gebhart/patrepeval huggingface dataset:
Brain imaging evidence of preclinical Alzheimer's disease in normal aging (2006)

These results indicate that temporal and parietal glucose metabolism predict decline in global cognitive function, and medial temporal brain volumes predict memory decline in normal older people. The anatomical location of these findings suggests detection of preclinical Alzheimer's disease pathology.
Deamidation of Amino Acids on the Surface of Adeno-Associated Virus Capsids Leads to Charge Heterogeneity and Altered Vector Function (2018)

Post-translational modification of the adeno-associated virus capsids is a poorly understood factor in the development of these viral vectors into pharmaceutical products. Here we report the extensive capsid deamidation of adeno-associated virus serotype 8 and seven other diverse adeno-associated virus serotypes, with supporting evidence from structural, biochemical, and mass spectrometry approaches. The extent of deamidation at each site depended on the vector's age and multiple primary-sequence and three-dimensional structural factors. However, the extent of deamidation was largely independent of the vector recovery and purification conditions. We demonstrate the potential for deamidation to impact transduction activity and, moreover, correlate an early time point loss in vector activity to rapidly progressing spontaneous deamidation at several adeno-associated virus 8 asparagines. We explore mutational strategies that stabilize side-chain amides, improving vector transduction and reducing the lot-to-lot molecular variability that presents a key concern in biologics manufacturing. This study illuminates a previously unknown aspect of adeno-associated virus capsid heterogeneity and highlights its importance in the development of these vectors for gene therapy.
cDNA Cloning, Expression, and Chromosomal Localization of Human N-Acetylglucosaminyltransferase III (GnT-III)1 (1993)

UDP-N-acetylglucosamine:beta-D-mannoside beta 1,4 N-acetylglucosaminyltransferase III (GnT-III) [EC 2.4.1.144] catalyzes the addition of N-acetylglucosamine in beta 1-4 linkage to the beta-linked mannose of the trimannosyl core of N-linked sugar chains to produce a bisecting GlcNAc residue. We have isolated six independent cDNA clones of human GnT-III from a fetal liver cDNA library. The cDNA sequence has an open reading frame that predicts a protein of 531 amino acids. The homology to rat GnT-III is 86% at the nucleotide level and is 91% at the amino acid level. The amino-terminal transmembrane domain and the catalytic domain are well conserved in the two species. Human GnT-III has a deletion of four amino acids in the "neck" region and several differences in the COOH-terminal region compared with the rat sequence. Using one of the human cDNA clones as the probe, two overlapping genomic clones have been isolated from a human cosmid library. The GnT-III gene has been mapped to chromosome 22q.13.1 using fluorescence in situ hybridization.
Production of liquid hydrocarbon transportation fuels by oligomerization of biomass-derived C9 alkenes (2010)

A process is described to produce renewable liquid fuels, similar to existing petroleum-derived transportation fuels, through the oligomerization over solid acid catalysts of C9-alkenes derived from γ-valerolactone (GVL). Larger, non-terminal alkenes are shown to be less reactive than short chain α-alkenes for oligomerization over solid acid sites, and Amberlyst-70 has been identified to be an active and stable catalyst with sufficient acidity to couple C9-alkenes. The inhibiting effect of water on alkene oligomerization can be minimized, because C9 alkenes derived from aqueous solutions of GVL separate spontaneously from water. The effect of other impurities arising from the cascade process for production of C9 alkenes from GVL, such as 5-nonanone and 5-nonanol, has been studied. Ketones are shown to be inert, while alcohols readily dehydrate on acid sites, producing an equivalent of water, which inhibits the rate of oligomerization. Small amounts of 5-nonanol present with C9-alkenes (< 1%) have a promotional effect, due to swelling of the catalyst by polar molecules; however, large amounts of 5-nonanol lead to inhibition of oligomerization. Other more reactive alkenes present in C9-alkenes produced from GVL, such as hexene and heptene isomers, compete for acid sites with the nonene feed. These smaller, more reactive alkenes are readily coupled at high conversion. Accordingly, with this process approximately 50 kg of liquid hydrocarbons can be produced from 100 kg of GVL retaining more than 90% of its energy content.
Ocular Irritation: Pathological Changes Occurring in the Rat with Surfactants of Unknown Irritancy (1998)

We believe the development and validation of in vitro alternatives to eliminate the need to use animals in ocular irritation testing must be based on a thorough understanding of the mechanisms of ocular irritation. We have recently undertaken the task of developing such an understanding for a panel of surfactants. The purpose of this study was to expand our current panel of surfactants for which the microscopic changes occurring over time have been characterized. Macroscopic and microscopic findings regarding the ocular irritation of 6 surfactants of relatively unknown irritancy were compared to those of 6 surfactants of known irritancy. The right eye of each rat was treated by placing 10 microliters of a surfactant directly on the cornea. Untreated left eyes served as the controls. At 3 hr and on days 1, 3, and 35, eyes and eyelids were collected for microscopic examination. Collectively, the macroscopic and microscopic findings revealed 3 surfactants to be similar to the mildly irritating surfactants previously studied, and 3 surfactants to be similar to the moderately irritating surfactant previously studied. Information such as this will be important to develop mechanistically based in vitro alternatives to replace the use of animals for ocular irritation testing.
Activity coefficient effects in spectral and solubility studies of molecular complex equilibriums (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTActivity coefficient effects in spectral and solubility studies of molecular complex equilibriumsSherril D. Christian, Jerry D. Childs, and Edwin H. LaneCite this: J. Am. Chem. Soc. 1972, 94, 19, 6861–6862Publication Date (Print):September 1, 1972Publication History Published online1 May 2002Published inissue 1 September 1972https://pubs.acs.org/doi/10.1021/ja00774a052https://doi.org/10.1021/ja00774a052research-articleACS PublicationsRequest reuse permissionsArticle Views127Altmetric-Citations12LEARN 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
Genetic Engineering of Drought Resistant Potato Plants by Introduction of the Trehalose-6-phosphate Synthase (TPS1) Gene from Saccharomyces cerevisiae (2000)

In yeast, trehalose-6-phosphate synthase is a key enzyme for trehalose biosynthesis, encoded by the structural gene TPS1. Trehalose affects sugar metabolism as well as osmoprotection against several environmental stresses, such as heat and desiccation. The TPS1 gene of Saccharomyces cerevisiae was engineered under the control of the CaMV 35S promoter for constitutive expression in transgenic potato plants by Ti-plasmid of Agrobacterium-mediated transformation. The resulting TPS1 transgenic potato plants exhibited various morphological phenotypes in culture tubes, ranging from normal to severely retarded growth, including dwarfish growth, yellowish lancet-shaped leaves, and aberrant root development. However, the plants recovered from these negative growth effects when grown in a soil mixture. The TPS1 transgenic potato plants showed significantly increased drought resistance. These results suggest that the production of trehalose not only affects plant development but also improves drought tolerance.
Increased fucosylation and reduced branching of serum glycoprotein N-glycans in all known subtypes of congenital disorder of glycosylation I (2003)

The N-glycans present on the total mixture of serum glycoproteins (serum N-glycome) were analyzed in 24 subjects with congenital disorder of glycosylation type I (CDG-I) and 7 healthy, age-matched individuals. No new N-glycan structures were observed in the sera of CDG-I patients as compared with normal sera. However, we observed in all subtypes a significantly increased degree of core alpha-1,6-fucosylation of the biantennary glycans as compared to normal, as well as a significant decrease in the amount of triantennary glycans. These serum N-glycome changes appear to be a milder manifestation of some of the changes observed in adult liver cirrhosis patients, which is compatible with the reported steatosis and fibrosis in CDG-I patients. In the CDG-Ia subgroup, the extent of the serum N-glycome changes correlates with the aberration of the serum transferrin isoelectric focusing pattern, which measures the severity of the lack of entire N-glycan chains (primary consequence of CDG-I) in the liver and is the standard diagnostic test for this category of inherited diseases.
A Cytosolic Acyltransferase Contributes to Triacylglycerol Synthesis in Sucrose-Rescued Arabidopsis Seed Oil Catabolism Mutants (2012)

Triacylglycerol (TAG) levels and oil bodies persist in sucrose (Suc)-rescued Arabidopsis (Arabidopsis thaliana) seedlings disrupted in seed oil catabolism. This study set out to establish if TAG levels persist as a metabolically inert pool when downstream catabolism is disrupted, or if other mechanisms, such as fatty acid (FA) recycling into TAG are operating. We show that TAG composition changes significantly in Suc-rescued seedlings compared with that found in dry seeds, with 18:2 and 18:3 accumulating. However, 20:1 FA is not efficiently recycled back into TAG in young seedlings, instead partitioning into the membrane lipid fraction and diacylglycerol. In the lipolysis mutant sugar dependent1and the β-oxidation double mutant acx1acx2 (for acyl-Coenzyme A oxidase), levels of TAG actually increased in seedlings growing on Suc. We performed a transcriptomic study and identified up-regulation of an acyltransferase gene, DIACYLGLYCEROL ACYLTRANSFERASE3 (DGAT3), with homology to a peanut (Arachis hypogaea) cytosolic acyltransferase. The acyl-Coenzyme A substrate for this acyltransferase accumulates in mutants that are blocked in oil breakdown postlipolysis. Transient expression in Nicotiana benthamiana confirmed involvement in TAG synthesis and specificity toward 18:3 and 18:2 FAs. Double-mutant analysis with the peroxisomal ATP-binding cassette transporter mutant peroxisomal ABC transporter1 indicated involvement of DGAT3 in the partitioning of 18:3 into TAG in mutant seedlings growing on Suc. Fusion of the DGAT3 protein with green fluorescent protein confirmed localization to the cytosol of N. benthamiana. This work has demonstrated active recycling of 18:2 and 18:3 FAs into TAG when seed oil breakdown is blocked in a process involving a soluble cytosolic acyltransferase.
Ambipolar solution-processed hybrid perovskite phototransistors (2015)

Organolead halide perovskites have attracted substantial attention because of their excellent physical properties, which enable them to serve as the active material in emerging hybrid solid-state solar cells. Here we investigate the phototransistors based on hybrid perovskite films and provide direct evidence for their superior carrier transport property with ambipolar characteristics. The field-effect mobilities for triiodide perovskites at room temperature are measured as 0.18 (0.17) cm(2) V(-1) s(-1) for holes (electrons), which increase to 1.24 (1.01) cm(2) V(-1) s(-1) for mixed-halide perovskites. The photoresponsivity of our hybrid perovskite devices reaches 320 A W(-1), which is among the largest values reported for phototransistors. Importantly, the phototransistors exhibit an ultrafast photoresponse speed of less than 10 μs. The solution-based process and excellent device performance strongly underscore hybrid perovskites as promising material candidates for photoelectronic applications.
Quality of life among long‐term non‐Hodgkin lymphoma survivors (2007)

From 5 to 15 years after diagnosis, the general health perceptions and vitality levels of non-Hodgkin lymphoma survivors remained significantly lower than those of their peers in the of general population. In addition, survivors faced practical problems with work and finances that deserve additional attention during the period of rehabilitation.
Impotence (1989)

IMPOTENCE is a common disorder that in many people has a profound effect on their well-being. Recently, the field of erectile dysfunction has undergone considerable change. There is now an improved understanding of the physiologic mechanisms of penile erection and how these can be altered to cause impotence. New diagnostic tests make possible the recognition of specific causes of erectile dysfunction. Treatments such as intracavernosal injection of vasoactive agents by patients, vascular reconstructive surgery, and vacuum erection devices have been added to the options of hormonal therapy, psychological counseling, and penile implants. In this article we will review the progress . . .
DNA aptamers and DNA enzymes (1997)

Investigators using combinatorial methods are revealing the surprising structural and functional abilities of DNA. A consequence of DNA's structure-forming potential is its ability to form highly specific receptors and ligands, and even its ability to catalyze chemical reactions. Unlike the classical images of double-stranded DNA, these DNA structures have many of the higher-ordered structural features that are found with ribozymes and other folded RNAs. Recent research is beginning to indicate that these new DNA structures are not rare exceptions, and that DNA, despite the absence of 2' hydroxyl groups, could rival RNA in its ability to form intricate structures and in its ability to function as an enzyme.
Metabolic engineering of biomass for high energy density: oilseed‐like triacylglycerol yields from plant leaves (2013)

High biomass crops have recently attracted significant attention as an alternative platform for the renewable production of high energy storage lipids such as triacylglycerol (TAG). While TAG typically accumulates in seeds as storage compounds fuelling subsequent germination, levels in vegetative tissues are generally low. Here, we report the accumulation of more than 15% TAG (17.7% total lipids) by dry weight in Nicotiana tabacum (tobacco) leaves by the co-expression of three genes involved in different aspects of TAG production without severely impacting plant development. These yields far exceed the levels found in wild-type leaf tissue as well as previously reported engineered TAG yields in vegetative tissues of Arabidopsis thaliana and N. tabacum. When translated to a high biomass crop, the current levels would translate to an oil yield per hectare that exceeds those of most cultivated oilseed crops. Confocal fluorescence microscopy and mass spectrometry imaging confirmed the accumulation of TAG within leaf mesophyll cells. In addition, we explored the applicability of several existing oil-processing methods using fresh leaf tissue. Our results demonstrate the technical feasibility of a vegetative plant oil production platform and provide for a step change in the bioenergy landscape, opening new prospects for sustainable food, high energy forage, biofuel and biomaterial applications.
Structural Insight into the Unique Properties of Adeno-Associated Virus Serotype 9 (2012)

Adeno-associated virus serotype 9 (AAV9) has enhanced capsid-associated tropism for cardiac muscle and the ability to cross the blood-brain barrier compared to other AAV serotypes. To help identify the structural features facilitating these properties, we have used cryo-electron microscopy (cryo-EM) and three-dimensional image reconstruction (cryo-reconstruction) and X-ray crystallography to determine the structure of the AAV9 capsid at 9.7- and 2.8-Å resolutions, respectively. The AAV9 capsid exhibits the surface topology conserved in all AAVs: depressions at each icosahedral two-fold symmetry axis and surrounding each five-fold axis, three separate protrusions surrounding each three-fold axis, and a channel at each five-fold axis. The AAV9 viral protein (VP) has a conserved core structure, consisting of an eight-stranded, β-barrel motif and the αA helix, which are present in all parvovirus structures. The AAV9 VP differs in nine variable surface regions (VR-I to -IX) compared to AAV4, but at only three (VR-I, VR-II, and VR-IV) compared to AAV2 and AAV8. VR-I differences modify the raised region of the capsid surface between the two-fold and five-fold depressions. The VR-IV difference produces smaller three-fold protrusions in AAV9 that are less "pointed" than AAV2 and AAV8. Significantly, residues in the AAV9 VRs have been identified as important determinants of cellular tropism and transduction and dictate its antigenic diversity from AAV2. Hence, the AAV9 VRs likely confer the unique infection phenotypes of this serotype.
Long-Term On-board Prediction of People in Traffic Scenes Under Uncertainty (2018)

Progress towards advanced systems for assisted and autonomous driving is leveraging recent advances in recognition and segmentation methods. Yet, we are still facing challenges in bringing reliable driving to inner cities, as those are composed of highly dynamic scenes observed from a moving platform at considerable speeds. Anticipation becomes a key element in order to react timely and prevent accidents. In this paper we argue that it is necessary to predict at least 1 second and we thus propose a new model that jointly predicts ego motion and people trajectories over such large time horizons. We pay particular attention to modeling the uncertainty of our estimates arising from the non-deterministic nature of natural traffic scenes. Our experimental results show that it is indeed possible to predict people trajectories at the desired time horizons and that our uncertainty estimates are informative of the prediction error. We also show that both sequence modeling of trajectories as well as our novel method of long term odometry prediction are essential for best performance.
A Sensitive Method to Quantify Human Long DNA in Stool: Relevance to Colorectal Cancer Screening (2006)

Human long DNA in stool may reflect nonapoptotic exfoliation and has been used as a colorectal cancer (CRC) marker. Targeting human-specific Alu repeats represents a logical but untested approach. A real-time Alu PCR assay was developed for quantifying long human DNA in stool and evaluated in this study. The accuracy and reproducibility of this assay and the stability of long DNA during room temperature fecal storage were assessed using selected patient stools and stools added to human DNA. Thereafter, long DNA levels were determined in blinded fashion from 18 CRC patients and 20 colonoscopically normal controls. Reproducibility of real-time Alu PCR for quantifying fecal long DNA was high (r2 = 0.99; P < 0.01). Long DNA levels in nonbuffered stools stored at room temperature fell a median of 75% by 1 day and 81% by 3 days. An EDTA buffer preserved DNA integrity during such storage. Human long DNA was quantifiable in all stools but was significantly higher in stools from CRC patients than from normal controls (P < 0.05). At a specificity of 100%, the sensitivity of long DNA for CRC was 44%. Results indicate that real-time Alu PCR is a simple method to sensitively quantify long human DNA in stool. This study shows that not all CRCs are associated with increased fecal levels of long DNA. Long DNA degrades with fecal storage, and measures to stabilize this analyte must be considered for optimal use of this marker.
Optical projection microtomography of transparent objects (2007)

We report first results in the development of a diffractive optical microtomography instrument for imaging transparent/semi-transparent biological samples without staining and sectioning. A brightfield transmission microscope was modified to form a Mach-Zehnder interferometer that was used to generate phase-shifted holograms recorded in image plane. Transparent/semi-transparent objects mixed with an index matching medium were inserted into a microcapillary and holograms of these objects were taken under different view angles by rotating the microcapillary. Precise rotation of the microcapillary was accomplished by clipping the microcapillary in a precisely machined V-groove, a system that when combined with software correction of the object centre achieved a precision of object positioning on the order of a micrometer. In this study, the observed objects were considered to be weakly diffracting and reconstructed by projection tomography of the phases of their measured scattered fields. The three-dimensional distribution of the refractive index was obtained by backprojecting the phases. Refractive index distributions are shown for a glass bead and a pollen grain. The measured difference between the refractive index of the glass bead and the microcapillary was within ±0.01. An isotropic spatial-resolution of the instrument in the micrometer range was obtained with an objective having a numerical aperture of 0.4.
Generation of Antibody Molecules Through Antibody Engineering (2003)

Twenty-five years ago, Georges Köhler and César Milstein invented a means of cloning individual antibodies, thus opening up the way for tremendous advances in the fields of cell biology and clinical diagnostics (1). However, in spite of their early promise, monoclonal antibodies (MAbs) were largely unsuccessful as therapeutic reagents resulting from insufficient activation of human effector functions and immune reactions against proteins of murine origin. These problems have recently been overcome to a large extent using genetic-engineering techniques to produce chimeric mouse/human and completely human antibodies. Such an approach is particularly suitable because of the domain structure of the antibody molecule (2), where functional domains carrying antigen-binding activities (Fabs or Fvs) or effector functions (Fc) can be exchanged between antibodies (see Fig. 1).
Nuclear and cytoplasmic LIMK1 enhances human breast cancer progression (2011)

Taken together, these data demonstrate that LIMK1 activity in both the cytoplasmic and nuclear compartments promotes breast cancer progression, underscoring that nuclear LIMK1 contributes to the transforming function of LIMK1.