gebhart/patrepeval huggingface dataset:
Quantitation of T-Cell Receptor Frequencies by Competitive PCR: Generation and Evaluation of Novel TCR Subfamily and Clone Specific Competitors (1999)

T cell receptor (TCR) V gene usage has been used to characterize the immune response to bacteria, viruses, allografts, self antigens, tumor antigens, and superantigens. Sensitive methods to detect changes in the frequency of TCR subfamilies or clonotypes might be useful in evaluating the efficacy of vaccines against infectious agents, immunotherapy treatments for cancer patients, or the status of autoimmune diseases. Two HLA-A2 restricted CTL clones expressing BV17 were isolated from a tumor infiltrating lymphocytes (TIL) culture of a patient with metastatic melanoma. One clone recognized the MART-1(27-35) peptide and the other clone recognized the gp100(209-217) peptide. The frequency of each of these CTL clones in an expanding TIL culture was measured using a novel competitive RT-PCR (cRT-PCR) strategy. cRT-PCR uses a single primer pair to amplify template cDNA simultaneously with a modified DNA competitor molecule. A rapid two-step PCR technique followed by a single cloning step was used to generate a TCR BV17 subfamily specific competitor or competitors specific for the MART-1(27-35) reactive CTL clone (CO-41) and the gp100(209-217) reactive CTL clone (CO-4). Each competitor contained a segment of the TCR BC region that served as an internal reference standard. Using the BV17 competitor we were able to accurately and reproducibly measure cDNA templates at a frequency as low as 1/100,000 using cDNA samples of known TCRBV subfamily composition. This competitor was used to monitor the frequency of BV17 expressing T cells in the TIL and PMBC of a patient with metastatic melanoma. We determined that the frequency of BV17 expressing T cells increased from 4.5% of the culture on day 35 to 60.7% of the culture on day 58. Expansion of the BV17 subfamily was due predominantly to the expansion of the CO-4 clone. This method can be used to meaningfully quantify the precursor frequency of T cell mRNA in prepared samples via TCR subfamily or TCR sequence specific primers.
Table S1 from <i>BRCA1</i> Promoter Methylation Is Linked to Defective Homologous Recombination Repair and Elevated <i>miR-155</i> to Disrupt Myeloid Differentiation in Myeloid Malignancies (2023)

&lt;p&gt;Table S1 shows the primer sequences used for qMSP, MSP, RT-qPCR&lt;/p&gt;
System issues in 2-photon absorption based 3-D optical memories (1995)

The 2-photon absorption based three dimensional memory 1 is an optical storage device where the bits of information are stored throughout the volume of a material. The use of optical beams for write/read operations allows the data to be densely packed inside the material, hence increasing the memory density. The third dimension allows the information to be accessed in parallel providing a high data transfer rate.
The Effect of Thyrotropin-Receptor Blocking Antibodies on Stimulating Autoantibodies from Patients with Graves' Disease (2003)

The hyperthyroidism of Graves' disease (GD) is caused by thyrotropin-receptor (TSHR) stimulating autoantibodies (TSAb), which lead to overproduction of thyroid hormones. In this study we tried to block the stimulatory effect of patients' TSAb to the TSHR with monoclonal antibodies (mAbs) and sera from hypothyroid patients. Two groups of blocking mAbs raised by different methods from two independent groups were tested for their ability to inhibit TSH binding to the TSHR, and also the binding of TSAb from the serum of patients with GD. Group 1 mAbs (7E3, 3H10, 4C1, 1B1, 4E9) bind to amino acids 378-387 and group 2 mAbs (23.1 and 31.7) to amino acids 382-415 of the human TSHR. These results were compared to the TSH- and TSAb-inhibiting effect of sera from hypothyroid patients containing bona fide thyroid blocking antibodies (TBAb) without agonistic activity. All studies were done in a conventional cyclic adenosine monophosphate (cAMP) or a modified luciferase reporter gene bioassay. TSH-induced cAMP/luciferase signal was reduced (> 70% inhibition) by all 7 mAbs, verifying the blocking nature. Comparable results (82.2%-96.3% inhibition) were seen when cells were preincubated with 8 TBAb sera. These TBAb sera also inhibited cAMP/luciferase induction of TSAb-positive sera from patients with GD (median of 27 experiments 62.2% inhibition; range, 26.8%-93.9%), and maintained inhibition greater than 20% even when diluted 1:150. However, when mAbs were incubated with these sera, results were heterogeneous: 17 of 30 sera (57%) incubated with mAb 31.7 caused reduced cAMP production compared to incubation with the control antibody, as did 18 of 34 sera (53%) incubated with mAb 7E3, 17 of 33 sera (52%) incubated with mAb 3H10, and 16 of 31 (52%) with mAb 23.1. Mixing all four mAbs did not enhance the cAMP-reductive effect (16/27 sera; 59% inhibited). Inhibition was less pronounced than with TBAb sera (0%-76% of a control antibody) and only present at antibody concentrations greater than 10 microg/mL. We conclude that despite the strong TBAb activity of the mAbs, their effect on TSAb-induced TSHR activation of sera from patients with GD was weaker than that of human TBAb autoantibodies. Thus, the latter are not only strong inhibitors of TSH activity, but also block the stimulatory effect of autoantibodies from patients with GD. However, this effect could not be reproduced by experimental mAbs to the same extent, because it may be the result of a broader spectrum of antibodies present in the TBAb sera, interacting with or in the vicinity of TSAb epitopes. Also of interest, when a TBAb serum was added to a TSAb serum, the TBAb effect was predominant even at high dilutions.
Infectious complications of TNF-α inhibitor monotherapy versus combination therapy with immunomodulators in inflammatory bowel disease: analysis of the Food and Drug Administration Adverse Event Reporting System. (2013)

TNF-α inhibitor and immunomodulator monotherapy increase the baseline odds of acquiring a serious infection. Combination therapy with these drugs does not further increase the odds of serious infections compared to monotherapy.
SignCRF: Scalable Channel-agnostic Data-driven Radio Authentication System (2023)

Radio Frequency Fingerprinting through Deep Learning (RFFDL) is a data-driven IoT authentication technique that leverages the unique hardware-level manufacturing imperfections associated with a particular device to recognize (fingerprint) the device based on variations introduced in the transmitted waveform. The proposed SignCRF is a scalable, channel-agnostic, data-driven radio authentication platform with unmatched precision in fingerprinting wireless devices based on their unique manufacturing impairments and independent of the dynamic channel irregularities caused by mobility. SignCRF consists of (i) a baseline classifier finely trained to authenticate devices with high accuracy and at scale; (ii) an environment translator carefully designed and trained to remove the dynamic channel impact from RF signals while maintaining the radio's specific signature; (iii) a Max-Rule module that selects the highest precision authentication technique between the baseline classifier and the environment translator per radio. We design, train, and validate the performance of SignCRF for multiple technologies in dynamic environments and at scale (100 LoRa and 20 WiFi devices). We demonstrate that SignCRF significantly improves the RFFDL performance by achieving as high as 5x and 8x improvement in correct authentication of WiFi and LoRa devices when compared to the state-of-the-art, respectively.
Information diffusion through blogspace (2004)

We study the dynamics of information propagation in environments of low-overhead personal publishing, using a large collection of weblogs over time as our example domain. We characterize and model this collection at two levels. First, we present a macroscopic characterization of topic propagation through our corpus, formalizing the notion of long-running chatter topics consisting recursively of spike topics generated by outside world events, or more rarely, by resonances within the community. Second, we present a microscopic characterization of propagation from individual to individual, drawing on the theory of infectious diseases to model the flow. We propose, validate, and employ an algorithm to induce the underlying propagation network from a sequence of posts, and report on the results.
Effect of schistosomiasis and hepatitis on liver disease. (1999)

Infection with hepatitis C virus (HCV) has become the most important public health problem in Egypt. In Egypt, viral hepatitis along with infection with Schistosoma mansoni is the major cause of chronic liver disease and liver cirrhosis. Although HCV infection is highly prevalent in Egypt, very little information is available on the distribution of the different genotypes of HCV. Our aims in this study were first to determine the prevalence of viral and parasite infections in patients with chronic liver disease and then to assess the distribution of HCV genotypes in these patients. In the present study, 151 individuals (50 with chronic liver disease, 51 with chronic diseases of organs other than the liver, and 50 apparently healthy persons) were investigated. The last 2 groups served as control groups. These individuals were subjected to routine liver function tests and detection of serum antibodies to bilharziasis, hepatitis B surface antigen (HBsAg), and HCV. Furthermore, the presence of hepatitis G virus (HGV) and HCV in the serum samples were tested for by a reverse transcription polymerase chain reaction (RT-PCR). Prevalence of different genotypes of HCV in patients positive for HCV were determined by RT-PCR using type-specific primers. Results of the study revealed that 84, 74, 12, and 20% of patients with chronic liver disease were positive for Schistosoma mansoni, HCV, HBsAg, and HGV, respectively, as compared to 51, 43.1, 2, and 4% of patients with other chronic diseases and 22, 6, 0, and 0% of apparently healthy individuals. One hundred percent of patients with chronic liver disease, 72.5% of those with other diseases, and 26% of normal controls were shown to have at least one of the studied infectious agents. Two or more of the agents were highly coincident in patients with chronic liver disease. In Egypt, HCV genotype 4a is highly prevalent, where it contributed 85% of the tested samples in comparison to 10, 2.5, and 2.5% for subtypes 1b, 2a, and 3a, respectively. In conclusion, these results suggest that in Egypt, HCV along with schistosomal parasite infection is the major risk factor for chronic liver disease. In most Egyptian patients, HCV genotype 4 is highly prevalent.
Role of the ptsN Gene Product in Catabolite Repression of the Pseudomonas putida TOL Toluene Degradation Pathway in Chemostat Cultures ▿ (2006)

The Pseudomonas putida KT2440 TOL upper pathway is repressed under nonlimiting conditions in cells growing in chemostat with succinate as a carbon source. We show that the ptsN gene product IIA(Ntr) participates in this repression. Crc, involved in yeast extract-dependent repression in batch cultures, did not influence expression when cells were growing in a chemostat with succinate at maximum rate.
The gene for T11 (CD2) maps to chromosome 1 in humans and to chromosome 3 in mice. (1988)

The chromosomal locations of the human and murine T11 (CD2) gene have been determined. Using recently cloned cDNA to probe Southern blots of mouse X human and Chinese hamster X mouse somatic cell hybrids, we have localized the human T11 gene to chromosome 1 and the murine T11 gene to chromosome 3. Based on previously determined blocks of homology between human chromosome 1 and mouse chromosome 3, it is suggested that the human T11 gene may lie on the short arm of chromosome 1 proximal to p221. Thus, the T11 gene is not linked to any other genes for T cell markers that have been mapped to date.
Development of a Gene Therapy Trial for Metastatic Prostate Cancer (2006)

Abstract : This award was to support the infrastructure and development of a Phase I clinical trial for men with metastatic prostate cancer. The Phase I trial under development employs a prostate restricted replicative adenovirus (PRRA) with excellent preclinical performance in vitro and in vivo in relevant animal models of human prostate cancer. Several components of the statement of work for this award have been completed. The key component of this trial the PRRA AdIU1 required a slight modification before proceeding with implementation of the trial as submitted. Reconfirmation of the activity of the modified AdIU1 was required prior to moving forward with the clinical trial. A majority of the funding from this award remains in the CTDA account and a no cost extension has been requested to allow continued development of the trail in order to apply for a 2007 DOD Clinical Trial Award to initiate a trial in 2008. Currently with the clinical trial team in place and modified AdIU1 verified the regulatory applications on hold can be filed.
Carbon Footprint Analysis of Gasoline and Diesel from Forest Residues and Algae using Integrated Hydropyrolysis and Hydroconversion Plus Fischer–Tropsch (IH2 Plus cool GTL) (2018)

Life cycle analysis was conducted with a focus on greenhouse gas (GHG) emissions of renewable gasoline and diesel produced by the integrated hydropyrolysis and hydroconversion (IH2) and the new IH2 plus Fischer–Tropsch (IH2 Plus cool GTL) processes. This new process has a primary objective of increasing the yield of biofuel relative to original IH2 process (increase of 26% to 38% wt) by processing the C1–C3 gas co-products through an integrated Fischer–Tropsch unit to produce liquid-range hydrocarbon biofuel. For both biofuel processes, woody biomass residues (forest logging and saw mills) and algae were investigated as feedstocks. The effect of the electricity generation mix of different states in the U.S. was also examined for algae cultivation. For woody residues as feedstock, life cycle GHG emission savings of about 86.8% and 63.3% were calculated for the IH2 and optimized-IH2 Plus cool GTL hydrocarbon biofuel, respectively, relative to fossil-derived fuel. For algae as feedstock, emission increases of about 140% and 103% were calculated for the IH2 and optimized-IH2 Plus cool GTL, respectively, relative to fossil-derived fuel. The electricity grid mix of the biorefinery location significantly impacts the GHG emissions of the processes for algae feedstock. GHG savings of about 42% can be potentially achieved if the plant was located in an area with a low GHG intensity grid. This study has shown that a significant biofuel yield boost can be achieved while retaining high GHG savings by using IH2 Plus cool GTL for a woody feedstock.
Applying C-DEEPSO to Solve Large Scale Global Optimization Problems (2018)

In this paper, a hybrid single-objective metaheuristic, named as C-DEEPSO (Canonical Differential Evolutionary Particle Swarm Optimization), is proposed to solve large-scale optimization problems. C-DEEPSO can be viewed as an evolutionary algorithm with recombination rules borrowed from PSO or an swarm optimization method with selection and self-adaptiveness properties. To assess the algorithm performance, the algorithm is run over 15 benchmark continuous problems presented in CEC'2015. The algorithm is also applied over a real world large-scale problem. The results indicate that the proposed algorithm is an efficient and competitive method to handle such problems. The experimental results also show that the new approach reaches competitive results when compared to the reference algorithm DECC-G. An application of C-DEEPSO were perform to solve the electric dispatch in a large scale energy network, the IEEE 57 Bus-System. The results show that the algorithm is a good way to solve nonlinear problems respecting many constraints associated.
Regionalization in a global hydrologic deep learning model: from physical descriptors to random vectors (2022)

Streamflow prediction is a long-standing hydrologic problem. Development of models for streamflow prediction often requires incorporation of catchment physical descriptors to characterize the associated complex hydrological processes. Across different scales of catchments, these physical descriptors also allow models to extrapolate hydrologic information from one catchment to others, a process referred to as “regionalization”. Recently, in gauged basin scenarios, deep learning models have been shown to achieve state of the art regionalization performance by building a global hydrologic model. These models predict streamflow given catchment physical descriptors and weather forcing data. However, these physical descriptors are by their nature uncertain, sometimes incomplete, or even unavailable in certain cases, which limits the applicability of this approach. In this paper, we show that by assigning a vector of random values as a surrogate for catchment physical descriptors, we can achieve robust regionalization performance under a gauged prediction scenario. Our results show that the deep learning model using our proposed random vector approach achieves a predictive performance comparable to that of the model using actual physical descriptors. The random vector approach yields robust performance under different data sparsity scenarios and deep learning model selections. Furthermore, based on the use of random vectors, high-dimensional characterization improves regionalization performance in gauged basin scenario when physical descriptors are uncertain, or insufficient.
Dispersive OPA at Very Near-Infrared Wavelengths (2021)

We present a serpentine-based 16-element dispersive OPA at very near-IR wavelengths that leverages SiN waveguide feeding. 2D beam steering is achieved by wavelength sweep, with tunability of 0.11°/nm on slow and 3.52°/nm on fast axis.
Simulation of nanofloating gate memory with high-k stacked dielectrics (2003)

Scaling of conventional floating gate nonvolatile memory cells towards the nanometer range is jeopardized by the lack of scalability of the tunnel oxide. In this paper, we discuss the advantages of using high-k materials for nanofloating gate memory structures by means of numerical device simulations.
Molybdate Inhibits Hsp90, Induces Structural Changes in Its C-Terminal Domain, and Alters Its Interactions with Substrates (1999)

To examine the biochemical mechanism by which hsp90 exerts its essential positive function on certain signal transduction proteins, we characterized the effects of molybdate and geldanamycin on hsp90 function and structure. Molybdate inhibited hsp90-mediated p56lck biogenesis and luciferase renaturation while enforcing salt-stable interactions with these substrates. Molybdate also reduced the amount of free hsp90 present in cell lysates, inhibited hsp90's ability to bind geldanamycin, and induced resistance to proteolysis at a specific region within the C-terminal domain of hsp90. In contrast, the hsp90 inhibitor geldanamycin prevented hsp90 from assuming natural or molybdate-induced conformations that allow salt-stable interactions with substrates. When these compounds were applied sequentially, the order of addition determined the effects observed, indicating that these agents had opposing effects on hsp90. We conclude that a specific region within the C-terminal domain of hsp90 (near residue 600) determines the mode by which hsp90 interacts with substrates and that the ability of hsp90 to cycle between alternative modes of interaction is obligatory for hsp90 function.
WebSphere Business Integration: An architectural overview (2004)

Business integration is a set of capabilities that characterize service-oriented architectures for e-business solutions. These capabilities include the ability to integrate and manage business operation systems, enterprise information assets, business partners, and a collaborative network of decision makers to address specific business problems. WebSphere® Business Integration is an IBM software platform that embodies these capabilities to offer rapid time to value for delivering integrated e-business solutions. In this paper, we provide an overview of the WebSphere Business Integration platform—the architecture, programming model, tools, and runtime.
In vitro simulation of immunosuppression caused by Trypanosoma brucei. (1991)

Macrophage populations derived from Trypanosoma brucei-infected mice suppress both interleukin-2 (IL-2) production and IL-2 receptor (IL-2R) expression. A prostaglandin-independent mechanism accounts for the suppression of IL-2R expression, while the suppression of IL-2 is prostaglandin-dependent. A macrophage hybridoma cell line (i.e. 2C11-12) was used to mimic the parasite-induced immunosuppression in vitro. It was found that 2C11-12 cells acquired a suppressive potential in vitro following interaction with opsonized living parasites. T. brucei-pulsed 2C11-12 cells failed to block IL-2 secretion in the presence of indomethacin but still suppressed the IL-2R expression. In contrast, addition of living T. brucei parasites to the cultures caused a complete suppression of IL-2 secretion and IL-2R expression, even in the presence of indomethacin. Hence, the addition of excess living parasites to the cultures could cause a depression which was different from the suppression associated with infection, whereas the addition of parasite-pulsed 2C11-12 cells mimicked the situation occurring during infection. This model system can be adopted as a suitable tool to unravel the mechanisms underlying the suppression of IL-2R expression during T. brucei infections.
Effects of isolectin B4‐conjugated saporin, a targeting cytotoxin, on bladder overactivity induced by bladder irritation (2004)

In order to clarify the functional role of the isolectin B4 (IB4)-binding afferent pathway in the micturition reflex, we investigated the effects on bladder activity of intrathecal application of the IB4-saporin conjugate, a targeting cytotoxin that destroys neurons binding IB4. In rats, IB4-saporin (2.5 micro m) or vehicle was administered through an intrathecal catheter implanted at the level of the L6-S1 spinal cord. Three weeks after IB4-saporin administration, cystometry in conscious animals revealed a reduction in bladder overactive responses induced by intravesical capsaicin or ATP infusion without affecting normal voiding function. In histochemical studies, double staining for IB4 and saporin was detected in L6 dorsal root ganglia (DRG) neurons 2 days after the treatment. Three weeks after the treatment, the area in lamina II of the L6 spinal cord stained with IB4 was significantly reduced compared with the area stained in control rats. The staining in the L1 spinal cord was not affected. The percentage of neurons in the L6 DRG intensely labeled with IB4 was also reduced in IB4-saporin-treated rats. These results indicate that intrathecal treatment with the IB4-saporin conjugate at the level of L6-S1 spinal cord, which reduces IB4 afferent nerve terminal staining in lamina II of the L6 spinal cord as well as the number of IB4-binding neurons in L6 DRG, suppressed bladder overactivity induced by bladder irritation without affecting normal micturition. Thus targeting IB4-binding, non-peptidergic afferent pathways sensitive to capsaicin and adenosine 5'-triphosphate may be an effective treatment for overactivity and/or pain responses in the bladder.
Donor-Related Risk Factors and Preoperative Recipient-Related Risk Factors for Graft Failure (2014)

This study demonstrated a success rate of 74%, which is consistent with previous studies. Various preoperative recipient-related factors seem to influence the outcome of penetrating keratoplasties, whereas few donor-related factors have a significant association with graft failure.