Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression in animal cells and characterization of the hepatitis E virus structural proteins

Hepatitis E virus (HEV) is a major human pathogen in much of the developing world. It is a positive-strand RNA virus with a 7.5-kb polyadenylated genome consisting of three open reading frames (ORFs). In the absence of an in vitro culture system, the replication and expression strategy of HEV and the nature of its encoded polypeptides are not well understood. We have expressed the two ORFs constituting the structural portion of the HEV genome in COS-1 cells by using simian virus 40-based expression vectors and in vitro by using a coupled transcription-translation system. We show here that the major capsid protein, encoded by ORF2, is an 88-kDa glycoprotein which is expressed intracellularly as well as on the cell surface and has the potential to form noncovalent homodimers. It is synthesized as a precursor (ppORF2) which is processed through signal sequence cleavage into the mature protein (pORF2), which is then glycosylated (gpORF2). The minor protein, pORF3, encoded by ORF3 is a 13.5-kDa nonglycosylated protein expressed intracellularly and does not show any major processing. pORF3 interacts with a cellular protein of about 18 kDa which we call 3IP, the pORF3-interacting protein. The significance of these findings are discussed in light of an existing model of HEV genome replication and expression.
5′‐Heterogeneity of the human excitatory amino acid transporter cDNA EAAT2 (GLT‐1)

TWO novel transcripts of the human excitatory amino acid transporter EAAT2 (GLT-1) were cloned using PCR cloning techniques. Comparative sequence analysis of the 5′-untranslated region (UTR) of five EAAT2 transcripts led to the definition of five putative 5′-untranslated exons that are combined in a variable manner. Alternative splicing is a likely mechanism for the 5′ complexity of the EAAT2 cDNA. The potential functional meaning of this finding such as differential expression of the EAAT2 transcripts in the central nervous system remains to be demonstrated.
OCEAN: Object Communication Environment for Arbitrary Network

In recent years, information devices with network communication ability have become very popular and many people actually own such devices. Those information devices, however do not share users' data in spite of their communication ability. This paper proposes OCEAN (Object Communication Environment for Arbitrary Network), which provides liaison of objects stored in each device according to their profiles and situations. It eliminates redundant user operation on information devices, and enables a novel communication scheme among users by sharing common objects in those devices. Furthermore, it is also adaptive for various network environments such as unstable wireless connection, low cost performance connection, or stable permanent wired connection. A prototype implementation is currently under development for commercial use.
Inhibition of BMP activity by the FGF signal promotes posterior neural development in zebrafish.

The expression patterns of region-specific neuroectodermal genes and fate-map analyses in zebrafish gastrulae suggest that posterior neural development is initiated by nonaxial signals, distinct from organizer-derived secreted bone morphogenetic protein (BMP) antagonists. This notion is further supported by the misexpression of a constitutively active form of zebrafish BMP type IA receptor (CA-BRIA) in the zebrafish embryos. It effectively suppressed the anterior neural marker, otx2, but not the posterior marker, hoxb1b. Furthermore, we demonstrated that the cells in the presumptive posterior neural region lose their neural fate only when CA-BRIA and Xenopus dominant-negative fibroblast growth factor (FGF) receptors (XFD) are coexpressed. The indications are that FGF signaling is involved in the formation of the posterior neural region, counteracting the BMP signaling pathway within the target cells. We then examined the functions of Fgf3 in posterior neural development. Zebrafish fgf3 is expressed in the correct place (dorsolateral margin) and at the correct time (late blastula to early gastrula stages), the same point that the most precocious posterior neural marker, hoxb1b, is first activated. Unlike other members of the FGF family, Fgf3 had little mesoderm-inducing activity. When ectopically expressed, Fgf3 expands the neural region with suppression of anterior neural fate. However, this effect was mediated by Chordino (zebrafish Chordin), because Fgf3 induces chordino expression in the epiblast and Fgf3-induced neural expansion was substantially suppressed in dino mutants with mutated chordino genes. The results obtained in the present study reveal multiple actions of the FGF signal on neural development: it antagonizes BMP signaling within posterior neural cells, induces the expression of secreted BMP antagonists, and suppresses anterior neural fate.
2-(fluorine-18)-fluoro-2-deoxy-D-glucose PET in detection of pancreatic cancer: value of quantitative image interpretation.

PURPOSE To evaluate use of positron emission tomography (PET) versus computed tomography (CT) in detection of pancreatic cancer and determine the value of quantitative and visual image interpretation of these techniques. MATERIALS AND METHODS Within 8 weeks before surgery, 73 patients with suspected pancreatic cancer or chronic pancreatitis underwent imaging with CT and with static PET after injection of 250-350 MBq of 2-(fluorine-18)-fluoro-2-deoxy-D-glucose (FDG). Focal FDG uptake, considered a sign of malignancy, was calculated with standardized uptake values (SUVs) 60 minutes after injection. RESULTS With FDG PET, pancreatic carcinoma was correctly diagnosed in 41 (95%) of 43 patients, and chronic pancreatitis in 27 (90%) of 30 patients. With an SUV cutoff value of 1.53, both sensitivity and specificity for detection of malignancy were 93%. With CT, pancreatic cancer was correctly diagnosed in 33 (80%) of 41 patients, whereas results in seven (26%) of 27 patients with chronic pancreatitis were false-positive (specificity, 74%). CONCLUSION FDG PET enabled reliable differentiation of pancreatic adenocarcinoma from chronic pancreatitis. The sensitivity and specificity of visual image interpretation with FDG PET was statistically significantly higher (P < .05) than with CT.
Prevention of malathion-induced depletion of cardiac cells mitochondrial energy and free radical damage by a magnetic magnesium-carrying nanoparticle

The present work was designed to examine the effect of a new 25Mg2+-carrying nanoparticle (PMC16) on energy and oxidative stress parameters inside the heart of the rats exposed to acute mild toxic dose of malathion, a widely used organophosphate. Post a single intraperitoneal (ip) injection of malathion (0.25 of LD50), PMC16 at different doses (0.05, 0.1, and 0.2 of LD50) was administered intravenously (iv) as a supplement to standard therapy of atropine and pralidoxime. MgSO4 was used as another supplement for comparison with PMC16. Oxidative stress biomarkers including lipid peroxidation (LPO) and reactive oxygen species (ROS), antioxidant enzymes including superoxide dismutase (SOD), glutathione peroxidase (GPx), catalase (CAT), ATP/ADP ratio, and Mg in the cardiac cells were determined. Results indicated a significant increase in LPO, ROS, ADP/ATP ratio, and a decrease in Mg post-malathion poisoning in comparison to controls. All of these parameters were improved by use of standard therapy either with MgSO4 or various doses of PMC16. The activities of SOD, CAT, and GPx did not change significantly in the present acute malathion poisoning model and neither MgSO4 or PMC16 had no considerable improvement on these parameters. Comparing groups that received normal Mg and those of various doses of PMC16, a significant difference was found with the PMC16 (0.2 LD50) group. PMC16 0.2 reduced cardiac cells LPO and ROS of Mal-exposed animals rather than that of MgSO4. PMC16 0.2 was also significantly better than MgSO4 in improving MAL-induced changes in ADP/ATP ratio and also intracellular Mg levels. This study illustrates that malathion-induced cardiac cells toxicity is improved by administration of Mg as a result of increasing cardiac ATP through active transport of Mg inside the cells. Finally, the results of this study support positive effects of this magnetic Mg nanoparticle carrier but do not confirm its absolute efficacy that remains to be explored by further tests in different animal models and organs before moving to a phase I human trial.
Combining a rule-based classifier with weakly supervised learning for twitter sentiment analysis

Microblog, especially Twitter, have become an integral part of our daily life, where millions of user sharing their thoughts daily because of its short length characteristics and simple manner of expression. Monitoring and analyzing sentiments from such massive amount of twitter posts provide enormous opportunities for companies and other organizations to learn about what user think and feel about their products and services. But the ever-growing unstructured and informal user-generated posts in twitter demands sentiment analysis tools that can perform well with minimum supervision. In this paper, we propose an approach for sentiment analysis on twitter, where we combine a rule-based classifier with weakly supervised Naive-Bayes classifier. To classify the tweets sentiment, we introduce a set of rules for the rule-based classifier based on the occurrences of emoticons and sentiment-bearing words, whereas several sentiment lexicons are applied to train the Naive-Bayes classifier. We conducted our experiments based on the Stanford sentiment140 dataset. Experimental results demonstrate the effectiveness of our method over the baseline in terms of recall, precision, F1 score, and accuracy.
Spatial Scale and Saccade Programming

The global effect in eye orienting occurs when saccades land at the ‘centre of gravity’ of a target stimulus configuration. Short-latency saccades are particularly prone to this effect whereas longer-latency saccades may show more influence of fine detail. Alternative explanations of these effects are considered and data are presented from an experiment in which the influence of different stimulus features on the global effect in a search task was examined. The effect shows a substantially different time course for target-distractor combinations differing in contrast polarity (black vs white) than for combinations differing in shape (circle vs square). It is concluded that the global effect cannot be explained either as a high-level strategic effect or as an effect of automatic fast processing of low-spatial-frequency information in early sensory channels. Instead it is suggested that the visual-spatial-integration characteristic of the global effect is an integral and unavoidable part of the process of selection of saccadic response.
Antioxidant Activity and Total Phenolic Contents of Three Bupleurum Taxa

Bupleuri Radix (Bupleurum spp. root) is one of the most important crude drugs in Korea, China and Japan. We investigated the total phenolic content and antioxidant activity of three Bupleurum taxa (B. falcatum, B. falcatum ‘Mishima’ and B. latissimum). The highest total phenolic content was found in B. latissimum (18.6±1.7 mg/g) and the least in B. falcatum ‘Mishima’ (9.4±0.5 mg/g). The ethyl acetate fractions obtained from B. falcatum and B. falcatum ‘Mishima’ showed higher DPPH radical scavenging activity than the other fractions. In the case of B. latissimum, the DPPH radical scavenging activity of the diethyl ether fraction was higher than that of the other fractions. These results suggest that the three Bupleurum plants may be used as a food additive as a natural antioxidant.
ENDOGENOUS LUTEINIZING HORMONE SURGE IN WOMEN DURING INDUCTION OF MULTIPLE FOLLICULAR DEVELOPMENT WITH PULSATILE FOLLICLE STIMULATING HORMONE

In this study nine consecutive normally cycling women undergoing in‐vitro fertilization (IVF) were superovulated with clomiphene citrate followed by pulsatile ‘pure’FSH injected s.c. via a pump (28 IU every 3 h). All women displayed an endogenous LH surge, which was markedly attenuated in most of the cases (peak value 44·5 ± 5·9 U/l, duration 29·2 ± 1·2 h, mean ± SEM) as compared to spontaneous cycles. An increase in serum progesterone levels before the onset of the LH surge was seen in only one woman at a time when the LH values were low. During the LH surge serum progesterone levels increased significantly in all patients (12·7 ± 1·90 nmol/l vs 4·74 ± 1·57 nmol/l at the onset of the surge, mean ± SEM, P < 0·05) indicating follicular luteinization. Very high oestradiol levels in serum were found at the onset of the LH surge (7504 ± 898 pmol/1, mean ± SEM). Preovulatory oocytes were recovered from all women through a laparoscope 34–36 h after the beginning of the LH surge and embryos were replaced to them after IVF. One ongoing clinical pregnancy occurred. In contrast to results in monkeys, these results demonstrate for the first time that normally cycling women superovulated with clomiphene pulsatile ‘pure’FSH will display an endogenous LH surge. Although the surge is attenuated implantation can occur.
Identification and Characterization of Outer Membrane Vesicle-Associated Proteins in Salmonella enterica Serovar Typhimurium

ABSTRACT Salmonella enterica serovar Typhimurium is a primary cause of enteric diseases and has acquired a variety of virulence factors during its evolution into a pathogen. Secreted virulence factors interact with commensal flora and host cells and enable Salmonella to survive and thrive in hostile environments. Outer membrane vesicles (OMVs) released from many Gram-negative bacteria function as a mechanism for the secretion of complex mixtures, including virulence factors. We performed a proteomic analysis of OMVs that were isolated under standard laboratory and acidic minimal medium conditions and identified 14 OMV-associated proteins that were observed in the OMV fraction isolated only under the acidic minimal medium conditions, which reproduced the nutrient-deficient intracellular milieu. The inferred roles of these 14 proteins were diverse, including transporter, enzyme, and transcriptional regulator. The absence of these proteins influenced Salmonella survival inside murine macrophages. Eleven of these proteins were predicted to possess secretion signal sequences at their N termini, and three (HupA, GlnH, and PhoN) of the proteins were found to be translocated into the cytoplasm of host cells. The comparative proteomic profiling of OMVs performed in this study revealed different protein compositions in the OMVs isolated under the two different conditions, which indicates that the OMV cargo depends on the growth conditions and provides a deeper insight into how Salmonella utilizes OMVs to adapt to environmental changes.
The effects of oxidative stress induced by prolonged low-dose diesel exhaust particle exposure on the generation of allergic airway inflammation differ between BALB/c and C57BL/6 mice

We have recently reported that airway inflammatory responses to the oxidative stress induced by prolonged low-dose diesel exhaust particle (DEP) exposure differ markedly between BALB/c and C57BL/6 mice. In the present study, the effects of genetic differences in the response to prolonged low-dose DEP exposure on the generation of ovalbumin-induced allergic airway inflammation were further explored using the same mouse strains. In BALB/c mice, eosinophils and mucous goblet cells in histopathological pulmonary specimens increased significantly after DEP exposure, and were more marked than in C57BL/6 mice. Interleukin (IL)-5 and IL-13 levels in bronchoalveolar lavage (BAL) fluid were increased significantly by DEP exposure only in BALB/c mice. The DEP-induced increases in peribronchial eosinophils and mucous goblet cells in the lung tissues, and of IL-5 and IL-13 in the BAL fluid, were significantly attenuated by the antioxidant N-acetylcysteine. Thus, the effects of prolonged low-dose DEP exposure on the generation of allergic airway inflammation differed markedly between the mouse strains. These differences may be caused by different antioxidant responses to the oxidative stress induced by DEP exposure. Our results contribute more information to the search for genetic susceptibility factors in the response to DEP, and may thus assist in the discovery of new biomarkers for DEP-related disease.
Temperature e ects on the diversity of soil heterotrophs and the d 13 C of soil-respired CO 2

We measured the respiration rates, dC of respired CO2, and microbial community composition in root-free bulk soils incubated at 4, 22 and 408C. The soils were obtained from the Duke Forest Free-Air CO2 Enrichment (FACE) experiment where organic carbon in soils sampled from the elevated CO2 plots contained a unique C label that was derived from FACE fumigation. The CO2 produced by soil heterotrophs at 48C was 2.2 to 3.5enriched in C relative to CO2 respired at 22 and 408C and was similarly enriched relative to bulk soil carbon. There was no isotopic dierence between CO2 produced at 22 and 408C. Respiration rates increased exponentially with temperature from 0.25 mg CO2 g soil ÿ1 dÿ1 at 48C to 0.73 mg CO2 g soil ÿ1 dÿ1 at 408C. Microbial community composition, as measured by the dierences in populations of morphology types, diered across the temperature range. Only eight of 67 microbial morphology types were common to all three incubation temperatures, while six types were unique to 48C soil, 17 to 228C soil and 18 to 408C soil. Species richness, approximated from morphology type, was signi®cantly lower at 48C than at 22 and 408C. This change in microbial community structure from 4 to 22 and 408C caused a shift in mineralizable carbon pools, resulting in a shift in the isotopic composition of CO2 respired at the low temperature. 7 2000 Elsevier Science Ltd. All rights reserved.
Concomitant radiotherapy and chemotherapy for early-stage nasopharyngeal carcinoma.

PURPOSE Early-stage nasopharyngeal carcinoma (NPC) continues to carry a failure rate of 15% to 30% when treated with radiotherapy alone; the benefit of concomitant radiotherapy and chemotherapy (CCRT) in early-stage NPC is unclear. The purpose of this report is to describe our efforts to improve treatment outcome in early-stage NPC after CCRT. PATIENTS AND METHODS Of 189 newly diagnosed NPC patients without evidence of distant metastases who were treated in our institution between 1990 and 1997, 44 presented with early-stage (stage I and II) disease according to the American Joint Committee on Cancer (AJCC) 1997 NPC staging system. Twelve of these patients were treated with radiotherapy alone and 32 with CCRT. Each patient's head and neck area was evaluated by magnetic resonance imaging or computed tomography. Radiotherapy was administered at 2 Gy per fraction per day, Monday through Friday, for 35 fractions for a total dose of 70 Gy. Chemotherapy consisting of cis-diamine-dichloroplatinum and fluorouracil was delivered simultaneously with radiotherapy in weeks 1 and 6 and sequentially for two monthly cycles after radiotherapy. RESULTS Patients who were treated with radiotherapy alone primarily had stage I disease, whereas none of those who were treated with CCRT had stage I disease (11 of 12 patients v none of 32 patients; P =.001). The locoregional control rate at 3 years for the radiotherapy group was 91.7% (median follow-up period, 34 months) and was 100% for the CCRT group (median follow-up period, 44 months) (P =.10). The 3-year disease-free survival rate in the radiotherapy group was 91.7% and was 96.9% in the CCRT group (P =.66). CONCLUSION Our results reveal excellent prognosis of AJCC 1997 stage II NPC treated with CCRT. Stage II patients with a greater tumor burden treated with CCRT showed an equal disease-free survival, compared with stage I patients treated with radiotherapy alone. A prospective randomized trial is underway to confirm the role of CCRT in stage II NPC.
Decision Support Tool to Improve Glucose Control Compliance After Cardiac Surgery

ABSTRACT Hyperglycemia control is associated with improved outcomes in patients undergoing cardiac surgery. The Surgical Care Improvement Project metric (SCIP‐inf‐4) was introduced as a performance measure in surgical patients and included hyperglycemia control. Compliance with the SCIP‐inf‐4 metric remains suboptimal. A novel real‐time decision support tool (DST) with guaranteed feedback that is based on the existing electronic medical record system was developed at a tertiary academic center. Implementation of the DST increased the compliance rate with the SCIP‐inf‐4 from 87.3% to 96.5%. Changes in tested clinical outcomes were not observed with improved metric compliance. This new framework can serve as a backbone for development of quality control processes for other metrics. Further and, ideally, multicenter studies are required to test if implementation of electronic DSTs will translate into improved resource utilization and outcomes for patients.
A novel fibrous material created by self-rolling of a patterned polymer thin film.

A new kind of a fibrous material is produced by controlled self-rolling of patterned thin poly(4-vinyl)pyridine films in acidic water. Self-rolling is induced by unequal swelling of the top and the bottom layers of the films in the solvent. Rolling starts from parallel scratches in the film and results in twin-scroll fibers. The fibers are stabilized by staining with CuCl(2) salt and freeze-dried. The output of the fiber material production is of the order of 1 cm(3) from approximately 50 cm(2) of the patterned polymer film. The approach opens new broad opportunities for creation of smart fibrous materials via loading the fibers with functional micro- and nanoparticles.
Reid's Paradox of Rapid Plant Migration Dispersal theory and interpretation of paleoecological records

James S. Clark, Jason Lynch, and Peter Wyckoff are in the Department of Botany, Duke University, Durham, NC 27708; Chris Fastie and Stephen T. Jackson are in the Department of Botany, University of Wyoming, Laramie, WY 82701; George Hurtt and Stephen Pacala are in the Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544-1003; Carter Johnson is in the Department of Horticulture and Forestry, South Dakota State University, Brookings, SD 57007; George A. King is at Dynamic Corporation, US EPA National Health and Environmental Effects Research Laboratory, Corvallis, OR 97333; Mark Lewis is in the Math Department, University of Utah, Salt Lake City, UT 84112; Colin Prentice is at the School of Ecology, Lund University, Lund, Sweden; Eugene W. Schupp is in the Department of Rangeland Resources, Utah State University, Logan, UT 84322; and Thompson Webb III is in the Department of Geological Sciences, Brown University, Providence, RI 029121846. 1998 American Institute of Biological Sciences. A plausible explanation
Bayesian model mixing for cold rolling mills: Test results

The contribution presents the results of a collaborative R&D effort of two private companies and two national research institutions, joined at the European level. It was aimed to develop an enhanced on-line predictor of the strip thickness in the rolling gap. The issue dealt with is the absence of a reliable delay-free measurement of the outgoing strip thickness or the gap size, making the thickness control a challenging task. Although several satisfactory solutions have been used for decades, and modern control theory has been exploited as well, the pervasive competition in the field of metal strip processing emphasizes the need of a novel, more precious measuring method. The solution developed within the completed project is based on a parallel run of several adaptive Bayesian predictors whose outputs are continuously mixed to provide the best available rolling gap size prediction. The system was already tested in open loop in a real industrial environment for two reversing cold rolling mills processing steel and copper alloys strips, respectively.