bluuebunny/crossref_metadata_2025_split huggingface dataset:
TULIP: An RNA-seq-based Primary Tumor Type Prediction Tool Using Convolutional Neural Networks
Authors: Jones Sara , Beyers Matthew , Shukla Maulik , Xia Fangfang , Brettin Thomas , Stevens Rick , Weil M Ryan , Ranganathan Ganakammal Satishkumar 
Published: December 2022

Background: With cancer as one of the leading causes of death worldwide, accurate primary tumor type prediction is critical in identifying genetic factors that can inhibit or slow tumor progression. There have been efforts to categorize primary tumor types with gene expression data using machine learning, and more recently with deep learning, in the last several years. Methods In this paper, we developed four 1-dimensional (1D) Convolutional Neural Network (CNN) models to classify RNA-seq count data as one of 17 highly represented primary tumor types or 32 primary tumor types regardless of imbalanced representation. Additionally, we adapted the models to take as input either all Ensembl genes (60,483) or protein coding genes only (19,758). Unlike previous work, we avoided selection bias by not filtering genes based on expression values. RNA-seq count data expressed as FPKM-UQ of 9,025 and 10,940 samples from The Cancer Genome Atlas (TCGA) were downloaded from the Genomic Data Commons (GDC) corresponding to 17 and 32 primary tumor types respectively for training and validating the models. Results: All 4 1D-CNN models had an overall accuracy of 94.7% to 97.6% on the test dataset. Further evaluation indicates that the models with protein coding genes only as features performed with better accuracy compared to the models with all Ensembl genes for both 17 and 32 primary tumor types. For all models, the accuracy by primary tumor type was above 80% for most primary tumor types. Conclusions: We packaged all 4 models as a Python-based deep learning classification tool called TULIP (TUmor CLassIfication Predictor) for performing quality control on primary tumor samples and characterizing cancer samples of unknown tumor type. Further optimization of the models is needed to improve the accuracy of certain primary tumor types.
Ten-year incidence of post-transplant Diabetes Mellitus in renal transplant patients
Authors: Habibnia Fatemeh , Oliaei Farshid , Shirafkan Hoda , Abbasi Firoozjah Mobarakeh , Rezaei Roshan Mobina , Akbari Roghayeh 
Published: December 2022

Background Kidney transplantation is the treatment of choice for renal failure. Development of New-Onset Diabetes After Transplantation (NODAT) significantly increases kidney graft loss and mortality. This study aimed to evaluate the 10-years prevalence of NODAT in renal transplant patients. Methods In this cross-sectional study, medical records of non-diabetic patients undergoing kidney transplant in Shahid-Beheshti Hospital of Babol, between March 2009–2019 were retrospectively reviewed. Results Totally 284 patients with the mean age of 40.83 ± 12.94 years were included. New-Onset Diabetes After Transplantation was identified in 57 (20.1%) patients and 92.98% developed NODAT during the first month after transplantation. New-Onset Diabetes After Transplantation and non-NODAT patients were 43.8% and 34.38% female. Graft rejection occurred in 18 (31%) of NODAT and 78 (34%) of non-NODAT patients ( p = .69). Patients with NODAT were about 10 years older (47.88 ± 11.06 vs 38.96 ± 13.12 years; p = .002). The pre-transplant Fasting Blood Sugar (FBS) was higher in the NODAT group (93.78 ± 13.78 vs 87.07 ± 11.56, p = .001) and post-transplantation cytomegalovirus (CMV) infection was higher in NODAT group (56% vs 40%, p = .021). New-Onset Diabetes After Transplantation patients had significantly higher BMI (27.16 ± 5.39 vs 23.94 ± 4.71, p < .001). Conclusion New-Onset Diabetes After Transplantation is more prevalent in subjects with older age, higher BMI, post-transplant CMV infection, and higher pre-transplant FBS but gender, pre-transplant CMV infection, type of dialysis and smoking were not associated with it. So, these patients should be followed-up more diligently.
Alternariol alleviates breast carcinoma by inhibiting cellular proliferation correlated with increased apoptotic events in rats
Authors: Xin Jian , Shang Yitai 
Published: December 2022

The breast cancer is most frequently diagnosed cancer in the women worldwide. Our study investigated the anticancer effect of alternariol, a secondary metabolite originated from endophytic fungi, against DMBA induced breast carcinoma on Wistar rats. The toxicity study investigated the LD50 and the subsequent doses of alternariol for the carcinogenic study. The breast cancer was developed in rats via induction of DMBA (5 mg/kg, i.v.) and the carcinogenic study was continued for 24 weeks. The induction of breast cancer and the chemotherapeutic effect of alternariol were assessed through histopathological analysis of rat mammary tissue, followed by immunohistochemical analysis, cell proliferation assay and apoptosis assay by TUNEL method. The result showed that alternariol therapy decreased the hyperplastic lesions of mammary tissue and restored the normal histopathological characteristics of breast tissue. Furthermore, alternariol treatment downregulated the expression of carcinogenic markers such as PI3K and Akt increased the expression of apoptotic markers including p53, caspase-3 and Bax. Alternariol therapy also decreased the cellular proliferation and enhanced the apoptotic events. In conclusion, the breast cancer progression was significantly reduced via induction of apoptotic events and inhibition of cell propagation which allowed constructing of suitable mechanism for alternariol mediated chemotherapeutic approach.
Mental health and neurodevelopment in children and adolescents with Turner syndrome
Authors: Wolstencroft Jeanne , Mandy William , Skuse David 
Published: December 2022

Objectives: Turner syndrome (TS) is a rare sex chromosome aneuploidy, with an incidence of four in 10,000 new-born girls. TS is often associated with impaired social communication skills, but the extent to which these are attributable to Autism Spectrum Disorders (ASD) is uncertain. We made standardized assessments of the mental health and associated neurodevelopmental disorders in children and adolescents with TS and report on the prevalence of concurrent conditions. Methods: Our sample comprised 127 girls with TS, 5–19 years of age. We obtained reports of their mental health from a combination of diagnostic interview (the Development and Wellbeing Assessment (DAWBA)), from the Strengths and Difficulties Questionnaire (SDQ) and from the Social Responsiveness Scale (SRS-2). Sources of information included parents, teachers and self-reports. The prevalence of mental health disorders in this sample was compared with age/sex matched national English data from typical controls. Results: Most individuals with TS (83%) had experienced significant social communication difficulties and nearly one in four (23%) met diagnostic criteria for ASD on the DAWBA. One-third (34%) had at least one mental health or neurodevelopmental condition, and those girls with an ASD were at a greater risk of a co-occurring emotional disorder and/or attention deficit hyperactivity disorder (ADHD). Conclusion: Children and adolescents with TS are substantially more likely to meet criteria for ASD than their typically developing peers. Our finding has clinical implications for appropriate behavioural management from preschool through to adolescence.
Prediction of gait independence using the Trunk Impairment Scale in patients with acute stroke
Authors: Ishiwatari Masahiro , Tani Mami , Isayama Reina , Honaga Kaoru , Hayakawa Masato , Takakura Tomokazu , Tanuma Akira , Kurosu Akihiro , Hatori Kozo , Wada Futoshi , Fujiwara Toshiyuki 
Published: December 2022

Background: Gait recovery is one of the primary goals of stroke rehabilitation. Gait independence is a key functional component of independent activities in daily living and social participation. Therefore, early prediction of gait independence is essential for stroke rehabilitation. Trunk function is important for recovery of gait, balance, and lower extremity function. The Trunk Impairment Scale (TIS) was developed to assess trunk impairment in patients with stroke. Objective: To evaluate the predictive validity of the TIS for gait independence in patients with acute stroke. Methods: A total of 102 patients with acute stroke participated in this study. Every participant was assessed using the TIS, Stroke Impairment Assessment Set (SIAS), and Functional Independence Measure (FIM) within 48 h of stroke onset and at discharge. Gait independence was defined as FIM gait scores of 6 and 7. Multiple regression analysis was used to predict the FIM gait score, and multiple logistic regression analysis was used to predict gait independence. Cut-off values were determined using receiver operating characteristic (ROC) curves for variables considered significant in the multiple logistic regression analysis. In addition, the area under the curve (AUC), sensitivity, and specificity were calculated. Results: For the prediction of the FIM gait score at discharge, the TIS at admission showed a good-fitting adjusted coefficient of determination ( R2 = 0.672, p < 0.001). The TIS and age were selected as predictors of gait independence. The ROC curve had a TIS cut-off value of 12 points (sensitivity: 81.4%, specificity: 79.7%) and an AUC of 0.911. The cut-off value for age was 75 years (sensitivity: 74.6%, specificity: 65.1%), and the AUC was 0.709. Conclusion: The TIS is a useful early predictor of gait ability in patients with acute stroke.
Determinants of neonatal hypoglycemia among neonates admitted at Hiwot Fana Comprehensive Specialized University Hospital, Eastern Ethiopia: A retrospective cross-sectional study
Authors: Sertsu Addisu , Nigussie Kabtamu , Eyeberu Addis , Tibebu Abel , Negash Abraham , Getachew Tamirat , Debella Adera , Dheresa Merga 
Published: December 2022

Objective: The study aimed to assess the magnitude and determinants of neonatal hypoglycemia among neonates admitted to the Neonatal Intensive Care Unit at Hiwot Fana Specialized University Hospital, Eastern Ethiopia. Methods: An institutional-based cross-sectional study was conducted among 698 randomly selected neonates at Hiwot Fana Comprehensive Specialized Hospital from 1 January 2018 to 31 December 2020. By looking at the charts, data were gleaned from the medical records. Data were entered into Epi-Data version 3.1 and analysis was performed using SPSS version 22. Bivariable and multivariable logistic regression analyses were conducted to identify determinant factors of neonatal hypoglycemia. Association was described using an adjusted odds ratio along with a 95% CI. Finally, a p-value <0.05 in the adjusted analysis was considered to declare a statistically significant association. Results: Out of 698 neonates, 148 (21.2%; 95% CI: 18.3, 24.5) neonates had hypoglycemia. Preterm birth (AOR = 3.06; 95% CI: 1.02, 9.17), hypothermia (AOR = 2.65; 95% CI: 1.22, 5.75), neonatal sepsis (AOR = 2.61; 95% CI: 1.03, 6.59), diabetic mother (AOR = 2.34; 95% CI: 1.03, 5.33), and delay in initiation of breastfeeding for more than 1 h (AOR = 3.89; 95% CI: 1.17, 12.89) were identified as determinant factors of neonatal hypoglycemia. Conclusion: The magnitude of neonatal hypoglycemia was quite common among neonates. Neonatal hypoglycemia was found to be predicted by preterm birth, hypothermia, neonatal sepsis, maternal diabetes mellitus, and delay in starting nursing. We therefore strongly suggest health-care workers work in the postnatal unit to manage and control these and other determinant factors of hypoglycemia to prevent the occurrence of neonatal hypoglycemia.
Associations between smartphone keystroke dynamics and cognition in MS
Authors: Chen Michelle H , Leow Alex , Ross Mindy K , DeLuca John , Chiaravalloti Nancy , Costa Silvana L , Genova Helen M , Weber Erica , Hussain Faraz , Demos Alexander P 
Published: December 2022

Objective Examine the associations between smartphone keystroke dynamics and cognitive functioning among persons with multiple sclerosis (MS). Methods Sixteen persons with MS with no self-reported upper extremity or typing difficulties and 10 healthy controls (HCs) completed six weeks of remote monitoring of their keystroke dynamics (i.e., how they typed on their smartphone keyboards). They also completed a comprehensive neuropsychological assessment and symptom ratings about fatigue, depression, and anxiety at baseline. Results A total of 1,335,787 keystrokes were collected, which were part of 30,968 typing sessions. The MS group typed slower ( P < .001) and more variably ( P = .032) than the HC group. Faster typing speed was associated with better performance on measures of processing speed ( P = .016), attention ( P = .022), and executive functioning (cognitive flexibility: P = .029; behavioral inhibition: P = .002; verbal fluency: P = .039), as well as less severe impact from fatigue ( P < .001) and less severe anxiety symptoms ( P = .007). Those with better cognitive functioning and less severe symptoms showed a stronger correlation between the use of backspace and autocorrection events ( P < .001). Conclusion Typing speed may be sensitive to cognitive functions subserved by the frontal–subcortical brain circuits. Individuals with better cognitive functioning and less severe symptoms may be better at monitoring their typing errors. Keystroke dynamics have the potential to be used as an unobtrusive remote monitoring method for real-life cognitive functioning among persons with MS, which may improve the detection of relapses, evaluate treatment efficacy, and track disability progression.
Molecular biomarkers predicting newly detected atrial fibrillation after ischaemic stroke or TIA: A systematic review
Authors: Ward Kirsty , Vail Andy , Cameron Alan , Katan Mira , Lip Gregory YH , Dawson Jesse , Smith Craig J , Kishore Amit K 
Published: December 2022

Background: Several molecular biomarkers are available that predict newly detected atrial fibrillation (NDAF). We aimed to identify such biomarkers that predict NDAF after an Ischaemic stroke (IS)/Transient Ischaemic Attack (TIA) and evaluate their performance. Methods: A systematic review was undertaken in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. Studies of patients with IS, TIA, or both, who underwent ECG monitoring for ⩾24 h, which reported molecular biomarkers and frequency of NDAF after electronic searches of multiple databases were included. Results: Twenty-one studies (76% IS, 24% IS and TIA) involving 4640 patients were included. Twelve biomarkers were identified, with cardiac biomarkers evaluated in the majority (75%) of patients. Performance measures were inconsistently reported. Among cohorts selecting high-risk individuals (12 studies), the most studied biomarkers were N-Terminal-Pro Brain Natriuretic Peptide (NT-ProBNP, five studies; C-statistics reported by three studies, 0.69–0.88) and Brain Natriuretic Peptide (BNP, two studies; C-statistics reported in two studies, 0.68–0.77). Among unselected cohorts (nine studies), the most studied biomarker was BNP (six studies; C-statistics reported in five studies, 0.75–0.88). Only BNP was externally validated (two studies) but using different thresholds to categorise risk of NDAF. Conclusion: Cardiac biomarkers appear to have modest to good discrimination for predicting NDAF, although most analyses were limited by small, heterogeneous study populations. Their clinical utility should be explored further, and this review supports the need to assess the role of molecular biomarkers in large prospective studies with standardised selection criteria, definition of clinically significant NDAF and laboratory assays.
Knee Multiligament Reconstruction: ACL / PCL / MCL
Authors: Quinn Courtney , Ignozzi Anthony J. , Taleghani Eric , Miller Mark 
Published: December 2022

Background: Multiligament knee injury (MLKI) is a rare, complex injury that requires surgical intervention. However, there is a lack of consensus regarding optimal timing, staging, and graft choice for ligament reconstruction. Indications: Delayed, single-stage reconstruction offers the advantage of attaining improved preoperative range of motion and potential healing of extra-articular ligaments and may be necessary in the setting of multitrauma. Technique Description: A hamstring graft was harvested and diagnostic arthroscopy performed. Three posterior portals were made for posterior cruciate ligament (PCL) reconstruction. Femoral and tibial pins were placed for both PCL and anterior cruciate ligament (ACL) tunnels, positions confirmed with fluoroscopy, and tunnels drilled over the pins. The Achilles allograft was shuttled through the femoral and tibial PCL tunnels in anterograde fashion and fixed with a metal interference screw on the femoral side. The hamstring autograft was passed through the ACL tunnels and suspended on the femoral side. Tibial fixation of both grafts was achieved with biocomposite interference. Medial collateral ligament reconstruction was performed through the medial incision from hamstring harvesting. The semitendinosis allograft was passed and fixed with screws and spiked washers. Fluoroscopy confirmed that screw trajectory did not interfere with the ACL or PCL tunnels. Results: Bagherifard et al reported a study of 41 consecutive patients with MLKI who underwent single-stage reconstruction with autograft and/or allograft. Mean postoperative Lysholm and International Knee Documentation Committee (IKDC) scores were 86.9 and 70, respectively, and only 7 patients experienced restricted range of motion. Billieres et al reported a study of 23 patients with MLKIs who underwent single-stage reconstruction with allograft only. Mean postoperative Lysholm and IKDC scores were 77.3 and 67.2, respectively, and 19 patients returned to sport. Goyal et al reported a study of 27 patients with MLKI who underwent single-stage reconstruction greater than 6 weeks after injury. At 2 years, there were significant improvements in Visual Analog Scale, IKDC, and Lysholm scores, and no patients had residual laxity of the knee joint. Discussion/Conclusion: Single-stage reconstruction of MLKIs is an effective intervention that has been supported in literature; however, further studies are necessary to determine optimal surgical timing and graft type. The author(s) attests that consent has been obtained from any patient(s) appearing in this publication. If the individual may be identifiable, the author(s) has included a statement of release or other written form of approval from the patient(s) with this submission for publication.
Influence of boundary conditions on acoustic emission propagation characteristics of Zelkova schneideriana
Authors: Zhao Yue , Li Ming , Fang Saiyin , Zhang Shaochun , Huang Changlin , Deng Tingting , Mao Feilong , Qin Gezhou , Zhu Daigen 
Published: December 2022

AbstractTo study the propagation characteristics of acoustic emission signals in Zelkova schneideriana under different boundary conditions, three types of boundary conditions were generated by applying aluminum plates and sound-absorbing cotton on the surface of Zelkova schneideriana specimens. Firstly, the sudden and continuous acoustic emission (AE) sources were simulated by PLB (pencil–lead break) tests and signal generator on the specimen surface, and the AE signals were collected by 5 sensors equally spaced on the surface of the specimen, and the sampling frequency was set to 500 kHz. Then, the detailed signals of different frequency bands were obtained by wavelet decomposition, and TDOA (the time difference of arrival) and correlation analysis method were used to calculate the time difference of longitudinal wave and surface transverse wave and the corresponding propagation velocity, respectively. Finally, the pulse trains with different energy levels generated by the signal generator were used as AE sources to study the attenuation law of AE signal energy with distance under different boundary conditions. The results show that the boundary changes can lead to a significant increase in the surface transverse wave velocity, and have no significant effect on the longitudinal wave velocity. At the same time, the energy attenuation of surface and longitudinal waves is faster after the aluminum plate and sound-absorbing cotton are affixed, and the distance of longitudinal waves attenuation to 90% is reduced from 186 to 139 mm, and the distance of surface transverse waves propagation is reduced from 312 to 226 mm.
MF-094 nanodelivery inhibits oral squamous cell carcinoma by targeting USP30
Authors: Zhang Xinyu , Han Yong , Liu Shuli , Guo Bing , Xu Shengming , He Yue , Liu Liu 
Published: December 2022

Abstract
Background
Oral squamous cell carcinoma (OSCC) is a common head and neck cancer, and the incidence of OSCC is increasing. As the mortality of OSCC keeps increasing, it is crucial to clarify its pathogenesis and develop new therapeutic strategies.

Methods
Confocal laser scanning microscopy was used to evaluate the uptake of nanoparticles (NPs). The potential functions of USP30 were evaluated by cell counting kit (CCK)-8, flow cytometry, biochemical assay, coimmunoprecipitation, qRT–PCR, and immunoblotting. The antitumor effect of NP-loaded USP30 inhibitor MF-094 was evaluated in vitro and in vivo.

Results
In this study, increased USP30 expression was found in OSCC specimens and cell lines through qRT–PCR and immunoblotting. CCK-8, flow cytometry, and biochemical assay revealed that the deubiquitylated catalytic activity of USP30 contributed to cell viability and glutamine consumption of OSCC. Subsequently, USP30 inhibitor MF-094 was loaded in ZIF-8-PDA and PEGTK to fabricate ZIF-8-PDA-PEGTK nanoparticles, which exhibited excellent inhibition of cell viability and glutamine consumption of OSCC, both in vitro and in vivo.

Conclusion
The results indicated the clinical significance of USP30 and showed that nanocomposites provide a targeted drug delivery system for treating OSCC.
Comprehensive analysis of pre-mRNA alternative splicing regulated by m6A methylation in pig oxidative and glycolytic skeletal muscles
Authors: Tan Baohua , Zeng Jiekang , Meng Fanming , Wang Shanshan , Xiao Liyao , Zhao Xinming , Hong Linjun , Zheng Enqin , Wu Zhenfang , Li Zicong , Gu Ting 
Published: December 2022

Abstract
Background
Different types of skeletal myofibers exhibit distinct physiological and metabolic properties that are associated with meat quality traits in livestock. Alternative splicing (AS) of pre-mRNA can generate multiple transcripts from an individual gene by differential selection of splice sites. N6-methyladenosine (m6A) is the most abundant modification in mRNAs, but its regulation for AS in different muscles remains unknown.

Results
We characterized AS events and m6A methylation pattern in pig oxidative and glycolytic muscles. A tota1 of 1294 differential AS events were identified, and differentially spliced genes were significantly enriched in processes related to different phenotypes between oxidative and glycolytic muscles. We constructed the regulatory network between splicing factors and corresponding differential AS events and identified NOVA1 and KHDRBS2 as key splicing factors. AS event was enriched in m6A-modified genes, and the methylation level was positively correlated with the number of AS events in genes. The dynamic change in m6A enrichment was associated with 115 differentially skipping exon (SE-DAS) events within 92 genes involving in various processes, including muscle contraction and myofibril assembly. We obtained 23.4% SE-DAS events (27/115) regulated by METTL3-meditaed m6A and experimentally validated the aberrant splicing of ZNF280D, PHE4DIP, and NEB. The inhibition of m6A methyltransferase METTL3 could induce the conversion of oxidative fiber to glycolytic fiber in PSCs.

Conclusion
Our study suggested that m6A modification could contribute to significant difference in phenotypes between oxidative and glycolytic muscles by mediating the regulation of AS. These findings would provide novel insights into mechanisms underlying muscle fiber conversion.