gebhart/patrepeval huggingface dataset:
Effective hydrostatic limits of pressure media for high-pressure crystallographic studies (2007)

The behavior of a number of commonly used pressure media, including nitrogen, argon, 2-propanol, a 4:1 methanol–ethanol mixture, glycerol and various grades of silicone oil, has been examined by measuring the X-ray diffraction maxima from quartz single crystals loaded in a diamond-anvil cell with each of these pressure media in turn. In all cases, the onset of non-hydrostatic stresses within the medium is detectable as the broadening of the rocking curves of X-ray diffraction peaks from the single crystals. The onset of broadening of the rocking curves of quartz is detected at ∼9.8 GPa in a 4:1 mixture of methanol and ethanol and at ∼4.2 GPa in 2-propanol, essentially at the same pressures as the previously reported hydrostatic limits determined by other techniques. Gigahertz ultrasonic interferometry was also used to detect the onset of the glass transition in 4:1 methanol–ethanol and 16:3:1 methanol–ethanol–water, which were observed to support shear waves above ∼9.2 and ∼10.5 GPa, respectively, at 0.8–1.2 GHz. By contrast, peak broadening is first detected at ∼3 GPa in nitrogen, ∼1.9 GPa in argon, ∼1.4 GPa in glycerol and ∼0.9 GPa in various grades of silicone oil. These pressures, which are significantly lower than hydrostatic limits quoted in the literature, should be considered as the practical maximum limits to the hydrostatic behavior of these pressure media at room temperature.
Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees (2015)

Lactobacillus kunkeei is the most abundant bacterial species in the honey crop and food products of honeybees. The 16 S rRNA genes of strains isolated from different bee species are nearly identical in sequence and therefore inadequate as markers for studies of coevolutionary patterns. Here, we have compared the 1.5 Mb genomes of ten L. kunkeei strains isolated from all recognized Apis species and another two strains from Meliponini species. A gene flux analysis, including previously sequenced Lactobacillus species as outgroups, indicated the influence of reductive evolution. The genome architecture is unique in that vertically inherited core genes are located near the terminus of replication, whereas genes for secreted proteins and putative host-adaptive traits are located near the origin of replication. We suggest that these features have resulted from a genome-wide loss of genes, with integrations of novel genes mostly occurring in regions flanking the origin of replication. The phylogenetic analyses showed that the bacterial topology was incongruent with the host topology, and that strains of the same microcluster have recombined frequently across the host species barriers, arguing against codiversification. Multiple genotypes were recovered in the individual hosts and transfers of mobile elements could be demonstrated for strains isolated from the same host species. Unlike other bacteria with small genomes, short generation times and multiple rRNA operons suggest that L. kunkeei evolves under selection for rapid growth in its natural growth habitat. The results provide an extended framework for reductive genome evolution and functional genome organization in bacteria.
p-Isothiocyanatophenyl 6-phospho-.alpha.-D-mannopyranoside coupled to albumin. A model compound recognized by the fibroblast lysosomal enzyme uptake system. 1. Chemical synthesis and characterization (1980)

We have developed a simple synthesis for a conjugate of albumin and isothio-nitrophenyl alpha-D-mannopyranoside to study the requirements of the fibroblast lysosomal enzyme recognition system. p-aminophenyl 6-phospho-alpha-D-mannopyranoside was prepared in two ways: (1) phosphorylation of isothio-nitrophenyl alpha-D-mannopyranoside and subsequent reduction of the nitro group by catalytic hydrogenation and (2) direct phosphorylation of p-aminophenyl alpha-D-mannopyranoside. Mannosides were phosphorylated in a reaction with phosphoryl chloride, pyridine, and water at 0 degrees C for 1 h, by a procedure selective for primary hydroxyl groups. Purified p-a minophenyl 6-phospho-alpha-D-mannopyranoside was characterized by chromatographic, enzymatic, and 13C nuclear magnetic resonance spectroscopic methods. Isothio-Isothiocyanatophenyl 6-phospho-alpha-D-mannopyranoside and the p-isothiocyanatophenyl glycosides of alpha-mannose, alpha-glucose, alpha- and beta-galactose, and alpha-L-fucose were formed by reaction of the respective p-aminophenyl glycosides with thiophosgene. Incubation of the p-isothiocyanatophenyl glycosides with bovine serum albumin at pH 8.5, 25 degrees C, for 18 h generally resulted in the coupling, primarily through lysine residues, of up to 20-30 mol of glycoside per mol of protein. Biological properties of the conjugates in the fibroblast lysosomal enzyme recognition system are described in the accompanying paper.
Interactions Between Evanescent Photons and Environment (2014)

The evanescent waves named as EW1, EW2, EW3 are described in 3 respective experimental setups: 1) total internal reflection; 2) scattering on an inhomogeneous planar target; and 3) propagation along a waveguide. Some interactions are considered between EW2 and the environment. The latter may include a beam of probing particles and/or the screen on which the EW2 are formed. Some new properties of EW are described, such as complex energy eigenvalues in case of a movable screen, and evanescence exchange between the interacting objects. This reveals the connection between evanescent states and the Gamow states of the studied system. The 4-momentum exchange between EW2 and the probe is highly selective and may collapse the superposition of studied EW2- eigenstates to a single EW-eigenstate of the probing particle. Possible imprints of EW2 in the far field are briefly discussed and a simple experiment is suggested for their observation. .
Polysome Profiling Analysis of mRNA and Associated Proteins Engaged in Translation (2018)

Post-transcriptional regulation is an important aspect of the control of gene expression. mRNAs are translated with variable efficiencies, and these efficiencies can change rapidly during adaptation to diverse environmental factors, including cellular stresses and microbial infections. Polysome profiling analysis utilizes ultracentrifugation to isolate complexes of mRNAs in the process of translation and corresponding proteins on the basis of density. Here we describe polysome profiling analysis using a continuous ultraviolet spectrophotometer and a gradient fractionator. We provide protocols for processing sucrose gradient fractions for isolation of RNA for RT-qPCR analysis and isolation of protein for SDS-PAGE and immunoblot analysis. © 2018 by John Wiley & Sons, Inc.
Performance of an Adaptive Routing Overlay under Dynamic Link Impairments (2007)

We propose an adaptive software routing overlay to improve the performance of TCP/IP-based internets over links with dynamic impairments. The routing overlay adaptively distributes traffic over a set of alternative paths based on real-time link status information provided by a system of network sensors. The routing overlay also provides explicit rate feedback to rate-aware TCP clients, allowing them to achieve higher throughputs than legacy clients under static link loss and delay impairments. We present performance results from a collection of Emulab experiments on simple network topologies with dynamic link impairments. The results show that the adaptive routing overlay achieves significantly higher bulk file transfer throughput than legacy systems in the presence of link impairments. Sensor-based adaptive routing provides substantial gains in TCP throughput even for legacy TCP clients. When rate-aware TCP clients are used, the performance gain of the adaptive routing overlay with respect to legacy systems improves dramatically.
Overexpression of IL-15 In Vivo Enhances Protection Against <i>Mycobacterium bovis</i> Bacillus Calmette-Guerin Infection Via Augmentation of NK and T Cytotoxic 1 Responses (2001)

To investigate the immunomodulating effects of IL-15 in vivo on mycobacterial infection, we used IL-15-transgenic (Tg) mice, which were recently constructed with cDNA-encoding secretable isoform of IL-15 precursor protein under the control of a MHC class I promoter. The IL-15-Tg mice exhibited resistance against infection with Mycobacterium bovis bacillus Calmette-Guérin (BCG), as assessed by bacteria growth. IFN-gamma level in serum was significantly higher in IL-15-Tg mice than in non-Tg mice after BCG infection. NK cells were remarkably increased, and Ag-specific T cytotoxic 1 response mediated by CD8+ T cells producing IFN-gamma was significantly augmented in the IL-15-Tg mice following BCG infection. Neutralization of endogenous IFN-gamma by in vivo administration of anti-IFN-gamma mAb deteriorated the clearance of the bacteria. Depletion of of NK cells or CD8+ T cells by in vivo administration of anti-asialo-GM(1) Ab or anti-CD8 mAb hampered the exclusion of bacteria. Thus, overexpression of IL-15 in vivo enhanced protection against BCG infection via augmentation of NK and T cytotoxic 1 responses.
Depressed Affect, Hopelessness, and the Risk of Ischemic Heart Disease in a Cohort of U.S. Adults (1993)

Major depression has been associated with mortality from ischemic heart disease (IHD). In addition, a symptom of depression--hopelessness--has been suggested as a determinant of health status. We studied the relation of both depressed affect and hopelessness to IHD incidence using data from a cohort of 2,832 U.S. adults age 45-77 years who participated in the National Health Examination Follow-up Study (mean follow-up = 12.4 years) and had no history of IHD or serious illness at baseline. We used the depression subscale of the General Well-Being Schedule to define depressed affect and a single item from the scale to define hopelessness. At baseline, 11.1% of the cohort had depressed affect; 10.8% reported moderate hopelessness, and 2.9% reported severe hopelessness. Depressed affect and hopelessness were more common among women, blacks, and persons who were less educated, unmarried, smokers, or physically inactive. There were 189 cases of fatal IHD during the follow-up period. After we adjusted for demographic and risk factors, depressed affect was related to fatal IHD [relative risk = 1.5; 95% confidence interval (CI) = 1.0-2.3]; the relative risks of fatal IHD for moderate and severe levels of hopelessness were 1.6 (95% CI = 1.0-2.5) and 2.1 (95% CI = 1.1-3.9), respectively. Depressed affect and hopelessness were also associated with an increased risk of nonfatal IHD. These data indicate that depressed affect and hopelessness may play a causal role in the occurrence of both fatal and nonfatal IHD.
Electron-Beam Patterning of Polymer Electrolyte Films To Make Multiple Nanoscale Gates for Nanowire Transistors (2013)

We report an electron-beam based method for the nanoscale patterning of the poly(ethylene oxide)/LiClO4 polymer electrolyte. We use the patterned polymer electrolyte as a high capacitance gate dielectric in single nanowire transistors and obtain subthreshold swings comparable to conventional metal/oxide wrap-gated nanowire transistors. Patterning eliminates gate/contact overlap, which reduces parasitic effects and enables multiple, independently controllable gates. The method's simplicity broadens the scope for using polymer electrolyte gating in studies of nanowires and other nanoscale devices.
Modelling of crosstalk among the GaAs-based VLSI interconnections (1989)

We have developed a computer-efficient model and carried out computer simulations of the crosstalk effects in the single-, bi- and trilevel high-density interconnections on the GaAs-based VHSIC. The self and coupling interconnection capacitances used in the model have been determined by a network analogue method developed for the finite-length interconnections, open substrates and finite dimensions of the bottom ground plane, as well as by the method of moments in conjunction with a Green&apos;s function appropriate for the geometry of the interconnections. The Green&apos;s function was obtained by using the method of multiple images. The results include the fringing fields, as well as the shielding by the neighbouring interconnections. Related software modules have been developed and run successfully on the mainframe computers. For a given set of the interconnection dimensions and other parameters, the algorithm takes less than 5 minutes of the computer processing time on a mainframe computer. The modules have been used to study the dependences of the crosstalk voltage on the interconnection dimensions such as their lengths, widths, separations and the interlevel distances. Dependence of the crosstalk signal on other parameters such as the driving transistor resistance and the load capacitance has also been investigated. The results can be utilised to obtain optimum values for the various interconnection parameters for minimum crosstalk.
Histamine H1 receptors identified in mammalian brain membranes with [3H]mepyramine. (1978)

The antihistamine [3H]mepyramine binds to H1 histamine receptors in mammalian brain membranes. Potencies of H1 antihistamines at the binding sites correlate with their pharmacological antihistamine effects in the guinea pig ileum. Specific [3H]mepyramine binding is saturable with a dissociation constant of about 4 nM in both equilibrium and kinetic experiments and a density of 10 pmol per gram of whole kinetic experiments and a density of 10 pmol per gram of whole brain. Some tricyclic antidepressants are potent inhibitors of specific [3H]mepyramine binding. Regional variations of [3H]mepyramine binding do not correlate with variations in endogeneous histamine and histidine decarboxylase activity.
Transition from Caspase-dependent to Caspase-independent Mechanisms at the Onset of Apoptotic Execution (1998)

We have compared cytoplasmic extracts from chicken DU249 cells at various stages along the apoptotic pathway. Extracts from morphologically normal "committed stage" cells induce apoptotic morphology and DNA cleavage in substrate nuclei but require ongoing caspase activity to do so. In contrast, extracts from frankly apoptotic cells induce apoptotic events in added nuclei in a caspase-independent manner. Biochemical fractionation of these extracts reveals that a column fraction enriched in endogenous active caspases is unable to induce DNA fragmentation or chromatin condensation in substrate nuclei, whereas a caspase-depleted fraction induces both changes. Further characterization of the "execution phase" extracts revealed the presence of an ICAD/DFF45 (inhibitor of caspase-activated DNase/DNA fragmentation factor)- inhibitable nuclease resembling CAD, plus another activity that was required for the apoptotic chromatin condensation. Despite the presence of active caspases, committed stage extracts lacked these downstream activities, suggesting that the caspases and downstream factors are segregated from one another in vivo during the latent phase. These observations not only indicate that caspases act in an executive fashion, serving to activate downstream factors that disassemble the nucleus rather than disassembling it themselves, but they also suggest that activation of the downstream factors (rather than the caspases) is the critical event that occurs at the transition from the latent to active phase of apoptosis.
Optimal Gabor filters for texture segmentation (1995)

Texture segmentation involves subdividing an image into differently textured regions. Many texture segmentation schemes are based on a filter-bank model, where the filters, called Gabor filters, are derived from Gabor elementary functions. The goal is to transform texture differences into detectable filter-output discontinuities at texture boundaries. By locating these discontinuities, one can segment the image into differently textured regions. Distinct discontinuities occur, however, only if the Gabor filter parameters are suitably chosen. Some previous analysis has shown how to design filters for discriminating simple textures. Designing filters for more general natural textures, though, has largely been done ad hoc. We have devised a more rigorously based method for designing Gabor filters. It assumes that an image contains two different textures and that prototype samples of the textures are given a priori. We argue that Gabor filter outputs can be modeled as Rician random variables (often approximated well as Gaussian rv's) and develop a decision-theoretic algorithm for selecting optimal filter parameters. To improve segmentations for difficult texture pairs, we also propose a multiple-filter segmentation scheme, motivated by the Rician model. Experimental results indicate that our method is superior to previous methods in providing useful Gabor filters for a wide range of texture pairs.
Split-Filter Computed Tomography (1980)

A simple technique for obtaining dual energy information from a single computed tomography (CT) scan is described. The method involves filtering the two halves of the X-ray fan beam differently. It is shown that during a 360 degree scan, this split-filtration geometry results in dual energy noise analysis, valid for polychromatic X-ray beams, is presented and used to determine the optimal parameters for the split-filter scans. Using the theoretically optimal split-filter design installed on a commercial CT scanner, photoelectric and Compton images of a head phantom were obtained. Recombination of the photoelectric and Compton components of attenuation at arbitrary energies demonstrates the ability to remove spectral artifacts from conventional CT images.
Cloning, sequencing, and expression of the gene encoding methylmalonyl-coenzyme A mutase from Streptomyces cinnamonensis (1993)

In streptomycetes, the conversion of succinyl-coenzyme A (CoA) into methylmalonyl-CoA, catalyzed by methylmalonyl-CoA mutase, most likely represents an important source of building blocks for polyketide antibiotic biosynthesis. In this work, the structural gene for methylmalonyl-CoA mutase from Streptomyces cinnamonensis was cloned by using a heterologous gene probe encoding the mutase from Propionibacterium shermanii. A 5,732-bp fragment was sequenced, within which four open reading frames were identified on one DNA strand. The two largest (mutA and mutB) overlap by 1 nucleotide and encode proteins of 616 and 733 residues showing high amino acid sequence similarities to each other and to methylmalonyl-CoA mutases from P. shermanii and mammalian sources. The transcriptional start of the mutA-mutB message, determined by S1 mapping, coincides with the first nucleotide of the translational start codon. Evidence that these two open reading frames encode a functional mutase in S. cinnamonensis was obtained by subcloning and expression in Streptomyces lividans TK64. The mutA and mutB gene products were detected in Western blots (immunoblots) with mutase-specific antibodies and by direct detection of mutase activity with a newly developed assay method. The methylmalonyl-CoA mutase was unable to catalyze the conversion of isobutyryl-CoA into n-butyryl-CoA, another closely related adenosylcobalamin-dependent rearrangement known to occur in S. cinnamonensis.
New approaches to the diagnosis and treatment of inborn errors or urea synthesis. (1981)

Long-term therapy of urea cycle enzymopathies using dietary manipulation alone has had limited success. Exploitation of alternative pathways of waste nitrogen excretion appears to improve control of these disorders. Arginine supplementation alone is sufficient therapy for AL deficiency. Arginine, protein restriction, and benzoate appear to be successful in managing AS deficiency. Sodium benzoate and/or phenylacetic acid combined with dietary manipulations may improve the prognosis in OTC and CPS deficiencies, but the long-term effectiveness of these drugs has yet to be tested. Acute therapy of hyperammonemic coma continues to be a vexing problem. Peritoneal dialysis appears to be more effective than exchange transfusion in removing accumulated nitrogen. Hemodialysis, if immediately available, is also effective. Sodium benzoate alone has avoided the necessity for peritoneal dialysis in many patients. However, at ammonium levels greater than tenfold normal, the effects of sodium benzoate have been equivocal. Intravenous arginine alone is effective therapy in treatment of hyperammonemic coma in AL and possibly AS deficiency.
Difluoro Ketone Peptidomimetics Suggest a Large S1 Pocket for Alzheimer's γ-Secretase:  Implications for Inhibitor Design (2000)

The final step in the generation of the amyloid-beta protein (Abeta), implicated in the etiology of Alzheimer's disease, is proteolysis within the transmembrane region of the amyloid precursor protein (APP) by gamma-secretase. Although considered an important target for therapeutic design, gamma-secretase has been neither well-characterized nor definitively identified. Previous studies in our laboratory using substrate-based difluoro ketone and difluoro alcohol transition-state analogue inhibitors suggest that gamma-secretase is an aspartyl protease with loose sequence specificity. To further characterize the active site of gamma-secretase, we prepared a series of difluoro ketone peptide analogues with varying steric bulkiness in the P1 position and tested the ability of these compounds to inhibit Abeta production in APP-transfected cells. Incorporation of bulky, aliphatic P1 side chains, such as sec-butyl or cyclohexylmethyl, led to increased gamma-secretase inhibitory potency, suggesting a large S1 pocket to accommodate these substituents and providing further evidence for loose sequence specificity. The cyclohexylmethyl P1 substituent allowed N-terminal truncation to a low-molecular-weight compound (<600 Da) that effectively blocked Abeta production (IC(50) approximately 5 microM). This finding suggests that optimal S1 binding may allow the development of potent inhibitors with ideal pharmaceutical properties. Moreover, a difluoro alcohol analogue with a cyclohexylmethyl P1 substituent was equipotent with its difluoro ketone counterpart, providing strong evidence that gamma-secretase is an aspartyl protease. All new analogues inhibited total Abeta and Abeta(42) production with the same rank order of potency and increased Abeta(42) production at low concentrations, providing further evidence for distinct gamma-secretases that are nevertheless closely similar with respect to active site topology and mechanism.