gebhart/patrepeval huggingface dataset:
Mesenchymal Stem Cells: Molecular Targets for Tissue Engineering (2007)

Mesenchymal stem cells (MSCs) represent an adherent, fibroblast-like population present not only in the bone marrow, but in a number of tissues, including blood, adipose tissue, muscle, and dermis. Their extensive proliferation and transdifferentiation potential makes them best suited for tissue engineering applications. Identification of growth factors and signaling pathways involved in self-renewal and differentiation is important for designing strategies to overcome replicative senescence and attain directed differentiation. Wnt, bone morphogenetic protein (BMP), and Notch pathways have been implicated to play key roles in self-renewal and differentiation of hematopoietic, intestinal, and epidermal stem cells. They are also involved in regulating MSC differentiation. However, MSC self-renewal has not received much attention, with Nucleostemin being the only recently identified proliferation molecule. Although immortalization using viral oncogenes and telomerase has been achieved, transformation in long-term cultures is a potential risk. Understanding of the mechanisms governing osteogenic differentiation of MSCs is expanding with the recent identification of two major transcription factors, Osterix and Runx2. Enhanced expansion as well as osteogenic differentiation of MSCs can be attained using a combinatorial approach involving co-expression of proliferation and differentiation genes. However, a thorough understanding of the molecular mechanism is necessary for enhancing the self-renewal ability and osteogenic potential in vitro.
Discovering web service workflows using web services interaction mining (2006)

Recovering and analysis of workflows executed in Service-Oriented Systems (SOS) can be expected to gain more and more relevance in service-oriented information technology in the not so distant future. Our work attempts to perform workflow mining in logs provided by service-oriented architectures. Firstly, we introduce the idea of Web Services Interaction Mining (WSIM) and give an overview of related fields of research. Secondly, we propose a classification of SOS according to the log information they provide and analyse mining opportunities in the respective classes. To illustrate the potential of WSIM, we describe a complete workflow mining cycle in a SOS of very rich log information. Since such rich logs are often not available, we then direct our attention to mining in limited logs. We present our first steps towards a workflow mining algorithm, specifically tailored to Web Services (WS). We conclude with a discussion of open issues and future work.
Global likelihood optimization via the cross-entropy method with an application to mixture models (2004)

Global likelihood maximization is an important aspect of many statistical analyses. Often the likelihood function is highly multi-extremal. This presents a significant challenge to standard search procedures, which often settle too quickly into an inferior local maximum. We present a new approach based on the cross-entropy (CE) method, and illustrate its use for the analysis of mixture models.
CD4+ T cells play a significant role in adoptive immunity to Chlamydia trachomatis infection of the mouse genital tract (1995)

The ability of CD4+ and CD8+ T cells to adoptively immunize mice against Chlamydia trachomatis infection of the mouse genital tract was studied. Adoptive transfer experiments were performed with splenic CD4+ or CD8+ T cells obtained from mice following resolution of a primary genital tract infection and after a secondary chlamydial challenge. The results show that donor CD4+ T cells, but not CD8+ T cells, obtained from mice following resolution of a primary infection or after secondary challenge were effective in transferring significant antichlamydial immunity to the genital tracts of naive animals. The lymphokine profiles in the culture supernatants of proliferating Chlamydia-specific CD4+ T cells obtained from mice following resolution of a primary infection and after secondary challenge were assayed by an enzyme-linked immunoadsorbent assay. Protective CD4+ T cells restimulated in vitro secreted interleukin 2, gamma interferon, and interleukin 6, lymphokine profiles characteristic of both Th1- and Th2-like responses. Resting CD4+ T cells obtained from mice 4 months following resolution of a primary infection were also capable of conferring significant levels of adoptive protective immunity to naive mice. These findings support an important role for CD4+ T cells in acquired immunity to chlamydial infection of the genital tract and indicate that protective CD4+ immune responses in this model are relatively long lived.
Determinants of GATA-1 Binding to DNA (2003)

Mammalian GATA transcription factors are expressed in various tissues in a temporally regulated manner. The prototypic member, GATA-1, is required for normal erythroid, megakaryocytic, and mast cell development. This family of DNA-binding proteins recognizes a consensus (A/T)GATA(A/G) motif and possesses homologous DNA binding domains consisting of two zinc fingers. The C-terminal finger of GATA-1 recognizes the consensus motif with nanomolar affinities, whereas the N-terminal finger shows a binding preference for a GATC motif, albeit with much reduced affinity (Kd approximately microm). The N-terminal finger of GATA-2 also shows a preference for an AGATCT binding site, with an increased affinity attributed to N- and C-terminal flanking basic residues (Kd approximately nm). To understand the differences in the binding specificities of the N- and C-terminal zinc fingers of GATA-1, we have constructed a series of swapped domain peptides. We show that the specificity for AGATAA over AGATCT arises from the C-terminal non-finger basic domain. Thus, the N-terminal finger binds preferentially to AGATAA once appended to the C-terminal arm of the C-terminal finger. We further show that this specificity arises from the highly conserved QTRNRK residues. The converse is, however, untrue in the case of the C-terminal finger; swapping of QTRNRK with the corresponding LVSKRA does not switch the DNA binding specificity from AGATAA to AGATCT. These results highlight the important role of residues adjacent to the CXXCX17CNAC zinc finger motif (i.e. non-finger residues) in the specific recognition of DNA residues.
Do Social Crises Cause Religious Revivals? What British Church Adherence Rates Show (2016)

A 2014 sociology of religion conference invitation asserted that it is ‘A long-standing assumption in the sociology of religion … that there is a correlation between religious resurgence and intense moments of political, economic and socio-cultural crisis.’ We test this proposition against various post-1900 British or uk church adherence data and find no evidence to support the claim. On the contrary, the trajectories of decline are remarkably smooth. We suggest that such smoothness better supports the sociological view of secularization as a long-run process with amorphous and deep causes than it supports the claim that religious change is a response to specific events.
OmniMVS: End-to-End Learning for Omnidirectional Stereo Matching (2019)

In this paper, we propose a novel end-to-end deep neural network model for omnidirectional depth estimation from a wide-baseline multi-view stereo setup. The images captured with ultra wide field-of-view (FOV) cameras on an omnidirectional rig are processed by the feature extraction module, and then the deep feature maps are warped onto the concentric spheres swept through all candidate depths using the calibrated camera parameters. The 3D encoder-decoder block takes the aligned feature volume to produce the omnidirectional depth estimate with regularization on uncertain regions utilizing the global context information. In addition, we present large-scale synthetic datasets for training and testing omnidirectional multi-view stereo algorithms. Our datasets consist of 11K ground-truth depth maps and 45K fisheye images in four orthogonal directions with various objects and environments. Experimental results show that the proposed method generates excellent results in both synthetic and real-world environments, and it outperforms the prior art and the omnidirectional versions of the state-of-the-art conventional stereo algorithms.
SIMPLE: Structured illumination based point localization estimator with enhanced precision (2019)

We present a structured illumination microscopy based point localization estimator (SIMPLE) that achieves a 2-fold increase in single molecule localization precision compared to conventional centroid estimation methods. SIMPLE advances the recently introduced MINFLUX concept by using precisely phase-shifted sinusoidal wave patterns as nanometric rulers for simultaneous particle localization based on photon count variation over a 20 μm field of view. We validate SIMPLE in silico and experimentally on a TIRF-SIM setup using a digital micro-mirror device (DMD) as a spatial light modulator.
Endothelin in myocardial ischaemia and reperfusion (1997)

Endothelin-1 (ET-1) is an extremely potent vasoconstrictor peptide derived from vascular endothelial cells. ET-1 can also be produced by other cell types such as smooth muscle cells and cardiomyocytes. Plasma levels of ET-1 are elevated during several different cardiovascular disorders like atherosclerosis, myocardial infarction and congestive heart failure. During and following myocardial ischaemia and reperfusion, the myocardial production and release of ET-1 is stimulated and the coronary constrictor response to ET-1 is enhanced. These findings all favour a pathophysiological role for ET-1 in the development of ischaemia/reperfusion injury. Accordingly, by using different pharmacological tools (monoclonal antibody, ET converting enzyme inhibitor or ET receptor antagonists) that block the biological actions of ET-1, myocardial ischaemia/reperfusion injury has been demonstrated to be reduced in experimental animal models, in terms of both reduction in final infarct size and improved recovery of myocardial performance and coronary flow. However, some studies have shown no cardioprotective effects of ET receptor antagonists. Possible explanations for these apparently conflicting results are differences in animal species used, route and timing of drug administration, experimental protocol and chemical nature of the antagonists. The potential mechanisms underlying the cardioprotective effects of ET antagonists are discussed and include prevention of no-reflow, inhibition of ET-induced neutrophil activation, abolishment of direct pro-ischaemic actions of ET on myocytes, and interruption of interference of ET with the renin-angiotensin system.
Modular PM generator/converter topologies, suitable for utility interface of wind/micro turbine and flywheel type electromechanical energy conversion systems (2002)

In this paper, modular PM generator and converter topologies, suitable for the utility interface of wind turbine, micro turbine and flywheel type electromechanical energy conversion systems are explored. It is shown that winding connections of the standard PM generator in the above applications can be reconnected into several single-phase and three-phase groups, each powering a separate PWM rectifier, resulting in high performance electromechanical energy conversion systems. The proposed approaches are fault tolerant and can continue to function at reduced power levels under faults. An example 3-phase, 10 hp, 4 pole, 60 Hz, 230 V/460 V PM motor/generator winding connection diagram along with the associated converter configurations is fully analyzed for the above listed applications.
The Response to Heat Shock and Oxidative Stress in<i>Saccharomyces cerevisiae</i> (2011)

A common need for microbial cells is the ability to respond to potentially toxic environmental insults. Here we review the progress in understanding the response of the yeast Saccharomyces cerevisiae to two important environmental stresses: heat shock and oxidative stress. Both of these stresses are fundamental challenges that microbes of all types will experience. The study of these environmental stress responses in S. cerevisiae has illuminated many of the features now viewed as central to our understanding of eukaryotic cell biology. Transcriptional activation plays an important role in driving the multifaceted reaction to elevated temperature and levels of reactive oxygen species. Advances provided by the development of whole genome analyses have led to an appreciation of the global reorganization of gene expression and its integration between different stress regimens. While the precise nature of the signal eliciting the heat shock response remains elusive, recent progress in the understanding of induction of the oxidative stress response is summarized here. Although these stress conditions represent ancient challenges to S. cerevisiae and other microbes, much remains to be learned about the mechanisms dedicated to dealing with these environmental parameters.
Comparative analysis between a low pathogenic and a high pathogenic influenza H5 hemagglutinin in cell entry (2009)

Avian influenza viruses continue to threaten globally with pandemic potential. The first step in a potential pandemic is the ability of the virus to enter human cells which is mediated by the viral surface glycoprotein hemagglutinin (HA). Viral entry of influenza is dependent upon the processing of the HA0 polypeptide precursor protein into HA1 and HA2 which is mediated by host cellular proteases. The sequence of the cleavage site which is recognized by host proteases has been linked with pathogenesis of various influenza viruses. Here we examined the effects of cleavage site sequences between a highly pathogenic H5N1 strain and a low pathogenic H5N2 strain to determine their effects on viral entry. From this analysis we determined that at the level of viral entry, the only observed difference between the low and high pathogenic strains is their ability to be cleaved by host cellular proteases.
Effect of synthesis conditions on properties of poly(<i>N</i>‐isopropylacrylamide) gels (1992)

Abstract Properties of poly( N ‐isopropylacrylamide) gels—equilibrium degree of swelling, shear modulus, effective crosslink density and clarity—depend significantly upon the conditions of synthesis. While it is well known that monomer and crosslinker concentrations affect gel properties, other variables are shown here to have significant effects on the properties of the resulting gels. Initiator type and concentration, synthesis temperature, mold geometry and polymerization time all significantly affect the properties, including the swelling degree. Evidence suggests that the microstructure of these gels is particularly sensitive to these variables.
Aligned carbon nanotube/polymer composite fibers with improved mechanical strength and electrical conductivity (2011)

In order to improve their practical applications, carbon nanotubes (CNTs) have been widely spun into fibers. However, both mechanical strength and electrical conductivity of the CNT fibers are far from the applications. Therefore, a second phase such as polymer has been introduced to increase their strength, but their conductivity further decreases due to the insulating or the low-conductivity action of the incorporated polymer. In this work, we have developed a general and effective route to fabricate CNT/polymer fibers through the introduction of monomers during an easy solution process followed by an in situ polymerization. The resulting composite fibers show an increased tensile strength and an improved electrical conductivity compared with either the pure CNT fibers or the CNT/polymer fibers prepared by the direct incorporation of polymers. This work demonstrates a fabrication methodology to design and synthesize high-quality CNT/polymer composite materials.
Anthracycline Cardiotoxicity: From Bench to Bedside (2008)

Anthracyclines remain among the most widely prescribed and effective anticancer agents. Unfortunately, life-threatening cardiotoxicity continues to compromise their usefulness. Despite more than four decades of investigation, the pathogenic mechanisms responsible for anthracycline cardiotoxicity have not been completely elucidated. In addition, new drugs and combination therapies often exacerbate the toxicity. The First International Workshop on Anthracycline Cardiotoxicity, held in fall 2006, in Como, Italy, focused on the state-of-the-art knowledge and discussed the research needed to address the cardiotoxicity of these drugs. Here, we incorporate these discussions into the framework of a broader review of preclinical and clinical issues.
Exploration of Solid Forms of Crisaborole: Crystal Engineering Identifies Polymorphism in Commercial Sources and Facilitates Cocrystal Formation (2018)

We report the discovery of three polymorphs of the very recently FDA-approved boron-containing active pharmaceutical ingredient, Crisaborole. Crisaborole displays polymorphism based on the syn (Form I) and anti (Form II) conformations of the hydroxyl group of the oxaborole ring as shown by single-crystal X-ray analysis. Forms I and II were discovered based on the availability from two different commercial suppliers, while Form III was obtained upon heating of Form I or II. A cocrystal based on 4,4′-bipyridine was also obtained.
Molecular Virology and the Development of Resistant Mutants: Implications for Therapy (2005)

Two of the key events in the viral life cycle of the hepatitis B virus (HBV) involve (1) generation from genomic DNA of the covalently closed circular DNA transcriptional template and (2) reverse transcription of the viral pregenomic RNA to form the HBV DNA genome. Because the virus employs reverse transcription to copy its genome, mutant viral genomes are found frequently. Particular selection pressures, both endogenous (host immune clearance) and exogenous (vaccines and antivirals), readily select out these escape mutants. The introduction of nucleoside/nucleotide analogue therapy has seen the emergence of drug resistance as the major factor limiting drug efficacy. The development of drug resistance is not unexpected if viral replication continues in the setting of ongoing treatment, especially monotherapy. Thus, prevention of resistance requires the adoption of strategies that effectively control virus replication.
2-D Layered Materials for Next-Generation Electronics: Opportunities and Challenges (2018)

Since the discovery of graphene in 2004, which proved the existence of 2-D crystals in nature, layered materials also known as van der Waals solids have received extensive reexamination, especially in the single-layer and multilayer forms because of their van der Waals type structure and unique properties that not only benefit many existing electronic components but also enable novel device concepts and design architectures. Numerous research efforts have been invested in these materials, and enormous quantities of results have been generated during the past 14 years. This paper provides an overview of the key physics and technology issues along with the most promising nanoelectronic applications of these materials and also identifies the challenges in this rapidly evolving field.
[Analysis of first flush effect of typical underlying surface runoff in Beijing urban city]. (2013)

Rapid increase of the urban impervious underlying surfaces causes a great increase of urban runoff and the accumulation of pollutants on the roof and road surfaces brings many pollutants into the drainage system with the runoff, and it thus becomes a great threat to the urban water environment. To know the runoff pollution process and to build scientific basis for pollutant control, runoff processes from the roof and road surfaces were monitored and analyzed from 2004 to 2006, and the runoff EMC (Event Mean Concentration) was calculated. It was found that two types of runoff were seriously polluted by COD and TN. The COD and TN of roof runoff exceeded the fifth level of the surface water environmental quality standard (GB 3838-2002) by 3.64 and 4.80 times, respectively, and the COD and TN of road runoff exceeded by 3.73 and 1.07 times, respectively. M (V) curve was used to determine the relation between runoff volume and runoff pollution load. Various degrees of the first flush phenomenon were found for TSS, COD, TN and TP in roof runoff. But this phenomenon occurred only for TSS and TP of the road runoff, and on the whole it was not obvious. Properties of the underlying surfaces, rainfall intensity, and pollutant accumulation are all important factors affecting the roof and road runoff pollutant emission characteristics.
Mechanisms of natural resistance to antifolates in human soft tissue sarcomas. (1992)

Efforts to use fresh human sarcoma cells for evaluating antifolate resistance with an in situ thymidylate synthesis assay using 5-[3H] deoxyuridine were unsuccessful because of low thymidylate synthesis activity in enzymatically disaggregated tumors. By incubating tumor cell suspensions in supplemented RPMI-1640 medium with 10% fetal bovine serum for 3 days, activity of the in situ thymidylate synthesis assay markedly increased (1.42 versus 0.03 pmol/h/10(7) cells), thus allowing 75% of samples to be evaluated for antifolate sensitivity. By criteria developed with a methotrexate-resistant and -sensitive cell line, this assay indicated that most sarcomas are naturally resistant to methotrexate (12 of 15). Natural resistance to 10-ethyl-10-deazaaminopterin and trimetrexate was also observed in 60% of the samples (nine of 15, respectively). The results from the 3-day in situ assay were confirmed by specific tests for resistance mechanisms in most sarcoma samples. The resistance mechanisms detected were impaired polyglutamylation, an increased level of dihydrofolate reductase, and amplification of this gene. These results encourage further exploration of this assay to predict response to antifolates in individual patients and to evaluate efficacy of new antifolates as candidates for clinical trial.
Enzyme-Activated Fluorogenic Probes for Live-Cell and <i>in Vivo</i> Imaging (2018)

Fluorogenic probes, small-molecule sensors that unmask brilliant fluorescence upon exposure to specific stimuli, are powerful tools for chemical biology. Those probes that respond to enzymatic catalysis illuminate the complex dynamics of biological processes at a level of spatiotemporal detail and sensitivity unmatched by other techniques. Here, we review recent advances in enzyme-activated fluorogenic probes for biological imaging. We organize our survey by enzyme classification, with emphasis on fluorophore masking strategies, modes of enzymatic activation, and the breadth of current and future applications. Key challenges such as probe selectivity and spectroscopic requirements are described alongside therapeutic, diagnostic, and theranostic opportunities.