gebhart/patrepeval huggingface dataset:
Modeling virtual machine performance (2010)

Data centers are increasingly employing virtualization and consolidation as a means to support a large number of disparate applications running simultaneously on server platforms. However, server platforms are still being designed and evaluated based on performance modeling of a single highly parallel application or a set of homogenous work-loads running simultaneously. Since most future datacenters are expected to employ server virtualization, this paper takes a look at the challenges of modeling virtual machine (VM) performance on a datacenter server. Based on vConsolidate (a server virtualization benchmark) and latest multi-core servers, we show that the VM modeling challenge requires addressing three key problems: (a) modeling the contention of visible resources (cores, memory capacity, I/O devices, etc), (b) modeling the contention of invisible resources (shared microarchitecture resources, shared cache, shared memory bandwidth, etc) and (c) modeling overheads of virtual machine monitor (or hypervisor) implementation. We take a first step to addressing this problem by describing a VM performance modeling approach and performing a detailed case study based on the vConsolidate benchmark. We conclude by outlining outstanding problems for future work.
Understanding 802.11e contention-based prioritization mechanisms and their coexistence with legacy 802.11 stations (2005)

The IEEE 802.11e task group has reached a stable consensus on two basic contention-based priority mechanisms to promote for standardization: usage of different arbitration interframe spaces and usage of different minimum/maximum contention windows. The goal of this article is to provide a thorough understanding of the principles behind their operation. To this purpose, rather than limit our investigation to high-level (e.g. throughput and delay) performance figures, we take a closer look at their detailed operation, also in terms of low-level performance metrics (e.g., the probability of accessing specific channel slots). Our investigation on one hand confirms that AIFS differentiation provides superior and more robust operation than contention window differentiation. On the other hand, it highlights performance issues related to the coexistence between 802.11e contention-based stations with legacy 802.11 stations, and provides guidelines for the 802.11e parameter settings when such a coexistence is the goal.
An LRE (leucine-arginine-glutamate)-dependent mechanism for adhesion of neurons to S-laminin (1991)

S-laminin is a homolog of laminin that is concentrated in the synaptic cleft of the neuromuscular junction. We previously showed that the tripeptide LRE is a crucial determinant for binding of ciliary motoneurons to recombinant s-laminin. Here, we describe a neuroblastoma-spinal neuron hybrid cell line, NSC-34, that binds to an LRE-containing s-laminin fragment and to a synthetic LRE-protein conjugate. NSC-34 cells exhibit several properties of motoneurons; other cell lines tested were not motoneuron-like and did not display LRE-dependent adhesion. We therefore used NSC-34 cells to characterize the LRE-dependent adhesion mechanism. Inhibition studies with a series of 20 tripeptide LRE analogs showed that the cells exhibit a high degree of selectivity for LRE, and suggested that ligand binding requires a combination of electrostatic and hydrophobic interactions. The effects of cations on LRE-dependent adhesion are unlike those of previously described adhesion molecules including the integrins, a family of receptors for extracellular matrix proteins, including laminin. Specifically, adhesion to LRE does not require divalent cations and is inhibited by Ca2+ (but not by Mg2+) in the physiological range. In contrast, adhesion of NSC-34 cells to laminin is LRE- and Ca2+ independent but Mg2+ dependent, and appears to be mediated by integrins. Additionally, experiments using mixed substrates demonstrated that LRE-protein conjugates inhibit neurite outgrowth promoted by laminin. Finally, we show that, under ionic conditions that minimize integrin-dependent adhesion, NSC-34 cells bind to s-laminin-rich basal laminae in tissue sections in an LRE-dependent manner. Together, these results suggest that LRE comprises a motoneuron-selective adhesion site that is accessible in native basal laminae and that acts to inhibit neurite outgrowth.
PCATMIP: Enhancing signal intensity in diffusion‐weighted magnetic resonance imaging (2010)

Diffusion-weighted MRI studies generally lose signal intensity to physiological motion, which can adversely affect quantification/diagnosis. Averaging over multiple repetitions, often used to improve image quality, does not eliminate the signal loss. In this article, PCATMIP, a combined principal component analysis and temporal maximum intensity projection approach, is developed to address this problem. Data are first acquired for a fixed number of repetitions. Assuming that physiological fluctuations of image intensities locally are likely temporally correlated unlike random noise, a local moving boxcar in the spatial domain is used to reconstruct low-noise images by considering the most relevant principal components in the temporal domain. Subsequently, a temporal maximum intensity projection yields a high signal-intensity image. Numerical and experimental studies were performed for validation and to determine optimal parameters for increasing signal intensity and minimizing noise. Subsequently, a combined principal component analysis and temporal maximum intensity projection approach was used to analyze diffusion-weighted porcine liver MRI scans. In these scans, the variability of apparent diffusion coefficient values among repeated measurements was reduced by 59% relative to averaging, and there was an increase in the signal intensity with higher intensity differences observed at higher b-values. In summary, a combined principal component analysis and temporal maximum intensity projection approach is a postprocessing approach that corrects for bulk motion-induced signal loss and improves apparent diffusion coefficient measurement reproducibility.
cfDNA analysis from blood in melanoma. (2015)

Testing of tumor tissue remains the recommended method for detecting the presence of somatic mutations in human malignancies. V600E is the most frequent somatic point mutation in metastatic melanoma, providing a unique molecular marker for this malignancy. In addition, tumors carrying this mutation are primary candidates for BRAF-targeted therapy. Although metastatic melanoma patients usually have sufficient tumor tissue available for genetic analyses, the detection of V600E in blood can have prognostic and predictive value. In addition, patients are rarely re-biopsied and genetic testing in blood can be useful for monitoring response to therapy. Cell-free DNA (cfDNA) and cell-free RNA (cfRNA), RNA associated to platelets and circulating tumor cells (CTCs) are some of the materials that can be derived from the blood of cancer patients. cfDNA can be easily purified from serum and plasma and contains DNA fragments of tumor origin. For this reason, it is the most widely used material for the detection of somatic mutations in blood. Several methodologies have been used to determine V600E status in the cfDNA of metastatic melanoma and some studies have demonstrated that the identification and follow-up of V600E in cfDNA can have prognostic and predictive value.
Identification of chromosomal fusion sites in<i>Arabidopsis</i>mutants using sequential bicolour BAC-FISH (2006)

Double stranded chromosomal breaks are repaired by homologous recombination or nonhomologous end joining (NHEJ). When broken chromosome ends are fused together by NHEJ, the resulting dicentric chromosomes can be detected as anaphase bridges during the subsequent mitosis. Telomeres in the absence of functional telomerase shorten, became unprotected, and are eventually recognized by the cell repair system as double stranded breaks. As result, chromosomes of Arabidopsis thaliana plants that are deficient in the gene for telomerase reverse transcriptase (TERT) are prone to chromosome fusions. We use Arabidopsis tert-/- mutants as a model system for analyzing terminal chromosome fusions. Here we report a novel and sensitive cytogenetic assay for the identification and characterization of chromosome-terminal fusion events by employing fluorescence in situ hybridization (FISH) with multiple probes and a repeated hybridization approach. A mixture of chromosome-specific subtelomeric probes is applied successively in 3 FISH reactions to the slides containing mitotic anaphase figures with anaphase bridges. Each figure is registered by a CCD camera after each in situ hybridization procedure. By comparing the signals presented on the bridge in successive images the assessment of the particular chromosome arms involved in fusion is possible. This experimental setup enables unambiguous identification of individual chromosome ends employed in fusion events.
Cytoskeletal architecture and epithelial differentiation: molecular determinants of cell interaction and cytoskeletal filament anchorage. (1993)

Desmosomes are morphologically well defined junctions between epithelial cells and also some other cells such as myocardiocytes, meningeal cells and dendritic reticulum cells of lymphatic follicles. Besides their function in cell coupling, desmosomes anchor components of the cytoskeleton, i.e. intermediate-sized filaments (IFs), through their cytoplasmic plaques, thereby contributing to cytoskeletal and tissue architecture. In molecular terms, desmosomes are specific assemblies of transmembrane glycoproteins of the cadherin family, desmoglein(s) and desmocollin(s), that contribute to cell adhesion via their extracellular, aminoterminal domains and to plaque formation and IF coupling through their cytoplasmic, carboxyterminal "tails". Using transfection assays, we analyzed the function of different tail domains in plaque assembly and IF anchorage. Furthermore, we present evidence that both desmogleins and desmocollins represent multigene subfamilies showing cell type specific expression and that a desmosomal plaque protein occurring in stratified and complex epithelia, the "band 6 protein", is related to the plakoglobin family.
Fabrication and Reliability of Rigid-Flexible Optical Electrical Printed Circuit Board for Mobile Devices (2008)

A rigid-flexible optical and electrical printed circuit board (RFOE-PCB) was fabricated using a conventional PCB manufacturing process for mobile devices. The RFOE-PCB was designed to be embedded with a flexible 45-ended optical waveguide. In order to apply it to mobile devices, a repeating folding test and an environment test were carried out for physical and optical reliability. The RFOE-PCB successfully passed the reliability tests.
A comparative analysis of several transformations for enhancement and segmentation of magnetic resonance image scene sequences (1992)

The performance of the eigenimage filter is compared with those of several other filters as applied to magnetic resonance image (MRI) scene sequences for image enhancement and segmentation. Comparisons are made with principal component analysis, matched, modified-matched, maximum contrast, target point, ratio, log-ratio, and angle image filters. Signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), segmentation of a desired feature (SDF), and correction for partial volume averaging effects (CPV) are used as performance measures. For comparison, analytical expressions for SNRs and CNRs of filtered images are derived, and CPV by a linear filter is studied. Properties of filters are illustrated through their applications to simulated and acquired MRI sequences of a phantom study and a clinical case; advantages and weaknesses are discussed. The conclusion is that the eigenimage filter is the optimal linear filter that achieves SDF and CPV simultaneously.
Theoretical and experimental characterization of nonsymmetrically shielded coplanar waveguides for millimeter-wave circuits (1989)

A quasi-planar structure, the nonsymmetrically shielded coplanar waveguide (NSCPW), is proposed as a quasi-TEM transmission line with advantageous characteristics for millimeter-wave circuit applications. Advantages in terms of broadband behavior and ease of machining, as well as device mounting and substrate mounting, are pointed out. An experimental method is developed which allows the evaluation of the transmission line spectrum in a very wide frequency band (15:1) with a single transmission measurement. The experimentally evaluated propagation characteristics of the dominant and higher order modes are shown to be in excellent agreement with the theoretical predictions based on the generalized transverse resonance technique. This method is also used for an extensive characterization of the structure in terms of characteristic impedance and useful frequency band.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Influence of Anabolic Steroids on Body Composition, Blood Pressure, Lipid Profile and Liver Functions in Body Builders (1991)

The effects of anabolic steroids on body composition, blood pressure, lipid profile and liver functions were studied in male body builders who received a weekly i.m. injection of nandrolone-decanoate (100 mg) or placebo for 8 weeks in a double blind way. In addition, 5 body builders received the same dosage of nandrolone-decanoate or placebo, in a double blind cross-over design during two 8-week periods, interspersed by 12 weeks. Anabolic steroids induced a 25-27% decrease in HDL-cholesterol, which was virtually reversed 6 weeks after cessation of drug use. In the SAD group an increase in diastolic blood pressure was observed, which returned to pre-anabolic values approximately 6 weeks after cessation of drug administration. No deleterious effects of anabolic drugs on plasma activity of liver enzymes were found. Increases in lean body mass were found in all groups, though the increase in the subjects who received anabolic steroids was superior to that in the placebo-treated subjects. The increase in lean body mass suggests increases in muscle mass.
Toward Building a Legal Knowledge-Base of Chinese Judicial Documents for Large-Scale Analytics (2017)

We present an approach for constructing a legal knowledge-base that is sufficiently scalable to allow for large-scale corpus-level analyses. We do this by creating a polymorphic knowledge representation that includes hybrid ontologies, semistructured representations of sentences, and unsupervised statistical extraction of topics. We apply our approach to over one million judicial decision documents from Henan, China. Our knowledge-base allows us to make corpus-level queries that enable discovery, retrieval, and legal pattern analysis that shed new light on everyday law in China.
A Scalable Multi-TeraOPS Core for AI Training and Inference (2018)

This letter presents a multi-TOPS AI accelerator core for deep learning training and inference. With a programmable architecture and custom ISA, this engine achieves >90% sustained utilization across the range of neural network topologies by employing a dataflow architecture to provide high throughput and an on-chip scratchpad hierarchy to meet the bandwidth demands of the compute units. A custom 16b floating point (fp16) representation with 1 sign bit, 6 exponent bits, and 9 mantissa bits has also been developed for high model accuracy in training and inference as well as 1b/2b (binary/ternary) integer for aggressive inference performance. At 1.5 GHz, the AI core prototype achieves 1.5 TFLOPS fp16, 12 TOPS ternary, or 24 TOPS binary peak performance in 14-nm CMOS.
Application of Culture-Independent Rapid Diagnostic Tests in the Management of Invasive Candidiasis and Cryptococcosis (2015)

The diagnosis of invasive candidiasis (IC) and cryptococcosis is often complicated by slow and insensitive culture-based methods. Such delay results in poor outcomes due to the lack of timely therapeutic interventions. Advances in serological, biochemical, molecular and proteomic approaches have made a favorable impact on this process, improving the timeliness and accuracy of diagnosis with resultant improvements in outcome. This paper will serve as an overview of recent developments in the diagnostic approaches to infections due to these important yeast-fungi.
Insulin-like growth factor-I regulates pro-B cell differentiation (1992)

Progression of B-lymphocyte development in the bone marrow of postnatal mammals is marked by progressive rearrangement and expression of immunoglobulin (Ig) heavy- and light-chain genes. Following productive VHDJH gene rearrangement in the Ig heavy-chain gene complex, mu-heavy chain is the first Ig gene product expressed in cells committed to the B-lymphoid differentiation pathway. Interleukin (IL)-7 has been shown to stimulate proliferation of pre-B cells following c mu expression and this proliferative stimulus is potentiated by kit ligand (KL). However, it appears that neither of these cytokines contributes to differentiation of pro-B cells or initiation of expression of Ig gene products. We previously demonstrated that differentiation of pro-B cells and expression of mu-heavy chain is stimulated by either bone marrow stromal cell line S17 or cell-free supernatants from that line. This biological activity was attributed to molecules with an apparent M(r) of less than 10 Kd and approximately 40 to 60 Kd. We now report that this biological activity resides with stromal cell-derived insulin-like growth factor-I (IGF-I). Recombinant IGF-I stimulated the expression of cytoplasmic mu-heavy chain in short-term bone marrow cultures and this stimulus was abrogated in the presence of anti-IGF-I antibody. We also demonstrate that either anti-IGF-I antibody or pretreatment of S17 cells with antisense oligonucleotide for IGF-I abrogated the pro-B cell differentiation activity of S17 stromal cell supernatants. Although IGF-I did not directly stimulate proliferation of B-lineage cells, like KL, it potentiated the proliferative stimulus provided by IL-7. Taken together, these data strongly suggest that IGF-I produced by bone marrow stromal cells in the hematopoietic microenvironment plays a key role in regulating primary B lymphopoiesis.
Endonuclease Regnase‐1/<scp>Monocyte chemotactic protein‐1‐induced protein‐1 (MCPIP1</scp>) in controlling immune responses and beyond (2017)

The activation of inflammatory cells is controlled at transcriptional and posttranscriptional levels. Posttranscriptional regulation modifies mRNA stability and translation, allowing for elaborate control of proteins required for inflammation, such as proinflammatory cytokines, prostaglandin synthases, cell surface co-stimulatory molecules, and even transcriptional modifiers. Such regulation is important for coordinating the initiation and resolution of inflammation, and is mediated by a set of RNA-binding proteins (RBPs), including Regnase-1, Roquin, Tristetraprolin (TTP), and AU-rich elements/poly(U)-binding/degradation factor 1 (AUF1). Among these, Regnase-1, also known as Zc3h12a and Monocyte chemotactic protein-1-induced protein-1 (MCPIP1), acts as an endoribonuclease responsible for the degradation of mRNAs involved in inflammatory responses. Conversely, the RBPs Roquin and TTP trigger exonucleolytic degradation of mRNAs by recruiting the CCR4-NOT deadenylase complex. Regnase-1 specifically recognizes stem-loop structures present in 3'-untranslated regions of cytokine mRNAs, and directly degrades the mRNAs in a translation- and ATP-dependent RNA helicase upframeshift 1 (UPF1)-dependent manner that is reminiscent of nonsense-mediated decay. Regnase-1 regulates the activation of innate and acquired immune cells, and is critical for maintaining immune homeostasis as well as preventing over-activation of the immune system under inflammatory conditions. Furthermore, recent studies have revealed that Regnase-1 and its family members are involved not only in immunity but also in various biological processes. In this article, I review molecular mechanisms of Regnase-1-mediated mRNA decay and its physiological roles. WIREs RNA 2018, 9:e1449. doi: 10.1002/wrna.1449 This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Turnover and Surveillance > Regulation of RNA Stability RNA in Disease and Development > RNA in Disease.
Synthetic gene design—The rationale for codon optimization and implications for molecular pharming in plants (2016)

Degeneracy in the genetic code allows multiple codon sequences to encode the same protein. Codon usage bias in genes is the term given to the preferred use of particular synonymous codons. Synonymous codon substitutions had been regarded as "silent" as the primary structure of the protein was not affected; however, it is now accepted that synonymous substitutions can have a significant effect on heterologous protein expression. Codon optimization, the process of altering codons within the gene sequence to improve recombinant protein expression, has become widely practised. Multiple inter-linked factors affecting protein expression need to be taken into consideration when optimizing a gene sequence. Over the years, various computer programmes have been developed to aid in the gene sequence optimization process. However, as the rulebook for altering codon usage to affect protein expression is still not completely understood, it is difficult to predict which strategy, if any, will design the "optimal" gene sequence. In this review, codon usage bias and factors affecting codon selection will be discussed and the evidence for codon optimization impact will be reviewed for recombinant protein expression using plants as a case study. These developments will be relevant to all recombinant expression systems; however, molecular pharming in plants is an area which has consistently encountered difficulties with low levels of recombinant protein expression, and should benefit from an evidence based rational approach to synthetic gene design. Biotechnol. Bioeng. 2017;114: 492-502. © 2016 Wiley Periodicals, Inc.
Les cercles de calcite de la « Lapa do Bezerra » (Sao Domingos, Goiás, Brésil) = Notes brèves (1993)

Un type rare de concretions a ete observe durant l'exploration et la topographie de la grotte Lapa do Bezerra, municipio de Sao Domingos, Goias (fig. 1). Il s'agit d'une bande annulaire de calcite qui entoure un noyau constitue d'une stalagmite recouverte de coralloides. Cette concretion se developpe dans deux secteurs differents de cette caverne. Des formes similaires ont deja ete observees dans la Gran Caverna de Santo Tomas a Cuba (JIMENEZ, 1993), dans Benarat Cavern, Borneo (MEREDITH & WOOLDRIDGE, 1992), et dans la Gruta do Padre, Bresil (Jose Ayrton LABEGALINI, comm. orale).