gebhart/patrepeval huggingface dataset:
An oncofetal antigen, IMP-3-derived long peptides induce immune responses of both helper T cells and CTLs (2016)

Insulin-like growth factor II mRNA-binding protein 3 (IMP-3), an oncofetal antigen identified using genome-wide cDNA microarray analyses, is overexpressed in several malignancies. IMP-3-derived cytotoxic T lymphocyte (CTL) epitopes have been used for peptide-based immunotherapies against various cancers. In addition to CTLs, induction of tumor-associated antigen (TAA)-specific helper T (Th) cells is crucial for establishment of effective antitumor immunity. In this study, we aimed to identify IMP-3-derived long peptides (IMP-3-LPs) carrying CTL and promiscuous Th-cell epitopes for use in cancer immunotherapy. IMP-3-derived Th-cell epitopes that bind to multiple HLA-class II molecules were predicted by in silico analysis, and their immunogenicity was determined by utilizing human T cells. We identified two highly immunogenic IMP-3-LPs presented by multiple HLA-class II molecules. One of the IMP-3-LPs encompassed two CTL epitopes that have been used for peptide-vaccine immunotherapy in ongoing clinical trials. IMP-3-LPs-specific Th cells responded to autologous dendritic cells (DCs) loaded with the recombinant IMP-3 proteins, suggesting that these s (LPs) can be naturally processed and presented. The IMP-3-LPs and specific Th cells augmented the expansion of IMP-3-specific CTLs, which was further enhanced by programmed cell death-1 (PD-1) blockade. In addition, IMP-3-LP encapsulated in liposomes was efficiently cross-presented in vitro, and this LP successfully cross-primed CTLs in HLA-A2 transgenic mice (Tgm) in vivo. Furthermore, one of the IMP-3-LPs induced IMP-3-specific Th cells from peripheral blood mononuclear cells (PBMCs) of head-and-neck malignant tumor (HNMT) patients. These findings suggest the potential usefulness of IMP-3-LPs in propagating both Th cells and CTLs and may have implications for IMP-3-LPs-based cancer immunotherapy.
Community-based benchmarking improves spike rate inference from two-photon calcium imaging data (2017)

In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. However, the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators. Different algorithms for estimating spike trains from noisy calcium measurements have been proposed in the past, but it is an open question how far performance can be improved. Here, we report the results of the spikefinder challenge, launched to catalyze the development of new spike inference algorithms through crowd-sourcing. We present ten of the submitted algorithms which show improved performance compared to previously evaluated methods. Interestingly, the top-performing algorithms are based on a wide range of principles from deep neural networks to generative models, yet provide highly correlated estimates of the neural activity. The competition shows that benchmark challenges can drive algorithmic developments in neuroscience.
Advanced Ground Systems Maintenance Prognostics Project (2015)

The project implements prognostics capabilities to predict when a component system or subsystem will no longer meet desired functional or performance criteria, called the end of life. The capability also provides an assessment of the remaining useful life of a hardware component. The project enables the delivery of system health advisories to ground system operators. This project will use modeling techniques and algorithms to assess components' health andpredict remaining life for such components. The prognostics capability being developed will beused:during the design phase and during pre/post operations to conduct planning and analysis ofsystem design, maintenance &amp; logistics plans, and system/mission operations plansduring real-time operations to monitor changes to components' health and assess their impacton operations.This capability will be interfaced to Ground Operations' command and control system as a part ofthe AGSM project to help assure system availability and mission success. The initial modelingeffort for this capability will be developed for Liquid Oxygen ground loading applications.
Optimal linear receivers for synchronizing pseudo random sequences (2002)

Much research work has been done in finding sequences with good autocorrelation properties. The conventional receiver structure for synchronizing with such a sequence transmitted periodically is a matched filter matched to the sequence. However, the synchronization performance of the receiver can be further improved if the receiver tries to match to the sequence and dematch the circular shifts of the sequence. In the problem at hand the data preceding the synchronization sequence is known. We derive the optimal linear receiver to synchronize with a given sequence and demonstrate the synchronization gain achieved by employing such a receiver over the conventional receiver. This gain is obtained by simply changing the receiver coefficients, leaving the receiver structure unchanged.
The relationship of actin to ligament contraction. (1986)

A surgical model of a contracting ligament was established in a Z-lengthened, rat medial collateral ligament. These lengthened ligaments contracted back to a normal degree of tightness in a three-week period. Immunofluorescent actin staining of cryostat ligament sections was increased in these contracted ligaments, compared with sham-operated ligaments that had not contracted. In vitro culture of ligament fibroblasts confirmed that they (like fibroblasts from other systems) produce large, actin, stress fibers thought to be involved in cell contraction. Transmission electron-microscopic examination of normal ligament demonstrated the cytoplasm of fibroblast cell processes extending out to and surrounding collagen fibrils, indicating a closer involvement with established fibrils than was expected. On the basis of these observations, it is hypothesized that intracellular proteins, such as actin, allow the fibroblast to exert forces and actively contribute to the contraction of ligamentous tissues.
Integrative structural studies of the SARS-CoV-2 spike protein during the fusion process (2022) (2022)

SARS-CoV-2 is the virus responsible for the COVID-19 pandemic and catastrophic, worldwide health and economic impacts. The spike protein on the viral surface is responsible for viral entry into the host cell. The binding of spike protein to the host cell receptor ACE2 is the first step leading to fusion of the host and viral membranes. Despite the vast amount of structure data that has been generated for the spike protein of SARS-CoV-2, many of the detailed structures of the spike protein in different stages of the fusion pathway are unknown, leaving a wealth of potential drug-target space unexplored. The atomic-scale structure of the complete S2 segment, as well as the complete fusion intermediate are also unknown and represent major gaps in our knowledge of the infectious pathway of SAR-CoV-2. The conformational changes of the spike protein during this process are similarly not well understood. Here we present structures of the spike protein at different stages of the fusion process. With the transitions being a necessary step before the receptor binding, we propose sites along the transition pathways as potential targets for drug development.
Immune Responses to Human Immunodeficiency Virus (HIV) Type 1 Induced by Canarypox Expressing HIV‐1Mngp120, HIV‐1SF2Recombinant gp120, or Both Vaccines in Seronegative Adults (1998)

A safety and immunogenicity trial was conducted in vaccinia-immune and vaccinia-naive human immunodeficiency virus (HIV)-uninfected adults who were randomized to receive 10(6) or 10(7) TCID50 of canarypox (ALVAC) vector expressing HIV-1MN gp160 or 10(5.5) TCID50 of ALVAC-rabies virus glycoprotein control at 0 and 1 or 2 months and ALVAC-gp160 or 50 microg of HIV-1SF2 recombinant (r) gp120 in microfluidized emulsion at 9 and 12 months; others received rgp120 at 0, 1, 6, and 12 months. All vaccines were well-tolerated. Neither vaccinia-immune status before vaccination nor ALVAC dose affected HIV immune responses. HIV-1MN and HIV-1SF2 neutralizing antibodies were detected more often (100%) in ALVAC-gp160/rgp120 recipients than in recipients of ALVAC-gp160 (<65%) or rgp120 (89%) alone. ALVAC-gp160/rgp120 also elicited more frequent HIV V3-specific and fusion-inhibition antibodies, antibody-dependent cellular cytotoxicity, lymphoproliferation, and cytotoxic CD8+ T cell activity than did either vaccine alone. Trials with ALVAC expressing additional HIV components and rgp120 are underway.
New method for the prediction of rain attenuation in terrestrial links using the concept of effective rainfall rate (2007)

A semi-empirical method for the prediction of rain attenuation in terrestrial links is presented in this paper. The proposed method is simple to apply and uses the concept of an effective rainfall rate and the full rainfall rate cumulative probability distribution to predict the attenuation distribution. Test results indicate that the proposed method provides significant improvement over the current ITU-R method and other methods available in the literature.
Variations in Antibiotic Prescribing of Acute Rhinosinusitis in United States Ambulatory Settings (2013)

Antibiotics were prescribed frequently despite recent consensus guidelines that discourage antibiotic use in mild cases. Furthermore, antibiotic prescription was more likely for younger patients and in primary care settings. This highlights the need to promote awareness of practice guidelines.
Advanced Scanning Tunneling Microscopy for Nanoscale Analysis of Semiconductor Devices (2016)

Significant attention has been addressed to high-spatial resolution analysis of modern sub-100-nm electronic devices to achieve new functions and energy-efficient operations. The chapter presents a review of ongoing research on charge carrier distribution analysis in nanoscale Si devices by using scanning tunneling microscopy (STM) employing advanced operation modes: a gap-modulation method, a molecule-assisted probing method, and a dual-imaging method. The described methods rely on detection and analysis of tunneling current, which is strongly localized within an atomic dimension. Representative examples of applications to nanoscale analysis of Si device cross-sections and nanowires are given. Advantages, difficulties, and limitations of the advanced STM methods are discussed in comparison with other techniques used in a field of device metrology.
A SUMOylation-Dependent Transcriptional Subprogram Is Required for Myc-Driven Tumorigenesis (2011)

Myc is an oncogenic transcription factor frequently dysregulated in human cancer. To identify pathways supporting the Myc oncogenic program, we used a genome-wide RNA interference screen to search for Myc-synthetic lethal genes and uncovered a role for the SUMO-activating enzyme (SAE1/2). Loss of SAE1/2 enzymatic activity drives synthetic lethality with Myc. Inactivation of SAE2 leads to mitotic catastrophe and cell death upon Myc hyperactivation. Mechanistically, SAE2 inhibition switches a transcriptional subprogram of Myc from activated to repressed. A subset of these SUMOylation-dependent Myc switchers (SMS genes) is required for mitotic spindle function and to support the Myc oncogenic program. SAE2 is required for growth of Myc-dependent tumors in mice, and gene expression analyses of Myc-high human breast cancers suggest that low SAE1 and SAE2 abundance in the tumors correlates with longer metastasis-free survival of the patients. Thus, inhibition of SUMOylation may merit investigation as a possible therapy for Myc-driven human cancers.
Latency Measurement of 100 km Fiber Using Correlation-OTDR (2020)

By means of C-OTDR (Correlation - Optical Time Domain Reflectometry), we measured the latency of100 km fiber with an accuracy of a few picoseconds. Based on iterating 49 measurements, we calculated a standard deviation of 12 ps between the round-trip latency values. To verify the reflection measurements, we used a single pass setup without reflector, which showed a maximum difference of only 11 ps.
Smart personalized learning system for energy management in buildings (2017)

Integration of energy management systems into existing buildings brings in several challenges and financial constraints. Some of the challenges in the existing smart building solutions are that they require large-scale deployment of sensors, high rate of data collection, real-time data analysis in short span of time, and lack of knowledge about the energy usage with respect to the behavior of individuals and groups. This work proposes an affordable wearable device system as an alternative for large-scale deployment of sensors in industrial buildings. For effective energy management in the buildings, a personalized behavior analysis has been done in machine learning and neural networks algorithm and integrated with the proposed system. The complete system is implemented and tested extensively. The results show that the proposed system could provide 85% user comfort and 23% energy savings.
Chemistry and Pharmacology of the Piperidine-Based Analogues of Cocaine. Identification of Potent DAT Inhibitors Lacking the Tropane Skeleton (1998)

To discover agents that might be useful in the treatment of cocaine abuse, we have chosen to re-explore a class of molecules that was first reported by Clarke et al. in 1973 and that was and shown to lack locomotor stimulatory activity in mice. These compounds are piperidine-3-carboxylic acid esters bearing a 4-chlorophenyl group in position 4, and as such, these structures may be viewed as truncated versions of the WIN series compounds, i.e., they lack the two-carbon bridge of the tropanes. All members of this class were synthesized starting from arecoline hydrobromide and obtained in optically pure form through resolution methods using either (+)- or (-)-dibenzoyltartaric acid. Interestingly, we have found that these piperidines do, in fact, exhibit substantial affinity in both WIN 35, 428 binding at the dopamine transporter and in the inhibition of [3H]dopamine uptake. Of all of the compounds synthesized, the 3-n-propyl derivative (-)-9 was found to be the most potent with a binding affinity of 3 nM. This simple piperidine is thus 33-fold more potent than cocaine in binding affinity and 29-fold more potent in its inhibition of dopamine uptake. Although no efforts have presently been made to "optimize" binding affinity at the DAT, the substantive activity found for the n-propyl derivative (-)-9 is remarkable; the compound is only about 10-fold less active than the best of the high-affinity tropanes of the WIN series. As a further point of interest, it was found that the cis-disubstituted piperidine (-)-3 is only about 2-fold more potent than its trans isomer (+)-11. This result stands in sharp contrast to the data reported for the tropane series, for the epimerization of the substituent at C-2 from beta to alpha has been reported to result in a lowering of activity by 30-200-fold. This smaller spread in binding affinities for the piperidines may reflect the smaller size of these molecules relative to the tropanes, which allows both the cis and the trans isomers to adjust themselves to the binding site on the DAT. Our present demonstration that these piperidine structures do, in fact, possess significant DAT activity, taken together with their reported lack of locomotor activity, provides a compelling argument for exploring this class of molecules further in animal behavioral experiments. The present work thus broadens the scope of structures that may be considered as lead structures in the search for cocaine abuse medications.
Impact of Carrier Configuration and Allocation Scheme on 3G Femtocell Offload Effect (2011)

The Macro offload of closed mode 3G Femtocells is studied; i.e. how much of downlink macrocellular traffic can be moved to a Femtocell layer. Taking the 3GPP dense urban reference model as our starting point we show that the combination of adaptive Femtocell power calibration together with a Macro-user frequency allocation method that considers the SINR difference between the mixed and a Macro-only carrier, improves offload. Additionally, the total number of carriers available to the operator is important for the offload potential. It is confirmed that a macro-only carrier is a desirable deployment strategy. At a 25% HNB penetration rate in apartments, 7% of the network traffic can be offloaded in the two-carrier case. This improves to 15% when three carriers are available. With Femto-aware macro-user carrier allocation, the offload performance improves further to 20% with 2 carriers.
Epitaxial Si-Ge-Sn Materials for Si-Based Optoelectronic Applications (2008)

Abstract not Available.
Long-wavelength VCSELs for sensing applications (2012)

Long-wavelength VCSELs with emission wavelengths beyond 1.3 &#956;m have seen a remarkable progress over the last decade. This success has been accomplished by using highly advanced device concepts which effectively overcome the fundamental technological drawbacks related with long-wavelength VCSELs such as inferior thermal properties and allow for the realization of lasers with striking device performance. In this presentation, we will give an overview on the state of the technology for long-wavelength VCSELs in conjunction with their opportunities in applications for optical sensing. While VCSELs based on InP are limited to maximum emission wavelengths around 2.3 &#956;m, even longer wavelengths up to the mid-infrared range beyond 3 &#956;m can be achieved with VCSELs based on GaSb. For near-infrared InP-based VCSELs, the output characteristics include sub-mA threshold currents, up to several milliwatts of singlemode output power and ultralow power consumption. New concepts for widely tunable VCSELs with tuning ranges up to 100 nm independent from the material system for the active region are also presented. Today, optical sensing by Tunable Diode Laser Spectroscopy is a fast emerging market. Gas sensing systems are used for a wide range of applications such as industrial process control, environmental monitoring and safety applications. With their inherent and compared to other laser types superior properties including enhanced current tuning rates, wavelength tuning ranges, modulation frequencies and power consumption, long-wavelength VCSELs are regarded as key components for TDLS applications.
IGBT SPICE model (1995)

During the last few years, great progress in the development of new power semiconductor devices has been made. The new generation of power semiconductors is capable of conducting more current and blocking higher voltage. The IGBT (insulated gate bipolar transistor) is an outgrowth of power MOSFET technology. More like a MOSFET than a bipolar transistor in structure, the IGBT has some of the electrical characteristics of both. Like a MOSFET, the gate of the IGBT is isolated, and drive power is very low. The on-state conduction voltage of an IGBT is similar to that of a bipolar transistor. However, SPICE users are constantly faced with the inability to analyze circuits that contain devices that are not in the SPICE library of the semiconductor models. With the authors' own computer program, a complete macromodel of the IGBT for the SPICE simulator has been computed. In this paper, a complete IGBT SPICE macromodel is described and verified with experimental results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Small Molecule Enhancers of Rapamycin-Induced TOR Inhibition Promote Autophagy, Reduce Toxicity in Huntington’s Disease Models and Enhance Killing of Mycobacteria by Macrophages (2007)

Upregulation of autophagy may have therapeutic benefit in a range of diseases that includes neurodegenerative conditions caused by intracytosolic aggregate-prone proteins, such as Huntington's disease, and certain infectious diseases, such as tuberculosis. The best-characterized drug that enhances autophagy is rapamycin, an inhibitor of the TOR (target of rapamycin) proteins, which are widely conserved from yeast to man. Unfortunately, the side effects of rapamycin, especially immunosuppression, preclude its use in treating certain diseases including tuberculosis, which accounts for approximately 2 million deaths worldwide each year, spurring interest in finding novel drugs that selectively enhance autophagy. We have recently reported a novel two-step screening process for the discovery of such compounds. We first identified compounds that enhance the growth-inhibitory effects of rapamycin in the budding yeast Saccharomyces cerevisiae, which we termed small molecule enhancers of rapamycin (SMERs). Next we showed that three SMERs induced autophagy independently, or downstream of mTOR, in mammalian cells, and furthermore enhanced the clearance of a mutant huntingtin fragment in Huntington's disease cell models. These SMERs also protected against mutant huntingtin fragment toxicity in Drosophila. We have subsequently tested two of the SMERs in models of tuberculosis and both enhance the killing of mycobacteria by primary human macrophages.
Improvement of Liver Cancer Detection with Simultaneous Assessment of Circulating Levels of Free Alpha-Fetoprotein (AFP) and Afp-Igm Complexes (2004)

We assessed the presence of alpha-fetoprotein (AFP) complexed with IgM (AFP-IgM IC) in serum of patients affected by hepatocellular carcinoma (HCC), cirrhosis and chronic hepatitis as well as in healthy subjects by means of a dedicated ELISA assay. The amount of AFP-IgM IC was expressed in arbitrary units (AU) on a reference standard curve. Free AFP (FAFP) levels were determined in parallel in each sample by means of an automated immunoassay system. The mean serum concentration of AFP-IgM IC was significantly higher in HCC patients (mean +/- SD: 1378.3 +/- 2935.7 AU/mL) than in cirrhotic patients (129.8 +/- 261.4 AU/mL) and in patients with chronic hepatitis (80.9 +/- 168.9 AU/mL) (p < 0.01). HCC patients had FAFP values above the 20 ng/mL cutoff in 44% of cases (22/50) and AFP-IgM IC values above the 120 AU/mL cutoff in 60% of cases (30/50). The occurrence of the free and IgM-complexed form of circulating AFP did not overlap, and 82% of patients (41/50) were positive for at least one marker. The results indicate that AFP-IgM IC is a complementary serological marker to FAFP and that the combination of these biomarkers may be useful in the diagnosis of liver cancer.
Effect of thermalization distance on stochastic phenomena in 7-nm-half-pitch line-and-space pattern fabrication using chemically amplified extreme ultraviolet resists (2016)

Abstract The thermalization of secondary electrons is an important process in the radiation effects on a condensed matter. In the lithography using ionizing radiations, it is expected that the effects of thermalization distance will become prominent in the sub-10 nm resolution region. In this study, the effects of thermalization distance on the stochastic phenomena in the fabrication of line-and-space patterns with 7 nm half-pitch were investigated on the basis of the sensitization mechanisms of chemically amplified extreme ultraviolet resists. All three factors related to the stochastic phenomena [the stochastic generation of pinching and bridges and line edge roughness (LER)] were improved by decreasing the thermalization distance. It was found that the suppression of LER and bridge generation was a more serious problem than that of pinching.