gebhart/patrepeval huggingface dataset:
Molecular definition of the bovine granulocytopathy syndrome: Identification of deficiency of the Mac-1 (CD11b/CD18) glycoprotein (1990)

Leukocytosis (34,600 WBC/microliter of blood) was detected in an apparently healthy 7-day-old Holstein heifer. Analysis of blood samples obtained over the next 41 days revealed chronic progressive neutrophilia, which peaked at greater than 85% neutrophils and exceeded 100,000 WBC/microliter. In vitro assessment of isolated blood neutrophils obtained from the heifer at 38 and 45 days of age revealed selected functional abnormalities. Endocytosis of immunoglobulin-opsonized Staphylococcus aureus and killing of this test organism by the calf's neutrophils were significantly diminished, as were phagocytosis-associated superoxide generation, chemiluminescence activity, and myeloperoxidase-catalyzed iodination. Diminished H2O2 elaboration by the calf's neutrophils was evident during ingestion of opsonized zymosan or on exposure to phorbol myristate acetate. Extracellular release (secretion) of elastase during ingestion of zymosan was also diminished, although total cell content of elastase was normal, compared with that of neutrophils from age-matched calves, and granular or other morphologic abnormalities of the calf's neutrophils were not evident by ultrastructural examination. Abnormalities of random migration were inconsistently detected, and normal or high degree of antibody-dependent cytotoxicity or natural killing by the calf's neutrophils was observed. Similar in vitro assessment of neutrophils obtained from the calf's dam revealed no functional abnormalities. The calf died at 48 days of age, with persistent fever and chronic diarrhea, despite administration of antibiotics. Histologic examination at necropsy revealed large numbers of intravascular neutrophils in most tissues, including massive neutrophil sequestration in spleen. However, a striking lack of extravascular neutrophils was evident in inflamed submucosa adjacent to intestinal ulcers heavily contaminated with enteric microorganisms. Bone marrow examination revealed diffuse myeloid hyperplasia, but no other abnormalities.
The value of anti-Mullerian hormone measurement in the long GnRH agonist protocol: association with ovarian response and gonadotrophin-dose adjustments (2012)

The serum AMH concentration at the start of the stimulation in IVF patients down-regulated with GnRH agonist in the long protocol revealed a positive relationship with ovarian response to gonadotrophins in terms of oocytes retrieved and accompanying endocrine response. AMH is a good predictor of the need for gonadotrophin-dose adjustment on stimulation day 6 for patients with a fixed starting dose, but a poor predictor of embryo quality and pregnancy chances in individual patients.
A Naturally Occurring hPMS2 Mutation Can Confer a Dominant Negative Mutator Phenotype (1998)

Defects in mismatch repair (MMR) genes result in a mutator phenotype by inducing microsatellite instability (MI), a characteristic of hereditary nonpolyposis colorectal cancers (HNPCC) and a subset of sporadic colon tumors. Present models describing the mechanism by which germ line mutations in MMR genes predispose kindreds to HNPCC suggest a "two-hit" inactivation of both alleles of a particular MMR gene. Here we present experimental evidence that a nonsense mutation at codon 134 of the hPMS2 gene is sufficient to reduce MMR and induce MI in cells containing a wild-type hPMS2 allele. These results have significant implications for understanding the relationship between mutagenesis and carcinogenesis and the ability to generate mammalian cells with mutator phenotypes.
Targeting, Imaging, and Therapy Using a Humanized Antiprostate Stem Cell Antigen (PSCA) Antibody (2007)

The murine 1G8 (micro1G8) monoclonal antibody directed against prostate stem cell antigen (PSCA) prevents prostate tumor establishment, growth, and metastasis in murine models. To further delineate in vivo targeting properties, micro1G8 was radiolabeled with In-111 and evaluated in nude mice bearing PC3-PSCA xenografts. Tumor activity ranged from 11.8% to 17.1% injected dose per gram (ID/g) at 24 to 96 hours postinjection. To extend the clinical applicability of micro1G8, a chimeric 1G8 antibody was produced that exhibited specific binding to PSCA and significant antitumor effect over micro1G8 in established LAPC-9 prostate cancer xenografts (P=0.0014). However, low expression yields and instability prompted us to humanize 1G8 by grafting the complementary determining regions onto the stable, human Fv framework of anti-p185 4D5v8 (trastuzumab). Two humanized 1G8 (hu1G8) versions (A and B) that differed in the number of murine residues present in the C-terminal half of CDR-H2, were produced. Biacore binding studies demonstrated affinities of 1.47 nM for micro1G8 and 3.74 nM for hu2B3-B, representing a 2.5-fold reduction. Tumor targeting of version B radioiodinated with I was evaluated by serial microPET imaging. Specific tumor targeting of I-hu1G8-B to PC3-PSCA [12.7 (+/-1.6)% ID/g at 94 h] and LAPC-9 [6.6 (+/-0.9)% ID/g at 168 h) xenografts was observed. Inhibition of tumor growth by hu1G8-B was demonstrated in mice bearing low-expressing SW-780-PSCA bladder carcinoma xenografts. In this model, the micro1G8 was ineffective, whereas the hu1G8-B exhibited approximately 50% inhibitory effect. These data support further development of hu1G8 anti-PSCA antibody for targeted imaging and therapy for tumors of urogenital origin.
Generation of human induced pluripotent stem cells from dermal fibroblasts (2008)

The generation of patient-specific pluripotent stem cells has the potential to accelerate the implementation of stem cells for clinical treatment of degenerative diseases. Technologies including somatic cell nuclear transfer and cell fusion might generate such cells but are hindered by issues that might prevent them from being used clinically. Here, we describe methods to use dermal fibroblasts easily obtained from an individual human to generate human induced pluripotent stem (iPS) cells by ectopic expression of the defined transcription factors KLF4, OCT4, SOX2, and C-MYC. The resultant cell lines are morphologically indistinguishable from human embryonic stem cells (HESC) generated from the inner cell mass of a human preimplantation embryo. Consistent with these observations, human iPS cells share a nearly identical gene-expression profile with two established HESC lines. Importantly, DNA fingerprinting indicates that the human iPS cells were derived from the donor material and are not a result of contamination. Karyotypic analyses demonstrate that reprogramming of human cells by defined factors does not induce, or require, chromosomal abnormalities. Finally, we provide evidence that human iPS cells can be induced to differentiate along lineages representative of the three embryonic germ layers indicating the pluripotency of these cells. Our findings are an important step toward manipulating somatic human cells to generate an unlimited supply of patient-specific pluripotent stem cells. In the future, the use of defined factors to change cell fate may be the key to routine nuclear reprogramming of human somatic cells.
Neural Mechanism of Atrial Fibrillation: Insight from Global High Density Frequency Mapping (2011)

The findings indicate that the AF was caused by an interaction between the PV ostial GPs during intrinsic autonomic stimulation, whereas the non-GP LA sites were responsible for the AF induced by an extrinsic neural input.
Intra-articular clodronate for the treatment of knee osteoarthritis: dose ranging study vs hyaluronic acid (2009)

This study indicates that IA clodronate provides symptomatic and functional improvements at least as good as those obtained with HA. Trial Registration. Osservatorio Nazionale sulla Sperimentazione Clinica dei Medicinali - Agenzia Italiana del Farmaco. Comitato Etico Azienda Ospedaliera Universitaria Senese number CLIO 22/02 http://oss-sper-clin.agenziafarmaco.it.
Discriminative Ferns Ensemble for Hand Pose Recognition (2014)

We present the Discriminative Ferns Ensemble (DFE) classifier for efficient visual object recognition. The classifier architecture is designed to optimize both classification speed and accuracy when a large training set is available. Speed is obtained using simple binary features and direct indexing into a set of tables, and accuracy by using a large capacity model and careful discriminative optimization. The proposed framework is applied to the problem of hand pose recognition in depth and infra-red images, using a very large training set. Both the accuracy and the classification time obtained are considerably superior to relevant competing methods, allowing one to reach accuracy targets with run times orders of magnitude faster than the competition. We show empirically that using DFE, we can significantly reduce classification time by increasing training sample size for a fixed target accuracy. Finally a DFE result is shown for the MNIST dataset, showing the method's merit extends beyond depth images.
Cell-permeable bicyclic peptidyl inhibitors against T-cell protein tyrosine phosphatase from a combinatorial library (2017)

Protein tyrosine phosphatases (PTPs) have been challenging targets for inhibitor design, because all PTPs share a highly conserved active site structure, which is positively charged and requires negatively charged moieties for tight binding. In this study, we developed cell-permeable bicyclic peptidyl inhibitors against T-cell PTP (TCPTP), which feature a cell-penetrating motif in one ring and a target-binding sequence in the second ring.
Quantum Two-Level Systems in Josephson Junctions as Naturally Formed Qubits (2006)

The two-level systems (TLSs) naturally occurring in Josephson junctions constitute a major obstacle for the operation of superconducting phase qubits. Since these TLSs can possess remarkably long decoherence times, we show that such TLSs can themselves be used as qubits, allowing for a well controlled initialization, universal sets of quantum gates, and readout. Thus, a single current-biased Josephson junction can be considered as a multiqubit register. It can be coupled to other junctions to allow the application of quantum gates to an arbitrary pair of qubits in the system. Our results indicate an alternative way to realize superconducting quantum information processing.
Visualizing attack graphs, reachability, and trust relationships with NAVIGATOR (2010)

A new tool named NAVIGATOR (Network Asset VIsualization: Graphs, ATtacks, Operational Recommendations) adds significant capabilities to earlier work in attack graph visualization. Using NAVIGATOR, users can visualize the effect of server-side, client-side, credential-based, and trust-based attacks. By varying the attacker model, NAVIGATOR can show the current state of the network as well as hypothetical future situations, allowing for advance planning. Furthermore, NAVIGATOR explicitly shows network topology, infrastructure devices, and host-level data while still conveying situational awareness of the network as a whole. This tool is implemented in Java and uses an existing C++ engine for reachability and attack graph calculations.
Down-regulation of HP1Hsalpha expression is associated with the metastatic phenotype in breast cancer. (2000)

We previously identified a down-regulation in heterochromatin-associated protein 1 (HP1)Hsalpha expression in MDA-MB-231 breast carcinoma cells (highly invasive/metastatic) compared with MCF-7 cells (poorly invasive/nonmetastatic). In this study, we demonstrate that HP1Hsalpha, but not HP1Hsbeta or HP1Hsgamma, is down-regulated at the mRNA and protein levels in highly invasive/metastatic breast cancer cell lines. In agreement, little to no nuclear HP1Hsalpha staining was observed in these cell lines. In contrast, poorly invasive/nonmetastatic cell lines showed HP1Hsalpha localization to the nucleus and nuclear membrane. Transfection of MDA-MB-231 cells with a green fluorescent protein-HP1Hsalpha expression vector decreased their ability to invade a collagen IV/laminin/gelatin matrix compared with green fluorescent protein-transfected controls. Consistent with the cell culture studies, immunohistochemical analysis of HP1Hsalpha protein localization in distant metastatic tissues from breast cancer patients revealed a decrease in the staining intensity and percentage of cells expressing HP1Hsalpha in seven of nine distant metastatic lesions compared with normal mammary and primary tumors. These results demonstrate a role for HP1Hsalpha in breast cancer invasion and metastasis. Given the role of HP1 in transcriptional silencing in Drosophila, we propose a model in which HP1Hsalpha normally silences genes involved in breast cancer invasion and metastasis.
TIFA activates IκB kinase (IKK) by promoting oligomerization and ubiquitination of TRAF6 (2004)

TRAF6 (tumor necrosis factor receptor-associated factor 6) is a RING (really interesting new gene) domain ubiquitin (Ub) ligase that mediates the activation of protein kinases, such as transforming growth factor beta-activated kinase (TAK1) and IkappaB kinase (IKK), by catalyzing the formation of a unique polyubiquitin chain linked through Lys-63 of Ub. Here, we present evidence that TIFA (TRAF-interacting protein with a forkhead-associated domain, also known as T2BP) activates IKK by promoting the oligomerization and Ub ligase activity of TRAF6. We show that recombinant TIFA protein, but not TRAF6-binding-defective mutant, can activate IKK in crude cytosolic extracts. Furthermore, TIFA activates IKK in an in vitro reconstitution system consisting of purified proteins, including TRAF6, the TAK1 kinase complex, and Ub-conjugating enzyme complex Ubc13-Uev1A. Interestingly, a fraction of recombinant TIFA protein exists as high-molecular-weight oligomers, and only these oligomeric forms of TIFA can activate IKK. Importantly, TIFA induces the oligomerization and polyubiquitination of TRAF6, which leads to the activation of TAK1 and IKK through a proteasome-independent mechanism.
An improved murine model of asthma: selective airway inflammation, epithelial lesions and increased methacholine responsiveness following chronic exposure to aerosolised allergen (1998)

This experimental model replicates many of the features of human asthma and should facilitate studies of pathogenetic mechanisms and of potential therapeutic agents.
ChemInform Abstract: SYNTHESIS, PROPERTIES, AND BIOLOGICAL ACTIVITY OF SOME NUCLEOSIDE CYCLIC PHOSPHORAMIDATES (1984)

Abstract Die Reaktion der entsprechenden Nucleoside (I) oder (III) mit Phosphorylchlorid und anschließend mit ,N‐Methylethanolamin oder N,N′‐Dimethylethylendiamin führt zu den cyclischen Phosphoramidaten (II) bzw. (IV) der Nucleoside.
An Intimate Relationship between Thyroid Hormone and Skin: Regulation of Gene Expression (2013)

Skin is the largest organ of the human body and plays a key role in protecting the individual from external insults. The barrier function of the skin is performed primarily by the epidermis, a self-renewing stratified squamous epithelium composed of cells that undergo a well-characterized and finely tuned process of terminal differentiation. By binding to their receptors thyroid hormones (TH) regulate epidermal cell proliferation, differentiation, and homeostasis. Thyroid dysfunction has multiple classical manifestations at skin level. Several TH-responsive genes, as well as genes critical for TH metabolism and action, are expressed at epidermal level. The role of TH in skin is still controversial, although it is generally recognized that TH signaling is central for skin physiology and homeostasis. Here we review the data on the epidermis and its function in relation to TH metabolism and regulation of gene expression. An understanding of the cellular and molecular basis of TH action in epidermal cells may lead to the identification of putative therapeutical targets for treatment of skin disorders.
Statistical Approaches to Effectiveness Measurement and Outcome-Driven Re-Randomizations in the Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE) Studies (2003)

The design of the Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE) schizophrenia and Alzheimer's disease studies pose several statistical challenges, including issues related to performing multiple comparisons, defining effectiveness outcomes, and collecting and analyzing data from a design with multiple outcome-driven re-randomizations. We discuss the CATIE strategy for addressing many hypotheses within the context of one clinical trial while controlling the overall type I error rate. We provide motivation for the use of two effectiveness outcomes: time to all-cause discontinuation and composite endpoints that combine outcomes from multiple domains, such as efficacy, safety, cost-effectiveness, and quality of life. Methods for statistical analysis of an outcome-driven re-randomization trial are compared and evaluated. We describe analysis within each phase, analysis based on the first randomization or treatment algorithms, and repeated measures modeling. Finally, strategies are described for designing an electronic data collection system for trials with repeated outcome-driven re-randomizations.
From point cloud to surface: the modeling and visualization problem (2003)

In this paper we address all the problems and solutions of converting a measured point cloud into a realistic 3D polygonal model thatcan satisfy high modeling and visualization demands. Close range photogrammetry deals since many years with manual or automaticimage measurements. Now 3D scanners are also becoming a standard source for input data in many application areas, providing formillions of points. As a consequence, the problem of generating high quality polygonal meshes of objects from unorganized pointclouds is receiving more and more attention. After reviewing the different 3D shape techniques for surface reconstruction, we willreport the full process of converting a usually unstructured point cloud into a consistent polygonal model. Some triangulationalgorithms, modeling methods and visualization techniques are also described and different examples are presented.
Signal transduction by the lipopolysaccharide receptor, Toll‐like receptor‐4 (2004)

An understanding of lipopolysaccharide (LPS) signal transduction is a key goal in the effort to provide a molecular basis for the lethal effect of LPS during septic shock and point the way to novel therapies. Rapid progress in this field during the last 6 years has resulted in the discovery of not only the receptor for LPS - Toll-like receptor 4 (TLR4) - but also in a better appreciation of the complexity of the signalling pathways activated by LPS. Soon after the discovery of TLR4, the formation of a receptor complex in response to LPS, consisting of dimerized TLR4 and MD-2, was described. Intracellular events following the formation of this receptor complex depend on different sets of adapters. An early response, which is dependent on MyD88 and MyD88-like adapter (Mal), leads to the activation of nuclear factor-kappaB (NF-kappaB). A later response to LPS makes use of TIR-domain-containing adapter-inducing interferon-beta (TRIF) and TRIF-related adapter molecule (TRAM), and leads to the late activation of NF-kappaB and IRF3, and to the induction of cytokines, chemokines, and other transcription factors. As LPS signal transduction is an area of intense research and rapid progress, this review is intended to sum up our present understanding of the events following LPS binding to TLR4, and we also attempt to create a model of the signalling pathways activated by LPS.
A local macrophage chemokine network sustains protective tissue-resident memory CD4 T cells (2014)

CD8 tissue-resident memory T (T(RM)) cells provide efficient local control of viral infection, but the role of CD4 T(RM) is less clear. Here, by using parabiotic mice, we show that a preexisting pool of CD4 T(RM) cells in the genital mucosa was required for full protection from a lethal herpes simplex virus 2 (HSV-2) infection. Chemokines secreted by a local network of macrophages maintained vaginal CD4 T(RM) in memory lymphocyte clusters (MLCs), independently of circulating memory T cells. CD4 T(RM) cells within the MLCs were enriched in clones that expanded in response to HSV-2. Our results highlight the need for vaccine strategies that enable establishment of T(RM) cells for protection from a sexually transmitted virus and provide insights as to how such a pool might be established.
Malondialdehyde-Modified LDL as a Marker of Acute Coronary Syndromes (1999)

The combination of MDA-modified LDL, which may reflect endothelial injury or plaque instability, and troponin I, which reflects myocardial cell injury, allows better discrimination between stable CAD and acute coronary syndromes than troponin I alone.
The Melanosomal Protein PMEL17 as a Target for Antibody Drug Conjugate Therapy in Melanoma (2012)

Melanocytes uniquely express specialized genes required for pigment formation, some of which are maintained following their transformation to melanoma. Here we exploit this property to selectively target melanoma with an antibody drug conjugate (ADC) specific to PMEL17, the product of the SILV pigment-forming gene. We describe new PMEL17 antibodies that detect the endogenous protein. These antibodies help define the secretory fate of PMEL17 and demonstrate its utility as an ADC target. Although newly synthesized PMEL17 is ultimately routed to the melanosome, we find substantial amounts accessible to our antibodies at the cell surface that undergo internalization and routing to a LAMP1-enriched, lysosome-related organelle. Accordingly, an ADC reactive with PMEL17 exhibits target-dependent tumor cell killing in vitro and in vivo.
Introduction to microlithography (1994)

An Introduction to Lithography The Lithographic Process: The Physics Organic Resist Materials Resist Processing Plasma Etching
TnphoA: a transposon probe for protein export signals. (1985)

We constructed a derivative of transposon Tn5 that permits the generation of hybrid proteins composed of alkaline phosphatase (EC 3.1.3.1) lacking its signal peptide fused to amino-terminal sequences of other proteins. Such a hybrid gives alkaline phosphatase activity if the protein fused to alkaline phosphatase contributes sequences that promote export and thus compensate for the missing alkaline phosphatase signal peptide. Fusions to both a secreted periplasmic protein and a complex cytoplasmic membrane protein led to alkaline phosphatase activity. TnphoA fusions should help localize export signals within the structure of a protein, such as a transmembrane protein, as well as identify new chromosomal genes for secreted and transmembrane proteins.
Neuropeptide-Derived Antimicrobial Peptides from Invertebrates for Biomedical Applications (2005)

Since the beginning of the 20th century, important medicinal progress has led medical doctors to think that the end of devastating epidemics has arrived. In 1930, the discovery of sulfamides and penicillin opened a wide area of applications able to fight against bacterial infections. However, almost all antibiotics were baffled by the great ability to adaptation of bacteria (1) and the emergence of new bacterial agents, discovered with up-dated technologies. The living world is perpetually in co-evolution and since more than 3 billion years, bacteria have developed resistance mechanisms to overcome external aggressions. Thus, in the middle of the 80th century, multi-resistant bacteria appeared and disseminated out from hospitals. In this context, researches have been developed in order to find new antimicrobial substances to destroy such new types of bacteria. Thus, several groups have turned their focus on invertebrates, which co-evoluad with human and have appeared on the planet since a long time. Evidence of new families of antimicrobial substances isolated from invertebrates different to the classical cationic peptide family i.e. dipeptides and anionic peptides been given. Moreover, these molecules are also present in human and may serve in the innate immune response as an important survival strategy.