bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic and metabolomic profiling of aged pork loin chops reveals molecular phenotypes linked to pork tenderness
Authors: Johnson Logan G , Zhai Chaoyu , Prusa Kenneth J , Nair Mahesh N , Prenni Jessica E , Chaparro Jacqueline M , Huff-Lonergan Elisabeth , Lonergan Steven M 
Published: November 2024

Abstract
The ability to predict fresh pork tenderness and quality is hindered by an incomplete understanding of molecular factors that influence these complex traits. It is hypothesized that a comprehensive description of the metabolomic and proteomic phenotypes associated with variation in pork tenderness and quality will enhance the understanding and inform the development of rapid and nondestructive methods to measure pork quality. The objective of this investigation was to examine the proteomic and metabolomic profiles of ~2-wk aged pork chops categorized across instrumental tenderness groups. One hundred pork loin chops from a larger sample (N = 120) were assigned to one of the four categories (n = 25) based on instrumental star probe value (Category A, x¯ =4.23 kg, 3.43–4.55 kg; Category B, x¯ =4.79 kg, 4.66–5.00 kg; Category C, x¯ =5.43 kg, 5.20–5.64 kg; and Category D, x¯ =6.21 kg, 5.70–7.41 kg). Soluble protein from ~2 wk aged pork loin was prepared using a low-ionic-strength buffer. Proteins were digested with trypsin, labeled with 11-plex isobaric tandem mass tag reagents, and identified and quantified using a Q-Exactive Mass Spectrometer. Metabolites were extracted in 80% methanol from lyophilized and homogenized tissue samples. Derivatized metabolites were identified and quantified using gas chromatography-mass spectrometry. Between Categories A and D, 84 proteins and 22 metabolites were differentially abundant (adjusted P &lt; 0.05). Fewer differences were detected in comparison between categories with less divergent tenderness measures. The molecular phenotype of the more tender (Category A) aged chops is consistent with a slower and less extended pH decline and markedly less abundance of glycolytic metabolites. The presence and greater abundance of proteins in the low-ionic-strength extract, including desmin, filamin C, calsequestrin, and fumarate hydratase, indicates a greater disruption of sarcoplasmic reticulum and mitochondrial membranes and the degradation and release of structural proteins from the continuous connections of myofibrils and the sarcolemma.
A new Col1a1 conditional knock-in mouse model to study osteogenesis imperfecta
Authors: Dimori Milena , Toulany Mahtab , Sultana Lira Samia , Onal Melda , Thostenson Jeff D , Carroll John L , O’Brien Charles A , Morello Roy 
Published: November 2024

Abstract
Osteogenesis imperfecta (OI) constitutes a family of bone fragility disorders characterized by both genetic and clinical heterogeneity. Several different mouse models reproduce the classic features of OI, and the most commonly studied carry either a spontaneous or genetically induced pathogenic variant in the Col1a1 or Col1a2 gene. When OI is caused by primary alterations of type I collagen, it represents a systemic connective tissue disease that, in addition to the skeleton, also affects several extra-skeletal tissues and organs, such as skin, teeth, lung, heart, and others, where the altered type I collagen is also expressed. Currently, existing mouse models harbor a disease-causing genetic variant in all tissues and do not allow assessing the primary vs secondary consequences of the mutation on a specific organ/system. Here, we describe the generation of the first conditional knock-in allele for Col1a1 that can express a severe OI-causing glycine substitution (p.Gly1146Arg) in the triple helical region of α1(I) but only after Cre-driven recombination in the tissue of choice. We called this new dominant allele Col1a1G1146R-Floxed/+ and introduced it into the murine model. We describe its validation by crossing mice carrying this allele with EIIA-Cre expressing mice and showing that offspring with the recombined allele reproduce the classic features of a severe form of OI. The new mouse model will be useful to study the tissue-specific impact of this severe mutation on organs, such as the lung, the heart, and others.
The role of vitamin D metabolism in regulating bone turnover in adolescents with perinatally-acquired HIV in Southern Africa: a cross-sectional study in Zimbabwe and Zambia
Authors: Madanhire Tafadzwa , Ward Kate A , Macdougall Amy , Mohammed Nuredin , Filteau Suzanne , Kasonka Lackson , Mabuda Hilda B , Chisenga Molly , Tang Jonathan , Fraser William D , Bandason Tsitsi , Dzavakwa Nyasha V , Simms Victoria , Ferrand Rashida A , Gregson Celia L 
Published: November 2024

Abstract
Vitamin D dysregulation can occur in people living with HIV, disrupting calcium homeostasis, and bone turnover. We aimed to investigate the potential mechanisms by which vitamin D regulates bone turnover in adolescents living with perinatally-acquired HIV (ALWH) in Southern Africa. A pre-planned secondary analysis was performed of baseline data from the vitamin D for adolescents with HIV to reduce musculoskeletal morbidity and immunopathology trial (PACTR20200989766029) which enrolled ALWH (11–19 yr) taking antiretroviral therapy for ≥6 mo, and recorded socio-demographic, clinical and dietary data. After over-night fasting, vitamin D metabolites (25(OH)D, 1,25(OH)2D, and 24,25(OH)2D), intact parathyroid hormone (PTH), and bone turnover markers (BTMs) (C-terminal telopeptide of type I collagen (CTX) and procollagen type 1 N-terminal propeptide (P1NP)) were measured. Tandem Mass Spectrometry measured vitamin D metabolites, while intact PTH and BTMs were analyzed by electrochemiluminescence immunoassay. Stratified by 25(OH)D (&lt;75 vs ≥75 nmol/L), associations between standardized concentrations (β = standard deviations) of vitamin D metabolites, intact PTH and BTMs were assessed using structural equations modelling (SEM) adjusted for age, sex, and country (Zimbabwe/Zambia). Among the 842 ALWH enrolled, the median dietary calcium intake was 100 mg (IQR: 55–145). The SEM showed PTH was positively associated (β: 0.21; 95% CI, 0.1, 0.32) with 1,25(OH)2D, only when 25(OH)D was &lt;75 vs ≥75 nmol/L (β: 0.23; 95%CI, −0.13, 0.59), with evidence of an interaction (β: −0.11; 95%CI, −0.20, −0.02). A positive relationship between 25(OH)D and 24,25(OH)2D was seen irrespective of 25(OH)D concentration. 24,25(OH)2D was inversely related to BTMs, particularly when 25(OH)D was &lt;75 nmol/L (CTX: β: −0.15; 95% CI, −0.24, −0.06 and P1NP: β: −0.14; 95%CI, −0.22, −0.06). There was interaction between dietary calcium and 25(OH)D on PTH (β: −0.15; 95% CI, −0.22, −0.07) suggesting an interaction between low 25(OH)D and low dietary calcium which increases PTH. In conclusion, associations between 25(OH)D, PTH, 1,25(OH)2D, and BTMs in ALWH appear dependent upon 25(OH)D concentrations &lt;75 nmol/L and calcium intake. A novel, potentially causal pathway between 25(OH)D, 24,25(OH)2D, and BTMs was seen. Findings enhance understanding of vitamin D metabolism in people living with HIV.
Assessing the potential spread of Zaprionus tuberculatus (Diptera: Drosophilidae) in the Americas: insights for proactive management and agricultural protection
Authors: Viana José Pedro Cavalcante , Viana Matheus Cavalcante , Cavalcanti Fábio André Gomes Silva , Mateus Rogério Pincela , Bitner-Mathé Blanche Christine , Garcia Flávio Roberto Mello , Jobim Karina , Madi-Ravazzi Lilian , Rohde Claudia , Martins Marlucia Bonifácio , Tidon Rosana 
Published: November 2024

Abstract
Invasive species pose significant ecological and economic threats globally. Zaprionus tuberculatus Malloch, a drosophilid fruit fly native to the Afrotropical region and Indian Ocean islands, is included in the pest list of the Center for Agriculture and Bioscience (CABI) because it uses fruit as breeding sites and can damage cultivated areas. This fly species extended its range across Europe in the late 20th century; in 2020, it was recorded in South America, and currently, it is widely distributed in Brazil. Here, we assess the potential spreading of Zaprionus tuberculatus in Central and North America based on 2 distinct origins of propagules: from South America and from Europe. To this end, we developed species distribution models using bioclimatic variables and elevation data to project potentially suitable habitats and infer invasion routes. In any case, our results indicate suitability for Z. tuberculatus colonization in Central and North America, including major fruit-producing areas in Central American countries and the United States (Florida and California). The rapid dispersal ability of Z. tuberculatus, coupled with its adaptability to diverse environments, underscores the urgency for proactive monitoring and control measures. Therefore, this study provides valuable insights for developing proactive measures to mitigate the spread of Z. tuberculatus and protect agricultural productivity in the Americas.
Direct and indirect effects of selective insecticides on 2 generalist predators of Bemisia tabaci (Hemiptera: Aleyrodidae)
Authors: Parkins Albertha J , Kheirodin Arash , Perier Jermaine D , Cremonez Paulo S G , Riley David G , Simmons Alvin M , Schmidt Jason M 
Published: November 2024

Abstract
Generalist arthropod predators have historically contributed to the suppression of arthropod pests in many agroecosystems. The successful implementation of integrated pest management (IPM) programs hinges on the incorporation of insecticides that are compatible with the biological attributes of natural enemies of pests. A potentially promising pathway is improving biological control by natural enemies through the timely application of selective insecticides. In our study, adult predators were exposed to commercially available insecticides (cyantraniliprole and pyriproxyfen) using a combined laboratory and field approach to assess their effects on survivorship and predation. We isolated 2 predators, Hippodamia convergens Guérin-Méneville and Geocoris punctipes (Say), in the laboratory to estimate the survivorship and consumption of whitefly nymphs, Bemisia tabaci (Gennadius). In the field, we deployed whitefly nymph-infested potted cotton plants in replicated cotton plots with both insecticide treatments. We enumerated whitefly nymph populations on enclosed (predator-exclusion) and open (predator-accessible) potted plants. While pyriproxyfen had a negligible effect on the predators, cyantraniliprole exposure directly affected H. convergence by reducing survivorship duration and indirectly influenced both predators by reducing prey consumption and altering the consumption of alternative prey. In field conditions, regardless of pesticide exposure, whitefly-infested potted plants that excluded predators had more whiteflies than predator-accessible potted plants. Overall, pyriproxyfen demonstrated minimal impact on the predators in the laboratory or field, while cyantraniliprole adversely influenced mortality and indirect foraging under controlled laboratory conditions but did not have a significant impact in the field.
Population records reveal expanded habitat preference for the endemic, predaceous Jamaican fungus gnat Neoditomyia farri (Diptera, Keroplatidae)
Authors: Stewart Ronald S , Kouwenberg Silvia , Pauel Johannes , Stellwagen Sarah 
Published: November 2024

Abstract
The predaceous fly Neoditomyia farri Coher is currently regarded as having an unknown population distribution in Jamaica. The larvae are known for their production of sticky “fishing lines” that are covered in adhesive droplets for prey capture and hang down from cave walls and ceilings. Published research beyond early observational records of the species is limited to one site—Dromilly Cave in the parish of Trelawny. The Jamaican Caves Organisation has observed larvae of the species at 26 caves visited over the last 2 decades and compiled a database with details of approximate numbers, internal and external environmental conditions, and accurate positions. Based on these records, we present evidence that the species is not cave obligate and describe factors that may suggest potential additional sites where the species can be found. Taken together, our observations paint a picture of a species which is ubiquitous and not under discernible threat, making it an excellent candidate for further research on its unique life history and behavior, which remain poorly understood.
Challenges in the Vespertilionidae phylogeny: resolving Pipistrellus nathusii placement and affirming generic status for Asian pipistrelles
Authors: Dool Serena E , Puechmaille Sébastien J 
Published: November 2024

Abstract
Vespertilionidae is a species-rich family of bats that experienced rapid diversification events and contains many morphologically conserved taxa, resulting in challenges to taxonomic and phylogenetic resolution for members of this family. One example of a challenging group is the pipistrelles, which several studies have recovered as paraphyletic. Pipistrellus nathusii is noteworthy for being recovered either as sister to other European Pipistrellus species, more closely related to Nyctalus, or sister to the clade comprising Nyctalus and European Pipistrellus species. Using a core data set of 6 nuclear introns, and an extended data set of 10 nuclear introns, we employ multiple independent phylogenetic methods that are robust in the presence of incomplete lineage sorting or hybridization to resolve the placement of P. nathusii. In addition, our data confirm the distinction of the Asian Pipistrelle taxa which form a distinct genus sister to the clade comprising Vansonia, Pipistrellus, and Nyctalus.
Elevated risk of lung cancer among Asian American women who have never smoked: an emerging cancer disparity
Authors: Gomez Scarlett Lin , DeRouen Mindy , Chen Jr Moon S , Wakelee Heather , Velotta Jeffrey B , Sakoda Lori C , Shariff-Marco Salma , Reynolds Peggy , Cheng Iona 
Published: November 2024

Abstract
Lung cancer is a leading cause of cancer mortality for most ethnic groups of Asian American women, including Chinese, Korean, Japanese, and Vietnamese Americans, a striking pattern given the exceedingly low prevalence of smoking among Asian American women in the general population. Recent research demonstrates that among Asian American women with a lung cancer diagnosis, the vast majority of patients have never smoked, a rate as high as 80% among Chinese and Asian Indian American women. Despite declining rates in lung cancer overall in the United States, rates among Asian American women who have never smoked appear to be increasing. This commentary articulates extant knowledge, based on studies in Asia, of a range of risk factors, such as a family history of lung cancer; a history of lung diseases, including tuberculosis and chronic obstructive pulmonary disease; exposure to cooking fumes and second-hand smoke; and various putative risk factors. Unique mutational profiles at the tumor level, including a higher prevalence of EGFR variations among Asian populations, highlight the importance of tumor genomic testing of newly diagnosed patients. Additional research is essential, given the high burden of disease among Asian American women who have never smoked and the limited knowledge regarding contributing risk factors specific to Asian American women, because the risk factors identified in Asian people living in Asia may not apply.
Potential of the pharmacological inhibition of CCL2-CCR2 axis via targeting FROUNT to prevent the initiation and the progression of intracranial aneurysms in rats
Authors: Ono Isao , Itani Masahiko , Okada Akihiro , Kawashima Akitsugu , Toda Etsuko , Arakawa Yoshiki , Terashima Yuya , Aoki Tomohiro 
Published: November 2024

Abstract
Intracranial aneurysms (IAs) affect 1%-5% of the public and are a major cause of subarachnoid hemorrhage. Currently, there is no medical treatment to prevent the progression or rupture of IAs. Recent studies have defined IA as a chronic inflammatory disease in which macrophages infiltrate intracranial arteries via the CCL2-CCR2 axis. The chemokine signal regulator FROUNT mediates this axis, and it can be inhibited by the anti-alcoholism drug disulfiram. Therefore, inhibition of macrophage infiltration by interfering with FROUNT using disulfiram may represent a strategy to prevent exacerbation of IAs. Here, effects of disulfiram were investigated in vitro and in an animal model of IAs. FROUNT expression was observed on infiltrated macrophages both in human IAs and in the rat IA model by immunohistochemistry. In vitro treatment with disulfiram suppressed CCL2-mediated migration of cultured rat macrophages in a transwell system. Disulfiram administered in a rat model of IAs inhibited both the initiation and the enlargement of IAs in a dose-dependent manner; this was accompanied by suppression of macrophage infiltration. These results suggest that pharmacological inhibition of the CCL2-CCR2-FROUNT signaling cascade could be a treatment of patients with IAs.
Use model averaging instead of model selection in pulsar timing
Authors: van Haasteren Rutger 
Published: November 2024

ABSTRACT
Over the past decade and a half, adoption of Bayesian inference in pulsar timing analysis has led to increasingly sophisticated models. The recent announcement of evidence for a stochastic background of gravitational waves by various pulsar timing array (PTA) projects highlighted Bayesian inference as a central tool for parameter estimation and model selection. Despite its success, Bayesian inference is occasionally misused in the pulsar timing community. A common workflow is that the data is analysed in multiple steps: a first analysis of single pulsars individually, and a subsequent analysis of the whole array of pulsars. A mistake that is then sometimes introduced stems from using the posterior distribution to craft the prior for the analysis of the same data in a second step, a practice referred to in the statistics literature as ‘circular analysis’. This is done to prune the model for computational efficiency. Multiple recent high-profile searches for gravitational waves by PTA projects have this workflow. This letter highlights this error and suggests that Spike and Slab priors can be used to carry out model averaging instead of model selection in a single pass. Spike and Slab priors are proved to be equal to log-uniform priors.
Linking the transcriptome to physiology: response of the proteome of Cupriavidus metallidurans to changing metal availability
Authors: Galea Diana , Herzberg Martin , Dobritzsch Dirk , Fuszard Matt , Nies Dietrich H 
Published: November 2024

Abstract
Cupriavidus metallidurans CH34 is a metal-resistant bacterium. Its metal homeostasis is based on a flow equilibrium of metal ion uptake and efflux reactions, which adapts to changing metal concentrations within an hour. At high metal concentrations, upregulation of the genes for metal efflux systems occurs within minutes. Here, we investigate the changes in the bacterial proteome accompanying these genetic and physiological events after 1.5 cell duplications, which took 3 h. To that end, C. metallidurans CH34 and its plasmid-free derivative, AE104, either were challenged with a toxic metal mix or were cultivated under metal-starvation conditions, followed by bottom-up proteomics. When metal-shocked or -starved cells were compared with their respective controls, 3540 proteins changed in abundance, with 76% appearing in one, but not the other, condition; the remaining 24% were up- or downregulated. Metal-shocked C. metallidurans strains had adjusted their proteomes to combat metal stress. The most prominent polypeptides were the products of the plasmid-encoded metal-resistance determinants in strain CH34, particularly the CzcCBA transenvelope efflux system. Moreover, the influence of antisense transcripts on the proteome was also revealed. In one specific example, the impact of an asRNA on the abundance of gene products could be demonstrated and this yielded new insights into the function of the transmembrane efflux complex ZniCBA under conditions of metal starvation.
Mercury records from natural archives reveal ecosystem responses to changing atmospheric deposition
Authors: Chen Qinqin , Wu Qingru , Cui Yuying , Wang Shuxiao 
Published: November 2024

ABSTRACT
Global ecosystems face mercury contamination, yet long-term data are scarce, hindering understanding of ecosystem responses to atmospheric Hg input changes. To bridge the data gap and assess ecosystem responses, we compiled and compared a mercury accumulation database from peat, lake, ice and marine deposits worldwide with atmospheric mercury deposition modelled by GEOS-Chem, focusing on trends, magnitudes, spatial–temporal distributions and impact factors. The mercury fluxes in all four deposits showed a 5- to 9-fold increase over 1700–2012, with lake and peat mercury fluxes that generally mirrored atmospheric deposition trends. Significant decreases in lake and peat mercury fluxes post-1950 in Europe evidenced effective environmental policies, whereas rises in East Asia, Africa and Oceania highlighted coal-use impacts, inter alia. Conversely, mercury fluxes in marine and high-altitude ecosystems did not align well with atmospheric deposition, emphasizing natural influences over anthropogenic impacts. Our study underscores the importance of these key regions and ecosystems for future mercury management.
Development of a City-wide Rapid Antiretroviral Therapy Initiation Toolkit for People Newly Diagnosed With HIV in the Southern United States
Authors: Pettit A C , Ahonkhai A A , Pierce L , Rebeiro P F , Valdebenito C M , Woods J , Gregory L , Walton C , Nash R , Summers N A , Van Wylen A , Thompson D , Hayes-Winton M , Eke A , Pichon L C , Audet C M 
Published: November 2024

Abstract

Background
Rapid antiretroviral therapy (ART) initiation, in which individuals with HIV start treatment within days of diagnosis, is a key component of the United States (US) Ending the HIV Epidemic initiative. The Memphis Metropolitan Statistical Area ranks second in the US for HIV incidence, yet only ∼60% of individuals link to treatment within 1 month of diagnosis. This study aimed to identify barriers and strategies for implementing rapid ART initiation in Memphis.

Methods
From August to December 2022, we conducted process mapping guided by the Consolidated Framework for Implementation Research to outline the steps from 3 HIV testing sites to ART prescription at 3 Ryan White-funded clinics in Memphis, Tennessee. We used modified conjoint analyses to prioritize barriers and identify strategies for improving rapid ART implementation, focusing on the importance and feasibility of changes.

Findings
Prioritized barriers included intersectional stigma and a lack of access to centralized information about the rapid ART program, branding and logo development, inter- and intra-organizational networking and communication, testing and treatment resources (HIV testing kits and ART starter packs), rapid ART knowledge, and organizational champions. Strategies to address these barriers were compiled into a local rapid ART toolkit.

Conclusions
We identified modifiable systemic barriers to rapid ART initiation in Memphis, a community disproportionately affected by HIV. The strategies developed to address these barriers informed the creation of a locally relevant rapid ART toolkit for future evaluation. These methods could be applied in other high-burden areas seeking to develop local rapid ART models.