gebhart/patrepeval huggingface dataset:
Pretreatment of biomass (1997)

This chapter reviews state-of-the-art lignocellulosic biomass pretreatment in preparation for enzymatic digestion, with emphasis on lignocellulose-to-ethanol production. Pretreatment techniques are classified by chemical application and type, and by product stream. The chapter provides various pretreatment reactor designs, reaction kinetics, and engineering constraints and challenges. It discusses the structural and Compositional Factors that affect the susceptibility of lignocellulosic biomass to enzyme attack, including cellulose crystallinity, lignin and hemicellulose protection of cellulose, accessible surface area of cellulose, and degree of acetylation of hemicelluloses. Pretreatment techniques can generally be grouped into three categories—physical, chemical, and biological—according to chemical and microorganism application. Physical pretreatment techniques do not involve chemical application. Typical examples are comminution, irradiation, steaming/steam explosion, and hydrothermolysis. The chapter summarizes the various product streams derived from the three major lignocellulosic material components—cellulose, hemicellulose, and lignin—as a result of pretreatment. The goal of pretreatment is to prepare biomass to facilitate bioconversion or paper-making.
Clinical Outcomes with Active versus Nutritional Vitamin D Compounds in Chronic Kidney Disease (2009)

Increasing confusion exists as to which vitamin D compounds are more appropriate for persons with chronic kidney disease (CKD). Some opinion-based guidelines recommend administration of such nutritional vitamin D agents as ergocalciferol or cholecalciferol as the first therapy in hyperparathyroidism associated with low circulating levels of 25-hydroxy vitamin D (<30 ng/ml) in nondialysis dependent CKD patients. Insufficient to deficient levels of 25-hydroxy vitamin D have been reported in the majority of individuals with CKD, including both nondialysis dependent and maintenance dialysis patients. Epidemiologic studies have almost consistently indicated the survival benefit of active vitamin D agents across all stages of CKD, including among dialysis patients with 25-hydroxy vitamin D deficiency. To date, no large observational or interventional studies have shown any survival advantage of nutritional vitamin D in CKD patients. Several recent (postguideline) small studies have yielded mixed results regarding the potential benefits of ergocalciferol in CKD, including satisfactory to inadequate lowering of PTH level to target ranges, improving response to erythropoietin stimulating agents, and salutary effects on glycemic controls. Compared with nutritional vitamin D agents, active vitamin D compounds appear to more effectively lower the circulating levels of alkaline phosphatase, a conveniently available biomarker associated with increased mortality and coronary artery calcification in CKD patients. The ideal vitamin D therapy for CKD patients should be the one that improves survival irrespective of suggested or imposed target ranges for arbitrary or opinion-based surrogate end points. Randomized controlled trials are needed to verify which agents offer superior survival advantages.
Nanopore sequencing and assembly of a human genome with ultra-long reads (2018)

We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ∼30× theoretical coverage, were produced. Reference-based alignment enabled detection of large structural variants and epigenetic modifications. De novo assembly of nanopore reads alone yielded a contiguous assembly (NG50 ∼3 Mb). We developed a protocol to generate ultra-long reads (N50 > 100 kb, read lengths up to 882 kb). Incorporating an additional 5× coverage of these ultra-long reads more than doubled the assembly contiguity (NG50 ∼6.4 Mb). The final assembled genome was 2,867 million bases in size, covering 85.8% of the reference. Assembly accuracy, after incorporating complementary short-read sequencing data, exceeded 99.8%. Ultra-long reads enabled assembly and phasing of the 4-Mb major histocompatibility complex (MHC) locus in its entirety, measurement of telomere repeat length, and closure of gaps in the reference human genome assembly GRCh38.
Saturated deep blue organic electrophosphorescence using a fluorine-free emitter (2005)

We demonstrate saturated, deep blue organic electrophosphorescence using the facial- and meridianal- isomers of the fluorine-free emitter tris(phenyl-methyl-benzimidazolyl)iridium(III)(f-Ir(pmb)3 and m-Ir(pmb)3, respectively) doped into the wide energy gap host, p-bis(triphenylsilyly)benzene (UGH2). The highest energy electrophosphorescent transition occurs at a wavelength of λ=389nm for the fac- isomer and λ=395nm for the mer- isomer. The emission chromaticity is characterized by Commission Internationale de l’Eclairage coordinates of (x=0.17,y=0.06) for both isomers. Peak quantum and power efficiencies of (2.6±0.3)% and (0.5±0.1)lm∕W and (5.8±0.6)% and (1.7±0.2)lm∕W are obtained using f-Ir(pmb)3 andm-Ir(pmb)3 respectively. This work represents a departure from previously explored, fluorinated blue phosphors, and demonstrates an efficient deep blue/near ultraviolet electrophosphorescent device.
Cloning of murine megakaryocyte progenitor cells in a fibrin clot culture system. (1987)

A fibrin clot culture system was applied to the cloning of mouse megakaryocyte colony-forming cells (CFU-Meg). The culture medium in this new method consists of Iscove's minimal essential medium containing fetal bovine serum, bovine fibrinogen, bovine thrombin, and pokeweed mitogen-stimulated mouse spleen cell-conditioned medium (PWM-SCM). CFU-Meg colony frequency with 10% PWM-SCM was maximal on days 5-6 of culture. Plating efficiencies averaged 36.1 +/- 3.9 and 51.9 +/- 6.0 per 1.5 X 10(5) BDF1 bone marrow cells and 1.0 X 10(6) spleen cells, respectively. The addition of bovine serum albumin to the culture medium had no effect on the efficiency of megakaryocyte colony growth in this culture system. This simplified and reproducible culture system supported not only the growth of colonies composed of megakaryocytes in "synchronous maturation," but also so-called "heterogenous" megakaryocyte colonies composed of cells in all stages of maturation.
The Effects of Nitric Oxide Inhibitor on Hyperdynamic Circulation in Portal Hypertensive Rats (1999)

Background: Nitric oxide, a vasodilator synthesized from L-arginine by vascular endothelial cells, accounts for the biological activity of endothelium derived relaxing factor. Previous studies demonstrated that nitric oxide inhibitor, -Nitro-L-Arginine(NNA) diminished the hyperdynamic splanchnic and systemic circulation in portal hypertensive rats The present study was done to determine the role of nitric oxide in the development of hyperdynamic circulations in the prehepatic portal hypertensive rat model produced by partial portal vein ligation. Methods: The portal hypertensive rats were divided into water ingestion group and NNA ingestion group. After partial portal vein ligation, NNA ingestion group and water ingestion group received NNA 1mg/kg/day and plain water through the mouth for 14 days, respectively. Cardiac output, mean arterial pressure, organ blood flow and porto-systemic shunting were measured by radioisotope labeled microsphere methods. Vascular resistances were calculated by standard equation. Results: There were significant decreases in mean arterial pressure, increases in cardiac output and cardiac index, and decreases in total systemic and splanchnic vascular resistance in portal hypertensive rats compared to normal control group (p
A collaborative survey of 80 mutations in the BRCA1 breast and ovarian cancer susceptibility gene. Implications for presymptomatic testing and screening. (1995)

The high frequency of protein-terminating mutations and the observation of many recurrent mutations found in a diverse set of samples could lead to a relatively simple diagnostic test for BRCA1 mutations. More data must be accumulated to address specifically the sensitivity and specificity of such a diagnostic testing procedure and to better estimate the age-specific risk for breast and ovarian cancer associated with such mutations.
Tandem arrayed Iigation of expressed sequence tags (TALEST): a new method for generating global gene expression profiles (1999)

We have developed a new and simple method for quantitatively analyzing global gene expression profiles from cells or tissues. The process, called TALEST, or tandem arrayed ligation of expressed sequence tags, employs an oligonucleotide adapter containing a type IIs restriction enzyme site to facilitate the generation of short (16 bp) ESTs of fixed position in the mRNA. These ESTs are flanked by GC-clamped punctuation sequences which render them resistant to thermal denaturation, allowing their concatenation into long arrays and subsequent recognition and analysis by high-throughput DNA sequencing. A major advantage of the TALEST technique is the avoidance of PCR in all stages of the process and hence the attendant sequence-specific amplification biases that are inherent in other gene expression profiling methods such as SAGE, Differential Display, AFLP, etc. which rely on PCR.
Cell Adhesion Molecules, Vascular Endothelial Growth Factor, and Basic Fibroblast Growth Factor in Patients with Non–Small Cell Lung Cancer Treated with Chemotherapy with or without Bevacizumab—an Eastern Cooperative Oncology Group Study (2008)

In this study, baseline ICAM levels were prognostic for survival and predictive of response to chemotherapy with or without bevacizumab. VEGF levels were predictive of response to bevacizumab but not survival.
Metabolic function and properties of 4-hydroxyphenylacetic acid 1-hydroxylase from Pseudomonas acidovorans (1975)

The enzyme 4-hydroxyphenylacetate, NAD(P)H:oxygen oxidoreductase (1-hydroxylating) (EC 1.14.13 ...; 4-hydroxyphenylacetate 1-monooxygenase; referred to here as 4-HPA 1-hydroxylase) was induced in Pseudomonas acidovorans when 4-hydroxyphenylacetate (4-PHA) was utilized as carbon source for growth; homogentisate and maleylacetoacetate were intermediates in the degradation of 4-HPA. A preparation of the hydroxylase that was free from homogentisate dioxygenase and could be stored at 4 C in the presence of dithioerythritol with little loss of activity was obtained by ultracentrifuging cell extracts; but when purified 18-fold by affinity chromatography the enzyme became unstable. Flavin adenine dinucleotide and Mg2+ ions were required for full activity. 4-HPA 1-hydrocylase was inhibited by KCl, which was uncompetitive with 4-HPA. Values of Ki determined for inhibitors competitive with 4-HPA were 17 muM dl-4-hydroxymandelic acid, 43 muM 3,4-dihydroxyphenylacetic acid, 87 muM 4-hydroxy-3-methylphenylacetic acid, and 440 muM 4-hydroxyphenylpropionic acid. Apparent Km values for substrates of 4-HPA 1-hydroxylase were 31 muM 4-HPA, 67 muM oxygen, 95 muM reduced nicotinamide adenine dinucleotide (NADH); AND 250 muM reduced nicotinamide adenine dinucleotide phosphate (NADPH). The same maximum velocity was given by NADH and NADPH. A chemical synthesis is described for 2-deutero-4-hydroxyphenylacetic acid. This compound was enzymatically hydroxylated with retention of half the deuterium in the homogentisic acid formed. Activity as substrate or inhibitor of 4-HPA 1-hydroxylase was shown only by those analogues of 4-HPA that possessed a hydroxyl group substituent at C-4 of the benze nucleus. A mechanism is suggested that accounts for this structural requirement and also for the observation that when 4-hydroxyphenoxyacetic acid was attacked by the enzyme, hydroquinone was formed by release of the side chain, probably as glycolic acid. Only one enantiometer of racemic 4-hydroxyhydratropic acid was attacked by 4-HPA 1-hydroxylase; the product, alpha-methylhomogentisic acid (2-(2,5-dihydroxyphenyl)-propionic acid), exhibited optical activity. This observation suggests that, during its shift from C-1 to C-2 of the nucleus, the side chain of the substrate remains bound to a site on the enzyme while a conformational change of the protein permits the necessary movement of the benzene ring.
A decision support tool for tuning parameters in a machine learning algorithm (1997)

Many machine learning algorithms require parameter tuning in order to adapt them to the particulars of a training set. This tuning task can be an expert task in its own right. Based on our observations of an expert tuning the HCV (Version 2.0) rule induction algorithm, we have built a simple decision support system (DSS) to automate tuning for that algorithm. We found that HCV plus DSS produced equal or better rule sets than standard HCV or C4.5. A surprising result from this study is that a very simple approach to tuning worked very well. We speculate that other research on machine learner tuning have indulged in complex solutions before experimenting adequately with simpler alternatives. Keywords: Decision support systems, machine learning, discretization, fine tuning 1 Introduction The dream of machine learning is that we can automatically build specifications from data without requiring tedious and time consuming human involvement. To date, this dream has not been realised. A repe...
A novel epithelial cell from neonatal rat lung: isolation and differentiated phenotype (1990)

A novel epithelial cell from normal neonatal rat lung has been isolated, established, and maintained for multiple passages in the absence of serum, without undergoing crisis or senescence. By careful manipulation of the nutrition/hormonal microenvironment, we have been able to select, from a heterogeneous population, a single epithelial cell type that can maintain highly differentiated features in vitro. This cell type has characteristics of bronchiolar epithelial cells. A clonal line, RL-65, has been selected and observed for greater than 2 yr in continuous culture. It has been characterized by ultrastructural, morphological, and biochemical criteria. The basal medium for this cell line is Ham's F12/Dulbecco's modified Eagle's (DME) medium plus insulin (1 micrograms/ml), human transferrin (10 micrograms/ml), ethanolamine (10(-4) M), phosphoethanolamine (10(-4) M), selenium (2.5 x 10(-8) M), hydrocortisone (2.5 x 10(-7) M), and forskolin (5 microM). The addition of 150 micrograms/ml of bovine pituitary extract to the defined basal medium stimulates a greater than 10-fold increase in cell number and a 50- to 100-fold increase in thymidine incorporation. The addition of retinoic acid results in further enhancement of cell growth and complete inhibition of keratinization. We have demonstrated a strategy that may be applicable to isolating other cell types from the lung and maintaining their differentiated characteristics for long-term culture in vitro. Such a culture system promises to be a useful model in which to study cellular events associated with differentiation and proliferation in the lung and to better understand the molecular mechanisms involved in these events.
Novel Euglycemic and Hypolipidemic Agents. 4. Pyridyl- and Quinolinyl-Containing Thiazolidinediones (1999)

A series of substituted pyridyl- and quinolinyl-containing 2, 4-thiazolidinediones having interesting cyclic amine as a linker have been synthesized. Both unsaturated thiazolidinediones 5 and saturated thiazolidinediones 6 and their various salts were evaluated in db/db mice for euglycemic and hypolipidemic effects and compared with BRL compound 11 and BRL-49653, respectively. Some of the potent compounds were converted to various salts in order to obtain improved activities. Among all the salts evaluated, the maleate salt of unsaturated TZD 5a was found to be a very potent euglycemic and hypolipidemic compound. Some of the more interesting compounds have also been evaluated in ob/ob mice and compared with rosiglitazone (maleate salt of BRL-49653). Oral glucose tolerance tests were performed in both db/db and ob/ob mice. Pharmacokinetic studies of 5a maleate are also reported. Receptor binding studies of PPARgamma by 5a/5a maleate did not show any significant transactivation of PPARalpha or PPARgamma.
Amorphous transparent conductive oxide InGaO3(ZnO)m (m≤ 4): a Zn4s conductor (2001)

Abstract With the purpose of creating ZnO-based amorphous transparent conductors, a range of amorphous films InGaoO3(ZnO)m (where m ≤ 4) was prepared using a pulsed-laser deposition method. The resulting films exhibited an optical bandgap of 2.8-3.0 eV, and an n-type electric conductivity of 170-400 Scm−1 at room temperature, displaying a slight dependence on the value of m, in which the carrier density was 1019-1020 cm−3 the electron mobili ty was 12-20 cm2 V−1 s−1 showing no p n anomaly between Hall and Seebeck coefficients. The conductivity displayed no significant dependence on the temperature ranging from 10 to 300 K. X-ray diffraction, transmission electron microscopy and extended X-ray absorption fine structure measurements confirmed that the films were amorphous phases. A combined use of bremsstrahlung isochromat spectroscopy and ultraviolet photoelectron spectroscopy revealed that the conduction band tail had a large dispersion and that the Fermi level was located at the conduction band edge. The percolation theory and overlap integral calculations suggest that the extended conduction band of the amorphous metal oxides are formed when the (n - 1)d10ws0 metal ions (n being the principal quantum number) occupy more than 20% of the atoms and the overlap integral between the vacant ns orbitals exceeds a threshold value of approximately 0.4. The present system is the first amorphous oxide semiconductor in which Zn4s orbitals form the extended conduction band.
Skeletal muscle metabolism during short-term, high-intensity exercise in prepubertal and pubertal girls (1999)

To test the hypothesis that glycolytic metabolism in muscle is attenuated in prepubertal children, (31)P-magnetic resonance spectroscopy was used to determine calf muscle intracellular pH (pH(i)) in nine prepubertal (Pre) and nine pubertal female swimmers (Pub). Maximal plantar flexion work capacity (100% MWC) was established by using a graded exercise test. Between 5 and 10 days later, calf muscle images (magnetic resonance imaging) and phosphorus spectra were acquired at rest, during 2 min of light exercise (40% MWC), and during 2 min of supramaximal exercise (140% MWC) in a 3.0-T NMR system. End-exercise pH(i) was 6.66 +/- 0.11 and 6.76 +/- 0.17 for Pub and Pre, respectively. No significant differences in the mean values for pH(i) or the P(i)-to-phosphocreatine ratio were observed between groups during the protocol; however, an interaction effect was found for the P(i)-to-phosphocreatine ratio during the supramaximal exercise challenge. Cross-sectional area of gastrocnemius was 15.12 +/- 0.46 and 9.37 +/- 0.37 cm(2) for Pub and Pre, respectively (P < 0.05). Differences in muscle size must be considered when interpreting the unlocalized magnetic resonance spectroscopy data. These results suggest that glycolytic metabolism in physically active children is not maturity dependent.
Applications and limitations of interspecies scaling and in vitro extrapolation in pharmacokinetics. (1998)

The search for new drugs is an extremely time-consuming and costly endeavor. Much of the time and cost are expended on generating data that support the efficacy and safety profiles of the drug. Because of ethical constraints, relevant pharmacological and toxicological assessments must be made in laboratory animals and in in vitro systems before human testing can begin. In support of the efficacy and safety evaluation during drug development, two fundamental challenges facing industrial drug metabolism scientists are (1) how to "scale-up" the pharmacokinetic data from animals to humans and (2) how to extrapolate the in vitro data to the in vivo situation. This review examines the applications and limitations of interspecies scaling and in vitro extrapolation in pharmacokinetics.
The blockade of Fc receptor-mediated clearance of immune complexes in vivo by a monoclonal antibody (2.4G2) directed against Fc receptors on murine leukocytes. (1984)

To evaluate the feasibility of using a monoclonal anti-Fc receptor antibody to alter Fc receptor function in vivo, the disappearance of radiolabeled human serum albumin-rabbit anti-human serum albumin (HSA-anti-HSA) complexes was studied in mice before and after the infusion of 2.4G2, a monoclonal antibody (developed by J. Unkeless). 2.4G2 specifically binds to Fc receptors on mouse macrophages. Under standardized conditions, 6.1% of an i.v. administered dose of anti-HSA was sequestered in the liver of B6/D2J mice. When HSA-anti-HSA complexes were administered, 53.4% were sequestered. If 8 micrograms/g body weight of 2.4G2 was infused i.p. 1.5 hr before HSA-anti-HSA, only 13.7% of the infused complexes were sequestered in the liver. The inhibition in Fc receptor-mediated sequestration produced by this dose of antibody persisted for at least 24 hr. A dose of 1 to 2 micrograms/g was sufficient to inhibit sequestration by 50%. Animals receiving daily injections of 2.4G2 cleared immune complexes from their blood much more slowly than untreated animals. Because 2.4G2 was not cytotoxic to peritoneal macrophages in vitro in the presence of serum, and because comparable inhibition of Fc receptor function was observed in vivo in C5-deficient mice, blockade of function does not depend upon complement-mediated lysis of macrophages. The maximal degree of inhibition of Fc receptor function obtained by using intact 2.4G2 was about twice that observed by using Fab fragments of 2.4G2 to block receptors. In addition to its effect on Fc receptor function, 2.4G2 also had a small but significant inhibitory effect upon the clearance of 125I-labeled heat-aggregated HSA by the mononuclear phagocyte system both in intact and C5-deficient mice. We conclude that 2.4G2 is a potent inhibitor of IgG Fc receptor-mediated immune clearance in vivo.
Synthesis of Fluorine-18 Functionalized Nanoparticles for use as in vivo Molecular Imaging Agents (2008)

Nanoparticles containing fluorine-18 were prepared from block copolymers made by ring opening metathesis polymerization (ROMP). Using the fast initiating ruthenium metathesis catalyst (H2IMes)(pyr)2(Cl)2Ru=CHPh, low polydispersity amphiphilic block copolymers were prepared from a cinnamoyl-containing hydrophobic norbornene monomer and a mesyl-terminated PEG-containing hydrophilic norbornene monomer. Self-assembly into micelles and subsequent cross-linking of the micelle cores by light-activated dimerization of the cinnamoyl groups yielded stable nanoparticles. Incorporation of fluorine-18 was achieved by nucleophilic displacement of the mesylates by the radioactive fluoride ion with 31% incorporation of radioactivity. The resulting positron-emitting nanoparticles are to be used as in vivo molecular imaging agents for use in tumor imaging.
Ultra-fast FFT protein docking on graphics processors (2010)

http://hex.loria.fr/ and http://hexserver.loria.fr/.
Adaptive sub-carrier, bit and power allocation for wireless multimedia using OFDM transmission (1999)

Adaptive sub-carrier, bit and power allocation for wireless multimedia using OFDM transmission by Wong Cheong Yui thesis 1999 viii, 67 leaves : ill. ; 30 cm Wideband wireless transmission often suffers from performance degradation caused by the varying channel characteristic…Read more ›