gebhart/patrepeval huggingface dataset:
Modulation of mesangial cell migration by extracellular matrix components. Inhibition by heparinlike glycosaminoglycans. (1988)

Extension of mesangial cells (MC) into the pericapillary space is a pathologic response seen in several forms of glomerulonephritis. This process may involve both cytoplasmic extension by MC and actual cellular migration. For investigation of whether extracellular matrix factors could modulate this process, the migratory responses of rat MC were quantitatively examined using a cell culture model. Denuding ("wounding") a portion of a confluent culture of MC was followed by migration of mesangial cells into the denuded area. The expected proliferative response to this treatment was blocked by irradiation. The migratory response began within 8 hours of wounding and continued for at least 80 hours. The MC migratory response was specifically inhibited in a dose-dependent and reversible manner by heparin and heparinlike glycosaminoglycans (GAGs). Chondroitin sulfates and hyaluronic acid did not significantly inhibit MC migration. Glomerular basement membrane heparinlike GAGs may normally prevent MC extension into the pericapillary space. Changes in the density or composition of these substances during glomerular inflammatory processes could permit the development of MC pericapillary extensions and thereby lead to further alterations in basement membrane integrity.
Two Pyrenylalanines in Dihydrofolate Reductase Form an Excimer Enabling the Study of Protein Dynamics (2012)

Because of the lack of sensitivity to small changes in distance by available FRET pairs (a constraint imposed by the dimensions of the enzyme), a DHFR containing two pyrene moieties was prepared to enable the observation of excimer formation. Pyren-1-ylalanine was introduced into DHFR positions 16 and 49 using an in vitro expression system in the presence of pyren-1-ylalanyl-tRNA(CUA). Excimer formation (λ(ex) 342 nm; λ(em) 481 nm) was observed in the modified DHFR, which retained its catalytic competence and was studied under multiple and single turnover conditions. The excimer appeared to follow a protein conformational change after the H transfer involving the relative position and orientation of the pyrene moieties and is likely associated with product dissociation.
PageNUCA: Selected policies for page-grain locality management in large shared chip-multiprocessor caches (2009)

As the last-level on-chip caches in chip-multiprocessors increase in size, the physical locality of on-chip data becomes important for delivering high performance. The non-uniform access latency seen by a core to different independent banks of a large cache spread over the chip necessitates active mechanisms for improving data locality. The central proposal of this paper is a fully hardwired coarse-grain data migration mechanism that dynamically monitors the access patterns of the cores at the granularity of a page to reduce the book-keeping overhead and decides when and where to migrate an entire page of data to amortize the performance overhead. The page-grain migration mechanism is compared against two variants of previously proposed cache block-grain dynamic migration mechanisms and two OS-assisted static locality management mechanisms. Our detailed execution-driven simulation of an eight-core chip-multiprocessor with a shared 16 MB L2 cache employing a bidirectional ring to connect the cores and the L2 cache banks shows that hardwired dynamic page migration, while using only 4.8% of extra storage out of the total L2 cache and book-keeping budget, delivers the best performance and energy-efficiency across a set of shared memory parallel applications selected from the SPLASH-2, SPEC OMP, DARPA DIS, and FFTW suites and multiprogrammed workloads prepared out of the SPEC 2000 and BioBench suites. It reduces execution time by 18.7% and 12.6% on average (geometric mean) respectively for the shared memory applications and the multiprogrammed workloads compared to a baseline architecture that distributes the pages round-robin across the L2 cache banks.
Ionizing radiation‐induced acoustics for radiotherapy and diagnostic radiology applications (2018)

Acoustic waves are induced via the thermoacoustic effect in objects exposed to a pulsed beam of ionizing radiation. This phenomenon has interesting potential applications in both radiotherapy dosimetry and treatment guidance as well as low-dose radiological imaging. After initial work in the field in the 1980s and early 1990s, little research was done until 2013 when interest was rejuvenated, spurred on by technological advances in ultrasound transducers and the increasing complexity of radiotherapy delivery systems. Since then, many studies have been conducted and published applying ionizing radiation-induced acoustic principles into three primary research areas: Linear accelerator photon beam dosimetry, proton therapy range verification, and radiological imaging. This review article introduces the theoretical background behind ionizing radiation-induced acoustic waves, summarizes recent advances in the field, and provides an outlook on how the detection of ionizing radiation-induced acoustic waves can be used for relative and in vivo dosimetry in photon therapy, localization of the Bragg peak in proton therapy, and as a low-dose medical imaging modality. Future prospects and challenges for the clinical implementation of these techniques are discussed.
Fabrication of Low-Loss Microstrip Band-Pass Filter Made from Double-Sided YBa<sub>2</sub>Cu<sub>3</sub>O<sub>x</sub> Films (1994)

A three-pole microstrip band-pass filter, with a center frequency of 9.5 GHz and bandwidth of 2%, has been fabricated using YBa 2 Cu 3 O x (YBCO) films deposited on both sides of (100)MgO substrates by pulsed laser ablation. A double-sided YBCO filter has a much lower passband insertion loss, 0.08 dB at 77 K and less than 0.04 dB below 60 K, compared with the 0.20 dB of a YBCO filter with a Au ground plane, and with the 1.1 dB of a conventional double-sided Au filter at 77 K. The extremely low insertion loss characteristics correspond to the element resonator unloaded quality factor ( Q u ) of 6000 at 77 K and greater than 10000 below 60 K. These results demonstrate that very compact high- Q u superconducting filters with waveguide-like performance can be achieved in planar microstrip configurations.
Visualizing call graphs (2011)

Developers navigate and reason about call graphs throughout investigation and debugging activities. This is often difficult: developers can spend tens of minutes answering a single question, get lost and disoriented, and erroneously make assumptions, causing bugs. To address these problems, we designed a new form of interactive call graph visualization - REACHER. Instead of leaving developers to manually traverse the call graph, REACHER lets developers search along control flow. The interactive call graph visualization encodes a number of properties that help developers answer questions about causality, ordering, type membership, repetition, choice, and other relationships. And developers remain oriented while navigating. To evaluate REACHER'S benefits, we conducted a lab study in which 12 participants answered control flow questions. Compared to an existing IDE, participants with REACHER were over 5 times more successful in significantly less time. All enthusiastically preferred REACHER, with many positive comments.
Nucleotide Frequency Variation Across Human Genes (2003)

The frequencies of individual nucleotides exhibit significant fluctuations across eukaryotic genes. In this paper, we investigate nucleotide variation across an averaged representation of all known human genes. Such a representation allows us to average out random fluctuations that constitute noise and uncover remarkable systematic trends in nucleotide distributions, particularly near boundaries between genetic elements--the promoter, exons, and introns. We propose that such variations result from differential mutational pressures and from the presence of specific regulatory motifs, such as transcription and splicing factor binding sites. Specifically, we observe significant GC and TA biases (excess of G over C and T over A) in noncoding regions of genes. Such biases are most probably caused by transcription-coupled mismatch repair, an effect that has recently been detected in mammalian genes. Subsequently, we examine the distribution of all hexanucleotides and identify motifs that are overrepresented within regulatory regions. By clustering and aligning such sequences, we recognize families of putative regulatory elements involved in exonic and intronic splicing control, and 3' mRNA processing. Some of our motifs have been identified in prior theoretical and experimental studies, thus validating our approach, but we detect several novel sequences that we propose as candidates for future functional assays and mutation screens for genetic disorders.
Test-driving Intel Xeon Phi (2014)

Based on Intel's Many Integrated Core (MIC) architecture, Intel Xeon Phi is one of the few truly many-core CPUs - featuring around 60 fairly powerful cores, two levels of caches, and graphic memory, all interconnected by a very fast ring. Given its promised ease-of-use and high performance, we took Xeon Phi out for a test drive. In this paper, we present this experience at two different levels: (1) the microbenchmark level, where we stress "each nut and bolt" of Phi in the lab, and (2) the application level, where we study Phi's performance response in a real-life environment. At the microbenchmarking level, we show the high performance of five components of the architecture, focusing on their maximum achieved performance and the prerequisites to achieve it. Next, we choose a medical imaging application (Leukocyte Tracking) as a case study. We observed that it is rather easy to get functional code and start benchmarking, but the first performance numbers can be far from satisfying. Our experience indicates that a simple data structure and massive parallelism are critical for Xeon Phi to perform well. When compiler-driven parallelization and/or vectorization fails, programming Xeon Phi for performance can become very challenging.
Big Data Analytics for Search Engine Optimization (2020)

In the Big Data era, search engine optimization deals with the encapsulation of datasets that are related to website performance in terms of architecture, content curation, and user behavior, with the purpose to convert them into actionable insights and improve visibility and findability on the Web. In this respect, big data analytics expands the opportunities for developing new methodological frameworks that are composed of valid, reliable, and consistent analytics that are practically useful to develop well-informed strategies for organic traffic optimization. In this paper, a novel methodology is implemented in order to increase organic search engine visits based on the impact of multiple SEO factors. In order to achieve this purpose, the authors examined 171 cultural heritage websites and their retrieved data analytics about their performance and user experience inside them. Massive amounts of Web-based collections are included and presented by cultural heritage organizations through their websites. Subsequently, users interact with these collections, producing behavioral analytics in a variety of different data types that come from multiple devices, with high velocity, in large volumes. Nevertheless, prior research efforts indicate that these massive cultural collections are difficult to browse while expressing low visibility and findability in the semantic Web era. Against this backdrop, this paper proposes the computational development of a search engine optimization (SEO) strategy that utilizes the generated big cultural data analytics and improves the visibility of cultural heritage websites. One step further, the statistical results of the study are integrated into a predictive model that is composed of two stages. First, a fuzzy cognitive mapping process is generated as an aggregated macro-level descriptive model. Secondly, a micro-level data-driven agent-based model follows up. The purpose of the model is to predict the most effective combinations of factors that achieve enhanced visibility and organic traffic on cultural heritage organizations’ websites. To this end, the study contributes to the knowledge expansion of researchers and practitioners in the big cultural analytics sector with the purpose to implement potential strategies for greater visibility and findability of cultural collections on the Web.
Evolutionary Relationships of Endemic/Epidemic and Sylvatic Dengue Viruses (2000)

Endemic/epidemic dengue viruses (DEN) that are transmitted among humans by the mosquito vectors Aedes aegypti and Aedes albopictus are hypothesized to have evolved from sylvatic DEN strains that are transmitted among nonhuman primates in West Africa and Malaysia by other Aedes mosquitoes. We tested this hypothesis with phylogenetic studies using envelope protein gene sequences of both endemic/epidemic and sylvatic strains. The basal position of sylvatic lineages of DEN-1, -2, and -4 suggested that the endemic/epidemic lineages of these three DEN serotypes evolved independently from sylvatic progenitors. Time estimates for evolution of the endemic/epidemic forms ranged from 100 to 1,500 years ago, and the evolution of endemic/epidemic forms represents relatively recent events in the history of DEN evolution. Analysis of envelope protein amino acid changes predicted to have accompanied endemic/epidemic emergence suggested a role for domain III in adaptation to new mosquito and/or human hosts.
A Study of Oil-Water Dispersion in a Pulsed Baffled Reactor (1996)

The preliminary results of studies on oil–water dispersion in a pulsed baffled reactor are reported in this paper. The effects of baffle design, oil-phase fraction, and the addition of surfactants and colloid on the dispersion were investigated, and the minimum oscillation frequencies to achieve a complete dispersion at different oscillation amplitudes were obtained and used for the interpretation of the state of dispersion. The results show that the orifice baffles with smaller orifice diameters are better suited for this type of dispersion than the other orifice baffles and disk baffles tested. The results have also shown that the complete dispersion characteristics in such a reactor were insensitive to oil-phase fractions but sensitive to the addition of surfactants and colloid.
Expression of active yeast pyruvate decarboxylase in Escherichia coli (1991)

We have shown by appropriate modification of the translational signals and using the strong T7 RNA polymerase promoter phi 10, that a cloned Saccharomyces cerevisiae pyruvate decarboxylase gene (pdc1) can be expressed in Escherichia coli. This protein, which migrated as a single band on SDS-polyacrylamide gels, was found to have a subunit molecular mass of approximately 62 kDa, similar to that of the enzyme produced by yeast. Polyclonal antibodies raised against purified yeast pyruvate decarboxylase recognized this bacterially produced protein. We found that this recombinant enzyme is active, indicating that the homotetramer encoded by the pdc1 gene is functional.
Hub Arc Location Problems: Part I—Introduction and Results (2005)

Hub networks play an important role in many transportation and telecommunications systems. This paper introduces a new model called the hub arc location model. Rather than locate discrete hub facilities, this model locates hub arcs, which have reduced unit flow costs. Four special cases of the general hub arc location model are examined in detail. We provide motivation for the new models, and present examples and optimal solutions, using data for U.S. air passenger traffic. Results are used to compare optimal costs, hub locations, and hub arc locations with corresponding hub median optimal solutions. The results reveal interesting spatial patterns and help identify promising cities and regions for hubs. A companion paper (Campbell et al. 2005) presents integer programming formulations and solution algorithms for the new hub arc problems. It also provides details and computation times for these solution algorithms.
Effects of familial risk factors and place of birth on the risk of autism: a nationwide register‐based study (2005)

The highest risk of autism was found in families with a history of autism, or Asperger's syndrome and other PDDs in siblings, supporting the commonly accepted knowledge that genetic factors are involved in the etiology of autism.
Polyamines are necessary for the survival of human small-cell lung carcinoma in culture. (1981)

Many human small-cell lung carcinoma culture lines grow as multicellular aggregate spheroids, for which high L-dopa decarboxylase activity is a marker. During the initial cell aggregation and the exponential growth phase, there is a marked increase in ornithine decarboxylase activity and an accumulation of polyamines. alpha-Difluoromethylornithine, a specific enzyme-activated, irreversible ornithine decarboxylase inhibitor, blocks the increase in ornithine decarboxylase activity and in polyamines and inhibits human small-cell lung carcinoma cell growth. After the onset of a decreased proliferation rate, the multicellular spheroid aggregates become poorly formed, cell loss ensues, and there is a decrease in L-dopa decarboxylase activity. These findings support the hypothesis that ornithine decarboxylase and the polyamines play an essential role not only in the proliferative phase but also in the viability of human small-cell lung carcinoma cells in culture. The results suggest that alpha-difluoromethylornithine, a virtually nontoxic compound, may be potentially useful in the therapy of this human tumor.
Controlling the Size of Taurine Crystals in the Cooling Crystallization Process (2013)

Taurine crystals (TC) with high fluidity, anticaking, and antisticking properties are commercially required by manufacturers. Crystal size and shape are two main factors controlling these properties. This study investigated the size and shape of TCs produced by a cooling crystallization processing. The addition of activated carbon to decolor the product exhibited negligible effects on the size of TCs. Increasing the crystallization temperature resulted in the formation of small-size crystals, whereas TC size decreased as the stirring rate increased. A careful control of post high-speed stirring aging in a slowly stirred system enabled the preparation of larger crystals. The estimation of optimal crystallization time is crucial as lengthening the crystallization time might not effectively increase the overall size of the crystals. It was found that the shape of the TC was not affected by various operating conditions, delineating a similar inherent molecular arrangement of taurine molecules under the range of operating conditions tested. These findings contribute to the understanding of controlling properties of TCs for industrial manufacturing via the cooling crystallization method.
Preventing cerebrospinal fluid leak following transection of a tight filum terminale (2011)

A longer hospital stay for maintaining patients flat after a simple tethered cord release appears not to prevent CSF leakage. However, a larger patient cohort will be needed to detect small differences in complication rates.
Calmodulin as an Ion Channel Subunit (2002)

A surprising variety of ion channels found in a wide range of species from Homo to Paramecium use calmodulin (CaM) as their constitutive or dissociable Ca(2+)-sensing subunits. The list includes voltage-gated Ca(2+) channels, various Ca(2+)- or ligand-gated channels, Trp family channels, and even the Ca(2+)-induced Ca(2+) release channels from organelles. Our understanding of CaM chemistry and its relation to enzymes has been instructive in channel research, yet the intense study of CaM regulation of ion channels has also revealed unexpected CaM chemistry. The findings on CaM channel interactions have indicated the existence of secondary interaction sites in addition to the primary CaM-binding peptides and the functional differences between the N- and C-lobes of CaM. The study of CaM in channel biology will figure into our understanding on how this uniform, universal, vital, and ubiquitous Ca(2+) decoder coordinates the myriad local and global cell physiological transients.
The Fas Counterattack In Vivo: Apoptotic Depletion of Tumor-Infiltrating Lymphocytes Associated with Fas Ligand Expression by Human Esophageal Carcinoma (1998)

Various cancer cell lines express Fas ligand (FasL) and can kill lymphoid cells by Fas-mediated apoptosis in vitro. FasL expression has been demonstrated in several human malignancies in vivo. We sought to determine whether human esophageal carcinomas express FasL, and whether FasL expression is associated with increased apoptosis of tumor-infiltrating lymphocytes (TIL) in vivo, thereby contributing to the immune privilege of the tumor. Using in situ hybridization and immunohistochemistry, respectively, FasL mRNA and protein were colocalized to neoplastic esophageal epithelial cells in all esophageal carcinomas (squamous, n = 6; adenocarcinoma, n = 2). The Extent of FasL expression was variable, with both FasL-positive and FasL-negative neoplastic regions occurring within tumors. TIL were detected by immunohistochemical staining for the leukocyte common Ag, CD45. FasL expression was associated with a mean fourfold depletion of TIL when compared with FasL-negative areas within the same tumors (range 1.6- to 12-fold, n = 6,p < 0.05). Cell death of TIL was detected by dual staining of CD45 (immunohistochemistry) and DNA strand breaks (TUNEL, terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling). There was a mean twofold increase in detectable cell death among TIL in FasL-positive areas compared with FasL-negative areas (range 1.6- to 2.4-fold, n = 6, p < 0.05). In conclusion, we demonstrate a statistically significant, quantitative reduction of TIL concomitant with significantly increased TIL apoptosis within FasL-expressing areas of esophageal tumors. Our findings suggest Fas-mediated apoptotic depletion of TIL in response to FasL expression by esophageal cancers, and provide the first direct, quantitative evidence to support the Fas counterattack as a mechanism of immune privilege in vivo in human cancer.
Sources of diversity in T cell epitope discovery (2011)

CD8-positive T cells respond to small antigenic peptide fragments presented on class I major histocompatibility complexes (MHCs). Those specific T cell epitopes capable of precipitating a cellular immune response are either derived from (altered) self (i.e. they are autoimmune- or cancer-associated) or come from foreign sources (i.e. they are pathogen-associated). Identification of T cell epitopes provides elementary information that can be employed in technologies that monitor and predict the likely outcome of an immune response, as well as in therapeutic and vaccine development efforts. The coexistence between host and pathogen has largely driven the diversification of both their systems of immune surveillance and their antigenic determinants, respectively. In this review, we discuss the multitude of factors that introduce diversity to the T cell response from both sides of the host-pathogen interaction. Furthermore, we provide an overview of a variety of commonly employed methods and tools to characterize class I MHC restricted antigen presentation and recent endeavors towards the harmonization of reporting data concerning T cell responses.