gebhart/patrepeval huggingface dataset:
Optimization of the surface and structural quality of N-face InN grown by molecular beam epitaxy (2006)

The authors demonstrate the impact of growth kinetics on the surface and structural properties of N-face InN grown by molecular beam epitaxy. Superior surface morphology with step-flow growth features is achieved consistently under In-rich conditions in a low-temperature region of 500–540°C. Remarkably, off-axis x-ray rocking curve (ω scans) widths are found to be independent of the growth conditions. The band gap determined from optical absorption measurements of optimized InN is 0.651eV, while photoluminescence peak emission occurs at even lower energies of ∼0.626eV. Hall measurements show room temperature peak electron mobilities as high as 2370cm2∕Vs at a carrier concentration in the low 1017cm−3 region. Analysis of the thickness dependence of the carrier concentration demonstrates a n-type surface accumulation layer with a sheet carrier concentration of ∼3×1013cm−2.
Phy M: an RNase activity specific for U and A residues useful in RNA sequence analysis (1980)

Physarum polycephalum, an acellular slime mold, produces an endoribonuclease activity (Phy M) useful in direct RNA sequence determination. Under conditions previously described for direct enzymatic RNA sequencing (7M urea, 50 degrees C, pH 5.0)1 Phy M cleaves almost exclusively and uniformly at Up-N and Ap-N. In the absence of urea Up-N, Ap-N, and Gp-N are attacked in a sequence specific way identical to that found with RNase Phy I2 digests performed under the same reaction conditions.
A dystrophic Duchenne mouse model for testing human antisense oligonucleotides (2018)

Duchenne muscular dystrophy (DMD) is a severe muscle-wasting disease generally caused by reading frame disrupting mutations in the DMD gene resulting in loss of functional dystrophin protein. The reading frame can be restored by antisense oligonucleotide (AON)-mediated exon skipping, allowing production of internally deleted, but partially functional dystrophin proteins as found in the less severe Becker muscular dystrophy. Due to genetic variation between species, mouse models with mutations in the murine genes are of limited use to test and further optimize human specific AONs in vivo. To address this we have generated the del52hDMD/mdx mouse. This model carries both murine and human DMD genes. However, mouse dystrophin expression is abolished due to a stop mutation in exon 23, while the expression of human dystrophin is abolished due to a deletion of exon 52. The del52hDMD/mdx model, like mdx, shows signs of muscle dystrophy on a histological level and phenotypically mild functional impairment. Local administration of human specific vivo morpholinos induces exon skipping and dystrophin restoration in these mice. Depending on the number of mismatches, occasional skipping of the murine Dmd gene, albeit at low levels, could be observed. Unlike previous models, the del52hDMD/mdx model enables the in vivo analysis of human specific AONs targeting exon 51 or exon 53 on RNA and protein level and muscle quality and function. Therefore, it will be a valuable tool for optimizing human specific AONs and genome editing approaches for DMD.
Preservation of Human Islet Cell Functional Mass by Anti-Oxidative Action of a Novel SOD Mimic Compound (2002)

The most commonly used technical approach to isolate human pancreatic islets intended for allotransplants generates a product that is hampered by mechanical and chemical insults, which dramatically reduce the mass of viable and functional transplantable cells. We tested a novel class of antioxidant chemical compounds (SOD mimics: AEOL10113 and AEOL10150) to protect human islets from oxidative stress in order to improve the preservation of the isolated tissue. Addition of SOD mimic in culture, after isolation, allowed for the survival of a significantly higher islet cell mass. Functional behavior and phenotypic cell characteristics of the SOD-treated islet preparations were preserved, as was the capacity to normalize diabetic mice, even when a marginal mass of islets was transplanted. The addition of SOD mimic during isolation, before culture, further reduced early cell loss. These results indicate that prompt interventions aimed at blocking oxidative stress can improve human islet survival, preserving a functional islet mass two- to threefold larger than the one usually obtained without adding any antioxidant compound. The ability to preserve functional islets without a dramatic loss represents a major advantage considering the scarce availability of islet tissue for clinical transplantation.
Fatal Outcome in Bacteremia is Characterized by High Plasma Cell Free DNA Concentration and Apoptotic DNA Fragmentation: A Prospective Cohort Study (2011)

Plasma cf-DNA concentration proved to be a specific independent prognostic biomarker in bacteremia. cf-DNA displayed a predominating low-molecular-weight cf-DNA band in nonsurvivors corresponding to the size of apoptotic nucleosomal DNA.
The Amadori Rearrangement under New Conditions and its Significance for Non-enzymatic Browning Reactions2 (1953)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Amadori Rearrangement under New Conditions and its Significance for Non-enzymatic Browning Reactions2John E. Hodge and Carl E. RistCite this: J. Am. Chem. Soc. 1953, 75, 2, 316–322Publication Date (Print):January 1, 1953Publication History Published online1 May 2002Published inissue 1 January 1953https://pubs.acs.org/doi/10.1021/ja01098a019https://doi.org/10.1021/ja01098a019research-articleACS PublicationsRequest reuse permissionsArticle Views1234Altmetric-Citations173LEARN 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
The delivery of foreign genes into fertilized fish eggs using high‐velocity microprojectiles (1991)

Fertilized eggs of loach (Misgurnus fossilis), rainbow trout (Salmo gairdneri) and zebrafish (Brachydanio rerio) were bombarded with high-velocity tungsten microprojectiles covered with plasmid DNA containing sequences of beta-galactosidase and neomycin phosphotransferase genes. About 70% of the eggs survived the bombardment. The activity of both transferred genes was revealed in the fish developed from the bombarded eggs. Neomycin phosphotransferase gene sequences were detected by means of PCR amplification and Southern hybridization in the total DNA of zebrafish that survived after G418 treatment.
Evaluation of circulating thyroid‐specific transcripts as markers of thyroid cancer relapse (2004)

Circulating thyroid-specific transcripts have been suggested as potential molecular markers of residual or recurrent thyroid cancer. We assessed the accuracy of real-time RT-PCR-based detection of a panel of thyroid-specific markers, including TG, TPO, TSHR, NIS and PDS, in comparison with serum TG measurements in a series of 55 patients operated for differentiated thyroid cancer (DTC). Serum TG levels were higher in patients with residual thyroid tissue or metastatic cancer than in disease-free patients during thyroid hormone suppressive therapy (THST) and after stimulation with rhTSH (P < 0.05). Recombinant hTSH increased serum TG values in patients with tumor relapse (P < 0.05), but not in disease-free patients. This assay showed high specificity and good sensitivity in detecting tumor relapse (accuracy under THST = 81.4%; after rhTSH stimulation = 90.9%). TPO and TSHR mRNA, either under THST or after rhTSH, showed a significant correlation with disease status for molecular assays. Qualitative analysis of baseline and stimulated TG, NIS and PDS mRNA showed high sensitivity but low specificity in the prediction of thyroid cancer recurrence or metastases (accuracy under THST = 51%, 43% and 54%, respectively), whereas TPO and TSHR mRNA assays had higher specificity but low sensitivity, with accuracy under THST of 67% and 61%, respectively, that improved when these tests were combined. Our findings indicate that serum TG assay after TSH stimulation is the most accurate test for monitoring DTC. Combined measurements of TPO and TSHR mRNA levels during THST may represent a specific test for early detection of DTC relapse.
Further characterization of amyloid-enhancing factor. (1982)

Amyloid-enhancing factor (AEF) is a transferable activity that in CBA/J mice reduces the induction time of splenic amyloid deposition to 48 hours. Azocasein, or AgNo3, can induce AEF in the spleen and liver. In the liver several subcellular organelles possess this activity. This is likely due to AEF's adherent properties. AEF is most effective when given by the intravenous route. After intravenous injection, AEF particulates localize to the perifollicular areas of the spleen and Kuppfer cells in the liver. The effects of AEF administration persist for at least 4 weeks. AEF can be solubilized in 4 M glycerol, is not the amyloid A protein, and is not likely to be the serum amyloid P component. The extract can be fractionated by Sepharose 4B column chromatography. The active component is of high molecular weight, and tentative identification by disc electrophoresis has been made.
Regulation of EGFR endocytic trafficking by rab proteins. (2006)

The Epidermal Growth Factor Receptor (EGFR) is a member of the receptor tyrosine kinase family and has important roles in development and cancer. Through ligand stimulation, the EGFR initiates a number of biochemical pathways that integrate to form specific physiological responses. In addition to these signaling pathways, the ligand stimulation also causes the EGFR to internalize and be transported through the endocytic pathway. The endocytic pathway regulates the rate of EGFR degradation and recycling, as well as the signaling mediated by the EGFR. In this review, the role of rabs, a family of small molecular weight guanine nucleotide binding proteins, is examined in how they regulate endocytic trafficking.
Polling Local Attitudes. (1982)

A computer simulation model of cardiac rhythm and heart-pacemaker interactions has been used to examine the response of short AV delay DDD pacing to an atrial premature depolarization in patients with a potential junctional reentry circuit. Special attention was given to the possibility of using the pacemaker to prevent atrioventricular reentry tachycardia mediated by a bidirectional accessory pathway. The computational experiments examined: (a) the differences between pacing modes with constant and quasi-Wenckebach prolongation of AV delay; (b) the effects of imposing the restrictions of a pacemaker atrial refractory period and upper rate limit; and (c) the effects of varying the ventricular refractory period so that it was either the same or longer than that of the atria. The computational results prove that some possible modes of initiation of junctional reentry tachycardia are beyond the prophylactic capabilities of current DDD pacemakers. Future possibilities involving the use of computer modeling to develop more sophisticated pacemaker modes are briefly discussed.
Novel Steroidal Inhibitors of Human Cytochrome P45017.alpha.-Hydroxylase-C17,20-lyase): Potential Agents for the Treatment of Prostatic Cancer (1995)

Steroidal compounds having a 17-(3-pyridyl) substituent together with a 16,17-double bond have been synthesized, using a palladium-catalyzed cross-coupling reaction of a 17-enol triflate with diethyl(3-pyridyl)borane, which are potent inhibitors of human testicular 17 alpha-hydroxylase-C17,20-lyase. The requirement for these structural features is stringent: compounds having 2-pyridyl (9), 4-pyridyl (10), or 2-pyridylmethyl (11) substituents instead of the 3-pyridyl substituent were either poor inhibitors or noninhibitory. Reduction of the 16,17-double bond to give 17 beta-pyridyl derivatives diminished potency with 3-pyridyl substitution (3-->27; IC50 for lyase, 2.9-->23 nM) but increased it with a 4-pyridyl substituent present (10-->28; IC50 1 microM-->53 nM). In contrast, a variety of substitution patterns in rings A-C of the steroid skeleton afforded inhibitors having potencies similar to those most closely related structurally to the natural substrates pregnenolone and progesterone, respectively 17-(3-pyridyl)androsta-5,16-dien-3 beta-ol (3, Kiapp < 1 nM; IC50 for lyase, 2.9 nM) and 17-(3-pyridyl)androsta-4,16-dien-3-one (15; IC50 for lyase, 2.1 nM). Thus compounds having variously aromatic ring A (18), saturated rings A/B (21, 22), and oxygenated ring C (26) exhibited IC50 values for lyase (1.8-3.0 nM) falling within a 2-fold range. The most potent compounds are candidates for development as drugs for the treatment of hormone-dependent prostatic carcinoma.
Bordetella holmesii DNA is not detected in nasopharyngeal swabs from Finnish and Dutch patients with suspected pertussis (2006)

Bordetella holmesii is a Gram-negative bacterium first identified in 1995. It can cause pertussis-like symptoms in humans. B. holmesii contains insertion sequences IS481 and IS1001, two frequently used targets in the PCR diagnosis of Bordetella pertussis and Bordetella parapertussis infections. To investigate the prevalence of B. holmesii in Finnish and Dutch patients with pertussis-like symptoms and whether B. holmesii has caused any false-positive results in diagnostic PCRs, B. holmesii-specific real-time PCRs were developed. The Finnish methods were conventional IS481 PCR and B. holmesii-specific real-time PCR (LightCycler, Roche) targeting the B. holmesii recA gene. The Dutch methods were IS481 and IS1001 PCRs with conventional or real-time formats and B. holmesii-specific real-time PCR targeting the homologue of IS1001. Of 11,319 nasopharyngeal swabs, 2804 were collected from Finnish patients from 2000 to 2003, and 8515 from Dutch patients from 1992 to 2003. B. holmesii DNA was not found in the samples analysed. The results suggest that B. holmesii is not among the causative agents of pertussis-like symptoms in Finnish and Dutch patients and thus does not in practice confound IS481 and IS1001 PCRs.
Evolutionary aspects of immunoglobulin heavy chain variable region (VH) gene subgroups. (1983)

We isolated and determined the sequences of two human germ-line heavy chain variable region (VH) genes and compared them with mouse VH genes. The results show that the human VHI subgroup is evolutionarily related to the mouse VHII subgroup. Evolutionary preservation of homologies in VH genes of the same subgroup includes not only the coding region but also intron size and homology in noncoding regions. This suggests that a VH gene subgroup constitutes a multigene family that undergoes concerted evolution. The homology between genes of the same subgroup in different species is greater than that between genes of different subgroups within a species. One of the VHII genes contains, in complementarity-determining region 2 (CDR2), a 13-base-pair previously shown to be in CDR2 of a VHIII gene and in a heavy chain diversity region gene, DH [Wu, T. T. & Kabat, E. A. (1982) Proc. Natl. Acad. Sci. USA 79, 5031-5032], suggesting the insertion of diversity region gene sequences into the VH gene. One of the human VH genes is a pseudogene because of a terminator, which, together with our previous results, shows that the VH gene repertoire contains 40% pseudogenes. In one of the VH genes, direct and inverted repeats at both 5' and 3' ends of the gene suggest a potential transposable element that encompasses the entire VH gene. It is possible that such a structure may facilitate saltatory replication and rapid expansion of VH gene families.
Exploiting dead value information (1997)

We describe Dead Value Information (DVI) and introduce three new optimizations which exploit it. DVI provides assertions that certain register values are dead, meaning they will not be read before being overwritten. The processor can use DVI to track dead registers and dynamically eliminate unnecessary save and restore instructions from the execution stream at procedure calls and context switches. Our results indicate that dynamic saves and restore instances can be reduced by 46% for procedure calls and by 51% for context switches. In addition, save/restore elimination for procedure calls can improve overall performance by up to 5%. DVI also allows the processor manage physical registers to efficiently, reducing the size requirements of the physical register file. When the system clock rate is proportional to the register file cycle time, this optimization can improve performance. All of these optimizations can be supported with only a few new instructions and minimal additional hardware structures.
The effect of particle shape and grain‐scale properties of shale: A micromechanics approach (2009)

Abstract Traditional approaches for modeling the anisotropic elasticity response of the highly heterogeneous clay fabric in shale have mainly resorted to geometric factors such as definitions of particles shapes and orientations. However, predictive models based on these approaches have been mostly validated using macroscopic elasticity data. The recent implementation of instrumented indentation aimed at probing nano‐scale mechanical behaviors has provided a new context for characterizing and modeling the anisotropy of the porous clay in shale. Nanoindentation experimental data revealed the significant contribution of the intrinsic anisotropy of the solid clay to the measured elastic response. In this investigation, we evaluate both the effects of geometric factors and of the intrinsic anisotropic elasticity of the solid clay phase on the observed anisotropy of shale at multiple length scales through the development of a comprehensive theoretical micromechanics approach. It was found that among various combinations of these sources of anisotropy, the elastic response of the clay fabric represented as a granular ensemble of aligned effective clay particles with spherical morphology and anisotropic elasticity compares satisfactorily to nanoindentation and ultrasonic pulse velocity measurements at nano‐ and macroscopic length scales, respectively. Other combinations of sources of anisotropy could yield comparable predictions, particularly at macroscopic scales, at the expense of requiring additional experimental data to characterize the morphology and orientations of particles. Copyright © 2009 John Wiley &amp; Sons, Ltd.
Real-time meeting recognition and understanding using distant microphones and omni-directional camera (2010)

This paper presents our newly developed real-time meeting analyzer for monitoring conversations in an ongoing group meeting. The goal of the system is to automatically recognize “who is speaking what” in an online manner for meeting assistance. Our system continuously captures the utterances and the face pose of each speaker using a distant microphone array and an omni-directional camera at the center of the meeting table. Through a series of advanced audio processing operations, an overlapping speech signal is enhanced and the components are separated into individual speaker's channels. Then the utterances are sequentially transcribed by our speech recognizer with low latency. In parallel with speech recognition, the activity of each participant (e.g. speaking, laughing, watching someone) and the situation of the meeting (e.g. topic, activeness, casualness) are detected and displayed on a browser together with the transcripts. In this paper, we describe our techniques and our attempt to achieve the low-latency monitoring of meetings, and we show our experimental results for real-time meeting transcription.
A novel genetic variant of BMP2K contributes to high myopia (2009)

Loss of eye growth regulation may cause myopia, because modulation of optic globe size is essential for the generation of normal optic power. Evidence has implied variations of BMP2 gene expression mediate ocular development and retinal tissue remodeling. Given BMP2 as a potential regulator involved in myopia development, we investigate whether gene BMP2-inducible kinase (BMP2K, BIKe), whose expression is up-regulated during BMP2-induced osteoblast differentiation, contributes to susceptibility of high myopia. Participants grouped into high myopia had a spherical equivalent greater than -6.00 D, compared with a control group of spherical equivalent less than -0.5 D. Genotyping of polymorphisms 1379 G/A (rs2288255) and 3171 C/G (rs12507099), corresponding with 405 Gly/Ser and 1002 Thr/Ser variation in the BMP2K gene were determined by PCR-restriction fragment length polymorphism and associative study performed by comparing high myopic subjects and healthy controls. The frequency of A allele in the BMP2K gene 1379 G/A polymorphism showed a significant difference between cases and controls (P<0.001, OR=2.99, 95% CI=1.62-5.54) and subjects with either AA or AG genotype show higher risk than GG genotype (P<0.001, OR=3.07, 95% CI=1.59-5.92), while 3171 C/G polymorphism was not significant from this survey. These data suggest that BMP2K gene 1379 G/A variant is strongly correlated with high myopia and may contribute to a genetic risk factor for high degrees of myopic pathogenesis.
Activity of Pulmonary Surfactant Protein-D (SP-D) in Vivo Is Dependent on Oligomeric Structure (2001)

Pulmonary surfactant protein-D (SP-D) is a member of the collectin family of C-type lectins that is synthesized in many tissues including respiratory epithelial cells in the lung. SP-D is assembled predominantly as dodecamers consisting of four homotrimeric subunits each. Association of these subunits is stabilized by interchain disulfide bonds involving two conserved amino-terminal cysteine residues (Cys-15 and Cys-20). Mutant recombinant rat SP-D lacking these residues (RrSP-Dser15/20) is secreted in cell culture as trimeric subunits rather than as dodecamers. In this study, transgenic mice that express this mutant were generated to elucidate the functional importance of SP-D oligomerization in vivo. Expression of RrSP-Dser15/20 failed to correct the pulmonary phospholipid accumulation and emphysema characteristic of SP-D null (mSP-D-/-) mice. Expression of high concentrations of the mutant protein in wild-type mice reduced the abundance of disulfide cross-linked oligomers of endogenous SP-D in the bronchoalveolar lavage fluid and demonstrated a phenotype that partially overlapped with that of the SP-D-/- mice; the animals developed emphysema and foamy macrophages without the associated abnormalities in alveolar phospholipids typical of SP-D-/- mice. Development of foamy macrophages in SP-D-deficient mice is not secondary to the increased abundance of surfactant phospholipids. Disulfide cross-linked SP-D oligomers are required for the regulation of surfactant phospholipid homeostasis and the prevention of emphysema and foamy macrophages in vivo.