gebhart/patrepeval huggingface dataset:
Structural features and kinetic characterization of alanine racemase fromStaphylococcus aureus(Mu50) (2011)

Staphylococcus aureus is an opportunistic Gram-positive bacterium which causes a wide variety of diseases ranging from minor skin infections to potentially fatal conditions such as pneumonia, meningitis and septicaemia. The pathogen is a leading cause of nosocomial acquired infections, a problem that is exacerbated by the existence of methicillin- and glycopeptide antibiotic-resistant strains which can be challenging to treat. Alanine racemase (Alr) is a pyridoxal-5'-phosphate-dependent enzyme which catalyzes reversible racemization between enantiomers of alanine. As D-alanine is an essential component of the bacterial cell-wall peptidoglycan, inhibition of Alr is lethal to prokaryotes. Additionally, while ubiquitous amongst bacteria, this enzyme is absent in humans and most eukaryotes, making it an excellent antibiotic drug target. The crystal structure of S. aureus alanine racemase (Alr(Sas)), the sequence of which corresponds to that from the highly antibiotic-resistant Mu50 strain, has been solved to 2.15 Å resolution. Comparison of the Alr(Sas) structure with those of various alanine racemases demonstrates a conserved overall fold, with the enzyme sharing most similarity to those from other Gram-positive bacteria. Structural examination indicates that the active-site binding pocket, dimer interface and active-site entryway of the enzyme are potential targets for structure-aided inhibitor design. Kinetic constants were calculated in this study and are reported here. The potential for a disulfide bond in this structure is noted. This structural and biochemical information provides a template for future structure-based drug-development efforts targeting Alr(Sas).
A constant‐volume ventilator and gas recapture system for hyperpolarized gas MRI of mouse and rat lungs (2011)

Abstract We present a ventilator that enables high‐resolution proton and hyperpolarized gas MR imaging of mice and rats. The design differs from previous approaches by eliminating the need for a custom pneumatic valve located near the trachea. This permits the system to be constructed from off‐the‐shelf components and reduces dead volumes sufficiently to make HP gas MRI feasible in the mouse. The constant‐volume ventilator routinely ventilates mice and rats for period of time up to 6 hrs and maintains reproducible tidal volumes over extended image acquisition periods, as we demonstrate with high‐resolution 3D lung images in the mouse using 1 H, 3 He and 129 Xe. The ventilator is designed to deliver a constant tidal volume regardless of changes in airway resistance, which we demonstrate with 3 He MR images acquired during severe broncho‐constriction. While the images reveal clear airway narrowing, the 3 He signal intensity remained within ±10% of baseline level. Finally, given the paucity of 3 He and the high cost of enriched 129 Xe, the ventilator has been designed to enable the recapture of these rare gases and we demonstrate a compact system to compress and store them for subsequent reprocessing. We expect that this constant‐volume ventilator will be readily reproducible by other laboratories, which we facilitate by providing extensive parts lists, detailed wiring diagrams and complete plumbing schematics. © 2011 Wiley Periodicals, Inc. Concepts Magn Reson Part B (Magn Reson Engineering) 39B: 78–88, 2011
Hdac6 and Sirtuin Inhibitors Protect Against Tachypacing-Induced Contractile Dysfunction in in vitro and in vivo Models for Atrial Fibrillation. (2010)

Introduction: Atrial Fibrillation (AF) is the most common persistent clinical tachyarrhythmia. Its self-perpetuating nature is due to AF-induced remodeling of cardiomyocytes. Recently, it has been ...
Akkermansia muciniphila administration exacerbated the development of colitis-associated colorectal cancer in mice (2021)

Colorectal cancer (CRC) is one of the most common digestive tract malignancies and inflammation and gut microbiota are well-known key factors to influence CRC development. <i>Akkermansia mucinipila</i> is an important gram-negative anaerobic bacterium that can degrade mucin in gut. Previous studies suggested that <i>A. muciniphila</i> may affect inflammation and cell proliferation, but the relationship between <i>A. muciniphila</i> and CRC is not clarified. Here C57BL/6 mice were administrated with <i>A. muciniphila</i> or PBS and then treated with azoxymethane (AOM)/dextran sodium sulphate (DSS) to induce CRC. The mice receiving <i>A. muciniphila</i> administration had more serious weight loss, shorter colon length and more intestinal tumors than those receiving PBS administration after AOM/DSS treatment. More colon damage and less goblet cells were also observed in <i>A. muciniphila</i> treated mice. Furthermore, <i>A. muciniphila</i> administration induced more Ki67<sup>+</sup> proliferating cells, higher PCNA expression and elevated gene expression of proliferation-associated molecules including <i>Snrpd1</i>, <i>Dbf4</i> or <i>S100A9</i>. At early stage of CRC development, in comparison with controls, the mice receiving <i>A. muciniphila</i> administration also had more body weight loss and shorter colon length, as well as higher gene expression of inflammatory cytokines. Furthermore, the <i>in vitro</i> experimental results showed that the co-culture of colon epithelial cells with <i>A. muciniphila</i> enhanced the cell proliferation and gene expression of proliferation-associated molecules. Therefore, <i>A. mucinipila</i> may promote the formation of CRC in mice through increasing the early level of inflammation and the proliferation of intestinal epithelial cells.
ChemInform Abstract: Chiral Building Blocks from Amino Acids via an Electrochemical Key Step: Synthesis of (R)‐2‐tert‐Butyl‐3‐methoxycarbonyl‐1,3‐oxazolines from (S)‐Serine and (S)‐Threonine. (1988)

Abstract The hydroxyaminocarboxylic acids (I) are converted to the oxazolidinecarboxylic acids (VIII) which form the acetoxyoxazolidines (X) during an electrochemical reaction.
Absolute Peripheral Blood Lymphocyte Count and Subsequent Mortality of Elderly Men (1986)

In this 16-year longitudinal study of 105 healthy elderly men, we analyzed one aspect of immunosenescence--a decline in the absolute number of peripheral blood lymphocytes--with particular reference to its relationship with subsequent mortality. It was found that there was a significantly (P less than .01) lower absolute lymphocyte count (1432 +/- 55/mm3; mean +/- SEM) within three years of death when compared with five years (1719 +/- 89/mm3) or 10 years (1715 +/- 98/mm3) before death. There was no relationship between this decrease in lymphocytes and age at death, smoking status, or prior cardiac illness. Previous cross-sectional studies have yielded conflicting data on age-related decreases in lymphocytes which may have been the result of an unrecognized selection process that either eliminated or included subjects who were close to death.
Hyperconcentrated Sweet Whey, a New Culture Medium That Enhances Propionibacterium freudenreichii Stress Tolerance (2016)

In this study, we demonstrate that sweet whey, a dairy industry by-product, not only allows the growth of probiotic dairy propionibacteria, but also triggers a multitolerance response through osmoadaptation and general stress response. We also show that propionibacteria accumulate compatible solutes under these culture conditions, which might account for the limited loss of viability after spray drying. This work opens new perspectives for more energy-efficient production of dairy starters and probiotics.
A Fall and Near-Fall Assessment and Evaluation System (2009)

The FANFARE (Falls And Near Falls Assessment Research and Evaluation) project has developed a system to fulfill the need for a wearable device to collect data for fall and near-falls analysis. The system consists of a computer and a wireless sensor network to measure, display, and store fall related parameters such as postural activities and heart rate variability. Ease of use and low power are considered in the design. The system was built and tested successfully. Different machine learning algorithms were applied to the stored data for fall and near-fall evaluation. Results indicate that the Naïve Bayes algorithm is the best choice, due to its fast model building and high accuracy in fall detection.
Thermodynamic Investigation of Thin Films of Ethane Adsorbed on Magnesium Oxide (2005)

The layering properties of ethane on MgO(100) were measured between 91 and 144 K using high-resolution adsorption isotherms. In contrast to previous studies, the results demonstrate that only three layers are formed. The thermodynamic functions derived from the data (isosteric heat, differential enthalpy, and entropy of adsorption) compare well with literature values and show a steady trend toward the bulk properties as the number of layers increased. Phase transitions for two of the layers were identified by monitoring the changes in the two-dimensional isothermal compressibility as a function of chemical potential. Both of these phase transitions occur at approximately 127 K and within 1 K of each other. Through the use of neutron diffraction, it is possible to identify at least one solid surface phase that melts at approximately 75 K. The transition at 127 K is therefore a transition between a liquidlike phase and a hyper-critical fluid. A comparison is made between the present data and our recent study of methane on MgO.
The Development of Therapeutic Antibodies That Neutralize Homologous and Heterologous Genotypes of Dengue Virus Type 1 (2010)

Antibody protection against flaviviruses is associated with the development of neutralizing antibodies against the viral envelope (E) protein. Prior studies with West Nile virus (WNV) identified therapeutic mouse and human monoclonal antibodies (MAbs) that recognized epitopes on domain III (DIII) of the E protein. To identify an analogous panel of neutralizing antibodies against DENV type-1 (DENV-1), we immunized mice with a genotype 2 strain of DENV-1 virus and generated 79 new MAbs, 16 of which strongly inhibited infection by the homologous virus and localized to DIII. Surprisingly, only two MAbs, DENV1-E105 and DENV1-E106, retained strong binding and neutralizing activity against all five DENV-1 genotypes. In an immunocompromised mouse model of infection, DENV1-E105 and DENV1-E106 exhibited therapeutic activity even when administered as a single dose four days after inoculation with a heterologous genotype 4 strain of DENV-1. Using epitope mapping and X-ray crystallographic analyses, we localized the neutralizing determinants for the strongly inhibitory MAbs to distinct regions on DIII. Interestingly, sequence variation in DIII alone failed to explain disparities in neutralizing potential of MAbs among different genotypes. Overall, our experiments define a complex structural epitope on DIII of DENV-1 that can be recognized by protective antibodies with therapeutic potential.
ChemInform Abstract: Horseradish Peroxidase‐Catalyzed Enantioselective Reduction of Racemic Hydroperoxy Homoallylic Alcohols: A Novel Enzymatic Method for the Preparation of Optically Active, Unsaturated Diols and Hydroperoxy Alcohols. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Currently Used Markers for CTC Isolation - Advantages, Limitations and Impact on Cancer Prognosis (2011)

Circulating tumor cells (CTC) released from primary tumor tissues into the bloodstream or lymphatic vessels are able to colonize distant organs giving rise to metastasis, which is the major factor contributing to poor survival of cancer patients. Thus, molecular characterization of CTC is thought to hold the key to enable an early clinical assessment of metastasis and to lead to improved therapeutic measurements. A number of markers have been described for the detection of CTC. However, for CTC isolation from blood samples only six markers have been used up to now. CTC isolation is a prerequisite of a better molecular characterization of these rare cells. Thus, we have focused on these six markers. Current approaches to capture CTC by specific marker molecules are still complex, and characterized by poor yield and low purity. This mini-review, which is not meant to be exhaustive, is specifically focused on what markers have been used for isolation of CTCs derived from solid cancers and on what are the advantages, limitations and impact of these markers. It aims to attract the interest of oncologists to this new exciting research field and to help them to critically review the wide variety of reported markers with sometimes conflicting results, in order to find better criteria how to identify references expected to provide reliable clinical information. MEDLINE and PubMed databases were searched using the keywords “circulating tumor cells”, “CTC isolation” and “surface markers”. Reviews, casecontrolled studies and reports published from 1989 through 2011 in English were analyzed, and the six markers EpCAM, E phB4, E GFR, C EA, H ER2 and MUC-1 were chosen for further discussion.
Top-Down Layout for Hierarchical Custom Design (1987)

Champ, a chip floor-plan program, and Alpha, an automatic cell placement and routing system, provide a method for hierarchical custom VLSI design that is highly automated and completely top-down. The system can handle standard cell blocks as well as macro cells such as RAMs, ROMs, PLAs. Champ consists of initial block placement and block packing Designers can execute initial block placement either manually or automatically using a method based on attractive-repulsive forces. Block packing is performed automatically or interactively through the moving and reshaping of blocks, which is done as the chip boundaries are being shrunk. Following the floor-plan design, Alpha automatically executes cell placement and routing. Using Champ/Alpha, only seven mandays are needed to design a 20,000-gate VLSI layout, using a predesigned standard cell library and predesigned macro cells.
Tamoxifen augments the innate immune function of neutrophils through modulation of intracellular ceramide (2015)

Tamoxifen is a selective oestrogen receptor modulator widely used for the treatment of breast cancer. In addition to its activity as an oestrogen receptor agonist/antagonist, tamoxifen also modulates sphingolipid biosynthesis, which has been shown to play an important role in the regulation of neutrophil activity. Here, we find that tamoxifen stimulation enhances several pro-inflammatory pathways in human neutrophils, including chemotaxis, phagocytosis and neutrophil extracellular trap (NET) formation. The enhancement of NET production occurs via a ceramide/PKCζ-mediated pathway, and treatment with synthetic ceramide is sufficient to promote NET formation. Pretreatment of human neutrophils with tamoxifen boosts neutrophil bactericidal capacity against a variety of pathogens in vitro and enhances clearance of the leading human pathogen methicillin-resistant Staphylococcus aureus in vivo. Our results suggest that tamoxifen, and the lipid signalling pathways it modulates, merit further exploration as targets for boosting host innate immune function.
Design and Application of GPRS Wjreless Data transmission System (2004)

For the remarkable advantage of GPRS communication technology applying to middle and low speed rate data transmission, a scheme for system of GPRS wireless data transmission with high feasibility and high performance-price ratio is designed and implemented. The scheme is all-purpose and can be applied to many fields, such as industry control, finance industry and transportation, etc.
ChemInform Abstract: REACTIONS AND REARRANGEMENTS OF 5,6‐DISUBSTITUTED BICYCLO(2.1.1)HEXENES (1980)

Abstract Benzvalen (I) liefert bei der Halogenierung die beiden Dihalogenide (IIa) und (IIb), die sich leicht zu (IIIa) und (IIIb) umlagern.
Real-Time Detection of Slug Velocity in Microchannels (2020)

Microfluidics processes play a central role in the design of portable devices for biological and chemical samples analysis. The bottleneck in this technological evolution is the lack of low cost detection systems and control strategies easily adaptable in different operative conditions, able to guarantee the processes reproducibility and reliability, and suitable for on-chip applications. In this work, a methodology for velocity detection of two-phase flow is presented in microchannels. The approach presented is based on a low-cost optical signals monitoring setup. The slug flow generated by the interaction of two immiscible fluids {air and water} in two microchannels was investigated. To verify the reliability of the detection systems, the flow nonlinearity was enhanced by using curved geometries and microchannel diameter greater than 100 μ m . The optical signals were analyzed by using an approach in a time domain, to extract the slug velocity, and one in the frequency domain, to compute the slug frequency. It was possible to distinguish the water and air slugs velocity and frequency. A relation between these two parameters was also numerically established. The results obtained represent an important step in the design of non-invasive, low-cost portable systems for micro-flow analysis, in order to prove that the developed methodology was implemented to realize a platform, easy to be integrated in a System-on-a-Chip, for the real-time slug flow velocity detection. The platform performances were successfully validated in different operative conditions.
Oxidative injury in the nervous system (1998)

A free radical is a highly reactive chemical species that can react with organic macromolecules leading to cell and tissue damage and consequent functional disruption. Free radical or oxidative injury is increasingly recognized as an important factor in the pathophysiology of many human diseases, including those that affect the nervous system. This review summarizes important evidence implicating oxidative injury in the pathogenesis and progression of many important neurological disorders, including cerebrovascular disease, epilepsy, amyotrophic lateral sclerosis, and Huntington's disease. Results of controlled clinical trials of various antioxidant therapies in neurological disease performed to date are also highlighted.
Inorganic write-once disc for high speed recording (2003)

Write-once media has been used as storage media for medical data, official documents in order to prevent tampering. In addition, write-once media, such as CD-R or DVD-R are the most popular storage media for the computer in the world by reason of the interchangeability with the ROM disc. On the other hand, in order to obtain much larger capacity, DVR-blue system (/spl lambda/ = 405 nm, NA = 0.85) has been proposed. Many storage media, such as rewritable discs, write-once discs, ROM discs have been developed to apply this system. We have already reported high speed rewritable disc for this system. We have developed write-once disc for this system, too. And we have achieved wide data recording rate in the range of 35 Mbps to 140 Mbps on a disc with inorganic recording material. In this report, we show the read and write characteristics of the write-once disc with inorganic write-once material.
Decomposing Complex Cooperative Ligand Binding into Simple Components:  Connections between Microscopic and Macroscopic Models (2004)

Cooperative ligand-binding curves may often appear deceptively featureless, yet the underlying microscopic models may be rather complex, and the connection between them is not intuitive. To address some of these issues, we have extended the framework of the decoupled sites representation (DSR), previously developed in the context of pH titration, to include cooperative ligand binding as well as multiple conformations and multiple ligands. The extended framework is based on general thermodynamic arguments and is applicable to both anti-cooperative and cooperative binding. It can be used to elucidate the connection between the experimentally observed binding curves and parameters of underlying microscopic models. It is demonstrated that any binding curve can be decomposed into simple standard components that permit a model-independent physical interpretation in terms of noninteracting (quasi) groups. A simple mathematical form of the DSR is proposed, that is well-suited for use in least-squares fitting of experimental binding curves; the fitting procedure produces an integer parameter indicative of the degrees of cooperativity possible in the system. A two-site example is worked out in detail. We demonstrate that the same macroscopic binding behavior observed experimentally can have qualitatively different origins at the level of the underlying microscopic mechanism. We also show that, in the absence of the microscopic model, it is not possible to draw a meaningful distinction between non-cooperative and anti-cooperative scenarios. We define a new measure of cooperativity and show that it is in many cases more adequate than the Hill coefficient when used to characterize complex binding curves. The extended DSR is applied to experimental data sets on oxygen binding to carp hemoglobin at different pHs, where the framework is used to interpret the degree of cooperativity in the system and provides an indication as to whether specific microscopic models are applicable.
Photoluminescence fine structures in the fractional quantum Hall effect regime (2014)

We investigate polarization-resolved fine structure in the photoluminescence (PL) in the fractional quantum Hall effect regime at $B=4$--6 T, where small Zeeman energy allows spin-depolarized ground states. We observe up to five distinct peaks with characteristic polarization and temperature dependence in the vicinity of $\ensuremath{\nu}=1/3$ and quenching of the PL from triplet charged quasiexcitons at around $\ensuremath{\nu}=1/4$. Those findings appear to be consistent with results of exact diagonalization on a Haldane sphere including all spin configurations and are understood to be PL from fractionally charged quasiexcitons.
Focusing capability of a phononic crystal based on a hollow metallic structure (2014)

The dispersion curves of a phononic crystal (PC) based on a hollow metallic structure are presented. They exhibit a negative refraction dispersion branch and perfect refractive index matching with the surrounding water, leading to focusing capability. Numerical and experimental results are reported for a flat PC lens. The characteristics of the focal spot (intensity, dimensions, etc.) are numerically and experimentally investigated with the goal of finding the frequency of the optimal imaging performance.