gebhart/patrepeval huggingface dataset:
Control of Pore Size and Functionality in Isoreticular Zeolitic Imidazolate Frameworks and their Carbon Dioxide Selective Capture Properties (2009)

Five new crystalline zeolitic imidazolate frameworks (ZIFs), ZIF-78 to -82, were prepared from zinc(II) nitrate and mixtures of 2-nitroimidazole and five different functionalized imidazoles and were found to have the GME topology. These structures, along with three previously reported GME ZIFs, constitute a series of highly porous materials with Brunauer-Emmet-Teller surface areas ranging from 620 to 1730 m(2)/g. The pore diameters and apertures vary incrementally from 7.1 to 15.9 A and 3.8 to 13.1 A, respectively, and the functionalities decorating the pores vary from polar cyano- and nitro- groups to nonpolar alkyl groups. The variability expressed in these materials makes them highly attractive for study as gas-separation media. Selectivity values calculated for separation of CO(2) and CH(4) predict that the ZIFs with polar functionality, ZIF-78 (10.6:1) and -82 (9.6:1), retain CO(2) gas to a greater degree than the other members of the GME series and BPL-activated carbon. These predictions are borne out in dynamic breakthrough studies, which confirm the increased capacity of ZIF-78 and -82 and demonstrate the promise of this class of materials.
Recent advances in targeted genome engineering in mammalian systems (2012)

Targeted genome engineering enables researchers to disrupt, insert, or replace a genomic sequence precisely at a predetermined locus. One well-established technology to edit a mammalian genome is known as gene targeting, which is based on the homologous recombination (HR) mechanism. However, the low HR frequency in mammalian cells (except for mice) prevents its wide application. To address this limitation, a custom-designed nuclease is used to introduce a site-specific DNA double-strand break (DSB) on the chromosome and the subsequent repair of the DSB by the HR mechanism or the non-homologous end joining mechanism results in efficient targeted genome modifications. Engineered homing endonucleases (also called meganucleases), zinc finger nucleases, and transcription activator-like effector nucleases represent the three major classes of custom-designed nucleases that have been successfully applied in many different organisms for targeted genome engineering. This article reviews the recent developments of these genome engineering tools and highlights a few representative applications in mammalian systems. Recent advances in gene delivery strategies of these custom-designed nucleases are also briefly discussed.
Smad1, β-catenin and Tcf4 associate in a molecular complex with the Myc promoter in dysplastic renal tissue and cooperate to control Myc transcription (2004)

Renal dysplasia, the major cause of childhood renal failure in humans,arises from perturbed renal morphogenesis and molecular signaling during embryogenesis. Recently, we discovered induction of molecular crosstalk between Smad1 and β-catenin in the TgAlk3QD mouse model of renal medullary cystic dysplasia. Our finding that Myc, a Smad andβ-catenin transcriptional target and effector of renal epithelial dedifferentiation, is misexpressed in dedifferentiated epithelial tubules provided a basis for investigating coordinate transcriptional control by Smad1 and β-catenin in disease. Here, we report enhanced interactions between a molecular complex consisting of Smad1, β-catenin and Tcf4 and adjacent Tcf- and Smad-binding regions located within the Myc promoter in TgAlk3QD dysplastic renal tissue, and Bmp-dependent cooperative control of Myc transcription by Smad1, β-catenin and Tcf4. Analysis of nuclear extracts derived from TgAlk3QD and wild-type renal tissue revealed increased levels of Smad1/β-catenin molecular complexes, and de novo formation of chromatin-associated Tcf4/Smad1 molecular complexes in TgAlk3QD tissues. Analysis of a 476 nucleotide segment of the 1490 nucleotide Myc genomic region upstream of the transcription start site demonstrated interactions between Tcf4 and the Smad consensus binding region and associations of Smad1, β-catenin and Tcf4 with oligo-duplexes that encode the adjacent Tcf- and Smad-binding elements only in TgAlk3QD tissues. In collecting duct cells that express luciferase under the control of the 1490 nucleotide Myc genomic region, Bmp2-dependent stimulation of Myc transcription was dependent on contributions by each of Tcf4, β-catenin and Smad1. These results provide novel insights into mechanisms by which interacting signaling pathways control transcription during the genesis of renal dysplasia.
Inflammatory mechanisms in the lung (2008)

Inflammation is the body's response to insults, which include infection, trauma, and hypersensitivity. The inflammatory response is complex and involves a variety of mechanisms to defend against pathogens and repair tissue. In the lung, inflammation is usually caused by pathogens or by exposure to toxins, pollutants, irritants, and allergens. During inflammation, numerous types of inflammatory cells are activated. Each releases cytokines and mediators to modify activities of other inflammatory cells. Orchestration of these cells and molecules leads to progression of inflammation. Clinically, acute inflammation is seen in pneumonia and acute respiratory distress syndrome (ARDS), whereas chronic inflammation is represented by asthma and chronic obstructive pulmonary disease (COPD). Because the lung is a vital organ for gas exchange, excessive inflammation can be life threatening. Because the lung is constantly exposed to harmful pathogens, an immediate and intense defense action (mainly inflammation) is required to eliminate the invaders as early as possible. A delicate balance between inflammation and anti-inflammation is essential for lung homeostasis. A full understanding of the underlying mechanisms is vital in the treatment of patients with lung inflammation. This review focuses on cellular and molecular aspects of lung inflammation during acute and chronic inflammatory states.
User authentication by cognitive passwords: an empirical assessment (2002)

The concept of cognitive passwords is introduced, and their use as a method to overcome the dilemma of passwords that are either difficult to remember or easily guessed is suggested. Cognitive passwords are based on personal facts, interests, and opinions that are likely to be easily recalled by a user. A brief dialogue between a user and a system, where a user provides a system with exact answers to a rotating set of questions, is suggested to replace the traditional authentication method using a single password. The findings of an empirical investigation focusing on memorability and ease-of-guessing of cognitive passwords, are reported. They demonstrate that cognitive passwords are easier to recall than conventional passwords, while being difficult for others, even those close to the users, to guess.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Esrrb Is a Direct Nanog Target Gene that Can Substitute for Nanog Function in Pluripotent Cells (2012)

Embryonic stem cell (ESC) self-renewal efficiency is determined by the level of Nanog expression. However, the mechanisms by which Nanog functions remain unclear, and in particular, direct Nanog target genes are uncharacterized. Here we investigate ESCs expressing different Nanog levels and Nanog(-/-) cells with distinct functionally inducible Nanog proteins to identify Nanog-responsive genes. Surprisingly, these constitute a minor fraction of genes that Nanog binds. Prominent among Nanog-reponsive genes is Estrogen-related receptor b (Esrrb). Nanog binds directly to Esrrb, enhances binding of RNAPolII, and stimulates Esrrb transcription. Overexpression of Esrrb in ESCs maintains cytokine-independent self-renewal and pluripotency. Remarkably, this activity is retained in Nanog(-/-) ESCs. Moreover, Esrrb can reprogram Nanog(-/-) EpiSCs and can rescue stalled reprogramming in Nanog(-/-) pre-iPSCs. Finally, Esrrb deletion abolishes the defining ability of Nanog to confer LIF-independent ESC self-renewal. These findings are consistent with the functional placement of Esrrb downstream of Nanog.
Normally Functioning murF Is Essential for the Optimal Expression of Methicillin Resistance in Staphylococcus aureus (2003)

A carboxy-terminal fragment of murF was used to construct and insert a suicide plasmid into the chromosomal copy of the gene in the highly and homogeneously methicillin-resistant Staphylococcus aureus (MRSA) strain COL by Campbell type integration. The plasmid insertion generated a mutant in which the MIC value for oxacillin was reduced from 400 microg/ml of the parental strain to 0.75 microg/ml in 90% of the cells of the mutant cultures that were heterogeneous: they contained subpopulations of bacteria with a frequency of 10(-3) that were capable of expressing resistance at nearly the parental level. The impact of the murF mutation on antibiotic resistance was selective for beta-lactam antibiotics: there was no change in the susceptibility of the mutant to D-cycloserine, fosfomycin, beta-D-chloro-alanine, moenomycin, bacitracin, or vancomycin. Analysis of the mutant peptidoglycan showed decrease in the percentage of oligomeric components in rough proportion to the accumulation of several abnormal muropeptide components, which were identified as structural variants of the disaccharide tripeptide monomer. An abnormal cell wall precursor identified as UDP MurNac tripeptide was also detected in the cytoplasmic pool of the mutant strain. A normal proportion of oligomers and a greatly reduced representation of the disaccharide tripeptide were demonstrated in the cell wall of the murF mutant's subpopulation that has retained the parental level of resistance. Northern analysis demonstrated a drastic reduction in the transcription rate of mecA in mutant F9 whereas mecA transcription increased in the subpopulation of bacteria that retained high-level resistance.
Synthesis of 3-deuterated diazepam and nordiazepam 4-oxides and their use in the synthesis of other 3-deuterated derivatives (1996)

The protons at 3-positions of diazepam 4-oxide and nordiazepam 4-oxide underwent an efficient deuterium exchange via keto-enol tautomerism in deuterated alkaline methanol. The 3-dideuterated 4-oxides were each used as a starting material to synthesize 3-monodeuterated oxazepam and its 3-acetate, 3-monodeuterated temazepam and its 3-acetate, and 3-dideuterated diazepam and nordiazepam.
Analysis of interactions among the CLAVATA3 receptors reveals a direct interaction between CLAVATA2 and CORYNE in Arabidopsis (2009)

In Arabidopsis, CORYNE (CRN), a new member of the receptor kinase family, was recently isolated as a key player involved in the CLAVATA3 (CLV3) signaling pathway, thereby playing an important role in regulating the development of shoot and root apical meristems. However, the precise relationships among CLAVATA1 (CLV1), CLAVATA2 (CLV2), and CRN receptors remain unclear. Here, we demonstrate the subcellular localization of CRN and analyze the interactions among CLV1, CLV2, and CRN using firefly luciferase complementation imaging (LCI) assays in both Arabidopsis mesophyll protoplasts and Nicotiana benthamiana leaves. Fluorescence targeting showed that CRN was localized to the plasma membrane. The LCI assays coupled with co-immunoprecipitation assays demonstrated that CLV2 can directly interact with CRN in the absence of CLV3. Additional LCI assays showed that CLV1 did not interact with CLV2, but can interact weakly with CRN. We also found that CLV1 can interact with CLV2-CRN heterodimers, implying that these three proteins may form a complex. Moreover, CRN, rather than CLV1 and CLV2, was able to form homodimers without CLV3 stimulation. Taken together, our results add direct evidence to the newly proposed two-parallel receptor pathways model and therefore provide new insights into the CLV3 signaling pathway.
A Retinal Ganglion Cell Neurotrophic Factor Purified from the Superior Colliculus (1990)

Dissociated neonatal rat retinal ganglion cells can be maintained by the addition of an extract from the neonatal superior colliculus. This extract can support 95% of ganglion cells over 24 h in culture; in addition it promotes the expression of neurites from these cells. This report describes the purification of a neurotrophic factor from the superior colliculus which supports the survival of 80% of retinal ganglion cells over 24 h in vitro. The purification procedure involves a combination of dye-ligand, anion-exchange, and molecular sieve chromatography. The purified neurotrophic factor has a Stokes radius of approximately 200 A using molecular sieve chromatography in the presence of a chaotropic agent. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the purified factor indicates that it is a glycoprotein that migrates with a molecular mass greater than 400 kDa. Further characterization of this high-molecular-mass glycoprotein by enzymatic digestion demonstrated that it is a chondroitin sulfate proteoglycan. This factor is clearly distinguishable from other neurotrophic factors that have an effect on retinal ganglion cells such as brain-derived neurotrophic factor and fibroblast growth factor. The chondroitin sulfate proteoglycan from the neonatal superior colliculus is the first proteoglycan to be identified as a neurotrophic factor.
CHARACTERIZING THE ROLE OF THE NELL1 GENE IN CARDIOVASCULAR DEVELOPMENT (2007)

PA). Her hometown is Silver Spring, Maryland. Cymbeline Culiat is a senior staff scientist at the Biological Sciences Division
Unique silane modified perfluorosulfonic acids as versatile reagents for new solid acid catalysts (1997)

A new versatile reagent, a perfluorosulfonate/trisilanol [(OH) 3 Si(CH 2 ) 3 (CF 2 ) 2 O(CF 2 ) 2 SO 3 - M + ], is synthesized and a series of surface bound strong solid acid catalysts developed which are active for catalyzing a range of reactions, for example alkene isomerization, alkylations and acylations.
Iron intake and the risk of colorectal cancer. (1996)

Prospectively gathered data from the National Health and Nutrition Examination Survey I and the National Health Evaluation Follow-Up Study were analyzed to evaluate the risk of colorectal cancer due to consumption of iron. Morbidity and mortality data due to colorectal cancer were available on 14,407 persons first interviewed in 1971 and followed through 1986. A total of 194 possible colorectal cancers occurred in this group over the 15-year period. Subsite analysis showed that the risk of colon cancer due to iron intake was elevated throughout the colon for both men and women, with the highest adjusted risks for the interquartile range seen in the proximal colon for females (relative risk, 1.51; 95% confidence interval, 1.41-1.60). The risk of rectal cancer was not significantly elevated for men or women. Elevated serum iron was also associated with increased risk; however, this effect was strongest in the distal (rather than proximal) colon and was significant only among females (adjusted relative risk, 1.73; 95% confidence interval, 1.03-2.92). The mean transferrin saturation was higher among cases than controls (30.7 versus 28.7%), but total iron-binding capacity did not seem to predict the occurrence of colorectal cancer. Proportional hazards models confirmed that the effects of iron and serum iron were not confounded by age, gender, energy consumption, fat intake, or other known risk factors for colorectal cancer. These data suggest that iron may confer an increased risk for colorectal cancer, and that the localization of risk may be attributable to the mode of epithelial exposure. It seems that luminal exposure to iron increases risk proximally, whereas humoral exposure increases risk distally. These differences may be due to such factors as oxidation state, binding proteins and the presence of other cofactors such as bile acids, products of bacterial metabolism.
Observation and quantitation of exocytosis from the cell body of a fully developed neuron in Planorbis corneus (1995)

We have discovered a neuronal system that releases neurotransmitter via exocytosis from the cell body. In the large dopamine cell of the pond snail Planorbis corneus, depolarization induces rhythmic release of dopamine from the cell body. When a stimulant is applied extracellularly or intracellularly in situ to the cell body, transient dopamine concentration packets that appear in a bursting pattern are observed. Dopamine release is calcium dependent and release is on the time scale expected for exocytosis (2 to 4 msec rise times). Quantitation of individual events reveals an average of 818,000 molecules per exocytotic event. As many as 89,000 individual exocytotic events have been observed following a single stimulation of one cell. Neurotransmitter exocytosis from the neuronal cell body appears to represent an alternative form of neurocommunication to synaptic transmission.
Aberrant Distribution of ADAM3 in Sperm from Both Angiotensin-Converting Enzyme (Ace)- and Calmegin (Clgn)-Deficient Mice1 (2006)

Male mice deficient for the calmegin (Clgn) or the angiotensin-converting enzyme (Ace) gene show impaired sperm migration into the oviduct and loss of sperm-zona pellucida binding ability in vitro. Since CLGN is a molecular chaperone for membrane transport of target proteins and ACE is a membrane protein, we looked for ACE on the sperm membranes from Clgn-/- mice. ACE was present and showed normal activity, indicating that CLGN is not involved in transporting ACE to the sperm membranes. The ablation of the Adam2 and Adam3 genes generated animals whose sperm did not bind the zona pellucida, which led us to examine the presence of ADAM2 and ADAM3 in Clgn-/- and Ace-/- sperm. ADAM3 was absent from Clgn-/- sperm. In the Ace-/- mice, while ADAM2 was found normally in the sperm, ADAM3 disappeared from the Triton X-114 detergent-enriched phase after phase separation, which suggests that ACE is involved in distributing ADAM3 to a location where it can participate in sperm-zona pellucida binding. This diminished amount of ADAM3 in the Triton X-114 detergent-enriched phase may explain the inability of Clgn-/- and Ace-/- sperm to bind to the zona pellucida.
Alternative Sources of Omega-3 Fats: Can We Find a Sustainable Substitute for Fish? (2013)

Increasing demand for eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) containing fish oils is putting pressure on fish species and numbers. Fisheries provide fish for human consumption, supplement production and fish feeds and are currently supplying fish at a maximum historical rate, suggesting mass-scale fishing is no longer sustainable. However, the health properties of EPA and DHA long-chain (LC) omega-3 polyunsaturated fatty acids (PUFA) demonstrate the necessity for these oils in our diets. EPA and DHA from fish oils show favourable effects in inflammatory bowel disease, some cancers and cardiovascular complications. The high prevalence of these diseases worldwide indicates the requirement for alternative sources of LC-PUFA. Strategies have included plant-based fish diets, although this may compromise the health benefits associated with fish oils. Alternatively, stearidonic acid, the product of α-linolenic acid desaturation, may act as an EPA-enhancing fatty acid. Additionally, algae oils may be a promising omega-3 PUFA source for the future. Algae are beneficial for multiple industries, offering a source of biodiesel and livestock feeds. However, further research is required to develop efficient and sustainable LC-PUFA production from algae. This paper summarises the recent research for developing prospective substitutes for omega-3 PUFA and the current limitations that are faced.
Proteoglycan Core Protein Families (1986)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Algorithms for distributed decision-making for multi-agent microgrid power management (2011)

A key component to future smart grids may be microgrid systems capable of integrating generation, load, and storage assets into an autonomous power system entity. As a potential building block for expanding power networks, microgrids can enable the broad integration of distributed energy resources (DER), as well as providing customers a means to optimize local assets based on multiple objectives. Pivotal to the implementation of microgrids are the power management and control architectures that will operate the microgrid systems. In this paper, a multi-agent based control architecture for microgrids, capable of coordinating and cooperatively achieving user-defined objectives is presented. Herein, unique agents that comprise a distributed multi-agent system (MAS) are developed according to Foundation for Intelligent Physical Agents (FIPA) guidelines. The authors present a method for facilitating the fundamental self-organizing and cooperative behavior amongst the microgrid agents. The MAS formulation developed is intended to lay the groundwork for a power management architecture that incorporates the integrated and robust operation of microgrid assets.
Albumin in tears (2013)

Platinum-based anticancer agents are widely used as first-line drugs in cancer chemotherapy for various solid tumors. However, great side effects and occurrence of resistance remain as the major drawbacks for almost all the platinum drugs developed. To conquer these problems, new strategies should be adopted for platinum drug based chemotherapy. Modern nanotechnology has been widely employed in the delivery of various therapeutics and diagnostic. It provides the possibility of targeted delivery of a certain anticancer drug to the tumor site, which could minimize toxicity and optimize the drug efficacy. Here, in this review, we focused on the recent progress in polymer based drug delivery systems for platinum-based combination therapy.
Q829X, a novel mutation in the gene encoding otoferlin (OTOF), is frequently found in Spanish patients with prelingual non-syndromic hearing loss (2002)

Inherited hearing impairment is a highly heterogeneous group of disorders with an overall incidence of about 1 in 2000 newborns.1 Among them, prelingual, severe hearing loss with no other associated clinical feature (non-syndromic) is by far the most frequent.1 It represents a serious handicap for speech acquisition, and therefore early detection is essential for the application of palliative treatment and special education. Hence genetic diagnosis and counselling are being increasingly demanded.

Non-syndromic prelingual deafness is mainly inherited as an autosomal recessive trait. To date, 28 different loci for autosomal recessive non-syndromic hearing loss have been reported and 10 genes have been identified.2 Mutations in the gene encoding connexin-26 ( GJB2 , DFNB1 locus) are responsible for up to 50% of all cases of autosomal recessive deafness, with a frequent mutation (35delG) accounting for up to 86% of the GJB2 mutant alleles in several populations.3–10 Other mutations, 235delC and 167delT, account for the majority of GJB2 mutant alleles among the Japanese11 and Ashkenazi Jewish populations,12 respectively. However, little is known about the individual contribution of other genes and their mutations to the remaining uncharacterised cases. Two factors explain this lack of knowledge. First, most of the deafness genes identified so far are large, with many exons and no mutational hotspots, a problem that hampers routine molecular diagnosis. Second, the recent impressive progress in the investigation of genetic deafness has been the result of a research strategy based on the study of large pedigrees with many affected subjects.13 As a consequence, for most of the genes identified so far, genetic linkage has been reported only for a few families, and a small number of mutations have been published.14–23 In contrast, most of the families asking for a genetic diagnosis are small, with only …