gebhart/patrepeval huggingface dataset:
Direct numerical simulation of electrokinetic translocation of a cylindrical particle through a nanopore using a Poisson–Boltzmann approach (2011)

Nanopore-based sensing of single molecules is based on a detectable change in the ionic current arising from the electrokinetic translocation of individual nanoparticles through a nanopore. In this study, we propose a continuum-based model to investigate the dynamic electrokinetic translocation of a cylindrical nanoparticle through a nanopore and the corresponding ionic current response. It is the first time to simultaneously solve the Poisson-Boltzmann equation for the ionic concentrations and the electric field contributed by the surface charges of the nanopore and the nanoparticle, the Laplace equation for the externally applied electric field, and the modified Stokes equations for the flow field using an arbitrary Lagrangian-Eulerian method. Current blockade due to the particle translocation is predicted when the electric double layers (EDLs) of the particle and the nanopore are not overlapped, which is in qualitative agreement with existing experimental observations. Effects due to the electric field intensity imposed, the EDL thickness, the nanopore's surface charge, the particle's initial orientation and lateral offset from the nanopore's centerline on the particle translocation including both translation and rotation, and the ionic current response are comprehensively investigated. Under a relatively low electric field imposed, the particle experiences a significant rotation and a lateral movement. However, the particle is aligned with its longest axis parallel to the local electric field very quickly due to the dielectrophoretic effect when the external electric field is relatively high.
[Effects of cernitin pollen-extract (Cernilton) on inflammatory cytokines in sex-hormone-induced nonbacterial prostatitis rats]. (2001)

Cernitin pollen-extract (Cernilton, CN) is a preparation made from eight kinds of pollen and has been used for various prostatic diseases in Japan and Europe. We reported previously that CN possessed a recovery action on the sex-hormone-induced nonbacterial prostatitis in rats. To clarify the possible mechanism of action of CN, we investigated the effects of CN on inflammatory cytokines (IL-1 beta, IL-6 and TNF-alpha) in the same model. Aged Wistar rats were castrated and injected 17 beta-estradiol (0.25 mg/kg/day, s.c.) for 30 days. CN (630 and 1,260 mg/kg, p.o.) or testosterone (2.5 mg/kg, s.c.) was administered for the last 14 days of the treatment of 17 beta-estradiol. In control rats, prostatic IL-6 and TNF-alpha contents were increased approximately 2-3 fold, and acinar glandular inflammation and stromal proliferation were found histopathologically, as compared with those of intact rats. On the other hand, CN decreased the increased contents of cytokines in a dose-dependent manner. The histopathological changes mentioned above were restored in rats treated with 1,260 mg/kg. Testosterone also ameliorated them significantly. These results indicate that CN has an anti-inflammatory action, and that the inhibitory effect of CN on the prostatic inflammatory cytokine is an important factor in its action.
Palladium(II)-Catalyzed Aerobic Hydroalkoxylation of Styrenes Containing a Phenol (2006)

An intermolecular Pd-catalyzed hydroalkoxylation of styrenes that contain a phenol is presented. The reaction can be performed on terminal, disubstituted, and trisubstituted olefins in a variety of alcoholic solvents. Initial mechanistic data suggest a mechanism that involves oxidation of the alcoholic solvent to provide a Pd-hydride that inserts into an olefin. This is followed by formation of a quinone methide and subsequent addition of an alcohol to yield the hydroalkoxylated product.
Neural model identification, variable selection and model adequacy (1999)

In recent years an impressive array of publications has appeared claiming considerable successes of neural networks in modelling financial data but sceptical practitioners and statisticians are still raising the question of whether neural networks really are ‘a major breakthrough or just a passing fad’. A major reason for this is the lack of procedures for performing tests for misspecified models, and tests of statistical significance for the various parameters that have been estimated, which makes it difficult to assess the model's significance and the possibility that any short-term successes that are reported might be due to ‘data mining’. In this paper we describe a methodology for neural model identification which facilitates hypothesis testing at two levels: model adequacy and variable significance. The methodology includes a model selection procedure to produce consistent estimators, a variable selection procedure based on statistical significance and a model adequacy procedure based on residuals analysis. We propose a novel, computationally efficient scheme for estimating sampling variability of arbitrarily complex statistics for neural models and apply it to variable selection. The approach is based on sampling from the asymptotic distribution of the neural model's parameters (‘parametric sampling’). Controlled simulations are used for the analysis and evaluation of our model identification methodology. A case study in tactical asset allocation is used to demonstrate how the methodology can be applied to real-life problems in a way analogous to stepwise forward regression analysis. Neural models are contrasted to multiple linear regression. The results indicate the presence of non-linear relationships in modelling the equity premium. Copyright © 1999 John Wiley & Sons, Ltd.
Early T-cell precursor acute lymphoblastic leukemia/lymphoma (ETP-ALL/LBL) in adolescents and adults: a high-risk subtype (2016)

Early T-cell precursor (ETP) acute lymphoblastic leukemia/lymphoma (ALL/LBL) is a recently recognized high-risk T lymphoblastic leukemia/lymphoma (T-ALL/LBL) subgroup. The optimal therapeutic approaches to adult patients with ETP-ALL/LBL are poorly characterized. In this study, we compared the outcomes of adults with ETP-ALL/LBL who received treatment on frontline regimens with those of patients with other T-ALL/LBL immunophenotypic subtypes. Patients with newly diagnosed T-ALL/LBL who received frontline chemotherapy between the years 2000 and 2014 at The University of Texas MD Anderson Cancer Center were identified and immunophenotypically categorized into early, thymic, and mature per the World Health Organization (WHO) classification using CD1a and surface CD3 status. Patients with ETP-ALL/LBL were identified on the basis of the following immunophenotypes: CD1a(-), CD8(-), CD5(-)(dim), and positivity for 1 or more stem cell or myeloid antigens. A total of 111 patients with T-ALL/LBL (68% T-ALL; 32% T-LBL) with adequate immunophenotype data were identified. The median age was 30 years (range, 13-79). There was no difference in the outcomes of patients based on the WHO subtypes. Nineteen patients (17%) had ETP-ALL/LBL. The complete remission rate /complete remission with incomplete platelet recovery rate in patients with ETP-ALL/LBL was significantly lower than that of non-ETP-ALL/LBL patients (73% vs 91%;P= .03). The median overall survival for patients with ETP-ALL/LBL was 20 months vs not reached for the non-ETP-ALL/LBL patients (P= .008). ETP-ALL/LBL represents a high-risk disease subtype of adult ALL. Novel treatment strategies are needed to improve treatment outcomes in this T-ALL/LBL subset.
Role of TL1A and its receptor DR3 in two models of chronic murine ileitis (2006)

TL1A is a TNF-like cytokine that binds to the death-domain receptor (DR)3 and provides costimulatory signals to activated lymphocytes. Through this interaction, TL1A induces secretion of IFN-gamma and may, therefore, participate in the development of T helper-1-type effector responses. In this study, we investigated whether interactions between TL1A and DR3 are involved in the pathogenesis of chronic murine ileitis. We demonstrate that alternative splicing of DR3 mRNA takes place during the activation of lymphocytes, which results in up-regulation of the complete/transmembrane (tm) form of DR3. Using two immunogenetically distinct animal models of Crohn's disease, we demonstrate that induction of intestinal inflammation is associated with significant up-regulation of TL1A and tm DR3 in the inflamed mucosa. In addition, within isolated lamina propria mononuclear cells from mice with inflammation, TL1A is primarily expressed on CD11c(high) dendritic cells. We also report that TL1A acts preferentially on memory CD4(+)/CD45RB(lo) murine lymphocytes by significantly inducing their proliferation, whereas it does not affect the proliferation of the naïve CD4(+)/CD45RB(hi) T helper cell subpopulation. Finally, we demonstrate that TL1A synergizes with both the cytokine-dependent IL-12/IL-18 pathway and with low-dose stimulation of the T cell receptor to significantly induce the secretion of IFN-gamma via an IL-18-independent pathway. Our results raise the possibility that interaction(s) between TL1A expressed on antigen-presenting cells and tm DR3 on lymphocytes may be of particular importance for the pathogenesis of chronic inflammatory conditions that depend on IFN-gamma secretion, including inflammatory bowel disease. Blockade of the TL1A/DR3 pathway may, therefore, offer therapeutic opportunities in Crohn's disease.
Some misconceptions about lines of code (2002)

Source lines of code (SLOC) is perhaps the oldest of software metrics, and still a benchmark for evaluating new ones. Despite the extensive experience with the SLOC metric, there are still a number of misconceptions about it. The paper addresses three of them: (1) that the format of SLOC is relevant to how to properly count it (a simple experiment shows that, in fact, it does not matter), (2) that SLOC is most useful as a predictor of software quality (in fact it is most useful as a covariate of other predictors), and (3) that there is an important inverse relationship between defect density and code size (in fact, this is an arithmetic artifact of plotting bugs-per-SLOC against SLOC).
Posterior Coronary Vein as the Substrate for an Epicardial Accessory Pathway (2013)

Catheter ablation of Wolff-Parkinson-White syndrome is associated with up to 5% of failure. Coronary sinus (CS) abnormalities or connections between CS myocardial coat and left ventricular epicardium are associated with posteroseptal and left posterior accessory pathways (AP). A 41-year-old patient with WPW syndrome was referred to our hospital after three unsuccessful ablations. The 12-lead ECG suggested a left posteroseptal AP. CT imaging and electro-anatomic mapping showed a relationship between AP electrical course and CS posterior branch. This finding supports the hypothesis CSAPs lie in the myocardial coat around CS and represent an extensive connection between atrial and ventricular epicardial surface.
Fabrication of high-packing-density vertical cavity surface-emitting laser arrays using selective oxidation (1996)

We describe the nearly-planar processing of two-dimensional vertical cavity laser arrays based on the selective conversion of AlAs to Al/sub x/O/sub y/. The individual lasers of 8×8 and 2×2 arrays are defined by native Al/sub x/O/sub y/ to achieve 4-μm square active regions on 12-μm center-to-center spacings. Interelement thermal coupling is characterized along with the optical mode structure.
Myosin-Binding Protein C DNA Variants in Domestic Cats (A31P, A74T, R820W) and their Association with Hypertrophic Cardiomyopathy (2013)

A31P mutation occurs frequently in MCO cats. The high incidence of HCM in homozygotes for the mutation supports the causal nature of the A31P mutation. Penetrance is incomplete for heterozygotes at A31P locus, at least at a young age. The A74T variant does not appear to be correlated with HCM.
Interleukin-2 with or without LAK cells in metastatic renal cell carcinoma: a report of a European multicentre study. (1989)

Between October 1987 and November 1988, 95 European patients with metastatic renal cell carcinoma have been treated with recombinant interleukin-2 (rIL-2) (EuroCetus) at 18 X 10(6) IU/m2/day (equivalent to 3 X 10(6) Cetus Units/m2/day) according to the West schedule in two trials. 1. Forty-two patients received rIL-2 alone. Median time between initial diagnosis and metastases was three months. Eighty-one percent of the patients had at least two involved sites at inclusion and 86% underwent prior nephrectomy. Twenty-seven patients (64%) received two successive courses. Over 80% of the planned dose was administered in 69% and 44% of patients during courses 1 and 2, respectively. Fever, hypotension, weight gain, rise in creatinine level, hepatic disturbances, anaemia and thrombocytopenia were commonly observed but resolved promptly after completion of therapy. No toxic death was recorded. Two (6%) complete responses (CR), four (13%) partial responses (PR), four stable diseases (SD) and 22 progressive diseases (PD) were observed. The response rate is 6/32 (19%); the median progression-free survival time is not reached at 218+ days (92-394). 2. Fifty-three patients received rIL-2 with lymphokine-activated killer (LAK) cells. Median time from primary diagnosis to metastases was three months. Eighty-five percent of patients had at least two involved sites though 73% had previously undergone nephrectomy. Forty patients (75%) received two successive induction courses. Most patients, i.e. respectively, 77% and 60%, were given at least 80% of the planned dose during courses 1 and 2. Median numbers of LAK cells infused were 13.1 and 11.6 X 10(9) nucleated cells per course, respectively. Toxicity was not different from that described above; no toxic death occurred; five CR (10%), nine PR (18%), 11 SD and 26 PD were observed. The response rate is 14/51 (27%) and the median progression-free survival time is not reached at 7.2+ months (3-13.1). In conclusion, rIL-2, with or without LAK cells, is obviously active on metastatic renal cell carcinoma. The difference in response rate between the two trials is not statistically significant but has to be paralleled with the difference in dose received by the patients rather than with the addition of a cellular therapy. Toxicity was always manageable and reversible. The association of rIL-2 with other lymphokines should represent a major issue to improve the response rate and will be considered in further European studies.
Increased prevalence of activated CD70+CD4+ T cells in the periphery of patients with systemic lupus erythematosus (2005)

Systemic lupus erythematosus (SLE) is characterized by loss of immune tolerance. A hallmark of SLE is the presence of autoantibodies resulting from B cell hyperactivity. Previous studies have shown that the presence of abnormal B cell subsets in the periphery, such as CD27highCD20- B cells, correlate with disease activity. We examined the relationship between the expression of CD70, the ligand for CD27 expressed by activated T cells, and indicators of disease activity. A significant increase in median CD70+CD4+ T cell frequencies and memory CD45RA-CD4+ T cell frequencies was observed in SLE samples as compared to healthy controls. The frequencies of CD70+CD4+ T cells correlated with disease duration but not age, treatment, or disease activity. Although a majority of CD70+CD4+ T cells appeared to be effector memory cells, mitogen-stimulated CD70+CD4+ T cells were capable of secreting a full repertoire of effector cytokines. Despite the presence of activated CD4+ T cells, no increase in immunosenescent CD4+ T cells, as defined by the loss of CD28 and/or the acquisition of CD57 was observed in samples from SLE patients. These studies indicate that increased CD70 expression might serve as a useful marker of abnormal T cell activity in SLE.
A 2-ns detecting time, 2- mu m CMOS built-in current sensing circuit (1993)

Built-in current testing is known to enhance the defect coverage in CMOS VLSI. An experimental CMOS chip containing a high-speed built-in current sensing (BICS) circuit design is described. This chip has been fabricated through MOSIS 2- mu m p-well CMOS technology. The power bus current of an 8*8 parallel multiplier is monitored. This BICS detects all implanted short-circuit defects and some implanted open-circuit defects at a clock speed of 30 MHz (limited by the test setup). SPICE3 simulations indicate a defect detection time of about 2 ns.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Molecular analysis of the bare lymphocyte syndrome. (1985)

The bare lymphocyte syndrome is a disorder in which class I histocompatibility antigens fail to be expressed normally on the surface of lymphocytes. Utilizing complementary DNA probes for both beta 2-microglobulin and class I genes, the molecular basis for this syndrome was investigated in a family with two siblings exhibiting the bare lymphocyte syndrome. Southern blot analysis demonstrated no gross internal defect in either class I or beta 2-microglobulin genes. Northern blot analysis of class I and beta 2-microglobulin messenger RNAs also revealed no qualitative difference between affected and unaffected family members. In contrast, quantitation of both class I and beta 2-microglobulin transcripts demonstrated each to be decreased in patients when compared to controls. Moreover, the decrease in both transcripts was coordinate. These results suggest that the bare lymphocyte syndrome may represent a pretranslational regulatory defect of both class I and beta 2-microglobulin gene expression.
Applying Deep Learning to Answer Selection: A Study and An Open Task (2015)

We apply a general deep learning framework to address the non-factoid question answering task. Our approach does not rely on any linguistic tools and can be applied to different languages or domains. Various architectures are presented and compared. We create and release a QA corpus and setup a new QA task in the insurance domain. Experimental results demonstrate superior performance compared to the baseline methods and various technologies give further improvements. For this highly challenging task, the top-1 accuracy can reach up to 65.3% on a test set, which indicates a great potential for practical use.
Lipid-Conjugated Oligonucleotides via “Click Chemistry” Efficiently Inhibit Hepatitis C Virus Translation (2008)

Conjugation of a lipid moiety via "click chemistry" potentiates the cellular uptake of oligonucleotides and allows their intracellular delivery. These nontoxic lipid conjugates efficiently inhibit hepatitis C virus internal ribosome entry site (IRES)-mediated translation in human hepatic Huh7 cells. The biological activity of the lipid-conjugated oligonucleotides is not affected by the presence of serum.
Endothelin antagonism in experimental hepatic fibrosis. Implications for endothelin in the pathogenesis of wound healing. (1996)

The liver's response to chronic injury is fibrosis, which is analogous to wound healing in other organs. Hepatic wounding is characterized by the "activation" of resident stellate cells (lipocytes, Ito cells) to myofibroblast-like cells that produce increased amounts of smooth muscle alpha-actin and extracellular matrix. Stellate cells possess abundant endothelin (ET) receptors (ETA/B) and, therefore, are subject to the effects of ET-1 and 3. In this study, we investigated whether ETs contribute to the activation of stellate cells and consequently, fibrogenesis. In cultured stellate cells, ET-1 and sarafotoxin S6C (a potent ETB receptor agonist) stimulated stellate cell activation, as assessed by expression of smooth muscle alpha-actin. Furthermore, the mixed ETA/B receptor antagonist, bosentan, blocked this process. Next, we administered bosentan during the induction of liver injury in two mechanistically distinct forms of hepatic wounding. Bosentan reduced levels of type I collagen and cellular fibronectin mRNAs in whole-liver tissue extracts in both models. In freshly isolated stellate cells from injured livers, bosentan reduced expression of activation markers, including smooth muscle alpha-actin and extracellular matrix mRNAs. We further demonstrate that endothelin antagonism after establishment of fibrosing injury reduced stellate cell activation and matrix production. These data indicate that ET contributes to stellate cell activation and fibrogenesis. Because ET is upregulated in diverse forms of parenchymal injury, we speculate that ET may play an important role in the wound-healing response.
A blind frequency tracking algorithm for OFDM transmission over frequency selective channels (2005)

This paper presents a blind frequency offset estimation algorithm for OFDM systems. The blind algorithm is compared to two popular frequency offset estimation algorithms. The first is the cyclic prefix-based (CPB) algorithm, which is blind but does not perform well in frequency selective channels. The second is the the pilot tone-aided (PTA) algorithm, which performs well in frequency selective channels but requires pilot subcarriers. Unlike the CPB and PTA algorithms, the blind algorithm in this paper does not require any training symbols or pilot subcarriers, and performs well in frequency selective channels. By simulation, it is shown that the performance of the blind algorithm is better than that of the PTA algorithm with subcarriers comprised of 25% pilot subcarriers anti 75% of data subcarriers.
Molecular cytogenetic alterations associated with rapid tumor cell proliferation in advanced urinary bladder cancer (2001)

Invasive urinary bladder carcinomas are characterized by a high number of cytogenetic alterations which are thought to pinpoint the location of critical genes, some of which may be involved in cell cycle control. To identify genomic alterations that may affect such genes the proliferative activity (Ki67 labeling index) was assessed in 93 invasively growing bladder carcinomas analyzed by comparative genomic hybridization. Only a few changes were significantly associated with rapid tumor cell proliferation, including 3p+ (p=0.0357), 6p+ (p=0.003), 8q+ (p=0.0273), and 11q- (p=0.0329). Among these alterations 6p+ is of particular interest because high level 6p22 amplifications occur frequently in bladder cancer. The particular strong association between 6p+ and a high tumor cell proliferation being independent of grade and stage suggests that a putative oncogene on 6p22 involved in cell cycle regulation.
Fluorine-18-altanserin: a radioligand for the study of serotonin receptors with PET: radiolabeling and in vivo biologic behavior in rats. (1991)

No-carrier-added [18F]altanserin was synthesized by nucleophilic substitution of the corresponding nitro compound with [18F]fluoride in the presence of kryptofix 222 and K2CO3. After purification by preparative HPLC, [18F]altanserin was produced in less than 2 hr with a radiochemical yield of 10% (EOS) and a specific activity of 0.8-1.3 Ci/mumol. In rats, the tracer localized rapidly in the whole brain (0.5% ID/g organ) with a high binding to the frontal cortex. The frontal cortex/cerebellum ratio increased with time and reached a plateau of 11 at 2 hr postinjection. This uptake in S2 receptor regions was saturable and could be blocked by pretreatment with various S2 antagonists. This radiopharmaceutical appears to be more selective for S2 receptor sites than other ligands available today and allows the study of S2 receptors under in vivo conditions.