gebhart/patrepeval huggingface dataset:
Structure and composition of the Shigella flexneri‘needle complex’, a part of its type III secreton (2001)

Type III secretion systems (TTSSs or secretons), essential virulence determinants of many Gram-negative bacteria, serve to translocate proteins directly from the bacteria into the host cytoplasm. Electron microscopy (EM) indicates that the TTSSs of Shigella flexneri are composed of: (1) an external needle; (2) a transmembrane domain; and (3) a cytoplasmic bulb. EM analysis of purified and negatively stained parts 1, 2 and a portion of 3 of the TTSS, together termed the "needle complex" (NC), produced an average image at 17 A resolution in which a base, an outer ring and a needle, inserted through the ring into the base, could be discerned. This analysis and cryoEM images of NCs indicated that the needle and base contain a central 2-3 nm canal. Five major NC components, MxiD, MxiG, MxiJ, MxiH and MxiI, were identified by N-terminal sequencing. MxiG and MxiJ are predicted to be inner membrane proteins and presumably form the base. MxiD is predicted to be an outer membrane protein and to form the outer ring. MxiH and MxiI are small hydrophilic proteins. Mutants lacking either of these proteins formed needleless secretons and were unable to secrete Ipa proteins. As MxiH was present in NCs in large molar excess, we propose that it is the major needle component. MxiI may cap at the external needle tip.
Laparoscopic hemicolectomy for a patient with situs inversus totalis: A case report (2017)

Laparoscopic colectomy is considered to be a safe and feasible option for patients with colorectal cancer and SIT.
Exploring and Evaluating Sound for Helping Children Self-Regulate with a Brain-Computer Application (2017)

Children in North America are more likely to suffer from attentional challenges than any other mental health issue. Studies suggest that neurofeedback treatments may be useful for helping these children learn to self-regulate. Applying neurofeedback treatments in real-world, school settings poses a challenge, however, as these environments are often noisy and filled with distractions. The addition of ambient audio to neurofeedback systems may help reduce these disruptions. Further, research suggests that certain auditory treatments, such as binaural beats and white noise, may improve children's focus and aid memory recall. In the following paper we present the theories supporting this idea as well as a mixed methods framework for evaluating whether sound can help children focus while learning to self-regulate using a neurofeedback system. Specifically, we wish to investigate whether these treatments may help children (1) achieve an attentive state sooner and (2) maintain an attentive state for longer, when compared to the same system without sound.
Contextual Treatment of Dissociative Identity Disorder (2001)

Evidence for the effectiveness of contextual therapy, a new approach for treating adult survivors of prolonged child abuse (PCA), is provided via case studies of three women with Dissociative Identity Disorder (DID). Contextual therapy is based on the premise that it is not only traumatic experiences that account for PCA survivors' psychological difficulties. Even more fundamentally, many survivors grow up in an interpersonal context in which adequate resources for secure attachment and acquisition of adaptive living skills are not available. As a result, they are left with lasting deficits that undermine not only their current functioning, but also their ability to cope with reliving their traumatic memories in therapy. The primary focus of this treatment approach, therefore, is on developing capacities for feeling and functioning better in the present, rather than on extensive exploration and processing of the client's trauma history or, in the case of DID, of identity fragments. Treatment of the three cases presented ranged from eight months to two and one-half years' duration, and culminated in very positive outcomes. The women's reports of achievements, such as obtaining and maintaining gainful employment, greater self-sufficiency, and the establishment of more intimate and gratifying relationships, indicated marked improvements in daily functioning. Objective test data obtained at admission and discharge, and in one case, at follow-up, documented substantial reductions in dissociative, posttraumatic stress, depressive, and other symptoms.
Probabilistic wavelet synopses (2004)

Recent work has demonstrated the effectiveness of the wavelet decomposition in reducing large amounts of data to compact sets of wavelet coefficients (termed "wavelet synopses") that can be used to provide fast and reasonably accurate approximate query answers. A major shortcoming of these existing wavelet techniques is that the quality of the approximate answers they provide varies widely, even for identical queries on nearly identical values in distinct parts of the data. As a result, users have no way of knowing whether a particular approximate answer is highly-accurate or off by many orders of magnitude. In this article, we introduce Probabilistic Wavelet Synopses , the first wavelet-based data reduction technique optimized for guaranteed accuracy of individual approximate answers. Whereas previous approaches rely on deterministic thresholding for selecting the wavelet coefficients to include in the synopsis, our technique is based on a novel, probabilistic thresholding scheme that assigns each coefficient a probability of being included based on its importance to the reconstruction of individual data values, and then flips coins to select the synopsis. We show how our scheme avoids the above pitfalls of deterministic thresholding, providing unbiased , highly accurate answers for individual data values in a data vector. We propose several novel optimization algorithms for tuning our probabilistic thresholding scheme to minimize desired error metrics. Experimental results on real-world and synthetic data sets evaluate these algorithms, and demonstrate the effectiveness of our probabilistic wavelet synopses in providing fast, highly accurate answers with improved quality guarantees.
Measurement of Fractional Flow Reserve to Assess the Functional Severity of Coronary-Artery Stenoses (1996)

Background. The clinical significance of coronary-artery stenoses of moderate severity can be difficult to determine. Myocardial fractional flow reserve (FFR) is a new index of the functional severity of coronary stenoses that is calculated from pressure measurements made during coronary arteriography. We compared this index with the results of noninvasive tests commonly used to detect myocardial ischemia, to determine the usefulness of the index.
Neurotrophic 3,9-Bis[(alkylthio)methyl]- and -Bis(alkoxymethyl)-K-252a Derivatives (1997)

A series of 3,9 disubstituted [(alkylthio)methyl]- and (alkoxymethyl)-K-252a derivatives was synthesized with the aim of enhancing and separating the neurotrophic properties from the undesirable NGF (trk A kinase) and PKC inhibitory activities of K-252a. Data from this series reveal that substitution in the 3- and 9-positions of K-252a with these groups reduces trk A kinase inhibitory properties approximately 100- to > 500-fold while maintaining or in certain cases enhancing the neurotrophic activity. From this research, 3,9-bis[(ethylthio)methyl]-K-252a (8) was identified as a potent and selective neurotrophic agent in vitro as measured by enhancement of choline acetyltransferase activity in embryonic rat spinal cord and basal forebrain cultures. Compound 8 was found to have weak kinase inhibitory activity for trk A, protein kinase C1 protein kinase A, and myosin light chain kinase. On the basis of the in vitro profile, 8 was evaluated in in vivo models suggestive of neurological diseases. Compound 8 was active in preventing degeneration of cholinergic neurons of the nucleus basalis magnocellularis (NBM) and reduced developmentally programmed cell death (PCD) of female rat spinal nucleus of the bulbocavernosus motoneurons and embryonic chick lumbar motoneurons.
Attention-Deficit/Hyperactivity Disorder: A Historical Neuropsychological Perspective (2017)

The behavior patterns of hyperactivity, impulsivity and inattention that would ultimately become recognized as Attention-Deficit Hyperactivity Disorder (ADHD) have been described for centuries. Nevertheless, in the past 35 years, advances in diagnostic methods, identification of biomarkers, and treatments have advanced at an exponential rate. ADHD is now recognized as the most common behavioral disorder of childhood, with risks extending well into adulthood for both males and females, leading to its identification as a significant public health issue. This historical neuropsychological review of ADHD emphasizes scientific highlights in the past 35 years related to ADHD, including the evolution of the diagnosis (from Hyperkinetic Reaction of Childhood to ADHD), influential theories (executive functions, cognitive-energetic, delay aversion), landmark treatment studies (Multimodal Treatment of ADHD [MTA] and Preschool ADHD Treatment Study [PATS]), and advances in brain mapping techniques (anatomic, functional, and resting state magnetic resonance imaging, diffusion tensor imaging). The review concludes by highlighting the challenges of studying and treating a heterogeneous neurodevelopmental disorder like ADHD, with emphasis on associated disorders and conditions (learning disabilities, sluggish cognitive tempo), special populations (girls, preschoolers, adults), and recommendations for scientific inquiry in the next 35 years. Neuropsychologists are well positioned to address the clinical and research challenges of the next generation of studies, especially involving advances in understanding the sexual dimor.phism, full developmental course, and dynamic risks associated with ADHD. (JINS, 2017, 23, 916-929).
Mass Spectrometric Resolution of Reversible Protein Phosphorylation in Photosynthetic Membranes ofArabidopsis thaliana (2001)

The use of mass spectrometry to characterize the phosphorylome, i.e. the constituents of the proteome that become phosphorylated, was demonstrated using the reversible phosphorylation of chloroplast thylakoid proteins as an example. From the analysis of tryptic peptides released from the surface of Arabidopsis thylakoids, the principal phosphoproteins were identified by matrix-assisted laser desorption/ionization and electrospray ionization mass spectrometry. These studies revealed that the D1, D2, and CP43 proteins of the photosystem II core are phosphorylated at their N-terminal threonines (Thr), the peripheral PsbH protein is phosphorylated at Thr-2, and the mature light-harvesting polypeptides LCHII are phosphorylated at Thr-3. In addition, a doubly phosphorylated form of PsbH modified at both Thr-2 and Thr-4 was detected. By comparing the levels of phospho- and nonphosphopeptides, the in vivo phosphorylation states of these proteins were analyzed under different physiological conditions. None of these thylakoid proteins were completely phosphorylated in the steady state conditions of continuous light or completely dephosphorylated after a long dark adaptation. However, rapid reversible hyperphosphorylation of PsbH at Thr-4 in response to growth in light/dark transitions and a pronounced specific dephosphorylation of the D1, D2, and CP43 proteins during heat shock was detected. Collectively, our data indicate that changes in the phosphorylation of photosynthetic proteins are more rapid during heat stress than during normal light/dark transitions. These mass spectrometry methods offer a new approach to assess the stoichiometry of in vivo protein phosphorylation in complex samples.
Function and Control of Recombination‐Activating Gene Activitya (1992)

The RAG-1 and RAG-2 genes synergistically confer VDJ recombinase activity to nonlymphoid cell lines. To unequivocally test RAG gene function, we created lines of mice that lack functional copies of these genes. Consistent with the possibility that RAG gene encode the tissue-specific components of VDJ recombinase, RAG-2-deficient mice are viable but have a severe combined immune deficiency due to inability to initiate VDJ recombination and thereby generate mature lymphocytes. RAG-2-deficient mice have no obvious defect in any tissue or lineage other than lymphocytes, indicating that VDJ recombinase activity and RAG-2-gene function is required only for lymphocyte development. Levels of RAG-1 and RAG-2 expression in primary murine lymphoid tissues and lymphoid bone marrow cultures generally are much higher than those of transformed precursor B-cell lines. Low-level RAG gene expression in permanent cell lines results from a decline during propagation due to outgrowth of cells with lower RAG expression levels. The low and variable level of RAG gene expression in transformed pre-B cell lines correlates with low and variable rates of endogenous VDJ recombination; therefore, such lines are not reliable models for experiments aimed at studying mechanisms that target this activity to particular variable region gene segments. To generate such a system, we introduced RAG genes into B-lineage lines under the control of a heat shock-inducible promoter; heat-shock treatment induces extremely high-level but transient RAG expression accompanied by parallel induction of VDJ recombinase activity. Such cells efficiently rearrange transfected VDJ recombination substrates in a regulated manner that is dependent on the activity of transcriptional control elements associated with the target V gene segments.
CYFIP2, a Direct p53 Target, is Leptomycin-B Sensitive (2007)

A number of target genes for the tumor suppressor, p53, have been identified, however, the mechanisms that contribute to p53-dependent apoptosis remain to be fully elucidated. In a comprehensive screen for p53 target genes, we have identified Cytoplasmic FMR Interacting Protein 2 (CYFIP2) as a p53-inducible gene. Here we show that the CYFIP2 promoter contains a p53-responsive element that confers p53 binding as well as transcriptional activation of a heterologous reporter. Inducible expression of CYFIP2 is sufficient for caspase activation and cellular apoptosis, reminiscent of p53 activation. Together, these results suggest that CYFIP2 is a direct p53 target gene that may be part of a redundant network of genes responsible for p53-dependent apoptosis. In addition, the sensitivity of CYFIP2 protein subcellular localization to Leptomycin-B, a CRM-1/Exportin inhibitor, suggests that the biological functions of CYFIP2 may extend from the cytoplasmic compartment into the nucleus of the cell.
A Practical Approach to Immunotherapy of Hepatocellular Carcinoma Using T Cells Redirected Against Hepatitis B Virus (2013)

Hepatocellular carcinoma (HCC) cells often have hepatitis B virus (HBV)-DNA integration and can be targeted by HBV-specific T cells. The use of viral vectors to introduce exogenous HBV-specific T-cell receptors (TCR) on T cells to redirect their specificity is complex and expensive to implement in clinical trials. Moreover, it raises safety concerns related to insertional mutagenesis and potential toxicity of long-lived HBV-specific T cells in patients with persistent infection. To develop a more practical and safer approach to cell therapy of HCC, we used electroporation of mRNA encoding anti-HBV TCR. Approximately 80% of CD8(+) T cells expressed functional HBV TCR 24 hours postelectroporation, an expression efficiency much higher than that obtained by retroviral transduction (~18%). Antigen-specific cytokine production of electroporated T cells was efficient within 72-hour period, after which the redirected T cells lost their HBV-specific function. Despite this transient functionality, the TCR-electroporated T cells efficiently prevented tumor seeding and suppressed the growth of established tumors in a xenograft model of HCC. Finally, we established a method for large-scale TCR mRNA electroporation that yielded large numbers of highly functional clinical-grade anti-HBV T cells. This method represents a practical approach to cell therapy of HCC and its inherently self-limiting toxicity suggests potential for application in other HBV-related pathologies.Molecular Therapy-Nucleic Acids (2013) 2, e114; doi:10.1038/mtna.2013.43; published online 13 August 2013.
G Protein-Coupled Receptors in Drug Discovery (2005)

The broad range of G protein-coupled receptors (GPCRs) encompasses all areas of modern medicine and have an enormous impact on the process of drug development. Using disease-oriented methods to cover everything from screening to expression and crystallization, G Protein-Coupled Receptors in Drug Discovery describes the physiological roles of GPCRs
Assessing the Invasion by Soybean Aphid (Homoptera: Aphididae): Where Will It End? (2004)

The invasion of soybean aphid, Aphis glycines Matsumura, into soybean (Glycine max L.) production areas of the northcentral United States has generated substantial concern over the ultimate impact of this pest on domestic agriculture. To evaluate the potential extent and severity of its invasion in the United States, we examined possible pathways for the arrival of the insect, considered the likelihood for establishment in different regions of the United States, and described patterns of spread. Historical records of aphid interceptions by the U.S. Department of Agriculture, Animal and Plant Health Inspection Service suggest that populations of soybean aphid most likely arrived in the United States from Japan or China, either carried by an international airline passenger or associated with horticultural cargo. Two methods of climate comparison suggest that the aphid may ultimately be present in all soybean producing areas of the United States. However, the severity of infestations within these areas is likely to vary considerably in space and time.
Systemic T Cell–independent Tumor Immunity after Transplantation of Universal Receptor–modified Bone Marrow into SCID Mice (1996)

Gene modification of hematopoietic stem cells (HSC) with antigen-specific, chimeric, or "universal" immune receptors (URs) is a novel but untested form of targeted immunotherapy. A human immunodeficiency virus (HIV) envelope-specific UR consisting of the extracellular domain of human CD4 linked to the zeta chain of the T cell receptor (CD4 zeta) was introduced ex vivo into murine HSC by retroviral transduction. After transplantation into immunodeficient SCID mice, sustained high level expression of CD4 zeta was observed in circulating myeloid and natural killer cells. CD4 zeta-transplanted mice were protected from challenge with a lethal dose of a disseminated human leukemia expressing HIV envelope. These results demonstrate the ability of chimeric receptors bearing zeta-signaling domains to activate non-T cell effector populations in vivo and thereby mediate systemic immunity.
The hepatitis B virus posttranscriptional regulatory element is composed of two subelements (1996)

The RNAs of the hepatitis B virus (HBV) contain a cis-acting regulatory element which facilitates the cytoplasmic localization of unspliced transcripts (J. Huang and T. J. Liang, Mol. Cell. Biol. 13:7476-7486, 1993, and Z. M. Huang and T. S. Yen, J. Virl. 68:3193-3199, 1994). Such localization is presumed to be mediated by cellular factors which interact with the element. The HBV posttranscriptional regulatory element (HBVPRE) can efficiently activate an RNA export reporter system in an orientation-dependent and position-independent manner. Deletion analysis reveals that the HBVPRE consists of two subelements which function synergistically. A synergistic effect was also observed when the 5' (PREalpha) or 3' (PREbeta) subelements were duplicated. The bipartite structure of the HBVPRE is reminiscent of reports that the high-affinity binding sites of the Rev-like proteins must be duplicated to function efficiently (M. Grone, E. Hoffmann, S. Berchtold, B.R. Cullen, and R. Grassmann, Virology 204:144-152, 1994; X. Huang, T.J. Hope, B.L. Bond, D. McDonald, K. Grahl, and T. G. Parslow, J. Virol. 65:2131-2134, 1991; and D. McDonald, T. J. Hope, and T. G. Parslow, J. Virol. 66:7232-7238, 1992).
The automated synthesis of sulfur-containing oligodeoxyribonucleotides using 3H-1,2-benzodithiol-3-one 1,1-dioxide as a sulfur-transfer reagent (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe automated synthesis of sulfur-containing oligodeoxyribonucleotides using 3H-1,2-benzodithiol-3-one 1,1-dioxide as a sulfur-transfer reagentRadhakrishnan P. Iyer, Lawrence R. Phillips, William Egan, Judith B. Regan, and Serge L. BeaucageCite this: J. Org. Chem. 1990, 55, 15, 4693–4699Publication Date (Print):July 1, 1990Publication History Published online1 May 2002Published inissue 1 July 1990https://pubs.acs.org/doi/10.1021/jo00302a039https://doi.org/10.1021/jo00302a039research-articleACS PublicationsRequest reuse permissionsArticle Views1192Altmetric-Citations200LEARN 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 Other access optionsGet e-Alertsclose Get e-Alerts
Effects Of Ozone-Hydrogen Peroxide Combination On The Formation Of Biodegradable Dissolved Organic Carbon (1993)

Abstract The effects of ozone and ozone/hydrogen peroxide on BDOC formation were studied with the “Ozotest” method, a laboratory technique that permits the assessment of oxidation efficiency. Oxidation treatments were performed on river water and sand filter effluent samples. Ozone consumption, reduction of UV absorbance, and BDOC formation were monitored during the experiments. The ratio of 0.35-0.45 mg H2O2 per mg O3 used to degrade pesticides also was optimal for the oxidation of organic matter. BDOC formation versus ozone dose curves with ozone alone or ozone/peroxide system were similar. BDOC formation was optimum at an applied ozone dose of 0.5-1 mg O3/mg C (contact time = 10 min). The ozone/peroxide system yielded lower BDOC values than ozone alone, a phenomenon related to differences in byproducts generated by the two oxidative systems. Moreover, reduction of the concentration of DOC was higher with ozone/hydrogen peroxide than with ozone alone. For both oxidant systems, BDOC formation occurred during the first minute of treatment.
Collagen Structure and Stability (2009)

Collagen is the most abundant protein in animals. This fibrous, structural protein comprises a right-handed bundle of three parallel, left-handed polyproline II-type helices. Much progress has been made in elucidating the structure of collagen triple helices and the physicochemical basis for their stability. New evidence demonstrates that stereoelectronic effects and preorganization play a key role in that stability. The fibrillar structure of type I collagen-the prototypical collagen fibril-has been revealed in detail. Artificial collagen fibrils that display some properties of natural collagen fibrils are now accessible using chemical synthesis and self-assembly. A rapidly emerging understanding of the mechanical and structural properties of native collagen fibrils will guide further development of artificial collagenous materials for biomedicine and nanotechnology.