gebhart/patrepeval huggingface dataset:
Halohydrin Dehalogenases Are Structurally and Mechanistically Related to Short-Chain Dehydrogenases/Reductases (2001)

Halohydrin dehalogenases, also known as haloalcohol dehalogenases or halohydrin hydrogen-halide lyases, catalyze the nucleophilic displacement of a halogen by a vicinal hydroxyl function in halohydrins to yield epoxides. Three novel bacterial genes encoding halohydrin dehalogenases were cloned and expressed in Escherichia coli, and the enzymes were shown to display remarkable differences in substrate specificity. The halohydrin dehalogenase of Agrobacterium radiobacter strain AD1, designated HheC, was purified to homogeneity. The k(cat) and K(m) values of this 28-kDa protein with 1,3-dichloro-2-propanol were 37 s(-1) and 0.010 mM, respectively. A sequence homology search as well as secondary and tertiary structure predictions indicated that the halohydrin dehalogenases are structurally similar to proteins belonging to the family of short-chain dehydrogenases/reductases (SDRs). Moreover, catalytically important serine and tyrosine residues that are highly conserved in the SDR family are also present in HheC and other halohydrin dehalogenases. The third essential catalytic residue in the SDR family, a lysine, is replaced by an arginine in halohydrin dehalogenases. A site-directed mutagenesis study, with HheC as a model enzyme, supports a mechanism for halohydrin dehalogenases in which the conserved Tyr145 acts as a catalytic base and Ser132 is involved in substrate binding. The primary role of Arg149 may be lowering of the pK(a) of Tyr145, which abstracts a proton from the substrate hydroxyl group to increase its nucleophilicity for displacement of the neighboring halide. The proposed mechanism is fundamentally different from that of the well-studied hydrolytic dehalogenases, since it does not involve a covalent enzyme-substrate intermediate.
Study of Light as a parameter in the growth of algae in a Photo-Bio Reactor (PBR) (2003)

A photo-bio Reactor is a system that provides an artificial environment for photosyntheticorganisms (Algae) to perform a chemical conversion. Light is an important parameter in aphotosynthetic process. Light is emitted both in visible and invisible wavelengths. Each wavelengthis associated with particular quantum energy. Like all living things algae is favorable to certainwavelengths in the light spectrum. Certain wavelengths of light are converted into useful energy inthe process of photosynthesis. It is important to investigate which wavelengths are important for thegrowth of algae in the PBR for achieving high yields. Different types of light sources with differentspectrum were chosen for further experimentation. Time, light intensity and the algae antenna alsocontrol the photosynthesis process. Excess light even in the appropriate wavelengths will beconverted in to heat and not used for photosynthesis. Light with wavelengths between 600-700nm isthe most efficient for photosynthesis. Light emitting diodes (LEDs) with a peak weavelength of643nm are the most cost effective light source if operation of the PBR is 1 year or more.
A More Versatile Route to Block Copolymers and Other Polymers of Complex Architecture by Living Radical Polymerization:  The RAFT Process (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTA More Versatile Route to Block Copolymers and Other Polymers of Complex Architecture by Living Radical Polymerization: The RAFT Process) Y. K. Chong, Tam P. T. Le, Graeme Moad, Ezio Rizzardo, and San H. ThangView Author Information CSIRO Molecular Science, Bag 10, Clayton South, Victoria 3169, Australia Cite this: Macromolecules 1999, 32, 6, 2071–2074Publication Date (Web):February 24, 1999Publication History Received16 September 1998Revised23 December 1998Published online24 February 1999Published inissue 1 March 1999https://pubs.acs.org/doi/10.1021/ma981472phttps://doi.org/10.1021/ma981472prapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views10296Altmetric-Citations770LEARN 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 SUBJECTS:Copolymerization,Copolymers,Monomers,Organic compounds,RAFT polymerization Get e-Alerts
Physical map of chromosomal nitrogen fixation ( nif ) genes of Klebsiella pneumoniae (1979)

We describe a method for the rapid determination of the physical location of mutations caused by insertion of transposable elements. We used this method to construct a detailed physical map of the nitrogen fixation (nif) gene cluster of Klebsiella pneumoniae and to correlate it with the genetic map. Total cellular DNA was isolated from individual strains, each carrying an insertion in 1 of 15 different nif genes. The DNA was digested with a restriction endonuclease, fractionated by agarose gel electrophoresis, denatured, and blotted onto nitrocellulose filter paper. The DNA on the filters was hybridized with (32)P-labeled DNA fragments derived from amplifiable plasmids carrying cloned nif DNA fragments from K. pneumoniae. Altered hybridization patterns caused by insertions into nif genes allowed us to map nif mutations with respect to the previously mapped cleavage sites for various restriction endonucleases. We have used the same method to map the end points of nif deletions. Using this procedure, we assigned physical locations on the K. pneumoniae chromosome to 86 nif insertion mutations and 13 nif deletion end points. This mapping procedure provides a convenient alternative to deletion mapping as a definitive method for mapping insertion mutations within a gene or for ordering genes within a gene cluster. This procedure will be especially useful for mapping mutations conferring phenotypes that are difficult to monitor and for mapping mutations in bacterial species in which techniques for conducting deletion mapping have not been devised.
Impact of the Intestinal Microbiota on the Development of Mucosal Defense (2008)

The gastrointestinal tract is a dynamic ecosystem composed of an organized matrix of host eukaryotic cells, including a fully functional immune system, and numerous microbial habitats normally colonized by a diverse array of microbes. Recent analyses of the gastrointestinal microbiota by use of molecular-based methods indicate that bacterial populations vary substantially among but appear relatively stable within individuals. These observations raise many important questions about the role of the normal microbiota in the development of both the innate and the adaptive immune systems of the host and about how perturbations in this relationship may contribute to various intestinal or immunologic disorders. Here, 3 critical issues pertaining to the intestinal microbiota are briefly reviewed: what are the microbes, where are the microbes, and what controls the composition of the microbiota.
Kilo-sequencing: an ordered strategy for rapid DNA sequence data acquisition (1983)

A strategy for rapid DNA sequence acquisition in an ordered, nonrandom manner, while retaining all of the conveniences of the dideoxy method with M13 transducing phage DNA template, is described. Target DNA 3 to 14 kb in size can be stably carried by our M13 vectors. Suitable targets are stretches of DNA which lack an enzyme recognition site which is unique on our cloning vectors and adjacent to the sequencing primer; current sites that are so useful when lacking are Pst, Xba, HindIII, BglII, EcoRI. By an in vitro procedure, we cut RF DNA once randomly and once specifically, to create thousands of deletions which start at the unique restriction site adjacent to the dideoxy sequencing primer and extend various distances across the target DNA. Phage carrying a desired size of deletions, whose DNA as template will give rise to DNA sequence data in a desired location along the target DNA, may be purified by electrophoresis alive on agarose gels. Phage running in the same location on the agarose gel thus conveniently give rise to nucleotide sequence data from the same kilobase of target DNA.
A minimum length of N gene sequence in transgenic plants is required for RNA-mediated tospovirus resistance (2000)

We showed previously that transgenic plants with the green fluorescent protein (GFP) gene fused to segments of the nucleocapsid (N) gene of tomato spotted wilt virus (TSWV) displayed post-transcriptional gene silencing of the GFP and N gene segments and resistance to TSWV. These results suggested that a chimeric transgene composed of viral gene segments might confer multiple virus resistance in transgenic plants. To test this hypothesis and to determine the minimum length of the N gene that could trans-inactivate the challenging TSWV, transgenic plants were developed that contained GFP fused with N gene segments of 24-453 bp. Progeny from these plants were challenged with: (i) a chimeric tobacco mosaic virus containing the GFP gene, (ii) a chimeric tobacco mosaic virus with GFP plus the N gene of TSWV and (iii) TSWV. A number of transgenic plants expressing the transgene with GFP fused to N gene segments from 110 to 453 bp in size were resistant to these viruses. Resistant plants exhibited post-transcriptional gene silencing. In contrast, all transgenic lines with transgenes consisting of GFP fused to N gene segments of 24 or 59 bp were susceptible to TSWV, even though the transgene was post-transcriptionally silenced. Thus, virus resistance and post-transcriptional gene silencing were uncoupled when the N gene segment was 59 bp or less. These results provide evidence that multiple virus resistance is possible through the simple strategy of linking viral gene segments to a silencer DNA such as GFP.
In Situ Electron Energy-Loss Spectroscopy in Liquids (2013)

In situ scanning transmission electron microscopy (STEM) through liquids is a promising approach for exploring biological and materials processes. However, options for in situ chemical identification are limited: X-ray analysis is precluded because the liquid cell holder shadows the detector and electron energy-loss spectroscopy (EELS) is degraded by multiple scattering events in thick layers. Here, we explore the limits of EELS in the study of chemical reactions in their native environments in real time and on the nanometer scale. The determination of the local electron density, optical gap, and thickness of the liquid layer by valence EELS is demonstrated. By comparing theoretical and experimental plasmon energies, we find that liquids appear to follow the free-electron model that has been previously established for solids. Signals at energies below the optical gap and plasmon energy of the liquid provide a high signal-to-background ratio regime as demonstrated for LiFePO4 in an aqueous solution. The potential for the use of valence EELS to understand in situ STEM reactions is demonstrated for beam-induced deposition of metallic copper: as copper clusters grow, EELS develops low-loss peaks corresponding to metallic copper. From these techniques, in situ imaging and valence EELS offer insights into the local electronic structure of nanoparticles and chemical reactions.
Augmentation Therapy With Serial Intravenous Ketamine Over 18 Months in a Patient With Treatment Resistant Depression (2015)

Major depressive disorder is a severe illness that affects 3% to 7% of adults annually in the United States. About 30% of these individuals are refractory to multiple treatment trials. Recent reports have found a significant and almost immediate improvement in depressive symptoms after single or multiple ketamine intravenous infusions (IVIs) in such patients. We present the case of A.B., a patient with treatment-resistant depression (TRD) including to subgenual deep brain stimulation, who went into remission after augmentation with 6 ketamine IVIs (0.5 mg/kg) over a 3-week period. However, she had a reemergence of depressive symptoms 4 months later and received a second series of 3 ketamine IVIs over the course of a week. A.B. again went into remission and maintained this for the next 8 months. At this time, she experienced a reemergence of depressive symptoms and was treated with the third series of ketamine IVIs (3 infusions over the course of a week). Because A.B. has now been in remission for 6 months. A.B. has received a total of 12 ketamine IVIs over the course of 18 months. No significant adverse events have occurred. To our knowledge, this is the first case of long-term ketamine efficacy as augmentation therapy in TRD over the course of 18 months. There is a need for studies examining the long-term management of TRD with IV ketamine. Guidelines for maintenance ketamine IVIs in TRD also need to be developed.
Characterization of a gastrointestinal tract microscale cell culture analog used to predict drug toxicity (2009)

The lining of the gastrointestinal (GI) tract is the largest surface exposed to the external environment in the human body. One of the main functions of the small intestine is absorption, and intestinal absorption is a route used by essential nutrients, chemicals, and pharmaceuticals to enter the systemic circulation. Understanding the effects of digestion on a drug or chemical, how compounds interact with and are absorbed through the small intestinal epithelium, and how these compounds affect the rest of the body is critical for toxicological evaluation. Our goal is to create physiologically realistic in vitro models of the human GI tract that provide rapid, inexpensive, and accurate predictions of the body's response to orally delivered drugs and chemicals. Our group has developed an in vitro microscale cell culture analog (microCCA) of the GI tract that includes digestion, a mucus layer, and physiologically realistic cell populations. The GI tract microCCA, coupled with a multi-chamber silicon microCCA representing the systemic circulation, is described and challenged with acetaminophen. Proof of concept experiments showed that acetaminophen passes through and is metabolized by the in vitro intestinal epithelium and is further metabolized by liver cells, resulting in liver cell toxicity in a dose-dependent manner. The microCCA response is also consistent with in vivo measurements in mice. The system should be broadly useful for studies on orally delivered drugs or ingestion of chemicals with potential toxicity.
Recent progress in the development of near-infrared fluorescent probes for bioimaging applications (2013)

Near-infrared (NIR) fluorescent dyes have emerged as promising modalities for monitoring the levels of various biologically relevant species in cells and organisms. The use of NIR probes enables deep photon penetration in tissue, minimizes photo-damage to biological samples, and produces low background auto-fluorescence from biomolecules present in living systems. The number of new analyte-responsive NIR fluorescent probes has increased substantially in recent years as a consequence of intense research efforts. In this tutorial review, we highlight recent advances (2010-2013) made in the development and applications of NIR fluorescent probes. The review focuses on NIR fluorescent probes that have been devised to sense various biologically important species, including ROS/RNS, metal ions, anions, enzymes and other related species, as well as intracellular pH changes. The basic principles involved in the design of functional NIR fluorescent probes and suggestions about how to expand applications of NIR imaging agents are also described.
8 GHz Low Noise Bias Tuned VCO (2005)

Design and performance of an 8 GHz cavity stabilized silicon bipolar transistor voltage controlled oscillator is presented. Very linear electronic frequency tuning with minimal output power variations are achieved without voractor by means of the transistor bias control. The VCO is mechanically tuned over 1 GHz frequency range with dialectic tuner. It delivers 50 mW of output power with 17% transistor efficiency and phase noise of -60 dBc/Hz at 1 kHz from carrier.
Phase 2 enzyme inducer sulphoraphane blocks matrix metalloproteinase production in articular chondrocytes (2009)

SPN was found to inhibit MMP production in pro-inflammatory cytokine-stimulated chondrocytes. Delineation of the biochemical mechanism regulating cartilage catabolism by SPN may identify safe and effective therapeutic targets for the inhibition of cartilage degradation.
Nasal Drug Delivery System-Factors Affecting and Applications (2007)

The nasal route is a potential alternative route for systemic availability of drugs restricted to intravenous administration, such as peptide and protein drugs and vaccines. This route is also advisable for drugs undergoing extensive first pass effect .Besides this, intranasal route has also been successfully exploited for bypassing the blood brain barrier [BBB] and subsequently delivering drug molecules to central nervous system [CNS]. The present article highlights the advantages, barriers, physicochemical factors and formulation related parameters affecting the nasal drug delivery. It also includes a note on nasal absorption enhancers. Also, the applications of nasal route for delivery of peptides and proteins, non-peptide drugs, vaccines and drug molecules to CNS have been summarized in depth. Keywords: Nasal route, nasal absorption enhancers, peptide, protein drugs, vaccines, central nervous system
Linkage analysis of the fibroin light chain gene in the silkworm, Bombyx mori. (1984)

The fibroin light chain of an inbred strain of Bombyx mori was shown to give a single band on SDS-polyacrylamide gel electrophoresis by a Laemmli system. From the electrophoretic mobility of the band, fibroin light chains from various inbred strains of the silkworm were classified into three groups, A, B and C. Linkage analysis of the fibroin light chain gene was performed by observing the relevant phenotypes, using a silkworm strain of Tamanashikasuri (light chain phenotype C) and sixteen silkworm stocks (light chain phenotype A or B) carrying genetic markers on each chromosome. The fibroin light chain gene was not linked to the fibroin H chain gene locating on the 25th chromosome carrying the Nd(2) mutation, but was found to be linked to the U gene locating on the 14th chromosome.
Treatment of Catheter-Induced Iliac Artery Injuries With Self-Expanding Endografts (2000)

Early model stent-grafts provided a safe and effective endovascular treatment for iliac perforations and large arterial dissections, showing a high mid-term patency rate. However, postimplantation syndrome appears to occur frequently with this type of Dacron-covered nitinol device.
Treponemal glycoconjugate inhibits Toll‐like receptor ligand‐induced cell activation by blocking LPS‐binding protein and CD14 functions (2003)

Spirochetes are well-known as causative agents of various chronic infectious diseases. Glycolipids of small-sized Treponema spirochetes have been shown to exhibit immunostimulating activities. In this study, we found that a glycoconjugate preparation obtained from Treponema medium (Tm-Gp), an intermediate-sized oral Treponema seen in subgingival plaque from patients with chronic periodontal diseases, diminished the LPS-induced activation of a human monocytic cell line, while TNF-alpha-induced activation was unaffected. NF-kappaB activation in Ba/F3 cells expressing murine Toll-like receptor (TLR) 4 and MD-2 was inhibited by Tm-Gp in a CD14/LPS-binding protein (LBP)-dependent manner when stimulated with LPS or its active center lipid A but not when stimulated with Taxol. Tm-Gp blocked the binding of LPS to immobilized CD14 and LBP and inhibited nitric oxide (NO) production by a murine Mphi cell line following stimulation with peptidoglycan and LPS in the presence of FBS, while NO production in response poly (I:C) RNA or CpG DNA remained unaffected. The inhibitory effects of Tm-Gp seem to be attributable to the lipophilic portion of the glycoconjugate. These results indicate that T. medium contains a glycoconjugate possessing an inhibitory effect on TLR-mediated cell activation through interaction with LBP and CD14.
Integrin Dynamics and Matrix Assembly (2000)

Fibronectin matrix assembly is a multistep, integrin-dependent process. To investigate the role of integrin dynamics in fibronectin fibrillogenesis, we developed an antibody-chasing technique for simultaneous tracking of two integrin populations by different antibodies. We established that whereas the vitronectin receptor alpha(v)beta(3) remains within focal contacts, the fibronectin receptor alpha(5)beta(1) translocates from focal contacts into and along extracellular matrix (ECM) contacts. This escalator-like translocation occurs relative to the focal contacts at 6.5 +/- 0.7 microm/h and is independent of cell migration. It is induced by ligation of alpha(5)beta(1) integrins and depends on interactions with a functional actin cytoskeleton and vitronectin receptor ligation. During cell spreading, translocation of ligand-occupied alpha(5)beta(1) integrins away from focal contacts and along bundles of actin filaments generates ECM contacts. Tensin is a primary cytoskeletal component of these ECM contacts, and a novel dominant-negative inhibitor of tensin blocked ECM contact formation, integrin translocation, and fibronectin fibrillogenesis without affecting focal contacts. We propose that translocating alpha(5)beta(1) integrins induce initial fibronectin fibrillogenesis by transmitting cytoskeleton-generated tension to extracellular fibronectin molecules. Blocking this integrin translocation by a variety of treatments prevents the formation of ECM contacts and fibronectin fibrillogenesis. These studies identify a localized, directional, integrin translocation mechanism for matrix assembly.
Advancing continuous IDEAs with mixture distributions and factorization selection metrics (2001)

Evolutionary optimization based on probabilistic models has so far been limited to the use of factorizations in the case of continuous representations. Furthermore, a maximum complexity parameter K was required previously to construct factorizations to prevent unnecessary complexity to be introduced in the factorization. In this paper, we advance these techniques by using clustering and the EM algorithm to allow for mixture distributions. Furthermore, we apply a search metric to eliminate the K parameter. We use these techniques in the IDEA framework to obtain new continuous evolutionary optimization algorithms and investigate their performance.