gebhart/patrepeval huggingface dataset:
FPGA-Based Processor Acceleration for Image Processing Applications (2019)

FPGA-based embedded image processing systems offer considerable computing resources but present programming challenges when compared to software systems. The paper describes an approach based on an FPGA-based soft processor called <i>Image Processing Processor</i> (IPPro) which can operate up to 337 MHz on a high-end Xilinx FPGA family and gives details of the dataflow-based programming environment. The approach is demonstrated for a <i>k</i>-means clustering operation and a traffic sign recognition application, both of which have been prototyped on an Avnet Zedboard that has Xilinx Zynq-7000 system-on-chip (SoC). A number of parallel dataflow mapping options were explored giving a speed-up of 8 times for the <i>k</i>-means clustering using 16 IPPro cores, and a speed-up of 9.6 times for the morphology filter operation of the traffic sign recognition using 16 IPPro cores compared to their equivalent ARM-based software implementations. We show that for <i>k</i>-means clustering, the 16 IPPro cores implementation is 57, 28 and 1.7 times more power efficient (fps/W) than ARM Cortex-A7 CPU, nVIDIA GeForce GTX980 GPU and ARM Mali-T628 embedded GPU respectively.
American Correctional Association (2013)

Abstract This entry provides an overview of the American Correctional Association (ACA) and its role as the premiere governing body for standards and guidelines among correctional practitioners in the United States. The goals of the ACA are outlined and discussed, making it clear that this organization serves as a key leadership entity within the field. The history of this organization, starting with its genesis as the National Prison Association in the late 1800s to its current day state of operations is presented. It is made clear that practitioners and scholars around the nation are impacted by the influence that the ACA has on correctional standards and practices.
Multidrug resistance in hematological malignancy. (2003)

The recent treatment of hematological malignancies appears to be unsatisfactory in child and adult patients with acute myeloid leukemia and adult patients with acute lymphocytic leukemia. A major problem in the treatment of leukemia is caused by the development of drug resistance to chemotherapeutic agents, which is already present at diagnosis or after chemotherapy as a minimal residual disease, their resistance having originated from genetic or epigenetic mutations during prior growth of the leukemia clone. It was suggested that the mechanisms of drug resistance consist of drug resistance proteins, which work as a drug efflux pump. These are the permeability-related glycoprotein (P-Gp), the multidrug-resistance associated protein (MRP), the lung resistance protein (LRP), and other MDR proteins such as the transporter associated with antigen processing (TAP), anthracyclin resistance associated protein (ARA), MRP 2-7, and breast cancer resistance protein (BCRP). In addition, anti-apoptosis mechanisms, alterations of tumor suppressor genes, altered immunogenicity, drug resistance mechanisms for individual drugs, and clinical risk factors such as white blood cell count, age, and other factors have been reported to act in drug resistance singly or in combinations. Here we describe the update of research on the biology of MDR in the hematological malignancies and also discuss how to overcome MDR and adapt the updated treatment methods in the clinical medical field.
Mbps experimental acoustic through-tissue communications: MEAT-COMMS (2016)

Methods for digital, phase-coherent acoustic communication date to at least the work of Stojanjovic, et al [20], and the added robustness afforded by improved phase tracking and compensation of Johnson, et al [21]. This work explores the use of such methods for communications through tissue for potential biomedical applications, using the tremendous bandwidth available in commercial medical ultrasound transducers. While long-range ocean acoustic experiments have been at rates of under 100kbps, typically on the order of 1-10kbps, data rates in excess of 120Mb/s have been achieved over cm-scale distances in ultrasonic testbeds [19]. This paper describes experimental transmission of digital communication signals through samples of real pork tissue and beef liver, achieving data rates of 20-30Mbps, demonstrating the possibility of real-time video-rate data transmission through tissue for in-body ultrasonic communications with implanted medical devices.
Parallel Prefix Scan with Compute Unified Device Architecture (CUDA) (2014)

Parallel prefix scan, also known as parallel prefix sum, is a building block for many parallel algorithms including polynomial evaluation, sorting and building data structures. This paper introduces prefix scan and also describes a step-bystep procedure to implement prefix scan efficiently with Compute Unified Device Architecture (CUDA). This paper starts with a basic naive algorithm and proceeds through more advanced techniques to obtain best performance. KeywordsScan, Parallel prefix sum, Prefix scan, CUDA, Parallel algorithms, Naive algorithm
Whole-Genome Expression Profiling Reveals That Inhibition of Host Innate Immune Response Pathways by Ebola Virus Can Be Reversed by a Single Amino Acid Change in the VP35 Protein (2008)

Ebola hemorrhagic fever is a rapidly progressing acute febrile illness characterized by high virus replication, severe immunosuppression, and case fatalities of ca. 80%. Inhibition of phosphorylation of interferon regulatory factor 3 (IRF-3) by the Ebola VP35 protein may block the host innate immune response and play an important role in the severity of disease. We used two precisely defined reverse genetics-generated Ebola viruses to investigate global host cell responses resulting from the inhibition of IRF-3 phosphorylation. The two viruses encoded either wild-type (WT) VP35 protein (recEbo-VP35/WT) or VP35 with an arginine (R)-to-alanine (A) amino acid substitution at position 312 (recEbo-VP35/R312A) within a previously defined IRF-3 inhibitory domain. When sucrose-gradient purified virus was used for infection, host cell whole-genome expression profiling revealed striking differences in human liver cell responses to these viruses differing by a single amino acid. The inhibition of host innate immune responses by WT Ebola virus was so potent that little difference in interferon and antiviral gene expression could be discerned between cells infected with purified WT, inactivated virus, or mock-infected cells. However, infection with recEbo-VP35/R312A virus resulted in a strong innate immune response including increased expression of MDA-5, RIG-I, RANTES, MCP-1, ISG-15, ISG-54, ISG-56, ISG-60, STAT1, IRF-9, OAS, and Mx1. The clear gene expression differences were obscured if unpurified virus stocks were used to initiate infection, presumably due to soluble factors present in virus-infected cell supernatant preparations. Ebola virus VP35 protein clearly plays a pivotal role in the potent inhibition of the host innate immune responses, and the present study indicates that VP35 has a wider effect on host cell responses than previously shown. The ability to eliminate this inhibitory effect with a single amino acid change in VP35 demonstrates the critical role this protein must play in the severe aspects this highly fatal disease.
Statistical properties of random scattering matrices (1996)

We discuss the statistical properties of eigenphases of S matrices in random models simulating quantum systems that exhibit chaotic scattering classically. The energy dependence of the eigenphases is investigated and the corresponding velocity and curvature distributions are obtained both theoretically and numerically. A simple formula describing the velocity distribution (and hence the distribution of the Wigner time delay) is derived that is capable of explaining the algebraic tail of the time delay distribution observed recently in microwave experiments. A dependence of the eigenphases on other external parameters is also discussed. We show that in the semiclassical limit (large number of channels) the curvature distribution of S-matrix eigenphases is the same as that corresponding to the curvature distribution of the underlying Hamiltonian and is given by the generalized Cauchy distribution. \textcopyright{} 1996 The American Physical Society.
Watershed calibration using multistart local optimization and evolutionary optimization with radial basis function approximation (2007)

Abstract Calibration of computationally expensive watershed models is more feasible with algorithms that require fewer simulations. This paper compares the performance of seven global optimization algorithms on a 14-parameter and an 8-parameter watershed calibration problem. The optimization algorithms include Shuffled Complex Evolution (SCE), Differential Evolution (DE), an evolutionary algorithm that uses Radial Basis Function (RBF) approximation (ESGRBF), and four types of local optimization methods coupled with the Multi-Level Single Linkage (MLSL) multistart procedure. The four local optimization algorithms are: Sequential Quadratic Programming, which is a derivative-based method; Unconstrained Optimization by Quadratic Approximation (UOBYQA), which is a derivativefree trust-region method; Pattern Search; and Implicit Filtering. The results indicate that ESGRBF is the most effective algorithm on the two calibration problems, followed by Implicit Filtering coupled with the MLSL multistart approach. Hence, this study provides some promising alternatives to the currently most widely used methods in watershed calibration, which did not perform as well.
The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in<i>Saccharomyces cerevisiae</i> (2013)

The YEASTRACT (http://www.yeastract.com) information system is a tool for the analysis and prediction of transcription regulatory associations in Saccharomyces cerevisiae. Last updated in June 2013, this database contains over 200,000 regulatory associations between transcription factors (TFs) and target genes, including 326 DNA binding sites for 113 TFs. All regulatory associations stored in YEASTRACT were revisited and new information was added on the experimental conditions in which those associations take place and on whether the TF is acting on its target genes as activator or repressor. Based on this information, new queries were developed allowing the selection of specific environmental conditions, experimental evidence or positive/negative regulatory effect. This release further offers tools to rank the TFs controlling a gene or genome-wide response by their relative importance, based on (i) the percentage of target genes in the data set; (ii) the enrichment of the TF regulon in the data set when compared with the genome; or (iii) the score computed using the TFRank system, which selects and prioritizes the relevant TFs by walking through the yeast regulatory network. We expect that with the new data and services made available, the system will continue to be instrumental for yeast biologists and systems biology researchers.
A Severe Outbreak of<i>Escherichia coli</i>O157:H7–Associated Hemorrhagic Colitis in a Nursing Home (1987)

In September 1985, an outbreak of Escherichia coli O157:H7 enteritis affected 55 of 169 residents and 18 of 137 staff members at a nursing home. The outbreak was characterized by two phases: a primary wave whose source was probably a contaminated sandwich meal and a secondary wave compatible with person-to-person transmission of infection. Among the elderly residents, the incubation period was 4 to 9 days (mean, 5.7 +/- 1.2). Older age and previous gastrectomy increased the risk of acquiring the infection (P = 0.01 and 0.03, respectively). Antibiotic therapy during exposure was associated with acquiring a secondary infection (P = 0.001). Hemolytic uremic syndrome developed in 12 affected residents (22 percent), 11 of whom died. Overall, 19 (35 percent) of the affected residents died, 17 (31 percent) from causes attributable to their infection. Antibiotic therapy after the onset of symptoms was associated with a higher case fatality rate in the more severe cases, possibly because patients with more severe disease tended to be treated with antibiotics. There were no complications or deaths among the affected members of the staff. Evidence of infection by verotoxin-producing E. coli O157:H7 was detected in 30 of 70 cases on the basis of isolation of this organism or demonstration of free verotoxin in stools. All isolates belonged to the same phage type. The high morbidity and mortality associated with this condition emphasize the need for proper food hygiene, rapid identification of outbreaks of disease, and prompt institution of infection-control techniques among the institutionalized elderly.
Mechanisms of postsynaptic plasticity: remodeling of the junctional acetylcholine receptor cluster induced by motor nerve terminal outgrowth (1987)

Motor nerve terminal outgrowth (NTO) at neuromuscular junctions (NMJs) occurs rapidly in response to denervation changes in muscle. We have previously found that NTO can produce an elongation of the synaptic area of the NMJ as defined by cholinesterase-silver staining. In the present study, we examined the effects of NTO on a postsynaptic muscle membrane component, the usually stable cluster of acetylcholine receptors (AChRs) at the NMJ. NTO was evoked in rat soleus muscles using botulinum toxin. AChRs were demonstrated using immunocytochemistry or autoradiography of alpha-bungarotoxin binding. Our results show that NTO induces rapid elongation of the cluster of AChRs at the NMJ within 7 d of treatment with botulinum toxin. The growth in the size of the AChR clusters was accompanied by an increase in the number of AChRs/NMJ. No elongation of AChR clusters was seen following surgical denervation, suggesting that cluster growth is related to NTO and not to denervation changes in muscle per se. Growth of NMJ-AChR clusters appeared to result primarily from 2 processes: insertion of new AChRs into the NMJ membrane and, surprisingly, redistribution of preexisting NMJ-AChRs. These results show that NTO can cause rapid changes in the normally stable cluster of AChRs at the NMJ. Motor nerve terminals provide a strong and anatomically precise control of AChRs at the NMJ.
On Device Architectures, Subthreshold Swing, and Power Consumption of the Piezoelectric Field-Effect Transistor (<inline-formula> <tex-math notation="LaTeX">${\pi }$ </tex-math></inline-formula>-FET) (2015)

This paper describes the potential of tunable strain in field-effect transistors to boost performance of digital logic. Voltage-controlled strain can be imposed on a semiconductor body by the integration of a piezoelectric material improving transistor performance. In this paper, we derive the relations governing the subthreshold swing in such devices to improve the understanding. Using these relations and considering the mechanical and technological boundary conditions, we discuss possible device architectures that employ this principle. Further, we review the recently published experimental and modeling results of this device, and give analytical estimates of the power consumption.
Antiangiogenic Gene Therapy in a Rat Glioma Model Using a Dominant-Negative Vascular Endothelial Growth Factor Receptor 2 (1999)

Malignant gliomas are a prominent target for cancer gene therapy approaches because of their poor prognosis despite all currently available therapies. Gene therapy strategies developed to interfere with the normal function of vascular endothelial growth factor receptors have been successfully used in different experimental models to block tumor angiogenesis and to inhibit tumor growth. In this study we examined whether retroviruses encoding a mutant VEGF receptor 2 (VEGFR-2) could suppress tumor angiogenesis and thereby prolong the survival of rats bearing syngeneic intracerebral glioma tumors. Survival time of rats with intracerebral tumors was significantly prolonged in a dose-dependent manner when retroviruses carrying a VEGFR-2 mutant were cotransplanted with tumor cells. No effect on survival was observed in rats that received virus-producing cells or virus supernatant intracerebrally after 5 days of tumor injection. In established subcutaneous tumors treatment with multiple injections of virus-producing cells also inhibited tumor growth in a dose-dependent manner. After implantation of tumor cells stably transfected with a truncated form of VEGFR-2, rats exhibited a rate of survival similar to that of animals treated with high numbers of virus-producing cells encoding the truncated form of VEGFR-2. Morphologically, tumors showed signs of impaired angiogenesis, such as extensive necrosis and reduced tumor vascular density. These results suggest a dual mode of function of truncated VEGFR-2, namely dominant-negative inhibition of VEGFR-2 function and VEGF depletion by receptor binding. We further explored the safety of retrovirus-mediated gene transfer. Although virus sequences were found in different tissues after intracerebral injection of virus-producing cells, no morphological changes were observed in any tissue after a follow-up time of 6 months. Our results indicate that VEGFR-2 inhibition is useful for the treatment of malignant gliomas.
A new protein evaluation system for pig feeds and its practical application (1998)

The present basis for determining the protein value in pig feeds is discussed and a proposal for a new protein evaluation system is presented. The system proposed includes (i) a quantification of digestible amino acids according to their ileal digestibility, determined using standardized methods; (ii) a characterization of the protein value according to the contribution of digestible amino acids to ideal protein; (iii) a calculation of surplus amino acid‐N; and (iv) a calculation of the physiologically available energy of surplus amino acids. Practical methods for improving the quantification of digestible amino acids in the actual samples are described. The methods include calculations of (i) total amino acids in feedstuffs from nitrogen analyses by the use of specific factors or regression equations and (ii) standardized digestible amino acids from in vitro digestible nitrogen and correction for the extra endogenous amino acid losses specifically induced by the feedstuff itself. An example calculation for the practical use of the proposed protein evaluation system is given.
RezRIDERS: A Tribally-Driven, Extreme Sport Intervention & Outcomes. (2018)

Reducing Risk through Interpersonal Development, Empowerment, Resiliency, and Self-Determination (RezRIDERS) is a tribally-driven youth empowerment program designed to deter substance abuse and depression symptomology among high-risk American Indian youth while increasing hope/optimism, self-efficacy, and pro-social bonding. The quasi-experimental intervention took place between 2012-2015 in the Pueblo of Jemez (New Mexico, USA). The community-based program served fifty-five total youth. RezRIDERS has four major curricular components: 1) Extreme Sport activity clusters paired with; 2) Indigenized behavioral-cognitive lessons; 3) Tribal Research Team providing program oversight and cultural mentoring; and 4) Community action projects addressing youth-identified community issues. This unique program is a modern version of challenge and journeying that Indigenous people historically experienced as norms. Using qualitative and quantitative data, intervention pilot-testing assessed feasibility and efficacy of the program.
A RecA Homologue in <i>Ustilago maydis </i>That Is Distinct and Evolutionarily Distant from Rad51 Actively Promotes DNA Pairing Reactions in the Absence of Auxiliary Factors (2001)

Two RecA homologues have been identified to date in Ustilago maydis. One is orthologous to Rad51 while the other, Rec2, is structurally quite divergent and evolutionarily distant. DNA repair and recombination proficiency in U. maydis requires both Rec2 and Rad51. Here we have examined biochemical activities of Rec2 protein purified after overexpression of the cloned gene. Rec2 requires DNA as a cofactor to hydrolyze ATP and depends on ATP to promote homologous pairing and DNA strand exchange. ATPgammaS was found to substitute for ATP in all pairing reactions examined. With superhelical DNA and a homologous single-stranded oligonucleotide as substrates, Rec2 actively promoted formation and dissociation of D-loops. When an RNA oligonucleotide was substituted it was found that R-loops could also be formed and utilized as primer/template for limited DNA synthesis. In DNA strand exchange reactions using oligonucleotides, we found that Rec2 exhibited a pairing bias that is opposite that of RecA. Single-stranded oligonucleotides were activated for DNA strand exchange when attached as tails protruding from a duplex sequence due to enhanced binding of Rec2. The results indicate that Rec2 is competent, and in certain ways even better than Rad51, in the ability to provide the fundamental DNA pairing activity necessary for recombinational repair. We propose that the emerging paradigm for homologous recombination featuring Rad51 as the essential catalytic component for strand exchange may not be universal in eukaryotes.
The large subunit of HIV-1 reverse transcriptase interacts with β-actin (1995)

HIV-1 reverse transcriptase is a dimeric enzyme mainly involved in the replication of the viral genome. A filamentous phage cDNA expression library from human lymphocytes was used to select cellular proteins interacting with HIV-1 reverse transcriptase Affinity selections using the bacterially expressed monomeric large subunit of reverse transcriptase (p66) yielded host beta-actin. This clone was expressed as glutathione-S-transferase fusion protein which was identified by using a specific antibody against beta-actin. Furthermore we show that also the eukaryotic beta-actin binds to either the large subunit of reverse transcriptase or to the Pol precursor polyprotein in vitro. The reverse transcriptase/beta-actin interaction might be important for the secretion of HIV-1 virions.
Vector Gaussian Multiple Description With Individual and Central Receivers (2007)

T multiple descriptions of a vector Gaussian source for individual and central receivers are investigated. The sum rate of the descriptions with covariance distortion measure constraints, in a positive semidefinite ordering, is exactly characterized. For two descriptions, the entire rate region is characterized. The key component of the solution is a novel information-theoretic inequality that is used to lower-bound the achievable multiple description rates. Jointly Gaussian descriptions are optimal in achieving the limiting rates. We also show the robustness of this description scheme: the distortions achieved are no larger when used to describe any non-Gaussian source with the same covariance matrix.
A Dissolvable Intralumental Stent for Sutureless Vascular Anastomasis (2005)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.