Miracle-dz/UniFAR-FTUs huggingface dataset:
Deciphering Novel Transcriptional Regulators of Soybean Hypocotyl Elongation Based on Gene Co-expression Network Analysis

Hypocotyl elongation is the key step of soybean seed germination, as well an important symbol of seedling vitality, but the regulatory mechanisms remain largely elusive. To address the problem, bioinformatics approaches along with the weighted gene co-expression network analysis (WGCNA) were carried out to elucidate the regulatory networks and identify key regulators underlying soybean hypocotyl elongation at transcriptional level. Combining results from WGCNA, yeast one hybridization, and phenotypic analysis of transgenic plants, a cyan module significantly associated with hypocotyl elongation was discerned, from which two novel regulatory submodules were identified as key candidates underpinning soybean hypocotyl elongation by modulating auxin and light responsive signaling pathways. Taken together, our results constructed the regulatory network and identified novel transcriptional regulators of soybean hypocotyl elongation based on WGCNA, which provide new insights into the global regulatory basis of soybean hypocotyl elongation and offer potential targets for soybean improvement to acquire cultivars with well-tuned hypocotyl elongation and seed germination vigor.
Chain Actions Generated High-Elevation and High-Relief Topography of the Eastern Margin of the Tibetan Plateau: From Deep Earth Forces to Earthquake-Induced Dams

High-elevation and high-relief topography is the most prominent geomorphological features of the eastern margin of the Tibetan Plateau. This paper proposes that the interaction of the endogenic and exogenic forces jointly determines the formation of such high and steep landform. Eastward propagation of the Tibetan Plateau has been portioned by NW-striking, large-scaled sinistral strike-slip faults due to resistance of rigid Yangtze craton to the east of the eastern margin of the Tibetan Plateau. The transpressional stress has emerged in eastern margin of the Tibetan Plateau and has resulted in several large-scale active faults. The transpressional behavior has changed the flowing direction of the rivers from NW-SE to nearly N-S. The transport capacity of these southward-flowing rivers decreases correspondingly. Since the late Cenozoic, intensive seismic events have occurred on the active faults of the eastern Tibetan Plateau which resulted in geohazards such as slope failures, landslides along these southward-flowing rivers. This resulted in the formation of a large number of dammed lakes in the eastern margin of the Tibetan Plateau. To a certain degree, these dammed lakes play an important role in lowering the upstream erosion rate and in accelerating downstream river incision which yields gravity unloading and uplift of the bedrock. The frequently and widely distributed damming events, therefore, forms an important supplementary factor with respect to the formation of high and steep landforms.
Identifying and Predicting Autism Spectrum Disorder Based on Multi-Site Structural MRI With Machine Learning

Although emerging evidence has implicated structural/functional abnormalities of patients with Autism Spectrum Disorder(ASD), definitive neuroimaging markers remain obscured due to inconsistent or incompatible findings, especially for structural imaging. Furthermore, brain differences defined by statistical analysis are difficult to implement individual prediction. The present study has employed the machine learning techniques under the unified framework in neuroimaging to identify the neuroimaging markers of patients with ASD and distinguish them from typically developing controls(TDC). To enhance the interpretability of the machine learning model, the study has processed three levels of assessments including model-level assessment, feature-level assessment, and biology-level assessment. According to these three levels assessment, the study has identified neuroimaging markers of ASD including the opercular part of bilateral inferior frontal gyrus, the orbital part of right inferior frontal gyrus, right rolandic operculum, right olfactory cortex, right gyrus rectus, right insula, left inferior parietal gyrus, bilateral supramarginal gyrus, bilateral angular gyrus, bilateral superior temporal gyrus, bilateral middle temporal gyrus, and left inferior temporal gyrus. In addition, negative correlations between the communication skill score in the Autism Diagnostic Observation Schedule (ADOS_G) and regional gray matter (GM) volume in the gyrus rectus, left middle temporal gyrus, and inferior temporal gyrus have been detected. A significant negative correlation has been found between the communication skill score in ADOS_G and the orbital part of the left inferior frontal gyrus. A negative correlation between verbal skill score and right angular gyrus and a significant negative correlation between non-verbal communication skill and right angular gyrus have been found. These findings in the study have suggested the GM alteration of ASD and correlated with the clinical severity of ASD disease symptoms. The interpretable machine learning framework gives sight to the pathophysiological mechanism of ASD but can also be extended to other diseases.
Effects and Interaction of Meteorological Parameters on Influenza Incidence During 2010–2019 in Lanzhou, China

Background Influenza is a seasonal infectious disease, and meteorological parameters critically influence the incidence of influenza. However, the meteorological parameters linked to influenza occurrence in semi-arid areas are not studied in detail. This study aimed to clarify the impact of meteorological parameters on influenza incidence during 2010–2019 in Lanzhou. The results are expected to facilitate the optimization of influenza-related public health policies by the local healthcare departments. Methods Descriptive data related to influenza incidence and meteorology during 2010–2019 in Lanzhou were analyzed. The exposure-response relationship between the risk of influenza occurrence and meteorological parameters was explored according to the distributed lag no-linear model (DLNM) with Poisson distribution. The response surface model and stratified model were used to estimate the interactive effect between relative humidity (RH) and other meteorological parameters on influenza incidence. Results A total of 6701 cases of influenza were reported during 2010–2019. DLNM results showed that the risk of influenza would gradually increase as the weekly mean average ambient temperature (AT), RH, and absolute humidity (AH) decrease at lag 3 weeks when they were lower than 12.16°C, 51.38%, and 5.24 g/m3, respectively. The low Tem (at 5th percentile, P5) had the greatest effect on influenza incidence; the greatest estimated relative risk (RR) was 4.54 (95%CI: 3.19–6.46) at cumulative lag 2 weeks. The largest estimates of RRs for low RH (P5) and AH (P5) were 4.81 (95%CI: 3.82–6.05) and 4.17 (95%CI: 3.30–5.28) at cumulative lag 3 weeks, respectively. An increase in AT by 1°C led to an estimates of percent change (95%CI) of 3.12% (−4.75% to −1.46%) decrease in the weekly influenza case counts in a low RH environment. In addition, RH showed significant interaction with AT and AP on influenza incidence but not with wind speed. Conclusion This study indicated that low AT, low humidity (RH and AH), and high air pressure (AP) increased the risk of influenza. Moreover, the interactive effect of low RH with low AT and high AP can aggravate the incidence of influenza.
Changing Oar Rotation Axis Position Increases Catch Angle During Indoor and In-Field Para-Rowing: A Randomized Crossover Trial Verified by a Repeated Measurement Trial

A long rowing stroke length is crucial for adequate rowing performance. Therefore, the relocation of the oar from traditional “in front” (NORM) to “behind the rotation axis” (GATE) may increase (para) rowing performance. Thus, 15 able-bodied rowers (21.4 ± 3.6 years; 187 ± 8 cm; 85.4 ± 8.2 kg) completed indoor TANK rowing 2 min TimeTrials (2 min-TT) of GATE and NORM in a randomized order. Additionally, one elite Paralympic oarsman (37 years, 185 cm, 67 kg) performed a multiple single case in-field BOAT testing (24x2min-TT of GATE and NORM in a randomized order). GATE revealed significantly larger catch angles during TANK (+97.1 ± 120.4%; p = 0.001, SMD = 0.84) and BOAT (+11.9 ± 3.2%; p < 0.021; SMD = 2.69; Tau-U = 0.70) compared to NORM. While total stroke length, rowing power, and work per stroke increased in GATE during TANK (p < 0.010, SMD > 0.634), no such significant changes of these performance parameters between GATE and NORM were observed during BOAT (p > 0.021; SMD < 0.58; Tau-U < 0.29). Rowing economy-related parameters (power or speed per oxygen uptake) and boat speed also showed no significant differences between GATE und NORM during BOAT (p > 0.61; SMD < 0.31; Tau-U < 0.19). The shape of the force–angle curve (position of peak force and ratio between average and maximal force) remained unaffected from GATE during both TANK (p > 0.73, SMD < 0.1) and BOAT (p > 0.63; SMD < 0.60; Tau-U < 0.27). In conclusion, GATE shifted the entire rowing stroke towards the catch (+6.6 ± 1.8°) without notably affecting relevant performance parameters during BOAT. Particularly during crew rowing, the minimization of detrimental boat movements for perfect synchrony should be aimed for. Accordingly, the combined application of GATE and NORM (for different athletes in crew boats) may be beneficial for rowing synchronization.
An Overview of Bite mark Analysis

Human bite mark analysis is by far the most demanding and complicated part of Forensic Dentistry. Although bite marks of an individual do have uniqueness due to specific characteristics and arrangement of the teeth, when it comes to bite mark analysis, it is complicated by numerous factors, being presented as a challenge to the Forensic Odontologists. The aim of this paper is to give a brief overview of bite mark analysis: its usefulness and limitations. The study and analysis of such injuries is challenging and complex. The correct protocol for collection, management, preservation, analysis and interpretation of this evidence should be employed if useful information is to be obtained for the courts.
Between-Subject and Within-Subject Variaton of Muscle Atrophy and Bone Loss in Response to Experimental Bed Rest

To improve quantification of individual responses to bed rest interventions, we analyzed peripheral quantitative computer tomography (pQCT) datasets of the lower leg of 76 participants, who took part in eight different bed rest studies. A newly developed statistical approach differentiated measurement uncertainty UMeas from between-subject-variation (BSV) and within-subject variation (WSV). The results showed that UMeas decreased 59.3–80% over the two decades of bed rest studies (p < 0.01), and that it was higher for muscles than for bones. The reduction of UMeas could be explained by improved measurement procedures as well as a higher standardization. The vast majority (89.6%) of the individual responses pci exceeded the 95% confidence interval defined by UMeas, indicating significant and substantial BSV, which was greater for bones than for muscles, especially at the epiphyseal measurement sites. Non-significant to small positive inter-site correlations between bone sites, but very large positive inter-site correlation between muscle sites suggests that substantial WSV exists in the tibia bone, but much less so in the calf musculature. Furthermore, endocortical circumference, an indicator of the individual’s bone geometry could partly explain WSV and BSV. These results demonstrate the existence of substantial BSV bone, and that it is partly driven by WSV, and likely also by physical activity and dietary habits prior to bed rest. In addition, genetic and epigenetic variation could potentially explain BSV, but not WSV. As to the latter, differences of bone characteristics and the bone resorption process could offer an explanation for its existence. The study has also demonstrated the importance of duplicate baseline measurements. Finally, we provide here a rationale for worst case scenarios with partly effective countermeasures in long-term space missions.
Disparate Associations of 24-h Central Aortic and Brachial Cuff Blood Pressure With Hypertension-Mediated Organ Damage and Cardiovascular Risk

Objective Aim of this study was to evaluate the associations of non-invasive central aortic and peripheral (brachial) blood pressure (BP) for Hypertension-mediated organ damage (HMOD) and atherosclerotic cardiovascular disease (ASCVD) risk. Methods We evaluated associations of HMOD with 24-h ambulatory blood pressure monitoring (ABPM) of central aortic and peripheral BP indices in patients with primary hypertension and presence of several cardiovascular risk factors. BP measurements were performed by means of a non-invasive automated oscillometric device (Mobil-O-Graph). HMOD was defined as the presence of carotid intima-media thickness (IMT) above normal values and/or carotid plaque, left ventricular hypertrophy (LVH), and/or renal abnormalities as assessed by urine albumin/creatinine ratio above normal values and/or estimated glomerular filtration rate (eGFR) <60 ml/min per 1.73 m2. Results In the study cohort of 273 (age 55.2 ± 13.4 years, 71.8% male) patients with primary hypertension, documented HMOD was present in 180 (65.9%), LVH in 70 (25.6%), increased IMT in 129 (47.3%). Fifty-six patients (20.5%) had kidney organ damage (20.5% albuminuria and 2.6% impaired eGFR). When accounting for confounding factors (age, sex, body-mass-index, antihypertensive treatment, smoking, triacylglycerol, statin treatment, glucose, hypoglycemic therapy, or heart rate) only peripheral 24-h pulse pressure (PP) maintained statistical significance with HMOD indices (OR: 1.126, 95% CI: 1.012~1.253; p = 0.029). Using ASCVD risk score as the independent continuous variable in multiple linear regression, 24-h central systolic pressure (SBP) (β = 0.179; 95% CI:0.019~0.387; p = 0.031), daytime central PP (β = 0.114; 95% CI:0.070~0.375; p = 0.005, night-time central SBP (β = 0.411; 95% CI:0.112~0.691; p = 0.007) and night-time PP (β = 0.257; 95% CI:0.165~0.780; p = 0.003) were all positively associated with ASCVD risk. Conclusions Blood pressure obtained by 24-h ABPM was better correlated with HMOD than office BP. Whilst 24-h peripheral BP showed a stronger association with HMOD than 24-h central BP, the prognostic value of 24-h central BP for the 10-year ASCVD risk was superior to 24-h peripheral BP.
Use of a Baculovirus-Mammalian Cell Expression-System for Expression of Drug-Metabolizing Enzymes: Optimization of Infection With a Focus on Cytochrome P450 3A4

Heterologous expression systems are important for analyzing the effects of genetic factors including single nucleotide polymorphisms on the functions of drug-metabolizing enzymes. In this study, we focused on a baculovirus-mammalian cell expression system (Bac-Mam) expression system as a safer and more efficient approach for this purpose. The baculovirus-insect cell expression system is widely utilized in large-scale protein expression. Baculovirus has been shown to also infect certain mammalian cells, although the virus only replicates in insect cells. With this knowledge, baculovirus is now being applied in a mammalian expression system called the Bac-Mam system wherein a gene-modified baculovirus is used whose promotor is replaced with one that can function in mammalian cells. We subcloned open-reading frames of cytochrome P450 3A4 (CYP3A4), UDP-glucuronosyltransferase (UGT) 1A1, and UGT2B7 into a transfer plasmid for the Bac-Mam system, and prepared recombinant Bac-Mam virus. The obtained virus was amplified in insect Sf9 cells and used to infect mammalian COS-1 cells. Expression of CYP3A4, UGT1A1, and UGT2B7 in COS-1 cell homogenates were confirmed by immunoblotting. Optimum infection conditions including the amount of Bac-Mam virus, culture days before collection, and concentration of sodium butyrate, an enhancer of viral-transduction were determined by monitoring CYP3A4 expression. Expressed CYP3A4 showed appropriate activity without supplying hemin/5-aminolevulinic acid or co-expressing with NADPH-cytochrome P450 reductase. Further, we compared gene transfer efficiency between the Bac-Mam system and an established method using recombinant plasmid and transfection reagent. Our results indicate that the Bac-Mam system can be applied to introduce drug-metabolizing enzyme genes into mammalian cells that are widely used in drug metabolism research. The expressed enzymes are expected to undergo appropriate post-translational modification as they are in mammalian bodies. The Bac-Mam system may thus accelerate pharmacogenetics and pharmacogenomics research.
Effects of Phragmites australis Shoot Remainder Silage on Growth Performance, Blood Biochemical Parameters, and Rumen Microbiota of Beef Cattle

The objective of the present study was to assess the effects of replacing corn silage with Phragmites australis shoot remainder (PSR) silage on intake, growth performance, serum biochemical parameters, and rumen microbial diversity of growing-finishing beef. Fifteen Angus beef cattle with an average body weight of 253 ± 2.94 kg were randomly divided into three groups (five replicas vs. each group vs. Angus beef cattle). The three treatments were group A fed 60% PSR silage + 40% concentrate, group B fed 30% PSR silage + 30% corn silage + 40% concentrate, and group C fed 60% corn silage + 40% concentrate. The adaptation period was 15 days, and the trial period lasted for 45 days. Results showed that the ADG was significantly higher, and FCR was significantly lower both in groups A and B compared with group C. The results of serum biochemical parameters showed that the concentration of GLU was significantly lower in group B than both groups A and C. Microbial diversity results showed that the OTUs, Shannon, Chao1, and ACE indices were significantly lower in group A compared with groups B and C. At the phyla level, the relative abundances of Tenericutes and Melainabacteria had significant differences among the three groups, and the relative abundances of Papillibacter, Anaeroplasma, and Anaerovorax had significant differences among the three groups at the genus level. Additionally, Rikenellaceae was the unique biomarker among the three groups. Furthermore, the results of function prediction showed that the gene families associated with metabolism of cofactors and vitamins, cellular processes and signaling, metabolism, biosynthesis of other secondary metabolites, infectious diseases, signaling molecules and interaction, nervous system, and digestive system were significantly decreased, while lipid metabolism was dramatically increased from groups A to C at KEGG level 2. At KEGG level 3, 11 metabolic pathways were significantly influenced among the three groups. In summary, these findings indicated that PSR silage substituted the corn silage totally or partially improved the growth performance, and altered the rumen microbial composition and diversity and the corresponding change in prediction function of rumen bacteria in Angus beef cattle.
Neurally Adjusted Ventilatory Assist vs. Conventional Mechanical Ventilation in Adults and Children With Acute Respiratory Failure: A Systematic Review and Meta-Analysis

Background Patient-ventilator asynchrony is a common problem in mechanical ventilation (MV), resulting in increased complications of MV. Despite there being some pieces of evidence for the efficacy of improving the synchronization of neurally adjusted ventilatory assist (NAVA), controversy over its physiological and clinical outcomes remain. Herein, we conducted a systematic review and meta-analysis to determine the relative impact of NAVA or conventional mechanical ventilation (CMV) modes on the important outcomes of adults and children with acute respiratory failure (ARF). Methods Qualified studies were searched in PubMed, EMBASE, Medline, Web of Science, Cochrane Library, and additional quality evaluations up to October 5, 2021. The primary outcome was asynchrony index (AI); secondary outcomes contained the duration of MV, intensive care unit (ICU) mortality, the incidence rate of ventilator-associated pneumonia, pH, and Partial Pressure of Carbon Dioxide in Arterial Blood (PaCO2). A statistical heterogeneity for the outcomes was assessed using the I2 test. A data analysis of outcomes using odds ratio (OR) for ICU mortality and ventilator-associated pneumonia incidence and mean difference (MD) for AI, duration of MV, pH, and PaCO2, with 95% confidence interval (CI), was expressed. Results Eighteen eligible studies (n = 926 patients) were eventually enrolled. For the primary outcome, NAVA may reduce the AI (MD = −18.31; 95% CI, −24.38 to −12.25; p < 0.001). For the secondary outcomes, the duration of MV in the NAVA mode was 2.64 days lower than other CMVs (MD = −2.64; 95% CI, −4.88 to −0.41; P = 0.02), and NAVA may decrease the ICU mortality (OR =0.60; 95% CI, 0.42 to 0.86; P = 0.006). There was no statistically significant difference in the incidence of ventilator-associated pneumonia, pH, and PaCO2 between NAVA and other MV modes. Conclusions Our study suggests that NAVA ameliorates the synchronization of patient-ventilator and improves the important clinical outcomes of patients with ARF compared with CMV modes.
The Relationship Between Low-Density Lipoprotein Cholesterol and Progression of Mild Cognitive Impairment: The Influence of rs6859 in PVRL2

Background: Genome-wide association studies have identified many Alzheimer’s disease (AD) genetic-risk single nucleotide polymorphisms (SNPs) and indicated the important role of the cholesterol/lipid metabolism pathway in AD pathogenesis. This study aims to investigate the effects of cholesterol and genetic risk factors on progression of mild cognitive impairment (MCI) to AD. Methods: We prospectively followed 316 MCI participants aged ≥50 years with a baseline cholesterol profile and SNP genotyping data for 4.5 years on average in a sub-cohort of the Shanghai Aging Study. Total cholesterol, low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol in serum were measured at baseline. SNP genotyping was performed using a MassARRAY system. At follow-up, consensus diagnosis of incident dementia and AD were established based on medical, neurological, and neuropsychological examinations. Cox regression models were used to assess the association of cholesterol and SNP with incident AD. Results: The AG/AA genotypes of PVRL2 rs6859 were significantly associated with increased incident AD in MCI participants, compared with GG genotype (adjusted hazard ratio [HR] 2.75, 95% confidence interval [CI] 1.32–5.76, p = .007, false discovery rate–adjusted p = .030). In PVRL2 rs6859 AG/AA carriers, each-1 mmol/L higher level of LDL-C was significantly associated with a 48% decreased risk of AD (adjusted HR 0.52, 95%CI 0.33–0.84, p = .007). Consistent results were obtained when using LDL-C as the categorical variable (P for trend = 0.016). Conclusion: The relationship between LDL-C and progression of MCI may be influenced by genetic variants.