gebhart/patrepeval huggingface dataset:
A Homochiral Porous Metal−Organic Framework for Highly Enantioselective Heterogeneous Asymmetric Catalysis (2005)

A homochiral porous noninterpenetrating metal-organic framework (MOF), 1, was constructed by linking infinite 1D [Cd(mu-Cl)2]n zigzag chains with axially chiral bipyridine bridging ligands containing orthogonal secondary functional groups. The secondary chiral dihydroxy groups accessible via the large open channels in 1 were utilized to generate a heterogeneous asymmetric catalyst for the addition of diethyzinc to aromatic aldehydes to afford chiral secondary alcohols at up to 93% enantiomeric excess (ee). Control experiments with dendritic aromatic aldehydes of different sizes indicate that the heterogeneous asymmetric catalyst derived from 1 is both highly active and enantioselective as a result of the creation of readily accessible, uniform active catalyst sites inside the porous MOF.
Topical aminolaevulinic acid-photodynamic therapy produces an inflammatory infiltrate but reduces Langerhans cells in healthy human skin in vivo (2011)

Reduction of Langerhans cells by topical PDT of human skin may play a significant role in PDT-induced local immunosuppression, potentially benefiting the treatment of immune-mediated skin disorders but negatively impacting on antitumour responses. Further exploration according to disease indication/treatment protocol is warranted.
Critical Reception (1988)

C. H. Sisson's claim in 1981 that Thomas had now become 'the centre of marked academic attention' is evidence of the slow climb to critical acclaim that the poetry had achieved in the 60 years since Thomas's death. The enthusiastic pages by F. R. Leavis in New Bearings in 1932 bore no obvious fruit, and during the thirties and forties Thomas's poetry seemed to vanish from the shelves of the critics.
BCL-2 Induction is Part of the Strategy of Epstein-Barr Virus (1994)

Epstein Barr virus can infect B lymphocytes and epithelial cells. Epithelial cells present the natural reservoir for the virus in man. In vitro, infected cells harbor the virus predominantly in a latent state with the expression of a set of nuclear (EBNA 1-6) and latent membrane genes (LMP 1-2) and virus-transformed B cells grow as permanently immortalized lymphoblastoid cell lines, that show increased resistance to various growth inhibiting factors. Here we show that the lymphoma-associated oncogene BCL-2 is upregulated by different latent Epstein-Barr virus genes in B lymphocytes as well as keratinocyte cell lines. Thus, the induction of BCL-2 gene expression seems to be part of the survival strategy of the virus independently of the host cell infected.
Bayesian transcriptome assembly (2014)

RNA sequencing allows for simultaneous transcript discovery and quantification, but reconstructing complete transcripts from such data remains difficult. Here, we introduce Bayesembler, a novel probabilistic method for transcriptome assembly built on a Bayesian model of the RNA sequencing process. Under this model, samples from the posterior distribution over transcripts and their abundance values are obtained using Gibbs sampling. By using the frequency at which transcripts are observed during sampling to select the final assembly, we demonstrate marked improvements in sensitivity and precision over state-of-the-art assemblers on both simulated and real data. Bayesembler is available at https://github.com/bioinformatics-centre/bayesembler.
Phosphoenolpyruvate Carboxykinase (GTP) Gene Transcription and Hyperglycemia Are Regulated by Glucocorticoids in Genetically Obesedb/db Transgenic Mice (1997)

The molecular mechanisms underlying increased hepatic phosphoenolpyruvate carboxykinase (PEPCK) gene transcription and gluconeogenesis in type II diabetes are largely unknown. To examine the involvement of glucocorticoids and the cis-acting insulin response sequence (IRS, -416/-407) in the genetically obese db/db mouse model, we generated crosses between C57BL/KsJ-db/+ mice and transgenic mice that express -460 or -2000 base pairs of the rat PEPCK gene promoter containing an intact or mutated IRS, linked to a reporter gene. Transgenic mice expressing the intact PEPCK(460)-CRP (C-reactive protein) transgene bred to near homozygosity at the db locus were obese, hyperinsulinemic, and developed fasting hyperglycemia (389 +/- 26 mg/100 ml) between 4 and 10 weeks of age. Levels of CRP reporter gene expression were increased 2-fold despite severe hyperinsulinemia compared with non-diabetic non-obese transgenic mice. Reporter gene expression was also increased 2-fold in transgenic obese diabetic db/db mice bearing a mutation in the IRS, -2000(IRS)-hGx, compared with non-obese non-diabetic transgenic 2000(IRS)-hGx mice. Treatment of obese diabetic db/db transgenic mice with the glucocorticoid receptor blocker RU 486 decreased plasma glucose by 50% and reduced PEPCK, GLUT2, glucose-6-phosphatase, tyrosine aminotransferase, CRP, and hGx reporter gene expression to levels similar to those of non-obese normoglycemic transgenic mice. Taken together, these results establish that -460 bp of 5'-flanking sequence is sufficient to mediate the induction of PEPCK gene transcription in genetically obese db/db mice during the development of hyperglycemia. The results further demonstrate that the mechanism underlying increased expression of gluconeogenic enzymes in the db/db mouse requires the action of glucocorticoids and occurs independently of factors acting through the PEPCK IRS (-416/-407) promoter binding site.
Oral health status and treatment needs amongst prison inmates of Nellore District in Andhra Pradesh (2011)

Aim: To assess the oral health status and treatment needs with special emphasis to oral mucosal lesions and wasting diseases among prison inmates of Nellore district in Andhra Pradesh. Methods: Data regarding oral health status was recorded on a WHO oral health assessment form 1997 using mouth mirror and CPI probe. WHO criteria for recording oral mucosal lesions were included in the form and wasting diseases were recorded using Smith & Knight index. Results: The inmates were suffering from periodontal disease with a Mean Number of Sextants for bleeding 1.3 ± 0.06, calculus 1.1 ± 0.7. Leukoplakia was found to be prevalent among 2.2% and Erythroplakia in 3.3% of study population. Wasting disease especially attrition was highly prevalent in the study population. Conclusions: This study demonstrates that the standard of past oral health care for prison inmates is low. There is a need to be more attentive to oral health promotion as eventually respondents will be returning to the community.
Time Course and Predictors of Autonomic Dysfunction After Ablation of the Slow Atrioventricular Nodal Pathway (2004)

Withdrawal of parasympathetic tone has been reported after ablation in the posteroseptal right atrium and has been attributed to injury of vagal efferent fibers. The purpose of this study was to assess the time course and predictors of autonomic dysfunction after slow pathway ablation. In 30 patients with AV nodal reentrant tachycardia, time- and frequency-domain measures of heart rate variability (HRV) were measured before, 30 minutes after, and 1 day after slow pathway ablation. There were significant reductions in mean RR interval (724 +/- 163 vs 836 +/- 164 ms, P < 0.05), SD of RR intervals (29 +/- 17 vs 40 +/- 18 ms, P < 0.05), root mean squared difference (15 +/- 8 vs 29 +/- 17 ms, P < 0.05), and high frequency power (4.1 +/- 0.4 vs 4.5 +/- 0.6 log10ms2, P < 0.05) 30 minutes after ablation. However, these parameters returned to baseline 1 day after ablation. Multivariate regression identified isoproterenol dose during the diagnostic study (P = 0.02) and radiofrequency duration (P = 0.02) as statistically significant predictors of heart rate change (R2= 0.45). These findings suggest that changes in autonomic tone after ablation in the posteroseptal right atrium are transitory and resolve within 1 day of the procedure. These short-term changes may be related to procedural variables rather than direct injury to vagal efferent fibers.
A polymerase chain reaction study of the stability of Ig heavy-chain and T-cell receptor delta gene rearrangements between presentation and relapse of childhood B-lineage acute lymphoblastic leukemia (1994)

Ig heavy-chain (IgH) and partial V delta 2-D delta 3 T-cell receptor (TCR) gene rearrangements were investigated, by polymerase chain reaction (PCR) amplification and sequence analysis, in 52 patients at presentation and first relapse and in 14 at both first and second relapse of B-lineage acute lymphoblastic leukemia. In combination, these techniques amplified one or more clonal markers at presentation in 90% of patients (IgH-PCR, 75%; V delta 2-D delta 3-PCR, 46%; both, 33%). Changes in the pattern of amplification between presentation and first relapse were seen in 31% of patients positive by IgH-PCR at presentation and in 25% of those positive by TCR delta-PCR. Only 3 patients showed complete change in their rearrangements, which is suggestive of relapse with a new clone. Furthermore, despite the high reported rates of oligoclonality and clonal evolution at the IgH locus, the results presented show that false-negative minimal residual disease (MRD) detection can be avoided by designing D-N-J probes to all presentation rearrangements. Using a PCR approach for both gene markers, false-negative testing because of clonal evolution would have only occurred in 3 (8%) of the IgH-positive patients, in contrast to 5 (21%) of V delta 2-D delta 3-positive patients. Combining these two systems increases the proportion of patients open to study to 90%, allows comparative studies of the sensitive of the two methods, and reduces the rate of false-negative assessment of MRD caused by clonal evolution to less than 10%. We conclude that large prospective PCR studies of MRD detection should examine gene rearrangements at multiple loci to maximize their applicability and to minimize false-negative relapse prediction.
Stress, Depression and Hippocampal Apoptosis (2006)

In this review, we summarize and discuss recent studies on structural plasticity changes, particularly apoptosis, in the mammalian hippocampus in relation to stress and depression. Apoptosis continues to occur, yet with very low numbers, in the adult hippocampal dentate gyrus (DG) of various species. Stress and steroid exposure modulate the rate of apoptosis in the DG. Contrary to earlier studies, the impact of chronic stress on structural parameters of the hippocampus like cell number and volume, is rather modest, and requires prolonged and severe stress exposure before only small reductions (< 10 %) become detectable. This does not exclude other structural parameters, like synaptic terminal structure, or dendritic arborization from being significantly altered in critical hippocampal subregions like the DG and/or CA3. Neither does it imply that the functional implications of the changes after stress are also modest. Of interest, most of the structural plasticity changes appear transient and are generally reversible after appropiate recovery periods, or following cessation or blockade of the stress or corticosteroid exposure. The temporary slowing down of both apoptosis and adult proliferation, i.e. the DG turnover, after chronic stress will affect the overall composition, average age and identity of DG cells, and will have considerable consequences for the connectivity, input and properties of the hippocampal circuit and thus for memory function. Modulation of apoptosis and neurogenesis, by drugs interfering with stress components like MR and/or GR, and/or mediators of the cell death cascade, may therefore provide important drug targets for the modulation of mood and memory.
The H2B ubiquitin ligase RNF40 cooperates with SUPT16H to induce dynamic changes in chromatin structure during DNA double-strand break repair (2011)

Many anticancer therapies function largely by inducing DNA double-strand breaks (DSBs) or altering the ability of cancer cells to repair them. Proper and timely DNA repair requires dynamic changes in chromatin assembly and disassembly characterized by histone H3 lysine 56 acetylation (H3K56ac) and phosphorylation of the variant histone H2AX (γH2AX). Similarly, histone H2B monoubiquitination (H2Bub1) functions in DNA repair, but its role in controlling dynamic changes in chromatin structure following DSBs and the histone chaperone complexes involved remain unknown. Therefore, we investigated the role of the H2B ubiquitin ligase RNF40 in the DSB response. We show that RNF40 depletion results in sustained H2AX phosphorylation and a decrease in rapid cell cycle checkpoint activation. Furthermore, RNF40 knockdown resulted in decreased H3K56ac and decreased recruitment of the facilitates chromatin transcription (FACT) complex to chromatin following DSB. Knockdown of the FACT component suppressor of Ty homolog-16 (SUPT16H) phenocopied the effects of RNF40 knockdown on both γH2AX and H3K56ac following DSB induction. Consistently, both RNF40 and SUPT16H were required for proper DNA end resection and timely DNA repair, suggesting that H2Bub1 and FACT cooperate to increase chromatin dynamics, which facilitates proper checkpoint activation and timely DNA repair. These results provide important mechanistic insights into the tumor suppressor function of H2Bub1 and provide a rational basis for pursuing H2Bub1-based therapies in conjunction with traditional chemo- and radiotherapy.
Enhanced Production of Recombinant Mycobacterium tuberculosis Antigens in Escherichia coli by Replacement of Low-Usage Codons (2000)

A major obstacle to development of subunit vaccines and diagnostic reagents for tuberculosis is the inability to produce large quantities of these proteins. To test the hypothesis that poor expression of some mycobacterial genes in Escherichia coli is due, in part, to the presence of low-usage E. coli codons, we used site-directed mutagenesis to convert low-usage codons to high-usage codons for the same amino acid in the Mycobacterium tuberculosis genes for antigens 85A and 85B and superoxide dismutase. Replacement of five codons in the wild-type gene for antigen 85B increased recombinant protein production in E. coli 54-fold. The recombinant antigen elicited proliferation and gamma interferon production by lymphocytes from healthy tuberculin reactors and was recognized by monoclonal antibodies to native antigen 85, indicating that the recombinant antigen contained T-cell and B-cell epitopes. Northern blotting demonstrated only a 1.7- to 2.5-fold increase in antigen 85B mRNA, suggesting that the enhanced protein production was due primarily to enhanced efficiency of translation. Codon replacement in the genes encoding antigen 85A and superoxide dismutase yielded four- to sixfold increases in recombinant protein production, suggesting that this strategy may be generally applicable to overexpression of mycobacterial genes in E. coli.
Clotting, Immune System, and Venous Thrombosis in Lung Adenocarcinoma Patients: A Prospective Study (2009)

Thrombosis is highly prevalent in cancer patients, being accepted as a bad prognosis marker. The importance of various mechanisms involved in the thrombophilic state of lung cancer patients is not well understood. In this prospective study, involving 109 unselected patients with lung adenocarcinoma, thrombosis was present in 24% of patients and affected survival in a bivariable model. However, in a multivariable evaluation, considering all the factors under study, only LAC and IgM anti-beta(2) GP I modified thrombosis risk, whereas in a Kaplan-Meyer regression model, thrombosis, IL-6, LAC, factor VIII, and IgM anti-beta(2) GP I interfered with patient's survival.
Regulation of caveolin and caveolae by cholesterol in MDCK cells (1998)

We have examined the expression of caveolin in MDCK cells under conditions that vary cellular cholesterol concentration. Caveolin mRNA levels dropped to one-sixth of control levels after treatment with simvastatin, an inhibitor of cholesterol synthesis, or beta-trimethyl cyclodextrin (CD), a cholesterol sequestering drug. Both simvastatin and CD treatment decreased total cellular cholesterol levels to about 50% of control values. The potent activator of the sterol regulatory element, 25-hydroxycholesterol, showed no direct regulation of caveolin mRNA levels. Caveolin protein concentration was also decreased to 50% of control values in cholesterol-depleted cells, giving rise to a severe attenuation of caveolin expression detected by indirect immunofluorescence labeling. Quantitative electron microscopy showed a total loss of morphologically recognizable invaginated caveolae after these cholesterol depletion treatments. When the number of invaginated caveolae per cell was expressed as a function of the cellular cholesterol content, a threshold phenomenon was observed, suggesting that caveolae only form when the steady state cellular cholesterol is above 50% of control values. These findings indicate that caveolins, and caveolae, may play an important part in cellular cholesterol homeostasis.
D2O-Fueled Fusion Power Reactor Using Electrochemically Induced D-Dn, D-Dp, and Deuterium-Tritium Reactions — Preliminary Design of a Reactor System (1989)

A 1000-MW(electric) fusion power reactor concept based on electrochemically induced D-Dn, D-Dp, and deuterium-tritium reactions is presented. A D- He reaction is not possible because He is not absorbed in the electrode. The concept of a tube-type fuel cell is presented. The inner surface of the tube is laminated with palladium. The cell provides a large cathode surface and efficient heat transport to the water coolant. The fuel assemblies and bundles of fuel tubes are installed in the pressure vessel. The reactor system is very similar to a pressurized water reactor, though the reactor internals are much simplified due to the elimination of fission fuel pellets and control rods. The spatial power distribution of the reactor core is very flat compared with that of fission reactors.
A cascade model for restenosis. A special case of atherosclerosis progression. (1992)

Several experimental observations support this novel mechanistic model. Leukocytes and smooth muscle cells express genes for cytokines and growth factors, and products of coagulation and thrombosis can activate mononuclear phagocytes. Cytokines and growth factors often augment their own gene expression and induce one another, providing a potential intralesional amplification loop. Experimental atheroma and advanced human atherosclerotic lesions do not express high levels of growth-stimulatory cytokines such as interleukin-1 or tumor necrosis factor in the basal state but exhibit inducible expression in response to an injurious stimulus. Thus, cascades of autocrine or paracrine mediators whose expression is triggered by vascular injury might contribute to deranged smooth muscle behavior during restenosis.
Glycomic Analysis of Membrane Glycoproteins with Bisecting Glycosylation from Ovarian Cancer Tissues Reveals Novel Structures and Functions (2014)

Biomarkers capable of detecting and targeting epithelial ovarian cancer cells for diagnostics and therapeutics would be extremely valuable. Ovarian cancer is the deadliest reproductive malignancy among women in the U.S., killing over 14 000 women each year. Both the lack of presenting symptoms and high mortality rates illustrate the need for earlier diagnosis and improved treatment of this disease. The glycosyltransferase enzyme GnT-III encoded by the Mgat3 gene is responsible for the addition of GlcNAc (N-acetylglucosamine) to form bisecting N-linked glycan structures. GnT-III mRNA expression is amplified in ovarian cancer tissues compared with normal ovarian tissue. We use a lectin capture strategy coupled to nano-ESI-RPLC-MS/MS to isolate and identify the membrane glycoproteins and unique glycan structures associated with GnT-III amplification in human ovarian cancer tissues. Our data illustrate that the majority of membrane glycoproteins with bisecting glycosylation are common to both serous and endometrioid histological subtypes of ovarian cancer, and several have been reported to participate in signaling pathways such as Notch, Wnt, and TGFβ.
Photochromic and Thermochromic Colorants in Textile Applications (2014)

Commercial photochromic and thermochromic colorants that change rapidly and reversibly from colorless to colored state when activated by stimuli like ultraviolet irradiation, temperature or pH are well established class of colorants for manufacturing of niche products. Use of photochromic and thermochromic systems in applications like medical thermography, plastic strip thermometers, photochromic lenses, food packaging and nondestructive testing of engineered articles and electronic circuitry is well documented. However, in the last few years, the research on application of these systems on textiles has picked up significantly which has the potential to unlock commercially significant nascent high-tech applications. This review paper presents a summary of the chemistry, mechanism, application on textiles and evaluation procedure of performance, other technical features, current and potential application areas as well as challenges encountered in wider acceptance of photochromic and thermochromic colorants on textiles.
A 1H and 13C nuclear magnetic resonance study of three quaternary salts of naloxone and oxymorphone (1986)

The information from 1H–1H and 1H–13C correlation n.m.r. spectra allowed a complete assignment of the 1H and 13C spectra of three N,N-dialkylmorphinanium chloride derivatives (one N,N-diallyl and two N-allyl-N-methyl diastereoisomers). In the case of the steroisomers the configuration of the asymmetric N atom could be established on the basis of 1H chemical shift data and nuclear Overhauser effects.
C-Nucleosides Derived from Simple Aromatic Hydrocarbons (1997)

We describe the synthesis, structure and DNA incorporation of a class of novel aromatic C-deoxynucleosides in which benzenes and larger polycyclic aromatics serve as DNA base analogs. Novel approaches have been developed for glycosidic bond formation and for epimenzation of the anomeric substitutents to β-configuration, and we describe some of the properties of such compounds in DNA.
Characterization of the platelet membrane glycoprotein abnormalities in Bernard-Soulier syndrome and comparison with normal by surface-labeling techniques and high-resolution two-dimensional gel electrophoresis. (1982)

The platelets from three patients with Bernard-Soulier syndrome have been analyzed by surface-labeling coupled with two-dimensional gel electrophoresis and compared with normals. As well as the previously described absence or deficiency in glycoprotein (GP) Ib(alpha) it could be shown that GP Ib beta and an additional low molecular weight glycoprotein GP17 were not detectable using carbohydrate-labeling methods or deficient to the same extent as the GPIb alpha subunit. In addition, the thrombin cleavable glycoprotein could not be detected using carbohydrate-labeling methods in two patients and was deficient in a third. This finding was confirmed in a fourth patient by one-dimensional gel electrophoresis. Thus, the changes in the membrane of Bernard-Soulier platelets are more complex than previously thought.