Miracle-dz/UniFAR-FTUs huggingface dataset:
Varied Relationship of Lipid and Lipoprotein Profiles to Liver Fat Content in Phenotypes of Metabolic Associated Fatty Liver Disease

Background Progressive overloads of intrahepatic triglycerides are related to metabolic dysregulation of multiple lipid and lipoprotein profiles, but whether similar dose effects are found in each subtype of metabolic associated fatty liver disease (MAFLD) remains unclear. We aimed to characterize the lipid profiles associated with liver fat content (LFC) in MAFLD patients who were overweight, lean/normal weight, or had diabetes. Methods We conducted a cross-sectional study enrolling 1,182 consecutive participants (144 non-MAFLD and 1,038 MAFLD) who underwent MRI proton density fat fraction measurement (MRI-PDFF) from 2011 to 2020. Lipid and apolipoprotein profiles, free fatty acid (FFA), liver and metabolism parameters, and anthropometric measurements were also assessed. Results MAFLD patients with type 2 diabetes or overweight/obesity had a higher proportion of abnormal lipid and lipoprotein profiles than those who were lean/normal weight. The degree of LFC had a positive correlation with total cholesterol, triglyceride, ApoB, and ApoE in patients with overweight/obesity and type 2 diabetes. In those with overweight/obesity, there were dose–response relationships between moderate-to-severe steatosis and total cholesterol, triglyceride, HDL-c, LDL-c, ApoB, ApoE, and Lp(a). A similar trend was observed for triglyceride in those with type 2 diabetes and for HDL-c in patients who were lean/normal weight (all p for trend <0.05). The combined model of relative lipid-related markers performed well in the prediction of moderate-to-severe steatosis (AUC: 0.762 for overweight/obesity; 0.742 for lean/normal weight). Conclusion LFC was associated with lipid profiles, including triglyceride, LDL-c, ApoB, ApoE, and FFA. These relationships were varied by the phenotype of MAFLD according to its diagnostic flow.
Can Compulsory Ecological Compensation for Land Damaged by Mining Activities Mitigate CO2 Emissions in China?

Chinese government has proposed a national contribution plan that involves achieving the peak CO2 emissions by 2030 and carbon neutrality by 2060. To explore the pathway of achieving carbon neutrality, we tried to use resources taxes and land reclamation deposits as compulsory ecological compensation (CEC). In order to test if CEC can affect CO2 emissions, energy intensity was selected as the intermediate variable. We found that the CO2 emissions trend in China is consistent with environmental Kuznets curve hypothesis and proved that CEC displayed a spillover effect on energy intensity. Likely, energy intensity presented a spillover effect on CO2 emissions. Therefore, CEC will spatially affect CO2 emissions. The generalized spatial two-stage least-squares estimate model was used to identify the impact mechanism of coal production on energy intensity with CEC as the instrumental variable. The results indicated that reducing coal production in neighboring regions may cause the mitigation of local CO2 emissions. Finally, regression analyses carried out by region suggested regional cooperation should be carried out in the process of carbon mitigation.
Experiences and Perceived Self-Efficacy in Distance Learning Among Teachers of Students With Special Educational Needs

The COVID-19 pandemic has had a great impact on school learning so far, creating a new and potentially stressful situation during school closures for teachers and students. The sudden switch to distance learning might have been especially hard to cope with for students with special educational needs (SEN). Teachers of student with SEN might thus face greater obstacles when establishing and dealing with distance learning. Teachers' self-efficacy (TSE) is a well-known factor for students' academic achievement and motivation. Little is yet known about TSE in distance learning, especially not with students with SEN. The present study aimed to investigate the experiences and the perceived TSE in distance learning of teachers teaching students with SEN at special schools and inclusive schools during the COVID-19 pandemic in Germany during June 2020 and January 2021. N = 96 teachers from both special schools and inclusive schools were involved in the study and were asked to complete a self-report online questionnaire. The study follows an exploratory design to give a first overview of the experiences of teachers of students with SEN and their TSE during the school closures and distance learning. Results showed that no major difference in overall teaching experiences could be found between teachers teaching at special schools or inclusive schools. The identification of difficulties in reading at distance and the support of students with difficulties in reading at distance was perceived by the teachers as most difficult. Difficulties in writing was being rated significantly less easy to identify at distance than difficulties in mathematics. Further, the support of students with difficulties in mathematics was perceived as being significant more challenging than the identification of difficulties in mathematics. TSE in distance learning was rather low, regardless if the teachers taught at a special school or inclusive school in this time period. TSE correlated positively with the perceived goodness of identification of difficulties and support of students with difficulties in reading, writing, and mathematics. Possible reasons and implications are discussed as well as implications of the overall results for distance learning of students with SEN.
Novel Partial Exon 51 Deletion in the Duchenne Muscular Dystrophy Gene Identified via Whole Exome Sequencing and Long-Read Whole-Genome Sequencing

Duchenne muscular dystrophy (DMD), one of the most common progressive and severely disabling neuromuscular diseases in children, can be largely attributed to the loss of function of the DMD gene on chromosome Xp21.2-p21.1. This paper describes the case of a 10-year-old boy diagnosed with DMD. Whole exome sequencing confirmed the hypothesized large partial exonic deletion of c.7310-11543_7359del (chrX:g.31792260_31803852del) spanning exon 51 and intron 50 in DMD. This large deletion was verified to be de novo by PCR, and the two breakpoints were further confirmed by Sanger sequencing and long-read whole-genome sequencing. Notably, this partial exonic deletion was the only complex variation in the deep intron regions or intron–exon junction regions in DMD. In addition, the case study demonstrates the clinical importance of using multiple molecular genetic testing methods for the diagnosis of rare diseases.
Effect of Weekly Long-Acting Growth Hormone Replacement Therapy Compared to Daily Growth Hormone on Children With Short Stature: A Meta-Analysis

Background We performed a meta-analysis to evaluate the efficacy and safety of weekly long-acting growth hormone replacement therapy compared to daily growth hormone in children with short stature. Methods A systematic literature search up to April 2021 was performed and 11 studies included 1,232 children with short stature treated with growth hormone replacement therapy at the start of the study; 737 of them were using weekly long-acting growth hormone replacement therapy and 495 were using daily growth hormone. They were reporting relationships between the efficacy and safety of long-acting growth hormone replacement therapy and daily growth hormone in children with short stature. We calculated the odds ratio (OR), and mean difference (MD) with 95% confidence intervals (CIs) to assess the efficacy and safety of weekly long-acting growth hormone replacement therapy compared to daily growth hormone in children with short stature using the dichotomous or continuous method with a random or fixed-effect model. Results Long-acting growth hormone replacement therapy had significantly lower height standard deviation scores chronological age (MD, −0.10; 95% CI, −0.13 to −0.08, p <0.001), and insulin-like growth factor binding protein-3 (MD, −0.69; 95% CI, −1.09 to −0.30, p <0.001) compared to daily growth hormone in children with short stature. However, growth hormone replacement therapy had no significantly difference in height velocity (MD, −0.09; 95% CI, −0.69–0.5, p = 0.76), height standard deviation scores bone age (MD, −0.04; 95% CI, −0.10–0.02, p = 0.16), insulin-like growth factor 1 standard deviation scores (MD, 0.26; 95% CI, −0.26–0.79, p = 0.33), and incidence of adverse events (OR, 1.16; 95% CI, 0.90–1.50, p = 0.25) compared to daily growth hormone in children with short stature. Conclusions Long-acting growth hormone replacement therapy had significantly lower height standard deviation scores chronological age, and insulin-like growth factor binding protein-3 compared to daily growth hormone in children with short stature. However, growth hormone replacement therapy had no significant difference in height velocity, height standard deviation scores bone age, insulin-like growth factor 1 standard deviation scores, and incidence of adverse events compared to daily growth hormone in children with short stature. Further studies are required to validate these findings.
Automated multi-target tracking with kinematic and non-kinematic information

The authors address an automated multi-target tracking (MTT) problem. In particular, our study is focused on robust data association considering an additional feature and the reliable track management by avoiding track duplications. As the additional feature, the amplitude information is combined with position measurements to improve the performance of the data association so as to effectively distinguish target-originated measurements from clutters. Because of its form of signal-to-noise ratio (SNR), which is often fluctuated according to targets' aspect and effective radar cross section, the usage of the amplitude information is not straightforward. To reduce the certain level of uncertainty of the SNR, the authors propose the SNR estimation algorithm. Moreover, the authors avoid the track duplication problem to achieve the reliability of track maintenance. Specifically, the authors solve the problem by exploiting well-known mean shift algorithm to merge duplications into appropriate clusters. Simulation results demonstrate the effectiveness and high estimation accuracy of the proposed MTT filter compared to existing methods.
Tropheryma whipplei Detection by Nanopore Sequencing in Patients With Interstitial Lung Disease

Tropheryma whipplei is a bacterium associated with Whipple’s disease, which commonly manifests as weight loss, arthralgia, and diarrhea. The most frequently involved organs comprise the heart and eyes, in addition to the central nervous system. Few studies have explored the relationship between T. whipplei and pneumonia. Herein, we report three patients with interstitial lung disease (ILD) of unknown cause, whose bronchoalveolar lavage fluid (BALF) were evaluated via Nanopore sequencing. In our in-house BALF Nanopore platform, human DNA was removed with saponin, to improve the reads ratio of microorganisms/host. T. whipplei was the sole or most abundant pathogen in all the patients, comprising 1,385, 826, and 285 reads. The positive result was confirmed via quantitative polymerase chain reaction (PCR) with two pairs of primers (cycle threshold value: 33.26/36.29; 31.68/32.01; 28.82/28.80) and Sanger sequencing. To our knowledge, this is the first report of T. whipplei detection using Nanopore-based sequencing. The turnaround time was approximately 6–8 h in clinical laboratories, including less than 1 h for analysis. In conclusion, the results of this study confirm that Nanopore sequencing can rapidly detect rare pathogens, to improve clinical diagnosis. In addition, diagnosis of Whipple’s disease should be combined other laboratory findings, such as periodic acid-Schiff (PAS) staining, and considered a possibility in middle-aged men presenting with ILD and a clinical history of unexplained arthralgia and/or fever.
Revealing Sea Turtle Behavior in Relation to Fishing Gear Using Color-Coded Spatiotemporal Motion Patterns With Deep Neural Networks

Incidental capture, or bycatch, of marine species is a global conservation concern. Interactions with fishing gear can cause mortality in air-breathing marine megafauna, including sea turtles. Despite this, interactions between sea turtles and fishing gear—from a behavior standpoint—are not sufficiently documented or described in the literature. Understanding sea turtle behavior in relation to fishing gear is key to discovering how they become entangled or entrapped in gear. This information can also be used to reduce fisheries interactions. However, recording and analyzing these behaviors is difficult and time intensive. In this study, we present a machine learning-based sea turtle behavior recognition scheme. The proposed method utilizes visual object tracking and orientation estimation tasks to extract important features that are used for recognizing behaviors of interest with green turtles (Chelonia mydas) as the study subject. Then, these features are combined in a color-coded feature image that represents the turtle behaviors occurring in a limited time frame. These spatiotemporal feature images are used along a deep convolutional neural network model to recognize the desired behaviors, specifically evasive behaviors which we have labeled “reversal” and “U-turn. ” Experimental results show that the proposed method achieves an average F1 score of 85% in recognizing the target behavior patterns. This method is intended to be a tool for discovering why sea turtles become entangled in gillnet fishing gear.
Substance Use Affects Type 1 Diabetes Pancreas Pathology: Implications for Future Studies

Access to human pancreas samples from organ donors has greatly advanced our understanding of type 1 diabetes pathogenesis; however, previous studies have shown that donors have a high rate of substance use, and its impact on pancreatic histopathology in this disease is not well described. One-hundred-thirty-one type 1 diabetes and 111 control organ donor pancreata from persons 12-89 years of age (mean 29.8 ± 15.5 years) within the Network for Pancreatic Organ donors with Diabetes (nPOD) were examined for insulin positivity, insulitis, amyloid staining, acute and chronic pancreatitis, and chronic exocrine changes (acinar atrophy, fibrosis, fatty infiltration, or periductal fibrosis); findings were compared by history of substance use. A secondary analysis compared exocrine pancreatic histopathologic findings in type 1 diabetes versus control organ donors regardless of substance use history. We observed a high but congruent rate of substance use in type 1 diabetes and control organ donors (66.4% and 64% respectively). Among donors with type 1 diabetes (but not controls), islet amyloid (OR 9.96 [1.22, 81.29]) and acute pancreatitis (OR 3.2 [1.06, 9.63]) were more common in alcohol users while chronic exocrine changes (OR 8.86 [1.13, 69.31]) were more common in cocaine users. Substance use impacted the pancreata of donors with type 1 diabetes more than controls. Overall, despite similar rates of substance use, acute pancreatitis (15.3% versus 4.5%, p=0.0061), chronic pancreatitis (29.8% versus 9.9%, p=0.0001), and chronic exocrine changes (73.3% versus 36.9%, p<0.0001) were more common in type 1 diabetes donors than controls. Alcohol and/or cocaine use in type 1 diabetes organ donors increases exocrine pancreas pathology and islet amyloid deposition but does not affect insulitis or insulin positivity. Exocrine pathology in type 1 diabetes donors is common, and further study of the pathophysiology of these changes is needed.
A Novel Bioimpedance-Based Detection of Miltefosine Susceptibility Among Clinical Leishmania donovani Isolates of the Indian Subcontinent Exhibiting Resistance to Multiple Drugs

The extent of susceptibility towards miltefosine (Mil), amphotericin B (AmpB), and paromomycin (Paro) was measured among 19 clinical isolates of Leishmania donovani (LD). Thirteen of these clinical isolates were reported to exhibit low susceptibility towards sodium stibogluconate (SSG-R), while six of them were highly susceptible (SSG-S). The degree of clearance of amastigotes (EC50) for these predefined SSG-R- and SSG-S-infected macrophages was determined against Mil, AmpB, and Paro. Two out of the 13 SSG-R isolates (BHU575 and BHU814) showed low susceptibility towards all three drugs studied, while the rest of the 11 SSG-R isolates showed varying degrees of susceptibility either towards none or only towards individual drugs. Interestingly, all the SSG-S isolates showed high susceptibility towards Mil/AmpB/Paro. The total intracellular non-protein thiol content of the LD promastigotes, which have been previously reported to be positively co-related with EC50 towards SSG, was found to be independent from the degree of susceptibility towards Mil/AmpB/Paro. Impedance spectra analysis, which quantifies membrane resistance, revealed lower impedimetric values for all those isolates exhibiting low efficacy to Mil (Mil-R). Our analysis points out that while non-protein thiol content can be an attribute of SSG-R, lower impedimetric values can be linked with lower Mil susceptibility, although neither of these parameters seems to get influenced by the degree of susceptibility towards AmpB/Paro. Finally, a correlation analysis with established biological methods suggests that impedance spectral analysis can be used for the accurate determination of lower Mil susceptibility among LD isolates, which is further validated in the LD-infected in vivo hamster model.
Competition Drives Group Formation and Reduces Within Nest Relatedness in a Facultatively Social Carpenter Bee

Animals respond to competition among kin for critical breeding resources in two ways: avoidance of direct fitness costs via dispersal of siblings to breed separately, and formation of kin-based societies in which subordinates offset direct fitness costs of breeding competition via altruism and increased indirect fitness. In the facultatively social eastern carpenter bee, nests are a critical breeding resource in perpetually short supply, leading to strong competition among females. Observations of individually marked and genotyped females in conditions of high and low resource competition demonstrate that competition leads to resource sharing and group nesting. However, in contrast to almost all known animal societies, females avoid nesting with relatives, and disperse from their natal nests to join social groups of non-relatives. This is the first example of a structured insect society with cooperation nestmates, the majority of which are unrelated; thus cooperation is more likely based on selection for direct, rather than indirect fitness. By forming social groups of non-kin, females avoid the indirect fitness costs of kin competition among sisters, yet increase their chances of successful reproduction, and thus direct fitness, when forming colonies of non-relatives.
Comparison of Gene Expression Between Resistant and Susceptible Families Against VPAHPND and Identification of Biomarkers Used for Resistance Evaluation in Litopenaeus vannamei

Acute hepatopancreatic necrosis disease (AHPND) has caused a heavy loss to shrimp aquaculture since its outbreak. Vibrio parahaemolyticus (VPAHPND) is regarded as one of the main pathogens that caused AHPND in the Pacific white shrimp Litopenaeus vannamei. In order to learn more about the mechanism of resistance to AHPND, the resistant and susceptible shrimp families were obtained through genetic breeding, and comparative transcriptome approach was used to analyze the gene expression patterns between resistant and susceptible families. A total of 95 families were subjected to VPAHPND challenge test, and significant variations in the resistance of these families were observed. Three pairs of resistant and susceptible families were selected for transcriptome sequencing. A total of 489 differentially expressed genes (DEGs) that presented in at least two pairwise comparisons were screened, including 196 DEGs highly expressed in the susceptible families and 293 DEGs in the resistant families. Among these DEGs, 16 genes demonstrated significant difference in all three pairwise comparisons. Gene set enrichment analysis (GSEA) of all 27,331 expressed genes indicated that some energy metabolism processes were enriched in the resistant families, while signal transduction and immune system were enriched in the susceptible families. A total of 32 DEGs were further confirmed in the offspring of the detected families, among which 19 genes were successfully verified. The identified genes in this study will be useful for clarifying the genetic mechanism of shrimp resistance against Vibrio and will further provide molecular markers for evaluating the disease resistance of shrimp in the breeding program.
Complete Chloroplast Genome Sequence of Erigeron breviscapus and Characterization of Chloroplast Regulatory Elements

Erigeron breviscapus is a famous medicinal plant. However, the limited chloroplast genome information of E. breviscapus, especially for the chloroplast DNA sequence resources, has hindered the study of E. breviscapus chloroplast genome transformation. Here, the complete chloroplast (cp) genome of E. breviscapus was reported. This genome was 152,164bp in length, included 37.2% GC content and was structurally arranged into two 24,699bp inverted repeats (IRs) and two single-copy areas. The sizes of the large single-copy region and the small single-copy region were 84,657 and 18,109bp, respectively. The E. breviscapus cp genome consisted of 127 coding genes, including 83 protein coding genes, 36 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. For those genes, 95 genes were single copy genes and 16 genes were duplicated in two inverted regions with seven tRNAs, four rRNAs, and five protein coding genes. Then, genomic DNA of E. breviscapus was used as a template, and the endogenous 5' and 3' flanking sequences of the trnI gene and trnA gene were selected as homologous recombinant fragments in vector construction and cloned through PCR. The endogenous 5' flanking sequences of the psbA gene and rrn16S gene, the endogenous 3' flanking sequences of the psbA gene, rbcL gene, and rps16 gene and one sequence element from the psbN-psbH chloroplast operon were cloned, and certain chloroplast regulatory elements were identified. Two homologous recombination fragments and all of these elements were constructed into the cloning vector pBluescript SK (+) to yield a series of chloroplast expression vectors, which harbored the reporter gene EGFP and the selectable marker aadA gene. After identification, the chloroplast expression vectors were transformed into Escherichia coli and the function of predicted regulatory elements was confirmed by a spectinomycin resistance test and fluorescence intensity measurement. The results indicated that aadA gene and EGFP gene were efficiently expressed under the regulation of predicted regulatory elements and the chloroplast expression vector had been successfully constructed, thereby providing a solid foundation for establishing subsequent E. breviscapus chloroplast transformation system and genetic improvement of E. breviscapus.