gebhart/patrepeval huggingface dataset:
HtaA Is an Iron-Regulated Hemin Binding Protein Involved in the Utilization of Heme Iron in Corynebacterium diphtheriae (2009)

Many human pathogens, including Corynebacterium diphtheriae, the causative agent of diphtheria, use host compounds such as heme and hemoglobin as essential iron sources. In this study, we examined the Corynebacterium hmu hemin transport region, a genetic cluster that contains the hmuTUV genes encoding a previously described ABC-type hemin transporter and three additional genes, which we have designated htaA, htaB, and htaC. The hmu gene cluster is composed of three distinct transcriptional units. The htaA gene appears to be part of an iron- and DtxR-regulated operon that includes hmuTUV, while htaB and htaC are transcribed from unique DtxR-regulated promoters. Nonpolar deletion of either htaA or the hmuTUV genes resulted in a reduced ability to use hemin as an iron source, while deletion of htaB had no effect on hemin iron utilization in C. diphtheriae. A comparison of the predicted amino acid sequences of HtaA and HtaB showed that they share some sequence similarity, and both proteins contain leader sequences and putative C-terminal transmembrane regions. Protein localization studies with C. diphtheriae showed that HtaA is associated predominantly with the cell envelope when the organism is grown in minimal medium but is secreted during growth in nutrient-rich broth. HtaB and HmuT were detected primarily in the cytoplasmic membrane fraction regardless of the growth medium. Hemin binding studies demonstrated that HtaA and HtaB are able to bind hemin, suggesting that these proteins may function as cell surface hemin receptors in C. diphtheriae.
Shaped inputs for a multimode system (2002)

A method for limiting vibration in flexible systems that have more than one characteristic frequency and mode is presented. It is only necessary to have knowledge of the component mode frequencies and damping ratios in order to be able to calculate the timing and magnitudes of the impulse sequence used in the shaping. Only two impulses, in the nonrobust case, or three impulses, in a more robust case, are necessary regardless of the number of component frequencies.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Immunochemical characterization of mammalian protein synthesis initiation factors (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTImmunochemical characterization of mammalian protein synthesis initiation factorsLaurence J. Meyer, Susan C. Milburn, and John W. B. HersheyCite this: Biochemistry 1982, 21, 18, 4206–4212Publication Date (Print):August 1, 1982Publication History Published online1 May 2002Published inissue 1 August 1982https://pubs.acs.org/doi/10.1021/bi00261a003https://doi.org/10.1021/bi00261a003research-articleACS PublicationsRequest reuse permissionsArticle Views75Altmetric-Citations58LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Interactions between the Escherichia coli MelR transcription activator protein and operator sequences at the melAB promoter (1994)

The Escherichia coli MelR protein binds to two sites at the melAB promoter and activates transcription in response to melibiose. The binding of purified MelR to the melAB promoter and to a number of derivatives carrying point mutations has been studied. A melAB promoter fragment that is very weakly activated by the melR gene product has been made by creating multiple symmetrical changes in both MelR-binding sites. A library of random substitutions in MelR was screened to find mutants that were able to activate this mutant promoter. One of these mutants contained a substitution in a proposed helix-turn-helix region that most likely relaxes the sequence-specificity of MelR binding. The other mutants contain substitutions throughout the central part of MelR and appear to alter the conformation of MelR, such that activity is triggered at lower melibiose concentrations and by arabinose.
Suppression of human DNA alkylation-repair defects by Escherichia coli DNA-repair genes. (1986)

The ada-alkB operon protects Escherichia coli against the effects of many alkylating agents. We have subcloned it into the pSV2 mammalian expression vector to yield pSV2ada-alkB, and this plasmid has been introduced into Mer- HeLa S3 cells, which are extremely sensitive to killing and induction of sister chromatid exchange by alkylating agents. One transformant (the S3-9 cell line) has several integrated copies of pSV2ada-alkB and was found to express a very high level of the ada gene product, the 39-kDa O6-methylguanine-DNA methyltransferase. S3-9 cells were found to have become resistant to killing and induction of sister chromatid exchange by two alkylating agents, N-methyl-N'-nitro-N-nitrosoguanidine and N,N'-bis(2-chloroethyl)-N-nitro-sourea. This shows that bacterial DNA alkylation-repair genes are able to suppress the alkylation-repair defects in human Mer- cells.
An Ultrasonic Through-Wall Communication (UTWC) System Model (2013)

Ultrasonic waves at 1 MHz are used to send information across solid walls without the needs for through wall penetrations. A communication channel is established by attaching a set of three ultrasonic transducers to the wall. The first transducer transmits a continuous ultrasonic wave into the wall. The second transducer is mounted on the opposite side of the wall (inside) and operates as a receiver and signal modulator. The third transducer, the outside receiving transducer, is installed on the same side as the first transducer where it is exposed to the signal reflected from the blended interface of the inside wall and inside transducer. Inside sensor data is digitized and the bit state is used to vary in time the electrical load connected to the inside transducer, changing its acoustic impedance in accordance with each data bit. These impedance changes modulate the amplitude of the reflected ultrasonic signal. The modulated signal is detected at the outside receiving transducer, where it is then demodulated to recover the data. Additionally, some of the ultrasonic power received at the inside transducer is harvested to provide energy for the communication and sensor system on the inside. The entire system (ultrasonic, solid wall, and electronic) is modeled in the electrical domain by means of electro-mechanical analogies. This approach enables the concurrent simulation of the ultrasonic and electronic components. A model of the communication system is implemented in an electronic circuit simulation package, which assisted in the analysis and optimization of the communication channel. Good agreement was found between the modeled and experimental results.
Design of a new indexing organization for a class-aggregation hierarchy in object-oriented databases (1999)

In an object-oriented database, a class consists of a set of attributes, and the values of the attributes are objects that belong to other classes; that is, the definition of a class forms a class-aggregation hierarchy of classes. A branch of such a hierarchy is called a path. Several index organizations have been proposed to support object-oriented query languages, including multiindex, join index, nested index and path index. All the proposed index organizations are helpful only for a query which retrieves the objects of the root class of a given path using a predicate which specifies the value of the attribute at the end of the path. In this paper, we propose a new index organization for evaluating queries, called full index, where an index is allocated for each class and its attribute (or nested attribute) along the path. From the analysis results, we show that a full index can support any type of query along a given path with a lower retrieval cost than all the other index organizations. Moreover, to reduce the high update cost for a long given path, we split the path into several subpaths and allocate a separate index to each subpath. Given a path, the number of subpaths and the index organization of each subpath define an index configuration. Since a low retrieval cost and a low update cost are always a trade-off in index organizations, we also propose
Increased Tau Phosphorylation and Tau Truncation, and Decreased Synaptophysin Levels in Mutant BRI2/Tau Transgenic Mice (2013)

Familial Danish dementia (FDD) is an autosomal dominant neurodegenerative disease caused by a 10-nucleotide duplication-insertion in the BRI(2) gene. FDD is clinically characterized by loss of vision, hearing impairment, cerebellar ataxia and dementia. The main neuropathologic findings in FDD are the deposition of Danish amyloid (ADan) and the presence of neurofibrillary tangles (NFTs). Here we investigated tau accumulation and truncation in double transgenic (Tg-FDD-Tau) mice generated by crossing transgenic mice expressing human Danish mutant BRI(2) (Tg-FDD) with mice expressing human 4-repeat mutant Tau-P301S (Tg-Tau). Compared to Tg-Tau mice, we observed a significant enhancement of tau deposition in Tg-FDD-Tau mice. In addition, a significant increase in tau cleaved at aspartic acid (Asp) 421 was observed in Tg-FDD-Tau mice. Tg-FDD-Tau mice also showed a significant decrease in synaptophysin levels, occurring before widespread deposition of fibrillar ADan and tau can be observed. Thus, the presence of soluble ADan/mutant BRI(2) can lead to significant changes in tau metabolism and synaptic dysfunction. Our data provide new in vivo insights into the pathogenesis of FDD and the pathogenic pathway(s) by which amyloidogenic peptides, regardless of their primary amino acid sequence, can cause neurodegeneration.
Determination of intracellular species at the level of a single erythrocyte via capillary electrophoresis with direct and indirect fluorescence detection (1992)

Intracellular contents reflect the specific history of a cell including innate physiological heterogeneity as well as differing levels of exposure to environmental influences. A method capable of analyzing a variety of species from within a single human erythrocyte is demonstrated. Guided by a microscope, individual cells can be drawn into open capillaries of 10-microns i.d. On contact with a low ionic strength buffer solution, the cell lyses and releases its intracellular fluid. The ionic components are then separated by capillary electrophoresis. For glutathione, microderivatization with a fluorescent reagent can be accomplished in vitro with monobromobimane. The effects of extracellular oxidizing and reducing agents on the glutathione levels can thus be followed. For sodium and potassium, or any other ionic species, charge displacement of a fluorescent cation results in indirect fluorescence detection. The two detection modes are suitable for intracellular components present at low-attomole and sub-femtomole levels, respectively.
Speech Coding: A Computer Laboratory Textbook (1995)

DSPLAB: The DSP Laboratory Software. Quantization: PCM and APCM. Waveform Coding with Fixed Prediction. Pitch-excited Linear Predictive Vocoder. Waveform Coding with Adaptive Prediction. Analysis-by-Synthesis LPC. Subband Coding. Projects. Appendices. Bibliography. Index.
Serum Leptin Concentrations in Women with Polycystic Ovary Syndrome (1997)

The role of gonadotropins, androgens, and insulin in the regulation of circulating leptin levels is obscure. In order to clarify the relationships of these parameters we studied serum leptin levels in 19 healthy control subjects and in 35 hyperandrogenic and hyperinsulinemic patients with polycystic ovary syndrome (PCOS). Serum leptin concentrations did not differ significantly between PCOS patients and control subjects. When PCOS and control groups were analyzed together by univariate analysis, serum leptin was positively correlated with body mass index (BMI), body weight, serum insulin, serum triglyceride, and serum free testosterone concentrations. Serum leptin was inversely correlated with serum sex hormone binding globulin (SHBG) concentrations. There were no significant correlations between serum leptin and testosterone, androstenedione, or gonadotropin concentrations. Serum insulin, triglyceride, and free testosterone concentrations were positively correlated, and serum SHBG was negatively correlated with BMI. However, when BMI on one hand and serum insulin, triglyceride, free testosterone, or SHBG on other hand were used as independent variables in the partial correlation analysis with leptin, BMI turned out to be the variable primarily responsible for all of the correlations with leptin. In conclusion, the concept that circulating leptin levels would be different in PCOS patients than in regularly menstruating control subjects is not supported by our data.
Functional analysis of the interaction between HCV 5'UTR and putative subunits of eukaryotic translation initiation factor eIF3 (1998)

Translation initiation in Hepatitis C Virus is controlled by the presence of an internal ribosome entry site element (IRES) principally located in its 5' untranslated region (UTR). Mutation/deletion analyses have shown that the integrity of this structure is essential for initiation of cap-independent protein synthesis. We have developed a strategy to swap the position of the two major domains (II and III) on the 5'UTR sequence. The aim was to further characterize this mechanism by preserving domain-specific interactions but possibly losing contacts that require any interdomain geometry. The expression of dicistronic mRNAs containing these different UTRs showed that the positioning of the different domains on the 5'UTR is essential for efficient IRES functioning. We then used these mutants to identify cellular factors implicated in IRES activity. Using UV crosslinking assays we found that domain III makes direct contact with two proteins (p170/p120) which can be associated with efficient IRES activity. In particular, we have mapped the binding sites of these proteins and shown that p120 binds to the apical loop segment of domain III, whilst p170 binds in the stem portion, independently of domain III position or context. Finally, we provide evidence showing that p170 and p120 represent two subunits of eukaryotic initiation factor eIF3: p170 and p116/p110.
Closed-loop electroosmotic microchannel cooling system for VLSI circuits (2002)

The increasing heat generation rates in VLSI circuits motivate research on compact cooling technologies with low thermal resistance. This paper develops a closed-loop two-phase microchannel cooling system using electroosmotic pumping for the working fluid. The design, fabrication, and open-loop performance of the heat exchanger and pump are summarized. The silicon heat exchanger, which attaches to the test chip (1 cm/sup 2/), achieves junction-fluid resistance near 0.1 K/W using 40 plasma-etched channels with hydraulic diameter of 100 /spl mu/m. The electroosmotic pump, made of an ultrafine porous glass frit with working volume of 1.4 cm/sup 3/, achieves maximum backpressure and flowrate of 160 kPa and 7 ml/min, respectively, using 1 mM buffered de-ionized water as working fluid. The closed-loop system removes 38 W with pump power of 2 W and junction-ambient thermal resistance near 2.5 K/W. Further research is expected to strongly reduce the thermal resistance for a given heating power by optimizing the saturation temperature, increasing the pump flowrate, eliminating the thermal grease, and optimizing the heat exchanger dimensions.
Model study detecting breast cancer cells in peripheral blood mononuclear cells at frequencies as low as 10(-7). (1995)

A flow cytometric assay was developed to detect rare cancer cells in blood and bone marrow. Multiple markers; each identified by a separate color of immunofluorescence (yellow and two shades of red), are used to reliably identify the cancer cells. Blood or bone marrow cells, which are not of interest but interfere in detecting the cancer cells, are identified by a panel of immunofluorescence markers, each of which has the same color (green). Thus, the rare cancer cells of interest are yellow and two different shades of red but not green. The requirement that the rare cancer cell be simultaneously positive for three separate colors (the specific markers) and negative for a fourth color (the exclusion color) allowed detection of as few as one cancer cell in 10(7) nucleated blood cells (a frequency of 10(-7). To test this rare-event assay prior to clinical studies, a model study was performed in which the clinical sample was simulated by mixing small numbers of cells from the breast carcinoma line BT-20 with peripheral blood mononuclear cells. We detected statistically significant numbers of BT-20 cells at mixing frequencies of 10(-5), 10(-6), and 10(-7). In control samples, no target events (BT-20) were observed when more than 10(8) cells were analyzed. For additional confirmation that the BT-20 cells in the model study were correctly identified and counted, the BT-20 cells (and only BT-20 cells) were covalently stained with a fifth fluorescence dye, 7-amino-4-chloromethylcoumarin (CMAC). CMAC fluorescence data were not used in the assay for detecting BT-20 cells. Only after the analysis using data from the specific and exclusion colors had been completed were the events identified as BT-20 cells checked for CMAC fluorescence. The putative BT-20 events were always found to be positive for CMAC fluorescence, which further increases confidence in the assay. Manual data analysis and an automated computer program were compared. Results were comparable with the manual and automated methods, but the automated "genetic algorithm" always found more BT-20 events. Cell sorting of BT-20 cells from samples that contained BT-20 at frequencies of 10(-5), 10(-6), and 10(-7) provided further evidence that these rare cells could be reliably detected. The good performance of the assay with the model system will encourage further studies on clinical samples.
Perspective on Genes and Mutations Causing Retinitis Pigmentosa (2007)

Exceptional progress has been made during the past two decades in identifying genes causing inherited retinal diseases such as retinitis pigmentosa. An inescapable consequence is that the relationship between genes, mutations, and clinical findings has become very complex. Success in identifying the causes of inherited retinal diseases has many implications, including a better understanding of the biological basis of vision and insights into the processes involved in retinal pathology. From a clinical point of view, there are two important questions arising from these developments: where do we stand today in finding disease-causing mutations in affected individuals, and what are the implications of this information for clinical practice? This perspective addresses these questions specifically for retinitis pigmentosa, but the observations apply generally to other forms of inherited eye disease.
The reaction of primate cytochromes c with cytochrome c oxidase. Analysis of the polarographic assay. (1983)

The steady state reactions of a number of native and chemically modified primate and nonprimate cytochromes c with beef and rhesus monkey cytochrome c oxidases, monitored polarographically, were analyzed by studying 1) the presteady state kinetics of the high affinity reaction between the cytochromes c and purified beef cytochrome c oxidase; 2) the corresponding binding of the cytochromes c to the purified beef enzyme; 3) the presteady state reaction of N,N,W,N*tetramethylphenylenediamine (TMPD), the reducing agent employed in the polarographic assay, with the various cytochromes c and their high affinity complexes with the purified beef enzyme; and 4) the presteady state low affinity reaction between ferrocytochrome c and the high affinity ferricytochrome c-beef cytochrome oxidase complex.It was concluded that the reduction of the enzyme-ferricytochrome c (EP) complex by TMPD is the rate-limiting step in the steady state polarographic assay, that the low maximal velocities for the high affinity reaction of simian cytochromes c with nonprimate cytochrome c oxidase result from a decreased rate of reduction of the EP complex by TMPD, and that this decrease may be due to evolutionary changes in the structures of the primate cytochromes c which result in the formation of too tight an EP complex.Finally, it was shown that the low affinity reaction of cytochrome c with beef cytochrome oxidase is dependent on whether a primate or a nonprimate cytochrome c is bound in the high affinity complex, demonstrating that the high and low affinity binding sites are interacting.Cytochrome c is a small, basic, water-soluble protein of the mitochondrial respiratory chain that is located in the space
Genotypic Correlates of Phenotypic Resistance to Efavirenz in Virus Isolates from Patients Failing Nonnucleoside Reverse Transcriptase Inhibitor Therapy (2001)

Efavirenz (also known as DMP 266 or SUSTIVA) is a potent nonnucleoside inhibitor of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) activity and of HIV-1 replication in vitro and in vivo. Most patients on efavirenz-containing regimens have sustained antiviral responses; however, rebounds in plasma viral load have been observed in some patients in association with the emergence of mutant strains of HIV-1. Virus isolates from the peripheral blood mononuclear cells (PBMCs) of patients with such treatment failures, as well as recombinant viruses incorporating viral sequences derived from patient plasma, show reduced in vitro susceptibility to efavirenz in association with mutations in the RT gene encoding K103N, Y188L, or G190S/E substitutions. Patterns of RT gene mutations and in vitro susceptibility were similar in plasma virus and in viruses isolated from PBMCs. Variant strains of HIV-1 constructed by site-directed mutagenesis confirmed the role of K103N, G190S, and Y188L substitutions in reduced susceptibility to efavirenz. Further, certain secondary mutations (V106I, V108I, Y181C, Y188H, P225H, and F227L) conferred little resistance to efavirenz as single mutations but enhanced the level of resistance of viruses carrying these mutations in combination with K103N or Y188L. Viruses with K103N or Y188L mutations, regardless of the initial selecting nonnucleoside RT inhibitor (NNRTI), exhibited cross-resistance to all of the presently available NNRTIs (efavirenz, nevirapine, and delavirdine). Some virus isolates from nevirapine or delavirdine treatment failures that lacked K103N or Y188L mutations remained susceptible to efavirenz in vitro, although the clinical significance of this finding is presently unclear.