gebhart/patrepeval huggingface dataset:
X10 and APGAS at Petascale (2016)

X10 is a high-performance, high-productivity programming language aimed at large-scale distributed and shared-memory parallel applications. It is based on the Asynchronous Partitioned Global Address Space (APGAS) programming model, supporting the same fine-grained concurrency mechanisms within and across shared-memory nodes. We demonstrate that X10 delivers solid performance at petascale by running (weak scaling) eight application kernels on an IBM Power--775 supercomputer utilizing up to 55,680 Power7 cores (for 1.7Pflop/s of theoretical peak performance). For the four HPC Class 2 Challenge benchmarks, X10 achieves 41% to 87% of the system’s potential at scale (as measured by IBM’s HPCC Class 1 optimized runs). We also implement K-Means, Smith-Waterman, Betweenness Centrality, and Unbalanced Tree Search (UTS) for geometric trees. Our UTS implementation is the first to scale to petaflop systems. We describe the advances in distributed termination detection, distributed load balancing, and use of high-performance interconnects that enable X10 to scale out to tens of thousands of cores. We discuss how this work is driving the evolution of the X10 language, core class libraries, and runtime systems.
Study of GeSn Mid-infrared Photodetectors for High Frequency Applications (2019)

In 2016, Thach et al. reported figures of merit of the GeSn photodiodes with large mesa sizes of 500 and 250 µm to show the potential of the GeSn materials in short-wave infrared photonics.23 However, there are only a few discussions about high frequency capabilities of GeSn photodetectors. It is needed to understand the potential of GeSn detectors as high frequency devices. This paper discusses comprehensively about the performance of GeSn photodiodes with 6.44 % and 9.24 % Sn for high frequency applications including high speed measurements and simulations. 6.449.24 %. With high Sn incorporation, the cutoff wavelength is extended up to 2.2 μm and 2.5 μm wavelengths for 6.44 % and 9.24 % Sn devices, respectively. The photodiodes’ bandwidth is 1.78 GHz, and the simulation shows excellent agreement with measurement results. The reported GeSn photodetectors together with recently reported GeSn lasers and other GeSn microwave photonic components will be a potential candidate for integrated microwave photonics.
Inhibitors of XIAP sensitize CD40-activated chronic lymphocytic leukemia cells to CD95-mediated apoptosis (2005)

Patients with chronic lymphocytic leukemia (CLL) treated with adenovirus CD154 (Ad-CD154, CD40 ligand [CD40L]) gene therapy experienced rapid reductions in leukemia cell counts and lymph node size associated with the induced expression of Fas (CD95). However, CLL cells initially resist CD95-mediated apoptosis within the first 3 days after CD40 ligation in vitro. Thereafter, they become sensitive, which is associated with the CD40-induced expression of the proapoptotic protein B-cell leukemia 2 homology 3 (BH3) interacting domain death agonist (Bid). We hypothesized that the initial resistance to CD95-mediated apoptosis may be due to the high-level expression of X-linked inhibitor of apoptosis protein (XIAP) by CLL cells. Consistent with this, CLL cells from patients 1 day after treatment with autologous Ad-CD154-transduced CLL cells became sensitive to CD95-mediated apoptosis following treatment with a novel XIAP inhibitor, 1540-14. Similarly, 1540-14 specifically enhanced CD95-mediated apoptosis of CLL cells following CD40 ligation in vitro. Immunoblot analyses demonstrated that treatment with 1540-14 allowed CD40-stimulated CLL cells to experience high-level activation of caspases-8 and -3 and cleavage of poly(adenosine diphosphate [ADP]-ribose) polymerase following CD95 ligation. This study demonstrates that distal apoptosis regulators contribute to the initial resistance of CD40-activated CLL cells to CD95-mediated apoptosis and suggests that XIAP inhibitors might enhance the effectiveness of immune-based treatment strategies that target CD40, such as CD154 gene therapy.
R: A Formal Model of Distributed Computation for Sensory-Based Robot (1986)

ROBOT SYSTEMS ARE BECOMING MORE AND MORE COMPLEX, BOTH IN TERMS OF AVAIL ABLE DEGREES OF FREEDOM AND IN TERMS OF SENSORS. IT IS NO LONGER POSSIBLE TO CONTINUE TO REGARD ROBOTS AS PERIPHERAL DEVICES OF A COMPUTER SYSTEM, AND TO PROGRAM THEM BY ADAPTING GENERAL-PURPOSE PROGRAMMING LANGUAGES. THIS DISSERTATION ANALYZES THE INHERENT COMPUTING CHARACTERISTICS OF THE ROBOT PROGRAMMING DOMAIN, AND FORMALLY CONSTRUCTS AN APPROPRIATE MODEL OF COMPU- TATION. THE PROGRAMMING OF A DEXTROUS ROBOT HAND IS THE EXAMPLE DOMAIN FOR THE DEVELOPMENT OF THE MODEL. THIS MODEL, CALLED RS, IS A MODEL OF DISTRIBUTED COMPUTATION: THE BASIC MODE OF COMPUTATION IS THE INTERACTION OF CONCURRENT COMPUTING AGENTS. A SCHEMA IN RS DESCRIBES A CLASS OF COMPUTING AGENTS. SCHEMAS ARE INSTANTI- ATED TO PRODUCE COMPUTING AGENTS, CALLED SIS, WHICH CAN COMMUNICATE WITH EACH OTHER VIA INPUT AND OUTPUT PORTS. A NETWORK OF SIS CAN BE GROUPED ATOMICALLY TOGETHER IN AN ASSEMBLAGE, AND APPEARS EXTERNALLY IDENTICAL TO A SINGLE SI. THE SENSORY AND MOTOR INTERFACE TO RS IS A SET OF PRIMITIVE, PREDEFINED SCHEMAS. THESE CAN BE GROUPED ARBITRARILY WITH BUILT-IN KNOW- LEDGE IN ASSEMBLAGES TO FORM TASK-SPECIFIC OBJECT MODELS. A SPECIAL KIND OF ASSEMBLAGE CALLED A TASK-UNIT IS USED TO STRUCTURE THE WAY ROBOT PRO- GRAMS ARE BUILT. THE FORMAL SEMANTICS OF RS IS AUTOMATA THEORETIC; THE SEMANTICS OF AN SI
Identification and Isolation of Lysogens with Induced Prophage (2009)

The fate of lysogens following prophage induction has assumed added significance with the finding that in many pathogens virulence genes are carried on prophages and, in some, the production and/or release of the virulence factor is under control of the phage lytic regulatory program. We outline a method for identifying and characterizing from a total lysogen population, the subpopulation in which the prophage is induced. The prophage is genetically altered so that on induction it does not go through the lytic pathway, but does express a resolvase that acts at a reporter cassette located at another site on the bacterial chromosome to irreversibly change the resistance of the bacterium from tetracycline to chloramphenicol. Thus, induced derivatives survive and are easily identified even if they make up a small fraction of the population.
ChemInform Abstract: A Short Synthesis of 3(R)‐Hydroxy‐2(R)‐isopropyltetrahydrothiophene: A Precursor to a High‐Affinity P2‐Ligand of HIV‐1 Protease Inhibitors. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Global View on Rare Diseases: A Mini Review (2017)

Therefore more research should be done in the space of rare diseases in order to broaden knowledge about them, their diagnosis and treatment, which will then lead to better training of medical staff, and ultimately will benefit the patients.
Large 2-D thinned array for the Microwave Imaging Radiometer with Synthetic Aperture (MIRAS) (2003)

The development and performance of the large two-dimensional thinned array antenna for the ESA Microwave Imaging Radiometer with Aperture Synthesis (MIRAS) is here presented. The radiating elements are distributed along three arms that form a Y-shape when deployed in space. Interferometry in two orthogonal linear polarisations is performed by coherent reception at element level in order to produce aperture synthesis, thus avoiding a larger antenna area. The overall instrument performance is enhanced by sequentially rotating or mirroring the radiating elements as in array design techniques. This work is being performed under a Demonstrator Pilot Project of the European Space Agency for the provision of one arm's segment and radiators.
Immunotherapy for HER2-positive medulloblastoma: Regression of experimental tumors by transfer of HER2-redirected T cells in vivo (2006)

9008 Background: The long-term objective of this project is to develop an innovative HER2-targeted immunotherapeutic approach for medulloblastoma, the most common malignant brain tumor of childhood. HER2 is expressed in 40% of medulloblastomas and at present less than one third of patients with HER2-positive tumors are cured by conventional therapies. The aim of this study was to determine if T cells grafted with a HER2-specific chimeric antigen receptor (CAR) recognize and kill HER2-positive medulloblastomas. Methods: Mitogen-activated T cells from healthy donors and medulloblastoma patients were transduced with a retroviral vector encoding a HER2-specific CAR with a ζ-signaling domain (HER2T-cells). We analyzed the ability of HER2T-cells to 1) proliferate, 2) produce immunostimulatory cytokines (IFN-γ and IL-2), and 3) kill HER2-positive targets in cytoxicity assays upon exposure to HER2-positive primary medulloblastoma cells and cell lines. The in vivo function was tested in an orthotopic murine xenograft model of human medulloblastoma, which allows for serial imaging by bioluminescence. Results: HER2T-cells killed both HER2-positive primary medulloblastoma cells and cell lines in cytotoxicity assays, whereas HER2-negative tumor cells were not killed. Stimulation of HER2T-cells resulted in T-cell proliferation and secretion of IFN-γ and IL-2 in a HER2-dependent manner. No functional difference was observed between cells generated from medulloblastoma patients receiving dexamethasone and healthy donors. In vivo, the adoptive transfer of HER2T-cells resulted in sustained regression of established medulloblastomas in an orthotopic murine xenograft model as judged by bioluminescence imaging. In contrast, delivery of non-transduced T cells did not change tumor growth in comparison to untreated tumors. Conclusions: This study shows for the first time that HER2 is a target antigen for the immunotherapy of medulloblastoma. HER2-redirected T-cells not only recognized and killed HER2-positive medulloblastomas ex vivo, but also induced regression of experimental medulloblastoma in vivo. Hence, adoptive transfer of HER2-redirected T-cells may represent a promising immunotherapeutic approach for medulloblastoma. No significant financial relationships to disclose.
Analysis of Hybrid CSMA/CA-TDMA Channel Access Schemes with Application to Wireless Sensor Networks (2013)

A wireless sensor network consists of a number of sensor devices and coordinator(s) or sink(s). A coordinator collects the sensed data from the sensor devices for further processing. In such networks, sensor devices are generally powered by batteries. Since wireless transmission of packets consumes significant amount of energy, it is important for a network to adopt a medium access control (MAC) technology which is energy efficient and satisfies the communication performance requirements. Carrier sense multiple access with collision avoidance (CSMA/CA), which is a popular access technique because of its simplicity, flexibility and robustness, suffers poor throughput and energy inefficiency performance in wireless sensor networks. On the other hand, time division multiple access (TDMA) is a collision free and delay bounded access technique but suffers from the scalability problem. For this reason, this thesis focuses on design and analysis of hybrid channel access schemes which combine the strengths of both the CSMA/CA and TDMA schemes. In a hybrid CSMA/CA-TDMA scheme, the use of the CSMA/CA period and the TDMA period can be optimized to enhance the communication performance in the network. If such a hybrid channel access scheme is not designed properly, high congestion during the CSMA/CA period and wastage of bandwidth during the TDMA period result in poor communication performance in terms of throughput and energy efficiency. To address this issue, distributed and centralized channel access schemes are proposed to regulate the activities (such as transmitting, receiving, idling and going into low power mode) of the sensor devices. This regulation during the CSMA/CA period and allocation of TDMA slots reduce traffic congestion and thus improve the network performance. In this thesis work, time slot allocation methods in hybrid CSMA/CA-TDMA schemes are also proposed and analyzed to improve the network performance. Finally, such hybrid CSMA/CA-TDMA schemes are used in a cellular layout model for the multihop wireless sensor network to mitigate the hidden terminal collision problem.
Grape Seed Proanthocyanidin Extract or Spirulina platensis alleviates blood biochemical and hepatic molecular derangements of experimentally-induced thyroid dysfunction in rats (2022)

Hyper or Hypothyroidism are an overactive or underactive thyroid gland that prevents the body from operating properly. The potential therapeutic effects of spirulina platensis and GSPE on experimental hypothyroidism and hyperthyroidism in rats were evaluated.A total 96 rats were split into two main experimental groups: Experiment A: carbimazole-induced hypothyroidism(1.8mg/kg b.wt) and experiment B: - induced hyperthyroidism(50, 100, 200ug/kg b.wt) for the first three weeks, respectively.The administered GSPE dose (150/kg b. wt/day) and Spirulina (300mg/kg b. wt/day) for 3 weeks.The Hyperthyroidism experiment (A)six sets of rats were used: Group 1(control normal), Group 2(hyperthyroidism),Group3 (GSPE Protected): GSPE administered for the first 3 weeks and continued with Thyroxine for another 3 week. Group 4 (GSPE treated): Thyroxine administeredfor 3 weeks, followed by GPSE as in group 3. Group 5 (Spirulina Protected); Spirulina and Thyroxine administration as in group 3. Group 6 (Spirulina treated): Spirulina andThyroxineadministration in group IV.The Hypothyroidism experiment (B) rats divided also into 6 groups similar the above design in Hyperthyroidism experiment (A) but carbimazole dose is stable (1.8mg/kg b.wt) in the 3 weeks.In Hyperthyroidism Spirulina and GPSE increase serum total cholesterol, triacylglycerols with down regulation of liver Caspase-8 and significant upregulation of Bcl2 gene. In HypothyroidismSpirulina and GPSE exhibited down regulation in liver miRNA 224, PKCα with significant upregulation of miRNA 382gene in Hypothyroid rats.Spirulina and grape seed may treat and prevent hyperthyroidism or Hypothroidsim in rats, according to a new study.
The Uniaxial Stress Effect on Normal-Incommensurate Phase Transition in K2SeO4–Observations of the Amplitude Mode by Raman Scattering– (1982)

The incommensurate phase transition of K 2 SeO 4 was studied under various uniaxial compressive stresses. The frequency and damping constant of the amplitude mode were measured by means of the Raman scattering as functions of applied stress X 3 at various temperatures. These results were analyzed by use of the Landau-type free-energy written in terms of the order parameter Q and strain component u 3 . The stress dependence of the amplitude mode frequency obeys well the relation ν amp = A [ X 3 0 ( T )- X 3 ] 1/2 , where X 3 0 ( T ) is the transition stress at a temperature T . The normal-incommensurate phase transition point T 2 decreases linearly with the increase of X 3 (d T 2 /d X 3 =-16 K/kbar).
704. Long-Term Correction of Crigler-Najjar Syndrome and Scale-Up Production of an Optimized AAV8 Vector Expressing the UGT1A1 Transgene (2015)

Crigler-Najjar syndrome (CN) is an autosomal recessive rare disorder caused by mutations in the UDP-glucuronosyltransferase 1 isotype A1 (UGT1A1) gene. In severe CN, lack or reduced activity of UGT1A1 results in high levels of serum unconjugated bilirubin (UCB), which can lead to brain damage and death. Treatment of CN consists of phototherapy for 10-12 hours per day to convert UCB into soluble photoisomers without the need of conjugation, which presents several limitations and has a major impact on life quality of the patients. Liver transplantation is the only curative option for CN. The limited therapeutic options available prompted us to develop a new therapy for CN based on the transfer of a corrected copy of the UGT1A1 gene to hepatocytes. We developed an AAV8 vector optimized for the liver expression of the hUGT1A1 transgene (AAV8-hUGT1A1). Safety and efficacy of correction of total serum bilirubin (TB) levels with AAV-hUGT1A1 were demonstrated in mouse and rat models of CN at vector doses as low as 5×10 11 vector genomes (vg)/kg, a result confirmed also by the detection of conjugated bilirubin in bile of treated rats. In juvenile CN rats, long-term correction of total bilirubin levels were observed for more than 8 months following AAV8-hUGT1A1 gene transfer. In neonate Ugt1a1–/– mice, intraperitoneal delivery of the vector at doses as low as 1×10 9 vg/mouse resulted in correction of TB at 4 weeks. However, vector delivery in P2 and P4 animals resulted in lower efficiency of correction when compared with P11-transduced mice, a finding likely due to the more advanced development of the liver at later time points. Based on these data, dose finding studies were performed in CN rats, which showed a profile of liver transduction with AAV8 vectors similar to humans, i.e. lower efficiency of transduction than mice. No differences in efficacy of correction of TB were observed in male vs. female rats. A scalable process for the production of AAV8-hUGT1A1 production was established based on a protocol of triple transfection of suspension HEK293 cells, leading to high yield vector preparations with excellent purity profile. In vitro transduction assays in human hepatocytes based on Western blot for hUGT1A1 protein and in vivo studies in CN rats demonstrated that vectors produced with the suspension process have potency characteristics undistinguishable from research grade vectors produced by triple transfection of adherent cells and purified by cesium chloride gradient centrifugation. In conclusion, our data demonstrate the safety and efficacy of gene transfer for Crigler-Najjar syndrome in two relevant animal models of the disease and provide tools and a strong rationale for the translation of these results in human subjects.
Partitioning of BTEX constituents and chloroorganics in high‐biomass systems (2003)

Abstract Henry's Law controls mass transfer rates for sparingly soluble organics and/or lower inlet VOC concentrations within a biofilter. We report measurements of apparent Henry's Law partitioning values for benzene, toluene, TCE, and chloromethane in systems that contain varying levels of biomass. The apparent air/liquid partition constant for benzene decreased from 2.9 × 10 −3 atm m 3 mol −1 to as low as 0.1 × 10 −3 atm m 3 mol −1 when biomass, in the form of yeast, was added to aqueous batch systems containing benzene. The constant for toluene decreased from 6.4 × 10 −3 to 0.17 × 10 −3 atm m 3 mol −1 . For TCE, the air/liquid partition constant decreased from 0.013 atm m 3 mol −1 to less than 0.00013 atm m 3 mol −1 . Experimentally measured partition values were also used to calculate intrinsic “pure biomass” partitioning constants, which can be used to interpolate behavior. Apparent partitioning values for TCE were most heavily impacted by biomass levels, changing by two orders of magnitude. These data should allow other researchers to estimate and extrapolate the influence of biomass on their own biofiltration processes.
Latent Contextual Bandits (2016)

Motivated by online recommendation and advertising systems, we consider a causal model for stochastic contextual bandits with a latent low-dimensional confounder. In our model, there are $L$ observed contexts and $K$ arms of the bandit. The observed context influences the reward obtained through a latent confounder variable with cardinality $m$ ($m \ll L,K$). The arm choice and the latent confounder causally determines the reward while the observed context is correlated with the confounder. Under this model, the $L \times K$ mean reward matrix $\mathbf{U}$ (for each context in $[L]$ and each arm in $[K]$) factorizes into non-negative factors $\mathbf{A}$ ($L \times m$) and $\mathbf{W}$ ($m \times K$). This insight enables us to propose an $\epsilon$-greedy NMF-Bandit algorithm that designs a sequence of interventions (selecting specific arms), that achieves a balance between learning this low-dimensional structure and selecting the best arm to minimize regret. Our algorithm achieves a regret of $\mathcal{O}\left(L\mathrm{poly}(m, \log K) \log T \right)$ at time $T$, as compared to $\mathcal{O}(LK\log T)$ for conventional contextual bandits, assuming a constant gap between the best arm and the rest for each context. These guarantees are obtained under mild sufficiency conditions on the factors that are weaker versions of the well-known Statistical RIP condition. We further propose a class of generative models that satisfy our sufficient conditions, and derive a lower bound of $\mathcal{O}\left(Km\log T\right)$. These are the first regret guarantees for online matrix completion with bandit feedback, when the rank is greater than one. We further compare the performance of our algorithm with the state of the art, on synthetic and real world data-sets.
Cookies along trust-boundaries (CAT): accurate and deployable flood protection (2006)

Packet floods targeting a victim’s incoming bandwidth are notoriously difficult to defend against. While a number of solutions have been proposed, such as network capabilities, thirdparty traffic scrubbing, and overlay-based protection, most suffer from drawbacks that limit their applicability in practice. We propose CAT, a new network-based flood protection scheme. In CAT, all flows must perform a three-way handshake with an in-network element to obtain permission to send data. The three-way handshake dissuades source spoofing and establishes a unique handle for the flow, which can then be used for revocation by the receiver. CAT offers the protection qualities of network capabilities, and yet does not require major architectural changes. 1
ChemInform Abstract: Novel 3‐Alkoxy‐1H‐pyrazolo[3,4‐d]pyrimidines as EGFR and erbB2 Receptor Tyrosine Kinase Inhibitors. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Prevalence and Clinical Impact of Early Repolarization Pattern and QRS-Fragmentation in High-Risk Patients With Brugada Syndrome (2016)

Fragmented QRS and ERP are common ECG findings in high-risk BrS patients, occurring in up to 27% of cases. When combined, f-QRS and ERP confer a higher risk of appropriate ICD interventions during a very long-term follow-up. (Circ J 2016; 80: 2109-2116).
Opportunity detection for OFDMA-based cognitive radio systems with timing misalignment (2009)

Accurate detection of spectrum opportunities within the frequency band of an orthogonal frequency division multiple access (OFDMA) system carries critical importance for OFDMAbased cognitive radios. In this paper, we analyze the opportunity detection performances of energy detection and ESPRIT (estimation of signal parameters by rotational invariance techniques) algorithms in the presence of timing misalignments in uplink (UL) OFDMA. For the energy detector, the statistics of subcarrier power are derived considering timing misalignments, and they are verified through computer simulations. Using these statistics, which take inter-carrier-interference (ICI) effects into account, receiver operating characteristics (ROCs) of the energy detector receiver are obtained. It is shown that energy detection has a considerably better performance than ESPRIT, especially when the subcarrier assignment changes frequently. Moreover, a closed form expression is derived for the UL-OFDMA synchronization point that minimizes the ICI. Finally, it is shown that employing resource allocation blocks with larger sizes in the primary network yields better opportunities for the cognitive radio.