bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taking stock of selective logging in the Andaman Islands, India: recent & legacy effects of timber extraction, assisted natural regeneration and a revamped working plan
Authors: Surendra Akshay , Sridhar Vanjulavalli , Osuri Anand M. , Ratnam Jayashree 
Published: June 2024

ABSTRACTForest management is an evolving balance between biodiversity conservation and economic needs. A shift in Andaman Islands’ Working Plan mandate in 2000s reflects this evolution. Our study independently assesses the impact of said policy change on post-logging recovery of forests in Baratang and Middle Andaman.In 2017-18, we placed seventy-six 0.49ha plots across evergreen and deciduous patches and compared large-tree (≥180cm girth) density and diversity across forests that were logged after 2005 focussing on sustainability, logged in 1990s focussing on timber, logged twice in 1990s and after 2005, and unlogged forests. We assessed forest regeneration in thirty 0.01ha plots along a coupe road within forests logged after 2005.Forests logged after 2005 had similar density of large trees as forests logged in 1990s (despite having 1/3rdthe recovery time), indicating reduced offtake or better recruitment. Along the unlogged—once-logged—twice-logged gradient, the dominance ofPterocarpus dalbergioidesin deciduous patches decreased while the dominance ofDiptercarpus sp.in evergreen patches increased. Compared to natural regeneration, proportionately more deciduous saplings were planted in both evergreen and deciduous patches.The new working plan maintains timber stock but not diversity. We make six simple recommendations to better align practice with the Working Plan mandate.SynthesisPost-2005 timber extraction policy in the Andaman Islands is partially successful but long-term forest health, in line with the working plan mandate, requires (1) lower timber offtake from deciduous patches and (2) targeted assisted regeneration of non-timber tree species.
Aquatic plant mycobiomes change with watershed urbanization
Authors: Mora Jacob , Olson Matt , Rocks Sara S. , Zahn Geoffrey 
Published: June 2024

AbstractUrban expansion, projected to triple globally from 2000 to 2030, significantly impacts biodiversity and ecosystem processes, including those of microbial communities. While extensive research has examined urbanization effects on macro-organisms, the impacts on microbial communities, particularly those associated with aquatic plants, remain underexplored. This study investigates the fungal endophyte communities in the pollution-tolerant aquatic plant Ranunculus aquatilis along an urbanization gradient in the Provo River, Utah, USA, a rapidly urbanizing region. We collected plant and adjacent water samples from ten locations along the river, spanning from rural to urbanized areas, and conducted DNA amplicon sequencing to characterize fungal community composition.Our results show a significant decline in fungal alpha diversity downstream, correlated with increased urbanization metrics such as impervious surface area and developed land cover. Specifically, fungal ASV richness and Shannon diversity decreased as urbanization intensified, driven primarily by a reduction in rare taxa. Despite a stable core microbiome dominated by a few taxa, the overall community structure varied significantly along the urban gradient, with notable shifts in dominant fungal taxa. Contrary to expectations, no detectable levels of heavy metals were found in water samples, suggesting that other urbanization-related factors, potentially including organic pollutants or plant stress responses, influence fungal endophyte communities.Our findings underscore the need for further investigation into the mechanisms driving these patterns, particularly the roles of organic pollution, nutrient loads, and plant stress. Understanding these interactions is crucial for predicting the impacts of continued urbanization on freshwater ecosystems and their associated microbial communities.
Why didn’t the nudibranch cross the ocean? Understanding biogeographic and evolutionary relationships ofHermissenda(Nudibranchia: Myrrhinidae) Bergh, 1878
Authors: Montana Katherine O. , Gosliner Terrence M. , Crews Sarah C. , Bonomo Lynn J. , Carlton James T. , Johnson Rebecca F. 
Published: June 2024

AbstractIn the aftermath of the 2011 east Japanese earthquake and tsunami, anthropogenic debris from the east coast of Japan floated across the Pacific Ocean to the west coast of North America. One such vessel from Iwate Prefecture arrived on the coast of Oregon, and the fouling community included specimens identified as the nudibranchHermissenda crassicornis, which was previously thought to range from Japan to Baja California but has since been split into three species:H. crassicornis(Alaska to southern CA),H. opalescens(British Columbia to Baja California), andH. emurai(Japan, Korea, Russian Far East). Previous work suggested that all of the motile invertebrates found in the tsunami debris fouling community were either pelagic or Japanese in origin. Our study sought to determine whether the nudibranch specimens collected from the Iwate vessel were, according to the new classification system, onlyH. emuraior whether the Eastern PacificHermissendawere present as well. Results from DNA sequencing and morphological analysis suggest that specimens ofH. crassicornis, as it is currently recognized, andH. opalescenswere found on the vessel.This finding indicates either that these species settled after arrival to the west coast of North America or thatH. crassicornisandH. opalescensis found in Japan, suggestingHermissendaranges need to be investigated further.Occurrence data shared on the iNaturalist platform were also used to assess current ranges. Our phylogenetic tree and haplotype network constructed from COI data from allHermissendaspecies indicate thatH. opalescensandH. emuraiare most closely related withH. opalescenssister to the clade that containsH. opalescensandH. emurai. This study demonstrates the power of combining volunteer naturalist data with lab-collected data to understand evolutionary relationships, species ranges, and biogeography.
Milk Fat Globule Membrane-Containing Protein Powder Promotes Fitness inCaenorhabditis elegans
Authors: Pitkänen Miina , Matilainen Olli 
Published: June 2024

AbstractMilk-derived peptides and milk fat globule membrane (MFGM) have gained interest as health-promoting food ingredients. However, the mechanisms by which these nutraceuticals modulate the function of biological systems often remain unclear. We utilizedCaenorhabditis elegansto elucidate how milk-derived Protein powders rich in MFGM, previously used in a clinical trial, affect the physiology of this model organism. Our results demonstrate that Protein powders do not affect lifespan but promote the fitness of the animals. Surprisingly, gene expression analysis revealed that Protein powders decrease the expression of genes functioning on innate immunity, which also translates into reduced survival on pathogenic bacteria. One of the innate immunity-associated genes showing reduced expression upon Protein powder supplementation iscpr-3, the homolog of human cathepsin B. Interestingly, knockdown ofcpr-3enhances fitness, but not in Protein powder-treated animals, suggesting that protein powders contribute to fitness by downregulating the expression of this gene. In summary, this research highlights the value ofC. elegansin testing the biological activity of food supplements and nutraceuticals. Furthermore, this study should encourage investigations into whether milk-derived peptides and MFGM mediate their beneficial effects through the modulation of cathepsin B expression in humans.
Hotwiring integrin endocytosis acutely modulates cell interactions
Authors: Kamboj Sahil , Boché Alphonse , Moret Anneline , Wang Zixu , Aimé Carole , Agniel Rémy , Leroy-Dudal Johanne , Carreiras Franck , Gallet Olivier , Royle Stephen J , Lambert Ambroise 
Published: June 2024

AbstractIntegrins are heterodimeric cell surface receptors that govern cell-cell interactions, which in turn can influence multiscale processes: cell migration, extracellular matrix remodeling and tissue formation. These processes occur over timescales which range from milliseconds to days. While various strategies exist to study integrin function across biological scales from cell to tissue, they are often chronic and fail to target specific cell-cell interactions acutely. We engineered cells to rapidly alter cell behavior by downregulating the surface population of α5β1 integrins through hot-wired clathrin-mediated endocytosis. This method allows for inducible, specific internalization of α5β1 integrins, achieving acute downregulation across various cell lines in 5-30 minutes. We show that induced internalization of α5β1 decreases the cell area, causes uptake of extracellular fibronectin, and decreases the rate of tumor spheroid compaction. This targeted control of multiscale processes by rapid downregulation of this important class of cell surface receptors demonstrates that hot-wired endocytosis is a useful tool to acutely modulate cell biology.
Instead of seeing it as a health care issue, you see it as you:Reasons for alcohol use, consequences of use, and barriers to help seeking among fathers in Kenya
Authors: Giusto Ali , Satinsky Emily N. , Jaguga Florence , Rono Wilter , Barasa Julius , Galán Chardée A. , Wainberg Milton L. 
Published: June 2024

AbstractIntroductionFather alcohol use negatively impacts family systems, yet research in this area is scarce in low- and middle-income countries like Kenya. An understanding of why fathers drink, consequences of alcohol use, and barriers to care is needed to refine and adapt clinical and implementation approaches to treating fathers.MethodsCommunity members, leaders, mental health providers, and fathers experiencing alcohol use problems in Eldoret, Kenya were recruited to participate in semi-structured qualitative interviews and focus groups. Participants were asked about why fathers engage in alcohol use, potential impacts of use, and barriers to accessing care. The frame method was employed to analyze the data. The study team read transcripts, iteratively memo-ed and discussed notes, developed a codebook, and coded transcripts. Broad codes were summarized and reviewed alongside transcripts.ResultsParticipants noted reasons for and consequences of fathers’ drinking at individual, family and interpersonal, and sociocultural levels. At the individual level, alcohol use facilitated an escape from mental distress and acted as a means to cope with “idleness” due to unemployment. Consequences included poor physical and mental health, such as depression. At the family/interpersonal level, fathers used alcohol to distract themselves from family conflicts. Consequences included violence and poor child outcomes. Gender and drinking norms were drivers at the sociocultural level. Consequences at this level included stigmatization and loss of social status, which can drive shame and isolation. Salient barriers to care included fathers’ lack of awareness of their alcohol use problem, limited-service access, and social stigma.ConclusionsFather motivations for drinking are influenced by multiple ecological levels, and drinking has a cascade of consequences on the family. These effects are worsened by barriers to care. Intervention and implementation strategies should consider masculinity norms, resources, and avoidant coping motivations in adaptation.
Diagnosis of the Beninese Health System: Progress, and Challenges for an Effective, Resilient, and Sustainable System
Authors: Nahini Amboise Tchando , Baranon Mouhamadou Djima , Sambieni Emmanuel N’Koé , Sanni Mouftaou Amadou 
Published: June 2024

AbstractThis work involved diagnosing the Beninese health system based on secondary data from several sources (statistical directories, surveys, censuses, and study reports). The descriptive analysis of the evolution of health indicators in Benin between 2002 and 2021 and in-depth interviews with resource people in the health sector made it possible to assess the efforts and progress made by those in power and system stakeholders. There have been many tangible efforts to improve accessibility to health services (the rates of health coverage and attendance at health facilities have increased from 86% to 96% and from 35% to 56% between 2002 and 2021). These efforts have significantly reduced morbidity and mortality rates. The results also indicate a drop in deaths due to malaria (141 deaths to 86 per 100,000 inhabitants between 2003 and 2021) and a drop in the prevalence of HIV AIDS up to 0.8% from 2019 ahead of several countries—neighbors of the sub-region. Early neonatal mortality fell from 10.1‰ to 4.7‰ as well as deaths of children under 5 years old, thus improving life expectancy at birth from 59.6 years in 2002 to 63.8 years in 2013. Despite these efforts, many challenges remain, adding to the strong demographic growth in the country, which clearly expresses the threats weighing on the daily state of health of the Beninese population and calling for a new way of thinking for a sustainable health system. The study ends with the prioritization of challenges and a proposal for strategies to have an efficient and resilient health system, capable of producing quality, healthy, and productive human capital.
Activity and function of the endothelial sodium channel is regulated by the effector domain of MARCKS like protein 1 in mouse aortic endothelial cells
Authors: Yu Ling , Bala Niharika , Nguyen Van-Anh L. , Kessler Leah , LaDisa John F. , Alli Abdel A. 
Published: June 2024

AbstractThe endothelial sodium channel (EnNaC) plays an important role in regulating vessel stiffness. Here, we investigated the regulation of EnNaC in mouse aortic endothelial cells (mAoEC) by the actin cytoskeleton and lipid raft association protein myristoylated alanine-rich C-kinase substrate like protein 1 (MLP1). We hypothesized that mutation of specific amino acid residues within the effector domain of MLP1 or loss of association between MLP1 and the anionic phospholipid phosphate PIP2 would significantly alter membrane association and EnNaC activity in mAoEC. mAoEC transiently transfected with a mutant MLP1 construct (three serine residues in the effector domain replaced with aspartate residues) showed a significant decrease in EnNaC activity compared to cells transfected with wildtype MLP1. Compared to vehicle treatment, mAoEC treated with the PIP2 synthesis blocker wortmannin showed less colocalization of EnNaC and MLP1. In other experiments, Western blot and densitometric analysis showed a significant decrease in MLP1 and caveloin-1 protein expression in mAoEC treated with wortmannin compared to vehicle. Finally, wortmannin treatment decreased sphingomyelin content and increased membrane fluidity in mAoEC. Taken together, our results suggest constitutive phosphorylation of MLP1 attenuates the function of EnNaC in aortic endothelial cells by a mechanism involving a decrease in association with MLP1 and EnNaC at the membrane, while deletion of PIP2 decreases MARCKS expression and overall membrane fluidity.
Scalable intracellular delivery via microfluidic vortex shedding enhances the function of chimeric antigen receptor T-cells
Authors: Sytsma Brandon J. , Allain Vincent , Bourke Struan , Faizee Fairuz , Fathi Mohsen , Berdeaux Rebecca , Ferreira Leonardo M.R. , Brewer W. Jared , Li Lian , Pan Fong L. , Rothrock Allison G. , Nyberg William A. , Li Zhongmei , Wilson Leah H. , Eyquem Justin , Pawell Ryan S. 
Published: June 2024

ABSTRACTAdoptive chimeric antigen receptor T-cell (CAR-T) therapy is transformative and approved for hematologic malignancies. It is also being developed for the treatment of solid tumors, autoimmune disorders, heart disease, and aging. Despite unprecedented clinical outcomes, CAR-T and other engineered cell therapies face a variety of manufacturing and safety challenges. Traditional methods, such as lentivirus transduction and electroporation, result in random integration or cause significant cellular damage, which can limit the safety and efficacy of engineered cell therapies. We present hydroporation as a gentle and effective alternative for intracellular delivery. Hydroporation resulted in 1.7- to 2-fold higher CAR-T yields compared to electroporation with superior cell viability and recovery. Hydroporated cells exhibited rapid proliferation, robust target cell lysis, and increased pro-inflammatory and regulatory cytokine secretion in addition to improved CAR-T yield by day 5 post-transfection. We demonstrate that scaled-up hydroporation can process 5 × 108cells in less than 10 s, showcasing the platform as a viable solution for high-yield CAR-T manufacturing with the potential for improved therapeutic outcomes.
Left-Right Brain-Wide Asymmetry of Neuroanatomy in the Mouse Brain
Authors: Silberfeld Andrew , Roe James M. , Ellegood Jacob , Lerch Jason P. , Qiu Lily , Kim Yongsoo , Lee Jong Gwan , Hopkins William D. , Grandjean Joanes , Ou Yangming , Pourquié Olivier 
Published: June 2024

AbstractLeft-right asymmetry of the human brain is widespread through its anatomy and function. However, limited microscopic understanding of it exists, particularly for anatomical asymmetry where there are few well-established animal models. In humans, most brain regions show subtle, population-average regional asymmetries in thickness or surface area, alongside a macro-scale twisting called the cerebral petalia in which the right hemisphere protrudes anteriorly past the left. Here, we ask whether neuroanatomical asymmetries can be observed in mice, leveraging 6 mouse neuroimaging cohorts from 5 different research groups (∼3,500 animals). We found an anterior-posterior pattern of volume asymmetry with anterior regions larger on the right and posterior regions larger on the left. This pattern appears driven by similar trends in surface area and positional asymmetries, with the results together indicating a small brain-wide twisting pattern, similar to the human cerebral petalia. Furthermore, the results show no apparent relationship to known functional asymmetries in mice, emphasizing the complexity of the structure-function relationship in brain asymmetry. By establishing a signature of anatomical brain asymmetry in mice, we aim to provide a foundation for future studies to probe the mechanistic underpinnings of brain asymmetry seen in humans – a feature of the brain with extremely limited understanding.Significance StatementThe human brain shows significant left-right anatomical asymmetry. Understanding its microscopic basis has implications for studies of autism and schizophrenia, evolution, embryonic brain development, and the relationship between structure and function in the brain. One of the biggest challenges to understanding this aspect of the brain is that animal models are limited. Here we show a brain-wide twisting pattern of asymmetry in the mouse brain using over 3,500 animals from six independent cohorts. These findings provide a basis for using mice to interrogate the microscopic underpinnings of anatomical asymmetry in humans and a roadmap for exploring anatomical asymmetry in additional species.
Shallow sequencing (Shall-seq) procedure: A method for determining the genetic lineages and detecting antimicrobial resistance genes of antimicrobial-resistant bacteria using minimum Nanopore sequencing data
Authors: Yagi Nobuyoshi , Miyagi Nanase , Uechi Ayumi , Hirai Itaru 
Published: June 2024

AbstractAntimicrobial-resistant bacteria could cause nosocomial infections and outbreaks in healthcare facilities. Phylogenetic analyses based on whole-genome sequencing (WGS) could become the gold-standard method for understanding the route of antimicrobial-resistant bacterial spreading. However, generally, the WGS needs to analyze much amount of data. Therefore, sufficient resources such as budget and data analysis system are needed and it is a burden for introduction of the WGS in the routine clinical examination of pathogenic bacterial isolates. In this study, we usedEscherichia colias a model and evaluated whether determination of the genetic background and detection of antimicrobial-resistance genes of 29E. coliclinical isolates were achieved by searching databases using sequence reads output by the Nanopore sequencer as the search keys. Consequently, only 66.2 MB data was sufficient to search for a genome sequence with ≥90% range of coverage rate. Importantly, AMR genes and plasmid replicon types were also detected with minimum data, and the detected AMR genes and phenotypes of theE. coliisolates did not present any discrepancy. Taken together, this shallow sequencing (Shall-seq) procedure consists of “shallow of coverage” sequencing using the Nanopore sequencer and data search using minimum data could be used to analyze bacterial isolates cost-effectively.
Increased Neonatal Deaths in Texas After SB8, a Cardiac Activity-Based Abortion Ban
Authors: Faust Jeremy Samuel , Chen Ji , Renton Benjamin , Otugo Onyekachi , Chen Alexander Junxiang , Yaver Miranda , Lin Zhenqiu , Rasmussen Sonja A. , Krumholz Harlan M. 
Published: June 2024

AbstractIntroductionOn September 1, 2021, Texas enacted Senate Bill 8 (SB8), a law banning abortions after the detection of fetal heart activity, without exceptions for early detectable fetal abnormalities with low survival probability. The effect on neonatal mortality is unknown.MethodsWe deployed difference-in-differences (primary analysis), and Joinpoint and seasonal autoregressive moving integrated averages (sensitivity analyses) to determine whether all-cause mortality among Texas neonates increased after SB8 was enacted, and compared the findings to states with permissive abortion laws. Changes in mortality due to congenital malformations, deformations and chromosomal abnormalities were also measured.ResultsCompared with states where abortion remained legal, approximately 177 all-cause excess neonatal deaths (2.3 per 10,000 births, interaction p<0.003) occurred in Texas. A sensitivity analysis using Joinpoint logistic regression spontaneously identified a mortality trend change in Texas coinciding with SB8 enactment. Approximately 113 excess deaths (1.5 per 10,000 births, interaction p<0.001) due to congenital malformations, deformations and chromosomal abnormalities occurred among Texas neonates after SB8 enactment. Compared to expected deaths based on prior internal trends (sARIMA), Texas recorded 289 (95% CI 18-559) excess neonatal deaths (3.7 per 10,000 births; 95% CI 0.2-7.2) in 2022-2023. A preliminary analysis of post-SB8 shares of neonates listed as “not alive” on birth certificates by race/ethnicity found increased relative contributions from non-Hispanic White and Hispanic populations.ConclusionTexas SB8 was responsible for between 177-289 excess neonatal deaths from Quarter 4, 2021-Quarter 4, 2023. These results suggest that if other SB8-like abortion bans are enacted, increases in neonatal mortality may occur elsewhere.