gebhart/patrepeval huggingface dataset:
SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins (2002)

Posttranslational modification of histones has emerged as a key regulatory signal in eukaryotic gene expression. Recent genetic and biochemical studies link H3-lysine 9 (H3-K9) methylation to HP1-mediated heterochromatin formation and gene silencing. However, the mechanisms that target and coordinate these activities to specific genes is poorly understood. Here we report that the KAP-1 corepressor for the KRAB-ZFP superfamily of transcriptional silencers binds to SETDB1, a novel SET domain protein with histone H3-K9-specific methyltransferase activity. Although acetylation and phosphorylation of the H3 N-terminal tail profoundly affect the efficiency of H3-K9 methylation by SETDB1, we found that methylation of H3-K4 does not affect SETDB1-mediated methylation of H3-K9. In vitro methylation of the N-terminal tail of histone H3 by SETDB1 is sufficient to enhance the binding of HP1 proteins, which requires both an intact chromodomain and chromoshadow domain. Indirect immunofluoresence staining of interphase nuclei localized SETDB1 predominantly in euchromatic regions that overlap with HP1 staining in nonpericentromeric regions of chromatin. Moreover, KAP-1, SETDB1, H3-MeK9, and HP1 are enriched at promoter sequences of a euchromatic gene silenced by the KRAB-KAP-1 repression system. Thus, KAP-1 is a molecular scaffold that is targeted by KRAB-ZFPs to specific loci and coordinates both histone methylation and the deposition of HP1 proteins to silence gene expression.
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB (2006)

A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.
Dual response regulators (NarL and NarP) interact with dual sensors (NarX and NarQ) to control nitrate- and nitrite-regulated gene expression in Escherichia coli K-12 (1993)

Two sensor proteins, NarX and NarQ, mediate nitrate regulation of anaerobic respiratory gene expression. Either of these sensors is sufficient to signal the presence of nitrate to the response regulator protein, NarL, a transcriptional activator and repressor. Two observations suggested the existence of a second response regulator that is also involved in nitrate regulation. First, narL null mutants retain residual nitrate induction of fdnG operon expression; this residual induction is absent in narX narQ double-null strains. Second, nitrate induction of aeg-46.5 operon expression is substantially enhanced in narL null strains (M.H. Choe and W.S. Reznikoff, J. Bacteriol. 173:6139-6146, 1991). We found that this nitrate induction requires either the NarX or the NarQ protein, consistent with the existence of a second response regulator. We designate this second regulator NarP. We isolated insertion mutants that are defective in aeg-46.5 operon expression. These insertions are in the narP gene, which encodes a response regulator that is 44% identical to the NarL protein. Null alleles of narP abolished aeg-46.5 induction and also eliminated the residual NarL-independent nitrate induction of fdnG operon expression. Both the NarX and NarQ proteins communicate with both the NarP and NarL proteins. We found that the primary signal for NarP-dependent aeg-46.5 operon induction is nitrite rather than nitrate. By contrast, nitrite is a relatively weak signal for NarL-dependent induction. In narX null strains, nitrate was an efficient signal for NarL-dependent induction, and this induction required the NarQ protein. We conclude that, in wild-type strains, the NarQ protein communicates the presence of nitrite to both the NarP and NarL proteins and that the NarX protein inhibits this communication with the NarL protein.
Squishy Non‐Spherical Hydrogel Microparticles (2009)

Recent advances in the synthesis of polymeric colloids have opened the doors to new advanced materials. There is strong interest in using these new techniques to produce particles that mimic and/or interact with biological systems. An important characteristic of biological systems that has not yet been exploited in synthetic polymeric colloids is their wide range of deformability. A canonical example of this is the human red blood cell (RBC) which exhibits extreme reversible deformability under flow. Here we report the synthesis of soft polymeric colloids with sizes and shapes that mimic those of the RBC. Additionally, we demonstrate that the mechanical flexibility of the colloids can be reproducibly varied over a large range resulting in RBC-like deformability under physiological flow conditions. These materials have the potential to impact the interaction between biological and synthetic systems.
In vivo Efficacy of Marimastat and Chemoradiation in Head and Neck Cancer Xenografts (2008)

Chemoradiation + marimastat therapy had delayed tumor growth, compared to the chemoradiation alone. Based on these results, marimastat may work in combination with chemotherapy and radiation to inhibit tumor growth.
A new look at logic synthesis (1980)

Despite many attempts to generate hardware implementations automatically from functional specifications, the literature does not record any commercial success. Previous efforts have dealt primarily with technology-independent primitives and have emphasized circuit minimization. However, larger scales of integration have made other design requirements and technology restrictions as important as circuit count, and have increased the cost of making an engineering change. Thus it is becoming increasingly important to insure that initial chip designs are correct. This paper outlines an investigation into the feasibility of logic synthesis in this new context. A system is described which will produce a naive implementation automatically from a functional specification, and then will interact with the designer, allowing him to evaluate it with respect to these many factors, and to improve it incrementally by applying local transformations until it is acceptable for manufacture. The use of simple local transformations will insure correct implementations, will isolate technology-specific data, and will allow the total process to be applied to larger VLSI designs. This approach has been tested on the design of a single chip with encouraging results. A prototype synthesis system is now being used to perform further experiments.
Majorana fermions in a tunable semiconductor device (2010)

The experimental realization of Majorana fermions presents an important problem due to their non-Abelian nature and potential exploitation for topological quantum computation. Very recently Sau et al. [Phys. Rev. Lett. 104, 040502 (2010)] demonstrated that a topological superconducting phase supporting Majorana fermions can be realized using surprisingly conventional building blocks: a semiconductor quantum well coupled to an $s$-wave superconductor and a ferromagnetic insulator. Here we propose an alternative setup, wherein a topological superconducting phase is driven by applying an in-plane magnetic field to a (110)-grown semiconductor coupled only to an $s$-wave superconductor. This device offers a number of advantages, notably a simpler architecture and the ability to tune across a quantum phase transition into the topological superconducting state while still largely avoiding unwanted orbital effects. Experimental feasibility of both setups is discussed in some detail.
Steroid hormone regulation of free secretory component in the rat uterus. (1983)

The present studies analysed the uterine free secretory component (SC) response to steroid hormones, and correlated effects on SC with those on IgA. Administration of oestradiol for 3 days to ovariectomized rats significantly increased the levels of SC in uterine secretions, when compared to those in saline-injected controls. This response was dose-dependent and specific for oestrogens, since progesterone, testosterone and glucocorticoids had no effect. The oestradiol-induced elevation in SC levels occurred in parallel with that of IgA. Time course studies of SC and IgA in uterine secretions indicated that both proteins accumulated in nearly identical patterns following oestradiol administration. The oestradiol-stimulated accumulation of SC, however, appears to be independent of IgA since dexamethasone treatment with oestradiol decreased IgA but not SC levels in uterine secretions. In contrast to dexamethasone, progesterone antagonized the oestradiol effect on both uterine IgA and SC. The uterine SC response to oestradiol was also observed in vitro. Incubation of uterine tissue following oestradiol exposure in vivo resulted in a significant accumulation of SC in the culture medium, when compared to levels from control uteri. Addition of either cycloheximide or colchicine to uterine incubation media significantly decreased the effect of oestradiol on SC accumulation. These results suggest that oestrogen regulation of uterine SC may involve stimulation of its synthesis. In addition, our findings indicate that oestradiol control of SC in uterine secretions may be responsible for the movement of IgA from uterine tissues to lumen.
Discovery of indolyl acrylamide derivatives as human diacylglycerol acyltransferase-2 selective inhibitors (2012)

A series of indolyl acrylamide derivatives was synthesized as potential diacylglycerol acyltransferase (DGAT) inhibitors. Furfurylamine containing indolyl acrylamide derivative 5h exhibited the most potent DGAT inhibitory activity using microsomes prepared from rat liver. Further evaluation against human DGAT-1 and DGAT-2 identified indolyl acrylamide analogues as selective inhibitors against human DGAT-2. In addition, the most potent compound 5h inhibited triglyceride synthesis dose-dependently in HepG2 cell lines.
Validating automated speaking tests (2010)

This paper presents evidence that supports the valid use of scores from fully automatic tests of spoken language ability to indicate a person’s effectiveness in spoken communication. The paper reviews the constructs, scoring, and the concurrent validity evidence of ‘facility-in-L2’ tests, a family of automated spoken language tests in Spanish, Dutch, Arabic, and English. The facility-in-L2 tests are designed to measure receptive and productive language ability as test-takers engage in a succession of tasks with meaningful language. Concurrent validity studies indicate that scores from the automated tests are strongly correlated with the scores from oral proficiency interviews. In separate studies with learners from each of the four languages the automated tests predict scores from the live interview tests as well as those tests predict themselves in a test-retest protocol (r = 0.77 to 0.92). Although it might be assumed that the interactive nature of the oral interview elicits performances that manifest a distinct construct, the closeness of the results suggests that the constructs underlying the two approaches to oral assessment have a stable relationship across languages.
Selected cysteine residues in transmembrane domains of mu-opioid receptor are critical for effects of sulfhydryl reagents. (2000)

The effects of sulfhydryl-specific methanethiosulfonate (MTS) derivatives on mu-opioid receptor binding were examined in Chinese hamster ovary (CHO) cells that stably express mu-opioid receptors (HmuCHO). Three charged MTS derivatives inhibited the binding of [(3)H][D-Ala(2),N-MePhe(4),Gly-ol(5)]-enkephalin to mu-opioid receptors with IC(50) values ranging from 0.12 to 13 mM. Further characterization of the mu-opioid receptor interactions with ethylammonium MTS (the most potent among tested MTS reagents) revealed that ethylammonium MTS inhibition of ligand binding to the receptor was irreversible, with both the maximal receptor binding (B(max)) and the binding affinity (K(d)) being changed. Preincubation of HmuCHO cells with [D-Ala(2),N-MePhe(4), Gly-ol(5)]-enkephalin or naloxone prevented the receptor inactivation normally caused by MTS derivatives, indicating that the reactions may occur within or near the ligand-binding pocket on the receptor. To identify the susceptible sulfhydryl groups, each of the cysteine residues in the mu-receptor transmembrane domains were substituted with serine by site-directed mutagenesis. All of the mutant receptors transiently expressed in COS cells had receptor binding properties similar to the wild-type receptors. However, four mutant receptors with a serine substitution in transmembrane domain III (C161S), IV (C192S), V (C237S), or VII (C332S) displayed significant resistance against MTS inhibition compared with the wild-type receptor. We conclude that these four cysteine residues react with MTS reagents and are responsible for the effect of the MTS reagents on mu-opioid receptor binding.
Effect of long-term vagal stimulation on food intake and body weight during diet induced obesity in rats. (2007)

Regulation of food intake and body weight is accomplished by several mechanisms. CNS receives information from periphery and modifies food intake mainly by vagal nerves that provide the major neuroanatomical link between gastrointestinal sites stimulated during food intake and CNS sites that control feeding behavior and metabolism. Gastric mechanoreceptors and jejunal chemoreceptors activated by food or vagal nerve stimulation (VNS), which mimic the physiological input, suppress feeding within short-term regulation. Our research was aimed on determination the role of electrical VNS in long-term control of food intake and body weight in diet induced obesity fed rats. Food intake, body weight and epididymal fat pad were assessed in male Wistar rats divided into three groups (controls vs. VNS). Rats were implanted with microchip and kept during the whole study (100 days) on diet induced obesity. Vagal nerve was stimulated by electrical rectangular pulses duration 10 ms, amplitude 200 mV, frequency 0.05 Hz generated by microchip. In control group surgery produced no significant changes in meal size and body weight gain as compared to intact group. In contrast, significantly decreased epididymal fat pad weight, decreased meal size with effect on decreased weight gain was observed in VNS rats. Data support theory that VNS can increase vagal afferent signal conduct to CNS and mimics the satiety signals leading to reduce food intake and body weight gain.
Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different human organs vulnerable to 2019-nCoV infection (2020)

It has been known that, the novel coronavirus, 2019-nCoV, which is considered similar to SARS-CoV, invades human cells via the receptor angiotensin converting enzyme II (ACE2). Moreover, lung cells that have ACE2 expression may be the main target cells during 2019-nCoV infection. However, some patients also exhibit non-respiratory symptoms, such as kidney failure, implying that 2019-nCoV could also invade other organs. To construct a risk map of different human organs, we analyzed the single-cell RNA sequencing (scRNA-seq) datasets derived from major human physiological systems, including the respiratory, cardiovascular, digestive, and urinary systems. Through scRNA-seq data analyses, we identified the organs at risk, such as lung, heart, esophagus, kidney, bladder, and ileum, and located specific cell types (i.e., type II alveolar cells (AT2), myocardial cells, proximal tubule cells of the kidney, ileum and esophagus epithelial cells, and bladder urothelial cells), which are vulnerable to 2019-nCoV infection. Based on the findings, we constructed a risk map indicating the vulnerability of different organs to 2019-nCoV infection. This study may provide potential clues for further investigation of the pathogenesis and route of 2019-nCoV infection.
Isolation of Intact Plastids from Protoplasts from Castor Bean Endosperm (1978)

Protoplasts were prepared from castor bean (Ricinus communis) endosperm by treatment with a mixture of the commercial enzymes Macerozyme R-10 and Cellulose "Onozuka" R-10. The protoplasts were gently ruptured by forcing the suspension through a hypodermic needle and the homogenate centrifuged on a linear sucrose gradient. From such a homogenate the mitochondria are recovered at their typical isopycnic density of 1.18 g/ml, but the glyoxysomes are retained, with other membranes, at a density of 1.13. The plastids reach their typical density of 1.22 on the gradient and are thus clearly separated from other organelles. Moreover, since essentially all of the ribulose bisphosphate carboxylase activity on the gradient is present in this fraction it can be concluded that the plastids are intact and have been recovered in high yield.
Thermal characteristics of a synthetic hydrotalcite-like material (1992)

The thermal and structural characteristics of a synthetic hydrotalcite-like material are described. Weight losses at 68 and 218 °C are observed, which are attributed to the loss of physisorbed and intercalated water, respectively. The loss of the intercalated water is accompanied by a decrease in the (003) repeat distance from 7.59 to 6.60 Å. A broad thermal transition is reported between 270 and 420 °C which results from dehydroxylation of the lattice and decomposition of the charge-balancing carbonate anion. During this decomposition, water and CO2are evolved simultaneously. The changes in crystal structure of the material which accompany these losses are described. Chemical analysis suggests that both carbonate and bicarbonate species are present within the interlayer region.
Publisher’s Note: Nanoparticle-Free Single Molecule Anti-Stokes Raman Spectroscopy [Phys. Rev. Lett.94, 058301 (2005)] (2005)

Received 29 March 2005DOI:https://doi.org/10.1103/PhysRevLett.94.139901©2005 American Physical Society
Different Expression of ICAM-1 and LFA-1 Alpha by Peripheral Leukocytes During Respiratory Syncytial Virus and Influenza Virus Infection in Young Children (2000)

We compared the expression of intercellular adhesion molecule (ICAM)-1 and lymphocyte function-associated antigen (LFA)-1 alpha (alpha) on the surfaces of peripheral immunocompetent cells of young children infected with respiratory syncytial virus (RSV) and influenza virus. Flow cytometric analysis revealed a significantly higher percentage of CD14 + monocytes/macrophages that were strongly ICAM-1-positive in the influenza group than in age-matched controls, whereas the ICAM-1 expression levels of the RSV and control groups did not differ significantly. Analysis of LFA-1alpha expression by CD3 + T lymphocytes showed a significantly higher percentage of strongly positive cells in the influenza group than in the age-matched controls. By contrast, the percentage of cells that were strongly LFA-1alpha-positive was significantly lower in the RSV group than in the age-matched controls. These results suggest that no increase of adhesion molecule expression occurs in vivo in patients with RSV infection, and also that there is little activation of peripheral blood monocytes/macrophages and T lymphocytes in young children with RSV infection.
Antibody‐Drug Conjugate Therapy (2009)

This chapter contains sections titled: Introduction The Role of Receptor-Mediated Endocytosis in Drug Delivery by Immunoconjugates Characteristics of an FDA-Approved Immunoconjugate Tumor Cell Surface Targets for ADCs Drug Delivery Vehicles The Choice of Drug Bystander Effect Linker Choice Drug Conjugation Site Optimizing the Number of Drugs per Antibody Summary References
Effect of different forest structures on growth of Bredia quadrangularis. (2009)

Distribution properties and growth of Bredia quadrangularis population under different forest structures was studied by quadrat in Qingliangfeng Nature Reserve,Zhejiang province.The results showed that B.quadrangularis mainly distributes in both sides of the shaded and wet valley.The diameter and height growth of the plant in Cyclobalanopsis glauca forest are significantly higher than that in Cunninghamia lanceolata forest and Pinus massoniana one.There are 214 species in B.quadrangularis community,most of them are shrubs(63 species) and herbs(115 species).The spatial distribution pattern of the community of B.quadrangularis is aggregation distribution,and it has strong vertical structure,high Simpson diversity,Pielou evenness and richness index.
An Efficient Palladium-Catalyzed Synthesis of Cinnamaldehydes from Acrolein Diethyl Acetal and Aryl Iodides and Bromides (2003)

The reaction of aryl iodides and bromides with acrolein diethyl acetal in the presence of Pd(OAc)(2), (n)()Bu(4)NOAc, K(2)CO(3), KCl, and DMF, at 90 degrees C until the disappearance of the acetal followed by the addition of 2 N HCl to the crude reaction mixture, affords cinnamaldehydes in good to high yields. A variety of functional groups are tolerated in the aryl halides, including ether, aldehyde, ketone, ester, dialkylamino, nitrile, and nitro groups. The presence of substituents close to the oxidative addition site does not hamper the reaction.
Combination chemotherapy (5-fluorouracil, methyl-CCNU, mitomycin C) versus 5-fluorouracil alone for advanced previously untreated colorectal carcinoma. A phase III study of the Piedmont Oncology Association. (1986)

One-hundred thirty eligible patients with advanced colorectal carcinoma who had received no prior chemotherapy were randomized to either methyl-CCNU, 70 mg/m2 orally every 6 weeks on day 1, mitomycin C, 10 mg/m2 intravenously every 6 weeks on day 1, and 5-fluorouracil (5-FU), 400 mg/m2 intravenously weekly--(MMF)--or 5-FU, 600 mg/m2 intravenously weekly (5-FU). One hundred twenty-six patients are evaluable for response. Of 62 patients treated with MMF, one (2%) achieved complete remission, and three (5%) attained partial remission. Of 64 patients treated with 5-FU, two (3%) achieved complete remission, and eight (13%) attained partial remission. The median survival for patients receiving MMF was 9.5 months compared with 10.3 months for patients receiving 5-FU. The survival distributions for the two regimens were not significantly different, either unadjusted or adjusted for pretreatment characteristics. Performance status and lactic dehydrogenase (LDH) were both significantly associated with survival. Patients with liver metastases only and normal liver function tests had a median survival of 19.8 months and a 40% response rate. This randomized phase III trial did not show any therapeutic advantage for MMF compared to 5-FU therapy alone in advanced colorectal cancer. In addition, hematologic toxicity was significantly greater with the combination (MMF) regimen.