gebhart/patrepeval huggingface dataset:
Bone Marrow Stromal Cell Regeneration Profile in Treated B-Cell Precursor Acute Lymphoblastic Leukemia Patients: Association with MRD Status and Patient Outcome (2022)

For the last two decades, measurable residual disease (MRD) has become one of the most powerful independent prognostic factors in B-cell precursor acute lymphoblastic leukemia (BCP-ALL). However, the effect of therapy on the bone marrow (BM) microenvironment and its potential relationship with the MRD status and disease free survival (DFS) still remain to be investigated. Here we analyzed the distribution of mesenchymal stem cells (MSC) and endothelial cells (EC) in the BM of treated BCP-ALL patients, and its relationship with the BM MRD status and patient outcome. For this purpose, the BM MRD status and EC/MSC regeneration profile were analyzed by multiparameter flow cytometry (MFC) in 16 control BM (10 children; 6 adults) and 1204 BM samples from 347 children and 100 adult BCP-ALL patients studied at diagnosis (129 children; 100 adults) and follow-up (824 childhood samples; 151 adult samples). Patients were grouped into a discovery cohort (116 pediatric BCP-ALL patients; 338 samples) and two validation cohorts (74 pediatric BCP-ALL, 211 samples; and 74 adult BCP-ALL patients; 134 samples). Stromal cells (i.e., EC and MSC) were detected at relatively low frequencies in all control BM (16/16; 100%) and in most BCP-ALL follow-up samples (874/975; 90%), while they were undetected in BCP-ALL BM at diagnosis. In control BM samples, the overall percentage of EC plus MSC was higher in children than adults (p = 0.011), but with a similar EC/MSC ratio in both groups. According to the MRD status similar frequencies of both types of BM stromal cells were detected in BCP-ALL BM studied at different time points during the follow-up. Univariate analysis (including all relevant prognostic factors together with the percentage of stromal cells) performed in the discovery cohort was used to select covariates for a multivariate Cox regression model for predicting patient DFS. Of note, an increased percentage of EC (>32%) within the BCP-ALL BM stromal cell compartment at day +78 of therapy emerged as an independent unfavorable prognostic factor for DFS in childhood BCP-ALL in the discovery cohort—hazard ratio (95% confidence interval) of 2.50 (1−9.66); p = 0.05—together with the BM MRD status (p = 0.031). Further investigation of the predictive value of the combination of these two variables (%EC within stromal cells and MRD status at day +78) allowed classification of BCP-ALL into three risk groups with median DFS of: 3.9, 3.1 and 1.1 years, respectively (p = 0.001). These results were confirmed in two validation cohorts of childhood BCP-ALL (n = 74) (p = 0.001) and adult BCP-ALL (n = 40) (p = 0.004) treated at different centers. In summary, our findings suggest that an imbalanced EC/MSC ratio in BM at day +78 of therapy is associated with a shorter DFS of BCP-ALL patients, independently of their MRD status. Further prospective studies are needed to better understand the pathogenic mechanisms involved.
A highly-efficient planar dielectric radiating structure (2013)

A novel highly-efficient planar dielectric antenna is presented in this work. As shown in Figure 1, the antenna consists of a thin layer of high-permittivity dielectric attached to a low-loss dielectric substrate. The thickness of the high-permittivity layer is much smaller than a wavelength in free space (i.e., in the micrometer range) and it can be precisely fabricated using screen printed ceramic thick-film technologies. The antenna is fed by proximity-coupled microstrip line. The high-permittivity layer is mainly utilized to change the boundary conditions and achieve a new radiating mode. Theoretical investigations are performed to derive closed-form expressions for the resonant frequencies of the antenna. Results on the antenna performance, including impedance bandwidth, radiation patterns, and efficiency, will be demonstrated, discussed, and compared to microstrip patch antennas and conventional dielectric resonator antennas in the conference.
Source separation based on binaural cues and source model constraints (2008)

We describe a system for separating multiple sources from a two-channel recording based on interaural cues and known characteristics of the source signals. We combine a probabilistic model of the observed interaural level and phase differences with a prior model of the source statistics and derive an EM algorithm for finding the maximum likelihood parameters of the joint model. The system is able to separate more sound sources than there are observed channels. In simulated reverberant mixtures of three speakers the proposed algorithm gives a signal-to-noise ratio improvement of 2.1 dB over a baseline algorithm using only interaural cues.
Fabrication of Carbon Disulfide Added Colloidal Gold Colorimetric Sensor for the Rapid and On-Site Detection of Biogenic Amines (2021)

Meat is often wasted due to the perceived concerns of its shelf life and preservation. Specifically, in meat formation, biogenic amines (BAs) are the major agents to spoil them. Herein, we have developed a carbon disulfide (CS<sub>2</sub>) added colloidal gold nanoparticles-based colorimetric sensor for the rapid and on-site detection of biogenic amines. Transmission electron microscopy is used to observe the morphological changes in colloidal gold nanoparticles and aggregation behavior of CS<sub>2</sub> added to the colloidal gold nanoparticles' solution. Raman spectroscopic analysis is further used to characterize the peaks of CS<sub>2</sub>, Cad and CS<sub>2</sub>-Cad molecules. Absorption spectroscopy is used to estimate the colorimetric differences and diffuse reflectance spectra of the samples. The sensing analysis is performed systematically in the presence and absence of CS<sub>2</sub>. CS<sub>2</sub> added colloidal gold nanoparticles colorimetric sensor detected the BAs with a limit of detection (LOD) value of 50.00 µM. Furthermore, the developed sensor has shown an LOD of 50.00 µM for the detection of multiple BAs at a single time. The observed differences in the colorimetric and absorption signals indicate that the structure of BAs is converted to the dithiocarbamate (DTC)-BA molecule, due to the chemical reactions between the amine groups of BAs and CS<sub>2</sub>. Significantly, the developed colorimetric sensor offers distinct features such as facile fabrication approach, on-site sensing strategy, rapid analysis, visual detection, cost-effective, possibility of mass production, availability to detect multiple BAs at a single time and appreciable sensitivity. The developed sensor can be effectively used as a promising and alternative on-site tool for the estimation of BAs.
Geometric Estimation with Orthogonal Bandlet Bases (2007)

This article presents the first adaptive quasi minimax estimator for geometrically regular images in the white noise model. This estimator is computed using a thresholding in an adapted orthogonal bandlet basis optimized for the noisy observed image. In order to analyze the quadratic risk of this best basis denoising, the thresholding in an orthogonal bandlets basis is recasted as a model selection process. The resulting estimator is computed with a fast algorithm whose theoretical performance can be derived. This efficiency is confirmed through numerical experiments on natural images.
DFT-Based Multi-Directions Directional Modulation (2019)

In this letter, a physically secure multi-directions directional modulation scheme is proposed. The scheme provides an adaptive beam-width assignment, where each user is granted a different beam width based on its channel condition. The scheme can be efficiently implemented using a discrete Fourier transform (DFT)-based algorithm that divides the spatial dimension into orthogonal narrow sub-beams. Each user is assigned multiple sub-beams that satisfies its pre-set direction of transmission and beam-width requirements. The scheme preserves the secrecy properties of directional modulation algorithms, where each legitimate user is guaranteed a secure communication link to its trusted receiver. The proposed scheme is practically efficient since it can be directly implemented using a DFT-based signal processing core.
Ontology based specification of web service policies (2004)

Abstract: An ever-growing number of XML-based languages are used to describe Web Service related issues such as security (WS-Security Policy), access control (XAC-ML), or privacy (P3P-WS). While it is desirable to specify policies in a declarative way, these languages expose great diversity in both syntax and semantics making it hard to realize a unified system. Our contribution to this problem is twofold. First, we present an expressive formal notation for policies. Second, we show how requester-, provider-, and third-party policies can be used for choosing a suitable service while making sure that all relevant policies are obeyed. 1
Reliability of lead-free SAC electronics under simultaneous exposure to high temperature and vibration (2012)

Electronics installed in automotive systems are subjected simultaneously to mechanical vibrations and thermal loads in underhood applications. Typical failure modes include solder joint failure, pad cratering, chip-cracking, copper trace fracture, and underfill fillet failures. The solder interconnects accrue damage much faster when vibrated at elevated temperatures. Industry migration to leadfree solders has resulted in a proliferation of a wide variety of solder alloy compositions. Presently, the literature on mechanical behavior of leadfree alloys under simultaneous harsh environment of high-temperature vibration is sparse. In this paper, a test vehicle with a variety of lead-free SAC305 daisy chain components including BGA, QFP, SOP, TSOP has been tested to failure by subjecting it to two elevated temperatures and harmonic vibrations at its first natural frequency. The test matrix includes variation in the amplitude of vibration from 10G to 14G as well as variation in temperature. Full field strain on the PCB has been extracted using high speed cameras operating at 100,000 fps in conjunction with digital image correlation. The vibration simulation using global-local finite element models is correlated with the system characteristics such as modal shapes and natural frequencies. The vibration simulation provides a fatigue life prediction that has been validated with the experimentally obtained cycles to failure. In addition, the packages have been cross-sectioned to study the failure modes. A comparison of failure modes for different surface mount packages at elevated test temperatures and vibration has been presented in this study.
[Prevalence of vancomycin-resistant enterococci in hospital and community environment.]. (2005)

In the Czech Republic, VRE were proved both in community and hospital settings. Their prevalence in rectal swabs is low and does not exceed the values reported in other European countries. The author describes the chief characteristics of the most important quinolone antibiotics, including preparations either in their development stage or whose development has been prematurely interrupted because of adverse side-effects. The list includes all preparations that are or were temporarily registered in the Czech Republic.
Grand Challenges in Chemistry for 2016 and Beyond (2016)

When several ACS Central Science Editors met for dinner at the 2015 Pacifichem meeting, conversation turned to the grand challenges facing science and society, and those we felt chemistry was in a unique position to solve. With the New Year, we thought we would share our ideas in our first editorial of 2016. The arenas in which we see chemistry having the largest influence are the molecular bases of disease and aging, alternative energy advancement, and the conservation of our elemental resources.
Tailoring graphite with the goal of achieving single sheets (1999)

We demonstrate the tailoring of highly oriented pyrolytic graphite (HOPG) to obtain uniformly sized islands of up to several microns in size. There has already been some research on manipulating individual sheets on HOPG surfaces with scanning probe microscope tips; such sheets were obtained either accidentally or with a less controllable indenting technique. Here we present a different approach, which is more reliable and controllable. The HOPG surface was first patterned to create an array of small graphite islands by reactive ion etching of the HOPG surface with an oxygen plasma. These islands were then manipulated with an atomic force microscope tip. Carbon nanotubes represent a promising material for nanotechnology and can be considered as a graphene sheet rolled into a seamless cylinder. While carbon nanotubes are synthesized successfully with laser ablation, carbon are. or chemical vapour deposition techniques, we speculate that it might be possible, by the controlled fabrication of graphene sheets, to form nanotubes or other novel motifs of use for nanotechnology.
Antiribosomal P antibodies in pediatric patients with systemic lupus erythematosus and psychosis (1996)

Elevated serum levels of antibodies to ribosomal P protein can distinguish SLE-associated psychosis from primary psychosis of childhood. In SLE, elevated antiribosomal P antibody levels were not specific for psychosis. Serial assays were useful for monitoring the disease activity.
Material innovation for MOL, BEOL, and 3D integration (2017)

This paper presents new materials and processes for advanced technology node of Si semiconductor devices. For MOL, Co contact plug and amorphous Co-Ti barrier showed a good adhesion, limited growth of Co silicide, and a low contact resistivity of the order of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−9</sup> Ωcm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> on both n+ and p+ Si. For BEOL, a CVD-MnOx layer could be formed conformally in high-aspect ratio contact holes. The ALD-MnOx layer of 1.2 nm thick showed a good diffusion barrier property at 400 °C. For 3D integration, TSV of 10 μm diameter and 80 μm depth could be filled with low resistivity sintered Cu paste without voids.
On the Efficiency of Decentralized Search in Expert Networks (2016)

Expert networks are formed by a group of expert-professionals with different specialties to collaboratively resolve specific queries posted to the network. In expert networks, decentralized search, operating purely on each expert's local information without any knowledge of network global structure, represents the most basic and scalable routing mechanism. However, there is still a lack of fundamental understanding of the efficiency of decentralized search. In this regard, we investigate decentralized search by quantifying its performance under a variety of network settings. Our key findings reveal that under certain network conditions, decentralized search can achieve significantly small query routing steps (i.e., between O(log n) and O(log <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> n), n: total number of experts in the network). To the best of our knowledge, this is the first work studying fundamental behaviors of decentralized search in expert networks.
Tunable and generic problem instance generation for multi-objective reinforcement learning (2014)

A significant problem facing researchers in reinforcement learning, and particularly in multi-objective learning, is the dearth of good benchmarks. In this paper, we present a method and software tool enabling the creation of random problem instances, including multi-objective learning problems, with specific structural properties. This tool, called Merlin (for Multi-objective Environments for Reinforcement LearnINg), provides the ability to control these features in predictable ways, thus allowing researchers to begin to build a more detailed understanding about what features of a problem interact with a given learning algorithm to improve or degrade the algorithm's performance. We present this method and tool, and briefly discuss the controls provided by the generator, its supported options, and their implications on the generated benchmark instances.
Web Access to Non-spatial Data using Internet Map Servers (2001)

Abstract: Current web interfaces to non-Geographic data are primarily text (html) and GIF/JPEG-based. GIS are increasingly being used for spatial analysis of non-Geographic data, for example genome maps, document retrieval, and citation analysis. I discuss webbased, visual, interactive access to non-spatial data, using an internet map server. I will explain how, as an example, online visual browsing and search of lexical data may be achieved, and demonstrate some results of spatial analysis.
Developing the 150%-FBW Ku-Band Linear Equalizer (2007)

This paper reports the development of a linear amplitude equalizer for the linearity of the slope of the amplitude over 150% fractional bandwidth in Ku-band. The circuit model is featured by the resistor placed between each pair of a transmission-line and a stub. The design includes finding the values of resistors and stubs to have the optimal linear slope and return loss performances. The measured data show the acceptable performances of the slope variation and return loss over 2-18 GHz.
CD4 and CD8 regulate interleukin 2 responses of T cells. (1992)

To characterize the T-cell surface molecules involved in regulation of T-cell interleukin 2 (IL-2) responses, we established several monoclonal antibodies (mAbs) that inhibit IL-2 responses of freshly isolated CD8+ T cells and the IL-2-dependent cell line CTLL-2. Here we show that two inhibitory mAbs are directed against Lyt-2 (CD8 alpha). In fact, all anti-Lyt-2 mAbs tested were able to inhibit the IL-2 response of the Lyt-2- and L3T4-deficient cell line HT-2 after transfection with a Lyt-2 cDNA clone. Similarly, anti-L3T4 mAbs inhibited the IL-2 response of CD4-transfected HT-2 cells. These inhibitory effects of anti-CD4 and anti-CD8 mAbs occur on normal T lymphocytes, since they also were observed with CD4+ and CD8+ T-cell blasts, and are specific for IL-2 responses, since IL-4 responses of CD4- and CD8-transfected HT-2 cells were not affected by the anti-CD4 and anti-CD8 mAbs. The inhibitory effects of anti-CD4 or anti-CD8 mAbs could not be explained by interference with IL-2 binding and depended on CD4 and CD8 crosslinking, because F(ab')2 or Fab plus crosslinking second antibody, but not Fab alone, were effective. A mutant Lyt-2 molecule lacking the cytoplasmic region that mediates p56lck binding could not mediate the inhibitory effect upon crosslinking. These results suggest that CD4 and CD8 mediate negative regulation of T-cell IL-2 responses via cytoplasmically associated p56lck.
Phenotypic Characterization of acopAMutant of Neisseria gonorrhoeae Identifies a Link between Copper and Nitrosative Stress (2011)

NGO0579 is annotated copA in the Neisseria gonorrhoeae chromosome, suggesting that it encodes a cation-transporting ATPase specific for copper ions. Compared to wild-type cells, a copA mutant was more sensitive to killing by copper ions but not to other transition metals. The mutant also accumulated a greater amount of copper, consistent with the predicted role of CopA as a copper efflux pump. The copA mutant showed a reduced ability to invade and survive within human cervical epithelial cells, although its ability to form a biofilm on the surface of these cells was not significantly different from that of the wild type. In the presence of copper, the copA mutant exhibited increased sensitivity to killing by nitrite or nitric oxide. Therefore, we concluded that copper ion efflux catalyzed by CopA is linked to the nitrosative stress defense system of Neisseria gonorrhoeae. These observations suggest that copper may exert its effects as an antibacterial agent in the innate immune system via an interaction with reactive nitrogen species.
Studies on the Activity of Barnase Toxins in Vitro and in Vivo (1996)

Pseudomonas exotoxin A (PE) is a protein toxin composed of three structural domains which are responsible for cell binding (domain Ia, amino acids 1-252), translocation into the cytosol (domain II, amino acids 253-364) and ADP-ribosylation activity (domain III, amino acids 405-613). We have previously described (Prior, T. I., FitzGerald, D. J., and Pastan, I. (1992) Biochem. 31, 3555-3559) a molecule composed of amino acids 1-412 of PE and the extracellular ribonuclease of Bacillus amyloliquefaciens, barnase (Bar), and shown that this protein (PE1-412-Bar) is toxic to cells due to its ribonuclease activity, which had been delivered to the cytosol. We have now used this model to evaluate the role played by the carboxyl end of domain II (amino acids 347-364), domain Ib, and the amino end of domain III (amino acids 405-412) in the translocation event. Toxins completely lacking domain III, termed PE1-380-Bar, or both domains Ib and III, termed PE1-364-Bar, were equally cytotoxic to a murine fibroblast cell line (L929) as was PE1-412-Bar. Extending the deletion to include part of the E-helix and all of the F-helix of domain II (amino acids 347-364) resulted in a toxin (PE1-346-Bar) that was 10-fold less toxic. Previously tested on only murine cell lines, we demonstrate that barnase toxins are cytotoxic also to a variety of human cell lines. Cytotoxicity was assessed by measuring inhibition of DNA synthesis. Surprisingly, PE1-380-Bar is not lethal when injected into mice, either intraperitoneally or intravenously, at 9 nmol, which is 2200-fold more than the amount required for killing by PE (4 pmol). In cell culture these barnase-containing toxins are 100-fold less toxic to murine fibroblast cells than PE. Barnase toxin has a greater survival time in the blood of mice than PE, with a half-life of 102 min. We conclude that domain II is sufficient to transport proteins into the cytosol. Further, since domain Ia can be replaced with other cell targeting moieties, we propose that barnase-toxins should be evaluated for utility in targeted cancer therapy.
Development of a Vaccine AgainstOnchocerca volvulus (2022)

Onchocerciasis or river blindness is a neglected parasitic disease that causes severe dermatitis and visual impairment, predominantly in Africa. The current strategy for controlling and/or eliminating this devastating disease relies on mass administration of a single drug, ivermectin. Neglected tropical disease experts doubt that onchocerciasis can be eliminated through mass drug administration (MDA) with IVM alone. We present in this chapter the rational strategy that was taken to develop a prophylactic vaccine that could accelerate elimination efforts and safeguard the enormous strides made in onchocerciasis control. This vaccine is based on two lead candidate antigens identified by an international partnership, The Onchocerciasis Vaccine for Africa Initiative (TOVA). The protective effects of two lead vaccine candidates in small animal models are presented, as well as the way forward for testing them in the Onchocerca ochengi cow infection system. Immune responses against these antigens in humans are reported with putative mechanisms of protective immunity described.