gebhart/patrepeval huggingface dataset:
Cbx7 is epigenetically silenced in glioblastoma and inhibits cell migration by targeting YAP/TAZ-dependent transcription (2016)

Glioblastomas (GBM) are the most malignant form of astrocytomas which are difficult to treat and portend a grave clinical course and poor prognosis. In this study, we identified Chromobox homolog 7 (Cbx7), a member of Polycomb Repressive Complex 1 (PRC1), as a downregulated gene in GBM owing to its promoter hypermethylation. Bisulphite sequencing and methylation inhibitor treatment established the hypermethylation of Cbx7 in GBM. Exogenous overexpression of Cbx7 induced cell death, inhibited cell proliferation, colony formation and migration/invasion of the glioma cells. GSEA of Cbx7 regulated genes identified Cbx7 as a repressor of transcription co-activators YAP/TAZ, the inhibitory targets of the Hippo signalling pathway. In good correlation, the exogenous expression of Cbx7 repressed the YAP/TAZ-dependent transcription and downregulated CTGF, a bonafide YAP/TAZ target. We also observed reduced levels of phospho-JNK in Cbx7 expressing cells. Additionally, CTGF silencing and pharmacological inhibition of JNK also inhibited glioma cell migration. Further, Cbx7 failed to inhibit cell migration significantly in the presence of exogenously overexpressed CTGF or constitutively active JNK. Thus, our study identifies Cbx7 as an inhibitor of glioma cell migration through its inhibitory effect on YAP/TAZ-CTGF-JNK signalling axis and underscores the importance of epigenetic inactivation of Cbx7 in gliomagenesis.
Classifying Microscopic Images of Reactive Lymphocytosis Using Two-Step Tandem AI Models (2023)

The practical applications of automatic recognition and categorization technology for next-generation systems are desired in the clinical laboratory. We approached the identification of reactive lymphocytosis using artificial intelligence (AI) technology and studied its clinical usefulness for blood smear screening. This study created one- and two-step AI models for the identification of reactive lymphocytosis. The ResNet-101 model was applied for deep learning. The original image set for supervised AI training consisted of 5765 typical nucleated blood cell images. The subjects for clinical assessment were 25 healthy cases, 25 erythroblast cases, and 25 reactive lymphocytosis cases. The total accuracy (mean ± standard deviation) of the one- and two-step models were 0.971 ± 0.047 and 0.977 ± 0.024 in healthy, 0.938 ± 0.040 and 0.978 ± 0.018 in erythroblast, and 0.856 ± 0.056 and 0.863 ± 0.069 in reactive lymphocytosis cases, respectively. The two-step AI model showed a sensitivity of 0.960 and a specificity of 1.000 between healthy and reactive lymphocytosis cases. As our two-step tandem AI model showed high performance for identifying reactive lymphocytosis in blood smear screening, we plan to apply this method to the development of AI models to differentiate reactive and neoplastic lymphocytosis.
A DNS reflection method for global traffic management (2010)

An edge network deployment consists of many (tens to a few hundred) satellite data centers. To optimize enduser perceived performance, a Global Traffic Management (GTM) solution needs to continuously monitor the performance between the users and the data centers, in order to dynamically select the “best ” data center for each user. Though widely adopted in practice, GTM solutions based on active measurement techniques suffer from limited probing reachability. In this paper, we propose a novel DNS reflection method, which uses the GTM DNS traffic itself to measure the performance between an arbitrary end-user and the data centers. From these measurements, the best data center can be selected for the user. We have implemented and deployed a prototype system involving 17 geographically distributed locations within the Microsoft global data center network infrastructure. Our evaluation of the prototype shows that the DNS reflection method is extremely accurate and suitable for GTM. In particular, at the 95 percentile, the measured latency is 6 ms away from Ping, and the selected data center is 2 ms away from the ground-truth best. 1
Development, Validation, and Utility of Species-Specific Diagnostic Markers for Detection of Peronospora belbahrii (2022)

<i>Peronospora belbahrii</i> is an oomycete and the cause of basil downy mildew, one of the most destructive diseases affecting basil production worldwide. Disease management is challenging due to wind-dispersed sporangia and contaminated seed; therefore, identifying <i>P. belbahrii</i> in seed lots before sale or planting or in the field before symptoms develop could allow for timely deployment of disease management strategies. In this study, a draft genome assembly and next-generation sequencing reads for <i>P. belbahrii</i>, as well as publicly available DNA-seq and RNA-seq reads of several other downy mildew pathogens, were incorporated into a bioinformatics pipeline to predict <i>P. belbahrii</i>-specific diagnostic markers. The specificity of each candidate marker was validated against a diverse DNA collection of <i>P. belbahrii</i>, host tissue, and related oomycetes using PCR. Two species-specific markers were identified and used as templates to develop a highly sensitive probe-based real-time quantitative PCR (qPCR) assay that could detect <i>P. belbahrii</i> in leaf tissue and seed samples. Both markers were capable of reliably detecting as low as 500 fg/µl of <i>P. belbahrii</i> genomic DNA and as few as 10 sporangia. The qPCR assay was then validated with seed samples collected from a basil cultivar experiment. In total, 48 seed samples were collected and tested; <i>P. belbahrii</i> was detected in samples of all cultivars at estimated concentrations of 600 fg/µl up to 250 pg/µl and at as few as 10 sporangia up to >1,000 sporangia. The markers and assays are valuable for diagnostics and identifying <i>P. belbahrii</i>-contaminated seed lots to mitigate the effects of future basil downy mildew epidemics.
Early detection of anastomotic leakage using oxygen and carbon dioxide sensor (2011)

Optical sensor has been introduced to detect anastomotic leakage (AL) in an early stage. AL is a most feared complication in anastomosis operation, because there is no tool that can detect this effectively. Therefore, oxygen and carbon dioxide have been introduced for constant monitoring of the condition of anastomosis. This thesis will represent the working principle of these two gas sensors and the wireless protocol that has been used for constant monitoring of the health condition.
Towards the Construction of Expressed Proteomes Using a Leishmania tarentolae Based Cell-Free Expression System (2010)

The adaptation of organisms to a parasitic life style is often accompanied by the emergence of novel biochemical pathways absent in free-living organisms. As a result, the genomes of specialized parasitic organisms often code for a large number (>50%) of proteins with no detectable homology or predictable function. Although understanding the biochemical properties of these proteins and their roles in parasite biogenesis is the next challenge of molecular parasitology, analysis tools developed for free-living organisms are often inadequate for this purpose. Here we attempt to solve some of these problems by developing a methodology for the rapid production of expressed proteomes in cell-free systems based on parasitic organisms. To do so we take advantage of Species Independent Translational Sequences (SITS), which can efficiently mediate translation initiation in any organism. Using these sequences we developed a single-tube in vitro translation system based on the parasitic protozoan Leishmania tarentolae. We demonstrate that the system can be primed directly with SITS containing templates constructed by overlap extension PCR. To test the systems we simultaneously amplified 31 of L. tarentolae's putative translation initiation factors and phosphatases directly from the genomic DNA and subjected them to expression, purification and activity analysis. All of the amplified products produced soluble recombinant proteins, and putative phosphatases could be purified to at least 50% purity in one step. We further compared the ability of L. tarentolae and E. coli based cell-free systems to express a set of mammalian, L. tarentolae and Plasmodium falciparum Rab GTPases in functional form. We demonstrate that the L. tarentolae cell-free system consistently produced higher quality proteins than E. coli-based system. The differences were particularly pronounced in the case of open reading frames derived from P. falciparum. The implications of these developments are discussed.
Reorientation Times for Solid-State Electrolyte Solvents and Electrolytes from NMR Spin–Lattice Relaxation Studies (2020)

Ionic and molecular plastic crystals have been studied recently as solid electrolytes or solvents, but the specific role of molecular reorientation has not been clarified. We use NMR spin-lattice relaxation times (<i>T</i><sub>1</sub> minima) to compare the time scale for magnetic fluctuations in a plastic crystal solvent to the molecular reorientation times, as established by dielectric spectroscopy. We focus on a mixture of succinonitrile and glutaronitrile, in which the rotationally disordered phase is stabilized against crystallization. Reorientation times can then be studied over 13 orders of magnitude, down to the glass transition temperature at 144 K. For each nucleus, <sup>1</sup>H and <sup>13</sup>C, the most probable magnetic fluctuation time is found to be slightly shorter than the reorientation time, but with practically indistinguishable temperature dependence. This facilitates investigation of the relation of solvent reorientation to ion conductivity relaxation times in ionic conducting systems in which the conductivity swamps the dielectric signature of solvent reorientation.
Model for Electrodes' Filaments of Hot Cathode Fluorescent Lamps, During Preheating With Constant rms Current (2007)

This paper presents a new model for the representation of electrodes' filaments of hot-cathode fluorescent lamps, during preheating processes based on the injection of currents with constant root mean square (rms) values. The main improvement obtained with this model is the prediction of the R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">h</sub> /R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> ratio during the preheating process, as a function of the preheating time and of the rms current injected in the electrodes. Using the proposed model, it is possible to obtain an estimate of the time interval and the current that should be provided by the electronic ballast, in order to ensure a suitable preheating process. This estimate of time and current can be used as input data in the design of electronic ballasts with programmed lamp start, permitting the prediction of the R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">h</sub> /R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> ratio during the initial steps of the design (theoretical analysis and digital simulation). Therefore, the use of the proposed model permits to reduce the necessity of several empirical adjustments in the prototype, in order to set the operation of electronic ballasts during the preheating process. This fact reduces time and costs associated to the global design procedure of electronic ballasts
Automatic Modulation Recognition of Radar Signals Based on Manhattan Distance-Based Features (2019)

Feature-based (FB) algorithms for automatic modulation recognition of radar signals have received much attention since they are usually simple to realize. However, existing FB approaches usually focus on several specific modulations and fail when applied to various modulations. To overcome this issue, we propose a simple and effective FB algorithm based on Manhattan distance-based features (MDBFs) in this paper. MDBFs are new features for radar signals that can be applied for recognition of different modulations. The main contributions of this paper are as follows. First, radar signals are represented as wavelet ridges, which includes important information that can distinguish different modulations, and the piecewise aggregate approximation algorithm is introduced to reduce signal dimensions. Then, the dynamic time warping averaging is employed instead of the traditional k-means algorithm to extract realistic centroids for each class. Finally, the Manhattan distances between each data sample and each centroid are used to construct MDBFs, and decisions are made using the k-nearest neighbor. In addition, we prove that MDBFs have better class separability power than the Euclidean-based features. MDBFs contain information about the correlations between different classes, which means that these features suitable for discriminating various modulations when their class distributions do not overlap badly in representation space. The extensive experiments on a synthetic dataset demonstrate the outstanding performance of our proposed method and are hardly affected by the pulse width of the signal. Thus, the proposed method with the effectiveness and robustness could be a promising modulation recognition method of the radar signal.
Report on temporal impact of identified entities on end-to-end-timing (2005)

Processing of high-quality streams is quite computationally expensive at the same time as video processing applications are more and more deployed in small embedded systems that traditionally exhibit limited processing and network resources, e.g. set top boxes, mobile phones or PDAs. Hence, for some combinations of streams and devices, the timing constraints on stream processing within a functional component will not automatically be met.\nThis task of WP2 analyses the identified functional components of a breeze processing and transmission with respect to their impact on the timing of end-to-end delivery chain processing. In particular it identifies parameters at a high level of abstraction, i.e., hiding the full internal details (which are addressed in WP3). The analysis is based on the list of devices selected in WP1 and the resources identified in close collaboration with WP3.\nWP2-3 results can be used to make trade-offs between timeliness, resource usage and energy consumption at system design time
Antioxidant Activity and Antifungal Activity of Chitosan Derivatives with Propane Sulfonate Groups (2018)

We successfully synthesized the water-soluble chitosan derivatives propane sulfonated chitosan (PSCS) and dipropane sulfonated chitosan (DPSCS) in this paper. These derivatives were characterized by FTIR, ¹H NMR, and <sup>13</sup>C NMR. Moreover, the antioxidant activity of the chitosan derivatives was evaluated by free radical scavenging ability (against DPPH-radical, hydroxyl-radical, and superoxide-radical) and ferric reducing power. Meanwhile, inhibitory effects against two fungi were also tested. Our results suggested antioxidant abilities and antifungal properties were in order of DPSCS > PSCS > CS, which were consistent with the number of propane sulfonated groups. The scavenging activity of DPSCS against superoxide-radical and DPPH-radical were 94.1% and 100% at 1.6 mg/mL, respectively. The inhibitory indices of DPSCS against <i>P. asparagi</i> and <i>F. oxysporum</i> were up to 82.2% and 94% at 1.0 mg/mL, respectively. Obviously, the number of propane sulfonated groups of chitosan derivatives not only contributes to antioxidant activity, but also to antifungal activity. Therefore, DPSCS with more propane sulfonated groups endowed with antioxidant and antifungal activity that can be used as a candidate material in the food and pharmaceutical industries.
GABAC RECEPTOR ION CHANNELS (2004)

1. The present review gives an overview of studies conducted on GABAC receptors over the past 10 years since the author started at the University of Sydney. It concentrates on the structure-activity relationship profiles of the receptor and how these studies were used to: (i) develop selective GABAC receptor ligands; and (ii) understand the impact of amino acid changes on GABAC receptor pharmacology and function. 2. Structure-activity relationship studies involving variations of both ligands and their receptor targets are vital to the discovery of drugs that interact selectively with particular native and mutant receptor subtypes. Such agents may be useful for treating anxiety, depression, epilepsy and memory related disorders, such as Alzheimer's disease.
Fabrication of Highly Oriented Cylindrical Polyacrylonitrile, Poly(lactide-co-glycolide), Polycaprolactone and Poly(vinyl acetate) Nanofibers for Vascular Graft Applications (2021)

Small-diameter vascular grafts fabricated from synthetic polymers have found limited applications so far in vascular surgeries, owing to their poor mechanical properties. In this study, cylindrical nanofibrous structures of highly oriented nanofibers made from polyacrylonitrile, poly (lactide-<i>co</i>-glycolide) (PLGA), polycaprolactone (PCL) and poly(vinyl acetate) (PVAc) were investigated. Cylindrical collectors with alternate conductive and non-conductive segments were used to obtain highly oriented nanofibrous structures at the same time with better mechanical properties. The surface morphology (orientation), mechanical properties and suture retention of the nanofibrous structures were characterized using SEM, mechanical tester and universal testing machine, respectively. The PLGA nanofibrous cylindrical structure exhibited excellent properties (tensile strength of 9.1 ± 0.6 MPa, suture retention strength of 27N and burst pressure of 350 ± 50 mmHg) when compared to other polymers. Moreover, the PLGA grafts showed good porosity and elongation values, that could be potentially used for vascular graft applications. The combination of PLGA nanofibers with extracellular vesicles (EVs) will be explored as a potential vascular graft in future.
Real-Time Centimeter-Accuracy GPS: Initializing While in Motion (Warm Start Versus Cold Start) (1992)

The initialization of real-time centimeter-accuracy GPS (i.e., based on carrier phases) can be performed while in motion. Although included results are postprocessed, the algorithms are currently being implemented for real-time navigation, and the results will be essentially the same. The goal of the initialization procedure is to determine the double-difference carrier phase integer ambiguities.



This paper reports the benefit to the initialization procedure of additional knowledge or constraints. As an example, it shows the speedup (meaning fewer epochs, not computational speed) of the initialization procedure and increased reliability using a priori knowledge of the average ellipsoidal height of the antenna phase center on a marine platform. As another example, it shows the benefit of prior knowledge of one or two double-difference integer biases, either alone or coupled with a priori knowledge of the ellipsoidal height of the antenna phase center.
Cover Feature: A peri‐Xanthenoxanthene Centered Columnar‐Stacking Organic Semiconductor for Efficient, Photothermally Stable Perovskite Solar Cells (Chem. Eur. J. 4/2019) (2019)

A low-cost peri-xanthenoxanthene-based hole-transporter has been developed for highly efficient and stable perovskite solar cells (PSCs). With strong π–π interactions, the planar π-conjugated two-dimensional heterocycles form core-to-core stacking, building a firm bridge between the perovskite and anode for holes to pass through. PSCs employing this new hole transporter attain a high efficiency of 19.8 % at the standard AM 1.5 G conditions, and good long-term stability under continuous full sunlight exposure at 40 °C. More information can be found in the Communication by P. Wang et al. on page 945.
Support materials for yeast immobilization affect the concentration of metal ions in the fermentation medium (2013)

Hydrogels are potential absorbers of ions present in the medium, but they can also release some cations (e.g. calcium in calcium alginates). Polyelectrolytes such as alginic acid and poly(acrylic acid) strongly bind polyvalent metal ions. In this paper, the impact of some materials used for the immobilization of yeast, in particular the concentration of certain ions, especially those that play a significant role in the process of fermentation such as calcium, magnesium, zinc and manganese, was assessed. The support for the immobilization of yeast (calcium alginate and polyacrylate) significantly affected the concentration of metal ions in a model solution. Calcium alginate decreased the concentration of Mg2+, Zn2+ and Mn2+ in the solution by about 10–25%, and greatly increased the Ca2+ concentration. Polyacrylate, while swelling, decreased the concentration of cations present by up to 50%. Based on the results in this work, no supplementation of wort with divalent metal salts is advised, since it may lead to a stronger cross-linking of polyelectrolytes used, and consequently result in a slower fermentation. Similarly, the relatively high concentration of calcium ions, caused by ion exchange, did not appear to affect the fermentation process. Copyright © 2013 The Institute of Brewing & Distilling
CONSTRUCTION OF TUNNELS USING SINGLE-SKIN CONCRETE LININGS (1976)

TUNNEL CONSTRUCTION WITH SINGLE LAYER LINING OF PRECAST CONCRETE SEGMENTS IS EXPLAINED WITH THE AID OF THREE COMPLETED PROJECTS, MAIN SEWERS IN STUTTGART AND HAMBURG AND AN UNDERGROUND RAILWAY TUNNEL IN MUNICH. THIS METHOD OF CONSTRUCTION DISPENSES WITH AN INTERNAL WATERPROOF LAYER OF IN SITU CONCRETE. WATERPROOFNESS MUST BE ACHIEVED SOLELY BY THE PRECAST CONCRETE SEGMENTS WHICH ARE LAID IN CIRCULAR OR HELICAL PATTERNS. THE JOINT DETAIL IS OF PARAMOUNT IMPORTANCE. WHILE IN STUTTGART POINTING WITH CEMENT MORTAR SUFFICED, IN HAMBURG AND MUNICH NEOPRENE GASKETS WERE REQUIRED TO RESIST THE HIGH WATER PRESSURE. IN THESE CASES GREATER DEMANDS ARE MADE ON THE DIMENSIONAL ACCURACY OF THE CONCRETE SEGMENTS. THE MANUFACTURE OF THE UNITS, THE DRIVING OF THE TUNNEL WITH THE AID OF COMPRESSED AIR AND THE ERECTION OF THE LININGS IS DESCRIBED. REINFORCED CONCRETE SEGMENTS OF THE TYPE DESCRIBED COST ABOUT HALF AS MUCH AS THE CONVENTIONAL CAST IRON LINING SEGMENTS. IT IS TO BE EXPECTED THAT THE USE OF CONCRETE LININGS WILL BECOME MORE WIDESPREAD IN THE FUTURE.
ChemInform Abstract: Manganese(III) Porphyrin Covalently Bound to Sol—Gel Derived Silica (Mn(III) Porphyrinosilica): A Reusable and Green Heterogeneous Photocatalyst for Oxidative Decarboxylation of α‐Arylacetic Acids with H2O2. (2011)

Abstract The activity of the heterogeneous title photocatalyst in the oxidative decarboxylation of α‐arylacetic acids (I) is significantly higher than that of the corresponding homogeneous system.
An Automated Vehicle Safety Concept Based on Runtime Restriction of the Operational Design Domain (2018)

Automated vehicles need to operate safely in a wide range of environments and hazards. The complex systems that make up an automated vehicle must also ensure safety in the event of system failures. This paper proposes an approach and architectural design for achieving maximum functionality in the case of system failures. The Operational Design Domain (ODD) defines the domain over which the automated vehicle can operate safely. We propose modifying a runtime representation of the ODD based on current system capabilities. This enables the system to react with context-appropriate responses depending on the remaining degraded functionality. In addition to proposing an architectural design, we have implemented the approach to prove its viability. The proof of concept has shown promising directions for future work and moved our automated vehicle research platform closer to achieving level 4 automation.