Miracle-dz/UniFAR-FTUs huggingface dataset:
Further Characterization of Clostridium perfringens Small Acid Soluble Protein-4 (Ssp4) Properties and Expression

Background Clostridium perfringens type A food poisoning (FP) is usually caused by C. perfringens type A strains that carry a chromosomal enterotoxin gene (cpe) and produce spores with exceptional resistance against heat and nitrites. Previous studies showed that the extreme resistance of spores made by most FP strains is mediated, in large part, by a variant of small acid soluble protein 4 (Ssp4) that has Asp at residue 36; in contrast, the sensitive spores made by other C. perfringens type A isolates contain an Ssp4 variant with Gly at residue 36. Methodology/Principal Findings The current study has further characterized Ssp4 properties and expression. Spores made by cpe-positive type C and D strains were found to contain the Ssp4 variant with Gly at residue 36 and were shown to be heat- and nitrite-sensitive; this finding may help to explain why cpe-positive type C and D isolates rarely cause food poisoning. Saturation mutagenesis indicated that both amino acid size and charge at Ssp4 residue 36 are important for DNA binding and for spore resistance. C. perfringens Ssp2 was shown to bind preferentially to GC-rich DNA on gel-shift assays, while Ssp4 preferred binding to AT-rich DNA sequences. Maximal spore heat and nitrite resistance required production of all four C. perfringens Ssps, indicating that these Ssps act cooperatively to protect the spore's DNA, perhaps by binding to different chromosomal sequences. The Ssp4 variant with Asp at residue 36 was also shown to facilitate exceptional spore survival at freezer and refrigerator temperatures. Finally, Ssp4 expression was shown to be dependent upon Spo0A, a master regulator. Conclusions/Significance Collectively, these results provide additional support for the importance of Ssps, particularly the Ssp4 variant with Asp at residue 36, for the extreme spore resistance phenotype that likely contributes to C. perfringens type A food poisoning transmission.
Luteolin and luteolin-7-O-glucoside inhibit lipopolysaccharide-induced inflammatory responses through modulation of NF-κB/AP-1/PI3K-Akt signaling cascades in RAW 264.7 cells

Luteolin is a flavonoid found in abundance in celery, green pepper, and dandelions. Previous studies have shown that luteolin is an anti-inflammatory and anti-oxidative agent. In this study, the anti-inflammatory capacity of luteolin and one of its glycosidic forms, luteolin-7-O-glucoside, were compared and their molecular mechanisms of action were analyzed. In lipopolysaccharide (LPS)-activated RAW 264.7 cells, luteolin more potently inhibited the production of nitric oxide (NO) and prostaglandin E2 as well as the expression of their corresponding enzymes (inducible NO synthase (iNOS) and cyclooxygenase-2 (COX-2) than luteolin-7-O-glucoside. The molecular mechanisms underlying these effects were investigated to determine whether the inflammatory response was related to the transcription factors, nuclear factor (NF)-κB and activator protein (AP)-1, or their upstream signaling molecules, mitogen-activated protein kinases (MAPKs) and phosphoinositide 3-kinase (PI3K). Luteolin attenuated the activation of both transcription factors, NF-κB and AP-1, while luteolin-7-O-glucoside only impeded NF-κB activation. However, both flavonoids inhibited Akt phosphorylation in a dose-dependent manner. Consequently, luteolin more potently ameliorated LPS-induced inflammation than luteolin-7-O-glucoside, which might be attributed to the differentially activated NF-κB/AP-1/PI3K-Akt pathway in RAW 264.7 cells.
Prevention of the onset and progression of collagen-induced arthritis in rats by the potent p38 mitogen-activated protein kinase inhibitor FR167653.

OBJECTIVE FR167653 is a potent inhibitor of p38 mitogen-activated protein kinase (MAPK) and inhibits tumor necrosis factor alpha (TNFalpha) and interleukin-1 beta (IL-1 beta) production in inflammatory cells. In this study we investigated the effect of FR167653 on collagen-induced arthritis (CIA). METHODS Rats with CIA were subcutaneously injected with FR167653 (32 mg/kg/day) starting on the day of the booster injection (day 7) in the prophylactic treatment group and after the onset of arthritis (day 21) in the therapeutic treatment group. Hind-paw swelling, body weight, radiographic and histologic scores, and osteoclast number were evaluated. Cytokine levels in the serum and tissue were assessed by enzyme-linked immunosorbent assays. Flow cytometric analysis of T lymphocytes from bone marrow was performed. The effect of FR167653 on in vitro osteoclast formation induced by soluble receptor activator of nuclear factor kappa B ligand (sRANKL) and TNFalpha was examined. RESULTS Swelling of hind paws and loss of weight occurred in the CIA rats, but this was not evident in the prophylactic treatment group. Therapeutic treatment also significantly reduced paw swelling. The mean radiographic and histologic scores as well as the osteoclast numbers were significantly lower in the treatment group than in the CIA rats without treatment. FR167653 treatment reduced the serum levels of TNFalpha and IL-1 beta, lowered the IL-1 beta concentration in the ankle joints, and decreased the CD4-,CD8a+ T cell population in bone marrow. Furthermore, FR167653 inhibited the osteoclast-like cell differentiation induced by both sRANKL and TNFalpha in vitro. CONCLUSION FR167653 prevents the onset of arthritis in a prophylactic treatment model and suppresses the progression of joint destruction in a therapeutic treatment model, suggesting that p38 MAPK is a potential therapeutic target for rheumatoid arthritis.
Biomarkers and Microfossils in the Murchison, Rainbow, and Tagish Lake meteorites

During the past six years, we have conducted extensive scanning electron and optical microscopy investigations and x-ray analysis to determine the morphology, life cycle processes, and elemental distributions in living and fossil cyanobacteria, bacteria, archaea, fungi, and algae sampled from terrestrial environments relevant to Astrobiology. Biominerals, pseudomorphs and microfossils have been studied for diverse microbial groups in various states of preservation in many types of rocks (e.g., oil shales, graphites, shungites, bauxites, limestones, pyrites, phosphorites, and hydrothermal vent chimneys). Results of these studies have been applied to the search for biosignatures in carbonaceous chondrites, stony, and nickel iron meteorites. We review important biomarkers found in terrestrial rocks and meteorites and present additional evidence for the existence of indigenous bacterial microfossils in-situ in freshly fractured surfaces of the Murchison, Rainbow and Tagish Lake carbonaceous meteorites. We provide secondary and backscatter electron images and spectral data obtained with Field Emission and Environmental Scanning Electron Microscopes of biominerals and microfossils. We discuss techniques for discriminating indigenous microfossils from recent terrestrial contaminants. Images are provided of framboidal magnetites in oil shales and meteorites and images and 2D x-ray maps are shown of bacterial microfossils embedded in the mineral matrix of the Murchison, Rainbow and Tagish Lake Carbonaceous Meteorites. These microfossils exhibit characteristics that preclude their interpretation as post-arrival contaminants and we interpret them as indigenous biogenic remains.
Postpartal Anxiety and Depression in Mothers of Term and Preterm Infants

This study examined differences in anxiety and depression in mothers of term and preterm infants in the first week postpartum and over the next 6 weeks. Mothers of 41 preterm infants were matched with 41 mothers of term infants on parity, type of delivery, age, and race. Sixteen mothers of preterm infants and 10 mothers of term infants completed all 7 weeks of data collection. Mothers of preterm infants were significantly more anxious and depressed than mothers of term infants in the first postpartal week but this difference did not persist over time. Maternal affect was unrelated to parity or type of delivery in the first postpartal week and over time. There were no differences among mothers of premature infants in initial anxiety or depression, based on the level of illness of the infant.
Proposition of an offline learning current modulation for torque-ripple reduction in switched reluctance motors: design and experimental evaluation

A new offline current modulation using a neuro-fuzzy compensation scheme for torque-ripple reduction in switched reluctance motors is presented. The main advantage of the proposed technique is that the torque signal is unnecessary. The compensating signal is learned prior to normal operation in a self-commissioning run, capturing the necessary current shape to reduce the torque ripple. Simulation results verify first the effects of speed and then load changes on the compensator performance. Implementation of the proposed technique in a laboratory prototype shows the feasibility and accuracy of the respective offline scheme.
Hypomagnesemia and Cause-specific Mortality in Hemodialysis Patients: 5-year follow-up Analysis

Introduction The aim of this prospective study was to evaluate the association between serum magnesium (Mg) and mortality, in particular the cause-specific mortality of Mg and other risk factors in hemodialysis (HD) patients. Methods We studied a cohort of 185 HD patients receiving thrice-weekly HD treatment, on a dialysate Mg concentration of 0.5 mmol/L. We stratified 3 patient groups according to the level of Mg: lower (<1.1 mmol/L), intermediate-reference (1.1 to <1.3 mmol/L), and higher (Mg >1.3 mm/L). Results During the 5-year follow-up, 60 patients died, with cardiovascular (CV) disease as the predominant cause (73.3%). Hazard ratio (HR) for all-cause and CV mortality were 2.55 and 2.67 in the lower versus intermediate Mg group, but there was no significant association between the higher and intermediate Mg group. Univariate Cox regression analysis showed that Mg <1.1 versus 1.1–1.30 mml/L with HR 2.34, was a significant univariate predictor for increased mortality in addition to the Hb <110 g/L, Alb <40 g/L, C-reactive protein (CRP) ≥10 mg/L and brain natriuretic peptide >1,200 pg/mL However, in the multivariate analysis only CRP ≥10 mg/L with HR 3.89 was a significant predictor of mortality. Subgroup analyses showed that among patients with CRP >10 mg/L, HR for all-cause and CV mortality of the lower versus intermediate Mg group were 1.96 and 2.39, respectively, not reaching significance for the higher versus intermediate Mg group. Conversely, there was no association between Mg level and all-cause and CV mortality within these 3 groups among patients with CRP <10 mg/L. Conclusions Lower serum Mg level was significantly associated with an increased all-cause and cardiovascular mortality in HD patients, especially in inflamed patients.
Cardiac protection by volatile anaesthetics: a multicentre randomized controlled study in patients undergoing coronary artery bypass grafting with cardiopulmonary bypass

Background and objectives: To evaluate the effects of total intravenous anaesthesia vs. volatile anaesthesia on cardiac troponin release in coronary artery bypass grafting with cardiopulmonary bypass, we performed a multicentre randomized controlled study to compare postoperative cardiac troponin release in patients receiving two different anaesthesia plans. Methods: We randomly assigned 75 patients to propofol (intravenous anaesthetic) and 75 patients to desflurane (volatile anaesthetic) in addition to an opiate‐based anaesthesia for coronary artery bypass grafting. Peak postoperative troponin I release was measured as a marker of myocardial necrosis. Results: There was a significant (P < 0.001) difference in the postoperative median (25th‐75th percentiles) peak of troponin I in patients receiving propofol 5,5 (2,3‐9,5) ng dL−1 when compared to patients receiving desflurane 2,5 (1,1‐5,3) ng dL−1. The median (interquartile) troponin I area under the curve analysis confirmed the results: 68 (30.5‐104.8) vs. 36.3 (17.9‐86.6) h ng dL−1 (P = 0.002). Patients receiving volatile anaesthetics had reduced need for postoperative inotropic support (24/75, 32.0% vs. 31/75, 41.3%, P = 0.04), and tends toward a reduction in number of Q‐wave myocardial infarction, time on mechanical ventilation, intensive care unit and overall hospital stay. Conclusions: Myocardial damage measured by cardiac troponin release could be reduced by volatile anaesthetics in coronary artery bypass surgery.
Long-term measurements of flow near the Aleutian Islands

In summer 1995, the Alaskan Stream at 173.5W was very intense; the peak geostrophic speed was ∼ 125 cm s -1 , and the computed volume transport above 1000 db, referred to 1000 db, was 9 × 10 6 m 3 s -1 . Flow north of the central Aleutians was shallow, convoluted and weak (2-3 × 10 6 m 3 s -1 ). A sequence of CTD casts across Amukta Pass, spaced irregularly in time during 1993-1996, showed a mean northward (southward) geostrophic transport of 1.0 (0.4) × 106 m 3 s -1 , for a net flow into the Bering Sea of 0.6 × 10 6 m 3 s -1 . The source of this flow was the Alaskan Stream except in 1995, when it was Bering Sea water. Results from two 13-month current moorings west and east of the pass were quite different. To the west, flow was weak and variable and appeared to have a barotropic component. To the east, flow was stronger and unidirectional eastward.
Radiative forcing and temperature trends from stratospheric ozone changes

Detailed shortwave and longwave radiative transfer models are used to calculate the radiative forcing and temperature trends due to stratospheric ozone depletion. These were calculated using the fixed dynamical heating approximation to adjust the stratospheric temperatures. Recent estimates of stratospheric ozone loss between 1979 and 1991 (from solar backscattered ultraviolet (SBUV) and stratospheric aerosol and gas experiment (SAGE) instruments) and updated radiative transfer schemes are used to obtain improved estimates of the radiative forcings. An annually and globally averaged radiative forcing of −0.13±0.02 W m−2 decade−1 (−0.22±0.03 W m−2 for the 1979–1996 period) was found from SBUV total column ozone trends, applying a constant percentage ozone depletion to a 7 km thick layer directly above the tropopause. SAGE ozone trends gave forcing estimates of −0.10±0.02 W m−2 decade−1 (−0.17±0.03 W m−2 for the 1979–1996 period), although assumptions needed to be made about the choice of the vertical profile of the ozone depletion below 17 km. Using Dobson instrument trends from 1964 to 1996, the total ozone forcing could be as negative as −0.26±0.05 W m−2. The quoted error bars derive from uncertainties in the total ozone trends. Using these values, the stratospheric ozone change may have offset about 30% of the forcing due to increases in well-mixed greenhouse gases since 1979, and about 15% of the forcing since 1964, at least on a global and annual mean. The ozone forcings are shown to be nearly a linear function of the ozone amount depleted from the atmospheric column, provided the vertical profile of the depletion remains constant. As in previous studies, it was found that stratospheric adjustment altered the sign of the ozone forcing by strongly cooling the lower stratosphere. It is shown that (depending on the vertical structure of ozone depletion) coolings of up to 0.4 K decade−1 can be found at altitudes of 35 km; this provides a mechanism for cooling the stratosphere nearly as large as that from well-mixed greenhouse gas increases, at altitudes where ozone changes were previously thought not to strongly affect stratospheric temperature trends. Previous studies have examined the effect of ozone trends by looking at the response of the surface temperature to a fixed absolute ozone change at different heights in the atmosphere. We argue that using absolute ozone perturbations places an unrealistically large emphasis on ozone changes near the tropopause. As the vertical profile of ozone change is more often reported as a percentage change, we present the sensitivity of the surface temperature to constant percentage, rather than absolute, changes in ozone.
Given Bilingual Terminology in Statistical Machine Translation: MWE-Sensitve Word Alignment and Hierarchical Pitman-Yor Process-Based Translation Model Smoothing

This paper considers a scenario when we are given almost perfect knowledge about bilingual terminology in terms of a test corpus in Statistical Machine Translation (SMT). When the given terminology is part of a training corpus, one natural strategy in SMT is to use the trained translation model ignoring the given terminology. Then, two questions arises here. 1) Can a word aligner capture the given terminology? This is since even if the terminology is in a training corpus, it is often the case that a resulted translation model may not include these terminology. 2) Are probabilities in a translation model correctly calculated? In order to answer these questions, we did experiment introducing a Multi-Word Expression-sensitive (MWE-sensitive) word aligner and a hierarchical Pitman-Yor process-based translation model smoothing. Using 200k JP--EN NTCIR corpus, our experimental results show that if we introduce an MWE-sensitive word aligner and a new translation model smoothing, the overall improvement was 1.35 BLEU point absolute and 6.0% relative compared to the case we do not introduce these two.
The Histone Chaperone FACT: Structural Insights and Mechanisms for Nucleosome Reorganization*

Changes in chromatin architecture induced by epigenetic mechanisms are essential for normal cellular processes such as gene expression, DNA repair, and cellular division. Compact chromatin presents a barrier to these processes and is highly regulated by epigenetic markers binding to components of the nucleosome. Histone modifications directly influence chromatin dynamics and facilitate recruitment of additional factors such as chromatin remodelers and histone chaperones. One member of this last class of factors, FACT (facilitates chromatin transcription), is categorized as a histone chaperone critical for nucleosome reorganization during replication, transcription, and DNA repair. Significant discoveries regarding the role of histone chaperones and specifically FACT have come over the past dozen years from a number of independent laboratories. Here, we review the structural and biophysical basis for FACT-mediated nucleosome reorganization and discuss up-to-date models for FACT function.
wikiBABEL: community creation of multilingual data

In this paper, we present a collaborative framework -- wikiBABEL -- for the efficient and effective creation of multilingual content by a community of users. The wikiBABEL framework leverages the availability of fairly stable content in a source language (typically, English) and a reasonable and not necessarily perfect machine translation system between the source language and a given target language, to create the rough initial content in the target language that is published in a collaborative platform. The platform provides an intuitive user interface and a set of linguistic tools for collaborative correction of the rough content by a community of users, aiding creation of clean content in the target language. We describe the architectural components implementing the wikiBABEL framework, namely, the systems for source and target language content management, mechanisms for coordination and collaboration and intuitive user interface for multilingual editing and review. Importantly, we discuss the integrated linguistic resources and tools, such as, bilingual dictionaries, machine translation and transliteration systems, etc., to help the users during the content correction and creation process. In addition, we analyze and present the prime factors -- user-interface features or linguistic tools and resources -- that significantly influence the user experiences in multilingual content creation. In addition to the creation of multilingual content, another significant motivation for the wikiBABEL framework is the creation of parallel corpora as a by-product. Parallel linguistic corpora are very valuable resources for both Statistical Machine Translation (SMT) and Crosslingual Information Retrieval (CLIR) research, and may be mined effectively from multilingual data with significant content overlap, as may be created in the wikiBABEL framework. Creation of parallel corpora by professional translators is very expensive, and hence the SMT and CLIR research have been largely confined to a handful of languages. Our attempt to engage the large and diverse Internet user population may aid creation of such linguistic resources economically, and may make computational linguistics research possible and practical in many languages of the world.
What Happened to My Dog in That Network: Unraveling Top-down Generators in Convolutional Neural Networks

Top-down information plays a central role in human perception, but plays relatively little role in many current state-of-the-art deep networks, such as Convolutional Neural Networks (CNNs). This work seeks to explore a path by which top-down information can have a direct impact within current deep networks. We explore this path by learning and using "generators" corresponding to the network internal effects of three types of transformation (each a restriction of a general affine transformation): rotation, scaling, and translation. We demonstrate how these learned generators can be used to transfer top-down information to novel settings, as mediated by the "feature flows" that the transformations (and the associated generators) correspond to inside the network. Specifically, we explore three aspects: 1) using generators as part of a method for synthesizing transformed images --- given a previously unseen image, produce versions of that image corresponding to one or more specified transformations, 2) "zero-shot learning" --- when provided with a feature flow corresponding to the effect of a transformation of unknown amount, leverage learned generators as part of a method by which to perform an accurate categorization of the amount of transformation, even for amounts never observed during training, and 3) (inside-CNN) "data augmentation" --- improve the classification performance of an existing network by using the learned generators to directly provide additional training "inside the CNN".
Differentiation of Beach, Dune, and Aeolian Flat Environments by Size Analysis, Mustang Island, Texas

Mustang Island is a 16-mile-long barrier island on the south Texas Gulf coast. Sediments consist of very well sorted fine sands (mean size 2.82phi , average sigma I = 0.29phi ), and show exceedingly uniform properties lengthwise of the island. Beach, dune, and aeolian flat environments can be readily distinguished by size analysis. The best means of differentiating them is by plotting skewness versus kurtosis inasmuch as the geologic processes at work have their greatest effect on the tails of the size distribution. Beach sands form normal carves, dune sands are positively skewed but still mesokurtic, and aeolian flat sands are positively skewed and leptokurtic. Sands from the beach are more poorly sorted than those from the other two environments. These differences are extremely significant with P values between . 0002 and . 0000001. To explain these changes, it is proposed that as sand travels from the beach to the dunes, the coarse end of the parent normal population lags behind, rendering the size curves better sorted and also positively skewed. The aeolian flats are believed to be subject to infiltration of silt from the atmosphere; this imparts a "tail" of fines, registering a marked increase in kurtosis.