bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcranial magnetic stimulation of dorsomedial prefrontal cortex for cocaine use disorder: A pilot study
Authors: Webber Heather E. , Hong L. Elliot , Quevedo João , Weaver Michael F. , Schmitz Joy M. , Lane Scott D. 
Published: September 2024

AbstractCocaine use disorder (CUD) is a difficult-to-treat condition with no FDA-approved medications. Recent work has turned to brain stimulation methods to help rectify hypofrontality and dopamine reward system changes often observed in individuals with CUD. Preliminary studies using transcranial magnetic stimulation (TMS) have demonstrated promising results, but there is room for optimization of the stimulation site, stimulation pattern, and identification of relevant biomarkers of TMS effects. The current pilot study aimed to test the feasibility, safety, and preliminary effects of a double-blind, sham-controlled, cross-over, acute design using intermittent theta burst stimulation to dorsomedial prefrontal cortex (dmPFC) on electroencephalogram (EEG) as intermediate outcome assessment in CUD patients. This small pilot enrolled five individuals with moderate-to-severe CUD for feasibility and proof-of-concept. Participants completed safety, psychometric, and EEG measures before and after receiving two sessions of active or sham TMS to dmPFC on two separate days. All five participants completed all the study tasks and found the TMS to be tolerable. The side effects were minimal and consistent with an acute TMS design. Visible changes were observed in the electrical activity of the brain during a monetary guessing task, while minimal changes in psychometric measures were observed. These results indicate the feasibility and safety of the current approach and suggest that dmPFC is a viable target for treating CUD. Future work should expand upon these findings in a randomized controlled clinical trial.
Integrative modeling in the age of machine learning: a summary of HADDOCK strategies in CAPRI rounds 47-55
Authors: Reys Victor , Giulini Marco , Cojocaru Vlad , Engel Anna , Xu Xiaotong , Roel-Touris Jorge , Geng Cunliang , Ambrosetti Francesco , Jiménez-García Brian , Jandova Zuzana , Koukos Panagiotis I. , van Noort Charlotte , Teixeira Joao M. C. , van Keulen Siri C. , Réau Manon , Honorato Rodrigo V. , Bonvin Alexandre M.J.J. 
Published: September 2024

AbstractThe HADDOCK team participated in CAPRI rounds 47-55 as both server, manual predictor, and scorers. Throughout these CAPRI rounds, we used a plethora of computational strategies to predict the structure of protein complexes. Of the 10 targets comprising 24 interfaces, we achieved acceptable or better models for 3 targets in the human category and 1 in the server category. Our performance in the scoring challenge was slightly better, with our simple scoring protocol being the only one capable of identifying an acceptable model for Target 234. This result highlights the robustness of the simple, fully physics-based HADDOCK scoring function, especially when applied to highly flexible antibody-antigen complexes. Inspired by the significant advances in machine learning for structural biology and the dramatic improvement in our success rates after the public release of Alphafold2, we identify the integration of classical approaches like HADDOCK with AI-driven structure prediction methods as a key strategy for improving the accuracy of model generation and scoring.
Mechanical Profiling of Biopolymer Condensates through Acoustic Trapping
Authors: Nakajima Kichitaro , Sneideris Tomas , Good Lydia L. , Erkamp Nadia A. , Ogi Hirotsugu , Knowles Tuomas P. J. 
Published: September 2024

AbstractCharacterizing the mechanical properties of single colloids is a central problem in soft matter physics. It also plays a key role in cell biology through biopolymer condensates, which function as membraneless compartments. Such systems can also malfunction, leading to the onset of a number of diseases, including many neurodegenerative diseases; the functional and pathological condensates are commonly differentiated by their mechanical signature. Probing the mechanical properties of biopolymer condensates at the single particle level has, however, remained challenging. In this study, we demonstrate that acoustic trapping can be used to profile the mechanical properties of single condensates in a contactless manner. We find that acoustic fields exert the acoustic radiation force on condensates, leading to their migration to a trapping point where acoustic potential energy is minimized. Furthermore, our results show that the Brownian motion fluctuation of condensates in an acoustic potential well is an accurate probe for their bulk modulus. We demonstrate that this framework can detect the change in the bulk modulus of polyadenylic acid condensates in response to changes in environmental conditions. Our results show that acoustic trapping opens up a novel path to profile the mechanical properties of soft colloids at the single particle level in a non-invasive manner with applications in biology, materials science, and beyond.
Most Beefalo cattle have no detectable bison genetic ancestry
Authors: Shapiro Beth , Oppenheimer Jonas , Heaton Michael P , Kuhn Kristen L , Green Richard E , Blackburn Harvey D , Smith Timothy PL 
Published: September 2024

AbstractHybridization is common among lineages in the genusBos, often mediated through human management for the selection of adaptive or desirable traits. A recent example is the American Beefalo cattle breed, which was developed in the 1970s and defined as a hybrid between American bison (Bison bison) and cattle (Bos taurus). The American Beefalo Association typically require ⅜ bison ancestry to qualify as Beefalo. Here, we sought to characterize admixed ancestry among Beefalo as a component of a larger project to understand the role of hybridization in shaping present-day diversity in bison and cattle. We generated genomic data from 50 historical and present-day Beefalo and bison hybrids, including several important founding animals, as well as from 10 bison originating from commercial herds that represent potential sources of bison ancestry in Beefalo. We found that most Beefalo did not contain detectable bison ancestry. No individual Beefalo within our data set satisfies the ancestry requirements specified by the American Beefalo Association (ABA), although several Beefalo had smaller proportions of bison ancestry (2-18%). Some beefalo had detectable indicine cattle ancestry (2-38%), suggesting that hybridization of taurine and zebu cattle may contribute to morphological similarity between some Beefalo and bison. Overall, ancestry profiles of Beefalo and bison hybrid genomes are consistent with repeated backcrossing to either parental species rather than the breeding between hybrids themselves, implying significant barriers to gene flow between bison and cattle. Our results call into question the ⅜ bison ancestry targeted by the breed association and demonstrate the value of genomic information in examining claims of interspecies gene flow amongBosspecies.
Directional Cell-to-cell Transport in Plant Roots
Authors: Jacquier Léa , Fiorenza Celeste , Robe Kevin , Han Jian-Pu , Cléard Fabienne , Fuchs Christelle , Ramakrishna Priya , Loubéry Sylvain , Lefebvre-Legendre Linnka , Barberon Marie 
Published: September 2024

SummaryCell-to-cell communication is critical for multicellular organisms. In plants, plasmodesmata—cytoplasmic channels—enable molecular transport between adjacent cells. In roots, this transport is predicted to be essential in nutrient acquisition and delivery to the vasculature. We demonstrate that plasmodesmatal transport persists in differentiated roots, despite apoplastic barriers such as Casparian strips and suberin lamellae in the endodermis, suggesting plasmodesmata as the sole pathway for water and nutrient flow at this stage. We also reveal a developmental switch in plasmodesmata function resulting in an unidirectional transport in differentiated roots. A genetic screen identified mutations that disrupt this directionality, leading to bidirectional transport. These mutations correlate with larger plasmodesmatal apertures, linked to defects in pectin composition and cell wall organization. This discovery underscores the role of plasmodesmatal aperture regulation and pectin in controlling directional transport. Our findings provide insights into plasmodesmata function and their regulation in roots.
A long shelf-life melon created via CRISPR/Cas9 RNP-basedin plantagenome editing
Authors: Sasaki Kentaro , Mimida Naozumi , Nonaka Satoko , Ezura Hiroshi , Imai Ryozo 
Published: September 2024

AbstractWe developed a non-culture and DNA-free genome editing technique for melon using in plant Particle Bombardment (iPB-RNP). The method was employed to create CmACO1 mutants. One of the mutant lines exhibited an extended shelf life due to ethylene deficiency during fruit ripening. As no cell culture step is involved, the iPB-RNP method is expected to overcome limitations associated with conventional genome editing, such as genotype dependency and somatic variations. Thus, this methodology holds significant potential for application in commercial melon breeding and across a wide range of Cucurbitaceae species.
A transcontinental experiment elucidates (mal)adaptation of a cosmopolitan plant to climate in space and time
Authors: Albano Lucas J. , Bastias Cristina C. , Estarague Aurélien , Hendrickson Brandon T. , Innes Simon G. , King Nevada , Patterson Courtney M. , Tudoran Amelia , Vasseur François , Puentes Adriana , Violle Cyrille , Kooyers Nicholas J. , Johnson Marc T. J. 
Published: September 2024

AbstractClimate change and the global spread of invasive species are two of the most significant threats to biodiversity. Both of these phenomena subject populations to novel conditions, either in space (species invasion) or in time (climate change), yet the role of adaptation in how populations respond to these rapid environmental shifts is poorly understood. We conducted a large-scale trans-continental common garden experiment using white clover (Trifolium repens, Fabaceae) to test if adaptive evolution to spatiotemporal variation in climate could contribute to the ecological success of one of the most widespread invasive plant species in the world. Individuals from 96 populations ofTrifolium repens(white clover) from both its native (Europe) and introduced (North America) ranges were planted into four experimental common gardens located in northern (Uppsala, Sweden) and southern (Montpellier, France) Europe, and northern (Mississauga, Canada) and southern (Louisiana, USA) North America. We recorded plant sexual and clonal fitness in each common garden and assessed whether the strength of local adaptation differed between the native and introduced ranges and whether populations are rapidly adapting to climate change. Results show that local adaptation was only evident when populations were transplanted into common gardens located in the same range (native or introduced) from which they originated and was driven by stronger selection (due to climatic factors rather than herbivory) at lower latitudes in both ranges. Our results indicate that rapid local adaptation across a large latitudinal gradient has occurred inT. repenspopulations in less than 400 years since its introduction to North America. However, we find evidence of an adaptation lag in the northern common garden in the introduced range, with plants from historically slightly warmer climates exhibiting the greatest fitness. These findings support two major conclusions: 1) white clover can rapidly adapt to spatial variation in climate in its introduced range as well as the native range, and 2) despite rapid adaptation to novel ranges, introduced white clover populations are not keeping pace with rapid climate change. Overall, our results provide insight into the role of adaptation in facilitating the ecological success of invasive species in a rapidly changing world.
Effect of oral contraceptive consumption timing on substrate metabolism, cognition, and exercise performance in females: a randomised controlled trial
Authors: Martin D , Bargh M , Pennington K 
Published: September 2024

AbstractThe pharmacokinetic profile of oral contraceptives (OCs) results in an acute, transient increase in circulating synthetic reproductive hormones. The aim of this study was to examine the effects of acute OC ingestion on cognitive function, substrate metabolism and exercise performance. Sixteen combined OC (30µg ethinyl oestradiol and 150mg Levonorgestrel) users ingested either their OC or placebo (PLA) in a randomised, double-blind, crossover manner. After 60 minutes, participants completed tests of verbal memory and verbal fluency, followed by sub-maximal treadmill exercise for 6 minutes at 60% lactate threshold (LT) and 90% LT where respiratory exchange ratio (RER), carbohydrate oxidation, fat oxidation, heart rate (HR), rating of perceived exertion (RPE), felt arousal and feeling scale were recorded. Participants then completed an incremental ramp test to exhaustion to assess time to exhaustion (TTE) and peak oxygen uptake (VO2peak), before ingesting the pill corresponding to the condition, they were not in. RER, arousal and feeling scale were all significantly lower in the OC condition compared to PLA (all P < 0.05) with no difference in HR, carbohydrate oxidation, fat oxidation, RPE, TTE or VO2peak (all P > 0.05). Verbal fluency score was significantly higher in the OC condition compared to PLA (P < 0.05), with no differences between conditions for any aspect of verbal memory (all P < 0.05). Combined OC ingestion acutely affects substrate metabolism, affective responses to exercise and verbal fluency. The timing of OC ingestion should be considered in relation to aspects of physiological function.Key findingsIngestion of a combined oral contraceptive (OC) results in a transient increase in circulating synthetic reproductive hormones.The altered reproductive hormone profile affects substrate metabolism and affective responses to exercise.Cognitive performance in a verbal fluency task is also improved post OC ingestion.The within-day timing of OC ingestion can be manipulated to affect aspects of physiology, which may have implications for athletes, exercises and the general population, in addition to interpretation of prior research using OCs.
Meta-SAIGE: Scalable and Accurate Meta-Analysis for Rare Variants
Authors: Park Eunjae , Nam Kisung , Jeong Seokho , Keat Karl , Kim Dokyoon , Bansal Vikas , Zhou Wei , Lee Seunggeun 
Published: September 2024

AbstractA meta-analysis is a practical approach to increasing the power of rare variant tests by combining summary statistics from multiple cohorts. However, existing methods for rare variant meta-analysis often fail to correctly control type I error rates when analyzing low-prevalence binary traits and are computationally intensive when analyzing many phenotypes. This paper introduces Meta-SAIGE, a novel approach for rare variant meta-analyses that addresses these challenges. Meta-SAIGE reduces type I error inflation through precise estimation of the distribution of test statistics and allows the reuse of the linkage disequilibrium (LD) matrix across phenotypes, significantly improving computational efficiency for phenome-wide analyses. Simulation studies using UK Biobank whole-exome sequencing (WES) genotypes demonstrate that Meta-SAIGE effectively controls type I error rates and yields power similar to that of pooled individual-level data through SAIGE-GENE+. A meta-analysis of UK Biobank and All of Us WES data for 83 low prevalence disease phenotypes identified 237 associations. Notably, 80 of these associations were not significant in either dataset alone, underscoring the power of our meta-analysis.
Cas9AEY (Cas9-facilitated Homologous Recombination Assembly of non-specific Escherichia coli yeast vector) method of constructing large-sized DNA
Authors: ma xiaoshu , yang lei , ye hua 
Published: September 2024

AbstractSaccharomyces cerevisiae is widely used in DNA assembly due to their efficient homologous recombination [1], but DNA assembly through yeast recombination in vivo usually requires the vector to have the ability to replicate in yeast. The CRISPR-Cas9 system can efficiently edit DNA [2,3], and the system can also be used for DNA editing of plasmids. In this paper, a yeast universal element is selected, which can be inserted into the vector, so that the vector can replicate in yeast cells, and then the intermediate plasmid containing yeast universal element can be obtained by recombination in yeast. At the same time, a pCas-SmR plasmid was designed in this paper. After Donor DNA is added, the CRISPR-Cas9 system can accurately and efficiently knock out the yeast universal element in the intermediate plasmid, remove the pCas-SmR plasmid through sucrose screening, and finally obtain a pure plasmid. Saccharomyces cerevisiae cells are widely used in DNA assembly due to their efficient homologous recombination [1], but DNA assembly through yeast recombination in vivo usually requires the vector to have the ability to replicate in yeast. The CRISPR-Cas9 system can efficiently edit DNA [2,3], and the system can also be used for DNA editing of plasmids. In this paper, a yeast universal element is selected, which can be inserted into the vector, so that the vector has the ability to replicate in yeast cells, and then the intermediate plasmid containing yeast universal element can be obtained by recombination in yeast. At the same time, a pCas-SmR plasmid was designed in this paper. After Donor DNA is added, the CRISPR-Cas9 system can accurately and efficiently knock out the yeast universal element in the intermediate plasmid, remove the pCas-SmR plasmid through sucrose screening, and finally obtain a pure knocked out plasmid.
Differential translocation of bacteriophages across the intestinal barrier in health and Crohn’s disease
Authors: Douadi Clara , Theodorou Ilias , Lamy-Besnier Quentin , Schiettekatte Olivier , Sbardella Yanis , Brot Loïc , Costantini Paolo Emidio , Saporetti Roberto , Danielli Alberto , Calvaresi Matteo , De Paepe Marianne , Sokol Harry , Garcia-Weber Diego , Carrière Véronique , Thenet Sophie , De Sordi Luisa 
Published: September 2024

SUMMARYImpaired intestinal barrier function is a major feature of Crohn’s disease (CD), leading to exacerbated inflammation in response to the microbiota. In this context, the translocation of intestinal bacteriophages (phages) and their effects on the host have been little investigated. We used phage fluorescence imaging coupled with ex-vivo and in-vitro models that mimic physiological and inflammatory conditions and found that phages can translocate across the intestinal barrier without disrupting its integrity. Although the translocation rate across the intestinal epithelium depended on phage morphology and the condition of the barrier, these factors did not influence the crossing of phage across the vascular endothelium. Virome analysis confirmed that viral sequences shared between blood and stool samples are more abundant in CD patients than healthy subjects, indicating that a barrier defect facilitates phage translocation from the gut to the bloodstream.
Neural basis of collective social behavior during environmental challenge
Authors: Raam Tara , Li Qin , Gu Linfan , Elagio Gabrielle , Lim Kayla Y. , Zhang Xingjian , Correa Stephanie M. , Hong Weizhe 
Published: September 2024

ABSTRACTHumans and animals have a remarkable capacity to collectively coordinate their behavior to respond to environmental challenges. However, the underlying neurobiology remains poorly understood. Here, we found that groups of mice self-organize into huddles at cold ambient temperature during the thermal challenge assay. We found that mice make active (self-initiated) and passive (partner-initiated) decisions to enter or exit a huddle. Using microendoscopic calcium imaging, we found that active and passive decisions are encoded distinctly within the dorsomedial prefrontal cortex (dmPFC). Silencing dmPFC activity in some mice reduced their active decision-making, but also induced a compensatory increase in active decisions by non-manipulated partners, conserving the group’s overall huddle time. These findings reveal how collective behavior is implemented in neurobiological mechanisms to meet homeostatic needs during environmental challenges.
Monkeys Predict US Elections
Authors: Jiang Yaoguang , Huttunen Annamarie , Belkaya Naz , Platt Michael L 
Published: September 2024

AbstractHow people vote often defies rational explanation. Physical traits sometimes sway voters more than policies do–but why? Here we show that rhesus macaques, who have no knowledge about political candidates or their policies, implicitly predict the outcomes of U.S. gubernatorial and senatorial elections based solely on visual features. Given a pair of candidate photos, monkeys spent more time looking at the loser than the winner, and this gaze bias predicted not only binary election outcomes but also the candidates’ vote share. Analysis of facial features revealed candidates with more masculine faces were more likely to win an election, and vote share was a linear function of jaw prominence. Our findings endorse the idea that voters spontaneously respond to evolutionarily conserved visual cues to physical prowess and that voting behavior is shaped, in part, by ancestral adaptations shared with nonhuman primates.Significance StatementWe report that monkeys and humans alike respond spontaneously to evolutionarily conserved facial masculinity cues in political candidates, and this innate sensitivity partly shapes voting behavior, highlighting the imperative for voters to overcome this ancient heuristic by becoming more informed on candidates and their policies.
Temporal trends in the occurrence, mortality, and cost of brain disorders in Denmark
Authors: Fuglsang Cecilia Hvitfeldt , Rasmussen Thomas Bøjer , Rudolfsen Jan Håkon , Olsen Jens , Skipper Niels , Ulrichsen Sinna Pilgaard , Sørensen Henrik Toft , Christiansen Christian Fynbo 
Published: September 2024

AbstractBackgroundBrain disorders, including neurological and mental disorders, are common and burdensome diseases.AimTo examine temporal trends in occurrence, mortality, and cost of brain disorders in Denmark for the period of 2015–2021.MethodsWe conducted a nationwide population-based cohort study using individual-level data recorded in the Danish health registries during 2011–2021. We computed the prevalence of any brain disorder and 25 individual brain disorders for each year from 2015 to 2021 and the incidence for the periods 2011–2015 and 2016–2021 by combining hospital diagnoses and filled prescriptions for relevant medications. We computed one-year hazard ratios (HRs) for mortality by comparing individuals with brain disorders to matched controls without. We also calculated attributable direct and indirect costs (i.e., lost productivity) of brain disorders.ResultsThe prevalence of any brain disorder in Denmark was 33.2% in 2015, increasing to 35.2% in 2021. The three most prevalent conditions were depression (13.5% in 2021), sleep disorders (13.5% in 2021), and headache (7.9% in 2021). The incidence rate of any brain disorder was 1,792 and 1,634 per 100,000 person-years in 2011-2015 and 2016-2021, respectively. The one-year HR of mortality for any brain disorder was 5.5 (95% confidence internal [CI]: 5.4; 5.6) for 2011–2015 and 5.3 (95% CI: 5.2; 5.3) for 2016–2021. The total attributable direct costs for individuals with any brain disorder were €7.5 billion in both 2015 and 2021. In 2021, the total attributable indirect costs were highest for depression (∼€3.5 billion) and lowest for neuromuscular disorders (∼€53.5 million). Total indirect costs increased from €17.7 billion in 2015 to €23.2 billion in 2021. In 2021, the total indirect costs were highest for depression (∼€14 billion) and lowest for other neurodegenerative disorders (∼€60 million).ConclusionBrain disorders remain common, with a fivefold higher one-year mortality compared to persons without brain disorders. While total direct costs were similar in 2015 and 2021, total indirect costs increased over this period.