Miracle-dz/UniFAR-FTUs huggingface dataset:
Cloning, Expression, Sequence Analysis and Homology Modeling of the Prolyl Endoprotease from Eurygaster integriceps Puton

Eurygaster integriceps Puton, commonly known as sunn pest, is a major pest of wheat in Northern Africa, the Middle East and Eastern Europe. This insect injects a prolyl endoprotease into the wheat, destroying the gluten. The purpose of this study was to clone the full length cDNA of the sunn pest prolyl endoprotease (spPEP) for expression in E. coli and to compare the amino acid sequence of the enzyme to other known PEPs in both phylogeny and potential tertiary structure. Sequence analysis shows that the 5ꞌ UTR contains several putative transcription factor binding sites for transcription factors known to be expressed in Drosophila that might be useful targets for inhibition of the enzyme. The spPEP was first identified as a prolyl endoprotease by Darkoh et al., 2010. The enzyme is a unique serine protease of the S9A family by way of its substrate recognition of the gluten proteins, which are greater than 30 kD in size. At 51% maximum identity to known PEPs, homology modeling using SWISS-MODEL, the porcine brain PEP (PDB: 2XWD) was selected in the database of known PEP structures, resulting in a predicted tertiary structure 99% identical to the porcine brain PEP structure. A Km for the recombinant spPEP was determined to be 210 ± 53 µM for the zGly-Pro-pNA substrate in 0.025 M ethanolamine, pH 8.5, containing 0.1 M NaCl at 37 °C with a turnover rate of 172 ± 47 µM Gly-Pro-pNA/s/µM of enzyme.
Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology

High-throughput biological assays such as microarrays let us ask very detailed questions about how diseases operate, and promise to let us personalize therapy. Data processing, however, is often not described well enough to allow for exact reproduction of the results, leading to exercises in “forensic bioinformatics” where aspects of raw data and reported results are used to infer what methods must have been employed. Unfortunately, poor documentation can shift from an inconvenience to an active danger when it obscures not just methods but errors. In this report, we examine several related papers purporting to use microarray-based signatures of drug sensitivity derived from cell lines to predict patient response. Patients in clinical trials are currently being allocated to treatment arms on the basis of these results. However, we show in five case studies that the results incorporate several simple errors that may be putting patients at risk. One theme that emerges is that the most common errors are simple (e.g., row or column offsets); conversely, it is our experience that the most simple errors are common. We then discuss steps we are taking to avoid such errors in our own investigations.
Spectral modification for concatenative speech synthesis

Concatenative synthesis can produce high-quality speech but is limited to the allophonic variations and voice types that were captured in the database. It would be desirable to modify speech units to remove formant discontinuities and to create new speaking styles, such as hypo- or hyper-articulated speech. Unfortunately, manipulating the spectral structure often leads to degraded speech quality. We investigate two speech modification strategies, one based on inverse filtering and the other on sinusoidal modeling, and we explain their merits and shortcomings for changing the spectral envelope in speech. We then propose a method which uses sinusoidal modeling and represents the complex sinusoidal amplitudes by an all-pole model. The all-pole model approximates the sinusoidal spectrum well, both in the amplitude and in the phase domain. We use the sinusoidal+all-pole model to control the spectral envelope in recorded speech. High-quality modified speech is generated from the model using sinusoidal synthesis. A perceptual test was conducted, which shows that the model was effective at changing vowel identities and was preferable over residual excited LPC.
Infant feeding practices of low-income rural mothers.

PURPOSE To examine infant feeding practices at 1 to 2 months of age and at 4 to 6 months in a rural population of infants at risk for failure to thrive. DESIGN A descriptive/exploratory study with 52 mothers who were interviewed twice during the infant's first 6 months of life. Mothers were recruited from health care facilities in rural southeastern Kentucky. Mothers participated in two structured interviews about feeding practices conducted in health care clinics or in the home. RESULTS At birth 52% of mothers chose to use formula, 41.2% chose breastfeeding, and 8% were both breastfeeding and formula feeding. By 1 month, 71% of mothers were formula feeding and only 29% were breastfeeding. At 4 to 6 months postpartum 80% of mothers were formula feeding and 20% were breastfeeding. Mothers with more children, higher family income, and more education were more likely to breastfeed. Almost all mothers began solid foods before the infant was 4 months old. Infants were fed table foods including mashed potatoes and gravy, and beverages such as apple juice, fruit juices, and soda. Mothers relied on health professionals for support for feeding decisions at the first interview; however, they relied more on the grandmother for support at the time of the second interview. CONCLUSIONS AND CLINICAL IMPLICATIONS Breastfeeding mothers need additional support to continue breastfeeding beyond the first month. Mothers and grandmothers need education to discourage the practice of early introduction of inappropriate solid foods, including the practice of thickening bottles of formula with cereal. Nutrition teaching should be provided to mothers and grandmothers including how to select high nutrient, lower fat-weaning foods, and limiting infant intake of high-calorie drinks.
Modeling Pollyanna Phenomena in Chinese Sentiment Analysis

This paper proposes a method to enhance sentiment classification by utilizing the Pollyanna phenomena. The Pollyanna phenomena describe the human tendency to use positive words more frequently than negative words. This word-level linguistic bias can be demonstrated to be strong and universal in many languages. We perform detailed analyses of the Pollyanna phenomena in four Chinese corpora. Quantitative analyses show that for documents with few positive words, the word usages in documents from either the positive or the negative polarities become similar. Qualitative analyses indicate t hat this increase of similarity of word usage could be caused by the concentration of topics. By taking advantage of these results, we propose a partitioning strategy for sentiment classification and significantly improve the F1-score.
Acoustic measurements of the 1999 basaltic eruption of Shishaldin volcano , Alaska 2 . Precursor to the Subplinian phase

The 1999 eruption of Shishaldin volcano (Alaska, USA) displayed both Strombolian and Subplinian basaltic activity. The Subplinian phase was preceded by a signal of low amplitude and constant frequency (c2 Hz) lasting 13 h. This bhumming signalQ is interpreted as the coalescence of the very shallow part of a foam building up in the conduit, which produces large gas bubbles before bursting. The acoustic waveform of the hum event is modelled by a Helmholtz resonator: gas is trapped into a rigid cavity and can only escape through a tiny upper hole producing sound waves. At Shishaldin, the radius of the hole (c5 m) is close to that of the conduit (c6 m), the cavity has a length of c60 m, and gas presents only a small overpressure between (c1.2 10 3 and 4.5 10 3 MPa). Such an overpressure is obtained by the partial coalescence of a foam formed by bubbles with a diameter from c2.3 mm at the beginning of the episode towards c0.64 mm very close to the end of the phase. The intermittency between hum events is explained by the ripening of the foam induced by the H2O diffusion through the liquid films. The two extreme values, from 600 to 10 s, correspond to a bubble diameter from 2.2 to 0.3 mm at the beginning and end of the pre-Subplinian phase, respectively. The extremely good agreement between two independent estimates of bubble diameters in the shallow foam reinforces the validity of such an interpretation. The total gas volume lost at the surface during the humming events is at most 5.9 10 m. At the very end of the preSubplinian phase, there is a single large bubble with an overpressure of c0.42 MPa. The large overpressure suggests that it comes from significant depth, unlike other bubbles in the pre-Subplinian phase. This deep bubble may be responsible for the entire foam collapse, resulting in the Subplinian phase. D 2004 Elsevier B.V. All rights reserved.
A missense mutation in the SEDL gene results in delayed onset of X linked spondyloepiphyseal dysplasia in a large pedigree

Editor—Spondyloepiphyseal dysplasia (SED) is a rare osteochondroplasia, characterised by disproportionate short stature with a short neck and trunk and barrel chest. The pelvis tends to be narrow and deep, the femoral neck short, and the femoral head flattened. Mild to moderate epiphyseal dysplasia of the large joints may also be seen. The latter may lead to premature secondary osteoarthritis with significant morbidity.1 SED may occur sporadically; however, in many cases the family history indicates an inherited condition. In some of these pedigrees, the inheritance pattern seems autosomal dominant, while in others it is consistent with autosomal recessive or X linked recessive.2 Recently, mutations in the gene designated SEDL , located on Xp22, were identified as the cause of X linked spondyloephiphyseal dysplasia tarda in three families.3 We have previously described a large kindred of British descent spanning four generations affected by SED.1 Briefly, 14 males between the ages of 10 and 77 years were affected, with early adolescence development of progressive decline in growth rate accompanied by short stature, short trunk, and barrel chest. Although some of them had to limit their activities because of hip or back limitation of movement or pain, many continued with normal activity and were …
Notes on P-Algebra (2): Group Presentation of Process Structure

We give yet another presentation of the process structures introduced in [1] and prove its equivalence to the original one. The presentation enjoys several convenient features not found in the original presentation, though in compensation for a certain loss of simplicity. Among others, it dispenses with the use of a choice function for quotient construction. The new presentation o ers a di erent viewpoint on the theory of process structure, and may provide a useful tool for some purposes.
Barriers and motivators for owners walking their dog: results from qualitative research.

ISSUE ADDRESSED This qualitative research explored the relationship between dog ownership and dog-related, social environmental and physical environmental factors associated with walking with a dog. METHODS Seven focus groups with dog owners (n=51) were conducted. A pre-determined discussion guide was used and transcripts were analysed as group data, using content analysis to identify common themes. RESULTS Many of the physical environmental barriers and facilitators that influenced dog owners to walk were similar to those found in the literature for general walking. However, a number of key motivators for walking, specific to dog owners, were identified. Dog owners reported that their dog was a strong source of motivation, companionship and social support that encouraged them to walk with their dog. The availability and accessibility of public open space (POS) for dogs and the provision of dog-related infrastructure within POS were also important environmental factors that affected whether owners walked with their dog. CONCLUSIONS Results from this qualitative study were used to develop the Dogs and Physical Activity (DAPA) tool which is now being used to measure the walking behaviour of dog owners.
Supplementary Information for Controlled Finite Momentum Pairing and Spatially Varying Order Parameter in Proximitized HgTe Quantum Wells

Junctions were fabricated using HgTe/HgCdTe heterostructures grown in the [001] crystal direction (the z direction), composed as shown in Supplementary Figure 1. Wafer I contained an 8 nm quantum well with an electron density of 13.5 × 10/cm and a mobility of 390, 000 cm/Vs. Wafer II contained a 7.8 nm quantum well with an electron density of 2.9 × 10/cm and a mobility of 790, 000 cm/Vs. Josephson junctions fabricated on these wafers were aligned at varying angles with respect to the [110] and [11̄0] cleavage edges of the crystal, but we do not know which is which in our samples. Therefore, we can only specify that the angular alignment corresponds to a rotation angle θ with respect to the [100] crystal axis, modulo π/2. Although we do not know which principal axis θ is referenced to experimentally, our model predicts the same results when θ is referenced to either. The x and y axes always lie respectively perpendicular and parallel to the direction of current flow in devices (see Figure 1 of main text). Throughout this supplement, devices are referred to in the following manner. Device A was fabricated by depositing aluminum leads onto a mesa etched into Wafer I, and was oriented at an angle θ = π/4. Devices B, C, and D were concurrently fabricated by depositing aluminum leads on Wafer II, and were
Intermittent Hypoxia Induces Hyperlipidemia in Lean Mice

Obstructive sleep apnea, a syndrome leading to recurrent intermittent hypoxia (IH), has been associated previously with hypercholesterolemia, independent of underlying obesity. We examined the effects of experimentally induced IH on serum lipid levels and pathways of lipid metabolism in the absence and presence of obesity. Lean C57BL/6J mice and leptin-deficient obese C57BL/6J-Lepob mice were exposed to IH for five days to determine changes in serum lipid profile, liver lipid content, and expression of key hepatic genes of lipid metabolism. In lean mice, exposure to IH increased fasting serum levels of total cholesterol, high-density lipoprotein (HDL) cholesterol, phospholipids (PLs), and triglycerides (TGs), as well as liver TG content. These changes were not observed in obese mice, which had hyperlipidemia and fatty liver at baseline. In lean mice, IH increased sterol regulatory element binding protein 1 (SREBP-1) levels in the liver, increased mRNA and protein levels of stearoyl–coenzyme A desaturase 1 (SCD-1), an important gene of TG and PL biosynthesis controlled by SREBP-1, and increased monounsaturated fatty acid content in serum, which indicated augmented SCD-1 activity. In addition, in lean mice, IH decreased protein levels of scavenger receptor B1, regulating uptake of cholesterol esters and HDL by the liver. We conclude that exposure to IH for five days increases serum cholesterol and PL levels, upregulates pathways of TG and PL biosynthesis, and inhibits pathways of cholesterol uptake in the liver in the lean state but does not exacerbate the pre-existing hyperlipidemia and metabolic disturbances in leptin-deficient obesity.
Role of Oxidative RNA Damage in Chronic-Degenerative Diseases

Normal cellular metabolism and exposure to ionizing and ultraviolet radiations and exogenous agents produce reactive oxygen species (ROS). Due to their reactivity, they can interact with many critical biomolecules and induce cell damage. The reaction of ROS with free nucleobases, nucleosides, nucleotides, or oligonucleotides can generate numerous distinct modifications in nucleic acids. Oxidative damage to DNA has been widely investigated and is strongly implicated in the development of many chronic-degenerative diseases. In contrast, RNA damage is a poorly examined field in biomedical research. In this review, I discuss the importance of RNA as a target of oxidative damage and the role of oxidative damage to RNA in the pathogenesis of some chronic-degenerative diseases, such as neurological disorders, atherosclerosis, and cancer. Furthermore, I review recent evidence suggesting that RNA may be the target for toxic agents and indicating RNA degradation as a powerful tool to treat any pathology in which there is an aberrant expression of mRNA and/or its gene products.
On the Relationship of the Circumpolar Current to Southern Hemisphere Winds in Coarse-Resolution Ocean Models

Abstract The response of the Circumpolar Current to changing winds has been the subject of much debate. To date most theories of the current have tried to predict the transport using various forms of momentum balance. This paper argues that it is also important to consider thermodynamic as well as dynamic balances. Within large-scale general circulation models, increasing eastward winds within the Southern Ocean drive a northward Ekman flux of light water, which in turn produces a deeper pycnocline and warmer deep water to the north of the Southern Ocean. This in turn results in much larger thermal wind shear across the Circumpolar Current, which, given relatively small near-bottom velocities, results in an increase in Antarctic Circumpolar Current (ACC) transport. The Ekman flux near the surface is closed by a deep return flow below the depths of the ridges. A simple model that illustrates this picture is presented in which the ACC depends most strongly on the winds at the northern and southern edges of .
High-dose chemotherapy with autologous stem-cell support as adjuvant therapy in breast cancer: overview of 15 randomized trials.

PURPOSE Adjuvant high-dose chemotherapy (HDC) with autologous hematopoietic stem-cell transplantation (AHST) for high-risk primary breast cancer has not been shown to prolong survival. Individual trials have had limited power to show overall benefit or benefits within subsets. METHODS We assembled individual patient data from 15 randomized trials that compared HDC versus control therapy without stem-cell support. Prospectively defined primary end points were relapse-free survival (RFS) and overall survival (OS). We compared the effect of HDC versus control by using log-rank tests and proportional hazards regression, and we adjusted for clinically relevant covariates. Subset analyses were by age, number of positive lymph nodes, tumor size, histology, hormone receptor (HmR) status, and human epidermal growth factor receptor 2 (HER2) status. RESULTS Of 6,210 total patients (n = 3,118, HDC; n = 3,092 control), the median age was 46 years; 69% were premenopausal, 29% were postmenopausal, and 2% were unknown menopausal status; 49.5% were HmR positive; 33.5% were HmR negative, and 17% were unknown HmR status. The median follow-up was 6 years. After analysis was adjusted for covariates, HDC was found to prolong relapse-free survival (RFS; hazard ratio [HR], 0.87; 95% CI, 0.81 to 0.93; P < .001) but not overall survival (OS; HR, 0.94; 95% CI, 0.87 to 1.02; P = .13). For OS, no covariates had statistically significant interactions with treatment effect, and no subsets evinced a significant effect of HDC. Younger patients had a significantly better RFS on HDC than did older patients. CONCLUSION Adjuvant HDC with AHST prolonged RFS in high-risk primary breast cancer compared with control, but this did not translate into a significant OS benefit. Whether HDC benefits patients in the context of targeted therapies is unknown.
Interaction between Lactobacillus kefir and Saccharomyces lipolytica isolated from kefir grains: evidence for lectin-like activity of bacterial surface proteins

Several microbial interactions involving yeast and lactobacilli have been suggested in fermented products. Co-aggregation between Lactobacillus kefir and yeast Saccharomyces lipolytica isolated from kefir grains was studied by scanning electron microscopy and aggregation assays. Six out of twenty Lb. kefir strains were able to co-aggregate with Sacch. lipolytica CIDCA 812 and showed thermolabile non-covalently bound surface molecules involved in this interaction. Co-aggregation inhibition after Lb. kefir pre-treatment with 5 m-LiCl or 20 g SDS/l showed that bacterial S-layer proteins play an important role in this interaction. Presence of different sugar (mannose, sucrose and fructose) or yeast pre-treatment with sodium periodate inhibited co-aggregation between Lb. kefir and Sacch. lipolytica. Co-aggregating Lb. kefir strains were also able to agglutinate with human red blood cells and they lost this ability after treatment with 5 m-LiCl. These results and the capacity of purified S-layer proteins of Lb. kefir to haemagglutinate, strongly suggest that a lectin-like activity of bacterial surface proteins (S-layer) mediates the aggregation with yeast cells.
Effects of corn oil on the volatile fatty acids in horses with induced gastric ulcers

ABSTRACT Objetive. To determine the influence of corn oil on the volatile fatty acids (VFA) concentrations in the gastric juice in horses with phenylbutazone (PBZ) induced gastric ulcers and Correlate the gastroscopic findings with the VFA concentrations. Materials and methods. 15 horses were allotted in 3 groups. Group I (control) received placebo during first 6 days (induction period) and was treated with sucralfate for 2 weeks (treatment period). Groups II and III received PBZ during the induction phase. After 6 days, horses from group II received 70 mL of corn oil /100 kg of body weight/ po, twice a day, for 2 weeks and horses from group III received 90 mL of corn oil/100 kg of body weight/ po, twice a day, for 2 weeks. All horses were examined by gastroscopy at days 0, 7 and 21. The lesions were recorded and classified according to the number and severity. Samples from gastric fluid were taken to measure the concentrations of the acetic, propionic, butyric and lactic acids. Results . Both PBZ protocols produced lesions in the both non-glandular and glandular areas of the stomach. All the treatments produced healing of the injured mucosa glandular. Neither of the two corn oil treatments affected healing of the gastric ulcers located in the non-glandular area. Conclusions . The concentrations of acetic and butyric acids were highest in the gastric juice. The corn oil and sucralfate did not lead to differences in the concentration of acetic acid and butyric acid.
Prognostic significance of additional cytogenetic abnormalities at diagnosis of Philadelphia chromosome-positive chronic granulocytic leukemia.

Of 661 patients with Philadelphia chromosome (Ph)-positive, nonblastic chronic granulocytic leukemia, 58 had cytogenetic abnormalities in addition to the Ph at the time of diagnosis. Twenty patients had reduplication of the Ph in one or more metaphases. Twenty-one patients with a single Ph exhibited hyperdiploidy in one or more metaphases. Eleven patients had two or more hypodiploid metaphases as their only numerical abnormality. The remaining six patients had a variety of abnormalities. Many patients had more than one type of abnormality. Survival of patients in the different subgroups was similar, but these 58 patients had a shorter course than the 603 patients without additional cytogenetic abnormalities (P less than .02). Survival curves for the two populations did not diverge until the 2-year point, after which the annual death rate among patients with additional cytogenetic abnormalities was approximately 40% higher than that of patients without such abnormalities. The two populations had similar relative risk values according to a hazard ratio formula previously described by the International CGL Prognosis Study Group. Thus, they would have been expected to have essentially identical survival curves. We conclude that the presence of additional cytogenetic abnormalities at the time of diagnosis constitutes an independently significant prognostic feature with an unusually delayed influence on survival.