gebhart/patrepeval huggingface dataset:
Inhibition of pilus-mediated adhesion of Pseudomonas aeruginosa to human buccal epithelial cells by monoclonal antibodies directed against pili (1990)

The Pseudomonas aeruginosa PAK pilus is capable of mediating the binding of this strain to human respiratory epithelial cells. We have produced monoclonal antibodies (MAbs) to the PAK pilus in order to elucidate the location of the binding domain of the pilus for human buccal epithelial cells (BECs). Four MAbs are described. MAbs PK41C and PK34C were found to react with P. aeruginosa pilins produced by a large number of strains. The epitope recognized by PK41C was determined to lie within the N-terminal region of the pilin and is likely constituted by amino acid residues 22 through 33. The epitope for PK34C was located in the C-terminal region of the pilin and was partially dependent on an intact intrachain disulfide bridge between cysteine residues 129 and 142. PK99H and PK3B were found to react specifically with PAK pilin. The epitope for PK99H was also localized in the C-terminal region of the pilin protein and appears to reside between amino acid residues 130 and 138. The epitope for PK3B was not localized by using the methods of this study, but it is likely dependent on the three-dimensional structure of the pilin. Fab fragments of PK99H inhibited adhesion of strains PAK and 492c to BECs, but the adherence of five other strains was not affected. Fab fragments of PK34C inhibited adhesion of all piliated strains examined. Fab fragments from both of these antibodies inhibited PAK pilus binding to BECs. Fab fragments of PK41C and PK3B had no effect on P. aeruginosa binding to BECs. These results confirm that the C-terminal region of the pilin has adhesin qualities and that a conserved epitope lies within this region.
Coil compression for accelerated imaging with Cartesian sampling (2012)

MRI using receiver arrays with many coil elements can provide high signal-to-noise ratio and increase parallel imaging acceleration. At the same time, the growing number of elements results in larger datasets and more computation in the reconstruction. This is of particular concern in 3D acquisitions and in iterative reconstructions. Coil compression algorithms are effective in mitigating this problem by compressing data from many channels into fewer virtual coils. In Cartesian sampling there often are fully sampled k-space dimensions. In this work, a new coil compression technique for Cartesian sampling is presented that exploits the spatially varying coil sensitivities in these nonsubsampled dimensions for better compression and computation reduction. Instead of directly compressing in k-space, coil compression is performed separately for each spatial location along the fully sampled directions, followed by an additional alignment process that guarantees the smoothness of the virtual coil sensitivities. This important step provides compatibility with autocalibrating parallel imaging techniques. Its performance is not susceptible to artifacts caused by a tight imaging field-of-view. High quality compression of in vivo 3D data from a 32 channel pediatric coil into six virtual coils is demonstrated.
Statistical significance of variables driving systematic variation in high-dimensional data (2014)

jstorey@princeton.edu.
An adaptation of item modeling for developing test‐item banks (1992)

An adaptation of item modeling, an item‐writing procedure, is described. As with related methods, the procedure includes dividing the stem of an item into discrete elements of information and then altering the elements to create new items. In this adaptation, writers were instructed to change the elements so that each incorrect option in the original item becomes the correct answer to a new item. Another part of the process, an innovation that increases the number of items generated, is to change the question asked of examinees (e.g., from diagnosis to treatment) for each item and write new response options. Two novice item writers applied modeling to patient‐based, one‐best‐answer items. They found the procedure easy to use and intuitive. From 13 items, they produced 209 modeled items in 24 at‐home hours, plus 12 hr of meeting time. A consultant evaluated a subset of items and estimated that approximately half the items were of sufficient quality to appear on a subspecialty certifying examination. Though the project had several limitations, item modeling appears to have promise as an efficient item‐writing procedure. Conservative estimates suggest it is about four times more productive than a traditional committee‐based approach.
A Model of Platelet Aggregation Involving Multiple Interactions of Thrombospondin-1, Fibrinogen, and GPIIbIIIa Receptor (2001)

Thrombospondin-1 (TSP) may, after secretion from platelet alpha granules, participate in platelet aggregation, but its mode of action is poorly understood. We evaluated the capacity of TSP to form inter-platelet cross-bridges through its interaction with fibrinogen (Fg), using either Fg-coated beads or Fg bound to the activated GPIIbIIIa integrin (GPIIbIIIa*) immobilized on beads or on activated fixed platelets (AFP), i.e. in a system free of platelet signaling and secretion mechanisms. Aggregation at physiological shear rates (100-2000 s(-1)) was studied in a microcouette device and monitored by flow cytometry. Soluble TSP bound to and induced aggregation of Fg-coated beads dose-dependently, which could be blocked by the amino-terminal heparin-binding domain of TSP, TSP18. Soluble TSP did not bind to GPIIbIIIa*-coated beads or AFP, unless they were preincubated with Fg. The interaction of soluble TSP with Fg-GPIIbIIIa*-coated beads or Fg-AFP resulted in the formation of aggregates via Fg-TSP-Fg cross-bridges, as demonstrated in a system where direct cross-bridges mediated by GPIIbIIIa*-Fg on one particle and free GPIIbIIIa* on a second particle were blocked by the RGD mimetic Ro 44-9883. Soluble TSP increased the efficiency of Fg-mediated aggregation of AFP by 30-110% over all shear rates and GPIIbIIIa* occupancies evaluated. Surprisingly, TSP binding to Fg already bound to its GPIIbIIIa* receptor appears to block the ability of this occupied Fg to recognize another GPIIbIIIa* receptor, but this TSP can indeed cross-bridge to another Fg molecule on a second platelet. Finally, TSP-coated beads could directly coaggregate at shear rates from 100 to 2000 s(-1). Our studies provide a model for the contribution of secreted TSP in reinforcing inter-platelet interactions in flowing blood, through direct Fg-TSP-Fg and TSP-TSP cross-bridges.
Diagnosis of Bone and Joint Disorders (1987)

Volume I: Radiography and Related Diagnostic Techniques in the Evaluation of Bone, Joint and Soft Tissue Diseases. Imaging of the Postoperative Patient . Volume II: Basic Sciences of Musculoskeletal Diseases. Rheumatoid Arthritis and Related Diseases. Connective Tissue Diseases . Volume III: Degenerative Diseases. Crystal-Induced and Related Diseases. Temporomandibular Manifestations of Articular Diseases. Target Area Approach to Articular Diseases. Volume IV: Metabolic Disease. Endocrine Diseases. Diseases of the Hematopoietic System. Infectious Diseases. Volume V: Traumatic, Iatrogenic and Neurogenic Diseases. Osteonecrosis and Osteochondrosis. Volume VI: Tumours and Tumor-Like Diseases. Congenital Diseases. Miscellaneous Diseases
125 Gbit/s carrier-injection-based silicon micro-ring silicon modulators (2007)

We show a scheme for achieving high-speed operation for carrier-injection based silicon electro-optical modulator, which is optimized for small size and high modulation depth. The performance of the device is analyzed theoretically and a 12.5-Gbit/s modulation with high extinction ratio >9dB is demonstrated experimentally using a silicon micro-ring modulator.
Genetic linkage and complex diseases, with special reference to psychiatric disorders (1990)

Recent linkage findings for psychiatric disorders, in particular schizophrenia, manic-depression, and Alzheimer disease, have raised a number of important conceptual issues regarding the genetic etiology of these diseases, as well as the appropriate interpretation of linkage results in studying complex diseases. Perspectives on mode of inheritance, genetic heterogeneity, and phenotypic variation are given.
Gene of the month: Interleukin 6 (IL-6) (2014)

The Interleukin 6 (IL-6) gene encodes the classic proinflammatory cytokine IL-6. It is also known as interferon-β2 (IFN-β2), B cell stimulatory factor-2 and hybridoma/plasmacytoma growth factor. IL-6 is a multifunctional cytokine with a central role in many physiological inflammatory and immunological processes. Due to its major role in initiation as well as resolving inflammation, deregulation of IL-6 is a mainstay of chronic inflammatory and autoimmune diseases. Additionally, IL-6 has been shown to be implicated in pathogenesis of many human malignancies. Thus, a better understanding of IL-6 and its role in various pathological conditions could enable the development of strategies to use it as a therapeutic target. This short review focuses on the structure, regulation and biological activities of IL-6. In addition we discuss the role of IL-6 in diseases with inflammatory background and cancer and also the therapeutic applications of anti-IL-6 agents.
N‐Arylpiperazine‐1‐carboxamide Derivatives: A Novel Series of Orally Active Nonsteroidal Androgen Receptor Antagonists. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
EcoRII can be activated to cleave refractory DNA recognition sites (1988)

EcoRII restriction sites [5'-CC(A/T)GG] in phage T3 and T7 DNA are refractory to cleavage by EcoRII, but become sensitive to cleavage in the presence of DNAs which contain an abundance of EcoRII sensitive sites (e.g. pBR322 or lambda DNA). Studies using fragments of pBR322 containing different numbers of EcoRII sites show that the susceptibility to EcoRII cleavage is proportional to the number of sites in the individual fragment. We postulate that EcoRII is the prototype of restriction endonucleases which require at least 2 simultaneously bound substrate sites for their activation. EcoRII sites are refractory when they occur at relatively low frequency in the DNA. The restriction enzyme can be activated by DNA with a higher frequency of sites.
Phthalocyaninatoeisen mit Pyrazin als zweizähnigem Brückenliganden (1980)

Synthese und Eigenschaften eindimensionaler Leiter sind von aktuellem Interesse. Jetzt gelang die Herstellung von (1) und einem Polymer (2), in welchem PcFe- und Pyrazingruppen miteinander abwechseln. Die physikalischen Eigenschaften von (2) deuten auf eine hohe Elektronendelokalisation über die Pyrazinbrücken hin.
Isokinetic and isometric muscle strength in a healthy population with special reference to age and gender (2009)

We developed a model to compare the isometric and isokinetic muscle strength of all the major joint movements of an individual with values for a healthy man or woman at any age in the range of 20-80 years. In all age groups, women have lower muscle strength than men. Men's muscle strength declines with age, while women's muscle strength declines from the age of 41 years.
A system for distributed intrusion detection (2002)

The network intrusion-detection concept is extended from the LAN (local area network) environment to arbitrarily wider areas, with the network topology being arbitrary as well. The generalized distributed environment is heterogeneous, i.e. the network nodes can be hosts or servers from different vendors, or some of them could be LAN managers. The proposed architecture for this distributed intrusion-detection system consists of the following components: a host manager (namely a monitoring process or collection of processes running in background) in each host: LAN manager for monitoring each LAN in the system; and a central manager, placed at a single secure location, that receives reports from various host and LAN managers and processes these reports, correlates them, and detects intrusions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Human T-cell responses to HLA-A-restricted high binding affinity peptides of human papillomavirus type 18 proteins E6 and E7. (2001)

Human Papillomaviruses (HPVs) are sexually transmitted pathogens, which are implicated in the etiology of cervical cancer. The early proteins E6 and E7 of HPV have transforming capacity and interfere with the cell cycle control of infected host cells and are essential for the maintenance of the transformed state. Identification of MHC class I-restricted, immunogenic peptides derived from either the E6 or the E7 protein is essential for the design of vaccines as well as the monitoring of clinical trials and immunotherapeutic approaches for the treatment of HPV-18-induced carcinomas. We have determined the binding affinities for all possible 9-mer peptides spanning the entire E6 and E7 amino acid sequence for the HLA-A*0101, HLA-A*0201, HLA-A*0302, HLA-A*1102, and HLA-A*2402101 molecules by a competition assay with reference peptides, thereby establishing the binding peptides as potential cytotoxic T-cell epitopes. From the HLA-A*0201 binding peptides, we selected five E6-derived and one E7-derived peptide with high affinities for HLA-A*0201. These six peptides were tested for their immunogenicity by in vitro immunization assays with purified human CD8+ T cells. We identified three HPV-18 E6-derived peptides (ELTEVFEFA, KTVLELTEV, and KLPDLCTEL) and the E7-derived peptide TLQDIVLHL to be highly immunogenic. Overall, these results will help to design vaccines for the prevention or treatment of HPV-18-induced cervical cancer.
Mannosylphosphate transfer to cell wall mannan is regulated by the transcriptional level of the MNN4 gene in Saccharomyces cerevisiae (1997)

Mannosylphosphorylation is a major oligosaccharide modification that provides negative charge in the Saccharomyces cerevisiae cell wall. Although two genes, MNN6 and MNN4, which encode a mannosylphosphate transferase and its putative positive regulator, respectively, are involved in this modification, the amount of Mnn4p has been found to be a limiting factor for mannosylphosphorylation. The level of mannosylphosphorylation increased at late-logarithmic and stationary phases of cell growth, and this was correlated to the transcriptional enhancement of MNN4. We also find that mannosylphosphate transfer to mannan is negatively regulated by the protein kinase A pathway, while the presence of 0.5 M potassium chloride enhanced MNN4 transcription. This type of transcriptional regulation is observed in many stress response genes, implying that mannosylphosphate transfer is involved in the cellular response to a variety of stresses.
Methods of On-Board Misfire Detection (1990)

&lt;div class="htmlview paragraph"&gt;Misfiring of the engine can cause damage to the catalyst within short time and increase emissions. Under misfiring conditions, unburned fuel and oxygen are pumped into the catalyst, where its combustion heavily increases the temperature. For this reason there is a demand for fast detection of misfiring. Once judged, one can take countermeasures to avoid further temperature rise. Two methods of misfire detection with the prospect of future use in series production are discussed. A first approach uses the trace shape of the λ-sensor signal for evaluation. The second approach uses the speed fluctuations of the engine for detection. Efficient algorithms give the possibility of misfire detection in the full load-speed range with reasonable effort to protect the catalyst. However there will remain some misfire conditions, increasing the emissions above regulation limits, that cannot be detected by those methods.&lt;/div&gt;
D2 dopamine receptor response to endophyte-infected tall fescue and an antagonist in the rat (1994)

Effects on rat brain D2 dopamine receptors by endophyte-infected tall fescue seed consumption and antagonist injection were characterized. Forty-eight male Wistar rats (225 g) in three separate trials were exposed to either 22 or 32 degrees C. Diets, to maintain similar concentrations of ergovaline, contained 10% (Trial 1) or 15% (Trials 2 and 3) endophyte-infected (E+; 325 average ppb of ergovaline) or uninfected (E-; 0 ppb of ergovaline) tall fescue seed. Rats were injected i.p. daily with either placebo (PL) or an experimental D2 dopamine antagonist (DA, .0375 mg/kg BW). No effects (P > .10) on diet DM intake by E+ ingestion or DA injection were detected at 22 degrees C. However, ingestion of E+ reduced (P < .01) and injection of DA improved (P < .05) DM intake of rats housed in 32 degrees C (11.1 vs 15.4 g of DM/d for E+ vs E-, respectively). Whole brain D2 dopamine receptor density (Bmax) and mRNA were reduced (P < .05) by E+ and increased (P < .05) by DA in Trial 1. No treatment effects (P > .10) on cerebral cortex alpha 1- and alpha 2-adrenergic or striatal D2 dopamine receptor Bmax were measured in Trials 2 and 3. In summary, dietary E+ reduced whole brain D2 dopamine mRNA and Bmax, whereas injection of DA increased D2 dopamine mRNA. Thus, long-term regulation of monoamine receptors seems to be affected by E+ ingestion or DA injection.
A Single Asparagine-Linked Glycosylation Site of the Severe Acute Respiratory Syndrome Coronavirus Spike Glycoprotein Facilitates Inhibition by Mannose-Binding Lectin through Multiple Mechanisms (2010)

Mannose-binding lectin (MBL) is a serum protein that plays an important role in host defenses as an opsonin and through activation of the complement system. The objective of this study was to assess the interactions between MBL and severe acute respiratory syndrome-coronavirus (SARS-CoV) spike (S) glycoprotein (SARS-S). MBL was found to selectively bind to retroviral particles pseudotyped with SARS-S. Unlike several other viral envelopes to which MBL can bind, both recombinant and plasma-derived human MBL directly inhibited SARS-S-mediated viral infection. Moreover, the interaction between MBL and SARS-S blocked viral binding to the C-type lectin, DC-SIGN. Mutagenesis indicated that a single N-linked glycosylation site, N330, was critical for the specific interactions between MBL and SARS-S. Despite the proximity of N330 to the receptor-binding motif of SARS-S, MBL did not affect interactions with the ACE2 receptor or cathepsin L-mediated activation of SARS-S-driven membrane fusion. Thus, binding of MBL to SARS-S may interfere with other early pre- or postreceptor-binding events necessary for efficient viral entry.
Exploring large virtual environments with an HMD when physical space is limited (2007)

Virtual Environments presented through head-mounted displays (HMDs) are often explored on foot. Exploration on foot is useful since the afferent and efferent cues of physical locomotion aid spatial awareness. However, the size of the virtual environment that can be explored on foot is limited to the dimensions of the tracking space of the HMD unless other strategies are used. This paper presents a system for exploring a large virtual environment on foot when the size of the physical surroundings is small by leveraging people's natural ability to spatially update. This paper presents three methods of "resetting" users when they reach the physical limits of the HMD tracking system. Resetting involves manipulating the users' location in physical space to move them out of the path of the physical obstruction while maintaining their spatial awareness of the virtual space.
Real-Time Quantitative Polymerase Chain Reaction Measurement of Male Fetal DNA in Maternal Plasma (2007)

Cell-free fetal DNA can be detected in the blood plasma of pregnant women as early as 5 wk into pregnancy. At present noninvasive prenatal diagnosis has already begun to impact clinical practice. The established applications are for the determination of fetal sex and rhesus D blood group when the mother is rhesus D negative. Both methods are currently evaluated and standardized by a large laboratory network (the Special Non-Invasive Advances in Fetal and Neonatal Evaluation Network, or SAFE) that aims to implement widespread noninvasive prenatal diagnosis throughout the European Union. This chapter presents the basic methodology used in this noninvasive analysis.
THE SOCIALLY RESPONSIBLE EXISTENTIALIST (2006)

In an open and virtually boundless media environment, old responses to the question of who is a journalist, based primarily on roles associated with the process of gathering and disseminating information, no longer apply. This article suggests a reconceptualization of the journalist based instead on normative constructs. Specifically, it advocates a blend of two competing philosophical approaches, existentialism and social responsibility theory, as well as two roughly corresponding professional norms, independence and accountability. The combination produces a “socially responsible existentialist”, a journalist who chooses to act as a trustworthy source of information that serves the public interest. That framework is applied at both a concrete level, through consideration of weblogs and the proliferation of partisan information sources, and a conceptual level, through consideration of gatekeeping and agenda-setting functions.
DNA Methylation Biomarkers for Blood-Based Colorectal Cancer Screening (2007)

The stringent criteria applied at all steps of the selection and validation process enabled successful identification and ranking of blood-based marker candidates.
Colour indexing across devices and viewing conditions (2001)

This paper reports a negative result. It is well known that the colours in a scene do not depend only on the surface properties of the objects present but also on the illumination conditions and the capturing device&amp;apos;s characteristics. Indeed, this dependence is so strong that computer vision techniques based on colour, such as object recognition [18] fail unless this relationship is accounted for. Much effort has been put into finding colour normalization techniques and colour invariants (features that do not change with changing illuminant), and many different approaches have been reported in the literature. All of these techniques, however, rely on the linearity property of the imaging process and hence on calibrated images. In this paper we set out to evaluate current state- of-the-art normalization and invariant methods on an uncalibrated image database [3]. The results of this experiment show that none of the existing techniques performs well enough to support colour based object recognition, and so suggest the need for new, improved algorithms.
Hyperfunctional coagulation factor IX improves the efficacy of gene therapy in hemophilic mice (2012)

Gene therapy may provide a cure for hemophilia and overcome the limitations of protein replacement therapy. Increasing the potency of gene transfer vectors may allow improvement of their therapeutic index, as lower doses can be administered to achieve therapeutic benefit, reducing toxicity of in vivo administration. Here we generated codon-usage optimized and hyperfunctional factor IX (FIX) transgenes carrying an R338L amino acid substitution (FIX Padua), previously associated with clotting hyperactivity and thrombophilia. We delivered these transgenes to hemophilia B mice by hepatocyte-targeted integration-competent and -defective lentiviral vectors. The hyperfunctional FIX transgenes increased FIX activity reconstituted in the plasma without detectable adverse effects, allowing correction of the disease phenotype at lower vector doses and resulting in improved hemostasis in vivo. The combined effect of codon optimization with the hyperactivating FIX-R338L mutation resulted in a robust 15-fold gain in potency and therefore provides a promising strategy to improve the efficacy, feasibility, and safety of hemophilia gene therapy.