gebhart/patrepeval huggingface dataset:
Plasmodium berghei ANKA (PbA) Infection of C57BL/6J Mice: A Model of Severe Malaria (2013)

The term "severe malaria" refers to a wide spectrum of syndromes in Plasmodium-infected humans including cerebral malaria (CM), respiratory distress, severe anemia, liver dysfunction, and hypoglycemia. Mouse models have been employed to further our understanding of the pathology and immune responses that occur during Plasmodium infection. Evidence of brain, liver, lung, and spleen pathology, as well as anemia and tissue-sequestration of parasites, has been reported in various strains of inbred mice. While no single mouse model mimics all the various clinical manifestations of severe malaria in humans, here we describe a detailed protocol for Plasmodium berghei ANKA infection of C57BL/6J mice. For many years, this model has been referred to as "experimental cerebral malaria," but in fact recapitulates many of the symptoms and pathologies observed in most severe malaria syndromes.
Wavelet-based histograms for selectivity estimation (1998)

Query optimization is an integral part of relational database management systems. One important task in query optimization is selectivity estimation, that is, given a query P, we need to estimate the fraction of records in the database that satisfy P. Many commercial database systems maintain histograms to approximate the frequency distribution of values in the attributes of relations.In this paper, we present a technique based upon a multiresolution wavelet decomposition for building histograms on the underlying data distributions, with applications to databases, statistics, and simulation. Histograms built on the cumulative data distributions give very good approximations with limited space usage. We give fast algorithms for constructing histograms and using them in an on-line fashion for selectivity estimation. Our histograms also provide quick approximate answers to OLAP queries when the exact answers are not required. Our method captures the joint distribution of multiple attributes effectively, even when the attributes are correlated. Experiments confirm that our histograms offer substantial improvements in accuracy over random sampling and other previous approaches.
A transmembrane-anchored chimeric focal adhesion kinase is constitutively activated and phosphorylated at tyrosine residues identical to pp125FAK. (1994)

Focal adhesion kinase, pp125FAK, is a nonmyristylated cytosolic tyrosine kinase unrelated to protein-tyrosine kinase families categorized to date. The kinase activity and tyrosine phosphorylation of pp125FAK are induced by beta 1 and beta 3 integrin-mediated cell adherence or aggregation. pp125FAK is also a tyrosine phosphorylation substrate in v-src-transformed cells and is localized to focal adhesion contracts of adherent fibroblasts and carcinoma cells. In this report, we have transiently expressed in COS cells a transmembrane-anchored chimeric receptor kinase, CD2FAK, consisting of CD2 and pp125FAK. We analyzed its kinase activity and tyrosine phosphorylation and compared to those of pp125FAK. We found that CD2FAK exhibited constitutive kinase activity and a high basal tyrosine phosphorylation level when COS transfectants were suspended in serum-free media. The kinase activity of CD2FAK was similarly up-regulated upon beta 1 integrin-mediated cell adherence as the endogenous pp125FAK. Both CD2FAK and pp125FAK appeared to be active as autophosphorylating kinases as shown by mutation of the ATP binding site. We determined the major tyrosine phosphorylation site, Tyr397, identical for both the constitutively activated CD2FAK and pp125FAK in response to beta 1 integrin-mediated cell adherence by site-directed mutagenesis. Deletions of the NH2- or the COOH-terminal noncatalytic domain of FAK, including Tyr397 did not lead to abolition of the kinase activity of pp125FAK or CD2FAK. Taken together, CD2FAK exhibits properties of an activated pp125FAK and the kinase activity does not appear to require tyrosine phosphorylation in vitro or in vivo.
Preparation and Properties of Polydienes (1973)

Abstract In summary there are presented some new data on the initiation step for poly-(butadiene) polymerization with the AlEt 3 -Ni-BF 3 catalyst which describe what appears to be a “settling down” period of newborn chains at the π-bonded nickel catalyst site. This leads to a segment of higher trans content at the end of each high cis -1,4-poly(butadiene) chain. Comparisons between nickel and cobalt catalysts seem to point up their differences rather than their similarities. We have described the role of water in effectively changing the identity of the aluminum alkyl which in turn has a marked effect on the polymerization rate, on the polymer molecular weight and the extent of crosslinking.
Antisense RNA Amplification: A Linear Amplification Method for Analyzing the mRNA Population from Single Living Cells (1996)

Cell-specific gene expression is a fundamental area of investigation of various disciplines, but is often complicated by cell heterogeneity, paucity of material, or limits of detection for low-abundance mRNAs. Antisense RNA (aRNA) amplification presents a linear amplification method for analyzing the mRNA population from single living cells. Patch clamp electrodes containing reverse transcriptase, dNTPS, and a poly(T) primer modified 5' with a T7 RNA polymerase promoter sequence are used to isolate the cytoplasmic contents of individual living cells. The cDNAs transcribed therefore contain the T7 promoter sequence. Following subsequent processing for second-strand cDNA synthesis, T7 polymerase is used for amplification, which results in a 2000-fold amplification of antisense RNA. A second round of amplification results in a 10(6)-fold amplification of the initial material. The aRNA amplification method may be used in conjunction with other techniques. Electrophysiology may be conducted first to examine functional properties. Reverse Northerns may be performed, using the aRNA as a probe to identify specific cDNAs loaded onto a slot blot. PCR may be conducted to determine splice variants. Differential display and library construction may be employed to identify unknown or novel genes. Thus, the aRNA amplification may prove a valuable method for providing information on cell-specific gene expression in a variety of studies.
Constitutive STAT3 Phosphorylation Contributes to Skeletal Muscle Insulin Resistance in Type 2 Diabetes (2012)

Signal transducer and activator of transcription 3 (STAT3) is involved in cytokine- and nutrient-induced insulin resistance. The role of STAT3 in the development of skeletal muscle insulin resistance and type 2 diabetes (T2D) pathogenesis is incompletely defined. We tested the hypothesis that STAT3 signaling contributes to skeletal muscle insulin resistance in T2D. Protein abundance and phosphorylation of STAT3 signaling molecules were determined in skeletal muscle biopsy specimens from BMI- and age-matched overweight individuals with normal glucose tolerant (NGT) and T2D patients. The direct role of STAT3 in the development of lipid-induced skeletal muscle insulin resistance was determined using small interfering (si)RNA. Phosphorylated STAT3, phosphorylated Janus kinase 2 (JAK2), and suppressor of cytokine signaling 3 (SOCS3) protein abundance was increased in skeletal muscle from T2D patients. STAT3 phosphorylation positively correlated with free fatty acid level and measures of insulin sensitivity in NGT but not T2D patients. Palmitate exposure led to a constitutive phosphorylation of STAT3, increased protein abundance of SOCS3, and development of insulin resistance in L6 myotubes. These effects were prevented by siRNA-mediated STAT3 silencing. In summary, STAT3 is constitutively phosphorylated in skeletal muscle from T2D patients. STAT3 gene silencing prevents lipid-induced insulin resistance in cultured myotubes. Collectively, our results implicate excessive STAT3 signaling in the development of skeletal muscle insulin resistance in T2D.
Medical Simulation for Trauma Management (1996)

We have continued our work on developing the fundamental simulation technologies needed for battlefield trauma treatment training software. New approaches to including haptic feedback for trauma surgery have been created through the integration of robotics and physics-based tissue modeling into a real-time simulation architecture. We have demonstrated interactive models representing both flexible and rigid structures, are continuing to develop techniques for volume deformation and surface warping, and have begun work incorporating fast finite element modeling into our simulation approach. The Visible Human male dataset has been segmented to the extent necessary for the abdominal simulation and polygonal models appropriate for interactive display have been constructed. A novel method for real-time intravacular fluid flow taking advantage of techniques in cellular automata has been implemented. Lastly, we have evaluated software architectures and have developed an expandable distributed real-time control system that allows for the assignment of multiple processors to various computational tasks of the simulation system. We have achieved significant performance increases on our benchmark simulation tests over our previous software architecture.
Local Drug Delivery to Inner Ear for Treatment of Hearing Loss (2008)

Sensorineural hearing loss (SNHL) is one of the most common disabilities in our society. Experimentally, many candidates for use as therapeutic molecules have been discovered. However, a considerable obstacle to clinical application is the lack of an effective method for drug delivery to the cochlea. In order to overcome this obstacle, there needs to be development of a local cochlear drug delivery system. Advances in pharmacological technology have provided various drug delivery systems that use biomaterials, and which can be utilized for local drug delivery to the cochlea. Indeed, recent studies have demonstrated the potential of synthetic and natural biomaterials for local drug delivery to the cochlea, indicating that the clinical application of such local drug delivery systems could be used in the near future for therapeutic treatments. Recent progress in cell therapy research also offers a novel drug delivery method for the cochlea. In addition, transplantation of stem cells into the cochlea has been demonstrated to provide protective effects for the auditory function. Transplantation of genetically engineered cells has also resulted in the sustained delivery of aimed therapeutic molecules within the inner ear. Although problems involving clinical application still need to be resolved, these drug delivery systems for the inner ear may hold the future therapeutic options for treatment of SNHL. Keywords: Drug delivery system, cochlea, biodegradable polymer, cell transplantation, gene therapy
Crude oil water-cut sensing with disposable laser ablated and inkjet printed RF microfluidics (2014)

This paper presents the first microwave microfluidic crude oil/water cut sensor. Anhydrous crude oil is been tested and the device provides a measurable frequency shift of 500MHz at 50% (vol.) water content and a 50MHz shift for a 5% (vol.) water concentration. The sensor is realized with a low-cost direct write fabrication method. This involves laser ablation, inkjet printing, laser heating, along with low temperature thermal compression bonding of Poly (methylmethacrylate) (PMMA) sheets. By using localized laser sintering a conductivity of 2.5e <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> S/m is achieved for silver nanoparticle ink without the need to heat the entire substrate above its glass transition temperature of (105 °C). The dielectric properties of PMMA are characterized to 1 GHz and a simulation model is offered for analyzing the dielectric properties of crude oil. This work demonstrates that a small form factor and low cost device is capable of precise water-cut measurements.
Changes of Plasma Tissue Factor and Tissue Factor Pathway Inhibitor Antigen Levels and Induction of Tissue Factor Expression on the Monocytes in Coronary Artery Disease (2000)

The high levels of circulating TF are present in CAD, which were not sufficiently inhibited by the elevated TFPI plasma levels. Although the source of circulating TF is unclear, TF induction of monocytes by plasma from CAD patients may contribute to the hypercoagulable state.
Bronchioloalveolar lung cancer: occurrence, surgical treatment and survival☆ (2003)

BAC has a favourable survival, particularly in women. In spite of this, resection smaller than lobectomy is recommended only as a compromise. A multiple appearance does not imply a worse survival. The best survival rate was found in the non-mucinous BAC among the histological groups. TB seems to be frequent among BAC patients.
Validation of a Clinical-Grade Assay to Measure Donor-Derived Cell-Free DNA in Solid Organ Transplant Recipients (2016)

The use of circulating cell-free DNA (cfDNA) as a biomarker in transplant recipients offers advantages over invasive tissue biopsy as a quantitative measure for detection of transplant rejection and immunosuppression optimization. However, the fraction of donor-derived cfDNA (dd-cfDNA) in transplant recipient plasma is low and challenging to quantify. Previously reported methods to measure dd-cfDNA require donor and recipient genotyping, which is impractical in clinical settings and adds cost. We developed a targeted next-generation sequencing assay that uses 266 single-nucleotide polymorphisms to accurately quantify dd-cfDNA in transplant recipients without separate genotyping. Analytical performance of the assay was characterized and validated using 1117 samples comprising the National Institute for Standards and Technology Genome in a Bottle human reference genome, independently validated reference materials, and clinical samples. The assay quantifies the fraction of dd-cfDNA in both unrelated and related donor-recipient pairs. The dd-cfDNA assay can reliably measure dd-cfDNA (limit of blank, 0.10%; limit of detection, 0.16%; limit of quantification, 0.20%) across the linear quantifiable range (0.2% to 16%) with across-run CVs of 6.8%. Precision was also evaluated for independently processed clinical sample replicates and is similar to across-run precision. Application of the assay to clinical samples from heart transplant recipients demonstrated increased levels of dd-cfDNA in patients with biopsy-confirmed rejection and decreased levels of dd-cfDNA after successful rejection treatment. This noninvasive clinical-grade sequencing assay can be completed within 3 days, providing the practical turnaround time preferred for transplanted organ surveillance.
A simple single-source precursor route to the nanostructures of AlN, GaN and InN (2005)

In an effort to find a simple and common single-source precursor route for the group 13 metal nitride semiconductor nanostructures, the complexes formed by the trichlorides of Al, Ga and In with urea have been investigated. The complexes, characterized by X-ray crystallography and other techniques, yield the nitrides on thermal decomposition. Single crystalline nanowires of AlN, GaN and InN have been deposited on Si substrates covered with Au islands by using the complexes as precursors. The urea complexes yield single crystalline nanocrystals under solvothermal conditions. The successful synthesis of the nanowires and nanocrystals of these three important nitrides by a simple single-precursor route is noteworthy and the method may indeed be useful in practice.
A 250 MHz 14 dB-NF 73 dB-Gain 82 dB-DR Analog Baseband Chain With Digital-Assisted DC-Offset Calibration for Ultra-Wideband (2010)

A 250 MHz analog baseband chain for ultra-wideband was implemented in a 1.2 V 0.13 ¿ m CMOS process. The chip has an active area of 0.8 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . In the analog baseband, PGAs and filters are carried out by current-mode amplifiers to achieve wide bandwidth and wide dynamic range of gain, as well as low noise and high linearity. Besides, a current-mode Sallen-Key low-pass filter is adopted for effective rejection of out-of-band interferers. A 6 th-order Chebyshev low-pass filter realized in G <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> -C topology is designed in the baseband chain for channel selection. Digitally-assisted DC-offset calibration improves second-order distortion of the entire chain. The design achieves a maximum gain of 73 dB and a dynamic range of 82 dB. Measured noise figure is 14 dB, an IIP3 of -6 dBV, and IIP2 of -5 dBV at the maximum gain mode. The analog baseband chain consumes 56.4 mA under supply of 1.2 V.
Technique for injecting very large volumes in capillary supercritical fluid chromatography (1991)

Abstract A new technique for injecting very large volumes was developed for capillary supercritical fluid chromatography, which is based on dilution and venting techniques. Dilution of sample solution with carbon dioxide mobile phase made the selective venting of sample solvent very effective. Pressure at the end of the precolumn was also an important parameter for venting. With this method, injection of 100‐μL volumes was performed within 15 min. On‐line coupling of liquid chromatography to capillary supercritical fluid chromatography was demonstrated.
The CLAVATA1 Receptor-Like Kinase Requires CLAVATA3 for Its Assembly into a Signaling Complex That Includes KAPP and a Rho-Related Protein (1999)

Amy E. Trotochaud, Tong Hao, Guang Wu, Zhenbiao Yang, Steven E. Clark, The CLAVATA1 Receptor-Like Kinase Requires CLAVATA3 for Its Assembly into a Signaling Complex That Includes KAPP and a Rho-Related Protein, The Plant Cell, Vol. 11, No. 3 (Mar., 1999), pp. 393-405
Effects of bone marrow-derived mesenchymal stromal cells on gene expression in human alveolar type II cells exposed to TNF-<i>α</i>, IL-1<i>β</i>, and IFN-<i>γ</i> (2018)

The acute respiratory distress syndrome (ARDS) is common in critically ill patients and has a high mortality rate. Mesenchymal stromal cells (MSCs) have demonstrated therapeutic potential in animal models of ARDS, and their benefits occur in part through interactions with alveolar type II (ATII) cells. However, the effects that MSCs have on human ATII cells have not been well studied. Using previously published microarray data, we performed genome-wide differential gene expression analyses of human ATII cells that were (1) unstimulated, (2) exposed to proinflammatory cytokines (CytoMix), or (3) exposed to proinflammatory cytokines plus MSCs. Findings were validated by qPCR. Alveolar type II cells differentially expressed hundreds of genes when exposed either to proinflammatory cytokines or to proinflammatory cytokines plus MSCs. Stimulation with proinflammatory cytokines increased expression of inflammatory genes and downregulated genes related to surfactant function and alveolar fluid clearance. Some of these changes, including expression of some cytokines and genes related to surfactant, were reversed by exposure to MSCs. In addition, MSCs induced upregulation of other potentially beneficial genes, such as those related to extracellular matrix remodeling. We confirmed several of these gene expression changes by qPCR. Thus, ATII cells downregulate genes associated with surfactant and alveolar fluid clearance when exposed to inflammatory cytokines, and mesenchymal stromal cells partially reverse many of these gene expression changes.
On the Detection of Many Outliers (1975)

This article is concerned with “many outlier” procedures i.e., procedures that can detect more than one outlier in a sample. Several many outlier procedtues are proposed in Section 2 and via power comparisons in Section 3 are found to be much superior to one outlier procedures in detecting many outliers. We then compare several different. many outlier procedures in Section 4 and find that the procedutre based on the extreme studentized deviate (ESD) is slightly the best. Finally, 5%, 1% and .5% points are given for the ESD procedure for various sample sizes in Section 5.
Effects of stereospecific positioning of fatty acids in triacylglycerol structures in native and randomized fats: a review of their nutritional implications (2007)

Most studies on lipid lowering diets have focused on the total content of saturated, polyunsaturated and monounsaturated fatty acids. However, the distribution of these fatty acids on the triacylglycerol (TAG) molecule and the molecular TAG species generated by this stereospecificity are characteristic for various native dietary TAGs. Fat randomization or interesterification is a process involving the positional redistribution of fatty acids, which leads to the generation of new TAG molecular species. A comparison between native and randomized TAGs is the subject of this review with regards to the role of stereospecificity of fatty acids in metabolic processing and effects on fasting lipids and postprandial lipemia. The positioning of unsaturated versus saturated fatty acids in the sn-2 position of TAGs indicate differences in early metabolic processing and postprandial clearance, which may explain modulatory effects on atherogenecity and thrombogenecity. Both human and animal studies are discussed with implications for human health.
Physical and mental health comorbidity is common in people with multiple sclerosis: nationally representative cross-sectional population database analysis (2014)

People with MS have excess multiple chronic conditions, with associated increased mental health comorbidity. The low recorded cardiovascular comorbidity warrants further investigation.
DNA methyltransferase-3–dependent nonrandom template segregation in differentiating embryonic stem cells (2013)

Asymmetry of cell fate is one fundamental property of stem cells, in which one daughter cell self-renews, whereas the other differentiates. Evidence of nonrandom template segregation (NRTS) of chromosomes during asymmetric cell divisions in phylogenetically divergent organisms, such as plants, fungi, and mammals, has already been shown. However, before this current work, asymmetric inheritance of chromatids has never been demonstrated in differentiating embryonic stem cells (ESCs), and its molecular mechanism has remained unknown. Our results unambiguously demonstrate NRTS in asymmetrically dividing, differentiating human and mouse ESCs. Moreover, we show that NRTS is dependent on DNA methylation and on Dnmt3 (DNA methyltransferase-3), indicating a molecular mechanism that regulates this phenomenon. Furthermore, our data support the hypothesis that retention of chromatids with the "old" template DNA preserves the epigenetic memory of cell fate, whereas localization of "new" DNA strands and de novo DNA methyltransferase to the lineage-destined daughter cell facilitates epigenetic adaptation to a new cell fate.