bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations between body mass index, sleep-disordered breathing, brain structure, and behavior in healthy children
Authors: Cui Jianqi , Li Guanya , Zhang Minmin , Xu Jiayu , Qi Haowen , Ji Weibin , Wu Feifei , Zhang Yaqi , Jiang Fukun , Hu Yang , Zhang Wenchao , Wei Xiaorong , Manza Peter , Volkow Nora D , Gao Xinbo , Wang Gene-Jack , Zhang Yi 
Published: July 2023

Abstract
Pediatric overweight/obesity can lead to sleep-disordered breathing (SDB), abnormal neurological and cognitive development, and psychiatric problems, but the associations and interactions between these factors have not been fully explored. Therefore, we investigated the associations between body mass index (BMI), SDB, psychiatric and cognitive measures, and brain morphometry in 8484 children 9–11 years old using the Adolescent Brain Cognitive Development dataset. BMI was positively associated with SDB, and both were negatively correlated with cortical thickness in lingual gyrus and lateral orbitofrontal cortex, and cortical volumes in postcentral gyrus, precentral gyrus, precuneus, superior parietal lobule, and insula. Mediation analysis showed that SDB partially mediated the effect of overweight/obesity on these brain regions. Dimensional psychopathology (including aggressive behavior and externalizing problem) and cognitive function were correlated with BMI and SDB. SDB and cortical volumes in precentral gyrus and insula mediated the correlations between BMI and externalizing problem and matrix reasoning ability. Comparisons by sex showed that obesity and SDB had a greater impact on brain measures, cognitive function, and mental health in girls than in boys. These findings suggest that preventing childhood obesity will help decrease SDB symptom burden, abnormal neurological and cognitive development, and psychiatric problems.
Encoding, working memory, or decision: how feedback modulates time perception
Authors: Li Langyu , Hou Chunna , Peng Chunhua , Chen Youguo 
Published: July 2023

AbstractThe hypothesis that individuals can accurately represent temporal information within approximately 3 s is the premise of several theoretical models and empirical studies in the field of temporal processing. The significance of accurately representing time within 3 s and the universality of the overestimation contrast dramatically. To clarify whether this overestimation arises from an inability to accurately represent time or a response bias, we systematically examined whether feedback reduces overestimation at the 3 temporal processing stages of timing (encoding), working memory, and decisions proposed by the scalar timing model. Participants reproduced the time interval between 2 circles with or without feedback, while the electroencephalogram (EEG) was synchronously recorded. Behavioral results showed that feedback shortened reproduced times and significantly minimized overestimation. EEG results showed that feedback significantly decreased the amplitude of contingent negative variation (CNV) in the decision stage but did not modulate the CNV amplitude in the encoding stage or the P2–P3b amplitudes in the working memory stage. These results suggest that overestimation arises from response bias when individuals convert an accurate representation of time into behavior. Our study provides electrophysiological evidence to support the conception that short intervals under approximately 3 s can be accurately represented as “temporal gestalt.”
Systolic anterior motion of the anterior mitral valve leaflet begins in subclinical hypertrophic cardiomyopathy
Authors: Seitler Samuel , De Zoysa Anthony Surani , Obianyo Chinwe C C , Syrris Petros , Patel Vimal , Sado Daniel M , Maestrini Viviana , Castelletti Silvia , Walsh Stephen , O’Brien Ben , Moon James C , Captur Gabriella 
Published: July 2023

Abstract

Aims
Anterior mitral valve leaflet (AMVL) elongation is detectable in overt and subclinical hypertrophic cardiomyopathy (HCM). We sought to investigate the dynamic motion of the aorto-mitral apparatus to understand the behaviour of the AMVL and the mechanisms of left ventricular outflow tract obstruction (LVOTO) predisposition in HCM.

Methods and results
Cardiovascular magnetic resonance imaging using a 1.5 Tesla scanner was performed on 36 HCM sarcomere gene mutation carriers without left ventricular hypertrophy (G+LVH−), 31 HCM patients with preserved ejection fraction carrying a pathogenic sarcomere gene mutation (G+LVH+), and 53 age-, sex-, and body surface area–matched healthy volunteers. Dynamic excursion of the aorto-mitral apparatus was assessed semi-automatically on breath-held three-chamber cine steady-state free precession images. Four pre-defined regions of interest (ROIs) were tracked: ROIPMVL: hinge point of the posterior mitral valve leaflet; ROITRIG: intertrigonal mitral annulus; ROIAMVL: AMVL tip; and ROIAAO: anterior aortic annulus. Compared with controls, normalized two-dimensional displacement-vs.-time plots in G+LVH− revealed subtle but significant systolic anterior motion (SAM) of the AMVL (P &lt; 0.0001) and reduced longitudinal excursion of ROIAAO (P = 0.014) and ROIPMVL (P = 0.048). In overt and subclinical HCM, excursion of the ROITRIG/AMVL/PMVL was positively associated with the burden of left ventricular fibrosis (P &lt; 0.028). As expected, SAM was observed in G+LVH+ together with reduced longitudinal excursion of ROITRIG (P = 0.049) and ROIAAO (P = 0.008).

Conclusion
Dyskinesia of the aorto-mitral apparatus, including SAM of the elongated AMVL, is detectable in subclinical HCM before the development of LVH or left atrial enlargement. These data have the potential to improve our understanding of early phenotype development and LVOTO predisposition in HCM.
Critical role of insertion preference for invasion trajectory of transposons
Authors: Munasinghe Manisha , Springer Nathan , Brandvain Yaniv 
Published: July 2023

Abstract
It is unclear how mobile DNA sequences (transposable elements, hereafter TEs) invade eukaryotic genomes and reach stable copy numbers, as transposition can decrease host fitness. This challenge is particularly stark early in the invasion of a TE family at which point hosts may lack the specialized machinery to repress the spread of these TEs. One possibility (in addition to the evolution of host regulation of TEs) is that TE families may evolve to preferentially insert into chromosomal regions that are less likely to impact host fitness. This may allow the mean TE copy number to grow while minimizing the risk for host population extinction. To test this, we constructed simulations to explore how the transposition probability and insertion preference of a TE family influence the evolution of mean TE copy number and host population size, allowing for extinction. We find that the effect of a TE family’s insertion preference depends on a host’s ability to regulate this TE family. Without host repression, a neutral insertion preference increases the frequency of and decreases the time to population extinction. With host repression, a preference for neutral insertions minimizes the cumulative deleterious load, increases population fitness, and, ultimately, avoids triggering an extinction vortex.
Characterization of integration sites and transfer DNA structures in Agrobacterium-mediated transgenic events of maize inbred B104
Authors: Neelakandan Anjanasree K , Kabahuma Mercy , Yang Qin , Lopez Miriam , Wisser Randall J , Balint-Kurti Peter , Lauter Nick 
Published: July 2023

Abstract
In maize, the community-standard transformant line B104 is a useful model for dissecting features of transfer DNA (T-DNA) integration due to its compatibility with Agrobacterium-mediated transformation and the availability of its genome sequence. Knowledge of transgene integration sites permits the analysis of the genomic environment that governs the strength of gene expression and phenotypic effects due to the disruption of an endogenous gene or regulatory element. In this study, we optimized a fusion primer and nested integrated PCR (FPNI-PCR) technique for T-DNA detection in maize to characterize the integration sites of 89 T-DNA insertions in 81 transformant lines. T-DNA insertions preferentially occurred in gene-rich regions and regions distant from centromeres. Integration junctions with and without microhomologous sequences as well as junctions with de novo sequences were detected. Sequence analysis of integration junctions indicated that T-DNA was incorporated via the error-prone repair pathways of nonhomologous (predominantly) and microhomology-mediated (minor) end-joining. This report provides a quantitative assessment of Agrobacterium-mediated T-DNA integration in maize with respect to insertion site features, the genomic distribution of T-DNA incorporation, and the mechanisms of integration. It also demonstrates the utility of the FPNI-PCR technique, which can be adapted to any species of interest.
Interactions between the transcription factors FfmA and AtrR are required to properly regulate gene expression in the fungus Aspergillus fumigatus
Authors: Paul Sanjoy , Stamnes Mark A , Moye-Rowley W Scott 
Published: July 2023

Abstract
Transcriptional regulation of azole resistance in the filamentous fungus Aspergillus fumigatus is a key step in development of this problematic clinical phenotype. We and others have previously described a C2H2-containing transcription factor called FfmA that is required for normal levels of voriconazole susceptibility. Null alleles of ffmA exhibit a strongly compromised growth rate even in the absence of any external stress. Here, we employ an acutely repressible doxycycline-off form of ffmA to rapidly deplete FfmA protein from the cell. Using this approach, we carried out RNA-seq analyses to probe the transcriptome cells acutely deprived of FfmA. A total of 2,000 genes were differentially expressed upon acute depletion of FfmA, illustrating the broad transcriptomic effect of this factor. Interestingly, the transcriptome changes observed upon this acute depletion of FfmA expression only shared limited overlap with those found in an ffmAΔ null strain analyzed by others. Chromatin immunoprecipitation coupled with high throughput DNA sequencing analysis (ChIP-seq) identified 530 genes that were bound by FfmA. More than 300 of these genes were also bound by AtrR, a transcription factor important in azole drug resistance, demonstrating striking regulatory overlap with FfmA. However, while AtrR is an upstream activation protein with known specificity, our data suggest that FfmA is a chromatin-associated factor that binds DNA in a manner dependent on other factors. We provide evidence that AtrR and FfmA interact in the cell and show reciprocal expression modulation. Interaction of AtrR and FfmA is required for normal gene expression in A. fumigatus.
Recommendations for Standardizing MRI-based Evaluation of Perianal Fistulizing Disease Activity in Pediatric Crohn’s Disease Clinical Trials
Authors: Crowley Eileen , Ma Christopher , Guizzetti Leonard , Zou Guangyong , Lewindon Peter J , Gee Michael S , Hyams Jeffrey S , Rosen Michael J , von Allmen Daniel , de Buck van Overstraeten Anthony , Shackelton Lisa M , Remillard Julie , Schleicher Lauren , Dillman Jonathan R , Rimola Jordi , Taylor Stuart A , Fletcher Joel G , Church Peter C , Feagan Brian G , Griffiths Anne M , Jairath Vipul , Greer Mary-Louise C 
Published: July 2023

Abstract

Background
Perianal fistulas and abscesses occur commonly as complications of pediatric Crohn’s disease (CD). A validated imaging assessment tool for quantification of perianal disease severity and activity is needed to evaluate treatment response. We aimed to identify magnetic resonance imaging (MRI)-based measures of perianal fistulizing disease activity and study design features appropriate for pediatric patients.

Methods
Seventy-nine statements relevant to MRI-based assessment of pediatric perianal fistulizing CD activity and clinical trial design were generated from literature review and expert opinion. Statement appropriateness was rated by a panel (N = 15) of gastroenterologists, radiologists, and surgeons using modified RAND/University of California Los Angeles appropriateness methodology.

Results
The modified Van Assche Index (mVAI) and the Magnetic Resonance Novel Index for Fistula Imaging in CD (MAGNIFI-CD) were considered appropriate instruments for use in pediatric perianal fistulizing disease clinical trials. Although there was concern regarding the use of intravascular contrast material in pediatric patients, its use in clinical trials was considered appropriate. A clinically evident fistula tract and radiologic disease defined as at least 1 fistula or abscess on pelvic MRI were considered appropriate trial inclusion criteria. A coprimary clinical and radiologic end point and inclusion of a patient-reported outcome were also considered appropriate.

Conclusion
Outcomes of treatment of perianal fistulizing disease in children must include MRI. Existing multi-item measures, specifically the mVAI and MAGNIFI-CD, can be adapted and used for children. Further research to assess the operating properties of the indices when used in a pediatric patient population is ongoing.
Use of Tramadol vs Traditional Opioids and Adverse Outcomes in Patients with Inflammatory Bowel Disease: A Danish Nationwide Cohort Study
Authors: Dalal Rahul S , Lund Ken , Zegers Floor D , Friedman Sonia , Allegretti Jessica R , Nørgård Bente Mertz 
Published: July 2023

Abstract

Background
Use of traditional opioids (TOs) for pain management has been associated with adverse outcomes among patients with inflammatory bowel diseases (IBDs). It is unknown if similar associations exist for tramadol, a partial opioid agonist and serotonin and norephinephrine reuptake inhibitor. We sought to compare adverse outcomes associated with tramadol vs TOs in an IBD population.

Methods
This nationwide cohort study included adults with IBD diagnosed from 1995 to 2021 in Denmark with subsequent prescriptions for tramadol or TOs. For each analgesic, 2 populations were assessed: initial users (first prescription) and persistent users (first 3 consecutive prescriptions within 365 days). Outcomes included infection, bowel obstruction/ileus, IBD surgery, and mortality within 90 days after the initial use index date (date of first prescription) and within 365 days after the persistent use index date (date of third prescription). Odds ratios adjusted for demographics, comorbidities, and IBD severity were calculated using multivariable logistic regression.

Results
We identified 37 377 initial users and 15 237 persistent users of tramadol or TOs. Initial users of tramadol had lower adjusted odds of infection (adjusted odds ratio [OR], 0.80; 95% confidence interval [CI], 0.65-0.99), bowel obstruction/ileus (aOR, 0.74; 95% CI, 0.53-1.03), and mortality (aOR, 0.43; 95% CI, 0.35-0.55), and a higher adjusted odds of IBD-related surgery (aOR, 1.27; 95% CI, 1.02-1.60) vs initial users of TOs. Similar results were found for persistent users.

Conclusions
Tramadol was associated with lower odds of infection, bowel obstruction/ileus, and mortality vs TOs among patients with IBD. These associations may be impacted by residual confounding.
Analysis of artificial insemination center management factors that contribute to sperm parameters and boar longevity with a major focus on PGF2α treatment
Authors: Henneberg Sophie , Pieper Laura , Selige Christin , Jung Markus , Schulze Martin 
Published: July 2023

Abstract
Artificial insemination (AI) centers’ economic profitability is directly impacted by the amount of high-quality sperm doses. Many internal and external factors contribute to the quality of ejaculates. To enhance the libido and to reduce the time that is required to train boars for semen collection, prostaglandin products are used routinely at AI centers. The objectives of this study were to analyze sperm parameters of 40,765 ejaculates and the survival of 406 PGF2α-treated and 417 untreated AI boars of five breeds (Duroc [DU], Large White [LW], Landrace [LR], Pietrain [PI], and Large White Sire Line [LS]). Data were assessed in one AI center in Switzerland from 2018 to 2022 and sperm parameters were determined by computer-assisted sperm analysis immediately after semen collection. For further calculations, the ejaculates were divided into four groups depending on the boar’s age at semen collection day: 7 to 11, 12 to 18, 19 to 24, and 25 to 87 mo. Along with the boar age, breed, season, and semen collection frequency even the treatment with PGF2α had significant influence on sperm parameters. Overall, 19.5% ejaculates were collected after PGF2α treatment. For every age and breed group, higher ejaculate volume was found for untreated boars than for PGF2α-treated boars (P &lt; 0.001). Higher values for total and progressive sperm motility, total sperm number, and the proportion of morphologically normal sperm were observed in untreated boars across several age and breed groups. Only for sperm concentration, higher values were found for treated boars older than 11 mo (P &lt; 0.001) and the breeds DU, LW, and LR (P &lt; 0.001). The chance of ejaculates being rejected for AI purposes because of low sperm quality was 21% greater for treated boars. There was no difference in survival between treated and untreated boars. The hazard for boar removal increased with decreasing age at first semen collection and decreasing semen collection frequency. The results reveal better sperm quality for untreated boars than for PGF2α-treated boars, which might indicate that the underlying fertility of boars necessitating treatment is inferior compared to boars that can be collected without further treatment. Therefore, AI boar stations that are aiming to reduce PGF2α treatment should pay special attention to high libido and fertility of young prospective AI boars.
The Chilling Effects of Surveillance and Human Rights: Insights from Qualitative Research in Uganda and Zimbabwe
Authors: Murray Daragh , Fussey Pete , Hove Kuda , Wakabi Wairagala , Kimumwe Paul , Saki Otto , Stevens Amy 
Published: July 2023

AbstractStates are increasingly developing and deploying large scale surveillance and AI-enabled analytical capabilities. What is uncertain, however, is the impact this surveillance will have. Will it result in a chilling effect whereby individuals modify their behaviour due to the fear of the consequences that may follow? Understanding any such effect is essential: if surveillance activities interfere with the processes by which individuals develop their identity, or undermine democratic processes, the consequences may be almost imperceptible in the short term but profound over the long term. Currently, surveillance-related chilling effects are not well understood, meaning that insufficient weight is given to their potentially society-wide impacts. This article seeks to help redress this balance. Drawing on empirical research in Zimbabwe and Uganda it highlights how State surveillance has chilled behaviour, with significant implications for rights essential to individual development and democratic functioning, specifically the rights to freedom of expression and to freedom of assembly. Importantly, this qualitative research identifies a pattern of common themes or consequences associated with surveillance in general, allowing us to move beyond hypothetical or individual experiences, and providing a greater understanding of the nuances of surveillance-related effects that can help inform decision-making surrounding large scale digital surveillance.
The sarcopenia index measured using the lumbar paraspinal muscle is associated with prognosis in endometrial cancer
Authors: Uno Kaname , Yoshikawa Nobuhisa , Kitami Kazuhisa , Mori Sho , Shibata Takahiro , Iyoshi Shohei , Fujimoto Hiroki , Mogi Kazumasa , Yoshihara Masato , Tamauchi Satoshi , Ikeda Yoshiki , Yokoi Akira , Kato Kazuyoshi , Hoshiba Tsutomu , Oguchi Hidenori , Kajiyama Hiroaki 
Published: July 2023

Abstract

Objective
The number of type-II endometrial cancer patients has been increasing and the prognosis is not favorable. We aim to investigate whether sarcopenia index in any of several different muscles could serve as a novel biomarker of prognosis in patients with type-II endometrial cancer.

Methods
We retrospectively investigated a total of 194 patients at four hospitals. Ninety patients were treated as derivation set and the other 104 patients as validation set. Using preoperative computed tomography images, we measured the horizontal cross-sectional area at the third lumbar spine level: the (i) psoas major, (ii) iliac and (iii) paraspinal muscle. The clinical information including recurrence-free survival and overall survival were retrospectively collected. These results were validated with external data sets of three hospitals.

Results
The median values of the sarcopenia index (cm2/m2) ± standard deviation with the first data of 90 patients using the psoas, iliac and paraspinal muscle were 3.4 ± 1.0, 1.7 ± 0.6 and 12.6 ± 3.2, respectively. In univariate analyses, the sarcopenia indexes measured using the psoas or paraspinal muscle were associated with recurrence-free survival and overall survival. On the other hand, in multivariate analyses, only the sarcopenia index using paraspinal muscle was significantly related to recurrence-free survival (hazard ratio = 3.78, 95% confidence intervals = 1.29–5.97, P = 0.009) and overall survival (hazard ratio = 3.13, 95% confidence interval = 1.18–8.26, P = 0.022). Paraspinal sarcopenia index was also related to overall survival (hazard ratio = 3.74, 95% confidence interval = 1.31–10.72, P = 0.014) even in patients with advanced stage. Serum albumin was significantly correlated with the sarcopenia index (P = 0.012). Within the analysis of the validation set, sarcopenia index using paraspinal muscle was related to recurrence-free survival (hazard ratio = 2.06, P = 0.045) in multivariate analysis and recurrence-free survival (P = 0.009) in patients with advanced stage.

Conclusions
The sarcopenia index using the paraspinal muscle, not psoas, could be a suitable index to predict recurrence-free survival and overall survival in patients with type-II endometrial cancer even in advanced stage.
BioLiP2: an updated structure database for biologically relevant ligand–protein interactions
Authors: Zhang Chengxin , Zhang Xi , Freddolino Lydia , Zhang Yang 
Published: July 2023

Abstract
With the progress of structural biology, the Protein Data Bank (PDB) has witnessed rapid accumulation of experimentally solved protein structures. Since many structures are determined with purification and crystallization additives that are unrelated to a protein's in vivo function, it is nontrivial to identify the subset of protein–ligand interactions that are biologically relevant. We developed the BioLiP2 database (https://zhanggroup.org/BioLiP) to extract biologically relevant protein–ligand interactions from the PDB database. BioLiP2 assesses the functional relevance of the ligands by geometric rules and experimental literature validations. The ligand binding information is further enriched with other function annotations, including Enzyme Commission numbers, Gene Ontology terms, catalytic sites, and binding affinities collected from other databases and a manual literature survey. Compared to its predecessor BioLiP, BioLiP2 offers significantly greater coverage of nucleic acid-protein interactions, and interactions involving large complexes that are unavailable in PDB format. BioLiP2 also integrates cutting-edge structural alignment algorithms with state-of-the-art structure prediction techniques, which for the first time enables composite protein structure and sequence-based searching and significantly enhances the usefulness of the database in structure-based function annotations. With these new developments, BioLiP2 will continue to be an important and comprehensive database for docking, virtual screening, and structure-based protein function analyses.