gebhart/patrepeval huggingface dataset:
Balance Between Bone Morphogenetic Proteins and Their Antagonists in Kidney Injury (2007)

Abstract: Dialysis dependency is one of the leading causes of morbidity and mortality in the world, and once end‐stage renal disease develops, it cannot be reversed by currently available therapy. Although the administration of large dose of bone morphogenetic protein‐7 (BMP‐7) has been shown to repair established renal injuries and improves renal function, pathophysiological role of endogenous BMP‐7 and regulatory mechanism of its activities remain elusive. Here we show that uterine sensitization‐associated gene‐1 (USAG‐1), novel BMP antagonist abundantly expressed in the kidney, is the central negative regulator of BMP function in the kidney, and that mice lacking USAG‐1 ( USAG‐1 −/− mice) are resistant to kidney injuries. USAG‐1 −/− mice exhibited prolonged survival and preserved renal function in acute and chronic renal injuries. Renal BMP signaling, assessed by phosphorylation of Smad proteins, is significantly enhanced in USAG‐1 −/− mice during renal injury, indicating that the preservation of renal function is attributed to enhancement of endogenous BMP signaling. Furthermore, the administration of neutralizing antibody against BMP‐7 abolished reno‐protection in USAG‐1 −/− mice, indicating that USAG‐1 plays a critical role in the modulation of reno‐protective action of BMP, and that inhibition of USAG‐1 will be promising means of development of novel treatment for kidney diseases.
Thiolation of transfer RNA inEscherichia colivaries with growth rate (1992)

We have used an affinity electrophoresis assay which when combined with Northern hybridization techniques permits us to estimate the degree of thiolation of individual tRNA species in Escherichia coli. We observe that the levels of 4-thio 2'(3')-uridine (4-thioU) in many but not all tRNAs varies dramatically at different bacterial growth rates: Five tRNAs are completely thiolated at all growth rates, while another eight tRNAs are incompletely thiolated and the fraction of the unthiolated form of these tRNA species increases as the growth rates increase. Transfer RNA(2Glu) contains 4-thioU as well as (methylamino)methyl-2-thio uridine (mnm(5)2-thioU). The level of mnm(5)2-thioU of tRNA(2Glu) is invariant with growth rate. Surprisingly, none of the thirteen tRNA species that we have studied is completely unmodified in all growth media. In particular, at the slowest growth rates every tRNA class that we have studied contains a form that has 4-thioU residues.
Age-dependent accumulation of N.epsilon.-(carboxymethyl)lysine and N.epsilon.-(carboxymethyl)hydroxylysine in human skin collagen (1991)

N epsilon-(Carboxymethyl)lysine (CML) is formed on oxidative cleavage of carbohydrate adducts to lysine residues in glycated proteins in vitro [Ahmed et al. (1988) J. Biol. Chem. 263, 8816-8821; Dunn et al. (1990) Biochemistry 29, 10964-10970]. We have shown that, in human lens proteins in vivo, the concentration of fructose-lysine (FL), the Amadori adduct of glucose to lysine, is constant with age, while the concentration of the oxidation product, CML, increases significantly with age [Dunn et al. (1989) Biochemistry 28, 9464-9468]. In this work we extend our studies to the analysis of human skin collagen. The extent of glycation of insoluble skin collagen was greater than that of lens proteins (4-6 mmol of FL/mol of lysine in collagen versus 1-2 mmol of FL/mol of lysine in lens proteins), consistent with the lower concentration of glucose in lens, compared to plasma. In contrast to lens, there was a slight but significant age-dependent increase in glycation of skin collagen, 33% between ages 20 and 80. As in lens protein, CML, present at only trace levels in neonatal collagen, increased significantly with age, although the amount of CML in collagen at 80 years of age, approximately 1.5 mmol of CML/mol of lysine, was less than that found in lens protein, approximately 7 mmol of CML/mol of lysine. The concentration of N epsilon-(carboxymethyl)hydroxylysine (CMhL), the product of oxidation of glycated hydroxylysine, also increased with age in collagen, in parallel with the increase in CML, from trace levels at infancy to approximately 5 mmol of CMhL/mol of hydroxylysine at age 80.(ABSTRACT TRUNCATED AT 250 WORDS)
Commitment of bacterial spores to germinate A measure of the trigger reaction (1981)

The rate of commitment of bacterial spores to germinate after short exposure to L-alanine increases exponentially from the time of addition of L-alanine. This absence of a lag facilitates kinetic analysis and allows the dependence of commitment on temperature and pH to be determined. The pH profile of commitment has been compared with that obtained from measurements of absorbance decreases during germination, and the two profiles exhibit differing pK values. It is suggested that because the decrease in A600 of spore suspensions is a late event in germination, it is an unsuitable parameter for studying germination-triggering reactions. Commitment has been shown to be temperature-dependent, with an optimum at approx. 37 degrees C and an activation energy (mu) of 1.08 X 10(5) J/mol. The data obtained from the present studies have been used to develop a model for the triggering of germination.
Arabidopsis CYP85A2, a Cytochrome P450, Mediates the Baeyer-Villiger Oxidation of Castasterone to Brassinolide in Brassinosteroid Biosynthesis (2005)

The conversion of castasterone (CS) to brassinolide (BL), a Baeyer-Villiger oxidation, represents the final and rate-limiting step in the biosynthesis of BL in plants. Heterologously expressed Arabidopsis thaliana CYP85A2 in yeast mediated the conversion of CS to BL as well as the C-6 oxidation of brassinosteroids (BRs). This indicated that CYP85A2 is a bifunctional enzyme that possesses BR C-6 oxidase and BL synthase activity. CYP85A2 is thus a cytochrome P450 that mediates Baeyer-Villiger oxidation in plants. Biochemical, physiological, and molecular genetic analyses of Arabidopsis CYP85A2 loss-of-function and overexpression lines demonstrated that CS has to be a bioactive BR that controls the overall growth and development of Arabidopsis plants. Mutant studies also revealed that BL may not always be necessary for normal growth and development but that Arabidopsis plants acquire great benefit in terms of growth and development in the presence of BL.
Molecular Imaging of Tumor Angiogenesis (2004)

Advances in imaging provide new insights into the pathophysiology of many diseases. Established imaging technologies such as MRI, CT, PET, and ultrasound are routinely applied to determine features of tumor blood vessels that distinguish them from normal blood vessels. These techniques yield information on blood flow, blood volume, and vessel permeability. Often, an intravenously injected imaging contrast agent without affinity to a specific target structure is applied to enable detection of malignant lesions. One of the emerging innovations in diagnostic imaging is the evolution of molecular imaging techniques. Molecular imaging is a noninvasive approach to determine the expression of indicative marker molecules of the tumor angiogenesis process. Meanwhile, this approach has been established for all imaging modalities and may further improve sensitivity of diagnostic tumor imaging. Another goal is to provide information with respect to drug treatment monitoring and therapeutic vascular targeting strategies.
Gap junctions promote the bystander effect of herpes simplex virus thymidine kinase in vivo. (1997)

Transfer of the herpes simplex thymidine kinase gene (HSVtk) into tumor cells followed by the administration of ganciclovir (GCV) provides a potential strategy for the treatment of some malignancies. During GCV treatment, not only the cells that express the HSVtk gene are killed but also frequently neighboring tumor cells that are not genetically altered. This has been called the "bystander effect." Although the mechanism of the bystander effect in vivo remains elusive, our results suggest that gap junction formation between neighboring cells is an important contributing factor. The C6 rat glioma cell line, which exhibits a low level of intercellular communication by gap junctions and connexin43 (Cx43)-transfected clones of this cell line forming gap junctions from a moderate level (Cx43-12 and Cx43-14) to a high level (Cx43-13), were transduced with HSVtk. Transduced and nontransduced cells were mixed in various concentrations and then cultured in vitro or injected s.c. into C.B-17/SCID-beige mice followed by i.p. injections of GCV. Cx43-transfected clones showed a significant increase of the bystander effect compared with the less coupled C6 parental cell line. In 11 of 12 mice injected with cells of Cx43-transfected clones, no tumors were seen at the inoculation site when a mixture of 50% HSVtk-negative and HSVtk-positive cells was used. Moreover, in mice injected with cells of clone Cx43-13, which exhibits the highest intercellular communication, tumors were frequently undetectable at the inoculation site when using mixtures of 75% HSVtk-negative and 25% HSVtk-positive cells, and even mixtures containing 5% HSVtk-positive cells of Cx43-transfected clones showed tumor size reduction. All animals in control groups (n = 26) developed large tumors at every injection site. These results demonstrate that gap junctions are an important component in mediating the bystander effect in vivo.
Long-term treatment of Wilson's disease with triethylene tetramine dihydrochloride (trientine) (1995)

Long-term treatment with triethylene tetramine dihydrochloride, (trientine, TETA) was evaluated in 19 patients with Wilson's disease (WD). Two were given the drug as first choice and 17 after treatment with penicillamine. The change was made because of side-effects, lack of improvement or worsening of neurological symptoms. All penicillamine-induced side-effects reverted. Thirteen patients still receive trientine, and the mean total observation time on this treatment is 8.5 years/patient. Seven of the 13 are free from symptoms related to WD, five have mild to moderate neurological symptoms, mainly dysarthria. One patient with neurological symptoms who received trientine from the start of treatment deteriorated rapidly and is now severely dystonic. The symptoms initially worsened and later improved in one patient. All other patients improved during trientine treatment. Three patients died: two from a multifocal cancer including the liver and one non-complier from a ruptured spleen. Two patients underwent liver transplantation for progressive liver failure: one non-complier and one with liver cirrhosis whose liver function deteriorated despite treatment; both are now free from symptoms. Unexpectedly, two patients developed a serious colitis, one with duodenitis as well, that improved after withdrawal of the drug. No other unfavourable effects of trientine were recorded.
Promoting relaxation using virtual reality, olfactory interfaces and wearable EEG (2018)

The ability to relax is sometimes challenging to achieve, nevertheless it is extremely important for mental and physical health, particularly to effectively manage stress and anxiety. We propose a virtual reality experience that integrates a wearable, low-cost EEG headband and an olfactory necklace that passively promotes relaxation. The physiological response was measured from the EEG signal. Relaxation scores were computed from EEG frequency bands associated with a relaxed mental state using an entropy-based signal processing approach. The subjective perception of relaxation was determined using a questionnaire. A user study involving 12 subjects showed that the subjective perception of relaxation increased by 26.1 % when using a VR headset with the olfactory necklace, compared to not being exposed to any stimulus. Similarly, the physiological response also increased by 25.0 %. The presented work is the first Virtual Reality Therapy system that uses scent in a wearable manner and proves its effectiveness to increase relaxation in everyday life situations.
On the Methodological and Philosophical Challenges of Sociomaterial Theorizing: An Overview of Competing Conceptualizations : ICIS 2012 Panel Statement (2012)

This panel discusses how to take the ontological paradigm of Sociomateriality to the field using alternative theoretical lenses that embody sociomaterial ideas. Based on exemplary papers, Samer Faraj, Karlheinz Kautz, Daniel Robey, and Ulrike Schultze present the advantages of the lens they have drawn on to inform their empirical research. Through their discussion the panelists illustrate how they designed their studies accordingly and defend why their approach allows them to make empirical observations of the Sociomaterial.
Informed by this comparative debate, the audience gains insights into the panelists’ experiences with conducting, writing, and editing Sociomaterial research. The audience will thus understand the methodological differences of the alternative lenses as well as important commonalities that make a study sociomaterial. As a key takeaway, the panel provides guidance on how to contribute to sociomaterial theorizing, thus supporting the recent trend towards Sociomateriality in the IS research community.
Ricin A-Chain:  Kinetics, Mechanism, and RNA Stem−Loop Inhibitors (1998)

Ricin A-chain (RTA) catalyzes the depurination of a single adenine at position 4324 of 28S rRNA in a N-ribohydrolase reaction. The mechanism and specificity for RTA are examined using RNA stem-loop structures of 10-18 nucleotides which contain the required substrate motif, a GAGA tetraloop. At the optimal pH near 4.0, the preferred substrate is a 14-base stem-loop RNA which is hydrolyzed at 219 min-1 with a kcat/Km of 4.5 x 10(5) M-1 s-1 under conditions of steady-state catalysis. Smaller or larger stem-loop RNAs have lower kcat values, but all have Km values of approximately 5 microM. Both the 10- and 18-base substrates have kcat/Km near 10(4) M-1 s-1. Covalent cross-linking of the stem has a small effect on the kinetic parameters. Stem-loop DNA (10 bases) of the same sequence is also a substrate with a kcat/Km of 0.1 that for RNA. Chemical mechanisms for enzymatic RNA depurination reactions include leaving group activation, stabilization of a ribooxocarbenium transition state, a covalent enzyme-ribosyl intermediate, and ionization of the 2'-hydroxyl. A stem-loop RNA with p-nitrophenyl O-riboside at the depurination site is not a substrate, but binds tightly to the enzyme (Ki = 0.34 microM), consistent with a catalytic mechanism of leaving group activation. The substrate activity of stem-loop DNA eliminates ionization of the 2'-hydroxyl as a mechanism. Incorporation of the C-riboside formycin A at the depurination site provides an increased pKa of the adenine analogue at N7. Binding of this analogue (Ki = 9.4 microM) is weaker than substrate which indicates that the altered pKa at this position is not an important feature of transition state recognition. Stem-loop RNA with phenyliminoribitol at the depurination site increases the affinity substantially (Ki = 0.18 microM). The results are consistent with catalysis occurring by leaving group protonation at ring position(s) other than N7 leading to a ribooxocarbenium ion transition state. Small stem-loop RNAs have been identified with substrate activity within an order of magnitude of that reported for intact ribosomes.
Stereotyped and specific gene expression programs in human innate immune responses to bacteria (2002)

The innate immune response is crucial for defense against microbial pathogens. To investigate the molecular choreography of this response, we carried out a systematic examination of the gene expression program in human peripheral blood mononuclear cells responding to bacteria and bacterial products. We found a remarkably stereotyped program of gene expression induced by bacterial lipopolysaccharide and diverse killed bacteria. An intricately choreographed expression program devoted to communication between cells was a prominent feature of the response. Other features suggested a molecular program for commitment of antigen-presenting cells to antigens captured in the context of bacterial infection. Despite the striking similarities, there were qualitative and quantitative differences in the responses to different bacteria. Modulation of this host-response program by bacterial virulence mechanisms was an important source of variation in the response to different bacteria.
p75 Neurotrophin Receptor Protects Primary Cultures of Human Neurons against Extracellular Amyloid β Peptide Cytotoxicity (2003)

The cytotoxicity of extracellular amyloid beta peptide (Abeta) has been clearly demonstrated in many cell types. In contrast, primary human neurons in culture are resistant to extracellular Abeta-mediated toxicity. Here, we investigate the involvement of p75 neurotrophin receptor (p75NTR) in Abeta-treated human neurons. We find that Abeta1-40 and Abeta1-42, but not the reverse control peptide, Abeta40-1, rapidly increase the levels of p75NTR in a specific and dose-dependent manner. In contrast to observations in cell lines, enhanced expression of p75NTR in human neurons via a herpes simplex virus amplicon vector does not increase the susceptibility of neurons to Abeta. Unexpectedly, inhibition of p75NTR expression with an antisense expression construct or incubation of the cells with an antibody to the extracellular domain of p75NTR sensitizes human neurons to extracellular nonfibrillar or fibrillar Abeta1-42 cytotoxicity. Unlike intracellular Abeta, extracellular Abeta toxicity is independent of p53 and Bax activity. However, Abeta toxicity is inhibited by caspase inhibitors and the glycogen synthase kinase 3beta inhibitor lithium. Neuroprotection against Abeta is phosphatidylinositide 3-kinase dependent but Akt independent. These results are consistent with a neuroprotective role for p75NTR against extracellular Abeta toxicity in human neurons.
Attenuation of focal cerebral ischemic injury in transgenic mice overexpressing CuZn superoxide dismutase. (1991)

Oxygen-derived free radicals have been implicated in the pathogenesis of vasogenic edema and infarction caused by ischemia and reperfusion injury. In earlier studies, exogenously supplied liposome-entrapped CuZn superoxide dismutase (CuZn-SOD) ameliorated ischemic brain edema and infarction in rats following focal cerebral ischemia. To ascertain directly the role of SOD in the protection against superoxide radical-induced injury, we measured infarct size and water content 24 hr following focal cerebral ischemia in nontransgenic mice and in transgenic mice bearing the human SOD1 gene. These transgenic mice have 3.1-fold higher cellular CuZn-SOD activity in the brain than do their nontransgenic littermates. We also measured antioxidant levels (reduced glutathione and reduced ascorbate) of contralateral cortex, infarct cortex, surrounding cortex, and striatum. Infarct size and brain edema were significantly decreased in transgenic mice compared with nontransgenic mice. Reduced glutathione and reduced ascorbate levels decreased in the ischemic hemisphere, but levels in surrounding cortex and striatum were significantly higher in transgenic mice than in nontransgenic mice. These results indicate that increased endogenous SOD activity in brain reduces the level of ischemic damage and support the concept that superoxide radicals play an important role in the pathogenesis of infarction and edema following focal cerebral ischemia.
Robotic Partial Nephrectomy for Renal Hilar Tumors: A Multi-Institutional Analysis (2008)

Robotic partial nephrectomy is a safe and feasible approach for select patients with renal hilar tumors. Robotic assistance may facilitate tumor resection and renal reconstruction for challenging renal hilar tumors, offering a minimally invasive and nephron sparing surgical option for select patients who might otherwise require open surgery or total nephrectomy.
Molecular cloning and sequence analysis of the gene encoding OmpL1, a transmembrane outer membrane protein of pathogenic Leptospira spp (1993)

Pathogenic Leptospira spp. are spirochetes that have a low transmembrane outer membrane protein content relative to that of enteric gram-negative bacteria. In a previous study we identified a 31-kDa surface protein that was present in strains of Leptospira alstoni in amounts which correlated with the outer membrane particle density observed by freeze fracture electron microscopy (D. A. Haake, E. M. Walker, D. R. Blanco, C. A. Bolin, J. N. Miller, and M. A. Lovett, Infect. Immun. 59:1131-1140, 1991). The N-terminal amino acid sequence was used to design a pair of oligonucleotides which were utilized to screen a lambda ZAP II library containing EcoRI fragments of L. alstoni DNA. A 2.5-kb DNA fragment which contained the entire structural ompL1 gene was identified. The structural gene deduced from the sequence of this DNA fragment would encode a 320-amino-acid polypeptide with a 24-amino-acid leader peptide and a leader peptidase I cleavage site. Processing of OmpL1 results in a mature protein with a predicted molecular mass of 31,113 Da. Secondary-structure prediction identified repeated stretches of amphipathic beta-sheets typical of outer membrane protein membrane-spanning sequences. A topological model of OmpL1 containing 10 transmembrane segments is suggested. A recombinant OmpL1 fusion protein was expressed in Escherichia coli in order to immunize rabbits with the purified protein. Upon Triton X-114 extraction of L. alstoni and phase separation, anti-OmpL1 antiserum recognized a single band on immunoblots of the hydrophobic detergent fraction which was not present in the hydrophilic aqueous fraction. Immunoelectron microscopy with anti-OmpL1 antiserum demonstrates binding to the surface of intact L. alstoni. DNA hybridization studies indicate that the ompL1 gene is present in a single copy in all pathogenic Leptospira species that have been tested and is absent in nonpathogenic Leptospira species. OmpL1 may be the first spirochetal transmembrane outer membrane protein for which the structural gene has been cloned and sequenced.
Interaction between the A2 and A19 amino acid residues is of critical importance for high biological activity in insulin: [19-leucine-A]insulin (1984)

The replacement of tyrosine at position A19 by leucine in the insulin molecule led to an analogue, [19-leucine-A]insulin [( Leu19-A]insulin), displaying insignificant receptor binding affinity and in vitro biological activity less than 0.1 and 0.05%, respectively, compared to the natural hormone. This analogue along with the previously reported [2-glycine-A]-, [2-alanine-A]-, and [2-norleucine-A]insulins is the least potent insulin analogue we have examined. Circular dichroic studies showed that all these analogues are monomeric at concentrations at which insulin is primarily dimeric. We conclude that an aromatic ring at position A19 and the presence of the side chain of isoleucine at position A2 are each of critical importance for high biological activity in insulin. It appears that the van der Waals interaction between the side chain of isoleucine A2 and tyrosine A19, present in crystalline insulin, is among the most important determinants for high biological activity in insulin.