gebhart/patrepeval huggingface dataset:
Role of the gag and pol genes of human immunodeficiency virus in the morphogenesis and maturation of retrovirus-like particles expressed by recombinant vaccinia virus: an ultrastructural study (1991)

An ultrastructural study was performed on rabbit epithelial RK-13 cells and CD4+ human T lymphocyte lines infected with various recombinant vaccinia viruses (RVVs) expressing genes of human immunodeficiency virus (HIV): the mature p17 or p24 gag domain alone, the entire or truncated gag gene, the reverse transcriptase domain, or the gag-pol genes with a frameshift mutation. Cells infected with RVVs that produced the gag polyprotein with a predicted M r of more than 48K showed budding and release of HIV-like particles into the extracellular space. These particles were not observed in cells expressing a truncated gag gene (p17 and p24 regions). Mature HIV-like particles were observed extracellularly when the entire gag gene and the protease region of the pol gene were expressed. In contrast, in cells infected with RVVs that contained the gag-pol gene with a frameshift mutation, neither recognizable budding structures nor extracellular HIV-like particles could be detected. These results suggest that the gag gene, particularly its 3′ terminus, is necessary for the assembly of HIV particles. In addition, the protease region of the pol gene seems to be required for morphological maturation of HIV particles, but complete proteolytic cleavage of the gag protein may prevent bud formation.
Heparin-dependent Modification of the Reactive Center Arginine of Antithrombin and Consequent Increase in Heparin Binding Affinity (1997)

Antithrombin, the principal plasma inhibitor of coagulation proteinases, circulates in a form with low inhibitory activity due to partial insertion of its reactive site loop into the A-beta-sheet of the molecule. Recent crystallographic structures reveal the structural changes that occur when antithrombin is activated by the heparin pentasaccharide, with the exception of the final changes, which take place at the reactive center itself. Here we show that the side chain of the P1 Arg of alpha-antithrombin is only accessible to modification by the enzyme peptidylarginine deiminase on addition of the heparin pentasaccharide, thereby inactivating the inhibitor, whereas the natural P1 His variant, antithrombin Glasgow, is unaffected, indicating that only the P1 Arg becomes accessible. Furthermore, the deimination of P1 Arg converts antithrombin to a form with 4-fold higher affinity for the heparin pentasaccharide, similar to the affinity found for the P1 His variant, due to a lowered dissociation rate constant for the antithrombin-pentasaccharide complex. The results support the proposal that antithrombin circulates in a constrained conformation, which when released, in this study by perturbation of the bonding of P1 Arg to the body of the molecule, allows the reactive site loop to take up the active inhibitory conformation with exposure of the P1 Arg.
EL CONOCIMIENTO MÉDICO EN LAS ÚLTIMAS DÉCADAS Y LOS SABERES “TRONCALES” HACIA EL FUTURO. O ¿EL MÉDICO DEL FUTURO? (2015)

Desgrabación de la conferencia ““El médico del futuro”” dictada por el Profesor Luis Cámera en la VII Jornada de Estudiantes del Ciclo Clínico del Hospital Vélez Sarsfield el 2 de septiembre de 2015, desgrabada por el estudiante y presidente de dichas Jornadas, Franco Stampalia.
Catabolite Repression and Induction of the Mg 2+ -Citrate Transporter CitM of Bacillus subtilis (2000)

In Bacillus subtilis the citM gene encodes the Mg(2+)-citrate transporter. A target site for carbon catabolite repression (cre site) is located upstream of citM. Fusions of the citM promoter region, including the cre sequence, to the beta-galactosidase reporter gene were constructed and integrated into the amyE site of B. subtilis to study catabolic effects on citM expression. In parallel with beta-galactosidase activity, the uptake of Ni(2+)-citrate in whole cells was measured to correlate citM promoter activity with the enzymatic activity of the CitM protein. In minimal media, CitM was only expressed when citrate was present. The presence of glucose in the medium completely repressed citM expression; repression was also observed in media containing glycerol, inositol, or succinate-glutamate. Studies with B. subtilis mutants defective in the catabolite repression components HPr, Crh, and CcpA showed that the repression exerted by all these medium components was mediated via the carbon catabolite repression system. During growth on inositol and succinate, the presence of glutamate strongly potentiated the repression of citM expression by glucose. A reasonable correlation between citM promoter activity and CitM transport activity was observed in this study, indicating that the Mg(2+)-citrate uptake activity of B. subtilis is mainly regulated at the transcriptional level.
Use of marine controlled‐source electromagnetic sounding for sub‐basalt exploration (2000)

The problem of imaging sedimentary structure obscured by high‐velocity layers, such as carbonate, basalt or salt, using conventional seismic techniques is well known. When this problem is encountered in offshore areas, marine electromagnetic data can provide valuable, alternative and complementary constraints on the structure. We concentrate on the use of marine controlled‐source electromagnetic (CSEM) sounding in the frequency domain. The feasibility of mapping sub‐basalt sedimentary structure using this technique is explored by means of modelling studies which mimic a type of survey which could readily be employed in practice. As a starting point the problem is addressed in terms of 1D resistivity structure. We show that sub‐basalt sediments can be detected and their depth of burial quantified to within 200 m in the examples shown. The presence of small‐scale inhomogeneities in the basalt (which cause much of the scattering in seismic data) is shown to have no appreciable effect on the ability of the CSEM data to detect the sediments. The modelling is then extended to 2.5 dimensions. Again the presence of sub‐basalt sediments can be readily detected and their properties and geometry quantified, especially if the electromagnetic data are combined with constraints from complementary geophysical techniques.
A randomized phase III study of rubitecan (ORA) vs. best choice (BC) in 409 patients with refractory pancreatic cancer report from a North-American multi-center study (2004)

4013 Background: Rubitecan (Orathecin), an oral topoisomerase I inhibitor, showed promising activity in pancreatic cancer in previous single-center Phase 2 studies in US and Europe. Our objective was to compare ORA with BC (physicians' best choice of treatment or care). Primary end-point: Median survival (MS) . Secondary endpoints: Response rate (RR), progression- free survival (PFS) and safety. Methods: ORA was administered orally at a dose of 1.5 mg/m2 for 5 consecutive days each week for 8 or more weeks. BC consisted of standard regimens of best alternative chemotherapy (89%) or supportive care (11%). CT scans were followed every 8 weeks. Results: 198 patients (pts) were randomized to ORA and 211 to BC. More than 90% were resistant to prior chemotherapy and 70% were refractory to 2 or more prior regimens. 49% of BC patients crossed over to rescue therapy with ORA at time of failure. No significant difference was noted in MS time (ORA: 108 days, BC 94 days, p =0.626), whereas a significant survival advantage was observed for BC pts crossed over to ORA vs. BC non-rescue pts, 147 days vs. 60 days (P<0.0001). In pts with measurable disease (59%), there were 12 independently verified ( blinded radiology review) responders for ORA (2 CR and 10 PR) for a RR of 11%, compared to one responder (<1%; 1 CR) for BC (p< 0.001). Stable disease (SD) was also more common on ORA (44 pts vs. 27 pts). On an Intent-To-Treat basis, more than 2-fold more pts on ORA (28% vs. 13%) achieved tumor growth control (CR +PR +SD), a primary objective for palliative treatment in this disease (Heinemann et al., Oncology 60:8–18, 2001). Median PFS was significantly longer for ORA, 58 days vs. 48 days (p =0.003). ORA was well tolerated as <5% discontinued treatment due to toxicity. Grade 3–4 toxicity was more common for ORA (neutropenia 28% vs. 14%; anemia 21% vs. 9%; nausea/vomiting 14% vs. 9%; diarrhea 12% vs. 5%). Conclusions: The results of this study support the notion that rubitecan, a new oral medication with an acceptable risk-benefit ratio, is convenient to use, and can achieve tumor growth control in a disease with few treatment options. Author Disclosure Employment or Leadership Consultant or Advisory Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Supergen GlaxoSmithKline GlaxoSmithKline
N‐methyl‐d‐aspartate receptor‐mediated increase of neurogenesis in adult rat dentate gyrus following stroke (2001)

Neurogenesis in the adult rat dentate gyrus was studied following focal ischemic insults produced by middle cerebral artery occlusion (MCAO). Animals were subjected to either 30 min of MCAO, which causes damage confined to the striatum, or 2 h of MCAO, which leads to both striatal and cortical infarction. When compared to sham-operated rats, MCAO-rats showed a marked increase of the number of cells double-labelled for 5-bromo-2'-deoxyuridine-5'-monophosphate (BrdU; injected during 4-6 days postischemia) and neuronal-specific antigen (NeuN; a marker of postmitotic neurons) in the ipsilateral dentate granule cell layer and subgranular zone at 5 weeks following the 2 h insult. Only a modest and variable increase of BrdU-labelled cells was found after 30 min of MCAO. The enhanced neurogenesis was not dependent on cell death in the hippocampus, and its magnitude was not correlated to the degree of cortical damage. Systemic administration of the N-methyl-D-aspartate (NMDA) receptor blocker dizocilpine maleate (MK-801) completely suppressed the elevated neurogenesis following 2 h of MCAO. Our findings indicate that stroke leads to increased neurogenesis in the adult rat dentate gyrus through glutamatergic mechanisms acting on NMDA receptors. This modulatory effect may be mediated through changes in the levels of several growth factors, which occur after stroke, and could influence various regulatory steps of neurogenesis.
44.4: RGB‐LED Backlights for LCD‐TVs with 0D, 1D, and 2D Adaptive Dimming (2006)

Abstract Output luminance of an RGB‐LED backlight for an LCD‐TV was adaptively dimmed along with input video signal in fashions of 0D (uniform dimming), 1D (line dimming), and 2D (local dimming). It has been proven experimentally that the backlight power can be reduced to 83%, 71%, and 50%, respectively, for a typical sample movie having 8.0% post‐gamma average picture level (which is equal to the average luminance level). Further simulation study revealed that the power consumption can be reduced to the value equal to that of the post‐gamma APL.
Highly Selective Protein Patterning on Gold−Silicon Substrates for Biosensor Applications (2002)

Proteins were precisely patterned on 2D sensor surfaces using photolithography and chemical selectivity. Microarrays of gold squares were fabricated on silicon substrates. The gold regions were modified with mixed COOH-terminated self-assembled monolayers (SAMs) to have a high affinity for the desired proteins or peptides. The silicon regions were modified with polyethylene glycol (PEG) by silanization to provide a high resistivity to protein adsorption. Protein surface coverage was visualized by fluorescence microscopy and atomic force microscopy (AFM). AFM was also used for studying protein morphology to understand the interaction of proteins with SAMs at the molecular level. Proteins and peptides immobilized on SAMs were examined by Fourier transform infrared (FTIR) spectroscopy. Contact angle measurements for surface wettability were conducted to confirm the success of the surface modification reactions. Protein resistance by the PEGs immobilized on bare silicon substrates and on the silicon regions of gold-patterned silicon substrates was compared, and it was found that the latter has a higher resistivity to protein adsorption. Both fluorescence and high-resolution AFM images indicated that bovine serum albumin (BSA) and fibronectin molecules formed a densely packed layer on the gold regions of the patterned substrates, while the immunoglobulin's (IgG) coverage was low. Specific antigen−antibody binding (BSA−anti-BSA) was studied using the surface plasmon resonance (SPR) technique for characterizing the bioactivity of the antigen attached to the gold substrates. The SPR results showed that the BSA proteins bound covalently to the gold surfaces have a much better bioactivity than those bound physically. This study suggests that protein or peptide, molecular structures, and the immobilization technique influence the coverage, morphology, and bioactivity of the attached proteins on the substrates which is crucial to the operational behavior of biosensors.
An empirical analysis of target-resident dos filters (2004)

Numerous techniques have been proposed by which an end-system, subjected to a denial-of-service flood, filters the offending traffic. In this paper, we provide an empirical analysis of several such proposals, using traffic recorded at the border of a large network and including real DoS traffic. We focus our analysis on four filtering techniques, two based on the addresses from which the victim server typically receives traffic (static clustering and network-aware clustering), and two based on coarse indications of the path each packet traverses (hop-count filtering and path identifiers). Our analysis reveals challenges facing the proposed techniques in practice, and the implications of these issues for effective filtering. In addition, we compare techniques on equal footing, by evaluating the performance of one scheme under assumptions made by another. We conclude with an interpretation of the results and suggestions for further analysis.
A 2.4-GHz CMOS receiver for IEEE 802.11 wireless LANs (1999)

This paper describes a radio-frequency receiver targeting spread-spectrum wireless local-area-network applications in the 2.4-GHz band. Based on a direct-conversion architecture, the receiver employs partial channel selection filtering, dc offset removal, and baseband amplification. Fabricated in a 0.6-/spl mu/m CMOS technology, the receiver achieves a noise figure of 8.3 dB, IP/sub 3/ of -9 dBm, IP/sub 2/ of +22 dBm, and voltage gain of 34 dB while dissipating 80 mW from a 3-V supply.
Serologically verified human bocavirus pneumonia in children (2009)

The present results show that HBoV is able to induce significant antibody responses and suggest that HBoV may be a fairly common cause of pneumonia in children. Seroconversion to HBoV in most children takes place in early childhood.
hMre11 and hRad50 Nuclear Foci Are Induced During the Normal Cellular Response to DNA Double-Strand Breaks † (1997)

We previously identified a conserved multiprotein complex that includes hMre11 and hRad50. In this study, we used immunofluorescence to investigate the role of this complex in DNA double-strand break (DSB) repair. hMre11 and hRad50 form discrete nuclear foci in response to treatment with DSB-inducing agents but not in response to UV irradiation. hMre11 and hRad50 foci colocalize after treatment with ionizing radiation and are distinct from those of the DSB repair protein, hRad51. Our data indicate that an irradiated cell is competent to form either hMre11-hRad50 foci or hRad51 foci, but not both. The multiplicity of hMre11 and hRad50 foci is much higher in the DSB repair-deficient cell line 180BR than in repair-proficient cells. hMre11-hRad50 focus formation is markedly reduced in cells derived from ataxia-telangiectasia patients, whereas hRad51 focus formation is markedly increased. These experiments support genetic evidence from Saccharomyces cerevisiae indicating that Mre11-Rad50 have roles distinct from that of Rad51 in DSB repair. Further, these data indicate that hMre11-hRad50 foci form in response to DNA DSBs and are dependent upon a DNA damage-induced signaling pathway.
Negative cross-talk between hematopoietic regulators: GATA proteins repress PU.1 (1999)

The process through which multipotential hematopoietic cells commit to distinct lineages involves the induction of specific transcription factors. PU.1 (also known as Spi-1) and GATA-1 are transcription factors essential for the development of myeloid and erythroid lineages, respectively. Overexpression of PU.1 and GATA-1 can block differentiation in lineages in which they normally are down-regulated, indicating that not only positive but negative regulation of these factors plays a role in normal hematopoietic lineage development. Here we demonstrate that a region of the PU.1 Ets domain (the winged helix-turn-helix wing) interacts with the conserved carboxyl-terminal zinc finger of GATA-1 and GATA-2 and that GATA proteins inhibit PU.1 transactivation of critical myeloid target genes. We demonstrate further that GATA inhibits binding of PU.1 to c-Jun, a critical coactivator of PU.1 transactivation of myeloid promoters. Finally, PU.1 protein can inhibit both GATA-1 and GATA-2 transactivation function. Our results suggest that interactions between PU.1 and GATA proteins play a critical role in the decision of stem cells to commit to erythroid vs. myeloid lineages.
Kalman Filtering and Neural Networks (2001)

From the Publisher:
Kalman filtering is a well-established topic in the field of control and signal processing and represents by far the most refined method for the design of neural networks. This book takes a nontraditional nonlinear approach and reflects the fact that most practical applications are nonlinear. The book deals with important applications in such fields as control, financial forecasting, and idle speed control.
HTLV-I basic leucine zipper factor gene mRNA supports proliferation of adult T cell leukemia cells (2006)

Human T cell leukemia virus type I (HTLV-I) causes adult T cell leukemia (ATL) in 2-5% of carriers after a long latent period. An HTLV-I encoded protein, Tax, induces proliferation and inhibits apoptosis, resulting in clonal proliferation of infected cells. However, tax gene expression in ATL cells is disrupted by several mechanisms, including genetic changes in the tax gene and DNA methylation/deletion of the 5' long terminal repeat (LTR). Because Tax is the major target of cytotoxic T-lymphocytes in vivo, loss of Tax expression should enable ATL cells to escape the host immune system. The 5' LTR of HTLV-I is frequently hypermethylated or deleted in ATL cells, whereas the 3' LTR remains unmethylated and intact, suggesting the involvement of the 3' LTR in leukemogenesis. Here we show that a gene encoded by the minus strand of the HTLV-I proviral genome, HTLV-I basic leucine zipper factor (HBZ), is transcribed from 3'-LTR in all ATL cells. Suppression of HBZ gene transcription by short interfering RNA inhibits proliferation of ATL cells. In addition, HBZ gene expression promotes proliferation of a human T cell line. Analyses of T cell lines transfected with mutated HBZ genes showed that HBZ promotes T cell proliferation in its RNA form, whereas HBZ protein suppresses Tax-mediated viral transcription through the 5' LTR. Thus, the single HBZ gene has bimodal functions in two different molecular forms. The growth-promoting activity of HBZ RNA likely plays an important role in oncogenesis by HTLV-I.
Biomechanical Assessment of Rucksack Shoulder Strap Attachment Location: Effect on Load Distribution to the Torso (2001)

The objective of this study was to conduct biomechanical testing of pack component options to determine the optimal location for the lower attachment of the shoulder strap for the Clothe the Soldier (CTS) Integrated Patrol Pack and Rucksack. A model of a 50th percentile male torso has been split transversely at T12/L1 and instrumented with two six degree of freedom load cells. The shoulder area of the manikin was instrumented with Fscan(Trademark) sensors to record the contact pressure distribution in the axilla (armpit) and anterior of the shoulder under the shoulder strap. A 25 kg fixed payload was used for all test configurations. Waist belt, load lifter and shoulder strap tensions were constant during testing. Output variables were reaction forces at T12/L1, waist belt lifting force, average and peak contact pressures about the shoulder. These were examined as a function of the attachment point location and as a function of the angle the shoulder strap made with respect to the body long axis. Strap angles above 30 degrees resulted in peak axilla contact pressures ranging from 35 to 64 kPa. At strap angles less than 24 degrees, anterior shoulder peak pressures of &gt; 32 kPa were recorded. These two effects determined the upper and lower bounds of an optimal range of 24 to 30 degrees with respect to the vertical axis of the body. These results cannot be extrapolated to other attachment locations that were not tested and pertain only to the type of strap tested.
Partial repair of irreparable rotator cuff tears (1994)

This study analyzes the results of a previously unreported technique of reconstruction for the massive irreparable rotator cuff tear. The technique involves repair of the margins of the tear to restore the force couples and "suspension bridge" system of force transmission in the shoulder. Complete coverage of the defect was not considered to be essential as long as the normal mechanics of the shoulder were restored and the rotator cuff tear was converted to a "functional cuff tear." This procedure was performed on 14 patients. Improvement in function was dramatic. Active elevation (elevation denotes the plane of motion midway between the planes of shoulder abduction and shoulder flexion; elevation is reported because it is the most functional plane in which to raise the arm) improved by 90.8 degrees: from a preoperative average of 59.6 degrees to a postoperative average of 150.4 degrees. Strength improved an average of 2.3 grades on a 0-to-5-point scale. The average score on the UCLA Shoulder Rating Scale improved from a preoperative value of 9.8 to a postoperative value of 27.6. All but one patient was very satisfied with his or her result. The authors are of the opinion that this technique is preferable to other reconstructive techniques, such as tendon transposition, that emphasize coverage of the defect at the expense of destroying the normal mechanics of the shoulder. The authors suggest that partial repair of massive irreparable rotator cuff tears should supplant tendon transposition as the procedure of choice for this condition.
Structure and Process Optimization for the Use of a Polymeric Relative-Permeability Modifier in Conformance Control (2001)

Abstract For many years, relative-permeability modifiers (RPM's) have received a great deal of attention from the oil- and gas-production industry. Because of the completion techniques used in many wells, it is not always practical or cost-effective to protect the hydrocarbon interval properly during a water-shutoff treatment. RPM's offer the option of bullheading a treatment without zonal isolation, which is designed to decrease water production with little or no decrease in oil or gas production. This paper describes the laboratory development and optimization of a polymeric RPM. The resulting material can be best described as a brush polymer consisting of a polymeric back-bone grafted with polyethylene oxide (PEO). Various phases of the development will be discussed, such as the optimization of the molecular weight of the backbone polymer and the concentration of grafted PEO. Details of laboratory evaluations will also be provided, including a discussion of the use of multipressure-tap flow cells for permeability-reduction tests, the effect of polymer concentration, and the effect of saturations. These test results show that the RPM polymer should be placed with a systematic approach consisting of proper preflushes and post-flushes for optimum results. Additionally, current theories concerning how RPM's function will be discussed, along with other materials claimed to act as RPM's.