gebhart/patrepeval huggingface dataset:
A novel immunofluorescent assay to investigate oxidative phosphorylation deficiency in mitochondrial myopathy: understanding mechanisms and improving diagnosis (2015)

Oxidative phosphorylation defects in human tissues are often challenging to quantify due to a mosaic pattern of deficiency. Biochemical assays are difficult to interpret due to the varying enzyme deficiency levels found in individual cells. Histochemical analysis allows semi-quantitative assessment of complex II and complex IV activities, but there is no validated histochemical assay to assess complex I activity which is frequently affected in mitochondrial pathology. To help improve the diagnosis of mitochondrial disease and to study the mechanisms underlying mitochondrial abnormalities in disease, we have developed a quadruple immunofluorescent technique enabling the quantification of key respiratory chain subunits of complexes I and IV, together with an indicator of mitochondrial mass and a cell membrane marker. This assay gives precise and objective quantification of protein abundance in large numbers of individual muscle fibres. By assessing muscle biopsies from subjects with a range of different mitochondrial genetic defects we have demonstrated that specific genotypes exhibit distinct biochemical signatures in muscle, providing evidence for the diagnostic use of the technique, as well as insight into the underlying molecular pathology. Stringent testing for reproducibility and sensitivity confirms the potential value of the technique for mechanistic studies of disease and in the evaluation of therapeutic approaches.
Purification and molecular cloning of the “A” chain of a rat heteromeric CCAAT-binding protein. Sequence identity with the yeast HAP3 transcription factor. (1990)

CCAAT-binding factor (CBF) is a heteromeric mammalian transcription factor which binds to sequences containing a CCAAT motif in a number of promoters such as those for type I collagen, albumin, MHC Class II, beta-actin, and others. It consists of two different components that are both needed for DNA binding. We have purified the chain of CBF to apparent homogeneity by sequence-specific DNA affinity chromatography followed by Mono S and Mono Q ion-exchange chromatography and obtained the amino acid sequences of tryptic peptides of this polypeptide. Amino acid sequences of two of these tryptic peptides were used to synthesize oligonucleotide primers. The primers served to obtain a small cDNA by the polymerase chain reaction method, which was then further used to obtain larger cDNA clones. DNA sequence analysis of a representative cDNA clone revealed the presence of an open reading frame of 207 amino acids coding for a putative polypeptide of 25 kDa. Transcription of these cDNAs in vitro followed by translation in a reticulocyte lysate produced a polypeptide that migrated on sodium dodecyl sulfate-polyacrylamide gel electrophoresis with the same mobility as the native A chain. The deduced amino acid sequence of the A chain showed a remarkable identity over a length of 90-amino acid residues with a sequence of the Hap3 polypeptide, a component of a heteromeric multisubunit yeast transcription factor.
Release of leukotriene B4 and 5-hydroxyeicosatetraenoic acid during phagocytosis of artificial immune complexes by peripheral neutrophils in chronic inflammatory bowel disease. (1986)

The capacity of peripheral neutrophils for activation of the arachidonic acid (AA) metabolism was studied during phagocytosis of IgG containing immune complexes (ICs) binding to Fc-receptors. Release of approximately 9% of the intracellular pool of radiolabelled AA in phospholipids, and release of the pro-inflammatory mediators, leukotriene B4 (LTB4), constituting 1.8%, and 5-hydroxyeicosatetraenoic acid (5-HETE), constituting 2.9% of the total radioactivity released, were demonstrated in 15 patients with untreated Crohn's disease, 15 patients with ulcerative colitis, and in 15 healthy volunteers. The concentrations of LTB4 and 5-HETE released were within the range of chemotactic activity for the two lipoxygenase products. Multiple large IgG containing ICs were revealed in neutrophils after phagocytosis by immunofluorescence. A minor defect in the IC uptake in patients with Crohn's disease observed in the absence of complement only, did not result in a subnormal activation of arachidonic acid release or metabolism. The study suggests that complexes of the IgG-class previously demonstrated in chronic inflammatory bowel disease, particularly in Crohn's disease, may activate inflammatory neutrophils leading to release of significant amounts of the pro-inflammatory lipoxygenase metabolites, LTB4 and 5-HETE.
Allergy to bumblebee venom I. Occupational anaphylaxis to bumblebee venom: diagnosis and treatment (1995)

We describe six patients with severe occasional anaphylaxis, caused by stings of bumblebees. Sensitization to bumblebee venom was confirmed by intracutaneous tests and RAST with purified bumblebee venom. Three patients changed their occupation and will probably not be stung by bumblebees in the future. The other patients started immunotherapy with newly purified bumblebee venom extract. After 1 year of treatment, no severe side-effects had occurred and clinical benefit in two patients could be demonstrated, as both skin sensitivity or serum IgE to bumblebee venom had decreased. Moreover, both patients were unresponsive to in-hospital sting challenge.
Transcribed sequences of the Escherichia coli btuB gene control its expression and regulation by vitamin B12. (1991)

The Escherichia coli btuB gene product is an outer membrane protein required for the active transport of vitamin B12 and other cobalamins. Synthesis of BtuB is repressed when cells are grown in the presence of cobalamins. Mapping of the 5' end of the btuB transcript revealed that a 240-nucleotide transcribed leader precedes the coding sequence. Point mutations causing increased expression under repressing conditions were isolated by use of a btuB-lacZ gene fusion. Mutations at many sites within the leader region affected btuB-lacZ regulation, whereas some base changes upstream of the start of transcription affected the absolute level of expression but not its repressibility. Analysis of btuB-phoA gene fusions and btuB-lacZ operon and gene fusions of various lengths showed that sequences within the btuB coding region (between nucleotides +250 and +350) had to be present for proper expression and transcriptional regulation. Sequences within the leader region (up to +250) conferred regulation of translational fusions. These results indicate that btuB expression is controlled at both the transcriptional and translational levels and that different but possibly overlapping sequences in the transcribed region, including the coding region for the transport protein itself, mediate these two modes of regulation.
Behavior of Certain Pyridines, Quinolines, and Isoquinolines with Amino or Hydrazino Substituents Toward N-Acylamino Acids Under the Influence of Papain Catalysis (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBehavior of Certain Pyridines, Quinolines, and Isoquinolines with Amino or Hydrazino Substituents Toward N-Acylamino Acids Under the Influence of Papain CatalysisJOHN LEO ABERNETHY and WARREN KILDAYCite this: J. Org. Chem. 1960, 25, 11, 1924–1928Publication Date (Print):November 1, 1960Publication History Published online1 May 2002Published inissue 1 November 1960https://pubs.acs.org/doi/10.1021/jo01081a025https://doi.org/10.1021/jo01081a025research-articleACS PublicationsRequest reuse permissionsArticle Views75Altmetric-Citations2LEARN 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
A survey of high-density dynamic RAM cell concepts (1979)

The performance capabilities of a variety of dynamic RAM cell concepts proposed in recent years are compared to the industry standard one-transistor cell. The new concepts are divided into three categories. The lateral charge sensing cells such as the Charge-Coupled cell, Hi-C cell, Merged-Charge cell, and Stacked-Capacitor cell. Vertical cells such as VMOS, the Punchthrough Isolated, and the Buried-Bit-Line cell which make use of the third dimension to achieve higher density. The Stratified-Charge cell and Taper-Isolated cell use current sensing of a dynamic change in the threshold voltage of a buried-channel transistor. The various cells were fabricated and compared on the basis of signal size, leakage rates, packing density, and fabrication and operational complexity. An overall figure of merit for a dRAM cell is suggested which combines all three considerations. Based on the cell concepts reported to date and this figure of merit, the Stacked-Capacitor, VMOS, and Punchthrough-Isolated cells ate the most promising charge storage cells. The Taper-Isolated cell, however, is shown to have significant overall advantage compared to the charge storage cells.
Biofunctionalized, Ultrathin Coatings of Cross-Linked Star-Shaped Poly(ethylene oxide) Allow Reversible Folding of Immobilized Proteins (2004)

Dense, ultrathin networks of isocyanate terminated star-shaped poly(ethylene oxide) (PEO) molecules, cross-linked at their chain ends via urea groups, were shown to be extremely resistant to unspecific adsorption of proteins while at the same time suitable for easy biocompatible modification. Application by spin coating offers a simple procedure for the preparation of minimally interacting surfaces that are functionalized by suitable linker groups to immobilize proteins in their native conformations. These coatings form a versatile basis for biofunctional and biomimetic surfaces. We have demonstrated their advantageous properties by using single-molecule fluorescence microscopy to study immobilized proteins under destabilizing conditions. Biotinylated ribonuclease H (RNase H) was labeled with a fluorescence resonance energy transfer (FRET) pair of fluorescent dyes and attached to the surface by a biotin-streptavidin linkage. FRET analysis demonstrated completely reversible denaturation/renaturation behavior upon exposure of the surface-immobilized proteins to 6 M guanidinium chloride (GdmCl) followed by washing in buffer. A comparison with bovine serum albumin (BSA) coated surfaces and linear PEO brush surfaces yielded superior performance in terms of chemical stability, inertness and noninteracting nature of the star-polymer derived films.
Microfluidic-assisted growth of colloidal crystals (2012)

We investigate the concentration process of dilute dispersions of charge-stabilized colloids using a dedicated microfluidic tool based on evaporation. We observe the nucleation and growth of colloidal crystals with typical dimensions of 10 × 50 μm2 × several millimetres whose growth kinetics and structures are characterized using optical, confocal, and electron microscopy. We demonstrate with systematic screening experiments that microfluidics yields a precise control on the growth pace of these dense organized colloidal states. We then predict the growth rate of these colloidal structures with a model of the suspension (hard-spheres) that accounts for a diverging collective diffusion coefficient near the close-packing; this description helps us understand why the kinetics can be anticipated on the basis of a simple conservation law. Finally, our experiments unveil the important role played by ions which are also present in the initial dilute dispersion and therefore also get concentrated simultaneously with colloids, and their influence on the ordering.
Association of Prehospital Blood Product Transfusion During Medical Evacuation of Combat Casualties in Afghanistan With Acute and 30-Day Survival (2017)

Among medically evacuated US military combat causalities in Afghanistan, blood product transfusion prehospital or within minutes of injury was associated with greater 24-hour and 30-day survival than delayed transfusion or no transfusion. The findings support prehospital transfusion in this setting.
Automated Ultra-Thin-Layer SDS Gel Electrophoresis of Proteins Using Noncovalent Fluorescent Labeling (2000)

Ultra-thin-layer SDS gel electrophoresis in conjunction with automated laser-induced fluorescence detection is a novel and powerful method for the analysis of fluorophore-labeled proteins. The technique described in this paper employs instant, noncovalent fluorophore labeling by the addition of a fluorescent staining dye to the sample proteins either during or immediately prior to the sample loading process. Thus, the method does not require time-consuming post- or preseparation staining/labeling. By combining the multilane format of SDS polyacrylamide slab gel electrophoresis and the high separation efficiency of capillary SDS gel electrophoresis, ultra-thin-layer SDS gel electrophoresis features rapid, high-throughput, and high-resolution analysis of proteins in the molecular mass range of 14-116 kDa. The good heat dissipation inherent to the ultrathin format enables the use of agarose and agarose-based composite separation matrixes, which can be easily replaced within the separation platform. Labeling efficiency as a function of the concentration of the staining dye, SDS, and proteins is thoroughly discussed. Detection sensitivity of the method was found to be at the low-femtomole level (1.25 ng/band), determined by analyzing a set of serial dilutions of standard proteins. Practical example of molecular mass determination and characterization of a complex protein mixture are also shown.
An Effective Staff Detection and Removal Technique for Musical Documents (2012)

Musical staff line detection and removal techniques detect the staff positions in musical documents and segment musical score from musical documents by removing those staff lines. It is an important preprocessing step for ensuing the Optical Music Recognition tasks. This paper proposes an effective staff line detection and removal method that makes use of the global information of the musical document and models the staff line shape. It first estimates the staff height and space, and then models the shape of the staff line by examining the orientation of the staff pixels. At last the estimated model is used to find out the location of staff lines and hence to remove those detected staff lines. The proposed technique is simple, robust, and involves few parameters. It has been tested on the dataset of the recent staff removal competition held under the International Conference of Document Analysis and Recognition(ICDAR) 2011. Experimental results show the effectiveness and robustness of our proposed technique on musical documents with various types of deformations.
How Does Nature Cleave Sulfuric Acid Esters? A Novel Posttranslational Modification of Sulfatases (1998)

A rare inherited disease, multiple sulfatase deficiency, is attributed to a defect in a posttranslational protein modification which is essential for the catalytic activity of all known sulfatases. Structure analysis of arylsulfatase A, the enzyme that cleaves sulfatide 1, shows that the modification of a cysteine residue into a formylglycine residue is essential for catalytic activity.
Ka band satellite system architecture for local loop Internet access (2002)

A Ka-band satellite system architecture that provides wide-band local loop access to consumers and small businesses is described. It is based on the phased deployment of simple, low cost bent-pipe GEO satellites providing highly directive spot beam coverage over the continental United States. Each spot beam covers a desired service area, usually not well served by terrestrial communications systems. Internet Service Providers (ISP) use hub antennas within the spot beams to provide two-way Internet connections to the end users. The end users access the ISP hub via the GEO satellite using USATs (Ultra-Small Antenna Terminals). The downstream data rate can be as high as 90 Mbps, and the upstream rates vary from 64 kbps to as high as 2.048 Mbps.
Nanostructured Polyaniline Sensors (2004)

The conjugated polymer polyaniline is a promising material for sensors, since its conductivity is highly sensitive to chemical vapors. Nanofibers of polyaniline are found to have superior performance relative to conventional materials due to their much greater exposed surface area. A template-free chemical synthesis is described that produces uniform polyaniline nanofibers with diameters below 100 nm. The interfacial polymerization can be readily scaled to make gram quantities. Resistive-type sensors made from undoped or doped polyaniline nanofibers outperform conventional polyaniline on exposure to acid or base vapors, respectively. The nanofibers show essentially no thickness dependence to their sensitivity.
SRS—an indexing and retrieval tool for flat file data libraries (1993)

SRS (Sequence Retrieval System) is an information indexing and retrieval system designed for libraries with a flat file format such as the EMBL nucleotide sequence databank, the SwissProt protein sequence databank or the Prosite library of protein subsequence consensus patterns. SRS supports the data structure of these libraries by providing special indices for implementing lists of subentities (e.g. feature tables) or hierarchically structured data-fields (e.g. taxonomic classification). A language (ODD) has been designed for the convenient specification of library format and organization, representation of individual data-fields within the system (design of indices) and structuring other data needed during retrieval. This ensures flexibility required for coping with different library formats, which are subject to continuous change. Queries and inspection of retrieved entries can be performed from a user interface with pull-down menus and windows. SRS supports various input and output formats but is particularly well adapted to the GCG programs.
Temperature Uniformity and DNA Amplification Efficiency in Micromachined Glass PCR chip (2005)

This paper presented the relationship between the temperature uniformity and the DNA amplification efficiency in glass PCR chip. The top glass slide was laser drilled to form liquid access holes. The bottom glass slide was wet etched to get 100µm depth trench and deposited platinum thin-film as heater and sensor. Two Pyrex 7740 glass slides were thermally bonded together to form a chip of 4µl PCR reaction chamber. The DNA replications are successfully demonstrated in these chips by precision temperature control and oil sealing. Chips were fabricated with different patterns of heater and sensor. Thermochromic liquid crystal (Hallcrest, Chicago, IL) and Agilent Bioanalyzer 2100 were used to check temperature uniformity and amplification efficiency of each chip. According to the experimental result, we did not only design a micro-PCR chip with higher efficiency, but also provide a convenient and cheap temperature measurement solution in micro technology.
Adrenergic and Cholinergic Receptors in the Human Prostate, Prostatic Capsule and Bladder Neck (1975)

The adrenergic and cholinergic receptors of the human prostatic capsule, prostatic "adenoma", and bladder neck, were investigated by the in-vitro isometric technique. The prostatic capsule was found to be very rich in both alpha-adrenergic receptors and cholinergic receptors. The prostatic adenoma was moderately rich in alpha-adrenergic receptors, but cholinergic receptors were absent. Beta-adrenergic receptors were absent in the prostatic adenoma, and there was an equivocal response in less than half the specimens of the prostatic capsule. An attempt was made to distinguish between the trigonal component at the posterior bladder neck, and the true bladder neck muscle both posteriorly and antero-laterally. The results indicat that the "posterior bladder neck" seen at operation is predominantly trigonal muscle, and is poor in cholinergic receptors. The adrenergic response is variable in the true bladder neck muscle, but is present and strong in the trigonal muscle. This response is characteristically gradual in its development. In view of the findings in this investigation, it is suggested that certain instances of acute retention of urine in prostatic patients are due to over-stimulation of the alpha-adrenergic receptors, particularly those in the prostatic capsule. Similarly, the accepted clinical contraindication to the use of cholinergic drugs for retention in the prostatic patient is supported by the distribution of the cholinergic receptors in the tissues examined.
Recruitment of lymphocytes during cutaneous delayed hypersensitivity in nonhuman primates is dependent on E-selectin and vascular cell adhesion molecule 1. (1994)

Previous investigations of cutaneous delayed hypersensitivity (DHR) in humans and animals have demonstrated that lymphocyte recruitment from blood is temporally and spatially associated with the de novo, asynchronous expression of both vascular cell adhesion molecule 1 (VCAM-1) and E-selectin on dermal endothelium. In this study, DHR was induced in rhesus monkeys sensitized against tuberculin in order to investigate the contribution of E-selectin and VCAM-1 in lymphocyte recruitment to skin. Intravenous infusions of neutralizing doses of F(ab')2 fragments of murine antibodies to either E-selectin or VCAM-1 during the early inductive phases of DHR showed that murine IgG localized to dermal endothelium at the site of DHR in a pattern kinetically similar to the expression of each endothelial adhesion protein. Most importantly, the relative numbers of lymphocytes localized to the inflammatory site were significantly reduced in DHR modified with infusions of antibodies to either VCAM-1 or E-selectin, while the numbers of lymphocytes recruited to skin in the animal given F(ab')2 fragments of an irrelevant murine monoclonal antibody of the same isotype and at the same dose were not changed. Moreover, in individual animals, the relative inhibition achieved with a particular antibody was proportional to the magnitude of expression of the targeted adhesion protein. Therefore, both VCAM-1 and E-selectin are functionally relevant in the genesis of cutaneous DHR, and each appears to contribute to lymphocyte recruitment in relation to its relative degree of expression in any one particular animal.