Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of spreader nodes in human-SARS-CoV protein-protein interaction network

The entire world is witnessing the coronavirus pandemic (COVID-19), caused by a novel coronavirus (n-CoV) generally distinguished as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). SARS-CoV-2 promotes fatal chronic respiratory disease followed by multiple organ failure, ultimately putting an end to human life. International Committee on Taxonomy of Viruses (ICTV) has reached a consensus that SARS-CoV-2 is highly genetically similar (up to 89%) to the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), which had an outbreak in 2003. With this hypothesis, current work focuses on identifying the spreader nodes in the SARS-CoV-human protein–protein interaction network (PPIN) to find possible lineage with the disease propagation pattern of the current pandemic. Various PPIN characteristics like edge ratio, neighborhood density, and node weight have been explored for defining a new feature spreadability index by which spreader proteins and protein–protein interaction (in the form of network edges) are identified. Top spreader nodes with a high spreadability index have been validated by Susceptible-Infected-Susceptible (SIS) disease model, first using a synthetic PPIN followed by a SARS-CoV-human PPIN. The ranked edges highlight the path of entire disease propagation from SARS-CoV to human PPIN (up to level-2 neighborhood). The developed network attribute, spreadability index, and the generated SIS model, compared with the other network centrality-based methodologies, perform better than the existing state-of-art.
Effects of One-Fifth, One-Third, and One-Half of the Bodyweight Lumbar Traction on the Straight Leg Raise Test and Pain in Prolapsed Intervertebral Disc Patients: A Randomized Controlled Trial

The prolapsed intervertebral disc (PIVD) at the lumbar spine is one of the most common causes of low back pain (LBP) affecting humans worldwide. Lumbar traction is widely used as a part of physiotherapeutic modalities for its treatment; however, reports on its effectiveness and dosage are conflicting. This study is aimed at comparing the acute effects of three traction forces on the straight leg raise (SLR) test and LBP intensity. A total of 45 (age 35.53 yrs., ±3.09) participants with 15 participants in each group were recruited for the study. Participants were divided into groups A, B, and C wherein traction forces equal to one-fifth, one-third, and one-half of their bodyweight were applied, respectively. SLR range of motion (ROM) and pain were examined before and immediately after the application of traction. Significant improvement was observed in SLR ROM in all three groups (p < 0.05). However, for pain, significant improvement (p < 0.05) was observed only in the group with one-half of bodyweight force. There was no significant difference (p > 0.05) between the three groups for both variables. All three forces were equally effective in immediately improving SLR ROM in patients suffering from lumbar PIVD; however, pain improvement was observed with one-half of bodyweight only.
Polysaccharides Extracted From Panax Ginseng C.A. Mey Enhance Complement Component 4 Biosynthesis in Human Hepatocytes

Panax ginseng C.A. Mey (ginseng) is a classic medicinal plant which is well known for enhancing immune capacity. Polysaccharides are one of the main active components of ginseng. We isolated water-soluble ginseng polysaccharides (WGP) and analyzed the physicochemical properties of WGP including molecular weight, monosaccharide composition, and structural characteristics. WGP had minimal effect on the growth of hepatocytes. Interestingly, WGP significantly increased the mRNA and protein levels of complement component 4 (C4), one of the core components of the complement system. Promoter reporter gene assays revealed that WGP significantly enhanced activity of the C4 gene promoter. Deletion analyses determined that the E-box1 and Sp1 regions play key roles in WGP-induced C4 transcription. Taken together, our results suggest that WGP promotes C4 biosynthesis through upregulation of transcription. These results provide new explanation for the intrinsic mechanism by which ginseng boosts human immune capacity.
Detection and classification of neurons and glial cells in the MADM mouse brain using RetinaNet

The ability to automatically detect and classify populations of cells in tissue sections is paramount in a wide variety of applications ranging from developmental biology to pathology. Although deep learning algorithms are widely applied to microscopy data, they typically focus on segmentation which requires extensive training and labor-intensive annotation. Here, we utilized object detection networks (neural networks) to detect and classify targets in complex microscopy images, while simplifying data annotation. To this end, we used a RetinaNet model to classify genetically labeled neurons and glia in the brains of Mosaic Analysis with Double Markers (MADM) mice. Our initial RetinaNet-based model achieved an average precision of 0.90 across six classes of cells differentiated by MADM reporter expression and their phenotype (neuron or glia). However, we found that a single RetinaNet model often failed when encountering dense and saturated glial clusters, which show high variability in their shape and fluorophore densities compared to neurons. To overcome this, we introduced a second RetinaNet model dedicated to the detection of glia clusters. Merging the predictions of the two computational models significantly improved the automated cell counting of glial clusters. The proposed cell detection workflow will be instrumental in quantitative analysis of the spatial organization of cellular populations, which is applicable not only to preparations in neuroscience studies, but also to any tissue preparation containing labeled populations of cells.
Is Early Controlled Motion and Weightbearing Recommended for Nonoperatively Treated Acute Achilles Tendon Rupture? A Systematic Review and Meta-analysis

Background: There is disagreement as to whether early controlled motion and weightbearing confer a beneficial effect for nonoperatively treated acute Achilles tendon rupture (ATR) compared with immobilization and late weightbearing. Purpose: To conduct a meta-analysis of randomized controlled trials (RCTs) to determine whether early controlled motion and weightbearing results in different outcomes compared with immobilization and late weightbearing for nonoperatively treated patients with acute ATR. Study Design: Systematic review; Level of evidence, 1. Methods: We conducted a search in the PubMed, Web of Science, and EMBASE databases for relevant RCTs in humans from January 1981 to August 2020. The primary outcome was the Achilles Tendon Total Rupture Score (ATRS) at 1-year follow-up. The secondary outcomes were the rerupture rate, return to sports activity and work, and the heel-rise work (limb symmetry index [LSI]). Study quality was assessed using the Cochrane Collaboration risk of bias tool. Results: Included were 7 RCTs involving 424 participants (n = 215 treated with early controlled motion and weightbearing [early group], n = 209 treated with immobilization and late weightbearing [late group]). The quality assessment indicated a low risk of bias in all included RCTs. There was no difference between the early and late groups regarding the ATRS (mean difference [MD], -0.220; 95% CI, -4.489 to 4.049; P = .920). Likewise, we found no difference between the 2 groups in terms of the rerupture rate (odds ratio [OR], 1.107; 95% CI, 0.552 to 2.219; P = .775), the number of patients who returned to sports (OR, 0.766; 95% CI, 0.438 to 1.341; P = .351) and returned to work (OR, 0.706; 95% CI, 0.397 to 1.253; P = .234), the time to return to work (MD, -2.802 days; 95% CI, -6.525 to 0.921 days; P = .140), or the heel-rise work LSI (MD, -0.135; 95% CI, -6.243 to 5.973; P = .965). Conclusion: No significant differences were found between early controlled motion and weightbearing compared with immobilization and late weightbearing regarding the ATRS, the rerupture rate, return to sports activity and work, and the heel-rise work in nonoperatively treated patients with acute ATR.
Mitogenomic characterization and phylogeny of Scelimena melli Günther (Orthoptera: Tetrigoidea: Scelimeninae)

Abstract The mitochondrial genome (mitogenome) of Scelimena melli, which belongs to Orthoptera, Tetrigoidea, Tetrigidae, Scelimeninae was determined. The mitogenome has a length of 14,598 bp and consists of 37 genes including 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes. Phylogenetic analysis using 37 mitochondrial genes with other 22 Tetrigoidea species revealed that S. melli had a closer relationship with Paragavialidium sichuanense, but the monophyly of Scelimeninae was not recovered. The mitogenome data of S. melli would provide useful resources for further evolutionary studies of Scelimeninae and Tetrigoidea species.
A Prediction Model for Primary Anterior Cruciate Ligament Injury Using Artificial Intelligence

Background: Supervised machine learning models in artificial intelligence (AI) have been increasingly used to predict different types of events. However, their use in orthopaedic surgery has been limited. Hypothesis: It was hypothesized that supervised learning techniques could be used to build a mathematical model to predict primary anterior cruciate ligament (ACL) injuries using a set of morphological features of the knee. Study Design: Cross-sectional study; Level of evidence, 3. Methods: Included were 50 adults who had undergone primary ACL reconstruction between 2008 and 2015. All patients were between 18 and 40 years of age at the time of surgery. Patients with a previous ACL injury, multiligament knee injury, previous ACL reconstruction, history of ACL revision surgery, complete meniscectomy, infection, missing data, and associated fracture were excluded. We also identified 50 sex-matched controls who had not sustained an ACL injury. For all participants, we used the preoperative magnetic resonance images to measure the anteroposterior lengths of the medial and lateral tibial plateaus as well as the lateral and medial bone slope (LBS and MBS), lateral and medial meniscal height (LMH and MMH), and lateral and medial meniscal slope (LMS and MMS). The AI predictor was created using Matlab R2019b. A Gaussian naïve Bayes model was selected to create the predictor. Results: Patients in the ACL injury group had a significantly increased posterior LBS (7.0° ± 4.7° vs 3.9° ± 5.4°; P = .008) and LMS (–1.7° ± 4.8° vs –4.0° ± 4.2°; P = .002) and a lower MMH (5.5 ± 0.1 vs 6.1 ± 0.1 mm; P = .006) and LMH (6.9 ± 0.1 vs 7.6 ± 0.1 mm; P = .001). The AI model selected LBS and MBS as the best possible predictive combination, achieving 70% validation accuracy and 92% testing accuracy. Conclusion: A prediction model for primary ACL injury, created using machine learning techniques, achieved a >90% testing accuracy. Compared with patients who did not sustain an ACL injury, patients with torn ACLs had an increased posterior LBS and LMS and a lower MMH and LMH.
Clinicopathological Analysis of Neuroendocrine Carcinoma of the Uterine Cervix: A Single-Institution Retrospective Review of 9 Cases

Aim To evaluate the clinicopathological features affecting the recurrence and survival of 9 cases of neuroendocrine cancer of the cervix. Method We retrospectively analyzed 9 cervical neuroendocrine cancer cases identified among 453 cervical cancer patients between 2004 and 2021 at Akdeniz University Gynecological Oncology Outpatient Clinic. Kaplan–Meier survival analysis was used for progression-free survival (PFS) and overall survival (OS). Mathematical functions of mean, standard deviation, median, Min–Max values, and frequencies were used for descriptive statistics. The categorical data were expressed in numbers and percentages (%). Results Nine patients with neuroendocrine histological subtype were selected out of 453 patients diagnosed with cervical cancer (1.98%). The average overall survival time of the patients was 26 months. The 5-year survival rate was 53.3%, while the PFS was 62.5%. The most common subtype was small cell neuroendocrine cancer. Tumours were mostly locally advanced at the time of diagnosis. 3 patients' stage was 1b2, while 4 patients were 2b, 1 patient was 3c2r, and 1 patient was 4b. All tumours showed the immunohistochemical staining properties of neuroendocrine cancer. The main treatment modality applied to our patients was surgery + adjuvant CRT. The most used chemotherapeutic agents were cisplatin/carboplatin and etoposide. Recurrence was found in 3 cases, including 5 deaths. Conclusion Neuroendocrine tumour of the cervix is a rare subtype with a poor prognosis. Unfortunately, there is not yet a standard treatment protocol due to the limited number of comparative studies of surgery, chemotherapy, and radiotherapy based treatment schemes.
A Longitudinal Randomized Controlled Trial Protocol to Evaluate the Effects of Wuqinxi on Dynamic Functional Connectivity in Parkinson’s Disease Patients

Background: Parkinson’s disease (PD) is a neurodegenerative movement disease that includes non-motor symptoms such as cognitive impairment. Long-term mind-body exercise has been shown to improve cognitive ability in PD patients, but the methods of assessment and intervention were inconsistent across studies. Wuqinxi is a mind-body exercise that is easy to learn, has few physical and cognitive demands, and is recommended for PD patients. Dynamic functional connectivity (DFC) has been associated with cognitive alterations in PD patients, but no studies have yet explored the effects of Wuqinxi on this association. The current protocol is designed to measure the effects of long-term Wuqinxi intervention on cognition in PD patients, and explore the underlying neural mechanisms through DFC. Methods: A long-term single-blind, randomized trial will be conducted. PD patients and age- and gender-matched HC will be recruited; PD patients will be randomly assigned to either Wuqinxi or balance groups, and HC will all receive health education. The Wuqinxi group will receive a 90-min session of Wuqinxi intervention three times a week for 24 weeks, while the balance group will receive balance exercise instruction on the same schedule. Primary outcomes will include assessment of cognitive domains and dynamic temporal characteristics of functional connectivity. Secondary outcomes will include severity of motor symptoms, mobility, balance, and emotional state. Assessments will be conducted at baseline, at the end of 24 weeks of intervention, and 12 weeks after interventions have ended. Discussion: This study will provide evidence to the effects of Wuqinxi exercise on cognitive improvements in PD patients from the perspective of DFC, and will contribute to the understanding of neural mechanisms underlying cognitive enhancement through Wuqinxi practice. Clinical Trial Registration: www.chictr. org.cn, identifier ChiCTR2000038517.
PD-1/PD-L1 Inhibitors versus Chemotherapy for Previously Treated Advanced Gastroesophageal Cancer: A Meta-Analysis of Randomized Controlled Trials

Patients with advanced gastroesophageal cancer refractory to the previous regimen of chemotherapy suffered from poor prognosis without many effective treatment options. Immune checkpoint inhibitors (ICIs) provide promising efficacy, but the relevant clinical trials have offered controversial data. We performed this meta-analysis to compare the efficacy and safety of inhibitors against programmed cell death receptor 1 (PD-1) and its ligand PD-L1 versus chemotherapy as second or third-line therapy in patients with advanced gastroesophageal cancer. Six randomized controlled trials (RCTs) including 2,648 patients were included. The meta-analysis results indicated that both ORR (RR = 1.39, 95% CI: 0.85∼2.25, P = 0.188) and PFS (HR = 1.14, 95% CI: 0.88∼1.46, P = 0.316) were not significantly improved by ICIs compared with chemotherapy. However, the OS was significantly prolonged (HR = 0.85, 95% CI: 0.75–0.97, P = 0.018) in the ICIs group compared with chemotherapy. Subgroup analysis showed that ICIs provide statistically significant OS benefits over chemotherapy in PD-L1-positive, squamous cell carcinoma, Asia origin, esophageal cancer, second-line treatment, male, and aged 65 or older patients. Compared with chemotherapy, the TRAEs risk of ICIs was reduced by 33% (RR = 0.67, 95% CI: 0.62–0.73, P ≤ 0.001). And the risk of grades 3–5 of TRAEs was reduced by 60% (RR = 0.40, 95% CI: 0.33–0.49, P ≤ 0.001). Compared to chemotherapy, ICIs appeared to improve OS and were better tolerated in previously treated patients with advanced esophageal cancer. We recommend PD-1/PD-L1 inhibitors as an optimal treatment option for positive PD-L1 expression, squamous cell carcinoma, Asia origin, esophageal cancer, second-line treatment, male, and ≥65 years of age patients.
Homologous Escherichia coli Identified in Cerebrospinal Fluid and Bloodstream

Background Escherichia coli is an opportunistic bacterium that causes a wide range of diseases, such as bloodstream infection and central nervous system infection. The traditional culture-based method to detect E. coli usually takes more than 2 days. The object of this study is to explore the value of metagenomic next-generation sequencing (mNGS) in identifying E. coli from human cerebrospinal fluid. In addition, we investigated the infection source of E. coli through whole genome sequencing and phylogenetic analysis. Methods We combined a clinical example to analyze the function of mNGS in pathogen detection from cerebrospinal fluid. NextSeq 550Dx platform was applied for mNGS. Next, whole genome sequencing was performed to obtain the genomic characterization of E. coli. Furthermore, we screened 20 E. coli strains from the National Center for Biotechnology Information and conducted a phylogenetic analysis. Results A middle-aged patient who attended our hospital was diagnosed with craniopharyngioma and received surgery. The patient had recurrent fever and persistent lethargy after surgery. Cerebrospinal fluid culture firstly failed to grow the bacteria. Next the cerebrospinal fluid sample was detected by mNGS and the sequence readings of E. coli were identified. Later, E. coli was reported via the second cerebrospinal fluid culture, certifying the result of mNGS. Moreover, we also cultured carbapenem-resistant E. coli from the patient’s bloodstream. Through whole genome sequencing and phylogenetic analysis, we found that the E. coli isolated from cerebrospinal fluid and the bloodstream was 100% homologous, indicating the E. coli central nervous system infection was originated from the bloodstream. Conclusion Metagenomic next-generation sequencing is a valuable tool to identify the pathogens from cerebrospinal fluid, and seeking the infection source is of great significance in clinical diagnosis and treatment. Furthermore, carbapenem-resistant E. coli is a serious problem as the cause of bloodstream infection and central nervous system infection, and effective and adequate measures to prevent and control the present circumstance are urgent.
Practice of Placenta Submission for Histopathological Examination, Experience of a Teaching/Tertiary Care Hospital in Saudi Arabia

Objectives The aim of this study is to determine the appropriateness of histopathologic examination of the placenta at King Abdulaziz University Hospital (KAUH), Jeddah, based on the guidelines of the College of American Pathologists (CAP). Methods It is a retrospective review of obstetric and pathologic records for all deliveries at KAUH, between January 1, 2017, and April 30, 2019. The placentae were assessed for eligibility to undergo pathologic examination. Furthermore, examined and non-examined placentae meeting the CAP criteria were compared based on their actual indications. Results There were 8,929 deliveries, of which 1,444 (16.2%) placentae met the CAP guidelines. A total of 583/1,444 placentae (40.4%; 95% confidence interval [CI] = 37.8-43) were sent for pathologic examination. Of the 7,485 placentae that did not require submission for pathological examination, as determined by the pathologist, 7,456 (99.6%; 95% CI = 99.4-99.7) were not submitted appropriately. The labor and delivery staff were more likely to submit placentae with fetal/neonatal indications rather than those with maternal indications for examination, which was statistically significant (odds ratio = 6.5; 95% CI = 5.08-8.30). Conclusion While most of the examined placentae at KAUH met the CAP guidelines, there was a substantial under-submission of eligible placentae. Further studies are advised to reveal the reasons behind this underestimation so that correctional measures may be adopted, as placenta examination is a valuable tool to understand the risk factors and pathogenesis of deleterious maternal, neonatal, and fetal events.
Does Interaction between Sleep Quality and Major Dietary Patterns Predicts Depression among Overweight and Obese Women in Iran?

Background: Although major dietary patterns and sleep quality independently affect psychiatric disorders, their interactive association on depression is not clear. This study assesses the independent association of dietary patterns and sleep quality on depression, and also investigates their interactive associations on depression among overweight and obese women in Iran Methods: Cross-sectional study was conducted among 304 participants, age 18 and above in 2018 at Tehran Iran. Usual dietary intake was collected with 174-FFQ. Participants’ biochemical parameters and depression were measured using standard protocol. Major dietary patterns were extracted by factor analysis and grouped into Fruits&Vegetable group (healthy dietary pattern), High Fat diary&Red Meat group (unhealthy dietary pattern) and Crackers&High Energy Drinks group (western dietary patterns). Results: After adjusting for confounders poor sleep was associated with moderate and high depression; AOR (95%CI): 0.41(0.19–0.90) and 0.29(0.13–0.60) respectively. However, healthy dietary patterns (tertiles 2nd and 3rd) interact with sleep for depression; AOR (95%CI): 4.168(1.166–14.992) and 2.966(1.068–8.234) respectively. Unhealthy dietary pattern tertiles 2nd and 3rd interact with sleep for depression; AOR (95%CI): 2.925(1.055–8.113) and 4.216(1.182–15.042) respectively and Western dietary pattern tertile 3rd interacts with sleep for depression; AOR (95%CI): 4.264(1.494–12.169). Conclusion: Sleep deprivation could be associated with depression. However, sleep quality could interacts with dietary patterns to be associate with depression among overweight and obese people.