Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal Soil Bacterial Community Responses to Cropping Systems and Crop Identity in Dryland Agroecosystems of the Northern Great Plains

Industrialized agriculture results in simplified landscapes where many of the regulatory ecosystem functions driven by soil biological and physicochemical characteristics have been hampered or replaced with intensive, synthetic inputs. To restore long-term agricultural sustainability and soil health, soil should function as both a resource and a complex ecosystem. In this study, we examined how cropping systems impact soil bacterial community diversity and composition, important indicators of soil ecosystem health. Soils from a representative cropping system in the semi-arid Northern Great Plains were collected in June and August of 2017 from the final phase of a 5-year crop rotation managed either with chemical inputs and no-tillage, as a USDA-certified organic tillage system, or as a USDA-certified organic sheep grazing system with reduced tillage intensity. DNA was extracted and sequenced for bacteria community analysis via 16S rRNA gene sequencing. Bacterial richness and diversity decreased in all farming systems from June to August and was lowest in the chemical no-tillage system, while evenness increased over the sampling period. Crop species identity did not affect bacterial richness, diversity, or evenness. Conventional no-till, organic tilled, and organic grazed management systems resulted in dissimilar microbial communities. Overall, cropping systems and seasonal changes had a greater effect on microbial community structure and diversity than crop identity. Future research should assess how the rhizobiome responds to the specific phases of a crop rotation, as differences in bulk soil microbial communities by crop identity were not detectable.
Host-Directed Therapies for Cutaneous Leishmaniasis

Cutaneous leishmaniasis exhibits a wide spectrum of clinical presentations from self-resolving infections to severe chronic disease. Anti-parasitic drugs are often ineffective in the most severe forms of the disease, and in some cases the magnitude of the disease can result from an uncontrolled inflammatory response rather than unrestrained parasite replication. In these patients, host-directed therapies offer a novel approach to improve clinical outcome. Importantly, there are many anti-inflammatory drugs with known safety and efficacy profiles that are currently used for other inflammatory diseases and are readily available to be used for leishmaniasis. However, since leishmaniasis consists of a wide range of clinical entities, mediated by a diverse group of leishmanial species, host-directed therapies will need to be tailored for specific types of leishmaniasis. There is now substantial evidence that host-directed therapies are likely to be beneficial beyond autoimmune diseases and cancer and thus should be an important component in the armamentarium to modulate the severity of cutaneous leishmaniasis.
Novel STMN2 Variant Linked to Amyotrophic Lateral Sclerosis Risk and Clinical Phenotype

Objective There is a critical need to establish genetic markers that explain the complex phenotypes and pathogenicity of ALS. This study identified a polymorphism in the Stathmin-2 gene and investigated its association with sporadic ALS (sALS) disease risk, age-of onset and survival duration. Methods The candidate CA repeat was systematically analyzed using PCR, Sanger sequencing and high throughput capillary separation for genotyping. Stathmin-2 expression was investigated using RT-PCR in patient olfactory neurosphere-derived (ONS) cells and RNA sequencing in laser-captured spinal motor neurons. Results In a case-control analysis of a combined North American sALS cohort (n = 321) and population control group (n = 332), long/long CA genotypes were significantly associated with disease risk (p = 0.042), and most strongly when one allele was a 24 CA repeat (p = 0.0023). In addition, longer CA allele length was associated with earlier age-of-onset (p = 0.039), and shorter survival duration in bulbar-onset cases (p = 0.006). In an Australian longitudinal sALS cohort (n = 67), ALS functional rating scale scores were significantly lower in carriers of the long/long genotype (p = 0.034). Stathmin-2 mRNA expression was reduced in sporadic patient ONS cells. Additionally, sALS patients and controls exhibited variable expression of Stathmin-2 mRNA according to CA genotype in laser-captured spinal motor neurons. Conclusions We report a novel non-coding CA repeat in Stathmin-2 which is associated with sALS disease risk and has disease modifying effects. The potential value of this variant as a disease marker and tool for cohort enrichment in clinical trials warrants further investigation.
Advanced Life Support vs. Basic Life Support for Patients With Trauma in Prehospital Settings: A Systematic Review and Meta-Analysis

Background: Advanced Life Support (ALS) is regarded to be associated with improved survival in pre-hospital trauma care when compared to Basic Life Support (BLS) irrespective of lack of evidence. The aim of this study is to ascertain ALS improves survival for trauma in prehospital settings when compared to BLS. Methods: We searched PubMed, EMBASE, and the Cochrane Central Register of Controlled Trials for published controlled trials (CTs), and observational studies that were published until Aug 2017. The population of interest were adults (>18 years old) trauma patients who were transported by ground transportation and required resuscitation in prehospital settings. We compared outcomes between the ALS and BLS groups. The primary outcome was in-hospital mortality and secondary outcomes were neurological outcome and time spent on scene. Results: We identified 2,502 studies from various databases and 10 studies were included in the analysis (two CTs, and eight observational studies). The outcomes were not statistically significant between the ALS and BLS groups (pooled OR 1.14; 95% CI 0.95 to 1.36 for mortality, pooled OR 1.12; 95% CI 0.88 to 1.42 for good neurological outcomes, pooled mean difference −0.96; 95% CI−6.64 to 4.72 for on-scene time) in CTs. In observational studies, ALS prolonged on-scene time and increased mortality (pooled OR 1.56; 95% CI: 1.31 to 1.86 for mortality, and pooled mean difference, 1.26; 95% CI: 0.07 to 2.45 for on-scene time). Conclusions: In prehospital settings, the present study showed no advantages of ALS on the outcomes in patients with trauma compared to BLS.
Sorption of Glyphosate on Soil Components: The Roles of Metal Oxides and Organic Materials

Predicting the behavior, fate, and transport potential of a herbicide in any soil involves understanding the sorption characteristics. The sorption characteristics of glyphosate (GPS) on soil and their main components were investigated, indicating that the mineral phase is more important than the organic carbon in adsorption of GPS. Sorption isotherms were determined from each component using the batch equilibrium method at various concentrations (5, 10, 15, 20, 25, and 30 mg L−1) and sorption affinity of GPS was approximated by the Freundlich equation. The sorption strength K f [mg kg−1 (L mg−1)−n] across the various components ranged from 2.1–134.9 while the organic carbon-normalized Freundlich sorption capacity values, K foc, ranged from 1.28–3.53 mg kg−1-OC/(mg L−1)n. Infrared Fourier transform spectroscopy (FTIR) of the components showed significant structural differences. The results suggest that the presence of the oxides and hydroxides iron, in particular in soil solutions, enhanced GPS adsorption. They also suggest that reduction in OC% due to various treatments may enhance the remobilization of GPS into the aqueous phase (i.e., groundwater), though at different rates. Comparatively, contribution of surface area to the adsorption of GPS on the various components proved more significant than contents of organic carbon.
Phosphoinositides: Roles in the Development of Microglial-Mediated Neuroinflammation and Neurodegeneration

Microglia are increasingly recognized as vital players in the pathology of a variety of neurodegenerative conditions including Alzheimer’s (AD) and Parkinson’s (PD) disease. While microglia have a protective role in the brain, their dysfunction can lead to neuroinflammation and contributes to disease progression. Also, a growing body of literature highlights the seven phosphoinositides, or PIPs, as key players in the regulation of microglial-mediated neuroinflammation. These small signaling lipids are phosphorylated derivates of phosphatidylinositol, are enriched in the brain, and have well-established roles in both homeostasis and disease.Disrupted PIP levels and signaling has been detected in a variety of dementias. Moreover, many known AD disease modifiers identified via genetic studies are expressed in microglia and are involved in phospholipid metabolism. One of these, the enzyme PLCγ2 that hydrolyzes the PIP species PI(4,5)P2, displays altered expression in AD and PD and is currently being investigated as a potential therapeutic target.Perhaps unsurprisingly, neurodegenerative conditions exhibiting PIP dyshomeostasis also tend to show alterations in aspects of microglial function regulated by these lipids. In particular, phosphoinositides regulate the activities of proteins and enzymes required for endocytosis, toll-like receptor signaling, purinergic signaling, chemotaxis, and migration, all of which are affected in a variety of neurodegenerative conditions. These functions are crucial to allow microglia to adequately survey the brain and respond appropriately to invading pathogens and other abnormalities, including misfolded proteins. AD and PD therapies are being developed to target many of the above pathways, and although not yet investigated, simultaneous PIP manipulation might enhance the beneficial effects observed. Currently, only limited therapeutics are available for dementia, and although these show some benefits for symptom severity and progression, they are far from curative. Given the importance of microglia and PIPs in dementia development, this review summarizes current research and asks whether we can exploit this information to design more targeted, or perhaps combined, dementia therapeutics. More work is needed to fully characterize the pathways discussed in this review, but given the strength of the current literature, insights in this area could be invaluable for the future of neurodegenerative disease research.
Female Pattern Hair Loss in Female and Male: A Quantitative Trichoscopic Analysis in Chinese Han Patients

Objectives: To investigate the trichoscopic features of female pattern hair loss (FPHL) in Chinese Han patients and analyze the difference between male and female patients with FPHL. Materials and Methods: Trichoscopic images were taken in four different scalp areas, including right frontal hairline, vertex, right parietal and occipital areas. Hair density, hair shaft diameter, vellus hair ratio and single hair follicle unit ratio were counted manually and analyzed. Results: Seventy-three subjects were enrolled in this study, including 38 patients with FPHL (28 females and 10 males) and 35 normal controls without hair loss. The hair density and hair shaft diameter of FPHL patients reduced in the whole scalp. Vellus hair ratio and single hair follicle unit ratio were both increased in FPHL compared to normal controls. The vertex was the most affected area and the hair shaft diameter showed the most significant difference. Parietal and occipital area were also affected in FPHL. The reduction or increase was correlated with the severity of Ludwig staging. Very few gender differences were detected in male and female FPHL patients. Conclusion: FPHL patients showed decreased hair density and hair shaft diameter, accompanied by increased vellus hair ratio and single hair follicle unit ratio. Parietal and occipital area can be also affected in FPHL, though not as severe as in vertex area. FPHL in male basically has the same characteristic as those in female patients. Limitation: The main limitation of the study is the small sample size which only enrolled 10 male FPHL patients, in comparison to the female cases. The findings could not be representative of the normal population with the limited sample size.
Comparative Study of the Rhizosphere and Root Endosphere Microbiomes of Cholistan Desert Plants

Microbial communities associated with the rhizosphere and roots of desert halophytes play an important role in plants’ growth and development. Very limited information has been available on the microbial diversity of arid environments of Pakistan. Hence in the current study, the microbial diversity of rhizosphere and root endosphere of desert halophytes, Zygophyllum simplex, Haloxylon salicoricum, Aerva javanica, and Capparis decidua was evaluated. The rhizosphere and root endosphere samples of desert halophytes collected from the three geographic sites of Cholistan desert, Punjab, Pakistan were analyzed by using 16S rRNA based Illumina sequencing. The results showed that Proteobacteria were more abundant in the rhizospheric soils while Actinobacteria were more dominant in the root endosphere of halophytes. Bacteroidetes, Firmicutes, and Deinococcus-Thermus were identified from all rhizospheric soils and roots across the three sites, with variable percentage. Bacillus, Kocuria, Pseudomonas, Halomonas, and Flavobacterium were commonly identified from the rhizosphere and root endosphere of halophytes across all the three sites. At the genus level, microbial diversity from Haloxylon showed the greatest variations between the rhizosphere and root endosphere from the site 2. This study revealed that microbial diversity analysis can be used to study how changes in abiotic factors such as soil moisture content and salinity affect the microbial communities associated with the rhizospheric soils and root endosphere of halophytes across the three sites. This study will also help in the discovery of potential inoculants for crops growing in arid and semi-arid regions of Pakistan.
Ultra-Processed Food Consumption Among Chilean Preschoolers Is Associated With Diets Promoting Non-communicable Diseases

Introduction: In adults, intake of ultra-processed foods (UPF) has been linked with poor diets and adverse health outcomes. In young children, evidence is scarcer but suggests a higher dietary share of UPF. Objective: To quantify the intake of UPF and its association with the nutrient composition of the diet in a sample of preschoolers in Santiago, Chile. Methods: Cross-sectional analysis of dietary data (24-h recall survey) from 960 preschoolers. Foods were categorized according to the extent and purpose of processing (NOVA classification) and participants were classified in quintiles of UPF intake. We explored the associations between UPF intake (% of the total energy) and intake of nutrients of concern for non-communicable disease development (carbohydrates, total sugars, fats, and sodium), and nutrients for promotion (proteins, polyunsaturated fats, iron, calcium, zinc, vitamins A, D, C, and B12, folate, and fiber) using multivariate regression after controlling for covariates. Results: UPF constituted 49% of the total energy intake. Preschoolers with higher intake consumed more energy, saturated and monounsaturated fats, carbohydrates, total sugars, and vitamin D, compared to preschoolers in the lowest quintile of UPF intake. In contrast, UPF intake was negatively associated with the consumption of proteins, polyunsaturated fats, fiber, zinc, vitamin A, and sodium (p < 0.05). Conclusion: In Chilean preschoolers, UPF was the primary source of energy intake. The dietary share of UPF was associated with the nutrient composition of the diet. Improving children's diet should consider not only promoting healthy food consumption but also limiting UPF consumption.
Histopathological Classification of Canine Cutaneous Round Cell Tumors Using Deep Learning: A Multi-Center Study

Canine cutaneous round cell tumors (RCT) represent one of the routine diagnostic challenges for veterinary pathologists. Computer-aided approaches are developed to overcome these restrictions and to increase accuracy and consistency of diagnosis. These systems are also of high benefit reducing errors when a large number of cases are screened daily. In this study we describe ARCTA (Automated Round Cell Tumors Assessment), a fully automated algorithm for cutaneous RCT classification and mast cell tumors grading in canine histopathological images. ARCTA employs a deep learning strategy and was developed on 416 RCT images and 213 mast cell tumors images. In the test set, our algorithm exhibited an excellent classification performance in both RCT classification (accuracy: 91.66%) and mast cell tumors grading (accuracy: 100%). Misdiagnoses were encountered for histiocytomas in the train set and for melanomas in the test set. For mast cell tumors the reduction of a grade was observed in the train set, but not in the test set. To the best of our knowledge, the proposed model is the first fully automated algorithm in histological images specifically developed for veterinary medicine. Being very fast (average computational time 2.63 s), this algorithm paves the way for an automated and effective evaluation of canine tumors.
Photonic Curing of Nickel Oxide Transport Layer and Perovskite Active Layer for Flexible Perovskite Solar Cells: A Path Towards High-Throughput Manufacturing

High-throughput roll-to-roll (R2R) manufacturing of perovskite solar cells (PSCs) is currently limited by thermal processes that take tens of minutes each, translating to impractically long annealing tools at high web speeds. In addition, PSCs are usually made with metal oxide transport layer materials that require high temperatures for thermal annealing. Here, we demonstrate the fabrication of PSCs using photonic curing, instead of thermal annealing, to convert NiOx directly from sol-gel precursors for hole transport layers and to crystallize methylammonium lead iodide (MAPbI3) active layers on flexible Willow® Glass substrates. Photonic curing uses short, intense pulses of light to process materials at a high speed, hence it is compatible with R2R manufacturing. We achieved power conversion efficiencies (PCEs) of 11.7% in forward-scan and 10.9% in reverse-scan for PSCs made with photonic cured NiOx and MAPbI3 films. Furthermore, both NiOx and MAPbI3 films could be processed with a single photonic curing pulse, with a web speed of 5.7 m/min, and still produce PCEs comparable to thermally annealed control samples. Based on the single-pulse photonic curing condition for each film, we project a web speed of 26 m/min, laying a pathway to high-throughput production of perovskite solar modules.
The Mediation Effect of Hyperarousal Symptoms on the Relationship Between Childhood Physical Abuse and Suicidal Ideation of Patients With PTSD

Objective: This study examined the relationship of childhood physical abuse, posttraumatic stress disorder (PTSD), depression, and suicide in patients with PTSD through path analysis. Materials and Methods: A total of 114 patients with PTSD (36 men and 78 women) were recruited and completed psychological assessments including the Childhood Trauma Questionnaire, the scale for suicidal ideation, the clinician-administered PTSD scale for the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition, the PTSD checklist, and the Hospital Anxiety and Depression Scale. Structural equation modeling was used to evaluate the results. We developed a model including childhood physical abuse experience as the causal variable, suicidal ideation as a result variable, and PTSD and depression as mediation variables. PTSD symptoms were divided into four clusters [intrusion, avoidance, negative cognition and mood, and altered arousal and reactivity (hyperarousal)] to determine predictive power for suicide. Results: PTSD symptoms fully mediated the relationship between childhood physical abuse and suicidal ideation. Furthermore, PTSD symptoms fully mediated the relationship between childhood physical abuse and depression. Among the PTSD symptoms, hyperarousal was the only symptom cluster that mediated the relationship between childhood physical abuse and suicidal ideation. The symptom clusters of negative cognition and mood as well as hyperarousal mediated the relationship between childhood physical abuse and depression. Conclusions: This study presents a link between childhood physical abuse and current symptoms in patients with PTSD, and highlights specific PTSD symptom clusters (i.e., hyperarousal, negative cognition and mood) that may increase the risk for psychopathology later in life.
Seismicity of the Northern Volcanic Zone of Iceland

A half century of monitoring of the Northern Volcanic Zone of Iceland, a branch of the North America—Eurasia plate boundary, shows that the seismicity is very unevenly distributed, both in time and space. The four central volcanoes at the boundary, Þeistareykir, Krafla, Fremrinámar, and Askja, show persistent but very low-level seismicity, spatially coinciding with their high-temperature geothermal systems. On their rift structures, on the other hand, seismicity is almost absent, except during rifting episodes. Krafla went through a rifting episode in 1975–1984 with inflation, interrupted by 20 diking events with extensive rifting, eruptive activity, and intense seismicity along an 80 km long section of the rift. During inflation periods, the seismicity was contained within the caldera of the volcano, reflecting the inflation level of the magma chamber. Diking events were marked by seismicity propagating away from the volcano into the fissure swarms to the south or north of the volcano, accompanied by rapid deflation of the caldera magma chamber. These events lasted from 1 day to 3 months, and the dike length varied between 1 and 60 km. The area around the Askja volcano is the only section of the Northern Volcanic Zone that shows persistent moderate seismicity. The largest events are located between fissure swarms of adjacent volcanic systems. Detailed relative locations of hypocenters reveal a system of vertical strike-slip faults, forming a conjugate system consistent with minimum principal stress in the direction of spreading across the plate boundary. A diking event into the lower crust was identified in the adjacent fissure swarm at Upptyppingar in 2007–2008. Four nests of anomalously deep earthquakes (10–34 km) have been identified in the Askja region, apparently associated with the movements of magma well below the brittle-ductile transition. Several processes have been pointed out as possible causes of earthquakes in the deformation zone around the plate boundary. These include inflation and deflation of central volcanoes, intrusion of propagating dikes, both laterally and vertically, strike-slip faulting on conjugate fault systems between overlapping fissure swarms, migration of magma in the lower, ductile crust, and geothermal heat mining.