bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeny, Ecology, and Gene Families Covariation Shaped the Olfactory Subgenome of Rodents
Authors: Courcelle Maxime , Fabre Pierre-Henri , Douzery Emmanuel J P 
Published: November 2023

Abstract
Olfactory receptor (OR) genes represent the largest multigenic family in mammalian genomes and encode proteins that bind environmental odorant molecules. The OR repertoire is extremely variable among species and is subject to many gene duplications and losses, which have been linked to ecological adaptations in mammals. Although they have been studied on a broad taxonomic scale (i.e., placental), finer sampling has rarely been explored in order to better capture the mechanisms that drove the evolution of the OR repertoire. Among placental mammals, rodents are well-suited for this task, as they exhibit diverse life history traits, and genomic data are available for most major families and a diverse array of lifestyles. In this study, 53 rodent published genomes were mined for their OR subgenomes. We retrieved more than 85,000 functional and pseudogene OR sequences that were subsequently classified into phylogenetic clusters. Copy number variation among rodents is similar to that of other mammals. Using our OR counts along with comparative phylogenetic approaches, we demonstrated that ecological niches such as diet, period of activity, and a fossorial lifestyle strongly impacted the proportion of OR pseudogenes. Within the OR subgenome, phylogenetic inertia was the main factor explaining the relative variations of the 13 OR gene families. However, a striking exception was a convergent 10-fold expansion of the OR family 14 among the phylogenetically divergent subterranean mole-rat lineages belonging to Bathyergidae and Spalacidae families. This study illustrates how the diversity of the OR repertoire has evolved among rodents, both shaped by selective forces stemming from species life history traits and neutral evolution along the rodent phylogeny.
Polysocial and Polygenic Risk Scores and All-Cause Dementia, Alzheimer’s Disease, and Vascular Dementia
Authors: Li Yueying , Zeng Zhiqing , Zhuang Zhenhuang , Zhao Yimin , Zhang Linjing , Wang Wenxiu , Song Zimin , Dong Xue , Xiao Wendi , Huang Ninghao , Jia Jinzhu , Liu Zhonghua , Qi Lu , Huang Tao 
Published: November 2023

Abstract

Background
To establish a polysocial risk score (PsRS) incorporating various social factors for capturing the dementia risk and investigate the benefits of favorable social conditions across different genetic backgrounds.

Methods
This prospective cohort study comprised 345 439 participants initially free of dementia from the UK Biobank. A total of 10 social factors were summed to create a PsRS. A polygenic risk score (PRS) was constructed based on genome-wide significant variants.

Results
During a median follow-up of 12.5 years, we documented 4 595 incident all-cause dementia events including 2 067 Alzheimer’s disease (AD) events and 1 028 vascular dementia (VD) events. Each additional PsRS was associated with a 19% increased risk of all-cause dementia (hazard ratio [HR], 1.19; 95% confidence interval [CI], 1.17 to 1.21), a 13% increased risk of AD (1.13; 1.10 to 1.16), and a 24% increased risk of VD (1.24; 1.19 to 1.29). 29% (24% to 33%) of dementia cases, 22% (14% to 29%) of AD cases, and 39% (28% to 48%) of VD cases were associated with a disadvantageous social environment. In addition, among participants at a high genetic risk, the low social risk was linked to a lower incidence rate of all-cause dementia, AD, and VD compared to those who had a high social risk, with reductions of 67.8%, 64.5%, and 84.2%, respectively.

Conclusions
The PsRS could be effectively used in discriminating individuals at high risk of dementia. Around a quarter of dementia events could have a connection with a disadvantageous social environment, especially for those genetically susceptible to dementia.
Genetic architecture and genomic prediction of plant height-related traits in chrysanthemum
Authors: Zhang Xuefeng , Su Jiangshuo , Jia Feifei , He Yuhua , Liao Yuan , Wang Zhenxing , Jiang Jiafu , Guan Zhiyong , Fang Weimin , Chen Fadi , Zhang Fei 
Published: November 2023

Abstract
Plant height (PH) is a crucial trait determining plant architecture in chrysanthemum. To better understand the genetic basis of PH, we investigated the variations of PH, internode number (IN), internode length (IL), and stem diameter (SD) in a panel of 200 cut chrysanthemum accessions. Based on 330 710 high-quality SNPs generated by genotyping by sequencing, a total of 42 associations were identified via a genome-wide association study (GWAS), and 16 genomic regions covering 2.57 Mb of the whole genome were detected through selective sweep analysis. In addition, two SNPs, Chr1_339370594 and Chr18_230810045, respectively associated with PH and SD, overlapped with the selective sweep regions from FST and π ratios. Moreover, candidate genes involved in hormones, growth, transcriptional regulation, and metabolic processes were highlighted based on the annotation of homologous genes in Arabidopsis and transcriptomes in chrysanthemum. Finally, genomic selection for four PH-related traits was performed using a ridge regression best linear unbiased predictor model (rrBLUP) and six marker sets. The marker set constituting the top 1000 most significant SNPs identified via GWAS showed higher predictabilities for the four PH-related traits, ranging from 0.94 to 0.97. These findings improve our knowledge of the genetic basis of PH and provide valuable markers that could be applied in chrysanthemum genomic selection breeding programs.
An Atlas Characterizing the Shared Genetic Architecture of Inflammatory Bowel Disease with Clinical and Behavioral Traits
Authors: Shaw Vikram R , Byun Jinyoung , Pettit Rowland W , Hou Jason K , Walsh Kyle M , Han Younghun , Amos Christopher I 
Published: November 2023

Abstract

Background
Inflammatory bowel disease (IBD) development is a complex, multifactorial process that involves extrinsic and intrinsic factors such as host genetics, the immune system, the gut microbiome, and environmental risks. To help understand the genetic contribution of clinical, behavioral, psychiatric, and diet-related traits, we aim to provide a deep and comprehensive characterization of the shared genetic architecture between IBD and hundreds of potentially related traits.

Methods
Utilizing publicly available summary statistics from a previously published IBD genome-wide association study and hundreds of traits from the United Kingdom BioBank (UKBB), we performed linkage disequilibrium score regression (LDSR) analysis to estimate cross-trait genetic correlations between Crohn’s disease (CD), ulcerative colitis (UC), and IBD summary statistics with the UKBB traits of interest.

Results
Nominally significant (P &lt; .05) genetic correlations were observed for 181 traits in overall IBD, 239 traits in CD, and 94 traits in UC. We replicate the known association between smoking behavior and CD/UC, namely that current tobacco smoking has a positive genetic correlation with CD (rg = 0.12, P = 4.2 × 10-4), while “ever smoking” has a negative genetic correlation with UC (rg = −0.07, P = .042). Globally, all 3 strata (IBD, CD, and UC) demonstrated increased genetic correlations for psychiatric-related traits related to anxiety and depression.

Conclusion
The present analysis reveals the shared genetic architecture between multiple traits and IBD, CD, and UC. Understanding the relevance of joint occurrences of IBD with psychiatric diseases may moderate management of these diseases for individuals jointly affected by them.
Influence of the new dispersible fixed-dose combination anti-Tuberculosis drug on treatment adherence among children with Tuberculosis in Osun State, Nigeria
Authors: Chijioke-Akaniro Obioma , Akinyemi Patrick A , Asuke Sunday , Anyaike Chukwuma , Uwaezuoke Ndubuisi A , Ochuko Urhioke , Ubochioma Emperor , Omoniyi Amos , Merle Corinne S , Daniel Soji 
Published: November 2023

Abstract

Background
The dispersible fixed-dose combination drug has been recommended as the mainstay of treatment for TB in children. However, more needs to be known about its effect on treatment. This study aimed to assess the effectiveness of the formulation on treatment adherence among children with TB.

Methods
A historical cohort design was used to assess and compare adherences of old loose non-dispersible and new dispersible fixed-dose anti-TB drugs, using a convergent parallel mixed-method approach for data collection. Determinants of treatment adherence were assessed using binary logistic regression.

Results
The proportion of children with good treatment adherence was higher in the new dispersible formulation group (82 [64.6%]) relative to the proportion among the loose non-dispersible formulation group (29 [23.4%]). Reports of forgetfulness, travelling and pill burden were significantly higher among those with poor adherence in the loose non-dispersible formulation group. Significant predictors of treatment adherence were acceptability (adjusted OR [AOR]=4.1, p=0.013, 95% CI 1.342 to 12.756), travelling from treatment areas (AOR=8.9, p=0.002, 95% CI 2.211 to 35.771) and forgetfulness (AOR=74.0, p&lt;0.001, 95% CI 23.319 to 234.725).

Conclusions
The determinants of treatment adherence are multifactorial. In addition to ensuring universal access to the drug, flexible referral in case of travelling and ensuring treatment partners' participation to minimise forgetfulness to take pills, are essential.
Population dynamics of Tribolium castaneum (Coleoptera: Tenebrionidae) in wheat and in wheat mixed with cracked wheat held in different types of containers
Authors: Jagadiswaran Bhagya , Jayas Digvir S , Jian Fuji 
Published: November 2023

Abstract
The population dynamics of Tribolium castaneum (Herbst), red flour beetle, was studied at 30 °C using long vertical columns (LVCs) (150 mm diameter and 1,020 mm long) and shallow containers (SCs) (460 mm long, 660 mm wide, and 150 mm high), containing 14 kg of whole wheat or a diet made of whole wheat and cracked wheat in 19:1 ratio by mass. The moisture content of the wheat or mixed diet was 14.5% (wb). Every 4 wk and up to 24 wk the live and dead adults were counted in the SCs or in each section of the LVCs. Each LVC was separated into 10 equal sections before removing grain from the LVC. After counting, the grains were incubated at 30 °C and 70% RH for 4 wk, and emerged adults after re-incubation were counted as offspring. The adults and offspring were mainly concentrated in the top section of the LVCs, which could be due to higher mortality in the lower sections and preference of T. castaneum for the surface of grain bulk. The diet influenced the population, and the insects developed better in the cracked wheat-based diet. Greater surface area of the container increased the multiplication and/ or survival of T. castaneum and insects inside SCs with larger surface area and with cracked wheat-based diet, had quicker population increase rate and larger carrying capacity than LVCs.
An Adaptive Targeted Field Experiment: Job Search Assistance for Refugees in Jordan
Authors: Caria A Stefano , Gordon Grant , Kasy Maximilian , Quinn Simon , Shami Soha Osman , Teytelboym Alexander 
Published: November 2023

AbstractWe introduce an adaptive targeted treatment assignment methodology for field experiments. Our Tempered Thompson Algorithm balances the goals of maximizing the precision of treatment effect estimates and maximizing the welfare of experimental participants. A hierarchical Bayesian model allows us to adaptively target treatments. We implement our methodology in Jordan, testing policies to help Syrian refugees and local jobseekers to find work. The immediate employment impacts of a small cash grant, information and psychological support are small, but targeting raises employment by 1 percentage-point (20%). After 4 months, cash has a sizable effect on employment and earnings of Syrians.
Lion (Panthera leo) movements in a multiuse area of the eastern Panhandle of the Okavango Delta, Botswana
Authors: LeFlore Eric G , Fuller Todd K , Stein Andrew B 
Published: November 2023

Abstract
As global large carnivore populations continue to decline due to human actions, maintaining viable populations beyond protected area (PA) borders is critical. African lions (Panthera leo) ranging beyond PA borders regularly prey on domestic livestock causing humans to retaliate or even preemptively kill lions to minimize impacts of lost livestock. To understand how lions navigate high-conflict areas in human-dominated landscapes, lions were observed and monitored in the eastern Panhandle of the Okavango Delta between October 2014 and December 2016, and five lions were fitted with GPS satellite collars from August 2015 to December 2016. Lion prides and coalitions were small, with all prides having four or fewer females and all coalitions having two or fewer males. Home range size varied between the sexes but was not statistically different (males: x¯ = 584 km2, n = 3; females: x¯ = 319 km2, n = 2). There was considerable spatial overlap in home ranges as nonassociating, neighboring collared individuals utilized high levels of shared space (female–female overlap = 152 km2, representing 41–56% of respective home ranges; male–male overlap = 125–132 km2, representing 16–31% of respective home ranges). However, neighboring lions varied use of shared space temporally as evidenced by low coefficients of association (&lt; 0.08), avoiding potentially costly interactions with neighboring individuals. Highest levels of overlap occurred during the wet and early dry seasons when flood waters minimized the amount of available land area. All collared individuals minimized time in close proximity (&lt; 3 km) to human habitation, but some individuals were able to rely heavily on areas where unmonitored livestock grazed. While most lions exist within PAs, anthropogenic impacts beyond PA boundaries can impact critical populations within PAs. Studying systems beyond park boundaries with high levels of human–lion conflict while also establishing conservation programs that account for both ecological and sociocultural dimensions will better aid lion conservation efforts moving forward.
Characterization of intrapuparial development of Musca domestica (Diptera: Muscidae), under different temperatures in laboratory conditions
Authors: do Couto Leiani Cristina Martins , Queiroz Margareth Maria de Carvalho 
Published: November 2023

Abstract
Musca domestica (Linnaeus, 1758) (Diptera: Muscidae), popularly known as “housefly”, is a highly synanthropic species, with economic, medical-sanitary, veterinary, and forensic importance. It is able to cause damage to health, transmit pathogenic agents, cause infection in domestic animals, and, in its immature stage, cause secondary myiasis. The scavenging habit of its immature stages makes these flies pioneers in colonizing both human and animal carcasses, from the initial stages of corpse decomposition to the final stages. Intrapuparial development studies of all stages of the biological cycle of these insects help estimate pupal age, being useful to forensic entomology to aid in determining the minimum postmortem interval (minPMI). This study describes, morphologically, the external structures of the pupae, under temperatures of 23, 27, and 30 ± 1 °C aiming to identify the characteristics that define their developmental stages and estimation of the pupae age of M. domestica. The whole experiment was carried out under laboratory conditions, with relative humidity 60 ± 10% and 12 hours of photoperiod. The process of pupariation and pupation including pre-pupae phases were observed; larvae pupae apolysis; early cryptocephalic pupae; late cryptocephalic pupae; phanerocephalic pupae; pharate adult, discriminated by eye color (transparent eyes, pink eyes, and red eyes); and the emergency of adults, which occurred in the intervals of 162–180; 138–144, and 96–102 hr, respectively, being described throughout the metamorphosis of the external morphological characteristics of the pupal stage of M. domestica.
METTL3-mediated maturation of miR-192-5p targets ATG7 to prevent Schwann cell autophagy in peripheral nerve injury
Authors: Liu Xing , Lv Jun , Tang Weilong , Hu Yuanbai , Wen Yiwei , Shen Hongtao 
Published: November 2023

Abstract
The inhibition of miR-192-5p can promote nerve repair in rats with peripheral nerve injury (PNI) but the precise mechanisms underlying this effect remain unclear. Schwann cell (SC) autophagy mediated by autophagy-related gene (ATG) proteins has a key role in PNI but it is uncertain whether miR-192-5p affects the involvement of SC autophagy in PNI. In this study, we investigated the impact of methyltransferase-like protein 3 (METTL3)/miR-192-5p/ATG7 on SC autophagy in a rat PNI model and in an SC oxygen and glucose deprivation model. The results revealed that METTL3 stimulated miR-192-5p maturation via m6A methylation to depress ATG7 and SC autophagy and aggravate PNI. These findings provide a new target and potential basis for the treatment of patients with PNI.
Handling Difficult Cryo-ET Samples: A Study with Primary Neurons from Drosophila melanogaster
Authors: Kim Joseph Y , Yang Jie E , Mitchell Josephine W , English Lauren A , Yang Sihui Z , Tenpas Tanner , Dent Erik W , Wildonger Jill , Wright Elizabeth R 
Published: November 2023

Abstract
Cellular neurobiology has benefited from recent advances in the field of cryo-electron tomography (cryo-ET). Numerous structural and ultrastructural insights have been obtained from plunge-frozen primary neurons cultured on electron microscopy grids. With most primary neurons having been derived from rodent sources, we sought to expand the breadth of sample availability by using primary neurons derived from 3rd instar Drosophila melanogaster larval brains. Ultrastructural abnormalities were encountered while establishing this model system for cryo-ET, which were exemplified by excessive membrane blebbing and cellular fragmentation. To optimize neuronal samples, we integrated substrate selection, micropatterning, montage data collection, and chemical fixation. Efforts to address difficulties in establishing Drosophila neurons for future cryo-ET studies in cellular neurobiology also provided insights that future practitioners can use when attempting to establish other cell-based model systems.
Characterization of the Small Intestine in the Southern White-breasted Hedgehog (Erinaceus concolor) Using Histological, Histochemical, Immunohistochemical, and Scanning Electron Microscopic Techniques
Authors: Massoud Diaa , Fouda Maged , Shaldoum Fayez , Alrashdi Barakat M , AbdRabou Mervat Ahmed , Soliman Soha A , Abd-Elhafeez Hanan H , Hassan Mervat , Abumandour Mohamed 
Published: November 2023

Abstract
The present study was designed to investigate the microscopic features of the small intestine in the southern white-breasted hedgehog (Erinaceus concolor). The histochemical profile of the small intestine was investigated using periodic acid Schiff (PAS), alcian blue (AB, pH 2.5), and aldehyde fuchsin. The expression of SOX9 was also evaluated immunohistochemically, and the detailed morphology of intestinal mucosa was studied by using a scanning electron microscope. The intestinal wall was composed of the tunica mucosa, tunica submucosa, tunica muscularis, and tunica serosa. Plica circulares and muscularis mucosa were present only in the duodenum. The jejunal villi were the tallest and the ileal villi were the shortest. From the duodenum to the ileum, the population density of goblet cells decreased significantly. The goblet cells throughout the small intestine reacted positively with PAS and AB. The expression rate of SOX9 was not statistically different between the three parts of the small intestine (p &gt; 0.05). In conclusion, despite the general characteristics of the small intestine in this species of hedgehog, there were some differences when compared with other mammalian and rodent species. These findings provide a baseline for future detailed research on the digestive system of the hedgehog species and other mammalian species.
The donor star radial velocity curve in the cataclysmic variable GY Cnc confirms white dwarf eclipse modelling mass
Authors: Littlefair S P , Rodríguez-Gil Pablo , Marsh T R , Parsons S G , Dhillon V S 
Published: November 2023

ABSTRACT
A large number of white dwarf and donor masses in cataclysmic variables have been found via modelling the primary eclipse, a method that relies on untested assumptions. Recent measurements of the mass of the white dwarf in the cataclysmic variable GY Cnc, obtained via modelling its ultraviolet spectrum, conflict with the mass obtained via modelling the eclipse light curve. Here we measure the radial velocity of the absorption lines from the donor star in GY Cnc to be Kabs = 280 ± 2  km s−1, in excellent agreement with the prediction based on the masses derived from modelling the eclipse light curve. It is possible that the white dwarf mass derived from the ultraviolet spectrum of GY Cnc is affected by the difficulty of disentangling the white dwarf spectrum from the accretion disc spectrum.
A near-infrared variability survey of young planetary-mass objects
Authors: Liu Pengyu , Biller Beth A , Vos Johanna M , Whiteford Niall , Zhang Zhoujian , Liu Michael C , Fontanive Clémence , Manjavacas Elena , Henning Thomas , Kenworthy Matthew A , Bonavita Mariangela , Bonnefoy Mickaël , Bubb Emma , Petrus Simon , Schlieder Joshua 
Published: November 2023

ABSTRACT
We present a photometric variability survey of young planetary-mass objects using the New Technology Telescope in the JS and KS bands. Surface gravity plays an important role in the atmospheric structure of brown dwarfs, as young low-gravity L dwarfs have a higher variability rate than field L dwarfs. In this study, we extend variability studies to young T-type planetary-mass objects and investigate the effects of surface gravity on the variability of L and T dwarfs across a large sample. We conduct continuous monitoring for 18 objects with spectral types from L5 to T8 and detect four new variables and two variable candidates. Combining with previous variability surveys of field and young L and T objects, we find that young objects tend to be more variable than field objects within peak-to-peak variability amplitude ranges of 0.5–10 per cent and period ranges of 1.5–20 h. For the first time, we constrain the variability rate of young T dwarfs to be $56_{-18}^{+20}$ per cent compared to $25_{-7}^{+8}$ per cent for field T dwarfs. Both field and young samples have higher variability rates at the L/T transition than outside the L/T transition. The differences in the variability rates between field and young samples are about 1σ and therefore larger sample sizes are needed to confirm and refine the results. Besides the L/T transition, young L dwarfs with strong variability tend to assemble in a narrow spectral type range of L6–L7.5. This work supports the critical role of surface gravity on the atmospheric structure from L to T spectral types.