Miracle-dz/UniFAR-FTUs huggingface dataset:
VCU Scholars Compass VCU Scholars Compass Applying model approaches in non-model systems: A review and Applying model approaches in non-model systems: A review and case study on coral cell culture case study on coral cell culture

Model systems approaches search for commonality in patterns underlying biological diversity and complexity led by common evolutionary paths. The success of the approach does not rest on the species chosen but on the scalability of the model and methods used to develop the model and engage research. Fine-tuning approaches to improve coral cell cultures will provide a robust platform for studying symbiosis breakdown, the calcification mechanism and its disruption, protein interactions, micronutrient transport/exchange, and the toxicity of nanoparticles, among other key biological aspects, with the added advantage of minimizing the ethical conundrum of repeated testing on ecologically threatened organisms. The work presented here aimed to lay the foundation towards development of effective methods to sort and culture reef-building coral cells with the ultimate goal of obtaining immortal cell lines for the study of bleaching, disease and toxicity at the cellular and polyp levels. To achieve this objective, the team conducted a thorough review and tested the available methods (i.e. cell dissociation, isolation, sorting, attachment and proliferation). The most effective and reproducible techniques were combined to consolidate culture methods and generate uncontaminated coral cell cultures for ~7 days (10 days maximum). The tests were conducted on scleractinian corals Pocillopora acuta of the same genotype to harmo-nize results and reduce variation linked to genetic diversity. The development of cell separation and identification methods in conjunction with further investigations into coral cell-type specific metabolic requirements will allow us to tailor growth media for optimized monocultures as a tool for studying essential reef-building coral traits such as symbiosis, wound healing and calcification at multiple scales.
Primary inguinal subcutaneous endometriosis accompanied with an inguinal hernia

Abstract Rationale: We report a case with inguinal subcutaneous endometriosis without typical cyclic dysmenorrhea and accompanied with a hernia sac treated with resection of the tumor and herniorrhaphy. Patient concerns: A 40-year-old woman had a painless enlarged inguinal nodule for 3 months. Diagnoses: Subcutaneous endometriosis accompanied with a hernia sac. Interventions: Ultrasonography showed a hypoechoic lesion (3.0 cm × 2.0 cm), and an inguinal subcutaneous tumor was first suspected. After surgical exploration, a cystic lesion was excised and the hernia hole was repaired by herniorrhaphy. The immunohistochemical analysis of the small endometriotic cyst-like lesion revealed calretinin (-) in epithelial cells and CD10 (+) in stromal cells, indicative of subcutaneous endometriosis accompanied with a hernia sac. Outcomes: The patient was followed up for 1 year and without recurrence. Lessons: Cutaneous endometriosis accompanied with a hernia sac can be presented without typical endometriosis-associated symptoms such as dysmenorrhea. Inguinal endometriosis might be the differential diagnosis of inguinal painless nodules.
Innovative alignment of sprinting prostheses for persons with transfemoral amputation: Exploratory study on a gold medal Paralympic athlete.

BACKGROUND Recommendations for the alignment of the socket and foot in the sprinting prosthesis of athletes with transfemoral amputation are either based on walking biomechanics or lack public scientific evidence. OBJECTIVES To explore the biomechanical changes and the sensations of a gold medal Paralympic sprinter, while running with three bench alignments: a conventional reference (A0), an innovative alignment based on the biomechanics of elite able-bodied sprinters (A2), and an intermediate alignment (A1). STUDY DESIGN Single subject with repeated measures. METHODS A1 and A2 feature a progressively greater socket tilt and a plantar-flexed foot compared to A0. The 30-year-old female athlete trained with three prostheses, one per alignment, for at least 2 months. We administered a questionnaire to collect her impressions. Then, she ran on a treadmill at full speed (5.5 m/s). We measured the kinematics and moments of the prosthetic side, and the ground reaction forces of both sides. RESULTS A2 reduced the prosthetic side hip extension at foot-off while preserving hip range of motion, decreased the impulse of the hip moment, and increased the horizontal propulsion, leaving sufficient margin to prevent knee buckling without increasing sound side braking forces. Biomechanical outcomes matched well with subjective impressions. CONCLUSIONS A2 appears promising to improve the performance and comfort of sprinters with transfemoral amputation, without compromising safety. CLINICAL RELEVANCE Observation of elite able-bodied sprinters led to the definition of a new specific alignment for the sprinting prosthesis of athletes with transfemoral amputation, which appears promising to improve performance and comfort, without compromising safety. This may constitute a major improvement compared to alignments based on walking biomechanics.
Homozygous GDF2 nonsense mutations result in a loss of circulating BMP9 and BMP10 and are associated with either PAH or an “HHT‐like” syndrome in children

Disrupted endothelial BMP9/10 signaling may contribute to the pathophysiology of both hereditary hemorrhagic telangiectasia (HHT) and pulmonary arterial hypertension (PAH), yet loss of circulating BMP9 has not been confirmed in individuals with ultra‐rare homozygous GDF2 (BMP9 gene) nonsense mutations. We studied two pediatric patients homozygous for GDF2 (BMP9 gene) nonsense mutations: one with PAH (c.[76C>T];[76C>T] or p.[Gln26Ter];[Gln26Ter] and a new individual with pulmonary arteriovenous malformations (PAVMs; c.[835G>T];[835G>T] or p.[Glu279Ter];[Glu279Ter]); both with facial telangiectases.
Resting-State Functional MRI for Determining Language Lateralization in Children with Drug-Resistant Epilepsy

BACKGROUND AND PURPOSE: Task-based fMRI is a noninvasive method of determining language dominance; however, not all children can complete language tasks due to age, cognitive/intellectual, or language barriers. Task-free approaches such as resting-state fMRI offer an alternative method. This study evaluated resting-state fMRI for predicting language laterality in children with drug-resistant epilepsy. MATERIALS AND METHODS: A retrospective review of 43 children with drug-resistant epilepsy who had undergone resting-state fMRI and task-based fMRI during presurgical evaluation was conducted. Independent component analysis of resting-state fMRI was used to identify language networks by comparing the independent components with a language network template. Concordance rates in language laterality between resting-state fMRI and each of the 4 task-based fMRI language paradigms (auditory description decision, auditory category, verbal fluency, and silent word generation tasks) were calculated. RESULTS: Concordance ranged from 0.64 (95% CI, 0.48–0.65) to 0.73 (95% CI, 0.58–0.87), depending on the language paradigm, with the highest concordance found for the auditory description decision task. Most (78%–83%) patients identified as left-lateralized on task-based fMRI were correctly classified as left-lateralized on resting-state fMRI. No patients classified as right-lateralized or bilateral on task-based fMRI were correctly classified by resting-state fMRI. CONCLUSIONS: While resting-state fMRI correctly classified most patients who had typical (left) language dominance, its ability to correctly classify patients with atypical (right or bilateral) language dominance was poor. Further study is required before resting-state fMRI can be used clinically for language mapping in the context of epilepsy surgery evaluation in children with drug-resistant epilepsy.
Antioxidant Supplementation Does Not Affect Bone Turnover Markers During 60 Days of 6° Head-Down Tilt Bed Rest: Results from an Exploratory Randomized Controlled Trial.

BACKGROUND Immobilization and related oxidative stress are associated with bone loss. Antioxidants like polyphenols, omega-3 fatty acids, vitamins, and micronutrients may mitigate these negative effects on bone metabolism through scavenging of free radicals. OBJECTIVES We hypothesized that antioxidant supplementation during 60 days of 6° head-down tilt bed rest (HDBR) would reduce bone resorption and increase bone formation compared to nonsupplemented controls. METHODS This exploratory randomized, controlled, single-blind intervention study conducted in a parallel design included 20 healthy male volunteers (age, 34 ± 8 years; weight, 74 ± 6 kg). The study consisted of a 14-day adaptation phase [baseline data collection (BDC)], followed by 60 days of HDBR and a 14-day recovery period (R). In the antioxidant group, volunteers received an antioxidant cocktail (741 mg/d polyphenols, 2.1 g/d omega-3 fatty acids, 168 mg/d vitamin E, and 80 μg/d selenium) with their daily meals. In the control group, volunteers received no supplement. Based on their body weight, all volunteers received an individually tailored and strictly controlled diet, consistent with DRIs. We analyzed biomarkers of calcium homeostasis, bone formation, and bone resorption during BDC, HDBR, and R, as well as for 30 days after the end of HDBR. Data were analyzed by linear mixed models. RESULTS The antioxidant supplement did not affect serum calcium, parathyroid hormone, urinary C-telopeptide of type I collagen (CTX), urinary N-telopeptide of type I collagen, serum β-C-telopeptide of type I collagen (β-CTX), bone alkaline phosphatase, aminoterminal propeptide of type I collagen, osteocalcin, or urinary calcium excretion. In both groups, typical bed rest-related changes were observed. CONCLUSIONS Supplementation of an antioxidant cocktail to a diet matching the DRIs did not affect bone resorption or formation during 60 days of HDBR in healthy young men. This trial was registered at clinicaltrials.gov as NCT03594799.
CT measures of adrenal gland length and caudal pole diameter are reproducible in large breed dogs: A pilot study

Abstract Computed tomography (CT) is increasingly available to evaluate dogs with suspected adrenal disease, however, published studies describing the reproducibility of CT methods for quantifying adrenal gland (AG) measurements are lacking. This prospective, pilot, observer agreement study aimed to evaluate reproducibility and repeatability of two different methods of measurement of AGs on CT to establish a usable technique and define standard reference ranges. Multiplanar reformatted (MPR) CT images of both AGs of six large breed dogs were obtained with the MPR axis parallel to the spine and parallel to the long axis of the AG. Ten measurements were performed: maximal length and diameter at cranial and caudal poles on dorsal, sagittal, and transverse images; and minimal diameter of cranial and caudal poles on transverse images. Three observers with different levels of experience repeated these measurements three times for each dog. Intra‐ and interobserver variability were calculated through intraclass correlation coefficient (ICC). The differences in time to perform measurements between the two methods were tested with Student's t‐test. Regardless of the measurement method used, length of AGs on dorsal and sagittal MPR images had the lowest intra‐ and inter‐observer variability (ICC = 0.93‐0.99), diameter of caudal pole on transverse plane showed low intra‐ and interobserver variability (ICC = 0.77‐0.80) and diameter of cranial pole had the highest variability (ICC = 0.12‐0.61). Although length was the less variable measurement, its use may be unrealistic in daily practice. Interestingly measurement of caudal pole on transverse plane was characterized by low intra‐ and interobserver variability. No difference in time performing the measurements was noted between the two methods.
A five-gene signature for predicting overall survival of esophagus adenocarcinoma

Supplemental Digital Content is available in the text Abstract Esophageal adenocarcinoma (EAC) is common and aggressive with increasing trend of incidence. Urgent need for an effective signature to assess EAC prognosis and facilitate tailored treatment is required. Differentially expressed mRNAs (DEMs) were identified by analyzing EAC tissues and adjacent normal samples from The Cancer Genome Atlas (TCGA). Then univariate regression analyses were performed to confirm prognostic DEMs. We used least absolute shrinkage and selection operator (LASSO) to build a prognostic mRNA signature whose performance was assessed by Kaplan–Meier curve, receiver operating characteristic (ROC). GSE72874 were used as an external test set. The performances of the signature were also validated in internal TCGA and external test sets. Gene set enrichment analysis (GSEA) and tumor immunity analysis were performed to decipher the biological mechanisms of the signature. A 5-mRNA signature consisted of SLC26A9, SINHCAF, MICB, KRT19, and MT1X was developed to predict prognosis of EAC. The 5-mRNA signature was promising as a biomarker for predicting 3-year survival rate of EAC in the internal test set, the entire TCGA set, and the external test set with areas under the curve (AUC) = 0.849, 0.924, and 0.747, respectively. Patients were divided into low- and high-risk groups based on risk scores of the signature. The high-risk group was mainly associated with cancer-related pathways and low levels of B cell infiltration. The 5-mRNA prognostic signature we identified can reliably predict prognosis and facilitate individualized treatment decisions for EAC patients.
Sexual dimorphism in hemispheric processing of faces in humans: A meta-analysis of 817 cases

Abstract A well-established neuroimaging literature predicts a right-sided asymmetry in the activation of face-devoted areas such as the fusiform gyrus (FG) and its resulting M/N170 response during face processing. However, the face-related response sometimes appears to be bihemispheric. A few studies have argued that bilaterality depended on the sex composition of the sample. To shed light on this matter, two meta-analyses were conducted starting from a large initial database of 250 ERP (Event-related potentials)/MEG (Magnetoencephalography) peer-reviewed scientific articles. Paper coverage was from 1985 to 2020. Thirty-four articles met the inclusion criteria of a sufficiently large and balanced sample size with strictly right-handed and healthy participants aged 18–35 years and N170 measurements in response to neutral front view faces at left and right occipito/temporal sites. The data of 817 male (n = 414) and female (n = 403) healthy adults were subjected to repeated-measures analyses of variance. The results of statistical analyses from the data of 17 independent studies (from Asia, Europe and America) seem to robustly indicate the presence of a sex difference in the way the two cerebral hemispheres process facial information in humans, with a marked right-sided asymmetry of the bioelectrical activity in males and a bilateral or left-sided activity in females.
Intra-Kernel Reallocation of Proteins in Maize Depends on VP1-Mediated Scutellum Development and Nutrient Assimilation[OPEN]

VP1 directly regulates embryo scutellum development and nutrient assimilation, which is required for protein reallocation from the endosperm to embryo. During maize (Zea mays) seed development, the endosperm functions as the major organ for storage of photoassimilate, serving to nourish the embryo. α-Zeins and globulins (GLBs) predominantly accumulate in the maize endosperm and embryo, respectively. Here, we show that suppression of α-zeins by RNA interference (αRNAi) in the endosperm results in more GLB1 being synthesized in the embryo, thereby markedly increasing the size and number of protein storage vacuoles. Glb genes are strongly expressed in the middle-to-upper section of the scutellum, cells of which are significantly enlarged by αRNAi induction. Elimination of GLBs caused an apparent reduction in embryo protein level, regardless of whether α-zeins were expressed or suppressed in the endosperm, indicating that GLBs represent the dominant capacity for storage of amino acids allocated from the endosperm. It appears that protein reallocation is mostly regulated at the transcriptional level. Genes differentially expressed between wild-type and αRNAi kernels are mainly involved in sulfur assimilation and nutrient metabolism, and many are transactivated by VIVIPAROUS1 (VP1). In vp1 embryos, misshapen scutellum cells contain notably less cellular content and are unable to respond to αRNAi induction. Our results demonstrate that VP1 is essential for scutellum development and protein reallocation from the endosperm to embryo.
Leprosy postexposure prophylaxis with single-dose rifampicin: Nepalese dermatologist’s dilemma

Nepal attained the status of leprosy elimination as a public health problem in 2010, however still struggling to sustain it. A recent World Health Organization (WHO) report has shown an increase in new case detection from Nepal in 2019 (3,844 new cases) which is an alarming situation [1]. In an effort to sustain the elimination status and reduce transmission, leprosy postexposure prophylaxis (LPEP) with single-dose rifampicin (SDR) has been implemented in some districts as a part of the national leprosy control program. The differences of opinions among leprosy experts on LPEP has created certain dilemmas. Although SDR is the only chemoprophylaxis recommended by WHO, we would like to share some of our dilemmas with LPEP with SDR with respect to these certain perspectives:
Mortality-related factors in patients with OXA-48 carbapenemase-producing Klebsiella pneumoniae bacteremia

Abstract Carbapenemase-producing Enterobacterales constitute a serious public health threat; however, information on the oxacilinasa (OXA-48)-type is limited. The objective of the study was to evaluate the risk factors associated with 14-day mortality for patients with bacteremia due to OXA-48 carbapenemase-producing Klebsiella pneumoniae. We conducted a retrospective, single-center observational study of adult patients with K. pneumoniae bacteremia, classifying the strains as carbapenem-susceptible K. pneumoniae (CSKp) and carbapenem-resistant K. pneumoniae (CRKp). All of the CRKp strains were the OXA-48-type. The study included 202 cases of bacteremia: 114 due to CSKp and 88 due to CRKp. The clinical cure rate was higher for the patients with CSKp (85% vs 69% for CSKp and CRKp, respectively; P = .010), while the 14-day mortality rate was lower (13% vs 30%, P = .005). An INCREMENT-CPE score ≥7 (HR 3.05, 95% CI 1.50–6.25, P = .002) was the only independent factor associated with 14-day mortality for the patients with Klebsiella spp. bacteremia. Other factors related to 14-day mortality were a rapidly fatal prognosis (McCabe) (HR 7.1, 95% CI 2.75–18.37, P < .001), dementia (HR 5.9, 95% CI 2.0–7.43, P = .001), and a high-risk source of infection (HR 2.7, 95% CI 1.06–6.82, P = .038). The most important factors associated with 14-day mortality for the patients with K. pneumoniae bacteremia was an INCREMENT-CPE score ≥7, dementia, a McCabe score indicating a rapidly fatal prognosis and a high-risk source of infection. We found no relationship between a poorer outcome and CRKp isolation or inadequate antibiotic therapy.
Reduced grip strength is associated with progression of depressive status in chronic liver diseases.

BACKGROUND The causal relationship between sarcopenia and depression in chronic liver disease (CLD) patients is unclear. To elucidate these issues, we aimed to investigate the impacts of muscle strength as assessed by grip strength (GS) and muscle mass as assessed by bioelectrical impedance analysis (BIA) on the progression of depression in CLD patients (n=189, 49 cirrhotic cases, and 87 males). METHODS The Beck Depression Inventory-2nd edition (BDI-II) was used for the evaluation of depression. Time interval from the date of baseline BDI-II and the first confirmed date of elevation of BDI-II score was calculated in each subject. We analyzed factors associated with the elevation of BDI-II score. RESULTS The baseline mean BDI-II score was 8.4 (median value, 7). Depression (BDI-II score >11) was found in 63 patients (33.33%). GS decline at baseline was found in 13 male patients (14.9%) and 37 female patients (36.3%). Skeletal muscle index (SMI) by BIA decline at baseline was found in 25 male patients (28.7%) and 40 female patients (39.2%). During the follow-up period, 84 patients (44.4%) had the elevation of BDIII score. For all cases, the 1-, 2- and 3-year cumulative elevation rates of BDI-II score were 39.2%, 46.6% and 54.9%. In patients with GS decline at baseline, the 1-, 2- and 3-year cumulative elevation rates of BDI-II score were 53.1%, 67.8% and 77.9%, while in patients with GS non-decline at baseline, the 1-, 2- and 3-year cumulative elevation rates of BDI-II score were 34.4%, 39.8% and 47.4% (P=0.0006). In patients with SMI decline at baseline, the 1-, 2- and 3-year cumulative elevation rates of BDI-II score were 43.5%, 50.8% and 62.1%, while in patients with SMI non-decline at baseline, the 1-, 2- and 3-year cumulative elevation rates of BDI-II score were 36.9%, 44.5% and 51.0% (P=0.2487). As per the multivariate analyses, only lower GS at baseline (P=0.0022) was identified to be a significant factor associated with the elevation of BDI-II score. CONCLUSIONS Reduced GS rather than loss of muscle mass can be independently associated with an elevated risk for the progression of depression.
The Etiology of Infertility Affects Fertility Quality of Life of Males Undergoing Fertility Workup and Treatment

This panel study explored the effects of male, female, mixed, or idiopathic factor of infertility on the fertility quality of life (FertiQoL) in involuntarily childless males undergoing fertility workup for the first time. A convenience sample of 255 married males (age range = 22–51 years, mean = 30.24 years), 254 (99.6%) of whom suffered from primary infertility were assessed (1) at the baseline, before their initial fertility evaluation (T1); (2) before their second andrological appointment, 2–3 months after diagnostic disclosure (T2); and (3) before subsequent treatment-related/ follow-up appointments (T3, T4). The timing of psychological assessment was strictly related to andrological appointments and routine medical procedures. Respondents completed Emotional, Mind–Body, Relational, and Social subscales of the Polish version of FertiQoL and a baseline demographic survey. The research demonstrated that the FertiQoL scores across the Emotional, Mind–Body, and Relational subscales markedly decreased after the diagnostic disclosure, particularly in the subgroups with male and concurrent male and female factor. Social subscale scores in all subgroups remained stable after the diagnostic disclosure (at T2) but significantly decreased in the follow-up (at T3 and T4). Significant differences in FertiQoL scores associated with respondents’ infertility factor could be demonstrated at each time point. The study identifies the FertiQoL in unintentionally childless males is significantly affected by their factor of infertility and evolves across the pathway of treatment-related/follow-up appointments.