gebhart/patrepeval huggingface dataset:
25 Gbit/s silicon microring modulator based on misalignment-tolerant interleaved PN junctions (2012)

A high-speed depletion-mode silicon-based microring modulator with interleaved PN junctions optimized for high modulation efficiency and large alignment tolerance is demonstrated. It is fabricated using standard 0.18 μm complementary metal-oxide-semiconductor processes and provides low V(π)L(π)s of 0.68 V·cm to 1.64 V·cm with a moderate doping concentration of 2 × 10(17) cm(-3). The measured modulation efficiency decreases by only 12.4% under ± 150 nm alignment errors. 25 Gbit/s non-return-zero modulation with a 4.5 dB extinction ratio is experimentally realized at a peak-to-peak driving voltage of 2 V, demonstrating the excellent performance of the novel doping profile.
A Framework for Recommender Systems in E-Commerce Based on Distributed Storage and Data-Mining (2010)

Recent technological advances in many networks and applications, particularly the Internet and the World Wide Web (WWW), have generated a huge amount of information available to users. A recommender system in E-Commerce is an intermediary program (or an agent) with a user interface that automatically and intelligently generates a list of information which suits an individual's needs. In this paper, a new recommender system framework based on Distributed Storage and Data-Mining is proposed. The recommendation systems work by collecting data from users, commodities, and transactions, examples of implicit data collection include the following: observing the items that a user views in an online store, keeping a record of the items that a user purchases online, obtaining a list of items that a user has listened to or watched on his/her computer, et al. This data ared stored by hadoop distributed file system(HDFS), and mined in Map Reduce that is a programming model and an associated implementation for processing and generating large data sets. The patterns (i.e., classification, cluster, and association rule ared used to complete recommender by hybrid recommendation method including (1) by analyzing the information content, i.e.), content-based filtering, (2) by referencing other user access behaviors, i.e., collaborative filtering, and (3) by referencing relations between commodity, i.e., association rule-based recommendation.
Rationale for interleukin-6 blockade in systemic lupus erythematosus (2004)

Interleukin-6 (IL-6) is a pleiotropic cytokine with a wide range of biological activities that plays an important role in immune regulation and inflammation. Among other actions, it induces terminal differentiation of B lymphocytes into antibody-forming cells and the differentiation of T cells into effector cells. IL-6 also has multiple potent proinflammatory effects. An association between IL-6 and lupus was demonstrated in murine models of SLE and blocking IL-6 improved lupus in all models tested. Data from several studies suggest that IL-6 plays a critical role in the B cell hyperactivity and immunopathology of human SLE, and may have a direct role in mediating tissue damage. Based on these data, we propose that blocking the effect of IL-6 in humans may improve lupus by interacting with the autoinflammatory process both systemically and locally.
Gene expression variation in the adult human retina (2003)

Despite evidence that differences in gene expression levels contribute significantly to phenotypic variation across individuals, there has been only limited effort to study gene expression variation in human tissue. To characterize expression variation in the normal human retina, we utilized a custom retinal microarray to analyze 33 normal retinas from 19 donors, aged 29-90 years. Statistical models were designed to separate and quantify biological and technical sources of variation, including age, gender, eye laterality, gene function and age-by-gender interaction. Although the majority of the 9406 genes analyzed showed relatively stable expression levels across different donors (for an average gene the expression level value of 95 out of a 100 individuals fell within a 1.23-fold range), 2.6% of genes showed significant donor-to-donor variation, with a false discovery rate of 10%. The mean expression ratio standard deviation was 0.15+/-0.8, log2, with a range of 0.09-0.99. Genes selectively expressed in photoreceptors showed higher expression variation than other gene classes. Gender, age and other donor-specific factors contributed significantly to the expression variation of multiple genes, and groups of genes with an age- and gender-associated expression pattern were identified. Our findings show that a significant fraction of gene expression variation in the normal human retina is attributable to identifiable biological factors. The greater expression variability of many genes central to retinal function (including photoreceptor-specific genes) may be partially explained by the dynamics of the vision process, and raises the possibility that photoreceptor gene expression levels may contribute to phenotypic diversity across normal adult retinas. In addition, as such diversity may result in different levels of disease susceptibility, exploring its sources may provide insights into the pathogenesis of retinal disease.
Intra-abdominal compartment syndrome as a complication of ruptured abdominal aortic aneurysm repair. (1989)

In four patients with ruptured abdominal aortic aneurysms increased intra-abdominal pressure developed after repair. It was manifested by increased ventilatory pressure, increased central venous pressure, and decreased urinary output associated with massive abdominal distension not due to bleeding. This set of findings constitutes an intra-abdominal compartment syndrome caused by massive interstitial and retroperitoneal swelling. The purpose of this report is to establish criteria for this syndrome and suggest a method of treatment. The syndrome developed within 24 hours; in one patient within 5 hours postoperatively. All four patients received more than 25 liters of fluid resuscitation (electrolyte and blood) during and within 16 hours after operation and had massive abdominal distension. Decompressive laparotomies were performed in the Intensive Care Unit with placement of Marlex (Bard Corp., Billerica, MA) mesh. In two additional patients, at the completion of the aneurysmectomy the abdominal incision was left open with interposition Marlex mesh. Opening the abdominal incision was associated with dramatic improvements in central venous pressure, urinary output, ventilatory pressure, arterial carbon dioxide tension, and oxygenation. The authors conclude that some patients with ruptured abdominal aortic aneurysm do not tolerate the closure of the abdominal wall, as manifested by increased ventilatory pressures, decreased oxygenation, and decreased urinary output. Opening the abdominal wound or delayed closure may reverse the oliguria and improve oxygenation. Recognition and treatment of this condition by opening the abdominal wound or delayed closure may affect outcome in some cases.
A One-Pot, Two-Step Synthesis of Tetrahydro Asterriquinone E (1999)

Bis(indolyl)dihydroxyquinone 2, the tetrahydro analogue of naturally occurring 1a, was synthesized by a novel, expeditious route. The short synthesis was accomplished by treating p-bromanil (3) with 2 equiv of indole 4 in the presence of cesium carbonate in acetonitrile at ambient temperature to provide a 1:1 mixture of the dibromo regioisomers 7 and 8, followed by hydrolysis of the mixture to afford 2. The synthetic compound 2 was found to inhibit the binding of the Grb2 adapter protein to tyrosine-phosphorylated EGF receptor (IC50 = 1.2 μM).
Desmin is present in proliferating rat muscle satellite cells but not in bovine muscle satellite cells (1991)

The presence of desmin was characterized in cultured rat and bovine satellite cells and its potential usefulness as a marker for identifying satellite cells in vitro was evaluated. In primary cultures, positive immunohistochemical staining for desmin and skeletal muscle myosin was observed in rat and bovine myotubes. A small number of mononucleated cells (20% of rat satellite cells and 5% of bovine satellite cells) were myosin-positive, indicative of post-mitotic differentiated myocytes. In bovine satellite cell cultures 13% of the mononucleated cells were desmin-positive, while 84% of the mononucleated cells in rat satellite cell cultures were desmin-positive. Rat satellite cell mass cultures and bovine satellite cell clonal density cultures were pulsed with 3H-thymidine, and autoradiographic data revealed that greater than 94% of dividing rat cells were desmin-positive, suggesting that desmin is synthesized in proliferating rat satellite cells. However, no desmin was seen in cells that incorporated labeled thymidine in bovine satellite cell clones. Analysis of clonal density cultures revealed that only 14% of the mononucleated cells in bovine satellite cell colonies were desmin-positive, whereas 98% of the cells in rat satellite cell colonies were desmin-positive. Fibroblast colonies from both species were desmin-negative. In order to further examine the relationship between satellite cell differentiation and desmin expression, 5-bromo-2'-deoxyuridine (BrdU) was added to culture medium at the time of plating to inhibit differentiation. Fusion was inhibited in rat and bovine cultures, and cells continued to divide. Very few desmin-positive cells were found in bovine cultures, but greater than 90% of the cells in rat cultures stained positive for desmin. The presence of desmin and sarcomeric myosin was also evaluated in regenerating rat tibialis anterior five days after bupivacaine injection. In regenerating areas of the muscle many desmin-positive cells were present, and only a few cells stained positive for skeletal muscle myosin. Application of desmin staining to rat satellite cell growth assays indicated that rat satellite cells cultured in serum-containing medium were contaminated with fibroblasts at levels that ranged from approximately 5% in 24 hr cultures to 15% in mature cultures. In defined medium 4 day cultures contain approximately 95% to 98% desmin-positive satellite cells.(ABSTRACT TRUNCATED AT 400 WORDS)
Proteolytic Cascade Enzymes Increase in Focal Cerebral Ischemia in Rat (1996)

Cerebral infarction initiates a cascade of molecular events, leading to proteolytic cell death. Matrix-degrading metalloproteinases (MMPs) are neutral proteases involved in extracellular matrix damage. Type IV collagenase is an MMP that increases cerebral capillary permeability after intracerebral injection and may be important along with plasminogen activators (PA) in secondary brain edema in stroke. Therefore, we measured MMPs and PAs in spontaneously hypertensive (SHR) or Wistar-Kyoto (WKY) rats with permanent middle cerebral artery occlusion (MCAO). Brain tissue was assayed for MMPs and PAs at 1, 3, 12, and 24 h and 5 days after occlusion, using substrate gel polyacrylamide electrophoresis (zymography). SHR showed an increase in 92-kDa type IV collagenase (gelatinase B) in the infarcted hemisphere compared with the opposite side at 12 and 24 h (p < 0.05). Gelatinase A remained the same in both infarcted and normal tissue until 5 days after injury, when it increased significantly (p < 0.05). Urokinase-type PA was increased significantly at 12 and 24 h and 5 days, while tissue-type PA was decreased significantly at 1, 12, and 24 h in the ischemic compared with the nonischemic hemisphere. Gelatinase B was markedly increased in SHR at 12 and 24 h compared with WKY (p < 0.05). Secondary vasogenic edema is maximal 1-2 days after a stroke, which is the time that gelatinase B was elevated. The time of appearance of gelatinase B suggests a role in secondary tissue damage and vasogenic edema, while gelatinase A may be involved in tissue repair.
Use of a Modified Tryptophanase Promoter to Direct High‐Level Expression of Foreign Proteins in E. coli (1996)

We have modified the tryptophanase promoter (PtnaA) for use as a temperature-independent promoter for the production of recombinant proteins. Although any protein will have a temperature range in which its expression is optimal, we find the tryptophanase promoter functions at all physiologically relevant temperatures (20 degrees C to 42 degrees C). Induction at temperatures below 37 degrees C avoids eliciting the heat-shock response and may favor the production of protein in the soluble state. A short segment of the E. coli tnaA promoter containing the catabolite gene activator protein (CAP) binding site but no tryptophan-responsive elements was used to direct synthesis of various proteins. Conditions for high cell density fermentation and induction control were developed. Expression was induced by depletion of glucose and was maximal when an alternative nonrepressing carbon source was supplied. Expression of certain proteins was tightly controlled; however, pre-induction expression was observed with other reporter genes. The tnaC leader portion of the tnaA promoter was found to reduce pre-induction expression in the presence of glucose, although maximal expression was observed only in the absence of this region. The effect of temperature on expression of several recombinant proteins was investigated. Although some proteins were produced only in inclusion bodies as insoluble material, the production of one protein in soluble form was clearly temperature dependent.
Importance of direct hepatocytolysis by liver macrophages in experimental fulminant hepatitis. (1992)

When lipopolysaccharide was administered to mice that had been injected with heat-killed Propionibacterium acnes, most of them died of massive liver necrosis. Previously, we demonstrated that a soluble hepatocytotoxic factor released by liver adherent cells fully activated by both P. acnes and lipopolysaccharide was attributable to the late stage of this severe liver injury. In this report, we focused on the hepatocytolysis by these liver adherent cells in a cell-cell interaction manner. Shortly after stimulation with lipopolysaccharide, the P. acnes-elicited liver adherent cells almost completely killed the hepatocytes prepared from both normal syngeneic mice and P. acnes-treated ones. Since P. acnes-elicited liver adherent cells also proved to produce various kinds of cytokines in a short time, the role of cytokines in this liver injury was analyzed. Only TNF-alpha enabled the P. acnes-elicited liver adherent cells to kill hepatocytes prepared from the same mice, but none from the normal ones. These results suggest that the liver adherent cells accumulated and partly stimulated by P. acnes-treatment might rapidly lyse the autologous hepatocytes once triggered by lipopolysaccharide and that the TNF-alpha these liver adherent cells produced might upregulate their own hepatocytotoxic ability.
Polyethyleneimine functionalized iron oxide nanoparticles as agents for DNA delivery and transfection (2007)

A novel, efficient DNA delivery and transfection agent has been developed by chemically attaching short chain polyethyleneimine (PEI) molecules (M.W. = 423 and 1800) to the surface of composite iron oxide nanoparticles (250 nm in diameter). These particles are not only capable of delivering DNA but also can be driven by an external magnetic field. During DNA binding experiments, a remarkably low N : P ratio of <1 was recorded. This is due to the more effective distribution of the PEI molecules across the surface of the nanoparticles in comparison to particles where PEI is attached to the surface via simple electrostatic interactions. This new attachment strategy allows the use of smaller amounts of PEI with potential reduction in toxic side-effects.
Comparative Evaluation of Hyperthermia Heating Modalities: II. Application of the Acceptable Power Range Technique (1984)

The acceptable power range technique previously described in a companion paper [R. B. Roemer, T. C. Cetas, J. R. Oleson, S. Halac, and A. Y. Matloubieh, Radiat. Res. 100, 450-472 (1984)] is applied to two heating modalities to demonstrate its application to simulated clinical situations. Comparisons of the abilities of the different modalities to heat given tumors are made using the relative sizes of the acceptable power ranges obtained for each modality. Similar comparisons are also possible for determining the efficacy of physiological manipulations and adjustments in power deposition patterns for a given heating modality. Predictions of the ability of modalities and configurations to properly heat tumors are made using the bracketing nature of the uniform and annular tumor perfusion models. These comparisons and predictions are possible because a single measure of the ability of any heating technique to heat an arbitrary tumor in any location is utilized (the size of the acceptable power range). While relatively simple models are presently utilized, this approach can be extended to take into account a host of physical and biological conditions that model the patient-device interaction to an arbitrarily high degree of detail. These refinements will be based on extended clinical and experimental data, particularly as tumor and normal tissue blood perfusion characteristics either become better known in general cases or can be specified for each real tumor. The applications of this approach should be far-reaching and complementary to clinical hyperthermia, especially as further model refinements are incorporated. Additional data are presented which reinforce the bracketing nature of the uniform and annular tumor perfusion models presented in the companion paper.
SoftSig (2008)

Many code analysis techniques for optimization, debugging, or parallelization need to perform runtime disambiguation of sets of addresses. Such operations can be supported efficiently and with low complexity with hardware signatures. To enable flexible use of signatures, this paper proposes to expose a Signature Register File to the software through a rich ISA. The software has great flexibility to decide, for each signature,which addresses to collect and which addresses to disambiguate against. We call this architecture SoftSig . In addition, as an example of SoftSig use, we show how to detect redundant function calls efficiently and eliminate them dynamically. We call this algorithm MemoiSE . On average for five popular applications, MemoiSE reduces the number of dynamic instructions by 9.3%, thereby reducing the execution time of the applications by 9%.
Measurement of second-order polarization-mode dispersion vectors in optical fibers (1999)

A polarization-mode dispersion (PMD) measurement technique is described that allows the determination of second- and higher order PMD vectors in optical fibers. The algorithm, based on Muller matrices, requires the launch of only two polarizations per wavelength and uses large rotation angles as well as interleaving to attain low-noise high-resolution PMD data. It has been applied to fibers ranging from 2 to 40 ps in mean PMD.
Surface-Cross-Linked Micelles as Multifunctionalized Organic Nanoparticles for Controlled Release, Light Harvesting, and Catalysis (2016)

Surfactant micelles are dynamic entities with a rapid exchange of monomers. By "clicking" tripropargylammonium-containing surfactants with diazide cross-linkers, we obtained surface-cross-linked micelles (SCMs) that could be multifunctionalized for different applications. They triggered membrane fusion through tunable electrostatic interactions with lipid bilayers. Antenna chromophores could be installed on them to create artificial light-harvesting complexes with efficient energy migration among tens to hundreds of chromophores. When cleavable cross-linkers were used, the SCMs could break apart in response to redox or pH signals, ejecting entrapped contents quickly as a result of built-in electrostatic stress. They served as caged surfactants whose surface activity was turned on by environmental stimuli. They crossed cell membranes readily. Encapsulated fluorophores showed enhanced photophysical properties including improved quantum yields and greatly expanded Stokes shifts. Catalytic groups could be installed on the surface or in the interior, covalently attached or physically entrapped. As enzyme mimics, the SCMs enabled rational engineering of the microenvironment around the catalysts to afford activity and selectivity not possible with conventional catalysts.
Induction of immunologic tolerance to cardiac allograft by simultaneous blockade of inducible co-stimulator and cytotoxic T-lymphocyte antigen 4 pathway1 (2003)

Inhibition of T-cell proliferation with ICOSIg and CTLA4Ig was more effective than that with ICOSIg alone. Thus, ICOS appears to be an important regulator of T-cell activation, and may be an effective therapy in clinical cardiac transplantation.
Intervertebral Disc Reconstitution After Chemonucleolysis With Chymopapain is Dependent on Dosage (1996)

This study demonstrates that an effective reduction in disc width compatible with later reconstitution of the nucleus pulposus can be achieved experimentally with an appropriate dose of chymopapain. These data clearly indicate that an optimal dose of chymopapain for chemonucleolysis in humans needs to be established.
Selective Release of MicroRNA Species from Normal and Malignant Mammary Epithelial Cells (2010)

MicroRNAs (miRNAs) in body fluids are candidate diagnostics for a variety of conditions and diseases, including breast cancer. One premise for using extracellular miRNAs to diagnose disease is the notion that the abundance of the miRNAs in body fluids reflects their abundance in the abnormal cells causing the disease. As a result, the search for such diagnostics in body fluids has focused on miRNAs that are abundant in the cells of origin. Here we report that released miRNAs do not necessarily reflect the abundance of miRNA in the cell of origin. We find that release of miRNAs from cells into blood, milk and ductal fluids is selective and that the selection of released miRNAs may correlate with malignancy. In particular, the bulk of miR-451 and miR-1246 produced by malignant mammary epithelial cells was released, but the majority of these miRNAs produced by non-malignant mammary epithelial cells was retained. Our findings suggest the existence of a cellular selection mechanism for miRNA release and indicate that the extracellular and cellular miRNA profiles differ. This selective release of miRNAs is an important consideration for the identification of circulating miRNAs as biomarkers of disease.
An accurate and interpretable model for siRNA efficacy prediction (2006)

The model proposed for prediction of siRNA potency is as accurate as a state-of-the-art nonlinear model and is easily interpretable in terms of biological features. It is freely available on the web at http://cbio.ensmp.fr/dsir.
Kinetics of cytokine production in experimental autoimmune anterior uveitis (EAAU) (1998)

Our study reveals an interesting correlation between the expression of TNF-alpha, IFN-gamma and disease progression in EAAU. Furthermore, they suggest that TNF-alpha is an important cytokine in the target tissue, while IFN-gamma is in the draining lymph node.
[Osteopontin of skin and hair follicle of rat]. (2000)

These results suggest a possible role of osteopontin in up-regulating growth and differentiation of dermal papilla during the catagen phase of the hair follicles.