gebhart/patrepeval huggingface dataset:
NetScope: traffic engineering for IP networks (2000)

Managing large IP networks requires an understanding of the current traffic flows, routing policies, and network configuration. However, the state of the art for managing IP networks involves manual configuration of each IP router, and traffic engineering based on limited measurements. The networking industry is sorely lacking in software systems that a large Internet service provider can use to support traffic measurement and network modeling, the underpinnings of effective traffic engineering. This article describes the AT&T Labs NetScope, a unified set of software tools for managing the performance of IP backbone networks. The key idea behind NetScope is to generate global views of the network on the basis of configuration and usage data associated with the individual network elements. Having created an appropriate global view, we are able to infer and visualize the networkwide implications of local changes in traffic, configuration, and control. Using NetScope, a network provider can experiment with changes in network configuration in a simulated environment rather than the operational network. In addition, the tool provides a sound framework for additional modules for network optimization and performance debugging. We demonstrate the capabilities of the tool through an example traffic engineering exercise of locating a heavily loaded link, identifying which traffic demands flow on the link, and changing the configuration of intradomain routing to reduce the congestion.
A Composite from Poly(m-phenylenevinylene-co-2,5-dioctoxy-p-phenylenevinylene) and Carbon Nanotubes: A Novel Material for Molecular Optoelectronics (1998)

A novel material for molecular optoelectronics consisting of a composite of carbon nanotubes and poly(m-phenylenevinylene-co-2,5-dioctoxy-p-phenylenevinylene) (PmPV) is reported. Incorporation of the nanotubes is demonstrated to increase the electrical conductivity of the polymer by up to eight orders of magnitude. The nanotubes appear to act as nanometric heat sinks, preventing the build up of large thermal effects, which degrade these conjugated systems. It is also shown that the composite can be used as the emissive layer in an organic light-emitting diode, which promises future applications in optoelectronics.
Primary Pulmonary Hypertension (1980)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), emerged in China in December 2019 and quickly spread around the globe, killing more than 4 million people and causing a severe economic crisis. ...Read More
Preselection of shotgun clones by oligonucleotide fingerprinting: an efficient and high throughput strategy to reduce redundancy in large-scale sequencing projects (1998)

Large-scale genomic sequencing projects generally rely on random sequencing of shotgun clones, followed by different gap closing strategies. To reduce the overall effort and cost of those projects and to accelerate the sequencing throughput, we have developed an efficient, high throughput oligonucleotide fingerprinting protocol to select optimal shotgun clone sets prior to sequencing. Both computer simulations and experimental results, obtained from five PAC-derived shotgun libraries spanning 535 kb of the 17p11.2 region of the human genome, demonstrate that at least a 2-fold reduction in the number of sequence reads required to sequence an individual genomic clone (cosmid, PAC, etc.) can be achieved. Treatment of clone contigs with significant clone overlaps will allow an even greater reduction.
Local density fluctuations, hyperuniformity, and order metrics (2003)

Questions concerning the properties and quantification of density fluctuations in point patterns continue to provide many theoretical challenges. The purpose of this paper is to characterize certain fundamental aspects of local density fluctuations associated with general point patterns in any space dimension d. Our specific objectives are to study the variance in the number of points contained within a regularly shaped window Omega of arbitrary size, and to further illuminate our understanding of hyperuniform systems, i.e., point patterns that do not possess infinite-wavelength fluctuations. For large windows, hyperuniform systems are characterized by a local variance that grows only as the surface area (rather than the volume) of the window. We derive two formulations for the number variance: (i) an ensemble-average formulation, which is valid for statistically homogeneous systems, and (ii) a volume-average formulation, applicable to a single realization of a general point pattern in the large-system limit. The ensemble-average formulation (which includes both real-space and Fourier representations) enables us to show that a homogeneous point pattern in a hyperuniform state is at a "critical point" of a type with appropriate scaling laws and critical exponents, but one in which the direct correlation function (rather than the pair correlation function) is long ranged. We also prove that the non-negativity of the local number variance does not add a new realizability condition on the pair correlation. The volume-average formulation is superior for certain computational purposes, including optimization studies in which it is desired to find the particular point pattern with an extremal or targeted value of the variance. We prove that the simple periodic linear array yields the global minimum value of the average variance among all infinite one-dimensional hyperuniform patterns. We also evaluate the variance for common infinite periodic lattices as well as certain nonperiodic point patterns in one, two, and three dimensions for spherical windows, enabling us to rank-order the spatial patterns. Our results suggest that the local variance may serve as a useful order metric for general point patterns. Contrary to the conjecture that the lattices associated with the densest packing of congruent spheres have the smallest variance regardless of the space dimension, we show that for d=3, the body-centered cubic lattice has a smaller variance than the face-centered cubic lattice. Finally, for certain hyperuniform disordered point patterns, we evaluate the direct correlation function, structure factor, and associated critical exponents exactly.
Modeling, post COVID-19 (2020)

Much of the public first learned about epidemiological modeling during the early months of the coronavirus disease 2019 (COVID-19) pandemic. The first models resulted in more confusion than clarity. Even though coronavirus cases were rising exponentially in the United States and Europe, some models predicted a rapid peak followed by a rapid decline, whereas other models predicted cycles of infection continuing over several years. Much has been learned since those early months. In retrospect, it is clear that modeling requires both reliable data and an accurate understanding of how disease spreads, and that the field of epidemiological modeling requires a diversity of approaches. Support for this field must increase and be coordinated, with a designation of responsibilities among funding agencies.
Possible Role of Cytomegalovirus in Atherogenesis (1990)

ATHEROSCLEROTIC plaques consist of complex accumulations produced by arterial smooth muscle cells, which proliferate excessively at the site of plaque formation. To explain the onset of this abnormal cellular proliferation, it has been suggested that injury to the endothelial lining of the artery results in exposure of underlying smooth muscle cells to hormones, low-density lipoproteins, and various growth-promoting factors associated with serum and platelets. It has also been suggested that a transforming event causes arterial smooth muscle cells to begin dividing and form a focus of proliferating cells. The possibility of viral infection playing a role in the pathogenesis of atherosclerosis is compatible with the hypotheses described above, since viruses may cause cell destruction, alter cellular metabolism, or induce transformation of infected cells. Recent work in this area has been stimulated by the finding that atherosclerotic lesions, strikingly similar to those in human disease, were reproducibly induced in chickens by
Laboratory Evaluation of Immunoassay Kits for the Detection of Cannabinoids in Biological Fluids (1982)

The Center for Human Toxicology has, together with other toxicology laboratories, been involved in the field evaluation of a radioimmunoassay procedure for the detection and quantitation of delta 9-THC in serum and an enzyme multiplied immunoassay procedure for the detection of the nor-carboxylic acid metabolite in urine. Each laboratory was selected on the basis of proven experience with commercially available immunoassay procedures. Initially, the study was designed to screen samples collected from accident casualties; however, at some of the study sites the data base was extended to include other samples. The radioimmunoassay procedure evaluated was developed at the Receptor Research Institute, and involves the use of a tritium-labeled delta 8-THC tracer. A total of eight laboratories participated in the evaluation of this method, which is prepared in kit form by the manufacturer. Thirteen laboratories evaluated the EMIT procedure developed at Syva Corporation. The study protocol required that each site screen serum and urine samples and forward all presumptive positive specimens to the Center for Human Toxicology. These positive specimens were then shipped to either Battelle Laboratories or Research Triangle Institute for confirmation analysis by gas chromatography-mass spectrometry. The results of these evaluations will be presented and will include: 1. Correlations of positive RIA and EMIT analysis with gas chromatography-mass spectrometry results; 2. The results of quality-control tests; 3. Criticisms and suggestions made by analysts at each site; 4. The results of evaluations performed at the Center for Human Toxicology.
Encorafenib, Binimetinib, and Cetuximab in BRAF V600E–Mutated Colorectal Cancer (2019)

A combination of encorafenib, cetuximab, and binimetinib resulted in significantly longer overall survival and a higher response rate than standard therapy in patients with metastatic colorectal cancer with the <i>BRAF</i> V600E mutation. (Funded by Array BioPharma and others; BEACON CRC ClinicalTrials.gov number, NCT02928224; EudraCT number, 2015-005805-35.).
Small Interfering RNAs and Antisense Oligonucleotides for Treatment of Neurological Diseases (2005)

The complexity of the central nervous system (CNS) exposes it to a number of different diseases, often caused by only small variations in gene sequence or expression level. Antisense oligonucleotides and RNA interference-mediated therapies hold great promise for the treatment of CNS diseases in which neurodegeneration is linked to overproduction of endogenous protein or to synthesis of aberrant proteins coded by dominant mutant alleles. Nevertheless, difficulties related to the crossing of the blood-brain barrier, expression vectors, molecule design and to the choosing of the correct target, should be effectively solved. This review summarizes some of the most recent findings concerning the administration of potential nucleic acid-based therapeutic drugs, as well as the most promising studies performed both in vitro and in animal models of disease. Finally, some current clinical trials involving antisense oligonucleotides or silencing RNA for therapy of neurological disorders are illustrated. Results of current studies and clinical trials are exciting, and further results will be certainly reached with increasing knowledge of blood-brain barrier transporters, of genes involved in neurological disease and in new vectors for efficient delivery to brain.
Effect Lines for Specifying Animation Effects (2005)

When we create 2D animations on a desktop computer using programs such as Microsoft PowerPoint or Macromedia Flash, we assign effects to objects and define their parameters, such as their path, speed, and time of movement. To do this, we use conventional interfaces like menus or dialog boxes. However, the motion effects associated with each object are not displayed on the canvas explicitly, so the user-can investigate the properties of each object only by opening a dialog box to see the animations that are associated with the object. Moreover, setting various parameters using menus and dialog boxes is time-consuming because the user must set each parameter individually. We have therefore developed a method that uses an effect line to set each effect and its parameters. Effect lines are a popular technique that is used in comics and cartoons. They depict information on the effects of an object, such as its speed, length of path, and degree of rotation. They enable us to set effects using simple gestures. In addition, the effect lines can be combined. That is, the effects each effect lines have are merged. The feature makes effect lines flexible for the users to create various animations. Effect lines enable the user to recognize animation by displaying the effect lines on each keyframe during on-screen editing. We have developed a prototype animation authoring system. On this system, the user can create various animations with effect lines. We have evaluated the effectiveness of our method as visual input method and pictorial output method, and have discussed about it. The user can set most of "start effect" of PowerPoint by using effect lines
Papillomavirus research update: highlights of the Barcelona HPV 2000 international papillomavirus conference (2001)

The 18th international papillomavirus conference took place in Barcelona, Spain in July 2000. The HPV clinical workshop was jointly organised with the annual meeting of the Spanish Association of Cervical Pathology and Colposcopy. The conference included 615 abstracts describing ongoing research in epidemiology, diagnosis/screening, treatment/prognosis, immunology/human immunodeficiency virus, vaccine development/trials, transformation/progression, replication, transcription/translation, viral protein functions, and viral and host interactions. This leader summarises the highlights presented at the conference (the full text of the abstracts and lectures can be found at www.hpv2000.com). Relevant material in Spanish can be found at www.aepcc.org.
Kinetics of crystal nucleation in undercooled droplets of Sb- and Te-based alloys used for phase change recording (2005)

Droplets of molten alloys of composition Ge12Sb88, Ag0.055In0.065Sb0.59Te0.29, Ge4Sb1Te5, and Ge2Sb2Te5, used for optical data storage, surrounded by a molten dehydrated B2O3 flux were undercooled to 40–80K below their liquidus temperature in a differential thermal analyzer. The crystal-melt interfacial energy was calculated from the nucleation temperature using the classical nucleation theory, which gave values of around 0.20 times the heat of fusion per atom in the interface for all alloys. This value should be a lower limit since we did not establish that nucleation was homogeneous in the experiments. The steady-state nucleation rate was calculated between the liquidus and glass transition temperatures and was higher for the GeSbTe alloys than for the Sb-rich alloys. Nevertheless, the nucleation rates appear too high to allow amorphization under operating conditions for the highest achievable cooling rates. Therefore, we conclude that it is the presence of an incubation time that makes amorphization and therefore phase change recording possible in both optical and electronic media.
Management of chronic refractory cough (2015)

Chronic refractory cough (CRC) is defined as a cough that persists despite guideline based treatment. It is seen in 20-46% of patients presenting to specialist cough clinics and it has a substantial impact on quality of life and healthcare utilization. Several terms have been used to describe this condition, including the recently introduced term cough hypersensitivity syndrome. Key symptoms include a dry irritated cough localized around the laryngeal region. Symptoms are not restricted to cough and can include globus, dyspnea, and dysphonia. Chronic refractory cough has factors in common with laryngeal hypersensitivity syndromes and chronic pain syndromes, and these similarities help to shed light on the pathophysiology of the condition. Its pathophysiology is complex and includes cough reflex sensitivity, central sensitization, peripheral sensitization, and paradoxical vocal fold movement. Chronic refractory cough often occurs after a viral infection. The diagnosis is made once the main diseases that cause chronic cough have been excluded (or treated) and cough remains refractory to medical treatment. Several treatments have been developed over the past decade. These include speech pathology interventions using techniques adapted from the treatment of hyperfunctional voice disorders, as well as the use of centrally acting neuromodulators such as gabapentin and pregabalin. Potential new treatments in development also show promise.
Chitinase 3–Like 1 Suppresses Injury and Promotes Fibroproliferative Responses in Mammalian Lung Fibrosis (2014)

Epithelial injury, alternative macrophage accumulation, and fibroproliferation coexist in the lungs of patients with idiopathic pulmonary fibrosis (IPF). Chitinase 3-like 1 (CHI3L1) is a prototypic chitinase-like protein that has been retained over species and evolutionary time. However, the regulation of CHI3L1 in IPF and its ability to regulate injury and/or fibroproliferative repair have not been fully defined. We demonstrated that CHI3L1 levels were elevated in patients with IPF. High levels of CHI3L1 are associated with progression--as defined by lung transplantation or death--and with scavenger receptor-expressing circulating monocytes in an ambulatory IPF population. In preterminal acute exacerbations of IPF, CHI3L1 levels were reduced and associated with increased levels of apoptosis. We also demonstrated that in bleomycin-treated mice, CHI3L1 expression was acutely and transiently decreased during the injury phase and returned toward and eventually exceeded baseline levels during the fibrotic phase. In this model, CHI3L1 played a protective role in injury by ameliorating inflammation and cell death, and a profibrotic role in the repair phase by augmenting alternative macrophage activation, fibroblast proliferation, and matrix deposition. Using three-dimensional culture system of a human fibroblast cell line, we found that CHI3L1 is sufficient to induce low grade myofibroblast transformation. In combination, these studies demonstrate that CHI3L1 is stimulated in IPF, where it represents an attempt to diminish injury and induce repair. They also demonstrate that high levels of CHI3L1 are associated with disease progression in ambulatory patients and that a failure of the CHI3L1 antiapoptotic response might contribute to preterminal disease exacerbations.
Construction and biological properties of yellow fever 17D/dengue type 1 recombinant virus (2006)

Dengue virus, a mosquito-borne flavivirus, is one of the most formidable public health threats in tropical and subtropical regions. As yet, there is no licensed vaccine to protect against the disease. A chimeric yellow fever (YF) 17D/dengue (DEN) type 1 virus was constructed by replacing the pre-membrane and envelope genes of YF 17D virus with those from DEN 1 VeMir95 virus, a Venezuelan isolate. The chimeric YF 17D/DEN 1 VeMir95 virus was regenerated from full-length infectious clones stably propagated in Escherichia coli by transfection of Vero cells with in vitro transcribed RNA. The chimeric virus proliferated efficiently in Vero cells ( approximately 6.6 log(10) plaque-forming units/ml). The chimeric virus was not neurovirulent to 3-week-old Swiss Webster mice inoculated by the intracerebral route, in contrast to the YF 17DD vaccine strain that was lethal for 90% of the mice. The YF 17D/DEN 1 virus at Passage 6 was more attenuated for rhesus monkeys than the YF 17DD commercial vaccine after intracerebral inoculation according to the standard neurovirulence test. This virus is a potential candidate to be included in a tetravalent DEN vaccine formulation. The availability of the cloned cDNA allows further structure/function studies on the viral envelope.
Metabolic and mechanistic studies on threonine degradation in Escherichia coli via the L-threonine dehydrogenase-initiated pathway. (1993)

The major route for the degradation of scL-threonine in both prokaryotes and eukaryotes is initiated by the enzymes, scL-threonine dehydrogenase and 2-amino-3-ketobutyrate (AKB) CoA lyase. Threonine dehydrogenase catalyzes the oxidation of scL-threonine to AKB with concomitant reduction of NAD$\sp+.$ The unstable $\beta$-keto acid formed in this reaction can then either undergo decarboxylation with release of aminoacetone or be utilized as a substrate (along with CoA) by the lyase to form glycine plus acetyl CoA. The first portion of this research focuses on the dynamics of the threonine dehydrogenase/AKB CoA lyase coupled reaction in the reverse direction (i.e. the formation of threonine from glycine (plus acetyl CoA and NADH)). In vitro and in vivo studies showed that AKB CoA lyase and threonine dehydrogenase are able to catalyze formation of threonine. The stability of the AKB intermediate was then examined. Half-life determinations showed a value that ranged from 8.6 minutes at pH 5.9 to 140 minutes at pH 11.1. Furthermore, the pH dependence of the decarboxylation rate constant predicted a pK$\sb{\rm a}$ of 8.15 for the $\alpha$-amino group of AKB. The relation of AKB to 2-amino-3-ketoadipate, which decarboxylates to 5-aminolevulinate, is also discussed along with homology exhibited between AKB CoA lyase and 5-aminolevulinate synthase. On the basis of assays performed during the half-life determinations of AKB, it was found that the lyase enzyme manifests threonine aldolase activity. This was proven by showing that a variety of purification and inactivation procedures affected both AKB CoA lyase and threonine aldolase activities identically. In mechanistic studies, scL-threonine dehydrogenase was found to be inactivated by the methylating agent, methyl p-nitrobenzenesulfonate, with concomitant incorporation of 1 methyl group per subunit. Substrate protection studies along with isolation and sequencing of the major radioactive peptide after inactivation with $\sp{14}$C-methyl p-nitrobenzenesulfonate showed that histidine residue-90 is at the active site of threonine dehydrogenase. Furthermore, examination and comparison with the primary and tertiary structures of LADH has allowed the tentative assignment of a hydrogen-bonding role for His-90 of TDH.
Long-term Drug Treatment for Obesity (2013)

Medications approved for long-term obesity treatment, when used as an adjunct to lifestyle intervention, lead to greater mean weight loss and an increased likelihood of achieving clinically meaningful 1-year weight loss relative to placebo. By discontinuing medication in patients who do not respond with weight loss of at least 5%, clinicians can decrease their patients' exposure to the risks and costs of drug treatment when there is little prospect of long-term benefit.
A GDP/GTP exchange protein for the Rab3 small G protein family up-regulates a postdocking step of synaptic exocytosis in central synapses (2002)

The Rab3 GDP/GTP exchange protein (Rab3 GEP) activates the Rab3 small GTP-binding protein (G protein) family, including Rab3A that is an important member controlling synaptic vesicle trafficking. Here, we examined the role of Rab3 GEP in regulating neurotransmitter release in autapses of mouse hippocampal neurons in culture. The release probability was markedly reduced in Rab3 GEP-/- neurons, whereas the readily releasable pool size was not different between WT and Rab3 GEP-/- neurons, indicating that Rab3 GEP up-regulates a postdocking step of synaptic exocytosis. Because Rab3A reportedly down-regulates Ca(2+)-triggered fusion of synaptic vesicles, these results provide evidence for a role of Rab3 GEP in the postdocking process distinct from Rab3A activation.