Miracle-dz/UniFAR-FTUs huggingface dataset:
Soil Surface Micro-Topography by Structure-from-Motion Photogrammetry for Monitoring Density and Erosion Dynamics

Soil erosion is a major threat to soil fertility, food security and water resources. Besides a quantitative assessment of soil loss, the dynamics of erosion-affected arable soil surfaces still poses challenges regarding field methods and predictions because of scale-dependent and soil management-related complex soil-crop-atmosphere processes. The objective was to test a photogrammetric Structure-from-Motion (SfM) technique for the mm-scale mapping of the soil surface micro-topography that allows the monitoring without special equipment and with widely available cameras. The test was carried out in May 2018 on three plots of 1.5 m2 (upper-, middle-, and footslope) covering surface structural features (tractor wheel lane, seed rows) along a Maize-cultivated hillslope with a coarse-textured topsoil and a runoff monitoring station. The changes in mm-scaled surface micro-topography were derived from repeatedly photographed images of the same surface area during a 2-weeks period with two rain events. A freely available SfM-program (VisualSfM) and the QGIS software were used to generate 3D-models of the surface topography. Soil cores (100 cm3) were sampled to gravimetrically determine the topsoil bulk density. The micro-topographical changes resulting from rainfall–induced soil mass redistribution within the plots were determined from the differences in SfM maps before and after rain. The largest decrease in mean soil surface elevation and roughness was observed after rain for the middle slope plot and primarily in initially less compacted regions. The spatially-distributed intra-plot changes in soil mass at the mm-scale derived from the digital micro-topography models indicated that local depressions were filled with sediments from surrounding knolls during rainfall. The estimated mass loss determined with the SfM technique decreased, if core sample-based soil settlement was considered. The effect of changes in the soil bulk density could be described after calibration also with an empirical model suggested in the Root-Zone-Water-Quality-Model. Uncertainties in the presented plot-scale SfM-technique were due to geo-referencing and the numerical limitations in the freely available SfM-software. The photogrammetric technique provided valuable information on soil surface structure parameters such as surface roughness. The successful application of SfM with widely available cameras and freely available software might stimulate the monitoring of erosion in regions with limited accessibility.
COVID-19 Pandemic and Overall Mental Health of Healthcare Professionals Globally: A Meta-Review of Systematic Reviews

Objective This meta-review aimed to provide a comprehensive overview of overall mental health of healthcare professionals during the COVID-19 pandemic. Method We conducted a comprehensive literature search on Academic Search Premier, CINAHL, Cochrane Library, and MEDLINE. A predefined eligibility criterion was used to screen the articles. The methodology quality of eligible studies was assessed using Joanna Briggs Institute checklist for systematic reviews. The data were narratively synthesised in line with the meta-review aim. Result Forty systematic reviews (represented as K = 40), which reported data from 1,828 primary studies (N) and 3,245,768 participants, met the inclusion criteria. The findings from a pooled prevalence indicate that anxiety (16–41%, K = 30, N = 701), depression (14–37%, K = 28, N = 584), and stress/post-traumatic stress disorder (18.6–56.5%, K = 24, N = 327) were the most prevailing COVID-19 pandemic-related mental health conditions affecting healthcare workers. Other reported concerns included insomnia, burnout, fear, obsessive-compulsive disorder, somatization symptoms, phobia, substance abuse, and suicidal thoughts. Considering regions/countries, the highest anxiety was reported in the United-Kingdom [22.3, 95% Confidence Interval (CI):7–38, N = 4] compared to other countries, while the highest depression was in the Middle-East, (41, 95% CI:16–60, N = 5) and stress in the Eastern Mediterranean region (61.6, 95% CI:56.4–66.8, N = 2) compared to other regions. The most significant risk factors include female gender, younger age, being a nurse, and frontline professional. The most-reported coping strategies include individual/group psychological support, family/relative support, training/orientation, and the adequacy of personal protective equipment. Conclusion It was concluded that healthcare professionals (nurses, doctors, allied health) have experienced various mental health issues during COVID-19 pandemic. The meta-review, therefore, recommends targeted interventions and health policies that address specific mental health issues to support health professionals worldwide during the duration of the COVID-19 pandemic and similar future health crises. Systematic Review Registration https://www.crd. york.ac. uk/prospero/display_record. php? ID=CRD4202126200, identifier: CRD42021262001.
Genome-Wide Investigation of the Zinc Finger-Homeodomain Family Genes Reveals Potential Roles in Apple Fruit Ripening

Zinc finger-homeodomain (ZF-HD) transcription factors play an important role in the regulation of plant growth and development, as well as the regulation of stress responses. Studies on the ZF-HD family genes have been conducted in many plants, however, the characteristics of this family in apple (Malus domestica) fruit remains to be poorly understood. In this study, we identified nineteen ZF-HD family genes in apple at the whole-genome scale, which were unevenly located on ten chromosomes. These MdZF-HD genes were phylogenetically divided into two subfamilies: zinc finger-homeodomain (ZHD) and MINI ZINC FINGER (MIF), and the ZHD subfamily was further classified into five groups (ZHDI–ZHDV). Analysis of the gene structures showed that most MdZF-HD genes lack introns. Gene expression analysis indicated that nine selected MdZF-HD genes were differentially responsive to 1-MCP (1-methylcyclopropene) treatment during the postharvest storage of “Qinguan” apple fruit. Moreover, the transcripts of six genes were further validated in “Golden Delicious” apple fruit, and five genes (MdZHD1/2/6/10/11) were significantly repressed and one gene (MdZHD7) was slightly induced by ethylene treatment. These results indicated that these six MdZF-HD genes may involve in the regulation of ethylene induced ripening process of postharvest apple fruit. These findings provide new clues for further functional investigation of ZF-HD genes, such as their roles in the regulation of fruit ripening.
BECN1 F121A mutation increases autophagic flux in aged mice and improves aging phenotypes in an organ-dependent manner

Autophagy is necessary for lifespan extension in multiple model organisms and autophagy dysfunction impacts age-related phenotypes and diseases. Introduction of an F121A mutation into the essential autophagy protein BECN1 constitutively increases basal autophagy in young mice and reduces cardiac and renal age-related changes in longer-lived Becn1F121A mutant mice. However, both autophagic and lysosomal activity have been described to decline with age. Thus, whether autophagic flux is maintained during aging and whether it is enhanced in Becn1F121A mice is unknown. Here we demonstrate that old wild type mice maintained functional autophagic flux in heart, kidney and skeletal muscle but not liver, and old Becn1F121A mice had increased autophagic flux in those same organs compared to wild type. In parallel, Becn1F121A mice were not protected against age-associated hepatic phenotypes but demonstrated reduced skeletal muscle fiber atrophy. These findings identify an organ-specific role for the ability of autophagy to impact organ aging phenotypes.
GR-regulated enhancers play a central role in the gene regulatory networks underlying drug addiction

Substance abuse and addiction represent a major public health problem that impacts multiple dimensions of society, including healthcare, economy, and workforce. In 2021, over 100,000 drug overdose deaths have been reported in the US with an alarming increase in fatalities related to opioids and psychostimulants. Understanding of the fundamental gene regulatory mechanisms underlying addiction and related behaviors could facilitate more effective treatments. To explore how repeated drug exposure alters gene regulatory networks in the brain, we combined capped small (cs)RNA-seq, which accurately captures nascent-like initiating transcripts from total RNA, with Hi-C and single nuclei (sn)ATAC-seq. We profiled initiating transcripts in two addiction-related brain regions, the prefrontal cortex (PFC) and the nucleus accumbens (NAc), from rats that were never exposed to drugs or were subjected to prolonged abstinence after oxycodone or cocaine intravenous self-administration (IVSA). Interrogating over 100,000 active transcription start regions (TSRs) revealed that most TSRs had hallmarks of bona-fide enhancers and highlighted the KLF/SP1, RFX and AP1 transcription factors families as central to establish brain-specific gene regulatory programs. Analysis of rats with addiction-like behaviors versus controls identified addiction-associated repression of transcription at regulatory enhancers recognized by nuclear receptor subfamily 3 group C (NR3C) factors, which include glucocorticoid receptors. Cell-type deconvolution analysis using snATAC-seq uncovered a potential role of glial cells in driving the gene regulatory programs associated with addiction-related phenotypes. These findings highlight the power of advanced transcriptomics methods to provide insight into how addiction perturbs gene regulatory programs in the brain.
Current Status and Hospital-Level Differences in Care and Outcomes of Patients With Acute Non-ST-Segment Elevation Myocardial Infarction in China: Insights From China Acute Myocardial Infarction Registry

Background With the growing burden of non-ST-elevation myocardial infarction (NSTEMI), developing countries face great challenges in providing equitable treatment nationwide. However, little is known about hospital-level disparities in the quality of NSTEMI care in China. We aimed to investigate the variations in NSTEMI care and patient outcomes across the three hospital levels (province-, prefecture- and county-level, with decreasing scale) in China. Methods Data were derived from the China Acute Myocardial Infarction Registry on patients with NSTEMI consecutively registered between January 2013 and November 2016 from 31 provinces and municipalities throughout mainland China. Patients were categorized according to the hospital level they were admitted to. Multilevel generalized mixed models were fitted to examine the relationship between the hospital level and in-hospital mortality risk. Results In total, 8,054 patients with NSTEMI were included (province-level: 1,698 patients; prefecture-level: 5,240 patients; county-level: 1,116 patients). Patients in the prefecture- and county-level hospitals were older, more likely to be female, and presented worse cardiac function than those in the province-level hospitals (P <0.05). Compared with the province-level hospitals, the rate of invasive strategies was significantly lower in the prefecture- and county-level hospitals (65.3, 43.3, and 15.4%, respectively, P <0.001). Invasive strategies were performed within the guideline-recommended timeframe in 25.4, 9.7, and 1.7% of very-high-risk patients, and 16.4, 7.4, and 2.4% of high-risk patients in province-, prefecture- and county-level hospitals, respectively (both P <0.001). The use of dual antiplatelet therapy in the county-level hospitals (87.2%) remained inadequate compared to the province- (94.5%, P <0.001) and prefecture-level hospitals (94.5%, P <0.001). There was an incremental trend of in-hospital mortality from province- to prefecture- to county-level hospitals (3.0, 4.4, and 6.9%, respectively, P-trend <0.001). After stepwise adjustment for patient characteristics, presentation, hospital facilities and in-hospital treatments, the hospital-level gap in mortality risk gradually narrowed and lost statistical significance in the fully adjusted model [Odds ratio: province-level vs. prefecture-level: 1.23 (0.73–2.05), P = 0.441; province-level vs. county-level: 1.61 (0.80–3.26), P = 0.182; P-trend = 0.246]. Conclusions There were significant variations in NSTEMI presentation and treatment patterns across the three hospital levels in China, which may largely explain the hospital-level disparity in in-hospital mortality. Quality improvement initiatives are warranted, especially among lower-level hospitals.
Association Between Vaginal Gardnerella and Tubal Pregnancy in Women With Symptomatic Early Pregnancies in China: A Nested Case-Control Study

The early diagnosis and treatment of ectopic pregnancy (EP) remains a major challenge. Despite a known link between vaginal microbiota and female reproductive health, few studies have focused on the association between vaginal microbiota and pregnancy location. This nested case-control study aimed to characterize the vaginal microbiota in tubal pregnancy (TP) among symptomatic women in early pregnancy. Women with symptomatic early pregnancy of unknown location (PUL) were included in this study. 16S rDNA gene sequencing was performed to assess vaginal microbial diversity and relative abundance. Machine learning and multivariate logistic regression were also used to evaluate the association between Gardnerella and TP. The results indicate that the vaginal microbiome in TP was more diverse (Shannon, p < 0.05) and was different in composition to that of women with intrauterine pregnancy (IUP) (weighted Unifrac, R = 0.08, p = 0.01). The genus Gardnerella was significantly enriched in TP. The XGBoost analysis was able to classify Gardnerella-induced TP more reliably (AUC = 0.621). Moreover, after adjusting potential confounders, our results indicate a robust association between Gardnerella and TP (as a continuous variable, adjusted OR: 12.0, 95% CI: 2.1–67.4, p < 0.01; as a categorical variable (≥0.85%), and adjusted OR: 4.2, 95% CI: 2.0–8.8, p < 0.01). In conclusion, we found that higher virginal Gardnerella levels were associated with TP in women with symptomatic early pregnancy.
Human Leucocyte Antigen G and Murine Qa-2 Are Critical for Myeloid Derived Suppressor Cell Expansion and Activation and for Successful Pregnancy Outcome

During pregnancy, maternal immune system has to balance tightly between protection against pathogens and tolerance towards a semi-allogeneic organism. Dysfunction of this immune adaptation can lead to severe complications such as pregnancy loss, preeclampsia or fetal growth restriction. In the present study we analyzed the impact of the murine MHC class Ib molecule Qa-2 on pregnancy outcome in vivo. We demonstrate that lack of Qa-2 led to intrauterine growth restriction and increased abortion rates especially in late pregnancy accompanied by a disturbed trophoblast invasion and altered spiral artery remodeling as well as protein aggregation in trophoblast cells indicating a preeclampsia-like phenotype. Furthermore, lack of Qa-2 caused imbalanced immunological adaptation to pregnancy with altered immune cell and especially T-cell homeostasis, reduced Treg numbers and decreased accumulation and functional activation of myeloid-derived suppressor cells. Lastly, we show that application of sHLA-G reduced abortion rates in Qa-2 deficient mice by inducing MDSC. Our results highlight the importance of an interaction between HLA-G and MDSC for pregnancy success and the therapeutic potential of HLA-G for treatment of immunological pregnancy complications.
Effects of Vitamin D and K on Interleukin-6 in COVID-19

Background Pathology during COVID-19 infection arises partly from an excessive inflammatory response with a key role for interleukin (IL)-6. Both vitamin D and K have been proposed as potential modulators of this process. Methods We assessed vitamin D and K status by measuring circulating 25-hydroxyvitamin D (25(OH)D) and desphospho-uncarboxylated Matrix Gla-Protein (dp-ucMGP), respectively in 135 hospitalized COVID-19 patients in relation to inflammatory response, elastic fiber degradation and clinical outcomes. Results Comparing good and poor disease outcomes of COVID-19 patients, vitamin 25(OH)D levels were not significantly different. IL-6 levels, however, were significantly higher in patients with poor outcome, compared to patients with good outcome (30.3 vs. 153.0 pg/mL; p < 0.0001). Dp-ucMGP levels as biomarker of extrahepatic vitamin K status was associated with IL-6 levels (r = 0.35; p < 0.0001). In contrast, 25(OH)D levels were only borderline statistically significant correlated with IL-6 (r = −0.14; p <0.050). A significant association was also found between IL-6 and elastic fiber degradation. Contrary to vitamin K status, 25(OH)D did not correlate with elastic fiber degradation. Conclusions Dp-ucMGP associates with IL-6 as a central component of the destructive inflammatory processes in COVID-19. An intervention trial may provide insight whether vitamin K administration, either or not in combination with vitamin D, improves clinical outcome of COVID-19.
Septins From Protists to People

Septin GTPases form nonpolar heteropolymers that play important roles in cytokinesis and other cellular processes. The ability to form heteropolymers appears to be critical to many septin functions and to have been a major driver of the high conservation of many septin domains. Septins fall into five orthologous groups. Members of Groups 1–4 interact with each other to form heterooligomers and are known as the “core septins. ” Representative core septins are present in all fungi and animals so far examined and show positional orthology with monomer location in the heteropolymer conserved within groups. In contrast, members of Group 5 are not part of canonical heteropolymers and appear to interact only transiently, if at all, with core septins. Group 5 septins have a spotty distribution, having been identified in specific fungi, ciliates, chlorophyte algae, and brown algae. In this review we compare the septins from nine well-studied model organisms that span the tree of life (Homo sapiens, Drosophila melanogaster, Schistosoma mansoni, Caenorhabditis elegans, Saccharomyces cerevisiae, Aspergillus nidulans, Magnaporthe oryzae, Tetrahymena thermophila, and Chlamydomonas reinhardtii). We focus on classification, evolutionary relationships, conserved motifs, interfaces between monomers, and positional orthology within heteropolymers. Understanding the relationships of septins across kingdoms can give new insight into their functions.
Prevalence of Sarcoidosis-Associated Pulmonary Hypertension: A Systematic Review and Meta-Analysis

Background Sarcoidosis-associated pulmonary hypertension (SAPH) is associated with poor prognosis, conferring up to a 10-fold increase in mortality in patients with sarcoidosis, but the actual prevalence of SAPH is unknown. Methods The PubMed, Embase, and Cochrane Library databases were systematically searched for epidemiological studies reporting the prevalence of SAPH up to July 2021. Two reviewers independently performed the study selection, data extraction, and quality assessment. Studies were pooled using random-effects meta-analysis. Results This meta-analysis included 25 high-quality studies from 12 countries, with a pooled sample of 632,368 patients with sarcoidosis. The prevalence of SAPH by transthoracic echocardiography in Europe, the United States and Asia was 18.8% [95% confidence interval (CI): 11.1–26.5%], 13.9% (95% CI: 5.4–22.4%) and 16.2% (95% CI: 7.1–25.4%) separately, and the overall pooled prevalence was 16.4% (95%CI: 12.2–20.5%). By right heart catheterization (RHC), the pooled prevalence of SAPH was 6.4% (95% CI: 3.6–9.1%) in general sarcoidosis population, and subgroup analyses showed that the prevalence of SAPH was 6.7% (95% CI: 2.4–11.0%) in Europe and 8.6% (95% CI: −4.1 to 21.3%) in the United States. Further, the prevalence of pre-capillary PH was 6.5% (95% CI: 2.9–10.2%). For the population with advanced sarcoidosis, the pooled prevalence of SAPH and pre-capillary PH by RHC was as high as 62.3% (95% CI: 46.9–77.6%) and 55.9% (95% CI: 20.1–91.7%), respectively. Finally, the pooled prevalence of SAPH in large databases with documented diagnoses (6.1%, 95% CI: 2.6–9.5%) was similar to that of RHC. Substantial heterogeneity across studies was observed for all analyses (I2 > 80%, P < 0.001). Conclusions The sarcoidosis population has a relatively low burden of PH, mainly pre-capillary PH. However, as the disease progresses to advanced sarcoidosis, the prevalence of SAPH increases significantly.
A Comparison of Caregiver Burden for Different Types of Dementia: An 18-Month Retrospective Cohort Study

Background This study aimed to elucidate the influence of dementia etiologies on the degree of caregiver burden and determine which factors predict a high caregiving burden. Methods This 18-month retrospective cohort study enrolled 630 patients and their caregivers from the Dementia Center of Changhua Christian Hospital. The care team performed face-to-face interviews every 6 months, for 18 months from when a diagnosis of dementia was made. The primary outcome was the change in Zarit Burden Interview (ZBI) scores. Generalized estimating equations were used for the longitudinal data analysis. Results Participants with Lewy body disease (LBD) had a significantly higher caregiving burden compared with those with Alzheimer's disease (AD) (β = 3.83 ± 1.47, Wald = 6.79, p = 0.009) after adjusting for patient and caregiver features. Caregivers of mixed-type dementia and frontotemporal dementia (FTD) experienced a greater burden than caregivers of AD, at 6- and 18-month follow-up. Patients with more severe dementia, neuropsychiatric symptoms, being cared for by more than two caregivers, or utilizing social resources were associated with higher ZBI scores; the depressive mood of caregiver also predicted higher ZBI scores. Conclusion This longitudinal study demonstrated that caregiver burden was influenced by the underlying dementia etiology of patients. The dementia care team should provide personalized education and transfer patients and caregivers to appropriate resources, especially for high-risk populations.
Gender Stereotypes and Expected Backlash for Female STEM Students in Germany and Japan

Although Germany and Japan are top-ranking in STEM, women are underrepresented in the STEM fields of physics, engineering, and computer science in both countries. The current research investigated widespread gender-science stereotypes in STEM in the two countries (Studies 1 and 2) and negative consequences of expected backlash (i.e., imagining negative reactions and lower ascribed communion in scenarios) for women’s emotions and motivation in STEM due to role incongruity and lack-of-fit (Study 3). Studies 1 (N = 87) and 2 (N = 22,556) showed that explicit and implicit gender-science stereotypes are widespread and comparable in Germany and Japan. Study 3 (N = 628) showed that lower ascribed communion was related to less positive emotions, more negative emotions and anxiety emotions, and less study motivation for STEM students (from the fields of physics, engineering, and computer science) from Germany and Japan. Results point to more subtle expected backlash effects for women in STEM than hypothesized. Theoretical and practical implications for gender equality in STEM are discussed.