Miracle-dz/UniFAR-FTUs huggingface dataset:
Knowledge needs, available practices, and future challenges in agricultural soils

Abstract. The goal of this study is to clarify research needs and identify effective practices for enhancing soil health. This was done by a synopsis of soil literature that specifically tests practices designed to maintain or enhance elements of soil health. Using an expert panel of soil scientists and practitioners, we then assessed the evidence in the soil synopsis to highlight practices beneficial to soil health, practices considered detrimental, and practices that need further investigation. A partial Spearman's correlation was used to analyse the panel's responses. We found that increased certainty in scientific evidence led to practices being considered to be more effective due to them being empirically justified. This suggests that for practices to be considered effective and put into practice, a substantial body of research is needed to support the effectiveness of the practice. This is further supported by the high proportion of practices (33 %), such as changing the timing of ploughing or amending the soil with crops grown as green manures, that experts felt had unknown effectiveness, usually due to insufficiently robust evidence. Only 7 of the 27 reviewed practices were considered to be beneficial, or likely to be beneficial in enhancing soil health. These included the use of (1) integrated nutrient management (organic and inorganic amendments); (2) cover crops; (3) crop rotations; (4) intercropping between crop rows or underneath the main crop; (5) formulated chemical compounds (such as nitrification inhibitors); (6) control of traffic and traffic timing; and (7) reducing grazing intensity. Our assessment, which uses the Delphi technique, is increasingly used to improve decision-making in conservation and agricultural policy, identified practices that can be put into practice to benefit soil health. Moreover, it has enabled us to identify practices that need further research and a need for increased communication between researchers, policy-makers, and practitioners, in order to find effective means of enhancing soil health.
ESTUDO DA VARIABILIDADE GENÉTICA E DOS FATORES DE VIRULÊNCIA DE ISOLADOS DE Ureaplasma diversum

MARQUES, L.M. Study of genetic variability and virulence factors of U. diversum isolates. 100 f. Tese (Doutorado) Instituto de Ciências Biomédicas da Universidade de São Paulo, São Paulo, 2009. Little is known about the pathogenicity and genetic characteristic of U. diversum. The aim of the present study was the study of genetic variability and virulence factors of U. diversum clinical isolates. Thirty four isolates of U. diversum and two type-strains, ATCC 49782 and 49783, were studied. Twenty four isolates were recovered from the vaginal mucus of a bovine vulvovaginitis and 10 isolates were recovered from frozen bovine semen. The strains were submitted to PCR assays for 16S rRNA and urease genes, and analyzed to genetic variability. Moreover, the strains were analyzed to the virulence factors: capsule, phospholipase C activity, IgA protease activity and adheson and invasion into Hep-2 cells. The sequencing of parcial 16S rRNA gene showed polymorphic patterns into 44 positions. This polymorphisms clustered the strins in seven groups. For the virulence factors, ureaplasma cells showed a dense-stained external capsule-like structure surrounding the cell membrane. This is the first description in U. diversum. A high level of phospholipase C activity was also detected in 31 studied ureaplasma. However, no strains showed IgA protease activity. For the invasion assay, the isolates and strains used were detected inside the cells after infection of one minute without difference in the arrangement for adhesion and invasion. The adhesion was scattered throughout the cells, and after three hours, the invasion, of the ureaplasmas surrounded the nuclear region but were not observed inside the nuclei. The gentamicin invasion assay detected that 1% of the ATCC strains were inside the infected Hep-2 cells in contrast to 10% to the clinical isolates. The results presented herein will help better understand U. diversum infections and genetic diversity, as much as cellular attachment and virulence.
GENETIC AFFINITIES BETWEEN SPIDER MITE TETRANYCHUS URTICAE (ACARINA:TETRANYCHIDAE) POPULATIONS IN A NON‐AGRICULTURAL AREA

Partial reproductive incompatibility between spider mite populations from adjacent glasshouses is a common phenomenon. It is demonstrated that such a multitude of incompatibilities is not found outdoors between populations collected from ground‐ivy (Glechoma hederacea) growing in a dune area on the west coast of the Netherlands.
S/GSK1349572 is a Potent Next Generation HIV Integrase Inhibitor

Background: S/GSK1349572 was selected as lead molecule from a series of two-metal binding integrase inhibitor scaffolds. We report here its antiviral potency, mechanism of action, and resistance profile. Methods: Antiviral activity of S/GSK1349572 was measured against different HIV strains in various cell lines. Mechanism of action was determined using in vitro integrase strand transfer and binding assays, effects on viral DNA integration, and resistance passage experiments. Fold change (FC) in susceptibility against integrase inhibitor (INI)-resistant mutants was determined with a HeLa-CD4 cell line assay. Results: S/GSK1349572 inhibited HIV integrase in an in vitro strand transfer assay. In PBMC cells, the antiviral EC50 and EC90 values were 0.51 and 2.0 nM, respectively. In MT-4 antiviral assays, the potency shift extrapolated to 100% human serum was 75-fold, resulting in estimated PA-EC90 of 152 nM in PBMCs. S/GSK1349572 had low nM potency against a broad clade panel of HIV-1 isolates representing Groups M and O, and against HIV-2. The mean EC50 against HIV-1 from thirteen subtype B clinical isolates was 0.52 nM. In cellular assays, S/GSK1349572 blocked viral DNA integration with a concomitant increase in 2-LTR circles. When virus was passaged in the presence of S/GSK1349572, highly resistant mutants were not isolated, but mutations which conferred low FC (maximum FC=4.1) were identified within the integrase active site. S/GSK1349572 demonstrated low fold change in activity against raltegravir resistant site directed molecular clones, including Y143R (S/GSK1349572 FC=1.4 and RAL FC=16), Q148K (S/GSK1349572 FC=1.1 and RAL FC=83), N155H (S/GSK1349572 FC=1.2 and RAL FC=11), and G140S, Q148H (S/GSK1349572 FC=2.6 and RAL FC=>130). Conclusions: S/GSK1349572 was a potent inhibitor of HIV integrase in vitro and in cellular HIV replication assays. S/GSK1349572 had a markedly different resistance profile as evidenced by limited cross-resistance to raltegravir resistant molecular clones and the low level maximum resistance to S/GSK1349572 in serial passage. 1 10
Multi-Step Unfolding and Rearrangement of α-Lactalbumin by SDS Revealed by Stopped-Flow SAXS

Interactions between proteins and surfactants are both of fundamental interest and relevant for applications in food, cosmetics and detergency. The anionic surfactant sodium dodecyl sulfate (SDS) denatures essentially all proteins. Denaturation typically involves a number of distinct steps where growing numbers of SDS molecules bind to the protein, as seen in multidisciplinary approaches combining several complementary techniques. We adopt this approach to study the SDS-induced unfolding of Ca2+-depleted α-lactalbumin (aLA), a protein particularly sensitive toward denaturation by surfactants. By combining stopped-flow mixing of protein and surfactant solutions with stopped-flow synchrotron small-angle X-ray scattering (SAXS), circular dichroism (CD) and Trp fluorescence, together with information from previous calorimetric studies, we construct a detailed picture of the unfolding process at the level of both protein and surfactant. A protein-surfactant complex is formed within the dead time of mixing (2.5 ms). Initially a cluster of SDS molecules binds asymmetrically, i.e., to one side of the protein, after which aLA redistributes around the SDS cluster. This occurs in two kinetic steps where the complex grows in number of both SDS and protein molecules, concomitant with protein unfolding. During these steps, the core-shell complex undergoes changes in shell thickness as well as core shape and radius. The entire process is very sensitive to SDS concentration and completes within 10 s at an SDS:aLA ratio of 9, decreasing to 0.2 s at 60 SDS:aLA. The number of aLA molecules per SDS complex drops from 1.9 to 1.0 over this range of ratios. While both CD and Trp kinetics reveal a fast and a slow conformational transition, only the slow transition is observed by SAXS, indicating that the protein-SDS complex (which is monitored by SAXS) adjusts to the presence of the unfolded protein. We attribute the rapid unfolding of aLA to its predominantly α-helical structure, which persists in SDS (albeit as isolated helices), enabling aLA to unfold without undergoing major secondary structural changes unlike β-sheet rich proteins. Nevertheless, the overall unfolding steps are broadly similar to those of the more β-rich protein β-lactoglobulin, suggesting that this unfolding model is representative of the general process of SDS-unfolding of proteins.
Understanding Needs, Breaking Down Barriers: Examining Mental Health Challenges and Well-Being of Correctional Staff in Ontario, Canada

Mental health challenges appear to be extremely prolific and challenging for correctional service employees, affecting persons working in community, institutional, and administrative correctional services. Focusing specifically on correctional workers employed by the Ontario Ministry of the Solicitor General, we shed light on their interpretations of the complexities of their occupational work and of how their work affects staff. Using a qualitative thematic approach to data analyses, we show that participants (n = 67) encounter barriers to treatment seeking, which they describe as tremendous, starting with benefits, wages, and shift work. We let the voices of staff elucidate what is needed to create a healthier correctional workforce. Recommendations include more training opportunities and programs; quarterly, semiannual, or annual appointments with a mental health professional who can assess changes in the mental health status of employees; offsite assessments to ensure confidentiality; and team building opportunities to reduce interpersonal conflict at work and increase moral by improving the work environment.
Reduced Cortical Thickness in the Right Caudal Middle Frontal Is Associated With Symptom Severity in Betel Quid-Dependent Chewers

Background Findings from brain structural imaging studies on betel quid dependence have supported relations between betel quid chewing and alterations in gray matter volume and white matter integrity. However, the effect of betel quid chewing on cortical thickness and the link between cortical thickness and symptom severity remains unascertained. Methods In this observational study, we compared cortical thickness measures from 24 male betel quid-dependent chewers with 27 male healthy controls. Using FreeSufer, we obtained three-dimensional T1-weighted images that were used to compute the thickness of the cerebral cortex throughout the cortical layer. Results Compared to healthy controls, betel quid dependent chewers displayed significant decreased cortical thickness in the precuneus, entorhinal, right paracentral, middle temporal, and caudal middle frontal gyri. Betel quid dependence scale scores negatively correlated (r = -0.604; p = 0.002) with reduced cortical thickness in the right caudal middle frontal of betel quid-dependent chewers. Conclusion The findings provide evidence for cortical thickness abnormality in betel dependent chewers and further propose that the severity of betel quid symptoms may be a critical aspect associated with the cortical alterations. The observed alterations may serve as potential mechanisms to explain why BQ chewing behavior is persistent among individuals with betel quid dependence.
Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of the CsrA Family in the Genus Pseudomonas

Gene expression is adjusted according to cellular needs through a combination of mechanisms acting at different layers of the flow of genetic information. At the posttranscriptional level, RNA-binding proteins are key factors controlling the fate of nascent and mature mRNAs. Among them, the members of the CsrA family are small dimeric proteins with heterogeneous distribution across the bacterial tree of life, that act as global regulators of gene expression because they recognize characteristic sequence/structural motifs (short hairpins with GGA triplets in the loop) present in hundreds of mRNAs. The regulatory output of CsrA binding to mRNAs is counteracted in most cases by molecular mimic, non-protein coding RNAs that titrate the CsrA dimers away from the target mRNAs. In γ-proteobacteria, the regulatory modules composed by CsrA homologs and the corresponding antagonistic sRNAs, are mastered by two-component systems of the GacS-GacA type, which control the transcription and the abundance of the sRNAs, thus constituting the rather linear cascade Gac-Rsm that responds to environmental or cellular signals to adjust and coordinate the expression of a set of target genes posttranscriptionally. Within the γ-proteobacteria, the genus Pseudomonas has been shown to contain species with different number of active CsrA (RsmA) homologs and of molecular mimic sRNAs. Here, with the help of the increasing availability of genomic data we provide a comprehensive state-of-the-art picture of the remarkable multiplicity of CsrA lineages, including novel yet uncharacterized paralogues, and discuss evolutionary aspects of the CsrA subfamilies of the genus Pseudomonas, and implications of the striking presence of csrA alleles in natural mobile genetic elements (phages and plasmids).
Gender Differences in Associated and Predictive Factors of Anxiety and Depression in People With Epilepsy

Purpose Comorbid anxiety and depression in people with epilepsy (PWE) are highly prevalent and contribute to low quality of life (QOL) and may even lead to poor outcomes of epilepsy. Among the various factors that affect these negative emotional comorbidities, possible gender differences remain poorly understood and are often neglected. This research aimed to determine whether there are discrepancies in the incidence and influence factors of anxiety and depression between men and women with epilepsy in a hospital in northwest China. Methods A total of 158 adult PWE (female: N = 65; 41.1%) completed self-report questionnaires, including the Self-rating Anxiety Scale (SAS), the Self-rating Depression Scale (SDS), the Chinese version of the Quality of Life in Epilepsy-31 (QOLIE-31) inventory and the Pittsburgh Sleep Quality Inventory (PSQI). The comparison between male and female PWE was made by regression analysis. Results For the prevalence of anxiety and depression in PWE, no gender difference was found in this study. However, the moderating factors of psychiatric comorbidities were significantly different between men and women: male PWE with comorbid anxiety were more likely to be affected by sleep quality, while anxiety symptoms in female PWE were closely associated with the frequency of seizures. Education years and QOL social function were significant indicators of depression in male PWE but not in female PWE. The important and common predictor for anxiety and depressive symptoms in PWE was QOL energy/fatigue, with male patients being more affected. Conclusion For the PWE included in this study, the incidence of comorbid anxiety and depression in PWE was similar for men and women, but the moderating factors affecting comorbid anxiety and depressive disorders differed between genders: male PWE were more likely to be affected by psychosocial factors, while female PWE were more influenced by epilepsy itself. This exploration suggests that gender-specific health care should be considered in epilepsy therapy to improve the psychiatric condition and QOL of PWE, and different treatments should be conducted for male and female PWE to prevent negative emotional comorbidities.
An Internet of things platform for Air Station remote sensing and smart monitoring

Air pollution is currently receiving more attention by international governments and organizations. Nevertheless, current systems for air quality monitoring lack essential requirements which are key in order to be effective concerning users’ access to the information and efﬁcient regarding real-time monitoring and notiﬁcation. This paper presents an Internet of Things platform for air station remote sensing and smart monitoring that combines Big Data and Cloud Computing paradigms to process and correlate air pollutant concentrations coming from multiple remote stations, as well as to trigger automatic and personalized alerts when a health risk for their particular context is detected. This platform has been tested by analyzing the results of observing Andalusian, South of Spain, sensor network during a long period of time. The results show that this novel solution can help to reduce the impact of air pollution on human health since citizens are alerted in real time.
TeenSensor: ?Gaussian processes for micro-blog based Teen's acute and chronic stress detection

Stress is a common problem all over the world. More and more teenagers today have to cope with different stressor events coming from school, family, peer relation, self-cognition, romantic relation, etc. Over-stress without proper guidance will lead to a series of potential problems including physical and mental disorders, and even suicide due to the shortage of teen’ s psychological endurance and controllability. Therefore, it is necessary and important to timely sense adolescents’ stress and help them release the stress properly. In this paper, we present a micro-blog based system called TeenSensor, aiming to detect teens acute and chronic stress from their tweeting contents (including linguistic text, song, picture, emoticon, punctuation) and tweeting context (time, and frequency) on micro-blog. We conduct a user study where 69 16/17-year-old high-school students got involved. The result shows that sensing teenagers acute and chronic stress is feasible through the open micro-blog, achieving 69.6% accuracy for acute and 72.2% for chronic, respectively. TeenSensor performs better in detecting the stress of introvert teens than extrovert teens. Among the four typical types of teens stress, self-cognition stress is revealed the least from micro-blog, compared to the study, inter-personal, and affection stress types.
Directly accessing the diversity of bacterial type I polyketide synthase gene in Chinese soil and seawater

Many bacteria are known to produce a wide range of biomedically important secondary metabolites synthesized by type I polyketide synthases (PKSs). These enzymes own a modular structure that could be used for combinatorial biosynthesis to yield novel drug candidates. To directly access PKS gene diversity of soil and seawater in China, a set of degenerate oligonucleotide primers were designed to amplify the ketoacyl synthase (KS)fragments belonging to the PKS I genes from the soil and the seawater samples. Twenty-three (23) new KS fragments were obtained. Their predicted amino acid sequences showed 45 to 85% identifies to the known KS domains in the GenBank. Phylogenetic analysis indicated that 14 of them belonged to the “normal” KS groups that catalyzed the condensation of the acyl groups and the other nine KS fragments belonged to the hybrid PKS/NRPS (non-ribosomal peptide synthase) groups which used an amino acid moiety as a starter unit. All the four KS fragments isolated from the seawater belonged to the former group. No significant difference was found between the soil KS fragments and the seawater KS fragments. Several KS fragments were endowed with some distinct characters that will be useful as probes for future studies. Key words: Uncultured microorganisms, polyketide synthase, ketoacyl synthase, soil, seawater.
Relational Memory at Short and Long Delays in Individuals With Moderate-Severe Traumatic Brain Injury

Memory deficits are a common and frequently-cited consequence of moderate-severe traumatic brain injury (TBI). However, we know less about how TBI influences relational memory, which allows the binding of the arbitrary elements of experience and the flexible use and recombination of relational representations in novel situations. Relational memory is of special interest for individuals with TBI, given the vulnerability of the hippocampus to injury mechanisms, as well as a growing body of literature establishing the role of relational memory in flexible and goal-directed behavior. In this study, participants with and without a history of moderate-severe TBI completed a continuous relational memory task for face-scene pairings. Participants with TBI exhibited a disruption in relational memory not only when tested after a delay, but also when tested with no experimenter-imposed delay after stimulus presentation. Further, canonical assessments of working and episodic memory did not correspond with performance on the face-scene task, suggesting that this task may tap into relational memory differently and with greater sensitivity than standardized memory assessments. These results highlight the need for rigorous assessment of relational memory in TBI, which is likely to detect deficits that have specific consequences for community reintegration and long-term functional outcomes.
INDUCTION OF CYTOCHROME P-450 1A1 IN HUMAN HEPATOMA HepG2 AND LUNG CARCINOMA NCI-H322 CELLS BY MOTORCYCLE EXHAUST PARTICULATE

The effects of motorcycle exhaust particulate (MEP) on human cytochrome P-450 (P-450)-dependent monooxygenases were determined using human hepatoma cell line HepG2 and lung carcinoma cell line NCI-H322 treated with organic extracts of MEP from a two-stroke engine. Gas chromatography and mass spectrometry analysis of MEP extract revealed the presence of carcinogens benzo[a]pyrene, benz[a]anthracene, benzo[b]fluoranthene, benzo[k]fluoranthene, benzo[g,h,i]perylene, chrysene, and indeno[1,2,3-c,d]pyrene in the chemical mixture. Treatment with MEP extract produced concentration- and time-dependent increases of monooxygenase activity in HepG2 cells. Treatment of the cells with 100 µg/ml MEP extract for 24 h markedly increased benzo[a]pyrene hydroxylation, 7-ethoxycoumarin, and 7-ethoxyresorufin O-deethylation activities in microsomes. Immunoblot analysis of microsomal proteins using mouse monoclonal antibody 1-12-3 against P-450 1A1 revealed that MEP extract induced a P-450-immunorelated protein in the hepatoma cells. RNA blot analysis of cellular total RNA using a human P-450 1A1 3? -end cDNA probe showed that MEP extract increased the level of a hybridizable P-450 mRNA. These P-450 1A1 inductive effects of MEP extract were similar to those from treatment with 10 µM benzo[a]pyrene or 3-methylcholanthrene (3-MC) in HepG2 cells. Treatment of lung carcinoma NCI-H322 cells with 100 µg/ml MEP extract, 10 µM benzo[a]pyrene, or 3-MC resulted in induction of monooxygenase activity, protein, and mRNA of P-450 1A1, similar to the induction observed with the hepatoma cells. The present study demonstrates that MEP extract has the ability to induce human hepatic and pulmonary P-450 1A1 in the liver- and lung-derived cell lines, and the induction involves a pretranslational mechanism. Induction of the human hepatic and pulmonary P-450 1A1 in vitro may provide important information in the assessment of MEP metabolism and toxicity in humans.