gebhart/patrepeval huggingface dataset:
Adeno-Associated Virus Serotypes 1, 8, and 9 Share Conserved Mechanisms for Anterograde and Retrograde Axonal Transport (2014)

Adeno-associated virus (AAV) vectors often undergo long-distance axonal transport after brain injection. This leads to transduction of brain regions distal to the injection site, although the extent of axonal transport and distal transduction varies widely among AAV serotypes. The mechanisms driving this variability are poorly understood. This is a critical problem for applications that require focal gene expression within a specific brain region, and also impedes the utilization of vector transport for applications requiring widespread delivery of transgene to the brain. Here, we compared AAV serotypes 1 and 9, which frequently demonstrate distal transduction, with serotype 8, which rarely spreads beyond the injection site. To examine directional AAV transport in vitro, we used a microfluidic chamber to apply dye-labeled AAV to the axon termini or to the cell bodies of primary rat embryonic cortical neurons. All three serotypes were actively transported along axons, with transport characterized by high velocities and prolonged runs in both the anterograde and retrograde directions. Coinfection with pairs of serotypes indicated that AAV1, 8, and 9 share the same intracellular compartments for axonal transport. In vivo, both AAV8 and 9 demonstrated anterograde and retrograde transport within a nonreciprocal circuit after injection into adult mouse brain, with highly similar distributions of distal transduction. However, in mass-cultured neurons, we found that AAV1 was more frequently transported than AAV8 or 9, and that the frequency of AAV9 transport could be enhanced by increasing receptor availability. Thus, while these serotypes share conserved mechanisms for axonal transport both in vitro and in vivo, the frequency of transport can vary among serotypes, and axonal transport can be markedly increased by enhancing vector uptake. This suggests that variability in distal transduction in vivo likely results from differential uptake at the plasma membrane, rather than fundamental differences in transport mechanisms among AAV serotypes.
Site-specific recombinases: molecular machines for the Genetic Revolution (2016)

The fields of molecular genetics, biotechnology and synthetic biology are demanding ever more sophisticated molecular tools for programmed precise modification of cell genomic DNA and other DNA sequences. This review presents the current state of knowledge and development of one important group of DNA-modifying enzymes, the site-specific recombinases (SSRs). SSRs are Nature's 'molecular machines' for cut-and-paste editing of DNA molecules by inserting, deleting or inverting precisely defined DNA segments. We survey the SSRs that have been put to use, and the types of applications for which they are suitable. We also discuss problems associated with uses of SSRs, how these problems can be minimized, and how recombinases are being re-engineered for improved performance and novel applications.
Transgenic expression of the Ly49A natural killer cell receptor confers class I major histocompatibility complex (MHC)-specific inhibition and prevents bone marrow allograft rejection. (1996)

Natural killer (NK) cells and some T cells are endowed with receptors specific for class I major histocompatibility complex (MHC) molecules that can inhibit cellular effector functions. The function of the Ly49 receptor family has been studied in vitro, but no gene transfer experiments have directly established the role of these receptors in NK cell functions. We show here that transgenic expression of the H-2Dd-specific Ly49A receptor in all NK cells and T cells conferred class I-specific inhibition of NK cell-mediated target cell lysis as well as of T cell proliferation. Furthermore, transgene expression prevented NK cell-mediated rejection of allogeneic H-2d bone marrow grafts by irradiated mice. These results demonstrate the function and specificity of Ly49 receptors in vivo, and establish that their subset-specific expression is necessary for the discrimination of MHC-different cells by NK cells in unmanipulated mice.
A Continuous Occlusion Model for Road Scene Understanding (2016)

We present a physically interpretable, continuous threedimensional (3D) model for handling occlusions with applications to road scene understanding. We probabilistically assign each point in space to an object with a theoretical modeling of the reflection and transmission probabilities for the corresponding camera ray. Our modeling is unified in handling occlusions across a variety of scenarios, such as associating structure from motion (SFM) point tracks with potentially occluding objects or modeling object detection scores in applications such as 3D localization. For point track association, our model uniformly handles static and dynamic objects, which is an advantage over motion segmentation approaches traditionally used in multibody SFM. Detailed experiments on the KITTI raw dataset show the superiority of the proposed method over both state-of-the-art motion segmentation and a baseline that heuristically uses detection bounding boxes for resolving occlusions. We also demonstrate how our continuous occlusion model may be applied to the task of 3D localization in road scenes.
ChemInform Abstract: Synthesis of Oxazolo(5,4‐g)‐1,2‐benzisoxazoles. (1987)

Abstract Title compounds of type (IV) and (VI) are synthesized via the common intermediate (II) and screened for their bacteriostatic activity.
Uncovering the roles of oxygen vacancies in cation migration in lithium excess layered oxides (2014)

A novel oxygen vacancy assisted transition metal (TM) diffusion mechanism is proposed for the first time to explain the near-surface phase transformation in lithium excess transition metal layered oxides. Oxygen vacancies and TM migration have been observed at nm scale spatial resolution by Scanning Transmission Electron Microscopy and Electron Energy Loss Spectroscopy. Formation of (dilute) oxygen vacancies and their roles in assisting transition metal ion diffusion were further investigated using first principles calculations. The activation barriers of TM diffusion in the presence of oxygen vacancies are drastically reduced and consistently in a reasonable range for room temperature diffusion.
Defects in type IIA von Willebrand disease: a cysteine 509 to arginine substitution in the mature von Willebrand factor disrupts a disulphide loop involved in the interaction with platelet glycoprotein Ib‐IX (1992)

Type IIA von Willebrand disease (vWD) is characterized by the loss of high and intermediate weight multimers of von Willebrand factor (vWF) from plasma. The 3' end of exon 28 in the vWF gene from four type IIA vWD patients was amplified by the polymerase chain reaction, cloned and sequenced. Sequencing identified two potential missense mutations resulting in the amino acid substitutions Arg 834-->Gln and Glu 875-->Lys in the mature vWF subunit within an area of vWF where mutations in type IIA vWD have been reported. Neither of these amino acid substitutions was found in over 100 normal alleles tested by allele specific oligonucleotide hybridization. A polymorphism (Val 802-->Leu) was identified in another patient. Other areas of exon 28 were analysed by denaturing gradient gel electrophoresis (DGGE) and DNA from one patient demonstrated an irregular DGGE pattern on the 5' end of the exon. Sequencing demonstrated an amino acid substitution of an arginine for cysteine at position 509 adjacent to an area of vWF where defects associated with type IIB vWD have been found. This substitution was not found in 100 normal chromosomes tested by restriction enzyme digestion. The Cys 509-->Arg substitution eliminates an intramolecular disulphide bridge formed by Cys 509 and Cys 695 which is important to maintain the configuration of vWF functional domains that interact with platelet glycoprotein Ib-IX.
Fluorescence detection of gadolinium chelates separated by reversed-phase high-performance liquid chromatography (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFluorescence detection of gadolinium chelates separated by reversed-phase high-performance liquid chromatographyJames J. Hagan, Susan Cicero. Taylor, and Michael F. TweedleCite this: Anal. Chem. 1988, 60, 6, 514–516Publication Date (Print):March 15, 1988Publication History Published online1 May 2002Published inissue 15 March 1988https://pubs.acs.org/doi/10.1021/ac00157a004https://doi.org/10.1021/ac00157a004research-articleACS PublicationsRequest reuse permissionsArticle Views1158Altmetric-Citations42LEARN 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
Influence of muscle temperature on maximal muscle strength and power output in human skeletal muscles (1979)

The influence of muscle temperature (Tm) on maximal muscle strength, power output, jumping, and sprinting performance was evaluated in four male subjects. In one of the subjects the electromyogram (EMG) was recorded from M. vastus lateralis, M. biceps femoris, and M. semitendinosus. Tm ranged from 30.0 degrees C to 39 degrees C. Maximal dynamic strength, power output, jumping, and sprinting performance were positively related to Tm. The changes were in the same order of magnitude for all these parameters (4-6% x degrees C-1) Maximal isometric strength decreased by 2% x degrees C-1 with decreasing Tm. The force-velocity relationship was shifted to the left at subnormal Tm. Thus in short term exercises, such as jumping and sprinting, performance is reduced at low Tm and enhanced at Tm above normal, primarily as a result of a variation in maximal dynamic strength.
Deletion mapping of chromosome 8p in prostate cancer by fluorescence in situ hybridization. (1994)

Double-target fluorescence in situ hybridization (FISH) was applied to 42 cases of prostate cancer and seven cases of histologically proven benign prostate hyperplasia for the detection of structural aberrations of chromosome 8. Cosmid probes for two chromosome 8p loci (LPL/8p22 and D8S7/8p23) were used in 34 specimens of malignant tumors obtained by the touch biopsy technique. Deletion was defined as when the number of cosmid signals was lower than the number of centromere signals in more than 35% of all nuclei observed. In total, thirty of the 42 (71%) specimens demonstrated any type of 8p deletion. Out of the 34 cases in which deletion mapping could be evaluated, distal deletion (D8S7) was detected in 17 (50%), of which 10 also showed deletion of LPL. Deletion of LPL was detected in 18 cases (53%), of which 8 (24%) retained the D8S7 (interstitial deletion). When the deletion pattern was graded as (1) no deletion (2) partial deletion (either D8S7 or LPL deleted) and (3) both deletions, the degree of deletion was well correlated with the tumor grade (P = 0.0009) and with stage (P = 0.0072, Fisher's Exact test). These data support the hypothesis that tumor suppressor gene(s) may be located in the chromosomal region 8p22, hence 8p deletions may play a crucial role in the pathogenesis of prostate cancer.
How do users know what to say? (1996)

article Free Access Share on How do users know what to say? Author: Nicole Yankelovich Sun Microsystems Laboratories Sun Microsystems LaboratoriesView Profile Authors Info & Claims InteractionsVolume 3Issue 6Nov./Dec. 1996 pp 32–43https://doi.org/10.1145/242485.242500Published:01 December 1996Publication History 62citation1,019DownloadsMetricsTotal Citations62Total Downloads1,019Last 12 Months47Last 6 weeks4 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP (1985)

The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
Mixed-backbone oligonucleotides as second generation antisense oligonucleotides: In vitro and in vivo  studies (1997)

Antisense oligonucleotides are being evaluated in clinical trials as novel therapeutic agents. To further improve the properties of antisense oligonucleotides, we have designed mixed-backbone oligonucleotides (MBOs) that contain phosphorothioate segments at the 3' and 5' ends and have a modified oligodeoxynucleotide or oligoribonucleotide segment located in the central portion of the oligonucleotide. Some of these MBOs indicate improved properties compared with phosphorothioate oligodeoxynucleotides with respect to affinity to RNA, RNase H activation, and anti-HIV activity. In addition, more acceptable pharmacological, in vivo degradation and pharmacokinetic profiles were obtained with these MBOs.
Deoxy Sugar Analogues of Triciribine:  Correlation of Antiviral and Antiproliferative Activity with Intracellular Phosphorylation (2000)

Triciribine (TCN) and triciribine monophosphate (TCN-P) have antiviral and antineoplastic activity at low micromolar or submicromolar concentrations. In an effort to improve and better understand this activity, we have conducted a structure-activity relationship study to explore requirements for the number of hydroxyl groups on the ribosyl moiety for biological activity. 2'-Deoxytriciribine (2'-dTCN), 3'-deoxytriciribine (3'-dTCN), 2', 3'-epoxytriciribine (2',3'-epoxyTCN), 2',3'-dideoxy-2', 3'-didehydrotriciribine (2',3'-d4TCN), and 2',3'-dideoxytriciribine (2',3'-ddTCN) were synthesized and evaluated for activity against human immunodeficiency virus (HIV-1), herpes simplex virus type 1 (HSV-1), and human cytomegalovirus (HCMV). Antiproliferative activity of the compounds also was tested in murine L1210 cells and three human tumor cell lines. All compounds were either less active than TCN and TCN-P or inactive at the highest concentration tested (100 microM) in both antiviral and antiproliferative assays. Reverse-phase HPLC of extracts from uninfected cells treated with the deoxytriciribine analogues only detected the conversion of 3'-dTCN and 2',3'-ddTCN to their respective monophosphates. Therefore, either the deoxytriciribine analogues were not transported across the cell membrane or, more likely, they were not substrates for a nucleoside kinase or phosphotransferase. We have concluded that the hydroxyl groups on the ribosyl ring system of TCN and TCN-P must be intact in order to obtain significant antiviral and antineoplastic activity.
Glu11 Site Cleavage and N-Terminally Truncated Aβ Production upon BACE Overexpression (2002)

Amyloid beta peptides (A beta) are generated by the proteolytic processing of the amyloid beta precursor protein (APP). The newly identified beta-site APP-cleaving enzyme (BACE) cleaves APP at Asp1 as well as between Tyr10 and Glu11 of A beta, producing C-terminal fragments (CTFs) C99 and C89, respectively. Subsequent cleavage by gamma-secretase gives rise to A beta 1-40/42 and A beta 11-40/42. Although both full-length and A beta peptides truncated at residue 11 have been identified in amyloid plaques in the AD brain, the relative proportion of these two cleavage products produced by BACE and secreted into the medium by cultured cells is unknown. Using cell lines stably overexpressing BACE, we found that A beta 11-40 and A beta 11-42 are major A beta cleavage products generated by BACE. We further showed that BACE utilizes both full-length APP as well as C99 as substrates for the production of C89, and that A beta 11-40/42 can be generated by sequential cleavage of single APP molecules by BACE and gamma-secretase. Taken together, the abundance of A beta 11-40/42 produced by BACE suggests that their roles in AD pathogenesis may be underestimated.
A low-noise low-offset chopper-stabilized capacitive-readout amplifier for CMOS MEMS accelerometers (2003)

A CMOS chopper-stabilized amplifier with both DC and AC offset cancellation, for capacitive readout of motion in MEMS structures, achieves 40 nV//spl radic/HZ noise floor, 10 mV DC offset, and 40 dB sensor offset reduction. The amplifier, integrated into a CMOS-MEMS accelerometer, achieves 50 /spl mu/g//spl radic/Hz noise floor.
Soil Loss and Silage Yield for Three Tillage Management Systems (1992)

Corn ( Zea mays L.) for silage is commonly grown in the southeastern USA in fields with rolling topography where rows often run up and down slope, promoting surface water runoff and soil erosion. The objective of this study was to assess one conventional and two nonconventional tillage‐management systems on silage yield, water runoff, and soil loss on sloping fields in the Piedmont of the southern USA. The study was conducted on an Appling sandy loam (clayey, kaolinitic, thermic Typic Hapludults) on a 4% slope with 12% clay and 66% sand in the Ap horizon. All tillage and planting operations were done up and down the slope. The three tillage‐management systems, each replicated six times, were (i) fall chisel plow to the 8‐in. depth and seeded to cover crops of rye ( Secufe cereufe L.) and hairy vetch ( Viciu vifosa Roth) in the wheel tracks (CPC); (ii) fall moldboard plow, seeded with hairy vetch over the entire surface and with rye seeded in the wheel tracks (MPC); and (iii) fall moldboard plow and disking before planting corn (MPD). Three‐year mean corn silage yield (65% by weight water) was least for treatment MPD, 15.75 ton/acre, as compared with 17.22 and 18.95 ton/acre for treatments CPC and MPC, respectively. Runoff and soil loss were collected in runoff collectors and measured after each single or group of closely spaced rains. Total runoff during the 3‐yr study was 19.7, 20.4, and 23.6 in. for the CPC, MPC, and MPD treatments, respectively. The percentages of total runoff lost between planting and harvest for the 3 yr were 59% for CPC, 52% for MPC, and 78% for MPD. Total soil loss during the 3‐yr study was 3.70, 3.30, and 41.3 tondacre, respectively, for treatments CPC, MPC, and MPD. Ninety‐nine percent of the soil loss for treatment MPD occurred between planting and harvest. The CPC and MPC systems were effective in increasing silage yields and in reducing soil loss below the soil loss tolerance (T value) of 5 tons/acre/year. Compared with treatment MPD, CPC increased silage yield by 9% while reducing soil loss 91%; MPC increased silage yield 20% and reduced soil loss 92%.
cRACE: a simple method for identification of the 5′ end of mRNAs (1995)

Journal Article cRACE: a simple method for identification of the 5′ end of mRNAs Get access Ichiro N. Maruyama, Ichiro N. Maruyama * Department of Cell Biology, The Scripps Research Institute10666 North Torrey Pines Road, La Jolla, CA 92037, USA *To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Terese L. Rakow, Terese L. Rakow Department of Cell Biology, The Scripps Research Institute10666 North Torrey Pines Road, La Jolla, CA 92037, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Hiroko I. Maruyama Hiroko I. Maruyama Department of Cell Biology, The Scripps Research Institute10666 North Torrey Pines Road, La Jolla, CA 92037, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 23, Issue 18, 25 September 1995, Pages 3796–3797, https://doi.org/10.1093/nar/23.18.3796 Published: 25 September 1995 Article history Received: 19 May 1995 Accepted: 18 August 1995 Published: 25 September 1995
Detection of HER-2/neu-positive circulating epithelial cells in prostate cancer patients (2004)

HER-2/neu may play a role in prostate carcinogenesis. The aim of this study was to use the expression of HER-2/neu as a molecular marker for the detection of circulating tumour cells (CTCs) in the blood of patients with prostate cancer (PC). Blood samples were collected from 42 patients with PC and nine healthy volunteers. Immunomagnetic beads were used to harvest epithelial cells from peripheral blood mononuclear cells. Total RNA was extracted and reverse transcribed before analysis by real-time PCR with HER-2/neu-specific primers. CTCs were HER-2/neu positive in six out of 11 (54%) patients with metastatic disease and in three out of 31 (9.6%) patients with localised PC (P=0.004). In blood samples from nine healthy volunteers, we detected no expression of HER-2/neu. The present method appears to be minimally invasive, highly sensitive and a specific approach for detecting CTCs in PC. Furthermore, it may help better target HER-2/neu in advanced PC.