gebhart/patrepeval huggingface dataset:
Nucleotide sequence of the type A streptococcal exotoxin (erythrogenic toxin) gene from Streptococcus pyogenes bacteriophage T12 (1986)

The gene specifying type A streptococcal exotoxin (speA), also known as erythrogenic toxin, was cloned from the Streptococcus pyogenes bacteriophage T12 genome and analyzed by nucleotide sequencing. The speA gene consists of 753 base pairs and codes for a 29,244-molecular-weight protein. The speA gene product contains a putative 30-amino acid signal peptide, resulting in a molecular weight of 25,787 for the secreted protein. A possible promoter and ribosome-binding site are present in the region upstream from the speA gene, and a transcriptional terminator is located 69 bases downstream from the translational termination codon. The amino acid sequence of the carboxy-terminal portion of the type A streptococcal exotoxin exhibits extensive homology with the carboxy terminus of Staphylococcus aureus enterotoxins B and C1.
Diminished virulence of a sar-/agr- mutant of Staphylococcus aureus in the rabbit model of endocarditis. (1994)

Microbial pathogenicity in Staphylococcus aureus is a complex process involving a number of virulence genes that are regulated by global regulatory systems including sar and agr. To evaluate the roles of these two loci in virulence, we constructed sar-/agr- mutants of strains RN6390 and RN450 and compared their phenotypic profiles to the corresponding single sar- and agr- mutants and parents. The secretion of all hemolysins was absent in the sar-/agr- mutants while residual beta-hemolysin activity remained in single agr- mutants. The fibronectin binding capacity was significantly diminished in both single sar- mutants and double mutants when compared with parents while the reduction in fibrinogen binding capacity in the double mutants was modest. In the rabbit endocarditis model, there was a significant decrease in both infectivity rates and intravegetation bacterial densities with the double mutant as compared to the parent (RN6390) at 10(3)-10(6) CFU inocula despite comparable levels of early bacteremia among various challenge groups. Notably, fewer bacteria in the double mutant group adhered to valvular vegetations at 30 min after challenge (10(6) CFU) than the parent group. These studies suggest that both the sar and agr loci are involved in initial valvular adherence, intravegetation persistence and multiplication of S. aureus in endocarditis.
Super-resolution mapping of scaffold nucleoporins in the nuclear pore complex (2017)

The nuclear pore complex (NPC), composed of ∼30 different nucleoporins (Nups), is one of the largest supramolecular structures in eukaryotic cells. Its octagonal ring scaffold perforates the nuclear envelope and features a unique molecular machinery that regulates nucleocytoplasmic transport. However, the precise copy number and the spatial location of each Nup in the native NPC remain obscure due to the inherent difficulty of counting and localizing proteins inside of the sub-micrometer supramolecular complex. Here, we combined super-resolution single-point edge-excitation subdiffraction (SPEED) microscopy and nanobody-specific labeling to reveal the spatial distribution of scaffold Nups within three separate layers in the native NPC with a precision of ∼3 nm. Our data reveal both the radial and axial spatial distributions for Pom121, Nup37 and Nup35 and provide evidence for their copy numbers of 8, 32 and 16, respectively, per NPC. This approach can help pave the path for mapping the entirety of Nups in native NPCs and also other structural components of macromolecular complexes.
Induction charge detector with multiple sensing stages (2007)

An induction charge detector yields the net charge and the time of flight of a particle. The unique ability to independently measure these two parameters sets apart this rather simple detection technique. The main shortcoming of this instrument is its high charge detection limit, resulting from the intrinsic noise of the detector electronics and the low signal associated with the charge to measure. The goal of the present work is to lower the detection limit of this detector. This article describes an induction charge detector whose main novelty is a sequence of aligned cylindrical electrodes for measuring the charge of a particle n times. In a time domain analysis, this feature reduces both the detection limit and the standard error of the charge measurement by factors of 2 and n. More importantly, sensing stages could be added to arbitrarily lower the detection limit in a frequency domain analysis.
Cellular Senescence in Type 2 Diabetes: A Therapeutic Opportunity (2015)

Cellular senescence is a fundamental aging mechanism that has been implicated in many age-related diseases and is a significant cause of tissue dysfunction. Accumulation of senescent cells occurs during aging and is also seen in the context of obesity and diabetes. Senescent cells may play a role in type 2 diabetes pathogenesis through direct impact on pancreatic β-cell function, senescence-associated secretory phenotype (SASP)-mediated tissue damage, and involvement in adipose tissue dysfunction. In turn, metabolic and signaling changes seen in diabetes, such as high circulating glucose, altered lipid metabolism, and growth hormone axis perturbations, can promote senescent cell formation. Thus, senescent cells might be part of a pathogenic loop in diabetes, as both a cause and consequence of metabolic changes and tissue damage. Therapeutic targeting of a basic aging mechanism such as cellular senescence may have a large impact on disease pathogenesis and could be more effective in preventing the progression of diabetes complications than currently available therapies that have limited impact on already existing tissue damage. Therefore, senescent cells and the SASP represent significant opportunities for advancement in the prevention and treatment of type 2 diabetes and its complications.
Expression of MUC1 splice variants in benign and malignant ovarian tumours (2002)

MUC1 is expressed on the surface of ovarian cancer cells. Nine different splice variants of MUC1 have been described, but no study has reported on the expression of MUC1 isoforms in human ovarian cancer. Our study compares patterns of expression of MUC1 splice variants of malignant and benign ovarian tumours. Ovarian tissue samples were taken from patients with benign ovarian tumours (n = 34) and from patients who had surgery for primary (n = 47) or recurrent (n = 8) ovarian cancer. RT-PCR for MUC1 splice variants A, B, C, D, X, Y, Z, REP and SEC was performed and their expression compared to clinical and histopathologic parameters. Variants A, D, X, Y and Z were more frequently expressed in malignant than in benign tumours. All primary ovarian cancer cases were positive for variant REP but negative for variant SEC. No significant association of the expression of MUC1 splice variants with the response to chemotherapy or patient survival could be demonstrated. Expression of MUC1 splice variants A, D, X, Y, Z and REP is associated with the presence of malignancy, whereas expression of MUC1/SEC is associated with the absence of malignancy.
[Formation of molecular hydrogen by the action of stratal microflora on oil]. (1981)

Methane and carbon dioxide were produced during the growth of a methane forming bacterial biocenosis from oil-bearing strata in the cultural broth of hydrocarbon oxidizing microorganisms grown in a medium with methane-naphthene oil. Molecular hydrogen can be produced by fermenting microorganisms isolated from stratal water in the course of their growth in the cultural broth of hydrocarbon oxidizing bacteria cultivated in media with methane oil, methane-naphthene oil and naphthene-aromatic oil.
Upcycling waste plastics into carbon nanomaterials: A review (2013)

ABSTRACT Polymer production and utilization are currently widespread and have greatly improved people's standards of living. However, due to their stable and nonbiodegradable nature, postconsumer polymers pose challenging issues to the environment and ecosystems. Efforts are being made not only to contain the generation of polymer wastes and associated littering but, also, to find ways of utilizing them sustainably. Aside from mechanical recycling, which turns postconsumer polymers into new polymer products, and thermal recycling, which releases the thermal energy contained within waste plastics through combustion, chemical recycling converts waste polymers into feedstock for chemicals/materials/fuels production. This manuscript reviews prior work on a special application of the particular chemical recycling route that converts polymers into carbon‐based nanomaterials. These materials feature extraordinary physical and chemical properties with tremendous applications potential. However, their production processes are both resource‐ and energy‐intensive. Yet, by taking advantage of the high carbon content of waste polymers, as well as of their high energy content, a cost‐effective, environmentally‐friendly, and self‐sustaining production of carbon nanomaterials can be achieved. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131 , 39931.
Biomedical Photonics Handbook (2004)

The <i>Journal of Biomedical Optics</i> (JBO) is a Gold Open Access journal that publishes peer-reviewed papers on the use of novel optical systems and techniques for improved health care and biomedical research.
Clonal growth of epithelial cells from normal adult human bronchus. (1981)

Normal primary epithelial cell cultures devoid of fibroblastic cells have been developed from tissue explants of adult human bronchi. Conditions for clonal growth of secondary cultures of bronchial epithelial cells were optimized by coculturing the human cells with mitomycin C growth-arrested Swiss 3T3 mouse feeder cells, lowering the calcium concentration of medium M199, and supplementing it with hydrocortisone, insulin, cholera toxin, epidermal growth factor, and 1.25% fetal bovine serum. The epithelial cells grew for an average of 35 population doublings and had the normal human karyotype, expressed keratin and blood group antigen epithelial cell markers, metabolized benzo(a)pyrene, and were capable of differentiating into both ciliated and squamous cells. This culture system makes it potentially possible to investigate various aspects of differentiation and carcinogenesis in human bronchial epithelial cells.
Subsite Structure and Action Mode of the α-Amylase fromThermoactinomvces vulgaris (1985)

The subsite structure of Thermoactinomyces vulgaris α-amylase was estimated from its action mode and rate parameters of hydrolysis on maltooligosaccharides. These results led to the conclusion that this α-amylase has six subsites with the catalytic site located between the third and fourth subsites from the non-reducing end side. Subsite affinities were calculated to be 0.38, 5.46, 2.72 and 0.23 kcal/mol for subsites 1, 2, 5 and 6, respectively, and the sum of the affinities of subsite 3 and 4 to be −3.41 kcal/mol. The unique action mode of this α-amylase on various substrates was interpreted in terms of the subsite structure.
Breakdown in cortical effective connectivity during midazolam-induced loss of consciousness (2010)

By employing transcranial magnetic stimulation (TMS) in combination with high-density electroencephalography (EEG), we recently reported that cortical effective connectivity is disrupted during early non-rapid eye movement (NREM) sleep. This is a time when subjects, if awakened, may report little or no conscious content. We hypothesized that a similar breakdown of cortical effective connectivity may underlie loss of consciousness (LOC) induced by pharmacologic agents. Here, we tested this hypothesis by comparing EEG responses to TMS during wakefulness and LOC induced by the benzodiazepine midazolam. Unlike spontaneous sleep states, a subject's level of vigilance can be monitored repeatedly during pharmacological LOC. We found that, unlike during wakefulness, wherein TMS triggered responses in multiple cortical areas lasting for >300 ms, during midazolam-induced LOC, TMS-evoked activity was local and of shorter duration. Furthermore, a measure of the propagation of evoked cortical currents (significant current scattering, SCS) could reliably discriminate between consciousness and LOC. These results resemble those observed in early NREM sleep and suggest that a breakdown of cortical effective connectivity may be a common feature of conditions characterized by LOC. Moreover, these results suggest that it might be possible to use TMS-EEG to assess consciousness during anesthesia and in pathological conditions, such as coma, vegetative state, and minimally conscious state.
CMOS Photonics For High Speed Interconnects (2006)

Abstract not Available.
Improved hole mobilities and thermal stability in a strained-Si∕strained-Si1−yGey∕strained-Si heterostructure grown on a relaxed Si1−xGex buffer (2005)

A dual channel heterostructure consisting of strained-Si∕strained-Si1−yGey on a relaxed Si1−xGex buffer (y&amp;gt;x), provides a platform for fabricating metal–oxide–semiconductor field-effect transistors with high hole mobilities. Ge outdiffusion during high temperature processing steps from the strained-Si1−yGey layer into the relaxed Si1−xGex buffer reduces the hole mobilities in these heterostructures. We present a strained-Si∕strained-Si1−yGey∕strained-Si heterostructure on relaxed Si1−xGex, in which the strained-Si layer between the strained-Si1−yGey and relaxed Si1−xGex reduces Ge outdiffusion. Improved hole mobilities in this heterostructure are also observed over similar dual channel heterostructures which could be a result of better hole confinement in the strained-Si1−yGey layer of the proposed heterostructure.
Idiopathic thrombocytopenic purpura: a practice guideline developed by explicit methods for the American Society of Hematology [see comments] (1996)

DIOPATHIC thrombocytopenic purpura (ITP, also I known as primary immune thrombocytopenic purpura) is a hematologic disorder for which appropriate diagnostic and treatment strategies are uncertain. In 1994, the American Society of Hematology (ASH) established a panel to produce explicitly developed practice guidelines for the diagnosis and management of ITP. “Explicitly developed,” evidencebased practice guidelines, which are being issued increasingly by medical specialty societies, combine a critical appraisal of scientific evidence with practice recommendations that state clearly to what extent the guidelines are based either on published scientific evidence or opinion (eg, clinical experience).I4 More details about the clinical practice guideline movement are provided elsewhere.’.’ This report begins with a brief summary of the panel’s recommendations, followed by a more detailed analysis of its methodology, the findings of the comprehensive literature review, and a full presentation of the recommendations. The report concludes with recommendations for future research. As explained later, the recommendations are based on the panel’s opinion, derived from a systematic scoring methodology. (Only recommendations receiving scores of 1 .O to 3.0 or 7.0 to 9.0, as defined later in the text, are cited in this summary.)
MicroRNA-486-3p Regulates γ-Globin Expression in Human Erythroid Cells by Directly Modulating BCL11A (2013)

MicroRNAs (miRNAs) play key roles in modulating a variety of cellular processes through repression of mRNAs target. The functional relevance of microRNAs has been proven in normal and malignant hematopoiesis. While analyzing miRNAs expression profile in unilineage serum-free liquid suspension unilineage cultures of peripheral blood CD34(+) hematopoietic progenitor cells (HPCs) through the erythroid, megakaryocytic, granulocytic and monocytic pathways, we identified miR-486-3p as mainly expressed within the erythroid lineage. We showed that miR-486-3p regulates BCL11A expression by binding to the extra-long isoform of BCL11A 3'UTR. Overexpression of miR-486-3p in erythroid cells resulted in reduced BCL11A protein levels, associated to increased expression of γ-globin gene, whereas inhibition of physiological miR-486-3p levels increased BCL11A and, consequently, reduced γ-globin expression. Thus, miR-486-3p regulating BCL11A expression might contributes to fetal hemoglobin (HbF) modulation and arise the question as to what extent this miRNA might contribute to different HbF levels observed among β-thalassemia patients. Erythroid cells, differentiated from PB CD34(+) cells of a small cohort of patients affected by major or intermedia β-thalassemia, showed miR-486-3p levels significantly higher than those observed in normal counterpart. Importantly, in these patients, miR-486-3p expression correlates with increased HbF synthesis. Thus, our data indicate that miR-486-3p might contribute to different HbF levels observed among thalassemic patients and, possibly, to the clinical severity of the disease.
Lipid-based colloidal carriers for peptide and protein delivery--liposomes versus lipid nanoparticles. (2007)

This paper highlights the importance of lipid-based colloidal carriers and their pharmaceutical implications in the delivery of peptides and proteins for oral and parenteral administration. There are several examples of biomacromolecules used nowadays in the therapeutics, which are promising candidates to be delivered by means of liposomes and lipid nanoparticles, such as solid lipid nanoparticles (SLN) and nanostructured lipid carriers (NLC). Several production procedures can be applied to achieve a high association efficiency between the bioactives and the carrier, depending on the physicochemical properties of both, as well as on the production procedure applied. Generally, this can lead to improved bioavailability, or in case of oral administration a more consistent temporal profile of absorption from the gastrointestinal tract. Advantages and drawbacks of such colloidal carriers are also pointed out. This article describes strategies used for formulation of peptides and proteins, methods used for assessment of association efficiency and practical considerations regarding the toxicological concerns.
The Serpin MNEI Inhibits Elastase-like and Chymotrypsin-like Serine Proteases through Efficient Reactions at Two Active Sites (2001)

MNEI (monocyte/neutrophil elastase inhibitor) is a 42 kDa serpin superfamily protein characterized initially as a fast-acting inhibitor of neutrophil elastase. Here we show that MNEI has a broader specificity, efficiently inhibiting proteases with elastase- and chymotrypsin-like specificities. Reaction of MNEI with neutrophil proteinase-3, an elastase-like protease, and porcine pancreatic elastase demonstrated rapid inhibition rate constants >10(7) M(-1) s(-1), similar to that observed for neutrophil elastase. Reactions of MNEI with chymotrypsin-like proteases were also rapid: cathepsin G from neutrophils (>10(6) M(-1) s(-1)), mast cell chymase (>10(5) M(-1) s(-1)), chymotrypsin (>10(6) M(-1) s(-1)), and prostate-specific antigen (PSA), which had the slowest rate constant at approximately 10(4) M(-1) s(-1). Inhibition of trypsin-like (plasmin, granzyme A, and thrombin) and caspase-like (granzyme B) serine proteases was not observed or highly inefficient (trypsin), nor was inhibition of proteases from the cysteine (caspase-1 and caspase-3) and metalloprotease (macrophage elastase, MMP-12) families. The stoichiometry of inhibition for all inhibitory reactions was near 1, and inhibitory complexes were resistant to dissociation by SDS, further indicating the specificity of MNEI for elastase- and chymotrypsin-like proteases. Determination of the reactive site of MNEI by N-terminal sequencing and mass analysis of reaction products identified two reactive sites, each with a different specificity. Cys(344), which corresponds to Met(358), the P(1) site of alpha1-antitrypsin, was the inhibitory site for elastase-like proteases and PSA, while the preceding residue, Phe(343), was the inhibitory site for chymotrypsin-like proteases. This study demonstrates that MNEI has two functional reactive sites corresponding to the predicted P(1) and P(2) positions of the reactive center loop. The data suggest that MNEI plays a regulatory role at extravascular sites to limit inflammatory damage due to proteases of cellular origin.
Characterization of oligodeoxyribonucleotide synthesis on glass plates (2001)

Achieving high fidelity chemical synthesis on glass plates has become increasingly important, since glass plates are substrates widely used for miniaturized chemical and biochemical reactions and analyses. DNA chips can be directly prepared by synthesizing oligonucleotides on glass plates, but the characterization of these micro-syntheses has been limited by the sub-picomolar amount of material available. Most DNA chip syntheses have been assayed using in situ coupling of fluorescent molecules to the 5'-OH of the synthesized oligonucleotides. We herein report a systematic investigation of oligonucleotide synthesis on glass plates with the reactions carried out in an automated DNA synthesizer using standard phosphoramidite chemistry. The analyses were performed using (32)P gel electrophoresis of the oligonucleotides cleaved from glass plates to provide product distribution profiles according to chain length of oligonucleotides. 5'-Methoxythymidine was used as the chain terminator, which permits assay of coupling reaction yields as a function of chain length growth. The results of this work reveal that a major cause of lower fidelity synthesis on glass plates is particularly inefficient reactions of the various reagents with functional groups close to glass plate surfaces. These problems cannot be detected by previous in situ fluorescence assays. The identification of this origin of low fidelity synthesis on glass plates should help to achieve improved synthesis for high quality oligonucleotide microarrays.
Proteome-wide Epitope Mapping of Antibodies Using Ultra-dense Peptide Arrays (2014)

Antibodies are of importance for the field of proteomics, both as reagents for imaging cells, tissues, and organs and as capturing agents for affinity enrichment in mass-spectrometry-based techniques. It is important to gain basic insights regarding the binding sites (epitopes) of antibodies and potential cross-reactivity to nontarget proteins. Knowledge about an antibody's linear epitopes is also useful in, for instance, developing assays involving the capture of peptides obtained from trypsin cleavage of samples prior to mass spectrometry analysis. Here, we describe, for the first time, the design and use of peptide arrays covering all human proteins for the analysis of antibody specificity, based on parallel in situ photolithic synthesis of a total of 2.1 million overlapping peptides. This has allowed analysis of on- and off-target binding of both monoclonal and polyclonal antibodies, complemented with precise mapping of epitopes based on full amino acid substitution scans. The analysis suggests that linear epitopes are relatively short, confined to five to seven residues, resulting in apparent off-target binding to peptides corresponding to a large number of unrelated human proteins. However, subsequent analysis using recombinant proteins suggests that these linear epitopes have a strict conformational component, thus giving us new insights regarding how antibodies bind to their antigens.