bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages
Authors: Chen Heidi I , Turakhia Yatish , Bejerano Gill , Kingsley David M 
Published: September 2023

AbstractFins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 percomorph fish species that span over 100 million years of evolution and either have complete or reduced pelvic and caudal fins. We identify 1,614 genomic regions that are well-conserved in fin-complete species but missing from multiple fin-reduced lineages. Recurrent deletions of conserved sequences in wild fin-reduced species are enriched for functions related to appendage development, suggesting that convergent fin reduction at the organismal level is associated with repeated genomic deletions near fin-appendage development genes. We used sequencing and functional enhancer assays to confirm that PelA, a Pitx1 enhancer previously linked to recurrent pelvic loss in sticklebacks, has also been independently deleted and may have contributed to the fin morphology in distantly related pelvic-reduced species. We also identify a novel enhancer that is conserved in the majority of percomorphs, drives caudal fin expression in transgenic stickleback, is missing in tetraodontiform, syngnathid, and synbranchid species with caudal fin reduction, and alters caudal fin development when targeted by genome editing. Our study illustrates a broadly applicable strategy for mapping phenotypes to genotypes across a tree of vertebrate species and highlights notable new examples of regulatory genomic hotspots that have been used to evolve recurrent phenotypes across 100 million years of fish evolution.
Inference of Coalescence Times and Variant Ages Using Convolutional Neural Networks
Authors: Nait Saada Juba , Tsangalidou Zoi , Stricker Miriam , Palamara Pier Francesco 
Published: September 2023

Abstract
Accurate inference of the time to the most recent common ancestor (TMRCA) between pairs of individuals and of the age of genomic variants is key in several population genetic analyses. We developed a likelihood-free approach, called CoalNN, which uses a convolutional neural network to predict pairwise TMRCAs and allele ages from sequencing or SNP array data. CoalNN is trained through simulation and can be adapted to varying parameters, such as demographic history, using transfer learning. Across several simulated scenarios, CoalNN matched or outperformed the accuracy of model-based approaches for pairwise TMRCA and allele age prediction. We applied CoalNN to settings for which model-based approaches are under-developed and performed analyses to gain insights into the set of features it uses to perform TMRCA prediction. We next used CoalNN to analyze 2,504 samples from 26 populations in the 1,000 Genome Project data set, inferring the age of ∼80 million variants. We observed substantial variation across populations and for variants predicted to be pathogenic, reflecting heterogeneous demographic histories and the action of negative selection. We used CoalNN’s predicted allele ages to construct genome-wide annotations capturing the signature of past negative selection. We performed LD-score regression analysis of heritability using summary association statistics from 63 independent complex traits and diseases (average N=314k), observing increased annotation-specific effects on heritability compared to a previous allele age annotation. These results highlight the effectiveness of using likelihood-free, simulation-trained models to infer properties of gene genealogies in large genomic data sets.
Evolutionarily conserved protein motifs drive interactions between the plant nucleoskeleton and nuclear pores
Authors: Mermet Sarah , Voisin Maxime , Mordier Joris , Dubos Tristan , Tutois Sylvie , Tuffery Pierre , Baroux Célia , Tamura Kentaro , Probst Aline V , Vanrobays Emmanuel , Tatout Christophe 
Published: September 2023

AbstractThe nucleoskeleton forms a filamentous meshwork under the nuclear envelope and contributes to the regulation of nuclear shape and gene expression. To understand how the Arabidopsis (Arabidopsis thaliana) nucleoskeleton physically connects to the nuclear periphery in plants, we investigated the Arabidopsis nucleoskeleton protein KAKU4 and sought for functional regions responsible for its localization at the nuclear periphery. We identified 3 conserved peptide motifs within the N-terminal region of KAKU4, which are required for intermolecular interactions of KAKU4 with itself, interaction with the nucleoskeleton protein CROWDED NUCLEI (CRWN), localization at the nuclear periphery, and nuclear elongation in differentiated tissues. Unexpectedly, we find these motifs to be present also in NUP82 and NUP136, 2 plant-specific nucleoporins from the nuclear pore basket. We further show that NUP82, NUP136, and KAKU4 have a common evolutionary history predating nonvascular land plants with KAKU4 mainly localizing outside the nuclear pore suggesting its divergence from an ancient nucleoporin into a new nucleoskeleton component. Finally, we demonstrate that both NUP82 and NUP136, through their shared N-terminal motifs, interact with CRWN and KAKU4 proteins revealing the existence of a physical continuum between the nuclear pore and the nucleoskeleton in plants.
MADS8 is indispensable for female reproductive development at high ambient temperatures in cereal crops
Authors: Shen Chaoqun , Zhang Yueya , Li Gang , Shi Jin , Wang Duoxiang , Zhu Wanwan , Yang Xiujuan , Dreni Ludovico , Tucker Matthew R , Zhang Dabing 
Published: September 2023

AbstractTemperature is a major factor that regulates plant growth and phenotypic diversity. To ensure reproductive success at a range of temperatures, plants must maintain developmental stability of their sexual organs when exposed to temperature fluctuations. However, the mechanisms integrating plant floral organ development and temperature responses are largely unknown. Here, we generated barley and rice loss-of-function mutants in the SEPALLATA-like MADS-box gene MADS8. The mutants in both species form multiple carpels that lack ovules at high ambient temperatures. Tissue-specific markers revealed that HvMADS8 is required to maintain floral meristem determinacy and ovule initiation at high temperatures, and transcriptome analyses confirmed that temperature-dependent differentially expressed genes in Hvmads8 mutants predominantly associate with floral organ and meristem regulation. HvMADS8 temperature-responsive activity relies on increased binding to promoters of downstream targets, as revealed by a cleavage under targets and tagmentation (CUT&Tag) analysis. We also demonstrate that HvMADS8 directly binds to 2 orthologs of D-class floral homeotic genes to activate their expression. Overall, our findings revealed a new, conserved role for MADS8 in maintaining pistil number and ovule initiation in cereal crops, extending the known function of plant MADS-box proteins in floral organ regulation.
Differences in adverse outcomes across race and ethnicity among Veterans with similar predicted risks of an overdose or suicide-related event
Authors: Garrido Melissa M , Legler Aaron , Strombotne Kiersten L , Frakt Austin B 
Published: September 2023

Abstract

Objective
To evaluate the degree to which differences in incidence of mortality and serious adverse events exist across patient race and ethnicity among Veterans Health Administration (VHA) patients receiving outpatient opioid prescriptions and who have similar predicted risks of adverse outcomes. Patients were assigned scores via the VHA Stratification Tool for Opioid Risk Mitigation (STORM), a model used to predict the risk of experiencing overdose- or suicide-related health care events or death. Individuals with the highest STORM risk scores are targeted for case review.

Design
Retrospective cohort study of high-risk veterans who received an outpatient prescription opioid between 4/2018–3/2019.

Setting
All VHA medical centers.

Participants
In total, 84 473 patients whose estimated risk scores were between 0.0420 and 0.0609, the risk scores associated with the top 5%–10% of risk in the STORM development sample.

Methods
We examined the expected probability of mortality and serious adverse events (SAEs; overdose or suicide-related events) given a patient’s risk score and race.

Results
Given a similar risk score, Black patients were less likely than White patients to have a recorded SAE within 6 months of risk score calculation. Black, Hispanic, and Asian patients were less likely than White patients with similar risk scores to die within 6 months of risk score calculation. Some of the mortality differences were driven by age differences in the composition of racial and ethnic groups in our sample.

Conclusions
Our results suggest that relying on the STORM model to identify patients who may benefit from an interdisciplinary case review may identify patients with clinically meaningful differences in outcome risk across race and ethnicity.
Are Humans the Only Rational Animals?
Authors: Melis Giacomo , Monsó Susana 
Published: September 2023

Abstract
While growing empirical evidence suggests a continuity between human and non-human psychology, many philosophers still think that only humans can act and form beliefs rationally. In this paper, we challenge this claim. We first clarify the notion of rationality. We then focus on the rationality of beliefs and argue that, in the relevant sense, humans are not the only rational animals. We do so by first distinguishing between unreflective and reflective responsiveness to epistemic reasons in belief formation and revision. We argue that unreflective responsiveness is clearly within the reach of many animals. We then defend that a key demonstration of reflective responsiveness would be the ability to respond to undermining defeaters. We end by presenting some empirical evidence that suggests that some animal species are capable of processing these defeaters, which would entail that even by the strictest standards, humans are not the only rational animals.
Flight to Safety: How Economic Downturns Affect Talent Flows to Startups
Authors: Bernstein Shai , Townsend Richard R , Xu Ting 
Published: September 2023

Abstract
Using proprietary data from AngelList Talent, we study how startup job seekers’ search and application behavior changed during the COVID-19 downturn. We find that workers shifted their searches and applications away from less-established startups and toward more-established ones, even within the same individual over time. At the firm level, this shift was not offset by an influx of new job seekers. Less-established startups experienced a relative decline in the quantity and quality of applications, ultimately affecting their hiring. Our findings uncover a flight-to-safety channel in the labor market that may amplify the procyclical nature of entrepreneurial activities.
Effect of smoking on thrombotic antiphospholipid syndrome: a 10-year prospective cohort study
Authors: Jiang Hui , Huang Can , Shi Yu , Wang Chu-Han , Chen Si-Yun , Li Jun , Wang Qian , Li Meng-Tao , Tian Xin-Ping , Zeng Xiao-Feng , Zhao Yan , Zhao Jiu-Liang 
Published: September 2023

Abstract

Objectives
Cigarette smoking is an established risk factor for autoimmune diseases. However, whether smoking plays a clear role in thrombotic APS (TAPS) has not been determined. We aimed to investigate the effects of smoking on the clinical characteristics and prognosis of TAPS.

Methods
This was a prospective cohort study from 2013 to 2022. During the study period, 297 patients were diagnosed with TAPS, including 82 smokers and 215 non-smokers. After propensity score matching, 57 smokers and 57 non-smokers matched by age and sex were analysed.

Results
Overall, smokers with TAPS had more cardiovascular risk factors than non-smokers, including hypertension (36.59% vs 14.42%, P &lt; 0.001), obesity (15.85% vs 7.44%, P = 0.029), dyslipidaemia (64.63% vs 48.37%, P = 0.012) and hyperhomocysteinaemia (62.20% vs 36.28%, P &lt; 0.001). Arterial thrombotic events were more common in smokers at diagnosis (62.20% vs 46.05%, P = 0.013), especially myocardial infarction, visceral thrombosis and peripheral vascular thrombosis. After matching, smokers showed balanced cardiovascular risk factors with non-smokers at baseline, but retained a higher prevalence of arterial thrombosis (59.65% vs 33.33%, P = 0.005), mainly distributed in cerebral vascular, cardiovascula and retinal vascular territories. During follow-up, smokers presented a tendency for more recurrent arterial thrombosis and less recurrent venous thrombosis. Smokers had significantly poorer outcomes for organ damage with higher Damage Index for APS score (median 2.00 vs 1.00, P = 0.008), especially in the cardiovascular (26.32% vs 3.51%, P = 0.001), gastrointestinal (15.79% vs 1.75%, P = 0.016) and ophthalmologic (10.53% vs 00.00%, P = 0.027) systems.

Conclusion
Smoking is related to increased arterial events and poor prognosis in TAPS patients. Patients with TAPS should be fully encouraged to avoid smoking.
Comparison of the conversion method with gravel unfolding to obtain dose values from photon spectra
Authors: Dombrowski Harald 
Published: September 2023

Abstract
Modern gamma-ray spectrometers based on solid-state scintillators are increasingly being used in fields where previously dosemeters were applied. From the spectra, precise fluence and dose information can be derived. The most important methods of doing this are investigated in detail; the conversion method, which is based on weighing functions; and unfolding, here using the GRAVEL algorithm. Both methods can be used to process any kind of spectra, regardless of the type of spectrometer employed. The GRAVEL algorithm is described in detail. The implementation of both methods is shown and results of examples are compared. Advantages and disadvantages of both techniques are discussed. For the first time, most precise conversion data up to 20 MeV are published, even extending the quantity H*(10) to this energy. They may serve for the improvement and harmonisation of dose rate measurements using scintillation spectrometers, e.g. those used in early warning systems.
Young Black Women’s Perceptions of Otherfather Involvement
Authors: Johnson Maria S 
Published: September 2023

Abstract
A limited number of studies have examined how Black children, particularly daughters, perceive Black men who provide care—financial, material, or emotional support—to children who are not their biological or legal children (these men are here conceptualized as “otherfathers”). Using accounts from in-depth interviews with twenty-six young Black women from two-parent and single-mother households, this study explores how daughters identify and assign meaning to otherfathers. Findings reveal a heterogeneous category with no single definition or set of criteria; rather, the young women enact a process of parental ascription to determine who “counts” as an otherfather. Otherfathers’ contributions are understood in relation to biological fathers’ involvement but not always in expected ways. The study challenges assumptions about how daughters think about otherfathers and reveals the importance of examining the perspectives of Black girl youth and young women.
Radiographic and Patient-Reported Outcomes in Anteriorly Placed Transforaminal Lumbar Interbody Fusion Cage Versus Anterior Lumbar Interbody Fusion With Posterior Instrumentation
Authors: Lee Yunsoo , Heard Jeremy C. , McCurdy Michael A. , Lambrechts Mark J. , Fras Sebastian I. , Purtill William , Millar Ben , Kolowrat Samantha , Issa Tariq Z. , D’Antonio Nicholas D. , Rihn Jeffrey A. , Kurd Mark F. , Kaye Ian David , Canseco Jose A. , Vaccaro Alexander R. , Hilibrand Alan S. , Kepler Christopher K. , Schroeder Gregory D. 
Published: September 2023

Study Design.
Retrospective cohort study.

Objective.
To compare outcomes in anteriorly placed transforaminal lumbar interbody fusions (TLIFs) and anterior lumbar interbody fusions (ALIFs).

Summary of Background Data.
TLIF and ALIF are surgical techniques that have become more prevalent in recent years. Although studies have compared the two, none have considered TLIFs with anteriorly placed cages, which may serve as a better comparison to ALIFs.

Patients and Methods.
Patients undergoing TLIF or ALIF with posterior instrumentation from 2010 to 2020 at a tertiary care institution were retrospectively identified. TLIF cage position was assessed and those with anterior placement were included. Electronic medical records were reviewed to identify patient characteristics and patient-reported outcomes. Radiographic outcomes included posterior disc height (DH), lumbar lordosis (LL), sacral slope, pelvic incidence, and pelvic tilt. Statistical analysis was performed to compare the two groups.

Results.
Of the 351 patients, 108 had ALIF with posterior instrumentation and 207 had a TLIF. Preoperatively, patients undergoing TLIF had less LL (53.7° vs. 60.6°, P < 0.001), sacral slope (38.3° vs. 43.7°, P < 0.001), and pelvic incidence (60.1° vs. 66.1°, P < 0.001), all of which remained significant at 1-year and long-term follow-up (P < 0.001). The TLIF group had less ∆DH (1.51° vs. 5.43°, P < 0.001), ∆LL (1.8° vs. 2.97°, P = 0.038), and ∆segmental lordosis (0.18° vs. 4.40°, P < 0.001) at 1 year postoperatively. At 2 to 3 years, ∆DH (P < 0.001) and ∆segmental lordosis (P = 0.001) remained significant, but ∆LL (P = 0.695) did not. Patients in the TLIF group had higher Visual Analog Scale-Back scores 1 year postoperatively (3.68 vs. 2.16, P = 0.008) and experienced less improvement in Oswestry Disability Index (−17.1 vs. −28.6, P = 0.012) and Visual Analog Scale-Back (−2.67 vs. −4.50, P = 0.008) compared with patients undergoing ALIF.

Conclusions.
Our findings suggest that ALIF with posterior instrumentation performed superiorly in radiographic outcomes and patient-reported outcomes compared with anteriorly placed TLIFs. Anteriorly placed TLIF cages may not achieve the same results as those of ALIF cages.
Cervical Total Disc Replacement in Athletes
Authors: Clohisy John C.F. , Maayan Omri , Asada Tomoyuki , Qureshi Sheeraz A. 
Published: September 2023

Study Design:
Systematic review.

Objective:
To perform a systematic review to describe clinical characteristics, outcomes, and return to play after cervical total disc replacement (cTDR) in athletes.

Summary of Background Data:
The role of cTDR in treating athletes with symptomatic cervical degenerative disc disease is undefined.

Methods:
A systematic search using MEDLINE through PubMed, EMBASE, and the Cochrane Library was conducted to identify all relevant literature. Data regarding study type, country in which the study was conducted, sample size, mean age, sex, type of sport, level of patient participation in sports, surgical indication, levels operated, type of implant, duration of follow-up, reoperations, surgical complications, extent of postoperative return to sports (RTSs), time to RTSs, and outcome notes were extracted from the included studies and analyzed.

Results:
Seven studies, including 4 case series and 3 case reports, and a total of 57 cTDR cases, were included. There was significant heterogeneity among the cTDR cases in terms of chosen sport and level of participation. Prestige LP was utilized in 51 out of 57 (89.5%) cases and 53 out of 57 (93%) cases were single-level. No reoperations were noted at a mean follow-up of 51.6 months. All patients returned to sports postoperatively. Return to training and competition occurred at a mean of 10.1 weeks and 30.7 weeks postoperatively, respectively.

Conclusions:
The available evidence regarding cTDR in athletes indicates that these patients RTSs at high rates, with return to training occurring around 10 weeks and return to competition occurring around 30 weeks. Clinical outcomes in these patients are like those reported for the general population. Low-level evidence, small numbers of cases, heterogeneity in chosen sport and participation level, and predominance of a single implant type limit the conclusions that can be drawn from the current literature on this patient population.
Technique Pearls for Successful Cervical Disc Arthroplasty From More Than 20 Years of Surgical Experience
Authors: Ye Jason , Sasso Willa , Boody Barrett , Sasso Rick 
Published: September 2023

Study Design:
Surgical technique paper.

Objective:
To describe tips and pearls for cervical disc arthroplasty (CDA).

Background:
CDA has proven to be an effective means of treatment for degenerative cervical disc disease and cervical radiculopathy in properly selected patients who have previously failed non-operative treatment.

Methods:
Surgical tips and pearls garnered from more than 20 years of experience with CDA surgery are described.

Results:
This discussion focuses on pearls for successful procedures, including patient selection, patient positioning, surgical technique, and postoperative protocols.

Conclusions:
In correctly selected patients, CDA can be effective in treating cervical degenerative disc disease and radiculopathy. The techniques described here can increase the chance of success and decrease complications.
Distinctive Characteristics of Thoracolumbar Junction Region Stenosis
Authors: Houten John K. , Spirollari Eris , Ng Christina , Greisman Jacob , Vaserman Grigori , Dominguez Jose F. , Kinon Merritt D. , Betchen Simone A. , Schwartz Amit Y. 
Published: September 2023

Study Design:
Retrospective case series and systemic literature meta-analysis.

Background:
Thoracolumbar junction region stenosis produces spinal cord compression just above the conus and may manifest with symptoms that are not typical of either thoracic myelopathy or neurogenic claudication from lumbar stenosis.

Objective:
As few studies describe its specific pattern of presenting symptoms and neurological deficits, this investigation was designed to improve understanding of this pathology.

Methods:
A retrospective review assessed surgically treated cases of T10–L1 degenerative stenosis. Clinical outcomes were evaluated with the thoracic Japanese Orthopedic Association score. In addition, a systematic review and meta-analysis was performed in accordance with guidelines provided by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA).

Results:
Of 1069 patients undergoing laminectomy at 1477 levels, 31 patients (16M/15F) were treated at T10–L1 a mean age 64.4 (SD=11.8). Patients complained of lower extremity numbness in 29/31 (94%), urinary dysfunction 11/31 (35%), and back pain 11/31 (35%). All complained about gait difficulty and objective motor deficits were detected in 24 of 31 (77%). Weakness was most often seen in foot dorsiflexion 22/31 (71%). Deep tendon reflexes were increased in 10 (32%), decreased in 11 (35%), and normal 10 (32%); the Babinski sign was present 8/31 (26%). Mean thoracic Japanese Orthopedic Association scores improved from 6.4 (SD=1.8) to 8.4 (SD=1.8) (P<0.00001). Gait subjectively improved in 27/31 (87%) numbness improved in 26/30 (87%); but urinary function improved in only 4/11 (45%).

Conclusions:
Thoracolumbar junction stenosis produces distinctive neurological findings characterized by lower extremity numbness, weakness particularly in foot dorsiflexion, urinary dysfunction, and inconsistent reflex changes, a neurological pattern stemming from epiconus level compression and the myelomeres for the L5 roots. Surgery results in significant clinical improvement, with numbness and gait improving more than urinary dysfunction. Many patients with thoracolumbar junction stenosis are initially misdiagnosed as being symptomatic from lumbar stenosis, thus delaying definitive surgery.