bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pangolin Genomes Offer Key Insights and Resources for the World’s Most Trafficked Wild Mammals
Authors: Heighton Sean P , Allio Rémi , Murienne Jérôme , Salmona Jordi , Meng Hao , Scornavacca Céline , Bastos Armanda D S , Njiokou Flobert , Pietersen Darren W , Tilak Marie-Ka , Luo Shu-Jin , Delsuc Frédéric , Gaubert Philippe 
Published: October 2023

Abstract
Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and purported medicinal properties. Despite their conservation concern, knowledge of their evolution is limited by a paucity of genomic data. We aim to produce exhaustive genomic resources that include 3,238 orthologous genes and whole-genome polymorphisms to assess the evolution of all eight extant pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera and highlighted the existence of an undescribed species closely related to Southeast Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of Southeast Asian pangolins, provide new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental versus island populations and species lineages, suggesting that conservation planning should consider intraspecific patterns. With the expected loss of genomic diversity from recent, extensive trafficking not yet realized in pangolins, we recommend that populations be genetically surveyed to anticipate any deleterious impact of the illegal trade. Finally, we produce a complete set of genomic resources that will be integral for future conservation management and forensic endeavors for pangolins, including tracing their illegal trade. These comprise the completion of whole-genomes for pangolins through the hybrid assembly of the first reference genome for the giant pangolin (Smutsia gigantea) and new draft genomes (∼43x–77x) for four additional species, as well as a database of orthologous genes with over 3.4 million polymorphic sites.
Genomic Signatures Associated with Transitions to Viviparity in Cyprinodontiformes
Authors: Yusuf Leeban H , Saldívar Lemus Yolitzi , Thorpe Peter , Macías Garcia Constantino , Ritchie Michael G 
Published: October 2023

AbstractThe transition from oviparity to viviparity has occurred independently over 150 times across vertebrates, presenting one of the most compelling cases of phenotypic convergence. However, whether the repeated, independent evolution of viviparity is driven by redeployment of similar genetic mechanisms and whether these leave a common signature in genomic divergence remains largely unknown. Although recent investigations into the evolution of viviparity have demonstrated striking similarity among the genes and molecular pathways involved across disparate vertebrate groups, quantitative tests for genome-wide convergent have provided ambivalent answers. Here, we investigate the potential role of molecular convergence during independent transitions to viviparity across an order of ray-finned freshwater fish (Cyprinodontiformes). We assembled de novo genomes and utilized publicly available genomes of viviparous and oviparous species to test for molecular convergence across both coding and noncoding regions. We found no evidence for an excess of molecular convergence in amino acid substitutions and in rates of sequence divergence, implying independent genetic changes are associated with these transitions. However, both statistical power and biological confounds could constrain our ability to detect significant correlated evolution. We therefore identified candidate genes with potential signatures of molecular convergence in viviparous Cyprinodontiformes lineages. Motif enrichment and gene ontology analyses suggest transcriptional changes associated with early morphogenesis, brain development, and immunity occurred alongside the evolution of viviparity. Overall, however, our findings indicate that independent transitions to viviparity in these fish are not strongly associated with an excess of molecular convergence, but a few genes show convincing evidence of convergent evolution.
Deciphering Evolutionary Trajectories of Lactate Dehydrogenases Provides New Insights into Allostery
Authors: Robin Adeline Y , Brochier-Armanet Céline , Bertrand Quentin , Barette Caroline , Girard Eric , Madern Dominique 
Published: October 2023

AbstractLactate dehydrogenase (LDH, EC.1.1.127) is an important enzyme engaged in the anaerobic metabolism of cells, catalyzing the conversion of pyruvate to lactate and NADH to NAD+. LDH is a relevant enzyme to investigate structure–function relationships. The present work provides the missing link in our understanding of the evolution of LDHs. This allows to explain (i) the various evolutionary origins of LDHs in eukaryotic cells and their further diversification and (ii) subtle phenotypic modifications with respect to their regulation capacity. We identified a group of cyanobacterial LDHs displaying eukaryotic-like LDH sequence features. The biochemical and structural characterization of Cyanobacterium aponinum LDH, taken as representative, unexpectedly revealed that it displays homotropic and heterotropic activation, typical of an allosteric enzyme, whereas it harbors a long N-terminal extension, a structural feature considered responsible for the lack of allosteric capacity in eukaryotic LDHs. Its crystallographic structure was solved in 2 different configurations typical of the R-active and T-inactive states encountered in allosteric LDHs. Structural comparisons coupled with our evolutionary analyses helped to identify 2 amino acid positions that could have had a major role in the attenuation and extinction of the allosteric activation in eukaryotic LDHs rather than the presence of the N-terminal extension. We tested this hypothesis by site-directed mutagenesis. The resulting C. aponinum LDH mutants displayed reduced allosteric capacity mimicking those encountered in plants and human LDHs. This study provides a new evolutionary scenario of LDHs that unifies descriptions of regulatory properties with structural and mutational patterns of these important enzymes.
Low Mutation Load in a Supergene Underpinning Alternative Male Mating Strategies in Ruff (Calidris pugnax)
Authors: Hill Jason , Enbody Erik D , Bi Huijuan , Lamichhaney Sangeet , Lei Weipan , Chen Juexin , Wei Chentao , Liu Yang , Schwochow Doreen , Younis Shady , Widemo Fredrik , Andersson Leif 
Published: October 2023

Abstract
A paradox in evolutionary biology is how supergenes can maintain high fitness despite reduced effective population size, the suppression of recombination, and the expected accumulation of mutational load. The ruff supergene involves 2 rare inversion haplotypes (satellite and faeder). These are recessive lethals but with dominant effects on male mating strategies, plumage, and body size. Sequence divergence to the wild-type (independent) haplotype indicates that the inversion could be as old as 4 million years. Here, we have constructed a highly contiguous genome assembly of the inversion region for both the independent and satellite haplotypes. Based on the new data, we estimate that the recombination event(s) creating the satellite haplotype occurred only about 70,000 yr ago. Contrary to expectations for supergenes, we find no substantial expansion of repeats and only a modest mutation load on the satellite and faeder haplotypes despite high sequence divergence to the non-inverted haplotype (1.46%). The essential centromere protein N (CENPN) gene is disrupted by the inversion and is as well conserved on the inversion haplotypes as on the noninversion haplotype. These results suggest that the inversion may be much younger than previously thought. The low mutation load, despite recessive lethality, may be explained by the introgression of the inversion from a now extinct lineage.
The dual economy, climate change, and the polarization of American politics
Authors: Oatley Thomas 
Published: October 2023

Abstract
This article explores two questions. What generates the political division over climate change policy in the United States? How is the division over climate change policy related to the broader polarization of contemporary American politics? I argue that the geographies of America’s dual economy—the knowledge economy and the carbon economy—and exposure to the climate crisis intersect to generate a new axis of conflict, which I call the carbon–climate cleavage. This cleavage produces political division over climate change and provides materialist elements that accompany the sociocultural factors that shape contemporary polarization. I demonstrate the existence of the cleavage and its impact using data on economic geography, political attitudes on climate change policy, and support for Trump in the 2016 and 2020 presidential elections. The empirical analysis indicates that carbon economy communities oppose climate change policy and support Trump, while knowledge economy residents support climate change policy and oppose Trump.
Three payment methods and the law of tracing
Authors: Chong Conrad 
Published: October 2023

Abstract
The law of tracing is an area of law that develops rapidly. This article analyses the area of law from the perspective of three payment methods (cash, a letter of credit, and overdrawn bank account) in a commercial context. This article extracts two prepositions that clarify the right to conduct a tracing exercise and advocates further exploration of the law of tracing.
From goal to outcome: Analyzing the progression of biomedical sciences PhD careers in a longitudinal study using an expanded taxonomy
Authors: Brown Abigail M. , Meyers Lindsay C. , Varadarajan Janani , Ward Nicholas J. , Cartailler Jean‐Philippe , Chalkley Roger G. , Gould Kathleen L. , Petrie Kimberly A. 
Published: October 2023

AbstractBiomedical sciences PhDs pursue a wide range of careers inside and outside academia. However, there is little data regarding how career interests of PhD students relate to the decision to pursue postdoctoral training or to their eventual career outcomes. Here, we present the career goals and career outcomes of 1452 biomedical sciences PhDs who graduated from Vanderbilt University between 1997 and 2021. We categorized careers using an expanded three‐tiered taxonomy and flags that delineate key career milestones. We also analyzed career goal changes between matriculation and doctoral defense, and the reasons why students became more‐ or less‐interested in research‐intensive faculty careers. We linked students' career goal at doctoral defense to whether they did a postdoc, the duration of time between doctoral defense and the first non‐training position, the career area of the first non‐training position, and the career area of the job at 10 years after graduation. Finally, we followed individual careers for 10 years after graduation to characterize movement between different career areas over time. We found that most students changed their career goal during graduate school, declining numbers of alumni pursued postdoctoral training, many alumni entered first non‐training positions in a different career area than their goal at doctoral defense, and the career area of the first non‐training position was a good indicator of the job that alumni held 10 years after graduation. Our findings emphasize that students need a wide range of career development opportunities and career mentoring during graduate school to prepare them for futures in research and research‐related professions.
Mechanical Power Correlates With Stress, Strain, and Atelectrauma Only When Normalized to Aerated Lung Size in Patients With Acute Respiratory Distress Syndrome
Authors: Pistillo Néstor , Castelluccio Pablo , Suzuki Ichiro , Castiblanco Lina 
Published: October 2023

OBJECTIVES:
First, to investigate whether the severity of acute respiratory distress syndrome (ARDS) influences ventilator-induced lung injury (VILI) risk in ventilated patients with similar mechanical power of respiratory system (MPRS). Second, to determine whether, under these circumstances, there is a relationship between transpulmonary mechanical power (MPTp) normalized to the aerated lung (specific lung mechanical power or SLMP) and VILI risk, and third, to determine whether normalizing MPRS to compliance of respiratory system (CRS) can replace SLMP to bedside.

DESIGN:
Prospective cohort study.

SETTING:
The study was conducted in a tertiary academic ICU.

PATIENTS:
The study included 18 patients with ARDS.

INTERVENTIONS:
Ventilatory settings were adjusted to achieve a similar MPRS.

MEASUREMENTS AND MAIN RESULTS:
Mechanical power was normalized to CRS (specific mechanical power or SMP = MPRS/CRS), and SLMP was calculated as the ratio between MPTp and end-expiratory lung volume (SLMP = MPTp/EELV). The strain was defined as the ratio between tidal volume and EELV (strain = Vt/EELV), stress as transpulmonary pressure at the end of inspiration, and atelectrauma as the difference between expiration and inspiration in the nonaerated lung. Although patients had been ventilated with similar MPRS = 23.75 (23–24) J/min and MPTp = 11.6 (10.8–12.8) J/min, SLMP increased linearly with the fall in Pao
2/Fio
2 (R = –0.83, p = 0.0001). MPRS only correlated positively with VILI-associated mechanisms when normalized to aerated lung size: correlations between SLMP and stress (R = 0.9, R
2 = 0.84, p = 0.00004), strain (R = 0.97, R
2 = 0.94, p < 0.00001) and atelectrauma (R = 0.82, R
2 = 0.70, p = 0.00002), and correlations between SMP and stress (R = 0.86, R
2 = 0.75, p = 0.00001), strain (R = 0.68, R2 = 0.47, p = 0.001) and atelectrauma (R = 0.67, R
2 = 0.46, p = 0.002).

CONCLUSIONS:
The results suggest that normalizing mechanical power to lung-aerated size or CRS may correlate positively with stress, strain, and atelectrauma.
Genetic risk assessment in breast and gynecologic malignancies- what's to know in 2024?
Authors: Kamara Daniella , Silver Erica , Niell-Swiller Mariana 
Published: October 2023

Purpose of review
Hereditary cancer risk assessment and counseling have become integral in oncology care, especially in breast and gynecologic malignancies where genetic test results impact management. However, a large number of patients who could benefit from genetic testing are not getting tested. As such, genetic risk assessment and counseling methods have had to evolve to meet the needs of this expanding patient population.

Recent findings
“Mainstreaming” genetic testing is an initiative to incorporate genetic testing into routine cancer care in lieu of the traditional genetic counseling model to improve uptake of testing while minimizing expansion of genetic counselor and clinic resources. These models have performed well in various institutions demonstrating an improvement in clinical efficacy. However, missed opportunities from the preventive care standpoint, a core value of cancer genetics risk assessment, have become apparent. The focus of these models is on the patient's cancer diagnosis and comprehensive/familial genetic risk assessment is not often completed.

Summary
Identifying patients at an increased risk of cancer, even in the absence of a hereditary cancer predisposition syndrome, is important in tailoring screening and preventive measures. As we look to the future, we need to critically approach mainstreaming and determine how to reincorporate comprehensive genetic risk assessment into our models.
Is It Appropriate to Completely Eliminate Contact Shielding during CT Examination? A Discourse Based on Experimental Findings
Authors: Chen Jiwei , Tu Jianchun , Huang Shengyan , Zhu Zhenhua , Tu Yu 
Published: October 2023

Objective
Through the integration of experimental data and literature, this study examines whether complete elimination of contact shielding during CT examination is warranted, with a particular focus on potential impacts to children's thyroid and pregnant women, as well as limitations associated with contact shielding. Methods: The thermoluminescent dosimeter (TLD) tablets were inserted into the phantom's five organs and tissues. Select fixed exposure, automatic exposure control (AEC), and use contact shielding combined into four experimental modes, with scanning of the phantom's four parts. Obtain the absorbed dose measurements within or outside the FOV. Statistical analysis was conducted using SPSS software. Results: (1) The AEC significantly reduces dose within and outside the FOV, with a dose reduction of 40%–60%. (2) The application of contact shielding outside the FOV significantly reduced the dose adjoin the FOV. (3) Both the use of AEC mode and contact shielding can effectively minimize the dose, with a reduction of 50–80%. (4) The shielding within the FOV may introduce image artifacts or interfere with AEC, the implementation of contact shielding outside FOV provides little reduction in radiation exposure risk through previous literature. (5) Contact shielding exhibits certain drawbacks in all aspects. Conclusion: The utilization of AEC mode in clinical CT should be widely adopted to minimize patient radiation exposure. In general, contact shielding both inside and outside the FOV should be avoided during exposure. However for children under 12 years old with thyroid gland examination, contact shielding could maximally reduce external radiation and may be appropriate. Pregnant women require careful evaluation when considering the use of contact shielding. Contact shielding should not be entirely abandoned.
Overgrowth syndromes, diagnosis and management
Authors: Klein Steven D. , Nisbet Alex , Kalish Jennifer M. 
Published: October 2023

Purpose of review
This review will focus on the current knowledge of the diagnosis and management of overgrowth syndromes with specific focus on mosaic conditions and treatment strategies.

Recent findings
With the implementation of massively parallel sequencing, the genetic etiology of many classically described overgrowth syndromes have been identified. More recently, the role of mosaic genetic changes has been well described in numerous syndromes. Furthermore, the role of imprinting and methylation, especially of the 11p15 region, has been shown to be instrumental for growth. Perhaps most importantly, many overgrowth syndromes carry an increased risk of neoplasm formation especially in the first 10 years of life and possibly beyond. The systematic approach to the child with overgrowth will aide in timely diagnosis and efficiently align them with appropriate screening strategies. In some cases, precision medical interventions are available to target the perturbed growth signaling pathways.

Summary
The systematic approach to the child with overgrowth aids in the standardization of the diagnostic pathway for these young patients, thereby expediting the diagnostic timeline, enabling rigorous monitoring, and delivering tailored therapeutic interventions.
Transplant tourism – a missed opportunity
Authors: Merhav Hadar 
Published: October 2023

Purpose of review
To explore the resurgence of transplant tourism (TT) despite the recent reiteration of the Declaration of Istanbul (DoI) in 2018. As demand grows exponentially and supply remains static, novel approaches to bridging the gap should be explored.

Recent findings
TT is estimated to comprise up to 10% of transplants worldwide. Prosecuting patients seeking organs through TT has been unsuccessful. Extra jurisdictional prosecution of brokers, vendors and institutions participating in illicit TT has been difficult. Resurgence of TT has occurred in both “traditional” and new countries. The public attitude towards TT and paid donation is largely positive. The Iranian experience with state regulated paid donors merits attention and perhaps emulation. Numerous philosophers, ethicists and transplant professionals find it acceptable to promote financial consideration for organ donors.

Summary
Acknowledging the autonomy of persons, including poor and vulnerable ones, to receive financial consideration for their sacrifice should not be considered morally reprehensible. Strict international regulation, oversight and legislation should be implemented to assure adequate compensation, donor wellbeing, elimination of brokers and excellent medical care. Implementing such a system internationally may eliminate kidney waiting lists, provide great benefits to vendors, improve transplant facilities in developing countries and provide substantial savings to insurers.
CD4dimCD8bright T cells are inversely associated with neuro-inflammatory markers among people with HIV
Authors: Albalawi Yasmeen A. , Shull Tanner , Virdi Amber K. , Subra Caroline , Mitchell Julie , Slike Bonnie M. , Jian Ningbo , Krebs Shelly J. , Sacdalan Carlo , Ratnaratorn Nisakorn , Hsu Denise C. , Phanuphak Nittaya , Spudich Serena , Trautmann Lydie , Al-Harthi Lena 
Published: October 2023

Objective:
HIV-associated neuroinflammation persists in the brain despite suppressive combination antiretroviral therapy (cART). We evaluated associations between a subset of CD8+ T cells, termed CD4dimCD8bright T cells, and soluble markers of immune activation and/or neuroinflammation in the cerebrospinal fluid (CSF) and plasma of people with HIV (PWH).

Design:
Fifteen cART-naive PWH were enrolled and underwent blood draw, lumbar puncture for CSF collection, and neuropsychological tests at week 0 (pre-cART) and 24 weeks after cART initiation.

Methods:
CSF and peripheral blood T cells were evaluated with flow cytometry and soluble markers of immune activation were measured by multiplex and singleplex assays. Spearman bootstrap correlation coefficients with 10 000 resamples were computed and reported with corresponding 95% confidence intervals (CIs) for each marker of interest and T-cell type.

Results:
The frequency of CSF CD4dimCD8bright T cells at week 0 was inversely related with CSF neopterin. In contrast, at week 24, CSF CD4−CD8+ T cells were positively correlated with CSF s100β, a marker of brain injury. In the blood, at week 0, CD4dimCD8bright T cells were inversely correlated with MCP-1, IP-10, IL-8, IL-6, G-CSF, and APRIL and positively correlated with plasma RANTES and MMP1. At week 0, the frequency of blood CD4−CD8+ were positively correlated with CRP and BAFF.

Conclusion:
CD4dimCD8bright T cells are associated with some anti-inflammatory properties, whereas CD4−CD8+ T cells may contribute to inflammation and injury. Assessing the contrast between these two cell populations in neuroHIV may inform targeted therapeutic intervention to reduce neuroinflammation and associated neurocognitive impairment.