bluuebunny/crossref_metadata_2025_split huggingface dataset:
CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images
Authors: Lee Michael Y. , Bedia Jacob S. , Bhate Salil S. , Barlow Graham L. , Phillips Darci , Fantl Wendy J. , Nolan Garry P. , Schürch Christian M. 
Published: January 2022

Abstract
Background
Algorithmic cellular segmentation is an essential step for the quantitative analysis of highly multiplexed tissue images. Current segmentation pipelines often require manual dataset annotation and additional training, significant parameter tuning, or a sophisticated understanding of programming to adapt the software to the researcher’s need. Here, we present CellSeg, an open-source, pre-trained nucleus segmentation and signal quantification software based on the Mask region-convolutional neural network (R-CNN) architecture. CellSeg is accessible to users with a wide range of programming skills.

Results
CellSeg performs at the level of top segmentation algorithms in the 2018 Kaggle Data Challenge both qualitatively and quantitatively and generalizes well to a diverse set of multiplexed imaged cancer tissues compared to established state-of-the-art segmentation algorithms. Automated segmentation post-processing steps in the CellSeg pipeline improve the resolution of immune cell populations for downstream single-cell analysis. Finally, an application of CellSeg to a highly multiplexed colorectal cancer dataset acquired on the CO-Detection by indEXing (CODEX) platform demonstrates that CellSeg can be integrated into a multiplexed tissue imaging pipeline and lead to accurate identification of validated cell populations.

Conclusion
CellSeg is a robust cell segmentation software for analyzing highly multiplexed tissue images, accessible to biology researchers of any programming skill level.
Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16S rRNA amplicon sequencing
Authors: Serrana Joeselle M. , Watanabe Kozo 
Published: January 2022

AbstractBackgroundSequential membrane filtration as a pre-processing step for capturing sediment-associated microorganisms could provide good quality and integrity DNA that can be preserved and kept at ambient temperatures before community profiling through culture-independent molecular techniques. However, the effects of sample pre-processing via filtration on DNA-based profiling of sediment-associated microbial community diversity and composition are poorly understood. Specifically, the influences of pre-processing on the quality and quantity of extracted DNA, high-throughput DNA sequencing reads, and detected microbial taxa need further evaluation.ResultsWe assessed the impact of pre-processing freshwater sediment samples by sequential membrane filtration (from 10, 5 to 0.22 μm pore size) for 16S rRNA-based community profiling of sediment-associated microorganisms. Specifically, we examined if there would be method-driven differences between non- and pre-processed sediment samples regarding the quality and quantity of extracted DNA, PCR amplicon, resulting high-throughput sequencing reads, microbial diversity, and community composition. We found no significant difference in the qualities and quantities of extracted DNA and PCR amplicons, and the read abundance after bioinformatics processing (i.e., denoising and chimeric-read filtering steps) between the two methods. Although the non- and pre-processed sediment samples had more unique than shared amplicon sequence variants (ASVs), we report that their shared ASVs accounted for 74% of both methods’ absolute read abundance. More so, at the genus level, the final collection filter identified most of the genera (95% of the reads) captured from the non-processed samples, with a total of 51 false-negative (2%) and 59 false-positive genera (3%). We demonstrate that while there were differences in shared and unique taxa, both methods revealed comparable microbial diversity and community composition.ConclusionsOur observations highlight the feasibility of pre-processing sediment samples for community analysis and the need to further assess sampling strategies to help conceptualize appropriate study designs for sediment-associated microbial community profiling.
Genome-wide association study of the candidate genes for grape berry shape-related traits
Authors: Zhang Chuan , Cui Liwen , Fang Jinggui 
Published: January 2022

Abstract
Background
In the breeding of new horticultural crops, fruit shape is an important selection characteristic. A variety of fruit shapes appeared during the gradual process of selection and domestication. However, few studies have been conducted on grape berry shape, especially studies related to mining candidate genes. To discover candidate genes related to grape berry shape, the present study first took the berry shape parameters analyzed by Tomato Analyzer as the target traits and used a genome-wide association analysis to analyze candidate genes.

Results
In total, 122 single-nucleotide polymorphism (SNP) loci had significant correlations with multiple berry shape traits in both years, and some candidate genes were further mined. These genes were mainly related to LRR receptor-like serine/threonine-protein kinase (At1g05700 and At1g07650), transcription factors (GATA transcription factor 23-like, transcription factor VIP1, transcription initiation factor TFIID, and MADS-box transcription factor 6), ubiquitin ligases (F-box protein SKIP19 and RING finger protein 44), and plant hormones (indole-3-acetic acid-amido synthetase GH3.6 and ethylene-responsive transcription factor ERF061). In addition, some important SNP loci were associated with multiple berry-shape traits. The study further revealed some genes that control multiple traits simultaneously, indicating that these berry shape traits are subject to the coordinated regulation of some genes in controlling berry shape.

Conclusions
In the present work, we identified interesting genetic determinants of grape berry shape-related traits. The identification of molecular markers that are closely related to these berry-shape traits is of great significance for breeding specific berry-shaped grape varieties.
Spatiotemporal prediction of vancomycin-resistant Enterococcus colonisation
Authors: van Niekerk J. M. , Lokate M. , Braakman-Jansen L. M. A. , van Gemert-Pijnen J. E. W. C. , Stein A. 
Published: January 2022

AbstractBackgroundVancomycin-resistant enterococci (VRE) is the cause of severe patient health and monetary burdens. Antibiotic use is a confounding effect to predict VRE in patients, but the antibiotic use of patients who may have frequented the same ward as the patient in question is often neglected. This study investigates how patient movements between hospital wards and their antibiotic use can explain the colonisation of patients with VRE.MethodsIntrahospital patient movements, antibiotic use and PCR screening data were used from a hospital in the Netherlands. The PageRank algorithm was used to calculate two daily centrality measures based on the spatiotemporal graph to summarise the flow of patients and antibiotics at the ward level. A decision tree model was used to determine a simple set of rules to estimate the daily probability of patient VRE colonisation for each hospital ward. The model performance was improved using a random forest model and compared using 30% test sample.ResultsCentrality covariates summarising the flow of patients and their antibiotic use between hospital wards can be used to predict the daily colonisation of VRE at the hospital ward level. The decision tree model produced a simple set of rules that can be used to determine the daily probability of patient VRE colonisation for each hospital ward. An acceptable area under the ROC curve (AUC) of 0.755 was achieved using the decision tree model and an excellent AUC of 0.883 by the random forest model on the test set. These results confirms that the random forest model performs better than a single decision tree for all levels of model sensitivity and specificity on data not used to estimate the models.ConclusionThis study showed how the movements of patients inside hospitals and their use of antibiotics could predict the colonisation of patients with VRE at the ward level. Two daily centrality measures were proposed to summarise the flow of patients and antibiotics at the ward level. An early warning system for VRE can be developed to test and further develop infection prevention plans and outbreak strategies using these results.
Triple gallbladder with heterotopic gastric mucosa: a case report
Authors: Ott Leah , O’Neill John , Cameron Danielle , Callahan Michael J. , Grover Amit , Fox Victor L. , Kim Heung Bae , Lillehei Craig , Cuenca Alex G. 
Published: January 2022

Abstract
Background
Triple gallbladder is a rare congenital anomaly of the biliary tract that can be associated with heterotopic tissue. Gallbladder triplication results from the failure of rudimentary bile ducts to regress during embryological development, and can be difficult to distinguish from Todani type II choledochal cysts and biliary duplication cysts.

Case presentation
A 2-year-old patient presented to our institution with intermittent abdominal pain for 1 year. She had elevated transaminases with imaging concerning for a choledochal cyst. After assessment with magnetic resonance cholangiopancreatography and endoscopic retrograde cholangiopancreatography, she was diagnosed with a gallbladder multiplication and a common bile duct stricture. She underwent laparoscopic cholecystectomy, which confirmed the diagnosis of triple gallbladder. One of the three gallbladders demonstrated heterotopic gastric mucosa on final pathology, including at the cystic duct margin. Follow up testing with a technetium 99 m scan demonstrated a subtle focus of increased activity in the right upper abdomen at the expected location of the common bile duct, concerning for the presence of residual gastric mucosa. The patient remains well without abdominal pain.

Conclusions
We describe the first case of heterotopic gastric mucosa in a triple gallbladder in a young patient presenting with chronic abdominal pain. We also demonstrate the safety and feasibility of laparoscopic cholecystectomy in young children with triple gallbladder. Finally, we propose an interdisciplinary approach to the management of common bile duct strictures in the setting of ectopic acid secretion, involving a combination of medical management, endoscopic intervention, and possible salvage laparoscopic Roux-en-Y hepaticojejunostomy.
Pharmacist assessment of drug-gene interactions and drug-induced phenoconversion in major depressive disorder: a case report
Authors: Del Toro-Pagán N. M. , Matos A. , Bardolia C. , Michaud V. , Turgeon J. , Amin N. S. 
Published: January 2022

Abstract
Background
Response to antidepressant therapy is highly variable among individuals. Pharmacogenomic (PGx) testing presents an opportunity to guide drug selection while optimizing therapy outcomes and/or decreasing the risk for toxicity.

Case presentation
A patient with multiple comorbidities, including severe major depressive disorder (MDD), experienced adverse drug events and undesirable response to multiple antidepressant medications (i.e., bupropion, escitalopram, and venlafaxine). A clinical pharmacist assessed significant drug-gene, drug-drug, and drug-drug-gene interactions as well as other clinical factors to provide recommendations for antidepressant therapy optimization.

Conclusion
This case highlights the importance of PGx testing and the key role of pharmacists in identifying and mitigating drug-related problems and optimizing drug therapy in patients with MDD.
Effective management of district-level malaria control and elimination: implementing quality and participative process improvements
Authors: Agins Bruce , Case Peter , Chandramohan Daniel , Chen Ingrid , Chikodzore Rudo , Chitapi Precious , Chung Amanda , Gosling Roly , Gosling Jonathan , Gumbi Matsiliso , Ikeda Daniel , Madinga Munashe , Mnguni Peliwe , Murungu Joseph , Gueye Cara Smith , Tulloch Jim , Viljoen Greyling ,   Leadership and Engagement for improved Accountability and Delivery of Services Framework Development Group, Agins Bruce , Case Peter , Chandramohan Daniel , Chen Ingrid , Chikodzore Rudo , Chitapi Precious , Chung Amanda , Gosling Roly , Gosling Jonathan , Gumbi Matsiliso , Ikeda Daniel , Madinga Munashe , Mnguni Peliwe , Murungu Joseph , Gueye Cara Smith , Tulloch Jim , Viljoen Greyling 
Published: January 2022

AbstractAlthough it is widely recognized that strong program management is essential to achieving better health outcomes, this priority is not recognized in malaria programmatic practices. Increased management precision offers the opportunity to improve the effectiveness of malaria interventions, overcoming operational barriers to intervention coverage and accelerating the path to elimination. Here we propose a combined approach involving quality improvement, quality management, and participative process improvement, which we refer to as Combined Quality and Process Improvement (CQPI), to improve upon malaria program management. We draw on evidence from other areas of public health, as well as pilot implementation studies in Eswatini, Namibia and Zimbabwe to support the proposal. Summaries of the methodological approaches employed in the pilot studies, overview of activities and an outline of lessons learned from the implementation of CQPI are provided. Our findings suggest that a malaria management strategy that prioritizes quality and participative process improvements at the district-level can strengthen teamwork and communication while enabling the empowerment of subnational staff to solve service delivery challenges. Despite the promise of CQPI, however, policy makers and donors are not aware of its potential. Investments are therefore needed to allow CQPI to come to fruition.
Estimating life expectancy adjusted by self-rated health status in the United States: national health interview survey linked to the mortality
Authors: Cho Hyunsoon , Wang Zhuoqiao , Yabroff K. Robin , Liu Benmei , McNeel Timothy , Feuer Eric J. , Mariotto Angela B. 
Published: January 2022

Abstract
Background
Life expectancy is increasingly incorporated in evidence-based screening and treatment guidelines to facilitate patient-centered clinical decision-making. However, life expectancy estimates from standard life tables do not account for health status, an important prognostic factor for premature death. This study aims to address this research gap and develop life tables incorporating the health status of adults in the United States.

Methods
Data from the National Health Interview Survey (1986–2004) linked to mortality follow-up through to 2006 (age ≥ 40, n = 729,531) were used to develop life tables. The impact of self-rated health (excellent, very good, good, fair, poor) on survival was quantified in 5-year age groups, incorporating complex survey design and weights. Life expectancies were estimated by extrapolating the modeled survival probabilities.

Results
Life expectancies incorporating health status differed substantially from standard US life tables and by health status. Poor self-rated health more significantly affected the survival of younger compared to older individuals, resulting in substantial decreases in life expectancy. At age 40 years, hazards of dying for white men who reported poor vs. excellent health was 8.5 (95% CI: 7.0,10.3) times greater, resulting in a 23-year difference in life expectancy (poor vs. excellent: 22 vs. 45), while at age 80 years, the hazards ratio was 2.4 (95% CI: 2.1, 2.8) and life expectancy difference was 5 years (5 vs. 10). Relative to the US general population, life expectancies of adults (age < 65) with poor health were approximately 5–15 years shorter.

Conclusions
Considerable shortage in life expectancy due to poor self-rated health existed. The life table developed can be helpful by including a patient perspective on their health and be used in conjunction with other predictive models in clinical decision making, particularly for younger adults in poor health, for whom life tables including comorbid conditions are limited.
Access to denture restoration services under removable dentures subsidy program for adults aged 65 years and older in Taiwan- an interpretive approach
Authors: Chu Kuan-Yu 
Published: January 2022

Abstract
Background
Access is an important issue in health equality. Availability of dental services and cost subsidies is an important factor affecting access to denture restoration for the elderly. This study aims to explore access to denture restoration services in the elderly removable denture’s subsidy program of Taiwan.

Methods
Access to the elderly removable dentures subsidy program was measured from two aspects, that is, availability of subsidies and payment for these services and the characteristics of patients and their treatment needs. The first aspect included reimbursements and the number and location of subsidy clinics, and the second aspect included the age and gender distribution of patients and denture types. Information on reimbursement regulations and the number and location of dental clinics providing subsidized services were obtained from the website of the Taoyuan City Public Health Bureau, Taoyuan Hospital, Department of Statistics and Ministry of Health and Welfare. Data on patient characteristics and denture type were obtained through a retrospective survey. We selected individuals who participated in the elderly removable denture’s subsidy program from 2015 to 2018 at the Geriatric Dentistry Department of Taoyuan Hospital. We conducted data analysis using an interpretive approach.

Results
This study found that reimbursement amounts are inadequate, and the availability of subsidized services is low. Moreover, the proportion of male applications is slightly higher than that of females. In addition, among the applicants, removable partial dentures for single or two arches are the most common.

Conclusions
Problems of insufficient numbers of contracted hospitals and low reimbursement amounts are observed in the subsidy program, which are the key factors affecting access to denture restoration services among the elderly. Policymakers should exclude wealthy individuals and offer subsidy only to low-income elderly individuals with missing teeth who are in dire need of financial support to improve their dental health.
Gut microbiome alterations and gut barrier dysfunction are associated with host immune homeostasis in COVID-19 patients
Authors: Sun Zhonghan , Song Zhi-Gang , Liu Chenglin , Tan Shishang , Lin Shuchun , Zhu Jiajun , Dai Fa-Hui , Gao Jian , She Jia-Lei , Mei Zhendong , Lou Tao , Zheng Jiao-Jiao , Liu Yi , He Jiang , Zheng Yuanting , Ding Chen , Qian Feng , Zheng Yan , Chen Yan-Mei 
Published: January 2022

Abstract
Background
COVID-19 is an infectious disease characterized by multiple respiratory and extrapulmonary manifestations, including gastrointestinal symptoms. Although recent studies have linked gut microbiota to infectious diseases such as influenza, little is known about the role of the gut microbiota in COVID-19 pathophysiology.

Methods
To better understand the host-gut microbiota interactions in COVID-19, we characterized the gut microbial community and gut barrier function using metagenomic and metaproteomic approaches in 63 COVID-19 patients and 8 non-infected controls. Both immunohematological parameters and transcriptional profiles were measured to reflect the immune response in COVID-19 patients.

Results
Altered gut microbial composition was observed in COVID-19 patients, which was characterized by decreased commensal species and increased opportunistic pathogenic species. Severe illness was associated with higher abundance of four microbial species (i.e., Burkholderia contaminans, Bacteroides nordii, Bifidobacterium longum, and Blautia sp. CAG 257), six microbial pathways (e.g., glycolysis and fermentation), and 10 virulence genes. These severity-related microbial features were further associated with host immune response. For example, the abundance of Bu. contaminans was associated with higher levels of inflammation biomarkers and lower levels of immune cells. Furthermore, human-origin proteins identified from both blood and fecal samples suggested gut barrier dysfunction in COVID-19 patients. The circulating levels of lipopolysaccharide-binding protein increased in patients with severe illness and were associated with circulating inflammation biomarkers and immune cells. Besides, proteins of disease-related bacteria (e.g., B. longum) were detectable in blood samples from patients.

Conclusions
Our results suggest that the dysbiosis of the gut microbiome and the dysfunction of the gut barrier might play a role in the pathophysiology of COVID-19 by affecting host immune homeostasis.
Strainline: full-length de novo viral haplotype reconstruction from noisy long reads
Authors: Luo Xiao , Kang Xiongbin , Schönhuth Alexander 
Published: January 2022

AbstractHaplotype-resolved de novo assembly of highly diverse virus genomes is critical in prevention, control and treatment of viral diseases. Current methods either can handle only relatively accurate short read data, or collapse haplotype-specific variations into consensus sequence. Here, we present Strainline, a novel approach to assemble viral haplotypes from noisy long reads without a reference genome. Strainline is the first approach to provide strain-resolved, full-length de novo assemblies of viral quasispecies from noisy third-generation sequencing data. Benchmarking on simulated and real datasets of varying complexity and diversity confirm this novelty and demonstrate the superiority of Strainline.
Striking sex differences in magnetic resonance imaging findings in the sacroiliac joints in the population
Authors: Braun J. , Baraliakos X. , Bülow R. , Schmidt C. O. , Richter A. 
Published: January 2022

Abstract
Background
In patients with axial spondyloarthritis (axSpA), magnetic resonance imaging (MRI) is used to detect bone marrow edema (BME) in sacroiliac joints (SIJ) but SIJ BME are also detected in the population. Not much is known about sex differences in that regard.

Objective
To explore sex-specific differences associated with the extent of BME in the SIJ suggestive of axSpA in a general population cohort study.

Methods
Taking advantage of 793 recently evaluated MRIs of subjects < 45 years taking part in the SHIP cohort, we used negative-binomial (NB) count data regression to analyze factors associated with the extent of SIJ BME. Predictors were explored by model-based boosting (MBB), a machine learning approach.

Results
Estimates of NB regression showed strong effects of sex in interaction with age, BMI, back pain, and particularly HLA-B27. The NB regression model showed incidence rate ratios (IRR) for the main effect of sex (females vs. males): 0.94 [95% CI: 0.63; 1.41], HLA-B27: 4.32 [2.09; 9.8], and for the interaction of sex to HLA-B27: 0.22 [0.06; 0.75]. According to MBB, HLA-B27 positivity, BMI, current smoking, back pain in the last 3 months, the interaction of sex and HLA-B27, and delivery in the last 12 months were of highest importance to explain the extent of SIJ BME.

Conclusions
Different factors were associated with the extent of SIJ BME in females and males. Most importantly, HLA-B27 was relevant only in males but not in females in whom a postpartal state was important. This finding may be relevant for the pathogenesis of axSpA.