gebhart/patrepeval huggingface dataset:
Real time multiple planar volume clipping based on the programmable graphics process unit (2009)

We propose a real time volume clipping method which is capable of using several analytical planes for virtual clipping, in order to display internal anatomical structures within volumetric data sets. A single proxy plane is used for computation of the direction of a ray that is cast from the viewpoint. Intersections between the rays and the planes are computed on graphics process unit (GPU). The start and end points for each ray are determined by analyzing relationships with the ray direction, intersections and the normal of planes. Then the volume integral is computed along the ray from the start point to the end point. To obtain immediate visual feedback of clipping effects, we implement translation and rotation of planes on GPU to interactively change the shape of clip object. At last, several experiments were performed on a standard PC with a GeForce FX8600 graphics card. Experimental results show that the method can freely clip and clearly visualize volumetric data sets at real time frame rates.
Variable Loop Glycan Dependency of the Broad and Potent HIV-1-Neutralizing Antibodies PG9 and PG16 (2010)

The HIV-1-specific antibodies PG9 and PG16 show marked cross-isolate neutralization breadth and potency. Antibody neutralization has been shown to be dependent on the presence of N-linked glycosylation at position 160 in gp120. We show here that (i) the loss of several key glycosylation sites in the V1, V2, and V3 loops; (ii) the generation of pseudoviruses in the presence of various glycosidase inhibitors; and (iii) the growth of pseudoviruses in a mutant cell line (GnT1(-/-)) that alters envelope glycosylation patterns all have significant effects on the sensitivity of virus to neutralization by PG9 and PG16. However, the interaction of antibody is not inhibited by sugar monosaccharides corresponding to those found in glycans on the HIV surface. We show that some of the glycosylation effects described are isolate dependent and others are universal and can be used as diagnostic for the presence of PG9 and PG16-like antibodies in the sera of HIV-1-infected patients. The results suggest that PG9 and PG16 recognize a conformational epitope that is dependent on glycosylation at specific variable loop N-linked sites. This information may be valuable for the design of immunogens to elicit PG9 and PG16-like antibodies, as well as constructs for cocrystallization studies.
Neural synchrony indexes disordered perception and cognition in schizophrenia (2004)

Current views of schizophrenia suggest that it results from abnormalities in neural circuitry, but empirical evidence in the millisecond range of neural activity has been difficult to obtain. In pursuit of relevant evidence, we previously demonstrated that schizophrenia is associated with abnormal patterns of stimulus-evoked phaselocking of the electroencephalogram in the gamma band (30-100 Hz). These patterns may reflect impairments in neural assemblies, which have been proposed to use gamma-band oscillations as a mechanism for synchronization. Here, we report the unique finding that, in both healthy controls and schizophrenia patients, visual Gestalt stimuli elicit a gamma-band oscillation that is phase-locked to reaction time and hence may reflect processes leading to conscious perception of the stimuli. However, the frequency of this oscillation is lower in schizophrenics than in healthy individuals. This finding suggests that, although synchronization must occur for perception of the Gestalt, it occurs at a lower frequency because of a reduced capability of neural networks to support high-frequency synchronization in the brain of schizophrenics. Furthermore, the degree of phase locking of this oscillation is correlated with visual hallucinations, thought disorder, and disorganization in the schizophrenia patients. These data provide support for linking dysfunctional neural circuitry and the core symptoms of schizophrenia.
Performance projections for ballistic carbon nanotube field-effect transistors (2002)

The performance limits of carbon nanotube field-effect transistors (CNTFETs) are examined theoretically by extending a one-dimensional treatment used for silicon metal–oxide–semiconductor field-effect transistors (MOSFETs). Compared to ballistic MOSFETs, ballistic CNTFETs show similar I–V characteristics but the channel conductance is quantized. For low-voltage, digital applications, the CNTFET with a planar gate geometry provides an on-current that is comparable to that expected for a ballistic MOSFET. Significantly better performance, however, could be achieved with high gate capacitance structures. Because the computed performance limits greatly exceed the performance of recently reported CNTFETs, there is considerable opportunity for progress in device performance.
Serum immunoglobulin A response to Norwalk virus infection (1989)

We describe the serum immunoglobulin A (IgA) antibody response to Norwalk virus infection in human volunteers and compare it with previously described IgM and total antibody responses. Whereas specific IgA and IgM peak within 2 weeks after onset of symptoms, titers of total blocking antibody continue to rise, implying mediation by IgG antibody.
Determining the Effects of Antiepileptic Drugs on Cognitive Function in Pediatric Patients With Epilepsy (2004)

The majority of children with epilepsy are of normal intelligence; however, a significant subset suffers from temporary or permanent cognitive impairment. Factors that affect cognitive function are myriad and include the neuropathology underlying the epilepsy, seizures, epileptiform activity, psychosocial problems, and antiepileptic drug side effects. Although cognitive impairment is often wrongly attributed to the effects of antiepileptic drugs, antiepileptic drugs do impair cognition in some children. Clinicians should be aware of the differential cognitive effects of antiepileptic drugs and should monitor cognitive function closely when adding or changing therapy. Based on published data from prospective, chronic dosing studies, phenobarbital and topiramate have the highest potential for causing cognitive dysfunction.
Distributed multiaxis fiber grating strain sensor applications for bridges (1998)

Fiber optic gratings have been widely used to measure longitudinal strain and temperature. By writing fiber gratings onto polarization maintaining optical fiber with substantial birefringence, transverse strain measurements may be made. For bridges and other civil structures, this opens up a series of new opportunities where multi axis strain sensing may be effectively used for health monitoring systems. (A) For the covering abstract see ITRD E127016.
A green-by-design biocatalytic process for atorvastatin intermediate (2009)

The development of a green-by-design, two-step, three-enzyme process for the synthesis of a key intermediate in the manufacture of atorvastatin, the active ingredient of the cholesterol lowering drug Lipitor®, is described. The first step involves the biocatalytic reduction of ethyl-4-chloroacetoacetate using a ketoreductase (KRED) in combination with glucose and a NADP-dependent glucose dehydrogenase (GDH) for cofactor regeneration. The (S) ethyl-4-chloro-3-hydroxybutyrate product is obtained in 96% isolated yield and >99.5% e.e. In the second step, a halohydrin dehalogenase (HHDH) is employed to catalyse the replacement of the chloro substituent with cyano by reaction with HCN at neutral pH and ambient temperature. The natural enzymes were highly selective but exhibited productivities that were insufficient for large scale application. Consequently, in vitro enzyme evolution using gene shuffling technologies was employed to optimise their performance according to predefined criteria and process parameters. In the case of the HHDH reaction, this afforded a 2500-fold improvement in the volumetric productivity per biocatalyst loading. This enabled the economical and environmentally attractive production of the key hydroxynitrile intermediate. The overall process has an E factor (kg waste per kg product) of 5.8 when process water is not included, and 18 if included.
Temporal zeta potential variations of 45S5 bioactive glass immersed in an electrolyte solution (2000)

45S5 bioactive glass (BG) is a bioactive material known to bond to bone in vivo through a surface calcium phosphate (Ca-P) layer. The goal of this study was to address the importance of BG surface charge in the bioactive response by examining the relationship between charge variations and the formation of the surface Ca-P layer. The zeta potential of BG in an electrolyte solution (TE) was measured by particle electrophoresis, and the formation of a Ca-P layer was characterized using SEM, EDXA, and FTIR. Si, Ca, and P solution concentrations also were determined. The initial BG surface was negatively charged, and two sign reversals were detected during 3 days of immersion. The first, from negative to positive after 1 day, is attributed to the adsorption of cations at the BG surface, and the second reversal was due to the precipitation of phosphate ions from solution. A strong correlation was found between the formation of a Ca-P layer and BG surface zeta potential variations. The dynamic shift in zeta potential from an initially negative surface to a positively charged surface directly corresponded with the formation of an amorphous Ca-P layer. In addition, when the glass surface matured into a crystalline Ca-P layer, it was associated with a reversal from a positive to a negative surface. Future work will focus on the effects of protein adsorption on BG surface charge and Ca-P layer formation kinetics as well as on cellular response to a changing BG surface.
A Constitutive Decay Element Promotes Tumor Necrosis Factor Alpha mRNA Degradation via an AU-Rich Element-Independent Pathway (2003)

Tumor necrosis factor alpha (TNF-α) expression is regulated by transcriptional as well as posttranscriptional mechanisms, the latter including the control of mRNA decay through an AU-rich element (ARE) in the 3′ untranslated region (UTR). Using two mutant cell lines deficient for ARE-mediated mRNA decay, we provide evidence for a second element, the constitutive decay element (CDE), which is also located in the 3′ UTR of TNF-α. In stably transfected RAW 264.7 macrophages stimulated with lipopolysaccharide (LPS), the CDE continues to target a reporter transcript for rapid decay, whereas ARE-mediated decay is blocked. Similarly, the activation of p38 kinase and phosphatidylinositol 3-kinase in NIH 3T3 cells inhibits ARE-mediated but not CDE-mediated mRNA decay. The CDE was mapped to an 80-nucleotide (nt) segment downstream of the ARE, and point mutation analysis identified within the CDE a conserved sequence of 15 nt that is required for decay activity. We propose that the CDE represses TNF-α expression by maintaining the mRNA short-lived, thereby preventing excessive induction of TNF-α after LPS stimulation. Thus, CDE-mediated mRNA decay is likely to be an important mechanism limiting LPS-induced pathologic processes.
Directed Evolution of Adeno-Associated Virus (AAV) as Vector for Muscle Gene Therapy (2010)

Adeno-associated virus (AAV) is emerging as a vector of choice for muscle gene therapy because of its effective and stable transduction in striated muscles. AAV naturally evolve into multiple serotypes with diverse capsid gene sequences that are apparently the determinants of their tissue tropism and infectivity. Certain AAV serotypes show robust gene transfer upon direct intramuscular injection, while others are effective in crossing the endothelial barrier to reach muscle when delivered intravenously. Muscular dystrophy gene therapy requires efficient body-wide muscle gene transfer. However, preferential liver transduction by nearly all natural AAV serotypes could be an undesirable feature for muscle-directed applications, especially by means of systemic gene delivery. Here we describe a method of in vitro evolution and in vivo selection of AAV capsids that target striated muscles and detarget the liver. Using DNA shuffling technology, we have generated a capsid gene library by in vitro scrambling and shuffling the capsid genes of natural AAV1 to AAV9. To minimize the bias and limitation of in vitro screening on culture cells, we performed direct in vivo panning in adult mice after intravenous injection of the shuffled capsid library that packaged their own coding sequences. The AAV variants enriched in the heart and muscle are retrieved by capsid gene PCR and subsequently characterized for their tissue tropisms. This directed evolution and in vivo selection method should be useful in generating novel gene therapy vectors for muscle and heart and other tissues.
Activation of bovine factor X (Stuart factor): conversion of factor Xaalpha to factor Xabeta. (1975)

Bovine factor X (molecular weight 55,100) is a blood coagulation factor present in plasma in a precursor or zymogen form. It is a glycoprotein which has been isolated as a two-chain structure held together by one or more disulfide bonds. During the coagulation process, factor X is converted to a serine protease by the hydrolysis of a specific peptide bond in the amino-terminal region of the heavy chain. This cleavage occurs between Arg-51 and Ile-52, giving rise to factor Xaalpha (molecular weight 45,300) and an activation peptide (molecular weight 9500). Factor Xaalpha is then converted to factor Xabeta (molecular weight 42,600) by hydrolysis of a second specific peptide bond in the carboxyl-terminal region of the heavy chain. This cleavage occurs between Arg-290 and Gly-291, giving rise to a second glycopeptide (molecular weight 2700). Factor Xaalpha and factor Xabeta have equivalent coagulant activity, indicating that the cleavage of the second peptide bond is unrelated to the activation process.
Dipolar-dephasing 13C NMR studies of decomposed wood and coalified xylem tissue: evidence for chemical structural changes associated with defunctionalization of lignin structural units during coalification (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDipolar-dephasing 13C NMR studies of decomposed wood and coalified xylem tissue: evidence for chemical structural changes associated with defunctionalization of lignin structural units during coalificationPatrick G. HatcherCite this: Energy Fuels 1988, 2, 1, 48–58Publication Date (Print):January 1, 1988Publication History Published online1 May 2002Published inissue 1 January 1988https://pubs.acs.org/doi/10.1021/ef00007a008https://doi.org/10.1021/ef00007a008research-articleACS PublicationsRequest reuse permissionsArticle Views416Altmetric-Citations122LEARN 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
Effect of mRNA secondary structure on the efficiency of translational initiation by eukaryotic ribosomes (1990)

We have used site-directed mutagenesis to determine whether the structural context surrounding the AUG triplet influences its ability to be selected as an initiation codon by the eukaryotic preinitiation complex. AUG triplets were introduced in a loop and stem structure naturally occurring at the midpoint of the 129-nucleotides-long 5'-untranslated region of the porcine proopiomelanocortin mRNA; one AUG triplet was inserted in the loop while another was inserted in the stem of the hairpin structure. The proopiomelanocortin cDNA and the mutant cDNAs were inserted downstream from the early promoter of an expression vector derived from simian virus 40 (SV40) and transfected into monkey kidney COS-1 cells. Analysis of the proopiomelanocortin-related peptides present in the culture medium 72 h after transfection revealed that both mutant cDNAs direct the synthesis of more proopiomelanocortin than the non-mutant cDNA. The increased translational efficiency observed with both mutants is probably due to the decreased secondary structures of the shortened 5'-untranslated region. In addition, comparison of the two mutants indicates that the mutant mRNA with the AUG triplet inserted in the loop region of the hairpin structure directs the synthesis of approximately 75% more proopiomelanocortin than the mutant mRNA with the AUG triplet inserted in the stem region of the same hairpin structure, supporting a role for the structural context in the efficiency of translational initiation.
Quantum Monte Carlo calculations of neutron matter (2003)

Uniform neutron matter is approximated by a cubical box containing a finite number of neutrons, with periodic boundary conditions. We report variational and Green's function Monte Carlo calculations of the ground state of fourteen neutrons in a periodic box using the Argonne ${v8}^{\ensuremath{'}}$ two-nucleon interaction at densities up to one and half times the nuclear matter density. The effects of the finite box size are estimated using variational wave functions together with cluster expansion and chain summation techniques. They are small at subnuclear densities. We discuss the expansion of the energy of low-density neutron gas in powers of its Fermi momentum. This expansion is strongly modified by the large $\mathrm{nn}$ scattering length, and does not begin with the Fermi-gas kinetic energy, as assumed in both Skyrme and relativistic mean field theories. The leading term of neutron gas energy is approximately half the Fermi-gas kinetic energy. The quantum Monte Carlo results are also used to calibrate the accuracy of variational calculations employing Fermi hypernetted and single operator chain summation methods to study nucleon matter over a larger density range, with more realistic Hamiltonians including three-nucleon interactions.
Cyclotetrahalo-p-phenylenes: simulations of halogen substituted cycloparaphenylenes and their interaction with C60 (2016)

Halogen substitution of cycloparaphenylenes (‘nanohoops’) shifts the HOMO and LUMO, for example eliminating redox coupling in the complex C<sub>60</sub>@[10]CPP-F.
The VP16 paradox: herpes simplex virus VP16 contains a long-range activation domain but within the natural multiprotein complex activates only from promoter-proximal positions (1997)

Removal of core promoter elements like the TATA box converts several regulatory upstream regions of viral and cellular genes into classical enhancers, i.e., cis-regulatory elements capable of activating transcription over long distances in an orientation-independent manner. This is not the case with herpes simplex virus (HSV) immediate-early gene promoters, which are strongly induced by the viral transactivator VP16 (Vmw65, alphaTIF, ICP25) complexed with the cellular factors Oct-1 and HCF. Here we report that the VP16 complex can readily bring about strong activation from a promoter-proximal position but fails to induce transcription from a distal downstream enhancer position. This is in striking contrast to results obtained with GAL fusion proteins: in this context, the C-terminal "general" activation domain of VP16 activates transcription to high levels over long distances. Thus, this paradoxical behavior suggests that the VP16 activation domain is not accessible to the transcription machinery when the VP16-Oct-1-HCF complex is bound in a remote position. Only upon specific interactions in a promoter-proximal position, perhaps with the basal transcription factors, can transcription be strongly induced. In agreement with such a proposed mechanism, VP16 proteins to which a heterologous general activation domain has been added strongly activate transcription from a downstream position. The biological role of this unexpected and sophisticated mechanism is most probably a limitation of the VP16 activity to the associated immediate-early genes, without undesired long-range effects on other viral promoters within the tightly packed HSV genome.
Development of Large Area (up to 1.5 cm<sup>2</sup>) 4H-SiC 10 kV Junction Barrier Schottky Rectifiers (2008)

DC characteristics and reverse recovery performance of 4H-SiC Junction Barrier Schottky (JBS) diodes capable of blocking in excess of 10 kV with forward conduction of 20 A at a forward voltage of less than 4 V are described. Performance comparisons are made to a similarly rated 10 kV 4H-SiC PiN diode. The JBS diodes show a significant improvement in reverse recovery stored charge as compared to PiN diodes, showing half of the stored charge at 25°C and a quarter of the stored charge at 125°C when switched to 3 kV blocking. These large area JBS diodes were also employed to demonstrate the tremendous advances that have recently been made in 4H-SiC substrate quality.
Few graphene layers/carbon nanotube composites grown at complementary-metal-oxide-semiconductor compatible temperature (2011)

We investigate the growth of the recently demonstrated composite material composed of vertically aligned carbon nanotubes capped by few graphene layers. We show that the carbon nanotubes grow epitaxially under the few graphene layers. By using a catalyst and gaseous carbon precursor different from those used originally we establish that such unconventional growth mode is not specific to a precise choice of catalyst–precursor couple. Furthermore, the composite can be grown using catalyst and temperatures compatible with complementary-metal-oxide-semiconductor processing (T&amp;lt;450 °C).
Partial purification and characterization of bovine liver aspartyl beta-hydroxylase. (1990)

In vitro hydroxylation of aspartic acid has recently been demonstrated in a synthetic peptide based on the structure of the first epidermal growth factor domain in human factor IX (Gronke, R. S., VanDusen, W. J., Garsky, V. M., Jacobs, J. W., Sardana, M. K., Stern, A. M., and Friedman, P. A. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 3609-3613). The putative enzyme responsible for the posttranslational modification, aspartyl beta-hydroxylase, has been shown to be a member of a class of 2-ketoglutarate-dependent dioxygenases, which include prolyl-4- and lysyl-hydroxylases. In the present study, we describe the solubilization with nonionic detergent of the enzyme from bovine liver microsomes and its purification using DEAE-cellulose followed by heparin-Sepharose. No additional detergent was required during purification. The partially purified enzyme preparation was found to contain no prolyl-4- or lysyl-hydroxylase activity. Using a synthetic peptide based on the structure of the epidermal growth factor-like region in human factor X as substrate, the apparent Km values for iron and alpha-ketoglutarate were 3 and 5 microM, respectively. The enzyme hydroxylated the factor X peptide with the same stereospecificity (erythro beta-hydroxyaspartic acid) and occurred only at the aspartate corresponding to the position seen in vivo. Furthermore, the extent to which either peptide (factor IX or X) was hydroxylated reflected the extent of hydroxylation observed for both human plasma factors IX and X.