Miracle-dz/UniFAR-FTUs huggingface dataset:
The InhA2 Metalloprotease of Bacillus thuringiensis Strain 407 Is Required for Pathogenicity in Insects Infected via the Oral Route

ABSTRACT The entomopathogenic bacterium Bacillus thuringiensis is known to secrete a zinc metalloprotease (InhA) that specifically cleaves antibacterial peptides produced by insect hosts. We identified a second copy of the inhA gene, named inhA2, in B. thuringiensis strain 407 Cry−. The inhA2 gene encodes a putative polypeptide showing 66.2% overall identity with the InhA protein and harboring the zinc-binding domain (HEXXH), which is characteristic of the zinc-requiring metalloproteases. We used a transcriptional inhA2′-lacZ fusion to show that inhA2 expression is induced at the onset of the stationary phase and is overexpressed in a Spo0A minus background. The presence of a reverse Spo0A box in the promoter region of inhA2 suggests that Spo0A directly regulates the transcription of inhA2. To determine the role of the InhA and InhA2 metalloproteases in pathogenesis, we used allelic exchange to isolate single and double mutant strains for the two genes. Spores and vegetative cells of the mutant strains were as virulent as those of the parental strain in immunized Bombyx mori larvae infected by the intrahemocoelic route. Exponential phase cells of all the strains displayed the same in vitro potential for colonizing the vaccinated hemocoel. We investigated the synergistic effect of the mutant strain spores on the toxicity of Cry1C proteins against Galleria mellonella larvae infected via the oral pathway. The spores of ΔinhA2 mutant strain were ineffective in providing synergism whereas those of the ΔinhA mutant strain were not. These results indicate that the B. thuringiensis InhA2 zinc metalloprotease has a vital role in virulence when the host is infected via the oral route.
Abnormal localization of cystic fibrosis transmembrane conductance regulator in primary cultures of cystic fibrosis airway epithelia

Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), a membrane glycoprotein that forms Cl- channels. Previous work has shown that when some CF- associated mutants of CFTR are expressed in heterologous cells, their glycosylation is incomplete. That observation led to the hypothesis that such mutants are not delivered to the plasma membrane where they can mediate Cl- transport. Testing this hypothesis requires localization of CFTR in nonrecombinant cells and a specific determination of whether CFTR is in the apical membrane of normal and CF epithelia. To test the hypothesis, we used primary cultures of airway epithelia grown on permeable supports because they polarize and express the CF defect in apical Cl- permeability. Moreover, their dysfunction contributes to disease. We developed a semiquantitative assay, using nonpermeabilized epithelia, an antibody directed against an extracellular epitope of CFTR, and large (1 microns) fluorescent beads which bound to secondary antibodies. We observed specific binding to airway epithelia from non-CF subjects, indicating that CFTR is located in the apical membrane. In contrast, there was no specific binding to the apical membrane of CF airway epithelia. These data were supported by qualitative studies using confocal microscopy: the most prominent immunostaining was in the apical region of non-CF cells and in cytoplasmic regions of CF cells. The results indicate that CFTR is either missing from the apical membrane of these CF cells or it is present at a much reduced level. The data support the proposed defective delivery of some CF-associated mutants to the plasma membrane and explain the lack of apical Cl- permeability in most CF airway epithelia.
ATF4 Degradation Relies on a Phosphorylation-Dependent Interaction with the SCFβTrCPUbiquitin Ligase

ABSTRACT The ubiquitin-proteasome pathway regulates gene expression through protein degradation. Here we show that the F-box protein βTrCP, the receptor component of the SCF E3 ubiquitin ligase responsible for IκBα and β-catenin degradation, is colocalized in the nucleus with ATF4, a member of the ATF-CREB bZIP family of transcription factors, and controls its stability. Association between the two proteins depends on ATF4 phosphorylation and on ATF4 serine residue 219 present in the context of DSGXXXS, which is similar but not identical to the motif found in other substrates of βTrCP. ATF4 ubiquitination in HeLa cells is enhanced in the presence of βTrCP. The F-box-deleted βTrCP protein behaves as a negative transdominant mutant that inhibits ATF4 ubiquitination and degradation and, subsequently, enhances its activity in cyclic AMP-mediated transcription. ATF4 represents a novel substrate for the SCFβTrCP complex, which is the first mammalian E3 ubiquitin ligase identified so far for the control of the degradation of a bZIP transcription factor.
Roles of Purinergic Receptor P2Y, G Protein–Coupled 12 in the Development of Atherosclerosis in Apolipoprotein E–Deficient Mice

Objective—The aim of the study was to evaluate the role of purinergic receptor P2Y, G protein–coupled 12 (P2Y12), an ADP receptor, in the development of atherosclerotic lesions. Methods and Results—Apolipoprotein E–null mice were crossed with P2y12−/− mice to generate double knockout mice. The double knockout mice and the control apolipoprotein E–null mice were fed a high-fat diet for 20 weeks. Assessment of the atherosclerotic lesions in the control and double knockout mice demonstrated that P2Y12 deficiency caused a diminished lesion area, an increased fibrous content at the plaque site, and decreased monocyte/macrophage infiltration of the lesions. Polymerase chain reaction studies revealed that white blood cells do not express significant levels of P2Y12. Bone marrow transplantation experiments confirmed that P2Y12 expressed on platelets is a key factor responsible for atherosclerosis, but do not exclude a role of smooth muscle cell P2Y12. Supernatant fluid from activated P2y12+/+ but not P2y12−/− platelets was capable of causing monocyte migration. In vitro studies showed that platelet P2Y12 deficiency suppressed platelet factor 4 secretion and P-selectin expression. Further work demonstrated that platelet P2Y12, through inhibition of the cAMP/protein kinase A pathway, critically regulates the release of platelet factor 4, and thereby affects monocyte recruitment and infiltration. Conclusion—These results demonstrate that P2Y12 modulates atherogenesis, at least in part by augmenting inflammatory cell recruitment via regulation of platelet &agr;-granule release.
Wide genetic variation in phenolic compound content of seed coats among black soybean cultivars

Black soybeans have been used as a food source and also in traditional medicine because their seed coats contain natural phenolic compounds such as proanthocyanidin and anthocyanin. The objective of this research is to reveal the genetic variation in the phenolic compound contents (PCCs) of seed coats in 227 black soybean cultivars, most of which were Japanese landraces and cultivars. Total phenolics were extracted from seed coats using an acidic acetone reagent and the proanthocyanidin content, monomeric anthocyanin content, total flavonoids content, total phenolics content, and radical scavenging activity were measured. The cultivars showed wide genetic variation in PCCs. Each of the contents was highly correlated with one another, and was closely associated with radical scavenging activity. PCCs were also moderately associated by flowering date but not associated by seed weight. Cultivars with purple flowers had a tendency to produce higher PCCs compared with cultivars with white flowers, suggesting that the W1 locus for flower color can affect phenolic compound composition and content. Our results suggest that developing black soybean cultivars with high functional phenolic compounds activity is feasible.
Proliferative Activity of Liver Growth Factor is Associated with an Improvement of Cigarette Smoke-Induced Emphysema in Mice

Cigarette smoke (CS)-induced emphysema is a major component of chronic obstructive pulmonary disease (COPD). COPD treatment is based on the administration of bronchodilators and corticosteroids to control symptoms and exacerbations, however, to date, there are no effective therapies to reverse disease progression. Liver growth factor (LGF) is an albumin-bilirubin complex with mitogenic properties, whose therapeutic effects have previously been reported in a model of emphysema and several rodent models of human disease. To approach the therapeutic effect of LGF in a model of previously established emphysema, morphometric and lung function parameters, matrix metalloproteinase (MMP) activity and the expression of several markers, such as VEGF, PCNA, 3NT and Nrf2, were assessed in air-exposed and CS-exposed C57BL/6J male mice with and without intraperitoneal (i.p.) injection of LGF. CS-exposed mice presented a significant enlargement of alveolar spaces, higher alveolar internal area and loss of lung function that correlated with higher MMP activity, higher expression of 3NT and lower expression of VEGF. CS-exposed mice injected with LGF, showed an amelioration of emphysema and improved lung function, which correlated with lower MMP activity and 3NT expression and higher levels of VEGF, PCNA and Nrf2. Taken together, this study suggests that LGF administration ameliorates CS-induced emphysema, highlights the ability of LGF to promote alveolar cell proliferation and may be a promising strategy to revert COPD progression.
The Holomorphic tension of vortices

We study the tension of vortices in = 2 SQCD broken to = 1 by a superpotential W(Φ), in color-flavor locked vacua. The tension can be written as T = T BPS+T non BPS . The BPS tension is equal to 4π|| where we call the holomorphic tension. This is directly related to the central charge of the supersymmetry algebra. Using the tools of the Cachazo-Douglas-Seiberg-Witten solution we compute the holomorphic tension as a holomorphic function of the couplings, the mass and the dynamical scale: = (W'2+f)1/2. A first approximation is given using the generalized Konishi anomaly in the semiclassical limit. The full quantum corrections are computed in the strong coupling regime using the factorization equations that relate the = 2 curve to the = 1 curve. Finally we study the limit in which the non-BPS contribution can be neglected because small with respect to the BPS one. In the case of linear superpotential the non-BPS contribution vanishes exactly and the holomorphic tension gets no quantum corrections.
Optimization strategies for complex queries

Previous research into the efficiency of text retrieval systems has dealt primarily with methods that consider inverted lists in sequence; these methods are known as term-at-a-time methods. However, the literature for optimizing document-at-a-time systems remains sparse.We present an improvement to the max_score optimization, which is the most efficient known document-at-a-time scoring method. Like max_score, our technique, called term bounded max_score, is guaranteed to return exactly the same scores and documents as an unoptimized evaluation, which is particularly useful for query model research. We simulated our technique to explore the problem space, then implemented it in Indri, our large scale language modeling search engine. Tests with the GOV2 corpus on title queries show our method to be 23% faster than max_score alone, and 61% faster than our document-at-a-time baseline. Our optimized query times are competitive with conventional term-at-a-time systems on this year's TREC Terabyte task.
Dietary pattern and oral cancer risk--a factor analysis study.

OBJECTIVES The role of diet in cancer risk has mainly been investigated based on intake of individual food items. However, food consumption is made up of a combination of various food items. This study aims to determine the association of dietary patterns with oral cancer risk. METHODS A total of 306 matched cases and controls were recruited in this study. Data on dietary intake were obtained using food frequency questionnaire (FFQ). Factor analysis (FA) was performed to identify dietary patterns based on the intake of nine major food groups, resulting in four factors/components being retained. The odds ratio (OR) was computed for each component using conditional logistic regression. RESULTS The first pattern labelled as 'modern' was loaded with processed foods and snacks, whereas the second pattern termed as 'prudent' was characterized by intake of fruits and vegetables. The third pattern labelled as 'traditional' consisted of beverages and starches, while the fourth pattern termed as 'combination' was loaded with intakes of dairy, fermented/salted and meat/by-products. A significant reduced risk was found for 'prudent' (OR 0.53, 95% CI = 0.28-0.98), whereas an increased risk was found for both 'combination' (OR 2.43, 95% CI = 1.33-4.45) and 'traditional' (OR 2.32, 95% CI = 1.23-4.25) patterns. However, after adjusting for risk habits of tobacco smoking, alcohol consumption and betel quid chewing, only 'combination' (aOR 2.99, 95% CI = 1.55-5.75) and 'traditional' (aOR 2.08, 95% CI = 1.09-3.97) patterns remained significant. CONCLUSION Consumption in the highest tertile of 'traditional' and 'combination' patterns may induce twice and thrice the risk of oral cancer, respectively.
The Modulation of Haptic Line Bisection by a Visual Illusion and Optokinetic Stimulation

Research has shown that a variety of different sensory manipulations, including visual illusions, transcutaneous nerve stimulation, vestibular caloric stimulation, optokinetic stimulation, and prism adaptation, can all influence people's performance on spatial tasks such as line bisection. It has been suggested that these manipulations may act upon the ‘higher-order’ levels of representation used to code spatial information. We investigated whether we could influence haptic line bisection in normal participants crossmodally by varying the visual background that participants viewed. In experiment 1, participants haptically bisected wooden rods while looking at a variant of the Oppel–Kundt visual illusion. Haptic-bisection judgments were influenced by the orientation of the visual illusion (in line with previous unimodal visual findings). In experiment 2, haptic-bisection judgments were also influenced by the presence of a leftward or rightward moving visual background. In experiments 3 and 4, the position of the to-be-bisected stimuli was varied with respect to the participant's body midline. The results confirmed an effect of optokinetic stimulation, but not of the Oppel–Kundt illusion, on participants' tactile-bisection errors, suggesting that the two manipulations might differentially affect haptic processing. Taken together, these results suggest that the ‘higher-order’ levels of spatial representation upon which perceptual judgments and/or motor responses are made may have multisensory or amodal characteristics.
The Binding of Substrate Analogs to Phosphotriesterase*

Phosphotriesterase (PTE) fromPseudomonas diminuta catalyzes the detoxification of organophosphates such as the widely utilized insecticide paraoxon and the chemical warfare agent sarin. The three-dimensional structure of the enzyme is known from high resolution x-ray crystallographic analyses. Each subunit of the homodimer folds into a so-called TIM barrel, with eight strands of parallel β-sheet. The two zinc ions required for activity are positioned at the C-terminal portion of the β-barrel. Here, we describe the three-dimensional structure of PTE complexed with the inhibitor diisopropyl methyl phosphonate, which serves as a mimic for sarin. Additionally, the structure of the enzyme complexed with triethyl phosphate is also presented. In the case of the PTE-diisopropyl methyl phosphonate complex, the phosphoryl oxygen of the inhibitor coordinates to the more solvent-exposed zinc ion (2.5 Å), thereby lending support to the presumed catalytic mechanism involving metal coordination of the substrate. In the PTE-triethyl phosphate complex, the phosphoryl oxygen of the inhibitor is positioned at 3.4 Å from the more solvent-exposed zinc ion. The two structures described in this report provide additional molecular understanding for the ability of this remarkable enzyme to hydrolyze such a wide range of organophosphorus substrates.
Unifying Conflicting Perspectives in Group Activities: Roles of Minority Individuals

For drawing higher-level perspectives in group activities, resolving conflicts among group members is crucial. We investigated group activities with four members wherein one member had a different perspective from the other three. Four members engaged in a rule discovery task in which they were required to unify conflicts for the solution. Through two experiments, we investigated two hypotheses: 1) Innovative high-level perspectives are more likely to emerge from a minority individual than from the majority of group members, 2) Group members on the majority side might tend to have more egocentric perspectives than an individual on the minority side. Both hypotheses were supported.
Bilingual response generation using semi-automatically-induced templates for a mixed-initiative dialog system

We have previously developed a framework for natural language response generation for mixed-initiative dialogs in the CUHK Restaurants domain. This paper investigates the use of semi-automatic technique for response templates generation. We adopt a semi-automatic approach for grammar induction to capture the language structures of responses from unannotated corpora. We wish to use this approach to induce a set of grammars from our response data. The induced grammars are coupled with a parser to produce response templates in a semi-automatic way. Our response data consists of 2349 waiter responses. It is used as the training corpus for grammar induction. Unsupervised grammar induction is first performed, followed by using the learned grammars as prior knowledge for seeding the clustering process. Results show that the semi-automatically-induced response templates cover more than 50% of the hand-designed templates in template coverage and provide more realization options. Performance evaluation indicates that the task completion rate is at least 90%, and most of the Grice's maxims as well as the overall user satisfaction scored at 3.5 points or above.
Impacts of Crop Residue and Cover Crops on Soil Hydrological Properties, Soil Water Storage and Water Use Efficiency of Soybean Crop

IMPACTS OF CROP RESIDUE AND COVER CROPS ON SOIL HYDROLOGICAL PROPERTIES, SOILL WATER STORAGE AND WATER USE EFFICIENCY OF SOYBEAN CROP KOPILA SUBEDI-CHALISE 2017 Cover crops and crop residue play a multifunctional role in improving soil hydrological properties, soil water storage and water use efficiency (WUE). This study was conducted to better understand the role of crop residue and cover crop on soil properties and soil water dynamics. The study was conducted at the USDA-ARS North Central Agricultural Research Laboratory, located in Brookings, South Dakota. Two residue removal treatments that include low residue removal (LRR) and high residue removal (HRR) were established in 2000 with randomized complete block design under no-till corn (Zea mays L.) and soybean (Glycine max L.) rotation. In 2005, cover crop treatments which include cover crops (CC) and no cover crops (NCC) were integrated into the overall design. Soil samples were collected in 2014, 2015 and 2016. Data from this study showed that the LRR treatment lowered the bulk density (BD) by 7 and 9% compared to HRR in 2015 and 2016, respectively, for the 0-5 cm depth. Similarly, LRR treatment significantly reduced soil penetration resistance (SPR) by 25% in the 0-5 cm depth compared with HRR treatment. Further, LRR treatment significantly increased soil organic carbon (SOC) concentrations and total nitrogen (TN) by 22 and 17%, respectively, in 0-5 cm. Similarly, CC treatment resulted in lower BD and SPR by 7% and 23%, respectively, at the 0-5 cm depth in 2015 compared with NCC treatment. The LRR significantly
Modulating the extension of axillary lymphadenectomy for early stage breast cancer

Axillary lymph node evaluation remains essential in breast cancer surgery, first as a prognostic factor, because it indicates the degree of dissemination of the disease to the main lymphatic drainage basin of the breast, and, on the other hand, as an element of preventing the local relapse. In the era of the sentinel lymph node, complete axillary lymphadenectomy, considered valuable until recently, but as therapeutic and diagnostic, has become an intervention performed increasingly rare in selected cases. Axillary lymphatic tissue resections are accompanied by morbidity (lymphedema, paresthesia, limitations of arm movement) and symptom magnitude is proportional to the extension of the intervention. For this reason, a solution to avoid these kinds of complications was looked for. Since Gould, in 1960, who mentioned cancer parotid and continuing with Cabanas, Morton, or Veronesi, many surgeons have contributed to the development of safe techniques with which the multidisciplinary team involved in the surgical treatment for breast cancer could perform a safe oncological intervention and at the same time could conserve the healthy tissue, thus limiting morbidity. To achieve this standard, axillary lymphadenectomy has passed through several stages, from over radical interventions that followed the Halsted era, in which, besides axillary lymph nodes, the internal mammary and jugulo-carotidian lymph nodes were excised, to the absence of axillary surgery and replacing it with radiation therapy.
Effect of Rotational Shepherding on Demographic and Genetic Connectivity of Calcareous Grassland Plants

Response to habitat fragmentation may not be generalized among species, in particular for plant communities with a variety of dispersal traits. Calcareous grasslands are one of the most species‐rich habitats in Central Europe, but abandonment of traditional management has caused a dramatic decline of calcareous grassland species. In the Southern Franconian Alb in Germany, reintroduction of rotational shepherding in previously abandoned grasslands has restored species diversity, and it has been suggested that sheep support seed dispersal among grasslands. We tested the effect of rotational shepherding on demographic and genetic connectivity of calcareous grassland specialist plants and whether the response of plant populations to shepherding was limited to species dispersed by animals (zoochory). Specifically, we tested competing dispersal models and source and focal patch properties to explain landscape connectivity with patch‐occupancy data of 31 species. We fitted the same connectivity models to patch occupancy and nuclear microsatellite data for the herb Dianthus carthusianorum (Carthusian pink). For 27 species, patch connectivity was explained by dispersal by rotational shepherding regardless of adaptations to zoochory, whereas population size (16% species) and patch area (0% species) of source patches were not important predictors of patch occupancy in most species. [Correction made after online publication, February 25, 2014: Population size and patch area percentages were mistakenly inverted, and have now been fixed. ] Microsite diversity of focal patches significantly increased the model variance explained by patch occupancy in 90% of the species. For D. carthusianorum, patch connectivity through rotational shepherding explained both patch occupancy and population genetic diversity. Our results suggest shepherding provides dispersal for multiple plant species regardless of their dispersal adaptations and thus offers a useful approach to restore plant diversity in fragmented calcareous grasslands.