bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the stellar properties of M dwarfs with high-resolution spectroscopy from the optical to the near-infrared
Authors: Rajpurohit A. S. , Allard F. , Rajpurohit S. , Sharma R. , Teixeira G. D. C. , Mousis O. , Kamlesh R. 
Published: November 2018

Context. Being the most numerous and oldest stars in the galaxy, M dwarfs are objects of great interest for exoplanet searches. The presence of molecules in their atmosphere complicates our understanding of their atmospheric properties. But great advances have recently been made in the modeling of M dwarfs due to the revision of solar abundances.
Aims. We aim to determine stellar parameters of M dwarfs using high resolution spectra (R ∼ 90 000) simultaneously in the visible and the near-infrared. The high resolution spectra and broad wavelength coverage provide an unique opportunity to understand the onset of dust and cloud formation at cool temperatures. Furthermore, this study will help in understanding the physical processes which occur in a cool atmospheres, particularly, the redistribution of energy from the optical to the near-infrared.
Methods. The stellar parameters of M dwarfs in our sample have been determined by comparing the high resolution spectra both in the optical and in the near-infrared simultaneously observed by CARMENES with the synthetic spectra obtained from the BT-Settl model atmosphere. The detailed spectral synthesis of these observed spectra both in the optical and in the near-infrared helps to understand the missing continuum opacity.
Results. For the first time, we derive fundamental stellar parameters of M dwarfs using the high resolution optical and near-infrared spectra simultaneously. We determine Teff, log g and [M/H] for 292 M dwarfs of spectral type M0 to M9, where the formation of dust and clouds are important. The derived Teff for the sample ranges from 2300 to 4000 K, values of log g ranges from 4.5 ≤ logg ≤ 5.5 and the resulting metallicity ranges from −0.5 ≤ [M/H] ≤ +0.5. We have also explored the possible differences in Teff, log g and [M/H] by comparing them with other studies of the same sample of M dwarfs.
Excitability of oxytocin neurons in paraventricular nucleus is regulated by voltage-gated potassium channels Kv4.2 and Kv4.3
Authors: Imai Ryota , Yokota Shoko , Horita Shoichiro , Ueta Yoichi , Maejima Yuko , Shimomura Kenju 
Published: November 2018

ABSTRACT
Oxytocin is produced by neurons in the paraventricular nucleus (PVN) and the supraoptic nucleus in the hypothalamus. Various ion channels are considered to regulate the excitability of oxytocin neurons and its secretion. A-type currents of voltage-gated potassium channels (Kv channels), generated by Kv4.2/4.3 channels, are known to be involved in the regulation of neuron excitability. However, it is unclear whether the Kv4.2/4.3 channels participate in the regulation of excitability in PVN oxytocin neurons. Here, we investigated the contribution of the Kv4.2/4.3 channels to PVN oxytocin neuron excitability. By using transgenic rat brain slices with the oxytocin-monomeric red fluorescent protein 1 fusion transgene, we examined the excitability of oxytocin neurons by electrophysiological technique. In some oxytocin neurons, the application of Kv4.2/4.3 channel blocker increased firing frequency and membrane potential with extended action potential half-width. Our present study indicates the contribution of Kv4.2/4.3 channels to PVN oxytocin neuron excitability regulation.
Abbreviation: PVN, paraventricular nucleus; Oxt-mRFP1, Oxt-monometric red fluorescent protein 1; PaTx-1, Phrixotoxin-1; TEA, Tetraethylammonium Chloride; TTX, tetrodotoxin; aCSF, artificial cerebrospinal fluid;PBS, phosphate buffered saline 3v, third ventricle.
BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks
Authors: Zheng Ruiqing , Li Min , Chen Xiang , Wu Fang-Xiang , Pan Yi , Wang Jianxin 
Published: November 2018

Abstract

Motivation
Reconstructing gene regulatory networks (GRNs) based on gene expression profiles is still an enormous challenge in systems biology. Random forest-based methods have been proved a kind of efficient methods to evaluate the importance of gene regulations. Nevertheless, the accuracy of traditional methods can be further improved. With time-series gene expression data, exploiting inherent time information and high order time lag are promising strategies to improve the power and accuracy of GRNs inference.

Results
In this study, we propose a scalable, flexible approach called BiXGBoost to reconstruct GRNs. BiXGBoost is a bidirectional-based method by considering both candidate regulatory genes and target genes for a specific gene. Moreover, BiXGBoost utilizes time information efficiently and integrates XGBoost to evaluate the feature importance. Randomization and regularization are also applied in BiXGBoost to address the over-fitting problem. The results on DREAM4 and Escherichia coli datasets show the good performance of BiXGBoost on different scale of networks.

Availability and implementation
Our Python implementation of BiXGBoost is available at https://github.com/zrq0123/BiXGBoost.

Supplementary information
Supplementary data are available at Bioinformatics online.
“The British Soldier is no Bolshevik”: The British Army, Discipline, and the Demobilization Strikes of 1919
Authors: Butler William 
Published: November 2018

Abstract
This article considers the breakdown in discipline in the British Army which occurred in Britain and on the Western Front during the process of demobilization at the end of the First World War. Many soldiers, retained in the army immediately after the Armistice, went on strike, and some formed elected committees, demanding their swifter return to civilian life. Their perception was that the existing demobilization system was unjust, and men were soon organized by those more politically conscious members of the armed forces who had enlisted for the duration of the war. At one stage in January 1919, over 50,000 soldiers were out on strike, a fact that was of great concern to the British civilian and military authorities who miscalculated the risk posed by soldiers. Spurred on by many elements of the press, especially the Daily Mail and Daily Herald, who both fanned and dampened the flames of discontent, soldiers’ discipline broke down, demonstrating that the patriotism which had for so long kept them in line could only extend so far. Though senior members of the government, principally Winston Churchill, and the military, especially Douglas Haig and Henry Wilson, were genuinely concerned that Bolshevism had ‘infected’ the army, or, at the very least, the army had been unionized, their fears were not realized. The article examines the government’s strategy regarding demobilization, its efforts to assess the risk of politicization and manage the press, and its responses to these waves of strikes, arguing that, essentially, these soldiers were civilians first and simply wanted to return home, though, in the post-war political climate, government fears were very real.
Serial Third-Trimester Ultrasonography Compared With Routine Care in Uncomplicated Pregnancies
Authors: Ashimi Balogun Olaide , Sibai Baha M. , Pedroza Claudia , Blackwell Sean C. , Barrett Tyisha L. , Chauhan Suneet P. 
Published: November 2018

OBJECTIVE:
Among uncomplicated pregnancies, serial third-trimester ultrasound examinations identified significantly more cases with a composite of fetal growth or amniotic fluid abnormalities (27%) than did routine fundal height measurements (8%).

METHODS:
Women without complications between 24 0/7 and 30 6/7 weeks of gestation were randomized (NCT0270299) to either routine care (control arm) or ultrasound examination every 4 weeks (intervention arm). The primary outcome was a composite of abnormalities of fluid volume and growth: oligohydramnios or polyhydramnios; fetal growth restriction; or large for gestational age. The secondary outcome was the presence of composite maternal or neonatal morbidity among the two groups. A total of 206 participants was needed to have 80% power to detect an increase in the primary composite outcome from 10% in control to 25% in the intervention group (baseline rate 10%; two-tailed; α=0.05; loss to follow-up 5%). All women were included in the intent-to-treat analysis. Fisher exact, χ2 tests, or two-sample t tests were used to assess group differences.

RESULTS:
From July 11, 2016, to May 24, 2017, 852 women were screened for eligibility and 206 were randomized as follows: 102 in routine care and 104 in serial ultrasound examinations. The two groups were comparable in baseline characteristics. The primary composite outcome was significantly higher among women who were in the ultrasound examination group than the routine care group (27% vs 8%; relative risk 3.43, 95% CI 1.64–7.17); five women (95% CI 3–11) were needed to identify at least one of the composite ultrasound abnormalities. Although we were underpowered to detect a significant difference, the following secondary endpoints occurred with similar frequency in the ultrasound examination group than the routine care group: induction resulting from abnormal ultrasound examination findings (14% vs 6%), cesarean delivery in labor (5% vs 6%), and prespecified composite maternal morbidity (9% in both groups) and composite neonatal morbidity (1% vs 4%).

CONCLUSION:
Among uncomplicated pregnancies between 24 0/7 and 30 6/7 weeks of gestation, serial third-trimester ultrasound examinations were significantly more likely to identify abnormalities of fetal growth or amniotic fluid than measurements of fundal height and indicated ultrasound examination. No differences in maternal and neonatal outcomes were noted, although we were underpowered for these endpoints.

CLINICAL TRIAL REGISTRATION:

ClinicalTrials.gov, NCT02702999.
Prognosis of a rare subtype of thyroid cancer
Authors: Liu Zeming , Zhao Qiuyang , Zeng Wen , Wang Shuntao , Xiong Yiquan , Guo Hui , Huang Tao , Cheng Hongtao , Guo Liang 
Published: November 2018

Abstract
Systemic illustrations of spindle cell thyroid cancer (SCTC), based on a large cohort, are few. We investigated the prognosis of SCTC compared to the most common subtypes, papillary thyroid cancer (PTC) and follicular thyroid cancer (FTC).
Information of patients with a diagnosis of SCTC, PTC, or FTC, between 2004 and 2013, was obtained from the Surveillance, Epidemiology, and End Results (SEER) database. Patient survival curves were investigated using Kaplan–Meier analyses, log-rank tests, and Cox proportional hazards regression analyses.
In a Kaplan–Meier analysis of the entire cohort of thyroid cancer patients, cancer specific survival declined sharply for patients with SCTC, but declined more modestly for patients with PTC and FTC. Unadjusted Cox regression analysis and Kaplan–Meier curve analysis showed that SCTC had a poorer cancer-specific mortality and all-cause mortality compared to PTC and FTC. Similar results were obtained after adjustment for different confounding factors.
Our study assessed the prognosis of SCTC, based on a large cohort, compared to PTC and FTC, and found relatively accurate hazard ratios of death rate in SCTC as compared to PTC and FTC. Thus, our findings would provide beneficial insights on patients with SCTC, and aid in treatment decision making, more radical treatment like total-thyoridectomy and/or plus central lymph node dissection should be performed for patients with SCTC.
Layer-specific strain analysis of left ventricular myocardium after alcohol septal ablation for hypertrophic obstructive cardiomyopathy
Authors: Zhang Juan , Zhu Linlin , Jiang Xiaomin , Hu Zuoying 
Published: November 2018

Abstract

Introduction:
We aimed to explore the layer-specific systolic strain of left ventricular (LV) myocardium in patients with hypertrophic obstructive cardiomyopathy (HOCM) before and after alcohol septal ablation (ASA).
The routine 2D (frame rate: >50 Hz) data sets were acquired using GE Vivi7 system for 44 consecutive HOCM patients and 21 matched normal subjects. Fifteen of HOCM patients had serial echocardiograms available for speckle tracking analyses before and 1 year after ASA. 2D strain was analyzed by EchoPAC software.
The layer strain from inner to mid-myocardial and outer layers in basal and middle segments in HOCM patients continuously declined. The absolute values of peak systolic strains from the endocardium to mid-myocardium and epicardium in the basal septum of the HOCM group were significantly lower than those of the normal group (P <.01). Meanwhile, the layer systolic strain of LV endocardium in the basal septum increased significantly during a 1-year follow-up (P <.05).

Conclusions:
The layer-specific strains of HOCM patients measured by tissue Doppler echocardiography decreased significantly compared to those of normal individuals. The increased specific layer strain of LV endocardium in the basal septum may be a valid marker of echocardiographic improvement in HOCM patients receiving ASA.
Routine coagulation test abnormalities caused by rivaroxaban
Authors: Song Zikai , Wu Haidi , Cao Hongyan , Yang Shuo , Tang Minglong , Qin Ling 
Published: November 2018

Abstract

Rationale:
Rivaroxaban is a non-vitamin K antagonist oral anticoagulant. Current recommendations state that coagulation monitoring is not required, and neither the dose nor dosing interval requires adjustment in response to changes in coagulation parameters when rivaroxaban is used for approved indications. Guidelines mainly discuss the indications for rivaroxaban and non-vitamin K antagonist oral anticoagulants in general; they offer less guidance regarding how to use these medications in specific clinical situations to bridge the gulf between guidelines and clinical practice.

Patient concerns:
An 88-year-old man with a long history of atrial fibrillation presented to the hospital with worsening dyspnea and chest pain. Significantly, he had an estimated glomerular filtration rate of 46.7 mL/min. He was prescribed oral rivaroxaban 20 mg once daily. After 7 days, the patient complained of maroon colored stools.

Diagnosis:
Laboratory investigations revealed that the patient's prothrombin time (PT) and activated partial thromboplastin time (aPTT) were elevated. Rivaroxaban induced gastrointestinal bleeding was suspected.

Interventions:
Rivaroxaban was discontinued and routine coagulation tests were monitored daily.

Outcomes:
Two days following the discontinuation of the drug, the bleeding was controlled and hemoglobin was normal, but the PT and aPTT remained abnormal. On the third day after discontinuing rivaroxaban, the patient experienced sudden syncope and pulselessness and expired.

Lessons:
This case indicates that in real-world situations, a small number of patients may develop changes in both PT and aPTT during rivaroxaban therapy. Therefore, coagulation monitoring should be considered in patients with risk factors for bleeding, such as elderly patients with renal insufficiency.
Chylous Ascites: Complication of Laparoscopic Donor Nephrectomy. Case Report and Review of Literature
Authors: Seth Abhinav , Sharma Ashish , Kenwar Deepesh Benjamin , Singh Sarbpreet 
Published: November 2018

Background.
Chylous ascites (CA) is an extremely rare complication after laparoscopic donor nephrectomy (LDN). It can increase the hospital stay, morbidity in postoperative period and thus negating the benefits of laparoscopic surgery. Most of the cases were managed conservatively, but surgical intervention may be occasionally required. This report describes the importance of accurate localization of the leaking chyle duct and its repair by endosuturing in a renal donor not responding to conservative treatment.

Methods.
A comprehensive review of literature regarding this rare complication after LDN was performed with Pubmed/Medline and Google Scholar using “chyle,” “complications,” and “laparoscopic donor nephrectomy” as keywords. The demographic profile and management of patients is discussed in detail. The various surgical modalities used to manage these patients are described.

Results.
Fifty-four cases of chyle leak/ascites have been reported after LDN in literature to date. Around 77% donors with CA could be successfully managed conservatively with dietary measures and total parenteral nutrition. Surgical intervention was required in nearly 23% donors ranging from clip application, use of argon coagulation, endosuturing with application of glue after 36.1 ± 19.07 days of failed conservative treatment. Donors with massive ascites or requiring frequent large-volume paracentesis on conservative treatment are likely to require surgical therapy. The present case was successfully managed with laparoscopic endosuturing and has no recurrence at 6 month follow-up.

Conclusions.
Chylous ascites is a rare complication after donor nephrectomy in experienced centers. Although conservative management remains the first line of treatment, early surgical treatment shall be undertaken in cases of massive ascites.
Regulatory mechanisms for the axonal localization of tau in neurons
Authors: Iwata Minori , Watanabe Shoji , Yamane Ayaka , Miyasaka Tomohiro , Misonou Hiroaki 
Published: November 2018

AbstractTau is a microtubule (MT)-associated protein, which precisely localizes to the axon of a mature neuron. Although it has been widely used as an axonal marker, the mechanisms for its axonal localization have been elusive. This might be largely due to the lack of an experimental system, as exogenously expressed tau, such as GFP-tau, mis-localizes to the soma and dendrites. In this study, we found that the expression of endogenous tau and its axonal localization in cultured rat hippocampal neurons mainly occur during early neuronal development and are coupled. By mimicking this early expression, we demonstrate that exogenously expressed human tau can be properly localized to the axon, thereby providing the first experimental model to study the mechanisms of tau localization. Using this model, we obtained surprising findings that the axonal localization of tau did not require the MT-binding domain nor correlate with the MT-binding ability. Instead, we identified a transport mechanism mediated by the proline-rich region 2 (PRR2), which contains a number of important phosphorylation sites. Mimicking phosphorylation and dephosphorylation in PRR2 disrupts the axonal localization, suggesting that it is regulated by the phosphorylation state of PRR2. These results shed new lights on the mechanism for the axonal localization of tau and indicate a link between the hyperphosphorylation and mis-localization of tau observed in tauopathies.Significance statementIn this paper, we present a first experimental system, in which expressed tau is properly localized to the axon, and which can therefore be used to study the mechanisms of tau localization and mis-localization. Using this system, we provide evidence that the microtubule binding domain of tau nor stable binding of tau to microtubules is not necessary for its axonal localization. Instead, we identified the proline-rich region and its phosphorylation-state dictate the localization of tau in neurons. These results provide a novel foundation to consider how axonal tau mis-localize to the soma and dendrites during early pathogenesis of Alzheimer’s disease.
Accumulation of prelamin A drives inflammation in the heart with implications for treatment of inherited and acquired cardiomyopathies
Authors: Brayson Daniel , Frustaci Andrea , Verardo Romina , Chimenti Cristina , Russo Matteo Antonio , Hayward Robert , Ahmad Sadia Munir , Vizcay-Barrena Gema , Protti Andrea , Zammit Peter S. , dos Remedios Cristobal G. , Ehler Elisabeth , Shah Ajay M. , Shanahan Catherine M. 
Published: November 2018

AbstractCardiomyopathies are complex heart muscle diseases that can be inherited e.g. dilated cardiomyopathy resulting from LMNA gene mutations, or acquired, e.g. cardiomyopathy associated with HIV. In both cases the lamin A precursor, prelamin A, may play a central role: mutations in LMNA and certain HIV protease inhibitors acting via the enzyme ZMPSTE24 both inhibit prelamin A processing. Firstly, we show that myocardial prelamin A accumulation occurs in both these cardiomyopathies in patients. Secondly, we developed a novel mouse model of cardiac specific prelamin A accumulation which mimicked tissue and molecular features of HIV associated cardiomyopathy, including inflammation. These findings: (1) confirm a central pathological role of prelamin A common to genetic and acquired cardiomyopathies; (2) have implications for the management of HIV patients with cardiac disease in whom protease inhibitors with low/no binding to ZMPSTE24 may be preferred; and (3) suggest that targeting inflammation may be a useful treatment strategy for some forms of inherited cardiomyopathy.
Ultra-sensitive sequencing for cancer detection reveals progressive clonal selection in normal tissue over a century of human lifespan
Authors: Salk Jesse J. , Loubet-Senear Kaitlyn , Maritschnegg Elisabeth , Valentine Charles C. , Williams Lindsey N. , Horvat Reinhard , Vanderstichele Adriaan , Nachmanson Daniela , Baker Kathryn T. , Emond Mary J. , Loter Emily , Soussi Thierry , Loeb Lawrence A. , Zeillinger Robert , Speiser Paul , Risques Rosa Ana 
Published: November 2018

ABSTRACTHigh accuracy next-generation DNA sequencing promises a paradigm shift in early cancer detection by enabling the identification of mutant cancer molecules in minimally-invasive body fluid samples. We demonstrate 80% sensitivity for ovarian cancer detection using ultra-accurate Duplex Sequencing to identify TP53 mutations in uterine lavage. However, in addition to tumor DNA, we also detect low frequency TP53 mutations in nearly all lavages from women with and without cancer. These mutations increase with age and share the selection traits of clonal TP53 mutations commonly found in human tumors. We show that low frequency TP53 mutations exist in multiple healthy tissues, from newborn to centenarian, and progressively increase in abundance and pathogenicity with older age across tissue types. Our results illustrate that subclonal cancer evolutionary processes are a ubiquitous part of normal human aging and great care must be taken to distinguish tumor-derived, from age-associated mutations in high sensitivity clinical cancer diagnostics.
Using Computer-vision and Machine Learning to Automate Facial Coding of Positive and Negative Affect Intensity
Authors: Haines Nathaniel , Southward Matthew W. , Cheavens Jennifer S. , Beauchaine Theodore , Ahn Woo-Young 
Published: November 2018

AbstractFacial expressions are fundamental to interpersonal communication, including social interaction, and allow people of different ages, cultures, and languages to quickly and reliably convey emotional information. Historically, facial expression research has followed from discrete emotion theories, which posit a limited number of distinct affective states that are represented with specific patterns of facial action. Much less work has focused on dimensional features of emotion, particularly positive and negative affect intensity. This is likely, in part, because achieving inter-rater reliability for facial action and affect intensity ratings is painstaking and labor-intensive. We use computer-vision and machine learning (CVML) to identify patterns of facial actions in 4,648 video recordings of 125 human participants, which show strong correspondences to positive and negative affect intensity ratings obtained from highly trained coders. Our results show that CVML can both (1) determine the importance of different facial actions that human coders use to derive positive and negative affective ratings, and (2) efficiently automate positive and negative affect intensity coding on large facial expression databases. Further, we show that CVML can be applied to individual human judges to infer which facial actions they use to generate perceptual emotion ratings from facial expressions.