gebhart/patrepeval huggingface dataset:
Phase Change Memory (2010)

In this paper, recent progress of phase change memory (PCM) is reviewed. The electrical and thermal properties of phase change materials are surveyed with a focus on the scalability of the materials and their impact on device design. Innovations in the device structure, memory cell selector, and strategies for achieving multibit operation and 3-D, multilayer high-density memory arrays are described. The scaling properties of PCM are illustrated with recent experimental results using special device test structures and novel material synthesis. Factors affecting the reliability of PCM are discussed.
El proceso de investigación en la elaboración de un diccionario de parlache (2009)

RESUMENEn este artículo sintetizamos el proceso de investigación que se siguió en la elaboración del diccionario de parlache. Explicamos cómo se recogieron y sistematizaron los datos y señalamos las características esenciales del diccionario de uso que realizamos.ABSTRACTIn this paper we summarize the research process followed in the preparation of The Parlache Dictionary. We explain how the data were collected and systematized and we show the essential features of this usage dictionary we carried out, as well.
Synthesis and Electronic Properties of Conjugated Pentacene Dimers (2008)

Conjugated pentacene dimers 1-3 were synthesized in two steps from readily available precursors. Noteworthy is the initial step, which assembles five independent fragments to form the carbon-rich molecular framework. Solution-cast films of these materials are air stable. Photocurrent measurements for solution-deposited thin films show that dimer 3 exhibits photoconductive gain >10.
Asthmatics with gastroesophageal reflux long term results of a randomized trial of medical and surgical antireflux therapies (2003)

In short term studies, asthma symptoms and pulmonary function have been reported to improve during and after medical treatment or surgical correction of gastroesophageal reflux (GER). In this study, we aimed to determine whether prolonged treatment of GER altered the long term natural history of asthma in asthmatics with GER. A total of 62 patients with both GER and asthma entered a randomized study of antireflux treatments for at least 2 yr: 24 controls (antacids as needed); 22 medical (ranitidine 150 mg t.i.d.); and 16 surgical (Nissen fundoplication). Asthma was defined as a previous diagnosis of asthma with discrete attacks of wheezing and 20% reversibility in airway disease. GER was defined as an abnormal ambulatory 24-h esophageal pH test and macroscopic or microscopic evidence of GER disease. Overall clinical status, asthma symptom scores, and pulmonary medication requirements were recorded monthly. Peak expiratory flow rates were recorded up to seven times per day for 1 wk of each month throughout the years. Pulmonary function, esophageal manometry, and endoscopy with biopsy were repeated yearly. The 62 patients were followed for up to 19.1 yr. In the surgical group, but not in the medical or control groups, there was an immediate and sustained reduction in acute nocturnal exacerbations of wheezing, coughing, and dyspnea. By the end of 2 yr, improvement, marked improvement, or cure in the overall asthma status occurred in 74.9% of the surgical group, 9.1% of the medical group and 4.2% of the control group, whereas the overall status worsened in 47.8% of the control group, 36.4% of the medical group, and 12.5% of the surgical group (p < 0.001, surgical vs medical and control). The mean asthma symptom score of the surgical group improved 43%, compared with less than 10% in the medical and control groups (p = 0.0009). As determined by changes in peak expiratory flow rates, there was no statistically significant difference in pulmonary function during the 2-yr period or during regularly scheduled follow-up. There was no difference in medication requirements among the groups. There was no difference between the groups in overall survival. In patients with both GER and asthma, antireflux surgery (but not medical therapy with ranitidine 150 mg t.i.d.) has minimal effect on pulmonary function, pulmonary medication requirements, or survival, but significantly improves asthma symptoms and overall clinical status.
Chemical Modification Patterns Compatible with High Potency Dicer-Substrate Small Interfering RNAs (2008)

Dicer-substrate small interfering RNAs (DsiRNAs) are synthetic RNA duplexes that are processed by Dicer into 21-mer species and show improved potency as triggers of RNA interference, particularly when used at low dose. Chemical modification patterns that are compatible with high potency 21-mer small interfering RNAs have been reported by several groups. However, modification patterns have not been studied for Dicer-substrate duplexes. We therefore synthesized a series of chemically modified 27-mer DsiRNAs and correlated modification patterns with functional potency. Some modification patterns profoundly reduced function although other patterns maintained high potency. Effects of sequence context were observed, where the relative potency of modification patterns varied between sites. A modification pattern involving alternating 2'-O-methyl RNA bases was developed that generally retains high potency when tested in different sites in different genes, evades activation of the innate immune system, and improves stability in serum.
Decondensation of Human Sperm Nuclei and Hp1 Protamine Degradation from Normospermia and Asthenospermia in Xenopus Egg Extracts (1992)

The process of human sperm decondensation has been studied in vitro in cytoplasmic extracts prepared from unfertilized Xenopus laevis eggs. The chromatin decondensation-recondensation cycle was divided into four stages according to chromatin appearance. Spermatozoa from normospermia and asthenospermia were evaluated according to their capacity to reach these stages, and their DNA integrity was assessed by acridine orange (AO) staining. We observed a significant difference between normospermia and asthenozoospermia in the ability to achieve the cycle of chromatin decondensation-recondensation. These results correlated with AO staining. The role of human protamine 1 degradation in the decondensation process was evaluated by immunostaining. It was found not to be a prerequisite for the earlier stage of chromatin decondensation and it was not implied in the latest stages of pronuclear development.
Active Plasma Kallikrein Localizes to Mast Cells and Regulates Epithelial Cell Apoptosis, Adipocyte Differentiation, and Stromal Remodeling during Mammary Gland Involution (2009)

The plasminogen cascade of serine proteases directs both development and tumorigenesis in the mammary gland. Plasminogen can be activated to plasmin by urokinase-type plasminogen activator (uPA), tissue-type plasminogen activator (tPA), and plasma kallikrein (PKal). The dominant plasminogen activator for mammary involution is PKal, a serine protease that participates in the contact activation system of blood coagulation. We observed that the prekallikrein gene (Klkb1) is expressed highly in the mammary gland during stromal remodeling periods including puberty and postlactational involution. We used a variant of ecotin (ecotin-PKal), a macromolecular inhibitor of serine proteases engineered to be highly specific for active PKal, to demonstrate that inhibition of PKal with ecotin-PKal delays alveolar apoptosis, adipocyte replenishment, and stromal remodeling in the involuting mammary gland, producing a phenotype resembling that resulting from plasminogen deficiency. Using biotinylated ecotin-PKal, we localized active PKal to connective tissue-type mast cells in the mammary gland. Taken together, these results implicate PKal as an effector of the plasminogen cascade during mammary development.
Chaos and order in the capital markets (1991)

Conversion THA after prior shelf acetabuloplasty provided encouraging short-term results with no major complications. Prior shelf acetabuloplasty did not complicate subsequent THA. Bone coverage of the acetabular component was inadequate in total hip arthroplasty, even with prior shelf acetabuloplasty.
In-Network Snoop Ordering (INSO): Snoopy coherence on unordered interconnects (2009)

Realizing scalable cache coherence in the many-core era comes with a whole new set of constraints and opportunities. It is widely believed that multi-hop, unordered on-chip networks would be needed in many-core chip multiprocessors (CMPs) to provide scalable on-chip communication. However, providing ordering among coherence transactions on unordered interconnects is a challenge. Traditional approaches for tackling coherence either have to use ordered interconnects (snoop-based protocols) which lead to scalability problems, or rely on an ordering point (directory-based protocols) which adds indirection latency. In this paper, we propose In-Network Snoop Ordering (INSO), in which coherence requests from a snoop-based protocol are inserted into the interconnect fabric and the network orders the requests in a distributed manner, creating a global ordering among requests. Essentially, when coherence requests enter the network, they grab snoop-orders at the injection router before being broadcasted. A snoop-order specifies the global ordering of the particular request with respect to other requests. Before requests reach their destinations, they get ordered along the way, at intermediate routers and destination network interfaces. Our logical ordering scheme can be mapped onto any unordered interconnect. This enables a cache coherence protocol which exploits the low-latency nature of unordered interconnects without adding indirection to coherence transactions. Our full-system evaluations compare INSO against a directory protocol and a broadcast based Token Coherence protocol. INSO outperforms these protocols by up to 30% and 8.5%, respectively, on a wide range of scientific and emerging applications.
Spatio-temporal Saliency detection using phase spectrum of quaternion fourier transform (2008)

Salient areas in natural scenes are generally regarded as the candidates of attention focus in human eyes, which is the key stage in object detection. In computer vision, many models have been proposed to simulate the behavior of eyes such as SaliencyToolBox (STB), neuromorphic vision toolkit (NVT) and etc., but they demand high computational cost and their remarkable results mostly rely on the choice of parameters. Recently a simple and fast approach based on Fourier transform called spectral residual (SR) was proposed, which used SR of the amplitude spectrum to obtain the saliency map. The results are good, but the reason is questionable.
Elevation of Intracellular Glucosylceramide Levels Results in an Increase in Endoplasmic Reticulum Density and in Functional Calcium Stores in Cultured Neurons (1999)

Gaucher disease is a glycosphingolipid storage disease caused by defects in the activity of the lysosomal hydrolase, glucocerebrosidase (GlcCerase), resulting in accumulation of glucocerebroside (glucosylceramide, GlcCer) in lysosomes. The acute neuronopathic type of the disease is characterized by severe loss of neurons in the central nervous system, suggesting that a neurotoxic agent might be responsible for cellular disruption and neuronal death. We now demonstrate that upon incubation with a chemical inhibitor of GlcCerase, conduritol-B-epoxide (CBE), cultured hippocampal neurons accumulate GlcCer. Surprisingly, increased levels of tubular endoplasmic reticulum elements, an increase in [Ca(2+)](i) response to glutamate, and a large increase in [Ca(2+)](i) release from the endoplasmic reticulum in response to caffeine were detected in these cells. There was a direct relationship between these effects and GlcCer accumulation since co-incubation with CBE and an inhibitor of glycosphingolipid synthesis, fumonisin B(1), completely antagonized the effects of CBE. Similar effects on endoplasmic reticulum morphology and [Ca(2+)](i) stores were observed upon incubation with a short-acyl chain, nonhydrolyzable analogue of GlcCer, C(8)-glucosylthioceramide. Finally, neurons with elevated GlcCer levels were much more sensitive to the neurotoxic effects of high concentrations of glutamate than control cells; moreover, this enhanced toxicity was blocked by pre-incubation with ryanodine, suggesting that [Ca(2+)](i) release from ryanodine-sensitive intracellular stores can induce neuronal cell death, at least in neurons with elevated GlcCer levels. These results may provide a molecular mechanism to explain neuronal dysfunction and cell death in neuronopathic forms of Gaucher disease.
Islet transplantation: present and future perspectives (1998)

Islet cell transplantation can potentially normalize blood glucose levels and stop the progression of clinical complications, and if the transplant is done early in the course of the disease complications may be prevented. Remarkable progress has been made in recent years and islet cell transplantation has resulted in normalization of metabolic control in several patients with Type 1 diabetes in the absence of hypoglycemia. Only a few patients, however, have achieved insulin independence. Issues relating to islet cell engraftment within the liver, prevention of rejection and recurrent autoimmunity, and identification of alternative immunosuppressive drugs that do not adversely affect islet cell function remain to be solved. Thus far, the need for chronic, generalized immunosuppression to prevent rejection of the islets has limited the indication to those patients who have already received another transplant or to those who simultaneously receive islets and another organ (generally a kidney). Identification of immunointervention protocols that allow for engraftment in the absence of deleterious effects on the islets and prevent rejection and recurrent autoimmunity would make this procedure suitable for all patients, including children who have not yet developed long-term complications of the disease.
ReX: A Suite of Computational Tools for the Design, Visualization, and Analysis of Chimeric Protein Libraries (2016)

Directed evolution has greatly facilitated protein engineering and provided new insights into protein structure-function relationships. DNA shuffling using restriction enzymes is a particularly simple and cost-effective means of recombinatorial evolution that is well within the capability of most molecular biologists, but tools for the design and analysis of such experiments are limited. Here we introduce a suite of freely available online tools to make the construction and analysis of chimeric libraries readily accessible to the novice. REcut (http://qpmf.rx.umaryland.edu/REcut.html) facilitates the choice of DNA fragmentation strategy, while Xover (http://qpmf.rx.umaryland.edu/Xover.html) analyzes chimeric mutants to reveal recombination patterns and extract quantitative data.
Her-2/neu oncogene amplification in clinically localised prostate cancer (2002)

Increased Her-2/neu oncogene copy number appears to be rare in clinically localised prostatic adenocarcinoma and is related to chromosome 17 polysomy rather than true amplification. As a result, it would not be a useful biomarker for identifying those patients who will have recurrences after radical prostatectomy.
Identification of protein phosphorylation sites by a combination of mass spectrometry and solid phase Edman sequencing. (2002)

The analysis of protein phosphorylation sites is one of the major challenges in the post-genomic age. To understand the role of reversible phosphorylation in cell signaling, the precise location of phosphorylation sites must be determined in a phosphoprotein as well as the effect that these post-translational modifications have on the function of the protein. The use of solid phase Edman degradation of (32)P-labeled phosphoproteins and peptides was described over 10 years ago as a method for the identification of phosphorylation sites. Since that time a number of laboratories have used this technique as the standard method for phosphorylation site analysis. In this report, we will describe how we routinely use this technology to perform hundreds of successful phosphorylation site analyses per annum. By combining mass spectrometry to identify the phosphopeptide and solid phase Edman degradation to localize the site of phosphorylation, subpmole quantities of phosphopeptides can be successfully characterized.
Developmental restriction of Mash2 expression in trophoblast correlates with potential activation of the Notch‐2 pathway (1997)

Mash-2 expression begins during preimplantation development, but is restricted to trophoblasts after the blastocyst stage. Within the trophoblast lineage, Mash-2 transcripts are first expressed in the ectoplacental cone and chorion, but not in terminally differentiated trophoblast giant cells. After day 8.5 of gestation, Mash-2 expression becomes further restricted to focal sites within the spongiotrophoblast and labyrinth. Downregulation is probably important for normal development since overexpression of Mash-2 reduces giant cell formation. We have investigated the role that the Notch signaling pathway may play in trophoblast development. Mash-2 is a homologue of Drosophila achaete/scute complex genes. In Drosophila, activation of the Notch receptor induces transcriptional repressors encoded by the hairy/Enhancer of split (HES) genes, which interact with the Groucho protein to shut off achaete-scute transcription. In the developing mouse placenta, we found that all elements of the Notch pathway were expressed. In particular, the Notch-2, HES-2, and HES-3 genes were coexpressed in trophoblast giant cells and in foci within the spongiotrophoblast at day 10.5 when Mash-2 transcription becomes restricted. Two members of the mammalian Groucho family were expressed in trophoblasts; TLE3 was expressed broadly in the giant cell, spongiotrophoblast, and labyrinthine regions, whereas TLE2 was limited to giant cells and focal regions of the spongiotrophoblast. These data suggest that Notch signaling through activation of HES transcriptional repressors may play a role in murine placental development. Dev. Genet. 21:21–30, 1997. © 1997 Wiley-Liss, Inc.
Mutations that disrupt DNA binding and dimer formation in the E47 helix-loop-helix protein map to distinct domains. (1990)

A common DNA binding and dimerization domain containing an apparent "helix-loop-helix" (HLH) structure was recognized recently in a number of regulatory proteins, including the E47 and E12 proteins that bind to the kappa E2 motif in immunoglobulin kappa gene enhancer. The effect of site-directed mutagenesis on E47 protein multimerization and DNA binding was examined. Mutations in either putative helix domain disrupted protein dimerization and DNA binding. No DNA binding was observed when mutations were introduced in the basic region, but these mutants were able to dimerize. These basic region mutants were not able to bind to DNA as heterodimers with the wild-type E47 proteins, demonstrating that two functional basic regions are required for binding to DNA. Therefore the basic region mutants are "transdominant."
Adjuvant effects of saponins on animal immune responses (2007)

Vaccines require optimal adjuvants including immunopotentiator and delivery systems to offer long term protection from infectious diseases in animals and man. Initially it was believed that adjuvants are responsible for promoting strong and sustainable antibody responses. Now it has been shown that adjuvants influence the isotype and avidity of antibody and also affect the properties of cell-mediated immunity. Mostly oil emulsions, lipopolysaccharides, polymers, saponins, liposomes, cytokines, ISCOMs (immunostimulating complexes), Freund's complete adjuvant, Freund's incomplete adjuvant, alums, bacterial toxins etc., are common adjuvants under investigation. Saponin based adjuvants have the ability to stimulate the cell mediated immune system as well as to enhance antibody production and have the advantage that only a low dose is needed for adjuvant activity. In the present study the importance of adjuvants, their role and the effect of saponin in immune system is reviewed.
Garbage collection without paging (2005)

Garbage collection offers numerous software engineering advantages, but interacts poorly with virtual memory managers. Existing garbage collectors require far more pages than the application's working set and touch pages without regard to which ones are in memory, especially during full-heap garbage collection. The resulting paging can cause throughput to plummet and pause times to spike up to seconds or even minutes. We present a garbage collector that avoids paging. This bookmarking collector cooperates with the virtual memory manager to guide its eviction decisions. Using summary information ("bookmarks") recorded from evicted pages, the collector can perform in-memory full-heap collections. In the absence of memory pressure, the bookmarking collector matches the throughput of the best collector we tested while running in smaller heaps. In the face of memory pressure, it improves throughput by up to a factor of five and reduces pause times by up to a factor of 45 over the next best collector. Compared to a collector that consistently provides high throughput (generational mark-sweep), the bookmarking collector reduces pause times by up to 218x and improves throughput by up to 41x. Bookmarking collection thus provides greater utilization of available physical memory than other collectors while matching or exceeding their throughput.
G Protein-Mediated Neuronal DNA Fragmentation Induced by Familial Alzheimer's Disease-Associated Mutants of APP (1996)

Missense mutations in the 695-amino acid form of the amyloid precursor protein (APP695) cosegregate with disease phenotype in families with dominantly inherited Alzheimer's disease. These mutations convert valine at position 642 to isoleucine, phenylalanine, or glycine. Expression of these mutant proteins, but not of normal APP695, was shown to induce nucleosomal DNA fragmentation in neuronal cells. Induction of DNA fragmentation required the cytoplasmic domain of the mutants and appeared to be mediated by heterotrimeric guanosine triphosphate-binding proteins (G proteins).
A biomimetic microfluidic chip to study the circulation and mechanical retention of red blood cells in the spleen (2015)

Red blood cells (RBCs) are deformable and flow through vessels narrower than their own size. Their deformability is most stringently challenged when they cross micrometer-wide slits in the spleen. In several inherited or acquired RBC disorders, blockade of small vessels by stiff RBCs can trigger organ damage, but a functional spleen is expected to clear these abnormal RBCs from the circulation before they induce such complications. We analyzed flow behavior of RBCs in a microfluidic chip that replicates the mechanical constraints imposed on RBCs as they cross the human spleen. Polymer microchannels obtained by soft lithography with a hydraulic diameter of 25 μm drove flow into mechanical filtering units where RBCs flew either slowly through 5- to 2-μm-wide slits or rapidly along 10-μm-wide channels, these parallel paths mimicking the splenic microcirculation. Stiff heated RBCs accumulated in narrow slits seven times more frequently than normal RBCs infused simultaneously. Stage-dependent retention of Plasmodium falciparum-infected RBCs was also observed in these slits. We also analyzed RBCs from patients with hereditary spherocytosis and observed retention for those having the most altered mechanical properties as determined by ektacytometry. Thus, in keeping with previous observations in vivo and ex vivo, the chip successfully discriminated poorly deformable RBCs based on their distinct mechanical properties and on the intensity of the cell alteration. Applications to the exploration of the pathogenesis of malaria, hereditary spherocytosis, sickle cell disease and other RBC disorders are envisioned.