gebhart/patrepeval huggingface dataset:
Detection and characterization of chemical vapor fugitive emissions by nonlinear optimal estimation: theory and simulation (2009)

This paper addresses detection and characterization of chemical vapor fugitive emissions in a nonscattering atmosphere by processing of remotely-sensed long-wavelength infrared spectra. The analysis approach integrates a parameterized signal model based on the radiative transfer equation with a statistical model for the infrared background. The maximum likelihood model parameter values are defined as those that maximize a Bayesian posterior probability and are estimated using a Gauss-Newton algorithm. For algorithm performance evaluation we simulate observation of fugitive emissions by augmenting plume-free measured spectra with synthetic plume signatures. As plumes become optically thick, the Gauss-Newton algorithm yields significantly more accurate estimates of chemical vapor column density and significantly more favorable plume detection statistics than clutter-matched-filter-based and adaptive-subspace-detector-based plume characterization and detection.
The triple helical structure of lentinan, a linear β-(1 → 3)-D-glucan (1977)

Probable models for the crystalline structure of lentinan, the β-(l → 3)-D-glucan of the fungus Lentinus elodes, were evaluated by X-ray fiber diffraction and theoretical conformational analysis of single and multiple helices. The X-ray diagram is consistent with a hexagonal unit cell with dimensions a = b = 15.8 Å and c (fiber repeat) = 6 Å. Conformational analysis predicts five probable models for this fiber repeat, of which one is a single helix, two are double helices, and two are triple helices. On the basis of packing of these helices into the unit cell and a comparison of their calculated Fourier transforms with the observed X-ray diffraction intensity distribution, all but the two triple helical models are eliminated from consideration. The two triple helices differ only in chirality and both left- and right-handed models are stabilized by interstrand [Formula: see text] hydrogen bonds, such as are found in the triple helical structure of β-(1 → 3)-D-xylan. The right-handed triple helix may be the more probable structure of the two, by analogy with the known structure of the β-(1 → 3)-D-xylan. It is likely that the β-(1 → 3)-D-glucan of curdlan and those of Armillaria mellea and Lilium longiflorum also possess the same structure.
ISSUES AND EXPERIENCES IN THE DESIGN OF A WINDOW MANAGEMENT SYSTEM (1986)

Window systems underlie many successful human-computer interfaces. But constructing them involves several fundamental design issues which are resolved in various ways by different implementations. These affect both user's and programmer's interface, and include tiling vs overlapping windows; program vs user control of windows; techniques for coping with changeable window sizes; design of transient windows; low-level vs high-level tools for the programmer; local vs distributed control; and the role of a controlling window manager process. There is no broad consensus among designers as to how best to make such decisions. This paper illuminates the issues involved by surveying characteristics of window systems and discussing dominant design questions. The philosophy and implementation underlying the JADE window manager constructed at the University of Calgary is revealed, and the design is reevaluated from the perspective of three years' experience of using the system and programming within it.
Rescue therapy with anti-programmed cell death protein 1 inhibitors of advanced cutaneous squamous cell carcinoma and basosquamous carcinoma: preliminary experience in five cases (2016)

Linked Comment:Soura et al.Br J Dermatol 2016; 175:1150–1151.
Home Life: Factors Structuring the Bacterial Diversity Found within and between Homes (2013)

Most of our time is spent indoors where we are exposed to a wide array of different microorganisms living on surfaces and in the air of our homes. Despite their ubiquity and abundance, we have a limited understanding of the microbial diversity found within homes and how the composition and diversity of microbial communities change across different locations within the home. Here we examined the diversity of bacterial communities found in nine distinct locations within each of forty homes in the Raleigh-Durham area of North Carolina, USA, using high-throughput sequencing of the bacterial 16S rRNA gene. We found that each of the sampled locations harbored bacterial communities that were distinct from one another with surfaces that are regularly cleaned typically harboring lower levels of diversity than surfaces that are cleaned infrequently. These location-specific differences in bacterial communities could be directly related to usage patterns and differences in the likely sources of bacteria dispersed onto these locations. Finally, we examined whether the variability across homes in bacterial diversity could be attributed to outdoor environmental factors, indoor habitat structure, or the occupants of the home. We found that the presence of dogs had a significant effect on bacterial community composition in multiple locations within homes as the homes occupied by dogs harbored more diverse communities and higher relative abundances of dog-associated bacterial taxa. Furthermore, we found a significant correlation between the types of bacteria deposited on surfaces outside the home and those found inside the home, highlighting that microbes from outside the home can have a direct effect on the microbial communities living on surfaces within our homes. Together this work provides the first comprehensive analysis of the microbial communities found in the home and the factors that shape the structure of these communities both within and between homes.
Biosynthesis of the prohormone convertase PC2 in Chinese hamster ovary cells and in rat insulinoma cells. (1993)

The biosynthesis of the prohormone convertase PC2 was studied in Chinese hamster ovary cells stably transfected with PC2 cDNA (CHO/PC2) and in rat insulinoma cells (Rin5f). The major form of PC2 synthesized by CHO/PC2 cells was a 75-kDa protein corresponding to proPC2; this protein was retained intracellularly for 2-4 h following synthesis, suggesting prolonged intracellular residence. In contrast, the major form of PC2 within Rin cells initially exhibited a molecular mass of 72 kDa and was then progressively converted to a 64-kDa species. This 64-kDa species, which required 1-2 h to be released, was the major PC2 form detectable in Rin cell medium. Calcium-dependent benzyloxycarbonyl-Arg-Ser-Lys-Arg-aminomethylcoumarin cleaving activity was found in spent Rin cell medium; this activity could be immunoprecipitated with a carboxyl-terminal PC2 antibody, but not with preimmune serum. In neither cell line did intracellular PC2 become endoglycosidase H-resistant over time. PC2 released from Rin cells was also endoglycosidase H-sensitive. Microsequencing and endoglycosidase H results indicate that 75-kDa CHO cell PC2 and 72-kDa Rin cell PC2 both represent proPC2. We speculate that (a) PC2 undergoes unusual glycosylation, which may be related to its slow release from cells, and (b) the 64-kDa molecule detectable in spent Rin cell medium represents the enzymatically active form of PC2.
Preparation of Cellobiose Octa(n-alkanoate)s and Their Thermal Properties (Commemoration Issue Dedicated to Professor Ken-ichi Katayama On the Occasion of His Retirement) (1991)

Cellobiose octa(n-alkanoate)s (CbOA's) of varying acyl length were prepared, and their thermal and structural properties were studied by differential scanning calorimetry, polarization optical microscopy, and polarization infrared spectroscopy (PIR).CbOA's with an acyl length between 6 and 14 in carbon number were found to form a thermotropic liquid crystal.Comparison of their thermal data with those of cellulose tri(n-alkanoate)s indicated different structuring principles for the oligomer and polymer systems, consistently with the previous studies by X-ray diffraction.The PIR data were apparently consistent with the proposed discotic columnar structuring of CbOA molecules.
Purification and properties of galactose oxidase from Gibberella fujikuroi. (1982)

Galactose oxidase was purified from the culture supernatant of Gibberella fujikuroi by ammonium sulfate precipitation, chromatographies on DEAE-cellulose and hydroxylapatite, and gel filtration on Bio-Gel P-100. The purified enzyme had a molecular weight of 90, 000 and an isoelectric point of pH 3.7, and contained about one atom of copper and about one atom of iron per mol of the enzyme protein. The enzyme was markedly inactivated by a copper-chelating agent, diethyldithiocarbamate, and reducing agents. The apoenzyme preparing on treatment of the enzyme with diethyldithiocarbamate could be reactivated only by the addition of either Cu+ or Cu2+. These results indicate that copper is involved in galactose oxidase activity of G. fujikuroi.
Beta Adrenergic Binding Sites in the Human Eye: An Autoradiographic Study (1990)

Beta adrenergic binding sites were localized and characterized in the human eye by means of "in vitro" autoradiography, using [125I] (-) iodocyanopindolol (125ICYP) as radioligand. Binding sites were visualized by apposition of isotope sensitive film to slide mounted eye sections. Receptor sites were present in the extraocular muscles, in the conjunctiva, in the epithelium and endothelium of the cornea, in the trabeculum and in the ciliary muscle. They were also present in the lens epithelium and in the retina. The pigmented ocular structures were heavily labelled but the binding was nonspecific. Characterization of these binding sites was achieved by testing the ability of selective adrenergic compounds to displace 125ICYP binding. These studies suggested that the majority of adrenergic binding sites in nonpigmented structures of human eye were of a beta2 type.
Design, Synthesis, and Antiviral Activity of 2‘-Deoxy-2‘-fluoro-2‘-C-methylcytidine, a Potent Inhibitor of Hepatitis C Virus Replication (2005)

The pyrimidine nucleoside beta-d-2'-deoxy-2'-fluoro-2'-C-methylcytidine (1) was designed as a hepatitis C virus RNA-dependent RNA polymerase (HCV RdRp) inhibitor. The title compound was obtained by a DAST fluorination of N(4)-benzoyl-1-(2-methyl-3,5-di-O-benzoyl-beta-d-arabinofuranosyl]cytosine to provide N(4)-benzoyl-1-[2-fluoro-2-methyl-3,5-di-O-benzoyl-beta-d-ribofuranosyl]cytosine. The protected 2'-C-methylcytidine was obtained as a byproduct from the DAST fluorination and allowed for the preparation of two biologically active compounds from a common precursor. Compound 1 and 2'-C-methylcytidine were assayed in a subgenomic HCV replicon assay system and found to be potent and selective inhibitors of HCV replication. Compound 1 shows increased inhibitory activity in the HCV replicon assay compared to 2'-C-methylcytidine and low cellular toxicity.
Decreased metastatic spread in mice homozygous for a null allele of the cystatin C protease inhibitor gene. (1999)

Cystatin C concentrations in vivo might influence metastasis in some tissues. The decreased metastatic spread of B16-F10 cells in CysC-/- mice is the result of both reduced seeding and reduced growth of tumour cells in their lungs.
Isosteric Substitutions of Urea to Thiourea and Selenourea in Aliphatic Oligourea Foldamers: Site‐Specific Perturbation of the Helix Geometry (2014)

Nearly isosteric oxo to thioxo substitution was employed to interrogate the structure of foldamers with a urea backbone and explore the relationship between helical folding and hydrogen-bonding interactions. A series of oligomers with urea bonds substituted by thiourea bonds at discrete or all positions in the sequence have been prepared and their folding propensity was studied by using a combination of spectroscopic methods and X-ray diffraction. The outcome of oxo to thioxo replacements on the helical folding was found to depend on whether central or terminal ureas were modified. The canonical helix geometry was not affected upon insertion of thioureas close to the negative end of the helix dipole, whereas thioureas close to the positive pole were found to increase the terminal flexibility and cause helix fraying. Perturbation was amplified when a selenourea was incorporated instead, leading to a structure that is only partly folded.
Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study (2010)

The potential of NDM-1 to be a worldwide public health problem is great, and co-ordinated international surveillance is needed.
Magnetic resonance chondro‐crassometry (MR CCM): A method for accurate determination of articular cartilace thickness? (1996)

A method for the assessment of articular cartilage thickness based on MRI is presented and its accuracy and reproducibility tested. Six specimens of human patellae were imaged, using a fat-suppressed FLASH 3D sequence, and sectioned with a high-precision band saw. The regional distribution of articular cartilage thickness was determined from the MR images and from the anatomical sections (intervals of 0.5 mm). With image analysis 50-90% of the image points were found to lie within exactly the same thickness interval in corresponding patterns, and less than 17% deviated more than 0.5 mm. More than 85% of all pixels were reproducible with MRI after new positioning of the joint. No influence of the read-out direction and no important differences between areas of thin and thick cartilage could be detected. The authors conclude that MR chondro-crassometry can provide accurate and reproducible information on cartilage thickness.
A family 26 mannanase produced by Clostridium thermocellum as a component of the cellulosome contains a domain which is conserved in mannanases from anaerobic fungi The GenBank/EMBL accession number for the sequence reported in this paper is AJ242666. (1999)

Cellulosomes prepared by the cellulose affinity digestion method from Clostridium thermocellum culture supernatant hydrolysed carob galactomannan during incubation at 60 degrees C and pH 6.5. A recombinant phage expressing mannanase activity was isolated from a library of C. thermocellum genomic DNA constructed in lambdaZAPII. The cloned fragment of DNA containing a putative mannanase gene (manA) was sequenced, revealing an ORF of 1767 nt, encoding a protein (mannanase A; Man26A) of 589 aa with a molecular mass of 66816 Da. The putative catalytic domain (CD) of Man26A, identified by gene sectioning and sequence comparisons, displayed up to 32% identity with other mannanases belonging to family 26. Immediately downstream of the CD and separated from it by a short proline/threonine linker was a duplicated 24-residue dockerin motif, which is conserved in all C. thermocellum cellulosomal enzymes described thus far and mediates their attachment to the cellulosome-integrating protein (CipA). Man26A consisting of the CD alone (Man26A") was hyperexpressed in Escherichia coli BL21(DE3) and purified. The truncated enzyme hydrolysed soluble and insoluble mannan, displaying a temperature optimum of 65 degrees C and a pH optimum of 6.5, but exhibited no activity against other plant cell wall polysaccharides. Antiserum raised against Man26A" cross-reacted with a polypeptide with a molecular mass of 70000 Da that is part of the C. thermocellum cellulosome. A second variant of Man26A containing the N-terminal segment of 130 residues and the CD (Man26A") bound to ivory-nut mannan and weakly to soluble Carob galactomannan and insoluble cellulose. Man26A" consisting of the CD alone did not bind to these polysaccharides. These results indicate that the N-terminal 130 residues of mature Man26A may constitute a weak mannan-binding domain. Sequence comparisons revealed a lack of identity between this region of Man26A and other polysaccharide-binding domains, but significant identity with a region conserved in the three family 26 mannanases from the anaerobic fungus Piromyces equi.
A New Multi-pulse Diode Rectifier Front End with Tapped Interphase Reactor Draws Near Sinusoidal Input Currents (1997)

In this paper, a new multi-pulse diode rectifier system is proposed. The proposed approach extends the conventional 12-pulse rectifier to a 24-pulse system and draws near sinusoidal currents from the utility line with 5th, 7th, 11th, 13th, 17th and 19th harmonics eliminated. With the addition of two controlled switches such as IGBT's, the pulse number is extended beyond 24 pulses. A generalized PWM technique is presented and an example 48-pulse system is demonstrated. Simulation results verify the proposed concept and experimental results arc provided from a 208V, 10kVA rectifier system.
Ultrastructural localization of capsules, cell wall polysaccharide, cell wall proteins, and F antigen in pneumococci (1988)

The localization of pneumococcal capsular and cell wall antigens was examined by immunoelectron microscopy. C polysaccharide (C-Ps), a common component of all pneumococci, was uniformly distributed on both the inside and outside of the cell walls. The thickness of the C-Ps varied with the strain. Encapsulated strains were covered by varied amounts of capsular polysaccharide concealing the C-Ps of the bacteria so as to render it inaccessible to anti-C-Ps antibodies. In addition to C-Ps, protein antigens were demonstrable on the surface of nonencapsulated pneumococci. The proteins were not masked by the C-Ps layer. An extra layer on the cell walls was conspicuous on electron micrographs of both rough and encapsulated pneumococci. The nature of this extra layer has not been disclosed. F antigen, another common antigen of pneumococci, was uniformly distributed on the surface of the plasma membranes. During the course of the experimental work a reproducible method of gold labeling immunoglobulins was developed.
Olanzapine-induced neutropenia (2015)

Olanzapine-induced neutropenia is a rare adverse effect that is currently poorly described in literature. Although neutropenia is a known adverse effect of clozapine, it has been associated with the use of other antipsychotic medications like olanzapine. This case report describes and reviews a case of olanza-pine-induced neutropenia in a schizophrenic patient. Although the mechanism of antipsychotic-induced neutropenia is still debated, this report attempts to discuss current theories as well as supply evidence in literature of this rare but potentially dangerous adverse effect.
Spontaneous Hibernomas in Sprague-Dawley Rats (2009)

Hibernomas are rare neoplasms originating in brown adipose tissue of humans and other animal species, including laboratory animals. Background incidence values for these tumors in all common strains of laboratory rats are generally accepted as being <0.1%. Between April 2000 and April 2007, however, sixty-two hibernomas (an overall prevalence of 3.52%) were observed in a total of 1760 Sprague-Dawley rats assigned to three carcinogenesis bioassays at two separate research laboratories. All rats were obtained from Charles River's breeding facilities in either Portage, Michigan, or Raleigh, North Carolina. Tumors (twenty-nine benign and thirty-three malignant) were randomly distributed among test article-treated and control groups and were considered to be spontaneous. Most tumors originated in the thoracic cavity, and they were usually described as soft, mottled to tan masses with nodular to lobulated profiles. Immunohistochemical procedures for uncoupling protein 1 (UCP1) confirmed brown adipose tissue as the site of origin rather than white fat. The marked increase in hibernomas in our studies suggests that greater numbers of spontaneous hibernomas may be sporadically encountered in future carcinogenesis studies with Sprague-Dawley rats. The increased potential for hibernomas to arise as spontaneous neoplasms has important implications in studies involving peroxisome proliferators-activated receptor (PPAR) drugs, lipophilic environmental chemicals (e.g., polychlorinated biphenyls), and other molecules or physiologic processes (e.g., beta-adrenergic stimulation) that may target brown fat adipocytes.
Conformation of Macromolecules in the Gas Phase: Use of Matrix-Assisted Laser Desorption Methods in Ion Chromatography (1995)

Conformational data for macromolecules in the gas phase have been obtained by the coupling of a matrix-assisted laser desorption ion source to an ion chromatograph. A series of polyethylene glycol (PEG) polymers "cationized" (converted to a cation) by sodium ions (Na(+)PEG9 to Na(+)PEG19) and a protonated neurotransmitter protein, bradykinin, were studied. Mobilities of Na(+)PEG9 to Na(+)PEG19 are reported. Detailed modeling of Na(+)PEG9 with molecular mechanics methods indicates that the lowest energy structure has the Na(+) ion "solvated" by the polymer chain with seven oxygen atoms as nearest neighbors. The agreement between the model and experiment is within 1 percent for Na(+)PEG9, Na(+)PEG13, and Na(+)PEG17, giving strong support to both the method and the deduced structures. Similar agreement was obtained in initial studies that modeled experimental data for arginine-protonated bradykinin.
The Pro-Factor D Cleaving Activity of MASP-1/-3 Is Not Required for Alternative Pathway Function (2014)

We recently reported in The Journal of Immunology ([1][1]) the presence of a functional alternative pathway in a human patient with Malpuech–Michels–Mingarelli–Carnevale (3MC) syndrome caused by a genetic defect in the MASP1 gene. This defect abolished the production of all three splice
Activation of the ISR mediates the behavioral and neurophysiological abnormalities in Down syndrome (2019)

Down syndrome (DS) is the most common genetic cause of intellectual disability. Protein homeostasis is essential for normal brain function, but little is known about its role in DS pathophysiology. In this study, we found that the integrated stress response (ISR)-a signaling network that maintains proteostasis-was activated in the brains of DS mice and individuals with DS, reprogramming translation. Genetic and pharmacological suppression of the ISR, by inhibiting the ISR-inducing double-stranded RNA-activated protein kinase or boosting the function of the eukaryotic translation initiation factor eIF2-eIF2B complex, reversed the changes in translation and inhibitory synaptic transmission and rescued the synaptic plasticity and long-term memory deficits in DS mice. Thus, the ISR plays a crucial role in DS, which suggests that tuning of the ISR may provide a promising therapeutic intervention.
Biological activity of selected tyrosine-containing 2,5-diketopiperazines. (2005)

The study investigates two cyclic dipeptides, cyclo(Tyr-Tyr) (cTT) and cyclo(Phe-Tyr) (cPT) with respect to their biological activity. Investigations using the whole-cell patch-clamp technique testing the effects of 100 microM cyclic dipeptide on ion channels, revealed reversible voltage-dependant blockade for cTT, while cPT exhibited irreversible time-dependant blockade of L-type calcium channels. The isolated retrogradely-perfused rat heart was used to determine the effects of 100 microM of either cTT or cPT on heart rate (HR), coronary flow rate (CFR), left ventricular systolic pressure (LVSP) and cardiac conduction speed. Results indicated opposing effects for the two compounds, where cTT increased HR and CF while cPT decreased HR, CF, LVSP as well as conduction speed. Other biological investigations included opioid binding and anti-neoplastic assays. Competitive binding curves, using tritiated DAMGO, revealed significant binding to micro-opioid receptors with IC50 values for cTT and cPT being 0.82 microM and 69.7 microM respectively. Anti-neoplastic activity was tested using three cultured cell lines: HT-29, MCF-7 and HeLa which were exposed to 2.5 mM cyclic dipeptide or 0.1 mM melphalan as a positive control. While cTT showed little activity against these lines, cPT resulted in as much as a 75.6% growth inhibition of MCF-7 cells, while also being active against HeLa (73.4% inhibition) and HT-29 (60.6%). The results indicate potential biological activity, showing a need for more investigation into tyrosine containing cyclic dipeptides and their analogues as potential bioactive compounds.