Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Analysis of Genomics and Proteomics in the New Isolated Bacillus thuringiensis X022 Revealed the Metabolic Regulation Mechanism of Carbon Flux Following Cu2+ Treatment

Bacillus thuringiensis (Bt) X022 is a novel strain isolated from soil in China, and showed strong insecticidal activity against several Lepidopteran pests. In this work, we performed whole genome sequencing of this Bt strain using the next-generation sequencing technology, and further conducted a comparative analysis with the proteomics data of the specific spore-release period based on LC-MS/MS approach. The Bt X022 genome consisted of one circular chromosomal DNA and seven plasmids, which were further functionally annotated using the RAST server. Comparative analysis of insecticidal substances showed that X022 contained genes coding for three Cry proteins (Cry1Ac, Cry1Ia and Cry2Ab) and a vegetative insecticidal protein (Vip3A). However, three insecticidal crystal proteins (ICPs) (Cry1Ca, Cry1Ac and Cry1Da) were detected by proteomics in the spore-release period. Moreover, a putative biosynthetic gene cluster and the metabolic pathway for poly-β-hydroxybutyrate in Bt X022 were deduced based on the comparative analysis of genomic and proteomic data, which revealed the metabolic regulation mechanism of carbon flux correlated with increased production of ICPs caused by Cu2+. Hence, these results provided a deeper understanding of the genetic background and protein expression profile of Bt X022. This study established a foundation for directed genetic modification and further application of this new isolated Bt strain.
Role of vacA and cagA inHelicobacter pylori Inhibition of Mucin Synthesis in Gastric Mucous Cells

ABSTRACT The aim of this study was to investigate the effect ofHelicobacter pylori on the function of gastric mucous cells. H. pylori (104 to 107CFU/well) was incubated with the mucin-producing gastric cell line HM02 for 12 and 24 h. Mucin synthesis and secretion were determined by the incorporation ofd-N-[acetyl-14C]glucosamine into intracellular and released high-molecular-weight glycoproteins.cagA-positive, cytotoxin-producing and non-cytotoxin-producing H. pylori strains impaired the incorporation ofd-N-[acetyl-14C]glucosamine into intracellular glycoproteins. Significant inhibition of mucin synthesis was noted after 12 and 24 h of cocultivation with a bacterial load of ≥105 bacteria (bacterium/cell ratio = 0.25). The cagA-positive, cytotoxin-producing strains (HP64, HP57, and HP87) caused significantly stronger inhibition of intracellular mucin synthesis than the cagA-positive, non-cytotoxin-producing strains (HP05, HP83, and HP84). ThecagA-negative, non-cytotoxin-producing strains (HP01, HP04, and HP85) did not affect intracellular mucin synthesis. The results indicate that H. pylori directly impairs mucin synthesis in gastric mucous cells and that cytotoxic cagA-positive strains cause more profound inhibition of mucin synthesis. We suggest that the increased inhibitory effect of cagA-positive, cytotoxin-producing strains on mucin synthesis can be considered one possible factor responsible for the increased risk of developing peptic ulceration with these H. pylori strains.
Long-term follow-up of the MAINTAIN Nephritis Trial, comparing azathioprine and mycophenolate mofetil as maintenance therapy of lupus nephritis

Objective To report the 10-year follow-up of the MAINTAIN Nephritis Trial comparing azathioprine (AZA) and mycophenolate mofetil (MMF) as maintenance therapy of proliferative lupus nephritis, and to test different definitions of early response as predictors of long-term renal outcome. Methods In 2014, data on survival, kidney function, 24 h proteinuria, renal flares and other outcomes were collected for the 105 patients randomised between 2002 and 2006, except in 13 lost to follow-up. Results Death (2 and 3 in the AZA and MMF groups, respectively) and end-stage renal disease (1 and 3, respectively) were rare events. Time to renal flare (22 and 19 flares in AZA and MMF groups, respectively) did not differ between AZA and MMF patients. Patients with good long-term renal outcome had a much more stringent early decrease of 24 h proteinuria compared with patients with poor outcome. The positive predictive value of a 24 h proteinuria <0.5 g/day at 3 months, 6 months and 12 months for a good long-term renal outcome was excellent (between 89% and 92%). Inclusion of renal function and urinalysis in the early response criteria did not impact the value of early proteinuria decrease as long-term prognostic marker. Conclusions The long-term follow-up data of the MAINTAIN Nephritis Trial do not indicate that MMF is superior to AZA as maintenance therapy in a Caucasian population suffering from proliferative lupus nephritis. Moreover, we confirm the excellent positive predictive value of an early proteinuria decrease for long-term renal outcome. Trial registration number NCT00204022.
Systematic review of home physiotherapy after hip fracture surgery.

OBJECTIVE To compare the benefits of home physiotherapy, institution-based physiotherapy and no physiotherapy following hip fracture surgery. DESIGN Systematic review and meta-analysis of randomized controlled trials. METHODS Two reviewers independently extracted data from 5 included studies. Standardized mean differences were pooled for health-related quality of life and performance-based outcomes. Review Manager Version 5 was used for data analysis. RESULTS Analysis of the 5 included studies indicated that home physiotherapy was better than no physiotherapy and similar to outpatient physiotherapy in improving patient-reported health-related quality of life. Performance-based outcomes were marginally better following outpatient physiotherapy compared with home physiotherapy 3 and 6 months after surgery. The risk of bias was high for most outcomes due to methodological issues in the included studies. DISCUSSION There was a trend of better results with increasing intensity of physiotherapy intervention, but this did not convert into significant effect sizes. The results of this review do not build a strong consensus for recommending one mode of physiotherapy over the others. The quality of evidence was low mainly due to the high risk of bias in the included studies. CONCLUSION In light of no strong consensus, physiotherapists should continue to follow their current workplace practice policies for determining suitable discharge settings.
Compositional distributional semantics with compact closed categories and Frobenius algebras

The provision of compositionality in distributional models of meaning, where a word is represented as a vector of co-occurrence counts with every other word in the vocabulary, offers a solution to the fact that no text corpus, regardless of its size, is capable of providing reliable co-occurrence statistics for anything but very short text constituents. The purpose of a compositional distributional model is to provide a function that composes the vectors for the words within a sentence, in order to create a vectorial representation that re ects its meaning. Using the abstract mathematical framework of category theory, Coecke, Sadrzadeh and Clark showed that this function can directly depend on the grammatical structure of the sentence, providing an elegant mathematical counterpart of the formal semantics view. The framework is general and compositional but stays abstract to a large extent. This thesis contributes to ongoing research related to the above categorical model in three ways: Firstly, I propose a concrete instantiation of the abstract framework based on Frobenius algebras (joint work with Sadrzadeh). The theory improves shortcomings of previous proposals, extends the coverage of the language, and is supported by experimental work that improves existing results. The proposed framework describes a new class of compositional models thatfind intuitive interpretations for a number of linguistic phenomena. Secondly, I propose and evaluate in practice a new compositional methodology which explicitly deals with the different levels of lexical ambiguity (joint work with Pulman). A concrete algorithm is presented, based on the separation of vector disambiguation from composition in an explicit prior step. Extensive experimental work shows that the proposed methodology indeed results in more accurate composite representations for the framework of Coecke et al. in particular and every other class of compositional models in general. As a last contribution, I formalize the explicit treatment of lexical ambiguity in the context of the categorical framework by resorting to categorical quantum mechanics (joint work with Coecke). In the proposed extension, the concept of a distributional vector is replaced with that of a density matrix, which compactly represents a probability distribution over the potential different meanings of the specific word. Composition takes the form of quantum measurements, leading to interesting analogies between quantum physics and linguistics.
Time-Dependent Properties of Lightweight Concrete Using Sedimentary Lightweight Aggregate

A kind of lightweight aggregate (LWA) has been successfully developed in Taiwan, which was made by expanding under heat fine sediments dredged from the Shihmen Reservoir. In this study the performances of concrete made from the aforementioned LWA were tested and compared with those of the companion normal weight concrete (NC). The test results show that the so produced lightweight concrete (LWAC) exhibited a comparable time-dependent properties (i.e., compressive strength, elastic modulus, drying shrinkage, and creep) as compared with those of the companion NC. Based on the results, it can be concluded that the use of prewetted LWAs and the incorporation of pozzolan materials can effectively control the drying shrinkage of LWAC. The specific creep of the LC mixture was obviously higher than that of the NC mixture at the same curing time.
Osteoporosis Is Associated With High Risk for Coronary Heart Disease

AbstractWe employed a population-based cohort sample to explore the risk of coronary heart disease (CHD) in relation to osteoporosis in an Asian population.We designed a retrospective population-based cohort study from 2000 to 2010 with data obtained from Taiwan's Longitudinal Health Insurance Database. A total of 19,456 patients aged 45 years or older who had no history of CHD and had a diagnosis of osteoporosis were identified as the osteoporosis cohort. The patients in the comparison cohort were randomly selected and frequency matched according to age, sex, and year of index date at a 1:1 ratio. Both cohorts were followed from the index date until a new diagnosis of CHD was made. Baseline variables, comorbidities, and bisphosphonate and estrogen prescriptions were collected.The overall incidence of CHD was 23.5 (per 1000 person-years) for the osteoporosis cohort and 16.7 for the comparison cohort, with a mean follow-up of 6.54 years and 6.63 years, respectively. The hazard ratio (HR) for developing CHD during follow-up was 1.30 (95% confidence interval [CI], 1.23–1.38) for the osteoporosis cohort compared with the comparison cohort after adjusting for age, sex, comorbidities, and estrogen medication. Patients with osteoporosis who received treatment with bisphosphonates or with both bisphosphonates and estrogen exhibited a significantly lower risk for CHD (adjusted HR = 0.37 and 0.23) than those who did not receive either of these 2 medications.The results support an association between osteoporosis and CHD in Asian population.
The effect of minimum quantity lubrication and cryogenic pre-cooling on cutting performance in the micro milling of Inconel 718

In this study, the effects of different cutting conditions on the cutting performance were investigated in the micro milling of Inconel 718. In this context, dry cutting, minimum quantity lubrication and cryogenic pre-cooling were considered as the cutting conditions. Tool wear, surface roughness and burr formation were determined as performance criteria in the cutting processes carried out using an AlCrN-coated tool. At the end of the study, cryogenic pre-cooling led to increased tool wear. In contrast, a significant reduction in surface roughness as well as burr formation was observed in the cutting process with cryogenic pre-cooling. However, the minimum quantity lubrication process increased tool life, but it was not seen as the clear effect for decreasing surface roughness and burr formation.
Hypergraph Partitioning for Community Discovery in Complex Network

Hypergraph partitioning has been considered as a promising method to address the challenges of high dimensionality in clustering. Many complex networks possess the scale-free property, which makes the task of community discobery from these networks difficult. In this paper we present a method of detecting community structure based on hypergraph model to address this problem. The hypergraph model maps the relationship in the original data into a hypergraph. A hyperedge represents a relationship among subsets of data and the weight of the hyperedge reflects the strength of this affinity. We assign the density of a hyperedge to its weight. We present and illustrate the results of experiments on the Enron data set. The experiments demonstrate that our approach is applicable and effective.
The Role of Imagistic Simulation in Scientific Thought Experiments

Interest in thought experiments (TEs) derives from the paradox: "How can findings that carry conviction result from a new experiment conducted entirely within the head? " Historical studies have established the importance of TEs in science but have proposed disparate hypotheses concerning the source of knowledge in TEs, ranging from empiricist to rationalist accounts. This article analyzes TEs in think-aloud protocols of scientifically trained experts to examine more fine-grained information about their use. Some TEs appear powerful enough to discredit an existing theory-a disconfirmatory purpose. In addition, confirmatory and generative purposes were identified for other TEs. One can also use details in transcript data, including imagery reports and gestures, to provide evidence for a central role played by imagistic simulations in many TEs, and to suggest that these simulations can generate new knowledge using several sources, including the "extended application" of perceptual motor schemas, implicit prior knowledge, and spatial reasoning operations, in contrast to formal arguments. These sources suggest what it means for TEs to be grounded in embodied processes that can begin to explain the paradox above. This leads to a rationalistic view of TEs as using productive internal reasoning, but the view also acknowledges the historical role that experience with the world can play in forming certain schemas used in TEs. Understanding such processes could help provide a foundation for developing a larger model of scientific investigation processes grounded on imagistic simulation (Clement, 2008).
www.econstor.eu Zentrum für Europäische Integrationsforschung Center for European Integration Studies

It is common in applied econometrics to test the null hypothesis of a level-stationary process against the alternative of a unit root process. We show that the use of conventional asymptotic critical values for the stationarity tests of Kwiatkowski et al. (1992) and Leybourne and McCabe (1994) may cause extreme size distortions, if the model under the null hypothesis is highly persistent. The existence of such size distortions has not been recognized in the previous literature. We illustrate the practical importance of these distortions for the problem of testing for long-run purchasing power parity under the recent float. Size distortions of tests of the unit root null hypothesis may be overcome by the use of finite-sample or bootstrap critical values. We show that such corrections are not possible for tests of the null hypothesis of stationarity. Our results suggest that the common practice of viewing tests of stationarity as complementary to tests of the unit root null will tend to result in contradictions or in spurious acceptances of the unit root hypothesis. We conclude that tests of the null hypothesis of stationarity cannot be recommended for applied work unless the sample size is very large.
Cholinergic modulation in the olfactory bulb influences spontaneous olfactory discrimination in adult rats

Cholinergic neuromodulation in the olfactory bulb has been hypothesized to regulate mitral cell molecular receptive ranges and the behavioral discrimination of similar odorants. We tested the effects of cholinergic modulation in the olfactory bulb of cannulated rats by bilaterally infusing cholinergic agents into the olfactory bulbs and measuring the rats' performances on separate spontaneous and motivated odor‐discrimination tasks. Specifically, 6 µL/bulb infusions of vehicle (0.9% saline), the muscarinic antagonist scopolamine (7.6 mm and 38 mm), the nicotinic antagonist mecamylamine hydrochloride (3.8 mm and 19 mm), a combination of both antagonists, or the acetylcholinesterase inhibitor neostigmine (8.7 mm) were made 20 min prior to testing on an olfactory cross‐habituation task or a rewarded, forced‐choice odor‐discrimination task. Spontaneous discrimination between chemically related odorants was abolished when nicotinic receptors were blocked in the olfactory bulb, and enhanced when the efficacy of cholinergic inputs was increased with neostigmine. Blocking muscarinic receptors reduced but did not abolish odor discrimination. Interestingly, no behavioral effects of modulating either nicotinic or muscarinic receptors were observed when rats were trained on a reward‐motivated odor‐discrimination task. Computational modeling of glomerular circuitry demonstrates that known nicotinic cholinergic effects on bulbar neurons suffice to explain these results.
Bleomycin‐induced chromosomal damage and shortening of telomeres in peripheral blood lymphocytes of incident cancer patients

Disruption of genomic integrity due to deficient DNA repair capacity and telomere shortening constitute hallmarks of malignant diseases. Incomplete or deficient repair of DNA double‐strand breaks (DSB) is manifested by chromosomal aberrations and their frequency reflects inter‐individual differences of response to exposure to mutagenic compounds. In this study, we investigated chromosomal integrity in peripheral blood lymphocytes (PBL) from newly diagnosed cancer patients, including 47 breast (BC) and 44 colorectal cancer (CRC) patients and 90 matched healthy controls. Mutagen sensitivity was evaluated by measuring chromatid breaks (CTAs) induced by bleomycin and supplemented by the chemiluminescent measurement of γ‐H2AX phosphorylation in 19 cancer patients (11 BC, 8 CRC). Relative telomere length (RTL) was determined in 22 BC, 32 CRC, and 64 controls. We observed statistically significant increased level of CTAs (P = .03) and increased percentage of aberrant cells (ACs) with CTAs (P = .05) in CRC patients compared with controls after bleomycin treatment. No differences were observed between BC cases and corresponding controls. CRC and BC patients with shorter RTL (below median) exhibited significantly higher amount of ACs (P = .02), CTAs (P = .02), and cells with high frequency of CTAs (≥12 CTAs/PBL; P = .03) after bleomycin treatment. No such associations were observed in healthy controls. γ‐H2AX phosphorylation after bleomycin treatment in PBL did not differ between CRC and BC patients. Our results suggest that altered DSB repair measured by sensitivity towards mutagen in PBL occurs particularly in CRC carcinogenesis. Irrespective of cancer type, telomere shortening may be associated with a decreased capacity to repair DSB.
Nurses learning family-oriented interprofessional collaboration

Objectives. A two-year family-oriented interprofessional education programme for professionals working in the field of primary services (e.g. health care, social welfare, school, day care) was started in the Province of Oulu, Finland in 2000. The programme aimed to provide the participants (n=76) with skills to work with families in interprofessional collaboration. The study investigated the views and working methods of all the 14 nurses who participated in the course. Study design. Qualitative study employing the content analysis method. Methods. The data were collected by using open-ended questions at the beginning and at the end of the education and analysed with the method of content analysis. Results. Initially, the nurses were aware of the significance and the premises of family-oriented interprofessional collaboration, but seldom implemented them in practice. At the end of the programme, their working methods had changed from expert-to client-and family-oriented direction. They began to appreciate interprofessional collaboration and found that client-and familyoriented working methods supported families’ own resources. Conclusions. In order to change the theoretical framework and practical working methods of the professionals a sufficiently long process of education is needed where the interprofessional collaboration is put into practice already during the education. Even though this education programme was developed and implemented for professionals working in the primary social and health care services in the Northern Finland, we believe that it is applicable to the teaching of interprofessional collaboration in different settings in different countries. (Int J Circumpolar Health 2006:65(3):206–218. )
The GISMOE challenge: constructing the pareto program surface using genetic programming to find better programs (keynote paper)

Optimising programs for non-functional properties such as speed, size, throughput, power consumption and bandwidth can be demanding; pity the poor programmer who is asked to cater for them all at once! We set out an alternate vision for a new kind of software development environment inspired by recent results from Search Based Software Engineering (SBSE). Given an input program that satisfies the functional requirements, the proposed programming environment will automatically generate a set of candidate program implementations, all of which share functionality, but each of which differ in their non-functional trade offs. The software designer navigates this diverse Pareto surface of candidate implementations, gaining insight into the trade offs and selecting solutions for different platforms and environments, thereby stretching beyond the reach of current compiler technologies. Rather than having to focus on the details required to manage complex, inter-related and conflicting, non-functional trade offs, the designer is thus freed to explore, to understand, to control and to decide rather than to construct.