gebhart/patrepeval huggingface dataset:
Inhibition of Both HIV-1 Reverse Transcription and Gene Expression by a Cyclic Peptide that Binds the Tat-Transactivating Response Element (TAR) RNA (2011)

The RNA response element TAR plays a critical role in HIV replication by providing a binding site for the recruitment of the viral transactivator protein Tat. Using a structure-guided approach, we have developed a series of conformationally-constrained cyclic peptides that act as structural mimics of the Tat RNA binding region and block Tat-TAR interactions at nanomolar concentrations in vitro. Here we show that these compounds block Tat-dependent transcription in cell-free systems and in cell-based reporter assays. The compounds are also cell permeable, have low toxicity, and inhibit replication of diverse HIV-1 strains, including both CXCR4-tropic and CCR5-tropic primary HIV-1 isolates of the divergent subtypes A, B, C, D and CRF01_AE. In human peripheral blood mononuclear cells, the cyclic peptidomimetic L50 exhibited an IC(50) ∼250 nM. Surprisingly, inhibition of LTR-driven HIV-1 transcription could not account for the full antiviral activity. Timed drug-addition experiments revealed that L-50 has a bi-phasic inhibition curve with the first phase occurring after HIV-1 entry into the host cell and during the initiation of HIV-1 reverse transcription. The second phase coincides with inhibition of HIV-1 transcription. Reconstituted reverse transcription assays confirm that HIV-1 (-) strand strong stop DNA synthesis is blocked by L50-TAR RNA interactions in-vitro. These findings are consistent with genetic evidence that TAR plays critical roles both during reverse transcription and during HIV gene expression. Our results suggest that antiviral drugs targeting TAR RNA might be highly effective due to a dual inhibitory mechanism.
Treemaps for space-constrained visualization of hierarchies (2005)

During 1990, in response to the common problem of a filled hard disk, I became obsessed with the idea of producing a compact visualization of directory tree structures. Since the 80 Megabyte hard disk in the HCIL was shared by 14 users it was difficult to determine how and where space was used. Finding large files that could be deleted, or even determining which users consumed the largest shares of disk space were difficult tasks.
Familial lipoprotein disorders in patients with premature coronary artery disease. (1992)

Our data indicate that more than half of patients with premature CAD have a familial lipoprotein disorder, with Lp(a) excess, hypertriglyceridemia with hypoalphalipoproteinemia, and combined hyperlipidemia with hypoalphalipoproteinemia being the most common abnormalities.
Indomethacin-induced gastric ulceration in rats: Ameliorative roles ofSpondias mombinandFicus exasperata (2015)

These findings are indicative of gastroprotective and antioxidative potentials of the extracts which is also evident in the degree of % inhibition against ulceration. The available data in this study suggest that the extracts proved to be capable of ameliorating indomethacin-induced gastric ulceration and the probable mechanisms are via antioxidative and proton pump inhibition.
Large scale, highly conductive and patterned transparent films of silver nanowires on arbitrary substrates and their application in touch screens (2011)

The application of silver nanowire films as transparent conductive electrodes has shown promising results recently. In this paper, we demonstrate the application of a simple spray coating technique to obtain large scale, highly uniform and conductive silver nanowire films on arbitrary substrates. We also integrated a polydimethylsiloxane (PDMS)-assisted contact transfer technique with spray coating, which allowed us to obtain large scale high quality patterned films of silver nanowires. The transparency and conductivity of the films was controlled by the volume of the dispersion used in spraying and the substrate area. We note that the optoelectrical property, σ(DC)/σ(Op), for various films fabricated was in the range 75-350, which is extremely high for transparent thin film compared to other candidate alternatives to doped metal oxide film. Using this method, we obtain silver nanowire films on a flexible polyethylene terephthalate (PET) substrate with a transparency of 85% and sheet resistance of 33 Ω/sq, which is comparable to that of tin-doped indium oxide (ITO) on flexible substrates. In-depth analysis of the film shows a high performance using another commonly used figure-of-merit, Φ(TE). Also, Ag nanowire film/PET shows good mechanical flexibility and the application of such a conductive silver nanowire film as an electrode in a touch panel has been demonstrated.
Microwave Imaging for Breast Cancer (2011)

Microwaves and millimeter waves have been used extensively to image dielectric bodies. The application of microwaves in biomedical imaging and diagnostics, however, remains a field with many uncharted territories. This article is an overview on medical imaging using microwave imaging for breast cancer and its challenges, hopes, and outlook.
Spatial Representations in the Parietal Cortex May Use Basis Functions (1994)

The parietal cortex is thought to represent the egocentric positions of objects in particular coordinate systems. We propose an alternative approach to spatial perception of objects in the parietal cortex from the perspective of sensorimotor transformations. The responses of single parietal neurons can be modeled as a gaussian function of retinal position multiplied by a sigmoid function of eye position, which form a set of basis functions. We show here how these basis functions can be used to generate receptive fields in either retinotopic or head-centered coordinates by simple linear transformations. This raises the possibility that the parietal cortex does not attempt to compute the positions of objects in a particular frame of reference but instead computes a general purpose representation of the retinal location and eye position from which any transformation can be synthesized by direct projection. This representation predicts that hemineglect, a neurological syndrome produced by ...
PREDICTORS OF MORTALITY IN PEDIATRIC ARDS (1995)

Reda, Zacharia MD; Boctor, Wagih MD; Maggi, J. Carlos MD; Mendoza, Patricia MD; Davis, Alan MD; Chin, Terry MD. Author Information
Midtrimester abortion induced by Radix trichosanthis: morphologic observations in placenta and fetus. (1982)

Since 1971 Radix trichosanthis has been used to induce midtrimester abortion in China. Radix trichosanthis is a traditional Chinese drug extracted from the root of Trichosanthis kirilowii maxim. Intramuscular, intravenous, or intraamniotic injection of the drug may lead to abortion. The time from induction to delivery and the clinical and morphologic changes occurring in the placenta and fetus vary somewhat, depending on the route of injection. The essential changes in the placenta are degeneration and necrosis of the syncytiotrophoblast and thrombosis of the intervillous spaces. In comparison with intramuscular or intravenous injection, intraamniotic injection has the advantage of a shorter interval from induction to delivery (normally 1 to 3 days), milder pathologic changes, and, generally, absence of systemic side effects. The chief element of the agent is vegetable protein, which may cause allergic reactions. A skin test before treatment is strongly recommended.
Combination of text-mining algorithms increases the performance (2006)

The LDD corpus presented is available by request to the author. The system will be available shortly. For information and updates on CONAN please visit http://www.cs.uu.nl/people/rainer/conan.html.
FSK with direct detection in optical multiple-access FDM networks (1990)

High-performance optical data networks of the future may interconnect hundreds of users at gigabit rates for a reasonable cost. A novel approach is described that utilizes a passive star coupler for distribution, a multiplicity of frequency-shift keyed (FSK) tunable lasers to provide a frequency division multiplexed (FDM) network, and a tunable optical fiber Fabry-Perot filter to select the channels and convert the FSK signal to ASK (amplitude-shift keying) for direct detection. The design of high-speed FDM-FSK direct detection networks and the performance of critical devices, such as tunable FM lasers, tunable filters, integrated star couplers, and optical amplifiers, are reviewed and discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Sporogenic Effect of Polyunsaturated Fatty Acids on Development of Aspergillus spp (1999)

Aspergillus spp. are frequently occurring seed-colonizing fungi that complete their disease cycles through the development of asexual spores, which function as inocula, and through the formation of cleistothecia and sclerotia. We found that development of all three of these structures in Aspergillus nidulans, Aspergillus flavus, and Aspergillus parasiticus is affected by linoleic acid and light. The specific morphological effects of linoleic acid include induction of precocious and increased asexual spore development in A. flavus and A. parasiticus strains and altered sclerotium production in some A. flavus strains in which sclerotium production decreases in the light but increases in the dark. In A. nidulans, both asexual spore production and sexual spore production were altered by linoleic acid. Spore development was induced in all three species by hydroperoxylinoleic acids, which are linoleic acid derivatives that are produced during fungal colonization of seeds. The sporogenic effects of these linoleic compounds on A. nidulans are similar to the sporogenic effects of A. nidulans psi factor, an endogenous mixture of hydroxylinoleic acid moieties. Light treatments also significantly increased asexual spore production in all three species. The sporogenic effects of light, linoleic acid, and linoleic acid derivatives on A. nidulans required an intact veA gene. The sporogenic effects of light and linoleic acid on Aspergillus spp., as well as members of other fungal genera, suggest that these factors may be significant environmental signals for fungal development.
Oxygen free radicals and pelvic adhesion formation: I. Blocking oxygen free radical toxicity to prevent adhesion formation in an endometriosis model. (1991)

Intraperitoneal superoxide dismutase (SOD) and catalase were used to block the toxic effects of superoxide anion (O2) and hydrogen peroxide (H2O2), associated with the production of endometriosis and inflammation in a rabbit model. In a two-part animal study, the combined instillation of SOD and catalase significantly reduced the formation of intraperitoneal adhesions at endometriosis sites.
Expression of multiple immune checkpoint molecules on Tï¿½cells in malignant ascites from epithelial ovarian carcinoma (2018)

Expression of immune checkpoint molecules, including programmed cell death protein-1 (PD-1), has been reported on T cells in various types of cancer. However, the expression status of these molecules in the tumor microenvironment of epithelial ovarian cancer (EOC) has not yet been studied. A total of 54 cases of malignant ascites from patients with EOC were analyzed in the present study. The expression of PD-1, lymphocyte-activation gene-3 (LAG-3), T-cell immunoglobulin and mucin-domain containing-3 (TIM-3) and B and T lymphocyte attenuator (BTLA) on cluster of differentiation (CD)4<sup>+</sup> and CD8<sup>+</sup> T cells in malignant EOC ascites were investigated using multicolor flow cytometric analysis. The expression of PD-L1 in tumor cells, PD-L2 in HLA-DR-positive cells and galectin-9 in ascitic fluid was also analyzed. In addition, cytokine profiling of ascitic fluid was performed to understand the immune microenvironment of EOC. PD-1, LAG-3 TIM-3, and BTLA were expressed on 65.8, 10.6, 4.3 and 37.6% of CD4<sup>+</sup> T cells, and on 57.7, 5.0, 4.9 and 15.7% of CD8<sup>+</sup> T cells, respectively. Programmed cell death protein-1 (PD-1), LAG-3 and BTLA were more frequently expressed on CD4<sup>+</sup> compared with CD8<sup>+</sup> T cells. The co-expression of immune checkpoints was further investigated and results indicated that 39 (72.2%) and 37 patients (68.5%) expressed multiple immune checkpoints on CD4<sup>+</sup> T cells and CD8<sup>+</sup> T cells, respectively. In addition, lower levels of TNF-α and interleukin-6 in ascitic fluid were significantly associated with multiple immune checkpoint expression on CD8<sup>+</sup> T cells. The present findings indicated that multiple immune checkpoint molecules were expressed on T cells in the EOC tumor microenvironment and the results may suggest the significance of simultaneous blockade of immune checkpoints to control EOC.
Endocytosis of Receptor Tyrosine Kinases (2013)

Endocytosis is the major regulator of signaling from receptor tyrosine kinases (RTKs). The canonical model of RTK endocytosis involves rapid internalization of an RTK activated by ligand binding at the cell surface and subsequent sorting of internalized ligand-RTK complexes to lysosomes for degradation. Activation of the intrinsic tyrosine kinase activity of RTKs results in autophosphorylation, which is mechanistically coupled to the recruitment of adaptor proteins and conjugation of ubiquitin to RTKs. Ubiquitination serves to mediate interactions of RTKs with sorting machineries both at the cell surface and on endosomes. The pathways and kinetics of RTK endocytic trafficking, molecular mechanisms underlying sorting processes, and examples of deviations from the standard trafficking itinerary in the RTK family are discussed in this work.
Pretreatment with a monoclonal antibody/interleukin-2 fusion protein directed against DNA enhances the delivery of therapeutic molecules to solid tumors. (1999)

The efficacy of molecular therapies for human malignancies is limited by inadequate accumulation within solid tumors. Our laboratory has developed a novel approach that uses monoclonal antibodies (MAbs) to direct vasoactive proteins to tumor sites to increase local vascular permeability and, in turn, improve the delivery of therapeutic reagents. Previously, we demonstrated that pretreatment with immunoconjugates containing interleukin-2 (IL-2) enhances specific tumor uptake of radiolabeled MAbs without affecting normal tissues. In the present study, we describe a fusion protein consisting of a chimeric antinuclear antibody and IL-2 (chTNT-3/IL-2) and illustrate its potential for improving the delivery of both MAbs and drugs. The ability of pretreatment with chTNT-3/IL-2 to increase specific tumor uptake of the MAb B72.3 was demonstrated in LS174T colon tumor-bearing mice. Tumor accretion of B72.3 increased nearly 3-fold, with no changes in normal tissues. Abrogation of this effect with N(G)-methyl-1-arginine, a chemical inhibitor of nitric oxide synthase, suggests that rapid generation of nitric oxide in the tumor is responsible for the enhanced uptake. To demonstrate that pretreatment with chTNT-3/IL-2 can improve the uptake of other clinically relevant MAbs in different tumor models, additional studies were performed in both lung and prostate xenograft models. Pretreatment with the fusion protein increased specific tumor uptake of the MAb NR-LU-10 in A427 lung tumor-bearing mice and enhanced tumor uptake of the MAb CYT-351 in LNCaP prostate tumor-bearing mice, 2.1-fold and 1.7-fold, respectively. Finally, tumor uptake of the radiolabeled thymidine analogue 125IUdR also increased approximately 3-fold after pretreatment, indicating that this approach can be extended to small molecules such as chemotherapeutic drugs. Because TNT-3 recognizes a universal nuclear antigen accessible in degenerating and necrotic cells within all solid tumors, this strategy may be applicable to the majority of human cancers.
Impact of multiple HPV infection on response to treatment and survival in patients receiving radical radiotherapy for cervical cancer (2002)

To obtain information on the incidence and the clinical significance of infection with various types of the human papillomavirus (HPV) in cancer of the uterine cervix, we retrospectively examined the HPV status of 106 patients who had received radical radiotherapy for cervical cancer stages IB to IIIB. DNA was extracted from formalin-fixed, paraffin-embedded biopsies and PCR was carried out to identify HPV types 16, 18, 31, 35, 33 and 45. To detect additional HPV types, consensus PCR products were cloned and sequenced. A catalyzed signal-amplified colorimetric in situ hybridization was carried out in 84 of 106 specimens as a positive control. Response to therapy, progression-free survival (PFS) and cervical cancer-specific survival (CCSS) were the statistical endpoints. Survival analysis was carried out using univariate and multivariate analysis (Cox regression). Ninety-six patients (90.6%) were HPV-positive and 42/96 (43.7%) were positive for multiple HPV types. Eight patients had persistent disease after radiotherapy. From these 8 patients, 7 were infected with multiple HPV types and only 1 patient had an infection with a single HPV type. After a median follow up period of 50 months, patients with multiple HPV infection had a significantly shorter PFS and CCSS compared to those with single HPV infection (24.8% and 34.9% vs. 64% and 60.8%, Log rank, p < 0.01 and 0.04). In multivariate analysis, the presence of multiple HPV types (RR 1.9), node status (RR 2.3), tumor size (RR 3.2) and histologic type (RR 4.8) were independent prognostic factors of CCSS. Our results demonstrate that the presence of multiple HPV types is associated with poor response and with reduced survival in cervical cancer patients who receive radiotherapy as the primary treatment.
Hyper-Connectivity of Subcortical Resting-State Networks in Social Anxiety Disorder (2013)

Social anxiety disorder-related alterations in basal ganglia regions, such as striatum and globus pallidus, though evident from metabolic imaging, remain to be explored using seed-based resting-state functional connectivity magnetic resonance imaging. Capitalizing on the enhanced sensitivity of a multichannel array coil, we collected high-resolution (2-mm isotropic) data from medication-naive patients and healthy control participants. Subcortical resting-state networks from structures including the striatum (caudate and putamen), globus pallidus, thalamus, amygdala, and periaqueductal gray were compared between the two groups. When compared with controls, the caudate seed revealed significantly higher functional connectivity (hyper-connectivity) in the patient group in medial frontal, prefrontal (anterior and dorsolateral), orbito-frontal, and anterior cingulate cortices, which are regions that are typically associated with emotional processing. In addition, with the putamen seed, the patient data exhibited increased connectivity in the fronto-parietal regions (executive control network) and subgenual cingulate (affective network). The globus pallidus seed showed significant increases in connectivity in the patient group, primarily in the precuneus, which is part of the default mode network. Significant hyper-connectivity in the precuneus, interior temporal, and parahippocampal cortices was also observed with the thalamus seed in the patient population, when compared with controls. With amygdala as seed region, between-group differences were primarily in supplementary motor area, inferior temporal gyrus, secondary visual cortex, angular gyrus, and cingulate gyrus. Seed from periaqueductal gray resulted in hyper-connectivity in the patient group, when compared with controls, in dorsolateral prefrontal cortex, precuneus, middle temporal gyrus, and inferior parietal lobule. In all the subcortical regions examined in this study, the control group did not have any significant enhancements in functional connectivity when compared with the patient group.
A Branch and Bound Approach to speed up the Sphere Decoder (2006)

In many communications applications, maximum-likelihood decoding reduces to solving an integer least-squares problem which is NP hard in the worst-case. However, as has recently been shown, over a wide range of dimensions and SNRs, the sphere decoder can be used to find the exact solution with an expected complexity that is roughly cubic in the dimension of the problem. However, the computational complexity becomes prohibitive if the SNR is too low and/or if the dimension of the problem is too large. We target these two regimes and attempt to find faster algorithms by pruning the search tree beyond what is done in the standard sphere decoder. The search tree is pruned by computing lower bounds on the possible optimal solution as we proceed down the tree. We observe a trade-off between the computational complexity required to compute the lower bound and the size of the pruned tree: the more effort spent computing a tight lower bound, the more branches that can be eliminated in the tree. Thus, even though it is possible to prune the search tree (and hence the number of points visited) by several orders of magnitude, this may be offset by the computations required to perform the pruning. All of which suggests the need for computationally-efficient tight lower bounds. We present three different lower bounds (based on spherical-relaxation, polytope-relaxation and duality), simulate their performances and discuss their relative merits.
Genetic Structure of Population of Bacillus cereus and B. thuringiensis Isolates Associated with Periodontitis and Other Human Infections (2000)

The genetic diversity and relationships among 35 Bacillus cereus and Bacillus thuringiensis isolates recovered from marginal and apical periodontitis in humans and from various other human infections were investigated using multilocus enzyme electrophoresis. The strains were isolated in Norway, except for three strains isolated from periodontitis patients in Brazil. The genetic diversity of these strains was compared to that of 30 isolates from dairies in Norway and Finland. Allelic variation in 13 structural gene loci encoding metabolic enzymes was analyzed. Twelve of the 13 loci were polymorphic, and 48 unique electrophoretic types (ETs) were identified, representing multilocus genotypes. The mean genetic diversity among the 48 genotypes was 0.508. The genetic diversity of each source group of isolates varied from 0.241 (periodontal infection) to 0.534 (dairy). Cluster analysis revealed two major groups separated at a genetic distance of greater than 0.6. One cluster, ETs 1 to 13, included solely isolates from dairies, while the other cluster, ETs 14 to 49, included all of the human isolates as well as isolates from dairies in Norway and Finland. The isolates were serotyped using antiflagellar antiserum. A total of 14 distinct serotypes were observed. However, little association between serotyping and genotyping was seen. Most of the strains were also analyzed with pulsed-field gel electrophoresis, showing the presence of extrachromosomal DNA in the size range of 15 to 600 kb. Our results indicate a high degree of heterogeneity among dairy strains. In contrast, strains isolated from humans had their genotypes in one cluster. Most strains from patients with periodontitis belonged to a single lineage, suggesting that specific clones of B. cereus and B. thuringiensis are associated with oral infections.