Miracle-dz/UniFAR-FTUs huggingface dataset:
Brain Gray Matter Atrophy and Functional Connectivity Remodeling in Patients With Chronic LHON

Purpose The aim of this study was to investigate the brain gray matter volume (GMV) and spontaneous functional connectivity (FC) changes in patients with chronic Leber's hereditary optic neuropathy (LHON), and their relations with clinical measures. Methods A total of 32 patients with chronic LHON and matched sighted healthy controls (HC) underwent neuro-ophthalmologic examinations and multimodel magnetic resonance imaging (MRI) scans. Voxel-based morphometry (VBM) was used to detect the GMV differences between the LHON and HC. Furthermore, resting-state FC analysis using the VBM-identified clusters as seeds was carried out to detect potential functional reorganization in the LHON. Finally, the associations between the neuroimaging and clinical measures were performed. Results The average peripapillary retinal nerve fiber layer (RNFL) thickness of the chronic LHON was significantly thinner (T = −16.421, p < 0.001), and the mean defect of the visual field was significantly higher (T = 11.28, p < 0.001) than the HC. VBM analysis demonstrated a significantly lower GMV of bilateral calcarine gyri (CGs) in the LHON than in the HC (p < 0.05). Moreover, in comparison with the HC, the LHON had significantly lower FC between the centroid of the identified left CG and ipsilateral superior occipital gyrus (SOG) and higher FC between this cluster and the ipsilateral posterior cingulate gyrus (p < 0.05, corrected). Finally, the GMV of the left CG was negatively correlated with the LHON duration (r = −0.535, p = 0.002), and the FC between the left CG and the ipsilateral posterior cingulate gyrus of the LHON was negatively correlated with the average peripapillary RNFL thickness (r = −0.522, p = 0.003). Conclusion The atrophied primary visual cortex of the chronic LHON may be caused by transneuronal degeneration following the retinal damage. Moreover, our findings suggest that the functional organization of the atrophied primary visual cortex has been reshaped in the chronic LHON.
Recruitment Traits Could Influence Species’ Geographical Range: A Case Study in the Genus Saxifraga L.

The reasons why some species occur widespread, while related species have restricted geographical ranges have been attributed to habitat specialization or ecological niche breadth. For species in the genus Saxifraga, habitat specialization alone cannot explain the distributional differences observed. We hypothesize that recruitment traits (i.e., germination, emergence, and survival) may account for differences in geographical ranges and that early life stages correlate to survival. We studied recruitment responses in 13 widespread and 12 narrow-ranged Saxifraga species in the laboratory and common garden experiments using seeds collected from 79 populations in the European Alps. We found that in the laboratory cold temperature led to higher germination percentages compared with warm temperature for both distribution groups. This represents an exception to the general assumption that alpine species require warm cues for germination. In warm laboratory temperatures, widespread species germinated better than narrow-ranged species, indicating a greater tolerance of warm temperatures for the former. Subsequent to germination, recruitment traits between the two distribution groups were lower or null in the common garden, suggesting that the impact of recruitment on species’ geographical ranges occurs at the earliest life stage. Mean time to emergence of narrow-ranged species showed lower variability than that of widespread species. Consistently, intraspecific variation of mean annual temperatures between seed collection sites was lower for narrow-ranged species, indicating a close relationship between home sites and emergence time. Emergence percentage was a strong predictor of survival only for widespread species, underlining that seed and seedling functional traits differ between distribution groups, which require further research. Our results support the view that early life stages are critical to population dynamics and thus can influence species’ geographical ranges. The wider responses to climatic conditions in widespread species may have facilitated their spread across the Alps. Our results also suggest that all Saxifraga species face a considerable threat from climate warming due to their overall cold-adapted recruitment niche.
Comparison Between Effects of Four Crystalloid Solutions on Acid-Base and Electrolyte Abnormalities in Stranded Juvenile Loggerhead Sea Turtles (Caretta caretta)

Dehydration, electrolyte abnormalities, and acid-base alterations are common findings in stranded sea turtles. Fluid therapy is essential for reestablishment of homeostasis. The aim of this study was to compare the efficacy and effects on acid-base and electrolyte status of four different crystalloids (0.9% NaCl solution, 0.9% NaCl and lactated Ringer's solutions 1:1 ratio, Plasmalyte, and Jarchow's solution) in 63 stranded juvenile loggerhead turtles (Caretta caretta). Crystalloid fluids were administered intracoelomically on the day of admission for a duration of three consecutive days at a rate of 20 mL/kg/day through the inguinal fossa. Blood samples were collected at three timepoints: on admission, 24 h after discontinuing fluid therapy and prior to release. Samples were analyzed using a portable electronic blood analyzer for pH, pCO2, pO2, bicarbonate, lactate, sodium, potassium, chloride, glucose, and BUN concentration. Thirty-four loggerhead turtles (53.9%) had some type of acid-base alteration at the time of admission. The combination of 0.9% NaCl and lactated Ringer's solutions resulted in the highest percentage of improved/resolved acid-base and electrolyte abnormalities (33.4 % more animals with normal acid-base status compared to the admission time) compared to Jarchow's solution, which was the least effective (15.8% decrease in the number of animals with normal acid-base status compared to the admission time). This study constitutes the second controlled study of fluid therapy in sea turtles, and corroborates the recommendation made previously on the use of 0.9% NaCl + lactated Ringer solution to resolve mild to moderate acid-base alterations in juvenile loggerhead turtles. In addition, convalescent acid-base, electrolyte and plasma biochemical reference intervals are also provided as a standard profile for sea turtle rehabilitation centers.
Heterogeneous Skeletal Muscle Cell and Nucleus Populations Identified by Single-Cell and Single-Nucleus Resolution Transcriptome Assays

Single-cell RNA-seq (scRNA-seq) has revolutionized modern genomics, but the large size of myotubes and myofibers has restricted use of scRNA-seq in skeletal muscle. For the study of muscle, single-nucleus RNA-seq (snRNA-seq) has emerged not only as an alternative to scRNA-seq, but as a novel method providing valuable insights into multinucleated cells such as myofibers. Nuclei within myofibers specialize at junctions with other cell types such as motor neurons. Nuclear heterogeneity plays important roles in certain diseases such as muscular dystrophies. We survey current methods of high-throughput single cell and subcellular resolution transcriptomics, including single-cell and single-nucleus RNA-seq and spatial transcriptomics, applied to satellite cells, myoblasts, myotubes and myofibers. We summarize the major myonuclei subtypes identified in homeostatic and regenerating tissue including those specific to fiber type or at junctions with other cell types. Disease-specific nucleus populations were found in two muscular dystrophies, FSHD and Duchenne muscular dystrophy, demonstrating the importance of performing transcriptome studies at the single nucleus level in muscle.
Speech Assistant System With Local Client and Server Devices to Guarantee Data Privacy

Users of speech assistant systems have reservations about the distributed approach of these systems. They have concerns that people might get access to the transmitted speech data or that somebody is able to access their microphone from outside. Therefore, we investigate the concept of a setup with local client and server systems. This comes along with the requirement of cost-efficient realizations of client and server. We examined a number of different cost-efficient server solutions depending on the required recognition capability of specific applications. A fairly cost-efficient solution is the use of a small computing device for recognizing a few dozens of words with a GMM-HMM based recognition. To perform a DNN-HMM based recognition, we looked at small computing devices with an integrated additional graphical processor unit (GPU). Furthermore, we investigated the use of low-cost PCs for implementing real-time versions of the Kaldi framework to allow the recognition of large vocabularies. We investigated the control of a smart home by speech as an exemplary application. For this, we designed compact client systems that can be integrated at certain places inside a room, e.g., in a standard outlet socket. Besides activating a client by a sensor that detects approaching people, the recognition of a spoken wake-up word is the usual way for activation. We developed a keyword recognition algorithm that can be implemented in the client despite its limited computing resources. The control of the whole dialogue has been integrated in our client, so that no further server is needed. In a separate study, we examined the approach of an extremely energy-efficient realization of the client system without the need of an external power supply. The approach is based on using a special microphone with an additional low-power operating mode detecting the exceeding of a preset sound level threshold only. This detection can be used to wake up the client's microcontroller and to make the microphone switch to normal operating mode. In the listening mode, the energy consumption of the microphone is so low that a client system can be active for months with an energy supply from standard batteries only.
Accurate 16S Absolute Quantification Sequencing Revealed Vaginal Microecological Composition and Dynamics During Mixed Vaginitis Treatment With Fufang FuRong Effervescent Suppository

Background The diagnosis and treatment of mixed vaginitis are more complicated than single pathogenic infections, and there may be adverse reactions and several contraindications to conventional antibiotic therapy. Therefore, this study aimed to evaluate the preliminary effects of Fufang Furong Effervescent Suppository for the management of aerobic vaginitis (AV) mixed with bacterial vaginosis (BV) using Accurate 16S absolute quantification sequencing (Accu16S). Methods In the present randomized, blind, multi-center clinical trial, women (20 to 55 years) who had received a diagnosis of AV+BV were randomly assigned into clindamycin positive control (n = 41) and Fufang Furong Effervescent Suppository (n = 39) groups. The follow-up occurred in three time periods (V1: -2~0 days; V2: 15-17 days; V3: 40 ± 3 days). At each visit, two vaginal swabs, one for clinical evaluation and one for laboratory examination, were taken from each patient. The Nugent score, Donders’ score, drug-related complications, recurrence rates, and microecological changes of vaginal swabs were assessed in the time three periods. Results At baseline, the two groups were similar in frequency of presentation with vaginal burning, odor, abnormal discharge, and itching. No meaningful differences in Nugent and Donders’ scores were detected between the two groups at stage V2 (Nugent: p = 0.67; Donders’: p = 0.85) and V3 (Nugent: p = 0.97; Donders: p = 0.55). The Furong group presented fewer complications compared to the Clindamycin group. However, this difference was not statistically significant (p = 0.15). Additionally, Accu16S indicated that the total abundance of bacteria in both groups sharply decreased in stage V2, but slightly increased in V3. In stage V3, the absolute abundance of Lactobacillus in the Furong group was considerably higher compared to untreated samples (p < 0.05). On the other hand, no momentous increase was detected in the Clindamycin group (p > 0.05). Conclusion Fufang Furong Effervescent Suppository can be as effective as clindamycin cream in the management of AV+BV while may restore the vagina microecosystem better.
Diagnostic Accuracy of Magnetic Resonance Enterography for the Evaluation of Active and Fibrotic Inflammation in Crohn’s Disease

Background Despite the success of standard magnetic resonance enterography (MRE) in detecting Crohn’s disease (CD), characterization of strictures and, thus, therapy guidance is still limited. The aim of the study was to determine diagnostic accuracy of MRE in detecting or ruling out active inflammation and identifying fibrotic lesions in patients with terminal ileal CD with histopathology as reference. Methods Sixty-seven consecutive patients (median age 32 years, range 19–79 years) with terminal ileal CD were retrospectively enrolled between January 2015 and October 2020. The median interval between MRE and surgery was 9 days (range 0–86 days). Sensitivity, specificity, positive and negative predictive value (PPV and NPV, respectively), and area under the curve (AUC) with 95% confidence intervals (CIs) were calculated for the MRE-based AIS (acute inflammation score) using the histopathology of surgical specimens as the reference standard. Results Sensitivity, specificity, PPV, and NPV for detecting or ruling out active inflammation were 100% (CI, 0.94–1.00; 0.44–1.00; 0.93–1.00; 0.31–1.00) using an AIS cut-off of >4.1. AUC was 1.00 (CI, 1.00–1.00; p < 0.01). In all patients with fibrotic changes only and no active inflammation, AIS was <4.1. Interobserver agreement was substantial (κ = 0.65, p < 0.01). Conclusion Our study has shown an excellent diagnostic performance of the MRE-based AIS for determining whether active inflammation is present or lesions are due to chronic changes in ileal CD using the histopathology of surgical specimens as reference. These findings indicate that the MRE-based AIS allows a better determination of the inflammatory stage of terminal ileal CD, which facilitates the decision to perform surgery.
Factor Structure of an ICF-Based Measure of Activity and Participations for Adults in Taiwan's Disability Eligibility Determination System

To assess activity and participation for adults in Taiwan's Disability Eligibility Determination System (DEDS), we developed a measure, the Functioning Disability Evaluation Scale—Adult version (FUNDES-Adult), based on the 36-item interviewer-administered version of the WHO Disability Assessment Schedule 2.0. The purpose of this study was to examine the factor structures of performance and capability dimensions of the FUNDES-Adult. This study followed a methodology research design to investigate the construct validity of the two dimensions of the FUNDES-Adult. Two samples were randomly stratified from the databank of adults with disabilities to examine structural validity by the exploratory factor analysis (EFA) (n = 8,730, mean age of 52.9 ± 16.81) and the confirmatory factor analysis (CFA) (n = 500, mean age of 54.3 ± 16.81). The results demonstrated that the EFA yielded 5-factor structures for both performance dimension (73.5% variance explained) and capability dimension (75.9% variance explained). The CFA indicated that the second-order factor structures of both dimensions were more parsimonious with adequate fit indices (GFI, NFI, CFI, and TLI ≥ 0.95, RMSEA < 0.09). The results of this study provide evidence that the FUNDES-Adult has acceptable structural validity for use in Taiwan's DEDS. Utility of the FUNDES-Adult in rehabilitation, employment, welfare, and long-term care services needs further study.
Transport and Barrier Functions in Rainbow Trout Trunk Skin Are Regulated by Environmental Salinity

The mechanisms underpinning ionic transport and barrier function have been relatively well characterised in amphibians and fish. In teleost fish, these processes have mostly been characterised in the gill and intestine. In contrast, these processes remain much less clear for the trunk skin of fish. In this study, we measured barrier function and active transport in the trunk skin of the rainbow trout, using the Ussing chamber technique. The effects of epithelial damage, skin region, salinity, and pharmacological inhibition were tested. Skin barrier function decreased significantly after the infliction of a superficial wound through the removal of scales. Wound healing was already underway after 3 h and, after 24 h, there was no significant difference in barrier function towards ions between the wounded and control skin. In relation to salinity, skin permeability decreased drastically following exposure to freshwater, and increased following exposure to seawater. Changes in epithelial permeability were accompanied by salinity-dependent changes in transepithelial potential and short-circuit current. The results of this study support the idea that barrier function in rainbow trout trunk skin is regulated by tight junctions that rapidly respond to changes in salinity. The changes in transepithelial permeability and short circuit current also suggest the presence of an active transport component. Immunostaining and selective inhibition suggest that one active transport component is an apical V-ATPase. However, further research is required to determine the exact role of this transporter in the context of the trunk skin.
Low Dose Gamma Irradiation of Trypanosoma evansi Parasites Identifies Molecular Changes That Occur to Repair Radiation Damage and Gene Transcripts That May Be Involved in Establishing Disease in Mice Post-Irradiation

The protozoan parasite Trypanosoma evansi is responsible for causing surra in a variety of mammalian hosts and is spread by many vectors over a wide geographical area making it an ideal target for irradiation as a tool to study the initial events that occur during infection. Parasites irradiated at the representative doses 100Gy, 140Gy, and 200Gy were used to inoculate BALB/c mice revealing that parasites irradiated at 200Gy were unable to establish disease in all mice. Cytokine analysis of mice inoculated with 200Gy of irradiated parasites showed significantly lower levels of interleukins when compared to mice inoculated with non-irradiated and 100Gy irradiated parasites. Irradiation also differentially affected the abundance of gene transcripts in a dose-dependent trend measured at 6- and 20-hours post-irradiation with 234, 325, and 484 gene transcripts affected 6 hours post-irradiation for 100Gy-, 140Gy- and 200Gy-irradiated parasites, respectively. At 20 hours post-irradiation, 422, 381, and 457 gene transcripts were affected by irradiation at 100Gy, 140Gy, and 200Gy, respectively. A gene ontology (GO) term analysis was carried out for the three representative doses at 6 hours and 20 hours post-irradiation revealing different processes occurring at 20 hours when compared to 6 hours for 100Gy irradiation. The top ten most significant processes had a negative Z score. These processes fall in significance at 140Gy and even further at 200Gy, revealing that they were least likely to occur at 200Gy, and thus may have been responsible for infection in mice by 100Gy and 140Gy irradiated parasites. When looking at 100Gy irradiated parasites 20 hours post-irradiation processes with a positive Z score, we identified genes that were involved in multiple processes and compared their fold change values at 6 hours and 20 hours. We present these genes as possibly necessary for repair from irradiation damage at 6 hours and suggestive of being involved in the establishment of disease in mice at 20 hours post-irradiation. A potential strategy using this information to develop a whole parasite vaccine is also postulated.
Association Between Antioxidant Nutrients, Oxidative Stress-Related Gene Polymorphism and Skeletal Fluorosis in Guizhou, China

Background Oxidative stress plays an important role in the pathogenesis of endemic fluorosis. We analyzed associations between oxidative stress-related gene polymorphisms (PON1 rs662, CAT rs769217, rs2300182, and SOD2 rs11968525) and skeletal fluorosis, and examined potential gene–environment interactions with dietary vitamin C, vitamin E, zinc, and selenium intake. Methods A cross-sectional study was conducted in the Zhijin County, Guizhou Province of China. Skeletal fluorosis was identified according to the Chinese Diagnostic Criteria of Endemic Skeletal Fluorosis. Dietary information was assessed through face-to-face interviews by trained interviewers using a 75-item food frequency questionnaire. The genotype was detected by high throughput TaqMan-MGB RT-PCR technology. Odds ratios (ORs) and 95% CIs were calculated using an unconditional logistic regression model. Results Intake of vitamin E, zinc, and selenium was found to be inversely associated with the risk of skeletal fluorosis. The multivariable-adjusted ORs were 0.438 (95% CI: 0.268 to 0.715, P-trend < 0.001) for vitamin E, 0.490 (95% CI: 0.298 to 0.805, P-trend = 0.001) for zinc, and 0.532 (95% CI: 0.324 to 0.873, P-trend = 0.010) for selenium when comparing the highest with the lowest quartile. The relationship for vitamin C was not observed after adjustment for risk factors. Furthermore, participants with PON1 rs662 AA genotype had a significantly decreased risk of skeletal fluorosis compared with those with the GG genotype (OR = 0.438, 95% CI: 0.231 to 0.830). GG + AG genotype carriers were 2.212 times more likely to have skeletal fluorosis than AA carriers (OR = 2.212, 95% CI: 1.197 to 4.090). Compared with AA carriers, AG carriers had a 2.182 times higher risk of skeletal fluorosis (OR = 2.182, 95% CI: 1.143 to 4.163). Although we observed the risk of skeletal fluorosis was higher with a lower intake of antioxidant nutrients, the potential interactions between nutrient intake and genetic polymorphisms were not observed. Conclusion Participants with a higher intake of vitamin E, zinc, and selenium have a lower likelihood of skeletal fluorosis. In addition, the PON1 rs662 polymorphism is related to skeletal fluorosis.
Preparation of High-Specific Surface Area-Activated Carbon with Oil-Bearing Mud Residue

Oil-bearing mud residue is a hazardous waste composed of minerals, mineral oil, and water. It is characterized by a high yield and a high content of heavy oil. It is not comprehensively utilized and is difficult to process. The primary sources are oil sludge and oil sand from petroleum exploration and development and from petrochemical production. Oil-bearing mud residue is declared a hazardous waste by Chinese law. Thus, its treatment and application is a problem requiring an immediate solution for petroleum and petrochemical industries. Using oil-bearing mud residue as feedstock and NaOH as the activator this study demonstrates production of activated carbon with high specific surface area. Features of this activated carbon include a specific surface area up to 2,700 m2/g and even pore size. Average pore size is less than 2 nm and total pore volume exceeds 2 cm3/g. This method provides a new approach for recycling oil-bearing mud residue.