gebhart/patrepeval huggingface dataset:
Imaging analysis of STAT1 and NF-kappaB translocation in dendritic cells at the single cell level. (2005)

Rapid assessment of immune or stem cells, which are now widely applied in the clinical setting of cancer treatment, is necessary to speed their development and to determine their quality. We have evaluated immature dendritic cells (iDC) by semiautomated imaging cytometry which provides detailed assessment at a single cell level. Nuclear translocation of NF-kappaB was studied by imaging analysis as well as electrophoretic mobility shift assay with an excellent correlation (r = 0.981) over a broad range of lipopolysaccharide (LPS) concentrations. Imaging analysis was time saving (5 h vs. 3 days), and required 30- to 100-fold less cells per analysis. Single cell information revealed remarkable heterogeneity between individual iDC and permitted detection of responses to 40 pg/ml of LPS. In IL-1beta/IFNgamma activated iDC, STAT1 responses preceded NF-kappaB responses, and the expression of both was strongly correlated in individual cells (p < 0.001). IFNgamma amplified IL-1-induced NF-kappaB responses. NF-kappaB responses to IL-1beta, CD40L, and LPS were donor-dependent (n = 7), correlated with the quality of iDC preparations (p = 0.002), and IL-12 p70 production (p = 0.010). NF-kappaB measurements in iDC within mixed cell cultures (iDC, NK, K562) demonstrated that these strategies are applicable for analyses of complex cell-cell interactions. Imaging analysis is a method that could be valuable for quality control of cell therapy preparations.
An area effective standard cell based channel decoder LSI for digital satellite TV broadcasting (2002)

A new channel decoder LSI, which will be used in digital satellite TV broadcasting set-top boxes, has been designed. This LSI's functions include AD/DA conversion, QPSK demodulation, Viterbi decoding, frame synchronization, convolutional deinterleaving, Reed-Solomon (RS) decoding, and descrambling. We use a new method for Viterbi decoding called the tracking survivor state information (TSSI) method, which not only reduces power consumption, but also solves the problem of increasing memory size. To reduce the size of the RS decoder circuit, we used a three-stage-pipeline structure as well as designed a new architecture to realize the Euclid algorithm. This device has been fabricated in a 0.35 /spl mu/m 3-metal CMOS standard cell-based process and is composed of 670 K transistors. We describe the TSSI method of the Viterbi decoder and the Reed-Solomon decoder's new 3-stage pipeline architecture.
Cortical localization of the Gα protein GPA-16 requires RIC-8 function during<i>C. elegans</i>asymmetric cell division (2005)

Understanding of the mechanisms governing spindle positioning during asymmetric division remains incomplete. During unequal division of one-cell stage C. elegans embryos, the Galpha proteins GOA-1 and GPA-16 act in a partially redundant manner to generate pulling forces along astral microtubules. Previous work focused primarily on GOA-1, whereas the mechanisms by which GPA-16 participates in this process are not well understood. Here, we report that GPA-16 is present predominantly at the cortex of one-cell stage embryos. Using co-immunoprecipitation and surface plasmon resonance binding assays, we find that GPA-16 associates with RIC-8 and GPR-1/2, two proteins known to be required for pulling force generation. Using spindle severing as an assay for pulling forces, we demonstrate that inactivation of the Gbeta protein GPB-1 renders GPA-16 and GOA-1 entirely redundant. This suggests that the two Galpha proteins can activate the same pathway and that their dual presence is normally needed to counter Gbetagamma. Using nucleotide exchange assays, we establish that whereas GPR-1/2 acts as a guanine nucleotide dissociation inhibitor (GDI) for GPA-16, as it does for GOA-1, RIC-8 does not exhibit guanine nucleotide exchange factor (GEF) activity towards GPA-16, in contrast to its effect on GOA-1. We establish in addition that RIC-8 is required for cortical localization of GPA-16, whereas it is not required for that of GOA-1. Our analysis demonstrates that this requirement toward GPA-16 is distinct from the known function of RIC-8 in enabling interaction between Galpha proteins and GPR-1/2, thus providing novel insight into the mechanisms of asymmetric spindle positioning.
Intrinsic Radiosensitivity and Cellular Characterization of 27 Canine Cancer Cell Lines (2016)

Canine cancer cell lines have progressively been developed, but are still underused resources for radiation biology research. Measurement of the cellular intrinsic radiosensitivity is important because understanding the difference may provide a framework for further elucidating profiles for prediction of radiation therapy response. Our studies have focused on characterizing diverse canine cancer cell lines in vitro and understanding parameters that might contribute to intrinsic radiosensitivity. First, intrinsic radiosensitivity of 27 canine cancer cell lines derived from ten tumor types was determined using a clonogenic assay. The 27 cell lines had varying radiosensitivities regardless tumor type (survival fraction at 2 Gy, SF2 = 0.19-0.93). In order to understand parameters that might contribute to intrinsic radiosensitivity, we evaluated the relationships of cellular radiosensitivity with basic cellular characteristics of the cell lines. There was no significant correlation of SF2 with S-phase fraction, doubling time, chromosome number, ploidy, or number of metacentric chromosomes, while there was a statistically significant correlation between SF2 and plating efficiency. Next, we selected the five most radiosensitive cell lines as the radiosensitive group and the five most radioresistant cell lines as the radioresistant group. Then, we evaluated known parameters for cell killing by ionizing radiation, including radiation-induced DNA double strand break (DSB) repair and apoptosis, in the radiosensitive group as compared to the radioresistant group. High levels of residual γ-H2AX foci at the sites of DSBs were present in the four out of the five radiosensitive canine cancer cell lines. Our studies suggested that substantial differences in intrinsic radiosensitivity exist in canine cancer cell lines, and radiation-induced DSB repair was related to radiosensitivity, which is consistent with previous human studies. These data may assist further investigations focusing on the detection of DSB for predicting individual response to radiation therapy for dogs, regardless of tumor type.
Guided acoustic Brillouin scattering measurements in optical communication fibers (2021)

Guided acoustic Brillouin (GAWBS) noise is measured using a novel, homodyne measurement technique for four commonly used fibers in long-distance optical transmission systems. The measurements are made with single spans and then shown to be consistent with separate multi-span long-distance measurements. The inverse dependence of the GAWBS noise on the fiber effective area is confirmed by comparing different fibers with the effective area varying between 80 µm<sup>2</sup> and 150 µm<sup>2</sup>. The line broadening effect of the coating is observed, and the correlation between the width of the GAWBS peaks to the acoustic mode profile is confirmed. An extensive model of the GAWBS noise in long-distance fibers is presented, including corrections to some commonly repeated mistakes in previous reports. It is established through the model and verified with the measurements that the depolarized scattering caused by TR<sub>2m</sub> modes contributes twice as much to the optical noise in the orthogonal polarization to the original source, as it does to the noise in parallel polarization. Using this relationship, the polarized and depolarized contributions to the measured GAWBS noise is separated for the first time. As a result, a direct comparison between the theory and the measured GAWBS noise spectrum is shown for the first time with excellent agreement. It is confirmed that the total GAWBS noise can be calculated from fiber parameters under certain assumptions. It is predicted that the level of depolarized GAWBS noise created by the fiber may depend on the polarization diffusion length, and consequently, possible ways to reduce GAWBS noise are proposed. Using the developed theory, dependence of GAWBS noise on the location of the core is calculated to show that multi-core fibers would have a similar level of GAWBS noise no matter where their cores are positioned.
&lt;title&gt;Development of silicon microcapacitive accelerometer for seismic measurement&lt;/title&gt; (1999)

We have developed a high sensitive and wide-band micro capacitive accelerometer for subsurface seismic measurements by using the micro machining technique which enables to fabricate three-dimensional micro structure and to realize small-size, low-cost and high performance sensors or actuators. The silicon capacitive micro accelerometers, which are used in automobiles for suspension control, brake control and air bags, are potentially be used for subsurface seismic measurements. However the sensitivity and the bandwidth of existing sensors are insufficient to detect seismic waves. The micromachining technique which we employed includes photolithography, anisotropic etching, reactive ion etching and anodic bonding. Problems in the fabrication process such as sticking of silicon mass on the electrode, buckling of spring beams, and a problem due to the squeezed film dumping effect have been resolved by improving the sensor structure and the silicon process. Finally, we have evaluated the characteristics of the sensor.
Detecting amyloid positivity in early Alzheimer disease using plasma biomarkers (2021)

Abstract Background Recent data suggest that blood biomarkers of amyloid‐β (Aβ) pathology (Aβ42/Aβ40), tau pathology (phosphorylated tau [P‐tau]) and neurodegeneration (neurofilament light [NfL]) in Alzheimer disease (AD) become abnormal very early in the disease course, albeit with different dynamics; Aβ42/Aβ40 starts to change first followed next by P‐tau and then by NfL. Method We studied the usefulness of plasma AD biomarkers measured using mass spectrometry (Aβ42/Aβ40) and immunoassays (P‐tau217 and NfL) to identify abnormal brain Aβ status (according to CSF Aβ42/Aβ40 or Aβ‐PET) in a total of 895 participants with early disease (cognitively unimpaired individuals [CU] and patients with mild cognitive impairment [MCI]) from two independent cohorts (BioFINDER‐1 and BioFINDER‐2). CSF Aβ42/Aβ40 measures were available in all study participants; 159 (26.9%) CU and 175 (57.6%) MCI were CSF Aβ42/Aβ40‐positive. Out of 858 subjects who underwent Aβ‐PET imaging, 142 (24.0%) CU and 169 (55.6%) MCI were Aβ‐PET positive. Result In CU, a combination of plasma Aβ42/Aβ40 and plasma P‐tau217 accurately detected abnormal CSF Aβ42/Aβ40 status (BioFINDER‐2, area under the curve [AUC]=0.86; BioFINDER‐1, AUC=0.83) with no significant difference in the accuracy compared with the model including all 3 plasma biomarkers (BioFINDER‐2, AUC=0.87, p=0.62; BioFINDER‐1, AUC=0.84, p=0.57). In MCI patients, plasma P‐tau217 alone showed high discriminative accuracy (BioFINDER‐2, AUC=0.88; BioFINDER‐1, AUC=0.86) which was not significantly different from the discriminative accuracy of the model combining all 3 plasma biomarkers (BioFINDER‐2, AUC=0.88, p=0.94; BioFINDER‐1, AUC=0.88, p=0.29). Adding APOE ε4 status improved model fit but did not significantly change the AUCs of the models. The results were similar when using Aβ‐PET as the outcome. Conclusion These findings suggest that different plasma biomarkers are not equally useful along the AD continuum. In the preclinical phase, plasma Aβ42/Aβ40 and plasma P‐tau217 would be needed to accurately detect abnormal brain Aβ status whereas in prodromal AD plasma P‐tau217 might alone be sufficient.
Nucleotides and Nucleic Acids; Oligo‐ and Polynucleotides (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access the actual ChemInform Abstract, please click on HTML or PDF.
Tumor removal limits prostate cancer cell dissemination in bone and osteoblasts induce cancer cell dormancy through focal adhesion kinase (2022)

Abstract Background Disseminated tumor cells (DTCs) can enter a dormant state and cause no symptoms in cancer patients. On the other hand, the dormant DTCs can reactivate and cause metastases progression and lethal relapses. In prostate cancer (PCa), relapse can happen after curative treatments such as primary tumor removal. The impact of surgical removal on PCa dissemination and dormancy remains elusive. Furthermore, as dormant DTCs are asymptomatic, dormancy-inducing can be an operational cure for preventing metastases and relapse of PCa patients. Methods We used a PCa subcutaneous xenograft model and species-specific PCR to survey the DTCs in various organs at different time points of tumor growth and in response to tumor removal. We developed in vitro 2D and 3D co-culture models to recapitulate the dormant DTCs in the bone microenvironment. Proliferation assays, fluorescent cell cycle reporter, qRT-PCR, and Western Blot were used to characterize the dormancy phenotype. We performed RNA sequencing to determine the dormancy signature of PCa. A drug repurposing algorithm was applied to predict dormancy-inducing drugs and a top candidate was validated for the efficacy and the mechanism of dormancy induction. Results We found DTCs in almost all mouse organs examined, including bones, at week 2 post-tumor cell injections. Surgical removal of the primary tumor reduced the overall DTC abundance, but the DTCs were enriched only in the bones. We found that osteoblasts, but not other cells of the bones, induced PCa cell dormancy. RNA-Seq revealed the suppression of mitochondrial-related biological processes in osteoblast-induced dormant PCa cells. Importantly, the mitochondrial-related biological processes were found up-regulated in both circulating tumor cells and bone metastases from PCa patients’ data. We predicted and validated the dormancy-mimicking effect of PF-562271, an inhibitor of focal adhesion kinase (FAK) in vitro . Decreased FAK phosphorylation and increased nuclear translocation were found in both co-cultured and PF-271-treated C4-2B cells, suggesting that FAK plays a key role in osteoblast-induced PCa dormancy. Conclusions Our study provides the first insights into how primary tumor removal enriches PCa cell dissemination in the bones, defines a unique osteoblast-induced PCa dormancy signature, and identifies FAK as a PCa cell dormancy gatekeeper.
Mesoscopic finite elements for woven fabrics : which model for which application - from 3D fine to coarse shell modelling (2012)

International audience
Atelier (2020)

The aim of the Atelier project1 is to develop an online platform that creates an atelier-like setting that emphasises collaboration and sharing of ideas. It is built for the Community of Practice [1] of students, student assistants, and lecturers involved in teaching programming in Processing in the first year of the bachelor programme Creative Technology (CreaTe) at the University of Twente. CreaTe is a design programme, with an engineering background in Computer Science and Electrical Engineering. It extols its own design philosophy, which emphasises autonomous design, creative thinking, multidisciplinary teams, tinkering and reflection. The motivation behind Atelier to help the creation of a Community of Practice where face-to-face tutoring is central. It is consciously not intended to replace face-to-face tutoring.
Selective Removal of <sup>226</sup>Ra<sup>2+</sup> from Gas-Field-Produced Waters (2005)

The 226Ra2+ selectivity of both the self-assembled (iso)guanosine-based systems and ionizable thiacalix[4]crown dicarboxylic acids was determined in gas-field-produced water and a metal ion-containing model solution (simulant). Seven gas-field-produced water samples have been analyzed. From a sample (K5D) with average metal ion concentrations ([metaltot] = 0.14 M), thiacalix[4]crown-5 dicarboxylic acid (10-4 M) extracts 60% of the 226Ra2+ content. Extractions performed with the model solution (MK5D) indicate that in K5D there is significant competition in 226Ra2+ extraction due to the organic constituents of K5D, in particular with self-assembled extractants guanosine and isoguanosine. Nevertheless, all four extractants extract 226Ra2+ both from the produced water K5D and the model solution MK5D, even with a 100-fold excess of [metaltot] to [extractant]. The extracted 226Ra2+ cations could effectively be stripped from the extractants by washing with pH 2 water. The results obtained with the extractants used, especially thiacalix[4]crown-5 dicarboxylic acid 3, clearly demonstrate the way to selectively remove Ra2+ from gas-field-produced waters.
Strong synaptic transmission impact by copy number variations in schizophrenia (2010)

Schizophrenia is a psychiatric disorder with onset in late adolescence and unclear etiology characterized by both positive and negative symptoms, as well as cognitive deficits. To identify copy number variations (CNVs) that increase the risk of schizophrenia, we performed a whole-genome CNV analysis on a cohort of 977 schizophrenia cases and 2,000 healthy adults of European ancestry who were genotyped with 1.7 million probes. Positive findings were evaluated in an independent cohort of 758 schizophrenia cases and 1,485 controls. The Gene Ontology synaptic transmission family of genes was notably enriched for CNVs in the cases (P = 1.5 x 10(-7)). Among these, CACNA1B and DOC2A, both calcium-signaling genes responsible for neuronal excitation, were deleted in 16 cases and duplicated in 10 cases, respectively. In addition, RET and RIT2, both ras-related genes important for neural crest development, were significantly affected by CNVs. RET deletion was exclusive to seven cases, and RIT2 deletions were overrepresented common variant CNVs in the schizophrenia cases. Our results suggest that novel variations involving the processes of synaptic transmission contribute to the genetic susceptibility of schizophrenia.
24-Hour Profiles of 11-Oxygenated C19 Steroids and Δ5-Steroid Sulfates during Oral and Continuous Subcutaneous Glucocorticoids in 21-Hydroxylase Deficiency (2021)

11-oxyandrogens and PregS could serve as biomarkers of disease control in 21OHD. The development of normative data for these promising novel biomarkers must consider their diurnal variability.
A Framework for Robust Watermarking of H.264-Encoded Video With Controllable Detection Performance (2007)

As H.264 digital video becomes more prevalent, the need for copyright protection and authentication methods that are appropriate for this standard will emerge. This paper proposes a robust watermarking algorithm for H.264. We employ a human visual model adapted for a 4 times 4 discrete cosine transform block to increase the payload and robustness while limiting visual distortion. A key-dependent algorithm is used to select a subset of the coefficients that have visual watermarking capacity. Furthermore, the watermark is spread over frequencies and within blocks to avoid error pooling. This increases the payload and robustness without noticeably changing the perceptual quality. We embed the watermark in the coded residuals to avoid decompressing the video; however, we detect the watermark from the decoded video sequence in order to make the algorithm robust to intraprediction mode changes. We build a theoretical framework for watermark detection based on a likelihood ratio test. This framework is used to obtain optimal video watermark detection with controllable detection performance. Our simulation results show that we achieve the desired detection performance in Monte Carlo trials. We demonstrate the robustness of our proposed algorithm to several different attacks
Evaluation and Treatment of Adult Growth Hormone Deficiency: An Endocrine Society Clinical Practice Guideline (2011)

GHD can persist from childhood or be newly acquired. Confirmation through stimulation testing is usually required unless there is a proven genetic/structural lesion persistent from childhood. GH therapy offers benefits in body composition, exercise capacity, skeletal integrity, and quality of life measures and is most likely to benefit those patients who have more severe GHD. The risks associated with GH treatment are low. GH dosing regimens should be individualized. The final decision to treat adults with GHD requires thoughtful clinical judgment with a careful evaluation of the benefits and risks specific to the individual.
Small Molecule-Induced Intramolecular Electron “Pitch and Catch” in a Rhodium<sup>I</sup> Complex with Substitutionally Inert Redox-Active Ligands (1999)

Chemically or electrochemically induced uptake and release of small molecules “L” by [RhI{Fe(C5H5)(C5H4SCH2CH2PPh2)}2]BF4 occurs via ferrocenyl group-centered oxidation/reduction to form [RhIII{Fe(C5H5)(C5H4SCH2CH2PPh2)}2(L)2][BF4]3. This reaction occurs via a novel intramolecular electron “pitch and catch” process involving the Fe and Rh centers.
Atomic-Layer Etching of Si by Low Energy Ion Irradiation. (1995)

原子層エッチングのためには,エッチャントの表面吸着過程と基板との反応過程を完全に分離し,さらに,おのおのの過程における吸着量や反応量が熱力学的飽和条件で自己制限されるようにすることが不可欠である。著者らは,高清浄雰囲気下での塩素吸着と低エネルギーイオン照射を交互に繰返すことにより,Siの原子層エッチングを,自己制限型にかつ方向性をもたせて実現した。Si(100),(111),(110),(211)面について調べた結果,1サイクル当たりのエッチング量は,表面の塩素吸着量とともに増加し各面方位ともそれぞれの1原子層厚に簡単な分数を掛けた値に飽和することがわかった。また,塩素分子のみを供給した場合,それらの飽和値は,塩素ラジカルの供給を含む場合の1/2倍になる。さらに,Si表面への塩素のLangmuir型吸着を仮定すると1サイクル当たりのエッチング量が定量的に説明でき,飽和エッチング量は各面方位の表面ボンド構造と塩素の吸着サイトとに単純な対応関係がある。本稿では,これら低エネルギーイオン照射によるSiの原子層エッチングの著者らの研究について解説する。
An algorithm for analysing probed partial digestion experiments (1995)

A partial digestion of DNA (e.g. cosmid. Lambda, YAC, chromosome) is performed and the lengths of thoses fragments which hybridize to a labeled probe are measured using gel electrophoresis. We give an efficient algorithm that takes as input this experimental data and proposes one or more candidate solutions. Each solution designates the location of each restriction site and specifies the endpoints of each fragment. (Further experiments can then be designed to select the correct solution from this small set of candidates.) The algorithm works well even when the experiment gives inexact values for the lengths.
Supplementary Figure and Table Legends from Novel Recombinant Human B7-H4 Antibodies Overcome Tumoral Immune Escape to Potentiate T-Cell Antitumor Responses (2023)

&lt;p&gt;Supplementary Figure and Table Legends - PDF file100K, Legend for Supplementary Figures S1-S5 and Supplementary Tables S1-S2&lt;/p&gt;
MAC layer frame design for millimeter wave cellular system (2016)

The MAC layer will need to be significantly redesigned to support the highly directional transmissions, very low latencies and high peak rates featured in 5G millimeter wave communication. This paper analyzes the frame structure and beamforming choices for mmWave MAC layer design. In this work we illustrate simple analytical methods to quantify the resource utilization and physical layer control overhead for millimeter wave cellular systems. It is observed that certain flexible frame design choices may lead to dramatically improved resource utilization under various traffic patterns. Moreover, it is shown that fully digital beamforming architectures offer significantly lower overhead than analog and hybrid beamforming under comparable power budgets.
Design and evaluation of taxi navigation displays [airports] (2003)

The presentation of an electronic map of the airport relative to the position of ownship is regarded as a means to improve the safety and efficiency of surface operations. This paper discusses the design rationale behind a surface moving map display based on an analysis of the surface navigation task and the associated information requirements. It is illustrated how the various elements depicted in the display aim to support the pilot with information collection, integration and extrapolation. Implementation, testing and evaluation are briefly addressed.