gebhart/patrepeval huggingface dataset:
Adipose Triglyceride Lipase and Hormone-sensitive Lipase Are the Major Enzymes in Adipose Tissue Triacylglycerol Catabolism (2006)

The mobilization of free fatty acids from adipose triacylglycerol (TG) stores requires the activities of triacylglycerol lipases. In this study, we demonstrate that adipose triglyceride lipase (ATGL) and hormone-sensitive lipase (HSL) are the major enzymes contributing to TG breakdown in in vitro assays and in organ cultures of murine white adipose tissue (WAT). To differentiate between ATGL- and HSL-specific activities in cytosolic preparations of WAT and to determine the relative contribution of these TG hydrolases to the lipolytic catabolism of fat, mutant mouse models lacking ATGL or HSL and a mono-specific, small molecule inhibitor for HSL (76-0079) were used. We show that 76-0079 had no effect on TG catabolism in HSL-deficient WAT but, in contrast, essentially abolished free fatty acid mobilization in ATGL-deficient fat. CGI-58, a recently identified coactivator of ATGL, stimulates TG hydrolase activity in wild-type and HSL-deficient WAT but not in ATGL-deficient WAT, suggesting that ATGL is the sole target for CGI-58-mediated activation of adipose lipolysis. Together, ATGL and HSL are responsible for more than 95% of the TG hydrolase activity present in murine WAT. Additional known or unknown lipases appear to play only a quantitatively minor role in fat cell lipolysis.
Circuit partitioning and RF isolation by through-substrate trenches (2004)

In this work, theoretical and experimental analysis of RF crosstalk suppression by substrate thinning and trenching is performed. Medici (2D solver) simulation results show that high isolation can be achieved by using high resistivity thinned substrate and through-substrate trenches. Measurements on dedicated G-S-G test structures implemented on thinned Si substrates (thickness 20-100 /spl mu/m) with and without through-substrate trenches (trench width 5-100 /spl mu/m) show that isolation between two single-ended capacitive substrate contacts can effectively be controlled by these trenches. While the partial trenches provide additional isolation of /spl sim/10 dB at 1 GHz, the full trenches (forming isolated silicon islands) provide additional isolation of /spl sim/30 dB at 1 GHz.
Cyclo‐bis‐[ω‐amino‐dodecansäure]‐amid (1965)

Abstract Cyclo‐bis‐[ω‐amino‐dodecansäure]‐amid wird dargestellt und charakterisiert.
Isoprenoid biosynthesis in bacteria: Two different pathways? (1993)

The biosynthesis of isopentenylpyrophosphate, a central intermediate of isoprenoid formation, was investigated in six different bacterial organisms. Cell-free extracts of Myxococcus fulvus, Staphylococcus carnosus, Lactobacillus plantarum and Halobacterium cutirubrum converted [14C]acetyl-CoA or [14C]hydroxymethylglutaryl-CoA to [14C]mevalonic acid. Furthermore, [14C]mevalonic acid, [14C]mevalonate-5-phosphate and [14C]mevalonate-5-pyrophosphate were metabolized to [14C]isopentenylpyrophosphate in bacteria. In contrast, no intermediates of this reaction sequence could be detected using cell-free extracts of Zymomonas mobilis and Escherichia coli. These results indicate that at least two different pathways for the biosynthesis of isopentenylpyrophosphate are present in bacteria.
The United Kingdom transient ischaemic attack (UK-TIA) aspirin trial: final results. (1991)

From 1979-85, 2435 patients with a transient ischaemic attack or minor ischaemic stroke were randomly allocated to receive long term "blind" treatment with aspirin 600 mg twice daily (n = 815), aspirin 300 mg once daily (n = 806) or placebo (n = 814). No patient was lost to follow up. The "intention to treat" comparison included all the serious vascular events and deaths which occurred before the end of the follow up period on 30 September 1986. There was no difference in efficacy between the 300 mg and 1200 mg daily doses of aspirin, but the lower dose was undoubtedly less gastrotoxic. Also, there was no definite difference in the response of males and females to aspirin. The odds of suffering a major stroke, myocardial infarction or vascular death were 15% less in the combined aspirin groups compared with the placebo group (95% confidence interval 29% reduction to 3% increase in odds) which is compatible with the continuing overview of all the similar trials of antiplatelet drugs where the relative reduction in odds was 25%. There was no statistically significant reduction in the likelihood of either disabling major stroke and vascular death or vascular death occurring.
A Noninvasive Computerized Tail-Cuff System for Measuring Blood Pressure in Mice (1995)

We have validated a noninvasive computerized tail-cuff system for measuring blood pressure in mice. The system was designed to perform all functions automatically, including a programmable routine of cuff inflation and deflation, analysis and assignment of pulse rate and blood pressure, and recording of data electronically. To evaluate this system over a range of blood pressures, we gave groups of mice enalapril or NG-nitro-L-arginine methyl ester in their drinking water. For each of these groups, an equal number of control mice were given nothing in their drinking water. Tail-cuff blood pressures were recorded as the means of blood pressures determined on at least 3 days after at least 7 days of training. Tail-cuff enalapril and control group means were measured both 3 and 4 months after enalapril (or no drug) was begun; the group means at 3 months were not significantly different from the group means at 4 months. These results demonstrate that the system gives reproducible results. After the tail-cuff measurements were completed, intra-arterial blood pressures were attempted in all mice under unrestrained, unanesthetized conditions, and individual mouse (n = 22) blood pressures with the use of the two methods were compared. The blood pressures from individual mice by tail-cuff and intra-arterial methods were highly correlated (r = .86, P < .01). The means for the four mouse groups were also highly correlated (r = .98, P < .02).(ABSTRACT TRUNCATED AT 250 WORDS)
Electrospinning of Collagen Nanofiber Scaffolds from Benign Solvents (2009)

Nanofiber scaffolds of collagen have been fabricated via electrospinning using benign solvent systems as a replacement for 1,1,1,3,3,3 hexafluoro-2-propanol. Simple binary mixtures of phosphate-buffered saline and ethanol have been found to be highly effective for electrospinning. FTIR spectra suggest that the triple helical structure of collagen was conserved after dissolution and electrospinning. Crosslinking of the electrospun collagen scaffolds was achieved with standard methods.
Individual differences in light sensitivity affect sleep and circadian rhythms (2020)

Artificial lighting is omnipresent in contemporary society with disruptive consequences for human sleep and circadian rhythms because of overexposure to light, particularly in the evening/night hours. Recent evidence shows large individual variations in circadian photosensitivity, such as melatonin suppression, due to artificial light exposure. Despite the emerging body of research indicating that the effects of light on sleep and circadian rhythms vary dramatically across individuals, recommendations for appropriate light exposure in real-life settings rarely consider such individual effects. This review addresses recently identified links among individual traits, for example, age, sex, chronotype, genetic haplotypes, and the effects of evening/night light on sleep and circadian hallmarks, based on human laboratory and field studies. Target biological mechanisms for individual differences in light sensitivity include differences occurring within the retina and downstream, such as the central circadian clock. This review also highlights that there are wide gaps of uncertainty, despite the growing awareness that individual differences shape the effects of evening/night light on sleep and circadian physiology. These include (1) why do certain individual traits differentially affect the influence of light on sleep and circadian rhythms; (2) what is the translational value of individual differences in light sensitivity in populations typically exposed to light at night, such as night shift workers; and (3) what is the magnitude of individual differences in light sensitivity in population-based studies? Collectively, the current findings provide strong support for considering individual differences when defining optimal lighting specifications, thus allowing for personalized lighting solutions that promote quality of life and health.
Altered gene expression in neurons during programmed cell death: identification of c-jun as necessary for neuronal apoptosis. (1994)

We have examined the hypothesis that neuronal programmed cell death requires a genetic program; we used a model wherein rat sympathetic neurons maintained in vitro are deprived of NGF and subsequently undergo apoptosis. To evaluate gene expression potentially necessary for this process, we used a PCR-based technique and in situ hybridization; patterns of general gene repression and selective gene induction were identified in NGF-deprived neurons. A temporal cascade of induced genes included "immediate early genes," which were remarkable in that their induction occurred hours after the initial stimulus of NGF removal and the synthesis of some required ongoing protein synthesis. The cascade also included the cell cycle gene c-myb and the genes encoding the extracellular matrix proteases transin and collagenase. Concurrent in situ hybridization and nuclear staining revealed that while c-jun was induced in most neurons, c-fos induction was restricted to neurons undergoing chromatin condensation, a hallmark of apoptosis. To evaluate the functional role of the proteins encoded by these genes, neutralizing antibodies were injected into neurons. Antibodies specific for either c-Jun or the Fos family (c-Fos, Fos B, Fra-1, and Fra-2) protected NGF-deprived neurons from apoptosis, whereas antibodies specific for Jun B, Jun D, or three nonimmune antibody preparations had no protective effect. Because these induced genes encode proteins ranging from a transcription factor necessary for death to proteases likely involved in tissue remodeling concurrent with death, these data may outline a genetic program responsible for neuronal programmed cell death.
FlowSOM: Using self‐organizing maps for visualization and interpretation of cytometry data (2015)

The number of markers measured in both flow and mass cytometry keeps increasing steadily. Although this provides a wealth of information, it becomes infeasible to analyze these datasets manually. When using 2D scatter plots, the number of possible plots increases exponentially with the number of markers and therefore, relevant information that is present in the data might be missed. In this article, we introduce a new visualization technique, called FlowSOM, which analyzes Flow or mass cytometry data using a Self-Organizing Map. Using a two-level clustering and star charts, our algorithm helps to obtain a clear overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise. R code is available at https://github.com/SofieVG/FlowSOM and will be made available at Bioconductor.
Thinking Ahead: Autonomic Buildings (2002)

A new type of rearrangement is described for 3-C-branched chain aldoses. The studied transformation is based on the Mo(VI)-catalyzed isomerization of carbohydrate carbon skeleton and allows preparation of C-3 isomers of 3-C-branched aldoses in a simple way without formation of side products. This rearrangement at C-3 carbon differs from the previously described epimerization at C-2 of aldoses catalyzed by Mo(VI) ions, known as Bílik reaction. The potential of this new transformation is illustrated on the preparation of new, 3-C-methyl-D-glucose and 3-C-vinyl-D-glucose from 3-C-methyl-d-allose and 3-C-vinyl-D-allose, respectively.
Emended Description of Buttiauxella agrestis with Recognition of Six New Species of Buttiauxella and Two New Species of Kluyvera: Buttiauxella ferragutiae sp. nov., Buttiauxella gaviniae sp. nov., Buttiauxella brennerae sp. nov., Buttiauxella izardii sp. nov., Buttiauxella noackiae sp. nov., Buttiauxella warmboldiae sp. nov., Kluyvera cochleae sp. nov., and Kluyvera georgiana sp. nov. (1996)

A total of 219 strains belonging to the genera Buttiauxella and Kluyvera were studied; 171 of these strains were isolated from mollusks, mainly snails and slugs, obtained from around the world. On the basis of DNA-DNA hybridization data, the strains were grouped into 11 genomospecies. A total of 44 phenotypic characters were used to differentiate the genera Buttiauxella and Kluyvera at the genus level and to identify genomospecies. There were significantly higher phenotypic probability distances between the genomospecies in the genus Battiauxella and the genomospecies in the genus Kluyvera than between the genomospecies in the same genus. Therefore, the existence of Buttiauxella and Kluyvera as different genera was confirmed. The existence of new species necessitated broadening the definitions of both genera. In two cases, Buttiauxella species could not be quantitatively differentiated biochemically, and several other pairs of species could be separated only by the results of one biochemical test. Nonetheless, combinations of several characteristics were used in differentiate all of the species with levels of certainly ranging from log 10.79 to log 57.77 (calculated as probability distances). The following new species are proposed: Buttiauxella ferragutiae (type strain, ATCC 51602 [DSM 9390]), Buttiauxella gaviniae (type strain, ATCC 51604 [DSM 9393]), Buttiauxella brennerae (type strain, ATCC 51605 [DSM 9396]), Buttiauxella izardii (type strain, ATCC 51606 [DSM 9397]), Buttiauxella noackiae (type strain, ATCC 51607 [DSM 9401]), Buttiauxella warmboldiae (type strain, ATCC 51608 [DSM 9404]), Kluyvera cochleae (type strain, ATCC 51609 [DSM 9406]), and Kluyvera georgiana (type strain, ATCC 51603 [DSM 9409]).
Signaling via β1 integrins and mitogen-activated protein kinase determines human epidermal stem cell fate in vitro (1999)

Human epidermal stem cells express higher levels of β1 integrins and are more adhesive than keratinocytes that are destined to differentiate. To investigate whether high β1 integrin expression and adhesiveness are essential for maintaining keratinocytes in the stem cell compartment, we introduced a dominant-negative β1 integrin mutant, CD8β1, into cultured human keratinocytes, thereby interfering with β1 integrin function. Surface β1 integrin levels, adhesiveness, and mitogen-activated protein (MAP) kinase activation on fibronectin were reduced, and exit from the stem cell compartment was stimulated. Adhesiveness and proliferative potential were restored by overexpressing wild-type β1 integrin or by constitutive MAP kinase activation. Conversely, a dominant-negative MAP kinase kinase 1 mutant decreased adhesiveness and stem cell number in the absence of CD8β1. MAP kinase activation by α6β4-mediated adhesion and mitogens was normal in CD8β1 cells, and constitutive MAP kinase activation did not affect adhesion and proliferation of control keratinocytes. We conclude that β1 integrins and MAP kinase cooperate to maintain the epidermal stem cell compartment in vitro .
Peptide and Protein Drug Analysis (1999)

Furthering efforts to simulate the potency and specificity exhibited by peptides and proteins in healthy cells, this remarkable reference supplies pharmaceutical scientists with a wealth of techniques for tapping the enormous therapeutic potential of these molecules-providing a solid basis of knowledge for new drug design.Provides a broad, comp
Obfuscated Gradients Give a False Sense of Security: Circumventing Defenses to Adversarial Examples (2018)

We identify obfuscated gradients, a kind of gradient masking, as a phenomenon that leads to a false sense of security in defenses against adversarial examples. While defenses that cause obfuscated gradients appear to defeat iterative optimization-based attacks, we find defenses relying on this effect can be circumvented. We describe characteristic behaviors of defenses exhibiting the effect, and for each of the three types of obfuscated gradients we discover, we develop attack techniques to overcome it. In a case study, examining non-certified white-box-secure defenses at ICLR 2018, we find obfuscated gradients are a common occurrence, with 7 of 9 defenses relying on obfuscated gradients. Our new attacks successfully circumvent 6 completely, and 1 partially, in the original threat model each paper considers.
Insulin stimulates the dephosphorylation and activation of acetyl-CoA carboxylase. (1988)

The mechanism underlying the ability of insulin to acutely activate acetyl-CoA carboxylase [acetyl-CoA: carbon-dioxide ligase (ADP-forming), EC 6.4.1.2; AcCoA-Case] has been examined in Fao Reuber hepatoma cells. Insulin promotes the rapid activation of AcCoACase, as measured in cell lysates, and this stimulation persists to the same degree after isolation of AcCoACase by avidin-Sepharose chromatography. The insulin-stimulated enzyme, as compared with control enzyme, exhibits an increase in both citrate-independent and -dependent activity and a decrease in the Ka for citrate. Direct examination of the phosphorylation state of isolated 32P-labeled AcCoACase after insulin exposure reveals a marked decrease in total enzyme phosphorylation coincident with activation. The dephosphorylation due to insulin appears to be restricted to the phosphorylation sites previously shown to regulate AcCoACase activity. All of these effects of insulin are mimicked by a low molecular weight autocrine factor, tentatively identified as an oligosaccharide, present in conditioned medium of hepatoma cells. These data suggest that insulin may activate AcCoACase by inhibiting the activity of protein kinase(s) or stimulating the activity of protein phosphatase(s) that control the phosphorylation state of the enzyme.
Stable genetic transformation of Arabidopsis thaliana by Agrobacterium inoculation in planta (1994)

Stable genetic transformation of Arabidopsis thaliana was achieved by simple in planta inoculation of Agrobacterium tumefaciens strain LBA4404 harboring a binary vector pBI121. The transformation procedure, which we call in planta transformation, involves severing of apical shoots at their bases, inoculation with Agrobacterium at the severed sites, and in planta generation of shoots from the severed sites. On average, 5.5% of the newly formed shoots produced transformed progenies. These progenies (T-2 generation) contained T-DNA in the genome as examined by assaying the T-DNA encoded beta-glucuronidase and kanamycin resistance and by genomic Southern blot analysis, the copy number of the T-DNAs in the Arabidopsis genome being single (33%) or multiple. The genetic behavior of the transformants examined at the T-3 and T-4 generations or with the F-2 progenies of the outcrosses between transformants and wild-type plants showed that most of the inserted T-DNA are inherited in a Mendelian fashion. This procedure provides a new approach for simple and efficient transformation of A. thaliana, obviating the need for plant regeneration from tissue explants in vitro.
Integrative analysis of RUNX1 downstream pathways and target genes (2008)

This work is the first large-scale study attempting to identify the genetic networks regulated by RUNX1, a master regulator in the development of the hematopoietic system and leukemia. The biological pathways and target genes controlled by RUNX1 will have considerable importance in disease progression in both familial and sporadic leukemia as well as therapeutic implications.
Nuclear localization signals and human disease (2009)

Abstract In eukaryotic cells, the physical separation of the genetic material in the nucleus from the translation and signaling machinery in the cytoplasm by the nuclear envelope creates a requirement for a mechanism through which macromolecules can enter or exit the nucleus as necessary. Nucleocytoplasmic transport involves the specific recognition of cargo molecules by transport receptors in one compartment followed by the physical relocation of that cargo into the other compartment through regulated pores that perforate the nuclear envelope. The recognition of protein cargoes by their transport receptors occurs via amino acid sequences in cargo proteins called nuclear targeting signals. Both nuclear import and export of proteins are highly regulated processes that control, not only what cargo can enter and/or exit the nucleus, but also when in the cell cycle and in what cell type, the cargo can be transported. Deregulation of the nuclear transport of specific cargoes has been linked to numerous cancers and developmental disorders highlighting the importance of understanding the mechanisms underlying nucleocytoplasmic transport and particularly the modulation of the specific interactions between transporter receptors and nuclear targeting signals within target cargo proteins. © 2009 IUBMB IUBMB Life 61(7): 697–706, 2009
Efficient in toto targeted recombination in mouse liver by meganuclease‐induced double‐strand break (2006)

We demonstrate for the first time that meganucleases can be successfully delivered in animal and induce targeted genomic recombination in mice liver in toto. These results are an essential step towards the use of designed meganucleases and show the high potential of this technology in the field of gene therapy.
Dietary (n-3) Polyunsaturated Fatty Acids Improve Adipocyte Insulin Action and Glucose Metabolism in Insulin-Resistant Rats: Relation to Membrane Fatty Acids (1996)

International audience
Survey of chemotherapy of metastatic renal cancer. (1988)

A critical survey is made of cytotoxic chemotherapy of metastatic renal cancer. On the basis of representative summaries, only a few substances such as vinblastine, CCNU, hydroxyurea, and ifosfamide seem to act with some degree of success, but no specific antirenal cancer agent has as yet become available. This outline should provide a more realistic view of the therapeutic possibilities and of the limits of cytostatic chemotherapy in the metastatic phase of renal cancer. It is postulated that chemotherapy should feature more prominently in future therapeutic strategies. Newer cytostatic substances, i.e., second-generation alkylating agents and anthracyclines as well as platinum analogues, may present an advance with regard to side effects and tolerance but are discouraging with regard to their therapeutic efficiency in metastatic renal cancer.
An Agonist Anti-Human CD40 Monoclonal Antibody that Induces Dendritic Cell Formation and Maturation and Inhibits Proliferation of a Myeloma Cell Line (1999)

CD40, a 48-50 KD cell membrane molecule, member of the nerve growth factor receptor and tumor necrosis factor receptor superfamily, is an important costimulatory molecule during the immune response. Anti-CD40 monoclonal antibody (MAb) has been shown earlier to costimulate with IgM or phorbol esters resting B cells to proliferate, differentiate, secrete immunoglobulins, and switch isotype. Here we report on an agonistic mouse anti-human CD40 MAb 5C11. The specificity of this MAb was verified by flow cytometry, Western blotting, and competition with anti-CD40 MAb 89. We studied the effects of MAb 5C11 on a multimyeloma cell line, XG2, that expresses the CD40 antigen strongly and found that this MAb caused the homotypic aggregation of XG2, strongly suppressed XG2 proliferation, and led to its apoptosis after 24 hr of treatment. Interestingly, MAb 5C11 also triggered the generation, proliferation, and maturation of dendritic cells from peripheral blood monocytes, either by itself or in combination with GM-CSF and IL-4.