gebhart/patrepeval huggingface dataset:
Molecular analysis of Hurler syndrome in Druze and Muslim Arab patients in Israel: multiple allelic mutations of the IDUA gene in a small geographic area. (1993)

The mutations underlying Hurler syndrome (mucopolysaccharidosis IH) in Druze and Muslim Israeli Arab patients have been characterized. Four alleles were identified, using a combination of (a) PCR amplification of reverse-transcribed RNA or genomic DNA segments, (b) cycle sequencing of PCR products, and (c) restriction-enzyme analysis. One allele has two amino acid substitutions, Gly409-->Arg in exon 9 and Ter-->Cys in exon 14. The other three alleles have mutations in exon 2 (Tyr64-->Ter), exon 7 (Gln310-->Ter), or exon 8 (Thr366-->Pro). Transfection of mutagenized cDNAs into Cos-1 cells showed that two missense mutations, Thr366-->Pro and Ter-->Cys, permitted the expression of only trace amounts of alpha-L-iduronidase activity, whereas Gly409-->Arg permitted the expression of 60% as much enzyme as did the normal cDNA. The nonsense mutations were associated with abnormalities of RNA processing: (1) both a very low level of mRNA and skipping of exon 2 for Tyr64-->Ter and (2) utilization of a cryptic splice site for Gln310-->Ter. In all instances, the probands were found homozygous, and the parents heterozygous, for the mutant alleles, as anticipated from the consanguinity in each family. The two-mutation allele was identified in a family from Gaza; the other three alleles were found in seven families, five of them Druze, residing in a very small area of northern Israel. Since such clustering suggests a classic founder effect, the presence of three mutant alleles of the IDUA gene was unexpected.
Optoelectronic Digital Rotary Angle Encoder (2007)

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Review of Kinase Inhibitor Drugs (2012)

ADVERTISEMENT RETURN TO ISSUEPREVBook ReviewNEXTReview of Kinase Inhibitor DrugsQiao-Hong ChenView Author Information California State University, FresnoFresno, CaliforniaCite this: J. Nat. Prod. 2012, 75, 12, 2269Publication Date (Web):November 20, 2012Publication History Published online20 November 2012Published inissue 28 December 2012https://pubs.acs.org/doi/10.1021/np300796hhttps://doi.org/10.1021/np300796hbook-reviewACS PublicationsCopyright © 2012 The American Chemical Society and American Society of PharmacognosyRequest reuse permissionsArticle Views1177Altmetric-Citations-LEARN 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 SUBJECTS:Drug discovery,Inhibitors,Kinase inhibitors,Medicinal chemistry,Peptides and proteins Get e-Alerts
The interaction between hybrid organic–inorganic halide perovskite and selective contacts in perovskite solar cells: an infrared spectroscopy study (2016)

The interaction of hybrid organic-inorganic halide perovskite and selective contacts is crucial to get efficient, stable and hysteresis-free perovskite-based solar cells. In this report, we analyze the vibrational properties of methylammonium lead halide perovskites deposited on different substrates by infrared absorption (IR) measurements (4000-500 cm(-1)). The materials employed as substrates are not only characterized by different chemical natures (TiO2, ZnO and Al2O3), but also by different morphologies. For all of them, we have investigated the influence of these substrate properties on perovskite formation and its degradation by humidity. The effect of selective-hole contact (Spiro-OmeTad and P3HT) layers on the degradation rate by moisture has also been studied. Our IR results reveal the existence of a strong interaction between perovskite and all ZnO materials considered, evidenced by a shift of the peaks related to the N-H vibrational modes. The interaction even induces a morphological change in ZnO nanoparticles after perovskite deposition, pointing to an acid-base reaction that takes place through the NH3(+) groups of the methylammonium cation. Our IR and X-ray diffraction results also indicate that this specific interaction favors perovskite decomposition and PbI2 formation for ZnO/perovskite films subjected to humid conditions. Although no interaction is observed for TiO2, Al2O3, and the hole selective contact, the morphology and chemical nature of both contacts appear to play an important role in the rate of degradation upon exposure to moisture.
Affine model for disparity estimation in multiview sequence coding (2010)

One major obstacle for the application of multiview sequences, including 3DTV, is the extremely large amount of data associated with a multiview sequence. To enable the storage or transmission of a multiview sequence at a reasonable cost, in this paper, we present a disparity estimation method based on affine model to overcome this problem. By modeling the disparity function on each patch of the multiview image, the proposed technique can improve the accuracy of the disparity estimation and gain the compressing performance efficiently.
Polymerase chain reaction-based methods for the detection of human papillomavirus DNA. (1992)

The unprecedented sensitivity of the polymerase chain reaction (PCR) DNA amplification technology provides numerous advantages for the detection of human papillomavirus (HPV) DNA. In this chapter, the principles of the method and its advantages are discussed; disadvantages of the technology and proposed solutions are also presented. To accommodate the complexity of the many distinct HPV types, both type-specific and consensus PCR-based detection methods have evolved. Consensus primer systems, which afford the amplification of a broad spectrum of HPV types, have proven particularly useful in epidemiological studies and in novel virus identification. Since the introduction of PCR into the HPV field, there have been rapid advances and improvements PCR technology. However, standardization of PCR methods for HPV detection is essential for research to fully benefit from the technology. To that end, specific guidelines regarding experimental controls, assessment of analytic sensitivity and data interpretation are outlined here.
Diagnostic application of kidney allograft-derived absolute cell-free DNA levels during transplant dysfunction (2018)

Graft-derived cell-free DNA (donor-derived cell-free DNA) is an emerging marker of kidney allograft injury. Studies examining the clinical validity of this biomarker have previously used the graft fraction, or proportion of total cell-free DNA that is graft-derived. The present study evaluated the diagnostic validity of absolute measurements of graft-derived cell-free DNA, as well as calculated graft fraction, for the diagnosis of graft dysfunction. Plasma graft-derived cell-free DNA, total cell-free DNA, and graft fraction were correlated with biopsy diagnosis as well as individual Banff scores. Sixty-one samples were included in the analysis. For the diagnosis of antibody mediated rejection, the receiver-operator characteristic area under the curves of graft-derived cell-free DNA and graft fraction were 0.91 (95% CI 0.82-0.98) and 0.89 (95% CI 0.79-0.98), respectively. Both measures did not diagnose borderline or type 1A cellular mediated rejection. Graft fraction was associated with a broader range of Banff lesions, including lesions associated with cellular mediated rejection, while graft-derived cell-free DNA appeared more specific for antibody mediated rejection. Limitations of this study include a small sample size and lack of a validation cohort. The capacity for absolute quantification, and lower barriers to implementation of this methodology recommend it for further study.
The Human Cytomegalovirus Major Immediate-Early Enhancer Determines the Efficiency of Immediate-Early Gene Transcription and Viral Replication in Permissive Cells at Low Multiplicity of Infection (2003)

To determine the effect of the human cytomegalovirus (CMV) major immediate-early (MIE) enhancer or promoter on the efficiency of viral replication in permissive human cells, we constructed recombinant viruses with their human MIE promoter, enhancer, and promoter plus enhancer replaced with the murine CMV components. After a low multiplicity of infection (MOI) (0.01 PFU/cell), recombinant human CMV with the murine CMV promoter replicated like the wild type but recombinant virus with the murine enhancer replicated less efficiently. Immediate-early (IE) viral protein pIE72 (UL123), early viral protein (UL44), and viral DNA synthesis were significantly decreased. The effect of the human CMV enhancer substitution with the murine CMV enhancer was also demonstrated in different cell types by using recombinant virus with the UL127 promoter, driving the expression of green fluorescent protein (GFP). After an MOI of 1, GFP expression was high with the human CMV enhancer and significantly lower with the murine CMV enhancer. Even though at a high MOI (10 PFU/cell), the murine CMV enhancer was as efficient as the human CMV enhancer for the transcription of IE genes in human foreskin fibroblast cells, at lower MOIs, the murine CMV enhancer was less efficient. Proximal and distal chimeras of the human and murine enhancers also replicated less efficiently at a low MOI and expressed lower levels of GFP from the UL127 promoter. These experiments demonstrate that the entire human CMV enhancer has evolved for the efficient expression of the viral IE and early genes in human cells. Possible functions of the human CMV enhancer and promoter at a low MOI are discussed.
A second generation user interface design environment (1993)

Several obstacles exist in the user interface design process which distract a developer from designing a good user interface. One of the problems is the lack of an application model to keep the designer in perspective with the application. The other problem is having to deal with massive user interface programming to achieve a desired interface and to provide users with correct help information on the interface. In this paper, we discuss an application model which captures information about the application to specifications of a desired interface. The application model is then used to control the dialogues at runtime and can be used by a help component to automatically generate animated and textual help. Specification changes in the application model will automatically result in behavioral changes in the interface.
BMP-dependent, injury-induced stem cell niche as a mechanism of heterotopic ossification (2019)

Available data provide evidence of a potential core mechanism in which multiple disease-specific cellular and extracellular molecular elements form a unique local microenvironment, i.e., an injury-induced stem cell niche, which regulates the proliferation and osteogenic differentiation of mesenchymal stem cells (MSCs). The implication for HO is that therapeutic approaches must consider several different disease specific factors as parts of a functional unit, instead of treating one factor at a time.
Plasma Triglyceride Level and Mortality from Coronary Heart Disease (1993)

Overall, the plasma triglyceride level showed no independent association with coronary mortality. However, in subgroups of subjects with lower HDL and LDL cholesterol levels and in younger subjects, defined a priori, an association between the triglyceride level and coronary mortality was observed, although this association was small and was not statistically significant after an adjustment for the plasma glucose level.
Developments in Luminescent Porous Si (1993)

The recent observation of room temperature photoluminescence (PL) from porous Si layers (PSLs) has received considerable attention. Bulk crystalline Si does not luminesce efficiently at room temperature due to the indirect nature of the energy bandgap minimum. The PL from PSLs has been attributed to quantum confinement effects in nanometer‐sized crystalline features found in PSLs, typically of high porosity. In this paper, we review some of the major results and discuss the controversies of subsequent research. The basic methods of fabricating luminescent PSLs are described, including conventional anodic etching and chemical etching. The latter technique requires no applied bias, but is modeled as an electrochemical process. Other processing issues are also addressed, particularly with respect to postanodization control of the PL spectrum. Microscopic and spectroscopic studies of the material and optical characteristics of PSLs fabricated by the various techniques are presented and discussed. The basic models for the luminescence mechanism are described, including quantum‐sized crystalline Si, surface passivation, , alloys, and molecular electronics. These models are discussed in terms of the supporting and contradicting evidence. Electroluminescence (EL) studies are discussed, including EL from anodic oxidation of PSLs as well as from light‐emitting diodes. The results are promising for optoelectronic applications. However, fundamental questions about the underlying chemistry, physics, and microstructure remain unanswered. More research will be required before any definitive statements can be conclusively made regarding the luminescence mechanism.
Sequences homologous to 5' splice sites are required for the inhibitory activity of papillomavirus late 3' untranslated regions. (1994)

Expression of bovine papillomavirus type 1 (BPV-1) late genes is limited to terminally differentiated keratinocytes in an infected epithelium. We have previously shown that although the BPV-1 late polyadenylation site is functional in nonpermissive cells, a 53-nucleotide (nt) fragment of the late 3' untranslated region acts posttranscriptionally to reduce polyadenylated cytoplasmic RNA levels. This 53-nt fragment does not appear to function by destabilizing polyadenylated cytoplasmic RNA (P. A. Furth and C. C. Baker, J. Virol. 65:5806-5812, 1991). In this study, we used site-directed mutagenesis and deletion analysis to demonstrate that the sequence AAG/GUAAGU, which is identical to the consensus 5' splice site sequence, was both necessary and sufficient for the inhibitory activity of the 53-nt fragment. Furthermore, base pairing between the 5' end of the U1 small nuclear RNA and this 5' splice site-like sequence was shown to be required for the inhibitory activity in vivo. We have also further mapped the human papillomavirus type 16 late 3' inhibitory element (I. M. Kennedy, J. K. Haddow, and J. B. Clements, J. Virol. 65:2093-2097, 1991) to a 51-nt region containing four overlapping sequence motifs with partial homology to 5' splice sites. Mutation of each of these motifs demonstrated that only one of these motifs is required for the inhibitory activity. However, the presence of the other motifs may contribute to the full inhibitory activity of the element. No BPV-1 or human papillomavirus type 16 mRNAs which are spliced by using the potential 5' splice sites present in the viral late 3' untranslated regions have been identified. This suggests that the primary function of these 5' splice site-like sequences is the inhibition of late gene expression. The most likely mechanism of action of these elements is reduction of polyadenylation efficiency, perhaps through interference with 3'-terminal exon definition.
TALEN-Mediated Somatic Mutagenesis in Murine Models of Cancer (2014)

Cancer genome sequencing has identified numerous somatic mutations whose biologic relevance is uncertain. In this study, we used genome-editing tools to create and analyze targeted somatic mutations in murine models of liver cancer. Transcription activator-like effector nucleases (TALEN) were designed against β-catenin (Ctnnb1) and adenomatous polyposis coli (Apc), two commonly mutated genes in hepatocellular carcinoma (HCC), to generate isogenic HCC cell lines. Both mutant cell lines exhibited evidence of Wnt pathway dysregulation. We asked whether these TALENs could create targeted somatic mutations after hydrodynamic transfection into mouse liver. TALENs targeting β-catenin promoted endogenous HCC carrying the intended gain-of-function mutations. However, TALENs targeting Apc were not as efficient in inducing in vivo homozygous loss-of-function mutations. We hypothesized that hepatocyte polyploidy might be protective against TALEN-induced loss of heterozygosity, and indeed Apc gene editing was less efficient in tetraploid than in diploid hepatocytes. To increase efficiency, we administered adenoviral Apc TALENs and found that we could achieve a higher mutagenesis rate in vivo. Our results demonstrate that genome-editing tools can enable the in vivo study of cancer genes and faithfully recapitulate the mosaic nature of mutagenesis in mouse cancer models. Cancer Res; 74(18); 5311-21. ©2014 AACR.
Toward High-Resolution de Novo Structure Prediction for Small Proteins (2005)

The prediction of protein structure from amino acid sequence is a grand challenge of computational molecular biology. By using a combination of improved low- and high-resolution conformational sampling methods, improved atomically detailed potential functions that capture the jigsaw puzzle-like packing of protein cores, and high-performance computing, high-resolution structure prediction (<1.5 angstroms) can be achieved for small protein domains (<85 residues). The primary bottleneck to consistent high-resolution prediction appears to be conformational sampling.
Epizootiology of insect diseases (1987)

Epidemiological Concepts Applied to Insect Epizootiology (J. Fuxa and Y. Tanada). Ecological Methods (J. Fuxa). Modeling (G. Brown). The Host Population (H. Watanabe). The Pathogen Population (Y. Tanada and J. Fuxa). Transmission (T. Andreadis). Environment (G. Benz). Patterns over Place and Time (J. Weiser). Noninfectious Diseases (R. Gaugler). Viral Diseases (H. Evans and P. Entwistle). Diseases Caused by Bacteria and Other Prokaryotes (A. Krieg). Fungal Diseases (R. Carruthers and R. Soper). Protozoan Diseases (J. Maddox). Diseases Caused by Nematodes (H. Kaya). Applied Epizootiology: Microbial Control of Insects (J. Harper). Epizootiology Prevention of Insect Diseases (T. Hukuhara). Author Index. Subject Index.
Antidepressant-Like Activity of 10-Hydroxy-Trans-2-Decenoic Acid, a Unique Unsaturated Fatty Acid of Royal Jelly, in Stress-Inducible Depression-Like Mouse Model (2011)

Symptoms of depression and anxiety appeared in mice after they had been subjected to a combination of forced swimming for 15 min followed by being kept in cages that were sequentially subjected to leaning, drenching, and rotation within 1-2 days for a total of 3 weeks. The animals were then evaluated by the tail-suspension test, elevated plus-maze test, and open-field test at 1 day after the end of stress exposure. Using these experimental systems, we found that 10-hydroxy-trans-2-decenoic acid (HDEA), an unsaturated fatty acid unique to royal jelly (RJ), protected against the depression and anxiety when intraperitoneally administered once a day for 3 weeks simultaneously with the stress loading. Intraperitoneally administered RJ, a rich source of HDEA, was also protective against the depression, but RJ given by the oral route was less effective. Our present results demonstrate that HDEA and RJ, a natural source of it, were effective in ameliorating the stress-inducible symptoms of depression and anxiety.
Apolipoprotein A-I is a selective target for myeloperoxidase-catalyzed oxidation and functional impairment in subjects with cardiovascular disease (2004)

In recent studies we demonstrated that systemic levels of protein-bound nitrotyrosine (NO 2 Tyr) and myeloperoxidase (MPO), a protein that catalyzes generation of nitrating oxidants, serve as independent predictors of atherosclerotic risk, burden, and incident cardiac events. We now show both that apolipoprotein A-I (apoA-I), the primary protein constituent of HDL, is a selective target for MPO-catalyzed nitration and chlorination in vivo and that MPO-catalyzed oxidation of HDL and apoA-I results in selective inhibition in ABCA1-dependent cholesterol efflux from macrophages. Dramatic selective enrichment in NO 2 Tyr and chlorotyrosine (ClTyr) content within apoA-I recovered from serum and human atherosclerotic lesions is noted, and analysis of serum from sequential subjects demonstrates that the NO 2 Tyr and ClTyr contents of apoA-I are markedly higher in individuals with cardiovascular disease (CVD). Analysis of circulating HDL further reveals that higher NO 2 Tyr and ClTyr contents of the lipoprotein are each significantly associated with diminished ABCA1-dependent cholesterol efflux capacity of the lipoprotein. MPO as a likely mechanism for oxidative modification of apoA-I in vivo is apparently facilitated by MPO binding to apoA-I, as revealed by cross-immunoprecipitation studies in plasma, recovery of MPO within HDL-like particles isolated from human atheroma, and identification of a probable contact site between the apoA-I moiety of HDL and MPO. To our knowledge, the present results provide the first direct evidence for apoA-I as a selective target for MPO-catalyzed oxidative modification in human atheroma. They also suggest a potential mechanism for MPO-dependent generation of a proatherogenic dysfunctional form of HDL in vivo.
High-speed, monolithic CMOS receivers at 1550nm with Ge on Si waveguide photodetectors (2007)

This talk discusses the technological challenges arising from the insertion of a Ge photodetectors step in a CMOS process and the advantages brought by monolithic integration.
Method for hand-feeding mouse pups with nursing bottles. (2004)

The purpose of this study was to establish a hand-feeding method for the mouse by using nursing bottles. Five different-sized nipples were tested. The largest nipple used for pups from 12 to 15 days of age was 5.5 mm in diameter and 10 mm long, with a tip of 1.5 mm in diameter. The size of the nipple was much larger than that of the mothers, and bloating due to air accumulation was observed in the artificially-reared pups. To prevent bloat, the nipple size was increased, and a piece of sponge was stuffed in the nipple. Among the 30 pups fed from 1 day of age, 26 were weaned and 4 died. Three pups died due to aspiration of milk into the lung, and the remaining one died due to bloating. The development of nursing bottles with nipples may be potentially useful for the studies of nutrition, behavior, immunology, psychology, and toxicology.