gebhart/patrepeval huggingface dataset:
Short-Term Effect of Antibiotics on Human Gut Microbiota (2014)

From birth onwards, the human gut microbiota rapidly increases in diversity and reaches an adult-like stage at three years of age. After this age, the composition may fluctuate in response to external factors such as antibiotics. Previous studies have shown that resilience is not complete months after cessation of the antibiotic intake. However, little is known about the short-term effects of antibiotic intake on the gut microbial community. Here we examined the load and composition of the fecal microbiota immediately after treatment in 21 patients, who received broad-spectrum antibiotics such as fluoroquinolones and β-lactams. A fecal sample was collected from all participants before treatment and one week after for microbial load and community composition analyses by quantitative PCR and pyrosequencing of the 16S rRNA gene, respectively. Fluoroquinolones and β-lactams significantly decreased microbial diversity by 25% and reduced the core phylogenetic microbiota from 29 to 12 taxa. However, at the phylum level, these antibiotics increased the Bacteroidetes/Firmicutes ratio (p = 0.0007, FDR = 0.002). At the species level, our findings unexpectedly revealed that both antibiotic types increased the proportion of several unknown taxa belonging to the Bacteroides genus, a Gram-negative group of bacteria (p = 0.0003, FDR<0.016). Furthermore, the average microbial load was affected by the treatment. Indeed, the β-lactams increased it significantly by two-fold (p = 0.04). The maintenance of or possible increase detected in microbial load and the selection of Gram-negative over Gram-positive bacteria breaks the idea generally held about the effect of broad-spectrum antibiotics on gut microbiota.
A model for the formation and interconversion of protein A-immunoglobulin G soluble complexes. (1984)

We present a model for the formation and interconversion of the soluble complexes formed by reacting staphylococcal protein A (SpA) with rabbit immunoglobulin G (IgG) antibodies. The basic elements of the model are developed from reported hydrodynamic and electron microscopic studies of these complexes (see accompanying companion paper), together with established structural and binding properties of IgG and SpA. The model includes specific symmetry and binding requirements for IgG-SpA combination, and a steric constraint between neighboring IgG molecules. We discuss how such a constraint could influence the assembly and distribution of equilibrium complexes. After formulating a convenient symbolism for representing IgG-SpA complexes, the suggested model is used to construct plausible structures for the four predominant complexes observed in moderate SpA excess. Distributions of these stable complexes at different IgG:SpA ratios, together with LeChatelier's principle and a straightforward thermodynamic derivation, are used to predict likely arrangements of equilibrium structures. Also, a scale model of the unique IgG4-SpA2 complex formed in IgG excess is constructed from reported x-ray diffraction and amino acid sequence data. An intuitive thermodynamic argument is used to show that the suggested steric constraint could cause the rather unprecedented reversible transformation of the four 7 to 15S complexes into the unique 17S complex. A computer simulation is used to predict equilibrium concentrations of the various proposed complexes at different IgG:SpA ratios. In support of the suggested structures, the calculated thermodynamic distributions agree surprisingly well with those measured with the ultracentrifuge. We point out how the proposed arrangements of the complexes, and in particular the 17S complex, can account for many of their novel properties, such as antigen-induced conformational changes. Reported differences in complement activation and precipitate formation by SpA complexes formed with antibodies from various species are also discussed with regard to possible differences in structural arrangements of the complexes.
Field Evaluation of Alternative Earthen Final Covers (2001)

ABSTRACT Five methods to assess percolation rate from alternative earthen final covers (AEFCs) are described in the context of the precision with which the percolation rate can be estimated: trend analysis, tracer methods, water balance method, Darcy's Law calculations, and lysimetry. Trend evaluation of water content data is the least precise method because it cannot be used alone to assess the percolation rate. The precision of percolation rates estimated using tracer methods depends on the tracer concentration, percolation rate, and the sensitivity of the chemical extraction and analysis methods. Percolation rates determined using the water balance method have a precision of approximately 100 mm/yr in humid climates and 50 mm/yr in semiarid and drier climates, which is too large to demonstrate that an AEFC is meeting typical equivalency criterion (30 mm/yr or less). In most cases, the precision will be much poorer. Percolation rates computed using Darcy's Law with measured profiles of water content and matric suction typically have a precision that is about two orders of magnitude (or more) greater than the computed percolation rate. The Darcy's Law method can only be used for performance assessment if the estimated percolation rate is much smaller than the equivalency criterion and preferential flow is not present. Lysimetry provides the most precise estimates of percolation rate, but the precision depends on the method used to measure the collected water. The lysimeter used in the Alternative Cover Assessment Program (ACAP), which is described in this paper, can be used to estimate percolation rates with a precision between 0.00004 to 0.5 mm/yr, depending on the measurement method and the flow rates. KEY WORDS: alternative coverevapotranspirationtranspirationstoragepercolationequivalencyfield demonstrationwater balanceAEFC
The characterization of IBF as a new selective dopamine D-2 receptor imaging agent. (1990)

The in vivo and in vitro studies of a new iodinated benzamide analog, [125I]IBF,5-iodo-7-N-[(1-ethyl-2-pyrrolidinyl)methyl]carboxamido-2,3- dihydrobenzofuran as a potential central nervous system (CNS) D-2 dopamine receptor imaging agent were investigated. In vivo biodistribution of IBF in rat indicated that this agent concentrated in the striatum region and displayed a remarkably high target-to-nontarget ratio (striatum/cerebellum = 48 at 120 min post-injection). The in vitro binding studies suggested that IBF binds selectively to D-2 dopamine receptors with high affinity and low nonspecific binding (Kd = 0.106 +/- 0.015 nM, Bmax = 448 +/- 18.2 fmole/mg protein). Ex vivo autoradiography results in rats further confirmed the high uptake and retention of this agent in the basal ganglia region. The planar images of monkey brains (lateral view of the head) after i.v. injection of [123I]IBF clearly demonstrated that D-2 dopamine receptors can be visualized. With the excellent in vivo stability to deiodination and high target-to-nontarget ratio, [123I]IBF may be useful as a CNS D-2 dopamine receptor imaging agent for single photon emission computed tomography (SPECT) in humans.
Interpretation of Dual Chamber Pacemaker Electrocardiograms (1985)

A diagramming system has been developed to assist in interpreting dual chamber pacemaker electrocardiograms. The system is based on the ladder diagram principle but uses two separate ladders, one for the ECG allowing proper representation of atrial A-V and ventricular activation, and a second ladder diagram below it for pacemaker events. The system is applicable to all current single and dual chamber pacing modes and is easy to draw. The ladder diagram allows the logical sequence of timing events to be easily illustrated, and pacemaker malfunction becomes clearly recognizable as a conflict between the ECG events ladder and the pacemaker timing ladder. The system is easy to apply and may eventually prove suitable for automatic generation by computer utilizing sophisticated pacemaker telemetry.
Sacrificial Adhesion Promotion Layers for Copper Metallization of Device Structures (2004)

The adhesion of copper films to adjacent device layers including TiN, Ta, and TaN diffusion barriers is a crucial reliability issue for integrated circuits. We report that ultrathin layers of poly(acrylic acid) (PAA) prepared on barrier surfaces or on the native oxide of Si wafers dramatically increase the interfacial adhesion of Cu films deposited by the H2 assisted reduction of bis(2,2,7-trimethyloctane-3,5-dionato)copper in supercritical carbon dioxide. Similar improvements were achieved on Si wafers using a simple vapor phase exposure of the substrate to acrylic acid prior to metallization. The deposited films and the substrate/Cu interfaces were analyzed by X-ray photoelectron spectroscopy (XPS), electron microscopy, atomic force microscopy, and variable-angle spectroscopic ellipsometry. No trace of the adhesion layer was detected at the interface, indicating it was sacrificial at the deposition conditions used. Moreover, the presence and subsequent decomposition of the PAA layer during deposition substantially reduced or eliminated metal oxides at the substrate interface. For depositions on PAA-treated Si wafers, copper was present primarily as Cu0 at the interface and Si was present only as Si0. On PAA-treated Ta substrates, XPS analysis indicated Ta was present primarily as Ta0 at the metallized interface whereas Ta2O5 dominated the interface of samples prepared without the adhesion layers. The technique can be extended to patterned substrates using adsorption of acrylic acid or thermal/UV polymerization of acrylic acid.
Twitter user behavior understanding with mood transition prediction (2012)

Human moods continuously change over time. Tracking moods can provide important information about psychological and health behavior of an individual. Also, history of mood information can be used to predict the future moods of individuals. In this paper, we try to predict the mood transition of a Twitter user by regression analysis on the tweets posted over twitter time line. Initially, user tweets are automatically labeled with mood labels from time 0 to t-1. It is then used to predict user mood transition information at time t. Experiments show that SVM regression attained less root-mean-square error compared to other regression approaches for mood transition prediction.
High performance UTBB FDSOI devices featuring 20nm gate length for 14nm node and beyond (2013)

We report, for the first time, high performance Ultra-thin Body and Box (UTBB) FDSOI devices with a gate length (L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</sub> ) of 20nm and BOX thickness (T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">BOX</sub> ) of 25nm, featuring dual channel FETs (Si channel NFET and compressively strained SiGe channel PFET). Competitive effective current (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff</sub> ) reaches 630μA/μm and 670μA/μm for NFET and PFET, respectively, at off current (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</sub> ) of 100nA/μm and V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dd</sub> of 0.9V. Excellent electrostatics is obtained, demonstrating the scalability of these devices to14nm and beyond. Very low A <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Vt</sub> (1.3mV·μm) of channel SiGe (cSiGe) PFET devices is reported for the first time. BTI was improved >20% vs a comparable bulk device and evidence of continued scalability beyond 14nm is provided.
Comparison of Two Methods for Determining Amylase Activity in Serum and Urine (1971)

Abstract Two methods for estimating amylase activity in serum and urine are compared. A method that uses a chromogenic substrate in a kit was shown to be preferable over the older amyloclastic procedure, which uses starch substrates. The precision of both methods was determined.
Safety and Efficacy of <i>Juniperus ashei</i> Sublingual-Swallow Ultra-Rush Pollen Immunotherapy in Cypress Rhinoconjunctivitis (2006)

The tolerability and safety of high-dose ultra-rush SLIT were comparable to those reported in previous SLIT studies. SLIT with J. ashei extract, due to its high Jun a 1 content, significantly reduced nasal steroid consumption in patients allergic to European cypress.
Influence of cell background on pharmacological rescue of mutant CFTR (2010)

Cystic fibrosis (CF) is caused by mutations in the CFTR chloride channel. Deletion of phenylalanine 508 (F508del), the most frequent CF mutation, impairs the maturation and gating of the CFTR protein. Such defects may be corrected in vitro by pharmacological modulators named as correctors and potentiators, respectively. We have evaluated a panel of correctors and potentiators derived from various sources to assess potency, efficacy, and mechanism of action. For this purpose, we have used functional and biochemical assays on two different cell expression systems, Fischer rat thyroid (FRT) and A549 cells. The order of potency and efficacy of potentiators was similar in the two cell types considered, with phenylglycine PG-01 and isoxazole UCCF-152 being the most potent and least potent, respectively. Most potentiators were also effective on two mutations, G551D and G1349D, that cause a purely gating defect. In contrast, corrector effect was strongly affected by cell background, with the extreme case of many compounds working in one cell type only. Our findings are in favor of a direct action of potentiators on CFTR, possibly at a common binding site. In contrast, most correctors seem to work indirectly with various mechanisms of action. Combinations of correctors acting at different levels may lead to additive F508del-CFTR rescue.
Helical Structure of Disodium 5′-Guanosine Monophosphate Self-Assembly in Neutral Solution (2009)

Nucleic acid molecules (DNA and RNA) are formed by linking many different basic units known as nucleotides together via covalent phosphodiester bonds. Nucleic acid molecules often form helical structures known as B-DNA (right-handed), A-DNA/RNA (right-handed), and Z-DNA (left-handed). We have found that spontaneous self-assembly of just one nucleotide, guanosine 5'-monophosphate (5'-GMP), leads to formation of a right-handed helix in neutral solution. The linkage between individual 5'-GMP molecules along the helix is provided by hydrogen bonds, as opposed to the covalent phosphodiester bonds found in regular polynucleotides. The most surprising finding is that this right-handed 5'-GMP helix has alternating C2'-endo and C3'-endo sugar puckers along the helical strand, a situation only seen to date in left-handed Z-DNA. The self-organized structure of 5'-GMP provides a perfect condition for phosphodiester bond formation which may provide a clue for formation of RNA oligomers under prebiotic conditions. We anticipate that similar helical structures could exist in other nucleic acid systems.
Anti‐allergic effects of <i>Lactobacillus crispatus</i> KT‐11 strain on ovalbumin‐sensitized BALB/c mice (2010)

In this study, we investigated the effects of oral ingestion of Lactobacillus crispatus KT-11 strain (KT-11) on the immune response in an allergic rhinitis mouse model, ovalbumin (OVA)-sensitized BALB/c mice. Sneezing activity in mice that were administered a KT-11-supplemented diet was significantly lower than that in mice administered a KT-11-free diet (control diet) at age 11 weeks. We found that serum OVA-specific immunoglobulin E (IgE) levels and total number of interleukin (IL)-4(+) CD4(+) spleen cells in mice that were administered a KT-11-supplemented diet were significantly lower than in mice administered a control diet. The ratio of spleen interferon-γ(+) CD4(+) /IL-4(+) CD4(+) cells was higher in the mice administered the KT-11-supplemented diet compared to that in mice administered the control or L. rhamnosus GG-supplemented diet. In contrast, the number of CD11b(+) CD80(+) and FcεRIα(+) CD117(+) cells was significantly lower in mice administered the KT-11-supplemented diet. These results suggested that KT-11 reduced OVA-induced allergic symptoms in BALB/c mice via the adjustment of the T helper type 1/T helper type 2 balance, and a decrease in the number of antigen-presenting cells and high affinity IgE receptor-positive mast cells.
Leaf blast suppression by pre-inoculation of some incompatible lesion-type isolates of Pyricularia oryzae. (1990)

The different lesion-type isolates of incompatible races of Pyricularia oryzae were used to compare the potential for suppressing leaf blast by pre-inoculation to rice plants. Although the leaf blast was suppressed by pre-inoculating any incompatible isolate of blast fungus, there were some differences in the degree of leaf blast suppression among the isolates used. The highest suppression of leaf blast was observed when the isolates inciting the quite small eyespots with brown margins (bg-type) were pre-inoculated to rice plants.
Femtosecond laser processing of crystalline silicon (2005)

This paper reports the surface morphologies and ablation of crystalline silicon wafers irradiated by infra-red 775 nm Ti:sapphire femtosecond laser. The effects of energy fluences (below and above single-pulse modification) with different number of pulses were studied. New morphological features such as pits, cracks formation, Laser-Induced Periodic Surface Structures (LIPSS) and ablation were observed. The investigation indicated that there are two distinct mechanisms under femtosecond laser irradiation: low fluence regime with different morphological features and high fluence regime with high material removal and without complex morphological features.
A Web-Based System for Family Health Record (2007)

During the past few years, a new and fast growing trend, defined as Personalized healthcare (pHealth) rose. It concerns the individualization of prevention, treatment and well being procedures available through the healthcare system. pHealth is realized through a number of capabilities stemming from the micro and nanosciences, information and communication technologies (ICTs). Electronic health record is one of them. Electronic health records are a fundamental support needed not only by healthcare providers, but also for individual patients. The idea of individuals collecting, organizing, and keeping in file folders their own paper-based medical information is not new. The widespread diffusion of the ICTs and the Internet has made this idea feasible using personal computers, personal digital assistants or smart-phones. We considered the management of healthcare data in the familiar environment and we designed and developed a system for family health record. The system permits an easy compilation and provides an effective visualization of the clinical data concerning family members also for friendly printing tasks.
Multimode optical-fiber loss-modulation acoustic sensor (1979)

We have measured the loss coefficient of the simple bending-loss transducer shown schematically in Fig. 1. The transducer structure consists of two mating, ridged plates (2.5 cm x 6 cm). The fiber is placed between the two plates and compressed with a variable load, and the resulting transmission loss is measured. We have investigated the response of various fiber types and also the effects of initial launch conditions. Figure 2 shows data from a short (2-m) length of Corning step-index fiber.
Identification of a<i>Naegleria fowleri</i>Membrane Protein Reactive with Anti-Human CD59 Antibody (2006)

Naegleria fowleri, the causative agent of primary amebic meningoencephalitis, is resistant to complement lysis. The presence of a complement regulatory protein on the surface of N. fowleri was investigated. Southern blot and Northern blot analyses demonstrated hybridization of a radiolabeled cDNA probe for CD59 to genomic DNA and RNA, respectively, from pathogenic N. fowleri. An 18-kDa immunoreactive protein was detected on the membrane of N. fowleri by Western immunoblot and immunofluorescence analyses with monoclonal antibodies for human CD59. Complement component C9 immunoprecipitated with the N. fowleri "CD59-like" protein from amebae incubated with normal human serum. In contrast, a gene or protein similar to CD59 was not detected in nonpathogenic, complement-sensitive N. gruberi amebae. Collectively, our studies suggest that a protein reactive with antibodies to human CD59 is present on the surface of N. fowleri amebae and may play a role in resistance to lysis by cytolytic proteins.
Comparative study of binary intensity mask and attenuated phase shift mask using hyper-NA immersion lithography for sub-45nm era (2008)

In this paper, we will present comparison of attenuated phase shift mask and binary intensity mask at hyper-NA immersion scanner which has been the main stream of DRAM lithography. Some technical issues will be reported for polarized illumination in hyper-NA imaging. One att.PSM (Phase Shift Mask) and three types of binary intensity mask are used for this experiment; those are ArF att.PSM ( MoSi:Å ), thick Cr ( 1030Å ) BIM (Binary Intensity Mask), thin Cr ( 590Å ) BIM and multi layer ( Cr:740Å / MoSi:930Å ) BIM. Simulation and experiment with 1.35NA immersion scanner are performed to study influence of mask structure, process margin and effect of polarization. Two types of DRAM cell patterns are studied; one is an isolation pattern with a brick wall shape and another is a storage node pattern with contact hole shape. Line and space pattern is also studied through 38nm to 50nm half pitch for this experiment. Lithography simulation is done by in-house tool based on diffused aerial image model. EM-SUITE is also used in order to study the influence of mask structure and polarization effect through rigorous EMF simulation. Transmission and polarization effects of zero and first diffraction order are simulated for both att.PSM and BIM. First and zero diffraction order polarization are shown to be influenced by the structure of masking film. As pattern size on mask decreases to the level of exposure wavelength, incident light will interact with mask pattern, and then transmittance changes for mask structure. Optimum mask bias is one of the important factors for lithographic performance. In the case of att.PSM, negative bias shows higher image contrast than positive one, but in case of binary intensity mask, positive bias shows better performance than negative one. This is caused by balance of amplitude between first diffraction order and zero diffraction order light. Process windows and mask error enhancement factors are measured with respect to various design rules, i.e., different k1 levels at fixed NA. In the case of one dimensional line and space pattern, thick Cr BIM shows the best performance through various pitches. But in case of two dimensional DRAM cell pattern, it is difficult to find out the advantage of BIM for sub-45nm. It needs further study for two dimensional patterns. Finally, it was observed that thick Cr binary intensity mask for sub-45nm has advantage for one dimensional line and space pattern.
On compression with two-way head machines (2002)

Motivated by the study of various kinds of machines as recognizers of formal languages, the authors compare the encoding and decoding power of finite state sequential machines and extensions thereof. They show that, with a forward moving head, the best compression achievable for a given sequence, to be decoded by a finite state decoder, is the same as the best ratio attainable for that sequence when encoded by a finite state information lossless encoder. They cannot gain in compression by allowing a finite state encoder to move its head back and forth on an input sequence, even if the decoder has unrestricted power. However, better compression can be achieved for specific infinite sequences using an unrestricted encoder and a two-way finite state decoder.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>