bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolomics for quality assessment of poultry meat and eggs
Authors: Yogeswari M S , Selamat Jinap , Jambari Nuzul Noorahya , Khatib Alfi , Mohd Amin Mohd Hishammfariz , Murugesu Suganya 
Published: January 2024

Abstract
The poultry industry is experiencing rapid growth worldwide. This accelerated growth has led to multiple food fraud incidents across the food supply chain, which consequently created a demand for precise determination of quality poultry production. This increase in demand for precise poultry production quality has necessitated advanced solutions. Metabolomics has emerged as a viable solution by offering detailed differentiation of biochemical indicators throughout the poultry supply chain. Additionally, this study provides a means to address risk factors affecting the poultry industry without compromising animal welfare, which is a critical concern. This review focuses on important issues related to poultry product quality assessment. Food adulteration has escalated in recent years as it is driven by the increasing focus on consuming high-quality and nutritious food. However, there is no specific guideline for such determinations, especially when appearance, texture, and taste can be manipulated by substituting for food components. Metabolomics can pave the way for a deeper understanding of existing and novel biochemical indicators responsible for determining the quality of poultry meat and eggs. This approach holds the potential to enhance the overall quality of poultry meat and egg products while also preventing food fraud.
Neighborhood Social Environment and Dementia: The Mediating Role of Social Isolation
Authors: Choi Eun Young , Cho Gawon , Chang Virginia W 
Published: January 2024

Abstract

Objectives
Despite the potential importance of the neighborhood social environment for cognitive health, the connection between neighborhood characteristics and dementia remains unclear. This study investigated the association between the prospective risk of dementia and three distinct aspects of neighborhood social environment: socioeconomic deprivation, disorder, and social cohesion. We also examined whether objective and subjective aspects of individual-level social isolation may function as mediators.

Methods
Leveraging data from the Health and Retirement Study (2006–2018; N = 9,251), we used Cox proportional hazards models to examine the association between time-to-dementia incidence and each neighborhood characteristic, adjusting for covariates and the propensity to self-select into disadvantaged neighborhoods. We used inverse odds weighting to decompose significant total effects of neighborhood characteristics into mediational effects of objective and subjective social isolation.

Results
The risk of dementia was associated with deprivation and disorder but not low cohesion. In deprived neighborhoods, individuals had an 18% increased risk of developing dementia (cause-specific hazard ratio [CHR] = 1.18, 95% CI: 1.02 to 1.38), and those in disordered areas had a 27% higher risk (CHR = 1.27, 95% CI: 1.03 to 1.59). 20% of the disorder’s effects were mediated by subjective social isolation, while the mediational effects of objective isolation were nonsignificant. Deprivation’s total effects were not partitioned into mediational effects given its nonsignificant associations with the mediators.

Discussion
Neighborhood deprivation and disorder may increase middle to older adults’ risks of dementia. The disorder may adversely affect cognitive health through increasing loneliness. Our results suggest a clear need for dementia prevention targeting upstream neighborhood contexts, including the improvement of neighborhood conditions to foster social integration among residents.
Retention of stress susceptibility in the mdx mouse model of Duchenne muscular dystrophy after PGC-1α overexpression or ablation of IDO1 or CD38
Authors: Johnson Erynn E , Southern W Michael , Doud Baird , Steiger Brandon , Razzoli Maria , Bartolomucci Alessandro , Ervasti James M 
Published: January 2024

Abstract
Duchenne muscular dystrophy (DMD) is a lethal degenerative muscle wasting disease caused by the loss of the structural protein dystrophin with secondary pathological manifestations including metabolic dysfunction, mood and behavioral disorders. In the mildly affected mdx mouse model of DMD, brief scruff stress causes inactivity, while more severe subordination stress results in lethality. Here, we investigated the kynurenine pathway of tryptophan degradation and the nicotinamide adenine dinucleotide (NAD+) metabolic pathway in mdx mice and their involvement as possible mediators of mdx stress-related pathology. We identified downregulation of the kynurenic acid shunt, a neuroprotective branch of the kynurenine pathway, in mdx skeletal muscle associated with attenuated peroxisome proliferator-activated receptor-gamma coactivator 1 alpha (PGC-1α) transcriptional regulatory activity. Restoring the kynurenic acid shunt by skeletal muscle-specific PGC-1α overexpression in mdx mice did not prevent scruff -induced inactivity, nor did abrogating extrahepatic kynurenine pathway activity by genetic deletion of the pathway rate-limiting enzyme, indoleamine oxygenase 1. We further show that reduced NAD+ production in mdx skeletal muscle after subordination stress exposure corresponded with elevated levels of NAD+ catabolites produced by ectoenzyme cluster of differentiation 38 (CD38) that have been implicated in lethal mdx response to pharmacological β-adrenergic receptor agonism. However, genetic CD38 ablation did not prevent mdx scruff-induced inactivity. Our data do not support a direct contribution by the kynurenine pathway or CD38 metabolic dysfunction to the exaggerated stress response of mdx mice.
Modified Commando procedure using a double valve composite through an aorto-annulo-septotomy
Authors: Matsuzaki Kanji , Mitomi Kisato , Imai Akito , Sato Masataka , Watanabe Yasunori 
Published: January 2024

Abstract
Double valve replacement of aortic and mitral valves with intervalvular fibrous body reconstruction (Commando procedure) is a challenging operation. Particularly in redo surgery for prosthetic valve endocarditis, special techniques are needed for approaching and reconstructing the valve complex. We performed a modified Commando procedure using a double valve composite through an aorto-annulo-septotomy. This approach provided a good field of vision at the combined aortic and mitral annuli without incising the left atrial roof. The double valve composite with four-layer patch wings was useful for performing double valve replacement en bloc and aorto-annulo-septotomy closure serially. Using these techniques, we successfully performed the Commando procedure for complicated prosthetic valve endocarditis.
The Ability to Voluntarily Regulate Theta Band Activity Affects How Pharmacological Manipulation of the Catecholaminergic System Impacts Cognitive Control
Authors: Prochnow Astrid , Mückschel Moritz , Eggert Elena , Senftleben Jessica , Frings Christian , Münchau Alexander , Roessner Veit , Bluschke Annet , Beste Christian 
Published: January 2024

Abstract

Background
The catecholaminergic system influences response inhibition, but the magnitude of the impact of catecholaminergic manipulation is heterogeneous. Theoretical considerations suggest that the voluntary modulability of theta band activity can explain this variance. The study aimed to investigate to what extent interindividual differences in catecholaminergic effects on response inhibition depend on voluntary theta band activity modulation.

Methods
A total of 67 healthy adults were tested in a randomized, double-blind, cross-over study design. At each appointment, they received a single dose of methylphenidate or placebo and performed a Go/Nogo task with stimuli of varying complexity. Before the first appointment, the individual’s ability to modulate theta band activity was measured. Recorded EEG data were analyzed using temporal decomposition and multivariate pattern analysis.

Results
Methylphenidate effects and voluntary modulability of theta band activity showed an interactive effect on the false alarm rates of the different Nogo conditions. The multivariate pattern analysis revealed that methylphenidate effects interacted with voluntary modulability of theta band activity at a stimulus processing level, whereas during response selection methylphenidate effects interacted with the complexity of the Nogo condition.

Conclusions
The findings reveal that the individual’s theta band modulability affects the responsiveness of an individual’s catecholaminergic system to pharmacological modulation. Thus, the impact of pharmacological manipulation of the catecholaminergic system on cognitive control most likely depends on the existing ability to self-modulate relevant brain oscillatory patterns underlying the cognitive processes being targeted by pharmacological modulations.
Energy partitioning and controlling factors of evapotranspiration in an alpine meadow in the permafrost region of the Qinghai-Tibet Plateau
Authors: Hu Zhaoyong , Wang Genxu , Sun Xiangyang , Huang Kewei , Song Chunlin , Li Yang , Sun Shouqin , Sun Juying , Lin Shan 
Published: January 2024

Abstract
Energy partitioning and evapotranspiration (ET) of alpine meadows in permafrost areas are crucial for water cycle on the Qinghai-Tibet Plateau. However, seasonal (freeze–thaw cycle) variations in energy partitioning and ET and their driving factors must be clarified. Therefore, 4-year energy fluxes [i.e. latent heat (LE) and sensible heat (H)] were observed, and bulk parameters [i.e. surface conductance, decoupling coefficient (Ω), and Priestley–Taylor coefficient (α)] were estimated in an alpine meadow in the Qinghai-Tibet Plateau. Mean daily LE (27.45 ± 23.89 W/m2) and H (32.51 ± 16.72 W/m2) accounted for 31.71% and 50.14% of available energy, respectively. More available energy was allocated to LE during the rainfall period, while 67.54 ± 28.44% was allocated to H during the frozen period. H was half the LE during rainfall period and seven times the LE during frozen period due to low soil water content and vegetation coverage during the frozen season. Mean annual ET was 347.34 ± 8.39 mm/year, close to mean annual precipitation. Low mean daily Ω (0.45 ± 0.23) and α (0.60 ± 0.29) throughout the year suggested that ET in the alpine meadow was limited by water availability. However, ET was constrained by available energy because of sufficient water supply from precipitation during rainfall season. In contrast, large differences between ET and precipitation indicated that soil water was supplied via lateral flow from melting upstream glaciers and snow during the transition season. The results suggest that seasonal variations in bulk parameters should be considered when simulating water and energy fluxes in permafrost regions.
On the conservation results for local reflection principles
Authors: Kogure Haruka , Kurahashi Taishi 
Published: January 2024

Abstract
For a class $\varGamma $ of formulas, $\varGamma $ local reflection principle $\textrm{Rfn}_{\varGamma }(T)$ for a theory $T$ of arithmetic is a scheme formalizing the $\varGamma $-soundness of $T$. Beklemishev (1997, Theoria, 63, 139–146) proved that for every $\varGamma \in \{\varSigma _{n}, \varPi _{n+1} \mid n \geq 1\}$, the full local reflection principle $\textrm{Rfn}(T)$ is $\varGamma $-conservative over $T + \textrm{Rfn}_{\varGamma }(T)$. We firstly generalize the conservation theorem to nonstandard provability predicates: we prove that the second condition $\textbf{D2}$ of the derivability conditions is a sufficient condition for the conservation theorem to hold. We secondly investigate the conservation theorem in terms of Rosser provability predicates. We construct Rosser predicates for which the conservation theorem holds and Rosser predicates for which the theorem does not hold.
Rapid human genomic DNA cloning into mouse artificial chromosome via direct chromosome transfer from human iPSC and CRISPR/Cas9-mediated translocation
Authors: Miyamoto Hitomaru , Kobayashi Hiroaki , Kishima Nanami , Yamazaki Kyotaro , Hamamichi Shusei , Uno Narumi , Abe Satoshi , Hiramuki Yosuke , Kazuki Kanako , Tomizuka Kazuma , Kazuki Yasuhiro 
Published: January 2024

Abstract
A ‘genomically’ humanized animal stably maintains and functionally expresses the genes on human chromosome fragment (hCF; &lt;24 Mb) loaded onto mouse artificial chromosome (MAC); however, cloning of hCF onto the MAC (hCF-MAC) requires a complex process that involves multiple steps of chromosome engineering through various cells via chromosome transfer and Cre-loxP chromosome translocation. Here, we aimed to develop a strategy to rapidly construct the hCF-MAC by employing three alternative techniques: (i) application of human induced pluripotent stem cells (hiPSCs) as chromosome donors for microcell-mediated chromosome transfer (MMCT), (ii) combination of paclitaxel (PTX) and reversine (Rev) as micronucleation inducers and (iii) CRISPR/Cas9 genome editing for site-specific translocations. We achieved a direct transfer of human chromosome 6 or 21 as a model from hiPSCs as alternative human chromosome donors into CHO cells containing MAC. MMCT was performed with less toxicity through induction of micronucleation by PTX and Rev. Furthermore, chromosome translocation was induced by simultaneous cleavage between human chromosome and MAC by using CRISPR/Cas9, resulting in the generation of hCF-MAC containing CHO clones without Cre-loxP recombination and drug selection. Our strategy facilitates rapid chromosome cloning and also contributes to the functional genomic analyses of human chromosomes.
Rif2 interaction with Rad50 counteracts Tel1 functions in checkpoint signalling and DNA tethering by releasing Tel1 from MRX binding
Authors: Pizzul Paolo , Casari Erika , Rinaldi Carlo , Gnugnoli Marco , Mangiagalli Marco , Tisi Renata , Longhese Maria Pia 
Published: January 2024

Abstract
The yeast Rif2 protein is known to inhibit Mre11 nuclease and the activation of Tel1 kinase through a short motif termed MIN, which binds the Rad50 subunit and simulates its ATPase activity in vitro. The mechanism by which Rif2 restrains Tel1 activation and the consequences of this inhibition at DNA double-strand breaks (DSBs) are poorly understood. In this study, we employed AlphaFold-Multimer modelling to pinpoint and validate the interaction surface between Rif2 MIN and Rad50. We also engineered the rif2-S6E mutation that enhances the inhibitory effect of Rif2 by increasing Rif2-Rad50 interaction. Unlike rif2Δ, the rif2-S6E mutation impairs hairpin cleavage. Furthermore, it diminishes Tel1 activation by inhibiting Tel1 binding to DSBs while leaving MRX association unchanged, indicating that Rif2 can directly inhibit Tel1 recruitment to DSBs. Additionally, Rif2S6E reduces Tel1-MRX interaction and increases stimulation of ATPase by Rad50, indicating that Rif2 binding to Rad50 induces an ADP-bound MRX conformation that is not suitable for Tel1 binding. The decreased Tel1 recruitment to DSBs in rif2-S6E cells impairs DSB end-tethering and this bridging defect is suppressed by expressing a Tel1 mutant variant that increases Tel1 persistence at DSBs, suggesting a direct role for Tel1 in the bridging of DSB ends.
COSMIC: a curated database of somatic variants and clinical data for cancer
Authors: Sondka Zbyslaw , Dhir Nidhi Bindal , Carvalho-Silva Denise , Jupe Steven , Madhumita  , McLaren Karen , Starkey Mike , Ward Sari , Wilding Jennifer , Ahmed Madiha , Argasinska Joanna , Beare David , Chawla Manpreet Singh , Duke Stephen , Fasanella Ilaria , Neogi Avirup Guha , Haller Susan , Hetenyi Balazs , Hodges Leonie , Holmes Alex , Lyne Rachel , Maurel Thomas , Nair Sumodh , Pedro Helder , Sangrador-Vegas Amaia , Schuilenburg Helen , Sheard Zoe , Yong Siew Yit , Teague Jon 
Published: January 2024

Abstract
The Catalogue Of Somatic Mutations In Cancer (COSMIC), https://cancer.sanger.ac.uk/cosmic, is an expert-curated knowledgebase providing data on somatic variants in cancer, supported by a comprehensive suite of tools for interpreting genomic data, discerning the impact of somatic alterations on disease, and facilitating translational research. The catalogue is accessed and used by thousands of cancer researchers and clinicians daily, allowing them to quickly access information from an immense pool of data curated from over 29 thousand scientific publications and large studies. Within the last 4 years, COSMIC has substantially expanded its utility by adding new resources: the Mutational Signatures catalogue, the Cancer Mutation Census, and Actionability. To improve data accessibility and interoperability, somatic variants have received stable genomic identifiers that are associated with their genomic coordinates in GRCh37 and GRCh38, and new export files with reduced data redundancy have been made available for download.
Are Rape Myths ‘Myths’?
Authors: Hayes David J 
Published: January 2024

Abstract
Little attention has been paid to what the word ‘myth’ contributes to the concept of rape myths. Rape myths tend to be regarded as widely believed falsehoods that need to be debunked in order to address patriarchal injustices. This account draws upon a long-standing vernacular English association between myth and falsehood which originated in the Enlightenment. But it is not the only possible definition of myth. This article draws upon mythological studies across a range of disciplines to argue that rape myths should be considered authentically mythic; that is, rape ‘myths’ are culturally significant folk narratives about sexual wrongdoing. This reappraisal enables a shift in our understanding of what rape myths are, what they could be—and what we can do to reduce their pernicious influence on the criminal justice system. It also enables legal scholars to more generally reassess how the concept of ‘myth’ is used across our discipline(s).
Circulating Tumor DNA to Predict Radiographic and Pathologic Response to Total Neoadjuvant Therapy in Locally Advanced Rectal Cancer
Authors: Alden Stephanie L , Lee Valerie , Narang Amol K , Meyer Jeffrey , Gearhart Susan L , Christenson Eric S 
Published: January 2024

Abstract
Despite advances in treatment and response assessment in locally advanced rectal cancer (LARC), it is unclear which patients should undergo nonoperative management (NOM). We performed a single-center, retrospective study to evaluate post-total neoadjuvant therapy (TNT) circulating tumor DNA (ctDNA) in predicting treatment response. We found that post-TNT ctDNA had a sensitivity of 23% and specificity of 100% for predicting residual disease upon resection, with a positive predictive value (PPV) of 100% and a negative predictive value (NPV) of 47%. For predicting poor tumor regression on MRI, ctDNA had a sensitivity of 16% and specificity of 96%, with a PPV of 75% and NPV of 60%. A commercially available ctDNA assay was insufficient to predict residual disease after TNT and should not be used alone to select patients for NOM in LARC.
The zinc finger protein DHHC09 S-acylates the kinase STRK1 to regulate H2O2 homeostasis and promote salt tolerance in rice
Authors: Tian Ye , Zeng Hui , Wu Ji-Cai , Dai Gao-Xing , Zheng He-Ping , Liu Cong , Wang Yan , Zhou Zheng-Kun , Tang Dong-Ying , Deng Guo-Fu , Tang Wen-Bang , Liu Xuan-Ming , Lin Jian-Zhong 
Published: January 2024

Abstract
Soil salinity results in oxidative stress and heavy losses to crop production. The S-acylated protein SALT TOLERANCE RECEPTOR-LIKE CYTOPLASMIC KINASE 1 (STRK1) phosphorylates and activates CATALASE C (CatC) to improve rice (Oryza sativa L.) salt tolerance, but the molecular mechanism underlying its S-acylation involved in salt signal transduction awaits elucidation. Here, we show that the DHHC-type zinc finger protein DHHC09 S-acylates STRK1 at Cys5, Cys10, and Cys14 and promotes salt and oxidative stress tolerance by enhancing rice H2O2-scavenging capacity. This modification determines STRK1 targeting to the plasma membrane or lipid nanodomains and is required for its function. DHHC09 promotes salt signaling from STRK1 to CatC via transphosphorylation, and its deficiency impairs salt signal transduction. Our findings demonstrate that DHHC09 S-acylates and anchors STRK1 to the plasma membrane to promote salt signaling from STRK1 to CatC, thereby regulating H2O2 homeostasis and improving salt stress tolerance in rice. Moreover, overexpression of DHHC09 in rice mitigates grain yield loss under salt stress. Together, these results shed light on the mechanism underlying the role of S-acylation in RLK/RLCK-mediated salt signal transduction and provide a strategy for breeding highly salt-tolerant rice.
Effects of Stimulus Type on 16-kHz Detection Thresholds
Authors: Buss Emily , Kane Stacey G. , Young Kathryn S. , Gratzek Chloe B. , Bishop Danielle M. , Miller Margaret K. , Porter Heather L. , Leibold Lori J. , Stecker G. Christopher , Monson Brian B. 
Published: January 2024

Objectives:Audiometric testing typically does not include frequencies above 8 kHz. However, recent research suggests that extended high-frequency (EHF) sensitivity could affect hearing in natural communication environments. Clinical assessment of hearing often employs pure tones and frequency-modulated (FM) tones interchangeably regardless of frequency. The present study was designed to evaluate how the stimulus chosen to measure EHF thresholds affects estimates of hearing sensitivity.Design:The first experiment used standard audiometric procedures to measure 8- and 16-kHz thresholds for 5- to 28-year olds with normal hearing in the standard audiometric range (250 to 8000 Hz). Stimuli were steady tones, pulsed tones, and FM tones. The second experiment tested 18- to 28-year olds with normal hearing in the standard audiometric range using psychophysical procedures to evaluate how changes in sensitivity as a function of frequency affect detection of stimuli that differ with respect to bandwidth, including bands of noise. Thresholds were measured using steady tones, pulsed tones, FM tones, narrow bands of noise, and one-third-octave bands of noise at a range of center frequencies in one ear.Results:In experiment 1, thresholds improved with increasing age at 8 kHz and worsened with increasing age at 16 kHz. Thresholds for individual participants were relatively similar for steady, pulsed, and FM tones at 8 kHz. At 16 kHz, mean thresholds were approximately 5 dB lower for FM tones than for steady or pulsed tones. This stimulus effect did not differ as a function of age. Experiment 2 replicated this greater stimulus effect at 16 kHz than at 8 kHz and showed that the slope of the audibility curve accounted for these effects.Conclusions:Contrary to prior expectations, there was no evidence that the choice of stimulus type affected school-age children more than adults. For individual participants, audiometric thresholds at 16 kHz were as much as 20 dB lower for FM tones than for steady tones. Threshold differences across stimuli at 16 kHz were predicted by differences in audibility across frequency, which can vary markedly between listeners. These results highlight the importance of considering spectral width of the stimulus used to evaluate EHF thresholds.