bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lyman-α transmission properties of the intergalactic medium in the CoDaII simulation
Authors: Gronke Max , Ocvirk Pierre , Mason Charlotte , Matthee Jorryt , Bosman Sarah E I , Sorce Jenny G , Lewis Joseph , Ahn Kyungjin , Aubert Dominique , Dawoodbhoy Taha , Iliev Ilian T , Shapiro Paul R , Yepes Gustavo 
Published: September 2021

ABSTRACT
The decline in abundance of Lyman-α (Lyα) emitting galaxies at z ≳ 6 is a powerful and commonly used probe to constrain the progress of cosmic reionization. We use the CoDaII simulation, which is a radiation hydrodynamic simulation featuring a box of ∼94 comoving Mpc side length, to compute the Lyα transmission properties of the intergalactic medium (IGM) at z ∼ 5.8 to 7. Our results mainly confirm previous studies, i.e. we find a declining Lyα transmission with redshift and a large sightline-to-sightline variation. However, motivated by the recent discovery of blue Lyα peaks at high redshift, we also analyse the IGM transmission on the blue side, which shows a rapid decline at z ≳ 6 of the blue transmission. This low transmission can be attributed not only to the presence of neutral regions but also to the residual neutral hydrogen within ionized regions, for which a density even as low as $n_{\rm HI}\sim 10^{-9}\, \mathrm{cm}^{-3}$ (sometimes combined with kinematic effects) leads to a significantly reduced visibility. Still, we find that $\sim 1{{\ \rm per\ cent}}$ of sightlines towards M1600AB ∼ −21 galaxies at z ∼ 7 are transparent enough to allow a transmission of a blue Lyα peak. We discuss our results in the context of the interpretation of observations.
Comparison of the characteristics of magnetars born in death of massive stars and merger of compact objects with swift gamma-ray burst data
Authors: Zou Le , Liang En-Wei , Zhong Shu-Qing , Yang Xing , Zheng Tian-Ci , Cheng Ji-Gui , Deng Can-Min , Lü Hou-Jun , Wang Shan-Qin 
Published: September 2021

ABSTRACT
Assuming that the shallow-decaying phase in the early X-ray light curves of gamma-ray bursts (GRBs) is attributed to the dipole radiations (DRs) of a newborn magnetar, we present a comparative analysis for the magnetars born in death of massive stars and merger of compact binaries with long and short GRB (lGRB and sGRB) data observed with the Swift mission. We show that the typical braking index (n) of the magnetars is ∼3 in the sGRB sample, and it is ∼4 for the magnetars in the lGRB sample. Selecting a sub-sample of the magnetars whose spin-down is dominated by DRs (n ≲ 3) and adopting a universal radiation efficiency of 0.3, we find that the typical magnetic field strength (Bp) is 1016 G versus 1015 G and the typical initial period (P0) is ∼20 ms versus 2 ms for the magnetars in the sGRBs versus lGRBs. They follow the same relation between P0 and the isotropic GRB energy as $P_0\propto E_{\rm jet}^{-0.4}$. We also extend our comparison analysis to superluminous supernovae (SLSNe) and stable pulsars. Our results show that a magnetar born in merger of compact stars tends to have a stronger Bp and a longer P0 by about one order of magnitude than that born in collapse of massive stars. Its spin-down is dominated by the magnetic DRs as old pulsars, being due to its strong magnetic field strength, whereas the early spin-down of magnetars born in massive star collapse is governed by both the DRs and gravitational wave (GW) emission. A magnetar with a faster rotation speed should power a more energetic jet, being independent of its formation approach.
A joint occultation and speckle investigation of the binary star TYC 1947-290-1 and of the asteroid (87) Sylvia
Authors: Dyachenko V , Richichi A , Obolentseva M , Beskakotov A , Maksimov A , Mitrofanova A , Balega Yu 
Published: September 2021

ABSTRACT
We report on the occultation of the star TYC 1947-290-1 by the asteroid (87) Sylvia. While asteroidal occultations occurring at fixed professional-level locations are relatively rare and are only recently starting to be observed with sufficiently high time resolution and sensitivity, they have the capability to measure sub-milliarcsecond angular diameters. The event described here was especially outstanding because the star was revealed to be a small-separation binary (≈10 mas at discovery), while at the same time the asteroid is not only one of the largest in size but it also has two satellite moons. The observations were carried out at the Russian 6-m telescope in 2019 December, and initially consisted of both a fast photometric series of the occultation itself, as well as of extensive speckle interferometry of the star and asteroid in the time immediately before and after the occultation. Subsequently, we obtained speckle data of TYC 1947-290-1 over a period of 1 yr after the event. We are able to present a detailed study of the binary star including measurements of the angular diameter of the stellar components, their geometry, and relative fluxes over several bandpasses, and to provide an accurate determination of the size of (87) Sylvia. We emphasize that we have been able to obtain the smallest ever directly measured stellar diameter, below the 100 micro-arcsecond level. Our data are also suitable for imaging of the asteroid by speckle holography, a task which we intend to carry out in a separate work.
scMethBank: a database for single-cell whole genome DNA methylation maps
Authors: Zong Wenting , Kang Hongen , Xiong Zhuang , Ma Yingke , Jin Tong , Gong Zheng , Yi Lizhi , Zhang Mochen , Wu Song , Wang Guoliang , Bao Yiming , Li Rujiao 
Published: September 2021

Abstract
Single-cell bisulfite sequencing methods are widely used to assess epigenomic heterogeneity in cell states. Over the past few years, large amounts of data have been generated and facilitated deeper understanding of the epigenetic regulation of many key biological processes including early embryonic development, cell differentiation and tumor progression. It is an urgent need to build a functional resource platform with the massive amount of data. Here, we present scMethBank, the first open access and comprehensive database dedicated to the collection, integration, analysis and visualization of single-cell DNA methylation data and metadata. Current release of scMethBank includes processed single-cell bisulfite sequencing data and curated metadata of 8328 samples derived from 15 public single-cell datasets, involving two species (human and mouse), 29 cell types and two diseases. In summary, scMethBank aims to assist researchers who are interested in cell heterogeneity to explore and utilize whole genome methylation data at single-cell level by providing browse, search, visualization, download functions and user-friendly online tools. The database is accessible at: https://ngdc.cncb.ac.cn/methbank/scm/.
A transcriptional complex of NGATHA and bHLH transcription factors directs stigma development in Arabidopsis
Authors: Ballester Patricia , Martínez-Godoy Maria A , Ezquerro Miguel , Navarrete-Gómez Marisa , Trigueros Marina , Rodríguez-Concepción Manuel , Ferrándiz Cristina 
Published: September 2021

AbstractThe stigma is an angiosperm-specific tissue that is essential for pollination. In the last two decades, several transcription factors with key roles in stigma development in Arabidopsis thaliana have been identified. However, genetic analyses have thus far been unable to unravel the precise regulatory interactions among these transcription factors or the molecular basis for their selective roles in different spatial and temporal domains. Here, we show that the NGATHA (NGA) and HECATE (HEC) transcription factors, which are involved in different developmental processes but are both essential for stigma development, require each other to perform this function. This relationship is likely mediated by their physical interaction in the apical gynoecium. NGA/HEC transcription factors subsequently upregulate INDEHISCENT (IND) and SPATULA and are indispensable for the binding of IND to some of its targets to allow stigma differentiation. Our findings support a nonhierarchical regulatory scenario in which the combinatorial action of different transcription factors provides exquisite temporal and spatial specificity of their developmental outputs.
The OsSPK1–OsRac1–RAI1 defense signaling pathway is shared by two distantly related NLR proteins in rice blast resistance
Authors: Yu Minxiang , Zhou Zhuangzhi , Liu Xue , Yin Dedong , Li Dayong , Zhao Xianfeng , Li Xiaobing , Li Shengping , Chen Renjie , Lu Ling , Yang Dewei , Tang Dingzhong , Zhu Lihuang 
Published: September 2021

Abstract
Resistance (R) proteins are important components of plant innate immunity. Most known R proteins are nucleotide-binding site leucine-rich repeat (NLR) proteins. Although a number of signaling components downstream of NLRs have been identified, we lack a general understanding of the signaling pathways. Here, we used the interaction between rice (Oryza sativa) and Magnaporthe oryzae to study signaling of rice NLRs in response to blast infection. We found that in blast resistance mediated by the NLR PIRICULARIA ORYZAE RESISTANCE IN DIGU 3 (PID3), the guanine nucleotide exchange factor OsSPK1 works downstream of PID3. OsSPK1 activates the small GTPase OsRac1, which in turn transduces the signal to the transcription factor RAC IMMUNITY1 (RAI1). Further investigation revealed that the three signaling components also play important roles in disease resistance mediated by the distantly related NLR protein Pi9, suggesting that the OsSPK1–OsRac1–RAI1 signaling pathway could be conserved across rice NLR-induced blast resistance. In addition, we observed changes in RAI1 levels during blast infection, which led to identification of OsRPT2a, a subunit of the 19S regulatory particle of the 26S proteasome. OsRPT2a seemed to be responsible for RAI1 turnover in a 26S proteasome-dependent manner. Collectively, our results suggest a defense signaling route that might be common to NLR proteins in response to blast infection.
Psychological Factors Change During the Rehabilitation of an Achilles Tendon Rupture: A Multicenter Prospective Cohort Study
Authors: Slagers Anton J , Dams Olivier C , van Zalinge Sara D , Geertzen Jan HB , Zwerver Johannes , Reininga Inge HF , van den Akker-Scheek Inge 
Published: September 2021

AbstractObjectiveThe authors sought to gain insight into the changes in psychological factors during rehabilitation after Achilles tendon rupture (ATR) and to explore the association between psychological factors during rehabilitation and functional outcome 12 months after ATR.MethodsFifty patients clinically diagnosed with ATR were invited to visit the hospital 3, 6, and 12 months after injury for data collection. They completed questionnaires assessing psychological factors: psychological readiness to return to sport (Injury Psychological Readiness to Return to Sport Questionnaire); kinesiophobia (Tampa Scale for Kinesiophobia); expectations, motivation, and outcome measures related to symptoms and physical activity (Achilles Tendon Total Rupture Score); and sports participation and performance (Oslo Sports Trauma Research Centre Overuse Injury Questionnaire). To determine whether psychological factors changed over time, generalized estimating equation analyses were performed. Multivariate regression analyses were used to study the association between psychological factors at 3, 6, and 12 months and outcome measures at 12 months after ATR.ResultsPsychological readiness to return to sport improved, and kinesiophobia decreased significantly during rehabilitation. Psychological readiness at 6 and 12 months showed significant associations with sports participation and performance. Kinesiophobia at 6 months was significantly associated with symptoms and physical activity. Motivation remained high during rehabilitation and was highly associated with symptoms and physical activity, sports participation, and performance.ConclusionPsychological factors change during rehabilitation after ATR. Patients with lower motivation levels during rehabilitation, low psychological readiness to return to sports, and/or high levels of kinesiophobia at 6 months after ATR need to be identified.ImpactAccording to these results, psychological factors can affect the rehabilitation of patients with ATR. Physical therapists can play an important role in recognizing patients with low motivation levels and low psychological readiness for return to sport and patients with high levels of kinesiophobia at 6 months post-ATR. Physical therapist interventions to enhance motivation and psychological readiness to return to sport and to reduce kinesiophobia need to be developed and studied in the post-ATR population.Lay SummaryWith Achilles tendon rupture, level of motivation, psychological readiness for return to sport, and fear of movement can affect rehabilitation outcome. A physical therapist can help recognize these factors.
Do peers share the same criteria for assessing grant applications?
Authors: Hug Sven E , Ochsner Michael 
Published: September 2021

Abstract
This study examines a basic assumption of peer review, namely, the idea that there is a consensus on evaluation criteria among peers, which is a necessary condition for the reliability of peer judgements. Empirical evidence indicating that there is no consensus or more than one consensus would offer an explanation for the disagreement effect, the low inter-rater reliability consistently observed in peer review. To investigate this basic assumption, we have surveyed all humanities scholars in Switzerland on 23 grant review criteria. We have employed latent class tree modelling to identify subgroups in which scholars rated criteria similarly (i.e. latent classes) and to explore covariates predicting class membership. We have identified two consensus classes, two consensus-close classes, and a consensus-far class. The consensus classes contain a core consensus (10 criteria related to knowledge gaps; feasibility; rigour; comprehensibility and argumentation; academic relevance; competence and experience of the applicant) and a broad consensus that include the core consensus plus eight contribution-related criteria, such as originality. These results provide a possible explanation for the disagreement effect. Moreover, the results are consistent with the notion of conservatism, which holds that original research is undervalued in peer review, while other aspects, such as methodology and feasibility, are overweighted. The covariate analysis indicated that age and having tenure increase from the consensus far to the consensus close to the consensus classes. This suggests that the more academic experience scholars accumulate, the more their understanding of review criteria conforms to the social norm.
Neotropical jewels in the moss: biodiversity, distribution and evolution of the genus Barbaria (Heterotardigrada: Echiniscidae)
Authors: Gąsiorek Piotr , Wilamowski Andrzej , Vončina Katarzyna , Michalczyk Łukasz 
Published: September 2021

Abstract
The genus Barbaria, recently established to accommodate the former Echiniscus bigranulatus group, is a tardigrade group emblematic for the South American tardigrade fauna. This unappendaged echiniscid lineage is widely recognized for the so-called ‘double’ sculpturing composed of endocuticular pillars and pseudopores or pores in the dorsal cuticle. The phylogenetic relationships in the genus have so far been completely unknown, but the discovery of two new species (B. paucigranulata sp. nov. and B. weglarskae sp. nov.), together with new genetic data for further six species (B. bigranulata, B. charrua comb. nov., B. danieli, B. jenningsi, B. madonnae and B. ollantaytamboensis), create an opportunity not only to uncover phyletic relationships, but also to reconstruct morphological evolution in the genus. To achieve this, we sequenced five genetic markers (18S rRNA, 28S rRNA, ITS1, ITS2, COI) for multiple populations of eight species of Barbaria (two-thirds of all known species) collected in Alabama (USA), Argentina and the Antarctic, and we analysed them in tandem with detailed morphological data. Our phylogentic analysis and the reconstruction of evolution of morphological traits suggests that the ancestor of the genus inhabited the Neotropics, and it was morphologically most similar to B. bigranulata. We also analyse literature records of Barbaria and conclude that the genus is most likely limited to the Neotropics, Antarctica and southern parts of the Nearctic. The findings are discussed in the context of the phylogeny of the Echiniscus evolutionary line.
Controversial Approval of New Drug to Treat Alzheimer's Disease
Authors: Aschenbrenner Diane S. 
Published: September 2021

Aducanumab (Aduhelm), the first new drug to treat Alzheimer's disease since 2003, has received accelerated approval from the Food and Drug Administration (FDA).This drug's approval has been highly contentious in the medical and scientific community owing to contradictory study findings and the FDA's advisory panel not recommending its approval.
Sugar-Sweetened Beverage Intake Linked to Early-Onset Colorectal Cancer Risk
Authors: Rosenberg Karen 
Published: September 2021

According to this study:

Among women, a higher intake of sugar-sweetened beverages in adulthood and adolescence is associated with a substantially higher risk of early-onset colorectal cancer.Reducing the intake of sugar-sweetened beverages in this population may reduce the incidence of early-onset colorectal cancer.
Anemia in Pregnancy
Authors: Stanley Angela Y. , Wallace Jerrol B. , Hernandez Andrea M. , Spell Jenna L. 
Published: September 2021

Abstract
Screening recommendations for anemia during pregnancy, etiologies of inherited and noninherited forms of anemia, their impact on maternal–fetal outcomes, and the clinical management of pregnant patients presenting with these conditions are reviewed. Anemia during pregnancy can cause adverse perinatal outcomes including preterm labor, premature rupture of membranes, and increased maternal and fetal mortality. Physiologic (dilutional) anemia and iron deficiency anemia are the two most common noninherited forms of anemia, and some cases may be the result of an underlying comorbidity such as diabetes or lupus. Aplastic anemia and autoimmune hemolytic anemia are uncommon forms of noninherited anemias that also merit discussion. Inherited forms of anemia include sickle cell disease, alpha-thalassemia, and beta-thalassemia. Timely diagnosis and treatment of anemia during pregnancy, whether inherited or noninherited, is imperative to protect mother and baby from potential adverse outcomes associated with these conditions.
Use of Lean Healthcare to Improve Hospital Throughput and Reduce LOS
Authors: Mangum Christopher D. , Andam-Mejia Rachel L. , Hale Leslie R. , Mananquil Ana , Fulcher Kyle R. , Hall Jason L. , McDonald Laura Anne C. , Sjogren Karl N. , Villalon Felicita D. , Mehta Ami , Shomaker Kyrie , Johnson Edward A. , Godambe Sandip A. 
Published: September 2021

Introduction:
Improving the discharge process is an area of focus throughout healthcare organizations. Capacity constraints, efficiency improvement, patient safety, and quality care are driving forces for many discharge process workgroups.

Methods:
Following the Pareto principle, we focused on improving the discharge process on the medical-surgical units that received the most patients admitted from the emergency department. Increased demand for medical-surgical beds, renovations, and diminished bed capacity made it imperative to improve efficiency using quality improvement techniques. A core team of frontline staff decreased the time between computer entry of discharge orders and patient’s departure from the unit to less than 60 minutes, with 80% compliance. The team developed a daily dashboard that detailed the process and outcome measures to create situational awareness and daily visual management. Additional observations of staff workflow uncovered excessive walking for printer use. Printers were placed at the point of use to reduce transport times. Next, using survey results provided by patients on discharge quality, a Treasure Map that aided with teach-back and Team Discharge were implemented to level the staff’s workload. Finally, physicians discharged patients earlier in the day. They standardized their discharge criteria to remove subjectivity from the discharge process and enable better team involvement.

Results:
After implementing 4 interventions, the average time between computer entry of discharge orders and patient’s departure from the unit decreased (94.26 versus 65.98 minutes; P < 0.001), simultaneously reducing our average length of stay from 5.62 to 4.81 days (P < 0.001).

Conclusions:
In conclusion, hardwiring proven interventions and complementing them with daily visual management led to significant, sustained results.
Outcomes following out-of-hours acute cholecystectomy: A systematic review and meta-analysis
Authors: Bhat Sameer , Varghese Chris , Xu William , Barazanchi Ahmed W.H. , Ratnayake Bathiya , O’Grady Gregory , Windsor John A. , Wells Cameron I. 
Published: September 2021

BACKGROUND
Cholecystectomy is one of the most commonly performed abdominal operations. Rising demands on acute operating theater availability and resource utilization in the daytime have led to acute cholecystectomy being performed out-of-hours (in the evenings, at night, or on weekends), although it remains unknown whether outcomes differ between out-of-hours and in-hours (during the daytime on weekdays) acute cholecystectomy. This systematic review and meta-analysis aimed to compare outcomes following out-of-hours versus in-hours acute cholecystectomy.

METHODS
The study protocol was prospectively registered on PROSPERO (ID: CRD42021226127). MEDLINE, EMBASE, and Scopus databases were systematically searched for studies comparing outcomes following out-of-hours and in-hours acute cholecystectomy in adults with any acute benign gallbladder disease. The outcomes of interest were rates of bile leakage, bile duct injury, overall postoperative complications, conversion to open cholecystectomy, specific intraoperative and postoperative complications, length of stay, readmission, and mortality. Subgroup (evening/night-time vs. daytime, weekend vs. weekday, acute surgical unit [ASU]-only, non-ASU, and laparoscopic-only) and sensitivity analyses of adjusted multivariate regression analysis results was also performed.

RESULTS
Eleven studies were included. There were no differences between out-of-hours and in-hours acute cholecystectomy for rates of bile leakage, bile duct injury, overall postoperative complications, conversion to open cholecystectomy, operative duration, readmission, mortality, and postoperative length of stay. Higher rates of postoperative sepsis (odds ratio, 1.58; 95% confidence interval, 1.04–2.41; p = 0.03) and pneumonia (odds ratio, 1.55; 95% confidence interval, 1.06–2.26; p = 0.02) were observed following out-of-hours acute cholecystectomy on univariate meta-analysis, but not after the adjusted multivariate meta-analysis. Higher conversion rates were observed when out-of-hours cholecystectomy was performed in centers without an ASU.

CONCLUSION
This systematic review and meta-analysis has not shown an increased risk in overall or specific complications associated with out-of-hours compared with in-hours acute cholecystectomy. However, future studies should assess the potential impact of structural hospital factors, such as an ASU, on outcomes following out-of-hours acute cholecystectomy.

LEVEL OF EVIDENCE
Systematic Review and Meta-Analysis Study, Level IV.