gebhart/patrepeval huggingface dataset:
Vaccine Injection Site Matters: Qualitative and Quantitative Defects in CD8 T Cells Primed as a Function of Proximity to the Tumor in a Murine Glioma Model (2012)

Malignant gliomas are lethal brain tumors for which novel therapies are urgently needed. In animal models, vaccination with tumor-associated Ags efficiently primes T cells to clear gliomas. In clinical trials, cancer vaccines have been less effective at priming T cells and extending survival. Generalized immune suppression in the tumor draining lymph nodes has been documented in multiple cancers. However, a systematic analysis of how vaccination at various distances from the tumor (closest to farthest) has not been reported. We investigated how the injection site chosen for vaccination dictates CD8 T cell priming and survival in an OVA-transfected murine glioma model. Glioma-bearing mice were vaccinated with Poly:ICLC plus OVA protein in the neck, hind leg, or foreleg for drainage into the cervical, inguinal, or axillary lymph nodes, respectively. OVA-specific CD8 T cell number, TCR affinity, effector function, and infiltration into the brain decreased as the vaccination site approached the tumor. These effects were dependent on the presence of the tumor, because injection site did not appreciably affect CD8 T cell priming in tumor-free mice. Our data suggest the site of vaccination can greatly impact the effectiveness of cancer vaccines. Considering that previous and ongoing clinical trials have used a variety of injection sites, vaccination site is potentially a critical aspect of study design that is being overlooked.
Syndromes of neurodegeneration with brain iron accumulation (NBIA): An update on clinical presentations, histological and genetic underpinnings, and treatment considerations (2011)

In recent years, understanding of the syndromes of neurodegeneration with brain iron accumulation (NBIA) has grown considerably. In addition to the core syndromes of pantothenate kinsase-associated neurodegeneration (PKAN, NBIA1) and PLA2G6-associated neurodegeneration (PLAN, NBIA2), several other genetic causes have been identified. The acknowledged clinical spectrum has broadened, age-dependent presentations have been recognized, and we are becoming aware of overlap between the different NBIA disorders as well as with other diseases. Autopsy examination of genetically confirmed cases has demonstrated Lewy bodies and/or tangles in some subforms, bridging the gap to more common neurodegenerative disorders such as Parkinson's disease. NBIA genes map into related pathways, the understanding of which is important as we move toward mechanistic therapies. Our aim in this review is to provide an overview of not only the historical developments, clinical features, investigational findings, and therapeutic results but also the genetic and molecular underpinnings of the NBIA syndromes.
A model for synchronisation and communication of distributed multimedia data streams (2002)

Effective means of communicating and synchronising multimedia data streams are extremely important in a distributed environment. We address the above problem by presenting a comprehensive model of multimedia objects communication and synchronisation in a high speed packet switched network such as the ATM. The model is based on the XOCPN model presented by Qazi, Woo and Ghafoor (see Proceedings of the ACM Multimedia, San Francisco, USA, 1993). The XOCPN model has been chosen for its inherent simplicity. Some of the deficiencies of the model are addressed.
Bisphosphonate-mediated gene vector delivery from the metal surfaces of stents (2005)

The clinical use of metallic expandable intravascular stents has resulted in improved therapeutic outcomes for coronary artery disease. However, arterial reobstruction after stenting, in-stent restenosis, remains an important problem. Gene therapy to treat in-stent restenosis by using gene vector delivery from the metallic stent surfaces has never been demonstrated. The present studies investigated the hypothesis that metal-bisphosphonate binding can enable site-specific gene vector delivery from metal surfaces. Polyallylamine bisphosphonate (PAA-BP) was synthesized by using Michael addition methodology. Exposure to aqueous solutions of PAA-BP resulted in the formation of a monomolecular bisphosphonate layer on metal alloy surfaces (steel, nitinol, and cobalt-chromium), as demonstrated by x-ray photoelectron spectroscopy. Surface-bound PAA-BP enabled adenoviral (Ad) tethering due to covalent thiol-binding of either anti-Ad antibody or a recombinant Ad-receptor protein, D1. In arterial smooth muscle cell cultures, alloy samples configured with surface-tethered Ad were demonstrated to achieve site-specific transduction with a reporter gene, (GFP). Rat carotid stent angioplasties using metal stents exposed to aqueous PAA-BP and derivatized with anti-knob antibody or D1 resulted in extensive localized Ad-GFP expression in the arterial wall. In a separate study with a model therapeutic vector, Ad-inducible nitric oxide synthase (iNOS) attached to the bisphosphonate-treated metal stent surface via D1, significant inhibition of restenosis was demonstrated (neointimal/media ratio 1.68 +/- 0.27 and 3.4 +/- 0.35; Ad-iNOS vs. control, P < 0.01). It is concluded that effective gene vector delivery from metallic stent surfaces can be achieved by using this approach.
Case of the Month (2009)

department editor Kate August works in cardiology at Emory University Hospital, Atlanta, Georgia. She has indicated no relationships to disclose relating to the content of this article.
Miniature Protein Inhibitors of the p53–hDM2 Interaction (2006)

Small but perfectly formed. A library of miniature protein variants was constructed that presented the minimal recognition epitope of the human double-minute 2 oncoprotein (hDM2), which was derived from the activation domain of p53 (p53AD). This library was optimized (see scheme) to yield several miniature proteins with robust folds and nanomolar affinity for hDM2. The inhibitory activities of these miniature proteins correlated with the stability of the protein fold. This emphasizes the benefit of presenting the p53AD epitope on a miniature protein scaffold.
Identification and characterization of an alternative cytotoxic T lymphocyte-associated protein 4 binding molecule on B cells. (1996)

To determine whether alternative cytotoxic T lymphocyte-associated protein 4 (CTLA4) binding proteins exist on B cells, we constructed (i) mCTLA4hIgG consisting of the extracellular region of a mouse CTLA4 molecule and the Fc portion of a human IgG1 molecule and (ii) PYAAhIgG, a mutant mCTLA4hIgG, having two amino acid substitutions on the conserved MYPPPY motif in the complementarity-determining region 3-like region and lacking detectable binding to both B7-1 and B7-2 molecules. Using these fusion proteins (mCTLA4hIgG and PYAAhIgG), we demonstrated that a mouse immature B-cell line, WEHI231 cells, expressed alternative CTLA4 binding molecules (ACBMs) that were distinct from both B7-1 and B7-2. ACBMs were 130-kDa disulfide-linked proteins. More importantly, ACBMs were able to provide costimulatory signal for T-cell proliferation in the presence of anti-CD3 monoclonal antibodies. In addition, we demonstrated that more than 20% of B220+ cells obtained from normal mouse spleen expressed ACBMs.
High levels of fetal erythroblasts and fetal extracellular DNA in the peripheral blood of a pregnant woman with idiopathic polyhydramnios: case report (2000)

Abnormal amniotic fluid volume can be associated with increased maternal risk as well as perinatal morbidity and mortality. Polyhydramnios is often indicative of fetal, placental or maternal problems. In a large proportion of patients the aetiology of the disorder is unclear. Here we report on a case in which numerous fetal erythroblasts and large quantities of extracellular fetal DNA were found in the peripheral blood of a pregnant woman with idiopathic polyhydramnios bearing a male fetus. Following enrichment of erythroblasts by magnetic separation (MACS) and anti-CD71 antibodies, approximately 45-fold more erythroblasts were determined per ml peripheral maternal blood than in matched controls (231 versus 5). Single cell multiplex polymerase chain reaction (PCR) of individually micromanipulated erythroblasts showed that approximately 122 of these were of fetal origin. The concentration of extracellular fetal circulatory DNA in maternal plasma was determined by real-time quantitative PCR and shown to be almost double that of the control group (749.2 versus 404 fetal genome equivalents per ml maternal plasma). It can be speculated that the increased intrauterine pressure in polyhydramnios leads to an enhanced influx of fetal cells and free extracellular fetal DNA into the maternal circulation. This hypothesis will have to be tested with further cases.
Regulation of gene expression by oxygen in Saccharomyces cerevisiae (1992)

The oxygen regulation of two broad categories of yeast genes is discussed in this review. The first is made up of genes regulated by heme, and the second is made up of genes whose regulation is heme independent. Heme-regulated genes fall into two classes: heme-activated and heme-repressed genes. Activation is achieved through one of two transcriptional activators, the heme-dependent HAP1 protein or the heme-activated, glucose-repressed HAP2/3/4 complex. Some of the properties and the DNA-binding sites of these activators are discussed. Heme repression is achieved through the action of the ROX1 repressor, the expression of which is transcriptionally activated by heme. Once ROX1 is synthesized, its function is heme independent. Evidence that ROX1 binds to DNA or is part of a DNA-binding complex is described. Factors which modulate the function of these regulatory proteins are discussed, and a schematic of heme activation and repression is presented. The mitochondrial subunits of cytochrome c oxidase are induced by oxygen in a heme-independent fashion. The translation of one, cytochrome c oxidase subunit III, is dependent upon three nucleus-encoded initiation factors. One of these, PET494, is itself translationally regulated by oxygen in a heme-independent fashion. The expression of at least four other mitochondrially encoded cytochrome subunits is dependent upon specific translation factors, raising the potential for translational regulation as a general mechanism. Finally, a number of anaerobic genes that show heme-independent, oxygen-repressed expression have been identified. These fall into two kinetic classes, suggesting that there are at least two different regulatory circuitries.
3DTV at home (2017)

Stereoscopic 3D (S3D) movies have become widely popular in the movie theaters, but the adoption of S3D at home is low even though most TV sets support S3D. It is widely believed that S3D with glasses is not the right approach for the home. A much more appealing approach is to use automulti-scopic displays that provide a glasses-free 3D experience to multiple viewers. A technical challenge is the lack of native multiview content that is required to deliver a proper view of the scene for every viewpoint. Our approach takes advantage of the abundance of stereoscopic 3D movies. We propose a real-time system that can convert stereoscopic video to a high-quality multiview video that can be directly fed to automultiscopic displays. Our algorithm uses a wavelet-based decomposition of stereoscopic images with per-wavelet disparity estimation. A key to our solution lies in combining Lagrangian and Eulerian approaches for both the disparity estimation and novel view synthesis, which leverages the complementary advantages of both techniques. The solution preserves all the features of Eulerian methods, e.g., subpixel accuracy, high performance, robustness to ambiguous depth cases, and easy integration of inter-view aliasing while maintaining the advantages of Lagrangian approaches, e.g., robustness to large disparities and possibility of performing non-trivial disparity manipulations through both view extrapolation and interpolation. The method achieves real-time performance on current GPUs. Its design also enables an easy hardware implementation that is demonstrated using a field-programmable gate array. We analyze the visual quality and robustness of our technique on a number of synthetic and real-world examples. We also perform a user experiment which demonstrates benefits of the technique when compared to existing solutions.
Manipulation of the growth rate of human breast cancer cells by antiandrogen followed by chemotherapy. (1990)

The effects induced by the antiandrogen Cyproterone Acetate (CPA) on the proliferation of EVSA-T human breast cancer cells endowed with androgen receptors were studied. Kinetic analyses were carried out by two autoradiographic techniques measuring the percentage of cells in S-phase and the growth fraction (GF). The exposure of the cultures to CPA for 24 h caused a marked inhibition on S-phase cells without significantly affecting the CF. The accumulation of cells in G1-phase, confirmed by cytometric analysis, was rescued to the S compartment by replacing the culture medium 24 h after CPA administration. Exposure of EVSA-T to Doxorubicin or Methotrexate after CPA and medium change at the time of maximal proliferative recruitment, led to an enhancement of cytotoxicity as demonstrated by colony survival assay.
Max-Margin Parsing (2004)

We present a novel discriminative approach to parsing inspired by the large-margin criterion underlying support vector machines. Our formulation uses a factorization analogous to the standard dynamic programs for parsing. In particular, it allows one to efficiently learn a model which discriminates among the entire space of parse trees, as opposed to reranking the top few candidates. Our models can condition on arbitrary features of input sentences, thus incorporating an important kind of lexical information without the added algorithmic complexity of modeling headedness. We provide an efficient algorithm for learning such models and show experimental evidence of the model’s improved performance over a natural baseline model and a lexicalized probabilistic context-free grammar.
Algorithms for Next-Generation High-Throughput Sequencing Technologies (2011)

Recent advances of DNA sequencing technologies are allowingresearchers to generateimmense amounts of data in a fast and cost effective fashion, enablinggenome-wide association study and populationgenetic research which could not be done a decade ago.There are quite numerous computational challenges arising from thisadvancement, however. Examples include efficient algorithms for processing rawdata generated by sequencing instruments, algorithms for detecting andcorrecting sequencing errors, algorithms for detecting genomevariations from sequence data, just to name a few. Because differentsequencing technologies can have drastically differentcharacteristics, these algorithms often need to be adapted in orderto produce most accurate results.In this thesis, I will address a few of the aforementioned problems. First, Iwill describe two model-based basecalling algorithms for the Illuminasequencing platforms: BayesCall and naiveBayesCall. The novelty of BayesCall algorithmis that it is fully unsupervised, requiring notraining data with known labels, and therefore it is applicable to data without a reference sequence.It also dramatically improves sequencing accuracies.Built upon BayesCall algorithm, naiveBayesCall dramatically improves computationalefficiency by approximating the original model without sacrificingaccuracy. We will also show that improved basecall can have positiveeffects on the downstream sequence analysis, such as the detection ofsingle nucleotide polymorphism and the assembly of novel genomes.In the third chapter, an algorithm, called ECHO, for correcting short-readsequencing errors will be described. The correction algorithm efficiently computesall overlaps between sequencing reads and corrects errorsby using statistical models. Since it does not rely on referencegenomes, ECHO can also be applied to &lt;italic&gt;de novo&lt;/italic&gt; sequencing.Most other error correction algorithms require users to specifykey parameters, but the optimal values for these parameters are unknown tousers and can be hard to specify. Without key parameters beingoptimized, the effectiveness of error correction algorithm couldsometimes be dramatically reduced.Based on statistical models, ECHO optimizes these parametersaccordingly. We will show that ECHO can significantly reducesequence error rates and also facilitate downstream sequenceanalysis. It is also demonstrated that ECHO can be extended to detectheterozygousity from sequencing data.These algorithms are developed in hopes tomake downstream analysis of sequence data easier and ultimatelyfacilitate genome researches.
Measuring locus of control: A critique of general, children's, health‐ and work‐related locus of control questionnaires (1993)

This paper attempts a critical review not so much of the concept of locus of control as the plethora of unidimensional or sphere-specific measures that have been developed in the past 25 years. After a brief history of the development of the concept of locus of control, various oft-repeated and some new criticisms are considered. One frequent response to problems associated with the original concept and scale has been to develop new psychometrically validated, sphere- or topic-specific measures. These are tabulated and reviewed under five headings: measures (either multidimensional or sphere-specific) of the general concept of locus of control; measures devised specifically for children and adolescents; measures that have concentrated on aspects of mental and physical health; work, career and economic locus of control measures; and finally, measures which have extended the locus of control concept into other areas. The advantages and disadvantages of this proliferation of measures is considered in some detail, especially the issue of incremental validity, and recommendations are made for future work in this area.
REVIEWS (1998)

REVIEWS Get access S. Lubensky. 1995. Random House Russian-English Dictionary of Idioms. New York: Random House. xxvii + 1017 pp. US $75.00. Adrian Room Adrian Room Stamford, Lincolnshire Search for other works by this author on: Oxford Academic Google Scholar International Journal of Lexicography, Volume 11, Issue 1, March 1998, Pages 79–84, https://doi.org/10.1093/ijl/11.1.79 Published: 01 March 1998
Direct Comparison of Two New Actigraphs and Polysomnography in Children and Adolescents (2011)

Similar to previous reports, both new actigraph brands were found to have good sensitivity (to detect sleep), but poorer specificity (to detect wake). Study results also suggest that researchers should adjust the scoring algorithm/sensitivity depending on a study's design (e.g., young children vs. adolescents, healthy children vs. youth with SDB). Further, inter-device reliability was poor, suggesting the need for caution when comparing results across studies that use different brands of actigraphic devices.
Predicting out of intensive care unit cardiopulmonary arrest or death using electronic medical record data (2013)

An automated model harnessing EMR data offers great potential for identifying RED and was superior to both a prior risk model and the human judgment-driven RRT.
Exploring hydrophobic sites in proteins with xenon or krypton (1998)

X-ray diffraction is used to study the binding of xenon and krypton to a variety of crystallised proteins: porcine pancreatic elastase; subtilisin Carlsberg from Bacillus licheniformis; cutinase from Fusarium solani; collagenase from Hypoderma lineatum; hen egg lysozyme, the lipoamide dehydrogenase domain from the outer membrane protein P64k from Neisseria meningitidis; urate-oxidase from Aspergillus flavus, mosquitocidal delta-endotoxin CytB from Bacillus thuringiensis and the ligand-binding domain of the human nuclear retinoid-X receptor RXR-alpha. Under gas pressures ranging from 8 to 20 bar, xenon is able to bind to discrete sites in hydrophobic cavities, ligand and substrate binding pockets, and into the pore of channel-like structures. These xenon complexes can be used to map hydrophobic sites in proteins, or as heavy-atom derivatives in the isomorphous replacement method of structure determination.
Small quantum-sized CdS particles assembled to form a regularly nanostructured porous film (1995)

Submicroporous CdS films were fabricated by a two-step replication process, in which porous anodic alumina was used as a template. The films were grown on a porous gold support of the same structure, resulting in a free-standing CdS/Au membrane. The diameter of the holes of the regular porous structure is in the order of 100 nm. Moreover, the replicated CdS film consists of small-sized quantized crystalline particles, the size of which are in the range of 5 nm. Thus, the film is ordered in the 5 and 100 nm domain forming a superstructure.
The mTORC1 signaling repressors REDD1/2 are rapidly induced and activation of p70S6K1 by leucine is defective in skeletal muscle of an immobilized rat hindlimb (2012)

Limb immobilization, limb suspension, and bed rest cause substantial loss of skeletal muscle mass, a phenomenon termed disuse atrophy. To acquire new knowledge that will assist in the development of therapeutic strategies for minimizing disuse atrophy, the present study was undertaken with the aim of identifying molecular mechanisms that mediate control of protein synthesis and mechanistic target of rapamycin complex 1 (mTORC1) signaling. Male Sprague-Dawley rats were subjected to unilateral hindlimb immobilization for 1, 2, 3, or 7 days or served as nonimmobilized controls. Following an overnight fast, rats received either saline or L-leucine by oral gavage as a nutrient stimulus. Hindlimb skeletal muscles were extracted 30 min postgavage and analyzed for the rate of protein synthesis, mRNA expression, phosphorylation state of key proteins in the mTORC1 signaling pathway, and mTORC1 signaling repressors. In the basal state, mTORC1 signaling and protein synthesis were repressed within 24 h in the soleus of an immobilized compared with a nonimmobilized hindlimb. These responses were accompanied by a concomitant induction in expression of the mTORC1 repressors regulated in development and DNA damage responses (REDD) 1/2. The nutrient stimulus produced an elevation of similar magnitude in mTORC1 signaling in both the immobilized and nonimmobilized muscle. In contrast, phosphorylation of 70-kDa ribosomal protein S6 kinase 1 (p70S6K1) on Thr(229) and Thr(389) in response to the nutrient stimulus was severely blunted. Phosphorylation of Thr(229) by PDK1 is a prerequisite for phosphorylation of Thr(389) by mTORC1, suggesting that signaling through PDK1 is impaired in response to immobilization. In conclusion, the results show an immobilization-induced attenuation of mTORC1 signaling mediated by induction of REDD1/2 and defective p70S6K1 phosphorylation.
Improved naming after transcranial direct current stimulation in aphasia (2007)

Transcranial direct current stimulation (tDCS) has been proposed as an adjuvant technique to improve functional recovery after ischaemic stroke. This study evaluated the effect of tDCS over the left frontotemporal areas in eight chronic non-fluent post-stroke aphasic patients. The protocol consisted of the assessment of picture naming (accuracy and response time) before and immediately after anodal or cathodal tDCS (2 mA, 10 minutes) and sham stimulation. Whereas anodal tDCS and sham tDCS failed to induce any changes, cathodal tDCS significantly improved the accuracy of the picture naming task by a mean of 33.6% (SEM 13.8%).