gebhart/patrepeval huggingface dataset:
Apoptotic photoreceptor cell death in mouse models of retinitis pigmentosa. (1994)

Retinitis pigmentosa (RP) is a group of inherited human diseases in which photoreceptor degeneration leads to visual loss and eventually to blindness. Although mutations in the rhodopsin, peripherin, and cGMP phosphodiesterase genes have been identified in some forms of RP, it remains to be determined whether these mutations lead to photoreceptor cell death through necrotic or apoptotic mechanisms. In this paper, we report a test of the hypothesis that photoreceptor cell death occurs by an apoptotic mechanism in three mouse models of RP: retinal degeneration slow (rds) caused by a peripherin mutation, retinal degeneration (rd) caused by a defect in cGMP phosphodiesterase, and transgenic mice carrying a rhodopsin Q344ter mutation responsible for autosomal dominant RP. Two complementary techniques were used to detect apoptosis-specific internucleosomal DNA fragmentation: agarose gel electrophoresis and in situ labeling of apoptotic cells by terminal dUTP nick end labeling. Both methods showed extensive apoptosis of photoreceptors in all three mouse models of retinal degeneration. We also show that apoptotic death occurs in the retina during normal development, suggesting that different mechanisms can cause photoreceptor death by activating an intrinsic death program in these cells. These findings raise the possibility that retinal degenerations may be slowed by interfering with the apoptotic mechanism itself.
Proton Sponge Trick for pH-Sensitive Disassembly of Polyethylenimine-Based siRNA Delivery Systems (2010)

Small interfering RNAs offer novel opportunities to inhibit gene expression in a highly selective and efficient manner but depend on cytosolic translocation with synthetic delivery systems. The polyethylenimine (PEI) is widely used for plasmid DNA transfection. However, the water-soluble PEI does not form siRNA polyplexes stable enough in extracellular media for effective delivery. We previously showed that rendering PEI insoluble in physiological media, without modifying drastically its overall cationic charge density, by simple conjugation with natural hydrophobic alpha-amino acids, can lead to effective siRNA delivery in mammalian cells. In here, we comprehensively investigated the mechanism behind the excellent efficacy of the leading PEIY vector. Our data revealed that the underlining proton sponge property is key to the effectiveness of the tyrosine-polyethylenimine conjugate as it may allow both endosomal rupture and siRNA liberation via an optimal pH-sensitive dissolution of the PEIY self-aggregates. Altogether, these results should facilitate the development of novel and more sophisticated siRNA delivery systems.
Bandwidth selection for kernel distribution function estimation (1995)

Leave-one-out cross-validation is a popular and readily implemented heuristic for bandwidth selection in nonparametric smoothing problems. In this note we elucidate the role of leave-one-out selection criteria by discussing a criterion introduced by Sarda (J. Statist. Plann. Inference 35 (1993) 65–75) for bandwidth selection for kernel distribution function estimators (KDFEs). We show that for this problem, use of the leave-one-out KDFE in the selection procedure is asymptotically equivalent to leaving none out. This contrasts with kernel density estimation, where use of the leave-one-out density estimator in the selection procedure is critical. Unfortunately, simulations show that neither method works in practice, even for samples of size as large as 1000. In fact, we show that for any fixed bandwidth, the expected value of the derivative of the leave-none-out criterion is asymptotically positive. This result and our simulations suggest that the criteria are increasing and that for sufficiently large samples (e.g., n = 100), the smallest available bandwidth will always be selected, thus contradicting the optimality result of Sarda for this estimator. As an alternative to minimizing a selection criterion, we propose a plug-in estimator of the asymptotically optimal bandwidth. Simulations suggest that the plug-in is a good estimator of the asymptotically optimal bandwidth even for samples as small as 10 observations and is not too far from the finite sample bandwidth.
AAA+ superfamily ATPases: common structure–diverse function (2001)

The AAA+ superfamily of ATPases, which contain a homologous ATPase module, are found in all kingdoms of living organisms where they participate in diverse cellular processes including membrane fusion, proteolysis and DNA replication. Recent structural studies have revealed that they usually form ring-shaped oligomers, which are crucial for their ATPase activities and mechanisms of action. These ring-shaped oligomeric complexes are versatile in their mode of action, which collectively seem to involve some form of disruption of molecular or macromolecular structure; unfolding of proteins, disassembly of protein complexes, unwinding of DNA, or alteration of the state of DNA-protein complexes. Thus, the AAA+ proteins represent a novel type of molecular chaperone. Comparative analyses have also revealed significant similarities and differences in structure and molecular mechanism between AAA+ ATPases and other ring-shaped ATPases.
Mutation in TET2 in Myeloid Cancers (2009)

Somatic mutations in TET2 occur in about 15% of patients with various myeloid cancers.
Influence of cross‐linker chemistry on release kinetics of PEG‐co‐PGA hydrogels (2008)

An investigation of encapsulated plasmid DNA release from degradable poly(ethylene glycol)-co-poly(glycolic acid) hydrogels (PEG-co-PGA) is presented. We determined by varying the chemistry of the cross-linker group, significant variations in hydrogel degradation kinetics could be achieved to control the release profiles of plasmid DNA. We prepared three analogues of PEG-co-PGA hydrogels by a photopolymerization process and measured variation in degradation rates by monitoring mechanical properties and release of plasmid DNA. 1H 1D DOSY NMR (one-dimensional diffusion ordered nuclear magnetic resonance spectroscopy) was used to measure conversion of vinyl groups after photocross-linking. Nearly full vinyl conversion was reached after 10 min exposure under ultraviolet light. Gel electrophoresis analysis confirmed that plasmid DNA remained structurally intact after photoencapsulation and release from the gels. This approach provides an additional strategy for controlling the release of biologically active compounds from hydrogels.
Identifying Key Properties of Electrolytes for Light-Emitting Electrochemical Cells (2014)

The electrolyte is a key component in light-emitting electrochemical cells (LECs), as it facilitates in situ electrochemical doping and associated attractive device features. LiCF3SO3 dissolved in hydroxyl-capped trimethylolpropane ethoxylate (TMPE-OH) constitutes an electrolyte with which we have attained high stability and efficiency for polymer LECs, but the turn-on time of such devices is unfortunately slow. By replacing hydroxyl with methoxy as the TMPE end-group, we produced LECs with a desired combination of high efficiency, good stability, and fast turn-on time. Specifically, we showed that the turn-on time to high luminance (300 cd/m2) at a current density of 7.7 mA/cm2 is lowered from 1740 to 16 s, that the efficiency is improved by ∼20%, and that the other device properties are either maintained or improved. In a parallel modeling and experimental effort, we demonstrated that the faster kinetics following the shift in the TMPE end-group is attributed to a marked decrease in the level of both inter- and intramolecular interactions of the electrolyte, as manifested in a lowered electrolyte viscosity, faster ion transport, and more facile ion release during doping.
Expression of c-erbB receptors, heregulin and oestrogen receptor in human breast cell lines (2000)

Members of the c-erbB family have been implicated in poor prognosis in breast cancer. Given the propensity for heterodimerisation within the erbB family, the pattern of co-expression of these receptors is likely to be as functionally important as aberrant expression of any given receptor alone. Therefore, the patterns of expression of the receptors, epidermal growth factor receptor (EGF-R), c-erbB-2, c-erbB-3, c-erbB-4, and one of the erbB ligands, heregulin (HRG), were examined in normal and malignant breast cell lines and compared with expression of oestrogen receptor (ER), a classical indicator of good prognosis. There was an inverse correlation between ER and EGF-R mRNA levels, as previously described, but no correlation between either of these receptors and c-erbB-2. c-erbB-3 expression was positively correlated with ER. In contrast, HRG expression was inversely related to ER. Expression of antisense-ER resulted in increased EGF-R mRNA, demonstrating a functional link between the expression of these 2 genes, however, there was no significant change in c-erbB-2 or c-erbB-3 mRNA, suggesting that ER is not directly involved in control of expression of these genes. A comparison of individual erbB receptors and HRG revealed that the majority of lines expressing increased levels of c-erbB-2 also expressed elevated levels of c-erbB-3 mRNA, and none of the cell lines that expressed both c-erbB-2 and either c-erbB-3 or c-erbB-4 expressed the ligand HRG. In summary, the levels of expression of c-erbB-1, -2, -3, and -4 varied in this series of breast cell lines, and the pattern of expression and the relationship of each growth factor receptor to the expression of ER was quite distinct. The lack of expression of HRG in cell lines that express receptors may be indicative of paracrine interactions between erbB ligands and their cognate receptors and may suggest that the ligand and receptors are expressed in different subtypes of breast epithelial cells from which the cell lines are derived.
Specific chromosomal abnormalities in acute nonlymphocytic leukemia correlate with drug susceptibility in vivo. (1988)

Specific chromosomal abnormalities are independent predictors of response to therapy in acute nonlymphocytic leukemia (ANLL) de novo. In a series of 149 patients with ANLL, we sought to determine whether the t(8;21), t(15;17), t(9;11) or other abnormalities of the long arm of chromosome 11, inv(16) or t(16;16), inv(3) or t(3;3), trisomy 8, and abnormalities of chromosome 5 (-5/5q-) or of chromosome 7 (-7/7q-) identify differences in susceptibility to chemotherapy drugs in vivo. The immediate outcome of the first cycle of remission induction chemotherapy was analyzed for patients in each cytogenetic subgroup as an index of the drug susceptibility of the leukemia cells in vivo. Patients with t(8;21), inv(16), t(16;16), or 11q abnormalities had high rates of complete remission after initial therapy (60-100%), whereas patients with -7/7q- or -5/5q- had low initial response rates (0-36%), suggestive of drug resistance in vivo. In general, cytogenetic groups with high initial complete remission rates ("drug sensitive") also had long disease-free survivals; those groups with low initial remission rates ("drug resistant") had short remission durations even if these patients eventually achieved complete remission with further therapy. Patients with acute promyelocytic leukemia (APL), all of whom had the t(15;17), were the exception; despite low initial remission rates, they had long disease-free survivals, possibly due to a more rapid cytotoxic effect of chemotherapy on the clonogenic APL cells than on the more numerous malignant promyelocytes. We conclude that the prognostic importance of specific chromosomal abnormalities in ANLL resides in part in differing susceptibilities to chemotherapy.
A large-scale in vivo analysis reveals that TALENs are significantly more mutagenic than ZFNs generated using context-dependent assembly (2013)

Zinc-finger nucleases (ZFNs) and TAL effector nucleases (TALENs) have been shown to induce targeted mutations, but they have not been extensively tested in any animal model. Here, we describe a large-scale comparison of ZFN and TALEN mutagenicity in zebrafish. Using deep sequencing, we found that TALENs are significantly more likely to be mutagenic and induce an average of 10-fold more mutations than ZFNs. We observed a strong correlation between somatic and germ-line mutagenicity, and identified germ line mutations using ZFNs whose somatic mutations rates are well below the commonly used threshold of 1%. Guidelines that have previously been proposed to predict optimal ZFN and TALEN target sites did not predict mutagenicity in vivo. However, we observed a significant negative correlation between TALEN mutagenicity and the number of CpG repeats in TALEN target sites, suggesting that target site methylation may explain the poor mutagenicity of some TALENs in vivo. The higher mutation rates and ability to target essentially any sequence make TALENs the superior technology for targeted mutagenesis in zebrafish, and likely other animal models.
A role for cadherins in cellular signaling and differentiation (1998)

Cadherins form a family of cell-cell adhesion proteins that are critical to normal embryonic development. Expression of the various family members is regulated in a complex pattern during embryogenesis. Both reduced and inappropriate expression of cadherins have been associated with abnormal tissue formation in embryos and tumorigenesis in mature organisms. Evidence is accumulating that signals unique to individual members of the cadherin family, as well as signals common to multiple cadherins, contribute to the differentiated phenotype of various cell types. While a complete understanding of the regulation of cadherin expression of the molecular nature of intracellular signaling downstream of cadherin adhesion is essential to an understanding of embryogenesis and tumorigenesis, our knowledge in both areas is inadequate. Clearly, elucidating the factors and conditions that regulate cadherin expression and defining the signaling pathways activated by cadherins are frontiers for future research. J. Cell. Biochem. Suppls. 30/31:168-176, 1998. © 1998 Wiley-Liss, Inc.
Coalbed Methane Potential of the Appalachians (1982)

ABSTRACT Coal mines in the Appalachian Basin emit approximately 180 million cubic feet (MMcf) of high-quality methane into the atmosphere daily. The existence of mines in West Virginia, southwest Virginia, eastern Kentucky, Ohio, Pennsylvania, Tennessee, and Alabama with high gas emissions of over 100 thousand cubic feet per day (Mcf/d) suggests that further investigation into the economic development of this unconventional energy source is warranted. Appalachian coals occur as multiple beds, individually up to 14 feet thick (Pittsburgh coalbed in Pennsylvania and West Virginia). The gas content of these bituminous coal seams has been measured at 93 cubic feet per ton (cu ft/t) from a depth of 149 feet (Waynesburg coalbed, Pennsylvania) to over 560 cu ft/t at 1,764 feet (Pocahontas No. 3 coalbed in West Virginia); in the anthracite region, 690 cu ft/t have been measured where the overburden is 685 feet thick (Peach Mountain coalbed). Detailed studies in the southern Warrior Basin indicate the presence of up to 20 trillion cubic feet (Tcf) of gas, and preliminary work in the Central and Northern Appalachian Basins suggests a resource of 50 and 80 Tcf, respectively. Many coal operators are realizing the production potential of coalbed methane. In Buchanan County, Virginia, the Island Creek Coal Company produced up to 434 Mcf/d from 12 horizontal boreholes drilled into the mine face. Waynesburg College in Pennsylvania will realize a savings of $25,000 toward their annual energy bill from a 1,450-foot vertical well drilled on campus. In Alabama, U.S. Steel's mines just began commercial production, and sold 25 Mmcf to a gas pipeline company in December 1981; and Jim Walters Resources has begun an ambitious program to drill up to 700 wells with a predicted total production of 60 billion cubic feet (Bcf). These examples of the successful exploitation of a resource formerly considered only a hazard to coal mining indicate a promising future for coalbed methane.
A Modified Thermal Treatment Method for the Up-Scalable Synthesis of Size-Controlled Nanocrystalline Titania (2016)

Considering the increasing demand for titania nanoparticles with controlled quality for various applications, the present work reports the up-scalable synthesis of size-controlled titanium dioxide nanocrystals with a simple and convenient thermal treatment route. Titanium dioxide nanocrystals with tetragonal structure were synthesized directly from an aqueous solution containing titanium (IV) isopropoxide as the main reactant, polyvinyl pyrrolidone (PVP) as the capping agent, and deionized water as a solvent. With the elimination of the drying process in a thermal treatment method, an attempt was made to decrease the synthesis time. The mixture directly underwent calcination to form titanium dioxide (TiO2) nanocrystalline powder, which was confirmed by FT-IR, energy dispersive X-ray spectroscopy (EDX), and X-ray diffraction (XRD) analysis. The control over the size and optical properties of nanocrystals was achieved via variation in calcination temperatures. The obtained average sizes from XRD spectra and transmission electron microscopy (TEM) images showed exponential variation with increasing calcination temperature. The optical properties showed a decrease in the band gap energy with increasing calcination temperature due to the enlargement of the nanoparticle size. These results prove that direct calcination of reactant solution is a convenient thermal treatment route for the potential large-scale production of size-controlled Titania nanoparticles.
iDNA-Prot: Identification of DNA Binding Proteins Using Random Forest with Grey Model (2011)

DNA-binding proteins play crucial roles in various cellular processes. Developing high throughput tools for rapidly and effectively identifying DNA-binding proteins is one of the major challenges in the field of genome annotation. Although many efforts have been made in this regard, further effort is needed to enhance the prediction power. By incorporating the features into the general form of pseudo amino acid composition that were extracted from protein sequences via the "grey model" and by adopting the random forest operation engine, we proposed a new predictor, called iDNA-Prot, for identifying uncharacterized proteins as DNA-binding proteins or non-DNA binding proteins based on their amino acid sequences information alone. The overall success rate by iDNA-Prot was 83.96% that was obtained via jackknife tests on a newly constructed stringent benchmark dataset in which none of the proteins included has ≥25% pairwise sequence identity to any other in a same subset. In addition to achieving high success rate, the computational time for iDNA-Prot is remarkably shorter in comparison with the relevant existing predictors. Hence it is anticipated that iDNA-Prot may become a useful high throughput tool for large-scale analysis of DNA-binding proteins. As a user-friendly web-server, iDNA-Prot is freely accessible to the public at the web-site on http://icpr.jci.edu.cn/bioinfo/iDNA-Prot or http://www.jci-bioinfo.cn/iDNA-Prot. Moreover, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results.
Pathogen analysis and genetic predisposition testing using microelectronic arrays and isothermal amplification. (2000)

We demonstrated two model clinical assays combining amplified materials and microelectronic arrays, one potentially suitable for pathogen screening and the other for a deleterious genetic mutation.
3-Aza-A-homoandrostenes (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT3-Aza-A-homoandrostenesArvin P. Shroff and C. H. HarperCite this: J. Med. Chem. 1969, 12, 1, 190–191Publication Date (Print):January 1, 1969Publication History Published online1 May 2002Published inissue 1 January 1969https://pubs.acs.org/doi/10.1021/jm00301a059https://doi.org/10.1021/jm00301a059research-articleACS PublicationsRequest reuse permissionsArticle Views26Altmetric-Citations7LEARN 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
Bile acid transporters in health and disease (2008)

In recent years the discovery of a number of major transporter proteins expressed in the liver and intestine specifically involved in bile acid transport has led to improved understanding of bile acid homeostasis and the enterohepatic circulation. Sodium (Na(+))-dependent bile acid uptake from portal blood into the liver is mediated primarily by the Na(+) taurocholate co-transporting polypeptide (NTCP), while secretion across the canalicular membrane into the bile is carried out by the bile salt export pump (BSEP). In the ileum, absorption of bile acids from the lumen into epithelial cells is mediated by the apical Na(+) bile salt transporter (ASBT), whereas exit into portal blood across the basolateral membrane is mediated by the organic solute transporter alpha/beta (OSTalpha/beta) heterodimer. Regulation of transporter gene expression and function occurs at several different levels: in the nucleus, members of the nuclear receptor superfamily, regulated by bile acids and other ligands are primarily involved in controlling gene expression, while cell signalling events directly affect transporter function, and subcellular localization. Polymorphisms, dysfunction, and impaired adaptive responses of several of the bile acid transporters, e.g. BSEP and ASBT, results in liver and intestinal disease. Bile acid transporters are now understood to play central roles in driving bile flow, as well as adaptation to various pathological conditions, with complex regulation of activity and function in the nucleus, cytoplasm, and membrane.
Wetting Mode Evolution of Steam Dropwise Condensation on Superhydrophobic Surface in the Presence of Noncondensable Gas (2011)

It is well known that heat transfer in dropwise condensation (DWC) is superior to that in filmwise condensation (FWC) by at least one order of magnitude. Surfaces with larger contact angle (CA) can promote DWC heat transfer due to the formation of “bare” condensation surface caused by the rapid removal of large condensate droplets and high surface replenishment frequency. Superhydrophobic surfaces with high contact angle (&gt; 150°) of water and low contact angle hysteresis (&lt; 5°) seem to be an ideal condensing surface to promote DWC and enhance heat transfer, in particular, for the steam-air mixture vapor. In the present paper, steam DWC heat transfer characteristics in the presence of noncondensable gas (NCG) were investigated experimentally on superhydrophobic and hydrophobic surfaces including the wetting mode evolution on the roughness-induced superhydrophobic surface. It was found that with increasing NCG concentration, the droplet conducts a transition from the Wenzel to Cassie-Baxter mode. And a new condensate wetting mode—a condensate sinkage mode—was observed, which can help to explain the effect of NCG on the condensation heat transfer performance of steam-air mixture on a roughness-induced superhydrophobic SAM-1 surface.