bluuebunny/crossref_metadata_2025_split huggingface dataset:
NGPINT: a next-generation protein–protein interaction software
Authors: Banerjee Sagnik , Velásquez-Zapata Valeria , Fuerst Gregory , Elmore J Mitch , Wise Roger P 
Published: November 2020

AbstractMapping protein–protein interactions at a proteome scale is critical to understanding how cellular signaling networks respond to stimuli. Since eukaryotic genomes encode thousands of proteins, testing their interactions one-by-one is a challenging prospect. High-throughput yeast-two hybrid (Y2H) assays that employ next-generation sequencing to interrogate complementary DNA (cDNA) libraries represent an alternative approach that optimizes scale, cost and effort. We present NGPINT, a robust and scalable software to identify all putative interactors of a protein using Y2H in batch culture. NGPINT combines diverse tools to align sequence reads to target genomes, reconstruct prey fragments and compute gene enrichment under reporter selection. Central to this pipeline is the identification of fusion reads containing sequences derived from both the Y2H expression plasmid and the cDNA of interest. To reduce false positives, these fusion reads are evaluated as to whether the cDNA fragment forms an in-frame translational fusion with the Y2H transcription factor. NGPINT successfully recognized 95% of interactions in simulated test runs. As proof of concept, NGPINT was tested using published data sets and it recognized all validated interactions. NGPINT can process interaction data from any biosystem with an available genome or transcriptome reference, thus facilitating the discovery of protein–protein interactions in model and non-model organisms.
Tits-type Alternative for Groups Acting on Toric Affine Varieties
Authors: Arzhantsev Ivan , Zaidenberg Mikhail 
Published: November 2020

Abstract
Given a toric affine algebraic variety $X$ and a collection of one-parameter unipotent subgroups $U_1,\ldots ,U_s$ of $\mathop {\textrm {Aut}}(X)$, which are normalized by the torus acting on $X$, we show that the group $G$ generated by $U_1,\ldots ,U_s$ verifies the following alternative of Tits type: either $G$ is a unipotent algebraic group or it contains a non-abelian free subgroup. We deduce that if $G$ is $2$-transitive on a $G$-orbit in $X$, then $G$ contains a non-abelian free subgroup and so is of exponential growth.
Gonococcal Adaptation to Palmitic Acid Through farAB Expression and FadD Activity Mutations Increases In Vivo Fitness in a Murine Genital Tract Infection Model
Authors: Gao Lingyu , Wang Zhemin , van der Veen Stijn 
Published: November 2020

Abstract
Neisseria gonorrhoeae is a bacterial pathogen that colonizes mucosal epithelia that are rich in antimicrobial molecules such as long-chain fatty acids. Here we studied the mechanisms involved in palmitic acid resistance and their impact on in vivo biological fitness in a murine genital tract infection model. A stable palmitic acid-resistant derivative was obtained by serial passage with incremental palmitic acid concentrations. This derivative outcompeted its parent strain for colonization and survival in the murine infection model. Subsequent whole-genome sequencing resulted in the identification of the 3 resistance-related SNPs ihfAC5T, fadDC772T, and farAG-52T (promoter) that were verified for resistance against palmitic acid. Subsequent characterization of the associated resistance determinants showed that ihfAC5T and farAG-52T induced gene expression of the FarAB efflux pump, whereas fadDC772T increased the maximum enzyme activity of the FadD long-chain fatty acid-coenzyme A ligase. Our results highlight the mechanisms involved in gonococcal adaptation to the murine host environment.
Treatment Outcomes Among Pediatric Patients With Highly Drug-Resistant Tuberculosis: The Role of New and Repurposed Second-Line Tuberculosis Drugs
Authors: Madzgharashvili Tea , Salindri Argita D , Magee Matthew J , Tukvadze Nestani , Avaliani Zaza , Blumberg Henry M , Kempker Russell R , Lomtadze Nino 
Published: November 2020

Abstract

Background
Among pediatric patients with multidrug-resistant tuberculosis (MDR-TB), limited data exist regarding treatment outcomes in the context of the new and repurposed second-line TB drugs (SLDs). We aimed to describe the treatment outcomes among pediatric MDR-TB patients receiving new and repurposed SLDs including the proportion who achieved favorable outcomes.

Methods
We conducted a retrospective cohort study among pediatric patients (age ≤18 years) treated for MDR-TB in the country of Georgia from 2009 to 2016. A “new and repurposed” SLD regimen was defined as a regimen that included linezolid, bedaquiline, and/or delamanid. Favorable treatment outcome was defined by treatment completion or documented microbial “cure” status at the end of treatment. We assessed the association between the use of the new and repurposed SLDs with MDR-TB treatment outcomes using bivariate analyses and log-binomial regression.

Results
There were 124 pediatric MDR-TB patients (median age: 13.7; interquartile range: 4.6-16.0) initiating treatment; 119 (96.0%) had a treatment outcome recorded and were included in our analyses. Eighteen (15.1%) patients received new and repurposed SLDs from 2015 or later. After adjusting for potential confounders, the proportion achieving favorable MDR-TB treatment outcomes was higher among patients treated with SLD regimens that included new and/or repurposed drugs when compared with those treated without (adjusted risk ratio: 1.17; 95% confidence interval: 0.51-2.72).

Conclusions
We observed a high proportion of favorable treatment outcomes among pediatric patients with MDR-TB receiving the new and repurposed SLDs. Further studies to evaluate the efficacy and children’s tolerability of the new and repurposed SLDs are still warranted.
Full circumference lower extremity degloving injury treated with hydrosurgical debridement and negative-pressure wound therapy with gauze wound filler for fixation of avulsed flap skin grafts
Authors: Nagama Tae , Kakudo Natsuko , Kuro Atsuyuki , Ozaki Yujiro , Shirasawa Yasuko , Kunieda Sakurako , Suzuki Kenji , Saito Fukuki , Kusumoto Kenji 
Published: November 2020

Abstract
Degloving, a skin and subcutis avulsion, is a severe traumatic injury sometimes caused by rolling wheels or machines. Although avulsed flaps are often readapted to its original site, most of these tissues become necrotic. Due to the extensive skin and soft tissue deficiency caused by necrosis, treatment becomes difficult. Skin grafts harvested from avulsed flaps may be used to treat degloving injuries, while negative pressure wound therapy (NPWT) is used to secure the grafts. Commonly used porous polyurethane foam wound fillers are difficult to set in circumferential extremity degloving injuries; gauze-based wound fillers are easier to use and cause less pain during dressing changes. We present a case of an extensive, full-circumference left lower-extremity degloving injury, treated using NPWT with gauze-based wound fillers for fixation of skin grafts harvested from avulsed flaps after hydrosurgical debridement. For complex wound geometries, gauze-based wound fillers can be easily applied for skin graft immobilization.
Traumatic pseudoaneurysm of the cavernous carotid: a lethal complication of craniofacial trauma
Authors: Ahmed Omar , Mahmood Sara , Aladham Youssef , Abdelnaby Moustafa Mohamed 
Published: November 2020

Abstract
Pseudoaneurysm of the cavernous carotid artery is a rare, yet life-threatening complication of craniofacial trauma. It may well present itself with delayed massive epistaxis up to several months after the initial insult. Early recognition and prompt treatment are the key in management and a high index of clinical suspicion is always required. In this article, we report a patient with a penetrating head injury who developed delayed epistaxis along with unilateral abducent and partial oculomotor palsy. Urgent diagnostic carotid angiography was undertaken, followed by endovascular coiling that resulted in no recurrence for a year of follow-up.
The Kimbalitos: The Plan Kimball, Cold War, and Medicine in Paraguay, 1956–64
Authors: María Chesterton Bridget 
Published: November 2020

Abstract
This article studies a faculty exchange from the medical school at the University of Buffalo (later the State University of New York, University at Buffalo) to the medical school in Asunción, Paraguay in the 1950s and 1960s. The arrival of U.S.-trained medical professionals spurred a new pedagogical program designed to improve medical education by reducing the number of students enrolled, making the curriculum more scientifically oriented, and demanding the professionalization of its future doctors. Moreover, the program was strategically designed to depoliticize the medical school in Asunción at the height of the Cold War. Using oral interviews of Paraguayans who participated in the reforms, government records, and documents produced by U.S. medical professionals, the article tracks how the program was started and under what conditions it operated, and concludes that both the United States and Paraguayan medical professionals considered the program a success—it improved the quality of Paraguayan medical professionals and, at least temporarily, neutralized the political leanings of the medical school.
The census of dense cores in the Serpens region from the Herschel Gould Belt Survey
Authors: Fiorellino E , Elia D , André Ph , Men’shchikov A , Pezzuto S , Schisano E , Könyves V , Arzoumanian D , Benedettini M , Ward-Thompson D , Bracco A , Di Francesco J , Bontemps S , Kirk J , Motte F , Molinari S 
Published: November 2020

ABSTRACT
The Herschel Gould Belt survey mapped the nearby (d &lt; 500 pc) star-forming regions to understand better how the prestellar phase influences the star formation process. Here, we report a complete census of dense cores in a ∼15 deg2 area of the Serpens star-forming region located between d ∼ 420 and 484 pc. The PACS and SPIRE cameras imaged this cloud from 70 to 500 μm. With the multiwavelength source extraction algorithm getsources, we extract 833 sources, of which 709 are starless cores and 124 are candidate protostellar cores. We obtain temperatures and masses for all the sample, classifying the starless cores in 604 prestellar cores and 105 unbound cores. Our census of sources is $80{{\ \rm per\ cent}}$ complete for M &gt; 0.8 M⊙ overall. We produce the core mass function (CMF) and compare it with the initial mass function (IMF). The prestellar CMF is consistent with lognormal trend up to ∼2 M⊙, after which it follows a power law with slope of −2.05 ± 0.34. The tail of its CMF is steeper but still compatible with the IMF for the region we studied in this work. We also extract the filaments network of the Serpens region, finding that $81{{\ \rm per\ cent}}$ of prestellar cores lie on filamentary structures. The spatial association between cores and filamentary structure supports the paradigm, suggested by other Herschel observations, that prestellar cores mostly form on filaments. Serpens is confirmed to be a young, low-mass and active star-forming region.
The Atacama Cosmology Telescope: a CMB lensing mass map over 2100 square degrees of sky and its cross-correlation with BOSS-CMASS galaxies
Authors: Darwish Omar , Madhavacheril Mathew S , Sherwin Blake D , Aiola Simone , Battaglia Nicholas , Beall James A , Becker Daniel T , Bond J Richard , Calabrese Erminia , Choi Steve K , Devlin Mark J , Dunkley Jo , Dünner Rolando , Ferraro Simone , Fox Anna E , Gallardo Patricio A , Guan Yilun , Halpern Mark , Han Dongwon , Hasselfield Matthew , Hill J Colin , Hilton Gene C , Hilton Matt , Hincks Adam D , Patty Ho Shuay-Pwu , Hubmayr J , Hughes John P , Koopman Brian J , Kosowsky Arthur , Van Lanen J , Louis Thibaut , Lungu Marius , MacInnis Amanda , Maurin Loïc , McMahon Jeffrey , Moodley Kavilan , Naess Sigurd , Namikawa Toshiya , Nati Federico , Newburgh Laura , Nibarger John P , Niemack Michael D , Page Lyman A , Partridge Bruce , Qu Frank J , Robertson Naomi , Schillaci Alessandro , Schmitt Benjamin , Sehgal Neelima , Sifón Cristóbal , Spergel David N , Staggs Suzanne , Storer Emilie , van Engelen Alexander , Wollack Edward J 
Published: November 2020

ABSTRACT
We construct cosmic microwave background lensing mass maps using data from the 2014 and 2015 seasons of observations with the Atacama Cosmology Telescope (ACT). These maps cover 2100 square degrees of sky and overlap with a wide variety of optical surveys. The maps are signal dominated on large scales and have fidelity such that their correlation with the cosmic infrared background is clearly visible by eye. We also create lensing maps with thermal Sunyaev−Zel’dovich contamination removed using a novel cleaning procedure that only slightly degrades the lensing signal-to-noise ratio. The cross-spectrum between the cleaned lensing map and the BOSS CMASS galaxy sample is detected at 10σ significance, with an amplitude of A = 1.02 ± 0.10 relative to the Planck best-fitting Lambda cold dark matter cosmological model with fiducial linear galaxy bias. Our measurement lays the foundation for lensing cross-correlation science with current ACT data and beyond.
Spectroscopic and photometric time series of the bright RRc star T Sex
Authors: Benkő József M , Sódor Ádám , Pál András 
Published: November 2020

ABSTRACT
We present spectroscopic time series observations on one of the brightest northern RRc stars, namely T Sex. Additionally, we also analysed extended photometric data sets, particularly the recent observations of the TESS space telescope. The main findings of our studies are as follows: T Sex, unlike all RRc stars whose space photometry has been analysed, shows only the 0.5fx frequency as an additional pulsation frequency. With this, T Sex may be the first represent of such rare RRc stars found from space photometry. The spectroscopic data show a periodic distortion of the H α line with the pulsation phase. This phenomenon has not been reported for any RR Lyrae stars. The characteristic line distortion is probably caused by the turbulent convection, which resulted in higher macroturbulent velocity for T Sex than that for typical RRab stars. Line doubling of the Na D line was observed between the 0.37 and 0.80 pulsation phases. The explanation of this phenomenon is that the two absorption components originate from different sources. The redder component comes from the pulsating atmosphere of the star, while the bluer one comes from the interstellar space. At phase 0.438, we detected emission on the Na D line, which may indicate a weak shock wave.
Infectious Disease Team Review Using Antibiotic Switch and Discharge Criteria Shortens the Duration of Intravenous Antibiotic: A Single-Center Cluster-Randomized Controlled Trial in Thailand
Authors: Wongkamhla Thanyarak , Khan-asa Buddharat , Tongsai Sasima , Angkasekwinai Nasikarn 
Published: November 2020

Abstract

Background
Strategies have been recommended to optimize early antibiotic (ATB) switching from intravenous (IV) to oral ATB. This study aimed to determine whether infectious disease (ID) team review using ATB switch and discharge criteria would shorten the duration of IV ATB and length of hospital stay (LOS).

Methods
This cluster-randomized controlled trial was conducted in 8 general medical wards as cluster units at Siriraj Hospital during January–October 2019. The ID team review with checklist criteria was performed on the third, fifth, and seventh day of IV-ATB treatment to determine (1) the suitability of switching to oral ATB or outpatient parenteral ATB therapy and (2) early discharge for patients receiving IV-ATB versus control. The primary outcomes were LOS and the duration or days of therapy (DOT) or defined daily dose (DDD) of IV-ATB therapy.

Results
Four wards each were randomly assigned to the intervention and control groups (46 patients/cluster, 184 patients/arm). No significant difference was observed between intervention and controls for median duration of IV-ATB therapy (7 vs 7 days) and LOS (9 vs 10 days). A significantly shorter duration of IV ATB was observed in patients without sepsis in the intervention group when measured by DOT (7 vs 8 days, P = .027) and DDD (7 vs 9, P = .017) in post hoc analysis.

Conclusions
Infectious disease team review using checklist criteria did not result in a shorter duration of IV-ATB and LOS in overall patients. Further study is needed to determine whether faster culture turnaround time or advanced testing will reduce the duration of IV-ATB therapy.
Retirement—a time to dread or to cherish?
Authors: Taylor-Robinson Simon D 
Published: November 2020

Abstract
Retirement is often a taboo subject amongst medical professionals. Many have dedicated a major part of their lives to the practice of medicine to the exclusion of anything else. The thought of empty days or lack of externally driven purpose is something that unsettles many who are approaching pensionable age. In reality, such fears rarely materialize. The challenge of transition to a new phase of life is all the more poignant if ill health intervenes early, causing premature cessation of work.
MEASUREMENT OF RADON ACTIVITY CONCENTRATION IN UNDERGROUND WATER OF BURETI SUB-COUNTY OF KERICHO COUNTY KENYA
Authors: Rotich Charles K , Hashim Nadir O , Chege Margaret W , Nyambura Catherine 
Published: November 2020

Abstract
The activity concentration of radon in underground water of Bureti sub-county was measured using liquid scintillating counter device. The average radon activity concentration in all the water samples was 12.41 Bql−1. The maximum and minimum activity concentrations of radon were 22.5 and 4.57 Bql−1, respectively. In total, 53% of the total samples analysed had radon concentration levels above the US Environmental Protection Agency-recommended limit of 11.1 Bql−1. The annual dose received by an individual as a result of waterborne radon was determined according to the United Nations Scientific Committee on the Effect of Atomic Radiation reports and was found to be 33.23 𝜇Svy−1. All the samples recorded a value &lt;100 𝜇Svy−1 recommended by the World Health Organization and the European Union council.
The Agency Myth: Persistence in Individual Explanations for Gender Inequality
Authors: Carian Emily K , Johnson Amy L 
Published: November 2020

AbstractWe leverage a unique longitudinal dataset—98 interviews with 30 college students—to investigate young people’s explanations for gender inequality over time and the implications of those explanations. Through five waves and four years of interviews, we show that young people struggled to internalize structural explanations, instead favoring explanations that conceptualized gender as an individual attribute. Individual perspectives were so intransigent because of respondents’ adherence to what we call the agency myth, the latent cultural idea that individuals, particularly women, have the power to overcome gender inequality through strategic behaviors. The agency myth offered young people a sense of self-efficacy, but prevented their imagining broader solutions for social change. Those who were able to think structurally did so only after rejecting the agency myth. This article shows how the durability of individualist perspectives contributes to persistent gender inequality by privileging individualized solutions over more effective structural ones. We discuss how individual subscription to the agency myth is structured by young people’s intersecting identities, and how the agency myth can be applied to other axes of inequality.
The Conserved Arginine Required for AvrRps4 Processing Is Also Required for Recognition of Its N-Terminal Fragment in Lettuce
Authors: Su Jianbin , Nguyen Quang-Minh , Kimble Ashten , Pike Sharon M. , Kim Sang Hee , Gassmann Walter 
Published: November 2020

Pathogens utilize a repertoire of effectors to facilitate pathogenesis, but when the host recognizes one of them, it causes effector-triggered immunity. The Pseudomonas type III effector AvrRps4 is a bipartite effector that is processed in planta into a functional 133–amino acid N-terminus (AvrRps4-N) and 88–amino acid C-terminus (AvrRps4-C). Previous studies found AvrRps4-C to be sufficient to trigger the hypersensitive response (HR) in turnip. In contrast, our recent work found that AvrRps4-N but not AvrRps4-C triggered HR in lettuce, whereas both were required for resistance induction in Arabidopsis. Here, we initially compared AvrRps4 recognition by turnip and lettuce using transient expression. By serial truncation, we identified the central conserved region consisting of 37 amino acids as essential for AvrRps4-N recognition, whereas the putative type III secretion signal peptide or the C-terminal 13 amino acids were dispensable. Surprisingly, the conserved arginine at position 112 (R112) that is required for full-length AvrRps4 processing is also required for the recognition of AvrRps4-N by lettuce. Mutating R112 to hydrophobic leucine or negatively charged glutamate abolished the HR-inducing capacity of AvrRps4-N, while a positively charged lysine at this position resulted in a slow and weak HR. Together, our results suggest an AvrRps4-N recognition-specific role of R112 in lettuce. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Fibromyalgia screening in patients with unexplained chronic fatigue
Authors: Aakre Christopher A. 
Published: November 2020

Abstract
Women often complain of symptoms of fatigue and generalized aches and pains around menopause. Even though fibromyalgia is more prevalent in midlife women, not all women presenting with aches and pain and disrupted sleep meet diagnostic criteria for fibromyalgia. This Practice Pearl addresses the distinction between chronic fatigue syndrome and fibromyalgia and the management of fibromyalgia in perimenopausal and postmenopausal women.
CLINICAL UTILITY OF MORPHOFUNCTIONAL CORRELATION OF MICROPERIMETRY AND OPTICAL COHERENCE TOMOGRAPHY
Authors: Sugiura Yoshimi , Dolz-Marco Rosa , Fernández-Avellaneda Pedro , Xu Xiaoyu , Ledesma-Gil Gerardo , Freund K. Bailey 
Published: November 2020

Purpose:
To demonstrate the clinical and research value of a simplified technique enabling alignment of functional microperimetry data with retinal structure imaged by eye-tracked optical coherence tomography (OCT) in eyes with macular disease.

Methods:
Normal and diseased eyes underwent sequential Spectralis OCT macular raster scans and Macular Integrity Assessment microperimetry using both standard central 10° analysis and custom scan patterns. The microperimetry data were imported into Spectralis research software program, which was automatically registered to the scanning laser ophthalmoscopy near-infrared reflectance image obtained during OCT acquisition. The OCT B-scans were directly correlated with the microperimetry data so that retina sensitivity and retinal microstructure at corresponding points could be evaluated simultaneously.

Results:
Seventy eyes of 41 patients (110 studies) aged 22 years to 95 years (mean 63.5 ± 18.0 years) with both normal and pathologic macular changes were included. The mean Macular Integrity Assessment retina sensitivity of all 110 studies was 22.2 ± 4.9 (range: 0.1–30.3). Retinal sensitivity showed good correspondence in structural changes seen on OCT B-scans.

Conclusion:
We demonstrate a practical method to align retina sensitivity data to anatomical tomographic findings. This technique provides data not obtainable with standard visual acuity measures.