gebhart/patrepeval huggingface dataset:
Laboratory Diagnosis of Invasive Pneumococcal Disease (2008)

The laboratory diagnosis of invasive pneumococcal disease (IPD) continues to rely on culture-based methods that have been used for many decades. The most significant recent developments have occurred with antigen detection assays, whereas the role of nucleic acid amplification tests has yet to be fully clarified. Despite developments in laboratory diagnostics, a microbiological diagnosis is still not made in most cases of IPD, particularly for pneumococcal pneumonia. The limitations of existing diagnostic tests impact the ability to obtain accurate IPD burden data and to assess the effectiveness of control measures, such as vaccination, in addition to the ability to diagnose IPD in individual patients. There is an urgent need for improved diagnostic tests for pneumococcal disease--especially tests that are suitable for use in underresourced countries.
Performance of 16 kbit/s GMSK Transmission with Postdetection Selection Diversity in Land Mobile Radio (1984)

Through laboratory simulation tests and field experiments in the Tokyo metropolitan area, 16 kbit/s Gaussian filtered minimum shift keying (GMSK) transmission performance has been experimentally clarified in the 920 MHz land mobile radio environment. The experimental results agree closely with theory, and they show that fast multipath fading severely degrades average bit error rate (BER) performance in GMSK transmission. However, a space diversity reception technique using a postdetection selection combining scheme is able to efficiently mitigate the fast multipath fading.
Interpreting and Reporting Results Based on Patient-Reported Outcomes (2021)

ABSTRACT This article deals with the incorporation of patient-reported outcomes (PROs) into clinical trials and focuses on issues associated with the interpretation and reporting of PRO data. The primary focus and context of this information relates to the evidentiary support and reporting for a labeling or advertising claim of a PRO benefit for a new or approved pharmaceutical product. This manuscript focuses on issues associated with assessing clinical significance and common pitfalls to avoid in presenting results related to PROs. Specifically, the questions addressed by this manuscript involve: What are the best methods to assess clinical significance for PROs? How should investigators present PRO data most effectively in a Food and Drug Administration (FDA) application? In labeling or in a scientific publication? Guidelinesfor interpreting clinical significance of PROs and for comprehensively reporting on the methods, measures and results of clinical trials that incorporate PROs are important for clinicians, regulatory agencies, and most of all to patients. Clear specifications for considering a finding on a PRO measure, as clinically meaningful, need to be determined by instrument developers and psychometricians; they need to be reported for all clinical trials involving PRO end points. Clinical trial reports need to be comprehensive, clear, and sufficient to enable any reader to understand the methods, PRO measures, statistical analysis, and results.
Inhibition of angiogenesis and vascular leakiness by angiopoietin-related protein 4. (2003)

Angiopoietins and angiopoietin-related proteins (ARPs) have been shown to regulate angiogenesis, a process essential for various neovascular diseases including tumors. Here, we identify ARP4/fasting-induced adipose factor/peroxisome proliferator-activated receptor gamma angiopoietin-related as a novel antiangiogenic modulatory factor. We hypothesized that ARP4 may regulate angiogenesis. In vitro experiments using purified recombinant ARP4 protein revealed that ARP4 markedly inhibited the proliferation, chemotaxis, and tubule formation of endothelial cells. Moreover, using corneal neovascularization and Miles permeability assays, we found that both vascular endothelial growth factor-induced in vivo angiogenesis and vascular leakiness were significantly inhibited by the addition of ARP4. Finally, we found remarkable suppression of tumor growth within the dermal layer associated with decreased numbers of invading blood vessels in transgenic mice that express ARP4 in the skin driven by the keratinocyte promoter. These findings demonstrate that ARP4 functions as a novel antiangiogenic modulatory factor and indicate a potential therapeutic effect of ARP4 in neoplastic diseases.
Comparison of intranasal triamcinolone acetonide with oral loratadine in the treatment of seasonal ragweed-induced allergic rhinitis. (1997)

A double-blind, randomized, multicenter, parallel-group controlled study compared the efficacy and safety of intranasal triamcinolone acetonide (220 micrograms/day) and oral loratadine (10 mg/day) in patients with at least two seasons of ragweed-induced seasonal allergic rhinitis. A 28-day screening period, including a 5-day baseline period, preceded a 4-week treatment period. Reduction in rhinitis symptom scores was evident in both groups as early as day 1, with no significant between-group differences during week 1. At weeks 2, 3, and 4, patients treated with triamcinolone acetonide were significantly (P < 0.05) more improved in total nasal score, nasal itch, nasal stuffiness, and sneezing than were patients treated with loratadine. At weeks 3 and 4, rhinorrhea and ocular symptoms were significantly (P < 0.05) more improved from baseline among triamcinolone acetonide patients compared with loratadine patients. There was no significant between-group difference in relief from postnasal drip at any time point. Physicians' global evaluations significantly (P = 0.002) favored triamcinolone acetonide at the final visit, with moderate to complete relief of symptoms attained by 68% of triamcinolone acetonide patients and 59% of loratadine patients. Over the 4-week treatment period, triamcinolone acetonide patients had significantly greater improvement in total nasal score, nasal itch, nasal stuffiness, sneezing, and ocular symptoms. Both treatments were well tolerated, with headache being the most frequently reported drug-related adverse effect in both the triamcinolone acetonide (15%) and loratadine (11%) groups. These results indicate that triamcinolone acetonide is more effective than oral loratadine in relieving the symptoms of ragweed-induced seasonal allergic rhinitis.
Secondary Structure of the Third Extracellular Loop Responsible for Ligand Selectivity of a Mammalian Gonadotropin-Releasing Hormone Receptor (2002)

The extracellular loop 3 (ECL3) of the mammalian gonadotropin-releasing hormone receptor (GnRH-R) contains an acidic amino acid (Glu(301) in the mouse GnRH-R) that confers agonist selectivity for Arg(8) in mammalian GnRH. It is proposed that a specific conformation of ECL3 is necessary to orientate the carboxyl side chain of the acidic residue for interaction with Arg(8) of GnRH, which is supported by decreased affinity for Arg(8) GnRH but not Gln(8) GnRH when an adjacent Pro is mutated to Ala. To probe the structural contribution of the loop domain to the proposed presentation of the carboxyl side chain, we synthesized a model peptide (CGPEMLNRVSEPGC) representing residues 293-302 of mouse ECL3, where Cys and Gly residues are added symmetrically at the N and C termini, respectively, allowing the introduction of a disulfide bridge to simulate the distances at which the ECL3 is tethered to the transmembrane domains 6 and 7 of the receptor. The ability of the ECL3 peptide to bind GnRH with low affinity was demonstrated by its inhibition of GnRH stimulation of inositol phosphate production in cells expressing the GnRH-R. The CD bands of the ECL3 peptides exhibited a superposition of predominantly unordered structure and partial contributions from beta-sheet structure. Likewise, the analysis of the amide I and amide III bands from micro-Raman and FT Raman experiments revealed mainly unordered conformations of the cyclic and of the linear peptide. NMR data demonstrated the presence of a beta-hairpin among an ensemble of largely disordered structures in the cyclic peptide. The location of the turn linking the two strands of the hairpin was assigned to the three central residues L(296), N(297), and R(298). A small population of structured species among an ensemble of predominantly random coil conformation suggests that the unliganded receptor represents a variety of structural conformers, some of which have the potential to make contacts with the ligand. We propose a mechanism of receptor activation whereby binding of the agonist to the inactive receptor state induces and stabilizes a particular structural state of the loop domain, leading to further conformational rearrangements across the transmembrane domain and signal propagating interaction with G proteins. Interaction of the Glu(301) of the receptor with Arg(8) of GnRH induces a folded configuration of the ligand. Our proposal thus suggests that conformational changes of both ligand and receptor result from this interaction.
Handling of packet dependencies (2002)

Network processors are being asked to perform increasingly complex operations on packets of information at faster and faster rates. Because processor performance and memory cycle times are not keeping up with this demand, there is a fundamental need for simultaneous processing of multiple packets, and the degree of this parallelism is increasing. Sometimes a dependency exists between two packets currently being operated on, and as the ratio of packet processing time to packet transmission time increases, these dependencies are more likely to impact performance. Thus, the way packet dependencies are handled will become critical. In this paper we show that there is potentially a dramatic difference in performance between optimal and non-optimal solutions. We argue that this is the key challenge that must be addressed in highly parallel network processors. We discuss how work in thread level speculation relates to this problem and describe a practical hardware implementation that requires little or no changes to software and with near optimal performance.
A Fiber-Optic Nerve Stimulation Probe Integrated with a Precise Common-Path Optical Coherence Tomography Distance Sensor (2010)

We have demonstrated a simple and effective common-path optical coherence tomography guided fiber probe for optical nerve stimulation which improves the spatial precision and safety of stimulation laser power delivery.
Distinct Ligand-binding Modes for Integrin αvβ3-Mediated Adhesion to Fibronectinversus Vitronectin (2001)

Cell surface integrins can adopt distinct conformations in response to ligand binding and intracellular signals. Several integrins including alpha(v)beta(3) can bind to multiple ligands. The binding of alpha(v)beta(3) to fibronectin and vitronectin was used as a model to determine whether the same or distinct forms of the receptor were utilized in strong binding to the two different ligands. A spinning-disc device was used to measure the relative strength of the alpha(v)beta(3)-ligand bonds. The initial binding reaction for both ligands occurred in the absence of metabolic energy and resulted in a strong adhesion to fibronectin but a weak adhesion to vitronectin. Increases in the strength of the alpha(v)beta(3)-vitronectin bond required phosphorylation of the beta(3) cytoplasmic domain, intracellular signals, and the binding of cytoskeletal proteins to cytoplasmic domains of beta(3) controlled by Tyr-747 and Tyr-759. In contrast, alpha(v)beta(3)-mediated adhesion to fibronectin was unaffected by phorbol 12-myristate 13-acetate, mutations of Tyr-747 and Tyr-759 to phenylalanine, or availability of metabolic energy. This suggests that strong adhesion to fibronectin used the initial binding conformation, whereas strong binding to vitronectin required signaling-induced changes in the conformation of alpha(v)beta(3).
Exponentiated backpropagation algorithm for multilayer feedforward neural networks (2004)

The gradient descent backpropagation learning algorithm is based on minimizing the mean square error. An alternate approach to gradient descent is the exponentiated gradient descent algorithm which minimizes the relative entropy. Exponentiated gradient descent applied to backpropagation is proposed for a multilayer feedforward neural network. The learning rules for changing weights in the output layer as well the hidden layer neurons in the network are developed. Simulations were performed to explore the convergence and learning of the backpropagation algorithm with exponentiated gradient descent. Accuracy obtained with exponentiated gradient descent back propagation was comparable to the gradient descent back propagation while convergence was faster. The results show that exponentiated gradient descent can be extended to a multilayer feedforward neural network and used in pattern classification applications.
Bile Duct Ligation in Mice: Induction of Inflammatory Liver Injury and Fibrosis by Obstructive Cholestasis (2015)

In most vertebrates, the liver produces bile that is necessary to emulsify absorbed fats and enable the digestion of lipids in the small intestine as well as to excrete bilirubin and other metabolic products. In the liver, the experimental obstruction of the extrahepatic biliary system initiates a complex cascade of pathological events that leads to cholestasis and inflammation resulting in a strong fibrotic reaction originating from the periportal fields. Therefore, surgical ligation of the common bile duct has become the most commonly used model to induce obstructive cholestatic injury in rodents and to study the molecular and cellular events that underlie these pathophysiological mechanisms induced by inappropriate bile flow. In recent years, different surgical techniques have been described that either allow reconnection or reanastomosis after bile duct ligation (BDL), e.g., partial BDL, or other microsurgical methods for specific research questions. However, the most frequently used model is the complete obstruction of the common bile duct that induces a strong fibrotic response after 21 to 28 days. The mortality rate can be high due to infectious complications or technical inaccuracies. Here we provide a detailed surgical procedure for the BDL model in mice that induce a highly reproducible fibrotic response in accordance to the 3R rule for animal welfare postulated by Russel and Burch in 1959.
Donor selection for natural killer cell receptor genes leads to superior survival after unrelated transplantation for acute myelogenous leukemia (2010)

Killer-cell immunoglobulin-like receptor (KIR) genes form a diverse, immunogenetic system. Group A and B KIR haplotypes have distinctive centromeric (Cen) and telomeric (Tel) gene-content motifs. Aiming to develop a donor selection strategy to improve transplant outcome, we compared the contribution of these motifs to the clinical benefit conferred by B haplotype donors. We KIR genotyped donors from 1409 unrelated transplants for acute myelogenous leukemia (AML; n = 1086) and acute lymphoblastic leukemia (ALL; n = 323). Donor KIR genotype influenced transplantation outcome for AML but not ALL. Compared with A haplotype motifs, centromeric and telomeric B motifs both contributed to relapse protection and improved survival, but Cen-B homozygosity had the strongest independent effect. With Cen-B/B homozygous donors the cumulative incidence of relapse was 15.4% compared with 36.5% for Cen-A/A donors (relative risk of relapse 0.34; 95% confidence interval 0.2-0.57; P < .001). Overall, significantly reduced relapse was achieved with donors having 2 or more B gene-content motifs (relative risk 0.64; 95% confidence interval 0.48-0.86; P = .003) for both HLA-matched and mismatched transplants. KIR genotyping of several best HLA-matched potential unrelated donors should substantially increase the frequency of transplants by using grafts with favorable KIR gene content. Adopting this practice could result in superior disease-free survival for patients with AML.
Silicon-substrate intracortical microelectrode arrays for long-term recording of neuronal spike activity in cerebral cortex (2003)

This study investigated the use of planar, silicon-substrate microelectrodes for chronic unit recording in the cerebral cortex. The 16-channel microelectrodes consisted of four penetrating shanks with four recording sites on each shank. The chronic electrode assembly included an integrated silicon ribbon cable and percutaneous connector. In a consecutive series of six rats, 5/6 (83%) of the implanted microelectrodes recorded neuronal spike activity for more than six weeks, with four of the implants (66%) remaining functional for more than 28 weeks. In each animal, more than 80% of the electrode sites recorded spike activity over sequential recording sessions during the postoperative time period. These results provide a performance baseline to support further electrode system development for intracortical neural implant systems for medical applications.
Statistical region merging (2004)

This paper explores a statistical basis for a process often described in computer vision: image segmentation by region merging following a particular order in the choice of regions. We exhibit a particular blend of algorithmics and statistics whose segmentation error is, as we show, limited from both the qualitative and quantitative standpoints. This approach can be efficiently approximated in linear time/space, leading to a fast segmentation algorithm tailored to processing images described using most common numerical pixel attribute spaces. The conceptual simplicity of the approach makes it simple to modify and cope with hard noise corruption, handle occlusion, authorize the control of the segmentation scale, and process unconventional data such as spherical images. Experiments on gray-level and color images, obtained with a short readily available C-code, display the quality of the segmentations obtained.
Genetically Engineered Nanofiber-Like Viruses For Tissue Regenerating Materials (2009)

Controlling structural organization and signaling motif display of biomimetic matrices at the nanometer scale is of great importance to the functional design of tissue regenerating materials. We have genetically engineered M13 bacteriophage (phage), naturally occurring nanofiber-like viruses, to display a high density of cell-signaling peptides on their major coat proteins. Structural orientation of these phage building blocks can be achieved due to their long-rod shape and monodispersity, which lead them to self-assemble into directionally organized liquid crystalline-like materials. We showed that the constructed viral nanofiber scaffolds were able to support neural progenitor cell proliferation and differentiation as well as direct orientation of their growth in three dimensions. Such functionalized and structurally aligned phage matrices offer promising opportunities for therapies that address challenging medical problems, such as nerve tissue regeneration after spinal cord injuries, or as in vitro model systems for studying complicated cell signaling environments.
Structure and Biodistribution Relationships of Photodynamic Sensitizers* (1996)

Photodynamic therapy (PDT) has, during the last quarter century, developed into a fully fledged biomedical field with its own association, the International Photodynamic Association (IPA) and regular conferences devoted solely to this topic. Recent approval of the first PDT sensitizer, Photofrin (porfimer sodium), by health boards in Canada, Japan, the Netherlands and United States for use against certain types of solid tumors represents, perhaps, the single most significant-indicator of the progress of PDT from a laboratory research concept to clinical reality. The approval of Photofrin will undoubtedly encourage the accelerated development of second-generation photosensitizers, which have recently been the subject of intense study. Many of these second-generation drugs show significant differences, when compared to Photofrin, in terms of treatment times postinjection, light doses and drug doses required for optimal results. These differences can ultimately be attributed to variations in either the quantum efficiency of the photosensitizer in situ, which is in turn affected by aggregation state, localized concentration of endogenous quenchers and primary photophysics of the dye, or the intratumoral and intracellular localization of the photosensitizer at the time of activation with light. The purpose of this review is to bring together data relating to the biodistribution and pharmacokinetics of second-generation sensitizers and attempt to correlate this with structural and electronic features of these molecules. As this requires a clear knowledge of photosensitizer structure, only chemically well-characterized compounds are included, e.g. Photofrin and crude sulfonated phthalocyanines have been excluded as they are known to be complex mixtures. Nonporphyrin-based photosensitizers, e.g. rose bengal and the hypericins, have also been omitted to allow meaningful comparisons to be made between different compounds. As the intracellular distribution of photosensitizers to organelles and other subcellular structures can have a large effect on PDT efficacy, a section will be devoted to this topic.
Parameter-free geometric document layout analysis (2001)

Automatic transformation of paper documents into electronic documents requires geometric document layout analysis at the first stage. However, variations in character font sizes, text line spacing, and document layout structures have made it difficult to design a general-purpose document layout analysis algorithm for many years. The use of some parameters has therefore been unavoidable in previous methods. The authors propose a parameter-free method for segmenting the document images into maximal homogeneous regions and identifying them as texts, images, tables, and ruling lines. A pyramidal quadtree structure is constructed for multiscale analysis and a periodicity measure is suggested to find a periodical attribute of text regions for page segmentation. To obtain robust page segmentation results, a confirmation procedure using texture analysis is applied to only ambiguous regions. Based on the proposed periodicity measure, multiscale analysis, and confirmation procedure, we could develop a robust method for geometric document layout analysis independent of character font sizes, text line spacing, and document layout structures. The proposed method was experimented with the document database from the University of Washington and the MediaTeam Document Database. The results of these tests have shown that the proposed method provides more accurate results than previous ones.