Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and Confirmation of Loci Associated With Canopy Wilting in Soybean Using Genome-Wide Association Mapping

Drought causes significant soybean [Glycine max (L.) Merr. ] yield losses each year in rain-fed production systems of many regions. Genetic improvement of soybean for drought tolerance is a cost-effective approach to stabilize yield under rain-fed management. The objectives of this study were to confirm previously reported soybean loci and to identify novel loci associated with canopy wilting (CW) using a panel of 200 diverse maturity group (MG) IV accessions. These 200 accessions along with six checks were planted at six site-years using an augmented incomplete block design with three replications under irrigated and rain-fed treatments. Association mapping, using 34,680 single nucleotide polymorphisms (SNPs), identified 188 significant SNPs associated with CW that likely tagged 152 loci. This includes 87 SNPs coincident with previous studies that likely tagged 68 loci and 101 novel SNPs that likely tagged 84 loci. We also determined the ability of genomic estimated breeding values (GEBVs) from previous research studies to predict CW in different genotypes and environments. A positive relationship (P ≤ 0.05;0.37 ≤ r ≤ 0.5) was found between observed CW and GEBVs. In the vicinity of 188 significant SNPs, 183 candidate genes were identified for both coincident SNPs and novel SNPs. Among these 183 candidate genes, 57 SNPs were present within genes coding for proteins with biological functions involved in plant stress responses. These genes may be directly or indirectly associated with transpiration or water conservation. The confirmed genomic regions may be an important resource for pyramiding favorable alleles and, as candidates for genomic selection, enhancing soybean drought tolerance.
Soil Freeze-Thaw and Water Transport Characteristics Under Different Vegetation Types in Seasonal Freeze-Thaw Areas of the Loess Plateau

In the arid and semi-arid regions of the Loess Plateau, seasonal freezing and thawing influence soil water movement, and water movement directly influences vegetation growth. However, currently, research with regard to freezing and thawing processes under various vegetation types and the mechanism of soil water movement is lacking. Therefore, the present study explored soil water migration characteristics of two typical vegetation types [arbor land (AL) and shrub land (SL)] on the Loess Plateau during seasonal freezing and thawing processes using bare land (BL) as a control. We used field measured data for hourly soil temperature (ST) and soil water content (SWC) at a depth of 100 cm below the soil surface from November 2017 to March 2018. Freezing and thawing process was divided into three stages based on ST change (initial freezing period, stable freezing period, and thawing period). Compared with previous studies in this area, ST is lower than expected, and SWC migration characteristics are also different. The results revealed that: 1) the maximum freezing depth of AL and SL was 60 cm, which was 30 cm less than that of BL. The freezing date of each soil layer in BL was the earliest and average ST value was the lowest. BL had the highest degree of freezing. The freezing of all soil layers in AL occurred at a later date than that of SL. ST and the minimum soil freezing temperatures were higher than those of SL, and the capacity of AL to resist freezing was higher; 2) the SWCs in AL and BL at depths of 0–10 cm and 10–30 cm decreased, whereas SWCs of AL and BL at a depth of 60 cm increased by 152 and 146%, respectively. The SWCs of SL at soil depths of 0–10 cm, 10–30 cm, and 30–60 cm increased by 46.3, 78.4 and 205%, respectively. The amount and distribution of soil moisture in SL were optimum when compared to those of AL and BL. The results of the present study could provide a scientific basis for vegetation restoration in arid and semi-arid areas of the Loess Plateau.
Quantifying Patterns of Supraglacial Debris Thickness and Their Glaciological Controls in High Mountain Asia

Mapping patterns of supraglacial debris thickness and understanding their controls are important for quantifying the energy balance and melt of debris-covered glaciers and building process understanding into predictive models. Here, we find empirical relationships between measured debris thickness and satellite-derived surface temperature in the form of a rational curve and a linear relationship consistently outperform two different exponential relationships, for five glaciers in High Mountain Asia (HMA). Across these five glaciers, we demonstrate the covariance of velocity and elevation, and of slope and aspect using principal component analysis, and we show that the former two variables provide stronger predictors of debris thickness distribution than the latter two. Although the relationship between debris thickness and slope/aspect varies between glaciers, thicker debris occurs at lower elevations, where ice flow is slower, in the majority of cases. We also find the first empirical evidence for a statistical correlation between curvature and debris thickness, with thicker debris on concave slopes in some settings and convex slopes in others. Finally, debris thickness and surface temperature data are collated for the five glaciers, and supplemented with data from one more, to produce an empirical relationship, which we apply to all glaciers across the entire HMA region. This rational curve: 1) for the six glaciers studied has a similar accuracy to but greater precision than that of an exponential relationship widely quoted in the literature; and 2) produces qualitatively similar debris thickness distributions to those that exist in the literature for three other glaciers. Despite the encouraging results, they should be treated with caution given our relationship is extrapolated using data from only six glaciers and validated only qualitatively. More (freely available) data on debris thickness distribution of HMA glaciers are required.
Is the Immunopeptidome Getting Darker?: A Commentary on the Discussion around Mishto et al., 2019

The immune system is perhaps the most ancient practitioner of proteomics; and as we delve into the more nuanced aspects of antigen processing and presentation, we learn more of the complexity of this essential process and Into a debate amongst the human practitioners of immunopeptidomics threatens to boil over and confer reputational damage to both the field and the investigators who use this technique. Traditionally the art of proteomics has used the identification of tryptic peptides to infer protein expression, a process termed “bottom-up” proteomics. Notably, an analogous process is used by antigen presenting cells to alert the immune system to the presence of infectious micro-organisms, malignancy and other abnormalities within the body. This process known as antigen processing and presentation relies on the selection of peptide fragments of antigens and their presentation on the surface of cells as a bound complex with Major Histocompatibility Complex (MHC) molecules. The isolation and characterisation of these MHC-bound peptides, most commonly through the use of liquid chromatography andmass spectrometry, is a rapidly growing field coined immunopeptidomics. Immunopeptidomics as a field has rapidly matured in the past decade and has moved from the domain of just a handful of specialised laboratories to now being more generally applied by the proteomics and immunology communities. The genesis of immunopeptidomics can be traced back to early work of the groups of Don Hunt with Victor Englehard and Alessandro Sette (1–5) and Hans-Georg Rammensee (6–9). It was in the early 90’s that I joined the field and was immediately struck by the generosity and encouragement of the established investigators – sharing anecdotes, methods and solutions to problems with a focus on growing the discipline and answering key questions of immune specificity whilst untangling the complexity of antigen presentation. This is something I have never forgotten and it has inspired me to “give back” to the field happily training the numerous visitors to my laboratory and publishing our methodology widely and in great depth (10, 11).
Study of Antibody-Dependent Reactions of Mast Cells In Vitro and in a Model of Severe Influenza Infection in Mice

We investigated the reaction of mouse peritoneal mast cells (MCs) in vitro after IgG-containing immune complex introduction using A/H5N1 and A/H1N1pdm09 influenza viruses as antigens. The sera of immune mice served as a source of IgG antibodies. The concentration of histamine in the supernatants was determined at 4 hours after incubation with antisera and virus. We compared the contribution of MCs to the pathogenesis of post-immunization influenza infection with A/H5N1 and A/H1N1 influenza viruses in mice. The mice were immunized parenterally with inactivated viruses and challenged with lethal doses of drift A/H5N1 and A/H1N1 influenza viruses on the 14th day after immunization. Simultaneously, half of the mice were injected intraperitoneally with a mixture of histamine receptor blockers (chloropyramine and quamatel). In in vitro experiments, the immune complex formed by A/H5N1 virus and antiserum caused a significant increase in the histamine release compared to immune serum or the virus alone. With regard to the A/H1N1 virus, such an increase was not significant. A/H1N1 immunization caused detectable HI response in mice at 12th day after immunization, in contrast to the A/H5N1 virus. After challenge of A/H5N1-immunized mice, administration of antihistamines increased the survival rate by up to 90%. When infecting the A/H1N1-immunized mice, 90% of the animals were already protected from lethal infection by day 14; the administration of histamine receptor blockers did not increase survival. Histological examination of the lungs has shown that toluidine blue staining allows to estimate the degree of MC degranulation. The possibility of in vitro activation of murine MCs by IgG-containing immune complexes has been shown. In a model of influenza infection, it was shown that the administration of histamine receptor blockers increased survival. When the protection was formed faster due to the earlier production of HI antibodies, the administration of histamine receptor blockers did not significantly affect the course of the infection. These data allow to propose that even if there are antibody-dependent MC reactions, they can be easily stopped by the administration of histamine receptor blockers.
Production and water-use efficiency of semi-arid grasslands of South Africa as affected by veld condition and rainfall

Water is one of the most important determinants of plant production, especially under semi-arid conditions. In the past, pasture science researchers in South Africa paid very little attention to water-balance studies under semi-arid conditions, thus identifying the need for this study. Plant production, runoff and water-use efficiency (i.e. above-ground phytomass production per unit of evapotranspiration) were determined on runoff plots on veld (rangeland) in 3 different conditions, over a period of 12 years. Evapotranspiration was calculated using the soil water-balance equation (.)
Primary Diffuse Large B-Cell Lymphoma of the Urinary Tract: A Population-Based Analysis

Objective Diffuse large B-cell lymphoma (DLBCL) is the most common histopathological type of non-Hodgkin’s lymphoma, which may arise from various extranodal sites. Little is known about the clinical characteristics and survival outcomes of primary DLBCL of the urinary tract (UT). Thus, we conducted this study to explore the independent prognostic factors of patients with UT-DLBCL using the Surveillance, Epidemiology, and End Results (SEER) database. Materials and Methods We searched the Surveillance, Epidemiology, and End Results (SEER) database for the data of patients diagnosed with UT-DLBCL between 1975 and 2016. Data, including demographic tumour stage and therapeutic strategies, such as surgical resection, radiation therapy, and chemotherapy, were collected. The impact of these factors on survival outcomes, including overall survival (OS) and disease-specific survival (DSS), was analysed using Kaplan–Meier curves. Results Four-hundred and eighty-nine patients who met the inclusion criteria were enrolled in the data analysis. The median age was 69 years old. Most cases of UT-DLBCL (72.39%) originated from the kidney, followed by the urinary bladder (24.95%). Both surgical resection and chemotherapy can significantly improve OS and DSS. Patients older than 75 years had the worst survival outcomes. Stage IV DLBCL may be a poor prognostic factor. Conclusion To the best of our knowledge, this is the largest population-based study of UT-DLBCL. Advanced age, male gender, lack of surgical resection or chemotherapy, and stage IV DLBCL were poor prognostic factors.
Looking for Earthquake Precursors From Space: A Critical Review

Starting from late seventies, many observations have been reported about observations in space of signals reconciled with earthquakes and claimed as possible preseismic measurements. The detected parameters range from electromagnetic field components (in a large band of frequencies) to plasmas parameters; from particles detection to thermal anomalies; etc. Up to the DEMETER mission, the analyses have been carried out on datasets gathered by not devoted satellites. Even beyond the results obtained, the DEMETER mission has constituted a milestone for space-based investigations of seismo-associated phenomena drawing a baseline for next missions with respect instruments, observational strategy and measurements uncertainty. Nowadays, the CSES-01 satellite – developed within a sino-italian collaboration with the participation also of Austrian Institutes – represents the most advanced mission for investigating near-Earth electromagnetic environment aimed at extending the observation of earthquake precursors to a long time series. The benefit of the mission is even higher by considering that CSES-01 is the first of a program of several LEO small satellites, the second of which will be launched on 2023 with the same instruments and orbit of CSES-01, but with a shift of half of an orbit in order to monitor each trace twice per orbit. The article gives a short survey of space-based observations of preseismic phenomena from the early studies up to the more recent ones, critically reviewing results, hypotheses and trends in this research field. The supposed physical processes proposed to explain the observations are still unable to explain the large variety of the phenomenology, the statistical significance of the results are highly debated, and more in general a common consensus is still missing. Anyway, the investigation of the seismo-associated phenomena from space is a challenge for near future Earth observation.
Effects of Day/Night Factor on the Detection Performance of FY4A Lightning Mapping Imager in Hainan, China

In this study, the effect of day/night factor on the detection performance of the FY4A lightning mapping imager (LMI) is evaluated using the Bayesian theorem, and by comparing it to the measurements made by a ground-based low-frequency magnetic field lightning location system. Both the datasets were collected in the summers of 2019–2020 in Hainan, China. The results show that for the observed summer thunderstorms in Hainan, the daytime detection efficiencies of LMI (DELMI) were 20.41~35.53% lower than the nighttime DELMI. Compared to other space-based lightning sensors (lightning imaging sensors/optical transient detectors (LIS/OTD) and geostationary lightning mapper (GLM)), the detection performance of LMI is more significantly influenced by the day/night factor. The DELMI rapidly dropped within about four hours after sunrise while it increased before sunset. For the storms that formed at night and lasted for an entire day, the DELMI remained relatively low during the daytime, even as the thunderstorms intensified. The poor detection performance of LMI during daytime is probably because of the sunlight reflection by clouds and atmosphere, which results in larger background radiative energy density (RED) than that at night. During night, LMI captured the lightning signals well with low RED (8.38~10.63 μJ sr−1 m−2 nm−1). However, during daytime, signals with RED less than 77.12 μJ sr−1 m−2 nm−1 were filtered, thus lightning groups could rarely be identified by LMI, except those with extremely high RED. Due to the limitations of the Bayesian theorem, the obtained DE in this study was “relative” DE rather than “absolute” DE. To obtain the absolute DE of LMI, the total lightning density is necessary but can hardly be measured. Nonetheless, the results shown here clearly indicate the strong impact of day/night factor on the detection performance of LMI, and can be used to improve the design and post-processing method of LMI.
The Impact of Common Epidemiological Factors on Gray and White Matter Volumes in Magnetic Resonance Imaging–Is Prevention of Brain Degeneration Possible?

Introduction: The aim of the study was to evaluate the impact of multiple risk factors (age, diabetes, hypertension, hyperlipidemia, BMI, smoking, alcohol) on the gray and white matter volumes as well as on the burden of white matter hyperintensities (WMH). Material and Methods: The study group consisted of 554 subjects (age range: 50–69 yrs, F/M: 367/187) recruited from the larger cohort of the Polish fraction of the Prospective Urban Rural Epidemiological (PURE) study. The participants answered questionnaires about their lifestyle, underwent physical and psychological examination (MoCA test), laboratory blood tests followed by brain MRI. Volumetric measurements of the total gray matter (GMvol), total white matter (WMvol) and WHM (WMHvol) normalized to the total intracranial volume were performed using the Computational Anatomy Toolbox 12 (CAT12) and Statistical Parametric Maps 12 (SPM12) based on 3D T1-weighted sequence. The influence of risk factors was assessed using multiple regression analysis before and after correction for multiple comparisons. Results: Older age was associated with lower GMvol and WMvol, and higher WMHvol (p < 0.001). Smaller GMvol volume was associated with higher WMHvol (p < 0.001). Higher WMHvol was associated with hypertension (p = 0.01) and less significantly with hyperlipidemia (only before correction p = 0.03). Diabetes, abnormal BMI, smoking and alcohol intake did not have any significant impact on GMvol, WMvol or WMHvol (p > 0.05). MoCA score was not influenced by any of the factors. Conclusions: Gray matter loss is strongly associated with the accumulation of WMH which seems to be potentially preventable by maintaining normal blood pressure and cholesterol levels.
Relationships Between the Therapeutic Alliance and Reactions to Artistic Experience With Art Materials in an Art Therapy Simulation

In art therapy, art-making plays an important role in the therapeutic relationship. To better understand the triangular relationship between the art therapist, the client and the artwork, this study investigated the association between the therapeutic alliance and reactions to artistic experiences with art materials in an art therapy simulation. The simulation consisted of a series of 6–8 sessions in which art therapy students were divided into teams composed of a permanent observer (art therapist) and creator (client). The client's role was to self-explore through art- making, and the art therapist's role was to accompany the client. Thirty-four students, all women, who played the art therapist role, and 37 students (one male) who played the client participated in the study. Of these participants, there were 24 pairs where both participants filled out all the questionnaires. A short version of the Working Alliance Inventory (WAI) was completed by the clients and the art therapists on the second session (T1) and on the penultimate session (T2). The clients also completed the Art-Based Intervention Questionnaire (ABI) at T2. Significant positive correlations were found between indices of the WAI for the art therapist and the client and the clients' reactions to the artistic experience with art materials on the ABI. The evaluation of the emotional bond between the art therapist and the client at the start of the simulation significantly predicted the client's reactions to the artistic experience with art materials at the end of the simulation and explained 45.4% of the variance for this variable. These findings highlight factors related to the development and influence of the therapeutic alliance, as well as the role of the artistic experience in art therapy and lay the groundwork for further research.
Patterns, Trends and Drivers of Water Transparency in Sri Lanka Using Landsat 8 Observations and Google Earth Engine

Addressing inland water transparency and driver effects to ensure the sustainability and provision of good quality water in Sri Lanka has been a timely prerequisite, especially under the Sustainable Development Goals 2030 agenda. Natural and anthropogenic changes lead to significant variations in water quality in the country. Therefore, an urgent need has emerged to understand the variability, spatiotemporal patterns, changing trends and impact of drivers on transparency, which are unclear to date. This study used all available Landsat 8 images from 2013 to 2020 and a quasi-analytical approach to assess the spatiotemporal Secchi disk depth (ZSD) variability of 550 reservoirs and its relationship with natural (precipitation, wind and temperature) and anthropogenic (human activity and population density) drivers. ZSD varied from 9.68 cm to 199.47 with an average of 64.71 cm and 93% of reservoirs had transparency below 100 cm. Overall, slightly increasing trends were shown in the annual mean ZSD. Notable intra-annual variations were also indicating the highest and lowest ZSD during the north-east monsoon and south-west monsoon, respectively. The highest ZSD was found in wet zone reservoirs, while dry zone showed the least. All of the drivers were significantly affecting the water transparency in the entire island. The combined impact of natural factors on ZSD changes was more significant (77.70%) than anthropogenic variables, whereas, specifically, human activity accounted for the highest variability across all climatic zones. The findings of this study provide the first comprehensive estimation of the ZSD of entire reservoirs and driver contribution and also provides essential information for future sustainable water management and conservation strategies.