gebhart/patrepeval huggingface dataset:
Analysis of ftsZ mutations that confer resistance to the cell division inhibitor SulA (SfiA) (1990)

In Escherichia coli, the ftsZ gene is thought to be an essential cell division gene. Several dominant mutations that make lon mutant cells refractory to the cell division inhibitor SulA, sulB9, sulB25, and sfiB114, have been mapped to the ftsZ gene. DNA sequence analysis of these mutations and the sfiB103 mutation confirmed that all of these mutations mapped within the ftsZ gene and revealed that the two sulB mutations were identical and by selection for resistance to higher levels of SulA, contained a second mutation within the ftsZ gene. We therefore propose that these mutations be redesignated ftsZ(Rsa) for resistance to SulA. A procedure involving mutagenesis of ftsZ cloned on low-copy-number vectors was used to isolate three additional ftsZ(Rsa) mutations. DNA sequence analysis of these mutations revealed that they were distinct from the previously isolated mutations. One of these mutations, ftsZ3(Rsa), led to an altered FtsZ protein that could no longer support cell growth but still conferred the Rsa phenotype in the presence of ftsZ+. In addition to being resistant to SulA, all ftsZ(Rsa) mutations also conferred resistance to a LacZ-FtsZ hybrid protein (ZZ). One possibility is that FtsZ functions as a multimer and that FtsZ(Rsa) mutant proteins have an increased ability for multimerization, making them resistant to SulA and ZZ.
A technique for the deconvolution of the renogram (1974)

The renogram in its standard form does not express the renal handling of Hippuran in its simplest and most explicit form. The curve obtained, R(t), is a convolution of the input function from the blood to the kidney, I(t), and the impulse response function of the kidney, H(t). H(t) is the response to a bolus injection and represents the renal handling in its simplest form. It can be calculated by deconvolution since I(t) and R(t) can both be obtained in the investigation. A method involving Laplace transforms is used.
Comprehensive Design and Optimization of a High-Power-Density Single-Phase Boost PFC (2009)

The design of a single-phase boost power-factor-correction (PFC) circuit is associated with a large variety of considerations, such as the following questions. Which operation mode should be selected (e.g., continuous or discontinuous operation)? How many interleaved boost cells are advantageous? Which switching frequency should be selected? What is the optimum number of EMI input filter stages? Which semiconductor technology should be chosen? All these issues have a significant influence on the converter efficiency and power density. In this paper, the aforementioned questions are addressed for exemplary specifications of the PFC (300-W output power, 400-V output voltage, and 230-V mains voltage), whereby the focus in the design is mainly put on very high power density. As a result, different design points are identified and comparatively evaluated. By considering different aspects such as volume, losses, capacitor lifetime, and also cost issues (e.g., by additional current sensors or expensive silicon carbide devices), a dual-interleaved PFC operated in discontinuous conduction mode at 200 kHz is selected. With an experimental prototype, a superior power density of 5.5 kW/L and a system efficiency of 96.4% are achieved, which is close to the values predicted by the design procedure. Furthermore, measurements verify a near-unity power factor (PF = 99.7%) and the compliance with electromagnetic compatibility conducted noise emission standards. Finally, it is investigated to which extent the power density could be further increased by an integration of the input filter in the PCB.
Interactions of CD4 with MHC class II molecules, T cell receptors and p56 lck (1993)

CD4 and CD8 are members of the immunoglobulin supergene family of proteins, and function as co-receptors with the T cell receptor (TCR) in binding MHC class II or class I molecules, respectively. Within this multimeric complex, CD4 interacts with three distinct ligands. CD4 interacts through its D1 and D2 domains with MHC class II proteins, through its D3 and D4 domains with T cell receptors, and through its cytoplasmic tail with p56lck, a src-related, protein tyrosine kinase. Each of these interactions is important in the function of CD4 and will be discussed in turn.
On the statistical assessment of classifiers using DNA microarray data (2006)

The method proposed provides statistically significant answers to precise questions relevant for the diagnosis and prognosis of cancer. We found that, with as few as 15 examples, it is possible to train statistically significant classifiers for colon cancer diagnosis. As for the definition of the number of genes sufficient for a reliable classification of colon cancer, our results suggest that it depends on the accuracy required.
Breaking boundaries: active information acquisition across learning and diagnosis (2009)

To date, the processes employed for active information acquisition during periods of learning and diagnosis have been considered as separate and have been applied in distinct phases of analysis. While active learning centers on the collection of information about training cases in order to build better predictive models, diagnosis uses fixed predictive models for guiding the collection of observations about a specific test case at hand. We introduce a model and inferential methods that bridge these phases of analysis into a holistic approach to information acquisition that considers simultaneously the extension of the predictive model and the probing of a case at hand. The bridging of active learning and real-time diagnostic feature acquisition leads to a new class of policies for learning and diagnosis. 1
[Phylogeny diversity of the nitrite reductase gene (nirS) in the sediments of the eutrophic East Lake, Wuhan]. (2011)

There are diverse and abundant NirS-like denitrifiers inhabited in the sediments of East Lake, Wuhan. The diversity indices and spatial distribution of these communities are affected by the content of TN, NH4- and NO3- nutrients in the sediments.
Integrated Profiling of MicroRNAs and mRNAs: MicroRNAs Located on Xq27.3 Associate with Clear Cell Renal Cell Carcinoma (2010)

Our study provided a two-dimensional map of the mRNA and miRNA expression profiles of ccRCC using deep sequencing technology. Our results indicate that the phenotypic status of ccRCC is characterized by a loss of normal renal function, downregulation of metabolic genes, and upregulation of many signal transduction genes in key pathways. Furthermore, it can be concluded that downregulation of miRNA genes clustered on Xq27.3 is associated with ccRCC.
Importance of Hydrolysis of Amino Acid Moiety in Water-Soluble Prodrugs of Disodium Cromoglycate for Increased Oral Bioavailability. (1992)

The relationship between physicochemical properties and oral absorption was investigated in prodrugs for the oral delivery of disodium cromoglycate (DSCG). To improve the lipophilicity of DSCG, various lipophilic moieties were introduced into the twin carboxyl groups. However, this did not lead to improved oral absorption in rabbits because of loss of water solubility, in spite of improved lipophilicity. Water-soluble prodrugs, in which an amino acid was introduced into a hydroxy group by ester linkage in addition to ethyl residues at twin carboxyl groups of DSCG, were synthesized and examined for oral absorption in rabbits and rats. The oral absorption of these prodrugs was affected by the species of amino acids introduced as a water-soluble moiety. Therefore, we examined the relation between the oral absorption of water-soluble prodrugs and the hydrolysis rate of the amino acid moiety. A good linear correlation was obtained between the oral absorption and the hydrolysis rate constant catalyzed by digestive enzymes, trypsin or alpha-chymotrypsin. It was thus concluded that the amino acid moiety of water-soluble prodrugs must be rapidly hydrolyzed to a permeable lipophilic prodrug still possessing the ethyl moiety at twin carboxyl groups in the small intestinal tract for good oral absorption.
WOUND COMPLICATIONS IN PARS PLANA VITRECTOMY (1993)

Eighteen eyes with examples of clinically important wound-related complications are reported. These include hemorrhage, fibrous ingrowth, and tractional or mechanical problems. Wound hemorrhages may occur early or late and can be the cause of substantial morbidity. Furthermore, intraocular blood is undesirable because it may provoke cataract formation, contribute to the postvitrectomy fibrin syndrome, induce fibrovascular proliferation, and lead to further surgery to remove the blood. Fibroplasia at the wound sites may in some patients contribute to the development of anterior hyaloid fibrovascular proliferation. Fibrous ingrowth may occur early or late and may be self-limited, with few side effects, or florid, with progression to retinal detachment or phthisis bulbi. Dilation of subconjunctival blood vessels entering the incision site suggests the presence of fibrous ingrowth or fibrovascular proliferation occurring in the vitreous base. Tractional or mechanical problems include retinal breaks, which may or may not lead to retinal detachment, and scarring within the vitreous base, which may contribute to the formation of anterior vitreoretinal traction or anterior proliferative vitreoretinopathy.
DX-9065a, a New Synthetic, Potent Anticoagulant and Selective Inhibitor for Factor Xa (1994)

DX-9065a is an orally active newly synthesized and specific inhibitor for factor Xa. We have examined the property of DX-9065a in vitro and ex vivo. DX-9065a prolonged human plasma recalcification time, APTT and PT. Its doubling concentrations for clotting times of each coagulation assay were 0.49, 0.97 and 0.52 microM, respectively. Kinetic study revealed that DX-9065a inhibited competitively human factor Xa (Ki value: 41 nM). Ki values (microM) for other human serine proteases were as follows; thrombin > 2000, trypsin 0.62, chymotrypsin > 2000, plasmin 23, t-PA 21, plasma kallikrein 2.3 and tissue kallikrein 1000. DX-9065a up to 100 microM had no effects on human platelet aggregation. After intravenous or oral administration, DX-9065a significantly prolonged APTT and PT with a dose dependent manner. These effects were well correlated with anti-Xa activity in plasma. These results suggest that DX-9065a may become an anticoagulant by means of the specific inhibition of factor Xa.
DNA Sensing by Silicon Nanowire: Charge Layer Distance Dependence (2008)

To provide a comprehensive understanding of the field effect in silicon nanowire (SiNW) sensors, we take a systematic approach to fine tune the distance of a charge layer by controlling the hybridization sites of DNA to the SiNW preimmobilized with peptide nucleic acid (PNA) capture probes. Six target DNAs of the same length, but differentiated successively by three bases in the complementary segment, are hybridized to the PNA. Fluorescent images show that the hybridization occurs exclusively on the SiNW surface between the target DNAs and the PNA. However, the field-effect response of the SiNW sensor decreases as the DNA (charge layer) moves away from the SiNW surface. Theoretical analysis shows that the field effect of the SiNW sensor relies primarily on the location of the charge layer. A maximum of 102% change in resistance is estimated based on the shortest distance of the DNA charge layer (4.7 A) to the SiNW surface.
When API Mass Spectrometry Meets Super Atmospheric Pressure Ion Sources (2015)

In a tutorial paper on the application of free-jet technique for API-MS, John Fenn mentioned that "…for a number of years and a number of reasons, it has been found advantageous in many situations to carry out the ionization process in gas at pressures up to 1000 Torr or more" (Int. J. Mass Spectrom. 200: 459-478, 2000). In fact, the first ESI mass spectrometer constructed by Yamashita and Fenn had a counter-flow curtain gas source at 1050 Torr (ca. 1.4 atm) to sweep away the neutral (J. Phys. Chem. 88: 4451-4459, 1984). For gaseous ionization using electrospray plume, theoretical analysis also shows that "super-atmospheric operation would be more preferable in space-charge-limited situations."(Int. J. Mass Spectrom. 300: 182-193, 2011). However, electrospray and the corona-based chemical ion source (APCI) in most commercial instrument are basically operated under an atmospheric pressure ambient, perhaps out of the concern of safety, convenience and simplicity in maintenance. Running the ion source at pressure much higher than 1 atm is not so common, but had been done by a number of groups as well as in our laboratory. A brief review on these ion sources will be given in this paper.
Transcription in vivo from SV40 early promoter deletion mutants without repression by large T antigen. (1983)

Transfection of monkey cells with recombinant plasmids containing a beta-globin coding region fused to wild-type or deleted simian virus 40 (SV40) early region promoters has allowed an analysis of the transcriptional activity of these promoters in the absence of repression by large T antigen. We find that deletion of the TATA sequence does not reduce the transcriptional effectiveness of the promoter; however, the 5' ends of the transcripts are heterogeneous rather than being restricted to the usual sites. The short GC-rich repeat sequences between nucleotides 37 and 107 and the tandemly repeated 72-bp segment between nucleotides 107 and 250 are each essential for promoter function. The GC-rich repeats are functionally redundant and probably interchangeable, since several subsets of two or three of the GC-rich segments are sufficient. One copy of the 72-bp sequence is sufficient to permit transcription. Moreover, the 72-bp repeat sequences function normally even if they are inverted relative to their normal orientation.
The alkylation of 3H‐phenoxazin‐3‐one derivatives (1982)

Abstract 2‐Alkyl‐, 4‐alkyl‐, and 2,4‐dialkyl‐3 H ‐phenoxazin‐3‐ones were prepared by reacting 3 H ‐phenoxazin‐3‐one with alkyl radicals in aqueous acetonitrile at 70–75°. The alkyl radicals were generated from the silver catalysed oxidative decarboxylation of acids with peroxydisulphate.
Enhancing DNA hybridization kinetics through constriction-based dielectrophoresis (2009)

The enhancement of signal sensitivity through the scaling-down of sensors presents mass transport limitations that can arrest the sensitivity gains obtained as a result of miniaturization. To alleviate these limitations, we study the application of constriction-based dielectrophoresis methods to enhance transport through pre-concentration of target DNA in the vicinity of the diffusion layer of the sensor, on which capture probe DNA molecules were immobilized. We demonstrate that constriction-based DEP pre-concentration was not impeded by scaling-down of the sensor, as long as the sensor electrode was composed of nanostructured edges and was coupled to an equally scaled down insulating constriction within a microfluidic channel to enhance the focusing effects of the constrictions and edges. Furthermore, as a result of the high focusing fields, pre-concentration of single-stranded target DNA occurred in the vicinity of the sensor pad within the relatively high ionic strength buffers required for DNA hybridization, with minimal degradation of capture probe molecules. Finally, constriction-based DEP resulted in an almost immediate pre-concentration of target DNA in the vicinity of the sensor electrode diffusion layer, resulting in a ten-fold enhancement of the DNA hybridization kinetics at target concentration values down to the sensitivity limit of 10 pM for the sensor platform.
Synthesis of the Functionalized Macrocyclic Core of Proteasome Inhibitors TMC-95A and B (2001)

An ordered assembly of four building blocks (2–5) forms the basis of the synthesis of 1, which contains the core structure of TMC-95A and B—two potent proteasome inhibitors (see scheme; TIPS=triisopropylsilyl, Cbz=benzoxycarbonyl, Boc=tert-butoxycarbonyl).
Detection of mutant Ha-ras genes in chemically initiated mouse skin epidermis before the development of benign tumors. (1992)

An activated Ha-ras oncogene has been consistently found in chemically initiated benign and malignant mouse skin tumors, and an activated ras oncogene has been shown to initiate the process of mouse skin carcinogenesis. However, the exact timing of mutational activation of the Ha-ras gene relative to application of the chemical carcinogen is not known. A sensitive mutation-specific PCR technique was used to experimentally address the timing of Ha-ras gene mutational activation. This technique can detect mutant Ha-ras alleles in the presence of a very large excess of normal ras alleles. Activated Ha-ras genes with 61st codon A----T mutations were found in the epidermis of mice 1 week after topical initiation with 7,12-dimethylbenz[a]anthracene or urethane by using this assay. These results were confirmed by Xba I restriction fragment length polymorphism analysis and direct DNA sequencing. One week after initiation is 1-2 months before the appearance of benign papillomas that harbor activated Ha-ras oncogenes when the initiated mice are promoted with the tumor promoter phorbol 12-myristate 13-acetate. Our data support the hypothesis that initiated epidermal cells containing an activated Ha-ras gene can remain dormant in the skin until a tumor promoter induces regenerative hyperplasia that allows for outgrowth of these cells with an activated ras oncogene to give rise to a benign papilloma.
MCPIP1 – an important RNase controlling intracellular RNA pool (2018)

Post-transcriptional regulation of mRNA pool is a key process coordinating the proper functioning of cells. This tight control of RNA molecules allows cells to quickly adapt to environmental conditions without the activation of translation. Degradation of RNA is one of the important mechanisms regulating RNA homeostasis. One of the protein involved in this process is a RNase called MCPIP1, whose function was described in 2009. The enzymatic activity of MCPIP1 is tightly linked to the zinc finger domain responsible for RNA binding and a catalytic domain that participates in endonucleolytic digestion of RNA molecules. MCPIP1 recognizes and cleaves a wide array of substrates, both endogenous mRNA, miRNA, and RNA viruses. Although MCPIP1 structure has not yet been resolved, it is known how an active center is formed and what motives in the RNA sequence are recognized and digested. MCPIP1 recognizes and cleaves RNA within the hairpin structure. Broad spectrum of MCPIP1 substrates makes this protein an important regulator of many biological processes such as inflammation, cell differentiation, tumor growth or viral infections. In this review we describe a structure, properties and biological function of RNase called MCPIP1.
Crystal Structure of Butyrate Kinase 2 from Thermotoga maritima , a Member of the ASKHA Superfamily of Phosphotransferases (2009)

The enzymatic transfer of phosphoryl groups is central to the control of many cellular processes. One of the phosphoryl transfer mechanisms, that of acetate kinase, is not completely understood. Besides better understanding of the mechanism of acetate kinase, knowledge of the structure of butyrate kinase 2 (Buk2) will aid in the interpretation of active-site structure and provide information on the structural basis of substrate specificity. The gene buk2 from Thermotoga maritima encodes a member of the ASKHA (acetate and sugar kinases/heat shock cognate/actin) superfamily of phosphotransferases. The encoded protein Buk2 catalyzes the phosphorylation of butyrate and isobutyrate. We have determined the 2.5-A crystal structure of Buk2 complexed with (beta,gamma-methylene) adenosine 5'-triphosphate. Buk2 folds like an open-shelled clam, with each of the two domains representing one of the two shells. In the open active-site cleft between the N- and C-terminal domains, the active-site residues consist of two histidines, two arginines, and a cluster of hydrophobic residues. The ATP binding region of Buk2 in the C-terminal domain consists of abundant glycines for nucleotide binding, and the ATP binding motif is similar to those of other members of the ASKHA superfamily. The enzyme exists as an octamer, in which four disulfide bonds form between intermolecular cysteines. Sequence alignment and structure superposition identify the simplicity of the monomeric Buk2 structure, a probable substrate binding site, the key residues in catalyzing phosphoryl transfer, and the substrate specificity differences among Buk2, acetate, and propionate kinases. The possible enzyme mechanisms are discussed.
Hypoadiponectinemia as a Marker of Adipocyte Dysfunction—Part II: The Functional Significance of Low Adiponectin Secretion (2007)

Low adiponectin expression is common in obesity and is tightly linked to insulin resistance and fat mass expansion. Whereas normal adipocytes offer effective metabolic buffering through well-controlled release and uptake of free fatty acids on demand, adipocyte expansion induced by caloric excess and modulated by genetic, regional, and systemic factors elicits major unfavorable changes in fat cell phenotypes. Large, dysfunctional adipocytes show increased lipolysis and enhanced expression and secretion of proinflammatory and pro-oxidative cytokines. Low adiponectin secretion is a hallmark of impaired adipocyte function; its secretion is inhibited by cytokines such as tumor necrosis factor alpha, interleukin 6 and plasminogen activator inhibitor 1 and by high oxidative stress induced by increased fatty acids that activate nicotinamide adenine dinucleotide phosphate-oxidase. The ensuing hypoadiponectinemia may aggravate insulin resistance and facilitate the evolution of type 2 diabetes. Only massive weight loss allows true and sustained recovery of normal fat cell function as reflected by adiponectin secretion.
Functional analysis of a relA/spoT gene homolog from Streptococcus equisimilis (1996)

We examined the functional attributes of a gene encountered by sequencing the streptokinase gene region of Streptococcus equisimilis H46A. This gene, originally called rel, here termed relS. equisimilis, is homologous to two related Escherichia coli genes, spoT and relA, that function in the metabolism of guanosine 5',3'-polyphosphates [(p)ppGpp]. Studies with a variety of E. coli mutants led us to deduce that the highly expressed rel S. equisimilis gene encodes a strong (p)ppGppase and a weaker (p)ppGpp synthetic activity, much like the spoT gene, with a net effect favoring degradation and no complementation of the absence of the relA gene. We verified that the Rel S. equisimilis protein, purified from an E. coli relA spoT double mutant, catalyzed a manganese-activated (p)ppGpp 3'-pyrophosphohydrolase reaction similar to that of the SpoT enzyme. This Rel S. equisimilis protein preparation also weakly catalyzed a ribosome-independent synthesis of (p)ppGpp by an ATP to GTP 3'-pyrophosphoryltransferase reaction when degradation was restricted by the absence of manganese ions. An analogous activity has been deduced for the SpoT protein from genetic evidence. In addition, the Rel S. equisimilis protein displays immunological cross-reactivity with polyclonal antibodies specific for SpoT but not for RelA. Despite assignment of rel S. equisimilis gene function in E. coli as being similar to that of the native spoT gene, disruptions of rel S. equisimilis in S. equisimilis abolish the parental (p)ppGpp accumulation response to amino acid starvation in a manner expected for relA mutants rather than spoT mutants.
Prospective Assessment of Genetic Effects on Progression to Different Stages of Age-Related Macular Degeneration Using Multistate Markov Models (2012)

Genes in different pathways influence progression to different stages of AMD.