bluuebunny/crossref_metadata_2025_split huggingface dataset:
Suitability of anthrax (Bacillus anthracis) in the Black Sea basin through the scope of distribution modelling
Authors: Arede Margarida , Allepuz Alberto , Beltran-Alcrudo Daniel , Casal Jordi , Romero-Alvarez Daniel 
Published: April 2024

AbstractThe Black Sea basin has a strategic geographical location bridging Asia and Europe and depends on traditional livestock practices. Anthrax, a zoonotic bacterial disease caused byBacillus anthracis, poses a significant global threat impacting public health, food security, pastoralist communities, and national economies. The disease is endemic or sporadic in the Black Sea basin, however, the study of its distribution has seldom been addressed, despite its burden and the presence of historicalB. anthracisburial sites in the region. The viability ofB. anthracisin a particular region is going to be influenced by multiple environmental factors, such as soil composition, climate, vegetation, and host abundance. To characterize the potential distribution ofB. anthracisin the Black Sea basin, and therefore, the potential for anthrax outbreaks, we applied an ecological niche modelling framework using the Maxent algorithm, analyzing multiple variable combinations, and proposing a novel approach for interpreting in-risk anthrax areas. Our findings underscored the importance of host abundance to the anthrax dynamics in the region. We identified anthrax-suitable areas spanning central and eastern Türkiye, Armenia, southern Georgia, southern Russia, Bulgaria, southern and eastern Romania, Hungary, Moldova, and southern Ukraine, which align with findings from previous global and regional studies on the potential suitability of anthrax. The insights gained from our research might facilitate the development of targeted interventions and policies to mitigate the spread of this disease in pastoralist communities in the Black Sea basin.
Electroconvulsive Therapy Modulates Loudness Dependence of Auditory Evoked Potentials: A Pilot MEG Study
Authors: Dib Michael , Lewine Jeffrey D. , Abbott Christopher C. , Deng Zhi-De 
Published: April 2024

ABSTRACTElectroconvulsive therapy (ECT) remains a critical intervention for treatment-resistant depression (MDD), yet its neurobiological underpinnings are not fully understood. This pilot study utilizes high-resolution magnetoencephalography (MEG) in nine depressed patients receiving right unilateral ECT, to investigate the changes in loudness dependence of auditory evoked potentials (LDAEP), a proposed biomarker of serotonergic activity, following ECT. We hypothesized that ECT would reduce the LDAEP slope, reflecting enhanced serotonergic neurotransmission. Contrary to this, our findings indicated a significant increase in LDAEP post-ECT (t8= 3.17,p= .013). The increase in LDAEP was not associated with changes in depression severity or cognitive performance, as assessed by the Hamilton Depression Rating Scale (HAMD-24) and Repeatable Battery for the Assessment of Neuropsychological Status (RBANS). We discussed potential mechanisms for the observed increase, including ECT’s impact on serotonergic, dopaminergic, glutamatergic, and GABAergic receptor activity, neuroplasticity involving brain-derived neurotrophic factor (BDNF), and inflammation modulators such as TNF-alpha. Our results suggest a complex interaction between ECT and these neurobiological systems, rather than a direct reflection of serotonergic neurotransmission.
State of the Interactomes: an evaluation of molecular networks for generating biological insights
Authors: Wright Sarah N. , Colton Scott , Schaffer Leah V. , Pillich Rudolf T. , Churas Christopher , Pratt Dexter , Ideker Trey 
Published: April 2024

ABSTRACTAdvancements in genomic and proteomic technologies have powered the use of gene and protein networks (“interactomes”) for understanding genotype-phenotype translation. However, the proliferation of interactomes complicates the selection of networks for specific applications. Here, we present a comprehensive evaluation of 46 current human interactomes, encompassing protein-protein interactions as well as gene regulatory, signaling, colocalization, and genetic interaction networks. Our analysis shows that large composite networks such as HumanNet, STRING, and FunCoup are most effective for identifying disease genes, while smaller networks such as DIP and SIGNOR demonstrate strong interaction prediction performance. These findings provide a benchmark for interactomes across diverse network biology applications and clarify factors that influence network performance. Furthermore, our evaluation pipeline paves the way for continued assessment of emerging and updated interaction networks in the future.
MIPDB: A maize image-phenotype database with multi-angle and multi-time characteristics
Authors: Wang Panpan , Chang Jianye , Deng Wenpeng , Liu Bingwen , Lai Haozheng , Hou Zhihao , Dong Linsen , Chen Qipian , Zhou Yun , Zhang Zhen , Liu Hailin , Ruan Jue 
Published: April 2024

AbstractPlant phenomics has become one of the most significant scientific fields in recent years. However, typical phenotyping procedures have low accuracy, low throughput, and are labor-intensive and time-consuming. Large-scale phenotypic collection equipment, on the other hand, is pricy, rigid, and inconvenient. The advancement of phenomics has been hampered by these restrictions. Lightweight picture collection equipment can now be used to capture plant phenotypic data thanks to the development of deep learning-based image identification. For the purpose of training the model, this approach needs high-quality annotated datasets. In this study, we used a handheld camera to gather multi-angle, multi-time series images and an unmanned aerial vehicle (UAV) to create a maize image phenotyping database (MIPDB). Over 30,000 high-resolution photos are available in the MIPDB, with 17,631 of those images having been carefully tagged with point-line method. The MIPDB can be accessed by the general public athttp://phenomics.agis.org.cn. We anticipate that the availability of this superior dataset will stimulate a new revolution in crop breeding and advance deep learning-based phenomics research.
Marmosets as model systems for the study of Alzheimer’s disease and related dementias: substantiation of physiological Tau 3R and 4R isoform expression and phosphorylation
Authors: Huhe Hasi , Shapley Sarah M. , Duong Duc , Wu Fang , Ha Seung-Kwon , Choi Sang-Ho , Kofler Julia , Mou Yongshan , Guimaraes Thais Rafael , Thathiah Amantha , Schaeffer Lauren K.H. , Carter Gregory W. , Seyfried Nicholas T. , Silva Afonso C. , Sukoff Rizzo Stacey J. 
Published: April 2024

ABSTRACTINTRODUCTIONMarmosets have been shown to spontaneously develop pathological hallmarks of Alzheimer’s disease (AD) during advanced age, including amyloid-beta plaques, positioning them as a model system to overcome the rodent-to-human translational gap for AD. However, Tau expression in the marmoset brain has been understudied.METHODSTo comprehensively investigate Tau isoform expression in marmosets, brain tissue from eight unrelated marmosets across various ages was evaluated and compared to human postmortem AD tissue. Microtubule-associated protein tau (MAPT) mRNA expression and splicing were confirmed by RT-PCR. Tau isoforms in the marmoset brain were examined by western blot, mass spectrometry, immunofluorescence, and immunohistochemical staining. Synaptic Tau expression was analyzed from crude synaptosome extractions.RESULTS3R and 4R Tau isoforms are expressed in marmoset brains at both transcript and protein levels across ages. Results from western blot analysis were confirmed by mass spectrometry, which revealed that Tau peptides in marmoset corresponded to the 3R and 4R peptides in the human AD brain. 3R Tau was primarily enriched in neonate brains, and 4R enhanced in adult and aged brains. Tau was widely distributed in neurons with localization in the soma and synaptic regions. Phosphorylation residues were observed on Thr-181, Thr-217, and Thr-231, Ser202/Thr205, Ser396/Ser404. Paired helical filament (PHF)-like aggregates were also detected in aged marmosets.DISCUSSIONOur results confirm the expression of both 3R and 4R Tau isoforms and important phosphorylation residues in the marmoset brain. These data emphasize the significance of marmosets with natural expression of AD-related hallmarks as important translational models for the study of AD.
Laminar fMRI in the locked-in stage of amyotrophic lateral sclerosis shows preserved activity in layer Vb of primary motor cortex
Authors: Knudsen Lasse , Jespersen Bo , Heintzelmann Mia B. , Zhang Peng , Yang Yan , Lund Torben E. , Blicher Jakob U. 
Published: April 2024

AbstractAmyotrophic lateral sclerosis (ALS) affects the cerebral cortex layer-dependently, most notably by the foremost targeting of upper motor neurons (UMNs) sited in layer Vb. Previous studies have shown a retained ability of paralysed patients to activate residual cortical motor networks, even in late-stage ALS. However, it is currently unknown whether such activation reflects a retained capacity to process sensorimotor inputs or if it is a result of actual motor output. Given the distinct function of individual cortical layers, layer-specific functional measurements may provide insight to this question. In this study, using submillimetre resolution laminar fMRI, we assessed the layer-dependent activation associated with attempted (motor) and passive (somatosensory) movements in a locked-in stage ALS patient. We found robust activation in both superficial and deep layers of primary motor cortex. The peak activation in deep layers was localised to layer Vb. These findings demonstrate preserved activity in deep output layers of M1, possibly reflecting a retained ability to engage residual UMNs despite years of paralysis. Our study underscores the capacity of laminar fMRI to discern subtle cortical activity and elucidates a promising pathway for probing in vivo human ALS pathology with unprecedented resolution.
Ambulatory physiological measures obtained under naturalistic urban mobility conditions have acceptable reliability
Authors: Korkmaz Dilber , Knauth Kilian , Brands Angela , Schmeck Marie , Büning Pia , Peters Jan 
Published: April 2024

AbstractAmbulatory assessment methods in psychology and clinical neuroscience are powerful research tools for collecting data outside of the laboratory. These methods encompass physiological, behavioral, and self-report measures obtained while individuals navigate in real-world environments, thereby increasing the ecological validity of experimental approaches. Despite the recent increase in applications of ambulatory physiology, data on the reliability of these measures is still limited. To address this issue, twenty-six healthy participants (N= 15 female, 18-34 years) completed an urban walking route (2.1 km, 30 min walking duration, temperatureM= 19.8° degree Celsius,Range= 12°-37° degrees Celsius) on two separate testing days, while GPS-location and ambulatory physiological measures (cardiovascular and electrodermal activity) were continuously recorded. Bootstrapped test-retest reliabilities of single measures and aggregate scores derived via principal component analysis (PCA) were computed. The first principal component (PC#1) accounted for 39% to 45% of variance across measures. PC#1 scores demonstrated an acceptable test-retest reliability (r= .60) across testing days, exceeding the reliabilities of most individual measures (heart rate:r= .53, heart rate variability:r= .50, skin conductance level:r= .53, no. of skin conductance responses:r= .28, skin conductance response amplitude:r= .60). Results confirm that ambulatory physiological measures recorded during naturalistic navigation in urban environments exhibit acceptable test-retest reliability, in particular when compound scores across physiological measures are analyzed, a prerequisite for applications in (clinical) psychology and digital health.Author summaryPsychophysiological assessments have been predominantly limited to controlled laboratory settings, leaving the reliability of field measurements unclear. In this study, we conducted a proof-of-concept investigation inN=26 healthy participants navigating the same urban route on two separate days. Cardiovascular and electrodermal activity were continuously recorded and combined with GPS-based location tracking. Psychophysiological measurements obtained under naturalistic urban mobility conditions showed acceptable test-retest reliability, in particular when multiple measures where combined into a compound score via principal component analysis. Shedding light on the reliability of ambulatory assessments in urban environments emphasizes the potential for psychophysiological measurements to contribute valuable insights beyond the constraints of traditional laboratory settings.
A Computational Model of Deep Brain Stimulation for Parkinson’s Disease Tremor
Authors: Nair Sandeep Sathyanandan , Chakravarthy V. Srinivasa 
Published: April 2024

ABSTRACTParkinson’s Disease (PD) is a progressive neurological disorder that is typically characterized by a range of motor dysfunctions and its impact extends beyond physical abnormalities into emotional well-being and cognitive symptoms. The loss of dopaminergic neurons in the Substantia nigra pars compacta (SNc) leads to an array of dysfunctions in the functioning of Basal Ganglia (BG) circuitry that manifests into PD. While active research is being carried out in finding the root cause of SNc cell deaths, various therapeutic techniques are prevalent to manage the symptoms of PD. The most common approach in managing the symptoms is replenishing the lost dopamine in the form of taking dopaminergic medications such as Levodopa amidst its long-term complications. Another commonly used intervention for PD is deep brain stimulation (DBS), which is a invasive technique where an electrode is surgically inserted into the skull and a high frequency current of appropriate characteristics is delivered to the brain region. DBS is most commonly used when levodopa medication efficacy reduces and also in combination with levodopa medication that will help reducing the required dosage of medication prolonging the therapeutic effect. DBS is also a go to option when motor complications such as dyskinesias emerge as a side effect of medication. Several studies have also reported that though DBS is found to be effective in suppressing severe motor symptoms such as tremor and rigidity, it has adverse effect on cognitive capabilities. Henceforth it is important to understand the exact mechanism of DBS in alleviating the motor symptoms. A computational model of DBS stimulation for motor symptoms will offer great insights in understanding the mechanisms underlying the DBS and in this line in our current study we model a cortico-basal ganglia circuitry of arm reaching where we simulate healthy controls (HC) and PD symptoms as well as the DBS effect on the PD tremor. With DBS current characteristics of 220 pA, 130 Hz and 100 microseconds pulse-width we were able to see maximum therapeutic effect using our model. This model can be extended to accommodate cognitive dynamics in future so as to study the impact of DBS on cognitive symptoms and optimizing the parameters to get optimal performance effect across modalities.
Gene pseudogenization in fertility-associated genes in cheetah (Acinonyx jubatus), a species with long-term low effective population size
Authors: Peers Jessica A. , Nash Will J. , Haerty Wilfried 
Published: April 2024

AbstractThe ongoing global biodiversity crisis is placing an increasing number of mammalian populations at risk of decline. Species that have survived severe historic bottlenecks, such as the cheetah (Acinonyx jubatus) exhibit symptoms of inbreeding depression including reproductive and developmental defects. Although it has long been suggested that such defects stem from an accumulation of weakly deleterious mutations, the implications of such mutations leading to pseudogenization has not been assessed.Here, we use comparative analysis of eight felid genomes to better understand the impacts of deleterious mutations in the cheetah. We find novel pseudogenization events specific to the cheetah. Through careful curation, we identify 89 genes with previously unreported premature termination codons that likely affect gene function, 65 of which are caused by point mutations. With the addition of population data, we find 22 PTCs fixed in wild populations, four of which (DEFB116, ARL13A, CFAP119 and NC5TD4) are also found in a more recent reference genome. Mutations within three of these genes are linked with sterility, including azoospermia, which is common in cheetahs. Our results highlight the power of comparative genomic approaches for the discovery of novel causative variants in declining species.
Generalizing the response and satisfaction threshold models for multiple task types: A maximal entropy approach
Authors: Lynch C.M. , Pavlic T.P. 
Published: April 2024

AbstractResponse threshold models are often used to test hypotheses about division of labor in social-insect colonies. Each worker’s probability to engage in a task rapidly increases when a cue associated with task demand crosses some “response threshold.” Threshold variability across workers generates an emergent division of labor that is consistent over time and flexibly adaptive to increasing demands, which allows for testable predictions about the shape of hypothetical response-threshold distributions. Although there are myriad different task types in a social-insect colony, the classical response-threshold model is built to understand variability in response to a single type of task. As such, it does not immediately allow for testing predictions about how different workers prioritize different task types or how demand for some tasks interferes with responding to demand for others. To rectify this, we propose a multi-task generalization that degenerates into the standard model for a single task. We replace the classical Hill response probability with a model that draws worker choices from a Boltzmann distribution, which is an approach inspired by multi-class machine learning.
Tap into non-symbiotic carbon? Exogenous myristate fuels the growth of symbiotic arbuscular mycorrhizal fungi but disrupts their carbon-phosphorus exchange with host plants
Authors: Chen Hanwen , Xiong Tian , Guan Baoxing , Huang Jiaqi , Zhao Danrui , Chen Yao , Liang Haoran , Li Yingwei , Wu Jingwen , Ye Shaoping , Li Ting , Shu Wensheng , Li Jin-tian , Wang Yutao 
Published: April 2024

AbstractArbuscular mycorrhizal fungi (AMF) form symbiotic relationships with the roots of most land plants. In this association, known as arbuscular mycorrhiza (AM), the obligate biotrophic fungi acquire host-derived (symbiotic) carbohydrates and, in return, facilitate plant uptake of mineral nutrients such as phosphate. However, the capacity of symbiotic AMF to access external non-symbiotic carbon sources remains unclear, complicating our understanding of the nutritional exchanges in AM and their ecosystem functions. In this study, we explored the direct uptake of exogenous13C1-labeled myristate by symbiotic AMF (Rhizophagus irregularis) and their growth responses using a two-compartment and a single-compartment AMF-carrot hairy root co-culture system, respectively. Additionally, we assessed the impact of exogenous myristate on the carbon-phosphorus exchange between AMF and two host species in a greenhouse experiment, using13C-neutral lipid fatty acid-isotope ratio mass spectrometry technology, alongside physiological and transcriptome analyses. Our findings reveal that symbiotic AMF can absorb external nonsymbiotic myristate, at least under the conditions tested, as evidenced by13C enrichment and transcriptional activation of putative fatty acid transport and metabolism genes in extraradical hyphae. Exogenous myristate increased both intraradical and extraradical fungal biomass, potentially due to suppressed mycorrhizal defense responses in host roots. Intriguingly, exogenous myristate reduced the mycorrhizal phosphorus benefits for both Medicago sativa and Oryza sativa and decreased their carbon allocation to symbiotic AMF, although these effects were influenced by host identity and soil phosphorus conditions. These findings advance our understanding of the nutritional interactions in AM, which are essential for comprehending and manipulating this symbiotic relationship.
Meta-analysis of the pathogenLeishmania donovani’s transcriptome reveals multiple modes of regulation including two reciprocally regulated gene modules
Authors: Paranjape Pradyumna , Vinod P K , Vaidya Tushar 
Published: April 2024

ABSTRACTLeishmania donovanicauses a neglected tropical disease called visceral leishmaniasis. Additionally, leishmaniasis also manifests opportunistically, under conditions of immune compromise. The continued non-availability of effectively curative interventions (drugs or vaccines) against this disease necessitates a deeper knowledge ofLeishmaniabiology in order to evolve novel strategies against the disease. We have used a meta-analysis approach to analyseLeishmania’s composite genetic network rather than investigating individual candidate genes. We performed Weighted Gene Co-expression Network Analysis (WGCNA) on publicly availableLeishmania donovanitranscriptome data to identify co-regulatory genetic modules. This clustering ofLeishmania donovanitranscriptomes revealed that genes fall in 30 distinct co-regulated modules with 32 to 3012 genes. In order to analyse the distribution of genes inLeishmaniagene modules, we queried the enrichment or depletion of various annotation-qualifiers in the modules. We observed that several modules are specifically and individually enriched or depleted for annotation qualifiers derived from GO-annotation and KEGG-pathways and are differentially associated with life-phases and experimental conditions. Additionally, modules are also enriched or depleted for sequence based genetic features such as chromosomal location, location on co-transcriptional segment, rank of transcript from initiation of transcription, skewed usage of known RNA Binding Protein motifs. Classification of uncharacterized transcripts into co-regulatory modules provides insights in their probable characteristics, aiding future empirical investigation. Strikingly, two of the modules have reciprocal features including individual associations with logarithmic or stationary growth phases ofLeishmania, two important life-phases that simulate the vector-dwelling pro-cyclic and the pre-infective meta-cyclic forms. Collectively, our analyses ofLeishmaniaco-regulated gene modules is suggestive of additional regulatory modes over the mere differential mRNA stabilization.