gebhart/patrepeval huggingface dataset:
Effects of the nematicide imicyafos on soil nematode community structure and damage to radish caused by Pratylenchus penetrans. (2011)

The effects of the non-fumigant nematicide imicyafos on soil nematode community structure and damage to radish caused by Pratylenchus penetrans were evaluated in two field experiments in consecutive years (2007 and 2008). Nematode densities in soil at 0 - 10 cm (the depth of nematicide incorporation) and 10 - 30 cm were measured. The application of imicyafos had a significant impact on the density of P. penetrans at 0 - 10 cm but had no effect on free-living nematode density. PCR-DGGE analysis conducted using extracted nematodes showed that the nematode community structure 12 d after application in 2007 was altered by the application of imicyafos at the 0 - 10 cm depth, but not at 10 - 30 cm. No significant differences were observed in the diversity of the nematode community at harvest (89 and 91 d after application) between the control and imicyafos treatments in both depths and both years. In both years, the damage to radish caused by P. penetrans was markedly suppressed by the nematicide. Overall, the nematicide imicyafos decreased populations of P. penetrans in soil and thereby decreased damage to radish, while having little impact on the soil nematode community.
Cell-to-substrate contacts in living fibroblasts: an interference reflexion study with an evaluation of the technique (1976)

The closeness of contact between cultured chick heart fibroblasts and glass substrates has been examined by interference reflexion microscopy. Evaluation of the optical technique demonstrated that both the film of medium between the cell and substrate and the cell itself act as two superimposed thin films which generate a complex interference pattern in reflected light or low illuminating numerical aperture (I.N.A.). The interference pattern generated by the cell consists of first and higher orders of interference and can be eliminated from the image by increasing the I.N.A. to greater than 1.0. The residual zero-order interference pattern at high I.N.A. originates from the thin film of medium between cell and substrate and corresponds to the closeness of contact between cell and substrate. Based on the zero-order interference pattern and a comparison of the same cells with differential interference optics, the following features were recognized in living chick heart fibroblasts. Focal contacts, 0.25-0.5 mum wide, 2-10 mum long, separated by 10-15 nm from the substrate, are located under the peripheral regions of the leading lamellae and near the edge of extended non-spreading regions of the cell margin in moving and stationary cells. Individual focal contacts are coincident with cytoplasmic fibres of the same dimensions as the contact or with the peripheral ends of longer fibres that extend from the focal contact toward the centre of the cell. In spreading cells a second type of contact is present under the peripheral regions of the leading lamellae. This close contact consists of a broad area of uniform cell-to-substrate separation distance (ca. 30 nm). Focal contacts are distributed within the close contact under the leading lamellae. Lamellipodia extend ahead of the close contact and are separated by 100 nm or more from the substrate. Depending on the previous motile history of the cell, the close contact extends to varying degrees under the centre of the cell but it is typically dissected here by discrete areas of distinctly greater cell-to-substrate separation (100-140 nm). Evidence for the adhesive nature of the focal contacts is considered. The common identity is discussed of the focal contacts and associated cytoplasmic fibres described here in living cells with the regions of closest apposition to the substrate and associated cytoplasmic plaques and bundles of microfilaments seen in EM studies.
Assembly of Functional U1 and U2 Human-Amphibian Hybrid snRNPs in Xenopus laevis oocytes (1988)

Oligonucleotides complementary to regions of U1 and U2 small nuclear RNAs (snRNAs), when injected into Xenopus laevis oocytes, rapidly induced the specific degradation of U1 and U2 snRNAs, respectively, and then themselves were degraded. After such treatment, splicing of simian virus 40 (SV40) late pre-mRNA transcribed from microinjected viral DNA was blocked in oocytes. If before introduction of SV40 DNA into oocytes HeLa cell U1 or U2 snRNAs were injected and allowed to assemble into small nuclear ribonucleoprotein particle (snRNP)-like complexes, SV40 late RNA was as efficiently spliced as in oocytes that did not receive U1 or U2 oligonucleotides. This demonstrates that oocytes can form fully functional hybrid U1 and U2 snRNPs consisting of human snRNA and amphibian proteins.
Targeting CD47 Enhances the Efficacy of Anti-PD-1 and CTLA-4 in an Esophageal Squamous Cell Cancer Preclinical Model (2017)

Esophageal squamous cell cancer is a highly aggressive cancer with a dismal 5-year survival rate. CD47 is a cell transmembrane protein that is involved in cell apoptosis, proliferation, adhesion, migration, and antigen presentation in the immune system. By interacting with signal regulatory protein-α expressed in antigen-presenting cells (APCs), CD47 acts as an antiphagocytic mechanism to inhibit APC-dependent antigen presentation. Overexpression of CD47 was found in various types of cancer. However, its role in esophageal squamous cell cancer is not yet clear. Anti-CD47 is an antagonist of CD47 signaling pathways by competing with its ligand. In the current study, we investigated the effects of anti-CD47 treatment on the antitumor immune response in an esophageal squamous cell cancer preclinical model. We found that anti-CD47 treatment enhanced proinflammatory responses and increased CD8+ T-cell infiltration in tumor tissue in the animal model. T cells in anti-CD47-treated tumors showed higher PD-1 and CTLA-4 expression, indicating T-cell activation and the rationale of combining anti-CD47 with anti-PD-1 and CLTA-4. The combinatory treatment showed the best antitumor response, implying a novel treatment strategy. The effects of anti-CD47 depended on dendritic cell function. In patient samples, expression of CD47 was negatively correlated with CD8+ T-cell infiltration in esophageal squamous cell cancer patients. Taken together, CD47 might be a novel target to enhance anti-PD-1 and CLTA-4 efficacy in esophageal squamous cell cancer.
All-normal-dispersion femtosecond fiber laser with pulse energy above 20nJ (2007)

We report a study of the scaling and limits to pulse energy in an all-normal-dispersion femtosecond fiber laser. Theoretical calculations show that operation at large normal cavity dispersion is possible in the presence of large nonlinear phase shifts, owing to strong pulse shaping by spectral filtering of the chirped pulse in the laser. Stable pulses are possible with energies of tens of nanojoules. Experimental results from Yb-doped fiber lasers agree with the trends of numerical simulations. Stable and self-starting pulses are generated with energies above 20 nJ, and these can be dechirped to <200 fs duration. Femtosecond pulses with peak powers near 100 kW are thus available from this simple and practical design.
Oligomerization of Monoolefins by Homogeneous Catalysts (2009)

In this article are summarized the different mechanistic pathways for the oligomerization of monoolefins by homogeneous catalysts, particularly for ethylene and alpha olefins. The major topics are: the production of non regioselective and also regioselective olefin dimers, the production of linear alpha olefins by ethylene oligomerization as well as the selective dimerization of ethylene and its selective trimerization. Several industrial developments initiated by IFP are presented to illustrate this topic.
Learning Depth from Single Monocular Images Using Deep Convolutional Neural Fields (2015)

In this article, we tackle the problem of depth estimation from single monocular images. Compared with depth estimation using multiple images such as stereo depth perception, depth from monocular images is much more challenging. Prior work typically focuses on exploiting geometric priors or additional sources of information, most using hand-crafted features. Recently, there is mounting evidence that features from deep convolutional neural networks (CNN) set new records for various vision applications. On the other hand, considering the continuous characteristic of the depth values, depth estimation can be naturally formulated as a continuous conditional random field (CRF) learning problem. Therefore, here we present a deep convolutional neural field model for estimating depths from single monocular images, aiming to jointly explore the capacity of deep CNN and continuous CRF. In particular, we propose a deep structured learning scheme which learns the unary and pairwise potentials of continuous CRF in a unified deep CNN framework. We then further propose an equally effective model based on fully convolutional networks and a novel superpixel pooling method, which is about 10 times faster, to speedup the patch-wise convolutions in the deep model. With this more efficient model, we are able to design deeper networks to pursue better performance. Our proposed method can be used for depth estimation of general scenes with no geometric priors nor any extra information injected. In our case, the integral of the partition function can be calculated in a closed form such that we can exactly solve the log-likelihood maximization. Moreover, solving the inference problem for predicting depths of a test image is highly efficient as closed-form solutions exist. Experiments on both indoor and outdoor scene datasets demonstrate that the proposed method outperforms state-of-the-art depth estimation approaches.
Outcome of positive antinuclear antibodies in individuals without connective tissue disease. (2003)

Patients tended to remain ANA positive on repeat testing. Three out of 53 patients had developed CTD, reflecting the more sensitive but less specific nature of ANA testing. Another common condition associated with ANA positivity was hypothyroidism. Continued longterm followup with larger cohorts is needed.
AN EMPIRICAL STUDY ON OPERATIONAL DETERMINANTS OF CUSTOMERSATISFACTION IN CALL CENTERS (2008)

As more and more companies focus on CRM (customer
					relationship management), call centers which are at the forefront
					of the customer-company relationship, are being used as a core
					channel for CRM activities. A call center can be understood as
					either a strategic customer marketing center which provides
					solutions for customer needs as well as answers questions about the
					products and services, or customer communication center that plays
					key roles in executing CRM strategies. With the development of
					information and communication technology, the traditional call
					center is recently evolving into an intelligent IP contact center,
					where customer contact and information exchange is enabled by
					concurrently using diverse media such as telephone, Web, e-mail,
					chat, voice over IP, and ultimately video conversation. Because
					call centers handle over 70% of all customer-company interactions
					in many companies, customer satisfaction with call center service
					is crucial for the success of a company. Consequently, companies
					should periodically assess how customers feel about the quality of
					service of their call center and should reflect the information on
					the call center operations. In order to provide high quality of
					service and achieve customer satisfaction, call center is being
					managed and monitored through a number of key performance
					indicators (KPIs). The problem here is that these KPIs are not
					based on the theoretical examination and empirical evidence. Thus,
					there is a need to identify what KPIs are really associated with
					customer satisfaction in call centers. The purpose of this study is
					to investigate the operational determinants affecting customer
					satisfaction in the call centers. For this purpose, we have
					extracted from the literature 10 key performance indicators:
					average speed of answer, average time in queue, percentage of calls
					closed on first contact, average abandonment rate, average talk
					time, adherence to schedule, average after call work time,
					percentage of calls blocked, employment turnover rate and service
					level. From the statistical analysis performed we could confirm
					that the percentage of calls blocked, average speed of answer and
					service level are the critical factors of determining customer
					satisfaction. It is expected that the results of this study can
					help call center managers to improve their call center operations.
The CXCL8-CXCR1/2 pathways in cancer (2016)

Persistent infection or chronic inflammation contributes significantly to tumourigenesis and tumour progression. C-X-C motif ligand 8 (CXCL8) is a chemokine that acts as an important multifunctional cytokine to modulate tumour proliferation, invasion and migration in an autocrine or paracrine manner. Studies have suggested that CXCL8 and its cognate receptors, C-X-C chemokine receptor 1 (CXCR1) and C-X-C chemokine receptor 2 (CXCR2), mediate the initiation and development of various cancers including breast cancer, prostate cancer, lung cancer, colorectal carcinoma and melanoma. CXCL8 also integrates with multiple intracellular signalling pathways to produce coordinated effects. Neovascularisation, which provides a basis for fostering tumour growth and metastasis, is now recognised as a critical function of CXCL8 in the tumour microenvironment. In this review, we summarize the biological functions and clinical significance of the CXCL8 signalling axis in cancer. We also propose that CXCL8 may be a potential therapeutic target for cancer treatment.
A study on using data clustering for feature extraction to improve the quality of classification (2021)

Abstract There is a certain belief among data science researchers and enthusiasts alike that clustering can be used to improve classification quality. Insofar as this belief is fairly uncontroversial, it is also very general and therefore produces a lot of confusion around the subject. There are many ways of using clustering in classification and it obviously cannot always improve the quality of predictions, so a question arises, in which scenarios exactly does it help? Since we were unable to find a rigorous study addressing this question, in this paper, we try to shed some light on the concept of using clustering for classification. To do so, we first put forward a framework for incorporating clustering as a method of feature extraction for classification. The framework is generic w.r.t. similarity measures, clustering algorithms, classifiers, and datasets and serves as a platform to answer ten essential questions regarding the studied subject. Each answer is formulated based on a separate experiment on 16 publicly available datasets, followed by an appropriate statistical analysis. After performing the experiments and analyzing the results separately, we discuss them from a global perspective and form general conclusions regarding using clustering as feature extraction for classification.
Restoration of Microvascular Function in the Infarct-Related Artery by Intracoronary Transplantation of Bone Marrow Progenitor Cells in Patients With Acute Myocardial Infarction (2007)

Intracoronary BMC therapy after acute myocardial infarction restores microvascular function of the infarct-related artery, which is associated with a significant improvement in maximal vascular conductance capacity. These data provide clinical proof of concept that progenitor cell transplantation promotes vascular repair.
Tolerance and efficacy of autologous or donor-derived T cells expressing CD19 chimeric antigen receptors in adult B-ALL with extramedullary leukemia (2015)

The engineering of T lymphocytes to express chimeric antigen receptors (CARs) aims to establish T cell-mediated tumor immunity rapidly. In this study, we conducted a pilot clinical trial of autologous or donor- derived T cells genetically modified to express a CAR targeting the B-cell antigen CD19 harboring 4-1BB and the CD3ζ moiety. All enrolled patients had relapsed or chemotherapy-refractory B-cell lineage acute lymphocytic leukemia (B-ALL). Of the nine patients, six had definite extramedullary involvement, and the rate of overall survival at 18 weeks was 56%. One of the two patients who received conditioning chemotherapy achieved a three-month durable complete response with partial regression of extramedullary lesions. Four of seven patients who did not receive conditioning chemotherapy achieved dramatic regression or a mixed response in the haematopoietic system and extramedullary tissues for two to nine months. Grade 2-3 graft-versus-host disease (GVHD) was observed in two patients who received substantial donor-derived anti-CD19 CART (chimeric antigen receptor-modified T) cells 3-4 weeks after cell infusions. These results show for the first time that donor-derived anti-CD19 CART cells can cause GVHD and regression of extramedullary B-ALL. This study is registered at www.clinicaltrials.gov as NCT01864889.
Factor VII deficiency and the FVII mutation database (2000)

Factor VII (FVII) is a zymogen for a vitamin K-dependent serine protease essential for the initiation of blood coagulation. It is synthesized primarily in the liver and circulates in plasma at a concentration of approximately 0.5 microg/ml (10 nmol/L). The FVII gene (F7) is located on chromosome 13 (13q34), consists of 9 exons, and spans approximately 12kb. It encodes a mature protein of 406 amino acids, which has an N-terminal domain (Gla) post-translationally modified by gamma-carboxylation of glutamic acid residues, two domains with homology to epidermal growth factor (EGF1 and 2), and a C-terminal serine protease domain. The single chain zymogen is activated by proteolytic cleavage at Arg152-Ile153. There are 238 individuals described in the world literature with mutations in their F7 genes (FVII mutation database; europium.csc. mrc.ac.uk). Complete absence of FVII activity in plasma is usually incompatible with life, and individuals die shortly after birth due to severe hemorrhage. The majority of individuals with mutations in their F7 gene(s), however, are either asymptomatic or the clinical phenotype is unknown. In general, a severe bleeding phenotype is only observed in individuals homozygous for a mutation in their F7 genes with FVII activities (FVII:C) below 2% of normal, however, a considerable proportion of individuals with a mild-moderate bleeding phenotype have similar FVII:C by in vitro assay. The failure of in vitro tests to differentiate between these groups may be due to lack of sensitivity in the assays to the very low amounts of FVII:C, which are sufficient to initiate coagulation in vivo. A number of polymorphisms have been identified in the F7 gene and some have been shown to influence plasma FVII antigen levels.
Extracellular polysaccharide production by Klebsiella pneumoniae and its relationship to virulence (1985)

Klebsiella pneumoniae serotype 1 and serotype 2 and their capsular variants were examined for production of cell-associated capsular polysaccharides and extracellular capsular polysaccharides. The virulence of these organisms in experimental animals was examined via intraperitoneal injection in mice and transtracheal inoculation into the lungs of rats. It was found that the production of either polysaccharide component correlated with the observed virulence. The extracellular polysaccharides were purified by ethanol precipitation, electrodialysis, extraction with quaternary ammonium salts, and gel filtration. These purification steps allowed for the separation and purification of both the extracellular lipopolysaccharide and the extracellular capsular polysaccharide. Purified extracellular capsular polysaccharide and extracellular lipopolysaccharide were co-injected with K. pneumoniae intraperitoneally into mice to determine if either of these substances would produce an effect on the natural course of infection in these animals. These studies showed that only purified extracellular lipopolysaccharide enhanced the virulence of K. pneumoniae when co-injected into mice, and this virulence enhancement correlated with the content of extracellular lipopolysaccharide, but not extracellular capsular polysaccharide in mixtures of these polysaccharides. Saponification of K. pneumoniae serotype 1 extracellular polysaccharides significantly decreased their virulence-enhancing capabilities in mice, further suggesting that extracellular lipopolysaccharide may play a role in these infections.
IL-22 Is Expressed by Th17 Cells in an IL-23-Dependent Fashion, but Not Required for the Development of Autoimmune Encephalomyelitis (2007)

Lately, IL-17-secreting Th cells have received an overwhelming amount of attention and are now widely held to be the major pathogenic population in autoimmune diseases. In particular, IL-22-secreting Th17 cells were shown to specifically mark the highly pathogenic population of self-reactive T cells in experimental autoimmune encephalomyelitis (EAE). As IL-17A itself was found to only play a minor role during the development of EAE, IL-22 is now postulated to contribute to the pathogenic function of Th17 cells. The goal of this study was to determine the role and function of IL-22 during the development of CNS autoimmunity in vivo. We found that CNS-invading encephalitogenic Th17 cells coexpress IL-22 and that IL-22 is specifically induced by IL-23 in autoimmune-pathogenic CD4+ T cells in a time- and dose-dependent manner. We next generated IL-22-/- mice, which--in contrast to the prediction that expression of inflammatory cytokines by CNS-invading T cells inevitably confers pathogenic function--turned out to be fully susceptible to EAE. Taken together, we show that self-reactive Th cells coexpress IL-17 and IL-22, but that the latter also does not appear to be directly involved in autoimmune pathogenesis of the CNS.
Solution NMR Structure of the NlpC/P60 Domain of Lipoprotein Spr from Escherichia coli: Structural Evidence for a Novel Cysteine Peptidase Catalytic Triad (2008)

Escherichia coli Spr is a membrane-anchored cell wall hydrolase. The solution NMR structure of the C-terminal NlpC/P60 domain of E. coli Spr described here reveals that the protein adopts a papain-like alpha+beta fold and identifies a substrate-binding cleft featuring several highly conserved residues. The active site features a novel Cys-His-His catalytic triad that appears to be a unique structural signature of this cysteine peptidase family. Moreover, the relative orientation of these catalytic residues is similar to that observed in the analogous Ser-His-His triad, a variant of the classic Ser-His-Asp charge relay system, suggesting the convergent evolution of a catalytic mechanism in quite distinct peptidase families.
Recommendations for Improved Standardization of Immunohistochemistry (2007)

Immunohistochemistry (IHC) continues to suffer from variable consistency, poor reproducibility, quality assurance disparities, and the lack of standardization resulting in poor concordance, validation, and verification. This document lists the recommendations made by the Ad-Hoc Committee on Immunohistochemistry Standardization to address these deficiencies. Contributing factors were established to be underfixation and irregular fixation, use of nonformalin fixatives and ancillary fixation procedures divested from a deep and full understanding of the IHC assay parameters, minimal or absent IHC assay optimization and validation procedures, and lack of a standard system of interpretation and reporting. Definitions and detailed guidelines pertaining to these areas are provided.