bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring personalized structural connectomics for moderate to severe traumatic brain injury
Authors: Imms Phoebe , Clemente Adam , Deutscher Evelyn , Radwan Ahmed M. , Akhlaghi Hamed , Beech Paul , Wilson Peter H. , Irimia Andrei , Poudel Govinda , Domínguez Duque Juan F. , Caeyenberghs Karen 
Published: September 2022

Abstract
Graph theoretical analysis of the structural connectome has been employed successfully to characterize brain network alterations in patients with traumatic brain injury (TBI). However, heterogeneity in neuropathology is a well-known issue in the TBI population, such that group comparisons of patients against controls are confounded by within-group variability. Recently, novel single-subject profiling approaches have been developed to capture inter-patient heterogeneity. We present a personalized connectomics approach that examines structural brain alterations in five chronic patients with moderate to severe TBI who underwent anatomical and diffusion magnetic resonance imaging. We generated individualized profiles of lesion characteristics and network measures (including personalized graph metric GraphMe plots, and nodal and edge-based brain network alterations) and compared them against healthy reference cases (N = 12) to assess brain damage qualitatively and quantitatively at the individual level. Our findings revealed alterations of brain networks with high variability between patients. With validation and comparison to stratified, normative healthy control comparison cohorts, this approach could be used by clinicians to formulate a neuroscience-guided integrative rehabilitation program for TBI patients, and for designing personalized rehabilitation protocols based on their unique lesion load and connectome.
ortho2align: a sensitive approach for searching for orthologues of novel lncRNAs
Authors: Mylarshchikov Dmitry Evgenevich , Mironov Andrey Alexandrovich 
Published: September 2022

Abstract
Background
Many novel long noncoding RNAs have been discovered in recent years due to advances in high-throughput sequencing experiments. Finding orthologues of these novel lncRNAs might facilitate clarification of their functional role in living organisms. However, lncRNAs exhibit low sequence conservation, so specific methods for enhancing the signal-to-noise ratio were developed. Nevertheless, current methods such as transcriptomes comparison approaches or searches for conserved secondary structures are not applicable to novel, previously unannotated lncRNAs by design.

Results
We present ortho2align—a versatile sensitive synteny-based lncRNA orthologue search tool with statistical assessment of sequence conservation. This tool allows control of the specificity of the search process and optional annotation of found orthologues. ortho2align shows similar performance in terms of sensitivity and resource usage as the state-of-the-art method for aligning orthologous lncRNAs but also enables scientists to predict unannotated orthologous sequences for lncRNAs in question. Using ortho2align, we predicted orthologues of three distinct classes of novel human lncRNAs in six Vertebrata species to estimate their degree of conservation.

Conclusions
Being designed for the discovery of unannotated orthologues of novel lncRNAs in distant species, ortho2align is a versatile tool applicable to any genomic regions, especially weakly conserved ones. A small amount of input files makes ortho2align easy to use in orthology studies as a single tool or in bundle with other steps that researchers will consider sensible. ortho2align is available as an Anaconda package with its source code hosted at https://github.com/dmitrymyl/ortho2align.
Joint models for dynamic prediction in localised prostate cancer: a literature review
Authors: Parr Harry , Hall Emma , Porta Nuria 
Published: September 2022

Abstract
Background
Prostate cancer is a very prevalent disease in men. Patients are monitored regularly during and after treatment with repeated assessment of prostate-specific antigen (PSA) levels. Prognosis of localised prostate cancer is generally good after treatment, and the risk of having a recurrence is usually estimated based on factors measured at diagnosis. Incorporating PSA measurements over time in a dynamic prediction joint model enables updates of patients’ risk as new information becomes available. We review joint model strategies that have been applied to model time-dependent PSA trajectories to predict time-to-event outcomes in localised prostate cancer.

Methods
We identify articles that developed joint models for prediction of localised prostate cancer recurrence over the last two decades. We report, compare, and summarise the methodological approaches and applications that use joint modelling accounting for two processes: the longitudinal model (PSA), and the time-to-event process (clinical failure). The methods explored differ in how they specify the association between these two processes.

Results
Twelve relevant articles were identified. A range of methodological frameworks were found, and we describe in detail shared-parameter joint models (9 of 12, 75%) and joint latent class models (3 of 12, 25%). Within each framework, these articles presented model development, estimation of dynamic predictions and model validations.

Conclusions
Each framework has its unique principles with corresponding advantages and differing interpretations. Regardless of the framework used, dynamic prediction models enable real-time prediction of individual patient prognosis. They utilise all available longitudinal information, in addition to baseline prognostic risk factors, and are superior to traditional baseline-only prediction models.
Orbital apex syndrome secondary to apical periodontitis of a tooth: a case report
Authors: Xiang Wei , Wei Hongchun , Xu Luyao , Liang Zhigang 
Published: September 2022

Abstract
Background
Orbital apex syndrome (OAS) is a rare disease with a noticeable mortality rate. Although its etiology has been repeatedly assessed, few reports have concentrated on odontogenic infection. We presented a rare case of OAS secondary to apical periodontitis.

Case presentation
A 61-year-old male was admitted to our hospital for a 3-day history of left orbital and head pain, along with diplopia for 1-day. He also had toothache symptoms before his admission. Due to the atypical early symptoms of orbital apex and cranial nerve injury, no timely and effective diagnosis and treatment were initially provided. However, as the disease progressed and complications occurred, we timely adjusted the diagnosis and successfully controlled the infection. During the one-year follow-up, no recurrence of inflammation was observed; nevertheless, the ptosis and ophthalmoplegia persisted.

Conclusions
OAS is a rare, while severe complication of odontogenic infection. This case had various symptoms and nerve injury in the orbital apical area. When disease is atypical in its early stages, treatment is easily overlooked. Early detection and suspicion of orbital apex-related complications should be heightened.
The presence and co-incidence of geriatric syndromes in older patients with mild-moderate Lewy body dementia
Authors: Gan Jinghuan , Chen Zhichao , Liu Shuai , Shi Zhihong , Liu Yiming , Wang Xiao-Dan , Liu Chunyan , Ji Yong 
Published: September 2022

Abstract
Introduction
Geriatric symptoms are common in dementia cases, while few studies have focused on these symptoms in Lewy body dementia (LBD). The purpose of this study is to investigate the distributions of Apolipoprotein E (APOE) ε4 and geriatric symptoms, and explore their associaitons in Dementia with Lewy bodies (DLB) and Parkinson’s disease dementia (PDD).

Methods
A retrospective study with 185 mild-moderate probable DLB (n = 93) and PDD (n = 92) patients was assigned. Demographic and clinical characteristics, neuropsychological assessments, and APOE genotypes were recorded. Description, correlation and logistic regression models were used to analyze the presence of geriatric symptom complaints and their associations with APOE ε4.

Results
DLB patients displayed more frequency of fluctuating cognition, visual hallucination, rapid eye movement sleep behavior disorder, delusion, depression, anxiety, apathy, and loss of appetite, whereas the PDD cases had constipation, fear of falling, and insomnia more frequently. The APOE ε4 allele was more common in DLB than PDD (29.9% vs. 7.0%, p < 0.001), and the patients with DLB + APOE ε4 (+) were presented more delusions (p = 0.005) and apathy (p = 0.007) than patients with PDD + APOE ε4 (+). We also found that the APOE ε4 allele was significantly associated with hyperhidrosis (OR = 3.472, 95%CI: 1.082–11.144, p = 0.036) and depression (OR = 3.002, 95%CI: 1.079–8.353, p = 0.035) in DLB patients, while there were no significant associations between APOE ε4 allele and the age at visit, the age at onset, scores of MDS-UPDRS III, H&Y stage, ADL, MMSE, MOCA and NPI, as well as the presences of fluctuating cognition, VH, parkinsonism and RBD in both groups.

Conclusion
The presence and co-incidence of geriatric symptoms are common in patients with mild-moderate LBD. The presence of APOE ε4 allele is associated with hyperhidrosis and depression, but not global cognition, activitives of daily life, motor function and other neuropsychitric symptoms in DLB. These findings improve the awareness of geriatric symptoms, and contribute to the healthcare management of mild-moderate DLB and PDD.
Prevalence and associated risk factors for anxiety and depression in infertile couples of ART treatment: a cross-sectional study
Authors: Zhang Li , Shao Hongfang , Huo Mian , Chen Jie , Tao Minfang , Liu Zhangshun 
Published: September 2022

AbstractBackgroundInfertility now is a public health concern and is associated with increased psychological distress.MethodsWe enrolled 1247 infertile couples and assessed their anxiety and depression status before and during assisted reproductive technology (ART) treatment using the Self-Rating Anxiety Scale (SAS) and Self-Rating Depression Scale (SDS). The Chi-square or fisher’s exact test was used to analyze the prevalence of anxiety and depression in infertile couples. Multivariate logistical regression was performed to analyze the risk factors for anxiety and depression.ResultsThe prevalence of anxiety was 13.5% and 8.7% (p < 0.05), and that of depression was 9.4% and 7.9% (p = 0.2) in female and male partners, respectively. Female SAS and SDS scores were positively associated with male SAS and SDS scores, respectively (r = 0.52 andr = 0.50, respectively, bothp < 0.0001), and were positively associated with their own SDS and SAS scores, respectively (r = 0.63 andr = 0.62, respectively, bothp < 0.0001). Their own depression or partners’ anxiety was associated with the anxiety, and their own anxiety or partners’ depression was associated with the depression in infertile couples. No children, unemployment, and low education level were also associated with female anxiety. SAS and SDS scores were significantly decreased during ART treatment.ConclusionsFemales were more vulnerable to having anxiety than males in infertile couples. Anxiety and depression in infertile couples could interact, therefore, anxiety and depression would be simultaneously counseled, and their partners also should be given supportive psychotherapy.Trial registrationIt was an observational study and had no health care interventions on participants. So it was not registrated.
Medium-term oncological outcomes of totally laparoscopic colectomy with intracorporeal anastomosis for right-sided and left-sided colon cancer: propensity score matching analysis
Authors: Hamamoto Hiroki , Suzuki Yusuke , Takano Yoshiaki , Kuramoto Toru , Ishii Masatsugu , Osumi Wataru , Masubuchi Shinsuke , Tanaka Keitaro , Uchiyama Kazuhisa 
Published: September 2022

Abstract
Background
This retrospective study aimed to compare long-term oncological outcomes between laparoscopic-assisted colectomy (LAC) with extracorporeal anastomosis (EA) and totally laparoscopic colectomy (TLC) with intracorporeal anastomosis (IA) for colon cancers, including right- and left-sided colon cancers.

Methods
Patients with stage I–III colon cancers who underwent elective laparoscopic colectomy between January 2013 and December 2017 were analyzed retrospectively. Patients converted from laparoscopic to open surgery and R1/R2 resection were excluded. Propensity score matching (PSM) analysis (1:1) was performed to overcome patient selection bias.

Results
A total of 388 patients were reviewed. After PSM, 83 patients in the EA group and 83 patients in the IA group were compared. Median follow-up was 56.5 months in the EA group and 55.5 months in the IA group. Estimated 3-year overall survival (OS) did not differ significantly between the EA group (86.6%; 95% confidence interval (CI), 77.4–92.4%) and IA group (84.8%; 95%CI, 75.0–91.1%; P = 0.68). Estimated 3-year disease-free survival (DFS) likewise did not differ significantly between the EA group (76.4%; 95%CI, 65.9–84.4%) and IA group (81.0%; 95%CI, 70.1–88.2%; P = 0.12).

Conclusion
TLC with IA was comparable to LAC with EA in terms of 3-year OS and DFS. TLC with IA thus appears to offer an oncologically feasible procedure.
Anti-Indigenous bias of medical school applicants: a cross-sectional study
Authors: Roach Pamela , Hernandez Santanna , Carbert Amanda , Jalil Rabiya , Panaccione Remo , Ruzycki Shannon M. 
Published: September 2022

Abstract
Background
Structural and interpersonal anti-Indigenous racism is prevalent in Canadian healthcare. The Truth and Reconciliation Commission calls on medical schools to address anti-Indigenous bias in students. We measured the prevalence of interpersonal anti-Indigenous bias among medical school applicants to understand how the medical school selection process selects for or against students with high levels of bias.

Methods
All applicants to a single university in the 2020–2021 admissions cycle were invited to participate. Explicit anti-Indigenous bias was measured using two sliding scale thermometers. The first asked how participants felt about Indigenous people (from 0, indicating ‘cold/unfavourable’ to 100, indicating ‘warm/favourable’) and the second asked whether participants preferred white (scored 100) or Indigenous people (scored 0). Participants then completed an implicit association test examining preferences for European or Indigenous faces (negative time latencies suggest preference for European faces). Explicit and implicit anti-Indigenous biases were compared by applicant demographics (including gender and racial identity), application status (offered an interview, offered admission, accepted a position), and compared to undergraduate medical and mathematics students.

Results
There were 595 applicant respondents (32.4% response rate, 64.2% cisgender women, 55.3% white). Applicants felt warmly toward Indigenous people (median 96 (IQR 80–100)), had no explicit preference for white or Indigenous people (median 50 (IQR 37–55), and had mild implicit preference for European faces (− 0.22 ms (IQR -0.54, 0.08 ms)). There were demographic differences associated with measures of explicit and implicit bias. Applicants who were offered admission had warmer feelings toward Indigenous people and greater preference for Indigenous people compared to those were not successful.

Conclusions
Medical school applicants did not have strong interpersonal explicit and implicit anti-Indigenous biases. Outlier participants with strong biases were not offered interviews or admission to medical school.
Impact of the use of illicit and licit substances and anxiety disorders on the academic performance of medical students: a pilot study
Authors: Ferreira Pedro Marques , Alves Rauni Jandé Roama , Zantut-Wittmann Denise Engelbrecht 
Published: September 2022

Abstract
Background
Medical students have a considerable prevalence of anxiety and substance use disorders. Our aim was to assess the presence of anxiety disorders and the use of alcohol and licit and illicit substances, and their influence on the academic performance of medical students.

Methods
This is a cross-sectional, non-experimental pilot study, with quantitative analyses, in which 67 medical students at the Federal University of Rondonópolis, Mato Grosso, Brazil (UFR), were evaluated through the application of non-invasive anxiety assessment instruments, screening for involvement with tobacco, alcohol and other substances, related to school performance coefficient, between June 2019 and March 2020.

Results
Worse academic performance was associated with frequent use of tobacco and its derivatives (p = 0.0022), marijuana (p = 0.0020), hypnotics and sedatives (p = 0.0138). Also, the performance was negatively correlated with the use of tobacco (p = 0.0004), alcoholic beverages (p = 0.0261), cannabis (p = 0.0075), sedatives (p = 0.0116) and trait anxiety (p = 0.0036). Greater trait anxiety intensity was associated with previous use of tobacco (p = 0.0276), marijuana (p = 0.0466), amphetamines/ecstasy (p = 0.0151), and hypnotics/sedatives (p = 0.0103). State anxiety was positively correlated with heavy alcohol use (p = 0.0434). Higher state anxiety intensity was related to needing intervention due to the use of amphetamines/ecstasy (p = 0.00379). Students from the intermediate classes of the course (3rd and 4th years) had a higher frequency and intensity of use of tobacco and its derivatives (p = 0.0133), amphetamines or ecstasy (p = 0.0006), and inhalants (p = 0.0256).

Conclusions
Worse academic performance in medical students was correlated with licit and illicit substances use and anxiety disorders. Mid-course students had a higher frequency and intensity of substance use.
Three novel leaderless bacteriocins have antimicrobial activity against gram-positive bacteria to serve as promising food biopreservative
Authors: Zhang Xiaofeng , Xin Nie , Zhu Zhaolu , Li Xudong , Dai Dadong , Pan Chunmei , Peng Donghai , Sun Ming 
Published: September 2022

Abstract
Background
Due to the detrimental effects of chemical preservatives, there has been an increasing demand for safer, healthier and natural bio-preservatives. Bacteriocins have attracted increasing interest because of their potential as natural bio-preservatives.

Results
We screened a large number of Bacillus thuringiensis strains and isolated one strain (B. thuringiensis P86) with antimicrobial activity against several foodborne pathogens. Three novel leaderless bacteriocins, including thucin A1, thucin A2 and thucin A3, were purified and identified from the culture supernatant of B. thuringiensis P86, whose molecular masses were 5552.02, 5578.07 and 5609.06 Da, respectively. Thucin A1 was then selected as a representative to be tested, and it exhibited potent inhibitory activity against all tested gram-positive bacteria. More importantly, thucin A1 showed stronger antimicrobial activity than nisin A against two important foodborne pathogens Bacillus cereus and Listeria monocytogenes. In addition, thucin A1 exhibited strong acid–base adaptability (pH 2–11), high endurance to heat, good stability to trypsin and pepsin, no hemolysis activity and cytotoxicity, and could effectively inhibit or eliminate Bacillus cereus and Listeria monocytogenes in skim milk.

Conclusions
Our findings indicate that these novel leaderless bacteriocins are potentially promising food biopreservatives.
Micropeptide MIAC inhibits the tumor progression by interacting with AQP2 and inhibiting EREG/EGFR signaling in renal cell carcinoma
Authors: Li Mengwei , Liu Guangxiang , Jin Xinrong , Guo Hongqian , Setrerrahmane Sarra , Xu Xindi , Li Tiantian , Lin Yunfei , Xu Hanmei 
Published: September 2022

Abstract
Background
Although, micropeptides encoded by non-coding RNA have been shown to have an important role in a variety of tumors processes, there have been no reports on micropeptide in renal cell carcinoma (RCC). Based on the micropeptide MIAC (micropeptide inhibiting actin cytoskeleton) discovered and named in the previous work, this study screened its tumor spectrum, and explored its mechanism of action and potential diagnosis and treatment value in the occurrence and development of renal carcinoma.

Methods
The clinical significance of MIAC in RCC was explored by bioinformatics analysis through high-throughput RNA-seq data from 530 patients with kidney renal clear cell carcinoma (KIRC) in the TCGA database, and the detection of clinical samples of 70 cases of kidney cancer. In vitro and in vivo experiments to determine the role of MIAC in renal carcinoma cell growth and metastasis; High-throughput transcriptomics, western blotting, immunoprecipitation, molecular docking, affinity experiments, and Streptavidin pulldown experiments identify MIAC direct binding protein and key regulatory pathways.

Results
The analysis of 600 renal carcinoma samples from different sources revealed that the expression level of MIAC is significantly decreased, and corelated with the prognosis and clinical stage of tumors in patients with renal carcinoma. Overexpression of MIAC in renal carcinoma cells can significantly inhibit the proliferation and migration ability, promote apoptosis of renal carcinoma cells, and affect the distribution of cells at various stages. After knocking down MIAC, the trend is reversed. In vivo experiments have found that MIAC overexpression inhibit the growth and metastasis of RCC, while the synthetized MIAC peptides can significantly inhibit the occurrence and development of RCC in vitro and in vivo. Further mechanistic studies have demonstrated that MIAC directly bind to AQP2 protein, inhibit EREG/EGFR expression and activate downstream pathways PI3K/AKT and MAPK to achieve anti-tumor effects.

Conclusions
This study revealed for the first time the tumor suppressor potential of the lncRNA-encoded micropeptide MIAC in RCC, which inhibits the activation of the EREG/EGFR signaling pathway by direct binding to AQP2 protein, thereby inhibiting renal carcinoma progression and metastasis. This result emphasizes that the micropeptide MIAC can provide a new strategy for the diagnosis and treatment of RCC.
Mucopolysaccharidoses and the blood–brain barrier
Authors: Sahin Onur , Thompson Hannah P. , Goodman Grant W. , Li Jun , Urayama Akihiko 
Published: September 2022

AbstractMucopolysaccharidoses comprise a set of genetic diseases marked by an enzymatic dysfunction in the degradation of glycosaminoglycans in lysosomes. There are eight clinically distinct types of mucopolysaccharidosis, some with various subtypes, based on which lysosomal enzyme is deficient and symptom severity. Patients with mucopolysaccharidosis can present with a variety of symptoms, including cognitive dysfunction, hepatosplenomegaly, skeletal abnormalities, and cardiopulmonary issues. Additionally, the onset and severity of symptoms can vary depending on the specific disorder, with symptoms typically arising during early childhood. While there is currently no cure for mucopolysaccharidosis, there are clinically approved therapies for the management of clinical symptoms, such as enzyme replacement therapy. Enzyme replacement therapy is typically administered intravenously, which allows for the systemic delivery of the deficient enzymes to peripheral organ sites. However, crossing the blood–brain barrier (BBB) to ameliorate the neurological symptoms of mucopolysaccharidosis continues to remain a challenge for these large macromolecules. In this review, we discuss the transport mechanisms for the delivery of lysosomal enzymes across the BBB. Additionally, we discuss the several therapeutic approaches, both preclinical and clinical, for the treatment of mucopolysaccharidoses.