bluuebunny/crossref_metadata_2025_split huggingface dataset:
IDeRare: a lightweight and extensible open-source phenotype and exome analysis pipeline for germline rare disease diagnosis
Authors: Harsono Ivan William , Ariani Yulia , Benyamin Beben , Fadilah Fadilah , Pujianto Dwi Ari , Hafifah Cut Nurul 
Published: June 2024

Abstract

Objectives
Diagnosing rare diseases is an arduous and challenging process in clinical settings, resulting in the late discovery of novel variants and referral loops. To help clinicians, we built IDeRare pipelines to accelerate phenotype-genotype analysis for patients with suspected rare diseases.

Materials and Methods
IDeRare pipeline is separated into phenotype and genotype parts. The phenotype utilizes our handmade Python library, while the genotype part utilizes command line (bash) and Python script to combine bioinformatics executable and Docker image.

Results
We described various implementations of IDeRare phenotype and genotype parts with real-world clinical and exome data using IDeRare, accelerating the terminology conversion process and giving insight on the diagnostic pathway based on disease linkage analysis until exome analysis and HTML-based reporting for clinicians.

Conclusion
IDeRare is freely available under the BSD-3 license, obtainable via GitHub. The portability of IDeRare pipeline could be easily implemented for semi-technical users and extensible for advanced users.
Governance of intersecting value chains in an era of polycentric trade: the case of Kenyan fresh fruit and vegetables
Authors: Alford Matthew , Pasquali Giovanni P , Barrientos Stephanie , Opondo Maggie 
Published: June 2024

Abstract
Domestic value chains (DVCs) led by retailers within the global South often overlap with global value chains (GVCs) as well as domestic arm’s length markets. DVCs incorporate some private governance, but we know little about the role of public governance. Based on analysis of Kenyan fresh fruit and vegetables, we ask: How is the power (or ability) of lead firms to govern producers being reshaped by the increased complexity of polycentric trade in the Kenyan horticultural sector? We reveal constraints to lead firms’ ability to directly exercise bargaining power; and shifts towards institutional power in a context of polycentric trade.
Volatility Shocks, Leverage Effects, and Time-Varying Conditional Skewness
Authors: Kirby Chris 
Published: June 2024

Abstract
I use GARCH-X specifications for stock index returns to investigate the connections between conditional skewness and variance shocks computed from realized variances. The evidence indicates that the conditional skewness of index returns is strongly influenced by variance shocks and displays a remarkable degree of persistence. Indeed, variance shocks not only drive changes in conditional skewness, but also act as a common factor that generates substantial negative correlation between contemporaneous changes in the conditional volatility and conditional skewness of index returns. The resultant linkages between these conditional moments could have important implications in asset pricing, portfolio selection, and risk management applications.
Cytoplasmic aggregation of TDP43 and topographic correlation with tau and α-synuclein accumulation in the rTg4510 mouse model of tauopathy
Authors: Nakayama Yutaro , Chambers James K , Takaichi Yuta , Uchida Kazuyuki 
Published: June 2024

Abstract
In patients with TDP43 proteinopathy, phosphorylated TDP43 (p-TDP43) accumulates in the cytoplasm of neurons. The accumulation of p-TDP43 has also been reported in patients with tauopathy and α-synucleinopathy. We investigated spatiotemporal changes in p-TDP43 accumulation in the brains of rTg4510 mice that overexpressed human mutant tau (P301L) and exhibited hyperphosphorylated tau (hp-tau) and phosphorylated αSyn (p-αSyn) accumulation. Immunohistochemically, p-TDP43 aggregates were observed in the cytoplasm of neurons, which increased with age. A significant positive correlation was observed between the number of cells with p-TDP43 aggregates and hp-tau and p-αSyn aggregates. Suppression of the human mutant tau (P301L) expression by doxycycline treatment reduces the accumulation of p-TDP43, hp-tau, and p-αSyn. Proteinase K-resistant p-TDP43 aggregates were found in regions with high hp-tau, and p-αSyn accumulation. Western blotting of the sarkosyl-insoluble fraction revealed bands of monomeric TDP43 and p-TDP43. These results indicate that the accumulation of mouse p-TDP43 is associated with the accumulation of human mutant tau (P301L) in rTg4510 mouse brains. The accumulation of hp-tau and p-αSyn may promote sarkosyl-insoluble p-TDP43 aggregates that are resistant to proteinase K. The synergistic effects of tau, TDP43, and αSyn may be involved in the pathology of proteinopathies, leading to the accumulation of multiple abnormal proteins.
Diffuse interstellar bands in the near-infrared: expanding the reddening range
Authors: Castellanos R , Najarro F , Garcia M , Patrick L R , Geballe T R 
Published: June 2024

ABSTRACT
We have investigated the behaviour of three strong near-infrared diffuse interstellar bands (DIBs) at λ13177 Å, λ14680 Å, and λ15272 Å, on a larger sample of sightlines and over a wider range of extinctions than previously studied, utilizing spectra from three observatories. We applied two telluric correction techniques to reduce atmospheric contamination and have used Gaussian fits to characterize the DIB profiles and measure equivalent widths. We confirmed strong and approximately linear correlations with reddening of the λ13177 Å, λ14680 Å, and λ15272 Å DIBs, extending them to higher reddening values and strengthening their link to interstellar matter. Modelling of the λ14680 Å DIB profiles revealed intrinsic variations, including line broadening, linked to their formation processes. This effect is particularly pronounced in the Galactic Centre (GC) environment, where multiple diffuse molecular clouds along the line of sight contribute to line broadening. We have detected one new DIB candidate at λ14795 Å on sightlines with high reddening.
LMC stars and where to find them: inferring birth radii for external galaxies
Authors: Lu Yuxi(Lucy) , Buck Tobias , Nidever David , Ratcliffe Bridget , Minchev Ivan , Macciò Andrea V , Obreja Aura 
Published: June 2024

ABSTRACT
It is well known that stars are subject to radial migration, i.e. over time, they move away from their birth location. This dynamical process tends to mix different stellar populations and hence hinders the determination of the true chemical evolution of a galaxy (e.g. metallicity gradients). One way to account for radial migration is to infer stellar birth radii for individual stars. Many attempts to do so have been performed over the last few years, but are limited to the Milky Way, as computing the birth position of stars requires precise measurements of stellar metallicity and age for individual stars that cover large Galactic radii. Fortunately, recent and future surveys will provide numerous opportunities for inferring birth radii for external galaxies such as the LMC. In this paper, we investigate the possibility of doing so using the NIHAO cosmological zoom-in simulations. We find that it is theoretically possible to infer birth radii with a ∼25 per cent median uncertainty for individual stars in galaxies with i) orderliness of the orbits, $\langle v_\phi \rangle /\sigma _{v} &gt; 2 $, ii) a dark matter halo mass greater or equal to approximately the LMC mass (∼2 × 1011 ${\rm M}_\odot$), and iii) after the average azimuthal velocity of the stellar disc reaches ∼70 per cent of its maximum. From our analysis, we conclude that it is possible and useful to infer birth radii for the LMC and other external galaxies that satisfy the above criteria.
Influence of cosmic voids on the propagation of TeV gamma-rays and the puzzle of GRB 221009A
Authors: Abdalla Hassan , Razzaque Soebur , Böttcher Markus , Finke Justin , Domínguez Alberto 
Published: June 2024

ABSTRACT
The recent detection of gamma-ray burst GRB 221009A has attracted attention due to its record brightness and first-ever detection of $\gtrsim 10$ TeV gamma-rays from a GRB. Despite being the second-nearest GRB ever detected, at a redshift of $z=0.151$, the distance is large enough for severe attenuation of gamma-ray flux at these energies due to $\gamma \gamma \rightarrow e^\pm$ pair production with the extragalactic background light (EBL). Here, we investigate whether the presence of cosmic voids along the line of sight can significantly impact the detectability of very high energy (VHE, $\gt $100 GeV) gamma-rays from distant sources. Notably, we find that the gamma–gamma opacity for VHE gamma-rays can be reduced by approximately 10 per cent and up to 30 per cent at around 13 TeV, the highest-energy photon detected from GRB 221009A, for intervening cosmic voids along the line of sight with a combined radius of 110 Mpc, typically found from void catalogues, and 250 Mpc, respectively. This reduction is substantially higher for TeV photons compared to GeV photons, attributable to the broader target photon spectrum that TeV photons interact with. This finding implies that VHE photons are more susceptible to variations in the EBL spectrum, especially in regions dominated by cosmic voids. Our study sheds light on the detection of $\gtrsim 10$ TeV gamma-rays from GRB 221009A in particular, and on the detection of extragalactic VHE sources in general.
Self-consistent dynamical models with a finite extent – IV. Wendland models based on compactly supported radial basis functions
Authors: Baes Maarten 
Published: June 2024

ABSTRACT
We present a new step in our systematic effort to develop self-consistent dynamical models with a finite radial extent. The focus is on models with simple analytical density profiles allowing for analytical calculations of many dynamical properties. In this paper, we introduce a family of models, termed Wendland models, based on compactly supported radial basis functions. The family of models is characterized by a parameter k that controls the smoothness of the transition at the truncation radius. In the limit $k\rightarrow \infty$, the Wendland model reduces to a non-truncated model with a Gaussian density profile. For each Wendland model, the density, mass and gravitational potential are simple truncated polynomial functions of radius. Via the sphecow tool we demonstrate that all Wendland models can be supported by isotropic distribution functions. Surprisingly, the isotropic distribution function exhibits varied behaviour across different Wendland models. Additionally, each model can be supported by a continuum of Osipkov–Merritt orbital structures, ranging from radially anisotropic to completely tangential at the truncation radius. To the best of our knowledge, the Wendland models presented here are the first family of models accommodating both radial and tangential Osipkov–Merritt distribution functions. Using linear superposition, these models can easily be combined to generate Wendland models with even more diverse orbital structures. While the Wendland models are not fully representative of real dynamical systems due to their Gaussian-like density profile, this study lays important groundwork for constructing more realistic models with truncated density profiles that can be supported by a range of orbital structures.
JWST observations of galaxy-damping wings during reionization interpreted with cosmological simulations
Authors: Keating Laura C , Bolton James S , Cullen Fergus , Haehnelt Martin G , Puchwein Ewald , Kulkarni Girish 
Published: June 2024

ABSTRACT
Spectra of the highest redshift galaxies taken with JWST are now allowing us to see into the heart of the reionization epoch. Many of these observed galaxies exhibit strong damping wing absorption redward of their Lyman-$\alpha$ emission. These observations have been used to measure the redshift evolution of the neutral fraction of the intergalactic medium and sizes of ionized bubbles. However, these estimates have been made using a simple analytic model for the intergalactic damping wing. We explore the recent observations with models of inhomogeneous reionization from the Sherwood–Relics simulation suite. We carry out a comparison between the damping wings calculated from the simulations and from the analytic model. We find that although the agreement is good on the red side of the Lyman-$\alpha$ emission, there is a discrepancy on the blue side due to residual neutral hydrogen present in the simulations, which saturates the intergalactic absorption. For this reason, we find that it is difficult to reproduce the claimed observations of large bubble sizes at $z \sim 7$, which are driven by a detection of transmitted flux blueward of the Lyman-$\alpha$ emission. We suggest instead that the observations can be explained by a model with smaller ionized bubbles and larger intrinsic Lyman-$\alpha$ emission from the host galaxy.
Evolutionary Dynamics of Accelerated Antiviral Resistance Development in Hypermutator Herpesvirus
Authors: Höfler Thomas , Nascimento Mariana Mara , Zeitlow Michaela , Kim Ji Yoon , Trimpert Jakob 
Published: June 2024

Abstract
Antiviral therapy is constantly challenged by the emergence of resistant pathogens. At the same time, experimental approaches to understand and predict resistance are limited by long periods required for evolutionary processes. Here, we present a herpes simplex virus 1 mutant with impaired proofreading capacity and consequently elevated mutation rates. Comparing this hypermutator to parental wild type virus, we study the evolution of antiviral drug resistance in vitro. We model resistance development and elucidate underlying genetic changes against three antiviral substances. Our analyzes reveal no principle difference in the evolutionary behavior of both viruses, adaptive processes are overall similar, however significantly accelerated for the hypermutator. We conclude that hypermutator viruses are useful for modeling adaptation to antiviral therapy. They offer the benefit of expedited adaptation without introducing apparent bias and can therefore serve as an accelerator to predict natural evolution.
Synteruptor: mining genomic islands for non-classical specialized metabolite gene clusters
Authors: Haas Drago , Barba Matthieu , Vicente Cláudia M , Nezbedová Šarká , Garénaux Amélie , Bury-Moné Stéphanie , Lorenzi Jean-Noël , Hôtel Laurence , Laureti Luisa , Thibessard Annabelle , Le Goff Géraldine , Ouazzani Jamal , Leblond Pierre , Aigle Bertrand , Pernodet Jean-Luc , Lespinet Olivier , Lautru Sylvie 
Published: June 2024

Abstract
Microbial specialized metabolite biosynthetic gene clusters (SMBGCs) are a formidable source of natural products of pharmaceutical interest. With the multiplication of genomic data available, very efficient bioinformatic tools for automatic SMBGC detection have been developed. Nevertheless, most of these tools identify SMBGCs based on sequence similarity with enzymes typically involved in specialised metabolism and thus may miss SMBGCs coding for undercharacterised enzymes. Here we present Synteruptor (https://bioi2.i2bc.paris-saclay.fr/synteruptor), a program that identifies genomic islands, known to be enriched in SMBGCs, in the genomes of closely related species. With this tool, we identified a SMBGC in the genome of Streptomyces ambofaciens ATCC23877, undetected by antiSMASH versions prior to antiSMASH 5, and experimentally demonstrated that it directs the biosynthesis of two metabolites, one of which was identified as sphydrofuran. Synteruptor is also a valuable resource for the delineation of individual SMBGCs within antiSMASH regions that may encompass multiple clusters, and for refining the boundaries of these SMBGCs.
The Effect of Adult Smoking Behavior on Children’s Exposure to Secondhand Smoke. An Analysis Based on Salivary Cotinine Levels Among Children in Dhaka and Karachi
Authors: Siddiqi Kamran , Welch Charlie , Huque Rumana , Iqbal Romania , Kanaan Mona , Mishu Masuma Pervin , Khokhar Mariam Ahmad , Semple Sean ,   CLASS III Trial Team, Sheikh Aziz , Hewitt Catherine , Jackson Catherine , Kellar Ian , Parrott Steve 
Published: June 2024

Abstract

Introduction
Exposure to secondhand smoke (SHS) risks children’s health. However, biomarkers are rarely used to study SHS exposure among children in low- and middle-income countries.

Aims and Methods
We analyzed cross-sectional data collected between March and November 2022 for a cluster-randomized controlled trial investigating a Smoke-Free Intervention in 2769 children aged 9–15 in 74 schools (34 in Dhaka, Bangladesh, and 40 in Karachi, Pakistan). Children’s saliva was tested for the concentration of cotinine—a highly sensitive and specific biomarker for SHS exposure. Based on their reports, children’s homes were categorized as Nonsmoking Homes (NSH) when residents were nonsmokers; Smoke-free Homes (SFH) when residents and visitors smoked outdoors only; and Smoke-permitted Homes (SPH) when either residents or visitors smoked indoors. We compared cotinine concentrations across these home types and the two cities using a proportional odds model.

Results
Overall, 95.7% of children (92% in Dhaka; and 99.4% in Karachi) had cotinine levels between 0.1 and 12 ng/mL, indicating SHS exposure. Median cotinine levels were higher in Karachi (0.58 ng/mL, IQR 0.37 to 0.93) than in Dhaka (0.27 ng/mL, IQR 0.16 to 0.49). Median cotinine concentration was also higher among children living in SPH than those in either NSH or SFH; with absolute differences of approximately 0.1–0.3 and 0.05 ng/mL, respectively.

Conclusions
The level of SHS exposure in Dhaka and Karachi indicates widespread and unrestricted smoking. Smoking restrictions in households and enforcement of smoking bans are urgently needed.

Implications
The high levels of SHS exposure in children living in SFH suggest parental behavior to hide their smoking and/or exposure in private vehicles or public spaces. It is important to advocate for SFH and cars to protect children from SHS exposure. However, these initiatives alone may not be enough. There is a need to enforce smoking bans in enclosed public places and transportation, as well as extend these bans to playgrounds, parks, fairgrounds, and other public spaces that children frequently visit. It is essential to complement smoking restrictions with tobacco cessation advice and support in these settings.
Renal Hyperfiltration as a New Mechanism of Smoking-Related Mortality
Authors: Aissani Mohamed Smail , Niskanen Leo , Tuomainen Tomi-Pekka , Ould Setti Mounir 
Published: June 2024

Abstract

Introduction
Renal hyperfiltration (RHF), an established risk factor for mortality, is prevalent among tobacco smokers. The aim of this study was to assess the mediating role of RHF in the association between smoking and mortality.

Aims and Methods
Data of this study were retrieved from the cohort of the Kuopio Ischemic Heart Disease Risk Factor Study (KIHD), including 2064 males from Finland. Study participants were followed over a 35-year period. Using classic and counterfactual mediation analysis approaches, we estimated the mediative effect of RHF in the association between smoking and each of the following outcomes: All-cause mortality, cardiovascular disease (CVD) mortality, and non-CVD mortality.

Results
The risk of all-cause mortality in smokers was twice that in nonsmokers (hazard ratio [HR], 2.06; 95% confidence interval [CI]: 1.84 to 2.31). Under the counterfactual framework the direct effect of smoking on all-cause mortality, controlled for RHF, corresponded to an HR of 2.00 (95% CI: 1.78 to 2.30). Of the effect of smoking on mortality, 5% (p-value = .016) was mediated by RHF. This finding concerned particularly non-CVD mortality.

Conclusions
RHF mediated the effect of smoking on non-CVD and all-cause mortality, but not on CVD mortality. The generalizability of our study results is however limited by its focus on a Finnish male cohort, underscoring the need for further investigation into RHF’s broader implications across diverse populations.

Implications
This study elucidates the complex interplay between smoking, renal hyperfiltration (RHF), and mortality, offering novel insights into the mediating role of RHF. Our findings demonstrate that RHF significantly mediates the relationship between smoking and non-cardiovascular disease (non-CVD), but not CVD mortality. This distinction underscores the multifaceted role of RHF beyond its established association with cardiovascular events. By highlighting the specific pathways through which RHF mediates some of the smoking-attributed mortality, this research contributes to our understanding of the mechanisms linking smoking to mortality.
Association of MC4R rs17782313 Genotype With Energy Intake and Appetite: A Systematic Review and Meta-analysis
Authors: Álvarez-Martín Cristina , Caballero Francisco Félix , de la Iglesia Rocio , Alonso-Aperte Elena 
Published: June 2024

Abstract

Context
The melanocortin-4 receptor gene (MC4R) is associated with a higher risk of obesity by the presence of the C allele in rs17782313, but the mechanisms are not clear.

Objective
The present systematic review and meta-analysis aimed to explore the association between the different genotypes of MC4R rs17782313 and energy intake and appetite.

Data Sources
A literature search was conducted up to June 2023 in PubMed, Scopus, Web of Science, and Cochrane Collaboration databases, following PRISMA guidelines.

Data Extraction
Inclusion criteria were studies in humans measuring energy intake, appetite, or satiety in all ages and physiological conditions. Studies dealing solely with body mass index were excluded. Twenty-one articles representing 48 560 participants were included in the meta-analysis.

Data Analysis
According to the NHLBI (National Heart, Lung, and Blood Institute) quality-assessment criteria, all case-control studies and 6 out of 17 cohort and cross-sectional studies were classified as “good,” while the rest scored as “fair.” Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated in a (CT+CC) vs TT dominant model, and both random-effects and fixed-effects models were used. A statistically significant association between the presence of the C allele and increased appetite was found (OR = 1.25; 95% CI: 1.01–1.49; P = .038) using the fixed-effects model, but the random-effects model proved nonsignificant. However, no association with energy intake was found. None of the variables considered (sample size, year of publication, sex, age group, type of population, origin, and quality) were identified as effect modifiers, and no publication biases were found after subgroup and meta-regression analyses.

Conclusion
To our knowledge, this is the first systematic review and meta-analysis that has analyzed the association between rs17782313 of MC4R and energy intake and appetite. Identifying people genetically predisposed to increased appetite may be of great interest, not only to prevent obesity in younger populations but also to avoid malnutrition in elderly persons. This paper is part of the Nutrition Reviews Special Collection on Precision Nutrition.

Systematic Review Registration
PROSPERO registration no. CRD42023417916.