gebhart/patrepeval huggingface dataset:
XAS Study of Iron and Arsenic Speciation during Fe(II) Oxidation in the Presence of As(III) (2005)

The speciation of As and Fe was studied during the oxidation of Fe(II)-As(III) solutions by combining XAS analysis at both the Fe and As K-edges. Fe(II) and As(III) were first hydrolyzed to pH 7 under anoxic conditions; the precipitate was then allowed to oxidize in ambient air for 33 h under vigorous stirring. EXAFS analysis at the As K-edge shows clear evidence of formation of inner-sphere complexes between As(III) and Fe(II), i.e., before any oxidation. Inner-sphere complexes were also observed when Fe became sufficiently oxidized, in the form of edge-sharing and double-corner linkages between AsIIIO3 pyramids and FeIIIO6 octahedra. XAS analyses at the Fe K-edge reveal that the presence of As(III) in the solution limits the polymerization of Fe(II) and the formation of green rust and inhibits the formation of goethite and lepidocrocite. Indeed, As(III) accelerates the Fe(II) oxidation kinetics and leads to the formation of nanosized Fe-As subunits of amorphous aggregates. These observations, rather than a presumed weaker affinity of As(III) for iron oxyhydroxides, might explain why As(III) is more difficult to remove than As(V) by aerating reducing groundwater.
A speckle-based method for fast blood flow measurement in deep tissue (2021)

Blood flow measurement in deep tissue is important because the circulatory system transports oxygen and nutrition to the tissue and removes carbon dioxide out from the tissue. Several non-invasive optical methods were developed for blood flow measurement in deep tissue, such as diffuse correlation spectroscopy (DCS) and diffuse speckle contrast analysis (DSCA). In this paper we will introduce a new speckle-based method for fast blood flow measurement in deep tissue: diffuse speckle pulsatile flowmetry (DSPF). By using a multi-mode fiber for speckle pattern detection, DSPF achieves high blood flow measurement rate of 300 Hz. It has one of the fastest measurement rates of blood flow among non-invasive modalities.
Efficient mining of correlated sequential patterns based on null hypothesis (2012)

Frequent pattern mining has been a widely studied topic in the research area of data mining for more than a decade. However, pattern mining with real data sets is complicated - a huge number of co-occurrence patterns are usually generated, a majority of which are either redundant or uninformative. The true correlation relationships among data objects are buried deep among a large pile of useless information. To overcome this difficulty, mining correlations has been recognized as an important data mining task for its many advantages over mining frequent patterns.
GNSS Collaborative Positioning and Performance Analysis (2014)

As the rapid development of global navigation satellite systems (GNSS) and their related applications in recent years, there will be many scenarios that multiple users work in certain region in the near future. However, facing occlusions and other issues in challenging environments such as urban canyons and forests, up to now there is no good positioning solutions. The ability for most conventional standalone GNSS receivers to independently estimate their locations using GNSS may be degraded in these environments.

With the popularity of the applications of GNSS and wireless networks, the GNSS collaborative positioning is becoming possible. In collaborative positioning, each user shares its processed data with the user group, measures the relative distances with its neighboring users and conducts joint data processing to improve the positioning performance such as availability, stability and accuracy. Compared with standalone positioning, the measurements utilized in collaborative positioning are obtained by the user group, which can help to solve the issues such as lack of visible satellites in challenging environments. 

In this paper, the collaborative data model and weighted least square (WLS) positioning algorithm are presented first. Then, the theoretical performance analysis and simulation tests are proposed by using the collaborative dilution of precision (CDOP) model, which focuses on the impacts of the number and distribution of collaborative users and the accuracy of relative distance measurements that are not considered in standalone positioning. Finally, the collaborative positioning algorithm is tested in some real scenarios such as building roof, balcony, windowsill by using several real-time GNSS receivers. Theoretical analysis and experimental results both verify the impacts of various factors on the positioning performance, and prove that the positioning availability and accuracy can be improved by collaboration.
[Epigallocatechin-3-gallate induces apoptosis in human hepatocellular carcinoma cells]. (2008)

EGCG induces apoptosis in HCC cells through down-regulation of COX-2 and Bcl-2 and consequently activating caspase-9 and caspase-3.
Sporozoites and merozoites of Cryptosporidium parvum share a common epitope recognized by a monoclonal antibody and two-dimensional electrophoresis. (1992)

Sporozoites and merozoites of Cryptosporidium parvum were analyzed for the presence of a 15 kDa surface antigen using a monoclonal antibody probe. Both were found to possess the antigen by immunofluorescence, and further analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis confirmed these observations. When separated by two-dimensional electrophoresis the isoelectric point was found to be similar, with major spots at 4.25 and minor spots at 4.15.
Probing the Roles of Calcium-Binding Sites during the Folding of Human Peptidylarginine Deiminase 4 (2017)

Our recent studies of peptidylarginine deiminase 4 (PAD4) demonstrate that its non-catalytic Ca<sup>2+</sup>-binding sites play a crucial role in the assembly of the correct geometry of the enzyme. Here, we examined the folding mechanism of PAD4 and the role of Ca<sup>2+</sup> ions in the folding pathway. Multiple mutations were introduced into the calcium-binding sites, and these mutants were termed the Ca1_site, Ca2_site, Ca3_site, Ca4_site and Ca5_site mutants. Our data indicate that during the unfolding process, the PAD4 dimer first dissociates into monomers, and the monomers then undergo a three-state denaturation process via an intermediate state formation. In addition, Ca<sup>2+</sup> ions assist in stabilizing the folding intermediate, particularly through binding to the Ca3_site and Ca4_site to ensure the correct and active conformation of PAD4. The binding of calcium ions to the Ca1_site and Ca2_site is directly involved in the catalytic action of the enzyme. Finally, this study proposes a model for the folding of PAD4. The nascent polypeptide chains of PAD4 are first folded into monomeric intermediate states, then continue to fold into monomers, and ultimately assemble into a functional and dimeric PAD4 enzyme, and cellular Ca<sup>2+</sup> ions may be the critical factor governing the interchange.
Epidemiologia de Desastres Naturais (2011)

Los sismos, inundaciones, huracanes, tsunamis, etc., son todos fenómenos naturales que han estado presentes a lo largo de millones de años en la conformación dinámica de nuestro planeta. Dichos fenómenos naturales no son en sí mismos un problema, sino se convierten en agentes perturbadores capaces de generar un desastre cuando se presentan en lugares donde se encuentran asentamientos humanos. Por su origen, los desastres pueden ser naturales o antropogénicos, aunque en ambos se presentan daños a las personas, a los bienes materiales y al ambiente. La epidemiología, como disciplina científica dedicada al estudio de los factores que determinan la distribución y frecuencia de los procesos de salud y enfermedad, no puede estar ajena al estudio de los desastres. Estos representan un campo de acción donde pueden aplicarse directamente los métodos epidemiológicos, desde el estudio de los efectos en salud relacionados con la exposición a los diferentes agentes perturbadores, la identificación de grupos vulnerables, el diseño de planes de emergencia, la evaluación de las intervenciones y de las medidas de mitigación implementadas durante y posterior a la ocurrencia de desastres, así como la propuesta de medidas de seguridad que minimicen los futuros impactos en la salud pública. El establecimiento de un extenso Plan Nacional en cada país que atienda los problemas de salud y seguridad derivados de la ocurrencia de desastres naturales, el cual incluya aspectos de salud mental en grupos vulnerables, debe ser una prioridad reflejada en términos prácticos y en apoyos a la investigación en este campo.
Replacements of Amino Acid Residues at Subsites and Their Effects on the Catalytic Properties of Rhizomucor pusillus Pepsin, an Aspartic Proteinase from Rhizomucor pusillus (2001)

Site-directed mutagenesis was carried out to investigate the functional roles of amino acid residues of Rhizomucor pusillus pepsin (RMPP) in substrate-binding and catalysis. Mutations of two amino acid residues, E13 in the S3 subsite and N219 in the S3/S4 subsites, caused marked changes in kinetic parameters for two substrate peptides with different sequences. Further site-directed mutagenesis at E13 suggested that E13 plays a critical role in forming the correct hydrogen bond network around the active center. In the crystal structure of Rhizomucor miehei pepsin (RMMP), which is an aspartic proteinase produced by Rhizomucor miehei and shows 81% amino acid identity to RMPP, the Oepsilon atom of N219 forms a hydrogen bond with the N-H of isovaline in pepstatin A, a statine-type inhibitor, at the P3 position, suggesting that the loss of the hydrogen bond causes an unfavorable arrangement of the P3 residue. Among the mutants constructed, the E13A mutant showed a 5-fold increase in the ratio of clotting versus proteolytic activity without significant loss of clotting activity. This mutant may present a promising candidate for a useful milk coagulant.
Biohybrid actuators for robotics: A review of devices actuated by living cells (2017)

Actuation is essential for artificial machines to interact with their surrounding environment and to accomplish the functions for which they are designed. Over the past few decades, there has been considerable progress in developing new actuation technologies. However, controlled motion still represents a considerable bottleneck for many applications and hampers the development of advanced robots, especially at small length scales. Nature has solved this problem using molecular motors that, through living cells, are assembled into multiscale ensembles with integrated control systems. These systems can scale force production from piconewtons up to kilonewtons. By leveraging the performance of living cells and tissues and directly interfacing them with artificial components, it should be possible to exploit the intricacy and metabolic efficiency of biological actuation within artificial machines. We provide a survey of important advances in this biohybrid actuation paradigm.
Intestinal Microbiota and Relapse After Hematopoietic-Cell Transplantation (2017)

Purpose The major causes of mortality after allogeneic hematopoietic-cell transplantation (allo-HCT) are relapse, graft-versus-host disease (GVHD), and infection. We have reported previously that alterations in the intestinal flora are associated with GVHD, bacteremia, and reduced overall survival after allo-HCT. Because intestinal bacteria are potent modulators of systemic immune responses, including antitumor effects, we hypothesized that components of the intestinal flora could be associated with relapse after allo-HCT. Methods The intestinal microbiota of 541 patients admitted for allo-HCT was profiled by means of 16S ribosomal sequencing of prospectively collected stool samples. We examined the relationship between abundance of microbiota species or groups of related species and relapse/progression of disease during 2 years of follow-up time after allo-HCT by using cause-specific proportional hazards in a retrospective discovery-validation cohort study. Results Higher abundance of a bacterial group composed mostly of Eubacterium limosum in the validation set was associated with a decreased risk of relapse/progression of disease (hazard ratio [HR], 0.82 per 10-fold increase in abundance; 95% CI, 0.71 to 0.95; P = .009). When the patients were categorized according to presence or absence of this bacterial group, presence also was associated with less relapse/progression of disease (HR, 0.52; 95% CI, 0.31 to 0.87; P = .01). The 2-year cumulative incidences of relapse/progression among patients with and without this group of bacteria were 19.8% and 33.8%, respectively. These associations remained significant in multivariable models and were strongest among recipients of T-cell-replete allografts. Conclusion We found associations between the abundance of a group of bacteria in the intestinal flora and relapse/progression of disease after allo-HCT. These might serve as potential biomarkers or therapeutic targets to prevent relapse and improve survival after allo-HCT.
Humoral immune response to membrane components of Chlamydia trachomatis and expression of human 60 kDa heat shock protein in follicular fluid of in-vitro fertilization patients (1997)

Recent evidence suggests that Chlamydia trachomatis can persist in the female upper genital tract in an unculturable state. Since unsuspected C. trachomatis infection has been associated with adverse in-vitro fertilization (IVF) outcome we sought to detect further evidence of C. trachomatis in the genital tracts of women undergoing IVF. The prevalence and distribution of antibodies to the major structural proteins of C. trachomatis in paired follicular fluid and sera of women undergoing IVF were examined. Sera and follicular fluid samples from 149 women were assayed for immunoglobulin (Ig)G and IgA antibodies to two C. trachomatis antigens, the major outer membrane protein (MOMP) and a recombinant lipopolysaccharide (rLPS) fragment. Additionally, the expression of human 60 kDa heat shock protein (hsp 60) in follicular fluid was determined. All cervical and follicular fluid samples were negative for C. trachomatis by polymerase chain reaction, ligase chain reaction and DNA probe. Sera from 60% of the subjects were positive for antichlamydial rLPS IgG; 36% were positive for anti-MOMP IgG. Similarly, rLPS-directed and MOMP-directed IgA were detected in sera of 34 and 14% of the subjects respectively. IgG antibodies to MOMP and rLPS were detected in 42 and 41% of the follicular fluid examined respectively. Anti-MOMP IgA was identified in 8.7% of the follicular fluid while 27.5% were positive for anti-rLPS IgA. Human hsp 60 expression was documented in 11.6% of the follicular fluid tested. IgA antibodies to both MOMP (P = 0.03) and rLPS (P = 0.02) in follicular fluid were associated with a failure to become pregnant after embryo transfer. IgG antibodies in sera and follicular fluid and IgA antibodies in sera were unrelated to IVF outcome. Similarly only anti-MOMP IgA (P = 0.02) and anti-rLPS IgA (P = 0.04) in follicular fluid were correlated with human hsp 60 expression in follicular fluid. The unique association between IgA antibodies to two chlamydial antigens in follicular fluid and both hsp 60 expression and IVF failure provides further support for the possibility that a persistent upper genital tract chlamydial infection contributes to IVF failure in some women.
Fibronectin Protects Prostate Cancer Cells from Tumor Necrosis Factor-α-induced Apoptosis via the AKT/Survivin Pathway (2003)

Integrins are cell surface heterodimeric transmembrane receptors that, in addition to mediating cell adhesion to extracellular matrix proteins modulate cell survival. This mechanism may be exploited in cancer where evasion from apoptosis invariably contributes to cellular transformation. The molecular mechanisms responsible for matrix-induced survival signals begin to be elucidated. Here we report that the inhibitor of apoptosis survivin is expressed in vitro in human prostate cell lines with the highest levels present in aggressive prostate cancer cells such as PC3 and LNCaP-LN3 as well as in vivo in prostatic adenocarcinoma. We also show that interference with survivin in PC3 prostate cancer cells using a Cys84--> Ala dominant negative mutant or survivin antisense cDNA causes nuclear fragmentation, hypodiploidy, cleavage of a 32-kDa proform caspase-3 to active caspase-3, and proteolysis of the caspase substrate poly(ADP-ribose) polymerase. We demonstrate that in the aggressive PC3 cell line, adhesion to fibronectin via beta1 integrins results in up-regulation of survivin and protection from apoptosis induced by tumor necrosis factor-alpha (TNF-alpha). In contrast, survivin is not up-regulated by cell adhesion in the non-tumorigenic LNCaP cell line. Dominant negative survivin counteracts the ability of fibronectin to protect cells from undergoing apoptosis, whereas wild-type survivin protects non-adherent cells from TNF-alpha-induced apoptosis. Evidence is provided that expression of beta1A integrin is necessary to protect non-adherent cells transduced with survivin from TNF-alpha-induced apoptosis. In contrast, the beta1C integrin, which contains a variant cytoplasmic domain, is not able to prevent apoptosis induced by TNF-alpha in non-adherent cells transduced with survivin. Finally, we show that regulation of survivin levels by integrins are mediated by protein kinase B/AKT. These findings indicate that survivin is required to maintain a critical anti-apoptotic threshold in prostate cancer cells and identify integrin signaling as a crucial survival pathway against death receptor-mediated apoptosis.
Synthesis of 2-Keto-imidazoles Utilizing <i>N</i>-Arylamino-Substituted N-Heterocyclic Carbenes (2011)

A new method for the synthesis of 2-aroyl-, 2-heteroaroyl-, and 2-cinnamoyl-substituted imidazoles in very good yields has been developed. The reaction employs novel nitrogen heterocyclic carbenes (NHCs), namely, N-arylamino-substituted NHCs, formed in situ from the corresponding imidazolium salts, and subsequent reaction with aromatic, heteroaromatic, and cinnamic aldehydes without utilizing transition metals or expensive specialized catalysts.
A (FM/DRDPE)-based approach to improve federated learning optimizer (2007)

Recently, there is a growing need for query optimization algorithm that can effectively deal with federated database systems. Modern optimizers use a cost model to choose the best query execution plan (QEP) which heavily dependent on statistics maintained in the system catalog. Keeping such statistics up to date in the federation is troublesome due to local autonomy. The main objective of this paper is to introduce a general framework for federated database system based on DB2 II to improve federated learning optimizer and enhancing global query optimization. In addition it will suggest two algorithms which may be evolved within the proposed framework to give the federation the full autonomy, precise statistics collection, efficiency in processing federated queries and permitting mid-query execution.
Network traffic classification via neural networks (2022)

The importance of network traffic classification has grown over the last decade. Coupled with advances in software and theory, the range of classification techniques has also increased. Network operators can predict demands in future traffic to high accuracy and better identify anomalous behavior. Multiple machine learning tools have been developed in this field and each have had varying degrees of success. In this paper we use supervised machine learning within a frequentist neural network to develop a model capable of achieving high classification accuracy and maintaining low system throughput. We will compare our model to previous work on Bayesian neural networks and other standard classification techniques in the context of real-time classification. The spatial and temporal stabilities of the different models will also be compared. Finally, we investigate the relationship between the convergence times of each model and the size of training dataset. Emphasis will be placed on experimental design and methodology to adequately justify and contextualize our analysis, as well as clarify the limitations of our results. Challenges in the field and areas for further work will also be discussed.
Alkyne Metathesis with d<sup>2</sup> Re(V) Alkylidyne Complexes Supported by Phosphino-Phenolates: Ligand Effect on Catalytic Activity and Applications in Ring-Closing Alkyne Metathesis (2022)

A family of d<sup>2</sup> Re(V) alkylidyne complexes bearing two decorated phosphino-phenolates (POs) and a labile pyridine ligand were prepared that can efficiently promote alkyne metathesis reactions in toluene. The relative activity of these complexes varies with the PO ligands. Complexes with an electron-rich metal center have a higher activity. Ligand exchange experiments suggest that the pyridine ligands of the Re(V) alkylidynes with more electron-donating PO ligands are more labile and are more easily released to generate catalytically active species. However, complexes with electron-withdrawing PO ligands are more air-stable than those with electron-donating PO ligands. These Re(V) alkylidyne catalysts can promote the homometathesis of functionalized internal alkyl- and aryl-alkynes, as well as ring-closing alkyne metathesis (RCAM) of methyl-capped diynes, forming macrocycles with a ring size ≥12 efficiently for concentrations ≤5 mM. These reactions represent the first examples of RCAM mediated by non-d<sup>0</sup> alkylidyne complexes. The Re(V) alkylidyne catalysts tolerate a wide range of functional groups including ethers, esters, ketones, aldehydes, alcohols, phenols, amines, amides, and heterocycles. Moreover, the catalytic RCAM reactions promoted by robust Re(V) alkylidyne catalysts could also proceed normally in wet toluene.
A Photonic Crystal Protein Hydrogel Sensor for <i>Candida albicans</i> (2015)

Abstract We report two‐dimensional (2D) photonic crystal (PC) sensing materials that selectively detect Candida albicans ( C. albicans ). These sensors utilize Concanavalin A (Con A) protein hydrogels with a 2D PC embedded on the Con A protein hydrogel surface, that multivalently and selectively bind to mannan on the C. albicans cell surface to form crosslinks. The resulting crosslinks shrink the Con A protein hydrogel, reduce the 2D PC particle spacing, and blue‐shift the light diffracted from the PC. The diffraction shifts can be visually monitored, measured with a spectrometer, or determined from the Debye diffraction ring diameter. Our unoptimized hydrogel sensor has a detection limit of around 32 CFU/mL for C. albicans . This sensor distinguishes between C. albicans and those microbes devoid of cell‐surface mannan such as the gram‐negative bacterium E. coli . This sensor provides a proof‐of‐concept for utilizing recognition between lectins and microbial cell surface carbohydrates to detect microorganisms in aqueous environments.