bluuebunny/crossref_metadata_2025_split huggingface dataset:
Violent injury prevention does not equal to violent crime prevention: an analysis of violence intervention program efficacy using propensity score methods
Authors: Holler, MPH Emma , Ortiz, MD Damaris , Mohanty, MD, MS Sanjay , Meagher, MD, MPH Ashley D , Boustani, MD, MPH Malaz , Zarzaur, MD, MPH Ben L , Simons, MD Clark J 
Published: October 2022

ObjectiveThe purpose of this study was to determine if exposure to Prescription for Hope (RxH), a hospital-based violence intervention program (HVIP), is associated with reduced violent reinjury and new convictions for violent crime in the 2-year period after index hospitalization for a violent injury.MethodsThis was a retrospective cohort study analyzing patients from two level I trauma centers in Indianapolis, Indiana. RxH participants (n=260) enrolled between January 1, 2015 and December 31, 2018 and who had trauma registry data were included. RxH eligibility criteria: admitted for a violent injury (excluding sexual violence), at least 15 years of age, live in Marion County, Indiana, and stay in the hospital for at least 24 hours. RxH exclusion criteria: heavy active substance use, acute psychosis, dementia, severe traumatic brain injury, intentional self-harm, and incarceration. All patients admitted to IU Health Methodist Hospital, a nearby level I trauma center, for an assault, stabbing, or gunshot wound during the same period and met the RxH eligibility criteria were included as a comparison group (n=732). Doubly adjusted logistic regression with inverse probability of treatment weighting was used to estimate the average treatment effect of RxH participation on violent reinjury and new convictions for violent crime.ResultsData from 992 patients were analyzed. RxH was significantly associated with reduced odds of violent reinjury (OR=0.35, 95% CI 0.20 to 0.59) and increased odds of conviction for a violent crime (OR=2.43, 95% CI 1.64 to 3.61).ConclusionRxH was associated with decreased odds of violent reinjury but increased odds of new conviction for a violent crime. Our results highlight the importance of robust, routine evaluation of HVIP efficacy and recommend inclusion of other outcomes in addition to violent reinjury when evaluating program success. High-quality randomized controlled trials are needed to further investigate the impact of HVIPs on a variety of outcomes.Level of evidenceIV: retrospective study with more than one negative criterion ((1) limited control of confounding and (2) heterogeneous populations).
Pre- and Early Peri-menopausal Physical Function and Risk of Cardiovascular Events: The Study of Women’s Health Across the Nation
Authors: Lange-Maia Brittney S. , El Khoudary Samar R. , Crandall Carolyn J. , Zhang Yanyu , Karvonen-Gutierrez Carrie A. , Gabriel Kelley Pettee , Appelhans Bradley M. , Strotmeyer Elsa S. , Ylitalo Kelly R. , Karavolos Kelly , Kravitz Howard M. , Dugan Sheila A. , Janssen Imke 
Published: October 2022

Objectives To determine whether physical function (PF) before menopause is related to cardiovascular disease (CVD) risk. Methods Participants were N = 2950 pre-/early peri-menopausal women (median age 46, (25th–75th percentile: 43–48 years). Physical function was assessed at baseline using the Physical Function subscale of the SF-36 and scores were trichotomized (no, some, or substantial limitations). Clinical CVD events were ascertained at annual/biennial clinical assessments through the 15th follow-up visit. Risk of CVD was determined with Cox proportional hazards models. Results: Women were followed for a median of 19.1 years, during which 220 women had a CVD event. In fully adjusted models, women with substantial limitations at baseline had higher CVD risk compared to women with no limitations (hazards ratio [HR] = 1.55, 95% confidence interval [CI]: 1.12–2.33). Discussion: Substantial PF limitations in pre- and early peri-menopausal women are associated with higher risk of clinical CVD events, consistent with literature in older adults.
Anti-Inflammatory and Chondro-Protective Effects of Acidic Polysaccharide from Enteromorpha Prolifera in Experimental Models of Osteoarthritis In-Vitro and In-Vivo
Authors: Wang Chih-Chien , Lu Jeng-Wei , Chiang Kuang-Hsing , Cheng Yu-Shuan , Chu You-Hsiang , Peng Yi-Jen , Cheng Chia-Hui , Chang Chia-Yu , Chuu Jiunn-Jye 
Published: October 2022

Objective Osteoarthritis (OA) progression has been shown to increase the expression of inflammatory cytokines in joints, leading to the destruction of cartilage matrix. Interleukin (IL)-1β is a potent inflammatory cytokine associated with osteoarthritic synovial fluid. The protective effects of polysaccharides from Enteromorpha prolifera against acute hepatic injury was reported. Design In this study, we examined the effects of Enteromorpha polysaccharide extracts (EPEs) in the treatment of OA. The effects of the EPEs were assessed using an IL-1β-stimulated SW1353 and SW982 cells. The expression levels of specific mRNA and proteins were evaluated using semi-quantitative reverse transcription polymerase chain reaction (sqRT-PCR) and western immunoblotting. An OA animal study involving C57BL/6J mice was also conducted to assess the effects on tactile sensitivity and anterior cruciate ligament transection (ACLT). Results Acidic polysaccharide extract (APE) was shown to significantly reduce cytokine and chemokine mRNA levels in IL-1β-stimulated SW1353 and SW982 cells and attenuate the expression of proinflammatory cytokines and p38/AP-1 in SW1353 cells. APE was also shown to minimize the effect of osteolytic lesions in the knee joints of ACLT-induced osteoarthritic mice. Conclusions APE is a potent inhibitor of joint degeneration associated with OA.
Development of an Artificial Intelligence-Based Machine Tool to Predict Outcome in Intracerebral Hemorrhage
Authors: Menon Girish , KS Hareesha , Gajula Karthik , Kumar Sampath , Hegde Ajay 
Published: October 2022

Introduction: Spontaneous intracerebral hemorrhage is the second most common type of stroke with high morbidity and mortality. Outcome prediction is very important in this disease, to enable us tailor treatment strategies especially in a low- and middle-income countries. Today, prediction is predominantly limited to few clinical factors and may not be very accurate. We explore the application of an artificial intelligence-based platform for outcome prediction with a combination of clinical, radiological, and biochemical parameters. Methods: Data from our prospectively maintained stroke register was cleaned and processed using the XGBoost machine learning (ML) algorithm to predict outcome at discharge and 90 days using the modified Rankin scale. A total of 1,000 patients were included in the study, 129 variables were pruned to 19 significant features during the phase of preprocessing. Results: The data set was split 9:1 with 900 cases being used for training and the remaining 100 for validation. The models were evaluated based on the mean absolute error (MAE). Model-1 trained for predicting “mRS_Discharge” had a MAE of 0.34 and model-2 trained for predicting “mRS_3months” had a MAE of 0.63. Conclusion: ML algorithms can be successfully applied for the prediction of outcome in intracerebral hemorrhage.
Distinct clonal identities of B-ALLs arising after lenolidomide therapy for multiple myeloma
Authors: Barnell Erica K. , Skidmore Zachary L. , Newcomer Kenneth F. , Chavez Monique , Campbell Katie M. , Cotto Kelsy C. , Spies Nicholas C. , Ruzinova Marianna B. , Wang Tianjiao , Abro Brooj , Kreisel Friederike , Parikh Bijal A. , Duncavage Eric J. , Frater John L. , Lee Yi-Shan , Hassan Anjum , King Justin A. , Kohnen Daniel R. , Fiala Mark A. , Welch John S. , Uy Geoffrey L. , Vij Kiran , Vij Ravi , Griffith Malachi , Griffith Obi L. , Wartman Lukas D. 
Published: October 2022

Abstract
Patients with multiple myeloma (MM) who are treated with lenalidomide rarely develop a secondary B-cell acute lymphoblastic leukemia (B-ALL). The clonal and biological relationship between these sequential malignancies is not yet clear. We identified 17 patients with MM treated with lenalidomide, who subsequently developed B-ALL. Patient samples were evaluated through sequencing, cytogenetics/fluorescence in situ hybridization (FISH), immunohistochemical (IHC) staining, and immunoglobulin heavy chain (IgH) clonality assessment. Samples were assessed for shared mutations and recurrently mutated genes. Through whole exome sequencing and cytogenetics/FISH analysis of 7 paired samples (MM vs matched B-ALL), no mutational overlap between samples was observed. Unique dominant IgH clonotypes between the tumors were observed in 5 paired MM/B-ALL samples. Across all 17 B-ALL samples, 14 (83%) had a TP53 variant detected. Three MM samples with sufficient sequencing depth (&gt;500×) revealed rare cells (average of 0.6% variant allele frequency, or 1.2% of cells) with the same TP53 variant identified in the subsequent B-ALL sample. A lack of mutational overlap between MM and B-ALL samples shows that B-ALL developed as a second malignancy arising from a founding population of cells that likely represented unrelated clonal hematopoiesis caused by a TP53 mutation. The recurrent variants in TP53 in the B-ALL samples suggest a common path for malignant transformation that may be similar to that of TP53-mutant, treatment-related acute myeloid leukemia. The presence of rare cells containing TP53 variants in bone marrow at the initiation of lenalidomide treatment suggests that cellular populations containing TP53 variants expand in the presence of lenalidomide to increase the likelihood of B-ALL development.
Clinical applications of machine learning in predicting 3D shapes of the human body: a systematic review
Authors: Wang Joyce Zhanzi , Lillia Jonathon , Kumar Ashnil , Bray Paula , Kim Jinman , Burns Joshua , Cheng Tegan L. 
Published: October 2022

AbstractBackgroundPredicting morphological changes to anatomical structures from 3D shapes such as blood vessels or appearance of the face is a growing interest to clinicians. Machine learning (ML) has had great success driving predictions in 2D, however, methods suitable for 3D shapes are unclear and the use cases unknown.Objective and methodsThis systematic review aims to identify the clinical implementation of 3D shape prediction and ML workflows. Ovid-MEDLINE, Embase, Scopus and Web of Science were searched until 28th March 2022.Results13,754 articles were identified, with 12 studies meeting final inclusion criteria. These studies involved prediction of the face, head, aorta, forearm, and breast, with most aiming to visualize shape changes after surgical interventions. ML algorithms identified were regressions (67%), artificial neural networks (25%), and principal component analysis (8%). Meta-analysis was not feasible due to the heterogeneity of the outcomes.Conclusion3D shape prediction is a nascent but growing area of research in medicine. This review revealed the feasibility of predicting 3D shapes using ML clinically, which could play an important role for clinician-patient visualization and communication. However, all studies were early phase and there were inconsistent language and reporting. Future work could develop guidelines for publication and promote open sharing of source code.
A web-based database server using 43,710 public RNA-seq samples for the analysis of gene expression and alternative splicing in livestock animals
Authors: Liu Jinding , Lang Kun , Tan Suxu , Jie Wencai , Zhu Yihua , Huang Shiqing , Huang Wen 
Published: October 2022

Abstract
Background
Livestock animals is of great significance in agricultural production. However, the role of specific gene expression, especially alternative splicing in determining phenotype, is not well understood. The livestock research community needs a gene expression and alternative splicing database contributing to livestock genetic improvement.

Description
We report the construction of LivestockExp (https://bioinfo.njau.edu.cn/livestockExp), a web-based database server for the exploration of gene expression and alternative splicing using 43,710 uniformly processed RNA-seq samples from livestock animals and several relative species across six orders. The database is equipped with basic querying functions and multiple online analysis modules including differential/specific expression analysis, co-expression network analysis, and cross-species gene expression conservation analysis. In addition to the re-analysis of public datasets, users can upload personal datasets to perform co-analysis with public datasets. The database also offers a wide range of visualization tools and diverse links to external databases enabling users to efficiently explore the results and to gain additional insights.

Conclusion
LivestockExp covers by far the largest number of livestock animal species and RNA-seq samples and provides a valuable data resource and analysis platform for the convenient utilization of public RNA-seq datasets.
Identification and characteristics of SnRK genes and cold stress-induced expression profiles in Liriodendron chinense
Authors: Li Rongxue , Radani Yasmina , Ahmad Baseer , Movahedi Ali , Yang Liming 
Published: October 2022

Abstract
Background
The sucrose non-fermenting 1 (SNF1)-related protein kinases (SnRKs) play a vivid role in regulating plant metabolism and stress response, providing a pathway for regulation between metabolism and stress signals. Conducting identification and stress response studies on SnRKs in plants contributes to the development of strategies for tree species that are more tolerant to stress conditions.

Results
In the present study, a total of 30 LcSnRKs were identified in Liriodendron chinense (L. chinense) genome, which was distributed across 15 chromosomes and 4 scaffolds. It could be divided into three subfamilies: SnRK1, SnRK2, and SnRK3 based on phylogenetic analysis and domain types. The LcSnRK of the three subfamilies shared the same Ser/Thr kinase structure in gene structure and motif composition, while the functional domains, except for the kinase domain, showed significant differences. A total of 13 collinear gene pairs were detected in L. chinense and Arabidopsis thaliana (A. thaliana), and 18 pairs were detected in L. chinense and rice, suggesting that the LcSnRK family genes may be evolutionarily more closely related to rice. Cis-regulation element analysis showed that LcSnRKs were LTR and TC-rich, which could respond to different environmental stresses. Furthermore, the expression patterns of LcSnRKs are different at different times under low-temperature stress. LcSnRK1s expression tended to be down-regulated under low-temperature stress. The expression of LcSnRK2s tended to be up-regulated under low-temperature stress. The expression trend of LcSnRK3s under low-temperature stress was mainly up-or down-regulated.

Conclusion
The results of this study will provide valuable information for the functional identification of the LcSnRK gene in the future.
ELOVL gene family plays a virtual role in response to breeding selection and lipid deposition in different tissues in chicken (Gallus gallus)
Authors: Wang Dandan , Li Xinyan , Zhang Panpan , Cao Yuzhu , Zhang Ke , Qin Panpan , Guo Yulong , Li Zhuanjian , Tian Yadong , Kang Xiangtao , Liu Xiaojun , Li Hong 
Published: October 2022

Abstract
Background
Elongases of very long chain fatty acids (ELOVLs), a family of first rate-limiting enzymes in the synthesis of long-chain fatty acids, play an essential role in the biosynthesis of complex lipids. Disrupting any of ELOVLs affects normal growth and development in mammals. Genetic variations in ELOVLs are associated with backfat or intramuscular fatty acid composition in livestock. However, the effects of ELOVL gene family on breeding selection and lipid deposition in different tissues are still unknown in chickens.

Results
Genetic variation patterns and genetic associations analysis showed that the genetic variations of ELOVL genes were contributed to breeding selection of commercial varieties in chicken, and 14 SNPs in ELOVL2-6 were associated with body weight, carcass or fat deposition traits. Especially, one SNP rs17631638T > C in the promoter of ELOVL3 was associated with intramuscular fat content (IMF), and its allele frequency was significantly higher in native and layer breeds compared to that in commercial broiler breeds. Quantitative real-time PCR (qRT-PCR) determined that the ELOVL3 expressions in pectoralis were affected by the genotypes of rs17631638T > C. In addition, the transcription levels of ELOVL genes except ELOVL5 were regulated by estrogen in chicken liver and hypothalamus with different regulatory pathways. The expression levels of ELOVL1-6 in hypothalamus, liver, abdominal fat and pectoralis were correlated with abdominal fat weight, abdominal fat percentage, liver lipid content and IMF. Noteworthily, expression of ELOVL3 in pectoralis was highly positively correlated with IMF and glycerophospholipid molecules, including phosphatidyl choline, phosphatidyl ethanolamine, phosphatidyl glycerol and phospholipids inositol, rich in ω-3 and ω-6 long-chain unsaturated fatty acids, suggesting ELOVL3 could contribute to intramuscular fat deposition by increasing the proportion of long-chain unsaturated glycerophospholipid molecules in pectoralis.

Conclusions
In summary, we demonstrated the genetic contribution of ELOVL gene family to breeding selection for specialized varieties, and revealed the expression regulation of ELOVL genes and their potential roles in regulating lipid deposition in different tissues. This study provides new insights into understanding the functions of ELOVL family on avian growth and lipid deposition in different tissues and the genetic variation in ELOVL3 may aid the marker-assisted selection of meat quality in chicken.
Arterial Glyceryl Trinitrate in Acute Ischemic Stroke after Thrombectomy for Neuroprotection (AGAIN): Rationale, design and protocol for a prospective randomized controlled trial
Authors: Gao Jie , Cheng Zhe , Jiang Shangqian , Wills Melissa , Wehbe Alexandra , Rajah Gary B. , Geng Xiaokun , Ding Yuchuan 
Published: October 2022

Abstract
Background
Although endovascular recanalization therapy demonstrates robust clinical efficacy in acute ischemic stroke (AIS), not all victims of these cerebrovascular accidents can benefit from it and achieve a favorable prognosis after successful reperfusion. Therefore, alternative neuroprotective strategies are urgently needed for AIS patients after vessel recanalization. Nitric oxide (NO) levels are low after AIS and NO donor drugs may be neuroprotective against cerebral ischemia–reperfusion injury. Glyceryl trinitrate (GTN), often used in the clinic as a NO donor, may provide a novel neuroprotective strategy. This rationale, design, and protocol for a prospective pilot study plans to explore the preliminary safety, feasibility, and neuroprotective benefits of Arterial Glyceryl Trinitrate in Acute Ischemic Stroke after Thrombectomy for Neuroprotection (AGAIN).

Methods
AGAIN, a prospective RCT, is proposed for AIS patients after mechanical thrombectomy. Subjects will be randomly assigned in a 1:1 fashion (n = 40) to either the control group or the intervention group. Participants assigned to the intervention group will be administered 800 μg GTN in the catheter immediately after recanalization, whereas those in the control group will be administered the same volume of normal saline. All participants from either group will be given concurrent treatment with standard of care therapies in accordance with the current guidelines for stroke management. The primary outcome is safety [symptomatic intracranial hemorrhage (ICH), hypotension, neurological deterioration, ICH, fatal ICH, as well as headache, tachycardia, emesis, and seizures], whereas secondary outcomes included changes in poststroke functional outcomes, infarction volumes, and blood nitrate index detection.

Discussions
This study is a prospective randomized controlled trial to test the safety and efficacy of intra-arterial GTN in AIS patients after endovascular therapy. The results from this study will give insight for future GTN studies and new neuroprotective strategies for future AIS treatment strategies.

Trial registration number
ChiCTR2100045254. Registered on March 21, 2021.
Reducing risks for infant mortality in the Midlands, UK: a qualitative study identifying areas for improvement in the delivery of key public health messages in the perinatal period
Authors: Pillay Thillagavathie , Feeney Jane , Walters Claire , Nelson Hollie , Thomas Lucy , Lewis Dawn , Anderson Karen , Petkar Anjali 
Published: October 2022

Abstract
Background:
The Midlands has amongst the highest rates of neonatal and infant mortality in the UK. A public health parent education and empowerment programme, aimed at reducing key risks associated with this mortality was established and evaluated in the region. This was undertaken in an attempt to identify areas for optimal delivery of the public health messages around reducing risks for neonatal and infant mortality.

Method:
Qualitatively assessment, using the software package Dedoose®, was undertaken. This involved analysis of reflections by the programme trainers, after the delivery of their training sessions to parents, families and carers, between 01 January and 31 December 2021. These were intended to capture insights from the trainers on parent, family, carer and staff perspectives, perceptions/misperceptions around reducing risks for infant mortality. Potential areas for improvement in delivery of the programme were identified from this analysis.

Results:
A total of 323 programmes, comprising 524 parents, family members and carers were offered the programme. Analysis of 167 reflections around these interactions and those of staff (n = 29) are reported. The programme was positively received across parents, families, carers and staff. Four overall themes were identified: (a) reach and inclusion, (b) knowledge, (c) practical and emotional support and (d) challenges for delivery of the programme. Recommendations for improved delivery of the programme were identified, based on qualitative analysis.

Conclusion:
This novel approach to empowerment and education around neonatal public health messaging is a valuable tool for parents, families, carers and staff in the Midlands. Key practical recommendations for enhancing delivery of these critical public health messages were identified from this qualitative research. These are likely to be of value in other parts of the UK and globally.
CD4 and FOXP3 as predictive markers for the recurrence of T3/T4a stage II colorectal cancer: applying a novel discrete Bayes decision rule
Authors: Nakagami Yuki , Hazama Shoichi , Suzuki Nobuaki , Yoshida Shin , Tomochika Shinobu , Matsui Hiroto , Shindo Yoshitaro , Tokumitsu Yukio , Matsukuma Satoshi , Watanabe Yusaku , Iida Michihisa , Tsunedomi Ryouichi , Takeda Shigeru , Fujita Tomonobu , Kawakami Yutaka , Ogihara Hiroyuki , Hamamoto Yoshihiko , Ioka Tatsuya , Tanabe Tsuyoshi , Ueno Tomio , Nagano Hiroaki 
Published: October 2022

Abstract
Background
We recently reported the relapse-free survival (RFS) significance of the combination of CD4+ and forkhead box P3+ (FOXP3) T-cell densities identified by immunohistochemistry in patients with stage I, II, and III colorectal cancer (CRC) who underwent curative resections. This study was designed to determine the optimal combination of markers that predict recurrence in patients with T factors of T3/T4a stage II CRC by applying a novel Bayes decision rule.

Methods
Using 137 cancer tissue specimens from T3/T4a stage II patients, 12 clinicopathologic and immune factors were analysed as predictive candidates for recurrence.

Results
Our study showed that the combination of low CD4+ and low FOXP3+ T-cell densities resulted in extremely poor RFS.

Conclusions
Adjuvant chemotherapy may be considered for patients with a combination of low CD4+ and low FOXP3+ T-cell densities. The discovery of this new prognostic indicator is important for the appropriate management of patients undergoing curative resection for T3/T4a stage II CRC.