gebhart/patrepeval huggingface dataset:
Lentivirus Mediated HO-1 Gene Transfer Enhances Myogenic Precursor Cell Survival After Autologous Transplantation in Pig (2007)

Cell therapy for Duchenne muscular dystrophy and other muscle diseases is limited by a massive early cell death following injections. In this study, we explored the potential benefit of heme oxygenase-1 (HO-1) expression in the survival of porcine myogenic precursor cells (MPCs) transplanted in pig skeletal muscle. Increased HO-1 expression was assessed either by transient hyperthermia or by HO-1 lentiviral infection. One day after the thermic shock, we observed a fourfold and a threefold increase in HSP70/72 and HO-1 levels, respectively. This treatment protected 30% of cells from staurosporine-induced apoptosis in vitro. When porcine MPC were heat-shocked prior to grafting, we improved cell survival by threefold at 5 days after autologous transplantation (26.3 +/- 5.5% surviving cells). After HO-1 lentiviral transduction, almost 60% of cells expressed the transgene and kept their myogenic properties to proliferate and fuse in vitro. Apoptosis of HO-1 transduced cells was reduced by 50% in vitro after staurosporine induction. Finally, a fivefold enhancement in cell survival was observed after transplantation of HO-1-group (47.5 +/- 9.1% surviving cells) as compared to the nls-LacZ-group or control group. These results identify HO-1 as a protective gene against early MPC death post-transplantation.
Profiling pH Gradients Across Nanocapillary Array Membranes Connecting Microfluidic Channels (2005)

Nanocapillary array membranes (NCAMs), comprised of thin (d approximately 5-10 microm) nuclear track-etched polycarbonate sheets containing approximately 10(8) cm(-2) nearly parallel nanometer-diameter capillaries, may act to gate fluid transport between microfluidic channels to effect, for example, sample collection. There is interest in H+-transport across these NCAMs because there is significant practical interest in being able to process analyte-containing samples under different pH conditions in adjacent layers of an integrated microfluidic circuit and because protons, with their inherently high mobility, present a challenge in separating microfluidic environments with different properties. To evaluate the capability of NCAMs to support pH gradients, the proton transport properties of NCAMs were studied using laser scanning confocal fluorescence microscopy (LSCFM). Spatiotemporal maps of [H+] in microfluidic channels adjacent to the NCAMs yield information regarding diffusive and electrokinetic transport of protons. The NCAMs studied here are characterized by a positive zeta potential, zeta > 0, so at small nanocapillary diameters, the overlap of electrical double layers associated with opposite walls of the nanocapillary establish an energy barrier for either diffusion or electrokinetic transport of cations through the nanometer-diameter capillaries due to the positive charge on the nanocapillary surface. Proton transfer through an NCAM into microchannels is reduced for pore diameters, d < or = 50 nm and ionic strengths I < or = 50 mM, while for large pore diameters or solution ionic strengths, the incomplete overlap of electric double layer allows more facile ionic transfer across the membranes. These results establish the operating conditions for the development of multilevel integrated nanofluidic/microfluidic architectures which can support multidimensional chemical analysis of mass-limited samples requiring sequential operations to be implemented at different pH values.
Familial hypomagnesemia maps to chromosome 9q, not to the X chromosome: genetic linkage mapping and analysis of a balanced translocation breakpoint (1997)

Familial hypomagnesemia with secondary hypocalcemia (HSH) (MIM 307600) was studied in three inbred Bedouin kindreds from Israel. The three kindreds, one extended and two nuclear families, contained 13 affected individuals, 11 males and two females. Assuming that the individuals affected with hypomagnesemia shared a chromosomal region inherited from a common ancestor, we used a DNA pooling strategy in a genome-wide search for loci which show homozygosity for shared alleles in affected individuals. DNA samples from affected individuals within a single kindred were pooled and used as the template for PCR amplification of short tandem repeat polymorphic markers (STRPs). Pooled DNA from unaffected siblings and parents were used as controls. A shift towards homozygosity was observed in the affected DNA pool compared with the control pools with D9S301 (GATA7D12). Genotyping of individual DNA samples with D9S301 and several flanking markers confirmed linkage to chromosome 9 with maximum LOD scores of 3.4 (theta = 0.05), 3.7 (theta = 0) and 2.3 (theta = 0) for the three families. We have identified a 14 cM interval on chromosome 9 (9q12-9q22.2), flanked by proximal marker D9S1874 and distal marker D9S1807, within which all affected individuals from the three kindreds are homozygous for a shared haplotype. The disease segregates with a common affected haplotype in the three families, suggesting that hypomagnesemia is caused by a common ancestral mutation in these families. Although HSH has been previously reported to be X linked, these linkage data demonstrate that the disorder is an autosomal recessive disease in these kindreds. Mapping of a chromosomal breakpoint in a somatic cell line established from a patient with HSH and a balanced X;9 translocation placed the chromosomal breakpoint in a 500 kb region flanked by D9S1844 and D9S273. Identification of the gene responsible for hypomagnesemia will provide insight into the regulation of this essential cation.
Chronic lymphocytic leukaemia cells drive the global CD4+ T cell repertoire towards a regulatory phenotype and leads to the accumulation of CD4+ forkhead box P3+ T cells (2011)

Advanced chronic lymphocytic leukaemia (CLL) is associated with profound immunodeficiency, including changes in T regulatory cells (T(regs)). We determined the pattern of expression of forkhead box P3 (FoxP3), CD25, CD27 and CD127 and showed that the frequency of CD4+ FoxP3+ T cells was increased in CLL patients (12% versus 8% in controls). This increase was seen only in advanced disease, with selective expansion of FoxP3-expressing cells in the CD4+ CD25(low) population, whereas the number of CD4+ CD25(high) FoxP3+ cells was unchanged. CD4+ CD25(low) cells showed reduced expression of CD127 and increased CD27, and this regulatory phenotype was also seen on all CD4 T cells subsets in CLL patients, irrespective of CD25 or FoxP3 expression. Incubation of CD4+ T cells with primary CLL tumours led to a sixfold increase in the expression of FoxP3 in CD4+ CD25- T cells. Patients undergoing treatment with fludarabine demonstrated a transient increase in the percentage of CD4+ FoxP3+ T cells, but this reduced to normal levels post-treatment. This work demonstrates that patients with CLL exhibit a systemic T cell dysregulation leading to the accumulation of CD4+ FoxP3+ T cells. This appears to be driven by interaction with malignant cells, and increased understanding of the mechanisms that are involved could provide novel avenues for treatment.
Deep Metric Learning via Lifted Structured Feature Embedding (2016)

Learning the distance metric between pairs of examples is of great importance for learning and visual recognition. With the remarkable success from the state of the art convolutional neural networks, recent works [1, 31] have shown promising results on discriminatively training the networks to learn semantic feature embeddings where similar examples are mapped close to each other and dissimilar examples are mapped farther apart. In this paper, we describe an algorithm for taking full advantage of the training batches in the neural network training by lifting the vector of pairwise distances within the batch to the matrix of pairwise distances. This step enables the algorithm to learn the state of the art feature embedding by optimizing a novel structured prediction objective on the lifted problem. Additionally, we collected Stanford Online Products dataset: 120k images of 23k classes of online products for metric learning. Our experiments on the CUB-200-2011 [37], CARS196 [19], and Stanford Online Products datasets demonstrate significant improvement over existing deep feature embedding methods on all experimented embedding sizes with the GoogLeNet [33] network. The source code and the dataset are available at: https://github.com/rksltnl/ Deep-Metric-Learning-CVPR16.
Adeno-associated virus vector integration junctions (1997)

Vectors derived from adeno-associated virus (AAV) have the potential to stably transduce mammalian cells by integrating into host chromosomes. Despite active research on the use of AAV vectors for gene therapy, the structure of integrated vector proviruses has not previously been analyzed at the DNA sequence level. Studies on the integration of wild-type AAV have identified a common site-specific integration locus on human chromosome 19; however, most AAV vectors do not appear to integrate at this locus. To improve our understanding of AAV vector integration, we analyzed the DNA sequences of several integrated vector proviruses. HeLa cells were transduced with an AAV shuttle vector, and integrated proviruses containing flanking human DNA were recovered as bacterial plasmids for further analysis. We found that AAV vectors integrated as single-copy proviruses at random chromosomal locations and that the flanking HeLa DNA at integration sites was not homologous to AAV or the site-specific integration locus of wild-type AAV. Recombination junctions were scattered throughout the vector terminal repeats with no apparent site specificity. None of the integrated vectors were fully intact. Vector proviruses with nearly intact terminal repeats were excised and amplified after infection with wild-type AAV and adenovirus. Our results suggest that AAV vectors integrate by nonhomologous recombination after partial degradation of entering vector genomes. These findings have important implications for the mechanism of AAV vector integration and the use of these vectors in human gene therapy.
Genome Erosion in a Nitrogen-Fixing Vertically Transmitted Endosymbiotic Multicellular Cyanobacterium (2010)

This is the first finding of genome degradation in a plant symbiont and phenotypically complex cyanobacterium and one of only a few extracellular endosymbionts described showing signs of reductive genome evolution. Our findings suggest an ongoing selective streamlining of this cyanobacterial genome which has resulted in an organism devoted to nitrogen fixation and devoid of autonomous growth. The cyanobacterial symbiont of Azolla can thus be considered at the initial phase of a transition from free-living organism to a nitrogen-fixing plant entity, a transition process which may mimic what drove the evolution of chloroplasts from a cyanobacterial ancestor.
EQUIVALENT GRAFT-VERSUS-HOST REACTIVITY OF SPLEEN CELLS FROM TWO LINES OF MICE GENETICALLY SELECTED FOR HIGH AND LOW HUMORAL ANTIBODY FORMATION (1972)

Department of Experimental Immunobiology Wellcome Research Laboratories Langley Court, Beckenham Kent BR3 3BS, England
Holonomic quantum computation with neutral atoms (2002)

We propose an all-geometric implementation of quantum computation using neutral atoms in cavity QED. We show how to perform generic single- and two-qubit gates, the latter by encoding a two-atom state onto a single, many-level atom. We compare different strategies to overcome limitations due to cavity imperfections.
Synthesis of simian virus 40 t antigen in Escherichia coli. (1979)

Plasmids are constructed by using recombination in vitro according to Roberts, T.M., Kacich, R. & Ptashne, M. (1979) Proc. Natl. Acad. Sci. USA 76, 760-764 in which the t antigen gene of simian virus 40 is fused to a promoter of the Escherichia coli lac operon. In the fusions, transcription commences at the lac promoter, and, in some of the fusions, translation begins at the ATG initiator codon of the t gene. This translation is directed most efficiently by those plasmids in which the lac sequences abut the t gene such that a hybrid ribosome binding is encoded. In this case, the Shine-Dalgarno sequence is of lac origin but the ATG derives from the t gene. translation from this initiator codon is greatly decreased if the lac sequences are separated from the ATG by 17 base pairs and is abolished if the AT of this triplet is deleted. Cells bearing the productive fusions synthesize a 20,000-dalton protein with t antigenic determinants. This protein has an isoelectric point(s) indistinguishable from that of t antigen isolated from simian virus 40-transformed cells. Moreover, a partial sequence of the amino-terminal region of the bacterial product is that predicted for authentic t antigen. We conclude that these bacteria are for authentic t antigen. We conclude that these bacteria are producing a protein, the sequence of which is identical to that of authentic t antigen unfused to other polypeptides.
The Sprite network operating system (1988)

A description is given of Sprite, an experimental network operating system under development at the University of California at Berkeley. It is part of a larger research project, SPUR, for the design and construction of a high-performance multiprocessor workstation with special hardware support of Lisp applications. Sprite implements a set of kernel calls that provide sharing, flexibility, and high performance to networked workstations. The discussion covers: the application interface: the basic kernel structure; management of the file name space and file data, virtual memory; and process migration.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Heuristics for the automatic identification of irregularities in spreadsheets (2005)

Spreadsheet programs turned out to be the most popular end-user programming environment that has ever been released. Important decisions are based on the results of spreadsheet programs and the list of known errors with large impact is growing daily- although it surely is only the top of an iceberg.One way out of the crisis might be the introduction of software engineering techniques into spreadsheet development. Suggestions for the improvement of spreadsheet development range back as far as into the late eighties, but none has been successful yet. We argue this is either because not enough effort is put into the roll-out of the technique to the users and, mainly, because they neglect the fact that spreadsheet programmers are end-users, not willing or not able to spend any time on learning software engineering methods. We found out that most end users are willing to verify their spreadsheets, but only view have the time and skills to do really systematic testing of spreadsheets.We developed an approach to generate two orthogonal abstract representations of spreadsheet programs that are then displayed to the user by different visualisation techniques to support the auditing process. Usually, irregularities in the visualisation point out hot-spots on the spreadsheet with a high likelihood of erroneous formulas. In this paper we present new heuristics for identifying hot spots that are very efficient for large spreadsheet programs.
Predation of human pathogens by the predatory bacteria Micavibrio aeruginosavorus and Bdellovibrio bacteriovorus (2010)

Infectious complications caused by micro-organisms that have become resistant to drug therapy are an increasing problem in medicine, with more infections becoming difficult to treat using traditional antimicrobial agents. The work presented here highlights the potential use of predatory bacteria as a biological-based agent for eradicating multidrug-resistant bacteria, with the hope of paving the way for future studies in animal models.
Quantifying the Extent of Ligand Incorporation and the Effect on Properties of TiO2 Thin Films Grown by Atomic Layer Deposition Using an Alkoxide or an Alkylamide (2020)

Atomic layer deposition (ALD) of TiO2 thin films on a Si substrate has been investigated using titanium isopropoxide (TTIP) and tetrakis(dimethylamino)titanium (TDMAT) in combination with water. The deposition rate and the chemical stability of the films are significantly different depending on the Ti precursor and process temperature (TALD). When the films are annealed a significant thickness shrinkage is reported for the first time on TiO2. A comprehensive analysis of the films with X-ray photoelectron spectroscopy, Fourier transform infrared, ellipsometry, and porosimetry demonstrates that some precursor ligands are incorporated (most likely as isopropanol) when ALD is performed at low temperature (i.e., TALD < 200 °C) using TTIP. The trapped ligand molecules can be removed by annealing but make the film porous and thus have a detrimental effect on the dielectric properties. Higher-quality nonporous films are grown by using TTIP at TALD ≥ 200 °C or by using TDMAT. It is shown that measuring the refractive index is a simple, nondestructive, and reliable way to determine film quality. Numerical simulations of ligand coverage show that the measured growth rates are consistent with a self-limiting ALD mechanism albeit with partial incorporation of ligands from TTIP at low temperature (TALD < 200 °C), which renders part of the surface inactive toward growth. Aside from this, the higher growth rate of TDMAT is due to more desorption of ligands during the Ti precursor pulse. The overall decrease in the growth rate with temperature is related quantitatively to decreasing coverage of hydroxyl groups on TiO2. Comparing the TTIP and TDMAT processes in this way reveals new aspects of the gas-surface chemistry during self-limiting ALD and how this affects film morphology and electrical properties.
Likelihood ratio gradient estimation for stochastic recursions (1995)

In this paper, we develop mathematical machinery for verifying that a broad class of general state space Markov chains reacts smoothly to certain types of perturbations in the underlying transition structure. Our main result provides conditions under which the stationary probability measure of an ergodic Harris-recurrent Markov chain is differentiable in a certain strong sense. The approach is based on likelihood ratio ‘change-of-measure' arguments, and leads directly to a ‘likelihood ratio gradient estimator' that can be computed numerically.
Polyamine Modification Increases the Permeability of Proteins at the Blood‐Nerve and Blood‐Brain Barriers (1996)

The permeability of the blood-nerve barrier (BNB) and the blood-brain barrier (BBB) to superoxide dismutase (SOD), insulin, albumin, and IgG in normal adult rats was quantified by measuring the permeability coefficient-surface area product (PS) with the intravenous bolus injection technique before and after covalent protein modification with naturally occurring polyamines-putrescine (PUT), spermidine (SPD), and spermine (SPM). The PS value of the BNB for PUT-SOD was 21.1-fold greater than the native SOD, and the PS values of the BBB for PUT-SOD ranged from 17.6-fold greater for the thalamus to 23.6-fold greater for the caudate-putamen compared with native SOD. In a similar manner, polyamine-modified insulin showed a 1.7-2.0-fold increase in PS of the BNB and BBB compared with the high values of native insulin. Polyamine-modified albumin showed a remarkable 54-165-fold increase in PS of the BNB and BBB compared with native albumin, whereas PUT-IgG resulted in an even higher increase in the PS that ranged from 111- to 349-fold for nerve and different brain regions compared with native IgG. Polyamine modification of proteins, therefore, can dramatically increase the permeability at the BNB and BBB of a variety of proteins with widely differing M(r) and function. It is surprising that the PS values of the BNB and BBB decreased with the increasing number of positive charges of the protonated amino groups on the polyamines (PUT>SPD>SPM). Although cationic proteins are known to interact with fixed anionic charges on the lumen of the microvascular endothelium, this observation of decreased permeability with increased positive charge distribution along the aliphatic carbon chain of the polyamines implies mechanisms other than simple electrostatic interaction involving charge density. It is suggested that the polyamine transporter may be responsible for the transport of these polyamine-modified proteins. Systemic administration of polyamine-modified peptides and proteins might prove to be an efficient approach to deliver therapeutic agents into the CNS and PNS for the treatment of a variety of neurological diseases.
Bacterial Cell Surface Techniques (1988)

Structure of Bacteria and Their Envelopes Culture of Bacteria Isolation and Purification of Cell Walls Separation and Purification of Surface Components Chemical Analysis of Envelope Polymers Immunochemistry of Cell Surfaces Current and Future Applications of Knowledge of Bacterial Surfaces.
Solid surface tension: the equation of state approach and the theory of surface tension components. Theoretical and conceptual considerations (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSolid surface tension: the equation of state approach and the theory of surface tension components. Theoretical and conceptual considerationsJ. K. Spelt and A. W. NeumannCite this: Langmuir 1987, 3, 4, 588–591Publication Date (Print):July 1, 1987Publication History Published online1 May 2002Published inissue 1 July 1987https://pubs.acs.org/doi/10.1021/la00076a026https://doi.org/10.1021/la00076a026research-articleACS PublicationsRequest reuse permissionsArticle Views1752Altmetric-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
Open networking in New Zealand (2002)

Open networking is becoming widely discussed and at least partial IN open networking is now considered to be technically a realistic possibility. Significant enhancement in competition in end-user value added services in New Zealand and in other countries is considered to be the likely result from the implementation of open networking. The authors discuss open networking (inter-networking) as associated with two goals: 1) standardisation of the services available at the interconnection (and hence provision of a competitive market in interconnection services) and (2) enhancing the capabilities available at the interconnection (and hence enabling greater innovation in end-user services).
Respiratory variations in pulse oximeter waveform amplitude are influenced by venous return in mechanically ventilated patients under general anaesthesia (2006)

DeltaPOP can be determined in the operating room and is influenced by changes in preload. This new index has potential clinical applications for the prediction of fluid responsiveness.
Distannoxane-catalysed transesterification of 1,n-diol diacetates. Selective transformation of either of chemically equivalent functional groups (1991)

Using catalysis by 1,3-dichlorotetrabutyldistannoxane, 1,n-diol diacetates were selectively converted into the corresponding monoacetates.