gebhart/patrepeval huggingface dataset:
SMEM++: A Pipelined and Time-Multiplexed SMEM Seeding Accelerator for Genome Sequencing (2018)

Next-generation sequencing motivates the researchof FPGA acceleration for genome sequencing algorithms. Therecently developed quadratic-time SMEM seeding algorithmbecomes a time-consuming computation kernel in genomesequencing, but it has not been well studied. The fundamentalchallenge of accelerating the SMEM algorithm is to handle itslarge volume of random memory accesses. While the state-ofthe-art SMEM accelerator attempts sacrifices the performanceof individual processing elements to maximize the task-levelparallelism, this methodology suffers a serious resource underutilizationissue. Therefore, we propose SMEM++, a pipelinedand time-multiplexed FPGA accelerator for SMEM algorithm.SMEM++ adopts the canonical non-blocking pipelinemethodology and implements a fully pipelined acceleratorwith initiation interval equal to one. Moreover, we designa communication interface adapter to make the acceleratorcompatible to the target platform interface and increase itsportability. Experiments on the Intel HARPv2 platform showthat SMEM++ outperforms the original software by 24x, andoutperforms the state-of-the-art SMEM accelerator design by6.3x, with 43% less logic resource usage.
Ruthenium Porphyrin Compounds for Photodynamic Therapy of Cancer (2008)

Five 5,10,15,20-tetra(4-pyridyl)porphyrin (TPP) areneruthenium(II) derivatives and a p-cymeneosmium and two pentamethylcyclopentadienyliridium and -rhodium analogues were prepared and characterized as potential photosensitizing chemotherapeutic agents. The biological effects of all these derivatives were assessed on human melanoma tumor cells, and their cellular uptake and intracellular localization were determined. All molecules, except the rhodium complex which was not cytotoxic, demonstrated comparable cytotoxicity in the absence of laser irradiation. The ruthenium complexes exhibited excellent phototoxicities toward melanoma cells when exposed to laser light at 652 nm. Cellular uptake and localization microscopy studies of [Ru 4(eta (6)-C 6H 5CH 3) 4(TPP)Cl 8] and [Rh 4(eta (5)-C 5Me 5) 4(TPP)Cl 8] revealed that they accumulated in the melanoma cell cytoplasm in granular structures different from lysosomes. The fluorescent porphyrin moiety and the metal component were localized in similar structures within the cells. Thus, the porphyrin areneruthenium(II) derivatives represent a promising new class of organometallic photosensitizers able to combine chemotherapeutic activity with photodynamic therapeutic treatment of cancer.
Экономические основы формирования трансакционных издержек в наукоемком бизнесе (2012)

Рассматриваются источники трансакционных издержек в наукоемком бизнесе, в том числе при взаимодействии с государственным сектором экономики. Приводятся основные комбинации ресурсных ограничений, способствующих внедрению инновационных технологий, росту эффективности, сокращению трансакционных издержек.
Alternative Lengthening of Telomeres and Loss of DAXX/ATRX Expression Predicts Metastatic Disease and Poor Survival in Patients with Pancreatic Neuroendocrine Tumors (2016)

ALT and DAXX/ATRX loss in PanNETs was associated with shorter DFS and DSS and likely plays a significant role in driving metastatic disease. Clin Cancer Res; 23(2); 600-9. ©2016 AACR.
The coiled Electric Double Layer Capacitors Formed with Carbon Nanotube (2009)

The carbon nanotube (CNT) was added into polarizable electrode instead of the acetylene black (AB) as conducting material of the coiled EDLCs. The capacitance of the EDLCs with addition of the CNTs or the ABs are almost same value.The series resistance of CNT-added EDLCs is lower than that of AB by 30[%]. Therefore, it is effective to add the CNTs into polarizable electrode as conducting material of the coiled EDLCs.
Determination of Phase Composition of MCM-48/Lamellar Phase Mixtures Using Nitrogen Adsorption and Thermogravimetry (2002)

It is shown that gas adsorption and thermogravimetry are suitable for the determination of the phase composition of MCM-48/lamellar phase mixtures, which often are formed at different stages of the MCM-48 synthesis. The occurrence of the lamellar phase can be easily detected by analyzing as-synthesized materials by X-ray diffraction (XRD). However, it is not convenient to use this technique to quantify the composition of MCM-48/lamellar mixtures because of the overlap of the characteristic XRD peaks of these two phases and an inherent difficulty in applying the quantitative analysis for materials with amorphous frameworks presenting solely low-angle XRD peaks due to the long-range ordering of the pore arrays. On the other hand, the quantification of the lamellar phase in MCM-48/lamellar mixtures can be readily achieved by fitting the nitrogen adsorption isotherm for the calcined mixed phase with a linear combination of nitrogen adsorption isotherms for pure calcined MCM-48 and pure calcined (collapsed) lamellar phases. When the pure phases are properly selected, a good fit is often achieved in the entire relative pressure range and the sum of fitting coefficients is close to 1. In such a case, the fitting coefficients can be regarded as weight fractions of the pure components in the mixture. A semiquantitative evaluation of the content of the lamellar phase in MCM-48/lamellar mixtures can also be made on the basis of thermogravimetric (TGA) weight change patterns of as-synthesized samples because of a dramatically different weight loss behavior for as-synthesized MCM-48 and lamellar phase. Phase composition estimates from gas adsorption and TGA data were found to be similar. Because of the fact that adsorption and TGA data are often acquired during a routine analysis of surfactant-templated materials, the methods reported in this study can readily be used to assess the phase purity of MCM-48.
Oncolytic Herpes Simplex Viral Therapy: A Stride toward Selective Targeting of Cancer Cells (2017)

Oncolytic viral therapy, which makes use of replication-competent lytic viruses, has emerged as a promising modality to treat malignancies. It has shown meaningful outcomes in both solid tumor and hematologic malignancies. Advancements during the last decade, mainly genetic engineering of oncolytic viruses have resulted in improved specificity and efficacy of oncolytic viruses in cancer therapeutics. Oncolytic viral therapy for treating cancer with herpes simplex virus-1 has been of particular interest owing to its range of benefits like: (a) large genome and power to infiltrate in the tumor, (b) easy access to manipulation with the flexibility to insert multiple transgenes, (c) infecting majority of the malignant cell types with quick replication in the infected cells and (d) as Anti-HSV agent to terminate HSV replication. This review provides an exhaustive list of oncolytic herpes simplex virus-1 along with their genetic alterations. It also encompasses the major developments in oncolytic herpes simplex-1 viral therapy and outlines the limitations and drawbacks of oncolytic herpes simplex viral therapy.
Scalable Solar dc Micrigrids: On the Path to Revolutionizing the Electrification Architecture of Developing Communities (2018)

There is a worldwide focus on the electrification of developing regions, as is evident from the sustainable development goals (SDGs) of the United Nations. In particular, the aim of SDG 7 is to ensure universal access to affordable, reliable, sustainable, and modern energy services for all by 2030. Because of these sustained efforts, more than 1 billion people worldwide have gained access to electricity since 2000. During this course, the electrification architecture of developing regions has taken different forms, ranging from extensive utility grid extensions to limited off-grid solutions. Off-grid solutions generally offer cost-effective and lower up-front cost alternatives in comparison to utility grid extensions and are deemed more suitable for developing economies. In developing economies, these off-grid electrification solutions have evolved from individual solar home-based systems to community-based microgrids in pursuit of achieving higher efficiency and reliability on a village scale. Community grids responsible for the electrification of developing regions are further categorized based on architecture, type of generation, and mode distribution.
Advances in active fibres (1989)

Rare-earth-doped fibre lasers and amplifiers have been demonstrated at several wavelengths in the visible and near infrared regions. As potential sources and amplifiers for telecommunications they have wide tunability, high pulse peak-power, high gain and complete compatibility with optical fibres.
On the relay gain of the fading relay channel with finite input constellations (2012)

We consider the wireless Rayleigh fading relay channel with finite complex input constellations. Assuming global knowledge of the channel state information and perfect synchronization, upper and lower bounds on the achievable rate, for the full-duplex relay, as well as the more practical half-duplex relay (in which the relay cannot transmit and receive simultaneously), are studied. Assuming the power constraint at the source node and the relay node to be equal, the gain in rate offered by the use of relay over the direct transmission (without the relay) is investigated. It is shown that for the case of finite complex input constellations, the relay gain attains the maximum at a particular SNR and at higher SNRs the relay gain tends to become zero. Since practical schemes always use finite complex input constellation, the above result means that the relay offers maximum advantage over the direct transmission when we operate at a particular SNR and offers no advantage at very high SNRs. This is contrary to the results already known for the relay channel with Gaussian input alphabet.
FEM simulation of welding distortion in thin curved structures during assembly considering gap and misalignment (2002)

Ships and automobiles are fabricated from thin curved plates. To assemble parts, welding is commonly used. However, it is impossible to avoid the deformation produced by welding. The deformation causes problems not only in the assembling process but also in the final products. The shrinkage of the weld zone is just one of the reasons for the distortion during assembly. Other factors, such as positioning, fixture and welding sequence must be controlled to achieve the required precision. Since it is influenced by various factors, the quantitative prediction and the control of the welding deformation is difficult. Regardless of the types of structures, the correction or straightening of the deformation, which requires skill and cost, is one of the essential parts of the assembly process. If the welding deformation can be predicted before welding, appropriate measure can be taken to maintain sufficient geometrical accuracy without special skill or large cost. In this research, a finite element method (FEM) for predicting the welding deformation of three-dimensional curved structures with considering welding sequences is proposed. In this method, the interface element is introduced to model the joining process. The usefulness of the proposed method is demonstrated through the prediction of the welding distortion of the curved plate structures and the influence of the gap correction is investigated.
Virus Assembly (2016)

Abstract Viral genomes are sequestered by capsid proteins to form nucleocapsids with icosahedral (pseudospherical) or helical symmetry. Mature virus particles (virions) may be naked (i.e. composed of nucleic acid and protein only) or enveloped within a lipid bilayer(s). There is great diversity in size and complexity across the virus spectrum; recently discovered giant viruses are larger than some bacteria. Virions assemble from relatively large numbers of a few identical subunits but may include additional proteins required for specialised functions. Various mechanisms ensure that only viral genomic nucleic acids are packaged. Virion components are transported by cellular processes to sites of assembly. Basic functions of virions are protection of the genome from environmental damage during extracellular existence and delivery to a susceptible cell to initiate a new infection. Proteolytic cleavage of specific proteins during virus maturation commonly induces a quasi‐stable ‘triggered’ state to allow conformational changes necessary for cell penetration and genome release. Key Concepts For genetic economy, virions are assembled from large numbers of a few components. Nucleocapsids comprise the viral genomic nucleic acid sequestered within a protein coat. The symmetry of nucleocapsids is usually icosahedral or helical. Virions are either nonenveloped (i.e. a naked nucleocapsid) or enveloped by a lipid membrane. Virus‐specific nucleic acids are selectively packaged within nucleocapsids. Intracellular transport mechanisms are hijacked by viruses to ensure that components are delivered to sites of assembly. Postassembly proteolytic cleavages are often used to induce a quasi‐stable state primed for cell entry.
Enhancement of Perfluoropolyether Boundary Lubrication Performance (1996)

A ball bearing simulator operating under starved conditions was used to perform screening tests to evaluate the boundary lubrication performance of a branched perfluoropolyether (PFPE), K-143 AB. Several approaches to enhance boundary lubrication were studied. These included soluble boundary additives, bearing surface modifications, run-in surface films and ceramic bearing components. In addition, results were compared with two nonperfluorinated liquid lubricant formulations. Based on these tests, the following tentative conclusions can be made: 1. Substantial improvements in boundary lubrication performance were observed with a β-diketone boundary additive and a tricresyl phosphate (TCP) liquid surface pretreatment. 2. The use of rough Si 3 N 4 balls (R a = 40 μ in) also provided increases in test duration, but with concomitant abrasive wear. 3. Moderate improvements were seen with two boundary additives (a phosphine and a phosphatriazine) and a neat (100%) fluid (a carboxylic acid terminated PFPE). Small improvements occurred with surface pretreatments with synthetic hydrocarbons, a polytetrafluoroethylene (PTFE) coating, and TiC-coated 440C and smooth Si 3 N 4 balls (R a = 1 μ in). 4. Two non-PFPE lubricant formulations (a polyalphaolefin (PAO) and a synthetic hydrocarbon) yielded substantial improvements.
Sparse Sampling in Helical Cone-Beam CT Perfect Reconstruction\n Algorithms (2014)

In the current paper we consider the Helical Cone Beam CT. This scanning\nmethod exposes the patient to large quantities of radiation and results in very\nlarge amounts of data being collected and stored. Both these facts are prime\nmotivators for the development of an efficient, reduced rate, sampling pattern.\nWe calculate bounds on the support in the frequency domain of the collected\ndata and use these to suggest an efficient sampling pattern. A reduction of up\nto a factor of 2 in sampling rate is suggested. Indeed, we show that\nreconstruction quality is not affected by this reduction of sampling rates.\n
Neuron-Specific Inactivation of the Hypoxia Inducible Factor 1 Increases Brain Injury in a Mouse Model of Transient Focal Cerebral Ischemia (2007)

In the present study, we show a biphasic activation of hypoxia inducible factor 1alpha (HIF-1) after stroke that lasts for up to 10 d, suggesting the involvement of the HIF pathway in several aspects of the pathophysiology of cerebral ischemia. We provide evidence that HIF-1-mediated responses have an overall beneficial role in the ischemic brain as indicated by increased tissue damage and reduced survival rate of mice with neuron-specific knockdown of HIF-1alpha that were subjected to transient focal cerebral ischemia. In addition, we demonstrated that drugs known to activate HIF-1 in cultured cells as well as in vivo had neuroprotective properties in this model of cerebral ischemia. This protective effect was significantly attenuated but not completely abolished in neuron-specific HIF-1alpha-deficient mice, suggesting that alternative mechanisms of neuroprotection are also implicated. Last, our study showed that hypoxia-induced tolerance to ischemia was preserved in neuron-specific HIF-1alpha-deficient mice, indicating that the neuroprotective effects of hypoxic preconditioning do not depend on neuronal HIF-1 activation.
Microcolins A and B, New Immunosuppressive Peptides from the Blue-Green Alga Lyngbya majuscula (1992)

Microcolin A [1] and microcolin B [2] are new immunosuppressive lipopeptides isolated from a Venezuelan sample of the blue-green alga Lyngbya majuscula. The microcolins are potent inhibitors of the murine mixed lymphocyte response and murine P-388 leukemia in vitro. Isolation and structure elucidation of 1 and 2 by nmr, mass spectral, and chemical methods are described.
Chemical diversity and cellular effects of antifungal cyclic lipopeptides from cyanobacteria (2021)

Cyanobacteria produce a variety of chemically diverse cyclic lipopeptides with potent antifungal activities. These cyclic lipopeptides have an amphipathic structure comprised of a polar peptide cycle and hydrophobic fatty acid side chain. Many have antibiotic activity against a range of human and plant fungal pathogens. This review article aims to summarize the present knowledge on the chemical diversity and cellular effects of cyanobacterial cyclic lipopeptides that display antifungal activity. Cyclic antifungal lipopeptides from cyanobacteria commonly fall into four structural classes; hassallidins, puwainaphycins, laxaphycins, and anabaenolysins. Many of these antifungal cyclic lipopeptides act through cholesterol and ergosterol-dependent disruption of membranes. In many cases, the cyclic lipopeptides also exert cytotoxicity in human cells, and a more extensive examination of their biological activity and structure-activity relationship is warranted. The hassallidin, puwainaphycin, laxaphycin, and anabaenolysin structural classes are unified through shared complex biosynthetic pathways that encode a variety of unusual lipoinitiation mechanisms and branched biosynthesis that promote their chemical diversity. However, the biosynthetic origins of some cyanobacterial cyclic lipopeptides and the mechanisms, which drive their structural diversification in general, remain poorly understood. The strong functional convergence of differently organized chemical structures suggests that the production of lipopeptide confers benefits for their producer. Whether these benefits originate from their antifungal activity or some other physiological function remains to be answered in the future. However, it is clear that cyanobacteria encode a wealth of new cyclic lipopeptides with novel biotechnological and therapeutic applications.
Inducing heuristics to decide whether to schedule (2004)

Instruction scheduling is a compiler optimization that can improve program speed, sometimes by 10% or more, but it can also be expensive. Furthermore, time spent optimizing is more important in a Java just-in-time (JIT) compiler than in a traditional one because a JIT compiles code at run time, adding to the running time of the program. We found that, on any given block of code, instruction scheduling often does not produce significant benefit and sometimes degrades speed. Thus, we hoped that we could focus scheduling effort on those blocks that benefit from it.Using supervised learning we induced heuristics to predict which blocks benefit from scheduling. The induced function chooses, for each block, between list scheduling and not scheduling the block at all. Using the induced function we obtained over 90% of the improvement of scheduling every block but with less than 25% of the scheduling effort. When used in combination with profile-based adaptive optimization, the induced function remains effective but gives a smaller reduction in scheduling effort. Deciding when to optimize, and which optimization(s) to apply, is an important open problem area in compiler research. We show that supervised learning solves one of these problems well.
On Engineered Cementitious Composites (ECC) (2003)

This article surveys the research and development of Engineered Cementitious Composites (ECC) over the last decade since its invention in the early 1990's. The importance of micromechanics in the materials design strategy is emphasized. Observations of unique characteristics of ECC based on a broad range of theoretical and experimental research are examined. The advantageous use of ECC in certain categories of structural, and repair and retrofit applications is reviewed. While reflecting on past advances, future challenges for continued development and deployment of ECC are noted. This article is based on a keynote address given at the International Workshop on Ductile Fiber Reinforced Cementitious Composites (DFRCC) - Applications and Evaluations, sponsored by the Japan Concrete Institute, and held in October 2002 at Takayama, Japan.
II.4.4 Characterization of Coal and Biomass Conversion Behaviors in Advanced Energy Systems (2004)

Introduction The goal of this project is to develop models that predict accurately coal and biomass gasification and combustion behaviors in the type of environments likely to be established in advanced energy systems. This requires acquiring the information needed to understand and characterize the fundamental chemical and physical processes that govern coal and biomass conversion at high temperatures and pressures. The models can be used to determine operating conditions that optimize thermal efficiency and to examine design strategies for integrating combined cycles for the production of synthesis gas and electric power with minimum impact on the environment.
The treatment of children's writing by student teachers (1989)

Abstract The research reported here investigates how student teachers respond to children's writing and if and how their responses change during teacher training. Results indicate that at the outset of their training students’ responses manifest the inadequacies commonly attributed to teachers’ marking behaviour. They place greater emphasis on what is wrong rather than what is right; their comments are very general, and are mainly about how the piece is written rather than what is written. As students go through college they put more emphasis on the content of the writing, correct fewer errors and develop a greater repertoire of comments. Their comments become more specific, less exclusively evaluative and more constructive. Nevertheless, even at the end of training, students do not comment on many of the strengths of the writing. This is particularly true of grammar; grammatical errors are noted but grammatical competence is generally not.