gebhart/patrepeval huggingface dataset:
The Oocyte as a Secretory Cell (1983)

Xenopus laevis oocytes secrete a large variety of foreign secretory proteins after the microinjection of mRNA or DNA. Two classes of such proteins are discussed in detail. These are the chick oviduct proteins ovalbumin and lysozyme, and the mouse MOPC 21 immunoglobulin. The injection of mRNAs for mouse immunoglobulin heavy or light chain leads to the synthesis, segregation, but not secretion of the encoded proteins unless the two mRNAs are simultaneously or sequentially injected into the same oocytes. Chicken ovalbumin and lysozyme are synthesized and secreted from oocyte after the injection of either oviduct mRNA or cloned DNA (ovalbumin). The secreted lysozyme is exported considerably faster than ovalbumin; however, 40% of the lysozyme synthesized cannot be secreted and, after fractionation of oocytes on sucrose gradients, is found in a higher density position than ovalbumin. No competition at the level of secretion or translation was noted when different amounts of immunoglobulin and ovalbumin mRNAs were injected into oocytes. However, the co-injection of ovalbumin mRNA and mRNAs encoding anti-ovalbumin immunoglobins resulted in the formation of a complex of the two types of protein within the oocyte. In these circumstances, secretion of the immunoglobulin was severely reduced.
Security-Aware Resource Allocation in Clouds (2013)

Elasticity and economic considerations make Infrastructure-as-a-Service (IaaS) clouds attractive propositions for hosting enterprise IT applications. However, for prospective cloud customers, that potential is tempered by concerns, chief among them being security. We consider the problem of resource allocation in IaaS clouds while factoring in reachability and access control requirements of the cloud virtual machines (VMs). We describe a security-aware resource allocation framework that allows for effective enforcement of defense-in-depth for cloud VMs by determining (1) the grouping of VMs into security groups based on the similarity of their reachability requirements, and (2) the placement of virtual machines in a manner that reduces residual risks for individual VMs as well as security groups. We formalize security-aware resource allocation as a Constraint Satisfaction Problem (CSP), which can be solved using widely available Satisfiability Modulo Theories (SMT) solvers. Our experimental evaluation shows the effectiveness of our approach in reducing risk and improving manageability of security configurations for the cloud VMs.
3D volume segmentation and reconstruction. Supervised image classification and automated quantification of superparamagnetic iron oxide nanoparticles in histology slides for safety assessment (2021)

This article presents an automated image-processing workflow for quantitative assessment of SPION accumulation in tissue sections stained with Prussian blue for iron detection. We utilized supervised machine learning with manually labeled features used for training the classifier. Performance of the classifier was validated by 10-fold cross-validation of obtained data and by measuring Dice and Jaccard Similarity Coefficients between manually segmented image and automated segmentation. The proposed approach provides time and cost-effective solution for quantitative imaging analysis of SPION in tissue with a precision similar to that obtained via thresholding method for stain quantification. Furthermore, we exploited the classifiers to generate segmented 3D volumes from histological slides. This enabled visualization of particles which were obscured in original 3D histology stacks. Our approach offers a powerful tool for preclinical assessment of the precise tissue-specific SPION biodistribution, which could affect both their toxicity and their efficacy as nanocarriers for medicines.
Distributed Distributionally Robust Dispatch for Integrated Transmission-Distribution Systems (2020)

This paper proposes a new distributed dispatch scheme to realize efficient coordinated real-time dispatch of the coupled transmission grid and active distribution grids (ADGs). In the proposed scheme, on the one hand, the concept of optimal power exchange interval is introduced to coordinate the transmission grid and ADGs so that the reserve capacity support from ADGs can be incorporated in the dispatch optimization of the transmission grid. On the other hand, uncertainties of renewable distributions are considered to ensure the robustness of dispatch decisions. With the analytical target cascading (ATC) method, the centralized distributionally robust dispatch model for the integrated transmission-distribution system is decoupled, leading to a number of independent small local optimization problems for the transmission grid and ADGs. Meanwhile, the diagonal quadratic approximation is adopted to develop an iterative coordination strategy where all local optimization problems are solved in a parallel manner, increasing the computational efficiency. By using the constrained cost variable technique (CCV) and a new affine policy, the original non-convex dispatch model is reformulated as a linear optimization problem, which ensures the convergence of the iterative process and further reduces the computational burden. Case studies on three test systems verify the effectiveness and efficiency of the proposed scheme.
Spontaneous parametric down-conversion in periodically poled KTP waveguides and bulk crystals (2007)

We present a theoretical and experimental comparison of spontaneous parametric down-conversion in periodically poled waveguides and bulk KTP crystals. We measured a waveguide pair generation rate of 2.9.10(6) pairs/s per mWof pump in a 1-nm band: more than 50 times higher than the bulk crystal generation rate.
Methyl (2′S,3′S)-3,4-O-(2′,3′-dimethoxybutane-2′,3′-diyl)-α-L-rhamnopyranoside: a glycosyl acceptor (2008)

The title compound, C(13)H(24)O(7), is the product of the ketalization of methyl l-(+)-rhamnopyran-oside with 2,3-butane-dione. It crystallizes with two mol-ecules in the asymmetric unit, which are connected by O-H⋯O hydrogen bonds. The C-3,4 diequatorial hydroxy groups of the methyl l-(+)-rhamnopyran-oside were protected, leaving the C-2 hydroxy group free. The l-(+)-rhamnopyran-oside and 2',3'-dimethoxy-butane-2',3'-diyl rings adopt chair conformations and all meth-oxy groups are in axial positions. The absolute configuration was assumed from the synthesis.
Real Time Extraction and Analysis of Key Morphological Features in the Electrocardiogram, for Data Compression and Clinical Decision Support (2011)

Massive amounts of clinical data can now be collected by stand-alone or wearable monitors over extended periods of time. One key challenge is to convert the volumes of raw data into clinically relevant and actionable information, ideally in real-time. This becomes imperative especially in the domain of wearable monitors, where power and memory constraints prevent continuous communication of raw, uncompressed data to a base station for a health care provider. We focus here on algorithmic approaches to extract clinically meaningful information from the electrocardiogram (ECG) in realtime. We use a curve-length transform to identify, and aggregate from beat to beat, physiologically relevant timing information, such as the onsets and offsets of P-waves, QRS complexes, and T-waves, along with their respective magnitudes. Each heartbeat is thus parametrized in terms of 12 variables. Assuming a nominal heart-rate of 70 beats per minute, and a sampling frequency of 250 Hz, each beat has approximately 215 samples. Reducing each beat to 12 samples thus gives an 18-fold compression. An exponentially-weighted sliding average of the identified morphological features over the preceding twenty beats is also stored. Whenever any feature deviates significantly from its stored weighted average, the algorithm registers an alarm and also retains the raw ECG data of the 5 beats immediately preceding and following the anomalous occurrence, for a later review by a clinician.
Blind estimation of multiple co-channel digital signals using an antenna array (1994)

Proposes a novel approach for separating and estimating multiple co-channel digital signals using an antenna array. The spatial response of the array is unknown. The authors exploit the temporal structure of the digital signals to simultaneously determine the array response and the bit sequence for each signal. Uniqueness of the estimates is established for signals with BPSK modulation format. This new approach is applicable to an unknown array geometry and propagation environment, which is particularly useful in digital mobile communications. Simulation results demonstrate its promising performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Modeling and bio-mimetic control for whole-arm dynamic cooperative manipulation (2005)

This paper studies modeling and bio-mimetic control of a three-dimensional 8-d.o.f. whole-arm cooperative manipulation system using sensitive skin. A sphere is considered here as a manipulated object. The control law is designed based on integration of voluntary movement and reflex considering the system's redundancy. The voluntary task of holding the object safely is realized via multi-point impedance control at the four contact points with the object using the contact force information from the sensitive skin. A reflex is introduced as a regulation problem of the direction between the points of end-effectors and elbows to determine the robot system's posture uniquely and to adapt to external disturbances. The solution of the redundant control is formulated and derived from the optimization point of view for different cases of the output function's dimensions. Further, desired functions for voluntary movement and reflex are adjusted according to the task situations. The validity of the proposed method is investigated by numerical simulations.
Electricity Price Forecasting via Statistical and Deep Learning Approaches: The German Case (2023)

Our research involves analyzing the latest models used for electricity price forecasting, which include both traditional inferential statistical methods and newer deep learning techniques. Through our analysis of historical data and the use of multiple weekday dummies, we have proposed an innovative solution for forecasting electricity spot prices. This solution involves breaking down the spot price series into two components: a seasonal trend component and a stochastic component. By utilizing this approach, we are able to provide highly accurate predictions for all considered time frames.
Studies on Pyruvate Metabolism by Lactic Acid Bacteria (1956)

乳酸菌をピルビン酸に作用させた場合,好気的には主としてpyruvic oxidase系の働くものと,アセトイン生成系の働くものとに二大別する事が出来る.この関係と乳酸醗酵型式との間には直接的な関連はない.このpyruvate oxidaseに対しては無機燐酸を要求し(L. delbrückii, L. fermentum),アセトイン生成系では燐酸の添加は反応を促進する場合と然らざる場合があり,更に醋酸はアセトイン生成反応を促進する. L. fermentum及びLeuc. mesenteroidesによる好気的なピルビン酸の代謝はpyruvic oxidaseとアセトイン生成系とが関与するが,次の(4), (5), (6)反応は行われないものと考えられる. CH3・CO・COOH+H2O→CH3・COOH+H・COOH…………………………………(4) CH3・CO・COOH+H2O→CH3・COOH+CO2+H2……………………………………(5) 2 CH3・CO・COOH+H2O→CH3・COOH+CH3・CHOH・COOH+CO2………………(6) 尚(4)反応はE. coli(21), (5)はCl. butylicum(22), (6)はSt. aureus(23)(24)について認められたものである.
Comparison of lung adenocarcinoma and squamous cell carcinoma genomes reveals distinct regions of amplification on chromosome 3q (2005)

879 Lung cancer is a leading cause of cancer death worldwide. Non-small cell lung cancer (NSCLC) is the major disease type, with squamous cell carcinoma (SqCC) and adenocarcinoma (AC) as the two main sub-types. SqCC and AC are distinguished by differences in their histopathological and molecular characteristics: SqCC develops more rapidly and is located in the central airways, whereas AC is thought to originate from the epithelium of the lung periphery. Previous findings suggest that, although a similar degree of genetic imbalance exists for AC and SqCC, each type is characterized by a unique pattern of genomic imbalance. Objective: To comprehensively identify the underlying differences in genetic alteration patterns between SqCC and AC, we performed genome-wide tiling resolution array CGH analysis. Novel variations in copy number detected by this high resolution technology may reveal cancer-related loci and will provide potential targets for diagnosis and treatment. Design, Materials and Methods: DNA was isolated from 15 AC cell lines and 9 SqCC cell lines. Sample DNA and a pooled reference genomic DNA sample were differentially labeled and applied to the submegabase resolution tiling-set (SMRT) array for CGH analysis. This array consists of >32,000 overlapping human bacterial artificial chromosome clones that span the entire human genome, allowing true genome-wide assessment of copy number changes for a given sample. SMRT array data was assessed using multiple software applications (SeeGH, weighted frequency, aCGH smooth) and alterations in identified regions are presently be validated by fluorescent in situ hybridization using loci specific probes. Results: In total, 24 whole genome array CGH profiles of lung cancer cell lines were generated. Numerous novel, subtype-specific chromosomal alterations were observed. This included differences of alteration at chromosome arms 2q, 6q, 8q, 9q, 12q, 13q and 16p. Of specific interest were the different locations of chromosomal amplification at 3q in the sub-types. AC showed frequent gains between 3q13 and 3q22 while SqCC displayed a similar frequency at 3q23-3q26. These regions have previously been implicated in lung cancer but not mapped according to sub-type. Further analysis of genes within distinct altered regions will determine if these loci help drive the development of different lung cancer subtypes. Conclusions: Tiling resolution array CGH analysis of AC and SqCC lung cancers revealed both shared and subtype-specific regions of DNA copy aberration, suggesting that differences in tumor genomes help define distinct disease subtypes. Further characterization of the novel aberrations and minimal regions we have identified will implicate additional genes in the two tumorigenesis processes and help tailor disease diagnosis. Supported by NCI SPORE CA 70907, NCI Contract N01-85188 and Genome Canada
Shear Viscosity of Superfluid3Heup to 15 Tesla (1997)

We present the first measurements of the viscosity of superfluid ${}^{3}\mathrm{He}$ in magnetic fields up to $15\mathrm{T}$, at temperatures down to $2\mathrm{mK}$ along the melting curve, using an assumption for the temperature dependence of the normal density. At fields higher than $4\mathrm{T}$, the viscosity shows a minimum in the ${A}_{1}$ phase, and reaches a local maximum at the ${A}_{2}$ transition which becomes global at $14.6\mathrm{T}$. The sharp decrease just below the ${A}_{1}$ transition can be understood within the Ginzburg-Landau framework and is consistent with both theory and experiments in lower fields. At temperatures below the minimum, the viscosity in the ${A}_{1}$ phase is dominated by a term with ${T}^{\ensuremath{-}2}$ dependence. Additionally, we have calculated the temperature dependence of the viscosity tensor in the low temperature limit using the method of temperature asymptotes.
ULTRASTRUCTURAL STUDIES ON THE PERMEABILITY OF THE MESOTHELIUM TO HORSERADISH PEROXIDASE (1968)

Peritoneal mesothelium was exposed for 2-60 min to solutions of horseradish peroxidase by incubation in vitro, or after intraperitoneal injection in vivo. Peroxidase was localized, with the electron microscope in the intercellular clefts of the mesothelium, often along their entire lengths, in vesicles adjoining or contiguous with the clefts, and along the peritoneal and basal surfaces of the cell, and also in intracytoplasmic vacuoles. The intercellular junctions of peroxidase-treated mesothelium did not differ from those of controls: open and closed junctions were present in both groups. Intercellular localization was also obtained when the mesothelium was exposed to peroxidase during or after fixation. Although intracellular absorption of peroxidase and its incorporation into larger vacuoles were observed, there was no clearcut evidence of vesicular transport across the mesothelium in these experiments. These findings are consistent with physiologic data which postulate that mesothelial transport can be accounted for, at least in part, by passive diffusion through a system of pores, and they suggest that these pores are located in the intercellular clefts.
Mass Spectrometry Analysis Of Msi2 Interacting Partners In K562 Cells (2017)

Mass spectrometry analysis of MSI2 interacting partners in K562 cells for manuscript "<strong>Functional screen of MSI2 interactors identifies an essential role for SYNCRIP in myeloid leukemia stem cells"</strong> by Vu et al. 2017.
A Security Architecture Based on Trust Management for Pervasive Computing Systems (2005)

Traditionally, stand-alone computers and small networks rely on user authentication and access control to provide security. These physical methods use system-based controls to verify the identity of a person or process, explicitly enabling or restricting the ability to use, change, or view a computer resource. However, these strategies are inadequate for the increased flexibility that distributed networks such as the Internet and ubiquitous/pervasive computing environments require, as these systems lack central control and in addition, their users are not all predetermined. Users in pervasive environments expect to access locally hosted resources and services anytime and anywhere leading to serious security risks and access control problems. We propose a solution based on distributed trust management which involves developing a security policy, assigning credentials to entities, verifying that the credentials conform to the policy, delegating trust to third parties, revoking rights and reasoning about users' access rights. This paper presents an infrastructure that complements existing security features like Public Key Infrastructure (PKI) and Role Based Access Control with distributed trust management to provide a highly flexible mode of enforcing security in a pervasive computing environments.
The challenge of Helicobacter pylori resistance to antibiotics: the comeback of bismuth-based quadruple therapy (2012)

A proton-pump inhibitor (PPI), clarithromycin-based, triple therapy has been the recommended treatment for Helicobacter pylori eradication for the past 15 years. Due to a steady increase in H. pylori resistance to clarithromycin, this triple clarithromycin-based treatment has become progressively less efficacious. Several approaches are available to address this situation: one is to test for clarithromycin resistance so that this triple clarithromycin-based regimen is given only to those who will benefit; a second is to prescribe the drugs sequentially, beginning with amoxicillin and a PPI followed by clarithromycin and metronidazole, again with a PPI or the four drugs prescribed concomitantly; a third alternative is to use bismuth-based quadruple therapy, PPI plus a standardized three-in-one capsule, bismuth subcitrate potassium, metronidazole, and tetracycline (BMT, sold under licence as Pylera®). The advantages of these different approaches are reviewed, including the relevance of BMT three-in-one capsule in clinical practice.
A case study in building layered DHT applications (2005)

Recent research has shown that one can use Distributed Hash Tables (DHTs) to build scalable, robust and efficient applications. One question that is often left unanswered is that of simplicity of implementation and deployment. In this paper, we explore a case study of building an application for which ease of deployment dominated the need for high performance. The application we focus on is Place Lab, an end-user positioning system. We evaluate whether it is feasible to use DHTs as an application-independent building block to implement a key component of Place Lab: its "mapping infrastructure." We present Prefix Hash Trees, a data structure used by Place Lab for geographic range queries that is built entire on top of a standard DHT. By strictly layering Place Lab's data structures on top of a generic DHT service, we were able to decouple the deployment and management of Place Lab from that of the underlying DHT. We identify the characteristics of Place Lab that made it amenable for deploying in this layered manner, and comment on its effect on performance.
Novel contrast enhancement scheme for infrared image using detail-preserving stretching (2011)

A novel contrast enhancement scheme for infrared (IR) image using detail-preserving stretching (DPS) is presented in this paper. Unlike CCD images, the histogram of the IR images is not distributed to the entire dynamic range of the input image. Therefore, in order to enhance the contrast, the proposed method adopts contrast stretching since it has a low computational complexity and preserves the global contrast of the original. However, the stretching often produces unpleasant images that do not contain clear details by limiting the output dynamic range. To solve this problem, we propose a new contrast stretching method based on gradient-domain processing (GDP) that can enhance the local image contrast while preserving the global contrast as well as the image details. Experimental results demonstrate that the proposed method outperforms the conventional stretching-based and other image enhancement methods with respect to the visual quality and computational complexity.
Subspace clothing simulation using adaptive bases (2014)

We present a new approach to clothing simulation using low-dimensional linear subspaces with temporally adaptive bases. Our method exploits full-space simulation training data in order to construct a pool of low-dimensional bases distributed across pose space. For this purpose, we interpret the simulation data as offsets from a kinematic deformation model that captures the global shape of clothing due to body pose. During subspace simulation, we select low-dimensional sets of basis vectors according to the current pose of the character and the state of its clothing. Thanks to this adaptive basis selection scheme, our method is able to reproduce diverse and detailed folding patterns with only a few basis vectors. Our experiments demonstrate the feasibility of subspace clothing simulation and indicate its potential in terms of quality and computational efficiency.
Optimization of Extraction Process of Protein Isolate from Mung Bean (2011)

Protein was extracted from mung bean by water. Study the best parameter extraction. Based on single factor experiments, investigated liquid ratio, extraction temperature, extraction ph, settlement ph, and extraction time. Design by design expert to optimize the response of the face of extraction of technology. Optimal parameters: Liquid ratio of 10%, extraction temperature 31.74°C, extraction ph 8.97, settlement ph 4.4, extraction time 33.24 min.
Evaluation of serum levels of oxidized and reduced glutathione and total antioxidant capacity in patients with head and neck squamous cell carcinoma (2018)

Since the levels of GSH and GSH/GSSG were significantly lower in the case group, GSH/GSSG could be used as a prognostic factor for the early diagnosis of HNSCC.
Welcome and Introduction to SPIE Conference 11672 (2021)

Welcome and Introduction to SPIE Photonics West LASE conference 11672: Laser Resonators, Microresonators, and Beam Control XXIII