crucially, the delay between excitation and inhibition decreases as excitatory input increases from a few synapses to tens of synapses. This creates a dynamic millisecond-range window for postsynaptic excitation, controlling membrane depolarization amplitude and timing via subthreshold divisive normalization. We suggest that this combination of precise EI balance and dynamic EI delays forms a general mechanism for millisecond-range input gating and subthreshold gain control in feedforward networks.
Scaling read aligners to hundreds of threads on general-purpose processors
Authors: Langmead Ben , Wilks Christopher , Antonescu Valentin , Charles Rone 
Published: October 2017

AbstractGeneral-purpose processors can now contain many dozens of processor cores and support hundreds of simultaneous threads of execution. To make best use of these threads, genomics software must contend with new and subtle computer architecture issues. We discuss some of these and propose methods for improving thread scaling in tools that analyze each read independently, such as read aligners. We implement these methods in new versions of Bowtie, Bowtie 2 and HISAT. We greatly improve thread scaling in many scenarios, including on the recent Intel Xeon Phi architecture. We also highlight how bottlenecks are exacerbated by variable-record-length file formats like FASTQ and suggest changes that enable superior scaling.