gebhart/patrepeval huggingface dataset:
Overexpression of PrP<sup>C</sup>by Adenovirus-Mediated Gene Targeting Reduces Ischemic Injury in a Stroke Rat Model (2005)

Prion diseases are induced by pathologically misfolded prion protein (PrPSc), which recruit normal sialoglycoprotein PrPC by a template-directed process. In this study, we investigated the expression of PrPC in a rat model of cerebral ischemia to more fully understand its physiological role. Immunohistochemical analysis demonstrated that PrPC-immunoreactive cells increased significantly in the penumbra of ischemic rat brain compared with the untreated brain. Western blot analysis showed that PrPC protein expression increased in ischemic brain tissue in a time-dependent manner. In addition, PrPC protein expression was seen to colocalize with neuron, glial, and vascular endothelial cells in the penumbric region of the ischemic brain. Overexpression of PrPC by injection of rAd (replication-defective recombinant adenoviral)-PGK (phosphoglycerate kinase)-PrPC-Flag into ischemic rat brain improved neurological behavior and reduced the volume of cerebral infarction, which is supportive of a role for PrPC in the neuroprotective adaptive cellular response to ischemic lesions. Concomitant upregulation of PrPC and activated extracellular signal-regulated kinase (ERK1/2) under hypoxia-reoxygenation in primary cortical cultures was shown to be dependent on ERK1/2 phosphorylation. During hypoxia-reoxygenation, mouse neuroblastoma cell line N18 cells transfected with luciferase rat PrPC promoter reporter constructs, containing the heat shock element (HSE), expressed higher luciferase activities (3- to 10-fold) than those cells transfected with constructs not containing HSE. We propose that HSTF-1 (hypoxia-activated transcription factor), phosphorylated by ERK1/2, may in turn interact with HSE in the promoter of PrPC resulting in gene expression of the prion gene. In summary, we conclude that upregulation of PrPC expression after cerebral ischemia and hypoxia exerts a neuroprotective effect on injured neural tissue. This study suggests that PrPC has physiological relevance to cerebral ischemic injury and could be useful as a therapeutic target for the treatment of cerebral ischemia.
A tissue-specific promoter that can drive a foreign gene to express in the suprabasal urothelial cells of transgenic mice. (1995)

Uroplakins are a group of integral membrane proteins that are synthesized as the major differentiation products of urothelium. The luminal portions of these proteins form 12-nm protein particles arranged in a two-dimensional crystalline array. The expression of uroplakin genes is bladder specific and differentiation dependent; little is known, however, about their molecular regulation. Here we describe the cloning of mouse uroplakin II gene and demonstrate, in transgenic mouse experiments, that a 3.6-kb 5'-flanking sequence of this gene can drive a bacterial lacZ (reporter) gene to express in the suprabasal cell layers of the urothelium. The transgene was not expressed in any tested (nonurothelial) epithelial and other tissues (except hypothalamus). These results suggest that most of the cis elements that confer the bladder-specific and differentiation-dependent expression of mouse uroplakin II gene must reside in the 3.6-kb sequence. The availability of a promoter capable of delivering a foreign molecule to the differentiated cell layers of bladder epithelium opens avenues for studying normal and pathological urothelial differentiation in transgenic mice.
DNA condensation by multivalent cations (1997)

In the presence of multivalent cations, high molecular weight DNA undergoes a dramatic condensation to a compact, usually highly ordered toroidal structure. This review begins with an overview of DNA condensation: condensing agents, morphology, kinetics, and reversibility, and the minimum size required to form orderly condensates. It then summarizes the statistical mechanics of the collapse of stiff polymers, which shows why DNA condensation is abrupt and why toroids are favored structures. Various ways to estimate or measure intermolecular forces in DNA condensation are discussed, all of them agreeing that the free energy change per base pair is very small, on the order of 1% of thermal energy. Experimental evidence is surveyed showing that DNA condensation occurs when about 90% of its charge is neutralized by counterions. The various intermolecular forces whose interplay gives rise to DNA condensation are then reviewed. The entropy loss upon collapse of the expanded wormlike coil costs free energy, and stiffness sets limits on tight curvature. However, the dominant contributions seem to come from ions and water. Electrostatic repulsions must be overcome by high salt concentrations or by the correlated fluctuations of territorially bound multivalent cations. Hydration must be adjusted to allow a cooperative accommodation of the water structure surrounding surface groups on the DNA helices as they approach. Undulations of the DNA in its confined surroundings extend the range of the electrostatic forces. The condensing ions may also subtly modify the local structure of the double helix.
Human bronchial epithelial cells transformed by the c-raf-1 and c-myc protooncogenes induce multidifferentiated carcinomas in nude mice: a model for lung carcinogenesis. (1991)

We have previously described the neoplastic transformation of immortalized human bronchial epithelial cells (BEAS-2B) by the combination of the c-raf-1 and c-myc protooncogenes and the concomitant induction of neuron-specific enolase mRNA expression (A. Pfeifer et al., Proc. Natl. Acad. Sci. USA, 86: 10075-10079, 1989). In this paper we describe the morphological, biochemical, and immunohistochemical characteristics of the primary c-raf-1/c-myc tumors, xenografts of these tumors, and tumors that originated from cell lines of the primary neoplasm. The tumors were morphologically characterized by the appearance of desmosomes and tonofilaments, microvilli, and dense core granules representing markers of squamous, glandular, and neuroendocrine differentiation, respectively. A total of 11 of 13 tumors were positive by immunohistochemical techniques for neuron-specific enolase, serotonin (nine of 13), and calcitonin (six of 13). Keratins were expressed in 11 of 13 tumors, and while specific keratins (K5, K7, K16/K17) decreased, there was an increase of vimentin in the tumor cells. Gastrin-releasing peptide immunoreactivity was detectable in a small number of tumors (five of 13). BEAS-2B cells transfected with the c-raf-1 and c-myc protooncogenes and cell lines established from the primary tumors expressed major histocompatibility Class II antigen which has been found on small cell lung carcinoma cells. The tumors induced by the c-raf-1 and c-myc protooncogenes resemble the multidifferentiated phenotype of small cell lung cancer frequently detected in vivo and present a defined model to study the relation between molecular markers, phenotypical appearance, and response to chemotherapeutic agents and radiation.
The clinical significance of soluble E-cadherin in nonsmall cell lung cancer. (2006)

Our data suggest that E-cad plays a role in the pathogenesis of NSCLC. sE-cad levels may be further studied as a potential prognostic biomarker.
Polymer Micelles Stabilization on Demand through Reversible Photo-Cross-Linking (2007)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTPolymer Micelles Stabilization on Demand through Reversible Photo-Cross-LinkingJinqiang Jiang, Bo Qi, Martin Lepage, and Yue ZhaoView Author Information Département de chimie and Département de médecine nucléaire et de radiobiologie and Centre d'imagerie moléculaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada J1K 2R1 Cite this: Macromolecules 2007, 40, 4, 790–792Publication Date (Web):January 17, 2007Publication History Received27 October 2006Revised7 December 2006Published online17 January 2007Published inissue 1 February 2007https://pubs.acs.org/doi/10.1021/ma062493jhttps://doi.org/10.1021/ma062493jrapid-communicationACS PublicationsCopyright © 2007 American Chemical SocietyRequest reuse permissionsArticle Views6230Altmetric-Citations319LEARN 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 SUBJECTS:Aromatic compounds,Micelles,Nucleic acid structure,Polymers,Solution chemistry Get e-Alerts
Bioinformatics for protein biomarker panel classification: what is needed to bring biomarker panels into<i>in vitro</i>diagnostics? (2009)

A large number of biomarkers have been discovered over the past few years using proteomics techniques. Unfortunately, most of them are neither specific nor sensitive enough to be translated into in vitro diagnostics and routine clinical practice. From this observation, the idea of combining several markers into panels to improve clinical performances has emerged. In this article, we present a discussion of the bioinformatics aspects of biomarker panels and the concomitant challenges, including high dimensionality and low patient number and reproducibility.
Nerve Regeneration Through a Pseudosynovial Sheath in a Primate Model (1985)

This study investigated nerve regeneration through a pseudosynovial sheath in a primate. After resecting a 3-cm segment of the ulnar nerve at the elbow, the two ends of the divided nerve were placed at either end of the pseudosynovial tube, positioning the nerve ends such that they were separated by a 3-cm gap. Histologic evaluation at 3, 5, 7, and 9 months demonstrated evidence of nerve regeneration across this gap. Nerve fiber diameter and density assessment demonstrated a maturation of the fiber pattern with time. The overall morphologic pattern of the regenerating nerve within the pseudosheath was that of multiple small fascicles, each within its own perineurial compartment. This pattern resembled neither the proximal nor distal nerve fascicular pattern.
Charge sensitivity of radio frequency single-electron transistor (1999)

A theoretical analysis of the charge sensitivity of the radio frequency single-electron transistor (rf-SET) is presented. We use the “orthodox” approach and consider the case when the carrier frequency is much less than I/e where I is the typical current through rf-SET. The optimized noise-limited sensitivity is determined by the temperature T, and at low T it is only 1.4 times worse than the sensitivity of conventional single-electron transistor.
Random Mutagenesis by Using Mixtures of dNTP and dITP in PCR (2003)

Generating random mutations in a DNA fragment of a specific size is often the method of choice for changing specific properties of an encoded protein or for studying the functional properties of a specific DNA fragment. In all these cases it is helpful and in some cases essential to have a screening method available that allows for distinction between phenotypic changes brought about by one or more random mutations in the DNA fragment of interest.
Safety of aerosol tobramycin administration for 3 months to patients with cystic fibrosis (1989)

To determine the potential toxicity of prolonged aerosol tobramycin administration, 22 patients with cystic fibrosis were monitored while receiving inhaled tobramycin three times a day for 12 weeks. Prior to, four times during administration and approximately 6 weeks after discontinuation of treatment, we assessed pulmonary function, weight, height, body temperature, eighth cranial nerve function, serum creatinine, blood urea nitrogen, urinary creatinine clearance, plasma iothalamate clearance, urinary beta-2 microglobulin concentration, and Pseudomonas aeruginosa density in sputum. There was no detectable laboratory evidence of nephrotoxicity. Neither a decrease in auditory acuity (range 250-20,000 Hz) nor vestibular dysfunction was detected. Pulmonary function tests significantly improved during the first month in all subjects (P less than 0.05) but returned to enrollment values by the end of the 12th week of administration of tobramycin aerosol. Sputum P. aeruginosa density initially decreased from a mean of 10(7) cfu/gm to a mean of 10(4) cfu/gm after 2 weeks of aerosol tobramycin administration and remained significantly below the enrollment value throughout. Coincident with the reduced bacterial density, a reduction in cough frequency and sputum production, as well as a weight gain was observed. Seventy-three percent of the patients with sputum P. aeruginosa isolates susceptible to tobramycin on enrollment yielded resistant organisms during aerosol administration. However, 1 year later all sputum P. aeruginosa isolates obtained from patients were susceptible to tobramycin. We conclude that thrice daily aerosol tobramycin administration for 3 months is not associated with detectable eighth cranial nerve or renal toxicity. Transient emergence of tobramycin resistant P. aeruginosa may occur.
Sensitive Dual Color In Vivo Bioluminescence Imaging Using a New Red Codon Optimized Firefly Luciferase and a Green Click Beetle Luciferase (2011)

We report here the re-engineering of different luciferase genes for in vitro and in vivo dual color imaging applications to address the technical issues of using dual luciferases for imaging. In respect to previously used dual assays, our study demonstrated enhanced sensitivity combined with spatially separate BL spectral emissions using a suitable spectral unmixing algorithm. This new D-luciferin-dependent reporter gene couplet opens up the possibility in the future for more accurate quantitative gene expression studies in vivo by simultaneously monitoring two events in real time.
A novel method for tracking and counting pedestrians in real-time using a single camera (2001)

This paper presents a real-time system for pedestrian tracking in sequences of grayscale images acquired by a stationary camera. The objective is to integrate this system with a traffic control application such as a pedestrian control scheme at intersections. The proposed approach can also be used to detect and track humans in front of vehicles. Furthermore, the proposed schemes can be employed for the detection of several diverse traffic objects of interest (vehicles, bicycles, etc.) The system outputs the spatio-temporal coordinates of each pedestrian during the period the pedestrian is in the scene. Processing is done at three levels: raw images, blobs, and pedestrians. Blob tracking is modeled as a graph optimization problem. Pedestrians are modeled as rectangular patches with a certain dynamic behavior. Kalman filtering is used to estimate pedestrian parameters. The system was implemented on a Datacube MaxVideo 20 equipped with a Datacube Max860 and was able to achieve a peak performance of over 30 frames per second. Experimental results based on indoor and outdoor scenes demonstrated the system s robustness under many difficult situations such as partial or full occlusions of pedestrians.
The histogenesis and biologic behavior of primary human malignant melanomas of the skin. (1969)

Summary This paper describes the histogenesis of 3 forms of human malignant melanoma: superficial spreading melanoma, nodular melanoma, and lentigo maligna melanoma. A comparative analysis by computer of the biologic behavior and clinical characteristics of the different neoplasms has been done. An additional 60 tumors have been studied by serial block sectioning. Evidence is presented suggesting that superficial spreading melanoma and lentigo maligna melanoma (Hutchinson9s melanotic freckle), though evolving at different rates, show a long period of superficial growth, followed by the relatively rapid appearance of nodules or deeper invasion within the primary lesion. This change in the nature of the primary lesion may be due to the appearance of one or more strains of cells of aggressive biologic potential. Thus the primary melanoma may exist for a relatively long period of time during which host selectional forces act to permit the growth of quite malignant strains of cells. It is these cells that seem to be capable of deeper growth. The subdivision of each of the forms of melanoma into 5 anatomic levels of invasion permits the accurate assignment of prognosis to each case. It is suggested that melanomas are tumors of the epidermal melanocytes and are not necessarily derived from melanocytic nevi. Each melanoma has a distinctive clinical appearance, even in its superficial and curable phases, and this appearance is the same whether or not the process arose in association with a melanocytic nevus.
A Bayesian Approach for Selective Image-Based Rendering using Superpixels (2015)

International audience
Tat-modified Leptin is more Accessible to Hypothalamus through Brain-blood Barrier with a Significant Inhibition of Body-weight Gain in High-fat-diet Fed Mice (2009)

Obesity in human was found mainly due to the poor transportation of leptin through brain-blood barrier (BBB), called as leptin resistance. To produce a leptin capable of penetrating BBB, we have added Tat-PTD(9) to the C terminal of leptin to construct a fusion protein. The fusion Tat-leptin and native leptin genes were synthesized by single-step insertion of a polymerase chain reaction and expressed in Escherichia coli BL21 (Rosseta). The expressing products were purified and renatured by Ni-NTA affinity chromatography, and identified by the molecular size in SDS-PAGE gel and by its immunoreactivity to specific antibody with Western-blotting assay. To bio-functionally evaluate the fusion protein, Balb/c mice fed with high-fat diet (HFD) were given Tat-leptin, leptin or saline for 19 days. The immunohistochemical staining showed the increases in positive stains for the leptin in the region of hypothalamus of the HFD mice with either Tat-leptin or leptin as compared to saline group, but the staining intensity and frequency in the group with Tat-leptin were stronger and higher than those in the group with leptin. Furthermore, the most efficiency in preventing the body-weight gain caused by HFD was found in Tat-leptin group among these three groups. These results suggest that Tat-modified leptin may become a great potential candidate for the prevention or therapy of obese patients.
Intimin-Specific Immune Responses Prevent Bacterial Colonization by the Attaching-Effacing Pathogen<i>Citrobacter rodentium</i> (2001)

The formation of attaching and effacing (A/E) lesions on gut enterocytes is central to the pathogenesis of enterohemorrhagic (EHEC) Escherichia coli, enteropathogenic E. coli (EPEC), and the rodent pathogen Citrobacter rodentium. Genes encoding A/E lesion formation map to a chromosomal pathogenicity island termed the locus of enterocyte effacement (LEE). Here we show that the LEE-encoded proteins EspA, EspB, Tir, and intimin are the targets of long-lived humoral immune responses in C. rodentium-infected mice. Mice infected with C. rodentium developed robust acquired immunity and were resistant to reinfection with wild-type C. rodentium or a C. rodentium derivative, DBS255(pCVD438), which expressed intimin derived from EPEC strain E2348/69. The receptor-binding domain of intimin polypeptides is located within the carboxy-terminal 280 amino acids (Int280). Mucosal and systemic vaccination regimens using enterotoxin-based adjuvants were employed to elicit immune responses to recombinant Int280alpha from EPEC strain E2348/69. Mice vaccinated subcutaneously with Int280alpha, in the absence of adjuvant, were significantly more resistant to oral challenge with DBS255(pCVD438) but not with wild-type C. rodentium. This type-specific immunity could not be overcome by employing an exposed, highly conserved domain of intimin (Int388-667) as a vaccine. These results show that anti-intimin immune responses can modulate the outcome of a C. rodentium infection and support the use of intimin as a component of a type-specific EPEC or EHEC vaccine.
Correlation of Segmental Carpal Tunnel Pressures with Changes in Hand and Wrist Positions in Patients with Carpal Tunnel Syndrome and Controls (1998)

We investigated pressures at 1 cm intervals along the carpal tunnel in 39 patients with carpal tunnel syndrome (CTS) and 12 controls. Pressures were measured for relaxed and gripping hand positions in combination with neutral, extended, and flexed wrist positions. Patient pressures exceeded control pressures, were below the previously reported 30 mmHg threshold for four of five locations in the relaxed neutral position and were typically greater in extension than in flexion. In the neutral position, both patient and control pressures were slightly above threshold levels just distal to the tunnel. Maximum intratunnel pressures were generally found in the central part of the tunnel and minimum pressures in the distal tunnel. Gripping hand pressures in the tunnel were lowest with the wrist flexed. In both controls and CTS patients, only in the neutral wrist and relaxed hand positions were pressures highest at the point where nerve conduction studies have indicated the nerve is most likely to be compromised (in the midpalm just distal to the distal margin of the carpal tunnel).
Middle East Respiratory Syndrome Coronavirus Spike Protein Delivered by Modified Vaccinia Virus Ankara Efficiently Induces Virus-Neutralizing Antibodies (2013)

Middle East respiratory syndrome coronavirus (MERS-CoV) has recently emerged as a causative agent of severe respiratory disease in humans. Here, we constructed recombinant modified vaccinia virus Ankara (MVA) expressing full-length MERS-CoV spike (S) protein (MVA-MERS-S). The genetic stability and growth characteristics of MVA-MERS-S make it a suitable candidate vaccine for clinical testing. Vaccinated mice produced high levels of serum antibodies neutralizing MERS-CoV. Thus, MVA-MERS-S may serve for further development of an emergency vaccine against MERS-CoV.