gebhart/patrepeval huggingface dataset:
Learning from Data (2012)

Machine learning allows computational systems to adaptively improve their performance with experience accumulated from the observed data. Its techniques are widely applied in engineering, science, finance, and commerce. This book is designed for a short course on machine learning. It is a short course, not a hurried course. From over a decade of teaching this material, we have distilled what we believe to be the core topics that every student of the subject should know. We chose the title `learning from data' that faithfully describes what the subject is about, and made it a point to cover the topics in a story-like fashion. Our hope is that the reader can learn all the fundamentals of the subject by reading the book cover to cover. ---- Learning from data has distinct theoretical and practical tracks. In this book, we balance the theoretical and the practical, the mathematical and the heuristic. Our criterion for inclusion is relevance. Theory that establishes the conceptual framework for learning is included, and so are heuristics that impact the performance of real learning systems. ---- Learning from data is a very dynamic field. Some of the hot techniques and theories at times become just fads, and others gain traction and become part of the field. What we have emphasized in this book are the necessary fundamentals that give any student of learning from data a solid foundation, and enable him or her to venture out and explore further techniques and theories, or perhaps to contribute their own. ---- The authors are professors at California Institute of Technology (Caltech), Rensselaer Polytechnic Institute (RPI), and National Taiwan University (NTU), where this book is the main text for their popular courses on machine learning. The authors also consult extensively with financial and commercial companies on machine learning applications, and have led winning teams in machine learning competitions.
Increased Accumulation of Intraneuronal Amyloid β in HIV-Infected Patients (2009)

In recent years, human immunodeficiency virus (HIV)-infected patients under highly active anti-retroviral therapy (HAART) regimens have shown a markedly improved general clinical status; however, the prevalence of mild cognitive disorders has increased. We propose that increased longevity with HIV-mediated chronic inflammation combined with the secondary effects of HAART may increase the risk of early brain aging as shown by intraneuronal accumulation of abnormal protein aggregates like amyloid beta (Abeta), which might participate in worsening the neurodegenerative process and cognitive impairment in older patients with HIV. For this purpose, levels and distribution of Abeta immunoreactivity were analyzed in the frontal cortex of 43 patients with HIV (ages 38-60) and HIV- age-matched controls. Subcellular localization of the Abeta-immunoreactive material was analyzed by double labeling and confocal microscopy and by immunono-electron microscopy (EM). Compared to HIV- cases, in HIV+ cases, there was abundant intracellular Abeta immunostaining in pyramidal neurons and along axonal tracts. Cases with HIV encephalitis (HIVE) had higher levels of intraneuronal Abeta immunoreactivity compared to HIV+ cases with no HIVE. Moreover, levels of intracellular Abeta correlated with age in the group with HIVE. Double-labeling analysis showed that the Abeta-immunoreactive granules in the neurons co-localized with lysosomal markers such as cathepsin-D and LC3. Ultrastructural analysis by immuno-EM has confirmed that in these cases, intracellular Abeta was often found in structures displaying morphology similar to autophagosomes. These findings suggest that long-term survival with HIV might interfere with clearance of proteins such as Abeta and worsen neuronal damage and cognitive impairment in this population.
Evidence Supporting a Zoonotic Origin of Human Coronavirus Strain NL63 (2012)

The relationship between bats and coronaviruses (CoVs) has received considerable attention since the severe acute respiratory syndrome (SARS)-like CoV was identified in the Chinese horseshoe bat (Rhinolophidae) in 2005. Since then, several bats throughout the world have been shown to shed CoV sequences, and presumably CoVs, in the feces; however, no bat CoVs have been isolated from nature. Moreover, there are very few bat cell lines or reagents available for investigating CoV replication in bat cells or for isolating bat CoVs adapted to specific bat species. Here, we show by molecular clock analysis that alphacoronavirus (α-CoV) sequences derived from the North American tricolored bat (Perimyotis subflavus) are predicted to share common ancestry with human CoV (HCoV)-NL63, with the most recent common ancestor between these viruses occurring approximately 563 to 822 years ago. Further, we developed immortalized bat cell lines from the lungs of this bat species to determine if these cells were capable of supporting infection with HCoVs. While SARS-CoV, mouse-adapted SARS-CoV (MA15), and chimeric SARS-CoVs bearing the spike genes of early human strains replicated inefficiently, HCoV-NL63 replicated for multiple passages in the immortalized lung cells from this bat species. These observations support the hypothesis that human CoVs are capable of establishing zoonotic-reverse zoonotic transmission cycles that may allow some CoVs to readily circulate and exchange genetic material between strains found in bats and other mammals, including humans.
Lateral diffusion of a hydrophobic peptide, N4-nitrobenz-2-oxa-1,3-diazole gramicidin S, in phospholipid multibilayers (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLateral diffusion of a hydrophobic peptide, N4-nitrobenz-2-oxa-1,3-diazole gramicidin S, in phospholipid multibilayersEn-Shinn Wu, Kenneth Jacobson, Francis Szoka, and Archie Portis, Jr.Cite this: Biochemistry 1978, 17, 25, 5543–5550Publication Date (Print):December 12, 1978Publication History Published online1 May 2002Published inissue 12 December 1978https://pubs.acs.org/doi/10.1021/bi00618a033https://doi.org/10.1021/bi00618a033research-articleACS PublicationsRequest reuse permissionsArticle Views102Altmetric-Citations49LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
C-Reactive Protein Alters Antioxidant Defenses and Promotes Apoptosis in Endothelial Progenitor Cells (2006)

CRP, at concentrations known to predict cardiovascular events, may serve to impair EPC antioxidant defenses, and promote EPC sensitivity toward oxidant-mediated apoptosis and telomerase inactivation. These data further support a direct role of CRP in the development and/or progression of atherothrombosis.
Partial stroke tests as a procedure for the extension of the proof test interval (2007)

Abstract: This paper describes a procedure to reduce the probability of failure on demand (PFD) for systems and to extend the proof test interval by using partial stroke test (PST). The goal of partial stroke tests is to discover a part of the dangerous undetected failures at an earlier time. The difference between a partial stroke test and a proof test (PT) is that a component is only partially tested by a PST. However, after carrying out a PST, the system has a residual of dangerous undetected failures. This residual can be eliminated by a proof test. The probability of failure can be improved with the diagnostic coverage factor for partial stroke tests. It is important to know the difference between probability of failure PFD and the average probability of failure PFDavg. The values of both PFDs with partial stroke test are lower than the probability of failure without partial stroke test. The factor B shows the improvement between a system with and without partial stroke tests at the time of the proof test. The larger the factor B is the larger is the system’s improvement.
Identifying program power phase behavior using power vectors (2004)

Characterizing program behavior is important for both hardware and software research. Most modern applications exhibit distinctly different behavior throughout their runtimes, which constitute several phases of execution that share a greater amount of resemblance within themselves compared to other regions of execution. These execution phases can occur at very large scales, necessitating prohibitively long simulation times for characterization. Due to the implementation of extensive clock gating and additional power and thermal management techniques in modern processors, these program phases are also reflected in program power behavior, which can be used as an alternative means of program behavior characterization for power-oriented research. In this paper, we present our methodology for identifying phases in program power behavior and determining execution points that correspond to these phases, as well as defining a small set of power signatures representative of overall program power behavior. We define a power similarity metric as an intersection of both magnitude based and ratio-wise similarities in the power dissipation of processor components. We then develop a thresholding algorithm in order to partition the power behavior into similarity groups. We illustrate our methodology with the gzip benchmark for its whole runtime and characterize gzip power behavior with both the selected execution points and defined signature vectors.
DMSO molecule as ancillary ligand in Ru-based catalysts for ring opening metathesis polymerization (2010)

The ring-opening metathesis polymerization (ROMP) of norbornene (NBE) occurs in the presence of the fac-[RuCl2(S-DMSO)3(O-DMSO)] complex and ethyldiazoacetate (5 μL), where DMSO is S- or O-bonded dimethylsulfoxide. The yield is 62% (PDI = 1.64) at room temperature for 5 min and 88% (PDI = 1.93) at 50 ºC for 30 min, with [NBE]/[Ru] = 516 in CHCl3. The yield is 90% (PDI = 1.64) in the presence of NBu4ClO4 at room temperature for 5 min. The complex is practically inactive when one or two molecules of DMSO are replaced by pyridine, imidazole, 2-methyl-imidazole or benzimidazole. The in situ formation of the catalytic species and the behavior of the DMSO molecules as ancillary ligands in the reactivity of the RuII complexes are discussed.
PCR Amplification and Sequencing of Single Copy DNA Molecules (2001)

DNA amplification via PCR (polymerase chain reaction) provides an unlimited supply of material for subsequent genetic analyses even in cases where only a single copy of the DNA molecule is present in the sample. There are several requirements for producing high quantities of uniformly amplified DNAs that are not altered, distorted or mutated by the process of the amplification, for example the choice of polymerase enzyme, cycling conditions and the starting copy number. In the case of single copy amplifications, high numbers of thermal cycles are needed to produce sufficient quantities of amplicons for follow-up analysis, which requires highly stable thermal polymerases and high fidelity in the polymerase to minimize misincorporations. In this paper, we examine the in-vitro amplification of single copy DNA molecules with subsequent sequence analysis of the PCR generated products from a single copy DNA molecule. Two different polymerases were investigated, including platinum Pfx polymerase and AmpliTaq® polymerase using hot-start PCR strategies. Amplification of a 500 bp segment of λ-DNA (48 kbp) with quantification using capillary gel electrophoresis and laser-induced fluorescence indicated that Pfx gave a higher yield of amplicons compared to AmpliTaq using similar cycling conditions with fewer false termination or side products, including primer-dimers. Following PCR amplification of single copy DNAs, the amplicons were sequenced using standard Sanger, dideoxy chain termination methods. Analysis of the sequencing data for single copy amplification products indicated that a read length of 424 bases could be achieved, with a read accuracy of 99.3%, similar to the results obtained for a starting copy number of 100.
Measurement of concentration profiles inside a nitrite ion-selective electrode membrane (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMeasurement of concentration profiles inside a nitrite ion-selective electrode membraneXizhong. Li and D. Jed. HarrisonCite this: Anal. Chem. 1991, 63, 19, 2168–2174Publication Date (Print):October 1, 1991Publication History Published online1 May 2002Published inissue 1 October 1991https://pubs.acs.org/doi/10.1021/ac00019a018https://doi.org/10.1021/ac00019a018research-articleACS PublicationsRequest reuse permissionsArticle Views218Altmetric-Citations54LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Automatic Locating of Anthropometric Landmarks on 3D Human Models (2006)

We present an algorithm for automatic locating of anthropometric landmarks on 3D human scans. Our method is based on learning landmark characteristics and the spatial relationships between them from a set of human scans where the landmarks are identified. The learned information is formulated by a pairwise Markov network. Each node of the network is a random variable corresponding to the position of a landmark. The edges of the network represent correlations between the positions of landmark pairs. Probabilistic inference is then performed over the Markov network to locate the landmarks. We evaluated the algorithm on 30 human models with different shapes. The results showed good accuracy for most of the landmarks.
Effect of the product layer on the kinetics of the CO<sub>2</sub>‐lime reaction (1983)

Abstract The kinetics of reaction between CO 2 and lime is investigated in the range of 673 to 998 K with a view to examining the effects of product layer deposition and variations in the limestone calcination atmosphere. The reaction is initially rapid and chemically controlled and goes through a sudden transition to a much slower regime controlled by diffusion in the product CaCO 3 layer. The magnitude of the estimated product layer diffusivity is in the range of 10 −18 to 10 −21 m 2 /s, the corresponding activation energy is 88.9 ± 3.7 kJ/mol below 688 K and 179.2 ± 7.0 kJ/mol above that temperature, suggestive of solid state diffusion. Plausible mechanisms are discussed.
Androgen Supplementation in Eugonadal Men with Osteoporosis: Effects of Six Months' Treatment on Markers of Bone Formation and Resorption (1997)

There is no established treatment for osteoporosis in men, a common and disabling condition the incidence of which is increasing rapidly. We conducted an open study to investigate the efficacy and mode of action of testosterone therapy in eugonadal men with osteoporotic vertebral crush fracture. Twenty-one men, aged 34-73 (mean 58), were treated with intramuscular testosterone esters (Sustanon 250) every 2 weeks for 6 months. Bone mineral density (BMD) measurement by dual-energy X-ray absorptiometry was performed at baseline and 6 months. We also measured biochemical markers of bone turnover, testosterone, estradiol, sex hormone binding globulin (SHBG), and gonadotrophins at baseline and after 3 and 6 months of treatment. Treatment was well tolerated, and side effects were uncommon. Lumbar spine BMD increased by 5% from 0.799 to 0.839 g/cm2 (p < 0.001). All bone markers decreased, indicating that treatment suppressed bone turnover. Although serum osteocalcin levels fell only slightly, there were large reductions in urinary deoxypyridinoline and N-telopeptide (p < 0.05), which were correlated with the increase in spinal BMD. Interpretation of the findings with other markers, such as bone-specific alkaline phosphatase and pyridinoline, was confounded by the wide scatter of values. Serum testosterone increased by 55%, while SHBG decreased by 20%, leading to a rise in free androgen of 90%. Serum estradiol also increased by 45%. The change in spine BMD was significantly correlated with a change in serum estradiol but not with a change in serum testosterone. We therefore conclude that testosterone is a promising treatment for men with idiopathic osteoporosis, acting to suppress bone resorption by a mechanism that may involve estrogen.
The emerging role of reactive oxygen and nitrogen species in redox biology and some implications for plasma applications to medicine and biology (2012)

Reactive oxygen species (ROS) and the closely related reactive nitrogen species (RNS) are often generated in applications of atmospheric pressure plasmas intended for biomedical purposes. These species are also central players in what is sometimes referred to as 'redox' or oxidation–reduction biology. Oxidation–reduction biochemistry is fundamental to all of aerobic biology. ROS and RNS are perhaps best known as disease-associated agents, implicated in diabetes, cancer, heart and lung disease, autoimmune disease and a host of other maladies including ageing and various infectious diseases. These species are also known to play active roles in the immune systems of both animals and plants and are key signalling molecules, among many other important roles. Indeed, the latest research has shown that ROS/RNS play a much more complex and nuanced role in health and ageing than previously thought. Some of the most potentially profound therapeutic roles played by ROS and RNS in various medical interventions have emerged only in the last several years. Recent research suggests that ROS/RNS are significant and perhaps even central actors in the actions of antimicrobial and anti-parasite drugs, cancer therapies, wound healing therapies and therapies involving the cardiovascular system. Understanding the ways ROS/RNS act in established therapies may help guide future efforts in exploiting novel plasma medical therapies. The importance of ROS and RNS to plant biology has been relatively little appreciated in the plasma biomedicine community, but these species are just as important in plants. It appears that there are opportunities for useful applications of plasmas in this area as well.
Application of an idealized model to morphometry of the mammalian tracheobronchial tree (1978)

Abstract Quantitative anatomical descriptions (morphometry) of the tracheobronchial airways are of importance in many applications including the preparation of successful mathematical models describing airflow patterns and deposition patterns of airborne particles in the lung. Morphometric data are also useful in studies of comparative anatomy and in describing normal and diseased states of an organ. The collection of such data is aided by the use of idealized models of airway branches of the tracheobronchial airways. Morphometric measurements from the lungs of several mammalian species are presented using a model that consists of three connected tubular segments. The morphometric model uniquely defines an identification number for each branch segment, a branching angle, an airway segment length and diameter, an inclination of a segment to gravity and the degree of alveolarization of each segment. Designed to be compatible with computerized data handling, the model is unambiguous and realistic, but flexible so that anomalous anatomical structures can be classified and noted. Morphometric data describing the variation of structure with depth in the tracheobronchial airways are presented in the form of graphical representations of anatomical measurements on replica casts of the human, dog, rat and hamster airways. These distributions describe the anatomical character of the tracheobronchial airways concisely, quantitatively, and characteristically for each species.
Biological comparison of isomers and chemical forms of vitamin A (retinol) (1974)

The effects were comparcd on mouse tail scale epidermis of vitamin A acid, acetate and alcohol (all as the trans isomer) and the cis aldehyde by regular topical applications. Increases in epidermal thickness produced by different doses were compared statistically, and the induction of a granular layer and of epidermal alkaline phosphatase activity was demonstrated. The different forms and isomers of vitamin A have similar effects on the epidermis, but vary individually in activity, Retinoic acid and trans‐retinyl acetate were very similar in their action when used in a water solubilizing vehicle. The fact that retinyl acetate is very much cheaper than retinoic acid is a point in favour of its use for the treatment of psoriasis.
Evaluation of a Multimodal Sonification and Visualisation of Depth of Market Stock Data (2002)

Day traders make minute by minute decisions from depth of market stock data read from a table. A visualisation has been designed to help traders make better decisions from extra context and history in the display. An expert review of the visualisation identified the need for more dynamic information and higher resolution in critical areas. We designed a sonification to complement the visualisation with this information in a multimodal display. We evaluated the visualisation, sonification and multimodal displays with 15 nonexperts. The subjects predicted price movements significantly better than chance, at 61.3 % correct with the visualisation, 70% with the sonification and 70 % with the multimodal display. The prediction of downward movements was significantly better than upward with a best of 83 % for downward with the sonification, compared with 65.5 % for upward with the multimodal display. There was no effect due to the order of experience with the different displays. The results suggest that the multimodal display is redundant for downward movements and complementary for upward. The subjects commented that the sonification provides recent trends while the visualisation provides context. 1.