bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of resistance training on physical function during chemotherapy in colon cancer
Authors: Brown Justin C , Yang Shengping , Compton Stephanie L E , Campbell Kristin L , Cespedes Feliciano Elizabeth M , Quinney Sara , Sternfeld Barbara , Caan Bette J , Meyerhardt Jeffrey A , Schmitz Kathryn H 
Published: July 2024

Abstract

Background
The decline of physical function during chemotherapy predicts poor quality of life and premature death. It is unknown if resistance training prevents physical function decline during chemotherapy in colon cancer survivors.

Methods
This multicenter trial randomly assigned 181 colon cancer survivors receiving postoperative chemotherapy to home-based resistance training or usual care control. Physical function outcomes included the short physical performance battery, isometric handgrip strength, and the physical function subscale of the Medical Outcomes Short-Form 36-item questionnaire. Mixed models for repeated measures quantified estimated treatment differences.

Results
At baseline, participants had a mean (SD) age of 55.2 (12.8) years; 67 (37%) were 60 years or older, and 29 (16%) had a composite short physical performance battery score of no more than 9. Compared with usual care control, resistance training did not improve the composite short physical performance battery score (estimated treatment difference = −0.01, 95% confidence interval [CI] = −0.32 to 0.31; P = .98) or the short physical performance battery scores for balance (estimated treatment difference = 0.01, 95% CI = −0.10 to 0.11; P = .93), gait speed (estimated treatment difference = 0.08, 95% CI = −0.06 to 0.22; P = .28), and sit-to-stand (estimated treatment difference = −0.08, 95% CI = −0.29 to 0.13; P = .46). Compared with usual care control, resistance training did not improve isometric handgrip strength (estimated treatment difference = 1.50 kg, 95% CI = −1.06 to 4.05; P = .25) or self-reported physical function (estimated treatment difference = −3.55, 95% CI = −10.03 to 2.94); P = .28). The baseline short physical performance battery balance score (r = 0.21, 95% CI = 0.07 to 0.35) and handgrip strength (r = 0.23, 95% CI = 0.09 to 0.36) correlated with chemotherapy relative dose intensity.

Conclusion
Among colon cancer survivors with relatively high physical functioning, random assignment to home-based resistance training did not prevent physical function decline during chemotherapy.

Clinical Trial Registration
NCT03291951.
Alternate bearing in ‘Hass’ avocado: fruit load-induced changes in bud auxin homeostasis are associated with flowering repression
Authors: Pochamreddy Madhuri , Haim Dor , Halon Eyal , Keinan Eti , Rai Avinash Chandra , Kamara Itzhak , Sadka Avi , Irihimovitch Vered 
Published: July 2024

Abstract
In ‘Hass’ avocado (Persea americana), fruit presence reduces next season flowering. Recent fruit tree studies proposed that heavy fruit load (HFL) generates an auxin (indole-3-acetic acid, IAA) signal in the buds that represses flowering. However, the nature of this signal remains unknown. Here, we investigated the effect of avocado HFL on bud IAA accumulation and flowering transition. We found that IAA–aspartate and IAA–glutamate conjugate levels were significantly higher in buds from fully loaded (‘on’) than low-loaded (‘off’) trees, hinting that free IAA levels were higher in the former. Expression analysis showed that coinciding with flowering reduction, HFL induced the floral repressor PaTFL1, and suggested that accumulation of IAA in buds as imposed by HFL was associated with its conjugation to aspartate and glutamate and resulted both from de novo IAA synthesis and from reduced IAA export. Accordingly, experiments involving radiolabelled [14C]IAA demonstrated that HFL reduced shoot basipetal IAA transport. Finally, we confirmed the negative effects of IAA on flowering, showing that IAA and polar auxin transport blocker (2,3,5-triiodobenzoic acid) treatments delayed ‘off’ trees’ inflorescence development, reducing their inflorescence axis and inducing PaTFL1 expression. Together, our data indicate that avocado HFL generates IAA signalling in buds that induces PaTFL1, leading to repression of inflorescence development.
Optical and H i observations of IC 443 and G189.6 + 3.3 in a complex environment
Authors: Bakış H , Paylı G , Aktekin E , Sano H , Sezer A 
Published: July 2024

ABSTRACT
The supernova remnant (SNR) IC 443 is one of the best-studied Galactic SNRs at many wavelengths. It is interacting with a very complex environment, including the SNR G189.6 + 3.3 and H ii regions. In this paper, we report on observations of IC 443 and G189.6 + 3.3 using 1.5- and 1-m telescopes to better understand the nature of these SNRs in the optical band. We obtain H$\alpha$ images showing both filamentary and diffuse structures, and long-slit spectra from many locations, with Balmer and forbidden lines detected for IC 443 and G189.6 + 3.3. The [S ii]/ H$\alpha$ ratios confirm the SNR nature of G189.6 + 3.3. The ranges of our estimated electron density and pre-shock cloud density clearly indicate the complex structure surrounding IC 443 and G189.6 + 3.3. We also investigate the archival H i data and newly find some shell-like distributions of H i that are possibly associated with G189.6 $+$ 3.3.
How does dark matter stabilize disc galaxies?
Authors: Aditya K 
Published: July 2024

ABSTRACT
The study presents a theoretical framework for understanding the role of dark matter on the stability of the galactic disc. We model the galaxy as a two-component system consisting of stars and gas in equilibrium with an external dark matter halo. We derive the equations governing the growth of perturbations and obtain a stability criterion that connects the potential of the dark matter halo and the gas fraction with the stability levels of the galaxy. We find that a two-component disc is more susceptible to the growth of gravitational instabilities than individual components, particularly as gas fractions increase. However, the external field, due to the dark matter halo, acts as a stabilizing agent and increases the net stability levels even in the presence of a cold gas component. We apply the stability criterion to models of the Milky Way, low surface brightness galaxies, and baryon-dominated cold rotating disc galaxies observed in the early universe. Our results show that the potential due to the dark matter halo plays a significant role in stabilizing nearby galaxies, such as the Milky Way, and low surface brightness galaxies, which would otherwise be prone to local gravitational instabilities. However, we find that the baryon-dominated cold disc galaxies observed in the early universe remain susceptible to the growth of local gravitational instabilities despite the stabilizing effect of the dark matter halo.
Adaptive Evolution of Two Distinct Adaptive Haplotypes of Neanderthal Origin at the Immunoglobulin Heavy-chain Locus in East Asian and European Populations
Authors: Ma Xixian , Lu Yan , Xu Shuhua 
Published: July 2024

Abstract
Immunoglobulins (Igs) have a crucial role in humoral immunity. Two recent studies have reported a high-frequency Neanderthal-introgressed haplotype throughout Eurasia and a high-frequency Neanderthal-introgressed haplotype specific to southern East Asia at the immunoglobulin heavy-chain (IGH) gene locus on chromosome 14q32.33. Surprisingly, we found the previously reported high-frequency Neanderthal-introgressed haplotype does not exist throughout Eurasia. Instead, our study identified two distinct high-frequency haplotypes of putative Neanderthal origin in East Asia and Europe, although they shared introgressed alleles. Notably, the alleles of putative Neanderthal origin reduced the expression of IGHG1 and increased the expression of IGHG2 and IGHG3 in various tissues. These putatively introgressed alleles also affected the production of IgG1 upon antigen stimulation and increased the risk of systemic lupus erythematosus. Additionally, the greatest genetic differentiation across the whole genome between southern and northern East Asians was observed for the East Asian haplotype of putative Neanderthal origin. The frequency decreased from southern to northern East Asia and correlated positively with the genome-wide proportion of southern East Asian ancestry, indicating that this putative positive selection likely occurred in the common ancestor of southern East Asian populations before the admixture with northern East Asian populations.
Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing
Authors: Tan Lu , Guo Zhihao , Shao Yanwen , Ye Lianwei , Wang Miaomiao , Deng Xin , Chen Sheng , Li Runsheng 
Published: July 2024

Abstract
Bacterial gene expression is a complex process involving extensive regulatory mechanisms. Along with growing interests in this field, Nanopore Direct RNA Sequencing (DRS) provides a promising platform for rapid and comprehensive characterization of bacterial RNA biology. However, the DRS of bacterial RNA is currently deficient in the yield of mRNA-mapping reads and has yet to be exploited for transcriptome-wide RNA modification mapping. Here, we showed that pre-processing of bacterial total RNA (size selection followed by ribosomal RNA depletion and polyadenylation) guaranteed high throughputs of sequencing data and considerably increased the amount of mRNA reads. This way, complex transcriptome architectures were reconstructed for Escherichia coli and Staphylococcus aureus and extended the boundaries of 225 known E. coli operons and 89 defined S. aureus operons. Utilizing unmodified in vitro-transcribed (IVT) RNA libraries as a negative control, several Nanopore-based computational tools globally detected putative modification sites in the E. coli and S. aureus transcriptomes. Combined with Next-Generation Sequencing-based N6-methyladenosine (m6A) detection methods, 75 high-confidence m6A candidates were identified in the E. coli protein-coding transcripts, while none were detected in S. aureus. Altogether, we demonstrated the potential of Nanopore DRS in systematic and convenient transcriptome and epitranscriptome analysis.
Adenovirus small E1A directs activation of Alu transcription at YAP/TEAD- and AP-1-bound enhancers through interactions with the EP400 chromatin remodeler
Authors: Cantarella Simona , Vezzoli Marco , Carnevali Davide , Morselli Marco , Zemke Nathan R , Montanini Barbara , Daussy Coralie F , Wodrich Harald , Teichmann Martin , Pellegrini Matteo , Berk Arnold J , Dieci Giorgio , Ferrari Roberto 
Published: July 2024

Abstract
Alu retrotransposons, which form the largest family of mobile DNA elements in the human genome, have recently come to attention as a potential source of regulatory novelties, most notably by participating in enhancer function. Even though Alu transcription by RNA polymerase III is subjected to tight epigenetic silencing, their expression has long been known to increase in response to various types of stress, including viral infection. Here we show that, in primary human fibroblasts, adenovirus small e1a triggered derepression of hundreds of individual Alus by promoting TFIIIB recruitment by Alu-bound TFIIIC. Epigenome profiling revealed an e1a-induced decrease of H3K27 acetylation and increase of H3K4 monomethylation at derepressed Alus, making them resemble poised enhancers. The enhancer nature of e1a-targeted Alus was confirmed by the enrichment, in their upstream regions, of the EP300/CBP acetyltransferase, EP400 chromatin remodeler and YAP1 and FOS transcription factors. The physical interaction of e1a with EP400 was critical for Alu derepression, which was abrogated upon EP400 ablation. Our data suggest that e1a targets a subset of enhancer Alus whose transcriptional activation, which requires EP400 and is mediated by the e1a-EP400 interaction, may participate in the manipulation of enhancer activity by adenoviruses.
The critical role of the iron–sulfur cluster and CTC components in DOG-1/BRIP1 function in Caenorhabditis elegans
Authors: Li Xiao , Perdomo Ivette Maria Menendez , Rodrigues Alves Barbosa Victoria , Diao Catherine , Tarailo-Graovac Maja 
Published: July 2024

Abstract
FANCJ/BRIP1, initially identified as DOG-1 (Deletions Of G-rich DNA) in Caenorhabditis elegans, plays a critical role in genome integrity by facilitating DNA interstrand cross-link repair and resolving G-quadruplex structures. Its function is tightly linked to a conserved [4Fe–4S] cluster-binding motif, mutations of which contribute to Fanconi anemia and various cancers. This study investigates the critical role of the iron–sulfur (Fe–S) cluster in DOG-1 and its relationship with the cytosolic iron–sulfur protein assembly targeting complex (CTC). We found that a DOG-1 mutant, expected to be defective in Fe–S cluster binding, is primarily localized in the cytoplasm, leading to heightened DNA damage sensitivity and G-rich DNA deletions. We further discovered that the deletion of mms-19, a nonessential CTC component, also resulted in DOG-1 sequestered in cytoplasm and increased DNA damage sensitivity. Additionally, we identified that CIAO-1 and CIAO-2B are vital for DOG-1’s stability and repair functions but unlike MMS-19 have essential roles in C. elegans. These findings confirm the CTC and Fe–S cluster as key elements in regulating DOG-1, crucial for genome integrity. Additionally, this study advances our understanding of the CTC’s role in Fe–S protein regulation and development in C. elegans, offering a model to study its impact on multicellular organism development.
Intrinsic PARG inhibitor sensitivity is mimicked by TIMELESS haploinsufficiency and rescued by nucleoside supplementation
Authors: Coulson-Gilmer Camilla , Littler Samantha , Barnes Bethany M , Brady Rosie M , Anagho Holda A , Pillay Nisha , Dey Malini , Macmorland William , Bronder Daniel , Nelson Louisa , Tighe Anthony , Lin Wei-Hsiang , Morgan Robert D , Unwin Richard D , Nielsen Michael L , McGrail Joanne C , Taylor Stephen S 
Published: July 2024

Abstract
A subset of cancer cells are intrinsically sensitive to inhibitors targeting PARG, the poly(ADP-ribose) glycohydrolase that degrades PAR chains. Sensitivity is accompanied by persistent DNA replication stress, and can be induced by inhibition of TIMELESS, a replisome accelerator. However, the nature of the vulnerability responsible for intrinsic sensitivity remains undetermined. To understand PARG activity dependency, we analysed Timeless model systems and intrinsically sensitive ovarian cancer cells. We show that nucleoside supplementation rescues all phenotypes associated with PARG inhibitor sensitivity, including replisome speed and fork stalling, S-phase completion and mitotic entry, proliferation dynamics and clonogenic potential. Importantly nucleoside supplementation restores PARG inhibitor resistance despite the continued presence of PAR chains, indicating that sensitivity does not correlate with PAR levels. In addition, we show that inhibition of thymidylate synthase, an enzyme required for dNTP homeostasis, induces PARG-dependency. Together, these observations suggest that PARG inhibitor sensitivity reflects an inability to control replisome speed and/or maintain helicase-polymerase coupling in response to nucleotide imbalances.
GLIM Achieves Best Diagnostic Performance in Non-Cancer Patients with Low BMI: A Hierarchical Bayesian Latent-Class Meta-Analysis
Authors: Wu Tiantian , Zhou Mingming , Xu Kedi , Zou Yuanlin , Zhang Shaobo , Cheng Haoqing , Guo Pengxia , Song Chunhua 
Published: July 2024

Abstract

Context
Global Leadership Initiative on Malnutrition (GLIM) and Patient-Generated Subjective Global Assessment (PG-SGA) are commonly used nutrition assessment tools, whose performance does not reach a consensus due to different and imperfect reference standards.

Objective
This study aimed to evaluate and compare the diagnostic accuracy of GLIM and PG-SGA, using a hierarchical Bayesian latent class model, in the absence of a gold standard.

Data Sources
A systematic search was undertaken in PubMed, Embase, and Web of Science from inception to October 2022. Diagnostic test studies comparing (1) the GLIM and/or (2) PG-SGA with “semi-gold” standard assessment tools for malnutrition were included.

Data Extraction
Two authors independently extracted data on sensitivity, specificity, and other key characteristics. The methodological quality of each included study was appraised according to the criteria in the Quality Assessment of Diagnostic Accuracy Studies-2.

Data Analysis
A total of 45 studies, comprising 20 876 individuals evaluated for GLIM and 11 575 for PG-SGA, were included. The pooled sensitivity was 0.833 (95% CI 0.744 to 0.896) for GLIM and 0.874 (0.797 to 0.925) for PG-SGA, while the pooled specificity was 0.837 (0.780 to 0.882) for GLIM and 0.778 (0.707 to 0.836) for PG-SGA. GLIM showed slightly better performance than PG-SGA, with a higher diagnostic odds ratio (25.791 vs 24.396). The diagnostic performance of GLIM was most effective in non-cancer patients with an average body mass index (BMI) of &lt;24 kg/m2, followed by non-cancer patients with an average age of ≥60 years. PG-SGA was most powerful in cancer patients with an average age of &lt;60 years, followed by cancer patients with an average BMI of &lt;24 kg/m2.

Conclusion
Both GLIM and PG-SGA had moderately high diagnostic capabilities. GLIM was most effective in non-cancer patients with a low BMI, while PG-SGA was more applicable in cancer patients.

Systematic Review Registration
PROSPERO registration No. CRD42022380409.
Gibberellin dynamics governing nodulation revealed using GIBBERELLIN PERCEPTION SENSOR 2 in Medicago truncatula lateral organs
Authors: Drapek Colleen , Rizza Annalisa , Mohd-Radzman Nadiatul A , Schiessl Katharina , Dos Santos Barbosa Fabio , Wen Jiangqi , Oldroyd Giles E D , Jones Alexander M 
Published: July 2024

Abstract
During nutrient scarcity, plants can adapt their developmental strategy to maximize their chance of survival. Such plasticity in development is underpinned by hormonal regulation, which mediates the relationship between environmental cues and developmental outputs. In legumes, endosymbiosis with nitrogen-fixing bacteria (rhizobia) is a key adaptation for supplying the plant with nitrogen in the form of ammonium. Rhizobia are housed in lateral root-derived organs termed nodules that maintain an environment conducive to Nitrogenase in these bacteria. Several phytohormones are important for regulating the formation of nodules, with both positive and negative roles proposed for gibberellin (GA). In this study, we determine the cellular location and function of bioactive GA during nodule organogenesis using a genetically encoded second-generation GA biosensor, GIBBERELLIN PERCEPTION SENSOR 2 in Medicago truncatula. We find endogenous bioactive GA accumulates locally at the site of nodule primordia, increasing dramatically in the cortical cell layers, persisting through cell divisions, and maintaining accumulation in the mature nodule meristem. We show, through misexpression of GA-catabolic enzymes that suppress GA accumulation, that GA acts as a positive regulator of nodule growth and development. Furthermore, increasing or decreasing GA through perturbation of biosynthesis gene expression can increase or decrease the size of nodules, respectively. This is unique from lateral root formation, a developmental program that shares common organogenesis regulators. We link GA to a wider gene regulatory program by showing that nodule-identity genes induce and sustain GA accumulation necessary for proper nodule formation.
People believe political opponents accept blatant moral wrongs, fueling partisan divides
Authors: Puryear Curtis , Kubin Emily , Schein Chelsea , Bigman Yochanan E , Ekstrom Pierce , Gray Kurt 
Published: July 2024

AbstractEfforts to bridge political divides often focus on navigating complex and divisive issues, but eight studies reveal that we should also focus on a more basic misperception: that political opponents are willing to accept basic moral wrongs. In the United States, Democrats, and Republicans overestimate the number of political outgroup members who approve of blatant immorality (e.g. child pornography, embezzlement). This “basic morality bias” is tied to political dehumanization and is revealed by multiple methods, including natural language analyses from a large social media corpus and a survey with a representative sample of Americans. Importantly, the basic morality bias can be corrected with a brief, scalable intervention. Providing information that just one political opponent condemns blatant wrongs increases willingness to work with political opponents and substantially decreases political dehumanization.
Perils and opportunities in using large language models in psychological research
Authors: Abdurahman Suhaib , Atari Mohammad , Karimi-Malekabadi Farzan , Xue Mona J , Trager Jackson , Park Peter S , Golazizian Preni , Omrani Ali , Dehghani Morteza 
Published: July 2024

Abstract
The emergence of large language models (LLMs) has sparked considerable interest in their potential application in psychological research, mainly as a model of the human psyche or as a general text-analysis tool. However, the trend of using LLMs without sufficient attention to their limitations and risks, which we rhetorically refer to as “GPTology”, can be detrimental given the easy access to models such as ChatGPT. Beyond existing general guidelines, we investigate the current limitations, ethical implications, and potential of LLMs specifically for psychological research, and show their concrete impact in various empirical studies. Our results highlight the importance of recognizing global psychological diversity, cautioning against treating LLMs (especially in zero-shot settings) as universal solutions for text analysis, and developing transparent, open methods to address LLMs’ opaque nature for reliable, reproducible, and robust inference from AI-generated data. Acknowledging LLMs’ utility for task automation, such as text annotation, or to expand our understanding of human psychology, we argue for diversifying human samples and expanding psychology’s methodological toolbox to promote an inclusive, generalizable science, countering homogenization, and over-reliance on LLMs.
The Trump Effect? Right-Wing Populism and Distrust in Voting by Mail in Canada
Authors: Wu Cary , Dawson Andrew 
Published: July 2024

Abstract
Do Donald Trump’s attacks on voting by mail influence how some Canadians view mail-in ballots? The Trump effect on views and behaviors surrounding voting by mail has been well documented in the United States. North of the border, more Canadians than ever voted by mail in the last general election. In this study, we consider how right-wing populism is associated with trust in voting by mail among Canadians. Specifically, we seek to test two main hypotheses. First, we consider whether Canadians holding populist views—and, in particular, those holding right-wing populist views (would-be Trump supporters)—are less trusting of voting by mail. Second, we consider whether political media exposure amplifies this association. We analyze data from both the 2021 Canadian Election Study and Democracy Checkup Survey. We find that those who hold populist views clearly have less trust in voting by mail. This is especially true among right-leaning individuals. Furthermore, as in the United States, this effect is moderated by one’s level of political media exposure, with higher levels of political media exposure amplifying the effect of populist views on trust in voting by mail. Our findings, therefore, suggest that the politicization of mail-in voting by President Trump has important implications for the legitimacy of the electoral system not only in the United States, but also in Canada and potentially in other parts of the world.