bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host, reproductive, and lifestyle factors in relation to quantitative histologic metrics of the normal breast
Authors: Abubakar Mustapha , Klein Alyssa , Fan Shaoqi , Lawrence Scott , Mutreja Karun , Henry Jill E. , Pfeiffer Ruth M. , Duggan Maire A. , Gierach Gretchen L. 
Published: August 2023

Abstract
Background
Emerging data indicate that variations in quantitative epithelial and stromal tissue composition and their relative abundance in benign breast biopsies independently impact risk of future invasive breast cancer. To gain further insights into breast cancer etiopathogenesis, we investigated associations between epidemiological factors and quantitative tissue composition metrics of the normal breast.

Methods
The study participants were 4108 healthy women ages 18–75 years who voluntarily donated breast tissue to the US-based Susan G. Komen Tissue Bank (KTB; 2008–2019). Using high-accuracy machine learning algorithms, we quantified the percentage of epithelial, stromal, adipose, and fibroglandular tissue, as well as the proportion of fibroglandular tissue that is epithelium relative to stroma (i.e., epithelium-to-stroma proportion, ESP) on digitized hematoxylin and eosin (H&E)-stained normal breast biopsy specimens. Data on epidemiological factors were obtained from participants using a detailed questionnaire administered at the time of tissue donation. Associations between epidemiological factors and square root transformed tissue metrics were investigated using multivariable linear regression models.

Results
With increasing age, the amount of stromal, epithelial, and fibroglandular tissue declined and adipose tissue increased, while that of ESP demonstrated a bimodal pattern. Several epidemiological factors were associated with individual tissue composition metrics, impacting ESP as a result. Compared with premenopausal women, postmenopausal women had lower ESP [β (95% Confidence Interval (CI)) = −0.28 (− 0.43, − 0.13); P < 0.001] with ESP peaks at 30–40 years and 60–70 years among pre- and postmenopausal women, respectively. Pregnancy [β (95%CI) vs nulligravid = 0.19 (0.08, 0.30); P < 0.001] and increasing number of live births (P-trend < 0.001) were positively associated with ESP, while breastfeeding was inversely associated with ESP [β (95%CI) vs no breastfeeding = −0.15 (− 0.29, − 0.01); P = 0.036]. A positive family history of breast cancer (FHBC) [β (95%CI) vs no FHBC = 0.14 (0.02–0.26); P = 0.02], being overweight or obese [β (95%CI) vs normal weight = 0.18 (0.06–0.30); P = 0.004 and 0.32 (0.21–0.44); P < 0.001, respectively], and Black race [β (95%CI) vs White = 0.12 (− 0.005, 0.25); P = 0.06] were positively associated with ESP.

Conclusion
Our findings revealed that cumulative exposure to etiological factors over the lifespan impacts normal breast tissue composition metrics, individually or jointly, to alter their dynamic equilibrium, with potential implications for breast cancer susceptibility and tumor etiologic heterogeneity.
Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture
Authors: Meadows Jennifer R. S. , Kidd Jeffrey M. , Wang Guo-Dong , Parker Heidi G. , Schall Peter Z. , Bianchi Matteo , Christmas Matthew J. , Bougiouri Katia , Buckley Reuben M. , Hitte Christophe , Nguyen Anthony K. , Wang Chao , Jagannathan Vidhya , Niskanen Julia E. , Frantz Laurent A. F. , Arumilli Meharji , Hundi Sruthi , Lindblad-Toh Kerstin , Ginja Catarina , Agustina Kadek Karang , André Catherine , Boyko Adam R. , Davis Brian W. , Drögemüller Michaela , Feng Xin-Yao , Gkagkavouzis Konstantinos , Iliopoulos Giorgos , Harris Alexander C. , Hytönen Marjo K. , Kalthoff Daniela C. , Liu Yan-Hu , Lymberakis Petros , Poulakakis Nikolaos , Pires Ana Elisabete , Racimo Fernando , Ramos-Almodovar Fabian , Savolainen Peter , Venetsani Semina , Tammen Imke , Triantafyllidis Alexandros , vonHoldt Bridgett , Wayne Robert K. , Larson Greger , Nicholas Frank W. , Lohi Hannes , Leeb Tosso , Zhang Ya-Ping , Ostrander Elaine A. 
Published: August 2023

Abstract
Background
The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function.

Results
We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.

Conclusions
We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.
Continuous passive paracentesis versus large-volume paracentesis in the prevention and treatment of intra-abdominal hypertension in the critically ill cirrhotic patient with ascites (COPPTRIAHL): study protocol for a randomized controlled trial
Authors: Pereira Rui Antunes , Virella Daniel , Perdigoto Rui , Marcelino Paulo , Saliba Faouzi , Germano Nuno 
Published: August 2023

Abstract
Background
Critically ill patients with cirrhosis and ascites are at high risk for intra-abdominal hypertension (IAH) which increases mortality. Clinical guidelines recommend maintaining intra-abdominal pressure (IAP) below 16 mmHg; nonetheless, more than three quarters of critically ill patients with cirrhosis develop IAH during their first week of ICU stay. Standard-of-care intermittent large-volume paracentesis (LVP) relieves abdominal wall tension, reduces IAP, optimizes abdominal perfusion pressure, and is associated with short-term improvement in renal and pulmonary dysfunction. However, there is no evidence of the superiority of different paracentesis strategies in the prevention and treatment of IAH in critically ill patients with cirrhosis.
This trial aims to compare the outcomes of continuous passive paracentesis versus LVP in the prevention and treatment of IAH in patients with cirrhosis and ascites.

Methods
An investigator-initiated, open label, randomized controlled trial, set in a general ICU specialized in liver disease, was initiated in August 2022, with an expected duration of 36 months. Seventy patients with cirrhosis and ascites will be randomly assigned, in a 1:1 ratio, to receive one of two methods of therapeutic paracentesis. A stratified randomization method, with maximum creatinine and IAP values as strata, will homogenize patient baseline characteristics before trial group allocation, within 24 h of admission.
In the control group, LVP will be performed intermittently according to clinical practice, with a maximum duration of 8 h, while, in the intervention group, continuous passive paracentesis will drain ascitic fluid for up to 7 days.
The primary endpoint is serum creatinine concentration, and secondary endpoints include IAP, measured creatinine clearance, daily urine output, stage 3 acute kidney injury and multiorgan dysfunction assessed at day 7 after enrollment, as well as 28-day mortality rate and renal replacement therapy-free days, and length-of-stay. Prespecified values will be used in case of renal replacement therapy or, beforehand ICU discharge, liver transplant and death. Safety analysis will include paracentesis-related complication rate and harm. Data will be analyzed with an intention-to-treat approach.

Discussion
This is the first trial to compare the impact of different therapeutic paracentesis strategies on organ dysfunction and outcomes in the prevention and treatment of IAH in critically ill patients with cirrhosis and ascites.

Trial registration
ClinicalTrials.gov NCT04322201. Registered on 20 December 2019
Effect of free-weight vs. machine-based strength training on maximal strength, hypertrophy and jump performance – a systematic review and meta-analysis
Authors: Haugen Markus E. , Vårvik Fredrik T. , Larsen Stian , Haugen Arvid S. , van den Tillaar Roland , Bjørnsen Thomas 
Published: August 2023

AbstractBackgroundThe effectiveness of strength training with free-weight vs. machine equipment is heavily debated. Thus, the purpose of this meta-analysis was to summarize the data on the effect of free-weight versus machine-based strength training on maximal strength, jump height and hypertrophy.MethodsThe review was conducted in accordance with the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines, and the systematic search of literature was conducted up to January 1st, 2023. Studies that directly compared free-weight vs. machine-based strength training for a minimum of 6 weeks in adults (18–60 yrs.) were included.ResultsThirteen studies (outcomes: maximal strength [n = 12], jump performance [n = 5], muscle hypertrophy [n = 5]) with a total sample of 1016 participants (789 men, 219 women) were included. Strength in free-weight tests increased significantly more with free-weight training than with machines (SMD: -0.210, CI: -0.391, -0.029,p = 0.023), while strength in machine-based tests tended to increase more with machine training than with free-weights (SMD: 0.291, CI: -0.017, 0.600,p = 0.064). However, no differences were found between modalities in direct comparison (free-weight strength vs. machine strength) for dynamic strength (SMD: 0.084, CI: -0.106, 0.273,p = 0.387), isometric strength (SMD: -0.079, CI: -0.432, 0.273,p = 0.660), countermovement jump (SMD: -0.209, CI: -0.597, 0.179,p = 0.290) and hypertrophy (SMD: -0.055, CI: -0.397, 0.287,p = 0.751).ConclusionNo differences were detected in the direct comparison of strength, jump performance and muscle hypertrophy. Current body of evidence indicates that strength changes are specific to the training modality, and the choice between free-weights and machines are down to individual preferences and goals.
Exploring the antibiogram of soil isolates from an indian hospital precinct: link to antibiotic usage
Authors: Kunhikannan Shalini , Thomas Colleen J. , Sumana M. N. , Franks Ashley E. , Kumar Sumana , Nagarathna S. , Petrovski Steve , Shindler Anya E. 
Published: August 2023

Abstract
Objective
Hospitals serve as hotspots of antibiotic resistance. Despite several studies exploring antibiotic resistance in hospitals, none have explored the resistance profile of soil bacteria from a hospital precinct. This study examined and compared the antibiogram of the soil isolates from a hospital and its affiliated university precinct, to determine if antibiotic resistant bacteria were present closer to the hospital.

Results
120 soil samples were collected from JSS Hospital and JSS University in Mysore, India across three consecutive seasons (monsoon, winter and summer). 366 isolates were randomly selected from culture. Antibiotic susceptibility testing was performed on 128 isolates of Pseudomonas (n = 73), Acinetobacter (n = 30), Klebsiella species (n = 15) and Escherichia coli (n = 10). Pseudomonas species exhibited the highest antibiotic resistance. Ticarcillin-clavulanic acid, an extended-spectrum carboxypenicillin antibiotic used to treat moderate-to-severe infections, ranked highest amongst the antibiotics to whom these isolates were resistant (n = 51 out of 73, 69.9%). Moreover, 56.8% (n = 29) were from the hospital and 43.1% (n = 22) were from the university precinct, indicating antibiotic resistant bacteria were closer to the hospital setting. This study highlights the effect of antibiotic usage in hospitals and the influence of anthropogenic activities in the hospital on the dissemination of antibiotic resistance into hospital precinct soil.
Cross-platform comparisons for targeted bisulfite sequencing of MGISEQ-2000 and NovaSeq6000
Authors: Sun Jin , Su Mingyang , Ma Jianhua , Xu Minjie , Ma Chengcheng , Li Wei , Liu Rui , He Qiye , Su Zhixi 
Published: August 2023

AbstractBackgroundAn accurate and reproducible next-generation sequencing platform is essential to identify malignancy-related abnormal DNA methylation changes and translate them into clinical applications including cancer detection, prognosis, and surveillance. However, high-quality DNA methylation sequencing has been challenging because poor sequence diversity of the bisulfite-converted libraries severely impairs sequencing quality and yield. In this study, we tested MGISEQ-2000 Sequencer’s capability of DNA methylation sequencing with a published non-invasive pancreatic cancer detection assay, using NovaSeq6000 as the benchmark.ResultsWe sequenced a series of synthetic cell-free DNA (cfDNA) samples with different tumor fractions and found MGISEQ-2000 yielded data with similar quality as NovaSeq6000. The methylation levels measured by MGISEQ-2000 demonstrated high consistency with NovaSeq6000. Moreover, MGISEQ-2000 showed a comparable analytic sensitivity with NovaSeq6000, suggesting its potential for clinical detection. As to evaluate the clinical performance of MGISEQ-2000, we sequenced 24 clinical samples and predicted the pathology of the samples with a clinical diagnosis model, PDACatch classifier. The clinical model performance of MGISEQ-2000’s data was highly consistent with that of NovaSeq6000’s data, with the area under the curve of 1. We also tested the model’s robustness with MGISEQ-2000’s data when reducing the sequencing depth. The results showed that MGISEQ-2000’s data showed matching robustness of the PDACatch classifier with NovaSeq6000’s data.ConclusionsTaken together, MGISEQ-2000 demonstrated similar data quality, consistency of the methylation levels, comparable analytic sensitivity, and matching clinical performance, supporting its application in future non-invasive early cancer detection investigations by detecting distinct methylation patterns of cfDNAs.
Stem cells and extracellular vesicles to improve preclinical orofacial soft tissue healing
Authors: Wang Zhihao , Knight Rob , Stephens Phil , Ongkosuwito E. M. , Wagener Frank A. D. T. G. , Von den Hoff Johannes W. 
Published: August 2023

AbstractOrofacial soft tissue wounds caused by surgery for congenital defects, trauma, or disease frequently occur leading to complications affecting patients' quality of life. Scarring and fibrosis prevent proper skin, mucosa and muscle regeneration during wound repair. This may hamper maxillofacial growth and speech development. To promote the regeneration of injured orofacial soft tissue and attenuate scarring and fibrosis, intraoral and extraoral stem cells have been studied for their properties of facilitating maintenance and repair processes. In addition, the administration of stem cell-derived extracellular vesicles (EVs) may prevent fibrosis and promote the regeneration of orofacial soft tissues. Applying stem cells and EVs to treat orofacial defects forms a challenging but promising strategy to optimize treatment. This review provides an overview of the putative pitfalls, promises and the future of stem cells and EV therapy, focused on orofacial soft tissue regeneration.
Optimization of differential filtration-based mitochondrial isolation for mitochondrial transplant to cerebral organoids
Authors: Bodenstein David F. , Powlowski Pavel , Zachos Kassandra A. , El Soufi El Sabbagh Dana , Jeong Hyunjin , Attisano Liliana , Edgar Landon , Wallace Douglas C. , Andreazza Ana Cristina 
Published: August 2023

Abstract
Background
Mitochondrial dysfunction is involved in several diseases ranging from genetic mitochondrial disorders to chronic metabolic diseases. An emerging approach to potentially treat mitochondrial dysfunction is the transplantation of autologous live mitochondria to promote cell regeneration. We tested the differential filtration-based mitochondrial isolation protocol established by the McCully laboratory for use in cellular models but found whole cell contaminants in the mitochondrial isolate.

Methods
Therefore, we explored alternative types of 5-μm filters (filters A and B) for isolation of mitochondria from multiple cell lines including HEK293 cells and induced pluripotent stem cells (iPSCs). MitoTracker™ staining combined with flow cytometry was used to quantify the concentration of viable mitochondria. A proof-of-principle mitochondrial transplant was performed using mitoDsRed2-tagged mitochondria into a H9-derived cerebral organoid.

Results
We found that filter B provided the highest quality mitochondria as compared to the 5-μm filter used in the original protocol. Using this method, mitochondria were also successfully isolated from induced pluripotent stem cells. To test for viability, mitoDsRed2-tagged mitochondria were isolated and transplanted into H9-derived cerebral organoids and observed that mitochondria were engulfed as indicated by immunofluorescent co-localization of TOMM20 and MAP2.

Conclusions
Thus, use of filter B in a differential filtration approach is ideal for isolating pure and viable mitochondria from cells, allowing us to begin evaluating long-term integration and safety of mitochondrial transplant using cellular sources.
RETRACTED ARTICLE: Intelligent monitoring methodology for large-scale logistics transport vehicles based on parallel Internet of Vehicles
Authors: Liang Chengzhang 
Published: August 2023

AbstractThe essence of the Internet of Vehicles is a social and physical information system, including the psychological and organizational factors of human beings. The complexity of the Internet will lead to certain deviations when monitoring vehicles. Therefore, the Parallel Internet of Vehicles is employed to monitor the information on large-scale logistics transport vehicles. This platform is built based on the ACP intelligent approach, which consists of three parts: An artificial system (A), a computational experiment (C), and parallel execution (P). The Adaboost algorithm is used to extract information on large-scale logistics transport vehicles from the ACP parallel Internet of Vehicles, and the Tabu search strategy is applied to optimize the Monte Carlo positioning algorithm. The approximate optimal estimation is obtained by optimizing the filtering to eliminate vehicle positions with fewer possibilities. The weight of important sampling values of the independent vehicle node positions is integrated to complete the posterior probability distribution estimation of the possible positions of vehicles, in order to realize vehicle position monitoring. It is verified that the root-mean square error of the algorithm when positioning a vehicle is less than 0.18, and the monitoring deviation is quite small.
Paneth cells in farm animals: current status and future direction
Authors: Cui Chenbin , Li Lindeng , Wu Lin , Wang Xinru , Zheng Yao , Wang Fangke , Wei Hongkui , Peng Jian 
Published: August 2023

AbstractA healthy intestine plays an important role in the growth and development of farm animals. In small intestine, Paneth cells are well known for their regulation of intestinal microbiota and intestinal stem cells (ISCs). Although there has been a lot of studies and reviews on human and murine Paneth cells under intestinal homeostasis or disorders, little is known about Paneth cells in farm animals. Most farm animals possess Paneth cells in their small intestine, as identified by various staining methods, and Paneth cells of various livestock species exhibit noticeable differences in cell shape, granule number, and intestinal distribution. Paneth cells in farm animals and their antimicrobial peptides (AMPs) are susceptible to multiple factors such as dietary nutrients and intestinal infection. Thus, the comprehensive understanding of Paneth cells in different livestock species will contribute to the improvement of intestinal health. This review first summarizes the current status of Paneth cells in pig, cattle, sheep, horse, chicken and rabbit, and points out future directions for the investigation of Paneth cells in the reviewed animals.
A novel strategy for screening mutations in the voltage-gated sodium channel gene of Aedes albopictus based on multiplex PCR-mass spectrometry minisequencing technology
Authors: Mu Qunzheng , Zhao Xin , Li Fengfeng , Li Wenyu , Zhou Xinxin , Lun Xinchang , Wang Yiguan , Hua Dongdong , Liu Qiyong , Xiao Di , Meng Fengxia 
Published: August 2023

Abstract
Background
The current prevention and control strategy for Aedes albopictus heavily relies on comprehensive management, such as environmental management and chemical control. However, the wide application of pyrethroids has facilitated the development of insecticide resistance, primarily via mutations in the voltage-gated sodium channel (VGSC) gene. This study aims to develop a novel strategy for detecting mutations in the VGSC gene in Ae. albopictus using multiplex PCR-mass spectrometry (MPCR-MS) minisequencing technology.

Methods
We established a new strategy for detecting mutations in the VGSC gene in Ae. albopictus using MPCR-MS minisequencing technology. MPCR amplification and mass probe extension (MPE) were first used, followed by single nucleotide polymorphism (SNP) typing mass spectrometry, which allows the simultaneous detection of multiple mutation sites of the VGSC gene in 96 samples of Ae. albopictus. A total of 70 wild-collected Ae. albopictus were used to evaluate the performance of the method by comparing it with other methods.

Results
Three target sites (1016, 1532, 1534) in the VGSC gene can be detected simultaneously by double PCR amplification combined with matrix-assisted laser desorption ionization–time-of-flight mass spectrometry, achieving a detection limit of 20 fg/μl. We applied this method to 70 wild-collected Ae. albopictus, and the obtained genotypes were consistent with the routine sequencing results, suggesting the accuracy of our method.

Conclusions
MPCR-MS minisequencing technology provides a sensitive and high-throughput approach to Ae. albopictus VGSC gene mutation screening. Compared with conventional sequencing, this method is economical and time-saving. It is of great value for insecticide resistance surveillance in areas with a high risk of vector-borne disease.

Graphical Abstract