bluuebunny/crossref_metadata_2025_split huggingface dataset:
schex avoids overplotting for large single-cell RNA-sequencing datasets
Authors: Freytag Saskia , Lister Ryan 
Published: November 2019

Abstract

Summary
Due to the scale and sparsity of single-cell RNA-sequencing data, traditional plots can obscure vital information. Our R package schex overcomes this by implementing hexagonal binning, which has the additional advantages of improving speed and reducing storage for resulting plots.

Availability and implementation
schex is freely available from Bioconductor via http://bioconductor.org/packages/release/bioc/html/schex.html and its development version can be accessed on GitHub via https://github.com/SaskiaFreytag/schex.

Supplementary information
Supplementary data are available at Bioinformatics online.
Heritability and Cognitive Relevance of Structural Brain Controllability
Authors: Lee Won Hee , Rodrigue Amanda , Glahn David C , Bassett Danielle S , Frangou Sophia 
Published: November 2019

Abstract
Cognition and behavior are thought to emerge from the connections and interactions among brain regions. The precise nature of these relationships remains elusive. Here we use tools provided by network control theory to determine how the structural connectivity profile of brain regions may shape individual variation in cognition. In a cohort of healthy young adults (n = 1066), we computed two fundamental brain regional control patterns, average and modal controllability, which index the degree of influence of a region over others. We first established that regional brain controllability measures were both reproducible and heritable. Regions with controllability profiles theoretically conducive to facilitating multiple cognitive operations were over-represented in higher-order resting-state networks. Finally, variation in regional controllability accounted for about 50% of interindividual variability in multiple cognitive domains. We conclude that controllability is a biologically plausible property of the structural connectome and provides a mechanistic explanation for how brain structural architecture may influence cognitive functions.
Serum amyloid A-type amyloidosis of the kidney and immune complex-mediated glomerulopathy in the setting of hyperimmunoglobulin E (Job’s) syndrome
Authors: Sekulic Miroslav , Rennke Helmut G , Rashidi Arash 
Published: November 2019

Abstract
Hyperimmunoglobulin E syndrome (HIES) is a rare immunodeficiency syndrome with characteristic features of pulmonary infections, eczema, recurrent skin abscesses and elevated serum IgE. We present a case of an HIES patient referred for nephrology consultation with elevated serum creatinine and nephrotic-range proteinuria. The subsequent kidney biopsy revealed AA-type amyloidosis and a separate and distinct inactive immune complex-mediated glomerulopathy with frequent glomerular capillary wall and mesangial polyclonal deposits. Potential kidney pathology in the setting of HIES has not been well described previously, and this case provides insight into associated renal comorbidities faced by patients with this rare syndrome.
Leakage-free ID-Based Signature, Revisited
Authors: Lin Xi-Jun , Sun Lin , Qu Haipeng 
Published: November 2019

Abstract
Recently, Tseng et al. proposed a new notion for identity-based signature (IBS) scheme to resist ephemeral secret leakage (ESL) attacks, called leakage-free identity-based signature (leakage-free IBS), and devised the first secure leakage-free IBS scheme. However, they only considered the situation of the leakage of ephemeral secrets used for generating the signatures. Notice that the private key extraction procedure is probabilistic as well in their scheme, that is, there are ephemeral secrets used by the key generation center to generate the signers’ private keys. It is practical to consider that if the adversary comprises these ephemeral secrets, then he can reveal the master key of the system. Therefore, it is desired to introduce a new security notion for the leakage-free IBS schemes to consider the ESL attacks on both private key extraction and signing procedures. In this paper, we present such security notion. Moreover, we propose two IBS schemes that are proved to be secure under the new security notion.
Potential of Electrical Neuromodulation for Inflammatory Bowel Disease
Authors: Cheng Jiafei , Shen Hong , Chowdhury Reezwana , Abdi Tsion , Selaru Florin , Chen Jiande D Z 
Published: November 2019

AbstractInflammatory bowel disease (IBD) is a common chronic inflammatory disease of the digestive tract that is often debilitating. It affects patients’ quality of life and imposes a financial burden. Despite advances in treatment with medications such as biologics, a large proportion of patients do not respond to medical therapy or develop adverse events. Therefore, alternative treatment options such as electrical neuromodulation are currently being investigated. Electrical neuromodulation, also called bioelectronic medicine, is emerging as a potential new treatment for IBD. Over the past decade, advancements have been made in electrical neuromodulation. A number of electrical neuromodulation methods, such as vagus nerve stimulation, sacral nerve stimulation, and tibial nerve stimulation, have been tested to treat IBD. A series of animal and clinical trials have been performed to evaluate efficacy with promising results. Although the exact underlying mechanisms of action for electrical neuromodulation remain to be explored, this modality is promising. Further randomized controlled trials and basic experiments are needed to investigate efficacy and clarify intrinsic mechanisms.
A lowest-order staggered DG method for the coupled Stokes–Darcy problem
Authors: Zhao Lina , Park Eun-Jae 
Published: November 2019

Abstract
In this paper we propose a locally conservative, lowest-order staggered discontinuous Galerkin method for the coupled Stokes–Darcy problem on general quadrilateral and polygonal meshes. This model is composed of Stokes flow in the fluid region and Darcy flow in the porous media region, coupling together through mass conservation, balance of normal forces and the Beavers–Joseph–Saffman condition. Stability of the proposed method is proved. A new regularization operator is constructed to show the discrete trace inequality. Optimal convergence estimates for all the approximations covering low regularity are achieved. Numerical experiments are given to illustrate the performances of the proposed method. The numerical results indicate that the proposed method can be flexibly applied to rough grids such as the trapezoidal grid and $h$-perturbation grid.
Givental’s Non-linear Maslov Index on Lens Spaces
Authors: Granja Gustavo , Karshon Yael , Pabiniak Milena , Sandon Sheila 
Published: November 2019

Abstract
Givental’s non-linear Maslov index, constructed in 1990, is a quasimorphism on the universal cover of the identity component of the contactomorphism group of real projective space. This invariant was used by several authors to prove contact rigidity phenomena such as orderability, unboundedness of the discriminant and oscillation metrics, and a contact geometric version of the Arnold conjecture. In this article, we give an analogue for lens spaces of Givental’s construction and its applications.
Repurposing drugs for treatment of Mycobacterium abscessus: a view to a kill
Authors: Gumbo Tawanda , Cirrincione Kayle , Srivastava Shashikant 
Published: November 2019

Abstract

Background
The current treatment regimens recommended for Mycobacterium abscessus subspecies abscessus (Mab) pulmonary disease are not effective. We identified 16 drugs with potential to build new regimens, translating to 560 possible three-drug combination regimens.

Objectives
To determine MICs and efficacy of drugs from different antibiotic classes for treatment against Mab, in order to winnow down the potential drugs for combination therapy to tractable numbers, for future use in hollow-fibre studies.

Methods
The MICs of levofloxacin, minocycline, meropenem, imipenem, tedizolid, bedaquiline, azithromycin, clarithromycin, amikacin, vancomycin, delafloxacin, tebipenem/avibactam and omadacycline were determined for 20 Mab isolates. In addition, concentration–response studies with tedizolid, bedaquiline, clarithromycin, amikacin, tebipenem/avibactam, cefdinir, faropenem, omadacycline and daunorubicin were performed and data were fitted to the inhibitory sigmoid Emax model. Efficacy was defined as maximal kill, expressed as cfu/mL kill below day 0 burden.

Results
The lowest MICs among the 13 antibiotics were of bedaquiline, tebipenem/avibactam and omadacycline. The antibiotics that killed Mab below the day 0 burden were the anticancer agent daunorubicin (3.36 log10 cfu/mL), cefdinir (1.85 log10 cfu/mL), faropenem (2.48 log10 cfu/mL) and tebipenem/avibactam (1.71 log10 cfu/mL kill). The EC50 values of these drugs were 11.67, 9.52, 48.2 and 0.33 mg/L, respectively, below peak concentrations of these drugs.

Conclusions
The low MICs and efficacy at clinically achievable concentrations mean that tebipenem/avibactam, daunorubicin, omadacycline and bedaquiline give a view of components of a three-drug regimen likely to effectively kill Mab. We propose pharmacokinetic/pharmacodynamic studies to identify such a regimen and the doses to be combined.
Managing Complex Peripheral Nerve Injuries Within the Military Health System: A Multidisciplinary Approach to Treatment, Education, and Research at Walter Reed National Military Medical Center
Authors: Wade Sean M , Nesti Leon J , Cook Glen A , Bresner Jonathan S , Happel Joseph P , Villahermosa Alexander J , Melendez-Munoz Angelica M , Gomez Yessenia D , Reece David E , Miller Matthew E , Souza Jason M 
Published: November 2019

Abstract

Introduction
Peripheral nerve injuries are a leading cause of disability within the Military Health System (MHS) patient population. Many peripheral nerve injuries (PNIs) are amenable to therapeutic intervention but require a timely diagnosis and prompt referral to a specialty center capable of intervention, as functional outcomes are directly related to the duration between injury and intervention. Even when appropriately identified, PNI management in the MHS is often challenged by the lack of an established pathway for care coordination and a limited awareness of available diagnostic and therapeutic resources. To address these potential shortcomings, the Walter Reed National Military Medical Center Peripheral Nerve Program (WRNMMC PNP) in Bethesda, MD, has been established to provide comprehensive, multidisciplinary care to peripheral nerve-injured patients across the MHS. Additionally, the WRNMMC PNP provides graduate medical education training in PNI management for multiple residency and fellowship programs, and it facilitates critical peripheral nerve research to advance knowledge within the field.

Materials and Methods
A retrospective review of all patients evaluated by the WRNMMC PNP between December 2015 and April 2019 was conducted in order to identify pertinent patient demographic information, referral patterns, and PNI etiology data.

Results
The WRNMMC PNP evaluated 356 patients consisting of active duty, dependents, retirees, and Veterans Affairs patients during the designated study period. These patients were referred by providers from more than nine different specialties from 78 commands across eight countries. The majority of these patients (222 patients) were referred for traumatic PNI. The WRNMMC PNP has also evaluated and treated patients with PNIs stemming from congenital and compressive etiologies. One hundred and one patients referred during this period were treated with surgery, while the remainder were managed through nonoperative means.

Conclusions
The WRNMMC PNP facilitates comprehensive, patient-centered care for PNI patients within the MHS. Moreover, the program helps to prepare the next generation of providers for evaluating and treating PNI patients through its involvement with graduate medical education training. It also conducts critical peripheral nerve research and lays the foundation for collaborations with other institutions involved with peripheral nerve research. In the years ahead, the WRNMMC PNP aims to expand its outreach and capabilities within the MHS through more expansive use of telemedicine consultation and the establishment of satellite peripheral nerve clinic sites.
The Victorian Guitar, Exoticism, and Extinction Discourse from Radcliffe to Wilde
Authors: Lovesey Oliver 
Published: November 2019

Abstract
This article examines the often-overlooked Victorian guitar and its place in the musicological history of the long nineteenth century and in various canonical and non-canonical literary representations from those of Ann Radcliffe and Charlotte Yonge to George Du Maurier and Oscar Wilde, in the light of some Victorian music historians’ and contemporary organologists’ search for a stringed cultural heritage extending to the far reaches of empire. Some Victorian music historians regarded instruments as developmental yardsticks, signifying a culture, nation, or people’s evolutionary progress, a process belonging to what Patrick Brantlinger has called ‘extinction discourse’. In the context of an interdisciplinary discussion of the guitar’s position amid the period’s obsession with uncovering origins and constructing archives, as well as fostering technical innovation—displayed at the Great Exhibition—and shifting modes of performance, this article argues that despite the changing instrument’s rise in status over the period, literary representations adhered to older, sentimental, exotic, spiritual, and, increasingly decadent and homoerotic associations. Anxiety about decadence in concert with calls for preservation but also rationalization of salvaged cultural forms, including musical instruments, led some to advocate a type of musical eugenics, ostensibly to facilitate the creation of a new music of the future.
The Cloud Factory I: Generating resolved filamentary molecular clouds from galactic-scale forces
Authors: Smith Rowan J , Treß Robin G , Sormani Mattia C , Glover Simon C O , Klessen Ralf S , Clark Paul C , Izquierdo Andrés F , Cabral Ana Duarte , Zucker Catherine 
Published: November 2019

ABSTRACT
We introduce a new suite of simulations, ‘The Cloud Factory’, which self-consistently forms molecular cloud complexes at high enough resolution to resolve internal substructure (up to 0.25 M⊙ in mass) all while including galactic-scale forces. We use a version of the arepo code modified to include a detailed treatment of the physics of the cold molecular ISM, and an analytical galactic gravitational potential for computational efficiency. The simulations have nested levels of resolution, with the lowest layer tied to tracer particles injected into individual cloud complexes. These tracer refinement regions are embedded in the larger simulation so continue to experience forces from outside the cloud. This allows the simulations to act as a laboratory for testing the effect of galactic environment on star formation. Here we introduce our method and investigate the effect of galactic environment on filamentary clouds. We find that cloud complexes formed after a clustered burst of feedback have shorter lengths and are less likely to fragment compared to quiescent clouds (e.g. the Musca filament) or those dominated by the galactic potential (e.g. Nessie). Spiral arms and differential rotation preferentially align filaments, but strong feedback randomizes them. Long filaments formed within the cloud complexes are necessarily coherent with low internal velocity gradients, which has implications for the formation of filamentary star-clusters. Cloud complexes formed in regions dominated by supernova feedback have fewer star-forming cores, and these are more widely distributed. These differences show galactic-scale forces can have a significant impact on star formation within molecular clouds.
Super Hot Cores in NGC 253: witnessing the formation and early evolution of super star clusters
Authors: Rico-Villas F , Martín-Pintado J , González-Alfonso E , Martín S , Rivilla V M 
Published: November 2019

ABSTRACT
Using 0.2 arcsec (∼3 pc) ALMA images of vibrationally excited HC3N emission (HC3N*) we reveal the presence of eight unresolved Super Hot Cores (SHCs) in the inner 160 pc of NGC 253. Our LTE and non-LTE modelling of the HC3N* emission indicate that SHCs have dust temperatures of 200–375 K, relatively high H2 densities of (1−6) × 106 cm−3 and high IR luminosities of (0.1–1) × 108 L⊙. As expected from their short-lived phase (∼104 yr), all SHCs are associated with young super star clusters (SSCs). We use the ratio of luminosities from the SHCs (protostar phase) and from the free–free emission (ZAMS star phase), to establish the evolutionary stage of the SSCs. The youngest SSCs, with the larges ratios, have ages of a few 104 yr (proto-SSCs) and the more evolved SSCs are likely between 105 and 106 yr (ZAMS-SSCs). The different evolutionary stages of the SSCs are also supported by the radiative feedback from the UV radiation as traced by the HNCO/CS ratio, with this ratio being systematically higher in the young proto-SSCs than in the older ZAMS-SSCs. We also estimate the SFR and the SFE of the SSCs. The trend found in the estimated SFE ($\sim 40{{\ \rm per\ cent}}$ for proto-SSCs and $\gt 85{{\ \rm per\ cent}}$ for ZAMS-SSCs) and in the gas mass reservoir available for star formation, one order of magnitude higher for proto-SSCs, suggests that star formation is still going on in proto-SSCs. We also find that the most evolved SSCs are located, in projection, closer to the centre of the galaxy than the younger proto-SSCs, indicating an inside-out SSC formation scenario.
The clockwork is moving on – a combined analysis of TESS and Kepler measurements of Kepler-13Ab
Authors: Szabó Gy M , Pribulla T , Pál A , Bódi A , Kiss L L , Derekas A 
Published: November 2019

ABSTRACT
Kepler-13Ab (KOI-13) is an exoplanet orbiting a rapidly rotating A-type star. The system shows a significant spin–orbit misalignment and a changing transit duration most probably caused by the precession of the orbit. Here, we present a self-consistent analysis of the system combining Kepler and Transiting Exoplanet Survey Satellite (TESS) observations. We model the light curves assuming a planet transits a rotating oblate star that has a strong surface temperature gradient due to rotation-induced gravity darkening. The transit chord moves slowly as an emergent feature of orbital precession excited by the oblate star with a decline rate in the impact parameter of db/dt = −0.011 yr−1, and with an actual value of b = 0.19 for the latest TESS measurements. The changing transit duration that was measured from Kepler Q2 and Q17 quarters and the TESS measurements indicates a linear drift of the impact parameter. The solutions for the stellar spin axis suggest a nearly orthogonal aspect, with inclination around 100°.
Childhood unintentional injury: The impact of family income, education level, occupation status, and other measures of socioeconomic status. A systematic review
Authors: Mahboob Afifa , Richmond Sarah A , Harkins Joshua P , Macpherson Alison K 
Published: November 2019

Abstract

Introduction
Unintentional injuries represent a substantial public health burden among children and adolescents, and previous evidence suggests that there are disparities in injury by socioeconomic status (SES). This paper reports on a systematic review of literature on injury rates among children and adolescents by measures of SES.

Methods
A systematic literature search was conducted using six electronic databases: MEDLINE, PsycINFO, CINAHL, HealthSTAR, EMBASE, and SportsDiscus. This review considered children ages 19 years and under and publications between 1997 and 2017—representing an update since the last systematic review examined this specific question. Fifty-four articles were summarized based on study and participant descriptions, outcome and exposure, statistical tests used, effect estimates, and overall significance.

Results
Most articles addressed risk factors across all injury mechanisms; however, some focused particularly on burns/scalds, road traffic injuries, falls/drowning cases, and playground/sports injuries. Other studies reported on specific injury types including traumatic dental injuries, traumatic brain injuries, and fractures. The studies were of moderate quality, with a median of 15.5 (95% confidence interval [CI]: 15.34 to 15.66) out of 19. Thirty-two studies found an inverse association between SES and childhood unintentional injury, three found a positive association while twenty were not significant or failed to report effect measures.

Conclusion
Given the variability in definition of the exposure (SES) and outcome (injury), the results of this review were mixed; however, the majority of studies supported a relationship between low SES and increased injury risk. Public health practice must consider SES, and other measures of health equity, in childhood injury prevention programming, and policy.
Nonsteroidal anti-inflammatory drugs and incidence of atrial fibrillation: a meta-analysis
Authors: Chokesuwattanaskul R , Chiengthong K , Thongprayoon C , Lertjitbanjong P , Bathini T , Ungprasert P , Cato L D , Mao M A , Cheungpasitporn W 
Published: November 2019

Abstract

Background
Nonsteroidal anti-inflammatory drugs (NSAIDs) are widely used for many inflammatory disorders and pain-related illnesses. Despite their widespread use, the association between NSAIDs and the incidence of atrial fibrillation (AF) remains unclear. The aim of this systematic review and meta-analysis is to investigate this association.

Methods
A systematic review was conducted in MEDLINE, EMBASE and Cochrane databases from inception through August 2019 to identify studies that evaluated the risk of AF among patients using NSAIDs. Pooled risk ratios (RRs) and 95% CI were calculated using a random-effect, generic inverse variance method. The protocol for this meta-analysis is registered with PROSPERO (International Prospective Register of Systematic Reviews; no. CRD42019141609).

Results
Eight observational studies (four case–control studies and four cohort studies) with a total of 14 806 420 patients were enrolled. When compared with nonNSAIDs users, the pooled RR of AF in patients with NSAIDs use was 1.29 (95% CI 1.19–1.39). Meta-analyses based on the type of study were additionally performed. Subgroup analysis by study design revealed a significant association between the use of NSAIDs and AF for both case–control studies (pooled RR 1.37; 95% CI, 1.15–1.63) and cohort studies (pooled RR 1.22; 95% CI, 1.14–1.31). Sub-analyses based on specific NSAIDs showed pooled RRs of AF in patients using ibuprofen of 1.30 (95% CI 1.22–1.39), naproxen of 1.44 (95% CI 1.18–1.76) and diclofenac of 1.37 (95% CI 1.10–1.71), respectively. Funnel plot and Egger’s regression asymmetry tests were performed and showed no publication bias.

Conclusion
NSAID use is associated with incident AF. Our study also demonstrated a consistent result among different NSAIDs.