Miracle-dz/UniFAR-FTUs huggingface dataset:
Intensity of Intraoperative Spinal Cord Hyperechogenicity as a Novel Potential Predictive Indicator of Neurological Recovery for Degenerative Cervical Myelopathy

Objective To analyze the correlations between intraoperative ultrasound and MRI metrics of the spinal cord in degenerative cervical myelopathy and identify novel potential predictive ultrasonic indicators of neurological recovery for degenerative cervical myelopathy. Materials and Methods Twenty-two patients who underwent French-door laminoplasty for multilevel degenerative cervical myelopathy were followed up for 12 months. The Japanese Orthopedic Association (JOA) scores were assessed preoperatively and 12 months postoperatively. Maximum spinal cord compression and compression rates were measured and calculated using both intraoperative ultrasound imaging and preoperative T2-weight (T2W) MRI. Signal change rates of the spinal cord on preoperative T2W MRI and gray value ratios of dorsal and ventral spinal cord hyperechogenicity on intraoperative ultrasound imaging were measured and calculated. Correlations between intraoperative ultrasound metrics, MRI metrics, and the recovery rate JOA scores were analyzed using Spearman correlation analysis. Results The postoperative JOA scores improved significantly, with a mean recovery rate of 65.0 ± 20.3% (p < 0.001). No significant correlations were found between the operative ultrasound metrics and MRI metrics. The gray value ratios of the spinal cord hyperechogenicity was negatively correlated with the recovery rate of JOA scores (ρ = −0.638, p = 0.001), while the ventral and dorsal gray value ratios of spinal cord hyperechogenicity were negatively correlated with the recovery rate of JOA-motor scores (ρ = −0.582, p = 0.004) and JOA-sensory scores (ρ = −0.452, p = 0.035), respectively. The dorsal gray value ratio was significantly higher than the ventral gray value ratio (p < 0.001), while the recovery rate of JOA-motor scores was better than that of JOA-sensory scores at 12 months post-surgery (p = 0.028). Conclusion For degenerative cervical myelopathy, the correlations between intraoperative ultrasound and preoperative T2W MRI metrics were not significant. Gray value ratios of the spinal cord hyperechogenicity and dorsal and ventral spinal cord hyperechogenicity were significantly correlated with neurological recovery at 12 months postoperatively.
Transcriptome analysis of buffalo granulosa cells in three dimensional culture systems

Hanging drop (HD) three‐dimensional (3D) culture model for buffalo granulosa cells (GC) was reported to mimic the preovulatory stage of ovarian follicles in our previous study. To further verify its reliability, the present study attempted a comparative transcriptome profile of buffalo GC freshly isolated from ovarian follicles (<8 mm diameter) (FC) and their cultures in normal culture dish (ND or 2D), polyHEMA coated dish (PH) and HD culture systems (3D). Out of 223 significantly (−log2 fold change: >3; p < .0005; false discovery rate [FDR]: <0.1) differentially expressed genes (SDEGs) among different culture systems, 137 were found unannotated, and 94, 29, and 66 were exclusively expressed in FC, PH, and HD, respectively. However, on eliminating the fixed points of p values and FDR from the entire raw data, only 11 genes related to long noncoding RNA, 12 genes related to luteinization, and 3 genes related to follicular maturation were exclusively expressed in FC, PH, and HD culture systems, respectively. The quantitative real time‐PCR validation and the next generation sequencing data had more than 90% correlation. Bioinformatics analyses of the exclusively expressed SDEG revealed that the freshly aspirated GCs were a true representative of GCs from small follicles (<8 mm diameter), the GC spheroids under PH maintained mitochondrial function, and those cultured in HD system for 6 days simulated the inflammatory milieu required for ovulation. Therefore, the comparative transcriptome profile also reinforced that HD culture system is better in vitro culture method than the other methods analyzed in this study for buffalo GC.
Ferroelectric domains in PZT ceramics at the morphotropic phase boundary. Can the splitting of reflections in SAED patterns be used for the distinction of different pseudo-cubic phases?

Tetragonal, rhombohedral and monoclinic ferroelectric domains can all occur in morphotropic PbZr1−xTixO3 (PZT) ceramics. In this article, the influence of these domains on the splitting of reflections in selected area electron diffraction (SAED) patterns along the main pseudo-cubic zone axes is reported. The orientation of the domain wall in a transmission electron microscopy image with respect to the splitting of reflections in the diffraction pattern has to be considered for the interpretation. The distinction of tetragonal and rhombohedral splitting is achieved for a pronounced splitting except for 〈111〉 with the domain wall edge on. As the monoclinic structure contains tetragonal as well as rhombohedral distortions, the distinction of monoclinic symmetry from tetragonal and rhombohedral based only on the splitting of reflections is not possible. Conceivable models of configurations of monoclinic subdomains inside the existing tetragonal or rhombohedral microdomains are derived from group–subgroup relations. Some experimental observations are given, which can only be explained by these models.
Biomarkers of environmental enteric dysfunction are not consistently associated with linear growth velocity in rural Zimbabwean infants

ABSTRACT Background Child stunting remains a poorly understood, prevalent public health problem. Environmental enteric dysfunction (EED) is hypothesized to be an important underlying cause. Objectives Within a subgroup of 1169 children enrolled in the SHINE (Sanitation Hygiene Infant Nutrition Efficacy) trial in rural Zimbabwe, followed longitudinally from birth to 18 mo of age, we evaluated associations between the concentration of 11 EED biomarkers and linear growth velocity. Methods At infant ages 1, 3, 6, 12, and 18 mo, nurses measured child length and collected stool and blood; the lactulose-mannitol urine test was also conducted at all visits except at 1 mo. Stool neopterin, α-1 antitrypsin, myeloperoxidase, and regenerating gene 1β protein; urinary lactulose and mannitol; and plasma kynurenine, tryptophan, C-reactive protein, insulin-like growth factor-1 (IGF-1), soluble CD14, intestinal fatty acid binding protein, and citrulline were measured. We analyzed the change in relative [∆ length-for-age z score (LAZ)/mo] and absolute (∆ length/mo) growth velocity during 4 age intervals (1–3 mo; 3–6 mo; 6–12 mo; and 12–18 mo) per SD increase in biomarker concentration at the start of each age interval. Results In fully adjusted models, we observed only 3 small, statistically significant associations: kynurenine:tryptophan ratio at 12 mo was associated with decreased mean LAZ velocity during the 12–18 mo interval (−0.015 LAZ/mo; 95% CI: −0.029, −0.001 LAZ/mo); mannitol excretion at 6 mo was associated with increased LAZ velocity during the 6–12 mo interval (0.013 LAZ/mo; 95% CI: 0.001, 0.025 LAZ/mo), and plasma IGF-1 at 1 mo was associated with increased LAZ velocity during the 1–3 mo interval (0.118 LAZ/mo; 95% CI: 0.024, 0.211 LAZ/mo). Results for absolute growth velocity were similar, except IGF-1 was also associated with growth during the 12–18 mo interval. We found no other associations between any EED biomarker and linear growth velocity. Conclusions None of 11 biomarkers of EED were consistently associated with linear growth among Zimbabwean children. This trial was registered at clinicaltrials.gov as NCT01824940.
The isotopic composition of soil organic carbon on a north–south transect in western Canada

The minor isotopes of carbon (13C and 14C) are widely used as tracers in studies of the global carbon cycle. We present carbon‐isotope data for the 0–5 cm layer of soil on a transect from 49.6°N to 68°N, from mature forest and tundra ecosystems in the boreal‐arctic zone of interior western Canada. Soil organic carbon in the < 2000 μm fraction of the soil decreases from 3.14 kg m−2 in the south to 1.31 kg m−2 in the north. The 14C activity of the organic carbon decreases as latitude increases from 118.9 to 100.7 per cent modern carbon (pMC). In addition, the 14C activities of organic carbon in the particle‐size fractions of each sample decrease as particle size decreases. These results suggest that organic carbon in the 0–5 cm layer of these soils transfers from standing biomass into the coarsest size fractions of the soil and is then degraded over time, with the residue progressively transferred into the more resistant finer particle sizes. We calculate residence times for the coarsest size fractions of 21 years in the south to 71 years in the north. Residence times for the fine size fractions (< 63 μm) are considerably longer, ranging from 90 years in the south to 960 years in the north. The δ13C of the organic carbon decreases from −26.8 ± 0.3‰ in soil under forest in the south to −26.2 ± 0.1‰ for tundra sites in the north. At all sites there is an increase in δ13C with decreasing particle size of 0.7–1.6‰. These changes in δ13C are due to the presence of ‘old’ carbon in equilibrium with an atmosphere richer in 13C, and to the effects of microbial degradation.
Dynamic imaging of enzymatic events at polyelectrolyte-disrupted phospholipid membranes using liquid crystals

In this study, we employed a simple liquid crystal (LC)-based system to dynamically image enzymatic events at the aqueous/LC interface decorated with polyelectrolyte-disrupted phospholipid membranes. Since polyelectrolytes were shown to disrupt the arrangement of the self-assembled phospholipid monolayer and induced a dark-to-bright shift in the optical response of LCs that support the phospholipid membrane, we observed that the transfer of an aqueous solution of protease onto the polyelectrolyte-disrupted phospholipid membrane resulted in a gradual recovery of the optical response of LCs from bright to dark appearance. Due to the enzymatic event that occurs at the aqueous/LC interface, the generated polyelectrolyte fragments desorbed from the interface to the bulk solution. This led to the restoration of the disrupted phospholipid monolayer, which resulted in recovery of the optical response. These results suggest that the polyelectrolyte-decorated membrane-supported LCs could be potentially used to examine a range of biological interactions that involve polyelectrolytes. Furthermore, the LC-based system holds great promise for label-free and real-time investigation and detection of biomolecular interactions coupled to membrane disruption and restoration, which might have potential utility in the clinical diagnosis and treatment of membrane-associated disease.
Influence of Proteome Profiles and Intracellular Drug Exposure on Differences in CYP Activity in Donor-Matched Human Liver Microsomes and Hepatocytes

Human liver microsomes (HLM) and human hepatocytes (HH) are important in vitro systems for studies of intrinsic drug clearance (CLint) in the liver. However, the CLint values are often in disagreement for these two systems. Here, we investigated these differences in a side-by-side comparison of drug metabolism in HLM and HH prepared from 15 matched donors. Protein expression and intracellular unbound drug concentration (Kpuu) effects on the CLint were investigated for five prototypical probe substrates (bupropion–CYP2B6, diclofenac–CYP2C9, omeprazole–CYP2C19, bufuralol–CYP2D6, and midazolam–CYP3A4). The samples were donor-matched to compensate for inter-individual variability but still showed systematic differences in CLint. Global proteomics analysis outlined differences in HLM from HH and homogenates of human liver (HL), indicating variable enrichment of ER-localized cytochrome P450 (CYP) enzymes in the HLM preparation. This suggests that the HLM may not equally and accurately capture metabolic capacity for all CYPs. Scaling CLint with CYP amounts and Kpuu could only partly explain the discordance in absolute values of CLint for the five substrates. Nevertheless, scaling with CYP amounts improved the agreement in rank order for the majority of the substrates. Other factors, such as contribution of additional enzymes and variability in the proportions of active and inactive CYP enzymes in HLM and HH, may have to be considered to avoid the use of empirical scaling factors for prediction of drug metabolism.
Increases in diagnosis and management of obstetric and neonatal complications in district hospitals during a high intensity nurse-mentoring program in Bihar, India

Maternal and neonatal mortality in Bihar, India was far higher than the aspirational levels set out by the Sustainable Development Goals. Provider training programs have been implemented in many low-resource settings to improve obstetric and neonatal outcomes. This longitudinal investigation assessed diagnoses and management of postpartum hemorrhage (PPH), hypertensive disorders of pregnancy, birth asphyxia (BA), and low birth weight (LBW), as part of the CARE’s AMANAT program in 22 District Hospitals in Bihar, between 2015 and 2017. Physicians and nurse mentors conducted clinical instruction, simulations and teamwork and communication activities, infrastructure and management support, and data collection for 6 consecutive months. Analysis of diagnosis included 11,259 non-referred and management included 11,800 total (non-referred and referred) admissions that were observed. Data were analyzed using the chi-square test for trend. PPH was diagnosed in 3.7% with no significant trend but diagnosis of hypertensive disorders increased from 1.0% to 1.7%, (ptrend = 0.04), over the 6 months. BA was diagnosed in 5.8% with no significant trend but LBW diagnoses increased from 11% to 16% (ptrend<0.01). Among PPH patients, 96% received fluids, 85% received uterotonics and 11% received Tranexamic Acid (TXA). There was a significant positive trend in the number of patients receiving TXA for PPH (6% to 13.8%, ptrend = 0.03). Of all neonates with BA, there were statistically significant increases in the proportion who were initially warmed, dried, and stimulated (78% to 94%, ptrend = 0.02), received airway suction (80% to 93%, ptrend = 0.03), and supplemental oxygen without positive pressure ventilation (73% to 86%, ptrend = 0.05). Diagnoses of hypertensive disorders and LBW as well as initial management of BA increased during the AMANAT program. However, underdiagnoses of PPH and hypertensive disorders relative to population levels remain critical barriers to improving maternal morbidity and mortality.
Relationships of rapeseed strength properties to seed size, colour and coat fibre composition

BACKGROUND: The size and strength of rapeseeds are factors likely to determine their suitability for storage and processing. The mechanical properties of whole seeds depend mainly on their coat composition. This study investigates variations in seed strength and colour between different-sized rapeseeds. The paper also presents an explanation of the differences in seed mechanical properties through analyses of coat fibre composition. RESULTS: The strength properties of seeds were dependent on seed size and correlated with seed equivalent diameter. All measured strength indices showed that seeds of diameter above 2 mm were the most resistant. The mechanical properties of seeds were also correlated with the colour of seed surface, indicating that the most resistant seeds were those with values of H > 60°, S < 15% and I < 19% in the HSI colour space. The resistance of individual seeds was attributed to the surface density of soluble and insoluble dietary fibre, especially cellulose and lignin. CONCLUSION: The results suggest that the highest mechanical resistance shown by the largest and blackest rapeseeds can be associated with the high surface density of fibre components in the seed coat. Copyright © 2008 Society of Chemical Industry
Complex changes of circadian proteins expression in inflammatory bowel disease.

OBJECTIVES AND BACKGROUND Recently, a possible role of circadian system in the pathogenesis of various gastrointestinal disorders gained an attention. The association of circadian system with immune system activity and reciprocal connection with intestinal microbiota indicate possible links with inflammatory bowel diseases (IBD). METHODS The retrospective study provided a semiquantitative immunohistochemical analysis of the expression of 8 core circadian proteins (BMAL1, BMAL2, PER1, PER2, PER3, CLOCK, NPAS2 and TIMELESS) in the epithelial cells of intestinal mucosa in 24 patients with Crohn's disease (CD) and 26 patients with ulcerative colitis (UC). Samples from patients without history of IBD served as the control. The BMAL1 protein expression in intramucosal inflammatory cells was explored as well. RESULTS The expression of 5 core circadian proteins (BMAL1, PER1, PER3, TIMELESS and NAPS2) was decreased in mucosal epithelium of patients with IBD in comparison with the control samples, whereas the expression of BMAL1 and PER1 was more noticeably decreased in UC patients and PER3, TIMELESS and NPAS2 in CD patients. There was a decreased BMAL1 expression in intramucosal inflammatory cells of IBD patients. CONCLUSION Decreased core circadian proteins expression in colonic mucosa and in intramucosal inflammatory cells of IBD patients indicated a circadian rhythm deregulation as contributing factor in the development of IBD. To our knowledge, this is so far the most extensive immunohistochemical analysis performed on the samples of IBD patients evaluating the changes in circadian protein expression in the intestinal mucosa (Tab. 1, Fig. 2, Ref. 31).
Dynamics of Adaptation During Three Years of Evolution Under Long-Term Stationary Phase

Abstract Many bacterial species that cannot sporulate, such as the model bacterium Escherichia coli, can nevertheless survive for years, following exhaustion of external resources, in a state termed long-term stationary phase (LTSP). Here we describe the dynamics of E. coli adaptation during the first three years spent under LTSP. We show that during this time, E. coli continuously adapts genetically through the accumulation of mutations. For nonmutator clones, the majority of mutations accumulated appear to be adaptive under LTSP, reflected in an extremely convergent pattern of mutation accumulation. Despite the rapid and convergent manner in which populations adapt under LTSP, they continue to harbor extensive genetic variation. The dynamics of evolution of mutation rates under LTSP are particularly interesting. The emergence of mutators affects overall mutation accumulation rates as well as the mutational spectra and the ultimate spectrum of adaptive alleles acquired under LTSP. With time, mutators can evolve even higher mutation rates through the acquisition of additional mutation rate–enhancing mutations. Different mutator and nonmutator clones within a single population and time point can display extreme variation in their mutation rates, resulting in differences in both the dynamics of adaptation and their associated deleterious burdens. Despite these differences, clones that vary greatly in their mutation rates tend to coexist within their populations for many years, under LTSP.
Mapping default mode connectivity alterations following a single season of subconcussive impact exposure in youth football

Repetitive head impact (RHI) exposure in collision sports may contribute to adverse neurological outcomes in former players. In contrast to a concussion, or mild traumatic brain injury, “subconcussive” RHIs represent a more frequent and asymptomatic form of exposure. The neural network‐level signatures characterizing subconcussive RHIs in youth collision‐sport cohorts such as American Football are not known. Here, we used resting‐state functional MRI to examine default mode network (DMN) functional connectivity (FC) following a single football season in youth players (n = 50, ages 8–14) without concussion. Football players demonstrated reduced FC across widespread DMN regions compared with non‐collision sport controls at postseason but not preseason. In a subsample from the original cohort (n = 17), players revealed a negative change in FC between preseason and postseason and a positive and compensatory change in FC during the offseason across the majority of DMN regions. Lastly, significant FC changes, including between preseason and postseason and between in‐ and off‐season, were specific to players at the upper end of the head impact frequency distribution. These findings represent initial evidence of network‐level FC abnormalities following repetitive, non‐concussive RHIs in youth football. Furthermore, the number of subconcussive RHIs proved to be a key factor influencing DMN FC.
Development and Validation of a Deep Learning–Based Model to Distinguish Glioblastoma from Solitary Brain Metastasis Using Conventional MR Images

A deep learning-based model may be a supportive tool for preoperative discrimination between glioblastoma and solitary brain metastasis using conventional MR images. BACKGROUND AND PURPOSE: Differentiating glioblastoma from solitary brain metastasis preoperatively using conventional MR images is challenging. Deep learning models have shown promise in performing classification tasks. The diagnostic performance of a deep learning–based model in discriminating glioblastoma from solitary brain metastasis using preoperative conventional MR images was evaluated. MATERIALS AND METHODS: Records of 598 patients with histologically confirmed glioblastoma or solitary brain metastasis at our institution between February 2006 and December 2017 were retrospectively reviewed. Preoperative contrast-enhanced T1WI and T2WI were preprocessed and roughly segmented with rectangular regions of interest. A deep neural network was trained and validated using MR images from 498 patients. The MR images of the remaining 100 were used as an internal test set. An additional 143 patients from another tertiary hospital were used as an external test set. The classifications of ResNet-50 and 2 neuroradiologists were compared for their accuracy, precision, recall, F1 score, and area under the curve. RESULTS: The areas under the curve of ResNet-50 were 0.889 and 0.835 in the internal and external test sets, respectively. The area under the curve of neuroradiologists 1 and 2 were 0.889 and 0.768 in the internal test set and 0.857 and 0.708 in the external test set, respectively. CONCLUSIONS: A deep learning–based model may be a supportive tool for preoperative discrimination between glioblastoma and solitary brain metastasis using conventional MR images.