bluuebunny/crossref_metadata_2025_split huggingface dataset:
PopGenAdapt: Semi-Supervised Domain Adaptation for Genotype-to-Phenotype Prediction in Underrepresented Populations
Authors: Comajoan Cara Marçal , Mas Montserrat Daniel , Ioannidis Alexander G. 
Published: October 2023

The lack of diversity in genomic datasets, currently skewed towards individuals of European ancestry, presents a challenge in developing inclusive biomedical models. The scarcity of such data is particularly evident in labeled datasets that include genomic data linked to electronic health records. To address this gap, this paper presents PopGenAdapt, a genotype-to-phenotype prediction model which adopts semi-supervised domain adaptation (SSDA) techniques originally proposed for computer vision. PopGenAdapt is designed to leverage the substantial labeled data available from individuals of European ancestry, as well as the limited labeled and the larger amount of unlabeled data from currently underrepresented populations. The method is evaluated in underrepresented populations from Nigeria, Sri Lanka, and Hawaii for the prediction of several disease outcomes. The results suggest a significant improvement in the performance of genotype-to-phenotype models for these populations over state-of-the-art supervised learning methods, setting SSDA as a promising strategy for creating more inclusive machine learning models in biomedical research.Our code is available athttps://github.com/AI-sandbox/PopGenAdapt.
Neurogenesis-mediated circuit remodeling reduces engram reinstatement and promotes forgetting
Authors: Guskjolen Axel , Dhaliwal Jagroop , de la Parra Juan , Epp Jonathan R. , Ko Sangyoon , Chahley Erin , de Snoo Mitch , Solari Michela , Panesar Prabdeep , Snyder Jason , Duan Xin , Sanes Joshua R. , Josselyn Sheena A. , Frankland Paul W. 
Published: October 2023

ABSTRACTPost-training increases in hippocampal neurogenesis are associated with forgetting of hippocampus-dependent memories in adult mice. This form of forgetting might be due to increased numbers of new neurons, remodeling of hippocampal circuitry or some combination of both. Here we tested the hypothesis that neurogenesis-mediated forgetting is caused by remodeling of hippocampal circuits by engineering mice in which adult-generated granule cells hypo- or hyper-integrate into hippocampal circuits. Using gene deletion, opto- and chemogenetic strategies, we find that hypo-integration of newborn neurons prevents post- training exercise-induced forgetting of contextual fear memories. Conversely, inducing hyper- integration of newborn neurons following contextual fear conditioning is sufficient to produce forgetting. Because these interventions did not affect survival of newborn neurons, these findings suggest that neurogenesis-mediated remodeling of hippocampal circuits represents a continuous and active form of interference that alters accessibility of engrams underlying hippocampal memories. Consistent with this, using engram-labeling approaches, we found that exercise-induced forgetting was associated with reduced engram reactivation.
Decoding Internal Decision Making During Reverse Engineering Tasks
Authors: Marsh Brianna , Rego Jocelyn , Levy Mia Matsuhisa , Sayer Mitchell Peter , Waagen Alexander , Barbieux Aidan , Cranford Edward A , Morrison Donald F , Maldonado Froylan , Johnson Jeremy Phillip , DiVita Joseph , Buch Jonathan Michael , Kim Tiffany Hyun-Jin , Lebiere Christian , Fugate Sunny , Bhattacharyya Rajan 
Published: October 2023

ABSTRACTNeural decoding is often limited to tasks with known stimuli and limited response options . Real world tasks, however, are often completely stimulus free with unconstrained user response possibilities. Real time decoding of internal decision making would allow for more complex and interactive Huma Machine Teaming in a way that is not currently possible. To address this problem, we present here a novel method of decoding moments of recognition and their associated internal value judgments in the context of highly complex software reverse engineering tasks. This is done through a combination of P300 detection (a neural marker of recognition) and the Engagement Index (a ratio of neural band powers) to determine whether an item has been identified as relevant to the task (to be further explored) or irrelevant to the task (to be quickly ignored). Artificial neural networks were trained to identify P300s in each subject during the reverse engineering tasks. Dimensionality reduction of neural data during the tasks showed the existence of separately clustering subgroups of P300s with differences in Engagement Index. Subgroups of P300s differentiated by Engagement were further verified as distinct groupings with pupil dilation and user behavior metrics. This decoded information could be used to aid in the reverse engineering process via cognitive offloading of the user’s own decision making on to the visual interface in a completely automated and personalized fashion. This represents a significant advance in domain of real-time neural decoding, and opens up many further possibilities for usage in a broad range of intelligent human systems integration applications.
A label-free approach for relative spatial quantitation of c-di-GMP in microbial biofilms
Authors: McCaughey Catherine S. , Trebino Michael A. , McAtamney Allyson , Isenberg Ruth , Mandel Mark J. , Yildiz Fitnat H. , Sanchez Laura M. 
Published: October 2023

AbstractMicrobial biofilms represent an important lifestyle for bacteria and are dynamic three dimensional structures. Cyclic dimeric guanosine monophosphate (c-di-GMP) is a ubiquitous signaling molecule that is known to be tightly regulated with biofilm processes. While measurements of global levels of c-di-GMP have proven valuable towards understanding the genetic control of c-di-GMP production, there is a need for tools to observe the local changes of c-di-GMP production in biofilm processes. We have developed a label-free method for the direct detection of c-di-GMP in microbial colony biofilms using matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI). We applied this method to the enteric pathogenVibrio cholerae, the marine symbiontV. fischeri, and the opportunistic pathogenPseudomonas aeruginosaPA14 and detected spatial and temporal changes in c-di-GMP signal that accompanied genetic alterations in factors that synthesize and degrade the compound. We further demonstrated how this method can be simultaneously applied to detect additional metabolites of interest in a single experiment.
Determinants of the willingness to pay and willingness to accept in the valuation of informal care. The CUIDARSE study
Authors: Oliva Juan , Peña Longobardo Luz María , García-Mochón Leticia , Abellán-Perpìñan José María , García-Calvente María del Mar 
Published: October 2023

PurposeThis paper aims to study the value of informal care (IC) time from the perspective of caregivers using two alternative contingent valuation tools – willingness to pay (WTP) and willingness to accept (WTA) – and to identify the variables that affect the stated values.Design/methodology/approachThe authors used data from a multi-centre study of 610 adult caregivers conducted in two Spanish regions in 2013. The existence of “protest zeros” and “economic zeros” because of the severe budgetary constraints of the households was also considered. Two-part multivariate models were used to analyse the main factors that explained the declared values of WTA and WTP.FindingsThe average WTP and WTA were €3.12 and €5.98 per hour of care, respectively (€3.2 and €6.3 when estimated values for “protest zeros” and “economic zeros” were considered). Some explanatory variables of WTA and WTP are coincident (place of residence and intensity of care time), whereas other variables only help to explain WTP values (household and negative coping with caregiving) or WTA values (age and burden of care). Some nuances are also identified when comparing the results obtained without protest and economic zeros with the estimated values of these special zeros.Originality/valueStudies analysing the determinants of WTP and WTA in IC settings are very scarce. This paper seeks to provide information to fill this gap. The results indicate that the variables that explain the value of IC from one perspective may differ from the variables that explain it from an alternative perspective. Given the relevance of contextual factors, studies on the topic should be expanded, and care should be taken with the extrapolation of results across countries and settings.
Ecology with artificial intelligence and machine learning in Asia: A historical perspective and emerging trends
Authors: Ryo Masahiro 
Published: October 2023

AbstractThe use of artificial intelligence (AI) and machine learning (ML) has significantly enhanced ecological research in Asia by improving data processing, analysis, and pattern extraction. Analyzing 1550 articles, I show an overview of the use of AI and ML for Asian ecological research. Following the last 20 year trend, I found that the topics in Asian ecological research have transitioned from technical perspectives to more applied issues, focusing on biodiversity conservation, climate change, land use change, and societal impacts. Non‐Asian countries, on the other hand, have focused more on theoretical understanding and ecological processes. The difference between Asian and non‐Asian regions may have emerged due to the ecological challenges faced by Asian countries, such as rapid economic growth, land development, and climate change impacts. In both regions, deep learning related technology has been emerging (e.g., big data collection including image and movement). Within Asia, China has been the Asia‐leading country for AI/ML applications followed by Korea, Japan, India, and Iran. The number of computer science education programs in China has been increasing 3.5× times faster than that in the United States, indicating that a nationwide strategy for computer science development is key for ecological science with AI. Overall, the adoption of AI and ML technologies in ecological studies in Asia has propelled the field forward and opened new avenues for innovative research and conservation practices.
Structure–activity relationships of bensulfuron methyl and its derivatives as novel agents against drug‐resistant Candida auris
Authors: Sun Xue‐Wen , Liu Yixuan , Wang Xiaofang , Li Hao‐Ran , Lin Xin , Tang Jin‐Yin , Xu Qing , Agnew‐Francis Kylie A. , Fraser James A. , Sun Zhi‐Juan , Guddat Luke W. , Wang Jian‐Guo 
Published: October 2023

AbstractWith the emergence of the human pathogen Candida auris as a threat to human health, there is a strong demand to identify effective medicines to prevent the harm caused by such drug‐tolerant human fungi. Herein, a series of 33 new derivatives of bensulfuron methyl (BSM) were synthesized and characterized by 1H NMR, 13C NMR, and HRMS. Among the target compounds, 8a possessed the best Ki value of 1.015 μM against C. auris acetohydroxyacid synthase (CauAHAS) and an MIC value of 6.25 μM against CBS10913, a clinically isolated strain of C. auris. Taken together the structures of BSM and the synthesized compounds, it was found that methoxy groups at both meta‐position of pyrimidine ring are likely to provide desirable antifungal activities. Quantum calculations and molecular dockings were performed to understand the structure–activity relationships. The present study has hence provided some interesting clues for the discovery of novel antibiotics with this distinct mode of action.
Sales manipulation strategies of competitive firms on an e‐commerce platform: Beneficial or harmful?
Authors: Zhang Qing , Li Juan , Xiao Tiaojun 
Published: October 2023

AbstractConsumers are affected by the relative sizes of products’ sales volumes, which is regarded as consumers’ sales comparison behavior when purchasing online. Therefore, some firms manipulate their sales volumes to attract consumers. To shed light on firms’ sales manipulation, we develop game theoretical models to investigate sales manipulation strategies for a high‐quality firm and a low‐quality firm on a platform. We identify conditions for firms’ sales manipulation and investigate its impact on the platform. We find the following: (1) A small amount of sales manipulation volumes may harm each firm. (2) When only the high‐quality (low‐quality) firm manipulates its sales volume, the total market share shrinks (expands), and the profit of the low‐quality (high‐quality) firm is damaged. In this case, the platform can only benefit from the high‐quality firm's sales manipulation. When both firms manipulate sales volumes, each firm aims to claim a higher sales volume than its competitor. (3) At equilibrium, when the unit sales manipulation cost is intermediate, only the high‐quality firm manipulates its sales volume. When the unit sales manipulation cost is low, both firms manipulate sales volumes and consequently get trapped in a Prisoner's Dilemma. In this case, the platform's profit cannot be improved. This study then incorporates considerations of consumers’ sales comparison behavior, nonlinear cost structures for sales manipulation, firms’ long‐term vision, and sales manipulation strategy in competitive supply chains to reveal that most aforementioned results are qualitatively robust.
Considerations in geriatric dermatopathology
Authors: Brent Ashley A. , Mancuso Elizabeth , Smith Emily 
Published: October 2023

AbstractThis review provides an overview of considerations in geriatric dermatopathology. The nuances of specimen collection and reporting in this population, including the importance of obtaining adequate tissue, providing detailed clinical information and ethical considerations surrounding specimen collection will be discussed. The histopathologic changes associated with aging and the morphologic features of common lesions related to photoaging are outlined followed by a discussion of common interpretation pitfalls, specifically entities at risk of overinterpretation and those related to hyper‐ and hypopigmentation. Finally, the recent literature is reviewed regarding special cases and what this implies for future research both in dermatology and dermatopathology.
The intra‐matrix and gastrointestinal parameters affecting the bioaccessibility of food biopeptides
Authors: Le Thanh‐Do , Suttikhana Itthanan , Ashaolu Tolulope Joshua 
Published: October 2023

SummaryThe discussions around biopeptides generated from foods are associated with the numerous physiologic functions and therapeutic interventions that they potentiate, especially toward cardiovascular and degenerative diseases. The recurring issue about these biopeptides, however, is the wide gap left between laboratory experimentations and human intervention studies, apart from the fact that the conditions of testing or validation are not the same in both instances. Therefore, the gastrointestinal processing of biopeptides must be on par with their bioaccessibility, which is a critical step toward their bioavailability. The checks and balances of bioaccessibility are associated with the effects of the gastrointestinal enzymes, the interplay of other micro‐ and macro‐nutrients in whole or part, as well as the disruption of the integrity of the intestinal mucosal cells. We herein discussed the interplay of biopeptides with food matrices with regard to metal‐, phenol‐, lipid‐, and sugar‐peptide complexes, including mucins and other gastrointestinal enzyme secretion. These most common parameters and mechanistic activities led to the proposition of novel techniques for ensuring peptides' bioaccessibility and physiologic functions, a backdrop for futuristic studies that would contribute to our understanding and actualisation of bioaccessible peptides well incorporated and maintained in desirable functional food products.
Dietary fibre concentrates from avocado and mango by‐products; antioxidant capacity and polyphenols evaluation by HPLC‐IDA‐EPI‐MS
Authors: Angulo‐López Jorge E. , Losoya‐Sifuentes Carolina , Palmieri Sara , Torres‐León Cristián , Flores‐Gallegos Adriana C. , Fanti Federico , Sergi Manuel , Ascacio‐Valdes Juan A. , Contreras Esquivel Juan C. , Rúelas‐Chácon Xochil , Aguilar Cristóbal N. , Compagnone Dario 
Published: October 2023

SummaryPhenolics bound to dietary fibres (DF‐PCs) represent a valuable source of antioxidants that are often wasted. DF‐PCs can be obtained as residues from conventional extraction processes of PCs derived from agro‐industrial by‐products. This study aimed to characterise DF‐PCs generated after the PC extraction process from the avocado peel (AP), mango peel (MP) and husk mango seed (testa) (MT), with a focus on solid residue or concentrated fibre (APFT: avocado peel fibre; MPFT: mango peel fibre; MTFT: mango testa fibre). The by‐products were evaluated under both non‐defatted and defatted conditions before simulating the PC extraction process. PCs were quantified (TPC) and identified (HPLC‐IDA‐EPI‐MS). Their antioxidant activity (AA) was determined (ABTS+, DPPH* and FRAP). Among the evaluated fibres, non‐defatted AP and defatted MP and MT exhibited the highest TPC content (22.64 ± 0.3, 37.31 ± 1.78 and 6.07 ± 0.08 mg GAE/g), respectively. Using the DPPH* assay, all fibre concentrates showed lower AA compared to the by‐products. Using FRAP assay, defatting gave the largest activity for mango samples. HPLC‐IDA‐EPI‐MS analysis of PC profiles resulted in the presence of 62 PC compounds in the fibre concentrates. These DF‐PCs, with a significant content of PCs, may be relevant as functional ingredients for food production.
Comparative molecular conformation, interaction, and network characteristics of wheat gluten modulated by sodium chloride and sodium carbonate
Authors: Kuang Jiwei , Xu Ke 
Published: October 2023

SummaryThe objective of the study was to investigate the configurational changes and aggregation mechanism of wheat gluten induced by sodium chloride (NaCl) and sodium carbonate (Na2CO3). The results showed that NaCl shielded surface charges of gluten, developed more hydrogen bonds with tyrosine, and stabilised the secondary structure, while Na2CO3 promoted significant transition of the secondary structure from random coils and β‐turn to β‐sheet. Both NaCl and Na2CO3 quenched tryptophan fluorescence and promoted the aggregation of gluten subunits, where Na2CO3 induced covalent bond formation other than disulphides and facilitated gluten network development. Atomic force microscopy images confirmed different molecular surface features in gluten network. In conclusion, both NaCl and Na2CO3 demonstrated the ability to promote rheology, aggregation, and network formation of gluten but different molecular mechanisms were involved. This work provides valuable insights for the processing of salted and alkaline noodles.
Noninvasive prenatal screening with conventional sequencing depth to screen fetal copy number variants: A retrospective study of 19 144 pregnant women
Authors: Wang Zhiwei , Tang Xinxin , Yang Shuting , Zhao Yali , Yin Ting , Chen Min , Zhang Yue , Wang Yongan , Zhang Fang , Wang Leilei 
Published: October 2023

AbstractAimTo investigate the detectability of noninvasive prenatal screening (NIPS) with conventional sequencing depth to detect fetal copy number variants.MethodsWe performed a retrospective study in a total of 19 144 pregnant women. Their cell‐free plasma DNA were assessed for trisomy 21, trisomy 18, trisomy 13, sex chromosome aneuploidies, and genome‐wide copy number variants by NIPS at conventional sequencing depth.ResultsThree hundred seventy‐four cases (2.0%, 374/19 144) with abnormal results were detected, which including 84 cases (0.4%, 84/19 144) with high risk of trisomy 21, 18, and 13, 90 cases (0.5%, 90/19 144) with high risk of sex chromosome abnormalities (SCA), and 44 cases (0.2%, 44/19 144) with high risk of other chromosome aneuploidies. One hundred fifty‐six cases (0.8%, 156/19 144) with high risk of copy number variations (CNVs) were also detected. In following prenatal diagnosis, composite positive predictive value (PPV) of trisomy 21, 18, and 13 was 69.6% (48/69). The PPV of SCAs was 37.3% (19/51). And the PPVs for CNVs was detected as 51.0% (<5 Mb), 71.4% (5 Mb ≤ CNV ≤10 Mb), 56.5% (>10 Mb). Finally, a follow‐up about the pregnancy outcomes were conducted for all available cases.ConclusionsNIPS yielded high PPVs for trisomy 21, 18, and 13 aneuploidies and moderate PPVs for SCAs and CNVs. The screening effectiveness was closely related to the size of CNV fragments. Larger CNVs, especially larger than 5 Mb, could be detected more accurately by NIPS in our analytic technique. Meanwhile, diagnostic confirmation by microarray analysis was highly recommended.
The effects of formulation on the pharmacokinetics of itraconazole and amiodarone in dogs after oral administration of a combination product, commercial products, and compounded products
Authors: Hunter Robert P. , Madigan Roy 
Published: October 2023

AbstractThis study evaluated four different formulations of itraconazole and amiodarone. Formulation 1 was Vida's combination tablet containing both active pharmaceutical ingredients (APIs). Formulation 2 was separate, commercially available human generic capsules and tablets of itraconazole and amiodarone, respectively. Formulation 3 was separate, compounded suspensions of itraconazole and amiodarone. Formulation 4 was a compounded chewable tablet of itraconazole. Eight female dogs were dosed with 5 mg/kg of itraconazole and 15 mg/kg amiodarone (except for formulation 4, which only received 5 mg/kg itraconazole) once weekly for 4 weeks using a modified Latin Square design, ensuring that all dogs received all formulations with a 7‐day washout between treatments. Animals were fasted overnight prior to each dose administration, with food returned to all animals 4 h post‐dose. Blood samples (3 mL) were collected pre‐treatment (0) and at appropriate time points over 72 h after each dose for a total of 14 samples per dog per treatment. There was high variability in the serum concentration data within treatment groups for itraconazole. The compounded suspensions were difficult to dose due to the nature of the formulations. The volumes dosed were accurate and consistent, but the suspension was thin and settled immediately when shaking was stopped for both itraconazole and amiodarone. All serum samples following itraconazole chewable tablet administration were not detectable or just above itraconazole's LOQ and thus did not allow for pharmacokinetic determination.