gebhart/patrepeval huggingface dataset:
Potent suppression of HIV viral replication by a novel inhibitor of Tat (2012)

Background Tat, the HIV Trans-Activator of Transcription is a potential antiviral target. Tat binds to the 5’ terminal region of HIV mRNAs stem-bulge-loop structure called the Trans-activation Responsive (TAR) element and activates transcription from the HIV promoter. Plasma viremia stubbornly persists in HIV-1 infected subjects despite receiving HAART, suggesting that residual levels of viral production originate from an integrated form of the HIV genome that is continuously transcribed at low levels. As current antiretrovirals (ARVs) fail to inhibit transcription from integrated viral genomes or viral production from stable cellular reservoirs, novel classes of ARVs are needed to inhibit this process.
Capacitively-Heated Fluidized Bed (1982)

Fluidized-bed chamber in which particles in bed are capacitively heated produces high yields of polycrystalline silicon for semiconductor devices. Deposition of unrecoverable silicon on chamber wall is reduced, and amount of recoverable silicon depositing on seed particles in bed is increased. Particles also have a size and density suitable for direct handling without consolidation, unlike silicon dust produced in heated-wall chambers.
Single frequency 1560nm Er:Yb fiber amplifier with 207W output power and 50.5% slope efficiency (2016)

High power fiber lasers/amplifiers in the 1550nm spectral region have not scaled as rapidly as Yb-, Tm-, or Ho-doped fibers. This is primarily due to the low gain of the erbium ion. To overcome the low pump absorption, Yb is typically added as a sensitizer. Although this helps the pump absorption, it also creates a problem with parasitic lasing of the Yb ions under strong pumping conditions, which generally limits output power. Other pump schemes have shown high efficiency through resonant pumping of erbium only without the need for Yb as a sensitizer [1-2]. Although this can enable higher power scaling due to a decrease in the thermal loading, resonant pumping methods require long fiber lengths due to pump bleaching, which may limit the power scaling which can be achieved for single frequency output. By using an Er:Yb fiber and pumping in the minima of the Yb pump absorption at 940nm, we have been able to simultaneously generate high power, single frequency output at 1560nm while suppressing the 1-micron ASE and enabling higher efficiency compared to pumping at the absorption peak at 976nm. We have demonstrated single frequency amplification (540Hz linewidth) to 207W average output power with 49.3% optical efficiency (50.5% slope efficiency) in an LMA Er:Yb fiber. We believe this is the highest reported efficiency from a high power 9XXnm pumped Er:Yb-doped fiber amplifier. This is significantly more efficient that the best-reported efficiency for high power Er:Yb doped fibers, which, to-date, has been limited to ~41% slope efficiency [3].
An effective BIST scheme for Booth multipliers (2002)

Booth multipliers are widely used in both general purpose datapath structures and specialized Digital Signal Processors. Such multipliers when embedded in complex ICs have low controllability and observability, so the use of a suitable BIST scheme is a necessity. No Such BIST schemes for Booth multipliers are available to our knowledge in the open literature. A very effective BIST scheme for Booth multipliers is introduced. The algorithmic BIST patterns that this scheme generates guarantee >99% fault coverage. The required Test Pattern Generator consists of a simple fixed-size binary counter or maximum length LFSR, independent of the site of the multiplier. Several count-based compaction schemes are evaluated and a new such compaction scheme is found to be the most effective. The novel BIST scheme is generic, i.e., independent of specific implementations of the multiplier cells and does not require DFT in the multiplier design. Due to its effectiveness and regularity this BIST architecture was adopted for automatic BIST synthesis via the parameterized multiplier generation tool.
Multicast and Group Security (2003)

From the Publisher:
Presenting detailed coverage of multicast and group security from the developer of the standards, this resource discusses a wide range of topics in: Multicast or group data protection; Access control in mass data distribution; and Multicast network infrastructure protection. New algorithms and protocols for multiparty secure communication are provided for easy reference. The book looks at multicast security issues and solutions under three broad categories - data authentication, key manegement, and policies.
The M2-2 protein of human respiratory syncytial virus is a regulatory factor involved in the balance between RNA replication and transcription (paramyxovirusyreverse geneticsyRNA regulationyvaccine development) (1999)

The M2 mRNA of human respiratory syncy- tial virus (RSV) contains two overlapping ORFs, encoding the transcription antitermination protein (M2-1) and the 90-aa M2-2 protein of unknown function. Viable recombinant RSV was recovered in which expression of M2-2 was ablated, identifying it as an accessory factor dispensable for growth in vitro. Virus lacking M2-2 grew less efficiently than did the wild-type parent in vitro, with titers that were reduced 1,000- fold during the initial 2-5 days and 10-fold by days 7-8. Compared with wild-type virus, the intracellular accumula- tion of RNA by M2-2 knockout virus was reduced 3- to 4-fold or more for genomic RNA and increased 2- to 4-fold or more for mRNA. Synthesis of the F and G glycoproteins, the major RSV neutralization and protective antigens, was increased in proportion with that of mRNA. In cells infected with wild-type RSV, mRNA accumulation increased dramatically up to ap- proximately 12-15 hr after infection and then leveled off, whereas accumulation continued to increase in cells infected with the M2-2 knockout viruses. These findings suggest that M2-2 mediates a regulatory ''switch'' from transcription to RNA replication, one that provides an initial high level of mRNA synthesis followed by a shift in the RNA synthetic program in favor of genomic RNA for virion assembly. With regard to vaccine development, the M2-2 knockout has a highly desirable phenotype in which virus growth is attenu- ated while gene expression is concomitantly increased.
Morphological transformations in a dually thermoresponsive coil–rod–coil bioconjugate (2012)

We report the conformational and assembly behavior of a thermoresponsive triblock biohybrid conjugate under aqueous conditions. The triblock comprises of poly(diethylene glycol methyl ether methacrylate) (PDEGMEMA) conjugated to the ends of a triple-helix forming collagen-like peptide. The circular dichroism (CD) experiment confirms the ability of the collagen-like peptide middle block to assemble as a triple helix in the hybrid conjugate. Above the LCST (~35 °C), the collapse of the thermoresponsive PDEGMEMA polymer at the ends of the peptide domain resulted in a concomitant increase in the conformational stability of the peptide domain towards thermal denaturation. Upon cooling back, the kinetic conformational refolding behavior was still observed for the peptide domain in the hybrid conjugate. Static light scattering (SLS) experiments suggested the formation of supramolecular structures upon increasing solution temperatures to above the LCST. The scattering intensity increased with increasing temperature, until at 75 °C then it was found to decrease. Cryogenic scanning electron microscopy and regular transmission electron microscopy suggested the formation of spherical aggregates that increased in size with increasing temperature up to 65 °C and a morphological transformation into fibrils was also observed at 75 °C. The synergistic effect of dual thermoresponsive behavior from the peptide and the polymer block in the triblock hybrid is suggested for the observed conformational and assembly behaviors.
Isotuberculosinol: the unusual case of an immunomodulatory diterpenoid from Mycobacterium tuberculosis (2012)

Despite having served as a primary source for pharmaceutical agents, the physiological role played by natural products in their bacterial hosts is typically unknown. In addition, while terpenoids comprise the largest class of known natural products, it is unusual for these to be produced by bacteria. Accordingly, the recent findings demonstrating that Mycobacterium tuberculosis (Mtb) produces a diterpenoid, isotuberculosinol, is unusual in and of itself, and the accumulating evidence that this functions in the infection process of this pernicious human pathogen indicates a physiological role with medical relevance, all of which is reviewed here. Also presented is conservation of the biosynthetic capacity for isotuberculosinol production, which suggests that this is particularly important in Mtb, leading to speculation that this natural product may contribute to the highly infectious nature of Mtb in humans.
Passive Sensors for Long Duration Internet of Things Networks (2017)

In this work, three different concepts are used to develop a fully passive sensor that is capable of measuring different types of data. The sensor was supplied by Wireless Power Transmission (WPT). Communication between the sensor and reader is established by a backscatter, and to ensure minimum energy consumption, low power techniques are used. In a simplistic way, the process starts by the transmission of two different waves by the reader to the sensor, one of which is used in power transmission and the other of which is used to communicate. Once the sensor is powered, the monitoring process starts. From the monitoring state, results from after processing are used to modulate the incoming wave, which is the information that is sent back from the reader to the tag. This new combination of technologies enables the possibility of using sensors without any cables or batteries to operate 340 cm from the reader. The developed prototype measures acceleration and temperature. However, it is scalable. This system enables a new generation of passive Internet of Things (IoT) devices.
Strain engineered Si∕SiGe resonant interband tunneling diodes with outside barriers grown on Si0.8Ge0.2 virtual substrates (2008)

Si-based resonant interband tunneling diodes (RITDs) grown on commercially available Si0.8Ge0.2 virtual substrates were studied. Peak-to-valley current ratios (PVCRs) were improved by utilizing strain induced band offsets to 3.5 with a peak current density (Jp) of 161A∕cm2. More specifically, a tensilely strained Si layer on the p-side and a compressively strained Si0.5Ge0.5 layer on the n-side were added to the design to form enhanced potential barriers away from the tunneling junction. The outside barriers deepen the respective hole and electron quantum wells and also block nonresonant tunneling current, which improved the PVCR significantly. However, due to the large surface roughness of the SiGe virtual substrates used in this study, the RITDs grown on Si0.8Ge0.2 substrates exhibit a smaller PVCR overall than RITDs optimized on standard Si substrates. Better performance is expected by using higher quality SiGe substrates with smaller surface roughness.
Shiga Toxin: Purification, Structure, and Function (1991)

Shiga toxin is a potent toxin produced by Shigella dysenteriae type 1 strains. The toxin has three biologic activities--cytotoxicity, enterotoxicity, and neurotoxicity--and one known biochemical effect: inhibition of protein synthesis. It consists of two polypeptide chains, an A chain (molecular weight, 32,225) and a B chain (molecular weight, 7,691). These two peptides associate with a stoichiometry of one A and five B subunits to form the holotoxin. The A chain is responsible for the biochemical effect of the holotoxin: cleavage of the N-glycosidic bond of adenine at nucleotide position 4324 in the 28S rRNA of the 60S ribosomal subunit. The B chain mediates binding of toxin to cell surface receptors. Shiga toxin is the prototype of a family of toxin molecules that have been termed Shiga-like in terms of both structural and functional analysis.
Positive Inductive Effect of Swine Interleukin-4 on Immune Responses Elicited by Modified Live Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Vaccine (2013)

Porcine reproductive and respiratory syndrome (PRRS) has become one of the most economically important diseases to the global pork industry. Currently, the efficacies of available commercial vaccines remain questionable: the modified live-PRRSV vaccines (MLVs) were generally effective but variable in sufficient protection, and the outcomes of inactivated-PRRSV vaccines (IVs) in the field were not very promising. In the present study, we investigated the effect of swine interleukin 4 (IL-4) on the development of virus-specific immune responses elicited by an MLV. The antibody titer against PRRSV membrane proteins in pigs elicited by MLV plus recombinant plasmid encoding IL-4 (group 3) was significantly higher than those elicited by MLV alone (group 1) and MLV plus empty plasmid (group 2) from 35 days post-inoculation (dpi). Similarly, the neutralizing efficacy of sera from group 3 was markedly enhanced compared with group 1 and group 2. In cellular immunity, the ratio of CD3⁺CD4⁺/CD3⁺CD8⁺ T lymphocyte subpopulations from group 3 monitored by flow cytometry (FCM) was significantly higher than those from group 1 and group 2 from 42 dpi to 21 days post-challenge (dpc). After viral challenge, pigs in group 3 showed significantly lower virus loads in peripheral blood measured by a real-time quantitative PCR (RT-qPCR), as compared with those in group 1 and group 2. Pigs in group 1 and group 2 had a low fever and displayed mild inappetence, lethargy, rough hair coats, and no lung lesions, while those in group 3 showed almost no clinical signs, no lung lesions. The scores of clinical signs of pigs in group 3 were significantly lower than those in both group 1 and group 2. Interestingly, the scores of lung lesions showed no significant differences among the three groups. Our results indicate that swine IL-4 markedly enhanced the protective immune response of pigs and improved the efficacy of the MLV in preventing PRRS disease.
Prospective Evaluation of a Whole-Blood Test Using <i>Mycobacterium tuberculosis</i> -Specific Antigens ESAT-6 and CFP-10 for Diagnosis of Active Tuberculosis (2005)

A new immunodiagnostic test based on the Mycobacterium tuberculosis-specific antigens CFP-10/ESAT-6(QFT-RD1) has been launched as an aid in the diagnosis of latent tuberculosis (TB) infection (LTBI). The aim of this study was to evaluate this test for the diagnosis of active TB. Eighty-two patients with suspicion of TB and 39 healthy BCG-vaccinated persons were enrolled. Forty-eight had active TB, 25 did not, and 9 were excluded. Sensitivity and specificity of the test for active TB were evaluated in a prospective blinded manner in patients suspected of TB. The sensitivity of the QFT-RD1 was 85% (40/48; confidence interval [CI], 75 to 96), and it was higher than the sensitivity of microscopy, 42% (20/48; CI, 27 to 56; P = 0.001), and culture, 59% (27/46; CI, 44 to 73; P = 0.009). Of patients with extrapulmonary TB, 92% (12/13) were QFT-RD1 positive, whereas only 31% (4/13) were positive by microscopy and 42% (5/12) by culture (P < 0.05), and 87% (13/15) of those who were negative by both microscopy and culture were QFT-RD1 positive. By combining microscopy and culture with the QFT-RD1 test, sensitivity increased to 96% (CI, 90 to 102). Ten of 25 (40%) non-TB patients were QFT-RD1 positive, resulting in a specificity of 60%. However, 80% (8/10) of these had risk-factors for TB, indicating latent infection in this group. In healthy controls, only 3% (1/39) were QFT-RD1 positive. In conclusion, the QFT-RD1 test is sensitive for diagnosis of TB, especially in patients with negative microscopy and culture. The accuracy of the QFT-RD1 test will vary with the prevalence of LTBI. We suggest that the QFT-RD1 test could be a very useful supplementary tool for the diagnosis of TB.
Detecting fingerprint distortion from a single image (2012)

Elastic distortion of friction ridge skin is one of the major challenges in fingerprint matching. Since existing fingerprint matching systems cannot match seriously distorted fingerprints, criminals may purposely distort their fingerprints to evade identification. Existing distortion detection techniques require availability of specialized hardware or fingerprint video, limiting their use in real applications. In this paper we conduct a study on fingerprint distortion and develop an algorithm to detect fingerprint distortion from a single image which is captured using traditional fingerprint sensing techniques. The detector is based on analyzing ridge period and orientation information. Promising results are obtained on a public domain fingerprint database containing distorted fingerprints.
Development of a Dry Plastic Insect Trap with Food-Based Synthetic Attractant for the Mediterranean and Mexican Fruit Flies (Diptera: Tephritidae) (1995)

A dry plastic insect trap for monitoring populations of tephritid fruit flies is described. The plastic trap is constructed of acetate film that is painted to provide a visual cue and contains a toxic ant panel that provides a visual cue and a feeding stimulant to flies that have entered the trap. The trap baited with a 2-component blend of ammonium acetate and putrescine was tested against feral populations of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), and the Mexican fruit fly, Anastrepha ludens (Loew), in field trials conducted in Guatemala. The combination of ammonium acetate and putrescine was better than either ammonium acetate-only, putrescine-only, or unbaited traps. More female Mediternmean fruit flies were trapped in green traps than in colorless traps, and capture of male Mediternmean fruit flies was greater in yellow traps than in orange traps. Neither female nor male Mexican fruit flies differentiated among orange, green, and yellow traps, but the percentage trapped in any colored trap was higher than in colorless traps. McPhail traps with standard protein bait caught more Mexican fruit flies than either of the plastic traps at any of the doses of synthetic baits tested. However, plastic traps baited with either the medium or high dose of synthetic blend caught equal numbers of Mediterranean fruit flies as McPhail traps. Although McPhail traps caught more female Mediterranean fruit flies than plastic traps baited with the low dose of synthetic blend, a greater percentage of females captured in plastic traps were unmated (55-65% versus 22% in McPhail traps). Increase in dose of the synthetic lure increased the percentage of mated females captured in the plastic traps. Unlike McPhail traps, which catch large numbers of miscellaneous Diptera, the plastic traps were highly specific and caught few nontarget flies.
An 11b 450 MS/s Three-Way Time-Interleaved Subranging Pipelined-SAR ADC in 65 nm CMOS (2016)

This paper presents an 11 bit 450 MS/s three-way time-interleaved (TI) subranging pipelined-successive approximation register (SAR) analog-to-digital converter (ADC). The proposed hybrid architecture combines the design benefits of different ADC structures to achieve a high conversion rate and accuracy with good power efficiency. The design employs multiple offset calibration schemes to compensate the offset mismatches at each stage. The solutions require less calibration efforts, thus allowing the ADC to achieve a compact area. Furthermore, a dynamic SAR controller embedded with error-decision-correction (EDC) logic is proposed to reduce large transition error. Measurement results on a 65 nm CMOS prototype operated at 450 MS/s and 1.2 V supply show 7.4 mW total power consumption with a peak signal-to-noise distortion ratio (SNDR) of 60.8 dB and an FOM of 32 fJ/conv.step at Nyquist.
Application of Projective Invariants in Hand Geometry Biometrics (2007)

Our research focuses on finding mathematical representations of biometric features that are not only distinctive, but also invariant to projective transformations. We have chosen hand geometry technology to work with, because it has wide public awareness and acceptance and most important, large space for improvement. Unlike the traditional hand geometry technologies, the hand descriptor in our hand geometry system is constructed using projective-invariant features. Hand identification can be accomplished by a single view of a hand regardless of the viewing angles. The noise immunity and the discriminability possessed by a hand feature vector using different types of projective invariants are studied. We have found an appropriate symmetric polynomial representation of the hand features with which both noise immunity and discrimminability of a hand feature vector are considerably improved. Experimental results show that the system achieves an equal error rate (EER) of 2.1% by a 5-D feature vector on a database of 52 hand images. The EER reduces to 0.00% when the feature vector dimension increases to 18. In this paper, we extend the concept of hand geometry from a geometrical size-based technique that requires physical hand constraints to a projective invariant-based technique that allows free hand motion.
Exterminator (2008)

Programs written in C and C++ are susceptible to memory errors, including buffer overflows and dangling pointers. These errors, which can lead to crashes, erroneous execution, and security vulnerabilities, are notoriously costly to repair. Tracking down their location in the source code is difficult, even when the full memory state of the program is available. Once the errors are finally found, fixing them remains challenging: even for critical security-sensitive bugs, the average time between initial reports and the issuance of a patch is nearly 1 month. We present Exterminator, a system that automatically corrects heap-based memory errors without programmer intervention. Exterminator exploits randomization to pinpoint errors with high precision. From this information, Exterminator derives runtime patches that fix these errors both in current and subsequent executions. In addition, Exterminator enables collaborative bug correction by merging patches generated by multiple users. We present analytical and empirical results that demonstrate Exterminator's effectiveness at detecting and correcting both injected and real faults.
Broadly-specific Cytotoxic T Cells Targeting Multiple HIV Antigens Are Expanded From HIV+ Patients: Implications for Immunotherapy (2014)

Antiretroviral therapy (ART) is unable to eradicate human immunodeficiency virus type 1 (HIV-1) infection. Therefore, there is an urgent need to develop novel therapies for this disease to augment anti-HIV immunity. T cell therapy is appealing in this regard as T cells have the ability to proliferate, migrate, and their antigen specificity reduces the possibility of off-target effects. However, past human studies in HIV-1 infection that administered T cells with limited specificity failed to provide ART-independent, long-term viral control. In this study, we sought to expand functional, broadly-specific cytotoxic T cells (HXTCs) from HIV-infected patients on suppressive ART as a first step toward developing cellular therapies for implementation in future HIV eradication protocols. Blood samples from seven HIV+ patients on suppressive ART were used to derive HXTCs. Multiantigen specificity was achieved by coculturing T cells with antigen-presenting cells pulsed with peptides representing Gag, Pol, and Nef. All but two lines were multispecific for all three antigens. HXTCs demonstrated efficacy as shown by release of proinflammatory cytokines, specific lysis of antigen-pulsed targets, and the ability to suppress HIV replication in vitro. In conclusion, we are able to generate broadly-specific cytotoxic T cell lines that simultaneously target multiple HIV antigens and show robust antiviral function.