gebhart/patrepeval huggingface dataset:
Transformation of vegetative cells of Bacillus thuringiensis by plasmid DNA (1987)

Plasmid DNA-mediated transformation of vegetative cells of Bacillus thuringiensis was studied with the following two plasmids: pBC16 coding for tetracycline resistance and pC194 expressing chloramphenicol resistance. A key step was the induction of competence by treatment of the bacteria with 50 mM Tris hydrochloride buffer (pH 8.9) containing 30% sucrose. Transformation frequency was strongly influenced by culture density during the uptake of DNA and required the presence of polyethylene glycol. Growth in a minimal medium supplemented with Casamino Acids gave 35 times more transformants than growth in a rich medium. The highest frequencies were obtained with covalently closed circular DNA. With all parameters optimized, the frequency was 10(-3) transformants per viable cell or 10(4) transformants per microgram of DNA. Cells previously frozen were also used as recipients in transformation experiments; such cells gave frequencies similar to those obtained with freshly grown cells. The procedure was optimized for B. thuringiensis subsp. gelechiae, but B. thuringiensis subsp. kurstaki, B. thuringiensis subsp. galleriae, B. thuringiensis subsp. thuringiensis, and B. thuringiensis subsp. israelensis were also transformed. Compared with protoplast transformation, our method is much faster and 3 orders of magnitude more efficient per microgram of added DNA.
Transgenic animals in integrative biology: approaches and interpretations of outcome (2000)

Technological innovations in methods for genetic manipulation of laboratory animals and in techniques for assessment of cardiovascular, respiratory, behavioral, and metabolic physiology in mouse models afford unprecedented opportunities for research in integrative biology. We provide here an overview of basic and advanced techniques for generation of transgenic mice and a discussion of how transgenic technology can be most advantageously applied to important physiological questions that can be addressed only within the intact organism.
Differentiating Soybean Responses to Heterodera Glycines Races (1992)

Physiological variation among populations of Heterodera glycines Ichinohe, the soybean cyst nematode, has been a problem for soybean [ Glycine max (L.) Merr.] growers and scientists. These populations have been classified into 16 races, but the system still leaves ambiguity, especially in the characterization of resistance. Two schemes are proposed: one to classify the nematoder aces and the other to designate the soybean response to the nematode. The existing race system by Riggs and Schmitt still serves as a basis for differentiating populations of H. glycines , but with soybean PI 437654 added as an additional nematode response parameter. A practical system using a popular resistant cultivar as the type for resistance is proposed for advisory purposes. Soybean reactions to parasitism by the nematode are denoted by four levels of resistance: resistant, moderately resistant, moderately susceptible, and susceptible.
Response to local inflammation of IL-1 beta-converting enzyme- deficient mice (1997)

IL-1 beta-converting enzyme (ICE) cleaves pro-IL-1 beta to the mature, released form. Although other proteases can process pro-IL-1 beta, ICE-deficient (ICE -/-) mice do not release mature IL-1 beta in response to endotoxin. The purpose of our study was to investigate the response of ICE -/- mice in two models of local inflammation, turpentine-induced tissue damage and zymosan-induced peritonitis. No differences were observed in the development of the systemic acute phase response after turpentine administration between wild-type and ICE -/- mice, but this response was completely impaired in IL-1 beta -/- mice. Accordingly, the levels of mature IL-1 beta produced in response to turpentine did not differ between wild-type and ICE -/- mice. In contrast, following zymosan-induced peritonitis, the levels of mature IL-1 beta were significantly lower in ICE -/- mice. This was associated with a 50% decrease in cellular infiltrate in ICE -/- mice compared with that in wild-type controls. The reduced production of zymosan-induced mature IL-1 beta in ICE -/- mice was also observed from cultured peritoneal or spleen cells. Our results demonstrate that in turpentine-induced tissue necrosis, precursor IL-1 beta is processed by non-ICE proteases, but in complement-mediated inflammation, ICE participates in the processing of the IL-1 beta precursor.
Laser straightness interferometer system with rotational error compensation and simultaneous measurement of six degrees of freedom error parameters (2015)

A laser straightness interferometer system with rotational error compensation and simultaneous measurement of six degrees of freedom error parameters is proposed. The optical configuration of the proposed system is designed and the mathematic model for simultaneously measuring six degrees of freedom parameters of the measured object including three rotational parameters of the yaw, pitch and roll errors and three linear parameters of the horizontal straightness error, vertical straightness error and straightness error's position is established. To address the influence of the rotational errors produced by the measuring reflector in laser straightness interferometer, the compensation method of the straightness error and its position is presented. An experimental setup was constructed and a series of experiments including separate comparison measurement of every parameter, compensation of straightness error and its position and simultaneous measurement of six degrees of freedom parameters of a precision linear stage were performed to demonstrate the feasibility of the proposed system. Experimental results show that the measurement data of the multiple degrees of freedom parameters obtained from the proposed system are in accordance with those obtained from the compared instruments and the presented compensation method can achieve good effect in eliminating the influence of rotational errors on the measurement of straightness error and its position.
HIV DRUG RESISTANCE (1994)

Departments of Pathology and Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093–0679, USA
New insights into the role and mechanism of c‐Jun‐N‐terminal kinase signaling in the pathobiology of liver diseases (2017)

The c-Jun-N-terminal-kinase (JNK) family is highly conserved across species such as Drosophila, C. elegans, zebrafish and mammals, and plays a central role in hepatic physiologic and pathophysiologic responses. These responses range from cell death to cell proliferation and carcinogenesis, as well as metabolism and survival, depending on the specific context and duration of activation of the JNK signaling pathway. Recently, several investigators identified the key molecules in the JNK activation loop which include apoptosis signal-regulating kinase (ASK1) and SH3-domain binding protein 5 (Sab) and their involvement in acute or chronic liver disease models. Thus, regulating JNK activation through modulating the JNK activation loop may represent an important new strategy in the prevention and treatment of acute and chronic liver diseases. In this review, we will discuss the molecular pathophysiology of the JNK activation loop and its role in the pathogenesis of liver diseases. (Hepatology 2018;67:2013-2024).
Interferon gamma-induced transcription of the high-affinity Fc receptor for IgG requires assembly of a complex that includes the 91-kDa subunit of transcription factor ISGF3. (1993)

A 39-nt DNA sequence, the interferon gamma (IFN-gamma) response region (GRR), is necessary for the IFN-gamma-induced transcription of the high-affinity Fc receptor for IgG (Fc gamma RI) and sufficient for the IFN-gamma-induced transcription of transfected plasmids. By using extracts from IFN-gamma-treated cells, three protein complexes will assemble in vitro on a 9-nt core region in the 3' domain of the GRR. The sequence of this core resembles the IFN-gamma-activated sequence (GAS) described for the GBP gene. Mutations in this GAS core region prevent complex assembly and result in the loss of IFN-gamma induction of reporter constructs containing the mutation. In addition to the GAS core region, a 5' region of the GRR is necessary for optimal IFN-gamma induction and for formation of one of the DNA-protein complexes. By antibody reactivity, we show that a 91-kDa protein, first identified as a component of ISGF3, the IFN-alpha-induced transcription complex, is present in at least two of the DNA-protein complexes. IFN-alpha can induce the formation of the faster-migrating 91-kDa protein-GAS complex but not the slower-migrating complex. Furthermore, IFN-alpha does not result in appreciable transcriptional activation of Fc gamma RI or constructs containing the GRR. Thus, these data demonstrate that the IFN-gamma-activated 91-kDa protein is required for IFN-gamma induction of Fc gamma RI and suggest that an additional complex may be required for optimal expression and specificity.
Novel Implantable Device to Detect Cardiac Allograft Rejection (2009)

The Soul Mate allograft rejection monitoring system accurately detected transplanted heart rejection in a canine model noninvasively with continuous sampling. This proof-of-concept study suggests that the Soul Mate could be used to more intensely and more frequently monitor cardiac allografts for rejection.
Prevention of cerebral malaria in children in Papua New Guinea by southeast Asian ovalocytosis band 3. (1999)

Southeast Asian ovalocytosis (SAO) occurs at high frequency in malarious regions of the western Pacific and may afford a survival advantage against malaria. It is caused by a deletion of the erythrocyte membrane band 3 gene and the band 3 protein mediates the cytoadherence of parasitized erythrocytes in vitro. The SAO band 3 variant may prevent cerebral malaria but it exacerbates malaria anemia and may also increase acidosis, a major determinant of mortality in malaria. We undertook a case-control study of children admitted to hospital in a malarious region of Papua New Guinea. The SAO band 3, detected by the polymerase chain reaction, was present in 0 of 68 children with cerebral malaria compared with six (8.8%) of 68 matched community controls (odds ratio = 0, 95% confidence interval = 0-0.85). Median hemoglobin levels were 1.2 g/dl lower in malaria cases with SAO than in controls (P = 0.035) but acidosis was not affected. The remarkable protection that SAO band 3 affords against cerebral malaria may offer a valuable approach to a better understanding of the mechanisms of adherence of parasitized erythrocytes to vascular endothelium, and thus of the pathogenesis of cerebral malaria.
A CRISPR Resource for Individual, Combinatorial, or Multiplexed Gene Knockout (2017)

We have combined a machine-learning approach with other strategies to optimize knockout efficiency with the CRISPR/Cas9 system. In addition, we have developed a multiplexed sgRNA expression strategy that promotes the functional ablation of single genes and allows for combinatorial targeting. These strategies have been combined to design and construct a genome-wide, sequence-verified, arrayed CRISPR library. This resource allows single-target or combinatorial genetic screens to be carried out at scale in a multiplexed or arrayed format. By conducting parallel loss-of-function screens, we compare our approach to existing sgRNA design and expression strategies.
Toxicological Evaluation of Thiol-Reactive Compounds Identified Using a La Assay To Detect Reactive Molecules by Nuclear Magnetic Resonance (2007)

We have recently reported on the development of a La assay to detect reactive molecules by nuclear magnetic resonance (ALARM NMR) to detect reactive false positive hits from high-throughput screening, in which we observed a surprisingly large number of compounds that can oxidize or form covalent adducts with protein thiols groups. In the vast majority of these cases, the covalent interactions are largely nonspecific (e.g., affect many protein targets) and therefore unsuitable for drug development. However, certain thiol-reactive species do appear to inhibit the target of interest in a specific manner. The question then arises as to the potential toxicology risks of developing a drug that can react with protein thiol groups. Here, we report on the evaluation of a large set of ALARM-reactive and -nonreactive compounds against a panel of additional proteins (aldehyde dehydrogenase, superoxide dismutase, and three cytochrome P450 enzymes). It was observed that ALARM-reactive compounds have significantly increased risks of interacting with one or more of these enzymes in vitro. Thus, ALARM NMR seems to be a sensitive tool to rapidly identify compounds with an enhanced risk of producing side effects in humans, including alcohol intolerance, the formation of reactive oxygen species, and drug-drug interactions. In conjunction with other toxicology assays, ALARM NMR should be a valuable tool for prioritizing compounds for lead optimization and animal testing.
Highly Ordered SnO2 Nanorod Arrays from Controlled Aqueous Growth (2004)

Without template, surfactant, applied field, or undercoating, well-defined and highly ordered rutile SnO2 nanorods were grown directly onto various substrates at low temperatures from aqueous solutions. These nanorods are elongated along the c axis and have stable prismatic (110) faces, which results in nanorods with a square cross section (see picture).
Spatially Resolved Measurements of the Chromatic Dispersion in Fibers (2014)

Technique for selective localization of four-photon mixing and its use for physical parameter extraction in fiber is described. The measurement method relies on localized counter-colliding power transfer and was applied to map dispersion and corresponding transverse geometry of different types of optical fibers. The technique is capable of resolving fiber core fluctuations comparable to a single silica molecular diameter.
Shape behavior of lipid vesicles as the basis of some cellular processes (2002)

The basic principles that govern the shape behavior of phospholipid vesicle shapes are discussed. The important membrane parameters of the system are defined by presenting the expressions for the relevant contributions to the system's mechanical energy. In the description of the rather unique shape behavior of lipid vesicles, the emphasis is on providing a qualitative understanding of the dependence of vesicle shape on the parameters of the system. The vesicle shape behavior is then related to biologically important phenomena. Some examples are given of how the results of the shape behavior of lipid vesicles can be applied to the analysis of cellular systems. Red blood cell shape and shape transformations, vesicle fission and fusion processes, and the phenomenon of cellular polarity are considered. It is reasoned that the current biological processes that involve changes of membrane conformation may have their origin in the general shape behavior of closed lamellar membranes.
Structural basis of specific inhibition of extracellular activation of pro- or latent myostatin by the monoclonal antibody SRK-015 (2020)

Myostatin (or growth/differentiation factor 8 (GDF8)) is a member of the transforming growth factor β superfamily of growth factors and negatively regulates skeletal muscle growth. Its dysregulation is implicated in muscle wasting diseases. SRK-015 is a clinical-stage mAb that prevents extracellular proteolytic activation of pro- and latent myostatin. Here we used integrated structural and biochemical approaches to elucidate the molecular mechanism of antibody-mediated neutralization of pro-myostatin activation. The crystal structure of pro-myostatin in complex with 29H4-16 Fab, a high-affinity variant of SRK-015, at 2.79 Å resolution revealed that the antibody binds to a conformational epitope in the arm region of the prodomain distant from the proteolytic cleavage sites. This epitope is highly sequence-divergent, having only limited similarity to other closely related members of the transforming growth factor β superfamily. Hydrogen/deuterium exchange MS experiments indicated that antibody binding induces conformational changes in pro- and latent myostatin that span the arm region, the loops contiguous to the protease cleavage sites, and the latency-associated structural elements. Moreover, negative-stain EM with full-length antibodies disclosed a stable, ring-like antigen-antibody structure in which the two Fab arms of a single antibody occupy the two arm regions of the prodomain in the pro- and latent myostatin homodimers, suggesting a 1:1 (antibody:myostatin homodimer) binding stoichiometry. These results suggest that SRK-015 binding stabilizes the latent conformation and limits the accessibility of protease cleavage sites within the prodomain. These findings shed light on approaches that specifically block the extracellular activation of growth factors by targeting their precursor forms.
CORONARY ARTERY ENDOTHELIAL DYSFUNCTION AFTER ISCHEMIA-REPERFUSION AND ACUTE UNTREATED REJECTION IN A CANINE HETEROTOPIC HEART TRANSPLANTATION MODEL (2001)

In the canine model of heterotopic heart transplantation, the early (24 hr) endothelial dysfunction seen after transplantation is specific to the thrombin receptor and the Gi-protein signaling pathway. Acute untreated rejection did not modify the alteration in endothelial reactivity to thrombin but enhanced the sensibility of the Gi-protein signaling pathways.
A Synthetic Antagonist for the Peroxisome Proliferator-activated Receptor γ Inhibits Adipocyte Differentiation (2000)

While searching for natural ligands for the peroxisome proliferator-activated receptor (PPAR) gamma, we identified a synthetic compound that binds to this receptor. Bisphenol A diglycidyl ether (BADGE) is a ligand for PPARgamma with a K(d(app)) of 100 microM. This compound has no apparent ability to activate the transcriptional activity of PPARgamma; however, BADGE can antagonize the ability of agonist ligands such as rosiglitazone to activate the transcriptional and adipogenic action of this receptor. BADGE also specifically blocks the ability of natural adipogenic cell lines such as 3T3-L1 and 3T3-F442A cells to undergo hormone-mediated cell differentiation. These results provide the first pharmacological evidence that PPARgamma activity is required for the hormonally induced differentiation of adipogenic cells.
An Analysis on Kinematically Contributing Factors at Impact of Forehand Drive Motion in Squash (2007)

This study were obtained elapsed time phase-by-phases, displacement, user angle, velocity and angular velocity to analyse kinematically contributing factors at impact of forehand drive motion, on targeting three male players. The results of the study were presented as follows; In the forehand drive swing, the elapsed time by phases was a total of .52 seconds: .30 seconds from backswing to impact and .22 seconds from impact to follow-through, Considering the mean change in locations of COM of each(part<TEX>$\rightarrow$</TEX>body segment) at impact, racket head, left shoulder, right wrist and left hip, the left-right directions(X-axis) were showm to be each <TEX>$.61{\pm}.03$</TEX>, <TEX>$1.19{\pm}.08$</TEX>, <TEX>$.66{\pm}.03$</TEX>, <TEX>$.94{\pm}.06$</TEX>, and <TEX>$.45{\pm}.03m$</TEX>. The displacement differences of COM of each body segment were shown to be -.57, -.05, -.33, and .16m. For the vertical direction(Z-axis), the center of mass was lowest at impact and highest at E3. For the displacement of the right wrist on the left hip, the right wrist moved to .82m to the lower direction without change in the locations of the hip from E1 from E2. When the left hip moved .02m from E2 to E3, the right wrist moved .7m in the upper direction. In respect to the velocity of each body segment, the hip and the shoulder joint accelerated and then the wrist followed. Then the right wrists of all the subjects and their racket heads showed maximum speed, and an effective swing was observed. At the angle of each part, the angle of the right wrist was the smallest at the backswing and the largest at the moment of the impact. Then it increased gradually in the follow-through section. In respect of angular velocity for subject A, the hip moved and the largest change occurred. Immediately before the impact, the subject made a swing using his right wrist, his hip, and the shoulder joint, showing the maximum value, which was judged to be effective.
Studies on the mechanism of action of protein kinase C and the isolation of molecular clones encoding the enzyme. (1986)

Protein kinase C (PKC) plays an important role in signal transduction and the action of phorbol ester tumor promoters, and it is of interest to isolate the coding sequence of this enzyme. Using a 53-base pair synthetic oligonucleotide probe that corresponds to an 18-amino acid peptide obtained from rat brain PKC, we have isolated rat brain cDNA clones corresponding to PKC. We have also isolated several closely related clones. Partial nucleotide sequence analysis of one of the PKC clones (RP41) identifies a 224-amino acid region with approximately 40% homology to the carboxy terminal and catalytic domains of both the cAMP-dependent and cGMP-dependent protein kinases. The levels of mRNA homologous to RP41 are very high in brain; very low but detectable levels are present in heart and liver. A second cDNA (RP16) was only partially sequenced, and based on its predicted amino acid sequence, it shares 65% homology with the corresponding region of the PKC clone RP41. The levels of mRNA corresponding to RP16 are also highest in rat brain, but they are of a different size than those detected with RP41. These and additional results indicate that the gene for the enzyme PKC shares considerable homology with other protein kinases and that PKC itself may belong to a new multigene family. The availability of these cDNA clones should greatly facilitate further studies on the role of PKC in growth control, differentiation, and multistage carcinogenesis.
Boron neutron-capture therapy (1990)

Abstract Boron Neutron Capture Therapy (BNCT) is a method of radiation therapy based on the 10B(n,4He)7Li reaction that shows promise in the treatment of some malignant tumors of the brain and of the skin. Considerable research on neutron beam development and on the chemistry, pharmacology and toxicology of boron-containing drugs for BNCT is in progress. BNCT with thermal neutrons may play a useful role as an adjunct therapy for localized malignant melanomas of the skin. BNCT with epithermal neutrons should improve the prognosis of patients with unifocal cerebral malignant gliomas. Several boron-containing drugs now available will enable clinical trials of BNCT for cerebral gliomas to begin within the next several years. Whether BNCT will be curative rather than palliative for most tumors so treated is arguable. However, present evidence suggests that BNCT should be beneficial in some clinical situations for which other methods of radiation therapy offer little benefit.