gebhart/patrepeval huggingface dataset:
Human immune response to multiple injections of murine monoclonal IgG. (1985)

Murine monoclonal antibody infusions in humans should induce a human anti-mouse immunoglobulin (mIgG) immune response, especially if multiple infusions over an extended period of time are necessary for therapeutic efficacy. We have administered multiple infusions of the murine monoclonal antibody T101 to patients with cutaneous T cell lymphoma (CTCL) or chronic lymphocytic leukemia (CLL). Five of 10 CTCL patients, compared with zero of six CLL patients, developed antibodies to mIgG. In those CTCL patients who did not demonstrate anti-mIgG antibodies, we were unable to correlate the lack of response to any of a large number of clinical parameters. Anti-mIgG antibodies were of both the mu and gamma isotypes and were detectable 14 days after the first infusion. Multiple infusions were associated with elevated titers. The anti-idiotypic portion of the anti-mIgG titer steadily increased with each infusion until eventually, in one patient receiving eight weekly infusions, well over one-half the serum anti-mIgG recognized only T101 and not four other murine IgG2AK antibodies tested. To increase our confidence in these findings, four separate assay systems were used to make these determinations. The identification of anti-idiotype antibodies as the dominant species of the immune response to multiple infusions of murine monoclonal antibody has major implications for future work with monoclonal antibodies. Although it has been suggested that human monoclonal antibodies would obviate an immune response, our work implies that such antibodies might still induce anti-idiotype antibodies if multiple infusions are administered.
Comparison of adjuvant formulations for cytotoxic T cell induction using synthetic peptides (1996)

We have investigated the capacity of synthetic peptides delivered in different adjuvant formulations to induce cytotoxic T lymphocyte (CTL) responses to a class I H-2Kd-restricted Plasmodium berghei circumsporozoite epitope, CS 252-260. Using three immunogen formulations: soybean emulsion; Montanide ISA720; and lipopeptide (P3-CS), we first evaluated the effects of immunization routes on CTL induction. No CTL response was induced in mice immunized s.c. or i.p. with CS peptide formulated in soybean emulsion. In contrast, immunization with lipopeptide P3-CS either s.c. or i.p. effectively primed for CTL. Interestingly, CS peptide emulsified in Montanide ISA720 induced a CTL response only when delivered s.c. and not i.p., indicating the critical influence of immunization routes on CTL induction. We then compared the effectiveness of eight adjuvant formulations to induce CTL response following a single s.c. immunization. Notably, lipopeptide P3-CS and CS peptide admixed with P3 or POE lipid molecules stimulated a vigorous CTL response. However, only mice immunized with P3-CS and CS peptide admixed with P3 molecule generated long-lived CTL which persisted in vivo for 5 months. Thus, based on a simultaneous comparison of the different adjuvant formulations, we demonstrated that the conjugated and unconjugated P3 lipopeptides were the most effective immunogens for eliciting primary and memory CTL in mice.
Patterns of Immune Infiltration in Breast Cancer and Their Clinical Implications: A Gene-Expression-Based Retrospective Study (2016)

Large differences in the cellular composition of the immune infiltrate in breast tumours appear to exist, and these differences are likely to be important determinants of both prognosis and response to treatment. In particular, macrophages emerge as a possible target for novel therapies. Detailed analysis of the cellular immune response in tumours has the potential to enhance clinical prediction and to identify candidates for immunotherapy.
Caffeine's Vascular Mechanisms of Action (2010)

Caffeine is the most widely consumed stimulating substance in the world. It is found in coffee, tea, soft drinks, chocolate, and many medications. Caffeine is a xanthine with various effects and mechanisms of action in vascular tissue. In endothelial cells, it increases intracellular calcium stimulating the production of nitric oxide through the expression of the endothelial nitric oxide synthase enzyme. Nitric oxide is diffused to the vascular smooth muscle cell to produce vasodilation. In vascular smooth muscle cells its effect is predominantly a competitive inhibition of phosphodiesterase, producing an accumulation of cAMP and vasodilation. In addition, it blocks the adenosine receptors present in the vascular tissue to produce vasoconstriction. In this paper the main mechanisms of action of caffeine on the vascular tissue are described, in which it is shown that caffeine has some cardiovascular properties and effects which could be considered beneficial.
Systematic assessment and evaluation of sliding interleaved ky (SLINKY) acquisition for 3D MRA (1998)

In comparison with the conventional three-dimensional multiple overlapped thin slab acquisition (MOTSA) for magnetic resonance angiography (MRA), we have developed a novel sliding interleaved kY (SLINKY) acquisition technique, which can eliminate the slab boundary artifact (SBA) or venetian blind artifact without any a priori knowledge of blood flow. This work addresses the systematic assessment and evaluation of the SLINKY technique and verifies the advantages of SLINKY in the following several aspects: (a) scan time efficiency; (b) signal-to-noise ratio (SNR), and signal-difference-to-noise ratio (SDNR); (c) sensitivity to flow velocity range; (d) sensitivity to flow direction; (e) signal loss in slow/reversal flow regions; and (f) reconstruction efficiency and feasibility. Both phantom and in vivo experiments verify the clinical significance of the technique. The new MRA images acquired with this imaging technique in 31 volunteer/patient examinations show highly reliable mapping of vascular morphology without the SBA and reduction of signal voids in complex/slow flow regions.
Emerging technologies in DNA sequencing (2005)

Demand for DNA sequence information has never been greater, yet current Sanger technology is too costly, time consuming, and labor intensive to meet this ongoing demand. Applications span numerous research interests, including sequence variation studies, comparative genomics and evolution, forensics, and diagnostic and applied therapeutics. Several emerging technologies show promise of delivering next-generation solutions for fast and affordable genome sequencing. In this review article, the DNA polymerase-dependent strategies of Sanger sequencing, single nucleotide addition, and cyclic reversible termination are discussed to highlight recent advances and potential challenges these technologies face in their development for ultrafast DNA sequencing.
PSAR-Align: improving multiple sequence alignment using probabilistic sampling (2013)

The PSAR-Align source code (implemented mainly in C++) is freely available for download at http://bioen-compbio.bioen.illinois.edu/PSAR-Align.
Genomics and the Continuum of Cancer Care (2011)

Microarray analysis, involving assay of the expression of thousands of genes, and systematic DNA sequencing have led to tools and medicines now used in the treatment of cancer. This article reviews recent progress in the genomic analysis of cancer.
Molecular Characterization of Barley β‐Glucans by Size‐Exclusion Chromatography with Multiple‐Angle Laser Light Scattering and Other Detectors (1997)

ABSTRACT Molecular characteristics were determined for mixed‐linkage (1→3) (1→4)‐β‐ d ‐glucans (β‐glucans) extracted from Azhul, Crystal, Waxbar, and Prowashonupana barleys. β‐Glucans in extracts (with or without α‐amylase, protease, hemicellulase, or xylanase treatment) were separated from other components by high‐performance size‐exclusion chromatography and detected with multiple‐angle laser light scattering, refractive index, and fluorometry following postrefractive index treatment with Calcofluor. Pretreatment of barley with 70% ethanol (80°C, 4 hr) reduced β‐glucanase activity by ~20%. Hot‐alcohol treatment also reduced β‐glucan extraction at 23 and 65°C by 42 and 14%, respectively. Molecular weights of β‐glucans in the first water extract were generally higher than in succeeding water and alkali extracts. Weight average molecular weights ranged from 0.44 × 10 6 to 2.34 × 10 6 g/mol after α‐amylase treatment to remove interfering starch. Interference due to pentosans was not demonstrated using enzyme treatments.
The lonely failing heart: a case for ECM genes (1995)

Journal Article The lonely failing heart: a case for ECM genes Get access Marvin O. Boluyt, Marvin O. Boluyt aLaboratory of Cardiovascular Science, Gerontology Research Center, Baltimore, MD 21224, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Oscar H.L. Bing Oscar H.L. Bing * bDepartment of Veterans Affairs Medical Center and the Department of Medicine, Boston University School of Medicine, Boston, MA, USA *Corresponding author. ACOS/R & D (151) Boston VA Medical Center, 150 S. Huntington Avenue, Boston, MA 02130, USA. Tel.: (+1-617) 232-9500, ext. 5591; fax: (+1-617) 278-4486. Search for other works by this author on: Oxford Academic PubMed Google Scholar Cardiovascular Research, Volume 30, Issue 6, December 1995, Pages 836–840, https://doi.org/10.1016/S0008-6363(96)88510-5 Published: 01 December 1995 Article history Received: 14 February 1995 Accepted: 27 April 1995 Published: 01 December 1995
Engraftment of engineered ES cell–derived cardiomyocytes but not BM cells restores contractile function to the infarcted myocardium (2006)

Cellular cardiomyoplasty is an attractive option for the treatment of severe heart failure. It is, however, still unclear and controversial which is the most promising cell source. Therefore, we investigated and examined the fate and functional impact of bone marrow (BM) cells and embryonic stem cell (ES cell)-derived cardiomyocytes after transplantation into the infarcted mouse heart. This proved particularly challenging for the ES cells, as their enrichment into cardiomyocytes and their long-term engraftment and tumorigenicity are still poorly understood. We generated transgenic ES cells expressing puromycin resistance and enhanced green fluorescent protein cassettes under control of a cardiac-specific promoter. Puromycin selection resulted in a highly purified (>99%) cardiomyocyte population, and the yield of cardiomyocytes increased 6-10-fold because of induction of proliferation on purification. Long-term engraftment (4-5 months) was observed when co-transplanting selected ES cell-derived cardiomyocytes and fibroblasts into the injured heart of syngeneic mice, and no teratoma formation was found (n = 60). Although transplantation of ES cell-derived cardiomyocytes improved heart function, BM cells had no positive effects. Furthermore, no contribution of BM cells to cardiac, endothelial, or smooth muscle neogenesis was detected. Hence, our results demonstrate that ES-based cell therapy is a promising approach for the treatment of impaired myocardial function and provides better results than BM-derived cells.
Broadway Corridor Study Public Outreach Report, Winter 2013 (2014)

The Broadway Corridor Study Public Outreach Report summarizes the public outreach efforts conducted as part of the process to develop alternative concepts for future development and circulation along the Broadway Corridor in Redwood City, California. These efforts were conducted as a class project by fourth year students in the City and Regional Planning Department at California Polytechnic State University from September of 2013 to March of 2014.
Synthesis and Properties of Diuridine Phosphate Analogues Containing Thio and Amino Modifications (1996)

Several analogues of diuridine phosphate (UpU) were synthesized in order to investigate why replacing the 2'-hydroxyl with a 2'-amino group prevents hydrolysis. These analogues were designed to investigate what influence the 2'-substituent and 5'-leaving group have upon the rate of hydrolysis. All the analogues were considerably more labile than UpU toward acid-base-catalyzed hydrolysis. In the pH region from 6 to 9, the rate of hydrolysis of uridylyl (3'-5') 5'-thio-5'-deoxyuridine (UpsU) hydrolysis rose, in a log linear fashion, from a value of 5 x 10(-)(6) s(-)(1) at pH 6 to 3200 x 10(-)(6) s(-)(1) at pH 9, indicating that attack on the phosphorus by the 2'-oxo anion is rate-limiting in the hydrolysis mechanism. In contrast, the rate of uridylyl (3'-5') 5'-amino-5'-deoxyuridine (UpnU) hydrolysis fell from a value of 1802 x 10(-)(6) s(-)(1) at pH 5 to 140 x 10(-)(6) s(-)(1) at pH 7.5, where it remained constant up to pH 11.5, thus indicating an acid-catalyzed reaction. The analogue 2'-amino-2'-deoxyuridylyl (3'-5') 5'-thio-5'-deoxyuridine (amUpsU) was readily hydrolyzed above pH 7, in contrast to the hydrolytic stability of amUpT, with rates between 85 x 10(-)(6) s(-)(1) and 138 x 10(-)(6) s(-)(1). The hydrolysis of 2'-amino-2'-deoxyuridylyl (3'-5') 5'-amino-5'-deoxythymidine (amUpnT) rose from 17 x 10(-)(6) s(-)(1) at pH 11.5 to 11 685 x 10(-)(6) s(-)(1) at pH 7.0, indicating an acid-catalyzed reaction, where protonation of the 5'-amine is rate limiting. The cleavage rates of UpsU, UpnU, and amUpsU were accelerated in the presence of Mg(2+), Zn(2+), and Cd(2+) ions, but a correlation with interaction between metal ion and leaving group could only be demonstrated for amUpsU. UpsU and UpnU are also substrates for RNase A with UpsU having similar Michaelis-Menten parameters to UpU. In contrast, UpnU is more rapidly degraded with an approximate 35-fold increase in catalytic efficiency, which is reflected purely in an increase in the value of k(cat).
Eotaxin and Obesity (2006)

Circulating eotaxin and eotaxin mRNA levels in visceral adipose tissue were increased in obesity in mice and humans. Adipose tissue explants secrete eotaxin, and the stromal/vascular component of adipose tissue seems to be the predominant source of eotaxin. Diet-induced weight loss in humans led to reduction in plasma eotaxin levels, demonstrating that clinical interventions that target obesity can modulate systemic eotaxin levels.
Cobaloxime-catalyzed hydroperfluoroalkylation of electron-deficient alkenes with perfluoroalkyl halides: reaction and mechanism (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCobaloxime-catalyzed hydroperfluoroalkylation of electron-deficient alkenes with perfluoroalkyl halides: reaction and mechanismChangming Hu and Yaoling QiuCite this: J. Org. Chem. 1992, 57, 12, 3339–3342Publication Date (Print):June 1, 1992Publication History Published online1 May 2002Published inissue 1 June 1992https://pubs.acs.org/doi/10.1021/jo00038a022https://doi.org/10.1021/jo00038a022research-articleACS PublicationsRequest reuse permissionsArticle Views546Altmetric-Citations54LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
<title>Affine-invariant moments and B-splines for object recognition from image curves</title> (1993)

In this paper we deal with the problem of matching and recognizing planar curves which are modeled as B-splines, independently of possible transformations that the original curve has been subjected to. Curve matching is achieved by using a finite set of B-spline moments which are compared to a set of B-spline prototype moments. When the observed curve is an unknown affine transformation (having four parameters) of one of the prototype curves, the affine parameters are estimated by relating the weighted moments of the original curve to that of the affine transformed curve. A set of up to a second order weighted B-spline moments are used toward that end, and results in a set of two single variable quadratic equations and two linear equations involving the four parameters of the linear transformation for which a closed form analytic expression exists. In the general linear case, the weight used is the affine length which weighs the moment integral by a kernel that results in having the affine parameters factoring out of the weighted moment integral. Once the transformation parameters are obtained, we undo the transformation, and use the set of third or fourth order B-spline moments for classification. The method is illustrated on classifying affine transformed silhouette of aircrafts.
Successful adjuvant-free vaccination of BALB/c mice with mutated amyloid β peptides (2008)

A recent human clinical trial of an Alzheimer's disease (AD) vaccine using amyloid beta (Aβ) 1–42 plus QS-21 adjuvant produced some positive results, but was halted due to meningoencephalitis in some participants. The development of a vaccine with mutant Aβ peptides that avoids the use of an adjuvant may result in an effective and safer human vaccine. All peptides tested showed high antibody responses, were long-lasting, and demonstrated good memory response. Epitope mapping indicated that peptide mutation did not lead to epitope switching. Mutant peptides induced different inflammation responses as evidenced by cytokine profiles. Ig isotyping indicated that adjuvant-free vaccination with peptides drove an adequate Th2 response. All anti-sera from vaccinated mice cross-reacted with human Aβ in APP/PS1 transgenic mouse brain tissue. Our study demonstrated that an adjuvant-free vaccine with different Aβ peptides can be an effective and safe vaccination approach against AD. This study represents the first report of adjuvant-free vaccines utilizing Aβ peptides carrying diverse mutations in the T-cell epitope. These largely positive results provide encouragement for the future of the development of human vaccinations for AD.
Retinal Pigment Epithelium Damage Enhances Expression of Chemoattractants and Migration of Bone Marrow–Derived Stem Cells (2006)

Damaged RPE secretes cytokines that have been shown to serve as chemoattractants for BM-derived stem cells (BMSCs). Retina-committed stem cells appear to reside in the BM and can be mobilized into the PB by G-CSF and FL. These stem cells may have the potential to serve as an endogenous source for tissue regeneration after RPE damage.
Glaucoma—2: Treatment (2004)

The main aim of treatment in glaucoma is to reduce intraocular pressure. Good evidence from multiple large randomised trials shows that reducing intraocular pressure is effective in preventing disease progression in ocular hypertension, primary open angle glaucoma, and even in so called normal tension glaucoma. Target pressures in the low teens are associated with the lowest progression rates.

### βblockers

blockers—for example, timolol, carteolol, betaxolol levobunolol, and metipranolol—reduce the secretion of aqueous and are the most commonly prescribed topical treatment. Contraindications to their use include a history of lung or heart disease, as the drops may cause systemic β blockade. Topical β blockers can unmask latent and previously undiagnosed chronic obstructive pulmonary disease in elderly people.

Systemic effects from eye drops can be reduced by occlusion of the punctum (finger pressed on the caruncle, which is felt as a lump at the inner canthus of the eye) or shutting the eyes for several minutes after putting in the drops. This reduces the lacrimal pumping mechanism and stops the drops running down the lacrimal passages and being absorbed systemically through the nasal mucosa or by inhalation directly into the lungs. It may also enhance ocular absorption of the drugs. Drops are usually given twice a day, but long acting forms can be given once a day, either alone or in combination with other drops.

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Eye closure to reduce systemic side effects after instilling drops

### Prostaglandin analogues

Prostaglandin analogues (such as, latanoprost, travoprost, and bimatoprost) reduce the intraocular pressure by increasing aqueous outflow from the eye through the uveoscleral pathway. These drugs can reduce intraocular pressure by 30-35%.

Systemic side effects are minimal, but a few patients with light irides experience a gradual, permanent darkening of the iris. Eyelashes may also increase in length and darken. For optimum effect, these drops are used once daily (at …

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(Leveled) fully homomorphic encryption without bootstrapping (2012)

We present a novel approach to fully homomorphic encryption (FHE) that dramatically improves performance and bases security on weaker assumptions. A central conceptual contribution in our work is a new way of constructing leveled fully homomorphic encryption schemes (capable of evaluating arbitrary polynomial-size circuits), without Gentry's bootstrapping procedure.
Structure and function of MRP20 and MRP49, the nuclear genes for two proteins of the 54 S subunit of the yeast mitochondrial ribosome. (1992)

MRP20 and MRP49 are proteins of the large subunit of the mitochondrial ribosome in Saccharomyces cerevisiae. Their genes were identified through immunological screening of a genomic library in the expression vector lambda gt11. Nucleotide sequencing revealed that MRP49 is tightly linked to TPK3 and encodes a 16-kDa, basic protein with no significant relatedness to any other known protein. MRP20 specifies a 263-amino-acid polypeptide with sequence similarity to members of the L23 family of ribosomal proteins. The levels of the mRNAs and proteins for both MRP20 and MRP49 were regulated in response to carbon source. In [rho0] strains lacking mitochondrial rRNA, the levels of the two proteins were reduced severalfold, presumably because the unassembled proteins are unstable. Null mutants of MRP20 converted to [rho-] or [rho0], a characteristic phenotype of mutations in essential genes for mitochondrial translation. Inactivation of MRP49 caused a cold-sensitive respiration-deficient phenotype, indicating that MRP49 is not an essential ribosomal protein. The mrp49 mutants were defective in the assembly of stable 54 S ribosomal subunits at the nonpermissive temperature. With the results presented here, there are now published sequences for 14 yeast mitochondrial ribosomal proteins, only five of which bear discernable relationships to eubacterial ribosomal proteins.
Methods for the Study of Protein-Protein Interactions in Cancer Cell Biology (2003)

Development of sensitive methods to monitor and quantitatively assess the expression levels of endogenous genes and the association-interaction of proteins in living cells and whole organisms is a complex and challenging problem. In this chapter, we have described basic methods for investigating protein-protein interactions which include immunoprecipitation, GST pull-down assays, peptide bead pull-down assays, chemical crosslinking and photoaffinity labeling. These methods should provide important tools to dissect crosstalk between proteins and the direct implications of this crosstalk in signaling pathways and cancer biology.