bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fine mapping and analysis of a candidate gene controlling Phytophthora blight resistance in cucumber
Authors: Wang R. , Lin Y.'e. , Zhang C. , Wu H. , Jin Q. , Guo J. , Cao H. , Tan D. , Wu T. 
Published: April 2024

ABSTRACT

Cucumber blight is a destructive disease. The best way to control this disease is resistance breeding. This study focuses on disease resistance gene mapping and molecular marker development.

We used the resistant cucumber, JSH, and susceptible cucumber, B80, as parents to construct F2 populations. Bulked segregant analysis (BSA) combined with specific length amplified fragment sequencing (SLAF‐seq) were used, from which we developed cleaved amplified polymorphic sequence (CAPs) markers to map the resistance gene.

Resistance in F2 individuals showed a segregation ratio of resistance:susceptibility close to 3:1. The gene in JSH resistant cucumber was mapped to an interval of 9.25 kb, and sequencing results for the three genes in the mapped region revealed three mutations at base sites 225, 302, and 591 in the coding region of Csa5G139130 between JSH and B80, but no mutations in coding regions of Csa5G139140 and Csa5G139150. The mutations caused changes in amino acids 75 and 101 of the protein encoded by Csa5G139130, suggesting that Csa5G139130 is the most likely resistance candidate gene. We developed a molecular marker, CAPs‐4, as a closely linked marker for the cucumber blight resistance gene.

This is the first report on mapping of a cucumber blight resistance gene and will provideg a useful marker for molecular breeding of cucumber resistance to Phytophthora blight.
Cover Image
Authors: Zhang Qingshuang , Yang Hongwei , Teame Tsegay , Ran Chao , Yang Yalin , Yao Yuanyuan , Ding Qianwen , Liu Shubin , Li Shengkang , Zhang Zhen , Zhou Zhigang 
Published: April 2024

The cover image is based on the Review Article Immune disorders induced by improper use of dietary immunostimulants in aquatic animals: Research progress and prospective solutions by targeting gut microbiota by Qingshuang Zhang and Hongwei Yang et al., https://doi.org/10.1111/raq.12852.[Correction added on 27 March 2024, after first online publication: Cover image has been changed]
image
Interdependent network restoration games with incomplete information and bounded rationality
Authors: Talebiyan Hesam , Duenas‐Osorio Leonardo 
Published: April 2024

AbstractCommunities face the challenge of finding restoration strategies in the aftermath of disasters. In particular, independent and self‐interested utility managers devise such strategies for infrastructure through a heuristic decentralized process. This paper takes a game‐theoretic approach to model the decentralized and strategic restoration decision making with application to interdependent infrastructure. Particularly, we model the decision process using simultaneous games to investigate decision makers' conflicting preferences. We employ Bayesian games to incorporate the realistic assumptions of poor interagent communication, resulting in incomplete information. Also, we account for behavioral biases such as bounded rationality, cooperative behavior or lack thereof, and equality‐driven resource allocations. We test our models using ideal, synthetic interdependent networks, and the realistic infrastructure of Shelby County, TN. Results show that cooperation leads to the best‐performing decisions even if others are not cooperative. The necessity of cooperation is even higher when there is a dominant player whose service is vital to other players. Our sensitivity results highlight the significant influence of resource availability and allocation on the performance of restoration plans. Our approach enhances the practicality of decision models for community resilience, and unravels novel policy strategies such as cooperation incentives.
Monitoring ESBL-
Escherichia coli
in Swiss wastewater between November 2021 and November 2022: insights into population carriage
Authors: Conforti Sheena , Holschneider Aurélie , Sylvestre Émile , Julian Timothy R. 
Published: April 2024

ABSTRACT

Antimicrobial resistance (AMR) poses a global health threat, causing millions of deaths annually, with expectations of increased impact in the future. Wastewater surveillance offers a cost-effective, non-invasive tool to understand AMR carriage trends within a population. We monitored extended-spectrum β-lactamase producing
Escherichia coli
(ESBL-
E. coli
) weekly in influent wastewater from six wastewater treatment plants (WWTPs) in Switzerland (November 2021 to November 2022) to investigate spatio-temporal variations, explore correlations with environmental variables, develop a predictive model for ESBL-
E. coli
carriage in the community, and detect the most prevalent ESBL-genes. We cultured total and ESBL-
E. coli
in 300 wastewater samples to quantify daily loads and percentage of ESBL-
E. coli
. Additionally, we screened 234 ESBL-
E. coli
isolates using molecular methods for the presence of 18 ESBL-gene families. We found a population-weighted mean percentage of ESBL-
E. coli
of 1.9% (95% confidence interval: 1.8–2%) across all sites and weeks, which can inform ESBL-
E. coli
carriage. Concentrations of ESBL-
E. coli
varied across WWTPs and time, with higher values observed in WWTPs serving larger populations. Recent precipitations (previous 24/96 h) showed no significant association with ESBL-
E. coli
, while temperature occasionally had a moderate impact (
P
< 0.05, correlation coefficients approximately 0.40) in some locations. We identified
bla
CTX-M-1
,
bla
CTX-M-9
, and
bla
TEM
as the predominant ESBL-gene families. Our study demonstrates that wastewater-based surveillance of culturable ESBL-
E. coli
provides insights into AMR trends in Switzerland and may also inform resistance. These findings establish a foundation for long term, nationally established monitoring protocols and provide information that may help inform targeted public health interventions.

IMPORTANCE

Antimicrobial resistance (AMR) is a global health threat and is commonly monitored in clinical settings, given its association with the risk of antimicrobial-resistant infections. Nevertheless, tracking AMR within a community proves challenging due to the substantial sample size required for a representative population, along with high associated costs and privacy concerns. By investigating high resolution temporal and geographic trends in extended-spectrum beta-lactamase producing
Escherichia coli
in wastewater, we provide an alternative approach to monitor AMR dynamics, distinct from the conventional clinical settings focus. Through this approach, we develop a mechanistic model, shedding light on the relationship between wastewater indicators and AMR carriage in the population. This perspective contributes valuable insights into trends of AMR carriage, emphasizing the importance of wastewater surveillance in informing effective public health interventions.
Phylogenetic analysis of the promoter element 2 of paramyxo- and filoviruses
Authors: Ashida Shoichi , Kojima Shohei , Okura Takashi , Kato Fumihiro , Furuyama Wakako , Urata Shuzo , Matsumoto Yusuke 
Published: April 2024

ABSTRACT

Paramyxo- and filovirus genomes are equipped with bipartite promoters at their 3
'
ends to initiate RNA synthesis. The two elements, the primary promoter element 1 (PE1) and the secondary promoter element 2 (PE2), are separated by a spacer region that must be precisely a multiple of 6 nucleotides (nts), indicating these viruses adhere to the “rule of six.” However, our knowledge of PE2 has been limited to a narrow spectrum of virus species. In this study, a comparative analysis of 1,647 paramyxoviral genomes from a public database revealed that the paramyxovirus PE2 can be clearly categorized into two distinct subcategories: one marked by C repeats at every six bases (exclusive to the subfamily
Orthoparamyxovirinae
) and another characterized by CG repeats every 6 nts (observed in the subfamilies
Avulavirinae
and
Rubulavirinae
). This unique pattern collectively mirrors the evolutionary lineage of these subfamilies. Furthermore, we showed that PE2 of the
Rubulavirinae
, with the exception of mumps virus, serves as part of the gene-coding region. This may be due to the fact that the
Rubulavirinae
are the only paramyxoviruses that cannot propagate without RNA editing. Filoviruses have three to eight consecutive uracil repeats every six bases (UN
5
) in PE2, which is located in the 3
'
end region of the genome. We obtained PE2 sequences from 2,195 filoviruses in a public database and analyzed the sequence conservation among virus species. Our results indicate that the continuity of UN
5
hexamers is consistently maintained with a high degree of conservation across virus species.

IMPORTANCE

The genomic intricacies of paramyxo- and filoviruses are highlighted by the bipartite promoters—promoter element 1 (PE1) and promoter element 2 (PE2)—at their 3
'
termini. The spacer region between these elements follows the “rule of six,” crucial for genome replication. By a comprehensive analysis of paramyxoviral genome sequences, we identified distinct subcategories of PE2 based on C and CG repeats that were specific to
Orthoparamyxovirinae
and
Avulavirinae
/
Rubulavirinae
, respectively, mirroring their evolutionary lineages. Notably, the PE2 of
Rubulavirinae
is integrated into the gene-coding region, a unique trait potentially linked to its strict dependence on RNA editing for virus growth. This study also focused on the PE2 sequences in filovirus genomes. The strict conservation of the continuity of UN
5
among virus species emphasizes its crucial role in viral genome replication.
Contrasting constraints on the temporal and spatial extents of normal faults from the Hilltop and Lewis mining districts, northern Shoshone Range, Nevada, USA
Authors: Richardson Carson A. , Seedorff Eric 
Published: April 2024

Abstract
Mapping of rock types, structural geology, and hydrothermal alteration, supported by geochronology and thermochronology, sheds light on the original spatial relationships of hydrothermal systems to intrusions in the northern Shoshone Range in north-central Nevada. Rocks in the Hilltop district are tilted ~35–40°E, as indicated by orientations of flattened pumice fiamme and bedding in sedimentary rocks along a single set of presently low-angle normal faults that initiated at 60–70°W dips. New U-Pb zircon geochronology from two sets of dikes in the Lewis district could suggest late Eocene–early Oligocene extension, but definitive crosscutting relations are lacking to demonstrably support this potential earlier period of normal faulting. Reinterpretation of previously reported apatite fission-track cooling ages with a new palinspastic restoration in the Lewis mining district concurs with middle Miocene extension as documented to the south at the Caetano caldera; however, the depth of burial of the Lewis district—and thus the significance of the apatite fission-track cooling ages—is uncertain.
The comparable orientations and tilting history, supported by fault scaling relations, suggest that the temporally coincident extension in the Caetano caldera to the south represents the along-strike continuation of the same system of normal faults as in the Hilltop and Lewis districts, with changes in observed offset, percent extension, and fault spacing attributed to the gradual tipping out of the fault system northward.
Cost Minimization of Digital Twin Placements in Mobile Edge Computing
Authors: Zhang Yuncan , Liang Weifa , Xu Wenzheng , Xu Zichuan , Jia Xiaohua 
Published: April 2024

In the past decades, explosive numbers of Internet of Things (IoT) devices (objects) have been connected to the Internet, which enable users to access, control, and monitor their surrounding phenomenons at anytime and anywhere. To provide seamless interactions between the cyber world and the real world, Digital twins (DTs) of objects (IoT devices) are key enablers for real time monitoring, behaviour simulations, and predictive decisions on objects. Compared to centralized cloud computing, mobile edge computing (MEC) has been envisioning as a promising paradigm for low latency IoT applications. Accelerating the usage of DTs in MEC networks will bring unprecedented benefits to diverse services, through the co-evolution between physical objects and their virtual DTs, and DT-assisted service provisioning has attracted increasing attention recently.
In this article, we consider novel DT placement and migration problems in an MEC network with the mobility assumption of objects and users, by jointly considering the freshness of DT data and the service cost of users requesting for DT data. To this end, we first propose an algorithm for the DT placement problem with the aim to minimize the sum of the DT update cost of objects and the total service cost of users requesting for DT data, through efficient DT placements and resource allocation to process user requests. We then devise an approximation algorithm with a provable approximation ratio for a special case of the DT placement problem when each user requests the DT data of only one object. Meanwhile, considering the mobility of users and objects, we devise an online, two-layer scheduling algorithm for DT migrations to further reduce the total service cost of users within a given finite time horizon. We finally evaluate the performance of the proposed algorithms through experimental simulations. The simulation results show that the proposed algorithms are promising.
Thymic Mimetic Cells: Ontogeny as Immunology
Authors: Michelson Daniel A. , Mathis Diane 
Published: April 2024

Medullary thymic epithelial cells (mTECs) generate immunological self-tolerance by ectopically expressing peripheral-tissue antigens (PTAs) within the thymus to preview the peripheral self to maturing T cells. Recent work, drawing inspiration from old histological observations, has shown that subtypes of mTECs, collectively termed mimetic cells, co-opt developmental programs from throughout the organism to express biologically coherent groups of PTAs. Here, we review key aspects of mimetic cells, especially as they relate to the larger contexts of molecular, cellular, developmental, and evolutionary biology. We highlight lineage-defining transcription factors as key regulators of mimetic cells and speculate as to what other factors, including Aire and the chromatin potential of mTECs, permit mimetic cell differentiation and function. Last, we consider what mimetic cells can teach us about not only the thymus but also other tissues.
Temporal Trends in Cardiovascular Disease Prevalence Among Asian American Subgroups
Authors: Nguyen Kaylin T. , Li Jiang , Peng Allison W. , Azar Kristen , Heidenreich Paul , Palaniappan Latha , Yong Celina M. 
Published: April 2024

Background
Asian and multiracial individuals represent the 2 fastest growing racial and ethnic groups in the United States, yet most prior studies report Asian American and Native Hawaiian or Other Pacific Islander as a single racial group, with limited data on cardiovascular disease (CVD) prevalence among subgroups. We sought to evaluate temporal trends in CVD burden among disaggregated Asian subgroups.

Methods and Results

Patients with CVD based on
International Classification of Diseases, Ninth Revision
and
Tenth Revision
(
ICD‐9
and
ICD‐10
) coding who received care from a mixed‐payer health care organization in California between 2008 and 2018 were classified into self‐identified racial and ethnic subgroups (non‐Hispanic White [NHW], Asian Indian, Chinese, Filipino, Japanese, Korean, Native Hawaiian or Other Pacific Islander, and multiracial groups). Adjusted trends in CVD prevalence over time by subgroup were compared using logistic regression. Among 3 494 071 patient‐years, prevalence of CVD increased faster among all subgroups except Japanese and Native Hawaiian or Other Pacific Islander patients (
P
<0.01 for each, reference: NHW). Filipino patients had the highest overall CVD prevalence, which increased from 34.3% to 45.1% over 11 years (increase from 17.3%–21.9%,
P
<0.0001, reference: NHW). Asian Indian patients had the fastest increase in CVD prevalence over time (16.9%–23.7%,
P
<0.0001, reference: NHW). Among subcategories of disease, hypertension increased faster among Asian Indian, Chinese, Filipino, Korean, and multiracial groups (
P
<0.01 for all, reference: NHW), and coronary artery disease increased faster among Asian Indian, Chinese, Filipino, and Japanese groups (
P
<0.05 for each, reference: NHW).

Conclusions
The increasing prevalence of CVD among disaggregated Asian, Native Hawaiian or Other Pacific Islander, and multiracial subgroups over time highlights the importance of tailored approaches to addressing CVD in these diverse subpopulations.
Cost‐Effectiveness of a Multicomponent Primary Care Intervention for Hypertension
Authors: Chay Junxing , Jafar Tazeen H. , Su Rebecca J. , Shirore Rupesh M. , Tan Ngiap Chuan , Finkelstein Eric A. 
Published: April 2024

Background
The SingHypertension primary care clinic intervention, which consisted of clinician training in hypertension management, subsidized single‐pill combination medications, nurse‐delivered motivational conversations and telephone follow‐ups, improved blood pressure control and cardiovascular disease (CVD) risk scores relative to usual care among patients with uncontrolled hypertension in Singapore. This study quantified the incremental cost‐effectiveness, in terms of incremental cost per unit reduction disability‐adjusted life years, of SingHypertension relative to usual care for patients with hypertension from the health system perspective.

Methods and Results
We developed a Markov model to simulate CVD events and associated outcomes for a hypothetical cohort of patients over a 10‐year period. Costs were measured in US dollars, and effectiveness was measured in disability‐adjusted life years averted. We present base‐case results and conducted deterministic and probabilistic sensitivity analyses. Based on a willingness‐to‐pay threshold of US $55 500 per DALY averted, SingHypertension was cost‐effective for patients with hypertension (incremental cost‐effectiveness ratio: US $24 765 per disability‐adjusted life year averted) relative to usual care. This result held even if risk reduction was assumed to decline linearly to 0 over 10 years but not sooner than 7 years. Incremental cost‐effectiveness ratios were most sensitive to the magnitude of the reduction in CVD risk; at least a 0.13% to 0.16% point reduction in 10‐year CVD risk is required for cost‐effectiveness. Probabilistic sensitivity analysis indicates that SingHypertension has a 78% chance of being cost‐effective at the willingness‐to‐pay threshold.

Conclusions
SingHypertension represents good value for the money for reducing CVD incidence, morbidity, and mortality and should be considered for wide‐scale implementation in Singapore and possibly other countries.

Registration Information

REGISTRATION: URL:
https://www.clinicaltrials.gov
; Unique identifier: NCT02972619.
LLaMA-LoRA Neural Prompt Engineering: A Deep Tuning Framework for Automatically Generating Chinese Text Logical Reasoning Thinking Chains
Authors: Chen Songlin , Wang Weicheng , Chen Xiaoliang , lu Peng , Yang Zaiyan , Du Yajun 
Published: April 2024

ABSTRACT
The exption of Chinese natural language processing (NLP) has stimulated research in the broader NLP domain. However, existing large language models have limitations in comprehending and reasoning in Chinese. This paper addresses these limitations by enhancing Chinese language models comprehension and reasoning capabilities while minimizing resource requirements. We propose LLaMA-LoRA, a neural prompt engineering framework that builds upon the LLaMA-13B model and incorporates the Low-Rank Adaptation (LoRA) of Large Language Models technique for refinement. Chain-of-Thought (CoT) are crucial for generating intermediate reasoning chains in language models, but their effectiveness can be limited by isolated language patterns. Erroneous reasoning resulting from conventional prompts negatively impacts model performance. Automatic prompts are introduced to encourage reasoning chain generation and accurate answer inference. Training the model with an extensive corpus of Chinese CoT data enhances its comprehension and reasoning abilities. The LLaMA-LoRA model demonstrates exceptional performance across numerous Chinese language tasks, surpassing benchmark performance achieved by related language models such as GPT-3.5, Chat-GLM, and OpenAssistant, delivering accurate, comprehensive, and professional answers. The availability of our open-source model code facilitates further research in the field of Chinese text logical reasoning thinking chains.
Disentangling reference frames in the neural compass
Authors: Dutriaux Léo , Xu Yangwen , Sartorato Nicola , Lhuillier Simon , Bottini Roberto 
Published: April 2024

Abstract
The neural system that encodes heading direction in humans can be found in the medial and superior parietal cortex and the entorhinal-retrosplenial circuit. However, it is still unclear whether heading direction in these different regions is represented within an allocentric or egocentric coordinate system. To investigate this problem, we first asked whether regions encoding (putatively) allocentric facing direction also encode (unambiguously) egocentric goal direction. Second, we assessed whether directional coding in these regions scaled with the preference for an allocentric perspective during everyday navigation. Before the experiment, participants learned different object maps in two geometrically similar rooms. In the MRI scanner, their task was to retrieve the egocentric position of a target object (e.g., Front, Left) relative to an imagined facing direction (e.g., North, West). Multivariate analyses showed, as predicted, that facing direction was encoded bilaterally in the superior parietal lobule (SPL), the retrosplenial complex (RSC), and the left entorhinal cortex (EC), a result that could be interpreted both allocentrically and egocentrically. Crucially, we found that the same voxels in the SPL and RSC also coded for egocentric goal direction but not for allocentric goal direction. Moreover, when facing directions were expressed as egocentric bearings relative to a reference vector, activities for facing direction and egocentric goal direction were correlated, suggesting a common reference frame. Besides, only the left EC coded allocentric goal direction as a function of the subject’s propensity to use allocentric strategies. Altogether, these results suggest that heading direction in the superior and medial parietal cortex is mediated by an egocentric code, whereas the entorhinal cortex encodes directions according to an allocentric reference frame.
Theta activity discriminates high-level, species-specific body processes
Authors: Chesley Jane , Riecke Lars , Lu Juanzhi , Vogels Rufin , de Gelder Beatrice 
Published: April 2024

Abstract
Among social stimuli that trigger rapid reactions, body images occupy a prominent place. Given that bodies carry information about other agents’ intentions, actions and emotional expressions, a foundational question concerns the neural basis of body processing. Previous functional magnetic resonance imaging (fMRI) studies have investigated this but were not yet able to clarify the time course and its functional significance. The present EEG study investigated the role of slow oscillatory cortical activity in body processing and species-specificity. Human participants viewed naturalistic images of human and monkey bodies, faces, and objects, along with mosaic-scrambled versions to control for low-level visual features. Analysis of event-related theta power (4–7 Hz) combined with data-driven methods revealed a strong, body-evoked neural response that is specific to human bodies and spans a widespread scalp region during a time window of 200–550 ms after the onset of the body image. Our results corroborate recent research proposing a species-specific cortical network of human body processing. We submit that this network may play an essential role in linking body processes to movement intentions.