gebhart/patrepeval huggingface dataset:
Similar and dissimilar aspects of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mrow><mml:mi mathvariant="normal">III</mml:mi><mml:mtext>−</mml:mtext><mml:mi mathvariant="normal">V</mml:mi></mml:mrow></mml:mrow></mml:math>semiconductors containing<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mrow><mml:mi mathvariant="normal">Bi</mml:mi></mml:mrow></mml:mrow></mml:math>versus<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mi mathvariant="normal">N</mml:mi></mml:mrow></mml:math> (2005)

We show through band structure calculations that $\mathrm{III}\text{\ensuremath{-}}\mathrm{V}\text{\ensuremath{-}}\mathrm{Bi}$ alloys, emerging as a new class of semiconductor materials, differ nontrivially from their counterparts $\mathrm{III}\text{\ensuremath{-}}\mathrm{V}\text{\ensuremath{-}}\mathrm{N}$ alloys which have been intensively studied in the past decade. For a prototype system, ${\mathrm{GaAs}}_{1\ensuremath{-}x}{\mathrm{Bi}}_{x}$ with a small amount of $\mathrm{Bi}$, a large band gap reduction, due to the shift of the perturbed host band edges, resembles the effect of $\mathrm{N}$ incorporation in $\mathrm{GaAs}$, but ${\mathrm{GaAs}}_{1\text{\ensuremath{-}}x}{\mathrm{Bi}}_{x}$ exhibits a number of striking differences from ${\mathrm{GaAs}}_{1\ensuremath{-}x}{\mathrm{N}}_{x}$: (1) $\mathrm{Bi}$ generates a resonant impurity state in the valence band as a strongly perturbed host state, while $\mathrm{N}$ produces a resonant impurity state additional to the host states in the conduction band; (2) Under pressure, the $\mathrm{Bi}$ impurity state sinks further into the valence band, while the $\mathrm{N}$ impurity state emerges as a bound state; (3) the spin-orbit splitting increases superlinearly with increasing $\mathrm{Bi}$ amount, while it decreases sublinearly with increasing $\mathrm{N}$ amount. Qualitative conclusions for $\mathrm{III}\text{\ensuremath{-}}\mathrm{V}\text{\ensuremath{-}}\mathrm{Bi}$ are generally applicable for other isoelectronic donors in semiconductors.
A highly automated heavy-atom search procedure for macromolecular structures (1999)

A new highly automated heavy-atom search procedure combines a fast Fourier transform translation function, Patterson superposition functions and Patterson correlation refinement. The search procedure can be applied to various native and difference Patterson maps and their statistically weighted averages. The procedure was tested with diffraction data for several crystal structures with up to 30 heavy-atom sites in the asymmetric unit and with minimum Bragg spacings ranging from 3 to 4 A. In all cases, the correct sites were found with modest computing time.
Accurate Imputation of Rare and Common Variants in a Founder Population From a Small Number of Sequenced Individuals (2012)

Advances in DNA sequencing technologies have greatly facilitated the discovery of rare genetic variants in the human genome, many of which may contribute to common disease risk. However, evaluating their individual or even collective effects on disease risk requires very large sample sizes, which involves study designs that are often prohibitively expensive. We present an alternative approach for determining genotypes in large numbers of individuals for all variants discovered in the sequence of relatively few individuals. Specifically, we developed a new imputation algorithm that utilizes whole-exome sequencing data from 25 members of the South Dakota Hutterite population, and genome-wide single nucleotide polymorphism (SNP) genotypes from >1,400 individuals from the same founder population. The algorithm relies on identity-by-descent sharing of phased haplotypes, a different strategy than the linkage disequilibrium methods found in most imputation algorithms. We imputed genotypes discovered in the sequence data to on average ∼77% of chromosomes among the 1,400 individuals. Median R(2) between imputed and directly genotyped data was >0.99. As expected, many variants that are vanishingly rare in European populations have risen to larger frequencies in the founder population and would be amenable to single-SNP analyses.
[Peritoneal dialysis, the method of treatment for end-stage renal insufficiency: development of indications during the past 10 years in relation to the initial renal disease and extra-renal pathology]. (1989)

A decade after its first introduction, the advantages and drawbacks of continuous ambulatory peritoneal dialysis over hemodialysis remain controversial. This present paper is a review of the literature, focused on the indications of this dialysis modality in different circumstances: extra-renal pathology, systemic diseases (lupus erythematosus--diffuse scleroderma--plasma cell disorders--amyloidosis--HIV infected patients) and complications related to hemodialysis.
Enhanced Vulnerability to NMDA Toxicity in Sublethal Traumatic Neuronal Injury <i>In Vitro</i> (2003)

Traumatic brain injury causes neuronal disruption and triggers secondary events leading to additional neuronal death. To study injuries triggered by secondary events, we exposed cultured cortical neurons to sublethal mechanical stretch, thus eliminating confounding death from primary trauma. Sublethally stretched neurons maintained cell membrane integrity, viability, and electrophysiological function. However, stretching induced in the cells a heightened vulnerability to subsequent challenges with L-glutamate or NMDA. This heightened vulnerability was specifically mediated by NMDA receptors (NMDARs), as stretched neurons did not become more vulnerable to either kainate toxicity or to that induced by the Ca(2+) ionophore A23187. Stretch-enhanced vulnerability to NMDA occurred independently of endogenous glutamate release, but required Ca(2+) and Na(+) influx through NMDARs. Stretch did not affect the electrophysiological properties of NMDARs nor excitatory synaptic activity, indicating that specificity of enhanced vulnerability to NMDA involves postsynaptic mechanisms downstream from NMDARs. To test whether this specificity requires physical interactions between NMDARs and cytoskeletal elements, we perturbed actin filaments and microtubules, both of which are linked to NMDARs. This had no effect on the stretch-induced vulnerability to NMDA, suggesting that sublethal stretch does not affect cell survival through the cytoskeleton. Our data illustrate that sublethal in vitro stretch injury triggers distinct signaling pathways that lead to secondary injury, rather than causing a generalized increase in vulnerability to secondary insults.
Analysis of a 3D antenna array by the synthetic-function expansion method (2004)

Abstract– Reducing the complexity of the MoM analysis of antenna andscattering problems is a challenging issue for computational electromagnetics:the Synthetic Function Expansion (SFX) method is one of the possible ways toaddress this issue. SFX acts by dividing the overall structure into portions,recognizing that the degrees of freedom of the field coupling among thesolutions on these portions are limited, and building basis functions that exploit this property. This communication presents an extension of the method to a 3D structure, a 12 elements helix array used in tracking applications. I. I NTRODUCTION A number of techniques like the Method of Moments (MoM), FDTD, GTD, PO, etc., or their combination, have been presented in the past years for the analysis oflarge and/or complex antennas. One of them, the Integral Equation (IE) approach iswidely used for the solution of these problems, through the Method of Moment (IE-MoM) discretization scheme, and/or the Generalized Admittance Matrix method(GAM).However, standard techniques are severely limited by the matrix size andcondition number involved in theproblems of interest.In these problems, thestructure of the solution can exhibit very different scales of variation: for example,local interactions in a geometry, like sub-wavelength details, edges anddiscontinuities, generate small-scale details of high spatial frequency, while distantinteractions as well as resonant lengths are responsible for the low-frequency, slowspatial variations. Consequently, one is typically forced to choose mesh cells of size comparable to the smallest foreseen scale of the solution, i.e. with the highestpossible spatial resolution, or likewise if waveguide modes are used as expansionfunctions.This leads to a large number of unknowns, densely populated MoMmatrices with a poor condition number, and renders the direct approach of largeproblems numerically intractable.This work belongs to a class of full-wave methods that end up in (drastically)reducing the actual size of the final Method-of-Moment (MoM) algebraic problem
Developmental biology of the pancreas. (2001)

All pancreatic cell types (endocrine, exocrine, and ductal) are derived from the same endodermal dorsal and ventral anlage, which grow together to form the definitive pancreas. Golosow and Grobstein were pioneers in the field of pancreatic developmental research, as were Wessells and Cohen, who already in the 1960s performed classic embryological experiments describing the morphogenesis of the pancreas and the epithelio-mesenchymal interactions that are instrumental for proper pancreas development. Recent findings suggest that follistatin and fibroblast growth factors represent some of these key mesenchymal factors that actively promote at least pancreatic exocrine development. The true endodermal origin of the pancreatic endocrine cells became evident by experiments performed by the groups of LeDouarin and Rutter in the 1970s. The newly acquired insights regarding the specification of pancreatic endocrine cells as controlled by the notch signaling pathway (i.e., similar to the mechanisms by which neurons are specified during neurogenesis) have provided a novel understanding of the long acknowledged similarities between neurons and the pancreatic endocrine cells. Last, the identification of a number of distinct transcription factors operating at various levels of pancreatic development and in different cell types has provided useful information both on pancreas development and on various pancreatic disorders such as diabetes. Interestingly, four of the hitherto defined five different maturity-onset diabetes of the young (MODY) genes correspond to transcription factors, and, in addition, several transcription factors have also been linked to type 2 diabetes.
Type I Interferon: Potential Therapeutic Target for Psoriasis? (2008)

Up-regulation of TNF-alpha and elevation of the TNF-alpha-inducible gene signature in lesional skin underscore the importance of this cytokine in psoriasis; these data describe a molecular basis for the therapeutic activity of anti-TNF-alpha agents. Furthermore, these findings implicate type I IFNs in the pathogenesis of psoriasis. Consistent and significant up-regulation of type I IFNs and their associated gene signatures in psoriatic skin suggest that type I IFNs may be potential therapeutic targets in psoriasis treatment.
Heart rate variability estimation and data visualisation for use in stress level determination in neuro-intensive care patients (2009)

A lot of research is being made on extracting useful information from biomedical measurements, and signal processing has been found to be a powerful diagnostics tool.We describe herein our effort to create a usable software implementation of certain analysis methods.As part of an ongoing project intending to study the effects that stress during care time can have on the final outcome of the treatment of neuro-intensive care patients, our tool is intended to provide estimates of the stress level in a patient.The focus is on the development of three main parts: algorithms for extracting estimates of stress levels based on Heart Rate Variability (HRV), means for visualisation of biomedical signals, and finally, an extendible framework for signal processing of this kind.The result is a piece of software where the user is presented with three different running estimates of stress-level.One is a statistical measure of HRV and the other two measure the level of correlation between variations in heart rate and the respiratory cycle.The correlation is determined, in one case using Fast Fourier Transform (FFT), and in the other, by a model-based approach using Kalman filtering.The information can be viewed over great ranges of scale in an easily browsable visualisation interface.At the foundation is our configurable and extendible library for signal analysis over large data sets.It is built on a concept of computation graphs of composable subalgorithms, enabling new processing methods to be built with ease; both by creating new computation graphs, and by implementing new sub-algorithms.We used our program on recorded data from several patients undergoing neuro-intensive care and found that our two correlation-based estimates show similar trends.The estimates show large variation, both from patient to patient, and over time in the same patient.These variations have not yet been satisfactorily linked to any other information about the patient, e.g.medication dosage or general observations.However, for the patients considered, the amount of stress-related information, was rather low and the medical links are hopefully due for further investigation.
Prefractionation, Enrichment, Desalting and Depleting of Low Volume and Low Abundance Proteins and Peptides Using the MF10 (2008)

The success of proteomics relies heavily in the ability to characterize very diverse species of proteins. This diversity stems from a proteins physicochemical properties, its copy number and abundance and its association with other proteins. Prefractionation and simplification of biological samples prior to downstream MS analysis is showing some virtue in obtaining greater depth of protein analysis. The MicroFlow MF10 is a prefractionation device for low volume, low abundance complex samples that can also enrich for very specific species of proteins based on charge and/or size either in native or denaturing format. It has also been used to desalt and deplete samples of contaminating ions or proteins. Although this instrument is only in its infancy in terms of exploring its capabilities, the technology has been used successfully for the fractionation of plasma proteins Wasinger(1), Omenn GS(2), as well as purification of human growth hormone Catzel D(3) antibodies Cheung(4) and IgY Gee(5) and other complex samples.
An International Intercomparison of Argon Triple Point Calibration Facilities, Accommodating Long-stem Thermometers (1990)

Argon triple point calibration facilities have been compared among eight laboratories with one transfer system, employing local long-stem standard platinum resistance thermometers. The apparatus intercompared, included a sealed cell and its associated cryostat. As is evidenced by the results of long-term investigations, previously performed at the INM, cells of the type employed may show a triple-point temperature, which is stable within the reproducibility of the measurements (≃0,1 mK) over a period of about 10 years. At each laboratory the mean difference between the Argon triple-point temperature of the transfer cell (t) and the local cell (i) has been determined, using a standard resistance thermometer previously calibrated at the fixed points, according to the IPTS-68; associated repeatabilities are typically of the order of 0,1 mK. The reproducibility attained by measuring the mean difference in different laboratories, using cells of the same type and origin (INM), amounts to 0,4 mK.
Neonatal Chest Computed Radiography: Image Processing and Optimal Image Display (2007)

Observers preferred brighter images with higher detail contrast and narrow to middle latitude for soft-copy display compared with the typical screen-film hard-copy appearance. Future research on low-dose neonatal chest imaging will be facilitated by an understanding of optimal soft-copy image display.
Selecting Semantically‐Resonant Colors for Data Visualization (2013)

Abstract We introduce an algorithm for automatic selection of semantically‐resonant colors to represent data (e.g., using blue for data about “oceans”, or pink for “love”). Given a set of categorical values and a target color palette, our algorithm matches each data value with a unique color. Values are mapped to colors by collecting representative images, analyzing image color distributions to determine value‐color affinity scores, and choosing an optimal assignment. Our affinity score balances the probability of a color with how well it discriminates among data values. A controlled study shows that expert‐chosen semantically‐resonant colors improve speed on chart reading tasks compared to a standard palette, and that our algorithm selects colors that lead to similar gains. A second study verifies that our algorithm effectively selects colors across a variety of data categories.
Improving load/store queues usage in scientific computing (2004)

Memory disambiguation mechanisms, coupled with load/store queues in out-of-order processors, are crucial to increase instruction level parallelism (ILP), especially for memory-bound scientific codes. Designing ideal memory disambiguation mechanisms is too complex because it would require precise address bits comparators; thus, modern microprocessors implement simplified and imprecise ones that perform only partial address comparisons. In this paper, we study the impact of such simplifications on the sustained performance of some real processors such that Alpha 21264, Power 4 and Itanium 2. Despite all the advanced features of these processors, we demonstrate in this article that memory address disambiguation mechanisms can cause significant performance loss. We demonstrate that, even if data are located in low cache levels and enough ILP exist, the performance degradation can be up to 21 times slower if no care is taken on the order of accessing independent memory addresses. Instead of proposing a hardware solution to improve load/store queues, as done in [G. Chrysos et al., (1998), S. Sethumadhavan et al., (2003), I. Park et al., (2003), A. Yoaz et al., (1999), S. Onder (2002)], we show that a software (compilation) technique is possible. Such solution is based on the classical (and robust) Id/st vectorization. Our experiments highlight the effectiveness of such method on BLAS 1 codes that are representative of vector scientific loops.
Contribution of the C-terminal end of apolipoprotein AI to neutralization of lipopolysaccharide endotoxic effect (2010)

It is well known that high density lipoprotein (HDL) binds bacterial lipopolysaccharide (LPS) and neutralizes its toxicity. The aim of this work was to study changes in the apolipoprotein (apo) AI structure after its interaction with LPS as well as to determine the protein domain involved in that interaction. The presented data indicate that LPS does not lead to major changes in the structure of apoAI, judging from Trp fluorescence spectra. However, analysis of denaturation behavior and binding of ANS show that LPS induces a loosened protein conformation. Further evidence for an apoAI-LPS specific interaction was obtained by incubation of the protein with (125)I-ASD-LPS. The results show that multiple regions of the protein were able to interact with LPS, according to its amphiphatic nature. Finally, the contribution of the purified C-terminal fragment of the protein in the endotoxin neutralization was evaluated in comparison with the effect of apoAI. In both cases, the same decrease in tumor necrosis factor-α released was observed. This result suggests that the C-terminal half of apoAI is the main domain responsible of the neutralization effect of this protein. Our data may provide innovative pharmacological tools in endotoxin neutralization therapies.
The Aryl Hydrocarbon Receptor Nuclear Transporter Is Modulated by the SUMO-1 Conjugation System (2002)

The aryl hydrocarbon receptor nuclear transporter (ARNT) is a member of the basic helix-loop-helix/PAS (Per-ARNT-Sim) family of transcription factors, which are important for cell regulation in response to environmental conditions. ARNT is an indispensable partner of the aryl hydrocarbon receptor (AHR) or hypoxia-inducible factor-1alpha. This protein is also able to form homodimers such as ARNT/ARNT. However, the molecular mechanism that regulates the transcriptional activity of ARNT remains to be elucidated. Here, we report that ARNT is modified by SUMO-1 chiefly at Lys(245) within the PAS domain of this protein, both in vivo and in vitro. Substitution of the target lysine with alanine enhanced the transcriptional potential of ARNT per se. Furthermore, green fluorescent protein-fused ARNT tended to form nuclear foci in approximately 20% of the transfected cells, and the foci partly colocalized with PML nuclear bodies. PML, one of the well known substrates for sumoylation, was found to augment the transcriptional activities of ARNT. ARNT bound AHR or PML, whereas the sumoylated form of ARNT associated with AHR, but not with PML, resulting in a reduced effect of PML on transactivation by ARNT. Our data suggest that the sumoylation of ARNT modulates its transcriptional role through affecting the ability of ARNT to interact with cooperative molecules such as PML. This exemplifies a crucial role of protein sumoylation in modulating protein-protein interactions.
All-copper chip-to-substrate interconnections for flip-chip packages (2010)

Avatrel 8000P's excellent photo-definition properties and mechanical strength make it an ideal polymer collar material. Avatrel 8000P is a high contrast, I-line sensitive mixture that can be developed in traditional aqueous-base developers. The great photolithographical performance of this photopolymer can be partly contributed to the minimal amount of light absorbed by the base norbornene polymer. The processing conditions noted in this work are an optimized version, which have been shown to give superior photolithographical performance. The simple baking procedures make Avatrel 8000P easier to process than SU-8. The ability to develop Avatrel 8000P in aqueous base can reduce chemical waste. As shown by SEM images, high fidelity structures with aspect ratios of 7:1 can be fabricated in thick films with vertical sidewalls. Bonding between two copper surfaces over various gap sizes was achieved by electroless deposition without the addition of surfactants or inhibitors in the bath. The effect of anneal temperature on the electroless bond formed was analyzed. The electroless bond strength increased with anneal temperature. However, the bond strength estimation for samples annealed at 80°C to 120°C is a minimum value due to the failure location of most of the pillars and the resulting area used in the calculation of bond strength. Grain growth from copper recrystallization and removal of small defects improve the bond strength. Large voids at the interface of the two pillars were related to rough starting surfaces for the electroplated pillars.
Molecular cloning and mapping of a human cDNA (SC5DL) encoding a protein homologous to fungal sterol-C5-desaturase (1996)

We have isolated a human cDNA clone homologous to fungal ERG3, a gene encoding sterol C-5 desaturase. The full nucleotide sequence of this human cDNA revealed a 708-bp open reading frame that encodes a 236-amino-acid polypeptide. The gene was expressed in all normal human tissues examined. We determined its location to chromosome 11q23.3 by fluorescence in situ hybridization.
China's new liquidity support facility explained. (2014)

The article discusses the liquidity support facility offered to Chinese firms involved in the offshore debt market. Topics explored include the expected benefits of this facility to investors, the statement issued by Andrew Malcolm of financial services firm Linklater regarding the purpose of the said facility, and the introduction of credit enhancement systems into the debt market. The offshore lending of the Chinese yuan approved by the People's Bank of China is also reported.