gebhart/patrepeval huggingface dataset:
Rate control in transform coding systems (2011)

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Characterization of UWB transmit-receive antenna system (2004)

An ultra-wideband (UWB), stripline-fed Vivaldi antenna is characterized both numerically and experimentally. Three-dimensional far-field measurements are conducted and accurate antenna gain and efficiency as well as gain variation versus frequency in the boresight direction are measured. Using two Vivaldi antennas, a free-space communication link is set up. The impulse response of the cascaded antenna system is obtained using full-wave numerical electromagnetic time-domain simulations. These results are compared with frequency-domain measurements using a network analyzer. Full-wave numerical simulation of the free-space channel is performed using a two step process to circumvent the computationally intense simulation problem. Vector transfer function concept is used to obtain the overall system transfer function and the impulse response.
Robust parametric modeling of Alzheimer’s disease progression (2020)

Quantitative characterization of disease progression using longitudinal data can provide long-term predictions for the pathological stages of individuals. This work studies the robust modeling of Alzheimer's disease progression using parametric methods. The proposed method linearly maps the individual's age to a disease progression score (DPS) and jointly fits constrained generalized logistic functions to the longitudinal dynamics of biomarkers as functions of the DPS using M-estimation. Robustness of the estimates is quantified using bootstrapping via Monte Carlo resampling, and the estimated inflection points of the fitted functions are used to temporally order the modeled biomarkers in the disease course. Kernel density estimation is applied to the obtained DPSs for clinical status classification using a Bayesian classifier. Different M-estimators and logistic functions, including a novel type proposed in this study, called modified Stannard, are evaluated on the data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) for robust modeling of volumetric magnetic resonance imaging (MRI) and positron emission tomography (PET) biomarkers, cerebrospinal fluid (CSF) measurements, as well as cognitive tests. The results show that the modified Stannard function fitted using the logistic loss achieves the best modeling performance with an average normalized mean absolute error (NMAE) of 0.991 across all biomarkers and bootstraps. Applied to the ADNI test set, this model achieves a multiclass area under the ROC curve (AUC) of 0.934 in clinical status classification. The obtained results for the proposed model outperform almost all state-of-the-art results in predicting biomarker values and classifying clinical status. Finally, the experiments show that the proposed model, trained using abundant ADNI data, generalizes well to data from the National Alzheimer's Coordinating Center (NACC) with an average NMAE of 1.182 and a multiclass AUC of 0.929.
Is B Cell-Targeted Therapy Effective in Systemic Lupus Erythematosus? (2015)

In the past decade we have witnessed a dramatic change in the management of autoimmune diseases, such as rheumatoid arthritis, due to the development of new biologic drugs designed to target key mediators in the autoimmune process. However, the development of similar target-specific drugs for the management of SLE has not been as successful. The B cell has long been considered central to the pathogenesis of SLE and has been regarded as an important target for biologic drugs. Several B cell-targeted drugs have been developed and although the mechanisms seem promising, most of the studies published to date have failed to achieve their primary endpoints, leading to an ongoing debate regarding the role of B cell therapy in SLE. The present report discusses the pros and cons of B cell-targeted therapy in SLE, reviews the clinical studies, and offers possible explanations forthe discrepancies between randomized control studies and real-life experience.
8 Multiparameter characterization of CAR T cells (2021)

<h3>Background</h3> Adoptive cell transfer of chimeric antigen receptor (CAR) modified T cells has demonstrated great therapeutic success against certain hematological malignancies. However, a substantial number of patients experienced relapse at some point after treatment with the underlying mechanisms not fully understood. Emerging data suggest that the undesired clinical outcome is related to different aspects, which include: the tumor heterogeneity, the tumor microenvironment, as well as intrinsic characteristics of the CAR T cells. In this work, we aimed to understand the diversity of CAR T cells generated from different donors, using multiparameter in vitro characterization. <h3>Methods</h3> Leukapheresis from healthy donors were collected to generate CAR T cells using the GMP-compliant CliniMACS Prodigy® platform, enabling an automated and closed engineering of CAR T cells in a highly reproducible manner. We performed an in-depth characterization of the resulting CAR T cells by exploring differences in the immunophenotype, cell fitness and effector function of the freshly prepared as compared to frozen CAR T cell samples. Specifically, we designed several flow cytometry panels for the extensive characterization of immunophenotypes of interest such as: proliferative capacity, differentiation, activation and exhaustion. Cell fitness status was determined by the rate at which cells undergo apoptosis following stress. Finally, effector function was determined by the ability of the activated CAR T cells to secrete proinflammatory cytokines including IFN-g, TNF-a and IL-2. The associations between these different parameters were analyzed using comprehensive statistical approaches. <h3>Results</h3> With our established workflow, over 20 healthy-donor derived CAR T cells were generated and characterized. We have observed donor-dependent variations and responses for most of the explored parameters. In general, the freezing and thawing process negatively affected cell fitness and effector function of the CAR T cells and resulted in altered immunophenotypes. Additionally, correlations between certain immunophenotypes and cell fitness/effector function were identified. <h3>Conclusions</h3> Collectively, we established a workflow for multiparameter characterization of CAR T cells and assessed the intrinsic variability of CAR T cells for both research and clinical application.
Histone Deacetylase inhibitors modulate mitochondrial biogenesis in skeletal muscle (2010)

The control of metabolic pathways occurs at the transcriptional level also through epigenetic mechanisms. Since it has been demonstrated that Histone Deacetylases (HDACs) are involved in muscle fiber type determination, our aim was to investigate the metabolic effects following the biochemical inhibition of HDACs in skeletal muscle and the underlying mechanisms. In C2C12 myotubes we observed that HDAC inhibitors (HDACi) upregulate the mRNA of PGC‐1alpha and its target genes. Additionally, transcriptome analysis in C2C12 treated with HDACi revealed an increase in OXPHOS genes and in genes coding for fatty acids catabolism enzymes, most likely linked to PGC‐1alpha‐dependent activation of gene transcription. Consistent with the increase of PGC‐1alpha, FACS analysis revealed increased density and activity of mitochondria in C2C12 myoblasts. As well, staining of myotubes treated with HDACi showed an increase in mitochondrial density and activity. Using Class specific HDAC inhibitors we observed that Class I HDACs are the most involved in the promotion of these effects. These results underscore a central role of HDACs, and most probably of Class I HDACs, in modulating metabolic adaptation in cells and suggest HDACi as valuable tools to study molecular mechanisms implicated in energy metabolism and possibly in metabolic diseases. (Funded by grants: EC FP6 LSHM‐CT‐2006‐037498 SOUTH, PRIN 2008 ZTN724)
Population Synthesis: A Different Perspective (2013)

Microsimulation of urban systems evolution requires synthetic population as a key input. Currently, the focus is on treating synthesis as a fitting problem and thus various techniques have been developed, including Iterative Proportional Fitting (IPF) and Combinatorial Optimization based techniques. The key shortcomings of fitting based procedures include: a) synthesis of only one weighting scheme, while there can be many solutions b) due to cloning rather than true synthesis of the population, losing the heterogeneity that may not have been captured in the microdata c) over reliance on the accuracy of the data to determine the cloning weights d) poor scalability and convergence with respect to the increase in number of attributes of the synthesized agents. In order to overcome these shortcomings, we propose a Markov Chain Monte Carlo (MCMC) simulation based approach. Partial views of the joint distribution of agents attributes that are available from various data sources can be used to simulate draws from the original distribution. The problem of association of different types of agents (person-households) is then treated as a maximum weight problem of a bipartite graph. The real population from Swiss census is used to compare the performance of simulation based synthesis with the standard IPF. The standard root mean square error statistics indicated that even the worst case simulation based synthesis (SRMSE=0.35) outperformed the best case IPF synthesis (SRMSE=0.64).
Synthesis of 3‐(Arylmethylene)isoindolin‐1‐ones from Ynamides by Heck—Suzuki—Miyaura Domino Reactions. Application to the Synthesis of Lennoxamine. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Plasma Melatonin Rhythms in Euthermic Marmots (Marmota flaviventris) (1984)

Plasma melatonin concentrations were measured in marmots (Marmota flaviventris) maintained under three short-day (4L:20D; 8L:10D; 10L:14D) and one long-day (14L:10D) photoperiod(s). Each animal had a daily rhythm of plasma melatonin with elevated plasma melatonin levels occurring during the dark period of the lighting cycle. There were no significant differences between any peak values during the night. The mean duration of elevated night melatonin concentrations was significantly different between long-day (16L:8D) and 8L:16D or 4L:20D animals (P less than 0.01). Daytime plasma melatonin levels were not significantly different among the photoperiods. These results characterize plasma melatonin rhythms in a sciurid rodent and demonstrate that this rhythm is modified by photoperiod. Therefore, the plasma melatonin profile could convey information about day length to the animal or, alternatively, the rhythm may be acting as a time-keeping mechanism for other physiological functions.
Analysis of the arabinoxylan arabinofuranohydrolase gene family in barley does not support their involvement in the remodelling of endosperm cell walls during development (2012)

Arabinoxylan arabinofuranohydrolases (AXAHs) are family GH51 enzymes that have been implicated in the removal of arabinofuranosyl residues from the (1,4)-β-xylan backbone of heteroxylans. Five genes encoding barley AXAHs range in size from 4.6 kb to 7.1 kb and each contains 16 introns. The barley HvAXAH genes map to chromosomes 2H, 4H, and 5H. A small cluster of three HvAXAH genes is located on chromosome 4H and there is evidence for gene duplication and the presence of pseudogenes in barley. The cDNAs corresponding to barley and wheat AXAH genes were cloned, and transcript levels of the genes were profiled across a range of tissues at different developmental stages. Two HvAXAH cDNAs that were successfully expressed in Nicotiana benthamiana leaves exhibited similar activities against 4-nitrophenyl α-L-arabinofuranoside, but HvAXAH2 activity was significantly higher against wheat flour arabinoxylan, compared with HvAXAH1. HvAXAH2 also displayed activity against (1,5)-α-L-arabinopentaose and debranched arabinan. Western blotting with an anti-HvAXAH antibody was used to define further the locations of the AXAH enzymes in developing barley grain, where high levels were detected in the outer layers of the grain but little or no protein was detected in the endosperm. The chromosomal locations of the genes do not correspond to any previously identified genomic regions shown to influence heteroxylan structure. The data are therefore consistent with a role for AXAH in depolymerizing arabinoxylans in maternal tissues during grain development, but do not provide compelling evidence for a role in remodelling arabinoxylans during endosperm or coleoptile development in barley as previously proposed.
Electrochemically Enhanced Dissolution of Silica and Alumina in Alkaline Environments (2019)

Dissolution of mineral surfaces at asymmetric solid-liquid-solid interfaces in aqueous solutions occurs in technologically relevant processes, such as chemical/mechanical polishing (CMP) for semiconductor fabrication, formation and corrosion of structural materials, and crystallization of materials relevant to heterogeneous catalysis or drug delivery. In some such processes, materials at confined interfaces exhibit dissolution rates that are orders of magnitude larger than dissolution rates of isolated surfaces. Here, the dissolution of silica and alumina in close proximity to a charged gold surface or mica in alkaline solutions of pH 10-11 is shown to depend on the difference in electrostatic potentials of the surfaces, as determined from measurements conducted using a custom-built electrochemical pressure cell and a surface forces apparatus (SFA). The enhanced dissolution is proposed to result from overlap of the electrostatic double layers between the dissimilar charged surfaces at small intersurface separation distances (<1 Debye length). A semiquantitative model shows that overlap of the electric double layers can change the magnitude and direction of the electric field at the surface with the less negative potential, which results in an increase in the rate of dissolution of that surface. When the surface electrochemical properties were changed, the dissolution rates of silica and alumina were increased by up to 2 orders of magnitude over the dissolution rates of isolated compositionally similar surfaces under otherwise identical conditions. The results provide new insights on dissolution processes that occur at solid-liquid-solid interfaces and yield design criteria for controlling dissolution through electrochemical modification, with relevance to diverse technologies.
Deep vein thrombosis after arthroplasty: Nanjing deep vein thrombosis study (2016)

Background: Deep vein thrombosis (DVT) remains a life-threatening complication of arthroplasty. It remains controversial for anticoagulation strategies after total hip arthroplasty (THA). Methods: A retrospective study was conducted to determine whether clinical risk factors and/or genetic variants might predict the development of DVT and find efficient anticoagulation strategies. Nanjing DVT study (NJDVTS), a retrospective and largest study conducted in a single center included 908 subjects who received knee or hip arthroplasty. Results: A total of 328 subjects (215 women and 113 men) who underwent uncemented THA were studied. Patients were followed up 3 months later after surgery. DVT was tested by contrast venography (CV). We checked genetic variants for DVT by a case-control study. Logistic regression analysis was performed to predict of the ability of each covariate and genetic factor. We also used logistic regression analysis with variable selection for obtaining the prediction model of DVT. Conclusions: DVT after THA was affected by personal (age) and clinical factors (mechanical compression, duration of surgery). THA with short duration of surgery did not require prophylactic anticoagulation. Extended anticoagulation was unnecessary for non-DVT patients after discharge from hospital.
Effect of molecular weight and protection ratio on line edge roughness and stochastic defect generation in chemically amplified resist processes of extreme ultraviolet lithography (2014)

The suppression of stochastic effects such as line edge roughness (LER) and stochastic defect generation is required for the high-volume production of semiconductor devices with 11 nm critical dimension using extreme ultraviolet (EUV) lithography. In this study, the effects of the molecular weight and protection ratio of a resist polymer on LER and stochastic defect generation were investigated, assuming line-and-space patterns with 11 nm half-pitch. By increasing the molecular weight, LER and the probability of stochastic defect generation were decreased. The negative effect caused by the increase of molecular weight is the increase of the minimum dissolution block size in the development process. By increasing the protection ratio, a similar effect was expected. However, LER and the probability of stochastic defect generation were not significantly decreased because of the decrease of the quantum efficiency of acid generation caused by the protection of proton sources. It is important to increase the protection ratio without decreasing the quantum efficiency of acid generation for the suppression of LER and stochastic defect generation.
Synthesis of α-Phenyltelluro Carbonyl Compounds (1987)

Several new α-phenyltelluro carbonyl compounds have been synthesized by the reaction of benzenetellurenyl iodide with lithium enolates derived from ketones, esters, and an amide in tetrahydrofuran at -78°C.
Correction of inter-crystal scatter effect in iterative image reconstruction of the jPET-D4 (2006)

A novel four-layered depth-of-interaction (DOI) positron emission tomography (PET) scanner is being developed at National Institute of Radiological Sciences, Japan. It aims to improve the image resolution, particularly at the edge of field of view while maintaining high sensitivity. However, inter-crystal scatter (ICS) occurs in the detector blocks of the jPET-D4. It is a phenomenon where there are multiple scintillations for a single irradiation of gamma photon due to Compton scatter in detecting crystals. Because of the Anger-type logic calculation, only one approximated position is detected by the jPET-D4 in the case of ICS. This causes error in position detection and ICS worsens the image contrast, particularly for smaller hotspot. In this paper, we propose to model an ICS probability by utilizing a Monte-Carlo simulator. It is a statistical relationship between gamma-ray first interaction crystal pair and the detected crystal pair. The ICS probability is then used to improve the system matrix of statistical image reconstruction algorithm ML-EM in order to correct the error of ICS. We have shown in computer simulation that image contrast is recovered successfully by applying the proposed method.
The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase (2020)

Efficient search for DNA damage embedded in vast expanses of the DNA genome presents one of the greatest challenges to DNA repair enzymes. We report here crystal structures of human 8-oxoguanine (oxoG) DNA glycosylase, hOGG1, that interact with the DNA containing the damaged base oxoG and the normal base G while they are nested in the DNA helical stack. The structures reveal that hOGG1 engages the DNA using different protein-DNA contacts from those observed in the previously determined lesion recognition complex and other hOGG1-DNA complexes. By applying molecular dynamics simulations, we have determined the pathways taken by the lesion and normal bases when extruded from the DNA helix and their associated free energy profiles. These results reveal how the human oxoG DNA glycosylase hOGG1 locates the lesions inside the DNA helix and facilitates their extrusion for repair.
Electrical Detection of Nucleic Acid Amplification Using an On-Chip Quasi-Reference Electrode and a PVC REFET (2014)

Electrical detection of nucleic acid amplification through pH changes associated with nucleotide addition enables miniaturization, greater portability of testing apparatus, and reduced costs. However, current ion-sensitive field effect transistor methods for sensing nucleic acid amplification rely on establishing the fluid gate potential with a bulky, difficult to microfabricate reference electrode that limits the potential for massively parallel reaction detection. Here we demonstrate a novel method of utilizing a microfabricated solid-state quasi-reference electrode (QRE) paired with a pH-insensitive reference field effect transistor (REFET) for detection of real-time pH changes. The end result is a 0.18 μm, silicon-on-insulator, foundry-fabricated sensor that utilizes a platinum QRE to establish a pH-sensitive fluid gate potential and a PVC membrane REFET to enable pH detection of loop mediated isothermal amplification (LAMP). This technique is highly amendable to commercial scale-up, reduces the packaging and fabrication requirements for ISFET pH detection, and enables massively parallel droplet interrogation for applications, such as monitoring reaction progression in digital PCR.
cis-5-Amino-6-hydroxycyclohexadiene as a Chiral Building Block: An Asymmetric Synthesis of (−)-Swainsonine (1999)

The four contiguous stereocenters of (−)-swainsonine were efficiently set in a 15-step synthesis with a 15 % overall yield and >99% ee. In order to differeniate the double bond in the key building block oxazolidin-2-one 2, a synthetic equivalent of oxazolidinone 3, is synthesized from the achiral diol 1 followed by a palladium-catalyzed desymmetrization of the meso-bis-carbamate.
Atorvastatin donor pre-treatment in a model of brain death and allogeneic kidney transplantation in rat (2012)

Atorvastatin donor pre-treatment of brain dead organ donors combined with 24h of cold preservation has no influence on graft rejection and infiltration with ED1 or MHCII positive cells in an allogeneic rat renal transplantation model. The detrimental combination of brain death and cold preservation might have overcome the possible protective effect of atorvastatin donor pre-treatment.
Key Homomorphic PRFs and Their Applications. (2015)

A pseudorandom function F: K ×X → Y is said to be key homomorphic if given F (k1, x) and F (k2, x) there is an efficient algorithm to compute F (k1 ⊕ k2, x), where ⊕ denotes a group operation on k1 and k2 such as xor. Key homomorphic PRFs are natural objects to study and have a number of interesting applications: they can simplify the process of rotating encryption keys for encrypted data stored in the cloud, they give one round distributed PRFs, and they can be the basis of a symmetric-key proxy re-encryption scheme. Until now all known constructions for key homomorphic PRFs were only proven secure in the random oracle model. We construct the first provably secure key homomorphic PRFs in the standard model. Our main construction is based on the learning with errors (LWE) problem. In the proof of security we need a variant of LWE where query points are non-uniform and we show that this variant is as hard as the standard LWE. We also construct key homomorphic PRFs based on the decision linear assumption in groups with an `-linear map. We leave as an open problem the question of constructing standard model key homomorphic PRFs from more general assumptions.
Risk of Pancreatic Cancer in Breast Cancer Families from the Breast Cancer Family Registry (2013)

This study clarifies the relationship between familial breast cancer and pancreatic cancer. Given its high mortality, pancreatic cancer should be included in risk assessment in familial breast cancer counseling.