bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-household environments make a major contribution to dengue transmission: Implications for vector control
Authors: Peña-García Víctor Hugo , LaBeaud A. Desiree , Ndenga Bryson A. , Mutuku Francis M. , Bisanzio Donal , Andrews Jason R. , Mordecai Erin A. 
Published: January 2024

AbstractThe incidence of Aedes-borne pathogens has been increasing despite vector control efforts. Control strategies typically target households, where Aedes mosquitoes breed in household containers and bite indoors. However, our study in Kenyan cities Kisumu and Ukunda (2019-2022) reveals high Aedes abundance in public spaces, prompting the question: how important are non-household (NH) environments for dengue transmission and control? Using field data and human activity patterns, we developed an agent-based model simulating transmission across household (HH) and five NH environments, which was then used to evaluate preventive (before an epidemic) and reactive (after an epidemic commences) vector control scenarios. Our findings estimate over half of infections occur in NH settings, particularly workplaces, markets, and recreational sites. Control efforts in NH areas proved more effective than HH, contradicting the current global focus. Greater reductions in dengue cases occurred with early, high-coverage interventions, especially in NH locations. Additionally, local ecological factors, such as uneven water container distribution, influence control outcomes. This study underscores the importance of vector control in both household and non-household environments in endemic settings. It highlights a specific approach to inform evidence-based decision making to target limited vector control resources for optimal control
An Ensemble Model for Acute Myeloid Leukemia Risk Stratification Recommendations by Combining Machine Learning with Clinical Guidelines
Authors: Chang Ming-Siang , Tsai Xavier Cheng-Hong , Chou Wen-Chien , Tien Hwei-Fang , Hou Hsin-An , Chen Chien-Yu 
Published: January 2024

AbstractAcute Myeloid Leukemia (AML) is a complex disease requiring accurate risk stratification for effective treatment planning. This study introduces an innovative ensemble machine learning model integrated with the European LeukemiaNet (ELN) 2022 recommendations to enhance AML risk stratification. The model demonstrated superior performance by utilizing a comprehensive dataset of 1,213 patients from National Taiwan University Hospital (NTUH) and an external cohort of 2,113 patients from UK-NCRI trials. On the external cohort, it improved a concordance index (c-index) from 0.61 to 0.64 and effectively distinguished three different risk levels with median hazard ratios ranging from 18% to 50% improved. Key insights were gained from the discovered significant features influencing risk prediction, including age, genetic mutations, and hematological parameters. Notably, the model identified specific cytogenetic and molecular alterations likeTP53, IDH2, SRSF2, STAG2, KIT, TET2, and karyotype (-5, -7, -15, inv(16)), alongside age and platelet counts. Additionally, the study explored variations in the effectiveness of hematopoietic stem cell transplantation (HSCT) across different risk levels, offering new perspectives on treatment effects. In summary, this study develops an ensemble model based on the NTUH cohort to deliver improved performance in AML risk stratification, showcasing the potential of integrating machine learning techniques with medical guidelines to enhance patient care and personalized medicine.
The longitudinal role of overweight and obesity women in mammographic breast screening participation: retrospective cohort study using linked data
Authors: McBride K.A. , Munasinghe S. , Sperandei S. , Page A. 
Published: January 2024

ABSTRACTObjectivesThis study investigated the association between prospective changes in BMI and longitudinal adherence to mammographic screening among overweight or obese women residing in New South Wales, AustraliaMethodsThis was a retrospective cohort study of women participating in the Australian Longitudinal Study on Women’s Health (ALSWH), with subsequent screening participation enumerated via BreastScreen New South Wales, Australia clinical records over the period 1996-2016. The association between BMI and subsequent adherence to screening was investigated in a series of marginal structural models, incorporating a range of socio-demographic, clinical, and health behaviour confounders. Models were also stratified by proxy measures of socio-economic status (private health insurance and educational achievement).ResultsParticipants who had overweight/obesity were more likely to be non-adherent to mammography screening, compared to normal or underweight participants (OR=1.29, [95% CI=1.07, 1.55). The association between overweight/obesity and non-adherence was slighter stronger among those who ever had private health insurance (OR=1.30, [95% CI=1.05, 1.61) compared to those who never had private health insurance (OR=1.19, [95% CI=0.83, 1.71), and among those with lower educational background (OR=1.38, [95% CI=1.08, 1.75) compared to those with higher educational background (OR=1.27, [95% CI=0.93, 1.73).ConclusionFindings show long-term impacts on screening participation with higher BMI women being less likely to participate in routinely organised breast screening. Women with a higher BMI should be a focus of efforts to improve breast screening participation, particularly given their increased risk of post-menopausal breast cancer and the association of higher BMI with more aggressive clinical presentations and histopathology of breast cancers.Key messagesOverweight and obesity increase risk of breast cancer, poorer prognostic features and worse outcomes.Long-term impacts on screening participation are evident among higher BMI women who are less likely to participate in routinely organised breast screening.This relationship is stronger among women of lower educational attainment.Women with a higher BMI should be a focus of targeted efforts to improve their breast screening participation
Effects of Alzheimer’s disease plasma marker levels on multilayer centrality in healthy individuals
Authors: García-Colomo Alejandra , López-Sanz David , Taguas Ignacio , Carrasco-Gómez Martín , Spuch Carlos , Comis-Tuche María , Maestú Fernando 
Published: January 2024

AbstractFinding early and non-invasive biomarkers that help identify individuals in the earliest stages of the Alzheimer’s disease continuum is paramount. Electrophysiology and plasma biomarkers are great candidates in this pursuit. Furthermore, the combination of functional connectivity metrics with graph-theory analyses allows for a deeper understanding of network alterations. Despite this, this is the first MEG study to assess multilayer centrality considering inter-band connectivity in an unimpaired population at high risk of Alzheimer’s disease. Our objective is twofold. First, to address the relationship between a compound centrality score designed to overcome previous inconsistencies stemming from the use of various individual metrics, and plasma pathology markers of Alzheimer’s disease in unimpaired individuals with elevated levels of the latter. Lastly, to evaluate whether hubs’ centrality is more affected by the pathology.33 individuals with available MEG recordings and elevated plasma pathology markers were included. A compound centrality score for each brain source of every subject was calculated combining widely used centrality metrics, considering intra- and inter-band connections.Spearman correlations were carried out to address the association between each node’s centrality score and biomarkers levels. Next, to test whether greater associations were found in hubs, a correlation between the obtained rho and the grand-average of the centrality score was carried out.Increasing concentrations of p-tau231 were associated with greater centrality within the network of posterior areas, which increased their connectedness in the theta range with the remaining areas, regardless of the latter’s frequency range. The opposite relationship was found for left areas, that decreased their connectedness in the gamma frequency range. Hubs’ centrality was significantly more affected by p-tau231 levels.Our results expand previous literature demonstrating early network reorganizations associated with elevated plasma p-tau231 in cognitively unimpaired individuals. Multilayer centrality increases in the theta band in posterior regions are congruent with previous results and theoretical models, that predict a longitudinal evolution towards a loss of centrality. On the other hand, the changes in multilayer centrality found in the gamma band could be associated with inhibitory neuron dysfunction, classical in AD pathology. Lastly, hubs were more likely to increase their centrality in association to p-tau231, thus corroborating hubs’ vulnerability.
Aβ-driven nuclear pore complex dysfunction alters activation of necroptosis proteins in a mouse model of Alzheimer’s Disease
Authors: Bansal Vibhavari Aysha , Tan Jia Min , Soon Hui Rong , Zainolabidin Norliyana , Saito Takashi , Ch’ng Toh Hean 
Published: January 2024

SUMMARYThe emergence of Aβ pathology is one of the hallmarks of Alzheimer’s disease (AD), but the mechanisms and impact of Aβ in progression of the disease is unclear. The nuclear pore complex (NPC) is a multi-protein assembly in mammalian cells that regulates movement of macromolecules across the nuclear envelope and its function is shown to undergo age-dependent decline during normal aging and is also impaired in multiple neurodegenerative disorders. Yet not much is known about the impact of Aβ on NPC function in neurons. Here, we examined NPC and nucleoporin (NUP) distribution and nucleocytoplasmic transport using a mouse model of AD (AppNL-G-F/NL-G-F) that expresses Aβ in young animals. Our studies revealed that a time-dependent accumulation of intracellular Aβ corresponded with a reduction of NPCs and NUPs in the nuclear envelope which resulted in the degradation of the permeability barrier and inefficient segregation of nucleocytoplasmic proteins, and active transport. As a result of the NPC dysfunctionAppKI neurons become more vulnerable to inflammation-induced necroptosis – a programmed cell death pathway where the core components are activated via phosphorylation through nucleocytoplasmic shutting. Collectively, our data implicates Aβ in progressive impairment of nuclear pore function and further confirms that the protein complex is vulnerable to disruption in various neurodegenerative diseases and is a potential therapeutic target.
Sound-seeking before and after hearing loss in mice
Authors: Mai Jessica , Gargiullo Rowan , Zheng Megan , Esho Valentina , Hussein Osama E , Pollay Eliana , Bowe Cedric , Williamson Lucas M , McElroy Abigail F , Goolsby William N , Brooks Kaitlyn A , Rodgers Chris C 
Published: January 2024

ABSTRACTHow we move our bodies affects how we perceive sound. For instance, we can explore an environment to seek out the source of a sound and we can use head movements to compensate for hearing loss. How we do this is not well understood because many auditory experiments are designed to limit head and body movements. To study the role of movement in hearing, we developed a behavioral task called sound-seeking that rewarded mice for tracking down an ongoing sound source. Over the course of learning, mice more efficiently navigated to the sound. We then asked how auditory behavior was affected by hearing loss induced by surgical removal of the malleus from the middle ear. An innate behavior, the auditory startle response, was abolished by bilateral hearing loss and unaffected by unilateral hearing loss. Similarly, performance on the sound-seeking task drastically declined after bilateral hearing loss and did not recover. In striking contrast, mice with unilateral hearing loss were only transiently impaired on sound-seeking; over a recovery period of about a week, they regained high levels of performance, increasingly reliant on a different spatial sampling strategy. Thus, even in the face of permanent unilateral damage to the peripheral auditory system, mice recover their ability to perform a naturalistic sound-seeking task. This paradigm provides an opportunity to examine how body movement enables better hearing and resilient adaptation to sensory deprivation.
Structured behavioral data format: An NWB extension standard for task-based behavioral neuroscience experiments
Authors: Ly Ryan , Avaylon Matthew , Wulf Michael , Kepecs Adam , Rübel Oliver 
Published: January 2024

AbstractUnderstanding brain function necessitates linking neural activity with corresponding behavior. Structured behavioral experiments are crucial for probing the neural computations and dynamics underlying behavior; however, adequately representing their complex data is a significant challenge. Currently, a comprehensive data standard that fully encapsulates task-based experiments, integrating neural activity with the richness of behavioral context, is lacking. We designed a data model, as an extension to the NWB neurophysiology data standard, to represent structured behavioral neuroscience experiments, spanning stimulus delivery, timestamped events and responses, and simultaneous neural recordings. This data format is validated through its application to a variety of experimental designs, showcasing its potential to advance integrative analyses of neural circuits and complex behaviors. This work introduces a comprehensive data standard designed to capture and store a spectrum of behavioral data, encapsulating the multifaceted nature of modern neuroscience experiments.
Elephants in a teacup: Ranging and Habitat-use of Asian elephantsElephas maximusin a Plantation Dominated Landscape in Southern Western Ghats, India
Authors: Vijayakrishnan Sreedhar , Raghunathan Ganesh , Ananda Kumar Mavatur , Sinha Anindya 
Published: January 2024

AbstractRanging patterns of four focal herds using a plantation-forest matrix of the Valparai plateau was studied by following the individuals on a regular basis, recording all possible sightings, for five years. Although surrounded by a network of protected areas, the focal herds were found to use the plateau extensively. There was minimal spatial overlap observed between the four herds, except between two, PTH and MON, which showed a fairly large overlap of 130 sq.km. The observed ranges of elephants were smaller (119.71 ± 24.11 sq.km) compared to previous studies on the species in India, but were comparable with those from Sri Lanka. Possible risk avoidance strategy is observed in their use of the landscape, as evidenced by the use of high intensity human activity areas mostly during night than day. Compared to previous studies from the same landscape, there is also an observed increase in the use of natural vegetation (in the form of rainforest fragments) than the plantation and monoculture habitats, indicating the importance of forest remnants for elephants on the plateau. The observations indicate importance of anthropogenic areas outside protected areas as potential habitats and, not just as movement pathways or as temporary refugia. Conservation planning should therefore consider such areas while initiating landscape-level management strategies for the species. The study also highlights the importance of longitudinal observation-based studies in ascertaining ranging, in the absence of logistically challenging techniques such as radio telemetry.
Role of microstructure of cellulosic mucilage in seed anchorage: A mechanical interpretation
Authors: Bhaskaran Krithika , Saveri Puchalapalli , Deshpande Abhijit P. , Varughese Susy 
Published: January 2024

AbstractCellulosic, hemicellulosic and pectinaceous mucilages produced by certain angiosperms as adaptation inmyxodiasporyare investigated in the past for seed dispersal. The present understanding ofzoochoryandtelechoryare based on mucilage amount, state of hydration and to a limited extent, role of mucilage microstructure studied using adhesion and friction. Pectinaceous mucilages have less adhesion and supports dispersal byzoochory. However, in the case of cellulosic mucilages, the role played by the cellulosic fibrils in seed dispersal is not clear, especially, since they have a negative correlation withendozoochory. Using fresh cellulosic seed mucilages from, sweet basil (Ocimum basilicum) and chia (Salvia hispanica) we investigate the role of microstructure of the mucilage in two key behaviours: anchoring and adhesion properties of the seeds through rheology. We report a special large deformation mechanism triggered through ‘strain stiffening’ operational in these cellulosic mucilages. In many biopolymers semi-flexible polymer chains and other aligning elements contribute to the strain stiffening. However, the strain stiffening and strong wet adhesion observed in these mucilages have a significant role from the cellulosic components. This behaviour is more pronounced in basil seeds and presents a plausible structure-property mechanism foranti-telechoryfavoured by plant species found in arid habitats.
Prefrontal cortical dynorphin peptidergic transmission constrains threat-driven behavioral and network states
Authors: Wang Huikun , Flores Rodolfo J. , Yarur Hector E. , Limoges Aaron , Bravo-Rivera Hector , Casello Sanne M. , Loomba Niharika , Enriquez-Traba Juan , Arenivar Miguel , Wang Queenie , Ganley Robert , Ramakrishnan Charu , Fenno Lief E , Kim Yoon , Deisseroth Karl , Or Grace , Dong Chunyang , Hoon Mark A. , Tian Lin , Tejeda Hugo A. 
Published: January 2024

SummaryPrefrontal cortical (PFC) circuits provide top-down control of threat reactivity. This includes ventromedial PFC (vmPFC) circuitry, which plays a role in suppressing fear-related behavioral states. Dynorphin (Dyn) has been implicated in mediating negative affect and mal-adaptive behaviors induced by severe threats and is expressed in limbic circuits, including the vmPFC. However, there is a critical knowledge gap in our understanding of how vmPFC Dyn-expressing neurons and Dyn transmission detect threats and regulate expression of defensive behaviors. Here, we demonstrate that Dyn cells are broadly activated by threats and release Dyn locally in the vmPFC to limit passive defensive behaviors. We further demonstrate that vmPFC Dyn-mediated signaling promotes a switch of vmPFC networks to a fear-related state. In conclusion, we reveal a previously unknown role of vmPFC Dyn neurons and Dyn neuropeptidergic transmission in suppressing defensive behaviors in response to threats via state-driven changes in vmPFC networks.Highlights●vmPFCDynneurons are activated by threats and threat-predictive cues●Characterization of a genetically-encoded kappa-opioid receptor sensor●vmPFCDynneurons rapidly release Dyn in response to threats and their predictors●vmPFCDynsignaling opposes threat-induced passive defensive behaviors●Dyn signaling promotes threat-evoked state transitions in vmPFC networks
Lateral Flow Assays Biotesting by Utilizing Plasmonic Nanoparticles Made of Inexpensive Metals – Replacing Colloidal Gold
Authors: Lorca Veronica A. Bahamondes , Ávalos-Ovando Oscar , Sikeler Christoph , Ijäs Heini , Santiago Eva Yazmin , Skelton Eli , Wang Yong , Yang Ruiqi , Cimatu Katherine Leslee A. , Baturina Olga , Wang Zhewei , Liu Jundong , Slocik Joseph M. , Wu Shiyong , Ma Dongling , Pastukhov Andrei I. , Kabashin Andrei V. , Kordesch Martin E. , Govorov Alexander O. 
Published: January 2024

AbstractNanoparticles (NPs) can be conjugated with diverse biomolecules and employed in biosensing to detect target analytes in biological samples. This proven concept was primarily used during the COVID-19 pandemic with gold NPs-based lateral flow assays (LFAs). Considering the gold price and its worldwide depletion, here we show that novel plasmonic nanoparticles (NPs) based on inexpensive metals, titanium nitride (TiN) and copper covered with a gold shell (Cu@Au), perform comparable or even better than gold nanoparticles. After conjugation, these novel nanoparticles provided high figures of merit for LFA testing, such as high signals and specificity and robust naked-eye signal recognition. To the best of our knowledge, our study represents the 1st application of laser-ablation-fabricated nanoparticles (TiN) in the LFA and dot-blot biotesting. Since the main cost of the Au NPs in commercial testing kits is in the colloidal synthesis, our development with TiN is very exciting, offering potentially very inexpensive plasmonic nanomaterials for various bio-testing applications. Moreover, our machine learning study showed that the bio-detection with TiN is more accurate than that with Au.
The J-Like Protein ARC6 Regulates Chloroplast FtsZ-Ring Assembly through Fine-tuning ARC3 Activity in Arabidopsis
Authors: Du Wenbin , Cao Lingyan , Zhou Yuelong , Jackson Shanelle , Naeem Maryam , Yang Yue , Glynn Jonathan M. , Porter Katie J. , He Qian , Xu Jie , Liang Wanqi , Osteryoung Katherine W. , Chen Cheng 
Published: January 2024

ABSTRACTChloroplast division is initiated by the establishment of the stromal FtsZ ring (Z ring). Assembly and positioning of the Z ring are governed by the chloroplast Min system, which inhibits Z-ring formation everywhere but the middle of the chloroplast. ACCUMULATION AND REPLICATION OF CHLOROPLASTS3 (ARC3), the core component of this system, is a direct inhibitor of Z-ring assembly. Regulation of ARC3 activity is vital thus for chloroplast division. Here, we report that ARC6, which localizes on the chloroplast inner envelope membrane, interacts with ARC3 and acts upstream of ARC3 during chloroplast division. We show that the C-terminal MORN domain of ARC3, demonstrated previously to prevent ARC3-FtsZ interaction, binds to the J-like domain (JLD) of ARC6, enabling full-length ARC3 to interact with FtsZ proteins and activating the inhibitory activity of ARC3 on the assembly of FtsZ filaments. Overexpression of a JLD-deleted version of ARC6 causes disruption of Z-ring formation in an ARC3-dependent manner. Finally, we reveal that ARC6 recruits ARC3 to the middle of the chloroplast. Our findings suggest a model whereby ARC6 regulates the assembly and positioning of the Z ring through fine-tuning the inhibitory activity of ARC3 at the chloroplast division site.One Sentence SummaryThe chloroplast membrane protein ARC6 recruits ARC3 to the chloroplast division site and regulates the assembly of the FtsZ ring by fine-tuning ARC3 activity through its J-like domain.The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (https://academic.oup.com/plcell/pages/General-Instructions) is: Cheng Chen (cgchen@sjtu.edu.cn).
High-Throughput DNA melt measurements enable improved models of DNA folding thermodynamics
Authors: Ke Yuxi , Sharma Eesha , Wayment-Steele Hannah K. , Becker Winston R. , Ho Anthony , Marklund Emil , Greenleaf William J. 
Published: January 2024

AbstractDNA folding thermodynamics are central to many biological processes and biotechnological applications involving base-pairing. Current methods for predicting stability from DNA sequence use nearest-neighbor models that struggle to accurately capture the diverse sequence-dependency of elements other than Watson-Crick base pairs, likely due to insufficient experimental data. We introduce a massively parallel method, Array Melt, that uses fluorescence-based quenching signals to measure equilibrium stability of millions of DNA hairpins simultaneously on a repurposed Illumina sequencing flow cell. By leveraging this dataset of 27,732 sequences with two-state melting behavior, we derived a refined NUPACK-compatible nearest-neighbor model, a richer parameterization nearest-neighbor model that exhibits higher accuracy, and a graph neural network (GNN) model that identifies relevant interactions within DNA beyond nearest neighbors. All models provide improved accuracy in predicting DNA folding thermodynamics, providing improvements relevant forin silicodesign of qPCR primers, oligo hybridization probes, and DNA origami.