bluuebunny/crossref_metadata_2025_split huggingface dataset:
IMFT of the sigmoid colon: a case report
Authors: Pandit Narendra , Yadav Tek Narayan , Shrestha Deepa , Adhikari Purbesh , Awale Laligen 
Published: October 2019

Abstract
Inflammatory myofibroblastic tumor (IMFT) of the colon is a very rare entity, characterized by proliferation of myofibroblast cells admixed with inflammatory infiltrates. The entity was first described in the late 1990s, and since then less than 30 cases have been described. It frequently mimics other neoplasm of the colon, such as adenocarcinoma, lymphoma and stromal tumor, and is very difficult to clinch the diagnosis preoperatively based on the clinical and radiological findings. Here, we discuss an uncommon case of sigmoid IMFT in a 35-year old male, presenting with bleeding per rectum and managed successfully by colectomy.
The Community Balance and Mobility Scale: Detecting Impairments in Military Service Members With Mild Traumatic Brain Injury
Authors: Pape Marcy M , Kodosky Paula N , Hoover Peter 
Published: October 2019

Abstract

Introduction
The objective of this study was to determine the utility of the Community Balance and Mobility scale (CB&M) among service members presenting with mild traumatic brain injury (mTBI), to compare the results against well-established balance assessments, and to find a new military-specific CB&M cut score to help differentiate those with and without mTBI.

Materials and Methods
The setting was a 4-week, intensive-outpatient, interdisciplinary program for active duty service members with mTBI. This was a nonrandomized, cross-sectional design that compared multiple measures between two groups: active duty service members with (n = 45) and without (n = 45) mTBI. The assessments, including the Activities-Specific Balance Confidence Scale, gait speed (comfortable and fast), the Functional Gait Assessment, and the CB&M, were provided to both sample groups.

Results
The mTBI group performed significantly worse (P ≤ 0.01) across all measures. A higher cut score for the CB&M of 81.5 is suggested. The CB&M demonstrated the best sensitivity (78%) and specificity (91%) ratio, as well as the largest effect size and area under the curve(0.92).

Conclusion
All objective measures distinguish participants with mTBI from controls, ranging from fair to excellent. The recommended CB&M cut score of 81.5 allows for good variance, standard deviation, and reduced risk of ceiling or floor effects. Further examination of the recommended CB&M cut score is warranted for use in the mTBI civilian populations.
LOFAR early-time search for coherent radio emission from GRB 180706A
Authors: Rowlinson A , Gourdji K , van der Meulen K , Meyers Z S , Shimwell T W , ter Veen S , Wijers R A M J , Kuiack M J , Shulevski A , Broderick J W , van der Horst A J , Tasse C , Hardcastle M J , Mechev A P , Williams W L 
Published: October 2019

ABSTRACT
The nature of the central engines of gamma-ray bursts (GRBs) and the composition of their relativistic jets are still under debate. If the jets are Poynting flux dominated rather than baryon dominated, a coherent radio flare from magnetic reconnection events might be expected with the prompt gamma-ray emission. There are two competing models for the central engines of GRBs; a black hole or a newly formed millisecond magnetar. If the central engine is a magnetar it is predicted to produce coherent radio emission as persistent or flaring activity. In this paper, we present the deepest limits to date for this emission following LOFAR rapid response observations of GRB 180706A. No emission is detected to a 3σ limit of 1.7 mJy beam−1 at 144 MHz in a 2-h LOFAR observation starting 4.5 min after the gamma-ray trigger. A forced source extraction at the position of GRB 180706A provides a marginally positive (1σ) peak flux density of 1.1 ± 0.9 mJy. The data were time sliced into different sets of snapshot durations to search for FRB like emission. No short duration emission was detected at the location of the GRB. We compare these results to theoretical models and discuss the implications of a non-detection.
The evolution of carbon-polluted white dwarfs at low effective temperatures
Authors: Blouin Simon , Dufour Patrick 
Published: October 2019

ABSTRACT
Taking advantage of the Gaia Data Release 2, recent studies have revisited the evolution of carbon-polluted white dwarfs (DQs) across a large range of effective temperatures. These analyses have clearly confirmed the existence of two distinct DQ evolutionary sequences: one with normal-mass white dwarfs and one with heavily polluted and generally more massive objects. The first sequence is thought to result from the dredge-up of carbon from the core, while the second could at least partially be made of descendants of hot DQs. However, the evolution of carbon-polluted white dwarfs below 6500 K remains unexplored, mainly due to the theoretical difficulties associated with modelling their dense atmospheres. In this work, we present a detailed star-by-star analysis of cool carbon-polluted white dwarfs. Our recently improved atmosphere models allow us to obtain good fits to most objects, including very cool DQpec white dwarfs with strongly shifted C2 molecular bands. We show that cool carbon-polluted white dwarfs keep following the two distinct evolutionary tracks previously identified at higher temperatures. We also find that most DQ white dwarfs transform into DQpec when their photospheric densities exceed ${\approx}0.15\, {\textrm{g\,cm}}^{-3}$. However, we identify stars for which the DQ→DQpec transition occurs at lower photospheric densities, possibly due to the presence of a strong magnetic field.
Gravitational waves from supernova mass loss and natal kicks in close binaries
Authors: Holgado A Miguel , Ricker Paul M 
Published: October 2019

ABSTRACT
Some fraction of compact binaries that merge within a Hubble time may have formed from two massive stars in isolation. For this isolated-binary formation channel, binaries need to survive two supernova (SN) explosions in addition to surviving common-envelope evolution. For the SN explosions, both the mass loss and natal kicks change the orbital characteristics, producing either a bound or unbound binary. We show that gravitational waves (GWs) may be produced not only from the core-collapse SN process, but also from the SN mass loss and SN natal kick during the pre-SN to post-SN binary transition. We model the dynamical evolution of a binary at the time of the second SN explosion with an equation of motion that accounts for the finite time-scales of the SN mass loss and the SN natal kick. From the dynamical evolution of the binary, we calculate the GW burst signals associated with the SN natal kicks. We find that such GW bursts may be of interest to future mid-band GW detectors like DECIGO. We also find that the energy radiated away from the GWs emitted due to the SN mass loss and natal kick may be a significant fraction, ${\gtrsim }10{\,{\rm {per\, cent}}}$, of the post-SN binary’s orbital energy. For unbound post-SN binaries, the energy radiated away in GWs tends to be higher than that of bound binaries.
Automatic detection and extraction algorithm of coronal loops based on match filter and oriented directivity
Authors: Zhiming Song , Xiaoli Yan , Zhongquan Qu , Hong-Bo Li 
Published: October 2019

ABSTRACT
In this paper, an efficient algorithm is developed to automatically detect and extract coronal loops. First of all, in the algorithm, three characteristics associated with coronal loops are used to construct a match filter able to enhance the loops. Secondly, the method combining a high-pass filter (unsharp-mask enhancement) with a global threshold is used to further enhance and segment the loops. Thirdly, to extract every individual coronal loop and obtain their parameters (the 2D projected space coordinates and lengths) from the segmented loops, a clustering method of the pixels with approximate local direction and connected domain is further used. Fourthly, to evaluate the performance of the developed algorithm, images observed by the Transition Region and Coronal Explorer (TRACE), the Atmospheric Imaging Assembly (AIA) of the Solar Dynamics Observatory (SDO) and the High-Resolution Coronal Imager (Hi-C) are used, and comparison experiments between the existing algorithms and the developed algorithm are performed. Finally, it is found that the developed algorithm is commensurate with the two most promising algorithms, oriented coronal curved loop tracing (OCCULT) and its improved version, OCCULT-2, in performance. Therefore, for scientific applications associated with coronal loops, the developed algorithm will be a powerful tool.
Deep learning predictions of galaxy merger stage and the importance of observational realism
Authors: Bottrell Connor , Hani Maan H , Teimoorinia Hossen , Ellison Sara L , Moreno Jorge , Torrey Paul , Hayward Christopher C , Thorp Mallory , Simard Luc , Hernquist Lars 
Published: October 2019

ABSTRACT
Machine learning is becoming a popular tool to quantify galaxy morphologies and identify mergers. However, this technique relies on using an appropriate set of training data to be successful. By combining hydrodynamical simulations, synthetic observations, and convolutional neural networks (CNNs), we quantitatively assess how realistic simulated galaxy images must be in order to reliably classify mergers. Specifically, we compare the performance of CNNs trained with two types of galaxy images, stellar maps and dust-inclusive radiatively transferred images, each with three levels of observational realism: (1) no observational effects (idealized images), (2) realistic sky and point spread function (semirealistic images), and (3) insertion into a real sky image (fully realistic images). We find that networks trained on either idealized or semireal images have poor performance when applied to survey-realistic images. In contrast, networks trained on fully realistic images achieve 87.1 per cent classification performance. Importantly, the level of realism in the training images is much more important than whether the images included radiative transfer, or simply used the stellar maps ($87.1{{\ \rm per\ cent}}$ compared to $79.6{{\ \rm per\ cent}}$ accuracy, respectively). Therefore, one can avoid the large computational and storage cost of running radiative transfer with a relatively modest compromise in classification performance. Making photometry-based networks insensitive to colour incurs a very mild penalty to performance with survey-realistic data ($86.0{{\ \rm per\ cent}}$ with r-only compared to $87.1{{\ \rm per\ cent}}$ with gri). This result demonstrates that while colour can be exploited by colour-sensitive networks, it is not necessary to achieve high accuracy and so can be avoided if desired. We provide the public release of our statistical observational realism suite, RealSim, as a companion to this paper.
Flybys in protoplanetary discs – II. Observational signatures
Authors: Cuello Nicolás , Louvet Fabien , Mentiplay Daniel , Pinte Christophe , Price Daniel J , Winter Andrew J , Nealon Rebecca , Ménard François , Lodato Giuseppe , Dipierro Giovanni , Christiaens Valentin , Montesinos Matías , Cuadra Jorge , Laibe Guillaume , Cieza Lucas , Dong Ruobing , Alexander Richard 
Published: October 2019

ABSTRACT
Tidal encounters in star clusters perturb discs around young protostars. In Cuello et al., we detailed the dynamical signatures of a stellar flyby in both gas and dust. Flybys produce warped discs, spirals with evolving pitch angles, increasing accretion rates, and disc truncation. Here, we present the corresponding observational signatures of these features in optical/near-infrared scattered light and (sub) millimetre continuum and CO line emission. Using representative prograde and retrograde encounters for direct comparison, we post-process hydrodynamical simulations with radiative transfer methods to generate a catalogue of multiwavelength observations. This provides a reference to identify flybys in recent near-infrared and submillimetre observations (e.g. RW Aur, AS 205, HV Tau and DO Tau, FU Ori, V2775 Ori, and Z CMa).
The 3D reconstructed skin micronucleus assay: considerations for optimal protocol design
Authors: Kidd Darren , Phillips Sarah , Chirom Teresa , Mason Nicky , Smith Robert , Saul Jim , Whitwell James , Clements Julie 
Published: October 2019

Abstract
Implementation of the seventh amendment to the EU Cosmetics Directive has driven much research into suitable in vitro alternative assays to support satisfactory risk assessments. One such assay is the reconstructed skin micronucleus (RSMN) assay. First reported in 2006, further development occurred and a standard protocol was published in 2011. To evaluate and optimise the assay at Covance Laboratories, we tested nine chemicals [4-nitrophenol (4-NP), cyclohexanone (CH), 2-ethyl-1,3-hexanediol (2-EHD), methyl methansulfonate (MMS), mitomycin C (MMC), ethyl nitrosourea (ENU), benzo[a]pyrene (BaP), cyclophosphamide (CPA) and vinblastine (VIN)] using the EpiDerm™ 3D skin model (MatTek Corporation®, IVLSL, Bratislava, Slovakia) and compared the data using the standard 48-h treatment regimen and also an emerging 72-h treatment protocol. The EpiDerm™ tissue has reportedly some metabolic capacity but data using 48-h treatments has provided mixed results. Our investigations demonstrate that the two chemicals requiring metabolic activation (BaP and CPA) were negative following the 48-h protocol but were clearly positive following 72-h treatment. Furthermore, Replication Index (RI) data showed higher RI values in vehicle control treatments (indicating increased cell division) across the treatment set following 72-h treatments. A general greater magnitude of micronucleus (MN) induction was also observed following test chemical treatment. These data suggest that the 72-h treatment protocol is more suitable as a standard approach for the detection of clastogenic, aneugenic and metabolically activated chemicals in the RSMN assay. For further assay optimisation, we compare the statistical power of scoring cells from duplicate or triplicate cultures per treatment concentration and provide recommendations.
DrugCombDB: a comprehensive database of drug combinations toward the discovery of combinatorial therapy
Authors: Liu Hui , Zhang Wenhao , Zou Bo , Wang Jinxian , Deng Yuanyuan , Deng Lei 
Published: October 2019

AbstractDrug combinations have demonstrated high efficacy and low adverse side effects compared to single drug administration in cancer therapies and thus have drawn intensive attention from researchers and pharmaceutical enterprises. Due to the rapid development of high-throughput screening (HTS), the number of drug combination datasets available has increased tremendously in recent years. Therefore, there is an urgent need for a comprehensive database that is crucial to both experimental and computational screening of synergistic drug combinations. In this paper, we present DrugCombDB, a comprehensive database devoted to the curation of drug combinations from various data sources: (i) HTS assays of drug combinations; (ii) manual curations from the literature; and (iii) FDA Orange Book and external databases. Specifically, DrugCombDB includes 448 555 drug combinations derived from HTS assays, covering 2887 unique drugs and 124 human cancer cell lines. In particular, DrugCombDB has more than 6000 000 quantitative dose responses from which we computed multiple synergy scores to determine the overall synergistic or antagonistic effects of drug combinations. In addition to the combinations extracted from existing databases, we manually curated 457 drug combinations from thousands of PubMed publications. To benefit the further experimental validation and development of computational models, multiple datasets that are ready to train prediction models for classification and regression analysis were constructed and other significant related data were gathered. A website with a user-friendly graphical visualization has been developed for users to access the wealth of data and download prebuilt datasets. Our database is available at http://drugcombdb.denglab.org/.
Strategies for in vitro engineering of the translation machinery
Authors: Hammerling Michael J , Krüger Antje , Jewett Michael C 
Published: October 2019

AbstractEngineering the process of molecular translation, or protein biosynthesis, has emerged as a major opportunity in synthetic and chemical biology to generate novel biological insights and enable new applications (e.g. designer protein therapeutics). Here, we review methods for engineering the process of translation in vitro. We discuss the advantages and drawbacks of the two major strategies—purified and extract-based systems—and how they may be used to manipulate and study translation. Techniques to engineer each component of the translation machinery are covered in turn, including transfer RNAs, translation factors, and the ribosome. Finally, future directions and enabling technological advances for the field are discussed.
G-quadruplex structures trigger RNA phase separation
Authors: Zhang Yueying , Yang Minglei , Duncan Susan , Yang Xiaofei , Abdelhamid Mahmoud A S , Huang Lin , Zhang Huakun , Benfey Philip N , Waller Zoë A E , Ding Yiliang 
Published: October 2019

Abstract
Liquid–liquid phase separation plays an important role in a variety of cellular processes, including the formation of membrane-less organelles, the cytoskeleton, signalling complexes, and many other biological supramolecular assemblies. Studies on the molecular basis of phase separation in cells have focused on protein-driven phase separation. In contrast, there is limited understanding on how RNA specifically contributes to phase separation. Here, we described a phase-separation-like phenomenon that SHORT ROOT (SHR) RNA undergoes in cells. We found that an RNA G-quadruplex (GQ) forms in SHR mRNA and is capable of triggering RNA phase separation under physiological conditions, suggesting that GQs might be responsible for the formation of the SHR phase-separation-like phenomenon in vivo. We also found the extent of GQ-triggered-phase-separation increases on exposure to conditions which promote GQ. Furthermore, GQs with more G-quartets and longer loops are more likely to form phase separation. Our studies provide the first evidence that RNA can adopt structural motifs to trigger and/or maintain the specificity of RNA-driven phase separation.
FoldamerDB: a database of peptidic foldamers
Authors: Nizami Bilal , Bereczki-Szakál Dorottya , Varró Nikolett , el Battioui Kamal , Nagaraj Vignesh U , Szigyártó Imola Cs , Mándity István , Beke-Somfai Tamás 
Published: October 2019

Abstract
Foldamers are non-natural oligomers that mimic the structural behaviour of natural peptides, proteins and nucleotides by folding into a well-defined 3D conformation in solution. Since their first description about two decades ago, numerous studies have been undertaken dealing with the design, synthesis, characterization and application of foldamers. They have huge application potential as antimicrobial, anticancer and anti-HIV agents and in materials science. Despite their importance, there is no publicly available web resource providing comprehensive information on these compounds. Here we describe FoldamerDB, an open-source, fully annotated and manually curated database of peptidic foldamers. FoldamerDB holds the information about the sequence, structure and biological activities of the foldamer entries. It contains the information on over 1319 species and 1018 activities, collected from more than 160 research papers. The web-interface is designed to be clutter-free, user-friendly and it is compatible with devices of different screen sizes. The interface allows the user to search the database, browse and filter the foldamers using multiple criteria. It also offers a detailed help page to assist new users. FoldamerDB is hoped to bridge the gap in the freely available web-based resources on foldamers and will be of interest to diverse groups of scientists from chemists to biologists. The database can be accessed at http://foldamerdb.ttk.hu/.
Prevalence and correlates of physical activity across kidney disease stages: an observational multicentre study
Authors: Wilkinson Thomas J , Clarke Amy L , Nixon Daniel G D , Hull Katherine L , Song Yan , Burton James O , Yates Thomas , Smith Alice C 
Published: October 2019

Abstract

Background
People with chronic kidney disease (CKD) report high levels of physical inactivity, a major modifiable risk factor for morbidity and mortality. Understanding the biological, psychosocial and demographic causes of physical activity behaviour is essential for the development and improvement of potential health interventions and promotional initiatives. This study investigated the prevalence of physical inactivity and determined individual correlates of this behaviour in a large sample of patients across the spectrum of kidney disease.

Methods
A total of 5656 people across all stages of CKD (1–2, 3, 4–5, haemodialysis, peritoneal dialysis and renal transplant recipients) were recruited from 17 sites in England from July 2012 to October 2018. Physical activity was evaluated using the General Practice Physical Activity Questionnaire. Self-reported cardiorespiratory fitness, self-efficacy and stage of change were also assessed. Binominal generalized linear mutually adjusted models were conducted to explore the associations between physical activity and correlate variables. This cross-sectional observational multi-centre study was registered retrospectively as ISRCTN87066351 (October 2015).

Results
The prevalence of physical activity (6–34%) was low and worsened with disease progression. Being older, female and having a greater number of comorbidities were associated with greater odds of being physically inactive. Higher haemoglobin, cardiorespiratory fitness and self-efficacy levels were associated with increased odds of being active. Neither ethnicity nor smoking history had any effect on physical activity.

Conclusions
Levels of physical inactivity are high across all stages of CKD. The identification of stage-specific correlates of physical activity may help to prioritize factors in target groups of kidney patients and improve the development and improvement of public health interventions.
The Relationship of Chemotherapy-Induced Peripheral Neuropathy and Obesity: A Systematic Review
Authors: Jesse Mary 
Published: October 2019

Background:Chemotherapy-induced peripheral neuropathy (CIPN) is a dose-limiting neurotoxic effect of chemotherapy that affects many survivors. Obesity is also known to have a negative effect on neuropathy. This review aimed to determine what relationship, if any, obesity might have with the incidence and severity of CIPN.Methods:Electronic databases PubMed, PEDro (Physiotherapy Evidence Database), CENTRAL (Cochrane Central Register of Controlled Trials), Ovid, and EBSCO were systematically searched from January 2008 to March 2019. All types of studies, data collections, and review articles were included in the adult population.Results:Twelve articles describing relationships between overweight/obesity and presence of CIPN were included in the review. Associations between body mass index (BMI), body surface area (BSA), and sarcopenic obesity and CIPN incidence and severity were described in patients who had received taxane therapy, platinum compound therapy, or bortezomib. Eleven of the 12 studies indicated an increased incidence of CIPN with higher BMI or BSA or sarcopenic obesity, and the 2 studies that analyzed severity of symptoms found an increase in those who were overweight/obese.Limitations:The number of studies specifically analyzing the relationship between overweight/obesity is limited. Also limiting comparison between studies is the categorization of obesity and the methods used to define CIPN.Conclusions:Overall, being overweight or obese would put one at a higher risk for development of CIPN. Clinicians should encourage healthy lifestyles to help decrease or control symptoms and/or limit dose reductions of chemotherapy. Further research regarding changes in severity of CIPN with weight loss or gain is needed.