Miracle-dz/UniFAR-FTUs huggingface dataset:
Relative Rates of Retroviral Reverse Transcriptase Template Switching during RNA- and DNA-Dependent DNA Synthesis

ABSTRACT Retroviral reverse transcriptases (RTs) frequently switch templates during DNA synthesis, which can result in mutations and recombination. The relative rates of in vivo RT template switching during RNA- and DNA-dependent DNA synthesis are unknown. To determine the relative rates of RT template switching during copying of RNA and DNA templates, we constructed spleen necrosis virus-based retroviral vectors containing a 400-bp direct repeat. The directly repeated sequences were upstream of the polypurine tract (PPT) in the RB-LLP vector; the same direct repeats flanked the PPT and attachment site (att) in the RB-LPL vector. RT template switching events could occur during either RNA- or DNA-dependent DNA synthesis and delete one copy of the direct repeat plus the intervening sequences. RB-LLP vectors that underwent direct repeat deletions during RNA- and DNA-dependent DNA synthesis generated viral DNA that could integrate into the host genome. However, any deletion of the direct repeats in the RB-LPL vector that occurred during RNA-dependent DNA synthesis resulted in deletion of the essential PPT and att site and generated a dead-end viral DNA product. Thus, only RB-LPL vectors that underwent direct repeat deletions during DNA-dependent DNA synthesis could integrate to form proviruses. The RB-LLP and RB-LPL vectors were permitted to undergo a single replication cycle, and the frequencies of direct repeat deletions were determined by PCR and Southern analysis of the resulting proviruses. A comparison of the frequency of direct repeat deletions in the RB-LLP and RB-LPL vectors indicated that the in vivo rates of RT template switching during RNA- and DNA-dependent DNA synthesis are nearly identical.
Most of ADP (cid:1) glucose linked to starch biosynthesis occurs outside the chloroplast in source leaves

Sucrose and starch are end products of two segregated gluconeogenic pathways, and their production takes place in the cytosol and chloroplast of green leaves, respectively. According to this view, the plastidial ADP (cid:1) glucose (ADPG) pyrophosphorylase (AGP) is the sole enzyme catalyzing the synthesis of the starch precursor molecule ADPG. However, a growing body of evidences indicates that starch formation involves the import of cytosolic ADPG to the chloroplast. This evidence is consistent with the idea that synthesis of the ADPG linked to starch biosynthesis takes place in the cytosol by means of sucrose synthase, whereas AGP channels the glucose units derived from the starch breakdown. To test this hypothesis, we ﬁrst investigated the subcellular localization of ADPG. Toward this end, we constructed transgenic potato plants that expressed the ADPG-cleav-ingadenosinediphosphatesugarpyrophosphatase(ASPP)from Escherichia coli either in the chloroplast or in the cytosol. Source leaves from plants expressing ASPP in the chloroplast exhibited reduced starch and normal ADPG content as compared with control plants. Mostimportantlyhowever,leavesfromplantsexpressingASPPinthe cytosol showed a large reduction of the levels of both ADPG and starch, whereas hexose phosphates increased as compared with control plants. No pleiotropic changes in photosynthetic parameters and maximum catalytic activities of enzymes closely linked to starch and sucrose metabolism could be detected in the leaves expressing ASPP in the cytosol. The overall results show that, essentially similar to cereal endosperms, most of the ADPG linked to starch biosynthesis in source leaves occurs in the cytosol.
Identification of critical paths in circuits with level-sensitive latches

An approach to timing verification of circuits with level-sensitive latches which focuses on the critical paths that constrain the operating speed of these circuits is described. The timing model used has been referred to as the 'SMO model' (Sakallah, Mudge and Olukotun, 1990). Three types of critical paths (long, short and loops) can arise in the SMO formulation; verifying their timing is sufficient to ensure correct operation. An algorithm for identifying these paths is presented, and its relationship to other approaches to solving the SMO model equations is discussed. Finally, results which demonstrate the algorithm on circuits from the ISCAS89 benchmark suite are presented. <<ETX>>
Aetiological diagnosis of community acquired pneumonia: Utility of rapid microbiological methods with respect to disease severity

The present study investigated the utility of rapid microbiological methods in the aetiological diagnosis of community acquired pneumonia (CAP) according to the severity of CAP. Between 1999 and 2004, 384 adult patients with CAP were studied prospectively. In addition to standard microbiological methods, PCR and antigen detection techniques were used to identify pathogens. A total of 230 microbial agents in 209 patients were identified, with 134 (58.2%) identified by antigen detection or PCR tests. Of these 134 microbial agents, 95 (70.9%) were identified only by these rapid methods. Streptococcus pneumoniae urinary antigen detection was positive in 24.3% (81/333) of the patients with a diagnostic yield of 38.7% in those with severe pneumonia. Respiratory viral antigen detection was positive in 11.1% (35/314) of the patients with the highest diagnostic yield (20.3%) in patients with severe pneumonia. Mycoplasma pneumoniae PCR was positive in 7.5% (13/174) of the patients, all of whom were low-risk patients. Only 1 case of Chlamydia pneumoniae was identified by PCR. In conclusion, besides yielding the aetiological diagnosis rapidly, new methods add to the total diagnostic yield in CAP. The diagnostic yield of rapid methods differs according to the severity of the pneumonia.
An FR II Radio Galaxy 15 ’ from Sagittarius A * : Implications for the Scattering Region in the Galactic Center

G359.87]0.18 is an enigmatic object located 15@ from Sgr A*. It has been variously classiÐed as an extragalactic source, a Galactic jet source, and a young supernova remnant. We present new observations of G359.87]0.18 between 0.33 and 15 GHz and an H I absorption spectrum and use these to argue that this source is an FR II radio galaxy. We are able to place a crude limit on its redshift of The source has a spectral index of a \[1 (S P la), suggestive of a radio galaxy with a redshift zZ 0.1. The scattering diameters of Sgr A* and several nearby OH masers (B1A at 1 GHz) indicate that a zZ 2. region of enhanced scattering is along the line of sight to the Galactic center. If the region covers the Galactic center uniformly, the implied diameter for a background source is at least 600A at 0.33 GHz, which is in contrast with the observed 20A diameter of G359.87]0.18. Using the scattering diameter of a nearby OH maser OH 359.762]0.120 and the widths of two nearby nonthermal threads, G0.08]0.15 and G359.79]0.17, we show that a uniform scattering region should cover G359.87]0.18. We therefore conclude that the Galactic center scattering region is inhomogeneous on a scale of 5@ (B10 pc at a distance of 8.5 kpc). This scale is comparable with the size scale of molecular clouds in the Galactic center. The close agreement between these two length scales is an indication that the scattering region is linked intimately to the Galactic center molecular clouds. Subject headings : galaxies : individual (G359.87]0.18) È Galaxy : center È radio continuum: galaxies È scattering
Performance of Multisite Silicon Microprobes Implanted Chronically in the Ventral Cochlear Nucleus of the Cat

A central auditory prosthesis based on microstimulation within the ventral cochlear nucleus (VCN) offers a means of restoring hearing to persons whose auditory nerve has been destroyed bilaterally and cannot benefit from cochlear implants. Arrays of silicon probes with 16 stimulating sites were implanted into the VCN of adult cats, for up to 314 days. Compound neuronal responses evoked from the sites in the VCN were recorded periodically in the central nucleus of the contralateral inferior colliculus (ICC). The threshold and growth of most of the responses were stable for at least 250 days after implantation of the arrays. The responses evoked from the deepest and shallowest electrode sites did exhibit some changes over time but none of the thresholds exceeded 10 muA. The thresholds and growth of the compound responses from most of the stimulating sites were very stable over time, and comparable to those of chronically implanted single-site iridium microelectrodes. Multiunit neuronal activity evoked from the stimulating sites in the VCN was recorded along the dorsolateral-ventromedial (DLVM) axis of the ICC. The distribution, span and degree of overlap of the multiunit activity demonstrated the utility of the multisite, multishank array configuration as a means of accessing the neuronal populations in the VCN that encode various acoustic frequencies. These findings are encouraging for the prospects of developing an auditory prosthesis employing multisite silicon microprobes
Intranasal and Intravenous Administration of Desmopressin: Effect on F VIII/vWF, Pharmacokinetics and Reproducibility

Summary A comparison was made of intranasal administration of 300 μg desmopressin (DDAVP) by spray, with intravenous administration of 0.2, 0.3 and 0.4 μg DDAVP/kg in 10 healthy volunteers. The effect of DDAVP was measured on F VIII/vWF complex and on plasminogen activator release. In addition, plasma levels of DDAVP were determined using a specific and sensitive radioimmunoassay. Moreover, the reproducibility of the spray effect in 10 healthy volunteers was tested after administration of 300 μg DDAVP intranasally by spray on 5 different occasions. Plasma levels of DDAVP showed a clear dose-response with the maximum levels at 0.4 μg/kg i.v. The effect of the spray approximated the 0.2 μg/kg response. However, the maximum response in both F VIII/vWF complex and plasminogen activator release was obtained after 0.3 μg/kg i. v. The response to 0.4 μg/kg i. v. was not significantly different from the response to 0.3 μg/kg indicating that maximum stimulation was reached with 0.3 μg/kg. There was no correlation between plasma levels of F VIII/vWF and DDAVP indicating that the biological response to DDAVP is subjected to saturation kinetics. The reproducibility of the effect of the spray dose on VIII : C was 21% (c.v.) and 27% for the intra-individual and interindividual variation, respectively, and compared favorably with intravenous administration. Intranasal DDAVP (300 μg) is as effective as 0.2 μg/kg intravenously and provides an accurate, reproducible and convenient alternative to parenteral administration.
An Agent Based Approach to Study Incubation in Innovation Ecosystems

The innovation ecosystems are clusters of economic entities creating high productivity and business diversity based on innovations. The business incubators are among the most well-known approaches to support economic growth in these ecosystems. Although the number of business incubators has increased substantially in the last decade, the absence of efficient assessment techniques for business incubation calls for novel approaches. In this paper, we present an approach for the analysis of innovation ecosystems by using an agent based modeling methodology with a focus on incubation. We model the role of business incubators considering different support methods and show their effects on global economy with our preliminary results.
The Impact of Matrix Metalloproteinase 2 on Prognosis and Clinicopathology of Breast Cancer Patients: A Systematic Meta-Analysis

Backgrounds Matrix metalloproteinase 2 (MMP-2) plays a crucial role in the progression of breast cancer (BC). The prognostic role of MMP-2 expression in BC patients has been widely reported, but the results were inconsistent. Thus, a meta-analysis was conducted to gain a better insight into the impact of MMP-2 expression on survival and clinicopathological features of BC patients. Methods Identical search strategies were used to search relevant literatures in electronic databases update to August 1, 2014. Individual hazard ratios (HRs) and odds ratios (ORs) with their 95% confidence intervals (CIs) were extracted and pooled to evaluate the strength of the association between positive MMP-2 expression and survival results and clinicopathological features of BC patients. Begg’s tests, Egger’s tests and funnel plots were used to evaluate publication bias. Heterogeneity and sensitivity analysis were also assessed. All the work was completed using STATA. Results Pooled HRs and 95% CIs suggested that MMP-2 expression had an unfavorable impact on both OS (HR: 1.53, 95% CI: 1.29–1.82) and DFS/RFS/DDFS (HR: 1.41, 95% CI: 1.07–1.86) in BC patients. Furthermore, MMP-2 expression was significantly associated with lymph node metastasis (positive vs negative: OR 1.91, 95% CI 1.17–3.12). Conclusion In conclusion, positive MMP-2 expression might be a significant predictive factor for poor prognosis in patients with BC.
Interference alignment with cyclic unidirectional cooperation

Recent results on interference alignment (IA) in a K-user n × n MIMO interference channel, have shown that the ratio of total degrees of freedom d̂ to the single user degrees of freedom varies from d̂/n <; 2 in the case of arbitrary MIMO channels (i.e., channels with no structure) to K/2 in the case of channels with diagonal structure (i.e., channels with time or frequency varying coefficients). These results confirm that the information theoretic upper bound on degrees of freedom with no channel extension can only be achieved for K ≤ 3 with an overwhelming overhead of the global channel knowledge or an extensive number of back-and-forth iterations between the transmitting and the receiving nodes [3]. In this paper, we show that this limit on the number of users can be extended to K ≤ 5 as a result of introducing a partial cooperation into the interference channel. This partial cooperation is such that the message of the kth transmitter or base station (BS) is known to the [k - 1)th transmitter (mod K) and each receiver or user is simultaneously served by two transmitters. We introduce a one-shot algorithm that utilizes the reciprocity of wireless network to achieve interference alignment with no iterations between the transmitting and the receiving nodes when d̂/n ≤ 2. Monte-Carlo simulation results show that the proposed partial cooperation used with the one-shot algorithm can considerably enhance the sum rate in an interference channel system at practical SNR levels as a result of improved spatial multiplexing gain.
The role of the EGFR signaling in tumor microenvironment

The epidermal growth factor receptor (EGFR) family comprehends four different tyrosine kinases (EGFR, ErbB‐2, ErbB‐3, and ErbB‐4) that are activated following binding to epidermal growth factor (EGF)‐like growth factors. It has been long established that the EGFR system is involved in tumorigenesis. These proteins are frequently expressed in human carcinomas and support proliferation and survival of cancer cells. However, activation of the EGFR in non‐malignant cell populations of the neoplastic microenvironment might also play an important role in cancer progression. EGFR signaling regulates in tumor cells the synthesis and secretion of several different angiogenic growth factors, including vascular endothelial growth factor (VEGF), interleukin‐8 (IL‐8), and basic fibroblast growth factor (bFGF). Overexpression of ErbB‐2 also leads to increased expression of angiogenic growth factors, whereas treatment with anti‐EGFR or anti‐ErbB‐2 agents produces a significant reduction of the synthesis of these proteins by cancer cells. EGFR expression and function in tumor‐associated endothelial cells has also been described. Therefore, EGFR signaling might regulate angiogenesis both directly and indirectly. In addition, activation of EGFR is involved in the pathogenesis of bone metastases. Within the bone marrow microenvironment, cancer cells stimulate the synthesis of osteoclastogenic factors by residing stromal cells, a phenomenon that leads to bone destruction. It has been shown that EGFR signaling regulates the ability of bone marrow stromal cells to produce osteoclastogenic factors and to sustain osteoclast activation. Taken together, these findings suggest that the EGFR system is an important mediator, within the tumor microenvironment, of autocrine and paracrine circuits that result in enhanced tumor growth. J. Cell. Physiol. 214: 559–567, 2008. © 2007 Wiley‐Liss, Inc.
Metabolic implications of ammonia production in the ruminant

NH3 is generated in the gut of all animal species as a result of two main processes: (1) microbial degradation of nitrogenous compounds such as proteins, peptides, amino acids and nucleic acids within the gut lumen and (2) microbial hydrolysis of urea passing across the gut wall from the blood and interstitial fluids. Whereas in most species the production of NH3 and its incorporation into microbial protein in the hindgut is considered of little nutritional benefit to the host (apart from coprophagic species), the pathway of N assimilation into microbial protein in the reticulo-rumen is an essential component of protein flow to the small intestine of ruminant animals. As such it has been that ruminants can sustain a modest level of productivity when provided only with non-protein-N in the diet Protein rationing for this group of livestock is on provision of N for microbial protein synthesis in to an component to of the of the to N to the which NH3 is within the and which affect its in
Premature Rupture of the Membranes at the Sylvanus Olympio University Hospital of Lomé, Togo: Microbiological Findings and Outcomes

Introduction: To prevent the risk of infections in cases of premature rupture of the membranes (PROM), a pregnancy complication, gynecologists of the Sylvanus Olympio University Teaching Hospital used clavulanic acid and amoxicillin as empiric antibiotic therapy intravenously. This study aims to identify and assess the susceptibility to antibiotics of bacteria involved in PROM. Methods: A cross-sectional study was conducted from February 25 to June 06, 2014 on 60 pregnant women presenting a PROM and their 65 newborns, recruited in the Gynecology and Obstetrics Service of the Sylvanus Olympio University Teaching Hospital of Lome, Togo. In mothers, cytological and bacteriological examinations of vaginal and endocervix swabs were carried out and among newborns, cytological and bacteriological examinations were performed on gastric fluid and ear swabs at the Microbiology Service of the university hospital. Results: The frequency of PROM was 6.8% of deliveries during the study period. Pathogens were isolated among 48.3% of mothers and 26.2% of newborns. Vaginal and endocervix swabs allowed isolation of pathogens in 45% and 28.3% of cases, respectively. The most isolated pathogens were Candida albicans (28.6%)(14/53) and enterobacteria (41.5%)(22/53), mainly represented by Escherichia coli (59.1%)(13/22). We also isolated Group B Streptococci (GBS) strains (7.5%)(4/53). Pathogen isolation rate among newborns was 26.2%(17/65). Of these pathogens, Escherichia coli represented 60%(15/25). Pathogens found in 10.7% of newborns were phenotypically identical to those isolated from their mothers. Among newborns, E. coli was the most isolated strain in gastric fluid (66.7%)(4/6) as well as from ear swabs (57.9%)(11/19). Conclusion: Half of PROM cases in this study were associated with presence of pathogen amongst pregnant women; E. coli and Group B Streptococcus known to cause neonatal meningitis were found. Unfortunately, a few isolated strains of E. coli were resistant to clavulanic acid-amoxicillin, a combination used as empiric antibiotic therapy by healthcare practitioners in our settings.
Polarimetric scanning radiometer C- and X-band microwave observations during SMEX03

Soil Moisture Experiment 2003 (SMEX03) was the second in a series of field campaigns using the National Oceanic and Atmospheric Administration Polarimetric Scanning Radiometer (PSR/CX) designed to validate brightness temperature (T/sub B/) data and soil moisture retrieval algorithms for the Advanced Microwave Scanning Radiometer (AMSR-E) for the Earth Observing System on the Aqua satellite. Objectives related to the PSR/CX during SMEX03 included: calibration and validation of AMSR-E T/sub B/ observations over different climate/vegetation regions of the U.S. [Alabama (AL), Georgia (GA), Oklahoma (OK)], identification of possible areas of radio-frequency interference (RFI), comparison of X-band observations from Tropical Rainfall Measurement Mission Microwave Imager (TMI), AMSR-E, and PSR/CX, and exploring the potential of soil moisture retrieval algorithms using C- and X-band imagery in diverse landscapes. In the current investigation, more than 100 flightlines of PSR/CX data were extensively processed to produce gridded T/sub B/ products for the four study regions. Due to the lack of significant rainfall in OK, generally dry soil moisture conditions were observed. Observations obtained over AL include a wide range of soil moisture and vegetation conditions. Results from the AL site clearly showed a lack of sensitivity to rainfall/soil moisture under forest canopy cover. Quantitative comparisons made with the TMI validated that both the PSR/CX and AMSR-E X-band channels were well calibrated. Spectral analyses indicated that the PSR/CX observations at C-band also are reasonable. As expected, there were varying degrees of RFI in the AMSR-E C-band data for the study sites that will prevent further soil moisture analysis using these data. X-band comparisons of the PSR/CX high-resolution and AMSR-E and TMI low-resolution data indicated a linear scaling for the range of conditions studied in SMEX03. These results will form the basis for further soil moisture investigations.
Mefloquine, an anti-malaria agent, causes reactive oxygen species-dependent cell death in mast cells via a secretory granule-mediated pathway

Mast cells are known to have a detrimental impact on a variety of pathological conditions. There is therefore an urgent need of developing strategies that limit their harmful effects. The aim of this study was to accomplish this by developing a means of inducing mast cell apoptosis. The strategy was to identify novel compounds that induce mast cell apoptosis by permeabilization of their secretory lysosomes (granules). As a candidate, we assessed mefloquine, an anti‐malarial drug that has been proposed to have lysosome‐permeabilizing activity. Mefloquine was added to mast cells and administered in vivo, followed by assessment of the extent and mechanisms of mast cell death. Mefloquine was cytotoxic to murine and human mast cells. Mefloquine induced apoptotic cell death of wild‐type mast cells whereas cells lacking the granule compounds serglycin proteoglycan or tryptase were shown to undergo necrotic cell death, the latter finding indicating a role of the mast cell granules in mefloquine‐induced cell death. In support of this, mefloquine was shown to cause compromised granule integrity and to induce leakage of granule components into the cytosol. Mefloquine‐induced cell death was refractory to caspase inhibitors but was completely abrogated by reactive oxygen species inhibition. These findings identify mefloquine as a novel anti‐mast cell agent, which induces mast cell death through a granule‐mediated pathway. Mefloquine may thus become useful in therapy aiming at limiting harmful effects of mast cells.