gebhart/patrepeval huggingface dataset:
Kinetic model for electric-field induced point defect redistribution near semiconductor surfaces (2014)

The spatial distribution of point defects near semiconductor surfaces affects the efficiency of devices. Near-surface band bending generates electric fields that influence the spatial redistribution of charged mobile defects that exchange infrequently with the lattice, as recently demonstrated for pile-up of isotopic oxygen near rutile TiO2 (110). The present work derives a mathematical model to describe such redistribution and establishes its temporal dependence on defect injection rate and band bending. The model shows that band bending of only a few meV induces significant redistribution, and that the direction of the electric field governs formation of either a valley or a pile-up.
Redirection of the Respiro-Fermentative Flux Distribution in <i>Saccharomyces cerevisiae</i> by Overexpression of the Transcription Factor Hap4p (2000)

Reduction of aerobic fermentation on sugars by altering the fermentative/oxidative balance is of significant interest for optimization of industrial production of Saccharomyces cerevisiae. Glucose control of oxidative metabolism in baker's yeast is partly mediated through transcriptional regulation of the Hap4p subunit of the Hap2/3/4/5p transcriptional activator complex. To alleviate glucose repression of oxidative metabolism, we constructed a yeast strain with constitutively elevated levels of Hap4p. Genetic analysis of expression levels of glucose-repressed genes and analysis of respiratory capacity showed that Hap4p overexpression (partly) relieves glucose repression of respiration. Analysis of the physiological properties of the Hap4p overproducer in batch cultures in fermentors (aerobic, glucose excess) has shown that the metabolism of this strain is more oxidative than in the wild-type strain, resulting in a significant reduced ethanol production and improvement of growth rate and a 40% gain in biomass yield. Our results show that modification of one or more transcriptional regulators can be a powerful and a widely applicable tool for redirection of metabolic fluxes in microorganisms.
The transceiver controller IC for home bus system (2003)

A transceiver controller IC has been developed for the improvement of the home bus system (HBS). The functions of the new IC cover the logical conditions of the physical layer of the OSI (open systems interconnection) reference model. Therefore, even a low cost, single chip microcomputer can easily control both home electronic products and the communication of HBS simultaneously by using the IC.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Universality in Elementary Cellular Automata (2004)

The purpose of this paper is to prove a conjecture made by Stephen Wolfram in 1985, that an elementary one dimensional cellular automaton known as "Rule 110" is capable of universal computation. I developed this proof of his conjecture while assisting Stephen Wolfram on research for A New Kind of Science [1].
Nokia Mobile Data Challenge: Predicting Semantic Place and Next Place via Mobile Data (2012)

The appearance of smartphones equipped with various sen-sors enables pervasive monitoring of mobile users ’ behaviors and mobility. The Nokia Mobile Data Challenge (MDC) [10] gives us a great opportunity to study the users ’ mobility models and location profiles from a rich mobile dataset. The realistic data analysis may benefit a wide range of fields from technology innovation to policy making. In this paper, we describe our proposed methods to predict the semantic meaning of the “important places ” (Task 1) and the users’ next destination (Task 2) based on released MDC data. For Task 1, we explore several features from the sequence of vis-ited places and accelerometer samples, and proposed two types of prediction methods: rule based and machine learn-ing based. For Task 2, we adopt a simple but effective ma-chine learning method to accomplish the prediction assign-ment via both temporal and spacial features. Our prelim-inary experimental results over released MDC data (Set A dataset) show that rule based methods produce good predic-tions for home and work locations in Task1, while machine learning methods are more scalable for different types of pre-diction tasks. But the prediction accuracy of machine learn-ing approaches heavily depends on the number of instances in the training data. 1.
Novel inducible antibacterial peptides from a hemipteran insect, the sap-sucking bug <i>Pyrrhocoris apterus</i> (1994)

Insects belonging to the recent orders of the endopterygote clade (Lepidoptera, Diptera, Hymenoptera and Coleoptera) respond to bacterial challenge by the rapid and transient synthesis of a battery of potent antibacterial peptides which are secreted into their haemolymph. Here we present the first report on inducible antibacterial molecules in the sap-sucking bug Pyrrhocoris apterus, a representative species of the Hemiptera, which predated the Endoptergotes by at least 50 million years in evolution. We have isolated and characterized from immune blood of this species three novel peptides or polypeptides: (i) a 43-residue cysteine-rich anti-(Gram-positive bacteria) peptide which is a new member of the family of insect defensins; (ii) a 20-residue proline-rich peptide carrying an O-glycosylated substitution (N-acetylgalactosamine), active against Gram-negative bacteria; (iii) a 133-residue glycine-rich polypeptide also active against Gram-negative bacteria. The proline-rich peptide shows high sequence similarities with drosocin, an O-glycosylated antibacterial peptide from Drosophila, and also with the N-terminal domain of diptericin, an inducible 9 kDa antibacterial peptide from members of the order Diptera, whereas the glycine-rich peptide has similarities with the glycine-rich domain of diptericin. We discuss the evolutionary aspects of these findings.
Structure-activity relationship studies in the field of calcium antagonists. Xanthone 1,4-dihydropyridines bearing a 2,3-lactone ring. (1995)

A series of xanthone 1,4-dihydropyridine derivatives bearing a 2,3-lactone ring and a 2-acetoxymethyl group were prepared. The compounds were evaluated for inotropic, chronotropic and calcium antagonist properties. The introduction of a 2,3-lactone ring improved the negative inotropic activity and selectivity.
Studies with an artificial endocrine pancreas (1977)

Short-term studies with an artificial endocrine pancreas have provided insights into the pathophysiology of diabetes and demonstrated the ability of such a system to restore and maintain glucose homeostasis in human subjects given either their usual diet, a 50 gm oral glucose tolerance test, or a moderate level of physical exercise. Animals were used to demonstrate that a peripheral route of insulin delivery by the artificial pancreas is equivalent to the portal route. (<i>Arch Intern Med</i>137:639-649, 1977)
THE REACTIONS OF <i>CLAVICEPS PURPUREA</i> TO VARIATIONS OF ENVIRONMENT (1931)

Peer Reviewed
Characterization of Shiga-like toxin I B subunit purified from overproducing clones of the SLT-I B cistron (1990)

The cistron encoding the B subunit of Escherichia coli Shiga-like toxin I (SLT-I) was cloned under control of the tac promoter in the expression vector pKK223-3 and the SLT-I B subunit was expressed constitutively in a wild-type background and inducibly in a lacIq background. The B subunit was located in the periplasmic space, and less than 10% was found in the culture medium after 24 h incubation. Polymyxin B extracts contained as much as 160 micrograms of B subunit/ml of culture. B subunit was purified to homogeneity by ion-exchange chromatography followed by chromatofocusing. Cross-linking analysis of purified native B subunit showed that it exists as a pentamer. In gels containing 0.1% SDS the native protein dissociated into monomers. B subunit was found to have the same glycolipid-receptor-specificity as SLT-I holotoxin. Competitive binding studies showed that B subunit and holotoxin had the same affinity for the globotriosylceramide receptor. We conclude that this recombinant plasmid is a convenient source of large amounts of purified SLT-I B subunit, which could be used for biophysical and structural studies or as a natural toxoid.
Chiral Phosphoric Acids as Versatile Catalysts for Enantioselective Transformations (2010)

Chiral phosphoric acids derived from axially chiral biaryls and related chiral Brønsted acids have emerged as an attractive and widely applicable class of enantioselective organocatalysts for a variety of organic transformations. This review focuses on recent achievements in the development of enantioselective transformations using these axially chiral phosphoric acids and their analogues as chiral Brønsted acid catalysts. The contents are arranged according to the specific types of carbon-carbon bond-forming reactions, followed by carbon-heteroatom bond-forming reactions and functional group transformations, including reduction and oxidation. Further applications to combined phosphoric acid and metal complex catalytic systems and new aspects in the development of chiral Brønsted acid catalysts are also highlighted.
Monitoring human papillomavirus prevalence in urine samples: a review (2013)

Human papillomavirus (HPV) is the main cause of cervical cancer, and many countries now offer vaccination against HPV to girls by way of government-funded national immunization programs. Monitoring HPV prevalence in adolescents could offer a near-term biological measure of vaccine impact, and urine sampling may be an attractive large-scale method that could be used for this purpose. Our objective was to provide an overview of the literature on HPV DNA detection in urine samples, with an emphasis on adolescents. We searched the PubMed database using the terms "HPV" and "urine" and identified 21 female and 14 male study populations in which HPV prevalence in urine samples was reported, four of which included only asymptomatic female adolescents. We provide herein an overview of the recruitment setting, age, urine sampling procedure, lesion type, HPV assay, and HPV prevalence in urine samples and other urogenital samples for the studies included in this review. In female study populations, concordance for any HPV type and type-specific concordance in paired urine and cervical samples are provided in addition to sensitivity and specificity. We concluded that few studies on HPV prevalence in urine samples have been performed in asymptomatic female adolescent populations but that urine samples may be a useful alternative to cervical samples to monitor changes in HPV prevalence in females in the post-HPV vaccination era. However, care should be taken when extrapolating HPV findings from urine samples to the cervix. In males, urine samples do not seem to be optimal for monitoring HPV prevalence due to a low human genomic DNA content and HPV DNA detection rate compared to other urogenital sites. In each situation the costs and benefits of HPV DNA detection in urine compared to alternative monitoring options should be carefully considered.
Two nuclear factors compete for the skeletal muscle actin promoter. (1987)

We show that DNA fragments, which span the skeletal muscle alpha-actin promoter, form specific complexes with proteins from nuclear extracts of 11 different cultured cell types. These include two myocyte stage specific cell types, myoblast and myotube. The myocyte nuclear extracts are distinguished from all of the others by the electrophoretic mobility of the predominant DNA complex. This complex is greatly diminished in the nine non-myocyte cell types, where a different complex predominates. The major myocyte and non-myocyte complexes are caused by distinct binding activities that compete for the same DNA sequence element. DNA footprint analysis shows that this element is located 78 nucleotides upstream of the transcription start site, within a region that appears essential for expression in developing myocytes.
Use of a pH Sensitive Polymer for Conformance Control (2002)

Abstract A new strategy of using pH sensitive polymers for conformance control is proposed. The rheological properties of some polymers such as anionic derivatives of polyacrylic acid are shown to be very pH sensitive. For example, their viscosity varies from 5 cp at a pH of 2.5 to 20,000 cp at a pH above 6.0. This rheological behavior is reversible as the pH is cycled. Rheological data is presented at different polymer concentrations, temperatures and in solutions with different ionic strength. The effect of temperature on the rheological properties of the polymer is shown to be small. Compatibility tests showed that this polymer is compatible with most brines (NaCl, NH4Cl, and KCl). Core flow experiments were conducted on Berea cores. The results showed that the polymer solution was easily propagated through 6 inch long cores due to its low initial viscosity (~5cp). The polymer solution formed a rigid gel inside the pores after a shut-in period of 24 hours as the pH of the fluid increased above 6. The gelled polymer was found to be stable up to the maximum examined pressure gradients of 4000 psi /ft across the core. Experiments were conducted by using acid pre-flushes ahead of the polymer solution. These results indicate that the polymer can be placed deep into a formation by using pre-flushes designed for a specific rock mineralogy. The pH sensitive polymers studied here are excellent candidates for conformance control. It may also be possible to use them for temporary zonal isolation since they can be easily broken down with a mild acid wash and flowback.
Investigation of the Interface in Silica-Encapsulated Liposomes by Combining Solid State NMR and First Principles Calculations (2011)

In the context of nanomedicine, liposils (liposomes and silica) have a strong potential for drug storage and release schemes: such materials combine the intrinsic properties of liposome (encapsulation) and silica (increased rigidity, protective coating, pH degradability). In this work, an original approach combining solid state NMR, molecular dynamics, first principles geometry optimization, and NMR parameters calculation allows the building of a precise representation of the organic/inorganic interface in liposils. {(1)H-(29)Si}(1)H and {(1)H-(31)P}(1)H Double Cross-Polarization (CP) MAS NMR experiments were implemented in order to explore the proton chemical environments around the silica and the phospholipids, respectively. Using VASP (Vienna Ab Initio Simulation Package), DFT calculations including molecular dynamics, and geometry optimization lead to the determination of energetically favorable configurations of a DPPC (dipalmitoylphosphatidylcholine) headgroup adsorbed onto a hydroxylated silica surface that corresponds to a realistic model of an amorphous silica slab. These data combined with first principles NMR parameters calculations by GIPAW (Gauge Included Projected Augmented Wave) show that the phosphate moieties are not directly interacting with silanols. The stabilization of the interface is achieved through the presence of water molecules located in-between the head groups of the phospholipids and the silica surface forming an interfacial H-bonded water layer. A detailed study of the (31)P chemical shift anisotropy (CSA) parameters allows us to interpret the local dynamics of DPPC in liposils. Finally, the VASP/solid state NMR/GIPAW combined approach can be extended to a large variety of organic-inorganic hybrid interfaces.
Isolation and Characterization of a Pathogenic Newcastle Disease Virus from a Natural Case in Indonesia (2010)

This study was performed to isolate a velogenic Newcastle disease virus (NDV) strain currently found in Indonesia for establishing a domestic reference virus for future pathological and molecular epidemiological studies. A chicken suspected to have contracted Newcastle disease (ND) in a local outbreak in Bali was selected for NDV isolation. Atrophy of lymphoid tissues such as the bursa of Fabricius, thymus, and spleen; intestinal haemorrhage; and oedema of the brain were observed in the chicken. Histopathological examination revealed severe non-suppurative meningoencephalomyelitis characterised by neuronal necrosis, multifocal to diffuse gliosis, and perivascular cuffing of mononuclear cells, hemorrhagic necrosis of the trachea, intestines and bursa of Fabricius, and various degree of lymphoid depletion and necrosis of the lymphoid tissues. After ND was confirmed immunohistochemically, the NDV was propagated by inoculating tissue homogenate of the diseased chicken in embryonated eggs. Phylogenetic analysis based on the F gene nucleotide sequence revealed that this isolate belonged to genotype VII. The deduced amino acid sequence of the isolated NDV F protein at the cleavage site was (112)RRQKRF(117), which is typically found in virulent NDV isolates. Pathogenicity indexes such as the mean death time (MDT) and intracerebral pathogenicity index (ICPI) were 54 hr and 1.77, respectively. Pathological findings, phylogenetic analysis, amino acid sequence of the F protein cleavage site, and pathogenicity index test results revealed the NDV isolate, designated as NDV/Bali-1/07, to be a novel Indonesian velogenic NDV strain belonging to group VII.
Enzyme Production by Species of <i>Cephalosporium</i> (1963)

The culture filtrates of ten species of Cephalosporium, which had been grown under conditions of submerged culture, were tested for enzymatic activity against each of seven substrates. The latter included casein, gelatin, milk, hemoglobin, human plasma clots, starch, and N-acetyl-beta-D-glucosaminide. All organisms tested were active, but to varying degrees. The most pronounced activities were obtained against the proteinaceous substrates. Two unidentified species of Cephalosporium exhibited the highest over-all activities, but no one organism predominated for all enzymatic functions. The ability of a filtrate to degrade a specific substrate was not always correlated with its ability to attack other substrates. The fibrinolytic properties of three of the cephalosporia were of particular interest. alpha-Amylase activity was not significant. The results obtained suggest the possible use of selected species of Cephalosporium as sources of a variety of microbial enzymes.
The effectiveness of a piezoelectric bimorph to perform mechanical work against various spring-type loads (1991)

The equations governing the energy and work relations for a piezoelectric bimorph working against a spring-type load are derived. A work cycle is assumed in which a piezoelectric bimorph pushes against a spring, compressing it, after which the spring is latched in position, ready to transfer its energy in a process where it can be used. The energy stored in the spring is calculated and related to the electrical energy taken in by the bimorph to enable it to compress the spring. An effectiveness μ is defined as the ratio of the energy transferred by the bimorph and the energy put in by the generator. Three types of springs are considered: a helical spring, attached at the tip to generate a moment M at the tip that depends on the rotation α of the tip; a coil spring, attached at the tip to provide a force F, proportional to the deflection; and a gas spring acting uniformly over the entire length of the bimorph, with a pressure p that is proportional to the displaced volume V. The effectivenesses μM, μF, μP are calculated. The maximum effectiveness is found as the spring constant KM, KF, Kp is varied.
Novel lithium-manganese composite oxide for the cathode of lithium secondary batteries (1990)

This paper reports on a heat treated LiNO{sub 3}-MnO{sub 2} mixture in the presence of nitric acid that has shown rechargeability as a cathode material for lithium secondary batteries. XRD patterns of this compound are different from those of known Li-Mn composite oxides, such as LiMn{sub 2}O{sub 4} or Li{sub 2}NmO{sub 3}. The presence of nitric acid during heating is preferable for reducing the content of the by-product such as LiMn{sub 2}O{sub 4}.
Interaction of R17 Coat Protein With Its RNA Binding Site For Translational Repression (1983)

The interaction between bacteriophage R17 coat protein and its RNA binding site for translational repression was studied as an example of a sequence-specific RNA-protein interaction. A nitrocellulose filter retention assay is used to demonstrate equimolar binding between the coat protein and a synthetic 21 nucleotide RNA fragment. The Kd at 2 degrees C in a buffer containing 0.19 M salt is about 1 nM. The relatively weak ionic strength dependence of Ka and a delta H = -19 kcal/mole indicates that most of the binding free energy is due to non-electrostatic interactions. Since a variety of RNAs failed to compete with the 21 nucleotide fragment for coat protein binding, the interaction appears highly sequence specific. We have synthesized more than 30 different variants of the binding site sequence in order to identify the portions of the RNA molecule which are important for protein binding. Out of the five single stranded residues examined, four were essential for protein binding whereas the fifth could be replaced by any nucleotide. One variant was found to bind better than the wild type sequence. Substitution of nucleotides which disrupted the secondary structure of the binding fragment resulted in very poor binding to the protein. These data indicated that there are several points of contact between the RNA and the protein and the correct hairpin secondary structure of the RNA is essential for protein binding.
The importance of the macrophage within the human endometrium (2012)

The human endometrium is exposed to cyclical fluctuations of ovarian-derived sex steroids resulting in proliferation, differentiation (decidualization), and menstruation. An influx of leukocytes (up to 15% macrophages) occurs during the latter stages of the menstrual cycle, including menses. We believe the endometrial macrophage is likely to play an important role during the menstrual cycle, especially in the context of tissue degradation (menstruation), which requires regulated repair, regeneration, and phagocytic clearance of endometrial tissue debris to re-establish tissue integrity in preparation for fertility. The phenotype and regulation of the macrophage within the endometrium during the menstrual cycle and interactions with other cell types that constitute the endometrium are currently unknown and are important areas of study. Understanding the many roles of the endometrial macrophage is crucial to our body of knowledge concerning functionality of the endometrium as well as to our understanding of disorders of the menstrual cycle, which have major impacts on the health and well-being of women.
Composite Nanofiber Network Membranes for PEM Fuel Cells (2008)

A new class of proton-exchange membranes has been developed and characterized, where an interconnected network of proton conducting polymer nanofibers is embedded in an inert (non-conducting) polymer matrix. In the present study the nanofiber network membrane contained electrospun fibers from sulfonated poly(arylene ether sulfone) solutions (with/without sulfonated polyhedral oligomeric silsesquioxane, sPOSS). The membranes were characterized in terms of morphology, proton conductivity, and water uptake. In-plane proton conductivity was measured using a BekkTech cell that was placed in a controlled temperature/humidity chamber. The data show: (1) There was a modest increase in nanofiber > 50%.membrane conductivity when the IEC of the fibers was increased from 2.1 to 2.6 mmol/g (in the absence of sPOSS), (2) There was a substantial increase in membrane conductivity when sPOSS was added to the fibers, and (3) The proton conductivity of the sPOSS-loaded membranes was significantly higher than that for a commercial Nafion 212 sample at 30oC for a relative humidity