gebhart/patrepeval huggingface dataset:
A Centralized, Tree-Based Approach to Network Repair Service for Multicast Streaming Media (2000)

IP multicast provides best-effort delivery. Packets encounter variable delays and may be lost because of transmission errors and buffer overflows. Real-time multimedia streaming services require that most packets arrive at the receivers prior to an application deadline. Multicast quality on the current Internet is often inadequate for these applications. We have solved this problem by placing repair servers inside the network. The repair servers recover missing packets by communicating with each other, then re-multicast the repaired stream to nearby receivers on a new address. Multicast reception in the constrained area is typically much better than in the wide area Internet. In this paper we address the problem of constructing a repair graph. The repair graph shows which repair servers each repair server communicates with to recover missing messages. Our objectives when constructing this graph conflict with each other. We want high reliability: every repair server to recover as many missing messages as possible, as quickly as possible. But we also want low cost: this recovery should use as little of the network bandwidth as possible. We present a centralized algorithm to generate repair graphs. We demonstrate through simulation that these graphs achieve a level of reliability that is almost as high as that achieved by repair graphs specifically designed for high reliability. At the same time, our graphs maintain a cost that is almost as low as the cost in repair graphs designed for low cost. 1
Tyrosine phosphorylation of the<i>Helicobacter pylori</i>CagA antigen after<i>cag</i>-driven host cell translocation (2000)

Helicobacter pylori strains associated with severe tissue damage and inflammation possess a unique genetic locus, cag, containing 31 genes originating from a distant event of horizontal transfer and retained as a pathogenicity island. The cag system is an Helicobacter-specific type IV secretion engine involved in cellular responses like induction of pedestals, secretion of IL-8, and phosphorylation of proteic targets. It has previously been reported that cocultivation of epithelial cells with Helicobacter pylori triggers signal transduction and tyrosine phosphorylation of a 145-kDa putative host cell protein. Herein, we demonstrate that this protein is not derived from the host but rather is the bacterial immunodominant antigen CagA, a virulence factor commonly expressed in peptic ulcer disease and thought to be an orphan of a specific biological function. Thus, CagA is delivered into the epithelial cells by the cag type IV secretion system where it is phosphorylated on tyrosine residues by an as yet unidentified host cell kinase and wired to eukaryotic signal transduction pathways and cytoskeletal plasticity.
Novel Ultrananocrystalline Diamond Probes for High‐Resolution Low‐Wear Nanolithographic Techniques (2005)

A hard, low-wear probe for contact-mode writing techniques, such as dip-pen nanolithography (DPN), was fabricated using ultrananocrystalline diamond (UNCD). Molding within anisotropically etched and oxidized pyramidal pits in silicon was used to obtain diamond tips with radii down to 30 nm through growth of UNCD films followed by selective etching of the silicon template substrate. The probes were monolithically integrated with diamond cantilevers and subsequently integrated into a chip body obtained by metal electroforming. The probes were characterized in terms of their mechanical properties, wear, and atomic force microscopy imaging capabilities. The developed probes performed exceptionally well in DPN molecular writing/imaging mode. Furthermore, the integration of UNCD films with appropriate substrates and the use of directed microfabrication techniques are particularly suitable for fabrication of one- and two-dimensional arrays of probes that can be used for massive parallel fabrication of nanostructures by the DPN method.
Estimation of eye penalty and PMD from frequency-resolved in-situ SOP measurements (2004)

We introduce frequency-resolved in-situ measurements of the output state-of-polarization 'strings' of an optical signal in operating 10 Gb/s channels, and show they permit estimation of the PMD-induced eye penalty, but, paradoxically, not the PMD vector itself.
The development of a "reduced logMAR" visual acuity chart for use in routine clinical practice (2001)

The RLM A chart offers an acceptable level of test-retest variability when compared with the gold standard ETDRS chart, while reducing the measurement time by half. Also, by allowing a faster, less variable acuity measurement than the Snellen chart, the RLM A chart can bring the benefits of logMAR acuity to routine clinical practice.
Flagellin-rPAc vaccine inhibits biofilm formation but not proliferation of<i>S. mutans</i> (2016)

As the main etiologic bacterium of dental caries, Streptococcus mutans (S. mutans) has been considered as the primary object of vaccine research. We previously constructed a recombinant flagellin-rPAc fusion protein (KF-rPAc) that consists of an alanine-rich region to proline-rich region fragment of PAc (rPAc) from S. mutans and flagellin KF from E.coli K12 strain. Intranasal (i.n) immunization of KF-rPAc could induce high level of rPAc-specific antibody responses and offer robust protection against dental caries. In caries development, biofilm formation was considered as the necessary process involved. As PAc possesses other activities besides affecting adherence of S. mutans to salivary glycoproteins, we wondered whether rPAc-specific antibody responses induced by KF-rPAc could inhibit biofilm formation. Hence, in the present study, a simple and convenient in vitro biofilm model of S. mutans was constructed without saliva pre-coated. Both serum and saliva from KF-rPAc immunized rats significantly inhibited biofilm formation. Moreover, with the presence of serum or saliva, the biofilm formation is negatively correlated with the level of rPAc-specific antibody, and positively correlated with caries scores in rat. Moreover, in immunized mice, the level of rPAc-specific antibody also negatively correlated with the biofilm formation. Unlike ampicillin, serum of KF-rPAc immunized mice only inhibited biofilm formation but not proliferation. All together, we discovered that besides the well known blocking adherence of S. mutans to salivary glycoproteins by rPAc-specific antibody, flagellin-rPAc vaccine could also protects tooth from caries by inhibiting biofilm structure formation in between bacteria.
Femtosecond time-domain phase comparator (1978)

Phase shift in test device is measured by summing output of mixer with ramp voltage and comparing time interval between zero crossings of summed signal and ramp reference frequency. Circuit can be used to test devices at other frequencies by changing only signal source, phase splitter, and mixer; divider and time-interval counter need not be driven by oscillator.
Prevalence of founderBRCA1 andBRCA2 mutations among breast and ovarian cancer patients in hungary (2000)

We have investigated the impact of BRCA1 and BRCA2 mutations that were frequently identified among Hungarian high-risk breast-ovarian cancer families (Ramus et al., 1997b, AJHG), on the development of breast and ovarian cancer in the general Hungarian population. The prevalence of 3 BRCA1 mutations (185delAG, 300T-->G and 5382insC) and 2 BRCA2 mutations (6174delT and 9326insA) was evaluated in a hospital-based consecutive series of 500 female breast cancer patients and 90 ovarian cancer patients, not selected for age at diagnosis or family history of cancer, as well as in 350 controls. Among breast cancer patients, 3.6% (18/500) carried a founder mutation: 9 BRCA1 300T-->G, 7 BRCA1 5382insC, 1 BRCA1 185delAG and 1 BRCA2 9326insA. Among ovarian cancer patients, 11% (10/90) carried a founder mutation: 5 BRCA1 185delAG, 4 BRCA1 300T-->G and 1 BRCA1 5382insC. One control carried a mutation, BRCA1 5382insC. Inherited breast cancer was more frequent among women with younger age at diagnosis: 6.1% of women younger than age 50 but 2.4% of women diagnosed at age 50 or older carried one of the founder mutations. There was no association between mutation status and age at diagnosis of ovarian cancer. Three of 23 medullary breast cancers were inherited (p = 0.038). Carrier status was also associated with a non-significant trend toward advanced tumor stage at diagnosis. These mutations could be evaluated among all ovarian cancer patients and breast cancer patients younger than age 60 and of Hungarian ancestry.
Characterization of Adipose-Derived Stem Cells: An Update (2010)

Adipose tissue is an attractive source of multipotent adult stem cells due to its wide-spread availability, accessibility, and ease of harvest. Adipose-derived stem cells (ASCs), the adherent stromal cell population present within adipose tissue, are easily expanded in culture, able to differentiate along multiple cell-lineage pathways, and have been shown to provide therapeutic benefit in models of injury and disease through immunomodulation, structural integation, and/or trophic support. Recent developments in the characterization of ASCs, specifically their isolation, gene and protein expression, differentiation, and expansion, are reviewed in this article.
Sensing Protein Surfaces with Targeted Fluorescent Receptors (2015)

A methodology for creating fluorescent molecular sensors that respond to changes that occur on the surfaces of specific proteins is presented. This approach, which relies on binding cooperatively between a specific His-tag binder and a nonspecific protein-surface receptor, enabled the development of a sensor that can track changes on the surface of a His-tag-labeled calmodulin (His-CaM) upon interacting with metal ions, small molecules, and protein binding partners. The way this approach was used to detect dephosphorylation of an unlabeled calmodulin-dependent protein kinase II (CaMKII), and the binding of Bax BH3 to His-tagged B-cell lymphoma 2 (Bcl-2) protein is also presented.
Transposon tagging of tobacco mosaic virus resistance gene N: its possible role in the TMV-N-mediated signal transduction pathway. (1995)

Plants can recognize and resist invading pathogens by signaling the induction of rapid defense responses. Often these responses are mediated by single dominant resistance genes (R genes). The products of R genes have been postulated to recognize the pathogen and trigger rapid host defense responses. Here we describe isolation of the classical resistance gene N of tobacco that mediates resistance to the well-characterized pathogen tobacco mosaic virus (TMV). The N gene was isolated by transposon tagging using the maize Activator (Ac) transposon. We confirmed isolation of the N gene by complementation of the TMV-sensitive phenotype with a genomic DNA fragment. Sequence analysis of the N gene shows that it encodes a protein with an amino-terminal domain similar to that of the cytoplasmic domains of the Drosophila Toll protein and the interleukin 1 receptor in mammals, a putative nucleotide-binding site and 14 imperfect leucine-rich repeats. The presence of these functional domains in the predicted N gene product is consistent with the hypothesis that the N resistance gene functions in a signal transduction pathway. Similarities of N to Toll and the interleukin 1 receptor suggest a similar signaling mechanism leading to rapid gene induction and TMV resistance.
Ru Complexes Bearing Bidentate Carbenes: From Innocent Curiosity to Uniquely Effective Catalysts for Olefin Metathesis (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
VLSI implementation of a CDMA blind adaptive interference-mitigating detector (2001)

This paper presents the design and the main performance results of a single-ASIC implementation of the recently proposed extended complex-valued blind anchored interference-mitigating detector (EC-BAID) for code division multiple access (CDMA) transmission. Such a detector, which exhibits a remarkable robustness to multiple access interference, operates in blind mode, i.e., it only requires knowledge of the timing of the wanted user's signature code, and it is therefore very well-suited for integration into handheld single-user terminal demodulators. The implementation of the interference-mitigating detector is based on a patented optimized architecture which leads, in 0.25-/spl mu/m CMOS technology, to a roughly 25 Kgate plus 23-Kbit RAM single-chip ASIC supporting chip rates up to 4 Mchip/s with a maximum internal clock frequency of 32.768 MHz. The main design drivers are thoroughly discussed, and the relevant performance results are compared to the theoretical behavior. A possible extension to multirate CDMA systems adopting orthogonal variable spreading factor (OVSF) sequences is also addressed.
A two-phase approach to fourier transform ion mobility time-of-flight mass spectrometry (2015)

It is well known that the duty cycle of common drift-tube ion mobility experiments is often below 1%. However, multiplexing approaches such as Fourier and Hadamard pulsing schemes have been shown to independently enhance the throughput of ion mobility spectrometry (IMS) experiments to levels that approach 50%. While challenges remain to their broad scale implementation we describe a new Fourier transform (FT) IMS experiment that is directly compatible with standard drift tube ion mobility mass spectrometers (DT-IMMS). Compared to previous FT-IMS experiments, our new approach requires only a single gate and circumvents the need for signal apodization by combining data from two frequency pulsing sequences 180° out of phase. Assessment of our initial results highlights an increase in signal-to-noise (SNR) relative to both previous implementations FT-IMS experiments and signal averaged (SA) experiments. For select tetraalkylammonium salts SNR improvements of more than one order of magnitude are routinely possible. To explore the performance metrics associated with the technique a number of experimental variables were systematically altered including frequency sweep range, sweep time, and data acquisition time. Using this experimental design we present the key aspects, considerations, and minimum resources necessary for other IMS researchers to incorporate this operational mode into their research. The two-phase FT-IMMS technique offers a tractable mechanism to enhance sensitivity for IMMS measurements and its broad-scale adoption by IMMS researchers promises to enhance the acquisition speed for mobility measurements using hybrid instrumentation.
Double strand RNA delivery system for plant-sap-feeding insects (2017)

Double-stranded RNA (dsRNA)-mediated gene silencing, also known as RNA interference (RNAi), has been a breakthrough technology for functional genomic studies and represents a potential tool for the management of insect pests. Since the inception of RNAi numerous studies documented successful introduction of exogenously synthesized dsRNA or siRNA into an organism triggering highly efficient gene silencing through the degradation of endogenous RNA homologous to the presented siRNA. Managing hemipteran insect pests, especially Halyomorpha halys (Stål) (Heteroptera: Pentatomidae), the brown marmorated stink bug (BMSB), is critical to food productivity. BMSB was recently introduced into North America where it is both an invasive agricultural pest of high value specialty, row, and staple crops, as well as an indoor nuisance pest. RNAi technology may serve as a viable tool to manage this voracious pest, but delivery of dsRNA to piercing-sucking insects has posed a tremendous challenge. Effective and practical use of RNAi as molecular biopesticides for biocontrol of insects like BMSB in the environment requires that dsRNAs be delivered in vivo through ingestion. Therefore, the key challenge for molecular biologists in developing insect-specific molecular biopesticides is to find effective and reliable methods for practical delivery of stable dsRNAs such as through oral ingestion. Here demonstrated is a reliable delivery system of effective insect-specific dsRNAs through oral feeding through a new delivery system to induce a significant decrease in expression of targeted genes such as JHAMT and Vg. This state-of-the-art delivery method overcomes environmental delivery challenges so that RNAi is induced through insect-specific dsRNAs orally delivered to hemipteran and other insect pests.
Abstract 2831: Development of selective GRP94 inhibitors for the treatment of cancer (2015)

Abstract Glucose Regulated Protein 94 (Grp94) is an Hsp90 paralog localized in the lumen of the endoplasmic reticulum (ER) of higher eukaryotes. While the mechanisms associated with Grp94-pathogenic expression are still actively studied, the focus thus far of most cancer related studies has been primarily on the immunogenic activity of Grp94/peptide complexes and the involvement of this protein in the secretion of IGF-I and IGF-II and the regulation of Toll-like receptors and integrins. This status quo has recently changed when work from our lab has shown that in certain breast cancers the maintenance of a high density HER2 species at the plasma membrane and its associated aberrant signaling also requires Grp94, rendering these tumors highly sensitive to Grp94 inhibition. The discovery of selective and potent Grp94 inhibitors has been hindered due to the high similarity of the ATP-binding regulatory pocket of the Hsp90 paralogs. However, recent work from our lab has shown that this apparent roadblock can be overcome by using library screening and structural and computational analysis to discover purine-based molecules that show 100-fold selectivity for the Grp94 isoform. Herein, we detail for the first time the structure activity relationship of the selective purine derived Grp94 molecules. This work provides insights on how to overcome the high structural similarity of Hsp90s in the ligand binding pocket, and also reports selective and therapeutically relevant Grp94 inhibitors based on a purine scaffold. These initial inhibitors have potent activity against cancer cells providing an important platform for the development of Grp94 inhibitors with drug-like features and potential for clinical translation. Citation Format: Stefan O. Ochiana, Tony Taldone, Hardik J. Patel, Pallav Patel, Yan Pengrong, Weilin Sun, Anna Rodina, Smit Shah, Daniel T. Gewirth, Gabriela Chiosis. Development of selective GRP94 inhibitors for the treatment of cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2831. doi:10.1158/1538-7445.AM2015-2831
Trusting your assistant (2002)

The assistant interface metaphor has the potential to shield the human user from low-level, task-specific details, while allowing the automation of the many idiosyncratic, mundane tasks falling between the capabilities of commercial software packages. However, a user will not willingly put resources (money, privacy, information) at risk unless the assistant can be trusted to carry out the task in accord with the user's goals and priorities. This risk is significant, because assistant behaviors, being idiosyncratic and highly customized, will not be as well supported or documented as is commercial software. This paper describes a solution to this problem, allowing the assistant to safely execute partially trusted behaviors and to interactively increase the user's trust in the behavior so that more of the steps can be carried out autonomously. The approach is independent of how the behavior was acquired and is based on using incremental formal validation to populate a trust library for the behavior.
Abstract 200: Computer-Assisted Monitoring of Hemodynamic Condition During a Simulated Experiment of Hypovolemia Using Lower Body Negative Pressure (2014)

Background: Real-time physiologic status monitoring of hemorrhaging war-fighter or civilian from the point of injury and along ensuing echelons of care in austere environments pose significant challenges. These challenges range for those arising from the environment to the physical profiles of monitors and the types of measures they make. Objective: To develop an automated clinical support system capable of using low level physiologic signals such as the electrocardiogram (ECG) to monitor hemodynamic compensation in response to injury or illness. Methods: An adapted low profile portable and wearable armband monitor was used to collect prolonged measurement of a single lead ECG from volunteer human subjects undergoing lower body negative pressure (LBNP) as a model of human hemorrhage. Fifty-five subjects underwent 5-minute intervals of progressive LBNP until hemodynamic decompensation at which time LBNP was halted. Using several advanced signal processing techniques including novel applications of the Stockwell Transform and L-1 Norm optimized taut-string theory, hidden underlying bio-markers were extracted from the ECG signal which was then used to develop a predictive model using support vector regression using radial basis kernel to predict the severity of blood loss with respect to LBNP levels. Results: Using by-subject cross validation for each of the 55 subjects, the Pearson’s correlation coefficient was calculated between the algorithm’s estimates and the actual LBNP levels for each subject. High correlation between the prediction and actual levels were observed with a mean correlation coefficient across all subjects of 0.862 and σ of 0.072. The mean r2 value was 0.928 with σ of 0.04. The system predicted changes in stability prior to any significant changes in heart rate and blood pressure among subjects during LBNP. Conclusions: The developed ECG analytic technique has provided encouraging results and has shown potential to be applicable in a variety of critical care environments and applications where detection of hemodynamic changes prior to overt decompensation would allow early intervention. This when used with wearable sensors opens up new possibilities for monitoring in different locations.
Human papillomavirus type 49, a type isolated from flat warts of renal transplant patients (1989)

The cloning and characterization of the genome of human papillomavirus type 49 (HPV-49) is described. The viral DNA, which is most closely related to the DNAs of HPVs seen in patients with epidermodysplasia verruciformis, was aligned to the HPV-5 genome by electron microscopic analysis of heteroduplexes between the cloned viral DNAs.
Adding Amino Acids with Novel Reactivity to the Genetic Code of <i>Saccharomyces Cerevisiae</i> (2003)

Using a novel genetic selection, we have identified a series of mutants of the E. coli tyrosyl-tRNA synthetase that selectively charge an amber suppressor tRNA with p-(propargyloxy)phenylalanine and p-azidophenylalanine in yeast. These evolved tRNA-synthetase pairs can be used to site-specifically label proteins with functional groups orthogonal to normal biological chemistries. As an example, we have shown that proteins containing these amino acids can be efficiently bioconjugated with small organic molecules by a [3 + 2] cycloaddition reaction that is mild enough for the manipulation of biological samples.
All-fiber-optic quantum random number generator (2006)

We built an all-fiber random number generator based on polarization-entangled photons that generates high-quality cryptographic random numbers. This setup allows active monitoring of the randomness and independent physics-based testing.