bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Cognitive, Age, Functioning, and Apolipoprotein E4 (CAFE) Scorecard to Predict the Development of Alzheimer’s Disease: A White-Box Approach
Authors: Wiranto Yumiko , Setiawan Devin R , Watts Amber , Ashourvan Arian ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: August 2024

AbstractObjectiveThis study aimed to bridge the gap between the costliness and complexity of diagnosing Alzheimer’s disease by developing a scoring system with interpretable machine learning to predict the risk of Alzheimer’s using obtainable variables to promote accessibility and early detection.Participants and MethodsWe analyzed 713 participants with normal cognition or mild cognitive impairment from the Alzheimer’s Disease Neuroimaging Initiative. We integrated cognitive test scores from various domains, informant-reported daily functioning,APOEgenotype, and demographics to generate the scorecards using the FasterRisk algorithm.ResultsVarious combinations of 5 features were selected to generate ten scorecards with a test area under the curve ranging from 0.867 to 0.893. The best performance scorecard generated the following point assignments: age < 76 (-2 points); noAPOEε4alleles (-3 points); Rey Auditory Verbal Learning Test <= 36 items (4 points); Logical Memory delayed recall <= 3 items (5 points); and Functional Assessment Questionnaire <= 2 (-5 points). The probable Alzheimer’s development risk was 4.3% for a score of -10, 31.5% for a score of -3, 50% for a score of -1, 76.3% for a score of 1, and greater than 95% for a score of > 6.ConclusionsOur findings highlight the potential of these interpretable scorecards to predict the likelihood of developing Alzheimer’s disease using obtainable information, allowing for applicability across diverse healthcare environments. While our initial scope centers on Alzheimer’s disease, the foundation we have established paves the way for similar methodologies to be applied to other types of dementia.
The Use of Wastewater Surveillance to Estimate SARS-CoV-2 Fecal Viral Shedding Pattern and Identify Time Periods with Intensified Transmission
Authors: Yang Wan , Omoregie Enoma , Olsen Aaron , Watts Elizabeth A. , Parton Hilary , Lee Ellen 
Published: August 2024

ABSTRACTBackgroundWastewater-based surveillance is an important tool for monitoring the COVID-19 pandemic. However, it remains challenging to translate wastewater SARS-CoV-2 viral load to infection number, due to unclear shedding patterns in wastewater and potential differences between variants.ObjectivesWe utilized comprehensive wastewater surveillance data and estimates of infection prevalence (i.e., the source of the viral shedding) available for New York City (NYC) to characterize SARS-CoV-2 fecal shedding pattern over multiple COVID-19 waves.MethodsWe collected SARS-CoV-2 viral wastewater measurements in NYC during August 31, 2020 – August 29, 2023 (N= 3794 samples). Combining with estimates of infection prevalence (number of infectious individuals including those not detected as cases), we estimated the time-lag, duration, and per-infection fecal shedding rate for the ancestral/Iota, Delta, and Omicron variants, separately. We also developed a procedure to identify occasions with intensified transmission.ResultsModels suggested fecal viral shedding likely starts around the same time as and lasts slightly longer than respiratory tract shedding. Estimated fecal viral shedding rate was highest during the ancestral/Iota variant wave, at 1.44 (95% CI: 1.35 – 1.53) billion RNA copies in wastewater per day per infection (measured by RT-qPCR), and decreased by ∼20% and 50-60% during the Delta wave and Omicron period, respectively. We identified around 200 occasions during which the wastewater SARS-CoV-2 viral load exceeded the expected level in any of 14 sewersheds. These anomalies disproportionally occurred during late January, late April - early May, early August, and from late-November to late-December, with frequencies exceeding the expectation assuming random occurrence (P< 0.05; bootstrapping test).DiscussionThese estimates may be useful in understanding changes in underlying infection rate and help quantify changes in COVID-19 transmission and severity over time. We have also demonstrated that wastewater surveillance data can support the identification of time periods with potentially intensified transmission.
The Impact of Myosteatosis on Cardiac Function in a Healthy Population: Insights from Abdominal CT Imaging
Authors: Kim Myung Jin , Nam Hyo-Jung , Cho Yun Kyung , Kim Eun Hee , Lee Min Jung , Lee Woo Je , Kim Hong-Kyu , Jung Chang Hee 
Published: August 2024

AbstractBackground:Ectopic fat deposition in skeletal muscle, termed myosteatosis, is a key factor in insulin resistance and contributes to various metabolic disturbances. This study evaluated the association between myosteatosis, assessed via abdominal computed tomography, and cardiac function in an asymptomatic Korean population.Methods:This cross-sectional study included 7,716 participants (4,902 [63.5%] men and 2,814 [36.5%] women, mean age 53.2 ± 8.0) who underwent routine health check-ups at Asan Medical Center (Seoul, Korea). Myosteatosis was evaluated by segmenting the total abdominal muscle area (TAMA) at the L3 vertebral level into normal-attenuation muscle area (NAMA), low-attenuation muscle area (LAMA), and inter-/intra-muscular adipose tissue (IMAT). Patients were categorized into quartiles based on the NAMA/TAMA index, calculated by dividing the NAMA by TAMA and multiplying by 100. Cardiac function was assessed by transthoracic echocardiography.Results:Higher NAMA/TAMA index levels were associated with decreased absolute values of the E/E’ ratio and increased E/A ratio in both men and women. Multiple linear regression analysis revealed a significant correlation between the NAMA/TAMA index and both the E/A and E/E’ ratios after adjusting for covariates. No significant correlation was found with left ventricular (LV) ejection fraction or LV mass index.Conclusions:The degree of myosteatosis was significantly associated with diastolic function in an asymptomatic population, while systolic function remained unaffected.
Nematodes Vector Bacteriophages in Compost and Soil
Authors: van Sluijs Lisa , Dietz Cassidy , van Noort Floris , Helder Johannes , Zwart Mark W. , Mason-Jones Kyle 
Published: August 2024

AbstractBacteriophages (phages) infect bacteria to reproduce and are often lethal to their host. To maintain the infection cycle, soil phages must travel from one suitable host to the next. However, traversing the soil matrix presents a dangerous journey for phages, which need to encounter the right hosts in this spatially complex habitat, but are not capable of active motion and can adsorb to soil particles. Here, we tested the hypothesis that bacterial-feeding nematodes (roundworms) present a reliable vehicle of soil transport for phages. First, we demonstrated that the bacterivorous nematodeCaenorhabditis elegansvectored the laboratory model phage T7 as well as the soil phage Φ Ppu-W11 on agar. Sorption assays carried out with paralyzed and non-paralyzed nematodes showed that phage transport can occur via both external cuticular attachment and ingestion, and that the presence of host bacteria is not required for phage vectoring. Finally, we designed a microcosm to test phage transfer in compost and sandy soil usingC. elegansand its sister species,C. remanei, respectively. This experiment confirmed that nematodes also enable phage movement through complex spatial habitats. This novel mechanism of phage vectoring extends our understanding of virus transmission in soil, revealing new multitrophic interactions that may influence soil functioning.
The multi-level effect of chlorpyrifos during clownfish metamorphosis
Authors: Reynaud Mathieu , Vianello Stefano , Lee Shu-Hua , Salis Pauline , Wu Kai , Frederich Bruno , Lecchini David , Besseau Laurence , Roux Natacha , Laudet Vincent 
Published: August 2024

AbstractChemical pollution in coastal waters, particularly from agricultural runoff organophosphates, poses a significant threat to marine ecosystems, including coral reefs. Pollutants such as chlorpyrifos (CPF) are widely used in agriculture and have adverse effects on marine life and humans. In this paper, we investigate the impact of CPF on the metamorphosis of a coral reef fish model, the clownfishAmphiprion ocellaris, focusing on the disruption of thyroid hormone (TH) signalling pathways. Our findings reveal that by reducing TH levels, CPF exposure impairs the formation of characteristic white bands in clownfish larvae, indicative of metamorphosis progression. Interestingly, TH treatment can rescue these effects, establishing a direct causal link between CPF effect and TH disruption. The body shape changes occurring during metamorphosis are also impacted by CPF exposure, shape changes are less advanced in CPF-treated larvae than in control conditions. Moreover, transcriptomic analysis elucidates CPF’s effects on all components of the TH signalling pathway. Additionally, CPF induces systemic effects on cholesterol and vitamin D metabolism, DNA repair, and immunity, highlighting its broader TH-independent impacts. Pollutants are often overlooked in marine ecosystems, particularly in coral reefs. Developing and enhancing coral reef fish models, such asAmphiprion ocellaris, offers a more comprehensive understanding of how chemical pollution affects these ecosystems. This approach provides new insights into the complex mechanisms underlying CPF toxicity during fish metamorphosis, shedding light on the broader impact of environmental pollutants on marine organisms.HighlightsChlorpyrifos (CPF) is an insecticide widely used in agriculture for the past five decades and has adverse effects on marine life and humansCPF exposure impairs the formation of characteristic white bands in clownfish larvae, indicative of metamorphosis progressionDuring metamorphosis, clownfish larvae lose their elongated body shape and transform into miniature ovoid-shaped adults, these shape changes are less advanced in CPF-treated larvaeCPF induces systemic effects on cholesterol and vitamin D metabolism, DNA repair, and immunity, highlighting its broader TH-independent impacts
Activity-dependent synapse elimination requires caspase-3 activation
Authors: Yu Zhou , Gutu Andrian , Kim Namsoo , O’Shea Erin K. 
Published: August 2024

AbstractDuring brain development, synapses are initially formed in excess and are later eliminated in an activity-dependent manner. Weak synapses are preferentially removed, but the mechanism linking neuronal activity to synapse removal is unclear. Here we show that, in the developing mouse visual pathway, inhibiting synaptic transmission induces postsynaptic activation of caspase-3. Caspase-3 deficiency results in defects in synapse elimination driven by both spontaneous and experience-dependent neural activity. Notably, caspase-3 deficiency blocks activity-dependent synapse elimination, as evidenced by reduced engulfment of inactive synapses by microglia. Furthermore, in a mouse model of Alzheimer’s disease, caspase-3 deficiency protects against synapse loss induced by amyloid-β deposition. Our results reveal caspase-3 activation as a key step in activity-dependent synapse elimination during development and synapse loss in neurodegeneration.
Reducing maladaptive behavior in neuropsychiatric disorders using network modification
Authors: Timme Nicholas 
Published: August 2024

AbstractNeuropsychiatric disorders are caused by many factors and produce a wide range of symptomatic maladaptive behaviors in patients. Despite this great variance in causes and resulting behavior, we believe the maladaptive behaviors that characterize neuropsychiatric disorders are most proximally determined by networks of neurons and that this forms a common conceptual link between these disorders. Operating from this premise, it follows that treating neuropsychiatric disorders to reduce maladaptive behavior can be accomplished by modifying the patient’s network of neurons. In this proof-of-concept computational psychiatry study, we tested this approach in a simple neural network model that produces aversion-resistant alcohol drinking – a key maladaptive behavior associated with alcohol use disorder. We demonstrated that it was possible to predict personalized network modifications that substantially reduced maladaptive behavior without inducing side effects. Furthermore, we found that it was possible to predict effective treatments with limited knowledge of the model and that information about neural activity during certain types of trials was more helpful in predicting treatment than information about model parameters. We hypothesize that this is a general feature of developing effective treatment strategies for networks of neurons. This computational study lays the groundwork for future studies utilizing more biologically realistic network models in conjunction within vivodata.
Experience-dependent modulation of collective behavior in larval zebrafish
Authors: Harpaz Roy , Phillips Morgan , Goel Ronan , Fishman Mark C. , Engert Florian 
Published: August 2024

AbstractComplex group behavior can emerge from simple inter-individual interactions. Commonly, these interactions are considered static and hardwired and little is known about how experience and learning affect collective group behavior. Young larvae use well described visuomotor transformations to guide interindividual interactions and collective group structure. Here, we use naturalistic and virtual-reality (VR) experiments to impose persistent changes in population density and measure their effects on future visually evoked turning behavior and the resulting changes in group structure. We find that neighbor distances decrease after exposure to higher population densities, and increase after the experience of lower densities. These adaptations develop slowly and gradually, over tens of minutes and remain stable over many hours. Mechanistically, we find that larvae estimate their current group density by tracking the frequency of neighbor-evoked looming events on the retina and couple the strength of their future interactions to that estimate. A time-varying state-space model that modulates agents’ social interactions based on their previous visual-social experiences, accurately describes our behavioral observations and predicts novel aspects of behavior. These findings provide concrete evidence that inter-individual interactions are not static, but rather continuously evolve based on past experience and current environmental demands. The underlying neurobiological mechanisms of experience dependent modulation can now be explored in this small and transparent model organism.
Mechanochemical forces regulate the composition and fate of stalled nascent chains
Authors: Khan Danish , Vinayak Ananya A , Sitron Cole S , Brandman Onn 
Published: August 2024

AbstractThe ribosome-associatedqualitycontrol (RQC) pathway resolves stalled ribosomes. As part of RQC, stalled nascent polypeptide chains (NCs) are appended withCArboxy-Terminal amino acids (CAT tails) in an mRNA-free, non-canonical elongation process. CAT tail composition includes Ala, Thr, and potentially other residues. The relationship between CAT tail composition and function has remained unknown. Using biochemical approaches in yeast, we discovered that mechanochemical forces on the NC regulate CAT tailing. We propose CAT tailing initially operates in an “extrusion mode” that increases NC lysine accessibility for on-ribosome ubiquitination. Thr in CAT tails enhances NC extrusion by preventing formation of polyalanine, which can form α-helices that lower extrusion efficiency and disrupt termination of CAT tailing. After NC ubiquitylation, pulling forces on the NC switch CAT tailing to an Ala-only “release mode” which facilitates nascent chain release from large ribosomal subunits and NC degradation. Failure to switch from extrusion to release mode leads to accumulation of NCs on large ribosomal subunits and proteotoxic aggregation of Thr-rich CAT tails.One sentence summaryMechanochemical forces regulate the composition of CAT tails to extrude or release stalled nascent chains and recycle ribosomes.
Isolation and molecular characterization of an enteric isolate of the Genotype-I Bovine coronavirus with notable mutations in the receptor binding domain of the spike glycoprotein and deletion downstream the RNA binding domain of the nucleocapsid protein
Authors: Shah Abid , Gauger Phillip , Hemida Maged Gomaa 
Published: August 2024

AbstractBovine coronavirus (BCoV) continues to be a significant threat to cattle populations despite the implementation of vaccination programs. The continuous circulation of BCoV highlights the necessity for ongoing genomic surveillance to understand better the virus’s evolution and its impact on cattle health. The main goal of this study was to do isolation and perform a comprehensive molecular characterization of a new enteric field isolate of the BCoV. To identify any genetic elements in the sequences of this BCoV isolate that could act as genetic markers for BCoV infection in cattle. To achieve these objectives, the newly identified BCoV isolate was propagated on the MDBK cell line for several subsequent blind passages. The immunofluorescence assay verified confirmation of the virus propagation. We plaque purified this isolate and titrated it by plaque assay using the HRT-18 cell line. We examined the viral protein expression using the SDS-PAGE followed by the Western blot using the BCoV/S and BCoV/N and BCoV/S antibodies. Our results show a substantial increase in the viral genome copy number, protein expression, and virus infectivity of this BCoV isolate with the increase in cell culture passages. The full-length genome sequence of this isolate using the NGS was drafted. The vial genome is 31 Kb in length. The viral genome has the typical BCoV organization (5’-UTR-Gene- 1- HE-S-M-E-N-UTR-3’). Our phylogenetic analysis based on the nucleotide sequences of the (full-length genome, S, HE, and N) showed that the BCoV-13 clustered with other members of the BCoV (genotype I-i). The sequence analysis shows several synonymous mutations among various domains of the S glycoprotein, especially the receptor binding domain. We found nine notable nucleotide deletions immediately downstream of the RNA binding domain of the nucleocapsid gene. Further gene function studies are encouraged to study the function of these mutations on the BCoV molecular pathogenesis and immune regulation/evasion. This research enhances our understanding of BCoV genomics and contributes to improved diagnostic and control measures for BCoV infections in cattle populations.
FoldToken4: Consistent & Hierarchical Fold Language
Authors: Gao Zhangyang , Tan Cheng , Li Stan Z. 
Published: August 2024

AbstractCreating protein structure language has attracted increasing attention in unifing the modality of protein sequence and structure. While recent works, such as FoldToken1&2&3 have made great progress in this direction, the relationship between languages created by different models at different scales is still unclear. Moreover, models at multiple scales (different code space size, like 25, 26, ⋯, 212) need to be trained separately, leading to redundant efforts. We raise the question:Could a single model create multiscale fold languages?In this paper, we propose FoldToken4 to learn the consistent and hierarchical of multiscale fold languages. By introducing multiscale code adapters and token mixing techniques, FoldToken4 can generate multiscale languages from the same model, and discover the hierarchical token-mapping relationships across scales. To the best of our knowledge, FoldToken4 is the first effort to learn multi-scale token consistency and hierarchy in VQ research; Also, it should be more novel in protein structure language learning.
Kaon superfluidity in the early Universe
Authors: Cao Gaoqing 
Published: August 2024

Previously, it was found that pion superfluidity could be realized in the quantum chromodynamics (QCD) epoch of the early Universe, when lepton flavor asymmetry |le+lμ| is large enough to generate a charge chemical potential |μQ| larger than vacuum pion mass. By following the same logic, kaon superfluidity might also be possible when |le+lμ| is so large that |μQ| becomes larger than vacuum kaon mass. Such a possibility is checked by adopting Ginzburg-Landau approximation within the three-flavor Polyakov–Nambu–Jona-Lasinio model. Consider the case with full chemical balance, though kaon superfluidity could be stable compared to the chiral phases with only σ condensations, it would get killed by the more favored homogeneous pion superfluidity. If we introduce mismatch between s and d quarks, kaon superfluidity would require so large s quark density that such a state is impossible in the early Universe.

Published by the American Physical Society
2024
Non-Hermitian lattice fermions in the 2D Gross-Neveu-Yukawa model
Authors: Guo Xingyu , Ma Chen-Te , Zhang Hui 
Published: August 2024

We work the lattice fermions and non-Hermitian formulation in the 2D Gross-Neveu-Yukawa (GNY) model and demonstrate the numerical implementation for two flavors by the hybrid Monte Carlo. Our approach has a notable advantage in dealing with chiral symmetry on a lattice by avoiding the Nielsen-Ninomiya theorem, due to the nonsymmetrized finite-difference operator. We restore the hypercubic symmetry by averaging over all possible orientations with the proper continuum limit. Our study is the first simulation for the interacting fermion formulated in a non-Hermitian way. We compare the numerical solution with the one-loop resummation. The resummation results matches with the numerical solution in ⟨ϕ⟩, ⟨ϕ2⟩, ⟨Tr(ψ¯1ψ1+ψ¯2ψ2)/2⟩, and ⟨Tr(ψ¯1ψ1+ψ¯2ψ2)ϕ/2⟩. We also used the one-loop resummation to provide the renormalization group flow and asymptotic safety in the 2D GNY model.

Published by the American Physical Society
2024
Indirect probe of electroweak-interacting particles at the
μTRISTAN

μ+μ+
collider
Authors: Okabe Risshin , Shirai Satoshi 
Published: August 2024

A novel collider, called μTRISTAN, was recently proposed, offering the capability to achieve high-energy collisions of antimuons. This high-energy collider presents an exceptional opportunity for the discovery of electroweak-interacting massive particles (EWIMPs), which are predicted by various new physics models. In a lepton collider like μTRISTAN, the potential for discovering EWIMPs extends beyond their direct production. Quantum corrections arising from EWIMP loops can significantly enhance our prospects for discovery by precise measurement of Standard Model processes. This study focuses on the indirect detection method within the μTRISTAN experiment, with a specific emphasis on TeV-scale EWIMP dark matter scenarios that yield the correct thermal relic density. At collision energies for s=O(1–10)  TeV, these EWIMPs introduce noticeable effects, typically in the range of O(0.1–1)%. Our findings indicate that at s=2(10)  TeV, with an integrated luminosity of 10  ab−1, μTRISTAN can detect Higgsinos at a mass of 1.3 (3.0) TeV and winos at a mass of 1.9 (4.4) TeV, assuming an optimistic level of systematic uncertainty in the observation of the Standard Model processes.

Published by the American Physical Society
2024