gebhart/patrepeval huggingface dataset:
Estimation of the size distribution of triaxial ellipsoidal particles from the distribution of linear intercepts (1970)

SUMMARY Methods for estimating particle‐size distributions in metallurgical structures from the distribution of linear intercepts observed on a metallographic section are extended to include systems in which the particle shape may be modelled by triaxial ellipsoids. Procedures are developed for oriented, partially oriented and randomly oriented systems of particles. Methods for determining the axial ratios appropriate to a given system are outlined for these cases.
Variations in Performance and Scalability When Migrating n-Tier Applications to Different Clouds (2011)

The increasing popularity of computing clouds continues to drive both industry and research to provide answers to a large variety of new and challenging questions. We aim to answer some of these questions by evaluating performance and scalability when an n-tier application is migrated from a traditional datacenter environment to an IaaS cloud. We used a representative n-tier macro-benchmark (RUBBoS) and compared its performance and scalability in three different test beds: Amazon EC2, Open Cirrus (an open scientific research cloud), and Emulab (academic research test bed). Interestingly, we found that the best-performing configuration in Emulab can become the worst-performing configuration in EC2. Subsequently, we identified the bottleneck components, high context switch overhead and network driver processing overhead, to be at the system level. These overhead problems were confirmed at a finer granularity through micro-benchmark experiments that measure component performance directly. We describe concrete alternative approaches as practical solutions for resolving these problems.
Evaluation of graphitized glass capillary columns (1978)

Abstract The performance of graphitized glass capillary columns obtained by precoating the inner glass walls with graphitized carbon black has been evaluated. It has been shown that according to the amount of stationary phase coated such columns can operate in gas–liquid‐solid chromatography and in gas–liquid chromatography so that tailor‐made columns for specific separations can be prepared. The versatility of these columns is shown in the separation of various mixtures (terpenes, pesticides, isomeric species and others) of analytical importance.
An Enrichment Strategy Yields Seven Novel Single Nucleotide Polymorphisms Associated With Mortality and Altered Th17 Responses Following Blunt Trauma (2017)

Trauma is the leading cause of death worldwide for individuals under the age of 55. Interpatient genomic differences, in the form of candidate single-nucleotide polymorphisms (SNPs), have been associated previously with adverse outcomes after trauma. However, the utility of these SNPs to predict outcomes based on a meaningful endpoint such as survival is as yet undefined. We hypothesized that specific SNP haplotypes could segregate trauma survivors from non-survivors. Genomic DNA samples were obtained from 453 blunt trauma patients, for whom complete daily clinical and biomarker data were available for 397. Of these, 13 patients were non-survivors and the remaining 384 were survivors. All 397 DNA samples were amplified, fragmented, and examined for 551,839 SNPs using the Illumina Infinium CoreExome-24 v1.1 BeadChip (Illumina). To enrich for likely important SNPs, we initially compared SNPs of the 13 non-survivors versus 13 matched survivors, who were matched algorithmically for injury severity score (ISS), age, and gender ratio. This initial enrichment yielded 126 SNPs; a further comparison to the haplotypes of the remaining 371 survivors yielded a final total of 7 SNPs that distinguished survivors from non-survivors. Furthermore, severely injured survivors with the same seven SNPs as non-survivor exhibited distinct inflammatory responses from similarly injured survivors without those SNPs, and specifically had evidence of altered Th17 cell phenotypes based on computational modeling. These studies suggest an interaction among genetic polymorphism, injury severity, and initial inflammatory responses in driving trauma outcomes.
Measurement Techniques for Multimode Waveguides (1955)

This paper surveys some of the techniques that have been worked out for multimode waveguide measurements. Equipment has been developed for measuring one mode at a time by taking advantage of the differences between the modes. Illustrations of its use are given.
Transformer-Coupled Power Amplifier Stability and Power Back-Off Analysis (2008)

We present a mathematical analysis of the common-mode instability and power back-off feature of a transformer-coupled Class-AB differential power amplifier (PA). The efficient impedance matching of the transformer combiner and efficiency improvement at power back-off, a major benefit of this structure, are illustrated. In addition, an analytical model is derived to predict the common-mode oscillations in PA. The analytical results, based on a simple hand-calculation model for the transistor, show good agreement with simulation results using complete 90-nm models. Two methods to suppress the common-mode oscillations are investigated and analyzed in detail.
Recombinant Expression and Phenotypic Screening of a Bioactive Cyclotide Against α‐Synuclein‐Induced Cytotoxicity in Baker′s Yeast (2015)

Abstract We report for the first time the recombinant expression of fully folded bioactive cyclotides inside live yeast cells by using intracellular protein trans‐splicing in combination with a highly efficient split‐intein. This approach was successfully used to produce the naturally occurring cyclotide MCoTI‐I and the engineered bioactive cyclotide MCoCP4. Cyclotide MCoCP4 was shown to reduce the toxicity of human α‐synuclein in live yeast cells. Cyclotide MCoCP4 was selected by phenotypic screening from cells transformed with a mixture of plasmids encoding MCoCP4 and inactive cyclotide MCoTI‐I in a ratio of 1:5×10 4 . This demonstrates the potential for using yeast to perform phenotypic screening of genetically encoded cyclotide‐based libraries in eukaryotic cells.
Design of a decision tree with action (2002)

Describes an algorithm for the design of a decision tree applied to the identification of objects where the action is built-in. The authors' main interest is the design of a decision tree with action applied to the sensorial integration problem, for instance a tactile application or vision system with the ability to change the light conditions, but it can be generalized to other applications. The knowledge representation is supported by a graph where each node represents a world state and where the arcs represent the actions of the world. Each world state is composed by a set of knowledge states. The intermediate and terminal knowledge states are in a world state. The intermediate states are defined considering that the knowledge of the possible classification object is incomplete. The terminal state means that the classification is done. Associated to each knowledge state there is the definition of a set of features its values and a training set. The training set is a table with feature values in which classification is known.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Reaction of Aromatic Heterocyclic Nitro Compounds with Potassium Cyanide. III. Some Nitroquinoline 1-Oxides (1971)

The reaction of 3-nitroquinoline 1-oxide with potassium cyanide in methanol was carried out producing 3-methoxycinchoninonitrile 1-oxide (I) and 3-methoxy-1H-pyrazolo [4, 3-b] quinoline-9-carboxamide (II). 5-Nitroquinoline 1-oxide gave 5-methoxyquinoline-6-carbonitrile 1-oxide (XIII) and 7-aminoisoxazolo [3, 4-f] quinoline 1-oxide (XIV), whereas 6-nitroquinoline 1-oxide gave methyl 5-cyano-6-methoxyquinaldimidate 1-oxide (VI), 5-cyano-6-methoxyquinaldamide 1-oxide (VII), and 1-hydroxy-6-nitrocarbostyril (VIII) by the similar type reactions. 4-Nitroquinoline 1-oxide produced 4-methoxyquinoline 1-oxide.
Type I pyridoxal 5′-phosphate dependent enzymatic domains embedded within multimodular nonribosomal peptide synthetase and polyketide synthase assembly lines (2013)

Abstract Background Pyridoxal 5′-phosphate (PLP)-dependent enzymes of fold type I, the most studied structural class of the PLP-dependent enzyme superfamily, are known to exist as stand-alone homodimers or homotetramers. These enzymes have been found also embedded in multimodular and multidomain assembly lines involved in the biosynthesis of polyketides (PKS) and nonribosomal peptides (NRPS). The aim of this work is to provide a proteome-wide view of the distribution and characteristics of type I domains covalently integrated in these assemblies in prokaryotes. Results An ad-hoc Hidden Markov profile was calculated using a sequence alignment derived from a multiple structural superposition of distantly related PLP-enzymes of fold type I. The profile was utilized to scan the sequence databank and to collect the proteins containing at least one type I domain linked to a component of an assembly line in bacterial genomes. The domains adjacent to a carrier protein were further investigated. Phylogenetic analysis suggested the presence of four PLP-dependent families: Aminotran_3, Beta_elim_lyase and Pyridoxal_deC, occurring mainly within mixed NRPS/PKS clusters, and Aminotran_1_2 found mainly in PKS clusters. Sequence similarity to the reference PLP enzymes with solved structures ranged from 24 to 42% identity. Homology models were built for each representative type I domain and molecular docking simulations with putative substrates were carried out. Prediction of the protein-protein interaction sites evidenced that the surface regions of the type I domains embedded within multienzyme assemblies were different from those of the self-standing enzymes; these structural features appear to be required for productive interactions with the adjacent domains in a multidomain context. Conclusions This work provides a systematic view of the occurrence of type I domain within NRPS and PKS assembly lines and it predicts their structural characteristics using computational methods. Comparison with the corresponding stand-alone enzymes highlighted the common and different traits related to various aspects of their structure-function relationship. Therefore, the results of this work, on one hand contribute to the understanding of the functional and structural diversity of the PLP-dependent type I enzymes and, on the other, pave the way to further studies aimed at their applications in combinatorial biosynthesis.
Sonic Boom Reduction Through the Use of Non-Axisymmetric Configuration Shaping (2003)

Traditional sonic boom minimization efforts have followed the approach of designing a Whitham “Ffunction” which produced the desired boom signature, followed by development of an airplane configuration representing the same equivalent distribution, and thus boom signature. With the computational resources available today, it is possible to reevaluate the solution approach of many aspects of the boom minimization problem. The near field solution about complex and highly non-axisymmetric configurations may be routinely solved in great detail without the slender body, weak shock, small disturbance assumptions and limitations necessary in the earlier mathematical approaches. Investigations of non-axisymmetric configurations have shown promise when the majority of the disturbance in the supersonic flow field is directed upward, resulting in reduced pressure disturbances, and thus reduced sonic boom below the configuration. CFD analysis and wind tunnel test results on axisymmetric and non-axisymmetric equivalent area distributions have shown good experiment/theory agreement and show that the concept has merit for reducing boom and should be developed further for more representative aircraft configurations.
Competitive regulation of CaT-like-mediated Ca <sup>2+</sup> entry by protein kinase C and calmodulin (2001)

A finely tuned Ca(2+) signaling system is essential for cells to transduce extracellular stimuli, to regulate growth, and to differentiate. We have recently cloned CaT-like (CaT-L), a highly selective Ca(2+) channel closely related to the epithelial calcium channels (ECaC) and the calcium transport protein CaT1. CaT-L is expressed in selected exocrine tissues, and its expression also strikingly correlates with the malignancy of prostate cancer. The expression pattern and selective Ca(2+) permeation properties suggest an important function in Ca(2+) uptake and a role in tumor progression, but not much is known about the regulation of this subfamily of ion channels. We now demonstrate a biochemical and functional mechanism by which cells can control CaT-L activity. CaT-L is regulated by means of a unique calmodulin binding site, which, at the same time, is a target for protein kinase C-dependent phosphorylation. We show that Ca(2+)-dependent calmodulin binding to CaT-L, which facilitates channel inactivation, can be counteracted by protein kinase C-mediated phosphorylation of the calmodulin binding site.
Antibody Dependent Enhancement Due to Original Antigenic Sin and the Development of SARS (2020)

Human coronavirus (HCoV) is one of the most common causes of respiratory tract infections throughout the world. Two phenomena observed so far in the development of the SARS-CoV-2 pandemic deserve further attention. First, the relative absence of clinical signs of infections in children, second, the early appearance of IgG in certain patients. From the point of view of immune system physiology, such an early rise of specific IgG is expected in secondary immune responses when memory to a cross-reactive antigen is present, usually from an earlier infection with a coronavirus. It is actually typical for the immune system to respond, to what it already knows, a phenomenon that has been observed in many infections with closely related viruses and has been termed ‘original antigenic sin’. The question then arises whether such cross-reactive antibodies are protective or not against the new virus. The worst scenario would be when such cross-reactive memory antibodies to related coronaviruses would not only be non-protective but even enhance infection and the clinical course. Such a phenomenon of antibody dependent enhancement (ADE) has already been described in several viral infections. Thus, the development of IgG against SARS-CoV-2 in the course of COVID-19 might not be a simple sign of viral clearance and developing protection against the virus. On the contrary, due to cross-reaction to related coronavirus strains from earlier infections, in certain patients IgG might enhance clinical progression due to ADE. The patient’s viral history of coronavirus infection might be crucial to the development of the current infection with SARS-CoV-2. Furthermore, it poses a note of caution when treating COVID-19 patients with convalescent sera.
Design and implementation of a configuration management system (2002)

The author has designed and implemented a configuration management system, which is based on the CMISE service. It provides several functions to configuration management users such as getting information about network resources, re-configuration of a managed network and so on. The author has introduced the network management domain concept and the object-oriented approach for defining managed objects. The service primitives supported by the configuration management system have been defined and the protocol between configuration managers for multi-domain management has been implemented. The author implemented CMISE service, simulator and management information base (MIB) based on the OSI network management framework. Fault and performance management functions are being implemented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Umbilical Cord Mesenchymal Stem Cells: The New Gold Standard for Mesenchymal Stem Cell-Based Therapies? (2014)

Due to their self-renewal capacity, multilineage differentiation potential, paracrine effects, and immunosuppressive properties, mesenchymal stromal cells (MSCs) are an attractive and promising tool for regenerative medicine. MSCs can be isolated from various tissues but despite their common immunophenotypic characteristics and functional properties, source-dependent differences in MSCs properties have recently emerged and lead to different clinical applications. Considered for a long time as a medical waste, umbilical cord appears these days as a promising source of MSCs. Several reports have shown that umbilical cord-derived MSCs are more primitive, proliferative, and immunosuppressive than their adult counterparts. In this review, we aim at synthesizing the differences between umbilical cord MSCs and MSCs from other sources (bone marrow, adipose tissue, periodontal ligament, dental pulp,…) with regard to their proliferation capacity, proteic and transcriptomic profiles, and their secretome involved in their regenerative, homing, and immunomodulatory capacities. Although umbilical cord MSCs are until now not particularly used as an MSC source in clinical practice, accumulating evidence shows that they may have a therapeutic advantage to treat several diseases, especially autoimmune and neurodegenerative diseases.
Measuring bacterial adaptation dynamics at the single-cell level using a microfluidic chemostat and time-lapse fluorescence microscopy (2014)

We monitored the dynamics of cell dimensions and reporter GFP expression in individual E. coli cells growing in a microfluidic chemostat using time-lapse fluorescence microscopy. This combination of techniques allows us to study the dynamical responses of single bacterial cells to nutritional shift-down or shift-up for longer times and with more precision over the chemical environment than similar experiments performed on conventional agar pads. We observed two E. coli strains containing different promoter-reporter gene constructs and measured how both their cell dimensions and the GFP expression change after nutritional upshift and downshift. As expected, both strains have similar adaptation dynamics for cell size rearrangement. However, the strain with a ribosomal RNA promoter dependent reporter has a faster GFP production rate than the strain with a constitutive promoter reporter. As a result, the mean GFP concentration in the former strain changes rapidly with the nutritional shift, while that in the latter strain remains relatively stable. These findings characterize the present microfluidic chemostat as a versatile platform for measuring single-cell bacterial dynamics and physiological transitions.
A vectorization technique of hashing and its application to several sorting algorithms (2002)

A vectorized algorithm for entering data into a hash table is presented. A program that enters multiple data could not be executed on vector processors by conventional vectorization techniques because of data dependences. The proposed method enables execution of multiple data entry by conventional vector processors and improves the performance by a factor of 12.7, compared with the normal sequential method, when 4099 pieces of data are entered on the Hitachi S-810. This method is applied to address calculation sorting and the distribution counting sort, whose main part was unvectorizable by previous techniques. It improves performance by a factor of 12.8 when n=2/sup 14/ on the S-810.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Estimation of pharmacokinetic parameters of lithium from saliva and urine (1974)

The salivary and urinary excretion of lithium was studied in three healthy male sub;ects after oral administration of two or three different doses. In all individuals the concentration of lithium in salivary fluid was found to be 2.2 to 3.3 times as high as the concentration in plasma. In each sub;ect the saliva:plasma concentration ratio remained constant over more than a 100 fold concentration range for at least 3 months. This ratio was not markedly affected by about tenfold changes in saliva flow rate. Thus, pharmacokinetic parameters obtained from salivary excretion data are in agreement with those obtained from plasma concentration and urinary excretion rate data, and renal clearance of lithium can be estimated from salivary excretion data. Diurnal rhythms in the urinary excretion rate of lithium were observed. Thus, once the saliva:plasma concentration ratio is established (by taking only a few blood samples), the measurement of saliva concentrations should prOVide all pharmacokinetic information necessary for rational dosage regimens.
Ion-exchanged glass waveguide technology: a review (2011)

We review the history and current status of ion exchanged glass waveguide technology. The background of ion exchange in glass and key developments in the first years of research are briefly described. An overview of fabrication, characterization and modeling of waveguides is given and the most important waveguide devices and their applications are discussed. Ion exchanged waveguide technology has served as an available platform for studies of general waveguide properties, integrated optics structures and devices, as well as applications. It is also a commercial fabrication technology for both passive and active wave-guide components.
Electrical Stimulation of the Anterior Nucleus of the Thalamus for the Treatment of Intractable Epilepsy (2004)

Electrical stimulation of the ANT appears to be well tolerated. Preliminary evidence suggests clinical improvement in seizure control in this small group of intractable patients. Further controlled study of deep brain stimulation of the anterior nucleus is warranted.
Stereochemical course of the reaction of 2-haloethyl isothiocyanates with nucleophiles. Stereospecific route to 4,5-disubstituted Δ2-thiazolines and thiazolidine-2-thiones (1981)

Diastereoisomeric 1-chloro-1-phenyl-2-isothiocyanatopropanes have been prepared. They reacted stereospecifically with CH 3 Ona, diethylamine, aniline and NaSH to give pure cis or trans -4,5-disubstituted Δ 2 -thiazolines and thiazolidine-2-thiones whose configuration was determined using the nuclear Overhauser effect. The preponderant conformation of diastereoisomeric 1-chloro-1-phenyl-2-isothiocyanatopropanes was estimated on the basis of coupling constants of vicinal protons.
The Promise of New Technologies to Reduce, Refine, or Replace Animal Use while Reducing Risks of Drug Induced Liver Injury in Pharmaceutical Development (2016)

Drug induced liver injury (DILI) has contributed more to marketed pharmaceutical withdrawals and clinical development failures than any other human organ toxicity. DILI seen in animal studies also frequently leads to the discontinuation of promising drug candidates very early in the pipeline. This manuscript reviews and critically assesses the current regulatory expectations; the current drug development approaches, strategies, and gaps; and the numerous exciting opportunities becoming available to address these gaps through technological advances. Emerging integrated pharmaceutical development strategies, while far from uniform, have generally evolved to currently inform early DILI risk potential using supplemental assays for reactive metabolite formation, mitochondrial toxicity, inhibition of bile salt transport, and cellular imaging endpoints including cytotoxicity. Despite these approaches and robust animal testing, significant gaps in addressing human DILI remain. Increasingly sophisticated in vitro humanized test systems, new animal models, emerging computational models, and novel translational biomarkers are being introduced to improve our ability to more accurately predict DILI. Expectations are high for a future state with more predictive tools and problem solving strategies that will improve pharmaceutical discovery and development in relation to understanding human DILI risk potential and make it less dependent on animal studies for successfully developing safer drug candidates.