gebhart/patrepeval huggingface dataset:
Insights into HLA-Restricted T Cell Responses in a Novel Mouse Model of Dengue Virus Infection Point toward New Implications for Vaccine Design (2011)

The frequency of dengue virus (DENV) infection has increased dramatically in the last few decades, and the lack of a vaccine has led to significant morbidity and mortality worldwide. To date, a convenient murine system to study human T cell responses to DENV has not been available. Mice transgenic for HLA are widely used to model human immune responses, and it has been shown that mouse-passaged DENV is able to replicate to significant levels in IFN-α/βR(-/-) mice. To cover a wide range of HLA phenotypes, we backcrossed IFN-α/βR(-/-) mice with HLA A*0201, A*0101, A*1101, B*0702, and DRB1*0101-transgenic mice. A DENV proteome-wide screen identified a total of 42 epitopes across all HLA-transgenic IFN-α/βR(-/-) strains tested. In contrast, only eight of these elicited responses in the corresponding IFN-α/βR(+/+) mice. We were able to identify T cell epitopes from 9 out of the 10 DENV proteins. However, the majority of responses were derived from the highly conserved nonstructural proteins NS3 and NS5. The relevance of this model is further demonstrated by the fact that most of the epitopes identified in our murine system are also recognized by PBMC from DENV-exposed human donors, and a dominance of HLA B*0702-restricted responses has been detected in both systems. Our results provide new insights into HLA-restricted T cell responses against DENV, and we describe in this study a novel murine model that allows the investigation of T cell-mediated immune mechanisms relevant to vaccine design.
Molecular Determinants of Melatonin Signaling Dysfunction in Adolescent Idiopathic Scoliosis (2007)

Presently, the genetic cause of adolescent idiopathic scoliosis (AIS), the most common form of scoliosis, remains unclear. Among many hypotheses, the neuroendocrine hypothesis involving a melatonin deficiency as the source for AIS generated the greatest interest and controversy since no decrease in circulating melatonin level has been observed in a majority of studies. Previously, we have reconciled the role of melatonin in AIS by demonstrating a melatonin signaling dysfunction occurring in osteoblasts derived from AIS patients, which contrasted with similar cells isolated from healthy subjects. We found that this difference is caused in AIS cells by increased phosphorylation of serine residues affecting the activity of G inhibitory proteins normally associated with melatonin cell surface receptors. Here we propose a preliminary molecular classification of patients with AIS based on the cellular response to the melatonin (cAMP) and distinct protein-protein interactions. These interactions include those between protein kinase C delta (PKCdelta) and MT2 melatonin receptors or PKCdelta and the receptor for activated protein C kinase 1. This finding could help in future molecular classification of patients with AIS.
Crosstalk rejection in parallel optical coherence tomography using spatially incoherent illumination with partially coherent sources (2010)

The continuing improvement of high-speed area-scan cameras has made possible the construction of parallel optical coherence tomography (OCT) systems that are competitive with the fastest demonstrated swept-source OCT systems. Unfortunately, when imaging through turbid media using a partially coherent source, parallel OCT suffers resolution loss from coherent multiple scattering, a phenomenon known as crosstalk. We demonstrate the use of a full-field OCT system employing multimode fiber in the illumination arm to reduce the spatial coherence of a partially coherent source. By reducing the spatial coherence area below the system's lateral resolution, we create a spatial coherence gate that rejects these multiply scattered photons. We quantify the image quality and resolution improvement of this method by comparing images of a USAF test chart acquired beneath turbid phantoms using both coherent and incoherent illumination and computing the resulting modulation transfer functions. We demonstrate the feasibility of this method for imaging biological specimens by imaging a Drosophila melanogaster sample.
Fracture Behavior under Impact. (1982)

Abstract : The physical behavior of cracks under impact loading is investigated. Single edge cracks or arrays of multiple cracks in rectangular specimens are considered. The specimens are loaded by time dependent tensile stress pulses moving perpendicular to the crack direction. The specimens are directly loaded by an impinging projectile or by a base plate which is accelerated by a projectile. The specimens are made from a transparent model material or a high strength steel. The initial crack lengths and impact velocities are varied throughout the experiments. Utilizing the shadow optical method of caustics in combination with high speed photography, the dynamic stress intensity factor at onset of rapid crack propagation, i.e. the dynamic fracture toughness KId, is determined and discussed with regard to the time tf at which the crack becomes unstable. The results are compare to corresponding static fracture toughness data. Within the second year of the three years research project many experiments of the proposed main investigations have been carried out: First the dependence of the impact fracture toughness KId on loading rate has been investigated. Specimens from the Araldite B with single edge cracks have been tested under base plate - and under direct impact loading conditions. Within the range of loading rates achieved so far, the measured impact fracture toughness KId do not show a dependence from loading rate.
Pathways that elicit long-term changes in gene expression in nociceptive neurons following nerve injury: contributions to neuropathic pain (2004)

Chronic neuropathic pain following nerve injury or inflammation is mediated by transcription-dependent changes in neurons that comprise the nociceptive pathway. Among these changes is often a long-term hyperexcitability (LTH) in primary nociceptors that persists long after the lesion has healed. LTH is manifest by a reduction in threshold and an increased tendency to fire action potentials. This increased excitability activates higher order neurons in the pathway, leading to the perception of pain. Efforts to ameliorate chronic pain would therefore benefit if we understood how LTH is induced, but studies toward this goal are impeded by the complexity and heterogeneity of vertebrate nervous systems. Fortunately, LTH is an evolutionarily conserved mechanism that underlies defensive behaviors across phyla, including invertebrates. Thus, the same electrophysiological changes that underlie LTH in vertebrate nociceptive neurons are seen in their counterparts in the experimentally favorable mollusk Aplysia californica. Nociceptive neurons of Aplysia are readily accessible and large enough to approach using a variety of cell and molecular approaches not possible in higher organisms. Studies of the molecular cascades activated by injury to Aplysia peripheral nerves has focused on a group of positive injury signals that are retrogradely transported from the injury site in the axon to the cell nucleus where they regulate gene transcription. One of these, protein kinase G, is activated by nitric oxide synthetase and its activation in axons is required for the induction of LTH after injury. This pathway, and the transcriptional events that it activates, are targets for therapeutic intervention for chronic pain.
Isobar suppression by photodetachment in a gas-filled rf quadrupole ion guide (2005)

A technique based on selective nonresonant laser photodetachment of unwanted negative ion species has been developed for efficient suppression of isobaric contaminants in negative ion beams. A radio-frequency quadrupole ion guide is employed to cool the negative ion beam and dramatically increase the interaction time of the ions with the laser, substantially increasing the efficiency of the photodetachment process. In a proof-of-principle experiment, we achieved 95% suppression of Co−59 ions by photodetachment while under identical conditions 10% of Ni−58 ions were neutralized.
Machine learned ranking of entity facets (2010)

The research described in this paper forms the backbone of a service that enables the faceted search experience of the Yahoo! search engine. We introduce an approach for a machine learned ranking of entity facets based on user click feedback and features extracted from three different ranking sources. The objective of the learned model is to predict the click-through rate on an entity facet. In an empirical evaluation we compare the performance of gradient boosted decision trees (GBDT) against a linear combination of features on two different click feedback models using the raw click-through rate (CTR), and click over expected clicks (COEC). The results show a significant improvement in retrieval performance, in terms of discounted cumulated gain, when ranking entity facets with GBDT trained on the COEC model. Most notably this is true when evaluated against the CTR test set.
SIP-based VoIP traffic behavior profiling and its applications (2007)

With the widespread adoption of SIP-based VoIP, understanding the characteristics of SIP traffic behavior is critical to problem diagnosis and security protection of IP Telephony. In this paper, we propose a general methodology for profiling SIP-based VoIP traffic behavior at multiple levels: SIP server host, server entity and individual user levels. Using SIP traffic traces captured in a production VoIP service, we illustrate the characteristics of SIP-based VoIP traffic behavior in an operational network and demonstrate the effectiveness of our general profiling methodology. In particular, we show how our profiling methodology can help identify performance anomalies through a case study.
Pilus biogenesis gene, pilC, of Neisseria gonorrhoeae: pilC1 and pilC2 are each part of a larger duplication of the gonococcal genome and share upstream and downstream homologous sequences with opa and pil loci (1995)

Pili of Neisseria gonorrhoeae mediate attachment of the bacteria to target cells and undergo both phase and antigenic variation. PilC is a 110 kDa minor pilus-associated protein involved in pilus biogenesis and attachment. The expression of PilC is turned on and off at high frequency and is controlled by frameshift mutations in a run of G residues positioned in the region encoding the signal peptide. Most strains of N. gonorrhoeae carry two copies of pilC. The DNA sequence of pilC1 of strain MS11 is presented and compared to the sequence of the 3' end of pilC2. These two genes are highly homologous, but not identical. The putative transcriptional terminator of pilC1 contains a pair of inverted uptake sequences for gonococcal DNA (5'-GCCGTCTGAA-3'). An 88 bp sequence located upstream of the pilC1 gene has also been reported to precede several opa genes of N. gonorrhoeae. Shorter regions positioned both downstream and upstream of pilC1 can also be found in silent pil loci as well as close to opa genes. The pilC genes are part of a duplication of a larger DNA region extending more than 2 kb downstream of the coding region.
<title>Novel modeling techniques for tumor diagnostics using pulsed laser sources</title> (2002)

In this paper, a two-dimensional transient radiation transport algorithm is developed to analyze short pulse laser transport through a tissue medium having tumors and inhomogeneities imbedded in it. Short pulse probing techniques have distinct advantages over conventional very large pulse width or cw lasers primarily due to the additional information conveyed about the tissue interior by the temporal variation of the observed signal. The distinct feature is the multiple scattering induced temporal signatures that persists for time periods greater than the duration of the source pulse and is a function of the source pulse width, the scattering/absorbing properties and nature of the medium, the location in the medium where the properties undergo changes. A wide range of parameters such as tissue and tumor size, scattering/absorbing properties and phase function of tissues and tumors, tumor location, laser beam diameter will affect the temporal and spatial distribution of the reflected and transmitted optical signals. The goal is to perform a parametric study in order to gain insight about laser-tissue interaction characteristics with the goal to detect tumors.
General Biochemical Characterization of Thermostable Extracellular β-Amylase from <i>Clostridium thermosulfurogenes</i> (1985)

Clostridium thermosulfurogenes, an anaerobic bacterium which ferments starch into ethanol at 62 degrees C, produced an active extracellular amylase and contained intracellular glucoamylase but not pullulanase activity. The extracellular amylase was purified 2.4-fold, and its general physicochemical and catalytic properties were examined. The extracellular amylase was characterized as a beta-amylase (1,4-alpha-d-glucan maltohydrolase) based on demonstration of exocleavage activity and the production of maltose with a beta-anomeric configuration from starch. The beta-amylase activity was stable and optimally active at 80 and 75 degrees C, respectively. The pH optimum for activity and the pH stability range was 5.5 to 6 and 3.5 to 6.5, respectively. The apparent [S](0.5V) and V(max) for beta-amylase activity on starch was 1 mg/ml and 60 U/mg of protein. Similar to described beta-amylase, the enzyme was inhibited by p-chloromercuribenzoate, Cu, and Hg; however, alpha- and beta-cyclodextrins were not competitive inhibitors. The beta-amylase was active and stable in the presence of air or 10% (vol/vol) ethanol. The beta-amylase and glucoamylase activities enabled the organism to actively ferment raw starch in the absence of significant pullulanase or alpha-amylase activity.
Binding of Complement Factor H (fH) to <i>Neisseria meningitidis</i> Is Specific for Human fH and Inhibits Complement Activation by Rat and Rabbit Sera (2008)

Complement factor H (fH), a molecule that downregulates complement activation, binds to Neisseria meningitidis and increases resistance to serum bactericidal activity. We investigated the species specificity of fH binding and the effect of human fH on downregulating rat (relevant for animal models) and rabbit (relevant for vaccine evaluation) complement activation. Binding to N. meningitidis was specific for human fH (low for chimpanzee fH and not detected with fH from lower primates). The addition of human fH decreased rat and rabbit C3 deposition on the bacterial surface and decreased group C bactericidal titers measured with rabbit complement 10- to 60-fold in heat-inactivated sera from human vaccinees. Administration of human fH to infant rats challenged with group B strain H44/76 resulted in an fH dose-dependent increase in CFU/ml of bacteria in blood 8 h later (P < 0.02). At the highest fH dose, 50 microg/rat, the geometric mean number of CFU per ml was higher than that in control animals (1,050 versus 43 [P < 0.005]). The data underscore the importance of binding of human fH for survival of N. meningitidis in vitro and in vivo. The species specificity of binding of human fH adds another mechanism toward our understanding of why N. meningitidis is strictly a human pathogen.
Wearable Sensors and the Assessment of Frailty among Vulnerable Older Adults: An Observational Cohort Study (2018)

<i>Background:</i> The geriatric syndrome of frailty is one of the greatest challenges facing the U.S. aging population. Frailty in older adults is associated with higher adverse outcomes, such as mortality and hospitalization. Identifying precise early indicators of pre-frailty and measures of specific frailty components are of key importance to enable targeted interventions and remediation. We hypothesize that sensor-derived parameters, measured by a pendant accelerometer device in the home setting, are sensitive to identifying pre-frailty. <i>Methods:</i> Using the Fried frailty phenotype criteria, 153 community-dwelling, ambulatory older adults were classified as pre-frail (51%), frail (22%), or non-frail (27%). A pendant sensor was used to monitor the at home physical activity, using a chest acceleration over 48 h. An algorithm was developed to quantify physical activity pattern (PAP), physical activity behavior (PAB), and sleep quality parameters. Statistically significant parameters were selected to discriminate the pre-frail from frail and non-frail adults. <i>Results:</i> The stepping parameters, walking parameters, PAB parameters (sedentary and moderate-to-vigorous activity), and the combined parameters reached and area under the curve of 0.87, 0.85, 0.85, and 0.88, respectively, for identifying pre-frail adults. No sleep parameters discriminated the pre-frail from the rest of the adults. <i>Conclusions:</i> This study demonstrates that a pendant sensor can identify pre-frailty via daily home monitoring. These findings may open new opportunities in order to remotely measure and track frailty via telehealth technologies.
The Design of Monolithic AC-coupled 1-Dimensional Voltage-Controlled-Oscillators (VCOs) Phased-array Network (2011)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Donald Y. C. Lie, J. Lopez; The Design of Monolithic AC‐coupled 1‐Dimensional Voltage‐Controlled‐Oscillators (VCOs) Phased‐array Network. AIP Conference Proceedings 19 April 2011; 1339 (1): 128–140. https://doi.org/10.1063/1.3574851 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
<i>Streptococcus gordonii</i> Strains Resistant to Fluorodeoxyuridine Contain Mutations in the Thymidine Kinase Gene and Are Deficient in Thymidine Kinase Activity (2000)

Mutants of Streptococcus gordonii resistant to 5-fluorodeoxyuridine (FUdR(r)) were isolated. Each strain contained a point mutation resulting in the premature termination of the thymidine kinase (TK) open reading frame (tdk). In vitro translation of the mutant tdk coding regions resulted in synthesis of truncated TK polypeptides deficient in TK activity.
Transducing Protease Activity into DNA Output for Developing Smart Bionanosensors (2019)

DNA can process information through sequence-based reorganization but cannot typically receive input information from most biological processes and translate that into DNA compatible language. Coupling DNA to a substrate responsive to biological events can address this limitation. A two-component sensor incorporating a chimeric peptide-DNA substrate is evaluated here as a protease-to-DNA signal convertor which transduces protease activity through DNA gates that discriminate between different input proteases. Acceptor dye-labeled peptide-DNAs are assembled onto semiconductor quantum dot (QD) donors as the input gate. Addition of trypsin or chymotrypsin cleaves their cognate peptide sequence altering the efficiency of Förster resonance energy transfer (FRET) with the QD and frees a DNA output which interacts with a tetrahedral output gate. Downstream output gate rearrangement results in FRET sensitization of a new acceptor dye. Following characterization of component assembly and optimization of individual steps, sensor ability to discriminate between the two proteases is confirmed along with effects from joint interactions where potential for cross-talk is highest. Processing multiple bits of information for a sensing outcome provides more confidence than relying on a single change especially for the discrimination between different targets. Coupling other substrates to DNA that respond similarly could help target other types of enzymes.
Effective Phagocytosis of Low Her2 Tumor Cell Lines with Engineered, Aglycosylated IgG Displaying High FcγRIIa Affinity and Selectivity (2012)

Glycans anchored to residue N297 of the antibody IgG Fc domain are critical in mediating binding toward FcγRs to direct both adaptive and innate immune responses. However, using a full length bacterial IgG display system, we have isolated aglycosylated Fc domains with mutations that confer up to a 160-fold increase in the affinity toward the low affinity FcγRIIa-R131 allele as well as high selectivity against binding to the remarkably homologous human inhibitory receptor, FcγRIIb. The mutant Fc domain (AglycoT-Fc1004) contained a total of 5 amino acid substitutions that conferred an activating to inhibitory ratio of 25 (A/I ratio; FcyRIIa-R131:FcγRIIb). Incorporation of this engineered Fc into trastuzumab, an anti-Her2 antibody, resulted in a 75% increase in tumor cell phagocytosis by macrophages compared to that of the parental glycosylated trastuzumab with both medium and low Her2-expressing cancer cells. A mathematical model has been developed to help explain how receptor affinity and the A/I ratio relate to improved antibody dependent cell-mediated phagocytosis. Our model provides guidelines for the future engineering of Fc domains with enhanced effector function.