gebhart/patrepeval huggingface dataset:
A nonsynonymous polymorphism in <i>IL23R</i> gene is associated with risk of gastric cancer in a Chinese population (2010)

Interleukin-23 receptor (IL-23R) is a key element in T helper (Th)17 cell-mediated inflammatory process, which plays an important role in pathogenesis of gastric cancer. Genetic variants of IL-23R have been identified as the predisposing factors for immunopathologic process. In this study, we hypothesized that the functional genetic variants of IL-23R gene may modify the risk of gastric cancer. To test this hypothesis, we conducted a case-control study including 1043 gastric cancer patients and 1089 controls in a Chinese population to assess the association between two potentially functional single nucleotide polymorphisms (SNPs) rs6682925 T>C and rs1884444 T>G of IL-23R and risk of gastric cancer. We found that the variant allele (G) of rs1884444 T>G, with amino acid His substituted by Gln at codon 3, was significantly associated with a decreased risk of gastric cancer [adjusted allelic odds ratio (OR) = 0.78, 95% confidence interval (CI) = 0.68-0.88]. In the stratified analysis, we found that this protective effect of rs1884444 G allele was mainly evident in intestinal-type gastric cancer (adjusted allelic OR = 0.75, 95% CI = 0.65-0.87) other than in diffuse-type gastric cancer (adjusted allelic OR = 0.96, 95% CI = 0.76-1.22). However, we did not find any significant association of rs6682925 T>C with gastric cancer risk. These findings indicate, for the first time, that the nonsynonymous variant rs1884444 T>G of IL-23R may contribute to gastric cancer susceptibility, especially in intestinal-type gastric cancer, in Chinese population.
Semi-blind decorrelating multiuser detection for synchronous CDMA (2004)

Multiuser detection is a key technology for combating multiple access interference (MAI) in CDMA systems. In this paper, we propose three effective one-shot multiuser semi-blind decorrelating detectors based on least squares (LS), total least squares (TLS) and mixed LS/TLS (MLS) formulations. All of the proposed algorithms are based on the classic decorrelating detector and a new semi-blind signature matrix. Different assumptions regarding the noise in the proposed semi-blind signature matrix lead to different detection algorithms. We also find that the classic decorrelating detector can be regarded as a special case of the proposed LS decorrelating detector. The proposed detection algorithms are simple and direct, where only the timing, signature and amplitude of the desired user are required. In addition, no search or convergence procedure is required. Finally, theoretical analysis and computer simulations are presented to illustrate the performance of the proposed algorithms.
Involvement of Viral and Chemical Factors with Oral Cancer in Taiwan (2004)

The data demonstrated that HPV, HSV-1 and betel quid chewing were significantly associated with OSCC, but HSV-2, CMV, EBV and HHV-8 were not. We suggest that the most determinative factor for oral cancer may be chemical in nature rather than viral infection.
Isolation of two forms of the high‐molecular‐mass serine protease, ingensin, from porcine skeletal muscle (1985)

Two forms of a neutral protease that catalyzed the hydrolysis of succinyl-Leu-Leu-Val-Tyr-MCA were isolated from porcine skeletal muscle cytosol by fractionation on DEAE-cellulose, hydroxyapatite and Sephadex G-100. The native enzyme had a molecular mass of above 1000 kDa. Peak A, which was eluted from hydroxyapatite at 50 mM phosphate, was activated 37-fold by the detergent, SDS, while peak B which was eluted at 150 mM phosphate, was activated only 2-fold. After dialysis against water, the B form showed restored ability to be activated by SDS (9.6-fold with 0.04% SDS). The activated peak B was extremely sensitive to divalent and monovalent cations such as Ca2+, Mg2+, Na+, K+ and NH+4 as well as protease inhibitors such as leupeptin, chymostatin and DFP. These results suggest that these proteases are generally latent in the cells and may be regulated by changes in the concentrations of cations in the cytosol. We call this new type of protease, ingensin.
Using Sacrificial Cell Spheroids for the Bioprinting of Perfusable 3D Tissue and Organ Constructs: A Computational Study (2019)

A long-standing problem in tissue engineering is the biofabrication of perfusable tissue constructs that can be readily connected to the patient's vasculature. It was partially solved by three-dimensional (3D) printing of sacrificial material (e.g., hydrogel) strands: upon incorporation in another cell-laden hydrogel, the strands were removed, leaving behind perfusable channels. Their complexity, however, did not match that of the native vasculature. Here, we propose to use multicellular spheroids as a sacrificial material and investigate their potential benefits in the context of 3D bioprinting of cell aggregates and/or cell-laden hydrogels. Our study is based on computer simulations of postprinting cellular rearrangements. The computational model of the biological system is built on a cubic lattice, whereas its evolution is simulated using the Metropolis Monte Carlo algorithm. The simulations describe structural changes in three types of tissue constructs: a tube made of a single cell type, a tube made of two cell types, and a cell-laden hydrogel slab that incorporates a branching tube. In all three constructs, the lumen is obtained after the elimination of the sacrificial cell population. Our study suggests that sacrificial cell spheroids (sacrospheres) enable one to print tissue constructs outfitted with a finer and more complex network of channels than the ones obtained so far. Moreover, cellular interactions might give rise to a tissue microarchitecture that lies beyond the bioprinter's resolution. Although more expensive than inert materials, sacrificial cells have the potential to bring further progress towards the biofabrication of fully vascularized tissue substitutes.
Structure and function in rhodopsin: correct folding and misfolding in point mutants at and in proximity to the site of the retinitis pigmentosa mutation Leu-125-->Arg in the transmembrane helix C. (1996)

L125R is a mutation in the transmembrane helix C of rhodopsin that is associated with autosomal dominant retinitis pigmentosa. To probe the orientation of the helix and its packing in the transmembrane domain, we have prepared and studied the mutations E122R, I123R, A124R, S127R, L125F, and L125A at, and in proximity to, the above mutation site. Like L125R, the opsin expressed in COS-1 cells from E122R did not bind 11-cis-retinal, whereas those from I123R and S127R formed the rhodopsin chromophore partially. A124R opsin formed the rhodopsin chromophore (lambda max 495 nm) in the dark, but the metarhodopsin II formed on illumination decayed about 6.5 times faster than that of the wild type and was defective in transducin activation. The mutant opsins from L125F and L125A bound 11-cis-retinal only partially, and in both cases, the mixtures of the proteins produced were separated into retinal-binding and non-retinal-binding (misfolded) fractions. The purified mutant rhodopsin from L125F showed lambda max at 500 nm, whereas that from L125A showed lambda max at 503 nm. The mutant rhodopsin L125F showed abnormal bleaching behavior and both mutants on illumination showed destabilized metarhodopsin II species and reduced transducin activation. Because previous results have indicated that misfolding in rhodopsin is due to the formation of a disulfide bond other than the normal disulfide bond between Cys-110 and Cys-187 in the intradiscal domain, we conclude from the misfolding in mutants L125F and L125A that the folding in vivo in the transmembrane domain is coupled to that in the intradiscal domain.
OpenAI Gym (2016)

OpenAI Gym is a toolkit for reinforcement learning research. It includes a growing collection of benchmark problems that expose a common interface, and a website where people can share their results and compare the performance of algorithms. This whitepaper discusses the components of OpenAI Gym and the design decisions that went into the software.
Genome-wide Specificity of Highly Efficient TALENs and CRISPR/Cas9 for T Cell Receptor Modification (2017)

In T cells with transgenic high-avidity T cell receptors (TCRs), endogenous and transferred TCR chains compete for surface expression and may pair inappropriately, potentially causing autoimmunity. To knock out endogenous TCR expression, we assembled 12 transcription activator-like effector nucleases (TALENs) and five guide RNAs (gRNAs) from the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas9) system. Using TALEN mRNA, TCR knockout was successful in up to 81% of T cells. Additionally, we were able to verify targeted gene addition of a GFP gene by homology-directed repair at the TALEN target site, using a donor suitable for replacement of the reporter transgene with therapeutic TCR chains. Remarkably, analysis of TALEN and CRISPR/Cas9 specificity using integrase-defective lentiviral vector capture revealed only one off-target site for one of the gRNAs and three off-target sites for both of the TALENs, indicating a high level of specificity. Collectively, our work shows highly efficient and specific nucleases for T cell engineering.
The coagulation system as a target for experimental therapy of human gliomas (2003)

The purpose of this paper is to review the rationale for the development of coagulation-reactive drugs for the experimental therapy of gliomas. Numerous reactants familiar to students of blood coagulation have been shown to contribute to neoplastic proliferation, invasion and metastasis. Recently, considerable progress has been made in demonstrating the ability of drugs capable of inhibiting these reactants to alter cancer progression. Biological features of gliomas within the realm of blood coagulation suggest that clinical trials of such drugs warrant consideration. This approach offers the prospect of a novel treatment for this devastating tumour type that does not share the toxicities of conventional cancer therapies.
A 5GHz phase-locked loop using dynamic phase-error compensation technique for fast settling in 0.18-µm CMOS (2009)

This paper presents a 5GHz phase-locked loop (PLL) with a fast-locking capability. During frequency locking, the proposed fast-settling technique dynamically adjusts the divide ratio of the frequency divider to keep the instantaneous phase error at the PFD input small. As a result, the locking time is greatly reduced. At a loop bandwidth of 20kHz, the measured settling time is less than 10µs, which is roughly 14× faster than a traditional PLL. Fabricated in a 0.18µm CMOS process, this PLL dissipates 9.5mA from a 1.8V supply. The measured phase noise is −117.5dBc/Hz at 1MHz offset.
The widest practicable dissemination - The NASA Technical Report Server (1995)

The National Aeronautics and Space Act of 1958 established NASA and charged it to 'provide for the widest practicable and appropriate dissemination of information concerning...its activities and the results thereof.' The search for innovative methods to distribute NASA's information lead a grass-roots team to create the NASA Technical Report Server (NTRS), which uses the World Wide Web and other popular Internet-based information systems as search engines. The NTRS is an inter-center effort which provides uniform access to various distributed publication servers residing on the Internet. Users have immediate desktop access to technical publications from NASA centers and institutes. The NTRS is comprised of several units, some constructed especially for inclusion in NTRS, and others that are existing NASA publication services that NTRS reuses. This paper presents the NTRS architecture, usage metrics, and the lessons learned while implementing and maintaining the services over the initial six-month period. The NTRS is largely constructed with freely available software running on existing hardware. NTRS builds upon existing hardware and software, and the resulting additional exposure for the body of literature contained will allow NASA to ensure that its institutional knowledge base will continue to receive the widest practicable and appropriate dissemination.
Genes Influenced by the Non-Muscle Isoform of Myosin Light Chain Kinase Impact Human Cancer Prognosis (2014)

The multifunctional non-muscle isoform of myosin light chain kinase (nmMLCK) is critical to the rapid dynamic coordination of the cytoskeleton involved in cancer cell proliferation and migration. We identified 45 nmMLCK-influenced genes by bioinformatic filtering of genome-wide expression in wild type and nmMLCK knockout (KO) mice exposed to preclinical models of murine acute inflammatory lung injury, pathologies that are well established to include nmMLCK as an essential participant. To determine whether these nmMLCK-influenced genes were relevant to human cancers, the 45 mouse genes were matched to 38 distinct human orthologs (M38 signature) (GeneCards definition) and underwent Kaplan-Meier survival analysis in training and validation cohorts. These studies revealed that in training cohorts, the M38 signature successfully identified cancer patients with poor overall survival in breast cancer (P<0.001), colon cancer (P<0.001), glioma (P<0.001), and lung cancer (P<0.001). In validation cohorts, the M38 signature demonstrated significantly reduced overall survival for high-score patients of breast cancer (P = 0.002), colon cancer (P = 0.035), glioma (P = 0.023), and lung cancer (P = 0.023). The association between M38 risk score and overall survival was confirmed by univariate Cox proportional hazard analysis of overall survival in the both training and validation cohorts. This study, providing a novel prognostic cancer gene signature derived from a murine model of nmMLCK-associated lung inflammation, strongly supports nmMLCK-involved pathways in tumor growth and progression in human cancers and nmMLCK as an attractive candidate molecular target in both inflammatory and neoplastic processes.
TNF-alpha, IL-6 and their soluble receptor serum levels and secretion by neutrophils in cancer patients. (2001)

Simultaneous evaluation of cytokines and their soluble receptor production and the serum levels can be helpful in understanding the local and systemic immune response of a tumor-bearing host. In the present study we examined serum levels of TNF-alpha, IL-6 and their soluble receptors: sTNFRp55, sTNFRp75 and sIL-6R confronted with their production by the polymorphonuclear neutrophils (PMN) from cancer patients. Examinations were carried out in patients with adenocarcinoma breast cancer and squamous cell carcinoma of the oral cavity and related to the clinical course and to different phases of therapy. Secretion of IL-6, sTNFRp55 and sTNFRp75 by PMN appeared to be dependent on tumor type, clinical progression of disease as well as on therapy, suggesting a significant role of these cells at different phases of the immune response to cancer associated with these mediators. Changes in values of TNF-alpha, IL-6 and their soluble receptors in sera of both cancer groups, dependent on tumor type, clinical progression and cancer therapy, could have a diagnostic and prognostic role in cancer disease.
COACERVATES : A NOVEL STATE OF SOFT MATTER — AN OVERVIEW (2008)

Coacervation is usually defined as the spontaneous formation of a dense liquid phase from a macromolecular solution of poor solvent affinity. In coacervation, the loss of solvation arises from the interaction of complementary macromolecular species. The formation of such macromolecule-rich fluids is well-known in mixtures of complementary polyelectrolytes; it can also occur from mixtures of polyelectrolytes with colloidal particles, leading to condensed soft matter phases with interesting properties. Though the polymer solution and gel states are adequately studied, characterized and mostly understood, the same for the coacervate phase is not true. Coacervates are macro-ionic hydrated complexes of a pair (self or complementary) of charge-neutralized polymers. Such a condensed phase remains in thermodynamic equilibrium with its supernatant that mostly contains a dilute dispersion of smaller intermolecular aggregates of the constituent polymers. This article intends to elucidate the salient features of this novel soft matter with some specific examples.
Towards answering opinion questions (2003)

Opinion question answering is a challenging task for natural language processing. In this paper, we discuss a necessary component for an opinion question answering system: separating opinions from fact, at both the document and sentence level. We present a Bayesian classifier for discriminating between documents with a preponderance of opinions such as editorials from regular news stories, and describe three unsupervised, statistical techniques for the significantly harder task of detecting opinions at the sentence level. We also present a first model for classifying opinion sentences as positive or negative in terms of the main perspective being expressed in the opinion. Results from a large collection of news stories and a human evaluation of 400 sentences are reported, indicating that we achieve very high performance in document classification (upwards of 97% precision and recall), and respectable performance in detecting opinions and classifying them at the sentence level as positive, negative, or neutral (up to 91% accuracy).
The use of indirect calorimetry in the intensive care unit (2013)

The role of indirect calorimetry in the ICU should be expected to increase in the near future, as predictive equations may be too inaccurate to identify the appropriate goals of nutrition therapy.
Neamine Inhibits Prostate Cancer Growth by Suppressing Angiogenin-Mediated rRNA Transcription (2009)

We confirmed that ANG is a molecular target for cancer drug development and that blocking nuclear translocation of ANG is an effective means to inhibit its activity. Our results also suggested that neamine is a lead compound for further preclinical evaluation.
Low complexity MPPT technique exploiting the effect of the PV cell series resistance (2008)

This paper proposes a method for estimating the maximum power point (MPP) of a photovoltaic (PV) module through a simple linear equation, exploiting the relation existing between the values of module voltage and current at the maximum power point (MPP locus). The analytical study of the electrical model shows that this relation tends to be linear for the higher irradiation conditions due to the effect of the PV cell series resistance. Based on that, a linear approximation of the MPP locus is derived, whose parameters are simply related to those of the electrical parameters of a PV cell. The proposed solution presents the same complexity but higher effectiveness when compared to other estimation MPPT methods. Furthermore, the estimation is inherently compensated for temperature variations by periodically sensing the module open circuit voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">oc</sub> ). The proposed method is suitable for low cost PV systems and was successfully tested in a solar powered 55 W battery charger circuit.
New multiplexing technique using polarization of light (1991)

A new scheme for coding optical signals using the polarization of light is described. The coding response is shown to be linear and invariant. As a consequence of the vectorial nature of the electromagnetic waves, this response takes a sinusoidal shape, which limits the number of channels to three. An application to fiber optics transmissions is presented; an experimental 50-m link is described. The performance and loss of the system are discussed as well as the influence of specific factors, such as the coherence length of the source and the random mode-coupling. As a conclusion, the compatibility of this new multiplexing principle with other multiplexing methods is examined.
Granulocytic myeloid‐derived suppressor cells from human cord blood modulate T‐helper cell response towards an anti‐inflammatory phenotype (2017)

Infections are a leading cause of perinatal morbidity and mortality. The outstandingly high susceptibility to infections early in life is mainly attributable to the compromised state of the neonatal immune system. One important difference to the adult immune system is a bias towards T helper type 2 (Th2) responses in newborns. However, mechanisms regulating neonatal T-cell responses are incompletely understood. Granulocytic myeloid-derived suppressor cells (GR-MDSC) are myeloid cells with a granulocytic phenotype that suppress various functions of other immune cells and accumulate under physiological conditions during pregnancy in maternal and fetal blood. Although it has been hypothesized that GR-MDSC accumulation during fetal life could be important for the maintenance of maternal-fetal tolerance, the influence of GR-MDSC on the immunological phenotype of neonates is still unclear. Here, we investigated the impact of GR-MDSC isolated from cord blood (CB-MDSC) on the polarization of Th cells. We demonstrate that CB-MDSC inhibit Th1 responses and induced Th2 responses and regulatory T (Treg) cells. Th1 inhibition was cell-contact dependent and occurred independent of other cell types, while Th2 induction was mediated independently of cell contact through expression of ArgI and reactive oxygen species by CB-MDSC and partially needed the presence of monocytes. Treg cell induction by CB-MDSC also occurred cell-contact independently but was partially mediated through inducible nitric oxide synthase. These results point towards a role of MDSC in regulating neonatal immune responses. Targeting MDSC function in neonates could be a therapeutic opportunity to improve neonatal host defence.
Bioassay for Nisin in Milk, Processed Cheese, Salad Dressings, Canned Tomatoes, and Liquid Egg Products (2006)

A sensitive nisin quantification bioassay was constructed, based on Lactococcus lactis chromosomally encoding the nisin regulatory proteins NisK and NisR and a plasmid with a green fluorescent protein (GFP) variant gfp(uv) gene under the control of the nisin-inducible nisA promoter. This strain, LAC275, was capable of transducing the signal from extracellular nisin into measurable GFPuv fluorescence through the NisRK signal transduction system. The LAC275 cells detected nisin concentrations of 10 pg/ml in culture supernatant, 0.2 ng/ml in milk, 3.6 ng/g in processed cheese, 1 ng/g in salad dressings and crushed, canned tomatoes, and 2 ng/g in liquid egg. This method was up to 1,000 times more sensitive than a previously described GFP-based nisin bioassay. This new assay made it possible to detect significantly smaller amounts of nisin than the presently most sensitive published nisin bioassay based on nisin-induced bioluminescence. The major advantage of this sensitivity was that foods could be extensively diluted prior to the assay, avoiding potential inhibitory and interfering substances present in most food products.
Development of medically hygienic socks loaded with antifungal microcapsules for patients with athlete's foot (2014)

7th Textile Bioengineering and Informatics Symposium (TBIS 2014) / 5th Asian Protective Clothing Conference (APCC 2014), Hong Kong, Peoples R China, 6-8 August 2014