gebhart/patrepeval huggingface dataset:
Coupling of ligand binding and dimerization of helix‐loop‐helix peptides: Spectroscopic and sedimentation analyses of calbindin D9k EF‐hands (2002)

Isolated Ca2+-binding EF-hand peptides have a tendency to dimerize. This study is an attempt to account for the coupled equilibria of Ca2+-binding and peptide association for two EF-hands with strikingly different loop sequence and net charge. We have studied each of the two separate EF-hand fragments from calbindin D9k. A series of Ca2+-titrations at different peptide concentrations were monitored by CD and fluorescence spectroscopy. All data were fitted simultaneously to both a complete model of all possible equilibrium intermediates and a reduced model not including dimerization in the absence of Ca2+. Analytical ultracentrifugation shows that the peptides may occur as monomers or dimers depending on the solution conditions. Our results show strikingly different behavior for the two EF-hands. The fragment containing the N-terminal EF-hand shows a strong tendency to dimerize in the Ca2+-bound state. The average Ca2+-affinity is 3.5 orders of magnitude lower than for the intact protein. We observe a large apparent cooperativity of Ca2+ binding for the overall process from Ca2+-free monomer to fully loaded dimer, showing that a Ca2+-free EF-hand folds upon dimerization to a Ca2+-bound EF-hand, thereby presenting a preformed binding site to the second Ca2+-ion. The C-terminal EF-hand shows a much smaller tendency to dimerize, which may be related to its larger net negative charge. In spite of the differences in dimerization behavior, the Ca2+ affinities of both EF-hand fragments are similar and in the range lgK = 4.6-5.3.
Sequence determinants of protein aggregation in human VH domains (2008)

Human antibody variable heavy (VH) domains tend to aggregate upon denaturation, for instance, by heat or acid. We have previously demonstrated that domains resisting protein aggregation can be selected from CDR-only repertoires by phage display. Here we analysed their sequences to identify determinants governing protein aggregation. We found that, while many different CDR sequences conferred aggregation-resistance, certain physico-chemical properties were strongly selected for. Thus, hydrophobicity and beta-sheet propensity were significantly lower among the selected domains, whereas net negative charge was increased. Our results provide guidelines for the design of human VH repertoires with reduced levels of protein aggregation.
An Effective Non-Commutative Encryption Approach withOptimized Genetic Algorithm for Ensuring Data Protection inCloud Computing (2020)

Nowadays, succeeding safe communication and protection-sensitive data from unauthorized access above public networks are the main worries in cloud servers. Hence, to secure both data and keys ensuring secured data storage and access, our proposed work designs a Novel Quantum Key Distribution (QKD) relying upon a non-commutative encryption framework. It makes use of a Novel Quantum Key Distribution approach, which guarantees high level secured data transmission. Along with this, a shared secret is generated using Diffie Hellman (DH) to certify secured key generation at reduced time complexity. Moreover, a non-commutative approach is used, which effectively allows the users to store and access the encrypted data into the cloud server. Also, to prevent data loss or corruption caused by the insiders in the cloud, Optimized Genetic Algorithm (OGA) is utilized, which effectively recovers the data and retrieve it if the missed data without loss. It is then followed with the decryption process as if requested by the user. Thus our proposed framework ensures authentication and paves way for secure data access, with enhanced performance and reduced complexities experienced with the prior works.
Recycling of homogeneous Pd catalysts using superparamagnetic nanoparticles as novel soluble supports for Suzuki, Heck, and Sonogashira cross-coupling reactions (2005)

Recycling of homogeneous catalysts could be achieved by using magnetic nanoparticles and solid-phase beads, but nanoparticle-supported catalysis proceeded much faster than its counterpart on resins.
Expected reciprocal rank for graded relevance (2009)

While numerous metrics for information retrieval are available in the case of binary relevance, there is only one commonly used metric for graded relevance, namely the Discounted Cumulative Gain (DCG). A drawback of DCG is its additive nature and the underlying independence assumption: a document in a given position has always the same gain and discount independently of the documents shown above it. Inspired by the "cascade" user model, we present a new editorial metric for graded relevance which overcomes this difficulty and implicitly discounts documents which are shown below very relevant documents. More precisely, this new metric is defined as the expected reciprocal length of time that the user will take to find a relevant document. This can be seen as an extension of the classical reciprocal rank to the graded relevance case and we call this metric Expected Reciprocal Rank (ERR). We conduct an extensive evaluation on the query logs of a commercial search engine and show that ERR correlates better with clicks metrics than other editorial metrics.
A WIDE-ANGLE PARABOLIC EQUATION FOR ACOUSTIC WAVES IN INHOMOGENEOUS MOVING MEDIA: APPLICATIONS TO ATMOSPHERIC SOUND PROPAGATION (2001)

Two new derivations of "vector" parabolic equations (PE) for use in acoustic propagation have recently been published. In these cases, PEs have been derived from first principles and incorporate velocity fluctuations of the medium as two additional vector terms. In the simpler case, large spatial-scale velocity fluctuations can be accommodated. In the more general case, multi-scale velocity fluctuations can be accommodated. In this paper we report on a series of two-dimensional numerical experiments which compares sound propagation predicted from traditional PEs with sound propagation predicted from these two "vector" PEs. Two types of velocity fields are simulated. One, suitable for approximating an atmospheric boundary layer, is a field in which velocity has only a horizontal component, but whose magnitude can depend on height, i.e., v=v x (z). The other is a field having random spatial fluctuations over a range of length scales and could be suggestive of atmospheric turbulence. In both cases celerity inhomogeneities are also included. Results suggest that at least, in two dimension, the standard PE using an effective index of refraction is not accurate to describe the effects of the mean and turbulent velocity on sound propagation near the ground. We suspect that in three-dimensional problems, the added terms in the "vector" PEs will significantly increase in importance.
BEHAB/brevican: an extracellular matrix component associated with invasive glioma. (2000)

The extracellular matrix (ECM) has a prominent role in many physiological processes, including organ development, wound healing, and neoplastic growth and invasion. In each of these processes, changes in the composition of the matrix can lead to increased cell movement. In this review, we discuss the role of ECM components in glioma invasion, with special emphasis on the brain-specific proteoglycan, Brain-Enriched Hyaluronan Binding (BEHAB)/brevican.
Molecular and epidemiological characterization of imported malaria cases in Chile (2020)

The timely detection of polymorphisms associated with drug resistance will contribute to understanding if current drug policies in the country are appropriate for treatment of imported malaria cases and provide information about the most frequent resistant genotypes entering Chile.
Assessment of autoantibodies to interferon-ω in patients with autoimmune polyendocrine syndrome type 1: using a new immunoprecipitation assay (2017)

We have developed a novel, highly sensitive and specific assay for measurement of IFN-ω Ab. It provides a simple and convenient method for the assessment of patients with APS-1 and selecting patients suspected of having APS-1 for AIRE gene analysis.
ECG signal acquisition and analysis for telemonitoring (2010)

The goal of this article is to present an algorithm for QRS complex detection in an electrocardiogram (ECG) signal, realized in Matlab software. The algorithm was tested on real ECG signals acquired with a commercial monitoring system Alive Heart Monitor and also for reference on signals from MIT-BIH online ECG signal database. The goal of our research is to import signals from the monitoring system to a PDA or a Smart Phone via wireless network for signal processing and use in telehealthcare and telemonitoring. Therefore, we examine the concept of wireless acquisition and digital signal processing of ECG (electrocardiogram) signal, which, in addition to traditional medicine is increasingly used in the field of telemedicine as well as in completely non-medical areas, such as sport, entertainment, marketing, etc. Furthermore, we describe the fundamental architecture of an electrocardiograph and describe and overview the basic methods for ECG signal processing.
Standardize Test Method of Reliability Evaluation for c-Si Photovoltaic Product (2017)

Shipping damage is one of the key problems of photovoltaic (PV) failures in the field. In addition, the detailed documents and industry standards are necessary, to avoid cell breakages or cracks during transportation. Therefore, ITRI coordinated some TFs to set up a series of experiments on the performance evaluation for PV-cell and PV-module caused by transportation and shipping. This work aims to standardize the test method for performance criteria of PV-cell and PV-module for transportation, and evaluates a guideline and risk analysis for shipped package of PV product to meet the relevant reliability concerns in a long-term perspective. PV products are shipped not only in a fab by forklift trucks or handling, but also transported outside a fab by shipping vehicles such as truck, train, aircraft and shipboard. Consequently, results were applied to SEMI Doc. 5431 and released as SEMI PV56 [1] by voting in 2014. PV product’s makers and buyers, or any other party interested like package designers, can thus have a common testing standard to refer to when desired.
An Investigation of Antibodies to Nerve Growth Factor in Diabetic Autonomic Neuropathy (1994)

Nerve growth factor (NGF) is required for development and maintenance of autonomic nervous function and is highly expressed in the iris. An association between sensory and autonomic diabetic neuropathy and NGF function has been postulated. In light of the evidence for an autoimmune component to the pathogenesis of autonomic neuropathy in Type 1 diabetes mellitus, an enzyme linked immunosorbent assay (ELISA) was established to investigate the presence of autoantibodies to mNGF in: 20 patients with long-standing Type 1 diabetes with abnormal autonomic function tests, of whom 14 had symptomatic autonomic neuropathy, 3 had an episode of iritis, and 6 had no autonomic symptoms; 9 age-matched patients with Type 1 diabetes and no complications; 10 healthy control subjects. Insulin antibodies by ELISA and autoantibodies to other endocrine targets were also measured. The specificity of anti-mNGF autoantibody ELISA was further confirmed by immunodepletion on mNGF-Sepharose 4B. No differences in antibody binding to mNGF were detected, between any of the patient groups and control subjects. There was no relationship between age, sex, and diabetes duration and mNGF binding. High levels of anti-mNGF autoantibodies were found in only one diabetic patient who had no evidence of neuropathy, raising the possibility that an autoimmune component to NGF might precede the development of autonomic dysfunction. It remains to be established whether autoantibodies to NGF play a role in diabetic autonomic neuropathy and prospective studies will be required to investigate whether the autoantibodies are a feature of evolving but not established neuropathy.
High-Throughput Screening of Small Molecule Ligands Targeted to Live Bacteria Surface (2013)

The discovery of small molecule ligands targeted to the surface of live pathogenic bacteria would enable an entirely new class of antibiotics. We report the development and validation of a microarray-based high-throughput screening platform for bacteria that exploits 300 μm diameter chemical spots in a 1 in. × 3 in. nanolayered glass slide format. Using 24 model compounds and 4 different bacterial strains, we optimized the screening technology, including fluorophore-based optical deconvolution for automated scoring of affinity and cyan-magenta-yellow-key (CMYK) color-coding for scoring of both affinity and specificity. The latter provides a lossless, one-dimensional view of multidimensional data. By linking in silico analysis with cell binding affinity and specificity, we could also begin to identify the physicochemical factors that affect ligand performance. The technology we describe could form the foundation for developing new classes of antibiotics.
X-VRML-XML based modeling of virtual reality (2003)

A new method of dynamic generation of virtual scenes for use in Internet virtual reality applications is presented. The virtual scenes are dynamically generated from virtual scene models coded in a high-level XML-based language called X-VRML. The language consists of a set of XML tags introducing new elements to programming of virtual reality. These new elements include object-orientation, access to databases, and programming techniques known from procedural languages like variables, conditions, and loops. The X-VRML language overcomes the main limitations of current virtual reality systems. Use of X-VRML simplifies the code of virtual scene models, allows retrieval of data from databases, selection of virtual scene contents, customization of virtual scenes, and efficient coding of elements that have repetitive structure. Applications of X-VRML include on-line data visualization, geographical information systems, scientific visualization, virtual games, and e-commerce applications such as virtual shops.
Nonphytate phosphorus requirement and phosphorus excretion of broiler chicks fed diets composed of normal or high available phosphate corn with and without microbial phytase (2000)

A study was conducted to evaluate the ability of the young (0 to 3 wk) broiler chicken to utilize the P provided by a high available P corn [HAPC; 0.27% total P and 0.17% nonphytate P] in comparison with yellow dent corn (YDC; 0.23% total P and 0.03% nonphytate P), and to determine the extent to which supplementation with exogenous phytase enzyme could reduce the demands for dietary P and subsequently reduce P excretion. Diets prepared using the two types of corn differed in the amount of phytate-bound P, with the HAPC diets containing approximately 50% less phytate-bound P. Treatment diets were prepared by varying the amount of dicalcium phosphate, and ranged from 0.10 to 0.50% nonphytate P for YDC diets, and from 0.18 to 0.50% nonphytate P for HAPC diets. Sublots of each diet were supplemented with 800 units/kg phytase. Each diet was fed to six pens of five male chicks of a commercial broiler strain from 1 to 21 d of age. Regression analysis was used to estimate nonphytate P requirements for each corn type with and without phytase supplementation. The greatest need for nonphytate P was for maximum tibia ash, with requirements of 0.39, 0.29, 0.37, and 0.32% in diets with YDC, YDC plus phytase, HAPC, and HAPC plus phytase, respectively. Addition of phytase liberated approximately 50% of the phytate-bound P from each diet. These levels were sufficient to support body weight, feed conversion, and livability. Fecal P content of broilers fed diets with YDC at the NRC (1994) recommended level of 0.45% nonphytate P was 1.21%, whereas at the respective requirement points indicated above, the P content was 1.09, 0.87, 0.78, and 0.64% in feces from broilers fed diets with YDC, YDC plus phytase, HAPC, and HAPC plus phytase, respectively. Thus, fecal P output could be reduced while maintaining optimum performance by the use of reduced dietary nonphytate P, introduction of HAPC, and phytase supplementation. One of the greatest benefits of phytase supplementation appeared to be maintaining livability at lower dietary levels of nonphytate P.
Neu3CA-RT: A framework for real-time fMRI analysis (2018)

Real-time functional magnetic resonance imaging (rtfMRI) allows visualisation of ongoing brain activity of the subject in the scanner. Denoising algorithms aim to rid acquired data of confounding effects, enhancing the blood oxygenation level-dependent (BOLD) signal. Further image processing and analysis methods, like general linear models (GLM) or multivariate analysis, then present application-specific information to the researcher. These processes are typically applied to regions of interest but, increasingly, rtfMRI techniques extract and classify whole brain functional networks and dynamics as correlates for brain states or behaviour, particularly in neuropsychiatric and neurocognitive disorders. We present Neu<sup>3</sup>CA-RT: a Matlab-based rtfMRI analysis framework aiming to advance scientific knowledge on real-time cognitive brain activity and to promote its translation into clinical practice. Design considerations are listed based on reviewing existing rtfMRI approaches. The toolbox integrates established SPM preprocessing routines, real-time GLM mapping of fMRI data to a basis set of spatial brain networks, correlation of activity with 50 behavioural profiles from the BrainMap database, and an intuitive user interface. The toolbox is demonstrated in a task-based experiment where a subject executes visual, auditory and motor tasks inside a scanner. In three out of four experiments, resulting behavioural profiles agreed with the expected brain state.
Fused Filament Fabrication of Small Ceramic Components (2018)

With respect to rapid prototyping of ceramic components, there are known only a few processes (stereo lithography, binder jetting). In this work, a new process chain is described in detail, showing that ceramics can be printed in a very cost-efficient way. We developed a ceramic⁻polymer composite as filament material that can be printed on a low-cost fused filament fabrication (FFF) desktop printer, even with very small nozzle sizes enabling very small geometric feature sizes. The thermal post-processing, with debinding and sintering, is very close to the ceramic injection molding (CIM) process chain.
Supplementary Figure 3 from The CD4<sup>+</sup> T-Cell Response of Melanoma Patients to a MAGE-A3 Peptide Vaccine Involves Potential Regulatory T Cells (2023)

Supplementary Figure 3 from The CD4&lt;sup&gt;+&lt;/sup&gt; T-Cell Response of Melanoma Patients to a MAGE-A3 Peptide Vaccine Involves Potential Regulatory T Cells
A Semi-Infinite Programming Approach to Preoperative Planning of Robotic Cardiac Surgery Under Geometric Uncertainty (2012)

In this paper, a computational framework for patient-specific preoperative planning of Robotics-Assisted Minimally Invasive Cardiac Surgery (RAMICS) is presented. It is expected that preoperative planning of RAMICS will improve the success rate by considering robot kinematics, patient-specific thoracic anatomy, and procedure-specific intraoperative conditions. Given the significant anatomical features localized in the preoperative computed tomography images of a patients thorax, port locations and robot orientations (with respect to the patients body coordinate frame) are determined to optimize qualities such as dexterity, reachability, tool approach angles and maneuverability. To address intraoperative geometric uncertainty, the problem is formulated as a Generalized Semi-Infinite Program (GSIP) with a convex lower-level problem to seek a plan that is less sensitive to geometric uncertainty in the neighborhood of surgical targets. It is demonstrated that with a proper formulation of the problem, the GSIP can be replaced by a tractable constrained nonlinear program that uses a multi-criteria objective function to balance between the nominal task performance and robustness to collisions and joint limit violations. Finally, performance of the proposed formulation is demonstrated by a comparison between the plans generated by the algorithm and those recommended by an experienced surgeon for several case studies.
Synthesis and Characterization of Silica-Chitosan Porous Hybrids for Tissue Engineering (2007)

A variety of types of organic polymers have been employed in the synthesis of hybrids with silica. In this work the sol-gel method was used for preparation of macroporous 3D hybrid scaffolds based on silica and chitosan in various compositions (10, 20 and 30% wt). The hybrids were analyzed by Scanning Electron Microscopy (SEM), X-ray Diffraction (DRX) and Infra-red Spectroscopy (FTIR) and the effect of addition of the polymer was evaluated. The foams obtained by sol-gel process were appropriate to produce hybrids based on chitosan-silica and showed large pore size distribution and porosity, except for hybrids with higher polymer content. The FTIR spectroscopy showed a band relative to Si-O-C bond that was also found to increase with the increasing the amounts of chitosan in the hybrid. This fact can suggest an interaction between the organic-inorganic phases in the material and provide new insights on the advantages of chitosansilica hybrid materials produced via sol-gel methodology.
Learning How to Teach or Selecting Minimal Surface Data (1991)

Learning a map from an input set to an output set is similar to the problem of reconstructing hypersurfaces from sparse data (Poggio and Girosi, 1990). In this framework, we discuss the problem of automatically selecting minimal surface data. The objective is to be able to approximately reconstruct the surface from the selected sparse data. We show that this problem is equivalent to the one of compressing information by data removal and the one of learning how to teach. Our key step is to introduce a process that statistically selects the data according to the model. During the process of data selection (learning how to teach) our system (teacher) is capable of predicting the new surface, the approximated one provided by the selected data. We concentrate on piecewise smooth surfaces, e.g. images, and use mean field techniques to obtain a deterministic network that is shown to compress image data.
Oncogene amplification in breast cancer. (1991)

To refine the analysis of gene amplification in breast cancer, the authors have developed sensitive methods that can be used to screen nucleic acid prepared from a variety of sources. In their analysis, Southern hybridization and DNA dot-blot analysis were used to screen 49 breast cancer DNAs for Myc, Neu, and Int-2 gene amplification. The analysis detected minimal one extra gene copy) as well as expanded (two or more extra gene copies) gene amplifications, and in addition, distinguished between gene amplification and aneuploidy as the cause of extra gene copies. These quantitative methods were adapted to patient specimens routinely available in the anatomic pathology laboratory, including fresh tumor tissue, tumor nuclei discarded during estrogen receptor analysis, and paraffin blocks. One minimal gene amplification was found in three cases of intraductal cancer. Of 25 cases of nonmetastatic invasive cancer, 28% had at least one extra Myc gene, whereas 24% had Neu, and 21% had Int-2 gene amplification. Of 21 cases of metastatic invasive cancer, 43% had Myc, 43% had Neu, and 40% had Int-2 gene amplification. Among the nonmetastatic cancers, 47% had one, 12% had two, and 4% had three amplified genes. Within the metastatic cancers, 48% had one, 28% had two, and 5% had three amplified genes. Our data suggest relationships between tumor progression and both incidence and size of Myc, Neu, and Int-2 gene amplification.