gebhart/patrepeval huggingface dataset:
Aristolochic acid nephropathy: Harbinger of a global iatrogenic disease (2012)

This review constitutes an overview of our investigations of aristolochic acid nephropathy, a chronic kidney disease associated with carcinomas of the upper urinary tract. Our studies began by confirming the hypothesis that chronic dietary poisoning by aristolochic acid was responsible for endemic (Balkan) nephropathy. A unique TP53 mutational signature in urothelial tumors and the presence of aristolactam-DNA adducts in the renal cortex, defined in the course of this research, proved to be robust biomarkers of exposure to this potent nephrotoxin and human carcinogen. Armed with this information, we used molecular epidemiologic approaches and novel mechanistic information to establish the causative role of aristolochic acid in upper urinary tract carcinoma in Taiwan, where one-third of the population had been prescribed herbal remedies containing Aristolochia, and the recorded incidence of upper urinary tract cancers is the highest in the world. As traditional Chinese medicine is practiced similarly in Taiwan and China, it is likely that upper urinary tract carcinomas and their attendant aristolochic acid nephropathy are prevalent in China and other Asian countries where Aristolochia herbs have been used for centuries in the treatment and prevention of disease, creating a potential public health problem of considerable magnitude.
Cyclic Testing of 3 All-Inside Meniscal Repair Devices (2009)

The Meniscal Cinch and Ultra FAST-FIX devices may be more desirable implants for use during all-inside meniscal repair as they have superior biomechanical properties when compared with the MaxFire device.
Pipeline vectorization (2001)

This paper presents pipeline vectorization, a method for synthesizing hardware pipelines based on software vectorizing compilers. The method improves efficiency and ease of development of hardware designs, particularly for users with little electronics design experience. We propose several loop transformations to customize pipelines to meet hardware resource constraints while maximizing available parallelism. For runtime reconfigurable systems, we apply hardware specialization to increase circuit utilization. Our approach is especially effective for highly repetitive computations in digital signal processor (DSP) and multimedia applications. Case studies using field programmable gate arrays (FPGAs)-based platforms are presented to demonstrate the benefits of our approach and to evaluate tradeoffs between alternative implementations. For instance, the loop-tiling transformation, has been found to improve vectorization performance 30-40 times above a PC-based software implementation, depending on whether runtime reconfiguration (RTR) is used.
DeViSE: A Deep Visual-Semantic Embedding Model (2013)

Modern visual recognition systems are often limited in their ability to scale to large numbers of object categories. This limitation is in part due to the increasing difficulty of acquiring sufficient training data in the form of labeled images as the number of object categories grows. One remedy is to leverage data from other sources – such as text data – both to train visual models and to constrain their pre-dictions. In this paper we present a new deep visual-semantic embedding model trained to identify visual objects using both labeled image data as well as seman-tic information gleaned from unannotated text. We demonstrate that this model matches state-of-the-art performance on the 1000-class ImageNet object recogni-tion challenge while making more semantically reasonable errors, and also show that the semantic information can be exploited to make predictions about tens of thousands of image labels not observed during training. Semantic knowledge improves such zero-shot predictions achieving hit rates of up to 18 % across thou-sands of novel labels never seen by the visual model. 1
Investigating the Effect of Ciliary Body Photodynamic Therapy in a Glaucoma Mouse Model (2006)

Ciliary body PDT resulted in morphologic changes in the ciliary body, significant reduction of IOP, and prevention of ganglion cell loss in a mouse glaucoma model. These results suggest that ciliary body PDT is a more selective cyclodestructive technique with potential clinical application in the treatment of glaucoma.
The vpx gene of simian immunodeficiency virus facilitates efficient viral replication in fresh lymphocytes and macrophage (1991)

vpx is a unique open reading frame found in simian immunodeficiency virus (SIV) and human immunodeficiency virus type 2 (HIV-2) but not in HIV-1. It encodes a 12- to 16-kDa virion-associated protein. Although vpx is dispensable for viral replication in several established human lymphocyte cell lines, there is no consensus regarding whether this gene is required for efficient viral replication in freshly isolated lymphocytes. We report here that the vpx mutant of SIVmac exhibits different degrees of impairment from wild-type SIVmac in freshly isolated lymphocytes. This defect is more pronounced in macrophages from the same donors. Our findings suggest that vpx is required for efficient viral replication in fresh lymphocytes and macrophages.
Gamma interferon regulates long terminal repeat-controlled oncogene expression in transformed mouse fibroblasts at the level of mRNA transcription (1988)

In transformed NIH 3T3 cells, murine gamma interferon reduces the expression of the long terminal repeat-controlled oncogenes v-mos, c-myc, and v-Ha-ras by a direct effect on the activity of retroviral promoters, as revealed by analyses of RNA half-life and transcriptional activity of retroviral genes as well as by analyses of chloramphenicol acetyltransferase activity in cells transformed with the cat gene under the control of long terminal repeats.
Novel therapies for Helicobacter pylori infection (1999)

Although in vitro data appeared promising, in vivo results were disappointing. Higher doses, longer duration of therapy, adjunctive acid suppression, or a combination could possibly yield better results.
Tolerogenic APC Generate CD8+ T Regulatory Cells That Modulate Pulmonary Interstitial Fibrosis (2004)

Transforming growth factor-beta2-treated Ag-pulsed APC mimic APC from the immune privileged eye, and provide signals that generate regulatory T (Tr) cells and mediate peripheral tolerance. We postulated that TGF-beta2-treated Ag-pulsed APC (tolerogenic APC (tol-APC)) might also orchestrate regulation of immune mediated pathogenesis in nonimmune privileged tissues such as the lung. We used an adoptive transfer model of autoimmune pulmonary interstitial fibrosis called hapten immune pulmonary interstitial fibrosis (ADT-HIPIF) in this study. Mice that received 2,4,6-trinitrobenzene sulfonic acid-sensitized cells and challenged (intratracheally) with the hapten developed pulmonary interstitial fibrosis. However, transfer (i.v.) of TGF-beta2-treated 2,4,6-trinitrobenzene sulfonic acid-pulsed bone marrow-derived APC (tol-APC) to experimental mice 1 day after intratracheal challenge reduced the collagen deposition in the interstitium of the lung that usually follows challenge. Furthermore, ADT-HIPIF mice that received tol-APC developed Ag-specific efferent CD8+ Tr cells. Adoptive transfer of the Tr cells to another set of presensitized mice mediated suppression of the efferent phase of Th1 immune response and the subsequent immune dependent pulmonary interstitial fibrosis. Thus, tol-APC induced efferent CD8+ Tr cells in immune mice, and the regulation of the immune response limited the development of autoimmune pulmonary fibrosis in sensitized and pulmonary-challenged mice. Because ADT-HIPIF shares etiological and pathological characteristics with a variety of human immune inflammatory conditions in the lung that eventuate into interstitial fibrosis, these studies provide insight into potential therapy to alter the course of pulmonary fibrosis in humans.
Stimulatory effect of low-power density He-Ne laser radiation on human fibroblasts in vitro. (1996)

Cultures of human embryonic fibroblasts in vitro were subjected to helium-neon laser single and double irradiation to investigate the influence of low-energy laser irradiation on fibroblast proliferation. Mean increase in the cell number values of irradiated cells were compared with increase values of non-irradiated control samples of fibroblasts. He-Ne laser was used as a coherent source of monochromatic radiation at 632.8 nm, and Petri-dishes with cultured fibroblasts were irradiated in way to receive radiation of energy doses of 0.5; 1; 1.5 and 2J/cm2. Single He-Ne laser irradiation exhibited a significant stimulation effect on human fibroblast proliferation in cell-culture.
Genome-derived vaccines (2004)

Vaccine research entered a new era when the complete genome of a pathogenic bacterium was published in 1995. Since then, more than 97 bacterial pathogens have been sequenced and at least 110 additional projects are now in progress. Genome sequencing has also dramatically accelerated: high-throughput facilities can draft the sequence of an entire microbe (two to four megabases) in 1 to 2 days. Vaccine developers are using microarrays, immunoinformatics, proteomics and high-throughput immunology assays to reduce the truly unmanageable volume of information available in genome databases to a manageable size. Vaccines composed by novel antigens discovered from genome mining are already in clinical trials. Within 5 years we can expect to see a novel class of vaccines composed by genome-predicted, assembled and engineered T- and Bcell epitopes. This article addresses the convergence of three forces--microbial genome sequencing, computational immunology and new vaccine technologies--that are shifting genome mining for vaccines onto the forefront of immunology research.
Spin-polarized current-induced magnetization reversal in perpendicularly magnetized L1-FePt layers (2006)

Current-induced magnetization reversal of perpendicularly magnetized layers was studied in current-perpendicular-to-plane giant magnetoresistance pillars with L10-FePt (001) layers. The FePt layers exhibited strong perpendicular magnetic anisotropy of the order of 107erg∕cm3. A series of magnetoresistance curves after applying pulse currents with different current densities showed that current-induced magnetization reversal from an antiparallel to a parallel alignment occurred at the current density of the order of 108A∕cm2 with the assistance of magnetic field.
An upstream, DNase I hypersensitive region of the hematopoietic-expressed transcription factor GATA-1 gene confers developmental specificity in transgenic mice (1997)

The transcription factor GATA-1, which is expressed in several hematopoietic lineages and multipotential progenitors, is required for the development of red blood cells and platelets. To identify control elements of the mouse GATA-1 gene, we analyzed DNase I hypersensitivity of the locus in erythroid chromatin and the expression of GATA-1/Escherichia coli beta-galactosidase (lacZ) transgenes in mice. Transgenes with 2.7 kb of promoter sequences are expressed infrequently and only within adult (definitive) erythroid cells. We show that inclusion of an upstream hypersensitive site (HS I) markedly enhances the frequency of expressing transgenic lines and activates expression in primitive erythroid cells. This pattern recapitulates the proper pattern of GATA-1 expression during development. By breeding a GATA-1/lacZ transgene into a GATA-1(-) background, we also have shown that the activation or maintenance of GATA-1 expression does not require the presence of GATA-1 itself, thereby excluding simple models of positive autoregulation. The transgene cassette reported here should be useful in directing expression of foreign sequences at the onset of hematopoiesis in the embryo and may assist in the identification of upstream regulators of the GATA-1 gene.
The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in Gram‐positive bacteria (1998)

The molecular mechanisms for regulation of the genes involved in the biosynthesis of methionine and cysteine are poorly characterized in Bacillus subtilis. Analyses of the recently completed B. subtilis genome revealed 11 copies of a highly conserved motif. In all cases, this motif was located in the leader region of putative transcriptional units, upstream of coding sequences that included genes involved in methionine or cysteine biosynthesis. Additional copies were identified in Clostridium acetobutylicum and Staphylococcus aureus, indicating conservation in other Gram-positive genera. The motif includes an element resembling an intrinsic transcriptional terminator, suggesting that regulation might be controlled at the level of premature termination of transcription. The 5' portion of all of the leaders could fold into a conserved complex structure. Analysis of the yitJ gene, which is homologous to Escherichia coli metH and metF, revealed that expression was induced by starvation for methionine and that induction was independent of the promoter and dependent on the leader region terminator. Mutation of conserved primary sequence and structural elements supported a model in which the 5' portion of the leader forms an anti-antiterminator structure, which sequesters sequences required for the formation of an antiterminator, which, in turn, sequesters sequences required for the formation of the terminator; the anti-antiterminator is postulated to be stabilized by the binding of some unknown factor when methionine is available. This set of genes is proposed to form a new regulon controlled by a global termination control system, which we designate the S box system, as most of the genes are involved in sulphur metabolism and biosynthesis of methionine and cysteine.
Characterization of Ag doped p -type ZnO films (2007)

Ag-doped ZnO thin films have been fabricated by pulsed laser deposition. Thermal analysis and X-ray photoelectron spectroscopy (XPS) were systematically investigated to verify the doping mechanism of Ag doped ZnO thin film depending on deposition temperature. The fabricated p-type Ag doped ZnO films shows the hole concentration in the range from 4.9x10<sup>16</sup> to 6.0x10<sup>17</sup> cm<sup>-3</sup>.
GLQ223: an inhibitor of human immunodeficiency virus replication in acutely and chronically infected cells of lymphocyte and mononuclear phagocyte lineage. (1989)

GLQ223 is a highly purified, formulated preparation of trichosanthin, a 26-kDa plant-derived ribosome-inactivating protein with potent inhibitory activity against human immunodeficiency virus (HIV) in vitro. The compound produced concentration-dependent inhibition of HIV replication in acutely infected cultures of T-lymphoblastoid cells (VB cell line). Treatment with GLQ223 selectively reduced levels of detectable viral proteins compared to total cellular protein synthesis and produced a selective decrease in levels of viral RNA relative to total cellular RNA in acutely infected cells. Substantial inhibition of viral replication was observed at concentrations of GLQ223 that showed little inhibition of parallel uninfected cultures. Selective anti-HIV activity was also observed in cultures of primary monocyte/macrophages chronically infected with HIV in vitro. When freshly drawn blood samples from HIV-infected patients were treated with a single 3-hr exposure to GLQ223. HIV replication was blocked for at least 5 days in subsequently cultured monocyte/macrophages, without further treatment. The anti-HIV activity of GLQ223 in both acutely and chronically infected cells and its activity in cells of both lymphoid and mononuclear phagocytic lineage make it an interesting candidate as a potential therapeutic agent in HIV infection and AIDS.
Arg—Gly—Asp peptides in polyurethanes: Design, synthesis, and characterization (1994)

Peptide‐containing polymers have been synthesized with the aim of using polymers as synthetic scaffolds for biologically active peptide sequences. Introducing the peptide shown in the figure during polyurethane synthesis resulted in a series of peptide‐polymer hybrids containing the Arg‐Gly‐Asp sequence, which plays a central role in cel adhesion. magnified image
The European Union: implications for developing countries (1995)

Examines the ramifications of the ongoing politico‐economic unification taking place in Europe. Viner′s theoretical contribution in analysing customs unions is applied to the European Union (EU) in order to determine the implications of the EU on developing countries. Additionally, examines the changes taking place in the formerly planned economies of Central and Eastern Europe in an effort to understand the diversion effect faced by developing countries better. Finally, identifies different levels of competition: competition within the EU and outside the EU, competition between EU and non‐EU firms, and competition among non‐EU actors.
Audio Coder Enhancement using Scalable Binaural Cue Coding with Equalized Mixing (2004)

This convention paper has been reproduced from the author’s advance manuscript, without editing, corrections, or consideration by the Review Board. The AES takes no responsibility for the contents. Additional papers
Acrylate-Based Block Copolymers Prepared by Atom Transfer Radical Polymerization as Matrices for Drug Delivery Applications (2006)

Block copolymers, synthesized by atom transfer radical polymerization (ATRP) processes, were evaluated as drug delivery matrices for the controlled release of paclitaxel (PTX) from coronary stents. The polymers were multi-block copolymers consisting of poly(butyl acrylate) or poly(lauryl acrylate) soft blocks and hard blocks composed of poly(methyl methacrylate), poly(isobornyl acrylate) or poly(styrene) homo or copolymers. The block copolymers had variable elastomeric properties which influenced the stent coating integrity when assessed by SEM imaging of over-expanded stents. In vitro PTX release kinetics from coronary stents coated with these copolymers typically showed an early burst followed by sustained release behavior which permitted the elution of the majority of the PTX over a 10 day time period. It was determined that neither the soft or the hard block appeared to affect the release kinetics of PTX at a loading of 25% drug by weight, whereas some effects were observed at 10% drug loading. DSC analysis showed that the PTX was at least partially miscible with the poly(n-butyl acrylate) phase of these block copolymers. Sterilization stability was evaluated by exposing both the copolymer alone and copolymer/PTX coated stents to e-beam radiation at doses of 25, 50 and 75 kGy. The block copolymers containing segments bearing quaternary carbons within the polymer backbone were found to be less stable to the radiation and showed a decrease in molecular weight as determined by gel permeation chromatography. Whereas, those without quaternary carbons showed no significant change in molecular weight when exposed to the same doses of radiation. There was no significant change in PTX release profile from any of the acrylate-based copolymers after exposure to up to 75 kGy of e-beam radiation, and this was attributed to the inherent radiation stability of the polyacrylate center blocks.
Incremental re-execution of programs (1987)

Interpreters replace the edit/compile/run cyle with edit/run. Dynamic computing environments, like spreadsheets, shorten this still more to just edit. So-called "Visiprog" environments, such as Maryland's XED, permit developing normal imperative programs in a dynamic computing environment, XED and similar environments, because they show the results of executing a program after every (reasonable) editing step, raise the issue of efficient incremental execution. Incremental execution optimizations are also applicable to any programming situation, including batch/cards, in which nearly the same program is run many times on nearly the same data. However, the requirement of remembering large amounts of internal state between runs make incremental exectution most natural for interpreted languages. This paper examines some algorithms for incremental execution. Based on the frequency of typical program editing changes, we predict the importance of optimizing certain kinds of incremental execution. We also examine actual speedups obtained in executing programs after subjecting them to these simulated incremental edits under these optimizations. The speedups range from factors of 1.1 to near 10. Finally, we discuss the feasibility of including these optimizations in an actual dynamic computing environment like XED, and in more traditional programming environments.
Distribution of Gibberellins in Lathyrus odoratus L. and Their Role in Leaf Growth (1993)

In sweet pea (Lathyrus odoratus L.) the mutant allele l reduced the level of gibberellin A1 (GA1) in expanding leaflets and resulted in smaller, more oval leaflets compared with the wild type. The apical portions of 6-d-old wild-type (L) seedlings also contained less GA1 and produced smaller, more oval leaflets than did comparable 20-d-old L seedlings. Application of GA1 markedly altered leaflet shape and, at certain dosages, restored the wild-type shape and size to leaflets of the l (dwarf) mutant. Taken together, these observations indicate that GA1 performs a regulatory role in the control of leaf growth in this species. The levels of GA1 precursors in the wild type were also determined. Rapidly expanding internodes contained much more gibberellin A19 (GA19) than gibberellin A20 (GA20), whereas the opposite was true for expanding leaflets. Although in entire apical portions of established seedlings the level of GA20 exceeded that of GA19, apical portions of very young seedlings contained more GA19 than GA20. Basal stem tissue of established seedlings also contained substantially more GA19 than GA20 or GA1. Both stems and leaflets from the basal portion of the plant contained much less GA20 and GA1 than did the rapidly expanding apical tissue. The implications of these results for the regulation of GA1 biosynthesis are discussed.
Electron microscopy of frozen hydrated sections of vitreous ice and vitrified biological samples (1983)

The preparation and high resolution observation of frozen hydrated thin sections has been studied by transmission electron microscopy (TEM and STEM) on model systems, including pure water, protein solutions, catalase crystals, myelin sheath and various tissues. The state of the ice is determined by electron diffraction. Mass measurement in the electron microscope is used to determine section thickness and control hydration. An adequate depth of vitrified material for sectioning can be obtained from many biological suspensions or untreated tissues. Frozen hydrated sections around 100 nm thick can be produced under optimal conditions from vitreous ice or from vitrified biological samples. Sectioning, transfer and observation in the electron microscope is feasible without alteration of the sample hydration or its initial vitrification. Biological structures can be preserved and observed down to 10 nm. Under favourable working conditions, specimen compression during sectioning and electron beam damage are the factors limiting high resolution observations.
Temperature compensated BAW resonator and its integrated thermistor for a 2.5GHz electrical thermally compensated oscillator (2009)

This paper presents a miniaturized 2.5 GHz frequency source based on compensated BAW resonator with its integrated temperature molybdenum sensor assembled on the differential Colpitts oscillator. The presence of silicon dioxide layer having a positive temperature coefficient compared to other layers is used to reduce the resonator's drift. A demonstration oscillator achieves a frequency drift of 40 ppm over a temperature range from -35degC to +85degC. The oscillator's phase noise of -113 dBc/Hz at 10 kHz offset from the carrier is reported at 2.5 GHz.
Differential gene expression in human lung adenocarcinomas and squamous cell carcinomas. (2002)

Many of these known and novel genes may be involved in human lung tumorigenesis; therefore, additional characterization is warranted and will be beneficial to the understanding of this deadly disease.