gebhart/patrepeval huggingface dataset:
Methods for high-throughput labelling and detection of biological features in situ using microscopy (2023)

Methods of labelling one or more subcellular components (e.g., an organelle and/or subcellular region) in vivo are provided. Methods of labelling a protein in vivo are provided. Methods of determining a nucleic acid sequence in situ are also provided.
Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells (2021)

While inhibition of T cell co-inhibitory receptors has revolutionized cancer therapy, the mechanisms governing their expression on human T cells have not been elucidated. Type 1 interferon (IFN-I) modulates T cell immunity in viral infection, autoimmunity, and cancer, and may facilitate induction of T cell exhaustion in chronic viral infection. Here we show that IFN-I regulates co-inhibitory receptor expression on human T cells, inducing PD-1/TIM-3/LAG-3 while surprisingly inhibiting TIGIT expression. High-temporal-resolution mRNA profiling of IFN-I responses enabled the construction of dynamic transcriptional regulatory networks uncovering three temporal transcriptional waves. Perturbation of key transcription factors on human primary T cells revealed unique regulators that control expression of co-inhibitory receptors. We found that the dynamic IFN-I response <i>in vitro</i> closely mirrored T cell features with IFN-I linked acute SARS-CoV-2 infection in human, with high <i>LAG3</i> and decreased <i>TIGIT</i> expression. Finally, our gene regulatory network identified <i>SP140</i> as a key regulator for differential <i>LAG3</i> and <i>TIGIT</i> expression, which were validated at the level of protein expression. The construction of IFN-I regulatory networks with identification of unique transcription factors controlling co-inhibitory receptor expression may provide targets for enhancement of immunotherapy in cancer, infectious diseases, and autoimmunity.
Integrated Sample Injection Chip for Micro-HPLC (2006)

In this paper we present a novel sample injection chip. Microvalves and microchannels are integrated on the chip. The valve is a passive lowpass valve that allows a liquid flow at a low flow rate and prohibits it when the flow rate exceeds a threshold. We can control the injection volume by changing the channel design. The chip consists of a channel substrate, an upper valve substrate and an under valve substrate. These substrates are separately fabricated and bonded by using MEMS techniques. The chip, not to leak at a pressure difference of 5.0 MPa, was successfully applied to high performance liquid chromatography (HPLC). A specific volume of sample (100 nl) was injected to the HPLC column. The results show that the sample injection chip has the possibility of being used in the micro-HPLC systems.
Load-Aware Energy Efficient Adaptive Large Scale Antenna System (2020)

This paper proposes an adaptive large scale antenna system (ALSAS) for enhancing energy efficiency in low density wireless network scenarios. The proposed ALSAS comprises of two stages, a novel adaptive discontinuous transmission (ADTx) stage and an antenna array optimization (AAO) one. The basic idea is to utilize prior knowledge of the users' quality of service (QoS) requirements as well as precoding selection in the ADTx stage to maximize the transmitter hibernation periods subject to a certain complexity constraint. In the AAO stage, further power saving is achieved by reducing the number of active antenna elements subject to a certain QoS requirement. It is shown that, relative to conventional large scale antenna system (LSAS), the proposed ALSAS system achieves significant energy efficiency improvements under various scenarios. The results show that the proposed technique can provide energy efficiency improvement between 125% and 1124% in the suburban scenario, and between 196% and 952% in the rural scenario. It is also demonstrated that for rural environments with relatively small short inter-site-distance (ISD) values, ALSAS can provide up to 500% power saving for the fixed bit rate requirement case.
Determination of Zak phase by reflection phase in 1D photonic crystals (2015)

For a one-dimensional (1D) periodic system with inherent mirror symmetry, the value of the geometric "Zak" phase in a bulk band is related to the sign of reflection phase for wavelengths inside the bandgaps sandwiching the bulk band. Here, we designed an interference setup which allows us to measure the reflection phase of 1D phonic crystal fabricated for the optical range; this, in turn, enabled us to determine the Zak phases of the bands. We then found interface states whose existence can be traced to the topological properties of the bandgaps and the geometric phases of the bulk bands.
Biomarkers of splenic function in infants with sickle cell anemia: baseline data from the BABY HUG Trial (2011)

We evaluated spleen function in 193 children with sickle cell anemia 8 to 18 months of age by (99m)Tc sulfur-colloid liver-spleen scan and correlated results with clinical and laboratory parameters, including 2 splenic biomarkers: pitted cell counts (PIT) and quantitative Howell-Jolly bodies (HJB) enumerated by flow cytometry. Loss of splenic function began before 12 months of age in 86% of infants in association with lower total or fetal hemoglobin and higher white blood cell or reticulocyte counts, reinforcing the need for early diagnosis and diligent preventive care. PIT and HJB correlated well with each other and liver-spleen scan results. Previously described biomarker threshold values did define patients with abnormal splenic function, but our data suggest that normal spleen function is better predicted by PIT of ≤1.2% or HJB ≤55/10(6) red blood cells and absent function by PIT ≥4.5% or HJB ≥665/10(6). HJB is methodologically advantageous compared with PIT, but both are valid biomarkers of splenic function. This trial was registered at www.clinicaltrials.gov as #NCT00006400.
Transverse momentum, rapidity, and centrality dependence of inclusive charged-particle production in sNN=5.02 TeV p+ Pb collisions measured by the ATLAS experiment (2016)

Measurements of the per-event charged-particle yield as a function of the charged-particle transverse momentum and rapidity are performed using p+Pb collision data collected by the ATLAS experiment at the LHC at a centre-of-mass energy of sNN=5.02TeV. Charged particles are reconstructed over pseudorapidity |η|&amp;lt;2.3 and transverse momentum between 0.1 GeV and 22 GeV in a dataset corresponding to an integrated luminosity of 1 μb−1. The results are presented in the form of charged-particle nuclear modification factors, where the p+Pb charged-particle multiplicities are compared between central and peripheral p+Pb collisions as well as to charged-particle cross sections measured in pp collisions. The p+Pb collision centrality is characterized by the total transverse energy measured in −4.9&amp;lt;η&amp;lt;−3.1, which is in the direction of the outgoing lead beam. Three different estimations of the number of nucleons participating in the p+Pb collision are carried out using the Glauber model and two Glauber–Gribov colour-fluctuation extensions to the Glauber model. The values of the nuclear modification factors are found to vary significantly as a function of rapidity and transverse momentum. A broad peak is observed for all centralities and rapidities in the nuclear modification factors for charged-particle transverse momentum values around 3 GeV. The magnitude of the peak increases for more central collisions as well as rapidity ranges closer to the direction of the outgoing lead nucleus.
Control of a three-phase four-wire shunt-active power filter based on DC-bus energy regulation (2008)

This paper presents a nonconventional three-phase four-wire shunt active power filter (APF) topology controlled by using an energy approach. A general study of power terms involved in the operation of the four-wire APF is conducted in order to evidence the relationship between instantaneous energy stored in the DC bus and active power requirements on the APF. Harmonics and imbalances both on the utility voltage and load current have been considered and the power developed by the active power filter has been evaluated. This study allows designing a controller for the APF based on the regulation of the energy-state of its DC-bus. The method has been experimentally tested on a four leg APF based on a neutral-point-clamped DC bus. Such topology allowed the test of the most general case, including harmonics and imbalance in utility voltage and in load currents.
A Compositional Approach to Embedded System Design (2002)

An important observable trend in embedded system design is the growing system complexity. Besides the sheer increase of functionality, the growing complexity has another dimension which is the resulting heterogeneity with respect to the different functions and components of an embedded system. This means that functions from different application domains are tightly coupled in a single embedded system. It is established industry practice that specialized specification languages and design environments are used in each application domain. The resulting heterogeneity of the specification is increased even further by reused components (legacy code, IP). Since there is little hope that a single suitable language will replace this heterogeneous set of languages, multi-language design is becoming increasingly important for complex embedded systems. The key problems in the context of multi-language design are the safe integration of the differently specified subsystems and the optimized implementation of the whole system. Both require the reliable validation of the system function as well as of the non-functional system properties. Current cosimulation-based approaches are well suited for functional validation and debugging. However, these approaches are less powerful for the validation of non-functional system properties. In this dissertation, a novel compositional approach to embedded system design is presented which augments existing cosimulation-based design flows with formal analysis capabilities regarding non-functional system properties such as timing or power consumption. Starting from a truly multi-language specification, the system is transformed into an abstract internal design representation which serves as basis for system-wide analysis and optimization.
The significance of shape and orientation in single-particle weak-scatterer models (2002)

Particles that have a density and compressibility comparable to those of the surrounding medium (weak scatterers) are often modeled as spherical scatterers of equivalent volume. The simplicity and symmetry of the spherical model does not however account for the effect of the angle of incidence of the incident field onto the particle. By performing a comparative study of scattering models for the case of a fluid sphere, it is shown that models derived using the Born approximation closely match the exact solution for weak scatterers. This approximation is therefore applied to produce a model for the fluid disk, which is used to investigate the significance of particle shape and orientation. Scattering by a red blood cell of given volume modeled as a sphere is compared to the result obtained by approximating its shape as a disk of varying aspect ratio and orientation. The spherical model is shown to provide a good description for frequencies up to 20 MHz, beyond which particle shape becomes significant. This effect could go undetected if the scattered field is only observed at 90 degrees relative to the direction of the incident field. Nevertheless, the significance of particle shape and orientation might form the basis of a novel detection technique.
Cell-Free Massive MIMO: Uniformly great service for everyone (2015)

We consider the downlink of Cell-Free Massive MIMO systems, where a very large number of distributed access points (APs) simultaneously serve a much smaller number of users. Each AP uses local channel estimates obtained from received uplink pilots and applies conjugate beamforming to transmit data to the users. We derive a closed-form expression for the achievable rate. This expression enables us to design an optimal max-min power control scheme that gives equal quality of service to all users. We further compare the performance of the Cell-Free Massive MIMO system to that of a conventional small-cell network and show that the throughput of the Cell-Free system is much more concentrated around its median compared to that of the smallcell system. The Cell-Free Massive MIMO system can provide an almost 20-fold increase in 95%-likely per-user throughput, compared with the small-cell system. Furthermore, Cell-Free systems are more robust to shadow fading correlation than smallcell systems.
Biodegradable Poly(ester) Urethane Acrylate Resins for Digital Light Processing: From Polymer Synthesis to 3D Printed Tissue Engineering Constructs (2023)

Digital light processing (DLP) is an accurate and fast additive manufacturing technique to produce a variety of products, from patient-customized biomedical implants to consumer goods. However, DLP's use in tissue engineering has been hampered due to a lack of biodegradable resin development. Herein, a library of biodegradable poly(esters) capped with urethane acrylate (with variations in molecular weight) is investigated as the basis for DLP printable resins for tissue engineering. The synthesized oligomers show good printability and are capable of creating complex structures with mechanical moduli close to those of medium-soft tissues (1-3 MPa). While fabricated films from different molecular weight resins show few differences in surface topology, wettability, and protein adsorption, the adhesion and metabolic activity of NCTC clone 929 (L929) cells and human dermal fibroblasts (HDFs) are significantly different. Resins from higher molecular weight oligomers provide greater cell adhesion and metabolic activity. Furthermore, these materials show compatibility in a subcutaneous in vivo pig model. These customizable, biodegradable, and biocompatible resins show the importance of molecular tuning and open up new possibilities for the creation of biocompatible constructs for tissue engineering.
ChemInform Abstract: Enhancement of Enantiocontrol/Diastereocontrol in Catalytic Intramolecular Cyclopropanation and Carbon‐Hydrogen Insertion Reactions of Diazoacetates with Rh2(4S‐MPPIM)4. (1996)

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.
DEGREE OF POLYMERIZATION OF A VESICLE MEMBRANE (SIZE-EXCLUSION-CHROMATOGRAPHY, GELIPEREATION) (1984)

The present work is aimed at determining the membrane composition of polymerized vesicles and determining how exactly the membrane composition and membrane stability are influenced by the specific method of polymerization used. Vesicle dispersions of dimethyl-n-hexadecyl-{11-(methacryloyloxy) undecyl} ammonium bromide in water (both well-sonicated and non-sonicated) were prepared and polymerized by the free radical initiator, 2,2' -azobis (2-methyl propionitrile) and by UV-irradiation. The polymers formed within the vesicles were isolated by freeze drying. The Mark-Houwink-Sakurada constants and absolute molecular weight averages for the polymers were determined by size-exclusion chromatography-viscometry. The non exclusion effects due to adsorption and polyelectrolyte expansion have been shown to be minimal in the size-exclusion chromatographic measurements. The degree of polymerization within AIBN-polymerized vesicles was considerably higher than that within UV-polymerized vesicles. Based on the number average degree of polymerization and using electron micrographic data the number of polymer molecules per vesicle was estimated to be 3 to 60 for AIBN-polymerized vesicles and 15 to 300 for UV-polymerized vesicles. Polymerization of the vesicles were also carried out under different conditions and the effect of polymerization condition on the degree of polymerization within the vesicles has been studied. Explanations for the observed results are given. The stability of the vesicles towards ethanol and Triton X-100 have also been determined and the results indicate that the stability of the vesicles increases as the degree of polymerization increases.
304. Atelocollagen-Based Cell Transfection Array Allows High-Throughput Screening of Gene Functions (2004)

The human genome project has been completed, and it is urgently required that genome information has been implicated in drug discovery, gene therapy and regenerative medicine. To achieve this goal, we have developed cell-based gene expression array that can elucidate the function of a large number of genes within a short time, designated Atelocollagen-based cell transfection array. It is essential to employ materials that condense or package DNA into nano-particles that can easily be taken up by cells and would allow DNA to be retained without degradation. Atelocollagen, biocompatible and low immunogenic biomaterial, is a promising carrier for gene delivery because it is considered safe and appropriate for practical use. We have successfully used Atelocollagen for high-throughput gene transfer into cells and expression screening of gene function. In this system, Atelocollagen/genetic material complexes with a nano-size particle are pre-coated on a micro-well plate on which the cells are then seeded. Through this method, the cells take up the genetic materials and express them by reverse transfection. Atelocollagen/genetic complexes allow for long-term gene expression and are free from cytotoxicity. Then, the cellular biology of the transduced cells could be studied at once with multiparameters including cell growth, cell morphology, subcellular localization of the protein products, number of apoptotic cells, and up- and down-regulation of signaling molecules by using conventional assay systems. We confirmed that the present method with Atelocollagen-based gene transfer is applicable to gene medicines, such as plasmid DNAs, adenovirus vectors, antisense oligonucleotides and siRNAs, and to various cells for cell-based assays.
Detection of mitochondrial deoxyribonucleic acid alterations in urine from urothelial cell carcinoma patients (2011)

Our study aims at understanding the timing and nature of mitochondrial deoxyribonucleic acid (mtDNA) alterations in urothelial cell carcinoma (UCC) and their detection in urine sediments. The entire 16.5 kb mitochondrial genome was sequenced in matched normal lymphocytes, tumor and urine sediments from 31 UCC patients and compared to different clinical stages and histological grades. The mtDNA content index was examined in all the specimens. Sixty-five percent (20/31) of the patients harbored at least 1 somatic mtDNA mutation. A total of 25 somatic mtDNA mutations were detected, which were more frequent in the respiratory complex coding regions (Complex I, III, IV and V) of the mtDNA and significantly affected respiratory Complex III compared to the other complexes (p = 0.021-0.039). Compared to Stage Ta, mtDNA mutation was higher in Stage T1 and significantly higher in Stage T2 (p = 0.01) patients. MtDNA mutation was also significantly higher (p = 0.04) in Stage T2 compared to Stage T1 patients. Ninety percent (18/20) of the patients harboring mtDNA mutation in the tumor also had mutation in their urine sediments. Eighty percent (20/25) of the tumor-associated mtDNA mutations was detectable in the urine sediments. Compared to the normal lymphocytes, the mtDNA content increased significantly in the tumor (p = 0.0013) and corresponding urine sediments (p = 0.0025) in 19/25 (76%) patients analyzed. Our results indicate that mtDNA alterations occur frequently in progressive stages of UCC patients and are readily detectable in the urine sediments. MtDNA mutations appear to provide a promising tool for developing early detection and monitoring strategies for UCC patients.
Optimal Multicast Service Chain Control: Packet Processing, Routing, and Duplication (2021)

Distributed computing (cloud) networks, e.g., mobile edge computing (MEC), are playing an increasingly important role in the efficient hosting, running, and delivery of real-time stream-processing applications such as industrial automation, immersive video, and augmented reality. While such applications require timely processing of real-time streams that are simultaneously useful for multiple users/devices, existing technologies lack efficient mechanisms to handle their increasingly multicast nature, leading to unnecessary traffic redundancy and associated network congestion. In this paper, we address the design of distributed packet processing, routing, and duplication policies for optimal control of multicast stream-processing services. We present a characterization of the enlarged capacity region that results from efficient packet duplication, and design the first fully distributed multicast traffic management policy that stabilizes any input rate in the interior of the capacity region while minimizing overall operational cost. Numerical results demonstrate the effectiveness of the proposed policy to achieve throughput- and cost-optimal delivery of stream-processing services over distributed computing networks.
Etude de la specificite et de la structure d'anticorps anti-histones et anti-motochondries presents dans le serum de patients atteints de maladies autoimmunes (1991)

La presence d'autoanticorps a des taux eleves dans le serum des patients est l'une des caracteristiques des maladies autoimmunes. Parmi ces autoanticorps, les anticorps anti-histones sont reveles au cours de differentes maladies autoimmunes non specifiques d'organes telles que le lupus erythemateux dissemine, la polyarthrite rhumatoide et l'arthrite chronique juvenile. Nous avons particulierement etudie l'activite d'autoanticorps anti-histones notamment a l'aide de peptides synthetiques et nous avons montre que 1) l'origine des anticorps anti-histones serait differente selon la maladie concernee puisque ces anticorps sont diriges contre des regions differentes des histones; 2) dans le lupus erythemateux dissemine, ces anticorps sont codes par des genes pouvant appartenir a differentes familles germinales; 3) l'activite anti-histone parfois portee par des anticorps de type facteurs rhumatoides (anticorps multireactifs) est reliee a des sites distincts de ceux liant le fe et l'ig sur l'anticorps. D'autres anticorps specifiques d'un antigene mitochondrial correspondant a la dihydrolipoamide acetyltransferase (e2) du complexe pyruvate deshydrogenase de la chaine respiratoire ont ete mis en evidence au cours de differentes maladies hepatiques autoimmunes specifiques d'organes comme la cirrhose biliaire primitive. Nous avons montrer que les anticorps anti-e2 produits au cours de cette maladie sont diriges contre un epitope conformationnel constitue par la sequence 167-184 de e2 sur laquelle une molecule d'acide lipoique (cofacteur de e2) est lie de facon covalente