gebhart/patrepeval huggingface dataset:
Determinants of the trans-Dominant Negative Effect of Truncated Forms of the CCR5 Chemokine Receptor (2001)

The human immunodeficiency virus, type 1 (HIV-1) entry process is triggered by interaction between the viral envelope and a seven membrane-spanning domain receptor at the cell surface, usually the CCR5 chemokine receptor. Different naturally occurring mutations in the CCR5 gene abolish receptor function, the most frequent being a 32-nucleotide deletion resulting in a truncated protein (Delta32) lacking the last three transmembrane domains (TM5-7). This mutant is retained in the endoplasmic reticulum and exerts a trans-dominant negative (TDN) effect on the wild type, preventing its exit from this compartment. This TDN effect is often considered as evidence for the oligomerization of CCR5 during transport to the cell surface. Here we use a genetic approach to define the structural determinants of the TDN effect of the Delta32 mutant. It was abolished by certain deletions and by mutations of cysteine residues preventing formation of a disulfide link between the first and second extracellular loops, suggesting that conformation of Delta32 is important for its interaction with CCR5. To circumvent this problem, we used chimeric forms of the Delta32 and wild type CCR5, consisting in substitutions with homologous domains from the mouse CCR5. All chimeric full-length receptors were expressed at the cell surface and were functional for interaction with HIV-1 or with a chemokine ligand, when assayed. The TDN effect was only observed if both the TM3 domain in CCR5 and the TM4 domain in Delta32 were from human origin, whereas the rest of the proteins could be from either origin. This suggests that the TDN effect involves some form of interaction between these transmembrane domains. Alternatively, but less likely to us, substitutions in TM4 could affect the conformation of CCR5 in the endoplasmic reticulum but not at the cell surface. However that may be, it seems that the TDN effect of the Delta32 mutant has no bearing to the issue of CCR5 dimerization and to its possible role in the processing of the receptor to the cell surface.
High power and low temperature coefficient of frequency oscillator based on a fully anchored and oxide compensated ALN contour-mode MEMS resonator (2012)

This paper reports on the design and experimental verification of the first high power and low temperature coefficient of frequency (TCF) oscillator based on a fully anchored and temperature compensated AlN contour-mode MEMS resonator operating at 950 MHz. Full anchoring of the AlN resonant body is introduced as an innovative design to improve the device linearity without altering the resonator quality factor. The enhanced power handling of the device enabled the implementation of a high power (6 dBm) and low phase noise (-85 dBc/Hz at 1 kHz offset and -172 dBc/Hz floor) oscillator with improved temperature stability (~600 ppm total frequency variation and no phase noise degradation over a 75 °C range).
Branched Peptides for the Modulation of Protein-Protein Interactions: More Arms are Better than One? (2011)

Combinatorial peptide libraries from synthetic or biological sources have been largely used in the last two-decades with the aim of identifying bioactive peptides that specifically bind proteins and modulate their interactions with other protein partners. Differently from biological libraries, synthetic methods allow the development of different kinds of libraries based on two main characteristics: i) the use of building blocks and chemical bonds different from those naturally occurring and ii) the possibility of designing scaffolds with non-linear shapes, as cyclic and branched structures. These two features, alone or in combination, have increased the chemical and structural diversity of peptide libraries expanding the offer of collections for the screenings. Here we describe our and other experiences with branched peptides and the results obtained in the last fifteen years. These clearly indicate how the use of short multimerized peptides can represent a successful approach for different applications ranging from affinity chromatography to the modulation of protein-protein interactions in different biological contexts.
Functional human antibody CDR fusions as long-acting therapeutic endocrine agonists (2015)

On the basis of the 3D structure of a bovine antibody with a well-folded, ultralong complementarity-determining region (CDR), we have developed a versatile approach for generating human or humanized antibody agonists with excellent pharmacological properties. Using human growth hormone (hGH) and human leptin (hLeptin) as model proteins, we have demonstrated that functional human antibody CDR fusions can be efficiently engineered by grafting the native hormones into different CDRs of the humanized antibody Herceptin. The resulting Herceptin CDR fusion proteins were expressed in good yields in mammalian cells and retain comparable in vitro biological activity to the native hormones. Pharmacological studies in rodents indicated a 20- to 100-fold increase in plasma circulating half-life for these antibody agonists and significantly extended in vivo activities in the GH-deficient rat model and leptin-deficient obese mouse model for the hGH and hLeptin antibody fusions, respectively. These results illustrate the utility of antibody CDR fusions as a general and versatile strategy for generating long-acting protein therapeutics.
Semi-perfluoroalkyl polyfluorene with varying fluorine content: synthesis and photophysical properties (2013)

Deposition of multilayer organic electronic devices by solution processing often requires clever material design to avoid intermixing of the various layers. The use of orthogonal solvents for multilayer processing is a simple and effective method to solve this problem. However, the introduction of fluorous substituents to materials normally functionalised with aliphatic side chains has been shown to affect the device performance of these materials. In this study, a series of 9,9-disubstituted polyfluorenes containing varying ratios of semi-perfluoroalkyl to alkyl side chains have been synthesised and characterised. The effect of the semi-perfluoroalkyl chains on photophysical, electrochemical and thermal properties of the polymers was examined. The results indicate that the semi-perfluoroalkyl chains have varying influence on these properties and this is reflected in the previously reported electroluminescent device performances.
Focused pulse of pressure for boosting sonoluminescence (2001)

Single bubble sonoluminescence is characterized by a great concentration of energy conducting to the generation of UV photon with ultrasound of centimetric wavelength. Several teams have tried to again increase more of the energy concentration, but most of these trials have rapidly reached the boundaries of the narrow stability domain of sonoluminescence. The idea developed in this work is to overcome this limitation by adding a high-frequency pressure pulse to the monochromatic low-frequency field used in the now classical setup. For instance, the pressure in the neighborhood of the bubble can be dramatically increased during a single collapse of the bubble. This pressure pulse is generated with eight high-frequency transducers adaptively focused on the bubble and synchronized with its low-frequency cycle. With this setup, a transient amplitude of 8 atmospheres has been reached on the bubble, without destroying it, and a significant increase of the emitted light intensity has been observed on a single flash. This process is no longer limited by the domain of stability of sonoluminescence and could lead, in the future, to much more efficient inertial confinement of the gas contained in the bubble.
ChemInform Abstract: A Pyrone Strategy for the Synthesis of 3‐Acyltetramic Acids. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Darinaparsin Inhibits Prostate Tumor–Initiating Cells and Du145 Xenografts and Is an Inhibitor of Hedgehog Signaling (2014)

Prostate cancer is the leading cause of cancer-related death in men in the United States. A major cause of drug resistance in prostate and other epithelial tumors may be due to the presence of a fraction of tumor cells that retain the ability to initiate tumors and hence are termed tumor-initiating cells (TIC) or cancer stem cells. Here, we report that darinaparsin, an organic derivative of arsenic trioxide, is cytotoxic to prostate cancer cell lines as well as fresh prostate cancer cells from patients at low micromolar concentrations, and importantly inhibits the TIC subpopulations. It also inhibits growth of the castrate-resistant Du145 prostate tumor propagated as xenograft in mice and inhibits the tumor-initiating potential of prostate cancer cells. Although the mechanism by which darinaparsin acts is not completely known, we show that it kills prostate cancer cells by blocking cells in the G2-M phase of the cell cycle and inhibits Hedgehog signaling by downregulating Gli-2 transcriptional activity. These data provide a rationale for evaluating darinaparsin in patients with castrate-resistant prostate cancer.
Orthogonal summing and power combining network in a 65-nm all-digital RF I/Q modulator (2011)

This paper elaborates on the recently introduced concept of an all-digital RF I/Q modulator. Orthogonal summation and design procedure of the power combining network are explained in more detail. A 65 nm CMOS prototype is implemented based on this concept. The prototype achieves 12.6 dBm peak output power and 20% peak drain efficiency at 2 GHz. While providing 6 dBm output power, the error vector magnitude (EVM) is 3.7%.
Development of Walking Analysis System Using by Motion Sensor with Mobile Force Plate (2012)

In walking analysis, which is one useful method for efficient physical rehabilitation, the ground reaction force, the center of pressure and the body orientation data are measured during walking. In the past, these data were measured by a 3D motion analysis system consisting of high-speed cameras and force plates, which must be installed in the floor. However, a conventional 3D motion analysis system can measure the ground reaction force and the center of pressure just on force plates during a few steps. In addition, the subjects' stride lengths are limited because they have to walk on the center of the force plate. These problems can be resolved by converting conventional devices into wearable devices. We used a measuring device consisting of portable force plates and motion sensors. We developed a walking analysis system that calculates the ground reaction force, the center of pressure, and the body orientations and measured a walking subject to estimate this system. We simultaneously used a conventional 3D motion analysis system to compare with our development system and showed its validity for measurements of ground reaction force, the center of pressure and posture of lower limb.
Heat Stress Risk Estimation for Workers from Wearable Sensor Data and Lifestyle Information (2021)

We are studying a worker monitoring system for early prevention of poor physical conditions due to heat stress. In this system, workers wear a wearable device that measures factors such as temperature, humidity, movement and pulse rate to estimate and monitor risk of heat stress during work. The primary issue for realizing this system is estimating heat stress risk with high accuracy under the low computational and storage limitations in a wearable device. For this issue, we propose a method for estimating risk of heat stress that (1) uses vital signs, profile information, and lifestyle information, (2) incorporates rules based on relations between information and health conditions, and (3) incurs low computational loads. We evaluate performance of the proposed method using input data consisting of correct answers regarding physical conditions, profile and lifestyle information, and environmental information, extracting correct answers from reports of poor physical conditions due to heat stress. We also extract profile and lifestyle information from a questionnaire, along with environmental information, vital signs, and action information from sensors in a wearable device attached to workers. We evaluate method robustness by using data collected at different times and places. The results show that when using only environmental information with a false rejection rate of 0%, the false acceptance rate is 92.4%. Using environmental information along with vital signs, action information, and profile information reduces this to 23.4%, and using the proposed method improves the false acceptance rate to 17.7%.
Rhythm in dyadic interactions (2021)

This review paper discusses <i>rhythmic</i> interactions and distinguishes them from <i>non-rhythmic</i> interactions. We report on communicative behaviours in social and sexual contexts, as found in dyads of humans, non-human primates, non-primate mammals, birds, anurans and insects. We discuss observed instances of rhythm in dyadic interactions, identify knowledge gaps and propose suggestions for future research. We find that most studies on rhythmicity in interactive signals mainly focus on one modality (acoustic or visual) and we suggest more work should be performed on multimodal signals. Although the social functions of interactive rhythms have been fairly well described, developmental research on rhythms used to regulate social interactions is still lacking. Future work should also focus on identifying the exact timing mechanisms involved. Rhythmic signalling behaviours are widespread and critical in regulating social interactions across taxa, but many questions remain unexplored. A multidisciplinary, comparative cross-species approach may help provide answers. This article is part of the theme issue 'Synchrony and rhythm interaction: from the brain to behavioural ecology'.
Retrospective Multi-Center Analysis of Canine Socket Prostheses for Partial Limbs (2019)

<b>Introduction:</b> Socket prostheses for treatment of distal limb pathology are becoming increasingly prevalent in veterinary medicine, however, limited objective data is available. Objectives of the present study were to retrospectively evaluate owner satisfaction, clinical outcomes, and prognostic factors associated with dogs receiving socket prostheses for partial limbs in a larger patient population. <b>Materials and Methods:</b> Client databases of a single prosthesis provider were reviewed to identify owners whose dogs had received a prosthetic device within the last 10 years. An online survey was developed to evaluate owner-reported outcomes. The survey inquired about anatomy of the residuum, concurrent disease, prosthesis use, rehabilitation, activity, complications, and owner satisfaction. Medical records and radiographs were requested from all participants. Radiographs were used to confirm level of amputation and evaluate for osseous complications. Survey responses were analyzed by assigning author-defined numeric scores defining clinical outcome and owner satisfaction. <b>Results:</b> One-hundred thirty-seven owners were contacted. The response rate was 50/137 (37%); 47 responses were analyzed. Forty-six of 47 owners reported positive satisfaction; 1/47 was displeased. Forty-two of 47 dogs were scored to have acceptable to full function; 5/47 had unacceptable clinical function using the author-defined scoring system. A 62% short-term complication rate and a 19% long-term complication rate were reported. Skin sores were the most common short and long-term complication. There was a significant correlation between both clinical outcome scores and owner satisfaction with days per week spent in the prosthesis. Additionally, clinical outcome scores and owner satisfaction significantly varied between dogs with different durations of prosthesis wear with a trend toward better outcomes associated with longer prosthesis wear. Radiographs were obtained for 23/47 dogs to further define level of defect. The most proximal level of defect was mid-radius for the forelimb and mid-tibia for the hind limb. There was no correlation between level of defect and either owner satisfaction or clinical outcome. <b>Discussion/Conclusion:</b> Results of this survey suggest a high degree of owner satisfaction despite substantial complication rates. Based on preliminary data, further evaluation of socket prostheses as a limb-sparing option for treatment of distal limb pathology should be considered. Prospective clinical trials with objective outcome measures are required to draw firm conclusions.
Amino Acid Composition of Ferredoxin and Rubredoxin Isolated from Desulfovibrio gigas (1969)

The composition of ferredoxin and rubredoxin from Desulfovibrio gigas was determined. Ferrodoxin contained five cysteines, two methionines, and four irons. The rubredoxin was not unique.
Abstract 1790: Functional importance of EpCAM for the activity of tumor-initiating cancer cells and their eradication by EpCAM/CD3-bispecific antibody MT110 (2011)

Abstract We have recently shown that tumor-initiating cells (TICs) derived from colorectal cancer tissue express EpCAM and can be eradicated in cell culture experiments as well as established xenograft mouse models by EpCAM/CD3-bispecific BiTE antibody MT110 (Hermann et al., 2010; PLoS ONE, 5: e13474). Here we show that TICs derived from liver and breast cancer tissue grow tumors in SCID mice at cell doses as low as 100 after a latency period of 37-58 days. Like colorectal cancer tissue-derived TICs, they expressed EpCAM and grew colonies in soft agar. In the presence of human T cells, breast and liver cancer-derived TICs could be eradicated by BiTE antibody MT110 as tested in a sensitive soft agar assay. In order to assess the role of EpCAM expression in colorectal TICs, we used short hairpin RNA molecules for specifically knocking down EpCAM expression. A shRNA molecule binding to the coding, non-translated 3’-UTR of the EpCAM mRNA showed the highest efficacy (ca 10-fold) in suppressing EpCAM expression, as shown at the mRNA level by RT-PCR and at the surface expression level by FACS analysis. Although the EpCAM knockdown was not complete and left ca 10% of the normal EpCAM expression, a strong impact on the phenotype of colorectal TICs was observed. Morphologically, TICs with reduced EpCAM expression adopted in cell culture an epithelial-like phenotype, could no longer efficiently close a scratch in a cell culture experiment, and reduced the expression of epithelial-mesenchymal transition (EMT)-associated proteins such as fibronectin, vimentin and slug. Compared to non-sense control shRNA, colony formation of TICs in soft agar was reduced by &amp;gt;60%. Most importantly, the tumor-initiating potential of TICs appeared to depend on a high level of EpCAM expression. TICs expressing the EpCAM-specific shRNA could no longer form a tumor at a dose of 500 cells after 116 days, whereas the non-sense shRNA-expressing TICs formed during this period a tumor of 0.5 cm3. Our data suggest that a certain EpCAM expression level is required for maintenance of a stem cell-like phenotype of colorectal TICs. This is consistent with a signal transducing role of EpCAM within a non-canonical wnt pathway (Maetzel et al. 2009; Nature Cell Biol. 11: 162-171), and in the process of EMT of colorectal cancer cells. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1790. doi:10.1158/1538-7445.AM2011-1790
Differentiating Double-Layer, Psuedocapacitance, and Battery-like Mechanisms by Analyzing Impedance Measurements in Three Dimensions (2020)

Electrochemical energy storage arises from processes that are broadly categorized as capacitive, pseudocapacitive, or battery-like. Advanced charge-storing materials that are designed to deliver high capacity at a high rate often exhibit a multiplicity of such mechanisms, which complicates the understanding of their charge-storage behavior. Herein, we apply a "3D Bode analysis" technique to identify key descriptors for fast Li-ion storage processes, where AC impedance data, such as the real capacitance (<i>C</i>') or phase angle (ϕ), are represented versus the frequency (<i>f</i>) and a third independent variable, the applied DC cell voltage. For double-layer processes, a near-constant <i>C</i>' or ϕ is supported across the entire voltage range, and the decrease in these values shows a near-linear decrease at higher <i>f</i>. For pseudocapacitance, an increase in <i>C</i>' is delivered, accompanied by high <i>C</i>' retention at higher <i>f</i> compared to double-layer processes. Interestingly, the lower ϕ values, where <i>C</i>' is highest, suggest that this is a key descriptor for pseudocapacitance, where high-rate charge storage is still facilitated within a kinetically limited regime. For battery-like processes, a high <i>C</i>' is only observed at the voltage at which the material stores charge, while outside that voltage, <i>C</i>' is negligible. The three-dimensional (3D) Bode analysis allows charge-storage dynamics to be mapped out in great detail with more delineation between mechanisms compared to the more frequently deployed kinetic analyses derived from cyclic voltammetry.
Paul Kecskemeti, The Unexpected Revolution: Social Forces in the Hungarian Uprising. Stanford, Calif.: Stanford University Press, 1961. vi + 178 pp. $4.75. - Ferenc A. Vali, Rift and Revolt in Hungary: Nationalism Versus Communism. Cambridge, Mass.: Harvard University Press, 1961. xvii + 590 pp. $9.75. (1962)

Paul Kecskemeti, The Unexpected Revolution: Social Forces in the Hungarian Uprising. Stanford, Calif.: Stanford University Press, 1961. vi + 178 pp. $4.75. - Ferenc A. Vali, Rift and Revolt in Hungary: Nationalism Versus Communism. Cambridge, Mass.: Harvard University Press, 1961. xvii + 590 pp. $9.75. - Volume 21 Issue 2
Enzymatic Labeling of Nucleic Acids (1992)

Extensive knowledge of the enzymology involved in biosynthesis and degradation of nucleic acids has permitted the development of simple methods for labeling RNA and DNA with radioisotopes or biotin. These labeled probes are used primarily for hybridization to nucleic acid fragments of interest in a variety of applications. A complete description of the methods available for such labeling is beyond the scope of this manual, but contained within this unit are protocols for oligonucleotide-primed synthesis of radiolabeled and biotinylated DNA probes, in vitro synthesis of radiolabeled RNA, and end labeling of synthetic oligonucleotide probes.