gebhart/patrepeval huggingface dataset:
Viral infection in community-acquired pneumonia: a systematic review and meta-analysis (2016)

The advent of PCR has improved the identification of viruses in patients with community-acquired pneumonia (CAP). Several studies have used PCR to establish the importance of viruses in the aetiology of CAP.We performed a systematic review and meta-analysis of the studies that reported the proportion of viral infection detected via PCR in patients with CAP. We excluded studies with paediatric populations. The primary outcome was the proportion of patients with viral infection. The secondary outcome was short-term mortality.Our review included 31 studies. Most obtained PCR via nasopharyngeal or oropharyngeal swab. The pooled proportion of patients with viral infection was 24.5% (95% CI 21.5-27.5%). In studies that obtained lower respiratory samples in >50% of patients, the proportion was 44.2% (95% CI 35.1-53.3%). The odds of death were higher in patients with dual bacterial and viral infection (OR 2.1, 95% CI 1.32-3.31).Viral infection is present in a high proportion of patients with CAP. The true proportion of viral infection is probably underestimated because of negative test results from nasopharyngeal or oropharyngeal swab PCR. There is increased mortality in patients with dual bacterial and viral infection.
Mixed-Variate Restricted Boltzmann Machines (2014)

Modern datasets are becoming heterogeneous. To this end, we present in this paper Mixed-Variate Restricted Boltzmann Machines for simultaneously modelling variables of multiple types and modalities, including binary and continuous responses, categorical options, multicategorical choices, ordinal assessment and category-ranked preferences. Dependency among variables is modeled using latent binary variables, each of which can be interpreted as a particular hidden aspect of the data. The proposed model, similar to the standard RBMs, allows fast evaluation of the posterior for the latent variables. Hence, it is naturally suitable for many common tasks including, but not limited to, (a) as a pre-processing step to convert complex input data into a more convenient vectorial representation through the latent posteriors, thereby offering a dimensionality reduction capacity, (b) as a classifier supporting binary, multiclass, multilabel, and label-ranking outputs, or a regression tool for continuous outputs and (c) as a data completion tool for multimodal and heterogeneous data. We evaluate the proposed model on a large-scale dataset using the world opinion survey results on three tasks: feature extraction and visualization, data completion and prediction.
Quality and matching performance analysis of three-dimensional unraveled fingerprints (2010)

The use of fingerprints as a biometric is both the oldest mode of computer-aided personal identification and the most-relied-on technology in use today. However, current acquisition methods have some challenging and peculiar difficulties. For higher performance fingerprint data acquisition and verification, a novel noncontact 3-D fingerprint scanner is investigated, where both the detailed 3-D and albedo information of the finger is obtained. The obtained high-resolution 3-D prints are further converted into 3-D unraveled prints, to be compatible with traditional 2-D automatic fingerprint identification systems. As a result, many limitations imposed on conventional fingerprint capture and processing can be reduced by the unobtrusiveness of this approach and the extra depth information acquired. To compare the quality and matching performances of 3-D unraveled with traditional 2-D plain fingerprints, we collect both 3-D prints and their 2-D plain counterparts. The print quality and matching performances are evaluated and analyzed by using National Institute of Standard Technology fingerprint software. Experimental results show that the 3-D unraveled print outperforms the 2-D print in both quality and matching performances.
Correction: IL-6 and Mouse Oocyte Spindle (2012)

Interleukin 6 (IL-6) is considered a major indicator of the acute-phase inflammatory response. Endometriosis and pelvic inflammation, diseases that manifest elevated levels of IL-6, are commonly associated with higher infertility. However, the mechanistic link between elevated levels of IL-6 and poor oocyte quality is still unclear. In this work, we explored the direct role of this cytokine as a possible mediator for impaired oocyte spindle and chromosomal structure, which is a critical hurdle in the management of infertility. Metaphase-II mouse oocytes were exposed to recombinant mouse IL-6 (50, 100 and 200 ng/mL) for 30 minutes and subjected to indirect immunofluorescent staining to identify alterations in the microtubule and chromosomal alignment compared to untreated controls. The deterioration in microtubule and chromosomal alignment were evaluated utilizing both fluorescence and confocal microscopy, and were quantitated with a previously reported scoring system. Our results showed that IL-6 caused a dose-dependent deterioration in microtubule and chromosomal alignment in the treated oocytes as compared to the untreated group. Indeed, IL-6 at a concentration as low as 50 ng/mL caused deterioration in the spindle structure in 60% of the oocytes, which increased significantly (P,0.0001) as IL-6 concentration was increased. In conclusion, elevated levels of IL-6 associated with endometriosis and pelvic inflammation may reduce the fertilizing capacity of human oocyte through a mechanism that involves impairment of the microtubule and chromosomal structure.
PLIF, a Novel Human Ferritin Subunit from Placenta with Immunosuppressive Activity (2002)

Ferritin is a ubiquitous iron storage protein existing in multiple isoforms composed of 24 heavy and light chain subunits. We describe here a third ferritin-related subunit cloned from human placenta cDNA library and named PLIF (placental immunomodulatory ferritin). The PLIF coding region is composed of ferritin heavy chain (FTH) sequence lacking the 65 C-terminal amino acids, which are substituted with a novel 48 amino acid domain (C48). In contrast to FTH, PLIF mRNA does not include the iron response element in the 5'-untranslated region, suggesting that PLIF synthesis is not regulated by iron. The linkage between the FTH and C48 domains created a restriction site for EcoRI. PLIF protein was found to localize in syncytiotrophoblasts of placentas (8 weeks of gestation) at the fetal-maternal interface. Increased levels of PLIF transcript and protein were also detected in the breast carcinoma cell lines T47D and MCF-7 but not in the benign corresponding cell line HBL-100. In vitro, PLIF was shown to down-modulate mixed lymphocyte reactions and to inhibit the proliferation of peripheral blood mononuclear cells stimulated with OKT3. The accumulated data indicate that PLIF is an embryonic immune factor involved in down-modulating the maternal immune recognition of the embryo toward anergy. This mechanism may have been adapted by breast cancer cells over expressing PLIF.
The contributions of specific amino acid side chains to signal intensities of peptides in matrix‐assisted laser desorption/ionization mass spectrometry (2004)

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis of complex peptide mixtures is often hampered by signal suppression effects as well as certain intrinsic properties of specific peptides that influence the desorption/ionization behavior. The present systematic study reports on the relationship between the occurrence of certain amino acids in peptides and the intensities of the related ions which appear during MALDI-MS analysis for both tryptic digests of proteins and synthetic peptide mixtures. The analysis of the tryptic digests revealed that the peptide sequences of the most intense peaks detected by MALDI-MS contained significantly higher proportions of arginine, phenylalanine, proline, and leucine than the average values for the measured proteins. The relationship between the relative signal intensities and amino acid compositions of peptides was studied in more detail by the partial least squares (PLS) method using equimolar mixtures of 144 well-characterized synthetic peptides. The regression coefficients clearly indicated that the presence of arginine, phenylalanine, leucine and proline tend to enhance the desorption/ionization process which results in higher MALDI-MS peak intensities. Furthermore, it was shown that the impact of arginine depends strongly on the identity of adjacent amino acids.
Quantification of Peptides for the Monitoring of Protease-Catalyzed Reactions by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Using Ionic Liquid Matrixes (2005)

Ionic liquid matrixes (ILM) have been shown to allow very homogeneous sample preparations, facilitating relative quantifications using internal standards in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). In the present work, the ability to perform quantifications of peptides without using internal standards in these matrixes was investigated. Linear correlations between peptide amount and signal intensities could be observed when increased molar matrix-to-analyte ratios were applied. The dynamic range of linearity was approximately 1 order of magnitude. The method was applied successfully to monitor the time-dependent evolution of substrates and products in trypsin-catalyzed digests of single peptides and peptide mixtures. Thus, ionic liquid matrixes allow quantitative MALDI-MS without the need for internal standards, making the method a suitable tool for the fast screening of new enzymes or the search for substrates or inhibitors.
<title>Pulsed-CO2 laser-material interaction: thermomechanical effects</title> (1993)

It's well known now that, under peculiar conditions, the laser-matter coupling is highly dependent on the plasma formation in front of the irradiated sample. The experiments with results presented here have been carried out over a range of intensity large enough to be able to discriminate the main stages of the interaction and particularly the effects of the plasma with the increasing intensity. The first part of this paper is devoted to the experimental conditions, whereas the results are discussed in a second part. Finally, a balance of the interaction is drawn up.
Dendritic cell subsets in blood and lymphoid tissue of rhesus monkeys and their mobilization with Flt3 ligand (2003)

We provide phenotypic and functional evidence of premonocytoid dendritic cells (DCs) and preplasmacytoid DCs in blood and of corresponding DC subsets in secondary lymphoid tissue of rhesus monkeys. Subsets were identified and sorted by 4-color flow cytometry using antihuman monoclonal antibodies cross-reactive with rhesus monkey. To mobilize pre-DC subsets, fms-like tyrosine 3 kinase ligand (Flt3L; 100 microg/kg subcutaneously) was administered for 10 days. Presumptive pre-DC subsets were identified within the lineage- (Lin-) major histocompatibility complex (MHC) class II+ fraction of blood mononuclear cells. Premonocytoid DCs were CD11c+CD123- (interleukin-3Ralpha- [IL-3Ralpha-]). Preplasmacytoid DCs were characterized as CD11c-CD123++ Flt3L increased the CD11c+ pre-DC (7-fold) and CD123++ pre-DC subsets (3-fold) in blood. The freshly isolated CD11c+ pre-DC subset induced modest proliferation of naive allogeneic T cells. After overnight culture with granulocyte macro-phage-colony-stimulating factor (GMCSF) and CD40L, both subsets up-regulated surface costimulatory molecules, and CD11c+ pre-DCs became potent allostimulators. Freshly isolated CD123++ pre-DCs showed typical plasmacytoid morphology and, when cultured with IL-3 and CD40L for 72 hours, developed mature DC morphology. Following stimulation with CD40L, CD11c+ pre-DCs secreted increased levels of IL-12p40. Importantly, herpes simplex virus-stimulated CD123++ pre-DCs, but not CD11c+ pre-DCs, secreted interferon-alpha (IFN-alpha). Corresponding DC subsets were identified by flow analysis and immunohistochemistry in lymph nodes wherein both populations were increased 2- to 3-fold by Flt3L administration. CD123+ pre-DCs produced IFN-alpha in response to in vivo viral infection. Thus, rhesus monkeys exhibit 2 distinct DC precursor populations that closely resemble those of humans. Both are mobilized into blood and lymphoid tissue by Flt3L, offering potential for their further characterization and possible therapeutic application.
Lung expansion and the perialveolar interstitial pressure gradient (1989)

We have determined the combined effects of lung expansion and increased extravascular lung water (EVLW) on the perialveolar interstitial pressure gradient. In the isolated perfused lobe of dog lung, we measured interstitial pressures by micropuncture at alveolar junctions (Pjct) and in adventitia of 30- to 50-microns microvessels (Padv) with stopped blood flow at vascular pressure of 3-5 cmH2O. We induced edema by raising vascular pressures. In nonedematous lobes (n = 6, EVLW = 3.1 +/- 0.3 g/g dry wt) at alveolar pressure of 7 cmH2O, Pjct averaged 0.5 +/- 0.8 (SD) cmH2O and the Pjct-Padv gradient averaged 0.9 +/- 0.5 cmH2O. After increase of alveolar pressure to 23 cmH2O the gradient was abolished in nonedematous lobes, did not change in moderately edematous lobes (n = 9, EVLW = 4.9 +/- 0.6 g/g dry wt), and increased in severely edematous lobes (n = 6, EVLW = 7.6 +/- 1.4 g/g dry wt). Perialveolar interstitial compliance decreased with increase of alveolar pressure. We conclude that increase of lung volume may reduce perialveolar interstitial liquid clearance by abolishing the Pjct-Padv gradient in nonedematous lungs and by compressing interstitial liquid channels in edematous lungs.
Balancing register allocation across threads for a multithreaded network processor (2004)

Modern network processors employ multi-threading to allow concurrency amongst multiple packet processing tasks. We studied the properties of applications running on the network processors and observed that their imbalanced register requirements across different threads at different program points could lead to poor performance. Many times application needs demand some threads to be more performance critical than others and thus by controlling the register allocation across threads one could impact the performance of the threads and get the desired performance properties for concurrent threads. This prompts our work.Our register allocator aims to distribute available registers to different threads according to their needs. The compiler analyzes the register needs of each thread both at the point of a context switch as well as internally. Compiler then designates some registers as shared and some as private to each thread. Shared registers are allocated across all threads explicitly by the compiler. Values that are live across a context switch can not be kept in shared registers due to safety reasons; thus, only those live ranges that are internal to the context switch can be safely allocated to shared registers. Spill can cause a context switch. and thus, the problems of context switch and allocation are closely coupled and we propose a solution to this problem. The proposed interference graphs (GIG,BIG,IIG) distinguish variables that must use a thread's private registers from those that can use shared registers. We first estimate the register requirement bounds, then reduce from the upper bound gradually to achieve a good register balance among threads. To reduce the register needs, move insertions are inserted at program points that split the live ranges or the nodes on the interference graph. We show that the lower bound is reachable via live range splitting and is adequate for our benchmark programs for simultaneously assigning them on different threads. As our objective, the number of move instructions is minimized.Empirical results show that the compiler is able to effectively control the register allocation across threads by maximizing the number of shared registers. Speed-up for performance critical threads ranges from 18 to 24% whereas degradation for performance of non-critical threads ranges only from 1 to 4%.
A 300-mm wafer-level three-dimensional integration scheme using tungsten through-silicon via and hybrid Cu-adhesive bonding (2008)

A 300-mm wafer-level three-dimensional integration (3DI) process using tungsten (W) through-silicon vias (TSVs) and hybrid Cu/adhesive wafer bonding is demonstrated. The W TSVs have fine pitch (5 mum), small critical dimension (1.5 mum), and high aspect ratio (17:1). A hybrid Cu/adhesive bonding approach, also called transfer-join (TJ) method, is used to interconnect the TSVs to a Cu BEOL in a bottom wafer. The process also features thinning of the top wafer to 20 mum and a Cu backside BEOL on the thinned top wafer. The electrical and physical properties of the TSVs and bonded interconnect are presented and show RLC values that satisfy both the power delivery and high-speed signaling requirements for high-performance 3D systems.
Object Detection and Motion Analysis in a Low Resolution 3-D Model (2011)

With augmenting security concerns and decreasing costs of surveillance and computing equipment, research on automated systems for object detection has been increasing, but the majority of the studies focus their attention on sequences where high-resolution objects are of interest. The main objective of the work reported here is the detection and extraction of information of low-resolution objects (e.g., objects that are so small or so far away from the camera that they occupy only tens of pixels) in order to provide a base for higher level information operations such as classification and behavioral analysis. The system proposed is composed of four stages (preprocessing, background modeling, information extraction, and post processing) and uses context-based region-of-importance selection, histogram equalization, background subtraction, biological motion analysis, and morphological filtering techniques. The result is a system capable of detecting and tracking low -resolution objects in a controlled background scene which can be a base for systems with higher complexity.
Algorithms for inferring haplotypes (2004)

Haplotype phase information in diploid organisms provides valuable information on human evolutionary history and may lead to the development of more efficient strategies to identify genetic variants that increase susceptibility to human diseases. Molecular haplotyping methods are labor-intensive, low-throughput, and very costly. Therefore, algorithms based on formal statistical theories were shown to be very effective and cost-efficient for haplotype reconstruction. This review covers 1) population-based haplotype inference methods: Clark's algorithm, expectation-maximization (EM) algorithm, coalescence-based algorithms (pseudo-Gibbs sampler and perfect/imperfect phylogeny), and partition-ligation algorithm implemented by a fully Bayesian model (Haplotyper) or by EM (PLEM); 2) family-based haplotype inference methods; 3) the handling of genotype scoring uncertainties (i.e., genotyping errors and raw two-dimensional genotype scatterplots) in inferring haplotypes; and 4) haplotype inference methods for pooled DNA samples. The advantages and limitations of each algorithm are discussed. By using simulations based on empirical data on the G6PD gene and TNFRSF5 gene, I demonstrate that different algorithms have different degrees of sensitivity to various extents of population diversities and genotyping error rates. Future development of statistical algorithms for addressing haplotype reconstruction will resort more and more to ideas based on combinatorial mathematics, graphical models, and machine learning, and they will have profound impacts on population genetics and genetic epidemiology with the advent of the human HapMap.
Physical organization of temporal data (1987)

In this paper, we propose a partitioning scheme of files in a temporal database system, and develop algorithms to minimize the overflow associated with that scheme. The proposed partitioning is suitable for range queries and aggregation operations along the time dimension. Simulation results show that the partitioning algorithms proposed in this paper result in better performance than in the case of a grid-type partitioning.
Measurement of skeletal muscle radiation attenuation and basis of its biological variation (2014)

Skeletal muscle contains intramyocellular lipid droplets within the cytoplasm of myocytes as well as intermuscular adipocytes. These depots exhibit physiological and pathological variation which has been revealed with the advent of diagnostic imaging approaches: magnetic resonance (MR) imaging, MR spectroscopy and computed tomography (CT). CT uses computer-processed X-rays and is now being applied in muscle physiology research. The purpose of this review is to present CT methodologies and summarize factors that influence muscle radiation attenuation, a parameter which is inversely related to muscle fat content. Pre-defined radiation attenuation ranges are used to demarcate intermuscular adipose tissue [from -190 to -30 Hounsfield units (HU)] and muscle (-29 HU to +150 HU). Within the latter range, the mean muscle radiation attenuation [muscle (radio) density] is reported. Inconsistent criteria for the upper and lower HU cut-offs used to characterize muscle attenuation limit comparisons between investigations. This area of research would benefit from standardized criteria for reporting muscle attenuation. Available evidence suggests that muscle attenuation is plastic with physiological variation induced by the process of ageing, as well as by aerobic training, which probably reflects accumulation of lipids to fuel aerobic work. Pathological variation in muscle attenuation reflects excess fat deposition in the tissue and is observed in people with obesity, diabetes type II, myositis, osteoarthritis, spinal stenosis and cancer. A poor prognosis and different types of morbidity are predicted by the presence of reduced mean muscle attenuation values in patients with these conditions; however, the biological features of muscle with these characteristics require further investigation.
Small-Molecule Inhibitors of the Wnt Pathway Potently Promote Cardiomyocytes From Human Embryonic Stem Cell–Derived Mesoderm (2011)

Pharmacological inhibition of Wnt signaling is sufficient to drive human mesoderm cells to form cardiomyocytes; this could yield novel tools for the benefit of pharmaceutical and clinical applications.