gebhart/patrepeval huggingface dataset:
N‐terminal methionine removal and methionine metabolism in Saccharomyces cerevisiae (2003)

Methionine aminopeptidase (MetAP) catalyzes removal of the initiator methionine from nascent polypeptides. In eukaryotes, there are two forms of MetAP, type 1 and type 2, whose combined activities are essential, but whose relative intracellular roles are unclear. Methionine metabolism is an important aspect of cellular physiology, involved in oxidative stress, methylation, and cell cycle. Due to the potential of MetAP activity to provide a methionine salvage pathway, we evaluated the relationship between methionine metabolism and MetAP activity in Saccharomyces cerevisiae. We provide the first demonstration that yeast MetAP1 plays a significant role in methionine metabolism, namely, preventing premature activation of MET genes through MetAP function in methionine salvage. Interestingly, in cells lacking MetAP1, excess methionine dramatically inhibits cell growth. Growth inhibition is independent of the ability of methionine to repress MET genes and does not result from inhibition of synthesis of another metabolite, rather it results from product inhibition of MetAP2. Inhibition by methionine is selective for MetAP2 over MetAP1. These results provide an explanation for the previously observed dominance of MetAP1 in terms of N-terminal processing and cell growth in yeast. Additionally, differential regulation of the two isoforms may be indicative of different intracellular roles for the two enzymes.
Absence of Correlation Between Delayed-Type Hypersensitivity and Protection in Experimental Systemic Candidiasis in Immunized Mice (1981)

We found that in mice which had been immunized intraperitoneally with 2 x 10(8) heat-killed Candida albicans cells there was a striking temporal relationship between resistance to systemic challenge with 10(6) living C. albicans cells and a number of measurable cellular parameters of the host response. These included the emergence of delayed-type hypersensitivity and the development of granulocytosis. Since it had been shown in previous work that granulocytosis was associated with an increase in resistance when nonspecific immunostimulation was used, we performed experiments to induce delayed-type hypersensitivity without any measurable modification of the granulocyte population. Adoptive transfer of delayed-type hypersensitivity with spleen cells from immune and resistant donor mice did not produce any increase in resistance in normal recipients. When separate groups of mice were immunized intraperitoneally or subcutaneously with varying doses of heat-killed C. albicans, we found that doses of less than 10(8) cells did induce significant delayed-type hypersensitivity without any increase in granulocytosis. In such mice, as well as in animals pretreated with immunomodulators before immunization with heat-killed C. albicans, the presence of cell-mediated immunity, as measured by the delayed-type hypersensitivity test, was not associated with an increase in resistance against systemic candidiasis. On the contrary, the results suggested that cell-mediated immunity was associated with an increase in the susceptibility of these mice. The same effect on candidiasis susceptibility was observed when animals were immunized with heat-killed filamentous C. albicans.
On the Effect of Cooperation in Wireless Content Distribution (2008)

In this paper we propose continuous time Markov chain models that capture the dynamics of content spreading in a disruption tolerant wireless content distribution system. We use our models to study the effect of cooperation among the mobile nodes and how limited node resources, such as battery lifetime and confined storage, affect the content distribution process. Based on our models and numerical results we deduce that limiting the number of times a node shares each content entry is a good method to conserve energy while at the same time only slightly reducing system performance. Our study also suggests that the effect of assisting nodes is greatest for content channels with few subscribers. For promoting fairness in distributing channels and giving new channels a chance to spread, assisting nodes should therefore solicit and help in spreading less popular channels.
Effect of stator chording and rotor skewing on average torque and torque ripple of reluctance synchronous machine (2003)

Low torque ripple in electrical machines is generally required to reduce acoustic noise and mechanical resonance vibration. To design for low torque ripple, however, affects the average torque and the power rating of the machine. In this paper, the effect of stator winding chording and rotor skewing on the average torque and torque ripple of the normal (transverse) laminated rotor reluctance synchronous machine is investigated. The 2-D finite element time-step method is used in the analysis. Only rotors with the number of flux barriers less than the number of stator slots are considered. It is shown and explained that chording has little effect on the torque ripple of the machine while it significantly reduces the average torque. Skewing the rotor, on the other hand, reduces torque ripple drastically, but has little effect on the average torque. It is further found that skewing the rotor by one stator slot pitch is not necessarily the optimum.
Adaptive data rate communications for high frequency radio channels (2002)

An alternative approach to the problem of multipath fading on HF ionospheric scatter channels is considered: that of adapting the data rate to the channel conditions. The performance of a simple on/off data rate system is only 4.3 dB shy of non-fading performance. A more sophisticated four-rate (three non-zero rates) trellis-coded system gains 6.7 dB more without interleaving and without bandwidth expansion. At a bit error rate of 10/sup -5/, this is equivalent to 39 dB of coding gain. Implementation problems for adaptive data rate systems include noisy feedback channels, increased overhead, synchronization, sensitivity to propagation delay, and buffer control. It is noted that these problems are challenging, but not insurmountable.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Improvement of aluminum-Si contact performance in native-oxide-free processing (1990)

The improvement of Al-to-Si contact performance to a low contact resistance of 0.4 mu Omega -cm/sup 2/ and a Schottky junction having an n factor of 1.02 without any thermal treatment has been achieved by a native-oxide-free processing technique. The technique consists of N/sub 2/-gas-sealed wet cleaning using pure water with low dissolved oxygen (20 p.p.b.), wafer transport and loading in an N/sub 2/ environment, and Al deposition by low-energy ion bombardment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Computational stabilization of human growth hormone (2002)

Recombinant human growth hormone (hGH) is used worldwide for the treatment of pediatric hypopituitary dwarfism and in children suffering from low levels of hGH. It has limited stability in solution, and because of poor oral absorption, is administered by injection, typically several times a week. Development has therefore focused on more stable or sustained-release formulations and alternatives to injectable delivery that would increase bioavailability and make it easier for patients to use. We redesigned hGH computationally to improve its thermostability. A more stable variant of hGH could have improved pharmacokinetics or enhanced shelf-life, or be more amenable to use in alternate delivery systems and formulations. The computational design was performed using a previously developed combinatorial optimization algorithm based on the dead-end elimination theorem. The algorithm uses an empirical free energy function for scoring designed sequences. This function was augmented with a term that accounts for the loss of backbone and side-chain conformational entropy. The weighting factors for this term, the electrostatic interaction term, and the polar hydrogen burial term were optimized by minimizing the number of mutations designed by the algorithm relative to wild-type. Forty-five residues in the core of the protein were selected for optimization with the modified potential function. The proteins designed using the developed scoring function contained six to 10 mutations, showed enhancement in the melting temperature of up to 16 degrees C, and were biologically active in cell proliferation studies. These results show the utility of our free energy function in automated protein design.
Generalised Pustular Psoriasis Induced by Cyclosporin A Withdrawal Responding to the Tumour Necrosis Factor Alpha Inhibitor Etanercept (2002)

We report a 50-year-old male patient with a 15-year history of psoriasis including mutilating psoriatic arthritis, in whom the withdrawal of cyclosporin A induced a generalised pustular exacerbation and a aggravation of the joint condition. Two weekly injections of 25 mg of the tumour necrosis factor alpha inhibitor etanercept led to a rapid improvement of his psoriatic arthritis, as well as regression of the pustular eruption, while residual erythema was still present. The clinical response was reflected by an increase in circulating interleukin (IL) 10 and a decrease in IL-6 and IL-8 serum levels during treatment. We conclude that etanercept may be a safe and effective therapy not only in severe psoriatic arthritis, but also in cases of pustular rebound after withdrawal of immunosuppressive agents.
Acute Respiratory Distress Syndrome in Critically Ill Surgical Patients (2012)

Acute respiratory distress syndrome (ARDS) is one of the causes of death in critically ill surgical patients. ARDS is a rapidly progressive pulmonary disorder that manifests respiratory failure. It is associated with postoperative infection, sepsis, and severe trauma, etc. The management of ARDS is complicate and targeting the underlying causes. In addition, many supportive managements such as nutritional support, prevention of stress ulcer and thromboembolism, with lung-protective ventilation strategies are necessary. (
Myostatin inhibitors as therapies for muscle wasting associated with cancer and other disorders (2013)

Myostatin inhibition remains a promising therapeutic strategy for a range of muscle wasting disorders.
Codon usage tabulated from the GenBank genetic sequence data (1992)

Journal Article Codon usage tabulated from the GenBank genetic sequence data Get access Ken-nosuke Wada, Ken-nosuke Wada 1Chukyo University, School of Computer and Congnitive SciencesJapan Search for other works by this author on: Oxford Academic PubMed Google Scholar Yoshiko Wada, Yoshiko Wada 2Niigata University, School of MedicineJapan Search for other works by this author on: Oxford Academic PubMed Google Scholar Fumie Ishibashi, Fumie Ishibashi Search for other works by this author on: Oxford Academic PubMed Google Scholar Takashi Gojobori, Takashi Gojobori Search for other works by this author on: Oxford Academic PubMed Google Scholar Toshimichi Ikemura Toshimichi Ikemura Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 20, Issue suppl, 11 May 1992, Pages 2111–2118, https://doi.org/10.1093/nar/20.suppl.2111 Published: 11 May 1992
2.5D forward and inverse modeling for interpreting low-frequency electromagnetic measurements (2008)

Abstract We present 2.5D fast and rigorous forward and inversion algorithms for deep electromagnetic (EM) applications that include crosswell and controlled-source EM measurements. The forward algorithm is based on a finite-difference approach in which a multifrontal LU decomposition algorithm simulates multisource experiments at nearly the cost of simulating one single-source experiment for each frequency of operation. When the size of the linear system of equations is large, the use of this noniterative solver is impractical. Hence, we use the optimal grid technique to limit the number of unknowns in the forward problem. The inversion algorithm employs a regularized Gauss-Newton minimization approach with a multiplicative cost function. By using this multiplicative cost function, we do not need a priori data to determine the so-called regularization parameter in the optimization process, making the algorithm fully automated. The algorithm is equipped with two regularization cost functions that allow us to reconstruct either a smooth or a sharp conductivity image. To increase the robustness of the algorithm, we also constrain the minimization and use a line-search approach to guarantee the reduction of the cost function after each iteration. To demonstrate the pros and cons of the algorithm, we present synthetic and field data inversion results for crosswell and controlled-source EM measurements.
A Tool for the Import of Natural and Unnatural Nucleoside Triphosphates into Bacteria (2018)

Nucleoside triphosphates play a central role in biology, but efforts to study these roles have proven difficult because the levels of triphosphates are tightly regulated in a cell and because individual triphosphates can be difficult to label or modify. In addition, many synthetic biology efforts are focused on the development of unnatural nucleoside triphosphates that perform specific functions in the cellular environment. In general, both of these efforts would be facilitated by a general means to directly introduce desired triphosphates into cells. Previously, we demonstrated that recombinant expression of a nucleoside triphosphate transporter from Phaeodactylum tricornutum (PtNTT2) in Escherichia coli functions to import triphosphates that are added to the media. Here, to explore the generality and utility of this approach, we report a structure-activity relationship study of PtNTT2. Using a conventional competitive uptake inhibition assay, we characterize the effects of nucleobase, sugar, and triphosphate modification, and then develop an LC-MS/MS assay to directly measure the effects of the modifications on import. Lastly, we use the transporter to import radiolabeled or 2'-fluoro-modified triphosphates and quantify their incorporation into DNA and RNA. The results demonstrate the general utility of the PtNTT2-mediated import of natural or modified nucleoside triphosphates for different molecular or synthetic biology applications.
Automatic Recognition of a Baby Gesture (2003)

We discuss and present a computer vision system that monitors a sitting baby of ages of 6 months old to one-year-old. The system tracks a baby's mouth and hands and alarms the guardians if it finds some objects in the baby's hand going towards his or her mouth. We use skin detection, grayscale based Sum of Square Differences (SSD) and template matching for tracking the hands and the head of a baby.
DIAGNOSTIC OVERLAP OF GENERALIZED ANXIETY DISORDER AND MAJOR DEPRESSIVE DISORDER IN A PRIMARY CARE SAMPLE (2012)

The results suggest that comorbidity of GAD and MDD is strongly influenced by diagnostic overlap. Results are discussed in terms of errors of diagnostic criteria, as well as models of shared psychopathology that account for diagnostic criteria overlap.
MOLECULAR WEIGHT AND SHAPE OF HUMIC ACID FROM SEDIMENTATION AND DIFFUSION MEASUREMENTS ON FRACTIONATED EXTRACTS (1972)

Summary Whole humic acid extracts are usually too polydisperse for reliable molecular‐weight measurement to be made in the ultracentrifuge by the sedimentation velocity technique. Consequently, the humic acid used in this study was fractionated with respect to molecular weight into fractions of low polydispersity by extensive use of gel‐permeation chromatography and other fractionation techniques. The sedimentation and diffusion coefficients of the fractions were determined and molecular‐weight values calculated. These values ranged approximately from 2 × 10 3 to 1.5 × 10 6 , the higher figure not necessarily representing the upper limit for these substances. On the basis of the frictional parameters calculated from the experimental data, it is proposed that the molecule adopts the solution conformation of a randomly coiled polymer in which branching may be significant, particularly at higher molecular weights.
An Overview of Tiles in HEVC (2013)

Tiles is a new feature in the High Efficiency Video Coding (HEVC) standard that divides a picture into independent, rectangular regions. This division provides a number of advantages. Specifically, it increases the “parallel friendliness” of the new standard by enabling improved coding efficiency for parallel architectures, as compared to previous sliced based methods. Additionally, tiles facilitate improved maximum transmission unit (MTU) size matching, reduced line buffer memory, and additional region-of-interest functionality. In this paper, we introduce the tiles feature and survey the performance of the tool. Coding efficiency is reported for different parallelization factors and MTU size requirements. Additionally, a tile-based region of interest coding method is developed.
In vitro allergy diagnosis: should we follow the flow? (2004)

Summary During the last 5 years, an increasing number of studies have demonstrated that flow cytometric quantification of in vitro basophil activation can be a quite performant and reliable tool to measure IgE‐dependent allergen‐specific responses in allergic patients. So far, most assays have used CD63 as a basophil activation marker and native allergen extracts for stimulation. However, other basophil markers and recombinant allergens have recently been introduced. The technique has been applied for the diagnosis of allergy to pollen, house dust mite, food, natural rubber latex, hymenoptera venom and drugs. In addition, the technique has proven to be useful in non‐IgE‐mediated reactions such as hypersensitivity to drugs as well as detection of auto‐antibodies in chronic urticaria. This review will focus on some specific issues: (1) principles of flow cytometric analysis of in vitro‐ activated basophils, (2) general technical aspects of the technique (including passive sensitization), (3) clinical applications and (4) recommendations for further development and evaluation of the technique.
Clonal heterogeneity of the sensitivity of human colon carcinoma cell lines to TGFβ isoforms (1995)

Spontaneously arising, TGF beta 1-resistant colonies were isolated directly from the soft agarose plates of MOSER human colon carcinoma cells grown in the presence of TGF beta 1 but in the absence of serum. The colonies were cloned by limiting dilution and screened in a monolayer proliferation assay for sensitivity to TGF beta 1 and TGF beta 2 isoforms. Cell clones selectively sensitive or resistant to these isoforms in the growth inhibition assay displayed similar differential sensitivities to TGF beta isoforms for production of the extracellular matrix proteins laminin and fibronectin, as well as for the expression of the colon cell differentiation marker carcinoembryonic antigen. Differential receptor binding profiles for TGF beta 1 and TGF beta 2 were observed among the clones. The isolation of cell clones selectively resistant or sensitive to TGF beta isoforms as well as the identification of differential receptor binding profiles among the clones indicate the heterogeneity of TGF beta responsiveness that exists naturally in human colon tumor cells and stress the importance of defining mechanisms underlying differential responsiveness to TGF beta isoforms.
The amino acid sequence of a major polypeptide chain of earthworm hemoglobin. (1982)

The amino acid sequence has been determined for polypeptide chain AIII of the major component of the hemoglobin (erythrocruorin) from the earthworm, Lumbricus terrestris. The chain has 157 residues and a molecular weight of 17,496. Although the extent of sequence identity with other globin chains is only 17-18%, analysis of the sequence leads to the conclusion that the secondary structure of the chain is very similar to those of vertebrate globins and that about 60-70% of the amino acid residues are in alpha helices. The D helix appears to be missing, as it is from the alpha chain of human hemoglobin and from the monomeric hemoglobin of Glycera dibranchiata, another annelid worm. This is the first sequence obtained from one of the "giant" extracellular hemoglobins of invertebrate animals.
Adaptive turbo equalizer with stopping rule based on LDPC codes (2009)

In this paper we propose a stopping rule for adaptive turbo equalizers based on low-density parity-check (LDPC) codes. Using an extrinsic information transfer (EXIT) chart, we analyze the convergence behavior of a turbo equalizer and devise an adaptive turbo equalizer with stopping rule. It monitors the status of iterative decoding and stops performing equalization when the decoding messages are reliable enough to converge successfully only by LDPC decoding. Simulation results show that the proposed scheme has lower complexity than the conventional schemes, while it has a similar performance.
Measurement of spectral correlation (1986)

Various methods for measurement/computation of spectral correlation functions for time series that exhibit cyclostationarity are described in a unifying theoretical framework. Some of these are amenable to digital hardware or software implementations, others are amenable to analog electrical or optical implementations, and other implementation types used for conventional spectral analysis are also possible. The interaction among reliability and temporal, spectral, and cycle resolutions is determined. Novel problems of computational complexity, cycle leakage and aliasing, cycle resolution, and cycle phasing are discussed. Sample spectral correlation functions are calculated with digital software for several simulated signals.
Inhibition of huntingtin fibrillogenesis by specific antibodies and small molecules: Implications for Huntington's disease therapy (2000)

The accumulation of insoluble protein aggregates in intra and perinuclear inclusions is a hallmark of Huntington's disease (HD) and related glutamine-repeat disorders. A central question is whether protein aggregation plays a direct role in the pathogenesis of these neurodegenerative diseases. Here we show by using a filter retardation assay that the mAb 1C2, which specifically recognizes the elongated polyglutamine (polyQ) stretch in huntingtin, and the chemical compounds Congo red, thioflavine S, chrysamine G, and Direct fast yellow inhibit HD exon 1 protein aggregation in a dose-dependent manner. On the other hand, potential inhibitors of amyloid-beta formation such as thioflavine T, gossypol, melatonin, and rifampicin had little or no inhibitory effect on huntingtin aggregation in vitro. The results obtained by the filtration assay were confirmed by electron microscopy, SDS/PAGE, and MS. Furthermore, cell culture studies revealed that the Congo red dye at micromolar concentrations reduced the extent of HD exon 1 aggregation in transiently transfected COS cells. Together, these findings contribute to a better understanding of the mechanism of huntingtin fibrillogenesis in vitro and provide the basis for the development of new huntingtin aggregation inhibitors that may be effective in treating HD.
UV-Curing of Fluorinated Systems: Synthesis and Properties (2003)

The study concerns the UV-curing of systems containing fluorinated products. New difunctional and monofunctional acrylic and methacrylic monomers bearing either a perfluoroalkyl chain or a perfluoropolyether structure were synthesized. The properties of the films obtained were investigated. By copolymerizing a small amount of the fluorinated acrylates with acrylic resins, while the bulk properties of the films were not changed, the surface properties were deeply modified and became highly hydrophobic. This behaviour was due to a selective enrichment of the fluorinated monomer at the film surface. The dependence of the surface properties on the monomer structure, on its concentration and on the type of substrate was studied.