Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying a rainfall event threshold triggering herbicide leaching by preferential flow

How can leaching risk be assessed if the chemical flux and/or the toxicity is highly uncertain? For many strongly sorbing pesticides it is known that their transport through the unsaturated zone occurs intermittently through preferential flow, triggered by significant rainfall events. In these circumstances the timing and frequency of these rainfall events may allow quantification of leaching risk to overcome the limitations of flux prediction. In this paper we analyze the leaching behavior of bromide and two herbicides, methabenzthiazuron and ethidimuron, using data from twelve uncropped lysimeters, with high‐resolution climate data, in order to identify the rainfall controls on rapid solute leaching. A regression tree analysis suggested that a coarse‐scale fortnightly to monthly water balance was a good predictor of short‐term increases in drainage and bromide transport. Significant short‐term herbicide leaching, however, was better predicted by the occurrence of a single storm with a depth greater than a 19 mm threshold. Sampling periods where rain events exceeded this threshold accounted for between 38% and 56% of the total mass of herbicides leached during the experiment. The same threshold only accounted for between 1% and 10% of the total mass of bromide leached. On the basis of these results, we conclude that in this system, the leaching risks of strongly sorbing chemicals can be quantified by the timing and frequency of these large rainfall events. Empirical and modeling approaches are suggested to apply this frequentist approach to leaching risk assessment to other soil‐climate systems.
A body joint improves vertical to horizontal transitions of a wall-climbing robot

Several recently-designed robots are able to scale steep surfaces using animal-inspired strategies for foot attachment and leg kinematics. These designs could be valuable for reaching high vantage points or for overcoming large obstacles. However, most of these robots cannot transition between intersecting surfaces. For example, our previous Climbing Mini-WhegsTM robot cannot make a 90deg transition from a vertical wall up onto a flat horizontal surface. It is known that cockroaches bend their body to accomplish such transitions. This concept has been simplified to a single-axis body joint which allows ground-walking robots to cross uneven terrain. In this work, we examine the effect of a body joint on wall-climbing vehicles using both a kinematic simulation and two prototype Climbing Mini-WhegsTM robots. The simulation accurately predicts that the better design has the body joint axle closer to the center of the robot than to the front wheel- legs for orthogonal exterior transitions for a wide range of initial conditions. In the future, the methods and principles demonstrated here could be used to improve the design of climbing robots for other environments.
Discovery of a Conjugative Megaplasmid in Bifidobacterium breve

ABSTRACT Bifidobacterium breve is a common and sometimes very abundant inhabitant of the human gut. Genome sequencing of B. breve JCM 7017 revealed the presence of an extrachromosomal element, designated pMP7017 consisting of >190 kb, thus representing the first reported bifidobacterial megaplasmid. In silico characterization of this element revealed several genomic features supporting a stable establishment of the megaplasmid in its host, illustrated by predicted CRISPR-Cas functions that are known to protect the host against intrusion of foreign DNA. Interestingly, pMP7017 is also predicted to encode a conjugative DNA transfer apparatus and, consistent with this notion, we demonstrate here the conjugal transfer of pMP7017 to representative strains of B. breve and B. longum subsp. longum. We also demonstrate the presence of a megaplasmid with homology to pMP7017 in three B. longum subsp. longum strains.
Identification of a Novel UT-B Urea Transporter in Human Urothelial Cancer

The urea transporter UT-B is widely expressed and has been studied in erythrocyte, kidney, brain and intestines. Interestingly, UT-B gene has been found more abundant in bladder than any other tissue. Recently, gene analyses demonstrate that SLC14A1 (UT-B) gene mutations are associated with bladder cancer, suggesting that urea transporter UT-B may play an important role in bladder carcinogenesis. In this study, we examined UT-B expression in bladder cancer with human primary bladder cancer tissues and cancer derived cell lines. Human UT-B has two isoforms. We found that normal bladder expresses long form of UT-B2 but was lost in 8 of 24 (33%) or significantly downregulated in 16 of 24 (67%) of primary bladder cancer patients. In contrast, the short form of UT-B1 lacking exon 3 was detected in 20 bladder cancer samples. Surprisingly, a 24-nt in-frame deletion in exon 4 in UT-B1 (UT-B1Δ24) was identified in 11 of 20 (55%) bladder tumors. This deletion caused a functional defect of UT-B1. Immunohistochemistry revealed that UT-B protein levels were significantly decreased in bladder cancers. Western blot analysis showed a weak UT-B band of 40 kDa in some tumors, consistent with UT-B1 gene expression detected by RT-PCR. Interestingly, bladder cancer associate UT-B1Δ24 was barely sialylated, reflecting impaired glycosylation of UT-B1 in bladder tumors. In conclusion, SLC14A1 gene and UT-B protein expression are significantly changed in bladder cancers. The aberrant UT-B expression may promote bladder cancer development or facilitate carcinogenesis induced by other carcinogens.
Helicobacter pylori and T Helper Cells: Mechanisms of Immune Escape and Tolerance

Helicobacter pylori colonizes the gastric mucosa of at least half of the human population, causing a worldwide infection that appears in early childhood and if not treated, it can persist for life. The presence of symptoms and their severity depend on bacterial components, host susceptibility, and environmental factors, which allow H. pylori to switch between commensalism and pathogenicity. H. pylori-driven interactions with the host immune system underlie the persistence of the infection in humans, since the bacterium is able to interfere with the activity of innate and adaptive immune cells, reducing the inflammatory response in its favour. Gastritis due to H. pylori results from a complex interaction between several T cell subsets. In particular, H. pylori is known to induce a T helper (Th)1/Th17 cell response-driven gastritis, whose impaired modulation caused by the bacterium is thought to sustain the ongoing inflammatory condition and the unsuccessful clearing of the infection. In this review we discuss the current findings underlying the mechanisms implemented by H. pylori to alter the T helper lymphocyte proliferation, thus facilitating the development of chronic infections and allowing the survival of the bacterium in the human host.
Determining Variables of Plyometric Training for Improving Vertical Jump Height Performance: A Meta-Analysis

Saez Saez de Villarreal, E, Kellis, E, Kraemer, WJ, and Izquierdo, M. Determining variables of plyometric training for improving vertical jump height performance: a meta-analysis. J Strength Cond Res 23(2): 495-506, 2009-Plyometric training improves vertical jump height (VJH). However, the effectiveness of plyometric training depends on various factors. A meta-analysis of 56 studies with a total of 225 effect sizes (ESs) was carried out to analyze the role of various factors on the effects of plyometrics on VJH performance. The inclusion criteria for the analysis were a) studies using plyometric programs for lower-limb muscles, b) studies employing true experimental designs and valid and reliable measurements, and c) studies including enough data to calculate ESs. Subjects with more experience in sport obtained greater enhancements in VJH performance (p < 0.01). Subjects in either good or bad physical condition benefit equally from plyometric work (p < 0.05), although men tend to obtain better power results than women after plyometric training (p < 0.05). With relation to the variables of performance, training volumes of more than 10 weeks and more than 20 sessions, using high-intensity programs (with more than 50 jumps per session), were the strategies that seemed to maximize the probability of obtaining significantly greater improvements in performance (p < 0.05). To optimize jumping enhancement, the combination of different types of plyometrics (squat jump + countermovement jump + drop jump) is recommended rather than using only 1 form (p < 0.05). However, no extra benefits were found to be gained from doing plyometrics with added weight. The responses identified in this analysis are essential and should be considered by strength and conditioning professionals with regard to the most appropriate dose-response trends for optimizing plyometric-induced gains.
Prevention of Pulmonary Hypertension by Angiotensin-Converting Enzyme 2 Gene Transfer

In spite of recent advancements in the treatment of pulmonary hypertension, successful control has yet to be accomplished. The abundant presence of angiotensin-converting enzyme 2 (ACE2) in the lungs and its impressive effect in the prevention of acute lung injury led us to test the hypothesis that pulmonary overexpression of this enzyme could produce beneficial outcomes against pulmonary hypertension. Monocrotaline (MCT) treatment of mice for 8 weeks resulted in significant increases in right ventricular systolic pressure, right ventricle:left ventricle plus septal weight ratio, and muscularization of pulmonary vessels. Administration of a lentiviral vector containing ACE2, 7 days before MCT treatment prevented the increases in right ventricular systolic pressure (control: 25±1 mm Hg; MCT: 44±5 mm Hg; MCT+ACE2: 26±1 mm Hg; n=6; P<0.05) and right ventricle:left ventricle plus septal weight ratio (control: 0.25±0.01; MCT: 0.31±0.01; MCT+ACE2: 0.26±0.01; n=8; P<0.05). A significant attenuation in muscularization of pulmonary vessels induced by MCT was also observed in animals overexpressing ACE2. These beneficial effects were associated with an increase in the angiotensin II type 2 receptor:angiotensin II type 1 receptor mRNA ratio. Also, pulmonary hypertension–induced increases in proinflammatory cytokines were significantly attenuated by lentiviral vector–containing ACE2 treatment. Furthermore, ACE2 gene transfer in mice after 6 weeks of MCT treatment resulted in a significant reversal of right ventricular systolic pressure. These observations demonstrate that ACE2 overexpression prevents and reverses right ventricular systolic pressure and associated pathophysiology in MCT-induced pulmonary hypertension by a mechanism involving a shift from the vasoconstrictive, proliferative, and fibrotic axes to the vasoprotective axis of the renin-angiotensin system and inhibition of proinflammatory cytokines.
Acute pulmonary and moderate cardiovascular responses of spontaneously hypertensive rats after exposure to single-wall carbon nanotubes

Abstract As a novel kind of nanomaterial with wide potential applications, the adverse effects of carbon nanotubes (CNTs) have recently received significant attention after respiratory exposure. In this study, single-wall carbon nanotubes (SWCNTs) containing different metal contents were intratracheally instilled into lungs of spontaneously hypertensive rats. Pulmonary and cardiovascular system alterations were evaluated at 24 and 72 h post-instillation. Biomarkers of inflammation, oxidative stress and cell damage in the bronchoalveolar lavage fluid (BALF) were increased significantly 24 h post-exposure of SWCNTs. The increased endothelin-1 levels in BALF and plasma and angiotensin I-converting enzyme in plasma suggested endothelial dysfunction in the pulmonary circulation and peripheral vascular thrombosis. These findings suggest that respiratory exposure to SWCNTs can induce acute pulmonary and cardiovascular responses and individuals with existing cardiovascular diseases are very susceptible to SWCNTs exposure. The co-existence of metal residues in SWCNTs can aggravate the adverse effects.
Interaction of complexes I, III, and IV within the bovine respirasome by single particle cryoelectron tomography

The respirasome is a multisubunit supercomplex of the respiratory chain in mitochondria. Here we report the 3D reconstruction of the bovine heart respirasome, composed of dimeric complex III and single copies of complex I and IV, at about 2.2-nm resolution, determined by cryoelectron tomography and subvolume averaging. Fitting of X-ray structures of single complexes I, III2, and IV with high fidelity allows interpretation of the model at the level of secondary structures and shows how the individual complexes interact within the respirasome. Surprisingly, the distance between cytochrome c binding sites of complexes III2 and IV is about 10 nm. Modeling indicates a loose interaction between the three complexes and provides evidence that lipids are gluing them at the interfaces.
Auditory activation of ‘visual’ cortical areas in the blind mole rat (Spalax ehrenbergi)

The mole rat (Spalax ehrenbergi) is a subterranean rodent whose adaptations to its fossorial life include an extremely reduced peripheral visual system and an auditory system suited for the perception of vibratory stimuli. We have previously shown that in this blind rodent the dorsal lateral geniculate nucleus, the primary visual thalamic nucleus of sighted mammals, is activated by auditory stimuli. In this report we focus on the manifestation of this cross‐modal compensation at the cortical level. Cyto‐ and myeloarchitectural analyses of the occipital area showed that despite the almost total blindness of the mole rat this area has retained the organization of a typical mammalian primary visual cortex. Application of the metabolic marker 2‐deoxyglucose and electrophysiological recording of evoked field potentials and single‐unit activity disclosed that a considerable part of this area is activated by auditory stimuli. Previous neuronal tracing studies had revealed the origin of the bulk of this auditory input to be the dorsal lateral geniculate nucleus which itself receives auditory input from the inferior colliculus.
Multiclass Classification Calibration Functions

In this paper we refine the process of computing calibration functions for a number of multiclass classification surrogate losses. Calibration functions are a powerful tool for easily converting bounds for the surrogate risk (which can be computed through well-known methods) into bounds for the true risk, the probability of making a mistake. They are particularly suitable in non-parametric settings, where the approximation error can be controlled, and provide tighter bounds than the common technique of upper-bounding the 0-1 loss by the surrogate loss. The abstract nature of the more sophisticated existing calibration function results requires calibration functions to be explicitly derived on a case-by-case basis, requiring repeated efforts whenever bounds for a new surrogate loss are required. We devise a streamlined analysis that simplifies the process of deriving calibration functions for a large number of surrogate losses that have been proposed in the literature. The effort of deriving calibration functions is then surmised in verifying, for a chosen surrogate loss, a small number of conditions that we introduce. As case studies, we recover existing calibration functions for the well-known loss of Lee et al. (2004), and also provide novel calibration functions for well-known losses, including the one-versus-all loss and the logistic regression loss, plus a number of other losses that have been shown to be classification-calibrated in the past, but for which no calibration function had been derived.
Iron monitoring of male and female rugby sevens players over an international season.

BACKGROUND Given the likely influence that high training loads, contact-induced hemolysis and female-specific requirements have on the incidence of iron deficiency, characterizing the direction and magnitude of fluctuations in iron status over an international season is important for managing player health and physical performance in rugby sevens. METHODS Australian national male (N.=27) and female (N.=23) rugby sevens players undertook blood tests at pre-season, mid-season, and end-season. Hemoglobin (Hb), hematocrit (Hct), ferritin, transferrin and transferrin saturation were quantified. Female athletes also reported oral contraceptive use and a subset (N.=7) provided 7-day food diaries to quantify iron intake. RESULTS Male players typically had a three-fold higher ferritin concentration than females. Pre-season ferritin concentrations in male (151±66 µg/L) and female (51±24 µg/L) players declined substantially (~20%) by mid-season but recovered by end-season. Over the season 23% of female players were classified as iron deficient (ferritin <30 µg/L) and prescribed supplementation. The greatest incidence of iron deficiency in female players occurred mid-season (30%). Oral contraception and dietary iron intake had an unclear influence on female players' ferritin concentration, while age was largely positively correlated (r=0.66±~0.33). CONCLUSIONS Given the relatively low ferritin concentrations evident in female rugby sevens players, and the potential for a further decline midway through a season when physical load may be at its highest, 6-monthly hematological reviews are suggested in combination with dietary management. Annual screening may be beneficial for male players, with further monitoring only when clinically indicated.
Lumbar Spinous Process Splitting Decompression Provides Equivalent Outcomes to Conventional Midline Decompression in Degenerative Lumbar Canal Stenosis: A Prospective, Randomized Controlled Study of 51 Patients

Study Design. Prospective, randomized controlled study. Objective. To compare the functional outcomes and extent of paraspinal muscle damage between 2 decompressive techniques for lumbar canal stenosis. Summary of Background Data. Lumbar spinous process splitting decompression (LSPSD) preserves the muscular and liga-mentous attachments of the posterior elements of the spine. It can potentially avoid problems such as paraspinal muscle atrophy and trunk extensor weakness that can occur after conventional midline decompression. However, large series prospective randomized controlled studies are lacking. Methods. Patients with lumbar canal stenosis were randomly allocated into 2 groups: LSPSD (28 patients) and conventional midline decompression (23 patients). The differences in operative time, blood loss, time to comfortable mobilization, and hospital stay were studied. Paraspinal muscle damage was assessed by postoperative rise in creatine phosphokinase and C-reactive protein levels. Functional outcome was evaluated at 1 year by Japanese Orthopaedic Association score, neurogenic claudication outcome score, and visual analogue scale for back pain and neurogenic claudication. Results. Fifty-one patients of mean age 56 years were followed-up for a mean 14.2 ± 2.9 months. There were no significant differences in the operative time, blood loss, and hospital stay. Both the groups showed significant improvement in the functional outcome scores at 1 year. Between the 2 groups, the Japanese Orthopaedic Association score, neurogenic claudication outcome score improvement, visual analogue scale for back pain, neurogenic claudication visual analogue scale, and the postoperative changes in serum C-reactive protein and creatine phosphokinase levels did not show any statistically significant difference. On the basis of the Japanese Orthopaedic Association recovery rate, it was found that 73.9% of conventional midline decompression group had good outcomes compared with only 60.7% after LSPSD. Conclusion. The functional outcome scores, back pain, and claudication pain in the immediate period and at the end of 1 year are similar in both the techniques. More patients had better functional outcomes after conventional decompression than the LSPSD technique. On the basis of this study, the superiority of one technique compared with the other is not established, mandating the need for further long-term studies. Level of Evidence: 2
Profiling of Substrate Specificity of SARS-CoV 3CLpro

Background The 3C-like protease (3CLpro) of severe acute respiratory syndrome-coronavirus is required for autoprocessing of the polyprotein, and is a potential target for treating coronaviral infection. Methodology/Principal Findings To obtain a thorough understanding of substrate specificity of the protease, a substrate library of 198 variants was created by performing saturation mutagenesis on the autocleavage sequence at P5 to P3' positions. The substrate sequences were inserted between cyan and yellow fluorescent proteins so that the cleavage rates were monitored by in vitro fluorescence resonance energy transfer. The relative cleavage rate for different substrate sequences was correlated with various structural properties. P5 and P3 positions prefer residues with high β-sheet propensity; P4 prefers small hydrophobic residues; P2 prefers hydrophobic residues without β-branch. Gln is the best residue at P1 position, but observable cleavage can be detected with His and Met substitutions. P1' position prefers small residues, while P2' and P3' positions have no strong preference on residue substitutions. Noteworthy, solvent exposed sites such as P5, P3 and P3' positions favour positively charged residues over negatively charged one, suggesting that electrostatic interactions may play a role in catalysis. A super-active substrate, which combined the preferred residues at P5 to P1 positions, was found to have 2.8 fold higher activity than the wild-type sequence. Conclusions/Significance Our results demonstrated a strong structure-activity relationship between the 3CLpro and its substrate. The substrate specificity profiled in this study may provide insights into a rational design of peptidomimetic inhibitors.
Selection of Suitable Reference Genes for qPCR Normalization under Abiotic Stresses and Hormone Stimuli in Carrot Leaves

Carrot, a biennial herb of the Apiaceae family, is among the most important vegetable crops in the world. In this study, nine candidate reference genes (GAPDH, ACTIN, eIF-4α, PP2A, SAND, TIP41, UBQ, EF-1α, and TUB) were cloned from carrot. Carrot plants were subjected to abiotic stresses (heat, cold, salt, and drought) and hormone stimuli (gibberellin, salicylic acid, methyl jasmonate, and abscisic acid). The expression profiles of the candidate reference genes were evaluated in three technical and biological replicates. Real-time qPCR data analyses were performed using three commonly used Excel-based applets namely, BestKeeper, geNorm, and NormFinder. ACTIN and TUB were the most stable genes identified among all sample groups, but individual analysis revealed changes in their expression profiles. GAPDH displayed the maximum stability for most of single stresses. To further validate the suitability of the reference genes identified in this study, the expression profile of DcDREB-A1 gene (homolog of AtDREB-A1 gene of Arabidophsis) was studied in carrot. The appropriate reference genes were selected that showed stable expression under the different experimental conditions.
The Design of Vertical R&D Collaborations

Suppliers play a major role in innovation processes. We analyze ownership allocations and the choice of R&D technology in vertical R&D cooperations. Given incomplete contracts on the R&D outcome, there is a tradeoff between R&D specifically designed towards a manufacturer (increasing investment productivity) and a general technology (hold-up reduction). We find that the market solution yields the specific technology in too few cases. More intense product market competition shifts optimal ownership towards the supplier. The use of exit clauses increases the gains from the collaboration.