gebhart/patrepeval huggingface dataset:
PDZ Interaction Sites in Integrin α Subunits (2001)

We used published peptide library data to identify PDZ recognition sequences in integrin alpha subunit cytoplasmic domains and found that the alpha(6)A and alpha(5) subunits contain a type I PDZ binding site (TSDA*) (asterisk indicates the stop codon). The alpha(6)A cytoplasmic domain was used for screening a two-hybrid library to find interacting proteins. The bulk of the captured cDNAs (60%) coded for TIP-2/GIPC, a cytoplasmic protein with one PDZ domain. The interaction of TIP-2/GIPC with different integrin subunits was tested in two-hybrid and in vitro binding assays. Surprisingly, TIP-2/GIPC bound strongly to the C terminus of both alpha(6)A and alpha(6)B, although the alpha(6)B sequence (ESYS*) is not suggestive of a PDZ binding site because of its polar C-terminal residue. For high affinity interaction with TIP-2/GIPC, at least one of the residues at positions -1 and -3 must be negatively charged. An aliphatic residue at position 0 increases the affinity of but is not required for this interaction. The alpha(5) integrin subunit also bound to TIP-2/GIPC. The alpha(6) integrin and TIP-2/GIPC co-localize in retraction fibers in carcinoma cells plated on laminin, a finding suggesting a functional interaction in vivo. Our results demonstrate that both splice variants of alpha(6) integrin contain a conserved PDZ binding site that enables interaction with TIP-2/GIPC. The binding site in alpha(6)B defines a new subclass of type I PDZ interaction site, characterized by a non-aliphatic residue at position 0.
Jet-Injected Insulin Is Associated With Decreased Antibody Production and Postprandial Glucose Variability When Compared With Needle-Injected Insulin in Gestational Diabetic Women (1993)

Jet injection is associated with a diminished antibody response and postprandial variability compared with needle-injected insulin. Thus, this warrants consideration as a therapeutic option for women with gestational diabetes mellitus and may also be applicable to nonpregnant, insulin-requiring diabetic patients.
Edaravone (3-Methyl-1-Phenyl-2-Pyrazolin-5-one), A Novel Free Radical Scavenger, for Treatment of Cardiovascular Diseases (2006)

Edaravone (3-methyl-1-phenyl-2-pyrazolin-5-one), a strong novel free radical scavenger, is used for treatment of patients with acute brain infarction. Edaravone has preventive effects on myocardial injury following ischemia and reperfusion in patients with acute myocardial infarction. Antioxidant actions of edaravone include enhancement of prostacyclin production, inhibition of lipoxygenase metabolism of arachidonic acid by trapping hydroxyl radicals, inhibition of alloxan-induced lipid peroxidation, and quenching of active oxygen, leading to protection of various cells, such as endothelial cells, against damage by reactive oxygen species (ROS). Recently, we have shown that edaravone improves endothelial function through a decrease in ROS in smokers. From a clinical perspective, it is important to select an appropriate drug that is effective in improving endothelial function in patients with cardiovascular diseases. The novel free radical scavenger edaravone may represent a new therapeutic intervention for endothelial dysfunction in the setting of atherosclerosis, chronic heart failure, diabetes mellitus, or hypertension. This review focuses on clinical findings and on putative mechanisms underlying the beneficial effects of the antioxidative agent edaravone on the artherosclerotic process in patients with cardiovascular diseases.
High‐Efficiency, Microscale GaN Light‐Emitting Diodes and Their Thermal Properties on Unusual Substrates (2012)

A method for forming efficient, ultrathin GaN light-emitting diodes (LEDs) and for their assembly onto foreign substances is reported. The LEDs have lateral dimensions ranging from ~1 mm × 1 mm to ~25 μm × 25 μm. Quantitative experimental and theoretical studies show the benefits of small device geometry on thermal management, for both continuous and pulsed-mode operation, the latter of which suggests the potential use of these technologies in bio-integrated contexts.
EARLY FLOWERING3 Encodes a Novel Protein That Regulates Circadian Clock Function and Flowering in Arabidopsis (2001)

Higher plants use photoperiodic cues to regulate many aspects of development, including the transition from vegetative to floral development. The EARLY FLOWERING3 (ELF3) gene is required for photoperiodic flowering and normal circadian regulation in Arabidopsis. We have cloned ELF3 by positional methods and found that it encodes a novel 695-amino acid protein that may function as a transcriptional regulator. ELF3 transcript level is regulated in a circadian manner, as is expected of a zeitnehmer input pathway component. Overexpression of the LATE ELONGATED HYPOCOTYL gene, which has been proposed to function as a clock component, did not abolish circadian regulation of ELF3 transcription, providing further evidence that ELF3 is a circadian clock input pathway component.
Rapid wavelength-swept spectrally encoded confocal microscopy (2005)

Spectrally encoded confocal microscopy (SECM) is a technique that allows confocal microscopy to be performed through the confines of a narrow diameter optical fiber probe. We present a novel scheme for performing SECM in which a rapid wavelength swept source is used. The system allows large field of view images to be acquired at rates up to 30 frames/second. Images of resolution targets and tissue specimens acquired ex vivo demonstrate high lateral (1.4 mum) and axial (6 mum) resolution. Imaging of human skin was performed in vivo at depths of up to 350 mum, allowing cellular and sub-cellular details to be visualized in real time.
Frame-Semantic Parsing (2013)

Frame semantics is a linguistic theory that has been instantiated for English in the FrameNet lexicon. We solve the problem of frame-semantic parsing using a two-stage statistical model that takes lexical targets (i.e., content words and phrases) in their sentential contexts and predicts frame-semantic structures. Given a target in context, the first stage disambiguates it to a semantic frame. This model uses latent variables and semi-supervised learning to improve frame disambiguation for targets unseen at training time. The second stage finds the target's locally expressed semantic arguments. At inference time, a fast exact dual decomposition algorithm collectively predicts all the arguments of a frame at once in order to respect declaratively stated linguistic constraints, resulting in qualitatively better structures than naïve local predictors. Both components are feature-based and discriminatively trained on a small set of annotated frame-semantic parses. On the SemEval 2007 benchmark data set, the approach, along with a heuristic identifier of frame-evoking targets, outperforms the prior state of the art by significant margins. Additionally, we present experiments on the much larger FrameNet 1.5 data set. We have released our frame-semantic parser as open-source software.
Applications of gene therapy to the CNS (1996)

Gene therapy is a new method with potential for treating a broad range of acquired and inherited neurologic diseases, where the causative gene defect or deletion has been identified. In addition to gene replacement the application of gene products that reduce cellular dysfunction or death represent new therapeutic options. Gene transfer techniques to express novel proteins using different viral vectors in vitro and in vivo, as well as animal models and human trials will be reviewed in this article. We will focus on a new lentiviral vector as a recent gene transfer method and degenerative disorders of the CNS, and their related model systems.
Quantitative analysis of SLC34A2 expression in different types of ovarian tumors. (2011)

The main purpose of this study was to estimate the SLC34A2 gene expression in normal ovary and different types of ovarian tumors.We have investigated SLC34A2 gene expression level in papillary serous, endometrioid, unspecified adenocarcinomas, benign tumors, and normal ovarian tissues using real-time PCR analysis. Differences in gene expression were calculated as fold changes in gene expression in ovarian carcinomas and benign tumors compared to normal ovary.We have found that SLC34A2 gene was highly expressed in well-differentiated endometrioid and papillary serous ovarian carcinomas compared to low-differentiated endometrioid carcinomas, benign serous cystoadenomas and normal ovary. Analysis of SLC34A2 gene expression according to tumor differentiation level (poor- and well-differentiated) showed that SLC34A2 is up-regulated in well differentiated tumors.Upregulation of SLC34A2 gene expression in well-differentiated tumors may reflect cell differentiation processes during ovarian cancerogenesis and could serve as potential marker for ovarian cancer diagnosis and prognosis.
The Making of a Portrait - Bringing it into Focus (2003)

The data generated by DNA arrays are often described as the molecular "portrait" of a particular physiological/pathological sample. Although the emotional reactions could range from revulsion to adoration when viewing those portraits, as it might be when viewing some contemporary art, array technology has fundamentally changed the way researchers approach many biomedical questions. With its ability to monitor the expression level of tens of thousands genes simultaneously, microarray technology has been able to identify "markers" for complex diseases such as cancer. While massive amounts of work lie ahead to validate those marker genes, many researchers are turning their attentions to the low-density, focused arrays. When incorporated with current knowledge on specific biological pathways, these specially tailored macroarrays may be better fitted for purposes such as diagnosis, drug discovery and validation, and prognostic assessment of clinical treatments.
Robust Estimation of Bioaffinity Assay Fluorescence Signals (2006)

In this paper, the challenging problem of robust mean-signal estimation of a single-step microparticle bioaffinity assay is investigated. For this purpose, a density estimation-based robust algorithm (DER) was developed. The DER algorithm was comparatively evaluated with four other parameter estimation methods (mean value, median filtering, least square estimation, Welsch robust m-estimator). Two important questions were raised and investigated: 1) Which of the five methods can robustly estimate the mean bioaffinity signal? and 2) How many microparticles need to be measured in order to obtain an accurate estimate of the mean signal value? To answer the questions, bootstrap and coefficient of variation (CV) analyses were performed. In the CV analysis, the DER algorithm gave the best results: The CV ranged from 0.8% to 4.9% when the number of microparticles used for the mean signal estimation varied from 800 to 30. In the bootstrap analysis of the standard error, the DER algorithm had the smallest variance. As a conclusion, it can be underlined that: 1) of all methods tested, the DER algorithm gave the most consistent and reproducible results according to the bootstrap and CV analysis; 2) using the DER algorithm accurate estimates could be calculated based on 80-100 particles, corresponding to a typical assay measurement time of 1 min; and 3) the investigated bioaffinity signals contained a large number of outliers (observations that severely deviate from the majority of data) and therefore robust techniques were necessary for the mean signal estimation tasks.
Error-prone bypass of certain DNA lesions by the human DNA polymerase κ (2000)

The Escherichia coli protein DinB is a newly identified error-prone DNA polymerase. Recently, a human homolog of DinB was identified and named DINB1. We report that the DINB1 gene encodes a DNA polymerase (designated polkappa), which incorporates mismatched bases on a nondamaged template with a high frequency. Moreover, polkappa bypasses an abasic site and N-2-acetylaminofluorene (AAF)-adduct in an error-prone manner but does not bypass a cis-syn or (6-4) thymine-thymine dimer or a cisplatin-adduct. Therefore, our results implicate an important role for polkappa in the mutagenic bypass of certain types of DNA lesions.
Functional human T-cell immunity and osteoprotegerin ligand control alveolar bone destruction in periodontal infection (2000)

Periodontitis, a prime cause of tooth loss in humans, is implicated in the increased risk of systemic diseases such as heart failure, stroke, and bacterial pneumonia. The mechanisms by which periodontitis and antibacterial immunity lead to alveolar bone and tooth loss are poorly understood. To study the human immune response to specific periodontal infections, we transplanted human peripheral blood lymphocytes (HuPBLs) from periodontitis patients into NOD/SCID mice. Oral challenge of HuPBL-NOD/SCID mice with Actinobacillus actinomycetemcomitans, a well-known Gram-negative anaerobic microorganism that causes human periodontitis, activates human CD4(+) T cells in the periodontium and triggers local alveolar bone destruction. Human CD4(+) T cells, but not CD8(+) T cells or B cells, are identified as essential mediators of alveolar bone destruction. Stimulation of CD4(+) T cells by A. actinomycetemcomitans induces production of osteoprotegerin ligand (OPG-L), a key modulator of osteoclastogenesis and osteoclast activation. In vivo inhibition of OPG-L function with the decoy receptor OPG diminishes alveolar bone destruction and reduces the number of periodontal osteoclasts after microbial challenge. These data imply that the molecular explanation for alveolar bone destruction observed in periodontal infections is mediated by microorganism-triggered induction of OPG-L expression on CD4(+) T cells and the consequent activation of osteoclasts. Inhibition of OPG-L may thus have therapeutic value to prevent alveolar bone and/or tooth loss in human periodontitis.
Antisense-mediated modulation of splicing: Therapeutic implications for Duchenne muscular dystrophy (2010)

While disruption of alternative splicing underlies many diseases, modulation of splicing using antisense oligonucleotides (AONs) can have therapeutic implications. The most notable example is Duchenne muscular dystrophy (DMD), where antisense-mediated exon skipping can restore the open reading frame and allow the synthesis of partly functional dystrophin proteins instead of non-functional ones. This approach is currently tested in early phase clinical trials. In this review the development of the exon skipping approach in patient-derived cell cultures, animal models and patients is described and hurdles that have to be overcome to make this personalized medicine type approach widely applicable are discussed.
Systemic lupus erythematosus patients with central nervous system involvement show autoantibodies to a 50-kD neuronal membrane protein. (1992)

An antibody was detected in the sera from patients with systemic lupus erythematosus (SLE) and central nervous system (CNS) involvement that reacted with a 50-kD antigen in the plasma membrane of brain synaptic terminals. The 50-kD antigen was solubilized with Triton X-100 from preparations enriched with synaptic plasma membranes, and was partially purified by molecular sieve filtration column chromatography. The sera of 19 of 20 CNS-SLE patients showed strong to moderate immunoreactivity with the 50-kD protein in Western blots. Immunoreactivity with the 50-kD protein was also detected in the cerebrospinal fluid of CNS-SLE patients. Control sera from healthy individuals did not react with the 50-kD protein. Low to background reactivity was detected in 35% of a group of SLE patients without CNS manifestations, and in 3% of patients displaying other connective tissue diseases. A total of 100 individuals were tested in this study. Purified autoantibodies to the 50-kD protein from CNS-SLE patients were used for immunofluorescent labeling of neuroblastoma cells. The immunofluorescent staining revealed a distinct macular distribution pattern on the surface of the cell membrane. Taken together, the data suggest that the 50-kD protein may be an important target for autoantibodies, preponderantly found in CNS-SLE patients, and that the antigen may play a role in the pathogenesis of some neurological manifestations in SLE.
Multiple description image coding for noisy channels by pairing transform coefficients (2002)

Multiple description coding (MDC) is a way of trading off coding gain with robustness to channel errors. This paper presents a new method for MDC using the framework of transform coding. Instead of using the Karhunen-Loeve transform (KLT) that decorrelates all the coefficients, we choose the transform bases so that the coefficients are correlated pair-wise. This is accomplished by rotating every two basis vectors in the KLT. Each pair of correlated coefficients are then split between two descriptions. Only 45/spl deg/ rotation is considered which leads to two balanced streams. In the actual implementation, the DCT is employed in place of the KLT and the rotation of transform bases is accomplished by rotating the DCT coefficients. Experimental results show that this method can lead to satisfactory image reconstruction from any one description with a relatively small (20% for "lena") overhead over a standard JPEG coder.
Psychosurgery (2001)

The author describes the three commonly practiced surgical methods in the treatment of mental illness, i.e., cingulotomy, anterior capsulotomy, and posteromedial hypothalamotomy.
Experimental Pseudomonas aeruginosa Infection of the Mouse Cornea (1971)

Pseudomonas aeruginosa infection of human cornea is rare but serious. The work of previous investigators using experimental infection primarily of rabbit cornea resulted in successful therapy for 10 to 50% of clinical cases. The advantage of using the mouse is demonstrated. The methods we adapted for characterizing the untreated experimental infection included: incising the cornea to enable establishing the infection; corneal examination with a steroscopic microscope; grading corneal pathology; qualitative and quantitative monitoring of the infecting bacteria by culturing and staining sectioned and dissected tissues. The characteristics of the tissue pathology, host response, and infection were similar to those reported for other animals and man. Corneal pathology was frequently nearly maximal 1 day after infection; host response involved a progression of events of long duration; pathology persisted well beyond the period of bacterial infection. The infection was essentially noncommunicable, and invasiveness was limited to the tissues of the incised eye. The results show the possibility of tests for invasiveness of clinical isolates and for screening for therapeutic and prophylactic measures.
Effect on cancer cells of plasmids that express antisense RNA of human papillomavirus type 18. (1992)

Some human squamous cell carcinomas contain DNA of human papillomaviruses (HPV) and express RNA from the E6 and E7 genes. We have examined the effect of plasmids that express antisense RNA of these genes on the growth of the human cancer cell lines HeLa, C4-1, and 1483, which contain HPV type 18 DNA. As controls, the human cancer cell line 183 and the Vero line of monkey kidney cells were used, which do not contain HPV. Plasmids were introduced into the cells by electroporation; cells that contained HPV type 18 accepted the antisense-expressing plasmids at a lower frequency than the cells that lacked HPV. Cell lines were developed from HeLa cells that contained sense- or antisense-expressing plasmids, and lines that contained antisense-expressing plasmids showed slower growth, reduced ability to form colonies in soft agar, and increased serum requirements. The use of antisense HPV RNA might be a suitable approach to gene therapy of HPV-expressing human cancers.
Extensive In Vivo Angiogenesis Following Controlled Release of Human Vascular Endothelial Cell Growth Factor: Implications for Tissue Engineering and Wound Healing (2001)

Vascular endothelial cell growth factor (VEGF) has strong stimulating effects on vascularization. Though very potent, VEGF is rapidly degraded due to its short half-life and when administrated by uncontrolled and nonspecific methods; however, its systemic administration in large doses can cause harmful side effects. Controlled release technology would allow delivering desired levels of bioactive VEGF within extended periods and permit examination of the in vivo effects of the compound in a broader way. The objective of this study was to determine the in vitro release behavior of VEGF from calcium alginate microspheres and the potency of this controlled release system in promoting localized neovascularization at the subcutaneous site of the rat model. In vitro release of human VEGF165 (2 and 4 microg/cm3 microsphere) was studied for 3 weeks under static conditions at 25 degrees C, and daily hormone release was measured using a competitive enzyme immunoassay. Following an uncontrolled release within the first 4 days, a quite constant zero-order VEGF release of 50 to 90 and 70 to 120 ng/day was achieved from 2 and 4 microg/cm3 polymer loaded microspheres respectively. In vivo angiogenesis was studied for a period of 8 weeks and evaluated using immunoperoidase staining and histopathological measurements. In vivo studies with rats (n = 24) showed a considerable level of capillary network formation at the epigastric groin fascia of VEGF microsphere-implanted rats starting from the first week. The most extensive neovascularization was observed in the group with 3 week postimplanted 4 microg VEGF containing microspheres; this level of vascularization was quite similar after 8 weeks. While the control group showed no evidence of angiogenesis, the difference in VEGF-induced neovascularization is statistically significant (p < 0.03). Immunostaining of the specimens showed a strong relationship between the release of human VEGF and neovascularization. The controlled VEGF release system described here promotes vigorous angiogenesis and has applicability for tissue engineering and wound healing studies.
Rotational allomerism and divergent evolution of domains in immunoglobulin light chains (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRotational allomerism and divergent evolution of domains in immunoglobulin light chainsA. B. Edmundson, K. R. Ely, E. E. Abola, M. Schiffer, and N. PanagiotopoulosCite this: Biochemistry 1975, 14, 18, 3953–3961Publication Date (Print):September 1, 1975Publication History Published online1 May 2002Published inissue 1 September 1975https://pubs.acs.org/doi/10.1021/bi00689a005https://doi.org/10.1021/bi00689a005research-articleACS PublicationsRequest reuse permissionsArticle Views86Altmetric-Citations182LEARN 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