gebhart/patrepeval huggingface dataset:
An Atm Network Interface for High-Speed Experimentation (2005)

To connect host computers to an Asynchronous Transfer Mode (ATM) network, a network interface is required. The interface must be able to move data between the network and the host and to convert between the data format used in the network (ATM cells) and that used in the host (eg. variable length protocol data units). In the work described here, the goal was to prototype such an interface and to satisfy two contradictory requirements: speed of operation and flexibility to support experimentation. To achieve this goal, we defined an architecture which uses microprocessors for those functions where most flexibility is required, such as the execution of Segmentation and Reassembly (SAR) algorithms, while more specialized hardware is used for critical high-speed functions such as data movement and formatting of ATM cells. The details of this architecture are described and the results that have been obtained so far with the experimental prototype implementation are presented.
Trajectory Optimization of Electric Aircraft Subject to Subsystem Thermal Constraints (2017)

Electric aircraft pose a unique design challenge in that they lack a simple way to reject waste heat from the power train. While conventional aircraft reject most of their excess heat in the exhaust stream, for electric aircraft this is not an option. To examine the implications of this challenge on electric aircraft design and performance, we developed a model of the electric subsystems for the NASA X-57 electric testbed aircraft. We then coupled this model with a model of simple 2D aircraft dynamics and used a Legendre-Gauss-Lobatto collocation optimal control approach to find optimal trajectories for the aircraft with and without thermal constraints. The results show that the X-57 heat rejection systems are well designed for maximum-range and maximum-efficiency flight, without the need to deviate from an optimal trajectory. Stressing the thermal constraints by reducing the cooling capacity or requiring faster flight has a minimal impact on performance, as the trajectory optimization technique is able to find flight paths which honor the thermal constraints with relatively minor deviations from the nominal optimal trajectory.
24‐Hour Survival of ACD‐ and CPD‐Stored Red Cells (1972)

Abstract. Using an automated differential agglutination procedure, 218 red cell survival studies were performed in patients requiring therapeutic transfusion. Blood was collected in acid‐citrate‐dextrose (ACD) or citrate‐phosphate‐dextrose (CPD). Some of the blood was stored as such and some as concentrated red cells. Adverse effects of storage on both washed and nonwashed whole blood and concentrated red cells were determined by 24‐hour posttransfusion survival measurements. There were no significant differences in the storage limitations of non‐washed ACD‐ and CPD‐collected whole blood, and concentrated red cells. Washing stored red cells with either buffered or nonbuffered 0.9% sodium chloride solution with or without glucose did not significantly affect 24‐hour survival. However, there was a significant decrease in survival when stored red cells were washed with CPD solution or with a buffered 0.9% sodium chloride solution supplemented with calcium and magnesium.
Evaluation of the Relative Performance of 12 Urinary Biomarkers for Renal Safety Across 22 Rat Sensitivity and Specificity Studies (2013)

Novel urinary kidney safety biomarkers have been identified recently that may outperform or add value to the conventional renal function biomarkers, blood urea nitrogen (BUN) and serum creatinine (SCr). To assess the relative performance of the growing list of novel biomarkers, a comprehensive evaluation was conducted for 12 urinary biomarkers in 22 rat studies including 12 kidney toxicants and 10 compounds with toxicities observed in organs other than kidney. The kidney toxicity studies included kidney tubular toxicants and glomerular toxicants. The 12 urinary biomarkers evaluated included Kim-1, clusterin, osteopontin, osteoactivin, albumin, lipocalin-2, GST-α, β2-microglobulin, cystatin C, retinol binding protein 4, total protein, and N-acetyl-β-D-glucosaminidase. Receiver operator characteristic (ROC) curves were generated for each biomarker and for BUN and SCr to compare the relative performance of the 12 biomarkers in individual animals against the microscopic histomorphologic changes observed in the kidney. Among the kidney toxicity biomarkers analyzed, Kim-1, clusterin, and albumin showed the highest overall performance for detecting drug-induced renal tubular injury in the rat in a sensitive and specific manner, whereas albumin showed the highest performance in detecting drug-induced glomerular injury. Although most of the evaluated kidney biomarkers were more sensitive in detecting kidney toxicity compared with BUN and SCr, all biomarkers demonstrated some lack of specificity, most notably NGAL and osteopontin, illustrating the need for caution when interpreting urinary biomarker increases in rat samples when organ toxicity is unknown.
Influence of bio-based solvents on the catalytic reductive fractionation of birch wood (2015)

In the reductive catalytic fractionation of lignocellulose, the choice of solvent significantly impacts the delignification efficiency, carbohydrate retention in the pulp and the macrostructure of the pulp.
Multi-Dimensional Coded Modulation in Long-Haul Fiber Optic Transmission (2015)

Multi-dimensional-coded modulation approaches the nonlinear Shannon limit due to its high SNR sensitivity and large Euclidean distance between multi-dimensional symbols. It also eliminates phase ambiguity to avoid cycle slips. In this paper, we review the design principles of bit-interleaved-coded modulation with multi-dimensional mapping, and its performance in long-haul transmission experiments with different spectral efficiencies in both dispersion managed and dispersion unmanaged fiber optic systems.
代谢综合征的诊断和治疗——美国心脏协会／国立心肺血液研究所指南概要 (2006)

近几年，代谢综合征越来越受到人们的关注。它包括了可能直接促进动脉粥样硬化性心血管疾病（ASCVD）的多种相关代谢性危险因素。这些代谢性危险冈素与2型糖尿病及其风险具有强相关性。这些代谢性危险因素包括致粥样硬化性血脂异常（甘油三酯、载脂蛋白B及小LDL颗粒升高，HDL-C浓度降低）、血压升高、血糖升高以及血栓前状态、前炎性状态。
Endogenous association of Bim BH3‐only protein with Mcl‐1, Bcl‐x<sub>L</sub> and Bcl‐2 on mitochondria in human B cells (2005)

Bim is an essential regulator of lymphoid system homeostasis and appears essential for B cell apoptosis induction. The mechanism by which Bim isoforms are held in an inactive form remains poorly documented in normal B cells. In the current study, we demonstrated that in normal tonsil B cells the three major Bim isoforms are strongly associated with the anti-apoptotic Bcl-2 family members Mcl-1, Bcl-2 and Bcl-x(L). On the other hand, only a weak association of BimEL and L with the dynein LC8 chain has been found. In addition, there is no free Bim in normal B cells. Moreover, subcellular fractionation demonstrated that Bim and the anti-apoptotic counterparts are localized preferentially in the mitochondria-rich fraction. The fact that most Bim was found in this fraction supports the hypothesis that it is sequestered by anti-apoptotic molecules in mitochondria where its pro-apoptotic activity is controlled. Of interest, BimS is essentially complexed to Mcl-1 and the Mcl-1/Bim complex is the most abundant among the three types of complexes. This supports the idea that this complex is critical for the control of B cell death. In conclusion, these results favor a model in which Bim release from anti-apoptotic proteins is a critical event for initiation of apoptosis.
Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c- <i>MYC</i> transcription (2002)

The nuclease hypersensitivity element III(1) upstream of the P1 promoter of c-MYC controls 85-90% of the transcriptional activation of this gene. We have demonstrated that the purine-rich strand of the DNA in this region can form two different intramolecular G-quadruplex structures, only one of which seems to be biologically relevant. This biologically relevant structure is the kinetically favored chair-form G-quadruplex, which is destabilized when mutated with a single G --> A transition, resulting in a 3-fold increase in basal transcriptional activity of the c-MYC promoter. The cationic porphyrin TMPyP4, which has been shown to stabilize this G-quadruplex structure, is able to suppress further c-MYC transcriptional activation. These results provide compelling evidence that a specific G-quadruplex structure formed in the c-MYC promoter region functions as a transcriptional repressor element. Furthermore, we establish the principle that c-MYC transcription can be controlled by ligand-mediated G-quadruplex stabilization.
Crown‐like macrocycle zinc complex derived from β‐diketone ligand for the polymerization of rac‐lactide (2007)

Abstract Enolic Schiff base zinc (II) complex 1 was synthesized. XRD revealed 1 was a novel crown‐like macrocycle structure consisted of hexanuclear units of (LZnEt) 6 via the coordination chelation between the Zn atom and adjacent amine nitrogen atom. Further reaction of 1 with one equivalent 2‐propanol at RT produced Zn‐alkoxide 2 by in situ alcoholysis. Complex 2 was used as an initiator to polymerize rac‐lactide in a controlled manner to give heterotactic enriched polylactide. Factors that influenced the polymerization such as the polymerization time and the temperature as well as the monomer concentration were discussed in detail in this paper. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 643–649, 2008
Synthetic essentiality of metabolic regulator PDHK1 in PTEN-deficient cells and cancers (2018)

SUMMARY PTEN is a tumor suppressor that is often inactivated in cancer and possesses both lipid and protein phosphatase activities. We report the metabolic regulator PDHK1 (pyruvate dehydrogenase kinase1) is a synthetic-essential gene in PTEN-deficient cancer and normal cells. The predominant mechanism of PDHK1 regulation and dependency is the PTEN protein phosphatase dephosphorylates NFκ;B activating protein (NKAP) and limits NFκB activation to suppress expression of PDHK1, a NFκB target gene. Loss of the PTEN protein phosphatase upregulates PDHK1 to drive aerobic glycolysis and induce PDHK1 cellular dependence. PTEN-deficient human tumors harbor increased PDHK1, which is a biomarker of decreased patient survival, establishing clinical relevance. This study uncovers a PTEN-regulated signaling pathway and reveals PDHK1 as a potential target in PTEN-deficient cancers. SIGNIFICANCE The tumor suppressor PTEN is widely inactivated in cancers and tumor syndromes. PTEN antagonizes PI3K/AKT signaling via its lipid phosphatase activity. The modest success of PI3K/AKT inhibition in PTEN-deficient cancer patients provides rationale for identifying other vulnerabilities in PTEN-deficient cancers to improve clinical outcomes. We show that PTEN-deficient cells are uniquely sensitive to PDHK1 inhibition. PTEN and PDHK1 co-suppression reduced colony formation and induced cell death in vitro and tumor regression in vivo . PDHK1 levels were high in PTEN-deficient patient tumors and associated with inferior patient survival, establishing clinical relevance. Our study identifies a PTEN-regulated signaling pathway linking the PTEN protein phosphatase to the metabolic regulator PDHK1 and provides a mechanistic basis for PDHK1 targeting in PTEN-deficient cancers.
Tests for the fractional active-site model in Flp site-specific recombination. Assembly of a functional recombination complex in half-site and full-site strand transfer (1993)

The Arg191-His305-Arg308 (the RHR triad) and Tyr343 of Flp site-specific recombinase correspond to the invariant tetrad residues of the integrase family of proteins. Flp mutants altered at these positions are blocked at the strand cleavage or the strand exchange step of recombination. Hybrid half-site-recombinase complexes formed by step-arrest mutants of Flp have revealed that an Flp monomer occupying a half-site does not cleave that half-site but rather cleaves a half-site occupied by a second Flp monomer. This trans-DNA cleavage is neatly accommodated by a model in which an Flp active site is assembled by contribution of amino acid residues from at least two protein monomers. Using a combination of wild type Flp, single, double, and triple step-arrest Flp mutants, critical predictions of the fractional active-site model have been verified. First, a wild type monomer paired with an RHR triad-Tyr343 double mutant is a catalytically inactive combination. Second, each pairwise combination of a single, double, or triple RHR mutant with Flp (Y343F) yields approximately equivalent levels of catalytic complementation. Half-site to half-site and half-site to full-site crosses suggest that execution of a strand transfer event within a half-site and between a half-site and a full site requires dimeric and tetrameric Flp configurations, respectively.
Microscopic theory of gain for an InGaN/AlGaN quantum well laser (1997)

This letter describes a microscopic gain theory for an InGaN/AlGaN quantum well laser. The approach, which is based on the semiconductor Bloch equations, with carrier correlations treated at the level of quantum kinetic theory in the Markovian limit, gives a consistent treatment of plasma and excitonic effects, both of which are important under lasing conditions. Inhomogeneous broadening due to spatial variations in quantum well thickness or composition is taken into account by a statistical average of the homogeneously broadened spectra.
502. The configurations of the isomeric forms of 1: 3-dimethylcyclopentane (1953)

S. F. Birch and R. A. Dean, J. Chem. Soc., 1953, 2477 DOI: 10.1039/JR9530002477
Warm forming of aluminium alloys: an overview and future directions (2004)

Aluminium offers the advantages of a high strength-to-weight ratio and corrosion resistance. However, the low formability of aluminium sheets limits their use in some products with complex shapes, such as automotive body parts. The warm forming process is intended to alleviate this problem by using an elevated forming temperature which is below the level for recrystallisation. This paper will review the existing knowledge of warm forming of aluminium as a way to improve formability. The appropriate constitutive material models as well as experimental work to date will be discussed. Several areas that require further study in order to realise the true potential of warm forming of aluminium will be identified.
Alginate synthesis in Pseudomonas aeruginosa: the role of AlgL (alginate lyase) and AlgX (1996)

Previous studies localized an alginate lyase gene (algL) within the alginate biosynthetic gene cluster at 34 min on the Pseudomonas aeruginosa chromosome. Insertion of a Tn501 polar transposon in a gene (algX) directly upstream of algL in mucoid P. aeruginosa FRD1 inactivated expression of algX, algL, and other downstream genes, including algA. This strain is phenotypically nonmucoid; however, alginate production could be restored by complementation in trans with a plasmid carrying all of the genes inactivated by the insertion, including algL and algX. Alginate production was also recovered when a merodiploid that generated a complete alginate gene cluster on the chromosome was constructed. However, alginate production by merodiploids formed in the algX::Tn501 mutant using an alginate cluster with an algL deletion was not restored to wild-type levels unless algL was provided on a plasmid in trans. In addition, complementation studies of Tn501 mutants using plasmids containing specific deletions in either algL or algX revealed that both genes were required to restore the mucoid phenotype. Escherichia coli strains which expressed algX produced a unique protein of approximately 53 kDa, consistent with the gene product predicted from the DNA sequencing data. These studies demonstrate that AlgX, whose biochemical function remains to be defined, and AlgL, which has alginate lyase activity, are both involved in alginate production by P. aeruginosa.
Dendritic Oxide Growth in Zero-Valent Iron Nanofilms Revealed by Atom Probe Tomography (2018)

Atom probe tomography (APT) analysis of chemically pure nanofilms of zero-valent iron (Fe(0), or ZVI) and their thermal oxide nano-overlayers reveals the presence of dendritic iron oxide features that extend from the oxide nano-overlayer surface into the ZVI bulk. The dendrites are observed by APT to be in the 5 nm x 10 nm size range and form quickly under natural atmospheric conditions. Their growth into the ZVI lalyer is, within the limit of our three-month long study, self-limiting (i.e. their initial growth appears to quickly discontinue). The atomistic views presented here shed first light on the atmospheric corrosion process of Fe(0)-bearing engineered nanostructures and their surfaces in the limit of low bulk impurities. Possible roles of the newly identified oxidized iron dendrites are also discussed in the context of passivation processes limiting technological applications of Fe(0).
Coral reef algal turfs: master producers in nutrient poor seas (1987)

Coral reef algal turfs were grown on submerged plastic screens near reef communities, in the trade wind belt of the southeastern Bahamas. Using harvest production methods, in a variety of depths and locations, mean harvest production rates up to 14 g (dry) m−2 d−1 were obtained at ambient nutrient levels below 0.2 μm for nitrogen as NO2 + NO3. A wide range in production rate was found; this resulted from light rather than nutrient differences. Peak harvest production occurs at light intensities of 1400–1700 μmol m−2 s−1, far above levels previously cited for most algae, including phytoplankton.A basic premise of biological oceanography has been that primary production in the sea, even under optimal conditions of solar radiation, is nutrient-limited and develops considerably lower levels than most plant production on land–both natural and under cultivation. However, the effects of nutrient limitation can be overcome by trade wind-driven currents, which provide an infinite nutrient source and nitrogen fixation by blue-green algae within the community. Wave surge maximizing of metabolite exchange, and perhaps light-flashing effects as well, enhance production potential. Actual harvest production demonstrated that, under these conditions, net and gross primary production can be very large even in the most nutrient-poor waters.
Book on Sakharov raises issues (2017)

We are disappointed that Physics Today would publish an alleged book review (July 2016, page 61) by Alexei Kojevnikov of Andrei Sakharov: The Conscience of Humanity, which was edited by us and includes papers presented at a conference in December 2014. Kojevnikov’s piece was not a review of the book at all, but an exposition of his own flawed personal interpretation of Sakharov’s life and views. Worse, the reviewer slurs the book’s essays by maintaining, falsely, that they use Sakharov’s views on human rights to justify recent wars. Kojevnikov misrepresents both the essays and Sakharov’s own ideas and the ways in which they continually evolved. He did not provide a single citation from the essays to support his description. The editors of Physics Today were remiss in trusting—but not verifying—his outrageous claims.An accurate statement of Sakharov’s views can be gained by reading his own writing. One example is his “Open Letter to Anatoly Aleksandrov, President of the USSR Academy of Sciences,” which reads in part, I am convinced that the prevention of thermonuclear war is our most important problem and must take absolute priority over all other issues. The resolution of that problem involves politics, economics, the creation of international trust among open societies, the unconditional observance of fundamental civil and political rights, and disarmament. Disarmament, especially nuclear disarmament, is mankind’s most important task.11. A. Babyonyshev, ed., On Sakharov, G. Daniels, trans., Vintage Books (1982), p. 213. [Editor’s note: With sadness we inform our readers that Sidney Drell died on 21 December 2016.]ReferencesSection:ChooseTop of pageReferences <<1. A. Babyonyshev, ed., On Sakharov, G. Daniels, trans., Vintage Books (1982), p. 213. Google Scholar© 2017 American Institute of Physics.
Characterization of Nonbiological Antimicrobial Polymers in Aqueous Solution and at Water−Lipid Interfaces from All-Atom Molecular Dynamics (2006)

We have applied molecular dynamics to investigate the structural properties and activity of recently synthesized amphiphilic polymethacrylate derivatives, designed to mimic the antimicrobial activity of natural peptides. The composition, molecular weight, and hydrophobicity (ratio of hydrophobic and cationic units) of these short copolymers can be modulated to achieve structural diversity, which is crucial in controlling the antimicrobial activity. We have carried out all-atom molecular dynamics to systematically investigate the conformations adopted by these copolymers in water and at the water-lipid interface as a function of sequence and the chemical nature of the monomers. For two sequences, we observe partial insertion into the bilayer. Formation of strong interactions between the lipid headgroups and the amine groups of the polymers assists in the initial association with the lipids. However, the primary driving force for the observed partial insertion appears to be the hydrophobic effect. Our results indicate sensitive dependence of the overall shape on the sequence, suggesting that experimentally observed changes in activity can be correlated with particular sequences, providing an avenue for rational design.
Evaluation of Fiber Clustering Methods for Diffusion Tensor Imaging (2006)

Fiber tracking is a standard approach for the visualization of the results of diffusion tensor imaging (DTI). If fibers are reconstructed and visualized individually through the complete white matter, the display gets easily cluttered making it difficult to get insight in the data. Various clustering techniques have been proposed to automatically obtain bundles that should represent anatomical structures, but it is unclear which clustering methods and parameter settings give the best results. We propose a framework to validate clustering methods for white-matter fibers. Clusters are compared with a manual classification which is used as a ground truth. For the quantitative evaluation of the methods, we developed a new measure to assess the difference between the ground truth and the clusterings. The measure was validated and calibrated by presenting different clusterings to physicians and asking them for their judgement. We found that the values of our new measure for different clusterings match well with the opinions of physicians. Using this framework, we have evaluated different clustering algorithms, including shared nearest neighbor clustering, which has not been used before for this purpose. We found that the use of hierarchical clustering using single-link and a fiber similarity measure based on the mean distance between fibers gave the best results.
Optimum inverse filters which shorten the spacing of velocity logs (1962)

Abstract A long-spacing velocity log contains almost the same information as an ideal short-spacing log, but in a distorted form with added noise. The distortion can be thought of as a moving average or smoothing filter. Its inverse, called a "sharpening" filter by astronomers, amplifies noise. If the inverse is to be useful, it must be designed with a balance between errors due to noise amplification and those due to incomplete sharpening. The Wiener optimum filter theory gives a prescription for achieving this balance. The result is called an optimum inverse filter. We have calculated finite-memory optimum inverse filters using the IBM 704. We have applied them to actual data, digitized in the field, to produce synthetic short-spacing velocity logs. These we have compared with their field counterparts. The synthetic logs have less calibration error and are free from noise spikes. The general agreement is good.