gebhart/patrepeval huggingface dataset:
Knockdown of lactate dehydrogenase <scp>A</scp> suppresses tumor growth and metastasis of human hepatocellular carcinoma (2012)

In previous studies, lactate dehydrogenase A (LDHA) was identified as one of the leading genes that promote the proliferative and tumorigenic potential of malignancies. However, less definitive evidence was reported in hepatocellular carcinoma (HCC) cells. Furthermore, the role of LDHA in promoting metastasis of HCC, and its possible mechanism, is not clear. In this study, RNA interference (RNAi) mediated by lentiviral vectors (which induce strong down-regulation of gene expression) was used to analyze the role of LDHA in tumor growth and metastasis in HCC. We performed transient and stable RNAi knockdowns of LDHA in HCCLM3 cells, a line that over-expresses LDHA and has a high metastatic potential. Our studies reveal that previously unidentified effects of LHDA may mediate tumor growth and metastasic effects in HCC. First, HCC cell lines over-express LDHA. Second, LDHA inhibition results in increased apoptosis via production of reactive oxygen species in HCCLM3 cells. Thus, LDHA knockdown resulted in significant reduction in metastatic potential in a xenograft mouse model. Furthermore, we found that FAK, MMP-2, VEGF and E-cadherin proteins contribute to inhibitory effects on metastasis in HCC cells. These studies have important implications for understanding the mechanisms by which LDHA promotes tumor growth and metastasis.
Fault Current Limitation and Contraction of Voltage Dips Thanks to D-FACTS and FACTS Cooperation (2012)

This paper presents the instantaneous response of the Distributed Static Series Compensator (DSSC) in fault current limitation of disturbed lines. The DSSC has the ability to adjust the impedance of the power system in order to increase the power transfer capacity. The injected voltage is implemented here to limit the fault currents.Moreover, the STATCOM which is a renowned FACTS device is also implemented for fault current limiting. The fault current will be greatly reduced, if the STATCOM make the bus voltage adjacent to the fault bus decrease its voltage. Furthermore, it is also revealed that, operation of both DSSC and STATCOM will greatly reduce the fault currents in the power systems. The effectiveness of the DSSC in reduction of instantaneous voltage dip range during fault current limiting mode, also is investigated. PSCAD/EMTC is used to validate the claims.
Specific membrane capacitance, cytoplasm conductivity and instantaneous Young’s modulus of single tumour cells (2017)

As label-free biomarkers, biophysical properties of cells are widely used for cell type classification. However, intrinsic biophysical markers, e.g., specific membrane capacitance (C<sub>specific membrane</sub>), cytoplasm conductivity (σ<sub>conductivity</sub>) and instantaneous Young's modulus (E<sub>instantaneous</sub>) measured for hundreds of single cells were not yet reported. In this study, single cells in suspension (adherent cells treated with trypsin) were aspirated through a microfluidic constriction channel at 25 °C, and the entry processes and impedance profiles were recorded and translated to C<sub>specific membrane</sub>, σ<sub>conductivity</sub> and E<sub>instantaneous</sub>. C<sub>specific membrane</sub>, σ<sub>conductivity</sub> and E<sub>instantaneous</sub> of five cell types were quantified as 2.10±0.38 μF cm<sup>-2</sup>, 0.91±0.15 S m<sup>-1</sup> and 5.52±0.95 kPa for H460 cells (n<sub>cell</sub>=437); 2.52±0.54 μF cm<sup>-2</sup>, 0.83±0.12 S m<sup>-1</sup> and 5.54±1.04 kPa for H446 cells (n<sub>cell</sub>=410); 2.45±0.57 μF cm<sup>-2</sup>, 0.99±0.18 S m<sup>-1</sup> and 5.16±1.68 kPa for A549 cells (n<sub>cell</sub>=442); 1.86±0.31 μF cm<sup>-2</sup>, 1.07±0.18 S m<sup>-1</sup> and 3.86±0.81 kPa for 95D cells (n<sub>cell</sub>=415); 2.03±0.35 μF cm<sup>-2</sup>, 0.99±0.16 S m<sup>-1</sup> and 3.49±0.70 kPa for 95C cells (n<sub>cell</sub>=290). The database of C<sub>specific membrane</sub>, σ<sub>conductivity</sub> and E<sub>instantaneous</sub> may serve as a reference for future studies of cellular biophysical properties.
Sound Source Separation in Monaural Music Signals (2006)

Sound source separation refers to the task of estimating the signals produced by individual sound sources from a complex acoustic mixture. It has several applications, since monophonic signals can be processed more efficiently and flexibly than polyphonic mixtures. This thesis deals with the separation of monaural, or, one-channel music recordings. We concentrate on separation methods, where the sources to be separated are not known beforehand. Instead, the separation is enabled by utilizing the common properties of real-world sound sources, which are their continuity, sparseness, and repetition in time and frequency, and their harmonic spectral structures. One of the separation approaches taken here use unsupervised learning and the other uses model-based inference based on sinusoidal modeling. Most of the existing unsupervised separation algorithms are based on a linear instantaneous signal model, where each frame of the input mixture signal is
The Bone-Forming Effects of HIF-1α-Transduced BMSCs Promote Osseointegration with Dental Implant in Canine Mandible (2012)

The presence of insufficient bone volume remains a major clinical problem for dental implant placement to restore the oral function. Gene-transduced stem cells provide a promising approach for inducing bone regeneration and enhancing osseointegration in dental implants with tissue engineering technology. Our previous studies have demonstrated that the hypoxia-inducible factor-1α (HIF-1α) promotes osteogenesis in rat bone mesenchymal stem cells (BMSCs). In this study, the function of HIF-1α was validated for the first time in a preclinical large animal canine model in term of its ability to promote new bone formation in defects around implants as well as the osseointegration between tissue-engineered bone and dental implants. A lentiviral vector was constructed with the constitutively active form of HIF-1α (cHIF). The ectopic bone formation was evaluated in nude mice. The therapeutic potential of HIF-1α-overexpressing canine BMSCs in bone repair was evaluated in mesi-implant defects of immediate post-extraction implants in the canine mandible. HIF-1α mediated canine BMSCs significantly promoted new bone formation both subcutaneously and in mesi-implant defects, including increased bone volume, bone mineral density, trabecular thickness, and trabecular bone volume fraction. Furthermore, osseointegration was significantly enhanced by HIF-1α-overexpressing canine BMSCs. This study provides an important experimental evidence in a preclinical large animal model concerning to the potential applications of HIF-1α in promoting new bone formation as well as the osseointegration of immediate implantation for oral function restoration.
<i>In</i> <i>vivo</i> laser computed tomographic imaging of human fingers by coherent detection imaging method using different wavelengths in near infrared region (1996)

We report in vivo laser computed tomographic images of the proximal interphalangeal joint region of a healthy human volunteer’s index finger. The laser computed tomographic (CT) images were obtained with a highly sensitive coherent detection imaging method that is based on the optical heterodyne detection method. These laser CT images are compared at the wavelengths of 715 nm and 1.064 μm and with images obtained by conventional imaging methods such as x-ray CT and magnetic resonance imaging. Internal structures of the proximal interphalangeal joint region could be clearly identified in the laser CT images.
Experimental study on intermediate and gradient index dielectric thin films by a novel reactive sputtering method (1997)

Here we report a novel reactive sputtering method, called two-stage high rate reactive sputtering method, its principles, and apparatus setup, and the results of optical properties of thin films obtained by this method. Then two typical antireflection coatings, one with an intermediate and homogeneous layer and the other with a gradient layer, have been successfully produced by this method. Their spectrum performances and microstructures are also presented.
Antimicrobial Properties of Amyloid Peptides (2011)

More than two dozen clinical syndromes known as amyloid diseases are characterized by the buildup of extended insoluble fibrillar deposits in tissues. These amorphous Congo red staining deposits known as amyloids exhibit a characteristic green birefringence and cross-β structure. Substantial evidence implicates oligomeric intermediates of amyloids as toxic species in the pathogenesis of these chronic disease states. A growing body of data has suggested that these toxic species form ion channels in cellular membranes causing disruption of calcium homeostasis, membrane depolarization, energy drainage, and in some cases apoptosis. Amyloid peptide channels exhibit a number of common biological properties including the universal U-shape β-strand-turn-β-strand structure, irreversible and spontaneous insertion into membranes, production of large heterogeneous single-channel conductances, relatively poor ion selectivity, inhibition by Congo red, and channel blockade by zinc. Recent evidence has suggested that increased amounts of amyloids not only are toxic to its host target cells but also possess antimicrobial activity. Furthermore, at least one human antimicrobial peptide, protegrin-1, which kills microbes by a channel-forming mechanism, has been shown to possess the ability to form extended amyloid fibrils very similar to those of classic disease-forming amyloids. In this paper, we will review the reported antimicrobial properties of amyloids and the implications of these discoveries for our understanding of amyloid structure and function.
Nanoparticle−Mirror Sandwich Substrates for Surface-Enhanced Raman Scattering (2005)

Sandwich surface-enhanced Raman scattering (SERS) substrates (3S) utilizing coupling between continuous metal films and plasmonic particles were fabricated using silver mirrors, electrochemically roughened films, and various sizes of silver nanoparticles. The effect of excitation wavelength and nanoparticle size on SERS spectra of poly(vinylpyridine), selected as a model compound, was studied to determine the optimum conditions for the strongest SERS signal. The Raman enhancement resulted from the plasmon coupling of silver nanoparticles to the underlying continuous film as well as the lateral plasmon coupling between the silver nanoparticles. The formation of the charge transfer complex was also observed. The 3S configuration was used to obtain SERS spectra of dipicolinic acid (DPA), a chemical signature for Bacillus anthracis.
Cytomegalovirus Antibody in Cerebrospinal Fluid of Schizophrenic Patients Detected by Enzyme Immunoassay (1982)

By means of enzyme immunoassay techniques to detect the presence of antibody to cytomegalovirus, the cerebrospinal fluid of 178 patients with schizophrenia, 17 patients with bipolar disorders, and 11 other psychiatric patients was compared with that of 79 neurological patients and 41 normal control subjects. The cerebrospinal fluid of 20 of the schizophrenic patients and 3 of the patients with bipolar disorders showed significant increases in immunoglobulin M antibody to cytomegalovirus; no difference was found in patients on or off psychotropic medications.
An Easy To Prepare Organic Salt as a Low Molecular Mass Organic Gelator Capable of Selective Gelation of Oil from Oil/Water Mixtures (2003)

Besides its capability to gelate various organic solvents, dicyclohexyl ammonium 4-chlorocinnamate 1 is shown to perform selective gelation of oil from oil/water mixtures. While the corresponding 3-chloro derivative 2 is an excellent gelator of nonpolar organic solvents, 2-chloro derivative 3 turned out to be a nongelator.
SDN-Based Multi-Tier Computing and Communication Architecture for Pervasive Healthcare (2018)

A large spectrum of healthcare applications, ranging from continuous blood sugar level monitoring to sleep apnea detection are nowadays facilitated by modern mobile gadgets. Wearable and ambient sensors generate enormous amounts of physiological data that demand high computation power for real-time processing and large storage area for recording the personal data. In order to conserve the energy on the battery-limited mainstream mobile devices of the end-users, the execution of the healthcare applications may be offloaded to a remote server. While cloud computing provides unlimited pool of resources for latency-tolerant services such as training a machine learning model, the personalization of healthcare services and the delay sensitivity of continuous health assessment necessitate a computation infrastructure in the vicinity of the end-users. As a remedy to address various demands of a wide range of pervasive healthcare applications, we propose a multi-tier computing and communication architecture composed of end-user devices, edge servers, and legacy cloud data-centers. The dynamic management of this architecture, policies to be applied within the network and the orchestration of the healthcare services are carried out by the concept of programmable networks, in the form of software-defined networking (SDN). As a concrete demonstration of our ideas, a fall risk assessment service is implemented and an experimental study is conducted to evaluate its accuracy and the performance of the multi-tier architecture. The results indicate that the proposed architecture is feasible to enable real-time healthcare services and has significant performance advantages over traditional cloud-based approaches.
DNA Binding Specificity of <i>Mun</i>I Restriction Endonuclease Is Controlled by pH and Calcium Ions:  Involvement of Active Site Carboxylate Residues (1997)

Gel shift analysis reveals [Lagunavicius, A., & Siksnys, V. (1997) Biochemistry 36 (preceding paper in this issue)] that at pH 8.3 in the absence of Mg2+, MunI restriction endonuclease exhibits little DNA binding specificity, as compared with the D83A and E98A mutants of MunI. This suggests that charged carboxylate residue(s) influence the DNA binding specificity of MunI. In our efforts to establish the determinants of MunI binding specificity, we investigated the possible role of the ionic milieu, and we found that lowering pH or elevating Ca2+ levels per se induces specific DNA recognition by WT MunI. In contrast to the binding experiments at pH 8.3, gel shift analysis at pH 6.5 indicated tight sequence-specific binding of WT MunI in the absence of Mg2+, suggesting that protonation of active site carboxylate residue(s) which manifest anomalously high pKa value(s) control binding specificity. Interestingly, Ca2+ ion concentrations, which did not support DNA cleavage by MunI also induced DNA binding specificity in WT MunI at pH 8.3. To explore possible structural changes upon DNA binding, we then used a limited proteolysis technique. Trypsin cleavage of MunI-DNA complexes indicated that in the presence of cognate DNA the MunI restriction endonuclease became resistant to proteolytic cleavage, suggesting that binding of specific DNA induced a structural change. CD measurements confirmed this observation, suggesting minor secondary structural differences between complexes of MunI with cognate and noncognate DNA. These results therefore suggest that binding of MunI to its recognition sequence triggers a conformational transition that correctly juxtaposes active site carboxylate residues, which then chelate Mg2+ ions. In the absence of Mg2+ ions, at pH 8.3, conditions in which carboxylate groups would be expected to be completely ionized, electrostatic repulsion between charged carboxylates and phosphate oxygens is enhanced such as to interfere with specific DNA binding. Elimination of such repulsive constraints by replacement of carboxylate residues, by lowering pH, or by metal ion binding, then promotes MunI binding specificity.
Emdogain<sup>®</sup> regulation of cellular differentiation in wounded rat periodontium (2003)

Emdogain is an enamel matrix derivative that may promote periodontal regeneration by recapitulating critical events in tooth morphogenesis. We hypothesized that Emdogain enhances periodontal regeneration by promoting the differentiation of cells required for the synthesis of periodontal ligament, bone and cementum. Cell differentiation was examined in rat periodontal window wounds in which there is no microbial biofilm or epithelial downgrowth, thereby simplifying the model system. Defects were filled with vehicle control or Emdogain (3 mg/ml or 30 mg/ml). Rats were sacrificed at 7, 14 and 21 d after wounding. Specimens of periodontium were immunostained for osteopontin, bone sialoprotein, osteocalcin as markers of osteogenic differentiation and for alpha-smooth muscle actin, a myofibroblastic marker. Morphometry and 3H-proline radioautography were used for assessment of tissue homeostasis and matrix production. Rats treated with Emdogain (only at 30 mg/ml) showed widening of the periodontal ligament at 7 d; by 14 and 21 d, periodontal ligament width was restored to normal values for all groups. Emdogain exerted no effect on cementum thickness, bone volume, osteoid deposition rates, or extracellular staining for osteopontin, bone sialoprotein or osteocalcin. Further, the percentage of cells with intracellular staining for osteopontin, osteocalcin or bone sialoprotein was unaffected by Emdogain. Staining for alpha-smooth muscle actin was abundant in the repopulating wound but was also unaffected by Emdogain. In conclusion, Emdogain does not apparently affect the expression of differentiation markers or bone matrix protein synthesis in the repopulation response of wounded rat molar periodontium. Therefore the effect of Emdogain on wound healing in the periodontium may be independent of differentiation in the cell populations examined in this model.
Carboxyl-terminal fragments of beta-amyloid precursor protein bind to microtubules and the associated protein tau. (1997)

Alzheimer's disease is a neurodegenerative disorder characterized by protein depositions in intracellular and extracellular spaces in the brain. The intraneuronal deposits are formed by neurofibrillary tangles composed mainly of abnormally phosphorylated tau, a microtubule-associated protein, whereas the major constituent of the amyloid deposited extracellularly in the brain parenchyma and vessel walls is amyloid beta-protein (A beta). The proteolytic processing of the beta-amyloid precursor protein (beta PP) results in the generation of a complex set of carboxyl-terminal peptides that contain A beta. In this study, we have used fusion proteins containing carboxyl-terminal fragments of beta PP to investigate the association of beta PP with cellular components. We demonstrate that specific domains within the carboxyl end of beta PP contain binding sites for cytoskeletal components; one, within residues 1 to 28 of A beta, binds directly to tubulin, and the second one, within sequences carboxyl-terminal to A beta, binds tau and tubulin. We propose that the two neuropathological hallmarks of Alzheimer's disease, A beta deposition and neurofibrillary tangles, represent the residual of a disrupted beta PP-tubulin-tau complex.
Application of Ultraviolet Radiation for Water Disinfection and Purification in Poland (1992)

A multi-disciplinary research project on water disinfection using UV radiation was carried out under laboratory conditions as well as in selected pools and waterworks. The influence of UV radiation on physical, chemical and microbiological properties of water was determined. The report describes prototype devices and disinfection systems, as well as methods of determining UV radiation dose and α absorption coefficient.
Preparation and evaluation of microspheres prepared from novel polyester-ibuprofen conjugates blended with non-conjugated ibuprofen (2009)

A novel polyester, poly(glycerol-adipate-co-omega-pentadecalactone) (PGA-co-PL), was conjugated with a model drug, ibuprofen, through the free hydroxyl groups of the former and the free carboxyl group of the latter at various levels of substitution. The conjugated material was processed into microspheres by both emulsion solvent evaporation and spray-drying methods. Samples of conjugated material were also blended with non-conjugated drug and the microspheres produced were evaluated by various methods. Morphologically, the microspheres produced were satisfactory. However, there was some initial burst drug release from all samples, probably due to the presence of non-conjugated drug. Subsequent drug release was very slow due to the relative stability of the covalent bonding of the drug-polyester conjugate. Stability tests showed that storage at high relative humidity resulted in increased burst release.
A solution of the mask overlay problem in microelectromechanical CAD (MEMCAD) (1992)

The authors present a computationally efficient algorithm for the processing of data from multiple multi-featured masks to produce a planar map of the device topography in a format compatible with mechanical CAD systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Native-like SARS-CoV-2 Spike Glycoprotein Expressed by ChAdOx1 nCoV-19/AZD1222 Vaccine (2021)

Vaccine development against the SARS-CoV-2 virus focuses on the principal target of the neutralizing immune response, the spike (S) glycoprotein. Adenovirus-vectored vaccines offer an effective platform for the delivery of viral antigen, but it is important for the generation of neutralizing antibodies that they produce appropriately processed and assembled viral antigen that mimics that observed on the SARS-CoV-2 virus. Here, we describe the structure, conformation, and glycosylation of the S protein derived from the adenovirus-vectored ChAdOx1 nCoV-19/AZD1222 vaccine. We demonstrate native-like post-translational processing and assembly, and reveal the expression of S proteins on the surface of cells adopting the trimeric prefusion conformation. The data presented here confirm the use of ChAdOx1 adenovirus vectors as a leading platform technology for SARS-CoV-2 vaccines.
<i>PHENIX</i>: a comprehensive Python-based system for macromolecular structure solution (2010)

Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.