Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimized cervical spinal cord perfusion MRI after traumatic injury in the rat

Despite the potential to guide clinical management of spinal cord injury and disease, noninvasive methods of monitoring perfusion status of the spinal cord clinically remain an unmet need. In this study, we optimized pseudo-continuous arterial spin labeling (pCASL) for the rodent cervical spinal cord and demonstrate its utility in identifying perfusion deficits in an acute contusion injury model. High-resolution perfusion sagittal images with reduced imaging artifacts were obtained with optimized background suppression and imaging readout. Following moderate contusion injury, perfusion was clearly and reliably decreased at the site of injury. Implementation of time-encoded pCASL confirmed injury site perfusion deficits with blood flow measurements corrected for variability in arterial transit times. The noninvasive protocol of pCASL in the spinal cord can be utilized in future applications to examine perfusion changes after therapeutic interventions in the rat and translation to patients may offer critical implications for patient management.
Data-Driven Boolean Network Inference Using a Genetic Algorithm With Marker-Based Encoding

The inference of Boolean networks is crucial for analyzing the topology and dynamics of gene regulatory networks. Many data-driven approaches using evolutionary algorithms have been proposed based on time-series data. However, the ability to infer both network topology and dynamics is restricted by their inflexible encoding schemes. To address this problem, we propose a novel Boolean network inference algorithm for inferring both network topology and dynamics simultaneously. The main idea is that, we use a marker-based genetic algorithm to encode both regulatory nodes and logical operators in a chromosome. By using the markers and introducing more logical operators, the proposed algorithm can infer more diverse candidate Boolean functions. The proposed algorithm is applied to five networks, including two artificial Boolean networks and three real-world gene regulatory networks. Compared with other algorithms, the experimental results demonstrate that our proposed algorithm infers more accurate topology and dynamics.
Observation of exchange bias below incommensurate antiferromagnetic (ICAFM) to canted A-type antiferromagnetic (cAAFM) transition in nanocrystalline orthorhombic EuMnO3

Detailed ac and dc magnetic properties of orthorhombic EuMnO3 were studied using a nanocrystalline powder sample. Orthorhombic EuMnO3 nanoparticles of 45 nm average size were synthesised using a hydrothermal method. Zero field cooled (ZFC) and field cooled (FC) magnetisation shows anomalies at ∼53, 44 and 24 K attributed to paramagnetic (PM) to an incommensurate antiferromagnetic phase (ICAFM), ICAFM to a canted A-type antiferromagnetic order (cAAFM) and spin reorientation transitions, respectively. No indication of a PM to ICAFM transition was observed in either the real or imaginary part of ac magnetisation. The real part of the ac magnetisation curve showed a peak at ∼24.7 K and anomalies at ∼46.8 and 21.8 K were observed in the imaginary part of ac magnetisation. Reduction in the width of the thermal hysteresis between the field cooling and heating magnetisation curve was observed with the nanocrystallites (∼1 K) compared with the bulk phase (∼3 K) EuMnO3. Isothermal magnetisation showed a large value of the exchange bias (2799 Oe at 3 K) below the ICAFM to cAAFM transition temperature.
EpiMOGA: An Epistasis Detection Method Based on a Multi-Objective Genetic Algorithm

In genome-wide association studies, detecting high-order epistasis is important for analyzing the occurrence of complex human diseases and explaining missing heritability. However, there are various challenges in the actual high-order epistasis detection process due to the large amount of data, “small sample size problem”, diversity of disease models, etc. This paper proposes a multi-objective genetic algorithm (EpiMOGA) for single nucleotide polymorphism (SNP) epistasis detection. The K2 score based on the Bayesian network criterion and the Gini index of the diversity of the binary classification problem were used to guide the search process of the genetic algorithm. Experiments were performed on 26 simulated datasets of different models and a real Alzheimer’s disease dataset. The results indicated that EpiMOGA was obviously superior to other related and competitive methods in both detection efficiency and accuracy, especially for small-sample-size datasets, and the performance of EpiMOGA remained stable across datasets of different disease models. At the same time, a number of SNP loci and 2-order epistasis associated with Alzheimer’s disease were identified by the EpiMOGA method, indicating that this method is capable of identifying high-order epistasis from genome-wide data and can be applied in the study of complex diseases.
Prevalence and antimicrobial susceptibility profiles of non‐typhoidal Salmonella isolated from chickens in Rajshahi, Bangladesh

Abstract Salmonellosis in poultry is an important disease that seriously impedes the development of the poultry industry. The increased resistance to antimicrobials against Salmonella has been a major public health concern worldwide. We conducted a study from January to June 2016 in and around the Rajshahi district of Bangladesh on the commercial chicken to isolate, identify and characterize poultry‐specific Salmonella, to assess the potential risk factors and to determine the antimicrobial resistance pattern of the isolates. The overall prevalence of Salmonella enterica was 41% (49/120) [95% CI: 31.95%–50.17%] with 41.7% in broiler chicken (25/60) [95% CI: 29.06%–55.12%] and 40% in layer chicken (24/60, 40%) [95% CI: 27.56%–53.46%]. Samples collected from Rajshahi city (OR = 1.37, 95% CI: 0.50–3.73) and Puthia Upazila (OR = 1.51, 95% CI: 0.56–4.12) were more likely to be positive for Salmonella than Charghat Upazila. Salmonella detection was 1.3 times higher in chicken, providing loose feed than those provided ready feed. All the isolates fermented dextrose, maltose and mannitol with the production of acid and gas, but did not ferment sucrose and lactose. The isolates showed catalase, MR, citrate utilization test and TSI agar test positive, but indole and V‐P tests negative. Salmonella isolates were sensitive to ciprofloxacin (90%), gentamycin (80%), amoxicillin (75%), streptomycin (70%), ampicillin (45%) and sulfamethoxazole‐trimethoprim (45%), whereas highly resistant to penicillin (100%) and nalidixic acid (100%) followed by sulfamethoxazole‐trimethoprim (55%), ampicillin (40%) and amoxicillin (25%). Salmonella enterica is endemic in commercial chicken production in Bangladesh with high prevalence. A considerable proportion of Salmonella isolates was found to be resistant to the majority of the common antimicrobial drugs. A good biosecurity system could be effective for the reduction of Salmonella. It is necessary to obtain universal commitments to establish prudent antibiotic use policies.
The application of scattering cross sections to ion flux models in discharge sheaths

We suggest consistent sets of Ar++Ar and Ar+++Ar differential and integral cross sections for modeling ion scattering that take into account differential scattering data and the fact that symmetric charge transfer collisions are one aspect of elastic scattering collisions. These suggestions make possible a considerable improvement in the accuracy of future Monte Carlo calculations of the angular, energy, and temporal distributions of Ar+ and Ar++ ions passing through the electrode sheaths of low‐pressure, rf, and dc discharges in Ar. The cross sections necessary for a proper modeling of the energy dissipation in the gas and at the electrodes by fast neutral Ar atoms formed in symmetric‐charge‐transfer collisions of Ar+ and Ar++ with Ar are also reviewed.
Physiological Indicators of Trail Running Performance: A Systematic Review.

PURPOSE To provide a systematic overview of physiological parameters used to determine the training status of a trail runner and how well these parameters correlate with real-world trail running performance. METHOD An electronic literature search of the PubMed and Scopus digital databases was performed. Combinations of the terms "trail run" or "trail runner" or "trail running" and "performance" were used as search terms. Seven studies met the inclusion criteria. RESULTS Trail running performance most commonly correlated (mean [SD]) with maximal aerobic capacity (71%; r = -.50 [.32]), lactate threshold (57%; r = -.48 [.28]), velocity at maximal aerobic capacity (43%; r = -.68 [.08]), running economy (43%; r = -.31 [.22]), body fat percentage (43%; r = .55 [.21]), and age (43%; r = .52 [.14]). Regression analyses in 2 studies were based on a single variable predicting 48% to 60% of performance variation, whereas 5 studies included multiple variable regression analyses predicting 48% to 99% of performance variation. CONCLUSIONS Trail running performance is multifaceted. The classic endurance model shows a weaker association with performance in trail running than in road running. Certain variables associated with trail running research (such as testing procedures, race profiles, and study participants) hinder the execution of comparative studies. Future research should employ trail-specific testing protocols and clear, objective descriptions of both the race profile and participants' training status.
Risk factors of Pancreatic Cancer in Vietnam: A Matched Case–Control Hospital-Based Study

Background: Data about the risk factors and pancreatic cancer in developing countries remain limited. We investigated for the first time the role of a number of risk factors (family cancer history, smoking, alcohol consumption, diabetes, inflammation disease, HBV infection) associated with pancreatic cancer among Vietnamese patients. Methods: We included all patients hospitalized at 4 Northern Vietnamese hospitals (Vietnam National Cancer Hospital, Bach Mai, Viet Duc, Thai Nguyen) and diagnosed with pancreatic cancer during the period from 2017 to 2019. Risk factors of eligible patients were collected and assessed the associations using a matched control study and logistic regression model analysis. Results: We identified 196 patients with diagnosis of pancreatic cancer of which 114 males and 82 females. The average age of the patient at the time of diagnosis was 58.28 years (standard deviation of 12.94, ranging from 25 to 87). Most of patients were diagnosed at advanced stage (85%). Smoking, diabetes, inflammation disease significantly increased the cancer risks (OR and 95% CI were 2.42 (1.38-4.37), 3.09 (1.54-6.68), 2.21 (1.42-3.45), respectively). HBV infection demonstrated a significant link with pancreatic cancer in univariate model (OR = 2.94 (1.08-9.36)), but not in multivariate model. However, cancer family history and alcohol drinkers did not show any significantly increased risk related to pancreatic cancer. Conclusions: Our finding showed smoking, diabetes, inflammation disease significantly increased the risk of pancreatic cancer in Vietnam.
Patient-Reported Outcomes and Knee Mechanics Correlate With Patellofemoral Deep Cartilage UTE-T2* 2 Years After Anterior Cruciate Ligament Reconstruction

Background: Patellofemoral joint degeneration and dysfunction after anterior cruciate ligament reconstruction (ACLR) are increasingly recognized as contributors to poor clinical outcomes. Purpose: To determine if greater deep cartilage matrix disruption at 2 years after ACLR, as assessed by elevated patellofemoral magnetic resonance imaging (MRI) ultrashort echo time–enhanced T2* (UTE-T2*), is correlated with (1) worse patient-reported knee function and pain and (2) gait metrics related to patellofemoral tracking and loading, such as greater external rotation of the tibia at heel strike, reduced knee flexion moment (as a surrogate of quadriceps function), and greater knee flexion angle at heel strike. Study Design: Cross-sectional study; Level of evidence, 3. Methods: MRI UTE-T2* relaxation times in patellar and trochlear deep cartilage were compared with patient-reported outcomes and ambulatory gait metrics in 60 patients with ACLR at 2 years after reconstruction. ACLR gait metrics were compared with those of 60 uninjured reference patients matched by age, body mass index, and sex. ACLR UTE-T2* values were compared with those of 20 uninjured reference patients. Results: Higher trochlear UTE-T2* values were associated with worse Knee injury and Osteoarthritis Outcome Scores (KOOS) Sport/Recreation subscale scores (rho = −0.32; P = .015), and showed a trend for association with worse KOOS Pain subscale scores (rho = −0.26; P = .045). At 2 years after ACLR, greater external rotation of the tibia at heel strike was associated with higher patellar UTE-T2* values (R = 0.40; P = .002); greater knee flexion angle at heel strike was associated with higher trochlear UTE-T2* values (rho = 0.39; P = .002); and greater knee flexion moment showed a trend for association with higher trochlear UTE-T2* values (rho = 0.30; P = .019). Patellar cartilage UTE-T2* values, knee flexion angle at heel strike, and external rotation of the tibia at heel strike were all elevated in ACLR knees as compared with reference knees (P = .029, .001, and .044, respectively). Conclusion: Patellofemoral deep cartilage matrix disruption, as assessed by MRI UTE-T2*, was associated with reduced sports and recreational function and with gait metrics reflective of altered patellofemoral loading. As such, the findings provide new mechanistic information important to improving clinical outcomes related to patellofemoral dysfunction after ACLR.
Machine Learning Analysis of Longevity-Associated Gene Expression Landscapes in Mammals

One of the important questions in aging research is how differences in transcriptomics are associated with the longevity of various species. Unfortunately, at the level of individual genes, the links between expression in different organs and maximum lifespan (MLS) are yet to be fully understood. Analyses are complicated further by the fact that MLS is highly associated with other confounding factors (metabolic rate, gestation period, body mass, etc.) and that linear models may be limiting. Using gene expression from 41 mammalian species, across five organs, we constructed gene-centric regression models associating gene expression with MLS and other species traits. Additionally, we used SHapley Additive exPlanations and Bayesian networks to investigate the non-linear nature of the interrelations between the genes predicted to be determinants of species MLS. Our results revealed that expression patterns correlate with MLS, some across organs, and others in an organ-specific manner. The combination of methods employed revealed gene signatures formed by only a few genes that are highly predictive towards MLS, which could be used to identify novel longevity regulator candidates in mammals.
Absence of B Cells in Brainstem and White Matter Lesions Associates With Less Severe Disease and Absence of Oligoclonal Bands in MS

Objective To determine whether B-cell presence in brainstem and white matter (WM) lesions is associated with poorer pathological and clinical characteristics in advanced MS autopsy cases. Methods Autopsy tissue of 140 MS and 24 control cases and biopsy tissue of 24 patients with MS were examined for CD20+ B cells and CD138+ plasma cells. The presence of these cells was compared with pathological and clinical characteristics. In corresponding CSF and plasma, immunoglobulin (Ig) G ratio and oligoclonal band (OCB) patterns were determined. In a clinical cohort of 73 patients, the presence of OCBs was determined during follow-up and compared to status at diagnosis. Results In 34% of active and 71% of mixed active/inactive lesions, B cells were absent, which correlated with less pronounced meningeal B-cell infiltration (p < 0.0001). The absence of B cells and plasma cells in brainstem and WM lesions was associated with a longer disease duration (p = 0.001), less frequent secondary progressive MS compared with relapsing and primary progressive MS (p < 0.0001 and p = 0.046, respectively), a lower proportion of mixed active/inactive lesions (p = 0.01), and less often perivascular T-cell clustering (p < 0.0001). Moreover, a lower CSF IgG ratio (p = 0.006) and more frequent absence of OCBs (p < 0.0001) were noted. In a clinical cohort, numbers of patients without OCBs in CSF were increased at follow-up (27.4%). Conclusions The absence of B cells is associated with a favorable clinical and pathological profile. This finding may reflect extremes of a continuum of genetic or environmental constitution, but also a regression of WM humoral immunopathology in the natural course of advanced MS.
Zika Virus Neutralizing Antibody Kinetics in Antenatally Exposed Infants.

BACKGROUND Zika virus (ZIKV) is associated with severe congenital abnormalities and laboratory diagnosis of antenatal infection is difficult. Here we evaluated ZIKV neutralizing antibody (Nab) kinetics in infants born to mothers with PCR-confirmed ZIKV infection during pregnancy. METHODS Neonates (n=98) had serum specimens tested repeatedly for ZIKV Nab over the first two years of life using virus neutralization test (VNT). ZIKV neonatal infection was confirmed by RT-PCR in blood or urine and/or presence of ZIKV IgM antibodies, and results were correlated with infant clinical features. RESULTS Postnatal laboratory evidence of ZIKV vertical transmission was obtained for 60.2% of children, while 32.7% exhibited clinical abnormalities. Congenital abnormalities were found in 37.3% of children with confirmed ZIKV infection and 31.0% of children without confirmed infection (p=0.734). All but one child displayed a physiologic decline in ZIKV Nab, reflecting maternal antibody decay, despite an early ZIKV-IgM response in 1/3 of infants. CONCLUSIONS Infants with antenatal ZIKV exposure do not develop ZIKV Nab despite an early IgM response. Therefore, ZIKV VNT in children is not useful for diagnosis of congenital infection. In light of these findings, it remains to be determined if children infected in utero are potentially susceptible to reinfection.
Multiscale Electron Microscopy for the Study of Viral Replication Organelles

During infection with positive-strand RNA viruses, viral RNA synthesis associates with modified intracellular membranes that form unique and captivating structures in the cytoplasm of the infected cell. These viral replication organelles (ROs) play a key role in the replicative cycle of important human pathogens like coronaviruses, enteroviruses, or flaviviruses. From their discovery to date, progress in our understanding of viral ROs has closely followed new developments in electron microscopy (EM). This review gives a chronological account of this progress and an introduction to the different EM techniques that enabled it. With an ample repertoire of imaging modalities, EM is nowadays a versatile technique that provides structural and functional information at a wide range of scales. Together with well-established approaches like electron tomography or labeling methods, we examine more recent developments, such as volume scanning electron microscopy (SEM) and in situ cryotomography, which are only beginning to be applied to the study of viral ROs. We also highlight the first cryotomography analyses of viral ROs, which have led to the discovery of macromolecular complexes that may serve as RO channels that control the export of newly-made viral RNA. These studies are key first steps towards elucidating the macromolecular complexity of viral ROs.
Do individuals with eating disorders dislike exposure therapy? Attitudes from children, adults, and parents toward exposure therapy and other treatments for eating disorders.

OBJECTIVE Exposure therapy appears underutilized in the treatment of eating disorders (EDs), perhaps due to clinicians' concerns that patients will dislike exposure therapy. The present study aims to investigate the attitudes of child patients, adult patients, and parents of child patients with EDs toward exposure therapy relative to four other treatments for EDs. METHOD A questionnaire was administered to patients and parents (N = 126) upon admission to a partial hospitalization program for EDs. Participants read vignettes describing five different treatments for EDs, and answered questions assessing attitudes about each treatment. RESULTS At admission, participants reported the most favorable attitudes toward cognitive therapy, and the least favorable attitudes toward psychiatric medication. Exposure therapy generally received similar scores as interpersonal and expressive art therapy, and was perceived as significantly more preferable and effective in the long-term than psychiatric medication. Relative to child and adult patients, parents reported greater preferences for all treatments except medication, and perceived all treatments as more credible except medication and art therapy. Preliminary findings from a subset of participants who also completed the questionnaire at discharge indicated that positive attitudes toward exposure therapy increased over the course of treatment. DISCUSSION Individuals with EDs and their parents may enter treatment with particularly favorable views toward cognitive therapy, and do not appear to have strong attitudes toward exposure therapy one way or the other. Clinicians' concerns that patients with EDs will dislike exposure therapy may be largely unfounded.
Hemorrhagic stroke caused by moyamoya disease in a patient with obstructive hypertrophic cardiomyopathy

A 42-year-old woman was admitted due to exertional dyspnea, chest pain, and dizziness. However, she denied a history of palpitation, headache, syncope, or seizure. She had been diagnosed as obstructive HCM and treated with metoprolol for 10 years. She was always found in sinus rhythm. Her mother was identified to have HCM due to mild exertional dyspnea at the age of 30 years, but she and other family members refused any further investigations. On admission, echocardiography showed asymmetrical left ventricular (LV) hypertrophy with a peak pressure gradient of 79 mmHg in the LV outflow tract (LVOT). Cardiac magnetic resonance imaging revealed remarkable hypertrophy of the interventricular septum with focal late gadolinium enhancement [Figure 1A] and a narrowed LVOT at mid-systole [Figure 1B]. The patient underwent a modified Morrow surgery and recovered successfully without symptoms during a regular follow up for 8 months. However, she was readmitted due to sudden onset of unconsciousness when computed tomography scan confirmed left parietal lobe and intraventricular hemorrhage in the brain. Transcatheter angiography demonstrated the typical feature of “moyamoya” as stenoocclusion of the distal part of bilateral internal carotid arteries and moyamoya-associated collateral networks at the base of brain [Figure 1C–F].