bluuebunny/crossref_metadata_2025_split huggingface dataset:
Establishing a clinical informatics umbilical cord: lessons learned in launching infrastructure to support dyadic mother/infant primary care
Authors: Bose-Brill Seuli , D’Amico Rachel , Bartley Adam , Ashmead Robert , Flores-Beamon Paola , Jallaq Shadia , Li Kevin , Mao Shengyi , Gillespie Shannon , Fareed Naleef , Venkatesh Kartik K , Crossnohere Norah L , Davis Jody , Bunger Alicia C , Lorenz Allison 
Published: August 2023

Abstract
The Multimodal Maternal Infant Perinatal Outpatient Delivery System (MOMI PODS) was developed to facilitate the pregnancy to postpartum primary care transition, particularly for individuals at risk for severe maternal morbidity, via a unique multidisciplinary model of mother/infant dyadic primary care. Specialized clinical informatics platforms are critical to ensuring the feasibility and scalability of MOMI PODS and a smooth perinatal transition into longitudinal postpartum primary care. In this manuscript, we describe the MOMI PODS transition and management clinical informatics platforms developed to facilitate MOMI PODS referrals, scheduling, evidence-based multidisciplinary care, and program evaluation. We discuss opportunities and lessons learned associated with our applied methods, as advances in clinical informatics have considerable potential to enhance the quality and evaluation of innovative maternal health programs like MOMI PODS.
Short-term changes in dietary fat levels and starch sources affect weight management, glucose and lipid metabolism, and gut microbiota in adult cats
Authors: Mo Ruixia , Zhang Mingrui , Wang Haotian , Liu Tianyi , Zhang Gang , Wu Yi 
Published: August 2023

Abstract
A 2 × 2 factorial randomized design was utilized to investigate the effects of fat level (8% or 16% fat on a fed basis) and starch source (pea starch or corn starch) on body weight, glycolipid metabolism, hematology, and fecal microbiota in cats. The study lasted for 28 d and included a low fat and pea starch diet (LFPS), a high fat and pea starch diet, a low fat and corn starch diet, and a high fat and corn starch diet. In this study, hematological analysis showed that all cats were healthy. The apparent total tract digestibility of gross energy, crude protein, and crude fat was above 85% in the four diets. After 28 d, cats fed the high fat diets (HF) gained an average of 50 g more than those fed the low fat diets (LF). The hematological results showed that the HF diets increased the body inflammation in cats, while the LFPS group improved the glucolipid metabolism. The levels of glucose and insulin were lower in cats fed the LF diets than those in cats fed the HF diets (P &lt; 0.05). Meanwhile, compared with the LF, the concentrations of total cholesterol, triglyceride, and high-density lipoprotein cholesterol in serum were greater in the cats fed the HF diets (P &lt; 0.05). Additionally, both fat level and starch source influenced the fecal microbiota, with the relative abundance of beneficial bacteria, such as Blautia being significantly greater in the LFPS group than in the other three groups (P &lt; 0.05). Reducing energy density and using pea starch in foods are both valuable design additions to aid in the management of weight control and improve gut health in cats. This study highlights the importance of fat level and starch in weight management in cats.
Adjuvant and neoadjuvant chemotherapy for biliary tract cancer: a review of randomized controlled trials
Authors: Nakachi Kohei , Gotohda Naoto , Hatano Etsuro , Nara Satoshi , Takahashi Shinichiro , Kawamoto Yasuyuki , Ueno Makoto 
Published: August 2023

Abstract
The first randomized controlled trial of adjuvant chemotherapy for biliary tract cancer was reported in 2002. Since then, studies have continued, with efficacy reported for capecitabine in 2018 and S-1 in 2023. Oral fluoropyrimidines have become established as the standard of care. This article reviews the evidence from the randomized controlled trials reported to date and those that are ongoing or from which results have not yet been reported.
Women in U.S. Law Schools, 1948–2021
Authors: Katz Elizabeth D , Rozema Kyle , Sanga Sarath 
Published: August 2023

AbstractWe study the progress of women’s representation and achievement in law schools. To do this, we assemble a new dataset on the number of women and men students, faculty, and deans at all ABA-approved U.S. law schools from 1948 to the present. These data enable us to study many unexplored features of women’s progress in law schools for the first time, including the process by which women initially gained access to each law school, the variance in women’s experiences across law schools, the relationship between women’s representation and student achievement, and the extent to which women disproportionally occupy interim and non-tenure track positions. We contextualize our findings by situating them within the vast qualitative literature on women’s experiences in law schools and the legal profession.
High-resolution emission spectroscopy retrievals of MASCARA-1b with CRIRES+: strong detections of CO, H2O, and Fe emission lines and a C/O consistent with solar
Authors: Ramkumar Swaetha , Gibson Neale P , Nugroho Stevanus K , Maguire Cathal , Fortune Mark 
Published: August 2023

ABSTRACT
The characterization of exoplanet atmospheres has proven to be successful using high-resolution spectroscopy. Phase curve observations of hot/ultra-hot Jupiters can reveal their compositions and thermal structures, thereby allowing the detection of molecules and atoms in the planetary atmosphere using the cross-correlation technique. We present pre-eclipse observations of the ultra-hot Jupiter, MASCARA-1b, observed with the recently upgraded CRIRES+ high-resolution infrared spectrograph at the VLT. We report a detection of Fe (≈ 8.3σ) in the K-band and confirm previous detections of CO (&gt;15σ) and H2O (&gt;10σ) in the day-side atmosphere of MASCARA-1b. Using a Bayesian inference framework, we retrieve the abundances of the detected species and constrain planetary orbital velocities, T–P profiles, and the carbon-to-oxygen ratio (C/O). A free retrieval results in an elevated CO abundance ($\log _{10}(\chi _{\rm {{}^{12}CO}}) = -2.85^{+0.57}_{-0.69}$), leading to a supersolar C/O ratio. More realistically, allowing for vertically-varying chemistry in the atmosphere by incorporating a chemical-equilibrium model results in a C/O of $0.68^{+0.12}_{-0.22}$ and a metallicity of $[\rm M/H] = 0.62^{+0.28}_{-0.55}$, both consistent with solar values. Finally, we also report a slight offset of the Fe feature in both Kp and vsys that could be a signature of atmospheric dynamics. Due to the 3D structure of exoplanet atmospheres and the exclusion of time/phase dependence in our 1D forward models, further follow-up observations and analysis are required to confirm or refute this result.
Genetic Architecture of Flowering Time Differs Between Populations With Contrasting Demographic and Selective Histories
Authors: Neto Célia , Hancock Angela 
Published: August 2023

Abstract
Understanding the evolutionary factors that impact the genetic architecture of traits is a central goal of evolutionary genetics. Here, we investigate how quantitative trait variation accumulated over time in populations that colonized a novel environment. We compare the genetic architecture of flowering time in Arabidopsis populations from the drought-prone Cape Verde Islands and their closest outgroup population from North Africa. We find that trait polygenicity is severely reduced in the island populations compared to the continental North African population. Further, trait architectures and reconstructed allelic histories best fit a model of strong directional selection in the islands in accord with a Fisher–Orr adaptive walk. Consistent with this, we find that large-effect variants that disrupt major flowering time genes (FRI and FLC) arose first, followed by smaller effect variants, including ATX2 L125F, which is associated with a 4-day reduction in flowering time. The most recently arising flowering time-associated loci are not known to be directly involved in flowering time, consistent with an omnigenic signature developing as the population approaches its trait optimum. Surprisingly, we find no effect in the natural population of EDI-Cvi-0 (CRY2 V367M), an allele for which an effect was previously validated by introgression into a Eurasian line. Instead, our results suggest the previously observed effect of the EDI-Cvi-0 allele on flowering time likely depends on genetic background, due to an epistatic interaction. Altogether, our results provide an empirical example of the effects demographic history and selection has on trait architecture.
HELZ2: a new, interferon-regulated, human 3′-5′ exoribonuclease of the RNB family is expressed from a non-canonical initiation codon
Authors: Huntzinger Eric , Sinteff Jordan , Morlet Bastien , Séraphin Bertrand 
Published: August 2023

Abstract
Proteins containing a RNB domain, originally identified in Escherichia coli RNase II, are widely present throughout the tree of life. Many RNB proteins have 3′-5′ exoribonucleolytic activity but some have lost catalytic activity during evolution. Database searches identified a new RNB domain-containing protein in human: HELZ2. Analysis of genomic and expression data combined with evolutionary information suggested that the human HELZ2 protein is produced from an unforeseen non-canonical initiation codon in Hominidae. This unusual property was confirmed experimentally, extending the human protein by 247 residues. Human HELZ2 was further shown to be an active ribonuclease despite the substitution of a key residue in its catalytic center. HELZ2 RNase activity is lost in cells from some cancer patients as a result of somatic mutations. HELZ2 harbors also two RNA helicase domains and several zinc fingers and its expression is induced by interferon treatment. We demonstrate that HELZ2 is able to degrade structured RNAs through the coordinated ATP-dependent displacement of duplex RNA mediated by its RNA helicase domains and its 3′-5′ ribonucleolytic action. The expression characteristics and biochemical properties of HELZ2 support a role for this factor in response to viruses and/or mobile elements.
Structural and functional characterization of MrpR, the master repressor of the Bacillus subtilis prophage SPβ
Authors: Kohm Katharina , Jalomo-Khayrova Ekaterina , Krüger Aileen , Basu Syamantak , Steinchen Wieland , Bange Gert , Frunzke Julia , Hertel Robert , Commichau Fabian M , Czech Laura 
Published: August 2023

Abstract
Prophages control their lifestyle to either be maintained within the host genome or enter the lytic cycle. Bacillus subtilis contains the SPβ prophage whose lysogenic state depends on the MrpR (YopR) protein, a key component of the lysis-lysogeny decision system. Using a historic B. subtilis strain harboring the heat-sensitive SPβ c2 mutant, we demonstrate that the lytic cycle of SPβ c2 can be induced by heat due to a single nucleotide exchange in the mrpR gene, rendering the encoded MrpRG136E protein temperature-sensitive. Structural characterization revealed that MrpR is a DNA-binding protein resembling the overall fold of tyrosine recombinases. MrpR has lost its recombinase function and the G136E exchange impairs its higher-order structure and DNA binding activity. Genome-wide profiling of MrpR binding revealed its association with the previously identified SPbeta repeated element (SPBRE) in the SPβ genome. MrpR functions as a master repressor of SPβ that binds to this conserved element to maintain lysogeny. The heat-inducible excision of the SPβ c2 mutant remains reliant on the serine recombinase SprA. A suppressor mutant analysis identified a previously unknown component of the lysis-lysogeny management system that is crucial for the induction of the lytic cycle of SPβ.
Physical interaction between MSL2 and CLAMP assures direct cooperativity and prevents competition at composite binding sites
Authors: Eggers Nikolas , Gkountromichos Fotios , Krause Silke , Campos-Sparr Aline , Becker Peter B 
Published: August 2023

Abstract
MSL2, the DNA-binding subunit of the Drosophila dosage compensation complex, cooperates with the ubiquitous protein CLAMP to bind MSL recognition elements (MREs) on the X chromosome. We explore the nature of the cooperative binding to these GA-rich, composite sequence elements in reconstituted naïve embryonic chromatin. We found that the cooperativity requires physical interaction between both proteins. Remarkably, disruption of this interaction does not lead to indirect, nucleosome-mediated cooperativity as expected, but to competition. The protein interaction apparently not only increases the affinity for composite binding sites, but also locks both proteins in a defined dimeric state that prevents competition. High Affinity Sites of MSL2 on the X chromosome contain variable numbers of MREs. We find that the cooperation between MSL2/CLAMP is not influenced by MRE clustering or arrangement, but happens largely at the level of individual MREs. The sites where MSL2/CLAMP bind strongly in vitro locate to all chromosomes and show little overlap to an expanded set of X-chromosomal MSL2 in vivo binding sites generated by CUT&RUN. Apparently, the intrinsic MSL2/CLAMP cooperativity is limited to a small selection of potential sites in vivo. This restriction must be due to components missing in our reconstitution, such as roX2 lncRNA.
When bargaining is and is not possible: the politics of bureaucratic expertise in the context of democratic backsliding
Authors: Koga Natália Massaco , Karruz Ana Paula , Palotti Pedro Lucas de Moura , Soares Filho Marcos Luiz Vieira , Couto Bruno Gontyjo do 
Published: August 2023

AbstractIn looking at the complex relationship between expertise and power in policymaking, what is amiss are studies on how the expertise exchange bargain between politicians and bureaucracy works in practice, especially in antidemocratic contexts. To deal with this limitation, we use Christensen’s (Christensen, J. (2022). When bureaucratic expertise comes under attack. Public Administration) expertise bargain change model for examining the authority transaction between politicians and bureaucrats. Upon external shocks, such as democratic backsliding with the sidelining of policy advice, the extant expertise bargain is challenged. We explore how the bureaucracy acted toward the government’s adversarial (and even antagonistic) stance and how that relationship toward the expertise bargain changed in two policy areas in Brazil (health and environment) during Bolsonaro’s administration (2019–2022). Notably, this article relies mainly on qualitative data from in-depth interviews with bureaucrats who provided expertise to the government on these policy areas during the Bolsonaro administration’s transition. Ancillary documentary sources were examined to detail the strategies of attack from government toward bureaucratic expertise and ancillary documentary sources of quantitative data from a survey with bureaucrats fielded during the Bolsonaro administration’s first year. Results show three factors that condition bureaucratic expertise’s resilience: the nature of the attack (local or extensive), the knowledge base’s and epistemic community’s level of cohesion, and the advice system’s degree of institutionalization. This case study sheds light on how different policy advice arrangements respond and function under antidemocratic contexts, allowing the application and enrichment of policy expertise literature outside regular democratic politics.
Local Effects of Global Capital Flows: A China Shock in the U.S. Housing Market
Authors: Li Zhimin , Shen Leslie Sheng , Zhang Calvin 
Published: August 2023

Abstract
This paper studies the real effects of foreign real estate capital inflows. Using transaction-level data, we document (i) a “China shock” in the U.S. housing market characterized by surging foreign Chinese housing purchases after 2008, and (ii) “home bias” in these purchases, as they concentrate in neighborhoods historically populated by ethnic Chinese. Exploiting their temporal and spatial variation, we find that these capital inflows raise local employment, with the effect transmitted through a housing net worth channel. However, they displace local lower-income residents. Our results show that real estate capital inflows can both stimulate the real economy and induce gentrification.
Performance of GAP and ILD-GAP models in predicting lung transplant or death in interstitial pneumonia with autoimmune features
Authors: Allen Michael R , Alevizos Michail K , Zhang David , Bernstein Elana J 
Published: August 2023

Abstract

Objectives
To assess the ability of two risk prediction models in interstitial lung disease (ILD) to predict death or lung transplantation in a cohort of patients with interstitial pneumonia with autoimmune features (IPAF).

Methods
We performed a retrospective cohort study of adults with IPAF at an academic medical centre. The primary outcome was a composite of lung transplantation or death. We applied the patient data to the previously described Gender–Age–Physiology (GAP) and ILD-GAP models to determine the ability of these models to predict the composite outcome. Model discrimination was assessed using the c-index, and model calibration was determined by comparing the incidence ratios of observed vs expected deaths.

Results
Ninety-four patients with IPAF were included. Mean (s.d.) age was 58 (13.5) years and the majority were female (62%). The majority met serologic and morphologic criteria for IPAF (94% and 91%, respectively). The GAP model had a c-index of 0.664 (95% CI 0.547–0.781), while the ILD-GAP model had a c-index of 0.569 (95% CI 0.440–0.697). In those with GAP stage 1 or GAP stage 2 disease, calibration of the GAP model was satisfactory at 2 and 3 years for the cumulative end point of lung transplantation or death.

Conclusion
In patients with IPAF, the GAP model performed well as a predictor of lung transplantation or death at 2 years and 3 years from ILD diagnosis in patients with GAP stage 1 and GAP stage 2 disease.
Universities of applied sciences’ EU research project participation through the lens of differentiation
Authors: Cavallaro Marco 
Published: August 2023

Abstract
In European universities of applied sciences (UASs), the intensity of research activities and the level of differentiation from universities vary across countries. We investigate whether the differentiation in the research function of UASs is reflected in their participation in the European Union Framework Programs for Research and Innovation (EU-FPs). We focus on the current and former UASs in four higher education systems with distinct levels of differentiation—the UK, Norway, Switzerland, and the Netherlands. Our results show significant cross-country differences in the intensity and type of EU-FP projects acquired. The former UASs in the UK and Norway had a participation profile similar to that of universities. In more differentiated higher education systems, Swiss and Dutch UASs were more geared toward applied projects. Variations both across and within countries emphasize the importance of research capacities. Our results carry implications for how national and European authorities can foster UAS participation in EU-FPs.
The Cauchy Process on Phylogenies: A Tractable Model for Pulsed Evolution
Authors: Bastide Paul , Didier Gilles 
Published: August 2023

Abstract
Phylogenetic comparative methods use random processes, such as the Brownian Motion, to model the evolution of continuous traits on phylogenetic trees. Growing evidence for non-gradual evolution motivated the development of complex models, often based on Lévy processes. However, their statistical inference is computationally intensive and currently relies on approximations, high-dimensional sampling, or numerical integration. We consider here the Cauchy Process (CP), a particular pure-jump Lévy process in which the trait increment along each branch follows a centered Cauchy distribution with a dispersion proportional to its length. In this work, we derive an exact algorithm to compute both the joint probability density of the tip trait values of a phylogeny under a CP and the ancestral trait values and branch increments posterior densities in quadratic time. A simulation study shows that the CP generates patterns in comparative data that are distinct from any Gaussian process, and that restricted maximum likelihood parameter estimates and root trait reconstruction are unbiased and accurate for trees with 200 tips or less. The CP has only two parameters but is rich enough to capture complex-pulsed evolution. It can reconstruct posterior ancestral trait distributions that are multimodal, reflecting the uncertainty associated with the inference of the evolutionary history of a trait from extant taxa only. Applied on empirical datasets taken from the Evolutionary Ecology and Virology literature, the CP suggests nuanced scenarios for the body size evolution of Greater Antilles Lizards and for the geographical spread of the West Nile Virus epidemics in North America, both consistent with previous studies using more complex models. The method is efficiently implemented in C with an R interface in package cauphy, which is open source and freely available online.
A new classification of the family Ariidae (Osteichthyes: Ostariophysi: Siluriformes) based on combined analyses of morphological and molecular data
Authors: Marceniuk Alexandre Pires , Oliveira Claudio , Ferraris Carl J 
Published: August 2023

AbstractWe present a new classification of the catfish family Ariidae based on a total-evidence hypothesis, which incorporates data from the examination of 249 morphological and 5603 molecular characters from 131 species. The named taxa in the proposed classification represent groups of species found in the Maximum Parsimony, Maximum Likelihood, and Bayesian Inference analyses or, in some cases, two of the three methods. Each named taxon is provided with a diagnosis derived from a comprehensive summary of the morphological characters and their character-state transformations, as interpreted from the most parsimonious version of the total-evidence tree. Taxa newly named herein are: Cathoropsini, new tribe; Genidentini, new tribe; Sciadeini, new tribe; Aceroichthys, new genus (type species Arius dioctes Kailola, 2000); Bleekeriella, new genus (type species Arius leptaspis Bleeker, 1862); Betancurichthys, new genus (type species Arius madagascariensis Vaillant, 1894); Jayaramichthys, new genus (type species Arius leptonotacanthus Bleeker, 1849); Kyataphisa, new genus (type species Pimelodus nenga Hamilton, 1822); Megalosciades, new genus (type species Arius augustus Roberts, 1978); Paracinetodus, new genus (type species Arius carinatus Weber, 1913); Papuarius, new genus (type species Arius latirostris Macleay, 1883); and Pseudosciades, new genus (type species Arius sona Hamilton, 1822). A key to the genera of Ariidae is presented.