gebhart/patrepeval huggingface dataset:
In Vitro/Ex Vivo Fluorescence Assays of CFTR Chloride Channel Function (2005)

Assays utilizing chloride-sensitive fluorescent indicators have been applied to study chloride transport by CFTR in native and transfected cell culture models, in ex vivo tissues in human gene therapy trials, and in high-throughput screening applications for discovery of CFTR inhibitors and activators. Our laboratory has developed a series of small molecule and genetically encoded chloride/halide-sensing fluorescent indicators to measure cellular chloride transport. Small molecule indicators, such as SPQ, MQAE and LZQ, require loading of cell cytoplasm and washing of excess extracellular dye.The genetically encoded indicators are expressed transiently or stably in cell cultures or in vivo by transfection, infection or gene targeting procedures. The general experimental strategy to assay CFTR-mediated chloride transport is to follow cell/tissue fluorescence continuously in response to solution exchanges that create chloride ionic gradients, and/or add CFTR activators or inhibitors. Fluorescence is followed by cuvette fluorimetry, microscopy/imaging or plate reader methods. The optimal choice of indicator, solution exchange protocol, and measurement method depends on the system, level of CFTR function, and questions to be addressed. Although fluorescent chloride sensors cannot provide information about single channel electrical properties, they have been very useful in quantifying CFTR function in analysis of CFTR mutations, protein-protein interactions, gene transfer, and high-throughput screening.
Bile Acids and Metabolic Regulation (2009)

Bile acids have long been known to facilitate digestion and absorption of lipids in the small intestine as well as regulate cholesterol homeostasis (1,2). Over the last decade, however, it has become clear that bile acids are not simply digestive detergents and the primary route governing cholesterol catabolism. Bile acids are now recognized as hormones involved in the regulation of various metabolic processes (3). Through activation of various signaling pathways, bile acids regulate not only their own synthesis and enterohepatic circulation, but also triglyceride, cholesterol, glucose, and energy homeostasis (2).

Manipulation of bile acid enterohepatic circulation by bile acid sequestration with nonsystemically absorbed resins can modulate the processes regulated by bile acids. Whereas bile acid sequestrants (BASs) have been used for over 40 years in the treatment of dyslipidemia (1), more recent data have emerged that have expanded their role in the treatment of dysglycemia in type 2 diabetes (4–9). The initial data suggesting such an effect were derived from post hoc analysis of a clinical trial for dyslipidemia that determined that BASs lowered glucose, particularly when compared with other lipid-lowering drugs (4). This concept was subsequently proven in several studies showing that BASs, such as colesevelam, lower glucose (5–8).

This review examines recent data exploring possible mechanisms involved in regulation of glucose metabolism by bile acids and the potential impact of disruption of their enterohepatic circulation on diabetes. We will also summarize the available clinical trial data that supported the regulatory approval of colesevelam for the treatment of hyperglycemia in type 2 diabetes.

Bile acids are potent “digestive surfactants” that promote absorption of lipids (including fat-soluble vitamins), acting as emulsifiers (1,2).

Bile acids represent the primary pathway for cholesterol catabolism and account for ∼50% of the daily turnover …
Replacement of potassium chloride by potassium glutamate dramatically enhances protein-DNA interactions in vitro (1987)

Although protein-nucleic acid interactions exhibit dramatic dependences on both ion concentration and type in vitro, large variations in intracellular ion concentrations can occur in Escherichia coli and other organisms without apparent effects on gene expression in vivo. E. coli accumulates K+ and glutamate as cytoplasmic osmolytes. The cytoplasmic K+ concentration in E. coli varies from less than 0.2 to greater than 0.9 m as a function of external osmolarity; corresponding cytoplasmic glutamate concentrations range from less than 0.03 to greater than 0.25 m. Only low levels of chloride occur in the cytoplasm of E. coli at all osmotic conditions. Since most in vitro studies have been performed in chloride salts, whereas glutamate is the more relevant physiological anion, we have measured the effects of the substitution of potassium glutamate (KGlu) for KCl on the kinetics and equilibria of a variety of site-specific protein-DNA interactions in vitro. Both the interaction of E. coli RNA polymerase with two phage lambda promoters and the interactions of various restriction enzymes with their DNA cleavage sites are enhanced by this substitution. Using the abortive initiation assay, we find a greater than 30-fold increase in the second-order rate constant for open complex formation at the lambda PR promoter and a 10-fold increase at the lambda PR' promoter, when KGlu is substituted for KCl. Replacement of KCl by KGlu does not affect the strong salt dependences of these interactions; increasing either KCl or KGlu concentrations decreases both reaction rates and extents. Substitution of glutamate for chloride does, however, shift the range of salt concentrations over which these interactions are observable to higher K+ concentrations.(ABSTRACT TRUNCATED AT 250 WORDS)
Early events and transient chemistry in the photohomolysis of alkylcobalamins (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEarly events and transient chemistry in the photohomolysis of alkylcobalaminsJohn F. Endicott and T. L. NetzelCite this: J. Am. Chem. Soc. 1979, 101, 14, 4000–4002Publication Date (Print):July 1, 1979Publication History Published online1 May 2002Published inissue 1 July 1979https://pubs.acs.org/doi/10.1021/ja00508a066https://doi.org/10.1021/ja00508a066research-articleACS PublicationsRequest reuse permissionsArticle Views180Altmetric-Citations106LEARN 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
Structure-guided Protein Engineering Modulates Helix Bundle Exchangeable Apolipoprotein Properties (2003)

Apolipoprotein (apo) E plays a major role in lipid metabolism by mediating cellular uptake of lipoprotein particles through interaction with members of the low density lipoprotein (LDL) receptor family. The primary region of apoE responsible for receptor binding has been limited to a cluster of basic amino acids between residues 134 and 150, located in the fourth helix of the N-terminal domain globular helix bundle structure. To investigate structural and functional requirements of this "receptor binding region" we engineered an apolipoprotein chimera wherein residues 131-151 of human apoE were substituted for residues 146-166 (helix 5) of Manduca sexta apolipophorin III (apoLp-III). Recombinant hybrid apolipoprotein was expressed in Escherichia coli, isolated, and characterized. Hybrid apolipoprotein and apoE3-N-terminal, but not apoLp-III, bound to heparin-Sepharose. Far UV circular dichroism spectroscopy revealed the presence of predominantly alpha-helix secondary structure, and stability studies revealed a urea denaturation midpoint of 1.05 m, similar to wild-type apoLp-III. Hybrid apolipoprotein-induced dimyristoylphosphatidylcholine (DMPC) bilayer vesicle solubilization activity was significantly enhanced compared with either parent protein, consistent with detection of solvent-exposed hydrophobic regions on the protein in fluorescent dye binding experiments. Unlike wild-type apoLp-III.DMPC complexes, disc particles bearing the hybrid apolipoprotein competed with 125ILDL for binding to the LDL receptor on cultured human skin fibroblasts. We conclude that a hybrid apolipoprotein containing a key receptor recognition element of apoE preserves the structural integrity of the parent protein while conferring a new biological activity, illustrating the potential of helix swapping to introduce desirable biological properties into unrelated or engineered apolipoproteins.
Allele loss on chromosome 16 associated with progression of human hepatocellular carcinoma. (1990)

Loss of heterozygosity on chromosome 16 is a common genetic alteration in human hepatocellular carcinoma (HCC). To clarify the pathogenetic significance of allele loss on chromosome 16, we performed restriction fragment length polymorphism analysis of 70 surgically resected tumors by using 15 polymorphic DNA markers for chromosome 16. Loss of heterozygosity on chromosome 16 was detected in 36 (52%) of 69 informative cases, and the common region of allele loss in these 36 tumors was located between the HP locus (16q22.1) and the CTRB locus (16q22.3-q23.2). These losses occurred more frequently in HCCs of poor differentiation, of larger size, and with metastasis, whereas they were not detected in HCC at the earliest stage. In addition, these losses were not associated with presence or absence of hepatitis B virus DNA integration or hepatitis C virus infection. These results show that loss of heterozygosity on chromosome 16 is a late event occurring after hepatocarcinogenesis and strongly suggest that this phenomenon is involved in enhancement of tumor aggressiveness during progression of HCC.
The Development of Reduced Size STR Amplicons as Tools for Analysis of Degraded DNA (2003)

New multiplex PCR sets of commonly used short tandem repeat (STR) markers have been developed to produce PCR products that are reduced in size when compared to standard commercial STR kits. The reduction in size of these amplicons can facilitate the examination and analysis of degraded DNA evidence by improving amplification efficiency. This "miniSTR" approach will permit current forensic practitioners to use STR markers and instrumentation already present in their laboratories and to generate genotyping data that is directly comparable to reference samples and searchable through the FBI's Combined DNA Index System (CODIS) databases. This paper discusses the development of these new primer sets and presents some initial results in the analysis of degraded and aged DNA samples. A method for removal of problematic fluorescent dye artifacts is also described. Comparison studies in over 100 samples have verified that these miniSTR primers can provide fully concordant results to commercial STR kits and can provide improved signal from degraded DNA specimens. These miniplex sets should prove valuable in the analysis of samples where allele dropout and reduced sensitivity of larger STR alleles occurs.
An Approach to Subjective Computing: A Robot That Learns From Interaction With Humans (2013)

We present an approach to subjective computing for the design of future robots that exhibit more adaptive and flexible behavior in terms of subjective intelligence. Instead of encapsulating subjectivity into higher order states, we show by means of a relational approach how subjective intelligence can be implemented in terms of the reciprocity of autonomous self-referentiality and direct world-coupling. Subjectivity concerns the relational arrangement of an agent's cognitive space. This theoretical concept is narrowed down to the problem of coaching a reinforcement learning agent by means of binary feedback. Algorithms are presented that implement subjective computing. The relational characteristic of subjectivity is further confirmed by a questionnaire on human perception of the robot's behavior. The results imply that subjective intelligence cannot be externally observed. In sum, we conclude that subjective intelligence in relational terms is fully tractable and therefore implementable in artificial agents.
The dioxin receptor and its nuclear translocator (Arnt) in the rat brain (1995)

Dioxins are environmental pollutants, whose detrimental effects on health are the cause of wide public concern due to their accumulation in the food chain and resistance to metabolism. The most well known dioxin is 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Dioxins exert their effects through a ligand activated transcription factor termed the dioxin or aryl hydrocarbon receptor (Ahr), which acts in concert with another structurally related protein: the aryl hydrocarbon nuclear translocator (Arnt). In the present study, we have employed in situ hybridization to study the localization of the mRNAs for these two proteins in the rat brain. We found mRNAs for both Ahr and Arnt predominantly in the same neuronal populations: in the olfactory bulb, the hippocampus, and the cerebral and cerebellar cortices. Arnt, however, had a more widespread expression than Ahr in the brain. The present results demonstrate that dioxins may act directly in the brain and that the effects of dioxin may occur in discrete neuronal populations. However, in some parts of the brain, e.g. the hypothalamus, that are thought to be targets of the toxic effects of dioxins, we did not observe detectable levels of Ahr mRNA. Furthermore, it appears that Arnt may have additional functions in the brain, apart from being the heterodimerization partner of Ahr, possibly through heterodimerizing with other transcription factors.
Interleukin-3 in gene therapy of cancer. (1994)

Retroviral Jzen vectors were used to introduce cytokine genes into cell lines established from a "moderately immunogenic" FSAR and a "non-immunogenic" FSAN murine fibrosarcoma. The effects of cytokine gene expression on tumour behaviour and host responses have been studied in vitro and in vivo. In this paper we report that, in comparison to other cytokines, interleukin-3 (IL-3) was surprisingly effective at enhancing the immunogenicity of irradiated tumour cell vaccines as seen by the development of protective immunity to parental tumour growth. Protection was tumour-specific and spleen cells from immunized mice could adoptively transfer immunity causing established parental tumours to regress in SCID mice. IL-3 acted through paracrine and endocrine pathways to induce largely a granulocyte infiltrate into tumours and through an autocrine pathway to increase major histocompatibility complex class I expression on both tumour types and CD44 expression on one. IL-3 gene transfer is worth further investigation as a method for enhancing the efficacy of tumour cell vaccines, but our study emphasizes that cytokine gene transduction can lead to stimulation of autocrine as well as paracrine pathways and both might be important in the generation of specific anti-tumour responses. These effects need to be carefully considered if cytokine gene transfer is to be effectively used in cancer immunotherapy.
High quality and low complexity pitch modification of acoustic signals (2002)

A high-quality and low-complexity algorithm for pitch modification of acoustic signals is proposed. It is high quality, because time-domain waveform shape and phase synchrony of a synthesized signal closely resemble that of its original signal. Low complexity is attained by performing the algorithm entirely in time domain with fast algorithm, and without resorting to complicated frequency domain analysis and synthesis. The time domain synthesis mostly consists of fast algorithms of finding minimum absolute error (MAE) and a cross fading operation for high correlation gain and phase synchrony. The MAE-based algorithm is shown to yield smaller complexity, and better performance, than other well-known correlation cost functions. Pitch modification is performed by selecting and synthesizing apposite frames from original input signals in a way such that the original waveform shape and phase synchrony are preserved. Subjective tests showed a comparable performance to that of the best known algorithms, but at much reduced complexity.
Recent progress in high performance and reliable n-type transition metal oxide-based thin film transistors (2015)

This review gives an overview of the recent progress in vacuum-based n-type transition metal oxide (TMO) thin film transistors (TFTs). Several excellent review papers regarding metal oxide TFTs in terms of fundamental electron structure, device process and reliability have been published. In particular, the required field-effect mobility of TMO TFTs has been increasing rapidly to meet the demands of the ultra-high-resolution, large panel size and three dimensional visual effects as a megatrend of flat panel displays, such as liquid crystal displays, organic light emitting diodes and flexible displays. In this regard, the effects of the TMO composition on the performance of the resulting oxide TFTs has been reviewed, and classified into binary, ternary and quaternary composition systems. In addition, the new strategic approaches including zinc oxynitride materials, double channel structures, and composite structures have been proposed recently, and were not covered in detail in previous review papers. Special attention is given to the advanced device architecture of TMO TFTs, such as back-channel-etch and self-aligned coplanar structure, which is a key technology because of their advantages including low cost fabrication, high driving speed and unwanted visual artifact-free high quality imaging. The integration process and related issues, such as etching, post treatment, low ohmic contact and Cu interconnection, required for realizing these advanced architectures are also discussed.
The synthesis of certain 8‐cyano‐2,4‐disubstituted‐imidazo[1,5‐a] pyrimidines (1974)

Abstract A number of imidazo[1,5‐ a ]pyrimidine‐8‐carboxamides were synthesized by reacting various β‐dicarbonyl compounds with 5(4)‐aminoimidazole‐4(5)carboxamide (AICA, 1 ), the non‐ribosylated form of AICAR, a key intermediate in the metabolic pathway of purine biosynthesis. Cyclization of 1 with ethylacetoacetate yielded 2‐methylimidazo[1,5‐ a ]pyrimidin‐1 H ‐4‐one‐8‐carboxamide ( 2 ). The treatment of 2 with phosphorus oxychloride gave 4‐chloro‐8‐cyano‐2‐methylimidazo[1,5‐ a ]pyrimidine ( 3 ). Various nucleophiles displaced the 4‐chloro substituent of 3 under mild conditions. However, the 4‐methylthio group of 8‐cyano‐2‐methyl‐4‐methylthioimidazo[1,5‐ a )pyrimidine ( 8a ) was also displaced under very mild conditions. Even more strangely, the 4‐diethylamino group of 8‐cyano‐4‐diethylamino‐2‐methylimidazo[1,5‐ a ]pyrimidine ( 5a ) was displaced by ammonia to give 4‐amino‐8‐cyano‐2‐methylimidazo[1,5‐ a ]pyrimidine ( 7 ).
Fatty muscle degeneration in cuff ruptures. Pre- and postoperative evaluation by CT scan. (1994)

A preoperative computed tomography (CT) scan grading muscular fatty degeneration in five stages was done in 63 patients scheduled for repair of a torn rotator cuff. The results were compared with postoperative evaluation done after a mean of 17.7 months in 57 patients. Postoperative arthrographies were also performed in 56 patients. Preoperative CT scans demonstrated that infraspinatus fatty degeneration can occur in the presence of large anterosuperior tears even when the infraspinatus tendon is not torn; it worsens with time. The subscapularis rarely degenerates, and when it does it degenerates moderately, even when its tendon is not torn. After an effective surgical repair, moderate supraspinatus degeneration regressed in six of 14 patients; that of the infraspinatus never regressed but rather, increased, in three patients. One of these deteriorations, involving both supra- and infraspinatus, could probably be attributed to a partial subscapular nerve injury. Infraspinatus degeneration was correlated with functional pre- and postoperative impairment of active external rotation. Recurrence of infraspinatus tear was never observed, but recurrence occurred in 25% of supraspinatus repairs. Infraspinatus degeneration had a highly negative influence on the outcome of supraspinatus repairs. It seems preferable to operate on wide tears before irreversible muscular damage takes place.
Design, Synthesis, and Biological Evaluation of Antibody−Drug Conjugates Comprised of Potent Camptothecin Analogues (2009)

Antibody−drug conjugates (ADCs) were prepared with potent camptothecin analogues attached to monoclonal antibodies (mAbs) via dipeptide or glucuronide-based linkers. Aniline-containing camptothecin analogues were employed to provide a site of linker attachment via carbamate bonds that would be stable in circulation. The camptothecin analogues, 7-butyl-10-amino-camptothecin and 7-butyl-9-amino-10,11-methylenedioxy-camptothecin, are generally 10−1000 times more potent than camptothecin. Dipeptide and glucuronide drug linkers were employed containing self-immolative spacers that release drug following lysosomal degradation upon ADC internalization into antigen-positive cell lines. The camptothecin drug linkers were conjugated to three antibodies: chimeric BR96, chimeric AC10, and humanized 1F6, which bind to the Lewis-Y antigen on carcinomas, CD30 on hematologic malignancies, and CD70 present on hematologic malignancies and renal cell carcinoma, respectively. ADCs bearing the potent camptothecin analogue, 7-butyl-9-amino-10,11-methylenedioxy-camptothecin, were highly potent and immunologically specific on a panel of cancer cell lines in vitro, and efficacious at well-tolerated doses in a renal cell carcinoma xenograft model.
Dispersion of Single-Walled Carbon Nanotubes of Narrow Diameter Distribution (2005)

The dispersibility and bundle defoliation of single-walled carbon nanotubes (SWNTs) of small diameter (<1 nm) have been evaluated on CoMoCAT samples with narrow distribution of diameters. As previously observed by photoluminescence and Raman spectroscopy, the CoMoCAT sample exhibits a uniquely narrow distribution of (n,m) structures that remains unchanged after different dispersion conditions. This narrow distribution allowed us to develop a method for quantifying the dispersability of the samples from their optical absorption spectra in terms of two ratios: the "resonance ratio" and the "normalized width." The former is defined as the quotient of the resonant band area and its nonresonant background. The latter is defined as the ratio of the width of the band at half-height to the peak height on a spectrum that has been normalized at 900 nm, making this an intensive property, rather than varying with the path length. In this study of the CoMoCAT sample, we have used the S22 transition corresponding to the (6,5) nanotube to do these calculations, which is the most abundant species. These two ratios provide a quantitative tool to compare different dispersion parameters (time of sonication, degree of centrifugation, etc.) on the same type of sample. From this comparison, an optimal procedure that maximizes the spectral features was selected; this procedure allowed us to contrast various surfactants at different pH values and concentrations. Several surfactants were as good or even better than the one we have used in previous studies, dodecylbenesulfonic acid sodium salt (NaDDBS). Despite differences in their dispersion abilities, none of the surfactants investigated generated new features in the absorption spectra nor changed the distribution of nanotube types, which confirms that the high selectivity of the CoMoCAT sample is in the original sample rather than caused by selective suspension of specific (n,m) nanotubes.