gebhart/patrepeval huggingface dataset:
A roadmap of clustering algorithms: finding a match for a biomedical application (2008)

Clustering is ubiquitously applied in bioinformatics with hierarchical clustering and k-means partitioning being the most popular methods. Numerous improvements of these two clustering methods have been introduced, as well as completely different approaches such as grid-based, density-based and model-based clustering. For improved bioinformatics analysis of data, it is important to match clusterings to the requirements of a biomedical application. In this article, we present a set of desirable clustering features that are used as evaluation criteria for clustering algorithms. We review 40 different clustering algorithms of all approaches and datatypes. We compare algorithms on the basis of desirable clustering features, and outline algorithms' benefits and drawbacks as a basis for matching them to biomedical applications.
Effect of external magnetic field on peroxidase synthesis and its activation during germination in wheat (1993)

The activity of peroxidase (POD)of wheat embryos increased gradually ingermination. The POD activity in ger-mination could be improved with mag-netic field. Electropherogram showedthat magnetic field induced two PODisozymic bands. Magnetic field treat-ment increased protein content. Therewas very significant positive correlationbetween POD activity and protein con-tent. This suggested that POD activityincrease could be due to an increase inenzyme protein synthesis. Cycloheximide (CHM ) inhibitedthe increase of POD activity in embryosduring germination and decreased thepromotive effect of magnetic field onPOD activity, thus proving that the in-crease of POD activity in germinatonwas due to the synthesis of POD enzymeprotein. Magnetic field could improvePOD synthesis. Actinomyin D (AMD)had not influence on the increase ofPOD activity in germination and thepromotion of magnetic field as well. In-dicating that the reason of POD synthe-sis was the translation from long--livemRNA and that the major link of syn-thesis of POD in germination promotedby magnetic field lied in translationstep. Electropherogram showed thatCHM inhibited gene expression of threebands and AMD had not effect. Mag-netic field deepened significantly the dyeof one band, therefore, magnetic fieldcould promote gene expression of specif-ic POD isozyme. Magnetic field in-creased speific activity of POD in thepresence of CHM in the early stage ofgermination. It suggested that the PODin seed could be still activited by mag-netic field. A possible mechanism of magneticfield promoting germination was pro-posed based on the results obtainedabove.
NUMERICAL INVESTIGATION OF CONVECTION HEAT TRANSFER IN A HEATED ROOM (2002)

Abstract We describe numerical investigation of airflow and temperature field in a room with a convective heat source. The simulation involves using computational fluid dynamics (CFD) to validate different turbulence models, i.e., the standard k- k model and the low Reynolds number k- k model. The comparisons between computations and experiments show good and acceptable agreement. It can be concluded that the CFD simulations can capture the main flow features and provide satisfactory results. It can be seen that the thermal wall jet created by the heat source greatly influences airflow pattern and temperature field in the room. It can also be seen that the advanced turbulence model may produce better results than the standard one under a suitable mesh scheme.
Faculty Opinions recommendation of Structural basis for Ca2+ selectivity of a voltage-gated calcium channel. (2013)

Voltage-gated calcium (CaV) channels catalyse rapid, highly selective influx of Ca(2+) into cells despite a 70-fold higher extracellular concentration of Na(+). How CaV channels solve this fundamental biophysical problem remains unclear. Here we report physiological and crystallographic analyses of a calcium selectivity filter constructed in the homotetrameric bacterial NaV channel NaVAb. Our results reveal interactions of hydrated Ca(2+) with two high-affinity Ca(2+)-binding sites followed by a third lower-affinity site that would coordinate Ca(2+) as it moves inward. At the selectivity filter entry, Site 1 is formed by four carboxyl side chains, which have a critical role in determining Ca(2+) selectivity. Four carboxyls plus four backbone carbonyls form Site 2, which is targeted by the blocking cations Cd(2+) and Mn(2+), with single occupancy. The lower-affinity Site 3 is formed by four backbone carbonyls alone, which mediate exit into the central cavity. This pore architecture suggests a conduction pathway involving transitions between two main states with one or two hydrated Ca(2+) ions bound in the selectivity filter and supports a 'knock-off' mechanism of ion permeation through a stepwise-binding process. The multi-ion selectivity filter of our CaVAb model establishes a structural framework for understanding the mechanisms of ion selectivity and conductance by vertebrate CaV channels. PMID: 24270805 Funding information This work was supported by: NIGMS NIH HHS, United States Grant ID: T32 GM008268 NHLBI NIH HHS, United States Grant ID: R01 HL112808 Howard Hughes Medical Institute, United States NHLBI NIH HHS, United States Grant ID: R01 HL117896 NINDS NIH HHS, United States Grant ID: R01NS015751 NIGMS NIH HHS, United States Grant ID: T32GM008268 NHLBI NIH HHS, United States Grant ID: R01HL112808 NINDS NIH HHS, United States Grant ID: R01 NS015751 More Less keyboard_arrow_down
AN EXPEDITIOUS ONE POT SYNTHESIS OF DIBENZO[a,g]FLUORENE (2001)

A convenient one-pot synthesis of dibenzo[a,g]fluorene via enolate alkylation and cyclodehydration-aromatisation route has been developed.
Immunization with the malaria heat shock like protein hsp70-1 enhances transmission to the mosquito (1995)

Mosquitoes fed on mice infected with Plasmodium yoelii after an immunization with the i72 recombinant form of the heat shock protein hsp70-1 developed significantly more oocysts than mosquitoes fed on controls. This effect was due to a marked increase in the relative numbers of gametocytes during the early stages of infection. A comparison of blood-induced and sporozoite-initiated infection showed that these gametocytes were derived from merozoites released from the liver. The stimulus for increased gametocyte production is unknown but is likely to be linked with antibody-dependent cellular cytotoxicity and associated cytokine responses.
3 dimensional analysis of Hemimetameric Segmental Shift (2015)

Hemimetameric Segmental Shift (HMMS) is defined as a hemivertebral deformation in which two or more hemivertebra exists on both left and right sides of the spine, where the hemivertebras are separated by at least 1 normal vertebra. 3D-CT analysis done by Kawakami et al on congenital scoliosis patients proved the existence of mismatch among the anterior and posterior segments, where they coined this phenomenon as discordant anomaly. The purpose of this study is to analyze the morphology and determine clinical features of HMMS 3 dimensionally.
Noggin recruits mesoderm progenitors from the dorsal aorta to a skeletal myogenic fate (2012)

Embryonic mesoangioblasts are the in vitro counterpart of vessel-associated progenitors, able to differentiate into different mesoderm cell types. To investigate signals recruiting these progenitors to a skeletal myogenic fate, we developed an in vitro assay, based upon co-culture of E11.5 dorsal aorta (from MLC3F-nLacZ transgenic embryos, expressing nuclear beta galactosidase only in striated muscle) with differentiating C2C12 or primary myoblasts. Under these conditions muscle differentiation from cells originating from the vessel can be quantified by counting the number of beta gal+nuclei. Results indicated that Noggin (but not Follistatin, Chordin or Gremlin) stimulates while BMP2/4 inhibits myogenesis from dorsal aorta progenitors; neutralizing antibodies and shRNA greatly reduce these effects. In contrast, TGF-β1, VEGF, Wnt7A, Wnt3A, bFGF, PDGF-BB and IGF1 have no effect. Sorting experiments indicated that the majority of these myogenic progenitors express the pericyte marker NG2. Moreover they are abundant in the thoracic segment at E10.5 and in the iliac bifurcation at E11.5 suggesting the occurrence of a cranio-caudal wave of competent cells along the aorta. BMP2 is expressed in the dorsal aorta and Noggin in newly formed muscle fibers suggesting that these two tissues compete to recruit mesoderm cells to a myogenic or to a perithelial fate in the developing fetal muscle.
Ammonolysis of Polycarbonates with (Supercritical) Ammonia: An alternative for Chemical Recycling (2005)

Ammonolysis of aliphatic and aromatic polycarbonates in liquid or in supercritical ammonia has been studied. Reaction products are alcohols (phenols) and urea. Ammonolysis of bisphenol A polycarbonate (BPA-PC) proceeds at room temperature at a high rate depending on the size and surface of particles. BPA-PC in composites like compact discs or car windows, consisting of a sandwich of glass layers bounded with a polyurethane adhesive to a polycarbonate, can be selectively ammonolyzed. Aliphatic poly(1,6-hexanediyl carbonate) can be fractionated without ammonolytic degradation in liquid ammonia up to 100 °C while ammonolysis occurs under supercritical conditions. If residence time and temperature (rate of reaction) are properly adjusted controlled degradation to oligomers is possible.
A Cross-Sectional and Longitudinal Study of Retinal Sensitivity inRPE65-Associated Leber Congenital Amaurosis (2018)

Volumetric assessment of central 30° visual field sensitivity, V30, is a useful independent measure of retinal function and, in our data, represented the best metric to monitor deterioration of retinal sensitivity in RPE65-LCA. Furthermore, functional correlation with genotype may enable more informed prognostic counseling. (ClinicalTrials.gov number, NCT02714816.)
Analysis of ovarian and adrenal activity in Namibian cheetahs : research article (2003)

Captive breeding of cheetahs ( Acinonyx jubatus ) has had limited success because a 
high percentage of captive females exhibit a lack of ovarian activity. This study examined 
concentrations of ovarian and adrenal hormones in wild-caught cheetahs ( n= 3) housed in 
large outdoor enclosures on private game ranches in Namibia. Cheetahs were monitored for 
a 16-month period to investigate the effect of season on ovarian and adrenal function. 
Secretory profiles of oestradiol, progestagen, and cortisol metabolites were quantified 
non-invasively using faecal steroid analysis. All three cheetahs exhibited ovarian activity; 
however, none cycled continuously. Periods of anoestrus occurred during overlapping 
periods between August and December 1994, but not during the same time period in 
1995. Mean duration of the oestrous cycle, oestrus period and baseline concentrations of 
reproductive hormones were consistent with those observed in other captive cheetah 
populations. Concentrations of faecal corticoids were lower than those from captive 
cheetahs in North America. There was no correlation between adrenal activity and ovarian 
function. Spontaneous ovulation was documented in one cheetah. These findings support 
those of earlier studies that even under natural and, therefore, presumably ideal 
environmental conditions, reproductive activity in captive cheetahs is not continuous.
Lithium phosphide/lithium chloride coating on lithium for advanced lithium metal anode (2018)

Lithium metal has been regarded as an ideal anode material for high-energy-density batteries.
Farm Family Pesticide Exposure Bibliography (2006)

Bibliography on farm family exposure to pesticides and minimizing exposures
Enhancement of antiproliferation activity of vincristine and adriamycin by interferon. (1984)

Vincristine (VCR) combined with interferon (IFN)-beta suppressed H.Ep #2 cell proliferation more than additively, whereas 6-mercaptopurine combined with IFN-beta suppressed it less than additively. Factors associated with the more-than-additive effect were examined. The enhanced antiproliferation was achieved in HeLa cells as well as H.Ep #2 cells but not in Daudi or M-14 cells, indicating cell dependency of the enhancement. This enhancement was not dependent on the IFN species, including IFN-beta, IFN-alpha (leukocyte), and IFN-alpha (lymphoblastoid), although the cells were variably sensitive to these IFN species. In contrast, the enhance antiproliferation was critically dependent on the species of antineoplastic agents, and was selective to VCR and adriamycin among those tested under the present experimental conditions. The sequential exposure of H.Ep #2 cells to IFN and VCR induced the enhancement but exposure to VCR followed by IFN did not, suggesting that IFN-induced cell modification made the cells more sensitive to VCR. Either IFN or VCR was successfully replaced by colchicine, an antimicrotubule agent, but not by cytochalasin D, an antimicrofilament agent, suggesting the involvement of microtubule modification in the enhanced antiproliferation observed with IFN and VCR.
Classification Of Textured Surfaces Based On Reflection Data (1986)

A statistical approach to classification of surfaces based on the spatial intensity distribution of reflected light is proposed. In this approach, a surface is modelled as a collection of randomly oriented mirror-like micro-facets which give rise to a spatial intensity distribution of reflected light. A correlation matrix is formulated based on the co-occurrence of two given reflected intensities at points separated by a given angular distance. Features based on this matrix are proposed, and two classification schemes based on maximum-likelihood and nearest neighbor decision rules are implemented on these features. Experimental results for the classification schemes are presented for a variety of sample surfaces such as paper, cloth, felt, cork, etc. Success rates of
An Enhanced Impulsive Noise Suppression Method Based on Wavelet Denoising and ICA for Power Line Communication (2021)

Aiming at the problem of noise suppression in power lines, traditional noise suppression methods need to know prior knowledge and other defects. In this paper, blind source separation methods that do not need prior knowledge are selected. In the case of low signal-to-noise ratio, the basic independent component analysis algorithm has poor denoising effect. Therefore, this paper proposes a joint independent component analysis algorithm based on Wavelet denoising and Power independent component analysis (WD-PowerICA). In this work, firstly, the pseudo observation signal is constructed by weighted processing, and the blind separation model of single channel is transformed into a multi-channel determined model. Then, the proposed WD-PowerICA algorithm is used to separate noise and source signals. Finally, the simulation results demonstrate that the proposed algorithm in this paper can effectively separate noise and source signal under low SNR. At the same time, the stronger the α pulse noise is, the closer the WD-PowerICA separated signal is to the source signal. The proposed algorithm is better than the state of the art PowerICA algorithm.
Introduction to dynamical systems analysis in quantitative systems pharmacology: basic concepts and applications (2020)

Quantitative systems pharmacology (QSP) can be regarded as a hybrid of pharmacometrics and systems biology. Here, we introduce the basic concepts related to dynamical systems theory that are fundamental to the analysis of systems biology models. Determination of the fixed points and their local stabilities constitute the most important step. Illustration of a phase portrait further helps investigate multistability and bifurcation behavior. As a motivating example, we examine a cell circuit model that deals with tissue inflammation and fibrosis. We show how increasing the severity and duration of inflammatory stimuli divert the system trajectories towards pathological fibrosis. Simulations that involve different parameter values offer important insights into the potential bifurcations and the development of efficient therapeutic strategies. We expect that this tutorial serves as a good starting point for pharmacometricians striving to widen their scope to QSP and physiologically-oriented modeling.
Preparation and Characterization of Alcogels Based on (Poly Ethylene Glycol Methyl Ether Methacrylate-Acrylic Acid) Copolymers (2013)

Abstract Alcohol absorbents based on poly ethylene glycol methyl ether methacrylate (PEGMEMA) macromer and acrylic acid (AA) were prepared via solution polymerization using trimethyl propane triacrylate (TMPTA) as crosslinker. Swelling capacity of gels was measured in water, ethanol and methanol. Alcohol absorbency was increased with increasing AA content, which can be related to the ability of an AA segment in formation of H-bonding and dissociation of COOH groups to produce of mobile ions. The alcogels absorb ethanol and methanol up to 14.8 and 17.4 g/g, respectively. TG analysis shows that increasing AA content caused an increase of thermal stability of alcogels. Keywords: Acrylic acidAlcogelAlcohol absorbencyPolyethylene glycol methyl ether methacrylate Notes *Precipitate was obtained.
Studies of GB hepatitis agent in tamarins (1989)

Three tamarins (Saguinus labiatus), two of which had previously been infected with hepatitis A virus and parenteral non-A, non-B hepatitis, were inoculated intravenously with the agent of GB hepatitis. All three animals developed alanine aminotransferase abnormalities 2 weeks after inoculation. Peak alanine aminotransferase levels were recorded 4 weeks postinoculation. These declined thereafter but continued to fluctuate at abnormal levels for 32 weeks. Liver biopsies showed liver cell swelling and inflammation with focal necrosis. Portal tracts and areas around central veins were heavily infiltrated with mononuclear cells. A fourth animal (no previous exposure to hepatitis viruses) inoculated with GB was killed on Day 15 postinoculation. Serum and extracts of liver and feces from this day were used as inocula for three other animals. Only the serum and liver extract transmitted GB hepatitis. The fecal specimen did not transmit and a fecal extract taken at a later date from another animal was also noninfectious. GB hepatitis virus is distinct from the viruses causing Type A and blood-borne non-A, non-B-hepatitis. Although the virus is present in serum and has previously been transmitted per os, it is not shed in feces.
Structural snapshots of nitrosoglutathione binding and reactivity underlying S-nitrosylation of photosynthetic GAPDH (2022)

S-nitrosylation is a redox post-translational modification widely recognized to play an important role in cellular signaling as it can modulate protein function and conformation. At the physiological level, nitrosoglutathione (GSNO) is considered the major physiological NO-releasing compound due to its ability to transfer the NO moiety to protein thiols but the structural determinants regulating its redox specificity are not fully elucidated. In this study, we employed photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Chlamydomonas reinhardtii (CrGAPA) to investigate the molecular mechanisms underlying GSNO-dependent thiol oxidation. We first observed that GSNO causes reversible enzyme inhibition by inducing S-nitrosylation. While the cofactor NADP<sup>+</sup> partially protects the enzyme from GSNO-mediated S-nitrosylation, protein inhibition is not observed in the presence of the substrate 1,3-bisphosphoglycerate, indicating that the S-nitrosylation of the catalytic Cys149 is responsible for CrGAPA inactivation. The crystal structures of CrGAPA in complex with NADP<sup>+</sup> and NAD<sup>+</sup> reveal a general structural similarity with other photosynthetic GAPDH. Starting from the 3D structure, we carried out molecular dynamics simulations to identify the protein residues involved in GSNO binding. The reaction mechanism of GSNO with CrGAPA Cys149 was investigated by quantum mechanical/molecular mechanical calculations, which permitted to disclose the relative contribution of protein residues in modulating the activation barrier of the trans-nitrosylation reaction. Based on our findings, we provide functional and structural insights into the response of CrGAPA to GSNO-dependent regulation, possibly expanding the mechanistic features to other protein cysteines susceptible to be oxidatively modified by GSNO.
Sulphide Scavengers in Oil and Gas Industry - A Review (2010)

The application of sulphide scavengers is a widely adopted practice in production and processing operations in the Oil and Gas Industry. Particularly challenging is the search and development of new chemistries, which is aimed at safeguarding the health of personnel and maintaining good protection of materials under a variety of conditions whilst being environmentally acceptable. This paper includes an up to date history of the efforts which have been put forth so far in the industry to minimize or eliminate the various problems caused by hydrogen sulphide during Oil and Gas drilling operations by the use of some chemicals. The advantages and disadvantages of using the various chemicals for scavenging hydrogen sulphide drilling fluids and produced fluids are compared.
Identifying bacterial spores and anthrax hoax materials by Raman spectroscopy (2004)

The distribution of Bacillus anthracis spores through the US postal system in the autumn of 2001, initiated a secondary form of terror, the mailing of hoax materials. In the past three years nearly 20,000 letters containing harmless powders have been mailed, creating additional anxiety. Thus, there is a need for analyzers that can not only identify anthrax-causing spores to save lives, but also identify hoax materials to eliminate time-consuming and costly shutdowns. Recently, we established that Raman spectroscopy has the ability to identify both Bacilli endospores and hoax materials. Here we present Raman spectra of several Bacilli spores along with the dipicolinate salts, to further define the abilities of this technology to not only identify hoax materials, but also identify spores at the genus and species level.
The Toolbox of Synthetic Reactions: A Key to Unlock the Design of Structure for Function (2014)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTThe Toolbox of Synthetic Reactions: A Key to Unlock the Design of Structure for FunctionBarry M. Trost*View Author Information Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States*E-mail: [email protected]Cite this: J. Org. Chem. 2014, 79, 21, 9913Publication Date (Web):October 27, 2014Publication History Published online27 October 2014Published inissue 7 November 2014https://pubs.acs.org/doi/10.1021/jo502354ahttps://doi.org/10.1021/jo502354aeditorialACS PublicationsCopyright © 2014 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views2672Altmetric-Citations2LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (123 KB) Get e-AlertscloseSUBJECTS:Chemical reactions,Chemical structure,Interfaces,Molecules,Rational design Get e-Alerts