gebhart/patrepeval huggingface dataset:
The Tail-Specific Protease Is Important for Legionella pneumophila To Survive Thermal Stress in Water and inside Amoebae (2021)

<i>Legionella pneumophila</i> (<i>Lp</i>) is an inhabitant of natural and human-made water systems, where it replicates within amoebae and ciliates and survives within biofilms. When <i>Lp</i>-contaminated aerosols are breathed in, <i>Lp</i> can enter the lungs and may infect human alveolar macrophages, causing severe pneumonia known as Legionnaires' disease. <i>Lp</i> is often found in hot water distribution systems (HWDS), which are linked to nosocomial outbreaks. Heat treatment is used to disinfect HWDS and reduce the concentration of <i>Lp</i> However, <i>Lp</i> is often able to recolonize these water systems, indicating an efficient heat shock response. Tail-specific proteases (Tsp) are typically periplasmic proteases implicated in degrading aberrant proteins in the periplasm and important for surviving thermal stress. In <i>Lp</i> Philadelphia-1, Tsp is encoded by the <i>lpg0499</i> gene. In this paper, we show that Tsp is important for surviving thermal stress in water and for optimal infection of amoeba when a shift in temperature occurs during intracellular growth. We also demonstrate that Tsp is expressed in the postexponential phase but repressed in the exponential phase and that the <i>cis</i>-encoded small regulatory RNA Lpr17 shows the opposite expression, suggesting that it represses translation of <i>tsp</i> In addition, our results show that <i>tsp</i> is regulated by CpxR, a major regulator in <i>Lp</i>, in an Lpr17-independent manner. Deletion of CpxR also reduced the ability of <i>Lp</i> to survive heat shock. In conclusion, our study shows that Tsp is likely an important factor for the survival and growth of <i>Lp</i> in water systems.<b>IMPORTANCE</b><i>Lp</i> is a major cause of nosocomial and community-acquired pneumonia. <i>Lp</i> is found in water systems, including hot water distribution systems. Heat treatment is a method of disinfection often used to limit the presence of <i>Lp</i> in such systems; however, the benefit is usually short term, as <i>Lp</i> is able to quickly recolonize these systems. Presumably, <i>Lp</i> responds efficiently to thermal stress, but so far, not much is known about the genes involved. In this paper, we show that the Tsp and the two-component system CpxRA are required for resistance to thermal stress when <i>Lp</i> is free in water and when it is inside host cells. Our study identifies critical systems for the survival of <i>Lp</i> in its natural environment under thermal stress.
Crystal Structure and Electrochemical Performance of LiNi1-xCoxO2(x=0.0~1.0) According to Co Substitution (2003)

[ <TEX>$LiNi_{1-x}Co_xO_2\;(x=0.0,\;0.3,\;05,\;0.7,\;1.0)$</TEX> ]을 구연산법을 이용하여 합성하고, Co 치환량에 따른 결정구조와 리튬 이차전지 양극특성을 조사하였다 X-선 회절분석 결과로부터 Co치환량에 무관하게 모든 조성에서 단일상의 고용체를 형성함을 알 수 있었다. 또한 Rietveld 구조정산을 통하여 고용체의 결정구조가 Co 치환량에 따라 크게 변화함을 확인하였다. 즉, Co치환량이 적은 경우는 (x=0-0.5)는 격자상수의 비가 작은(c/a<4.98) 입방구조에 가까웠으며, Co치환량이 큰 경우(x^gt;0.7)는 격자상수의 비가 큰<TEX>$(c/a\geq4.98)$</TEX> 층상구조를 보였다. 이와 같은 차이는 electrochemical voltage spectroscopy를 통하여 확인할 수 있었는데, 고용체를 형성하고 있는 Co성분은 Co치환량이 적을 경우는 <TEX>$3.7V\;(vs.\;Li/Li^+)$</TEX>, 그리고 치환량이 클 경우는 <TEX>$3.92V\;(vs.\;Li/Li^+)$</TEX>에서 충전되는 현상을 보였다. [ <TEX>$LiNi_{1-x}Co_xO_2\;(x=0.0\~1.0)$</TEX> ] powders were synthesized by citrate method, and their crystal structures and electrochemical performance as the cathode material in Li secondary batteries were analyzed. X-ray diffraction analysis revealed that all the samples carry a single phase regardless of the Co substitution. The results of Rietveld refinement suggested that the crystal structure of solid solutions varies according to the Co substitution. When the Co substitution is low <TEX>$(x=0.3\~0.5)$</TEX>, the solid solutions carry a cubic-like structure with a relatively small value in the ratio of lattice parameters (c/a). The solid solutions made with a higher Co substitution (x=0.7), however, exhibit a layered structure with a higher c/a ratio. This difference was also observed in the electrochemical voltage spectroscopy (EVS) profiles, whereby the Co component in scarcely substituted materials shows a charging reaction at <TEX>$3.7V\;(vs.\;Li/Li^+)$</TEX>, but in the heavily substituted ones at 3.92V.
Strategies for dietary intervention studies in colon cancer (1981)

As a result of many studies in descriptive and analytic epidemiology, in animal carcinogenesis, and in the direct examination of body fluids for mutagens/carcinogens, it is possible to develop a list of dietary factors that may be associated with the high rate of colon cancer and related cancers in Western countries. This paper is concerned with the design of intervention studies to clarify which of these factors is important. The size of such intervention trials is influenced primarily by two factors: the incidence of the disease outcome studied in a control population and the magnitude of risk reduction in a treated group. Calculations based on a variety of assumptions suggest that a randomized trial in which cancer mortality is measured as the outcome of the intervention in a healthy population is probably too costly to be justified by current evidence linking the disease to diet. However, precursor lesions can be considered as an alternative outcome. The choice of the precursor lesion depends on the link to the disease in question, the prevalence of the lesion in the population, and the ease of detection. Recent developments in the application of endoscopic methods and in the description of the pathologic process leading to cancer suggest the use of gastrointestinal polyps as "precursor lesions" as the outcome of a trial. We illustrate these points with a protocol for a study in progress, a randomized double-blind study of the effect of ascorbic acid and alpha-Tocopherol on the rate of recurrence of colorectal polyps.
Oligomerization of the Macrophage Mannose Receptor Enhances gp120-mediated Binding of HIV-1 (2009)

C-type lectin receptors expressed on the surface of dendritic cells and macrophages are able to bind glycoproteins of microbial pathogens via mannose, fucose, and N-acetylglucosamine. Langerin on Langerhans cells, dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin on dendritic cells, and mannose receptor (MR) on dendritic cells and macrophages bind the human immunodeficiency virus (HIV) envelope protein gp120 principally via high mannose oligosaccharides. These C-type lectin receptors can also oligomerize to facilitate enhanced ligand binding. This study examined the effect of oligomerization of MR on its ability to bind to mannan, monomeric gp120, native trimeric gp140, and HIV type 1 BaL. Mass spectrometry analysis of cross-linked MR showed homodimerization on the surface of primary monocyte-derived dendritic cells and macrophages. Both monomeric and dimeric MR were precipitated by mannan, but only the dimeric form was co-immunoprecipitated by gp120. These results were confirmed independently by flow cytometry analysis of soluble monomeric and trimeric HIV envelope and a cellular HIV virion capture assay. As expected, mannan bound to the carbohydrate recognition domains of MR dimers mostly in a calcium-dependent fashion. Unexpectedly, gp120-mediated binding of HIV to dimers on MR-transfected Rat-6 cells and macrophages was not calcium-dependent, was only partially blocked by mannan, and was also partially inhibited by N-acetylgalactosamine 4-sulfate. Thus gp120-mediated HIV binding occurs via the calcium-dependent, non-calcium-dependent carbohydrate recognition domains and the cysteine-rich domain at the C terminus of MR dimers, presenting a much broader target for potential inhibitors of gp120-MR binding.
Streamlined System for Purifying and Quantifying a Diverse Library of Compounds and the Effect of Compound Concentration Measurements on the Accurate Interpretation of Biological Assay Results (2004)

As part of an overall systems approach to generating highly accurate screening data across large numbers of compounds and biological targets, we have developed and implemented streamlined methods for purifying and quantitating compounds at various stages of the screening process, coupled with automated "traditional" storage methods (DMSO, -20 degrees C). Specifically, all of the compounds in our druglike library are purified by LC/MS/UV and are then controlled for identity and concentration in their respective DMSO stock solutions by chemiluminescent nitrogen detection (CLND)/evaporative light scattering detection (ELSD) and MS/UV. In addition, the compound-buffer solutions used in the various biological assays are quantitated by LC/UV/CLND to determine the concentration of compound actually present during screening. Our results show that LC/UV/CLND/ELSD/MS is a widely applicable method that can be used to purify, quantitate, and identify most small organic molecules from compound libraries. The LC/UV/CLND technique is a simple and sensitive method that can be easily and cost-effectively employed to rapidly determine the concentrations of even small amounts of any N-containing compound in aqueous solution. We present data to establish error limits for concentration determination that are well within the overall variability of the screening process. This study demonstrates that there is a significant difference between the predicted amount of soluble compound from stock DMSO solutions following dilution into assay buffer and the actual amount present in assay buffer solutions, even at the low concentrations employed for the assays. We also demonstrate that knowledge of the concentrations of compounds to which the biological target is exposed is critical for accurate potency determinations. Accurate potency values are in turn particularly important for drug discovery, for understanding structure-activity relationships, and for building useful empirical models of protein-ligand interactions. Our new understanding of relative solubility demonstrates that most, if not all, decisions that are made in early discovery are based upon missing or inaccurate information. Finally, we demonstrate that careful control of compound handling and concentration, coupled with accurate assay methods, allows the use of both positive and negative data in analyzing screening data sets for structure-activity relationships that determine potency and selectivity.
Temporal Properties of High Frequency Intra-QRS Signals in Myocardial Infarction and Healthy Hearts - Temporale Eigenschaften von hochfrequenten Intra-QRS-Signalen nach Myokardinfarkt und bei Herzgesunden (2000)

The prevalence of late potentials after myocardial infarction depends on the site of the infarction. This may be caused by the different activation onsets of the anterior and inferior myocardial segments. Therefore, in anterior infarcts the high frequency signals may be concealed within the QRS whereas in the inferior infarcts they last beyond the end of the QRS. We compared the timing and the spatial patterns of high frequency intra-QRS signals (IQSs) in the different infarction sites. We investigated 14 patients with anterior infarcts, 17 patients with inferior infarcts, and 10 healthy subjects. 31-lead magnetocardiograms were recorded in left precordial position and averaged. The QRS signals were smoothed with a Savitzky-Golay filter. The smoothed QRS signals were subtracted from the measured ones. The difference of the signals (frequency band of about 60-200 Hz) representing the high frequency components was quantified. The percentage of the high frequency signals was calculated for the entire QRS, for the first and for the second half, respectively. We found that in patients with anterior infarcts the high frequency components predominantly appeared in the first half of the QRS whereas in inferior infarcts these components predominantly appeared in the second half of the QRS. The different infarction sites were associated with different spatial patterns of the high frequency signals on the body surface. In healthy subjects there was not such a preferential association of time intervals and high frequency signals. Late potentials are the special case of high frequency signals appearing in the terminal QRS. It is the general property of the myocardium to generate high frequency signals associated with the depolarization of infarcted tissue. The timing of such signals and the spatial distribution patterns on the body surface may help to identify the location of the sources.
A Review on Effects of Nanoparticles on Freshwater Single-Celled Microalga Chlorella Spps. (2021)

With the increasing development in the field of nanotechnology and increased use of nanomaterials, there has been also increase in the release of Nanoparticles in the environment. These nanoparticles sometimes act as pollutants for living organisms. Due to release of these nanoparticles in the water bodies, they easily impact the aquatic organisms. Algae being the primary producers and acting as a food for higher aquatic animals, when encountered with nanoparticles, negatively affected by them or through biomagnifications, are directly or indirect become susceptible and also harmful for further food chain. Nanoparticles also hinder the growth of algae, thus providing less biomass. This review analyses the recent work done on the effect of different nanoparticles on the cellular structure of one of the most economically useful algae Chlorella spp.
Plant populations track rather than buffer climate fluctuations (2010)

Climate change not only affects mean temperature and precipitation but also exacerbates temporal fluctuations in these conditions. However, we know relatively little about how species respond to such climate fluctuations, with respect to variation in vital rates (i.e. survival, growth and reproduction of individuals) and population fluctuations. We examine whether populations display evidence of buffering against environmental variation in one of two ways: (1) through negative covariances among vital rates, or (2) reduction of variation in those vital rates to which population growth is most sensitive. We analyse time series of demographic data for 40 plant species and show that there is no evidence for either of these mechanisms. In species in which there is evidence for vital rate covariation, positive covariances between reproduction and survival rates predominate, and tend to magnify the effect of variability. Increasing climate variability is therefore expected to increase population fluctuations and extinction risks.
Effect of guest capture modes on molecular recognition by a dynamic cavity array at the air–water interface: soft vs. tight and fast vs. slow (2005)

Dynamic aspects of molecular recognition at the air-water interface have been investigated using a monolayer of a steroid cyclophane SC(OH) which consists of the rigid 1,6,20,25-tetraaza[6.1.6.1]paracyclophane ring, connected to four steroid moieties (cholic acid) through flexible -lysine spacers. An aqueous fluorescent guest (TNS) can be reversibly captured by SC(OH) with a variation in the accompanying fluorescence emission upon compression and expansion of the SC(OH) monolayer. Tight capture, by compression of the monolayer to a high surface pressure, efficiently enhances fluorescence intensity because of suppression of formation of the non-emissive state. On the other hand, rapid motion of the reversible cavity formation by a high rate of compression and expansion of the monolayer results in better reproducibility in the fluorescence change than that obtained under a slower motion, which can be explained by the suppression of unfavorable structural relaxation within the monolayer structures. This result has connotations for the development of novel molecular devices and machines that operate through mechanically driven molecular recognition.
HER1/EGFR Inhibitor-Associated Rash: Future Directions for Management and Investigation Outcomes from the HER1/EGFR Inhibitor Rash Management Forum (2005)

Skin rash associated with HER1/epidermal growth factor receptor (EGFR) inhibitors is common. The lack of clinical and patient guidance for this often chronic and sometimes distressing side effect makes rash management and etiology investigation high priorities. To address this, oncologists and dermatologists with experience with HER1/EGFR inhibitors attended the HER1/EGFR Inhibitor Rash Management Forum. Recommendations include continued analysis of the correlation between rash and clinical outcome and improving the accuracy and reproducibility of terminology and grading systems. Because acne vulgaris has a unique pathology, and the pathology and etiology of rash are unclear yet distinct from acne vulgaris, using such terms as acne, acne-like, or acneiform should be avoided. Until there is a specific dermatological definition, rash is best described using phenotypic terms for its appearance and location. It is currently unknown which agents are best for treating rash. Clinical trials of rash treatments are urgently required, and suggestions for agents to consider are made based on current knowledge. The effect of dose reduction or interruption on rash should also be investigated. Secondarily infected rash may be more frequent than has been previously recognized, and some investigators favor empiric use of an oral antibiotic if this appears to be the case. Suggestions for patients include makeup to camouflage the rash and an emollient to prevent and alleviate skin dryness. The increasing use of HER1/EGFR-targeted agents makes managing rash important. We hope the outcomes from this Forum provide background for future studies.
The Quasi-Steady-State Approximation: Numerical Validation (1998)

The quasi-steady-state approximation (QSSA) of chemical kinetics is a mathematical way of simplifying the differential equations describing some chemical kinetic systems. Originally devised by biochemists on an ad hoc basis, it is now recognized as belonging to singular perturbation theory. Ideally, this theory provides an error estimate for the QSSA, but it is too complicated for general use. Various investigations of special cases, invoking exact solutions, give some indications of the applicability of the QSSA. But further clarification is called for, especially since the QSSA is virtually unavoidable in introductory texts on chemical kinetics, while at the same time it is open to misuse in practice. In this note, we explore first the graphical representation of exact numerical solutions of partially nondimensionalized forms of the kinetic equations of some small systems of pedagogic interest, and thereby show that the QSSA is more widely applicable than is often assumed.Secondly, qualitative discussions of singular perturbation theory and of numerical stiffness are shown to lead to a simple computational test of QSSA validity, which works with intricate and large systems. This procedure is illustrated for the case of the Oregonator.
Designing Optimal Risk Mitigation and Risk Transfer Mechanisms to Improve the Management of Earthquake Risk in Chile (2011)

The property losses from the Feb 27 th 2010 Maule earthquake are assessed as $18.1Bn paid for 38% by insurers, 47% by the Government of Chile and 15% by individuals and businesses. Including $4Bn damage to infrastructure and the costs of lost economic activity the total loss in 2010 values is estimated to have been close to $28Bn. The report considers policy options for expanding the proportion of future Chilean earthquake losses that would be covered via new and expanded risk transfer mechanisms: for low income homeowners, small commercial enterprises and government buildings. Consideration is also given to how the overall levels of earthquake risk in Chile could be reduced through targeted efforts at risk mitigation. Recommendations are made for how the insurance industry and government in Chile should expand the use of probabilistic catastrophe loss models for defining and pricing risk management options.
Design and Fabrication of Bow-tie-shaped Meander Microstrip Patch Antenna on 5GHz Application (2005)

In this paper, a meander-type microstrip patch antenna for application in 5GHz-band is designed and fabricated. To obtain enough bandwidth in VSWR bandwidth in VSWRdBi, Unidirectional pattern.
Mutation in clpxoo4158Reduces Virulence and Resistance to Oxidative Stress in Xanthomonas oryzae pv. oryzae KACC10859 (2011)

Cyclic AMP receptor-like protein (Clp), is known to be a global transcriptional regulator for the expression of virulence factors in Xanthomonas campestris pv. campestris (Xcc). Sequence analysis showed that Xanthomonas oryzae pv. oryzae (Xoo) contains a gene that is strongly homologous to the Xcc clp. In order to determine the role of the Clp homolog in Xoo, a marker exchange mutant of <TEX>$clp_{xoo4158}$</TEX> was generated. Virulence and virulence factors, such as the production of cellulase, xylanase, and extracellular polysaccharides (EPS) and swarming motility were significantly decreased in the <TEX>$clp_{xoo4158}$</TEX> mutant. Moreover, the mutation caused the strain to be more sensitive to hydrogen peroxide and to over-produce siderophores. Complementation of the mutant restored the mutation-related phenotypes. Expression of <TEX>$clp_{xoo4158}$</TEX>, assessed by reverse-transcription realtime PCR and clp promoter activity, was significantly reduced in the rpfB, rpfF, rpfC, and rpfG mutants. These results suggest that the clp homolog, <TEX>$clp_{xoo4158}$</TEX>, is involved in the control of virulence and resistance against oxidative stress, and that expression of the gene is controlled by RpfC and RpfG through a diffusible signal factor (DSF) signal in Xanthomonas oryzae pv. oryzae KACC10859.
New Adamantane Derivatives with Sigma Affinity and Antiproliferative Activity (2012)

The synthesis of 4-(1-adamantyl)-4,4-diarylbutylamines 1, 5-(1-adamantyl)-5,5-diarylpentylamines 2 and 6-(1-adamantyl)-6,6-diarylhexylamines 3 is described and the σ1, σ2-receptors and sodium channels binding affinity of compounds 1 were investigated. The in vitro activity of compounds 1, 2 and 3 against main cancer cell lines is significant. One of the most active analogs, 1a, had an interesting in vivo anticancer profile against the ovarian cancer cell line IGROV-1, which was associated with an anagelsic activity against the neuropathic pain induced by the main anticancer drugs.
Genome-wide analysis of mRNA targets for Caenorhabditis elegans FBF, a conserved stem cell regulator (2010)

Stem cells are essential for tissue generation during the development of multicellular creatures, and for tissue homeostasis in adults. The great therapeutic promise of stem cells makes understanding their regulation a high priority. PUF RNA-binding proteins have a conserved role in promoting self-renewal of germline stem cells. Here we use a genome-wide approach to identify putative target mRNAs for the Caenorhabditis elegans PUF protein known as FBF. We find that putative FBF targets represent approximately 7% of all protein-coding genes in C. elegans, implicating FBF as a broad-spectrum gene regulator. These putative FBF targets are enriched for regulators of meiotic entry and other components of the meiotic program as well as regulators of key developmental pathways. We suggest that these targets may be critical for FBF's role in stem cell maintenance. Comparison of likely FBF target mRNAs with putative PUF target mRNAs from Drosophila and humans reveals 40 shared targets, including several established stem cell regulators. We speculate that shared PUF targets represent part of a broadly used module of stem cell control.