gebhart/patrepeval huggingface dataset:
Nicotinamide Adenine Dinucleotide Phosphate Oxidase 2 Regulates LPS-Induced Inflammation and Alveolar Remodeling in the Developing Lung (2016)

In premature infants, sepsis is associated with alveolar simplification manifesting as bronchopulmonary dysplasia. The redox-dependent mechanisms underlying sepsis-induced inflammation and alveolar remodeling in the immature lung remain unclear. We developed a neonatal mouse model of sepsis-induced lung injury to investigate whether nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2) regulates Toll-like receptor (TLR)-mediated inflammation and alveolar remodeling. Six-day-old NOX2<sup>+/+</sup> and NOX2<sup>-/-</sup> mice were injected with intraperitoneal LPS to induce sepsis. Lung inflammation and canonical TLR signaling were assessed 24 hours after LPS. Alveolar development was examined in 15-day-old mice after LPS on Day 6. The in vivo efficacy of a NOX2 inhibitor (NOX2-I) on NOX2 complex assembly and sepsis-induced lung inflammation were examined. Lung cytokine expression and neutrophil influx induced with sepsis in NOX2<sup>+/+</sup> mice was decreased by >50% in NOX2<sup>-/-</sup> mice. LPS-induced TLR4 signaling evident by inhibitor of NF-κB kinase-β and mitogen-activated protein kinase phosphorylation, and nuclear factor-κB/AP-1 translocation were attenuated in NOX2<sup>-/-</sup> mice. LPS increased matrix metalloproteinase 9 while decreasing elastin and keratinocyte growth factor levels in NOX2<sup>+/+</sup> mice. An LPS-induced increase in matrix metalloproteinase 9 and decrease in fibroblast growth factor 7 and elastin were not evident in NOX2<sup>-/-</sup> mice. An LPS-induced reduction in radial alveolar counts and increased mean linear intercepts were attenuated in NOX2<sup>-/-</sup> mice. LPS-induced NOX2 assembly evident by p67phox/gp91phox coimmunoprecipitation was disrupted with NOX2-I. NOX2-I also mitigated LPS-induced cytokine expression, TLR pathway signaling, and alveolar simplification. In a mouse model of neonatal sepsis, NOX2 regulates proinflammatory TLR signaling and alveolar remodeling induced by a single dose of LPS. Our results provide mechanistic insight into the regulation of sepsis-induced alveolar remodeling in the developing lung.
Human Immunodeficiency Virus Isolated from a Serum Sample Collected in 1976 in Central Africa (1987)

The screening of 454 serum samples from northern Zaire for antibodies to the Ebola virus has revealed the earliest human immunodeficiency virus (HIV) isolated identified to date. The serum tested in this study were collected in 1976; previously an HIV isolate collected in 1983 was believed to be the 1st such case. 5 (1%) of the 454 serum samples from 1976 were positive by ELISA and Western blot. 1 of the positive samples was obtained from a 26-year-old unmarried woman who died in 1978 of an illness suggestive of acquired immunodeficiency syndrome (AIDS). Her symptoms included prolonged fever substantial weight loss headaches oral lacerations dysphagia and persistent cough with hemoptysis. The women was from a small village in Northwest Zaire but had lived in Kinshasa in 1971-1975. The isolates obtained in this series were compared to HIV isolates from other populations in terms of viral proteins antigenic cross-reactivity and Southern hybridization. A unique pattern of reactivity was found for all 5 Zairian isolates. Homologous radioimmunoassay indicated that the major core proteins of Zairian HIV (CDC451) and HZ 321 were identical. All 5 isolates showed major bands at molecular bands of 18000 24000 and 41000. In addition the strains showed reactivity with the p65 polymerase gene product. The distinct nature of HZ 321 was further confirmed by the production of hybridization patterns different from human T-cell lymphotropic virus (HTLV-III). This study suggests that HIV was circulating in rural Zaire several years before its recognition in Kinshasa. The finding that HIV can be isolated from serum frozen initially at minus 70 C and later at minus 20 C should encourage additional analyses of serum samples collected in the 1970s in rural Africa.
IP address assignment in a mobile ad hoc network (2003)

A mobile ad hoc network (MANET) consists of a set of identical mobile nodes communicating with each other via wireless links. The network's topology may change rapidly and unpredictably. Such networks may operate in a stand-alone fashion, or may be connected to the larger Internet. In traditional networks, hosts rely on centralized servers like DHCP for configuration, but this cannot be extended to MANETs because of their distributed and dynamic nature. Many schemes have been proposed to solve this problem. Some of these approaches try to extend the IPv6 stateless autoconfiguration mechanism to MANETs, some use flooding the entire network to come up with a unique IP address, and others distribute IP addresses among nodes (using binary split) so that each node can independently configure new nodes. None of these existing solutions consider network partitioning and merging. In this paper, we propose a proactive scheme for dynamic allocation of IP addresses in MANETs. Our solution also uses the concept of binary split and takes into consideration the previously unsolved issues like partitioning and merging and abrupt departure of nodes from the system. We show that our solution is scalable and does not have the limitations of earlier approaches.
Entropy-biased models for query representation on the click graph (2009)

Query log analysis has received substantial attention in recent years, in which the click graph is an important technique for describing the relationship between queries and URLs. State-of-the-art approaches based on the raw click frequencies for modeling the click graph, however, are not noise-eliminated. Nor do they handle heterogeneous query-URL pairs well. In this paper, we investigate and develop a novel entropy-biased framework for modeling click graphs. The intuition behind this model is that various query-URL pairs should be treated differently, i.e., common clicks on less frequent but more specific URLs are of greater value than common clicks on frequent and general URLs. Based on this intuition, we utilize the entropy information of the URLs and introduce a new concept, namely the inverse query frequency (IQF), to weigh the importance (discriminative ability) of a click on a certain URL. The IQF weighting scheme is never explicitly explored or statistically examined for any bipartite graphs in the information retrieval literature. We not only formally define and quantify this scheme, but also incorporate it with the click frequency and user frequency information on the click graph for an effective query representation. To illustrate our methodology, we conduct experiments with the AOL query log data for query similarity analysis and query suggestion tasks. Experimental results demonstrate that considerable improvements in performance are obtained with our entropy-biased models. Moreover, our method can also be applied to other bipartite graphs.
Oral fluid as a diagnostic tool (2004)

Technological advances over the past decades have enabled oral fluid to expand its usefulness in the diagnosis of disease, prediction of disease progression, monitoring of therapeutic drug levels and detection of illicit drugs. The easy non-invasive nature of collection and the relationship between oral fluid and plasma levels make oral fluid a valuable clinical tool. This review describes advances over the past 5 years in the area of oral fluid as a diagnostic tool, its use in therapeutic and illicit drug monitoring, including proposed guidelines for cut-off values, and methods of collection.
Tumor-associated neurological dysfunction prevented by lazaroids in rats (1991)

The efficacy of U-74006F and U-78517F in the treatment of blood-tumor barrier permeability and tumor-associated neurological dysfunction was evaluated in a brain-tumor model in rats. U-74006F is a 21-aminosteroid and U-78517F is a 2-methylamino chroman. Rats with stereotactically implanted Walker 256 tumors were treated with methylprednisolone, U-74006F, U-78517F, or vehicle (0.05 N HCl) on Days 6 through 10 following implantation. Neurological function and vascular permeability were assessed on Day 10. Methylprednisolone and U-74006F were equally effective at preventing neurological dysfunction compared to the control group (p less than 0.01); U-78517F was slightly less effective than U-74006F and methylprednisolone but was significantly better than vehicle in preventing neurological dysfunction. Delivery of methylprednisolone resulted in a significant decrease in tumor vascular permeability (p less than 0.006) while U-74006F and U-78517F had no effect on permeability. This suggests that U-74006F and U-78517F prevented tumor-associated neurological dysfunction by a mechanism other than decreasing permeability in tumor capillaries, and that U-74006F or U-78517F could prove useful in the treatment of brain tumors.
Haptoglobin Polymorphism and Body Iron Stores (2002)

In humans the iron status is influenced by environmental and genetic factors. Among them, the genetic polymorphism of the hemoglobin (Hb)-binding plasma protein haptoglobin (Hp) has been shown to affect iron turnover. The best known biological function of Hp is capture of free Hb in plasma to allow hepatic recycling of heme iron and to prevent kidney damage during hemolysis. In healthy males, but not in females, the Hp 2-2 phenotype is associated with higher serum iron, higher transferrin saturation, and higher ferritin than Hp 1-1 and 2-1. Moreover, serum ferritin correlates with monocyte L-ferritin content, which is also highest in Hp 2-2 subjects due to endocytosis of multimeric Hb-Hp 2-2 complexes by the recently identified Hb scavenger receptor CD163 in macrophages. This iron delocalization pathway, occurring selectively in Hp 2-2 subjects, has important biological and clinical consequences. The Hp polymorphism is related to the prevalence and the outcome of various pathological conditions with altered iron metabolism such as hemochromatosis, infections, and atherosclerotic vascular disease.
Optimal routing and wavelength assignment in all-optical networks (2002)

The author consider the problem of routing connections in an optical network using wavelength division multiplexing, where each connection between a pair of nodes in the network is assigned a path through the network and a wavelength on that path, such that connections whose paths share a common link in the network are assigned different wavelengths. They derive an upper bound on the carried traffic of connections (or equivalently, a lower bound on the blocking probability) for any routing and wavelength assignment (RWA) algorithm in such a network. The bound scales with the number of wavelengths and is achieved asymptotically (when a large number of wavelengths is available) by a fixed RWA algorithm. Although computationally intensive, this bound can be used as a metric against which the performance of different RWA algorithms can be compared for networks of moderate size. They illustrate this by comparing the performance of a simple RWA algorithm via simulation with our bound. They also derive a similar bound for optical networks using dynamic wavelength converters, which are equivalent to circuit-switched telephone networks, and compare the two cases for different examples.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A survey of query recommendation techniques for data warehouse exploration (2011)

Lots of data are gathered in datawarehouses that are navigated andexplored for analytical purposes. Only recently has the problem of recommending a datawarehouse query to a datawarehouse user attracted attention. In this paper, we propose a simple formal framework for expressing datawarehouse queryrecommendations. We propose to see the problem of recommending a datawarehouse query for exploration purposes as a function computing a set of queriesand associated ratings given a query log, a session, a user profile, a datawarehouse instance, and an expectation function. The rating computed indicates theusefulness of each query for a session. With this viewpoint, we review and categorize the few techniques that, to the best of our knowledge, have been proposedand we illustrate them with a case study.
Inhibition of Rho via Arg and p190RhoGAP in the Postnatal Mouse Hippocampus Regulates Dendritic Spine Maturation, Synapse and Dendrite Stability, and Behavior (2007)

The RhoA (Rho) GTPase is a master regulator of dendrite morphogenesis. Rho activation in developing neurons slows dendrite branch dynamics, yielding smaller, less branched dendrite arbors. Constitutive activation of Rho in mature neurons causes dendritic spine loss and dendritic regression, indicating that Rho can affect dendritic structure and function even after dendrites have developed. However, it is unclear whether and how endogenous Rho modulates dendrite and synapse morphology after dendrite arbor development has occurred. We demonstrate that a Rho inhibitory pathway involving the Arg tyrosine kinase and p190RhoGAP is essential for synapse and dendrite stability during late postnatal development. Hippocampal CA1 pyramidal dendrites develop normally in arg-/- mice, reaching their mature size by postnatal day 21 (P21). However, dendritic spines do not undergo the normal morphological maturation in these mice, leading to a loss of hippocampal synapses and dendritic branches by P42. Coincident with this synapse and dendrite loss, arg-/- mice exhibit progressive deficits in a hippocampus-dependent object recognition behavioral task. p190RhoGAP localizes to dendritic spines, and its activity is reduced in arg-/- hippocampus, leading to increased Rho activity. Although mutations in p190rhogap enhance dendritic regression resulting from decreased Arg levels, reducing gene dosage of the Rho effector ROCKII can suppress the dendritic regression observed in arg-/- mice. Together, these data indicate that signaling through Arg and p190RhoGAP acts late during synaptic refinement to promote dendritic spine maturation and synapse/dendrite stability by attenuating synaptic Rho activity.
Weed management in conventional, no-till, and transgenic corn with mesotrione combinations and other herbicides (2002)

Weed management programs in corn typically include herbicides applied both preemergence (PRE) and postemergence (POST) for season-long weed control. Mesotrione is a new triketone herbicide registered for PRE and POST control of broadleaf weeds in corn. Triketone herbicides function through inhibition of the enzyme p-hydroxyphenylpyruvate dioxygenase. Mesotrione applied PRE did not adequately control common lambsquarters (Chenopodium album L.), smooth pigweed (Amaranthus hybridus L.), common ragweed (Ambrosia artemisiifolia L.), or morningglory species (Ipomoea spp.) in conventional tillage corn, but control of these weeds was generally improved in no-till corn. Mesotrione combinations with acetochlor did not always improve control of broadleaf weeds, but increased control of smooth pigweed and giant foxtail (Setaria faberi Herrm.). POST applications of mesotrione at 105 g ai/ha controlled most annual broadleaf weeds except common ragweed, but did not control giant foxtail. The addition of atrazine at 280 g ai/ha to mesotrione, however, improved control of common ragweed. Tank-mixtures of glyphosate, imazethapyr, or imazethapyr plus imazapyr with mesotrione improved control of giant foxtail in herbicide-resistant corn. Corn injury was usually low from PRE and POST mesotrione applications in non-genetically modified corn, however, greater injury occurred in glyphosate-resistant varieties. Corn treated with mesotrione combinations generally yielded similar to corn treated with commercial standards. Mesotrione applied POST also suppressed the perennial weeds horsenettle (Solanum carolinense L.) and Canada thistle [Cirsium arvense (L.) Scop.]. Additions of atrazine increased the rate of plant tissue necrosis on these perennial weeds as compared to the slower bleaching symptoms associated with mesotrione applied alone. In general, Canada thistle plants were more susceptible to mesotrione in the rosette stage of growth than when bolting. Absorption, translocation, and metabolism of 14C mesotrione in Canada thistle was generally low. However, higher levels of absorption and translocation and lower root metabolism of mesotrione in rosette stage plants compared to bolting stage plants may explain why Canada thistle is more susceptible to mesotrione in the rosette stage of growth. The changes in symptomology and increased control from mesotrione plus atrazine tank-mixtures is likely due to the interrelationship between the modes of action of atrazine and mesotrione.
Aging, Immunity, and Cancer (2000)

Senescent decline in immune surveillance leads to the accumulation of cellular and DNA mutations that could be a significant factor in the development of malignancy and programmed cell death or apoptosis observed in the elderly.
Blind deconvolution of linear systems with nonstationary discrete inputs (2002)

A method is proposed for blind deconvolution (equalization) of communication channels when their input signals are real- or complex-valued multilevel random sequences. The gist of the method is to apply a linear filter (equalizer) to the observed signal and to adjust it until a multilevel sequence is obtained from the output. It is shown that the problem can be solved with only scale/rotation and shift ambiguities. A cost function is proposed so that any minimizer of the function provides a solution to the problem. When the channel is parametric, a procedure is presented for the consistent estimation of the channel parameters. All these results are obtained for nonminimum phase linear systems without assuming the stationarity of the signal.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
[Polysulfates, anionic detergents, sodium phosphotungstate and electrophoretic mobility of plasmatic proteins]. (1978)

Anions with strong electro-negative charges, like sulphuric esters of polysaccharides (heparin, dextran sulphate M.W. 15 00), the sodium salt of polyanethol sulfonic acid (liquoid, Roche), anionic detergents (sodium dodecylsulphate, sodium oleate, sodium deoxycholate), and the sodium salt of phosphotungstic acid were added to human serum or citrated plasma. For each compound several final concentrations were adopted, the highest being 4%. By using microimmunoelectrophoresis and numerous specific antisera against human plasma proteins, it was demonstrated that at pH 8.60 anions increase electrophoretic mobility of the following antigens: lipoproteins alpha and beta; fibrinogen; beta 2-glycoprotein I; beta 2-glycoprotein II ; antithrombin III. All reagents utilized do not react with all these proteins; for instance, only detergents accelerate the migration rate of a lipoproteins. Besides, depending on the protein, this or that reagent may be the most active. Thus, in the polysulphate group, heparin has the highest affinity for antithrombin III, liquoid for fibrinogen and dextran sulphate for beta 2-glycoprotein I.
Structural Analysis of Sucrose-Derived Hard Carbon and Correlation with the Electrochemical Properties for Lithium, Sodium, and Potassium Insertion (2020)

Hard carbon possesses the ability to store Li, Na, and K ions between stacked sp2 carbon layers and voids (micropores). We have explored hard carbon as a candidate for negative electrode materials for Li-ion, Na-ion, and K-ion batteries. Hard carbon samples have been prepared by carbonizing sucrose at different heat treatment temperatures (HTTs) in the range of 700–2000 °C to make them structurally suitable for reversible Li, Na, and K insertion. Structures and particle morphology of the hard carbon samples synthesized at different HTTs were systematically characterized using X-ray diffraction, small-angle X-ray scattering, pair distribution function analysis, electron microscopy, Raman spectroscopy, and electron spin resonance spectroscopy. All these characterizations of hard carbon samples have revealed advanced ordering of carbons and reduction of carbon defects with increasing HTT. Thus, the average stacked carbon interlayer distance decreases, the number of the stacking layers increases, the layered domains grow in the in-plane direction, and interstitial voids enlarge. Electrochemical properties of the hard carbons were examined in nonaqueous Li, Na, and K cells. Potential profiles and reversible capacities upon galvanostatic charge/discharge processes in nonaqueous cells are significantly different depending on HTTs and different alkali metal ions. On the basis of these findings, strategies to design high-capacity hard carbon negative electrodes for high-energy-density Li-ion, Na-ion, and K-ion batteries are discussed.
Rate constrained adaptive control (1988)

The problem of direct adaptive control subject to a control rate constraint is considered. Theoretical results concerned with the system boundedness and control tracking properties are presented. These results require a finite gain stability condition of the associated non-adaptive control system. The results are applied to a stable plant.
Evaluating the impact of sequencing error correction for RNA-seq data with ERCC RNA spike-in controls (2016)

Sequencing errors are a major issue for several next-generation sequencing-based applications such as de novo assembly and single nucleotide polymorphism detection. Several error-correction methods have been developed to improve raw data quality. However, error-correction performance is hard to evaluate because of the lack of a ground truth. In this study, we propose a novel approach which using ERCC RNA spike-in controls as the ground truth to facilitate error-correction performance evaluation. After aligning raw and corrected RNA-seq data, we characterized the quality of reads by three metrics: mismatch patterns (i.e., the substitution rate of A to C) of reads aligned with one mismatch, mismatch patterns of reads aligned with two mismatches and the percentage increase of reads aligned to reference. We observed that the mismatch patterns for reads aligned with one mismatch are significantly correlated between ERCC spike-ins and real RNA samples. Based on such observations, we conclude that ERCC spike-ins can serve as ground truths for error correction beyond their previous applications for validation of dynamic range and fold-change response. Also, the mismatch patterns for ERCC reads aligned with one mismatch can serve as a novel and reliable metric to evaluate the performance of error-correction tools.