gebhart/patrepeval huggingface dataset:
Defining interferon β response status in multiple sclerosis patients (2004)

IFN-beta is effective in reducing relapses and magnetic resonance imaging (MRI) lesions in multiple sclerosis (MS). It is assumed that individual therapeutic responses vary, but methods to identify IFN-beta responsiveness have not been validated. Our objective was to evaluate methods to classify IFN-beta responder status using relapses and MRI lesions. Data was analyzed from 172 patients who were followed up in a placebo-controlled clinical trial of IFN-beta1a for 2 years. Patients were classified as responders or nonresponders using (1) the number of relapses during the 2-year trial; (2) the number of new T2 lesions after 2 years; and (3) the number of gadolinium-enhancing lesions at year 1 and year 2 on study. Outcomes included 2-year change in the Expanded Disability Status Scale, Multiple Sclerosis Functional Composite, and brain parenchymal fraction. We found that subgroups with high on-study relapse numbers had more disease progression, differences between responder subgroups were similar in the IFN-beta1a and placebo arms. In contrast, subgroups with high numbers of new MRI lesions had significantly more disease progression only in the IFN-beta1a arm. Baseline characteristics failed to account for differential outcome. New MRI lesion activity during IFN-beta1a treatment correlates with poor response to IFN-beta1a. MRI classification may facilitate rational therapeutic decisions, better clinical trial designs, and studies correlating biomarkers with therapeutic response.
FPGA-based DNA Basecalling Hardware Acceleration (2018)

Modern DNA sequencing technologies have greatly reduced their physical dimensions while still being able to process large numbers of molecules. Under ideal conditions the raw throughput of such devices may peak at the equivalent of 1 human genome per 3.5 hours. Such outputs present a large burden on the ensuing computing devices tasked with processing the raw data and completing the sequence. To approach the power and spatial footprint of the measurement devices, hardware-accelerated embedded computers are needed. The design of an FPGA-based accelerator customized for one aspect of this task - basecalling - is described herein. Simulations indicate a system capable of basecalling the equivalent of one human genome in 35 minutes within an estimated power budget of 10 W.
Vaccination against Chlamydial Genital Tract Infection after Immunization with Dendritic Cells Pulsed Ex Vivo with Nonviable Chlamydiae (1998)

Chlamydia trachomatis, an obligate intracellular bacterial pathogen of mucosal surfaces, is a major cause of preventable blindness and sexually transmitted diseases for which vaccines are badly needed. Despite considerable effort, antichlamydial vaccines have proven to be elusive using conventional immunization strategies. We report the use of murine bone marrow-derived dendritic cells (DC) pulsed ex vivo with killed chlamydiae as a novel approach to vaccination against chlamydial infection. Our results show that DC efficiently phagocytose chlamydiae, secrete IL-12 p40, and present chlamydial antigen(s) to infection sensitized CD4(+) T cells. Mice immunized intravenously with chlamydial-pulsed DC produce protective immunity against chlamydial infection of the female genital tract equal to that obtained after infection with live organisms. Immunized mice shed approximately 3 logs fewer infectious chlamydiae and are protected from genital tract inflammatory and obstructive disease. Protective immunity is correlated with a chlamydial-specific Th1-biased response that closely mimics the immune response produced after chlamydial infection. Thus, ex vivo antigen-pulsed DC represent a powerful tool for the study of protective immunity to chlamydial mucosal infection and for the identification of chlamydial protective antigens through reconstitution experiments. Moreover, these findings might impact the design of vaccine strategies against other medically important sexually transmitted diseases for which vaccines are sought but which have proven difficult to develop.
Homing of Human B Cells to Lymphoid Organs and B-Cell Lymphoma Engraftment Are Controlled by Cell Adhesion Molecule JAM-C (2012)

Junctional adhesion molecule C (JAM-C) is expressed by vascular endothelium and human but not mouse B lymphocytes. The level of JAM-C expression defines B-cell differentiation stages and allows the classification of marginal zone-derived (JAM-C-positive) and germinal center-derived (JAM-C-negative) B-cell lymphomas. In the present study, we investigated the role of JAM-C in homing of human B cells, using a xenogeneic nonobese diabetic/severe combined immunodeficient mouse model. Treatment with anti-JAM-C antibodies in short-term experiments reduced migration of normal and malignant JAM-C-expressing B cells to bone marrow, lymph nodes, and spleen. Blocking homing to the spleen is remarkable, as most other antiadhesion antibodies reduce homing of B cells only to bone marrow and lymph nodes. Long-term administration of anti-JAM-C antibodies prevented engraftment of JAM-Cpos lymphoma cells in bone marrow, spleen, and lymph nodes of mice. Plasmon resonance studies identified JAM-B as the major ligand for JAM-C, whereas homotypic JAM-C interactions remained at background levels. Accordingly, anti-JAM-C antibodies blocked adhesion of JAM-C-expressing B cells to their ligand JAM-B, and immunofluorescence analysis showed the expression of JAM-B on murine and human lymphatic endothelial cells. Targeting JAM-C could thus constitute a new therapeutic strategy to prevent lymphoma cells from reaching supportive microenvironments not only in the bone marrow and lymph nodes but also in the spleen.
The Pathophysiology of Angiogenesis (1995)

The formation of new capillary blood vessels, a process termed "angiogenesis", is one of the most pervasive and fundamentally essential biological processes encountered in mammalian organizations. Angiogenesis is an important event in a variety of physiological settings, such as embryonic development, chronic inflammation, and wound repair. It is a process that is tightly regulated in both time and space. Angiogenesis is driven by a cocktail of growth factors and pro-angiogenic cytokines and is tempered by an equally diverse group of inhibitors of neovascularization. Angiogenesis is also central to the etiology and pathogenesis of a number of pathological processes that include, among others, solid tumors, diseases of the eye, and chronic inflammatory disorders such as rheumatoid arthritis, psoriasis, and periodontitis. Based on recent work from several laboratories, it is now eminently clear that most if not all angiogenesis and vasoproliferative-dependent disease processes are not only a consequence of the unrestricted production of normal or aberrant forms of pro-angiogenic mediators but also the result of a relative deficiency in angiogenic-inhibitory molecules. In this review, I will describe how these multifunctional mediator systems function to coordinate and regulate the angiogenic response, and how disruption in the molecular controls that regulate the production of pro-angiogenic and angiostatic mediators leads to aberrant angiogenesis and disease. The implications of these findings in the development of novel therapeutic strategies for the treatment of diseases characterized by disregulated angiogenesis will also be discussed.
Atomic Force Microscope (1986)

The scanning tunneling microscope is proposed as a method to measure forces as small as ${10}^{\ensuremath{-}18}$ N. As one application for this concept, we introduce a new type of microscope capable of investigating surfaces of insulators on an atomic scale. The atomic force microscope is a combination of the principles of the scanning tunneling microscope and the stylus profilometer. It incorporates a probe that does not damage the surface. Our preliminary results in air demonstrate a lateral resolution of 30 \AA{}A and a vertical resolution less than 1 \AA{}.
A simple neural network module for relational reasoning (2017)

Relational reasoning is a central component of generally intelligent behavior, but has proven difficult for neural networks to learn. In this paper we describe how to use Relation Networks (RNs) as a simple plug-and-play module to solve problems that fundamentally hinge on relational reasoning. We tested RN-augmented networks on three tasks: visual question answering using a challenging dataset called CLEVR, on which we achieve state-of-the-art, super-human performance; text-based question answering using the bAbI suite of tasks; and complex reasoning about dynamic physical systems. Then, using a curated dataset called Sort-of-CLEVR we show that powerful convolutional networks do not have a general capacity to solve relational questions, but can gain this capacity when augmented with RNs. Our work shows how a deep learning architecture equipped with an RN module can implicitly discover and learn to reason about entities and their relations.
Next-generation sequencing: applications beyond genomes (2008)

The development of DNA sequencing more than 30 years ago has profoundly impacted biological research. In the last couple of years, remarkable technological innovations have emerged that allow the direct and cost-effective sequencing of complex samples at unprecedented scale and speed. These next-generation technologies make it feasible to sequence not only static genomes, but also entire transcriptomes expressed under different conditions. These and other powerful applications of next-generation sequencing are rapidly revolutionizing the way genomic studies are carried out. Below, we provide a snapshot of these exciting new approaches to understanding the properties and functions of genomes. Given that sequencing-based assays may increasingly supersede microarray-based assays, we also compare and contrast data obtained from these distinct approaches.
Citrate determines calcium oxalate crystallization kinetics and crystal morphology—studies in the presence of Tamm–Horsfall protein of a healthy subject and a severely recurrent calcium stone former (2000)

Citrate appears to be the main determinant of CaOx crystallization rates and crystal morphology in the presence of nTHP as well as SF-THP. Its effects appear to predominate over those of THP, since even promotory SF-THP is turned into a crystallization inhibitor in the presence of citrate. This re-emphasizes at a morphological level what has been concluded from functional as well from clinical studies, namely that citrate is needed in urine at equimolar concentrations to calcium in order to prevent the formation of large crystal aggregates in presence of abnormal THP.
Beta Blockers in Heart Failure (1993)

The efficacy of beta-blocking drugs in the treatment of chronic heart failure remains controversial. A major obstacle to their acceptance in this pharmacotherapeutic role has been their reputed negative inotropic effects and the resulting depression of cardiac function when given acutely to patients in heart failure. However, in a number of uncontrolled studies in patients in mild or moderate heart failure due to dilated cardiomyopathy, these drugs, when titrated from a low-dose starting point, have been shown to improve the surrogate endpoints of symptoms and certain haemodynamic parameters. It is presumed that this benefit is related to the improvement in myocardial contractile activity secondary to the gradual up-regulation of the depressed myocardial beta-receptors in patients with chronic heart failure. At present, the data regarding the improvement in exercise tolerance are conflicting and there are no published data on the influence of beta-adrenoceptor-blocking drugs on survival. The potential of beta-blocking drugs to improve the clinical state in some patients with heart failure is, however, being further explored in two prospective randomized trials.
Expression of indoleamine 2,3-dioxygenase by plasmacytoid dendritic cells in tumor-draining lymph nodes (2004)

During the preparation of this manuscript for publication, an error was introduced into the Results section, in the fourth sentence of the paragraph beginning with "The levels of the APP-derived soluble peptides A40 and A42 in brains of double-transgenic mice and APP [V717I] control animals at the age of 18 weeks were quantified by specific sandwich ELISAs." The correct sentence appears below. We regret this error.
Propolypeptide of von Willebrand Factor Circulates in Blood and Is Identical to von Willebrand Antigen II (1986)

The generally mild bleeding disorder of von Willebrand disease is associated with abnormalities of two distinct plasma proteins, the large multimeric von Willebrand factor (vWF), which mediates platelet adhesion, and von Willebrand antigen II (vW AgII), which is of unknown function. The two proteins were found to have a common biosynthetic origin in endothelial cells and megakaryocytes, which explains their simultaneous absence in the severe form of this hereditary disease. Shared amino acid sequences from a 100-kilodalton plasma glycoprotein and from vW AgII are identical to amino acid sequences predicted from a complementary DNA clone encoding the 5' end of vWF. In addition, these proteins have identical molecular weights and immunologic cross reactivities. Monoclonal antibodies prepared against both proteins recognize epitopes on the pro-vWF subunit and on a 100-kilodalton protein that are not present on the mature vWF subunit in endothelial cell lysates. In contrast, polyclonal antibodies against vWF recognize both pro-vWF and vWF subunits. Thus, the 100-kilodalton plasma glycoprotein and vW AgII are identical proteins and represent an extremely large propolypeptide that is first cleaved from pro-vWF during intracellular processing and then released into plasma.
Combination Foam/Fluid Fracturing (1980)

Abstract This paper describes the newly developed combination foam/fluid fracturing technique, dealing with the objectives of the process" the equipment required, a typical sand schedule, the calculation for frac area, fluid cleanup procedures and, finally, the advantages of combination fracturing. The areal extent of a combination fracturing treatment is discussed in the Appendix, along with fracture capacity and the fluid co-efficient for foam. Introduction One of the most significant innovations in fracturing technology in recent years -was the development of foam as a fracturing fluid in the fall of 1973. First conceived and researched by Blauer et al.(1) as a thesis project at the Colorado School of Mines, the process was quickly recognized by the oil and gas industry as a technique with a number of advantages resulting from the unique rheological properties of foam. Foam is now widely used as a fracturing fluid, for stimulating productivity of oil and gas wells, with a high ratio of success.(2,3) "Combination Fracturing" was first introduced in February of 1977 as a further improvement of the Blauer form frac process, incorporating the best features of both foam and conventional fluid fracturing treatments in one job. Results of jobs performed to date indicate that Combination Fracs achieve equal or higher productivity increases than either foam fracs or fluid fracs alone. Description of the Process A Combination Frac is actually two different fracturing operations conducted in sequence on a' well first a foam frac, followed by a fluid fracture treatment. These two fracs are continuous, with transition from one type of operation to the other effected by increasing the pumping rates of the liquid and at the same time reducing the rate of the gas volumes pumped. The first stage of a Combination Frac is generated by treated fluids and a specific N2 ratio to develop 75% quality foam at bottom-hole conditions. The foam is injected into the well as the base fluid of the fracturing treatment, with sand being added at concentrations of 1 to 2 pounds/gallon of foam. The rheological properties of foam, including its excellent sand carrying properties and low fluid loss, are such that it develops a fracture of considerable areal extent reaching deep into the formation. In the second stage of a Combination Frac, the aeration and the foaming agent ratios are reduced. Simultaneously, the pumping rate is increased and sand ratios are increased to concentrations as high as 8 to 10 pounds per gallon. The increased viscosity of this fluid stage, combined with the increased rate, develops a greater crack width. This widening of the fracture, as? described in the Appendix, results in a higher flow capacity over the total frac area developed by the treatment. Objective of a Combination Frac The productivity of a well following fracturing is proportional to both the permeability contrast (flow capacity of the fracture in md-ft divided by the flow capacity of the formation in md-ft) and the extent of the fracture area, as illustrated in Figure I.
An iterative multiuser decoder for near-capacity communications (1998)

The combination of forward error correction (FEC) coding and random interleaving is shown to overcome the limitations of multiuser detectors/decoders when the user cross correlations are high. In particular, one can asymptotically achieve single-user performance in a highly correlated multiuser system. In addition, an optimal iterative multiuser detector is derived from iterative techniques for cross-entropy minimization. A practical suboptimal implementation of this algorithm is presented, and simulations demonstrate that, even with highly correlated users, it achieves optimal asymptotic efficiency. The effects of the theoretical limits on channel capacity are evident in many of the simulation results. The complexity of the suboptimal algorithm is approximately (O(2/sup K/)+O(2/sup /spl kappa//)) per bit per iteration where K is the number of users and /spl kappa/ is the code constraint length.
Age-Related Differences in Movement Control: Adjusting Submovement Structure To Optimize Performance (1997)

In this experiment older and younger adults were compared on their ability to position a cursor with an electromechanical mouse. Distance of the movement, size of the target, and relative emphasis on the speed or accuracy of the movement were manipulated. The study was designed to isolate and evaluate the effects of age-related differences in the noise-to-force ratio, perceptual feedback efficiency, strategy differences, and the ability to produce force as explanations for age-related differences in movement control. This was done by using two types of movement tasks and by analyzing movement performance according to stages of movement. The study showed that all four factors, when isolated, are significantly different for the two age groups. However, in the task component where all factors could simultaneously affect performance, the age-related difference in performance was less than the difference in either the measure of noise-to-force ratio or perceptual efficiency. Analysis of the submovement structure revealed how older adults compensated for the greater noise and less perceptual efficiency by adjusting the velocity and number of submovements. These findings are discussed in light of the optimized submovement model.
A hermetic chip to chip bonding at low temperature with Cu/In/Sn/Cu joint (2008)

A bonding joint between Cu metallization and evaporated Sn/In composite solder was produced at temperature lower than 200°C in air in this work. The isothermal solidification and subsequent interdiffusion of Cu and Sn/In took place along the bonding couples held at 180°C for 20 minutes. The interfacial reaction and the bonding quality is studied and evaluated. Scanning electron microscopy (SEM) exhibits the joint is uniform along the bonding interface and no crack or voids present, which has an interfacial tensile strength of 52 kg/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The overall bonding is examined by C-mode scanning acoustic microscope (C-SAM). Fine leak rate test shows the leak rate is about 5.8x10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−9</sup> atm·cc/s which indicates a hermetic sealing. Intermetallic compounds (IMCs) such as AuIn <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> , Cu <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</inf> Sn <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</inf> and Cu <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</inf> In <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9</inf> have been detected by means of X-ray diffraction analysis (XRD) and transmission electron microscopy (TEM) accompanied with energy dispersive X-ray (EDX). The chemical composition analysis also reveals that solder interlayers, Sn and In, have been completely converted into IMCs by reacting with Cu. All IMCs formed in the joints have re-melting temperature above 300°C according to Cu-In, Cu-Sn and Au-In phase diagrams. Therefore, the joint can sustain high service temperature due to the presence of IMCs. Such technique producing the joints with the good bond quality and high re-melting point has great potential in electronics and microelectronics packaging such as MEMS packaging and photonic packaging.
The Impact of Contemporary Contact Lenses on Contact Lens Discontinuation (2012)

About 23% of those surveyed had discontinued CL wear permanently. The primary reasons for dropping out continue to be discomfort and dryness. Dropout rates were lower in silicone hydrogel wearers.
Yeast protocols : methods in cell and molecular biology (1996)

Yeast Protocols intends to offer a selection of well-proven proto­ cols in cell and molecular biology, applicable to yeasts including, but certainly not exclusively aimed at, Saccharomyces cerevisiae. Saccharomyces cerevisiae and its very distant cousin, Schizosacc- romyces pombe, are of course now foremost model eukaryotic organisms, and the focus of wide-ranging experimental studies, especially those using molecular genetic techniques. Many of the lat­ ter, such as DNA sequencing and in vitro mutagenesis, are general DNA techniques, well covered in other volumes of Humana's Meth­ ods in Molecular Biology series, and elsewhere. The inclusion of a number of non-DNA techniques in this book is meant to reflect the resurgent interest in yeast cell biology sparked by the development of gene manipulation methods—for example, cellular localization of cloned gene products using microscopical techniques. The presentation of protocols follows the successful Methods in Molecular Biology series format, with a clear sequence of steps and extensive troubleshooting notes. It is our hope that these protocols will be useful not only to established members of the full-time research community, but also to the less experienced—first degree level and masters students undertaking project work, as well as PhD students starting their experimental programs; I am well aware that these young apprentice scientists are not always able to receive the supervision time that they, and indeed their supervisors, would like
Evaluation of the clinical usefulness of isolation of fetal DNA from the maternal circulation (2003)

It is possible to isolate fetal DNA from maternal serum. It is a potentially clinically useful technique in our laboratory and can be used to detect male fetuses, and Rh negative fetuses. To be useful in clinical practice, it is necessary to safeguard against contamination at the time of sample handling, and to use the optimal range of primers available to cover the polymorphisms present within the RhD gene. Although not robust enough yet to be used with diagnostic certainty in our hands, immense improvements in technique, probes and real-time PCR equipment make this type of diagnosis a reality in the near future.