gebhart/patrepeval huggingface dataset:
Using NASA's GeneLab for VESGEN Systems Analysis of Vascular Phenotypes from Stress and Other Signaling Pathways (2016)

One fundamental requirement shared by humans with all higher terrestrial life forms, including other vertebrates, insects, and higher land plants, is a complex, fractally branching vascular system. NASA's VESsel GENeration Analysis (VESGEN) software maps and quantifies vascular trees, networks, and tree-network composites according to weighted physiological rules such as vessel connectivity, tapering and bifurcational branching. According to fluid dynamics, successful vascular transport requires a complex distributed system of highly regulated laminar flow. Microvascular branching rules within vertebrates, dicot leaves and the other organisms therefore display many similarities. A unifying perspective is that vascular patterning offers a useful readout of molecular signaling that necessarily integrates these complex pathways. VESGEN has elucidated changes in vascular pattern resulting from inflammatory, developmental and other signaling within numerous tissues and major model organisms studied for Space Biology. For a new VESGEN systems approach, we analyzed differential gene expression in leaves of Arabidopsis thaliana reported by GeneLab (GLDS-7) for spaceflight. Vascularrelated changes in leaf gene expression were identified that can potentially be phenocopied by mutants in ground-based experiments. To link transcriptional, protein and other molecular change with phenotype, alterations in the spatial and dynamic dimensions of vascular patterns for Arabidopsis leaves and other model species are being co-localized with signaling patterns of single molecular expression analyzed as information dimensions. Previously, Drosophila microarray data returned from space suggested significant changes in genes related to wing venation development that include EGF, Notch, Hedghog, Wingless and Dpp signaling. Phenotypes of increasingly abnormal ectopic wing venation in the (non-spaceflight) Drosophila wing generated by overexpression of a Notch antagonist were analyzed by VESGEN. Other VESGEN research applications include the mouse retina, GI and coronary vessels, avian placental analogs and translational studies in the astronaut retina related to health challenges for long-duration missions.
A Taxonomy of Telemedicine Efforts with Respect to Applications, Infrastructure, Delivery Tools, Type of Setting and Purpose (2005)

In the history of telemedicine, various definitions have been published and numerous terminologies have been coined. The introduction of new technologies played an important role in the changing definitions. After three decades of experience in telemedicine and its variations, the need for a single taxonomy that is detailed enough to define all the terms introduced until today is evident. Taxonomy we propose takes into account purpose, application area, delivery tools, communication infrastructure, and delivery setting dimensions. The purpose is to create a taxonomy that can explain how these dimensions fit together. Our taxonomy helps to categorize and compare current/future telemedicine efforts and plan several emerging telemedicine scenarios using new technology. The paper concludes with an explanation of how the proposed taxonomy can be used by parties involved in telemedicine as a diagnostic tool, and can help them to understand their needs and capabilities for participating in next generation healthcare environments.
Enhanced fluorescence from metal nanoapertures: physical characterizations and biophotonic applications (2010)

Nanoapertures milled in opaque metallic films offer a simple and robust photonic tool to significantly enhance the fluorescence of single molecules. We provide a detailed physical characterization of this phenomenon for apertures milled in gold and aluminum, and discuss its application to biophotonics. For the first time, the most general figures are provided to predict the awaited enhancement factors for almost every kind of fluorescent molecule. This knowledge is essential to discuss the ability to detect low-quantum yield species. We also report the first demonstration of single metal nanoapertures to perform DNA hybridization sensing, and measure similar enhancement factors as for experiments on diffusing molecules.
Clinical and Laboratory Risk Factors for Venous Thromboembolism in Patients with High-Grade Gliomas: Results of a Prospective Study of 107 Newly-Diagnosed Patients. (2008)

Abstract Introduction: Patients with malignant gliomas are at high risk for venous thromboembolism (VTE). The reason for this association is unclear. We sought to identify clinical and laboratory risk factors for VTE in adult patients with high-grade gliomas. Methods: The NABTT CNS Consortium prospectively enrolled patients with newly-diagnosed grade 3 or 4 malignant glioma prior to anti-neoplastic therapy. Patients with a previous history of VTE, anti-neoplastic therapy or on chronic anticoagulation were excluded. At enrollment, we collected demographic and clinical information (age, gender, ethnicity, tumor histopathology and grade, Karnofsky Performance Status (KPS), and ABO blood group) and blood samples for measurement of factor VIII activity (FVIII), fibrinogen, and quantitative D dimer using standard laboratory assays. Endogenous thrombin potential (ETP) was measured using Innovin® and a synthetic chromagenic thrombin substrate on a BCS® coagulation analyzer (Dade Behring Inc. Newark, DE). Fisher’s exact test and the Student’s-T test were used for individual comparison of categorical data and continuous data, respectively. Cox regression modeling was used to examine the association of factors with VTE. The probability of thrombosis-free survival was estimated using the product-limit method of Kaplan and Meier. Results: One hundred seven patients (49% male) with a median age 57 years (range 28–85) were enrolled between 6/05 and 4/08. Ninety patients (84%) had glioblastoma multiforme. Median KPS at enrollment was 90. After a median follow up of 324 days, twenty two patients (21%) have suffered VTE and 45 patients (42%) have died. Median time to VTE was 67 days post-operation (95% Confidence Interval 33–128). No fatal VTE have occurred. VTE was associated with a lower KPS (p=0.008), higher baseline FVIII (178% versus 151%, p=0.04) and greater ETP (473nmol/L versus 438nmol/L, p=0.04) but not with ABO blood group. Patients suffering VTE were more likely to die than patients without VTE (68% versus 35%, p&amp;lt;0.005). Conclusions: In a prospective cohort study of newly-diagnosed patients with high-grade gliomas, we have identified a substantial incidence of VTE. Patients with VTE had a lower initial KPS, higher factor VIII activity, greater ETP and were more likely to die than patients without VTE. With additional follow up, we hope to identify additional clinical and laboratory risk factors for VTE. These data should lead to greater insight into the pathogenesis of VTE in patients with high-grade gliomas and facilitate identification of patients in whom primary long-term VTE prophylaxis may be beneficial.
Fast computation of the ambiguity function and the Wigner distribution on arbitrary line segments (2001)

By using the fractional Fourier transformation of the time-domain signals, closed-form expressions for the projections of their auto or cross ambiguity functions are derived. Based on a similar formulation for the projections of the auto and cross Wigner distributions and the well known two-dimensional (2-D) Fourier transformation relationship between the ambiguity and Wigner domains, closed-form expressions are obtained for the slices of both the Wigner distribution and the ambiguity function. By using discretization of the obtained analytical expressions, efficient algorithms are proposed to compute uniformly spaced samples of the Wigner distribution and the ambiguity function located on arbitrary line segments. With repeated use of the proposed algorithms, samples in the Wigner or ambiguity domains can be computed on non-Cartesian sampling grids, such as polar grids.
Circuits of Surveillance. (2004)

This paper examines the increasing police use of DNA profiling and databasing as a developing instrumentality of modern state surveillance. It briefly notes previously published work on a variety of surveillance technologies and their role in the governance of social action and social order. It then argues that there are important differences amongst the ways in which several such technologies construct and use identificatory artefacts, their orientations to human subjectivity, and their role in the governmentality of citizens and others. The paper then describes the novel and powerful form of bio-surveillance offered by DNA profiling and illustrates this by reference to an ongoing empirical study of the police uses of the UK National DNA Database for the investigation of crime. It is argued that DNA profiling and databasing enable the construction of a 'closed circuit' of surveillance of a defined population.
Hydrogels as controlled drug delivery systems: Synthesis, crosslinking, water and drug transport mechanism (2006)

Hydrogels are presently under investigation as a delivery system for bioactive molecules, because of their similar physical properties as that of living tissue, which is due to their high water content, soft and rubbery consistency, and low interfacial tension with water or biological fluids. Anionic hydrogels are used in the design of intelligent controlled release devices for site-specific drug delivery of therapeutic proteins to the large intestine, where the biological activity of the proteins are prolonged, and cationic hydrogels are studied for the development of self-regulated insulin delivery system, which releases the insulin in response to changing glucose concentration. The different methods of preparation of hydrogels, novel methods of crosslinking used in the preparation of hydrogels, the mechanism of water transport through the ionic hydrogels, and the release mechanism of the solute from the hydrogels, are discussed in the present article.
Erratum: one dimensional particle systems as extended Pfaffian point processes (2015)

This erratum corrects the statement of the main result in <a href="http://dx.doi.org/10.1214/ECP.v17-2133">ECP volume 17 paper 40</a>, which establishes that the mulit-time particle densitites for certain intercating particle systems on the real line are extended Pfaffian point processes.
Age-related declines in hemispheric asymmetry as revealed in the binaural interaction component (2014)

The binaural interaction component (BIC) is a physiological index of binaural processing. The BIC is defined as the brain activity resulting from binaural (diotic or dichotic) stimulus presentation minus the brain activity summed across successive monaural stimulus presentations. Smaller binaural-induced activity relative to summed monaural activity is thought to reflect neural inhibition in the central auditory pathway. Since aging is commonly associated with reduced inhibitory processes, we evaluate the hypothesis that the BIC is reduced with increasing age. Furthermore, older listeners typically have reduced hemispheric asymmetry relative to younger listeners, interpreted in terms of compensation or recruitment of neural resources and considered an indication of age-related neural plasticity. Binaural stimuli designed to elicit a lateralized percept generate maximum neural activity in the hemisphere opposite the lateralized position. In this investigation, we evaluated the hypothesis that the BIC resulting from stimuli lateralized to one side (due to interaural time differences) results in less hemispheric asymmetry in older than younger listeners with normal hearing. Behavioral data were obtained to assess the acuity of binaural processing. Data support the interpretation that aging is marked by reduced central auditory inhibition, reduced temporal processing, and broader distribution of activity across hemispheres compared to young adults.
A role for exposed mannosylations in presentation of human therapeutic self-proteins to CD4+ T lymphocytes (2007)

Several therapeutic self-proteins elicit immune responses when administered to patients. Such adverse immune responses reduce drug efficacy. To induce an immune response, a protein must interact with different immune cells, including antigen-presenting cells, T cells, and B cells. Each cell type recognizes distinct immunogenic patterns on antigens. Mannose-terminating glycans have been identified as pathogen-associated molecular patterns that are essential for internalization of microbes by antigen-presenting cells, leading to presentation. Here, we have investigated the importance of exposed mannosylation on an immunogenic therapeutic self-protein, procoagulant human factor VIII (FVIII). Administration of therapeutic FVIII to hemophilia A patients induces inhibitory anti-FVIII antibodies in up to 30% of the cases. We demonstrate that entry of FVIII into human dendritic cells (DC) leading to T cell activation, is mediated by mannose-terminating glycans on FVIII. Further, we identified macrophage mannose receptor (CD206) as a candidate endocytic receptor for FVIII on DC. Saturation of mannose receptors on DC with mannan, and enzymatic removal of mannosylated glycans from FVIII lead to reduced T cell activation. The interaction between FVIII and CD206 was blocked by VWF, suggesting that, under physiological conditions, the intrinsic mannose-dependent immunogenicity of FVIII is quenched by endogenous immunochaperones. These data provide a link between the mannosylation of therapeutic self-proteins and their iatrogenic immunogenicity. Such a link would be of special relevance in the context of replacement therapy where mechanisms of central and peripheral tolerance have not been established during ontogeny because of the absence of the antigen.
Prescribing patterns in hypertension: the emerging role of fixed-dose combinations for attaining BP goals in hypertensive patients (2008)

Guidelines for hypertension management clearly support the greater use of multidrug therapy, especially in high-risk patients. FDCs (e.g., various emerging CCB/ARB combinations) are a valuable option for such high-risk patients, as these combinations offer the potential to reduce adverse events, increase compliance, lower treatment costs, and improve BP goal-attainment rates.
Sonochemical synthesis of supersaturated Ga–Al liquid-alloy fine particles and Al3+-doped γ-Ga2O3 nanoparticles by direct oxidation at near room temperature (2022)

In this study, we investigated the fabrication of supersaturated gallium (Ga)-aluminum (Al) liquid alloy and Al<sup>3+</sup>-doped γ-Ga<sub>2</sub>O<sub>3</sub> nanoparticles (NPs) at near room temperature (60 °C) using sonochemical and sonophysical effects. Supersaturated Ga-Al liquid alloy microparticles (D<sub>av</sub> = 1.72 µm) were formed and stabilized at 60 °C by the thermal nonequilibrium field provided by sonochemical hot spots. Compared with liquid Ga, supersaturated Ga-Al liquid alloy was rapidly oxidized to a uniform oxide without Al<sub>2</sub>O<sub>3</sub> or Al deposition. Thus, ultrafine Al<sup>3+</sup>-doped γ-Ga<sub>2</sub>O<sub>3</sub> NPs were obtained after only 1 h of ultrasonic irradiation at 60 °C. The oxidation of liquid Ga was remarkably accelerated by alloying with metallic Al and ultrasonic irradiation, and the time was shortened. The average diameter and surface area of the γ-Ga<sub>2</sub>O<sub>3</sub>-based NPs were 59 nm and 181 m<sup>2</sup>/g, respectively. Compared with γ-Ga<sub>2</sub>O<sub>3</sub>, the optical bandgap of the Al<sup>3+</sup>-doped γ-Ga<sub>2</sub>O<sub>3</sub> NPs was broadened, and the thermal stability improved, indicating Al<sup>3+</sup>-doping into the γ-Ga<sub>2</sub>O<sub>3</sub> lattice. However, the lattice constant of γ-Ga<sub>2</sub>O<sub>3</sub> was almost unchanged with or without Al<sup>3+</sup>-doping. Al<sup>3+</sup> was introduced into the defect sites of Ga<sup>3+</sup>, which were massively induced in the defective spinel structure during ultrasonic processing. Therefore, sonochemical processing, which provides nonequilibrium reaction fields, is suitable for the synthesis of supersaturated and metastable materials in metals and ceramics fields.
Model-Driven Development in the Enterprise (2008)

For decades, model-driven development has been the perfect example of software-engineering hype. Just as bees are attracted to honey, we software engineers look for ways of simplifying our work and automating endless change cycles. Today, after many years of experimenting with MDD, mostly in limited-size scientific environments, the three ingredients of methodology, notation, and tools seem to fit and support each other. Round-trip engineering might still be some years from day-to-day practice, but simple forward engineering with MDD is readily available to software practitioners now. And it works. In this issue's column, Axel Uhl, chief development architect in SAP's Office of the CTO, looks into MDD methodologies and tool support. He shares his many practical experiences to help you master the ramp-up for your own enterprise.
Use of VLANs for IPv4-IPv6 Coexistence in Enterprise Networks (2006)

Ethernet VLANs are quite commonly used in enterprise networks for the
purposes of traffic segregation. This document describes how such
VLANs can be readily used to deploy IPv6 networking in an enterprise,
which focuses on the scenario of early deployment prior to
availability of IPv6-capable switch-router equipment. In this method,
IPv6 may be routed in parallel with the existing IPv4 in the
enterprise and delivered at Layer 2 via VLAN technology. The IPv6
connectivity to the enterprise may or may not enter the site via the
same physical link. This memo provides information for the Internet
community.
Antibodies Specific for the Hia Adhesion Proteins of NontypeableHaemophilus influenzaeMediate Opsonophagocytic Activity (2009)

The Hia autotransporter proteins are highly immunogenic surface adhesins expressed by nontypeable Haemophilus influenzae (NTHI). The objective of our study was to assess the opsonophagocytic activity of anti-Hia antibodies against homologous and heterologous NTHI. A segment of the hia gene that encodes a surface-exposed portion of the H. influenzae strain 11 Hia protein was cloned into a pGEMEX-2 expression vector. Escherichia coli JM101 was transformed with the resulting pGEMEX-Hia BstEII del recombinant plasmid, and recombinant fusion protein was recovered. An immune serum against recombinant GEMEX-Hia (rGEMEX-Hia)-mediated killing of the homologous NTHI strain 11 at a 1:160 titer and five heterologous Hia-expressing strains at titers of > or =1:40. Immune serum did not mediate killing of two Hia-knockout strains whose hia genes were inactivated but did mediate killing of one knockout strain at a high titer after the strain was transformed with a plasmid containing the hia gene. Immune serum did not mediate killing of HMW1/HMW2-expressing NTHI strains, which do not express the Hia adhesin. However, when two representative HMW1/HMW2-expressing strains were transformed with the plasmid containing the hia gene, they expressed abundant Hia and were susceptible to killing by the immune serum. Immune serum did not mediate killing of HMW1/HMW2-expressing strains transformed with the plasmid without the hia gene. Our results demonstrate that the Hia proteins of NTHI are targets of opsonophagocytic antibodies and that shared epitopes recognized by such antibodies are present on the Hia proteins of unrelated NTHI strains. These data argue for the continued investigation of the Hia proteins as vaccine candidates for the prevention of NTHI disease.
Bee Identification Problem for DNA Strands (2023)

Motivated by DNA-based applications, we generalize the bee identification problem proposed by Tandon et al. (2019). In this setup, we transmit all <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$M$ </tex-math></inline-formula> codewords from a codebook over some channel and each codeword results in <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$N$ </tex-math></inline-formula> noisy outputs. Then our task is to identify each codeword from this unordered set of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$MN$ </tex-math></inline-formula> noisy outputs. First, via a reduction to a minimum-cost flow problem on a related bipartite flow network called the input-output flow network, we show that the problem can be solved in <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$O(M^{3})$ </tex-math></inline-formula> time in the worst case. Next, we consider the deletion and the insertion channels individually, and in both cases, we study the expected number of edges in their respective input-output networks. Specifically, we obtain closed expressions for this quantity for certain codebooks and when the codebook comprises all binary words, we show that this quantity is sub-quadratic when the deletion or insertion probability is less than 1/2. This then implies that the expected running time to perform joint decoding for this codebook is <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$o(M^{3})$ </tex-math></inline-formula>. For other codebooks, we develop methods to compute the expected number of edges efficiently. Finally, we adapt classical peeling-decoding techniques to reduce the number of nodes and edges in the input-output flow network.
On the mechanism of reductive degradation of dithiocarbonates by tributylstannane (1988)

Product analysis of the reaction between O-isopropyl S-4-phenylbut-3-enyl dithiocarbonate and tributylstannane, initiated by azoisobutyronitrile in boiling benzene or toluene, indicates that the first step in the reductive degradation of dithiocarbonates by trialkylstannanes involves the homolytic attack of trialkyltin radical on the thioxo sulphur according to the Barton mechanism, rather than on the thio sulphur as displayed in a proposed alternative mechanism.