bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling the formation of the first two neutron star–black hole mergers, GW200105 and GW200115: metallicity, chirp masses, and merger remnant spins
Authors: Chattopadhyay Debatri , Stevenson Simon , Broekgaarden Floor , Antonini Fabio , Belczynski Krzysztof 
Published: May 2022

ABSTRACT
The two neutron star–black hole mergers (GW200105 and GW200115) observed in gravitational waves by advanced LIGO and Virgo, mark the first ever discovery of such binaries in nature. We study these two neutron star–black hole systems through isolated binary evolution, using a grid of population synthesis models. Using both mass and spin observations (chirp mass, effective spin, and remnant spin) of the binaries, we probe their different possible formation channels in different metallicity environments. Our models only support LIGO data when assuming the black hole is non-spinning. Our results show a strong preference that GW200105 and GW200115 formed from stars with sub-solar metallicities Z ≲ 0.005. Only two metal-rich (Z = 0.02) models are in agreement with GW200115. We also find that chirp mass and remnant spins jointly aid in constraining the models, while the effective spin parameter does not add any further information. We also present the observable (i.e. post-selection effects) median values of spin and mass distribution from all our models, which may be used as a reference for future mergers. Further, we show that the remnant spin parameter distribution exhibits distinguishable features in different neutron star–black hole sub-populations. We find that non-spinning, first born black holes dominate significantly the merging neutron star–black hole population, ensuring electromagnetic counterparts to such mergers a rare affair.
Variable structure in the PDS 70 disc and uncertainties in radio-interferometric image restoration
Authors: Casassus Simon , Cárcamo Miguel 
Published: May 2022

ABSTRACT
The compact mm-wavelength signal in the central cavity of the PDS 70 disc, revealed by deep ALMA observations, is aligned with unresolved H α emission, and is thought to stem from a circumplanetary disc (CPD) around PDS 70c. We revisit the available ALMA data on PDS 70c with alternative imaging strategies, and with special attention to uncertainties and to the impact of the so-called ‘JvM correction’, which is thought to improve the dynamic range of restored images. We also propose a procedure for the alignment and joint imaging of multi-epoch visibility data. We find that the JvM correction exaggerates the peak signal-to-noise of the data, by up to a factor of 10. In the case of PDS 70, we recover the detection of PDS 70c from the 2019 July data, but only at 8 σ. However, its non-detection in 2017 Dec. suggests that PDS 70c is variable by at least $42{{\ \rm per\ cent}} \pm 13{{\ \rm per\ cent}}$ over a 1.75 yr time-span, so similar to models of the H α variability. We also pick up fine structure in the inner disc, such that its peak is offset by ∼0${_{.}^{\prime\prime}}$04 from the disc centre. The inner disc is variable too, which we tentatively ascribe to Keplerian rotation as well as intrinsic morphological changes.
Chromosomal synapsis defects can trigger oocyte apoptosis without elevating numbers of persistent DNA breaks above wild-type levels
Authors: Ravindranathan Ramya , Raveendran Kavya , Papanikos Frantzeskos , San-Segundo Pedro A , Tóth Attila 
Published: May 2022

Abstract
Generation of haploid gametes depends on a modified version of homologous recombination in meiosis. Meiotic recombination is initiated by single-stranded DNA (ssDNA) ends originating from programmed DNA double-stranded breaks (DSBs) that are generated by the topoisomerase-related SPO11 enzyme. Meiotic recombination involves chromosomal synapsis, which enhances recombination-mediated DSB repair, and thus, crucially contributes to genome maintenance in meiocytes. Synapsis defects induce oocyte apoptosis ostensibly due to unrepaired DSBs that persist in asynaptic chromosomes. In mice, SPO11-deficient oocytes feature asynapsis, apoptosis and, surprisingly, numerous foci of the ssDNA-binding recombinase RAD51, indicative of DSBs of unknown origin. Hence, asynapsis is suggested to trigger apoptosis due to inefficient DSB repair even in mutants that lack programmed DSBs. By directly detecting ssDNAs, we discovered that RAD51 is an unreliable marker for DSBs in oocytes. Further, SPO11-deficient oocytes have fewer persistent ssDNAs than wild-type oocytes. These observations suggest that oocyte quality is safeguarded in mammals by a synapsis surveillance mechanism that can operate without persistent ssDNAs.
ExpressVis: a biologist-oriented interactive web server for exploring multi-omics data
Authors: Liu Xian , Xu Kaikun , Tao Xin , Yin Ronghua , Ren Guangming , Yu Miao , Li Changyan , Chen Hui , Zhao Ke , Xiang Shensi , Gao Huiying , Bo Xiaochen , Chang Cheng , Yang Xiaoming 
Published: May 2022

Abstract
In the era of life-omics, huge amounts of multi-omics data have been generated and widely used in biomedical research. It is challenging for biologists with limited programming skills to obtain biological insights from multi-omics data. Thus, a biologist-oriented platform containing visualization functions is needed to make complex omics data digestible. Here, we propose an easy-to-use, interactive web server named ExpressVis. In ExpressVis, users can prepare datasets; perform differential expression analysis, clustering analysis, and survival analysis; and integrate expression data with protein–protein interaction networks and pathway maps. These analyses are organized into six modules. Users can use each module independently or use several modules interactively. ExpressVis displays analysis results in interactive figures and tables, and provides comprehensive interactive operations in each figure and table, between figures or tables in each module, and among different modules. It is freely accessible at https://omicsmining.ncpsb.org.cn/ExpressVis and does not require login. To test the performance of ExpressVis for multi-omics studies of clinical cohorts, we re-analyzed a published hepatocellular carcinoma dataset and reproduced their main findings, suggesting that ExpressVis is convenient enough to analyze multi-omics data. Based on its complete analysis processes and unique interactive operations, ExpressVis provides an easy-to-use solution for exploring multi-omics data.
Measuring Belief-dependent Preferences without Data on Beliefs
Authors: Bellemare Charles , Sebald Alexander 
Published: May 2022

Abstract
We derive bounds on the causal effect of belief-dependent preferences (reciprocity and guilt aversion) on choices in sequential two-player games without data on the (higher-order) beliefs of players. We show how informative bounds can be derived by exploiting a specific invariance property common to those preferences. We illustrate our approach by analysing data from an experiment conducted in Denmark. Our approach produces tight bounds on the causal effect of reciprocity in the games we consider. These bounds suggest there exists significant reciprocity in our population—a result also substantiated by the participants’ answers to a post-experimental questionnaire. On the other hand, our approach yields high implausible estimates of guilt aversion—participants would be willing, in some games, to pay at least three Danish crowns (DKK) to avoid letting others down by one DKK. We contrast our estimated bounds with point estimates obtained using data on stated higher-order beliefs, keeping all other aspects of the model unchanged. We find that point estimates fall within our estimated bounds, suggesting that elicited higher-order belief data in our experiment is weakly (if at all) affected by various reporting biases.
Effects of reducing the standardized ileal digestible lysine and tryptophan to lysine ratio to slow growth of finishing pigs
Authors: Tolosa Andres F , Tokach Mike D , Goodband Robert D , Woodworth Jason C , DeRouchey Joel M , Gebhardt Jordan T , Wolfe Matt L 
Published: May 2022

Abstract
The COVID-19 global pandemic greatly affected pork processing plants in the United States. These pork processing plants were forced to either temporarily close or operate at reduced capacity due to the increased number of health-related employee absences. Because finishing pigs could not be timely marketed, methods to reduce growth performance were required to keep pigs from becoming too heavy at slaughter weight. Therefore, our objective was to determine the extent that reducing dietary standardized ileal digestible (SID) Lys and tryptophan-to-lysine ratio (Trp:Lys) ratio would slow finishing pig average daily gain (ADG) in a commercial setting. A total of 1,080 finishing pigs (327 × 1050, PIC; initially 32.3 kg) were used in a 119-d growth trial. Pigs were allotted by initial body weight (BW) and randomly assigned to 1 of 4 dietary treatments in a completely randomized block design with 27 pigs per pen and 10 pens per treatment. Three dietary regimes were formulated to contain either 100%, 90%, or 80% of the estimated SID Lys requirement for pigs in this facility, with a SID Trp:Lys ratio of 19%, with the exception of the last dietary phase formulated to 17% SID Trp:Lys. Seven different dietary phases were fed. The SID Lys concentrations in the 100% diets were: 1.10%, 1.01%, 0.91%, 0.83%, 0.79%, 0.71%, or 0.67% SID Lys from 32 to 40, 40 to 51, 51 to 72, 72 to 85, 85 to 98, 98 to 112, and 112 to 130 kg, respectively. A fourth regime was formulated to 80% SID Lys with a SID Trp:Lys ratio of 16% (80–16% SID Trp:Lys) throughout all phases. Overall from d 0 to 119, ADG (linear, P &lt; 0.001), final BW (linear, P &lt; 0.001), and gain-to-feed (G:F) decreased (linear, P = 0.087) as SID Lys decreased from 100% to 80% of the estimated requirement. Pigs fed the 80–16% SID Trp:Lys diets had an additional decrease in ADG (P &lt; 0.05) and G:F (P &lt; 0.10) compared with pigs fed 80% of the SID Lys requirement with the normal Trp:Lys ratio. The reduction in SID Lys (from 100% to 80%) and reduction in SID Lys and Trp:Lys ratio resulted in an 8.6 and 11.7 kg, respectively, decrease in final BW compared with pigs fed Lys and Trp at the requirement (100%). This study provides alternatives for pork producers to reduce growth rate of finishing pigs.
Evaluation of increasing digestible threonine to lysine ratio in corn–soybean meal diets without and with distillers dried grains with solubles on growth performance of growing-finishing pigs
Authors: Tolosa Andres F , Tokach Mike D , Goodband Robert D , Woodworth Jason C , DeRouchey Joel M , Gebhardt Jordan T 
Published: May 2022

Abstract
Corn distillers dried grains with solubles (DDGS) is commonly available and often can lower diet cost for swine diets. This corn co-product is recognized to be a source of dietary insoluble fiber, which can not only increase the villous length of the gut mucosa but also increase intestinal production of mucin. Mucin structure, functions, and synthesis are correlated to Thr intake; consequently, the dietary Thr level may need to be increased when feeding an insoluble fiber source such as corn–DDGS. Thus, the objective of this study was to evaluate if feeding standardized ileal digestible (SID) Thr:Lys ratio at or above the estimated requirement in diets without and with DDGS would influence growth performance in finishing pigs. A total of 2,160 pigs (PIC 337 × 1,050; initially 35.1 ± 0.5 kg) were used in a 112-d growth trial. Pigs were randomly assigned to pens (27 pigs per pen) in a randomized complete block design by body weight (BW) with 20 replications per treatment. Pens of pigs were allotted to one of four dietary treatments that were arranged in a 2 × 2 factorial with main effects of dietary Thr level (normal vs. high) and DDGS (without or with). Treatment diets were formulated in four phases from 34 to 57, 57 to 79, 79 to 104, and 104 to 130 kg BW. Diets with high DDGS were formulated to include 40% DDGS in phases 1 and 2, 30% in phase 3, and 15% in phase 4. The normal Thr diets were formulated to contain 61%, 62%, 63%, and 65% SID Thr:Lys ratios for the four dietary phases, respectively. High Thr diets had SID Thr:Lys ratios of 67%, 68%, 69%, and 72%, respectively. There were no interactions (P &gt; 0.10) observed in any phase or overall between Thr level and added DDGS. For the overall period (day 0 to 112), pigs fed diets without DDGS had increased (P &lt; 0.001) average daily gain (ADG) but reduced (P &lt; 0.001) average daily feed intake (ADFI), leading to increased (P &lt; 0.001) feed efficiency (gain-to-feed ratio [G:F]). There was no evidence for difference (P &gt; 0.10) between pigs fed diets formulated at normal or high SID Thr:Lys ratio. In summary, feeding high levels of DDGS decreased ADG and increased ADFI, which resulted in decreased G:F and lower final BW, regardless of the dietary SID Thr:Lys ratio level. In the current study, increasing the level of digestible Thr in a diet that contained a highly insoluble fiber source did not increase the growth performance of grow-finish pigs.
Disparities in Research during Plastic Surgery Training: How Can We Level the Playing Field?
Authors: Murphy Alexander I. , Mellia Joseph A. , Iaconetti Emma K. , Asadourian Paul A. , Diatta Fortunay , Klifto Kevin M. , Morris Martin P. , Broach Robyn B. , Fischer John P. , Butler Paris D. 
Published: May 2022

Background:
Lack of female and ethnically underrepresented in medicine (UIM) surgeons remains concerning in academic plastic surgery. One barrier to inclusion may be unequal opportunity to publish research. This study evaluates the extent of this challenge for plastic surgery trainees and identifies potential solutions.

Methods:
Data were collected on academic plastic surgeons' research productivity during training. Bivariate analysis compared publication measures between genders and race/ethnicities at different training stages (pre-residency/residency/clinical fellowship). Multivariate analysis determined training experiences independently associated with increased research productivity.

Results:
Overall, women had fewer total publications than men during training (8.89 versus 12.46, P = 0.0394). Total publications were similar between genders before and during residency (P > 0.05 for both) but lower for women during fellowship (1.32 versus 2.48, P = 0.0042). Women had a similar number of first-author publications during training (3.97 versus 5.24, P = 0.1030) but fewer middle-author publications (4.70 versus 6.81, P = 0.0405). UIM and non-UIM individuals had similar productivity at all training stages and authorship positions (P > 0.05 for all). Research fellowship completion was associated with increased total, first-, and middle-author training publications (P < 0.001 for all).

Conclusions:
Less research productivity for female plastic surgery trainees may reflect a disparity in opportunity to publish. Fewer middle-author publications could indicate challenges with network-building in a predominately male field. Despite comparable research productivity during training relative to non- UIM individuals, UIM individuals remain underrepresented in academic plastic surgery. Creating research fellowships for targeting underrepresented groups could help overcome these challenges.
Does Dedicated Research Time During Residency Predict Resident Academic Productivity and a Future Academic Career?
Authors: Onyekaba Ginikanwa , Mauch Jaclyn T. , Barrero Carlos , Mellia Joseph A. , Diatta Fortunay , Card Elizabeth , Broach Robyn B. , Fischer John P. 
Published: May 2022

Objective
Dedicated research time is a component of certain plastic surgery programs, and yet, there is limited research examining its impact on academic productivity and career outcomes. This study aimed to assess the effect of dedicated research time on the academic productivity of residents and the likelihood of pursuing an academic career.

Methods
We conducted a cross-sectional study that examined bibliometric indices of integrated plastic surgery residency graduates from 2010 to 2020. Academic productivity was determined by the number of peer-reviewed publications and h-index 1 year after residency graduation. Results were analyzed using descriptive statistics, χ2 test, t test, and logistic regression.

Results
Data on plastic surgery residency graduates were analyzed (N = 490 from 46 programs). The mean numbers of publications and h-index per research track graduate were 26.1 and 8.23, respectively. The mean numbers of publications and h-index per nonresearch track graduate were 15.9 and 5.97, respectively. After controlling for the University of Alabama research ranking through multilinear regression analysis, we found that pursuing dedicated research time was an independent predictor of increased h-index and publication output, although it did not predict an increased likelihood of pursuing an academic career.

Conclusions
Participating in dedicated research during residency increases academic productivity, irrespective of the residency program’s research rank. Given this finding, offering research years can help support the mission of fostering academic opportunities within plastic surgery.
Investigating Patient-Level Radiation Exposure in Hand and Wrist Fracture Surgery
Authors: Xu Wen , Christopher Adrienne N. , Hu Sophia , Steinberg David R. , Bozentka David J. , Lin Ines C. 
Published: May 2022

Background
Although occupational exposure to radiation has been previously studied in the hand surgery literature, there is a paucity of studies looking at radiation exposure to the patient during fluoroscopy-guided hand surgery. We aimed to describe the level of radiation experienced by patients undergoing common hand and wrist fracture fixation and to identify risk factors for increased radiation exposure.

Methods
We performed a retrospective review of patients at a single institution who underwent fracture fixation of the hand, wrist, or forearm requiring mini c-arm fluoroscopic guidance from 2016 to 2020. Data points collected included patient demographics, procedural details, and indicators of radiation exposure including dose-area product (DAP), total intraoperative images, and total fluoroscopy time. Effective dose (ED) was calculated using DAP, field size, and a previously established conversion factor.

Results
The final sample included 361 patients with an average age of 46 years. Procedures included fixation of forearm fractures (3.3%), distal radius fractures (35.7%), metacarpal fractures (30.8%), and phalangeal fractures (30.2%). The median number of intraoperative images acquired was 36, median total fluoroscopy time was 43 seconds, median DAP was 4.8 cGycm2, and median ED was 0.13 μSv. Distal (metacarpal and phalangeal) fractures required more intraoperative images and longer total fluoroscopy time (49 images, 61 seconds) compared with proximal (forearm and distal radius) fractures (39 images, 47 seconds) (images, P = 0.004; exposure time, P = 0.004). However, distal fractures had a lower average ED compared with proximal fractures (0.15 vs 0.19 μSv, P = 0.020). When compared with open procedures, percutaneous procedures had higher DAPs (8.8 vs 4.9 cGycm2, P < 0.001), higher ED (0.22 vs 0.15 μSv, P < 0.001), more intraoperative images (65 vs 36 images, P < 0.001), and longer total fluoroscopy time (81.9 vs 44.4 seconds, P < 0.001).

Conclusions
Patient-level radiation exposure during fluoroscopy-guided hand and wrist procedures is low relative to other common imaging modalities, such as dental radiographs, chest x-rays, and computed tomography scans, and is comparable with less than a few hours of natural background radiation exposure, highlighting the overall safety of this important technology. Further study should be performed to establish reference ranges, which could lead to improved patient counseling and evidence-based guidelines on patient shielding.
Single-cell transcriptome analysis reveals evolutionarily conserved features during the transition from normal breast stromal cells to cancer-associated fibroblasts
Authors: Delgado Ana Paula , Nemajerova Alice , Nelson Brian J. , Rao Manisha , Li Jinyu , Marchenko Natalia , Preall Jonathan , Moll Ute M. , Egeblad Mikala , Powers Scott 
Published: May 2022

SummaryTo comprehend cancer-associated fibroblasts (CAFs) origins, single-cell RNA sequencing was conducted on normal and cancerous breast tissue from mice and humans. We found three conserved CAF subtypes, which based on GOterm analysis we designated as matrix CAFs-, chemokine CAFs, and contractile CAFs. Matrix and chemokine CAFs originated from resident fibroblasts, while contractile CAFs originated from normal pericytes. Both human and mouse CAFs displayed upregulated genes involved in extracellular matrix organization, cellular respiration, and cell migration. Key transcription factors in both species included NFKB1, SP1, TP53, and TWIST2. Trajectory inference suggested that in some cases a transitory state characterized by JUN expression precedes the maturation of CAFs. Computational analysis revealed a common mechanism for CAF education involving the overexpression of TGF-β, PDGF, TNF, and NOTCH-family ligands in different tumor microenvironment cell types, along with reciprocal overexpression of receptors in CAFs. These findings bolster and broaden current understandings of CAF genesis.
Endogenous retroviruses promote prion-like spreading of proteopathic seeds
Authors: Liu Shu , Heumüller Stefanie-Elisabeth , Hossinger André , Müller Stephan A. , Buravlova Oleksandra , Lichtenthaler Stefan F. , Denner Philip , Vorberg Ina M. 
Published: May 2022

AbstractEndogenous retroviruses, remnants of viral germline infections, make up a substantial proportion of the mammalian genome. While usually epigenetically silenced, retroelements can become upregulated in neurodegenerative diseases associated with protein aggregation, such as amyotrophic lateral sclerosis and tauopathies. Here we demonstrate that spontaneous upregulation of endogenous retrovirus gene expression drastically affects the dissemination of protein aggregates between murine cells in culture. Viral glycoprotein Env mediates membrane association between donor and recipient cells and promotes the intercellular transfer of protein aggregates packaged into extracellular vesicles. Proteopathic seed spreading can be inhibited by neutralizing antibodies targeting Env as well as drugs inhibiting viral protein processing. Importantly, we show that also overexpression of a human endogenous retrovirus Env elevates intercellular spreading of pathological Tau. Our data highlight the potential influence of endogenous retroviral proteins on protein misfolding diseases and suggest that antiviral drugs could represent promising candidates for inhibiting protein aggregate spreading.