gebhart/patrepeval huggingface dataset:
Induction of HLA Class I-Restricted CD8+ CTLs Specific for the Major Outer Membrane Protein of Chlamydia trachomatis in Human Genital Tract Infections (1999)

HLA class I-restricted CD8+ CTLs specific for the major outer membrane protein (MOMP) of Chlamydia trachomatis are present in the peripheral blood of humans who acquired genital tract infections with the organism. Three HLA-A2-restricted epitopes and two HLA-B51-restricted epitopes were identified in serovar E-MOMP. One of the five epitopes spans a variable segment of MOMP and is likely a serovar E-specific epitope. The other four epitopes are localized in constant segments and are C. trachomatis species specific. CTL populations specific for one or more of the four constant segment epitopes were isolated from all 10 infected subjects tested, regardless of infecting serovars, but from only one of seven uninfected subjects tested. The CTLs failed to recognize corresponding peptides derived from Chlamydia pneumoniae MOMP, further suggesting that they indeed resulted from genital tract infections with C. trachomatis. Significantly, ME180 human cervical epithelial cells productively infected with C. trachomatis were killed by the MOMP peptide-specific CTLs. Further investigations of the ability of such CTLs to lyse normal infected epithelial cells and their presence at inflamed sites in the genital tract will help understand the protective or pathological role of CTLs in chlamydial infections. The MOMP CTL epitopes may be explored as potential components of a subunit vaccine against sexually transmitted diseases caused by C. trachomatis. Moreover, the knowledge provided here will facilitate studies of HLA class I pathways of chlamydial Ag processing and presentation in physiologically relevant human APCs.
Automated Geometric Theorem Proving: Wu's Method (2006)

Wu’s Method for proving geometric theorems is well known. We investigate the underlying algorithms involved, including the concepts of pseudodivision, Ritt’s Principle and Ritt’s Decomposition algorithm. A simple implementation for these algorithms in Maple is presented, which we then use to prove a few simple geometric theorems to illustrate the method.
Functional specificity of Candida albicans Als3p proteins and clade specificity of ALS3 alleles discriminated by the number of copies of the tandem repeat sequence in the central domain (2005)

Candida albicans strain SC5314 contains two ALS3 alleles, which differ in sequence with respect to the number of copies of the 108 bp tandem repeat sequence within the central domain of the coding region. One allele (ALS3(12)) has 12 tandem repeat copies while the other (ALS3(9)) has 9 copies. Wild-type C. albicans (ALS3(12)/ALS3(9)) and those containing various ALS3 alleles (ALS3(12)/als3Delta(9), als3Delta(12)/ALS3(9) and als3Delta(12)/als3Delta(9)) were assayed for adhesion to monolayers of cultured vascular endothelial and pharyngeal epithelial cells. These assays showed obvious adhesive function for the larger Als3p protein, compared to a minor contribution to adhesion from the smaller protein. These functional differences in strain SC5314 prompted examination of ALS3 allelic diversity across the five major genetic clades of C. albicans. This analysis focused on the number of copies of the tandem repeat sequence within the central domain of the coding region and showed a range of alleles encoding from 6 to 19 tandem repeat copies. Clades differed with respect to prevalent ALS3 alleles and allele distribution, but were similar for the mean number of tandem repeat copies per ALS3 allele. Analysis of allelic pairing showed clade differences and the tendency for C. albicans strains to encode one longer and one shorter ALS3 allele. The allelic variability observed for ALS3 and its functional consequences observed in strain SC5314 highlight the importance of understanding ALS allelic diversity in order to draw accurate conclusions about Als protein function.
Present and potential future use of gene therapy for the treatment of non-insulin dependent diabetes mellitus (Review). (1999)

This review describes the latest approaches towards using gene therapy as a treatment for non-insulin dependent diabetes mellitus (NIDDM; Type 2 diabetes). We examine attempts to directly deliver the insulin gene to non-beta-cells, to improve insulin secretion from existing beta-cells and to develop ex vivo approaches to implanting genetically modified cells. Future research into the pathology of non-insulin dependent diabetes, combined with the latest developments in gene delivery systems, may potentially make gene therapy an attractive alternative NIDDM treatment in the future.
Efficacy of sirolimus (rapamycin) administered concomitantly with a subtherapeutic dose of cyclosporin in the treatment of severe psoriasis: a randomized controlled trial (2001)

The concomitant administration of sirolimus with a subtherapeutic dose of cyclosporin in severe psoriasis may permit a reduction in their respective toxicities, notably cyclosporin-induced nephrotoxicity.
Somatic cell nuclear transfer in pigs: recent achievements and future possibilities (2007)

During the past 6 years, considerable advancement has been achieved in experimental embryology of pigs. This process was mainly generated by the rapidly increasing need for transgenic pigs for biomedical research purposes, both for future xenotransplantation to replace damaged human organs or tissues, and for creating authentic animal models for human diseases to study aetiology, pathogenesis and possible therapy. Theoretically, among various possibilities, an established somatic cell nuclear transfer system with genetically engineered donor cells seems to be an efficient and reliable approach to achieve this goal. However, as the result of unfortunate coincidence of known and unknown factors, porcine embryology had been a handicapped branch of reproductive research in domestic animals and a very intensive and focused research was required to eliminate or minimise this handicap. This review summarises recent achievements both in the background technologies (maturation, activation, embryo culture) and the actual performance of the nuclear replacement. Recent simplified methods for in vivo development after embryo transfer are also discussed. Finally, several fields of potential application for human medical purposes are discussed. The authors conclude that although in this early phase of research no direct evidence can be provided about the practical use of transgenic pigs produced by somatic cell nuclear transfer as organ donors or disease models, the future chances even in medium term are good, and at least proportional with the efforts and sums that are invested into this research area worldwide.
One-sided polymerase chain reaction: the amplification of cDNA. (1989)

We report a rapid technique, based on the polymerase chain reaction (PCR), for the direct targeting, enhancement, and sequencing of previously uncharacterized cDNAs. This method is not limited to previously sequenced transcripts, since it requires only two adjacent or partially overlapping specific primers from only one side of the region to be amplified. These primers can be located anywhere within the message. The specific primers are used in conjunction with nonspecific primers targeted either to the poly(A)+ region of the message or to an enzymatically synthesized d(A) tail. Pairwise combinations of specific and general primers allow for the amplification of regions both 3' and 5' to the point of entry into the message. The amplified PCR products can be cloned, sequenced directly by genomic sequencing, or labeled for sequencing by amplifying with a radioactive primer. We illustrate the power of this approach by deriving the cDNA sequences for the skeletal muscle alpha-tropomyosins of European common frog (Rana temporaria) and zebrafish (Brachydanio rerio) using only 300 ng of a total poly(A)+ preparation. In these examples, we gained initial entry into the tropomyosin messages by using heterologous primers (to conserved regions) derived from the rat skeletal muscle alpha-tropomyosin sequence. The frog and zebrafish sequences are used in an analysis of tropomyosin evolution across the vertebrate phylogenetic spectrum. The results underscore the conservative nature of the tropomyosin molecule and support the notion of a constrained heptapeptide unit as the fundamental structural motif of tropomyosin.
Drug recognition of DNA. Proposal for GC minor groove specific ligands: vinylexins. (1988)

International audience
Stacked Attention Networks for Image Question Answering (2015)

This paper presents stacked attention networks (SANs) that learn to answer natural language questions from images. SANs use semantic representation of a question as query to search for the regions in an image that are related to the answer. We argue that image question answering (QA) often requires multiple steps of reasoning. Thus, we develop a multiple-layer SAN in which we query an image multiple times to infer the answer progressively. Experiments conducted on four image QA data sets demonstrate that the proposed SANs significantly outperform previous state-of-the-art approaches. The visualization of the attention layers illustrates the progress that the SAN locates the relevant visual clues that lead to the answer of the question layer-by-layer.
Track edge fluctuations (1990)

Track edge fluctuations on recording media affect signal-to-noise ratio and servo control, and can provide clues to the medium’s magnetic microstructure. We write track edges on longitudinal thin-film magnetic recording media by dc erasing the medium and writing a saturated dc track of opposite magnetization direction on the erased band. We then ‘‘read’’ the position fluctuations of the x-component reversal of one edge of the written track by centering a head on that edge, and by stepping the head across the edge. Since a straight track edge would not produce any flux change in the read head coil, the voltage output of the head arises from flux changes due to track edge fluctuations. The spectrum of the fluctuations can be deduced by decorrelating the read head sensitivity function from the voltage spectrum. We have used this procedure with several low- and high-noise thin-film media and we find in each case a k−b spectrum (k=wave number) with b near 1. We propose a model which interprets the fluctuations as a superposition of uncorrelated protuberances from a nominal straight edge, and we deduce the size distribution of the protuberances which will generate the observed fluctuation spectrum. Simulated reconstruction of the track edge resulting from a weighted superposition of the protuberances permits semiquantitative inferences to be drawn from the model about the medium microstructure.
Patched1 Regulates Hedgehog Signaling at the Primary Cilium (2007)

Primary cilia are essential for transduction of the Hedgehog (Hh) signal in mammals. We investigated the role of primary cilia in regulation of Patched1 (Ptc1), the receptor for Sonic Hedgehog (Shh). Ptc1 localized to cilia and inhibited Smoothened (Smo) by preventing its accumulation within cilia. When Shh bound to Ptc1, Ptc1 left the cilia, leading to accumulation of Smo and activation of signaling. Thus, primary cilia sense Shh and transduce signals that play critical roles in development, carcinogenesis, and stem cell function.
Isolation and characterization of recombinant lambda gt11 bacteriophages expressing eight different mycobacterial antigens of potential immunological relevance (1988)

A genomic lambda gt11 DNA library of Mycobacterium tuberculosis was screened for expression of mycobacterial protein antigens with murine monoclonal antibodies. The reactivity patterns of the monoclonal antibodies ranged from those showing a limited interspecies reactivity to antibodies widely cross-reactive among different mycobacterial species. Twelve recombinant bacteriophages were isolated, containing eight mycobacterial genes (paa, pab, pac, pad, paeA, paeB, pafA, and pafB) encoding protein antigens. Physical maps of the phages were generated and the products of the recombinant genes were analyzed by immunoblotting techniques. PaeA and PaeB are distinct proteins but were shown to share an epitope. A similar condition was observed between PafA and PafB. Among the phages isolated, two groups expressed epitopes specific for M. tuberculosis and Mycobacterium bovis BCG. One group of phages produced an antigenic determinant which is found in M. tuberculosis and Mycobacterium marinum but not in M. bovis BCG.
Photocatalytic Activity of Structured Mesoporous TiO2 Materials (2006)

Starting from colloidal TiO2 nanoparticles in combination with tetraethyl orthosilicate using neutral Pluronic or cationic cetyltrimethylammonium as templates, a series of structured mesoporous silicas has been obtained. The structure of the mesoporous titania was confirmed by isothermal gas adsorption, transmission electron microscopy, and X-ray diffraction. The pore diameter ranged between 3.8 and 10.9 nm, and the BET surface area varied from 99 to 584 m2 g(-1). The photocatalytic activity of these samples for the degradation of phenol in aqueous solution has been compared with that of standard P-25 TiO2. Even though the activity of these new mesostructured materials is lower that those found for P-25 TiO2, the turnover frequency of the photocatalytic activity (moles of phenol degraded per Ti atom present at initial reaction time) is much higher for the mesoporous titania, particularly with low titanium contents for those materials (mpTiO2-5 and TiO2SBA15-5).
MET Gene Amplification and MET Receptor Activation Are Not Sufficient to Predict Efficacy of Combined MET and EGFR Inhibitors in EGFR TKI-Resistant NSCLC Cells (2015)

Epidermal growth factor receptor (EGFR), member of the human epidermal growth factor receptor (HER) family, plays a critical role in regulating multiple cellular processes including proliferation, differentiation, cell migration and cell survival. Deregulation of the EGFR signaling has been found to be associated with the development of a variety of human malignancies including lung, breast, and ovarian cancers, making inhibition of EGFR the most promising molecular targeted therapy developed in the past decade against cancer. Human non small cell lung cancers (NSCLC) with activating mutations in the EGFR gene frequently experience significant tumor regression when treated with EGFR tyrosine kinase inhibitors (TKIs), although acquired resistance invariably develops. Resistance to TKI treatments has been associated to secondary mutations in the EGFR gene or to activation of additional bypass signaling pathways including the ones mediated by receptor tyrosine kinases, Fas receptor and NF-kB. In more than 30-40% of cases, however, the mechanisms underpinning drug-resistance are still unknown. The establishment of cellular and mouse models can facilitate the unveiling of mechanisms leading to drug-resistance and the development or validation of novel therapeutic strategies aimed at overcoming resistance and enhancing outcomes in NSCLC patients. Here we describe the establishment and characterization of EGFR TKI-resistant NSCLC cell lines and a pilot study on the effects of a combined MET and EGFR inhibitors treatment. The characterization of the erlotinib-resistant cell lines confirmed the association of EGFR TKI resistance with loss of EGFR gene amplification and/or AXL overexpression and/or MET gene amplification and MET receptor activation. These cellular models can be instrumental to further investigate the signaling pathways associated to EGFR TKI-resistance. Finally the drugs combination pilot study shows that MET gene amplification and MET receptor activation are not sufficient to predict a positive response of NSCLC cells to a cocktail of MET and EGFR inhibitors and highlights the importance of identifying more reliable biomarkers to predict the efficacy of treatments in NSCLC patients resistant to EGFR TKI.
Heterogeneity of Human Skin Mast Cells and Human Basophils (1996)

Skin mast cells and basophilic leukocytes are known as key elements of acute and subacute IgE-mediated immune responses of the skin. The present paper investigated pharmacological aspects of signal transduction pathways of both cell types using activators and inhibitors of protein kinase C (PKC). The nonselective inhibitor K252a suppressed Fc epsilon RI-mediated histamine release from basophils and skin mast cells dose-dependently with IC50 values of 0.01 and 0.28 mumol/l. However, preincubation of both cell populations with kinase inhibitors showing in vitro selectivity for PKC (Ro 31-7549, calphostin C, GF 109203X) revealed a distinct modulation of cell response: IgE-mediated mediator release was inhibited only in skin mast cells, whereas in experiments with basophils a concentration-dependent potentiation of exocytosis was observed. Further evidence for heterogenous biochemical signals following activation of both cell types derived from studies with the phorbol ester TPA. With respect to acute and late-phase IgE-mediated skin reactions, we suggest that distinct signal transduction mechanisms at the level of PKC (isozymes) in basophils and skin mast cells might reflect their functional heterogeneity.
Single-agent dose-finding cohort of a phase 1/2 study of lenvatinib (LEN) in children and adolescents with refractory or relapsed solid tumors. (2017)

10544 Background: LEN is an inhibitor of vascular endothelial growth factor (VEGF) receptors 1‒3, fibroblast growth factor receptors 1‒4, platelet-derived growth factor receptor α, RET, and KIT. LEN is approved in adults for radioiodine-refractory differentiated thyroid cancer (DTC) and in combination with everolimus in patients (pts) with advanced renal cell carcinoma. We show results from the single-agent LEN dose-finding part of a phase 1/2 study in children and adolescents with solid tumors. Methods: Pts had any relapsed or refractory solid tumor, evaluable or measurable disease, were aged 2 to ≤18 years, had &lt; 2 prior VEGF-targeted therapies, and adequate organ function. A starting dose of LEN 11 mg/m 2 was escalated with a time-to-event continual reassessment method. The primary endpoint was to determine the LEN recommended dose (RD). Secondary objectives included best overall response (BOR), objective response rate, safety, and pharmacokinetics (PK). Results: 23 pts enrolled (11 mg/m 2 : n = 5, 14 mg/m 2 : n = 11, 17 mg/m 2 : n = 7). The most common tumors were rhabdomyosarcoma (n = 5), Ewing sarcoma (n = 4), and neuroblastoma (n = 3). 3 Dose-limiting toxicities occurred in cycle 1 at 14 mg/m 2 (increased alanine aminotransferase: 1; hypertension: 2). All pts had any-grade treatment-emergent adverse events (TEAEs; grade 3/4: 65%). Most common any-grade TEAEs were vomiting (52%), abdominal pain (48%), decreased appetite (48%), diarrhea (44%), and hypothyroidism (44%). 1 Pt discontinued LEN due to a LEN-related TEAE (hypertension). BOR was stable disease (n = 10). Effect of age on oral clearance and central volume of distribution was not significant. Exposure was similar to that in adults. LEN 14 mg/m 2 /day was therefore identified as the RD. Updated cohort 1 data will be shown. Conclusions: The LEN RD in children and adolescents was similar to the adult dose and showed a reasonable safety profile. PK in these pts did not differ significantly from that in adults. The phase 1b dose-finding study of LEN in combination with chemotherapy in osteosarcoma (OS) and phase 2 LEN monotherapy (RD 14 mg/m 2 ) parts in DTC and OS are ongoing. Clinical trial information: NCT02432274.
Local Cooling: A Therapy for Intractable Neocortical Epilepsy (2003)

Therapy for many of the neocortical epilepsies remains unsatisfactory. Recent research has demonstrated that focal cooling, using thermoelectric (Peltier) devices, may be capable of terminating, or possibly even preventing, some types of seizures.
Technique for Enumeration of Heterotrophic and Phototrophic Nanoplankton, Using Epifluorescence Microscopy, and Comparison with Other Procedures (1983)

A new method is described that uses the fluorochrome primulin and epifluorescence microscopy for the enumeration of heterotrophic and phototrophic nanoplankton (2 to 20 mum). Phototrophic microorganisms are distinguished from heterotrophs by the red autofluorescence of chlorophyll a. Separate filter sets are used which allow visualization of the primulin-stained nanoplankton without masking chlorophyll a fluorescence, thus allowing easy recognition of phototrophic cells. Comparison with existing epifluorescence techniques for counting heterotrophic and phototrophic nanoplankton shows that primulin provides more accurate counts of these populations than the fluorescein isothiocyanate or proflavine techniques. Accuracy is comparable to that with the acridine orange technique, but this method requires only one filter preparation for the enumeration of both phototrophic and heterotrophic populations.
Monolithic silicon photonic crystal slab fiber tip sensor (2009)

We demonstrate that monolithic photonic crystals (PCs) confined to the facet, or tip, of single-mode optical fibers can be designed as highly sensitive refractive index point sensors. Monolithic photonic-crystal slabs are fabricated on silicon wafers and subsequently released and micro-assembled on the tip of optical fibers. The PC slab's reflection spectrum is modulated by the refractive index of the environment and shows sensitivity comparable to fiber Bragg gratings (FBGs). The compact sensing element is located at the tip of a fiber and hence is a highly localized sensor. The sensor is made of robust, high-temperature dielectric materials and therefore has the potential to be used for many applications including measurements in harsh environments.
Fabrication of self-supporting porous silicon membranes and tuning transport properties by surface functionalization (2010)

This study presents a simple approach to perform selective mass transport through freestanding porous silicon (pSi) membranes. pSi membranes were fabricated by the electrochemical etching of silicon to produce membranes with controlled structure and pore sizes close to molecular dimensions (approximately 12 nm in diameter). While these membranes are capable of size-exclusion based separations, chemically specific filtration remains a great challenge especially in the biomedical field. Herein, we investigate the transport properties of chemically functionalized pSi membranes. The membranes were functionalized using silanes (heptadecafluoro-1,1,2,2-tetrahydrodecyl)dimethylchlorosilane (PFDS) and N-(triethoxysilylpropyl)-o-polyethylene oxide urethane (PEGS) to give membranes hydrophobic (PFDS) and hydrophilic (PEGS) properties. The transport of probe dyes tris(2,2'-bipyridyl)dichlororuthenium(ii) hexahydrate (Rubpy) and Rose Bengal (RB) through these functionalized membranes was examined to determine the effect surface functionalization has on the selectivity and separation ability of pSi membranes. This study provides the basis for further investigation into more sophisticated surface functionalization and coupled with the biocompatibility of pSi will lead to new advances in membrane based bio-separations.