gebhart/patrepeval huggingface dataset:
Noninvasive identification of lineage-specific circular RNA for ER-positive breast cancer. (2020)

3543 Background: Non-invasive testing in plasma using RNA biomarkers has been limited by exoribonuclease-mediated degradation of RNA. Circular RNA (circRNA) are covalently closed RNA structures that resist this degradation due to their circular structure. Therefore circRNA are more stable than their linear counterparts. CircRNA are formed by alternative backsplicing of the 3’ end of a downstream exon to the 5’ end of an upstream exon. Here, we propose a novel method for non-invasive identification of circRNA and demonstrate circularized forms of several lineage and cancer specific targets for estrogen receptor-positive breast cancer. Methods: Capture RNA sequencing on cancer tissue was previously performed to determine the relative expression of potential circRNA isoforms in breast cancer patients. These isoforms as well as those predicted by intron length were screened using a quantitative PCR-based assay on ER-positive breast cancer cells. RNA extracted from breast cancer cells are exposed to ribonuclease R to demonstrate stability of circRNA. CircRNA derived from targets with known universal expression are used as positive controls as well as for analysis on plasma. Results: We identify the circRNA isoforms with highest expression for five genes, including ESR1, that are differentially expressed in ER-positive breast cancer compared to other cancers and normal breast tissue. We determine that the circRNA corresponding to all five targets is specifically expressed in breast cancer cell lines with at least 1000-fold higher expression than in non-ER positive breast cancer cell lines. We demonstrate that the highest expressing circRNA isoforms are resistant to degradation by ribonuclease R, whereas corresponding linear mRNA is susceptible. We also demonstrate the presence and stability of positive control circRNA in plasma from patients without cancer. Conclusions: CircRNA are promising biomarkers for early non-invasive detection of cancer due to their stability in plasma. This assay reliably detects ER-positive breast cancer specific circRNA, and exoribonuclease resistance has been validated. Application of this diagnostic assay to plasma from breast cancer patients is underway.
Advanced Na[Ni0.25Fe0.5Mn0.25]O2/C Cathode / EMS Electrolyte / Fe3O4 Anode for Sodium-Ion Batteries (2015)

Lithium is an attractive battery material because it is the lightest metal, but its resources are concentrated in large quantities mainly in South America with an associated risk of dependence on a single geographic area. 1 In addition, the price of lithium-ion batteries is affected by the high cost of their active materials, commonly based on cobalt compounds. As a result, there is an increasing interest worldwide in developing low cost and sustainable energy storage systems that do not use lithium or cobalt. Among them, rechargeable sodium batteries, due to the almost infinite supply of the metal, are the most appealing as immediate alternatives to lithium batteries. Recently reported results 2-4 have triggered an increasing industrial and academic interest in sodium-ion batteries operating at room temperature. Pioneering work by Hagenmuller et al. and Yamamoto et al. introduced O3-type NaMO 2 (M = Ni, Co, and Fe) in which Na+ could be inserted into a host structure. Since then, interest in developing sodium batteries declined because of the fast development and market domination of lithium-ion batteries. However, recent increasing demands for low-cost energy storage have renewed interest in sodium-based batteries and, accordingly, the O3 type NaMO 2 compounds are being revisited as a cathode material due to the facile synthesis and structural stability, including Na-Ni 0.5 Mn 0.5 O 2 , NaCoO 2 , NaCrO 2 , NaMn x M 1 − x O 2 (M =Co, Ni), Na[Ni 1/3 Fe 1/3 O 1/3 ]O 2 , and NaxVO 2 . At present, the electrochemical performance of these cathode materials has been limited due to the lack of electrolytes capable of withstanding voltages above 3.9 V versus Na/Na+. In response, we have developed a sodium-ion battery that has an electrolyte of NaClO 4 in a mixture of ethyl methanesulfonate electrolyte (EMS) and fluoroethylene carbonate (FEC) additive for increasing the stability and conductivity, along with an anode of carbon-coated Fe3O4 and a cathode of O3-type layered Na[Ni 0.25 Fe 0.5 Mn 0.25 ]O 2 . The electrolyte is a key component if sodium-ion batteries are to become competitive with or surpass lithium-ion batteries. The main requirement is a wide anodic stability window in order to allow complete desodiation of the cathode. A common choice has been 1 M sodium perchlorate in propylene carbonate (NaClO 4 −PC) with selected additives. For instance, as suggested by Komaba et al., the addition of a small amount of FEC to the PC-based solvent contributes to improved cycleability of sodium batteries, possibly because of a positive effect induced by the fluorination of the anode surfaces. (1) Scrosati, B.; Garche, J. J. Power Sources 2010, 195, 2419−2430. (2) Fouassier, C.; Matejka, G.; Reau, J.-M.; Hagenmuller, P. J. Solid State Chem. 1973, 6, 532−537. (3) Delmas, C.; Fouassier, C.; Hagenmuller, P. Physica B+C 1980, 99,81−85. (4) Braconnier, J.-J.; Delmas, C.; Fouassier, C.; Hagenmuller, P. Mater. Res. Bull. 1980, 15, 1797−1804.
Visible-Light-Induced Reversible Photomagnetism in Rubidium Manganese Hexacyanoferrate (2007)

The photoreversibility of a photoinduced phase transition was investigated in a rubidium manganese hexacyanoferrate, Rb0.88Mn[Fe(CN)6]0.96·0.5H2O. The present material shows a charge-transfer phase transition from the MnII−FeIII [high-temperature (HT)] phase to the MnIII−FeII [low-temperature (LT)] phase, and the LT phase shows ferromagnetism. Spectroscopic ellipsometry measurements of the dielectric constant suggest that the optical transitions in the LT and HT phases are a metal-to-metal charge transfer (FeII → MnIII) band at 420–540 nm and a ligand-to-metal charge transfer (CN– → FeIII) band of [FeIII(CN)6] at 410 nm, respectively. By irradiation with 532 nm light, the LT phase is transmitted to the photoinduced (PI) phase, which has a valence state similar to that of the HT phase, and photodemagnetization is observed. In contrast, irradiating the PI phase with 410 ± 30 nm light causes the reverse phase transition. Neutron powder diffraction measurement of an analogue compound, Rb0.58Mn[Fe(CN)6]0.86·2.3H2O, which does not show a charge-transfer phase transition and maintains the MnII−FeIII phase at a very low temperature, confirms that the PI phase is an antiferromagnet. Hence, the present visible-light-induced reversible photomagnetic effect is due to optical switching between the ferromagnetic LT phase and the antiferromagnetic PI phase.
Iterative Method for the Design of DFT Filter Bank (2004)

Multirate adaptive filters have numerous advantages such as low computational load, fast convergence, and parallelism in the adaptation. Drawbacks when using multirate processing are mainly related to aliasing and reconstruction effects. These effects can be minimized by introducing appropriate problem formulation and employing sophisticated optimization techniques. In this paper, we propose a formulation for the design of a filter bank which controls the distortion level for each frequency component directly and minimizes the inband aliasing and the residual aliasing between different subbands. The advantage of this problem formulation is that the distortion level can be weighted for each frequency depending on the particular practical application. A new iterative algorithm is proposed to optimize simultaneously over both the analysis and the synthesis filter banks. This algorithm is shown to have a unique solution for each iteration. For a fixed distortion level, the proposed algorithm yields a significant reduction in both the inband aliasing and the residual aliasing levels compared to existing methods applied to the numerical examples.
Abstract 13113: Dynamic Vessel Bioreactor Recapitulates in vivo Cell Viability and Phenotype in Response to Absorbable Magnesium-Based Stent (2019)

Introduction: Absorbable magnesium (Mg)-based stents are a promising option for treating stenotic artery disease. Animal and pre-clinical models have shown encouraging results; however, predictions...
Origin of yellow emission in white OLED with single emitting material (2010)

Abstract The photo‐luminescence (PL) and electro‐luminescence (EL) of a novel organic material, benzodithiophene/triphenylamine copolymer (P‐PBTx, n=5‐6) were investigated. The PL exhibited wide blue emission at room temperature, which is attributed to fluorescence from a chromophore, benzodithiophene moiety, from results of spectral analysis and decay profile. The EL, however, exhibited white emission consisting of wide blue (B) and yellow (Y) bands, although it was prepared with P‐PBTx as a single emitting material. The Y‐band was slightly observed at 7 K and found to possess long lived component of 19 ms lifetime. The origin of the Y‐band efficiently stimulated by carrier injection is supposed to be a charge‐transfer state between benzodithiophene and triphenylamine moieties. The long lived component could be explained by lowered transition probability caused by charge separation. (© 2011 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
ChemInform Abstract: Grazing Incidence X‐Ray and Electrochemical Study of Thin Film Copper( 111) on Mica. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Exoskeletons for Gait Assistance and Training of the Motor-Impaired (2007)

Robotics is emerging as a promising tool for training of human functional movement. The current research in this area is focused primarily on upper extremity movements. This paper describes novel designs of three lower extremity exoskeletons, intended for gait assistance and training of motor-impaired patients. The design of each of these exoskeletons is novel and different. Force and position sensors on the exoskeleton provide feedback to the user during training. The exoskeletons have undergone limited tests on healthy and stroke survivors to assess their potential for treadmill walking. GBO is a gravity balancing un-motorized orthosis which can alter the gravity acting at the hip and knee joints during swing. ALEX is an actively driven leg exoskeleton which can modulate the foot trajectory using motors at the joints. SUE is a bilateral swing-assist un-motorized exoskeleton to propel the leg during gait.
Origin of quasiperiodic dynamics in excitable media (2000)

Analysis of the dynamic instabilities of periodic waves in a one-dimensional excitable ring medium demonstrates that driven oscillations of a pulse width display different oscillatory behavior at different values of stimulation frequency. Initial periodicity evolves to quasiperiodic dynamics when the propagation speed of a pulse approaches its minimal value determined by the dispersion relation of a medium.
Electronic Skin to Feel “Pain”: Detecting “Prick” and “Hot” Pain Sensations (2019)

An artificial tactile system has attracted tremendous interest and intensive study, since it can be applied as a new functional interface between humans and electronic devices. Unfortunately, most previous works focused on improving the sensitivity of sensors. However, humans also respond to psychological feelings for sensations such as pain, softness, or roughness, which are important factors for interacting with others and objects. Here, we present an electronic skin concept that generates a "pain" warning signal, specifically, to sharp "prick" and "hot" sensations. To simplify the sensor structure for these two feelings, a single-body tactile sensor design is proposed. By exploiting "hot" feeling based on the Seebeck effect instead of the pyroelectric property, it is possible to distinguish points registering a "hot" feeling from those generating a "prick" feeling, which is based on the piezoelectric effect. The control of free carrier concentration in nanowire induced the appropriate level of Seebeck current, which enabled the sensor system to be more reliable. The first derivatives of the piezo and Seebeck output signals are the key factors for the signal processing of the "pain" feeling. The main idea can be applied to mimic other psychological tactile feelings.
Honeybee-mediated Controlled Pollinations in Cornus florida and C. kousa Intra- and Interspecific Crosses (2009)

Flowering ( Cornus florida L.) and kousa ( C. kousa Hance) dogwoods are ornamental trees valued for their four-season appeal, but also for their importance to retail and wholesale nurseries. The popularity of kousa dogwood has increased in recent years as a result of its resistance to dogwood anthracnose and powdery mildew as compared with flowering dogwood, which is typically susceptible to those diseases. This range of resistance allows the development of intra- and interspecific cultivars with multiple disease resistance or a combination of disease resistance and specific ornamental traits. Breeding requires controlled crosses that are usually done manually, which is a labor-intensive process. Cornus florida and C. kousa have generally been found to be self-incompatible allowing for the breeding process to be made more efficient by not having to emasculate flowers. We have capitalized on the natural ability of honeybees and the self-incompatible nature of dogwood to perform self- and crosspollinations of flowering and kousa dogwood. Self-pollinations were conducted in 2006 and 2007 with C. florida ‘Appalachian Spring’ and ‘Cherokee Brave’ and with C. kousa ‘Blue Shadow’ and Galilean®. The flowering dogwood self-pollinations resulted in no seed production, whereas the kousa dogwood self-pollinations resulted in low seed production, indicating self-incompatibility. Intra- and interspecific crosses of flowering and kousa dogwood cultivars and breeding lines were conducted in 2006 to 2008. Honeybees were effective in facilitating seed production for all intraspecific crosses conducted. Seedling phenotypes of putative intra- and interspecific hybrids are similar and practically indistinguishable, so dogwood-specific simple sequence repeats were used to verify a sample of the putative hybrids. The results demonstrated that honeybees were effective in performing controlled pollinations and that honeybee-mediated pollinations provide an alternative to time-consuming hand pollinations for flowering and kousa dogwood.
Differential gene expression patterns in porcine nuclear transfer embryos reconstructed with fetal fibroblasts and mesenchymal stem cells (2006)

The present study compared the developmental ability and gene expression pattern at 4-cell, 8-cell, morula, and blastocyst stages of porcine nuclear transfer (NT) embryos from fetal fibroblasts (FFs) and mesenchymal stem cells (MSCs), in vitro fertilized (IVF), and in vivo derived embryos. MSC-NT embryos showed enhanced blastocyst formation, higher total cell number, and a low incidence of apoptosis compared to FF-NT embryos. Alterations in the expression pattern of genes implicated in transcription and pluripotency (Oct4, Stat3, Nanog), DNA methylation (Dnmt1, Dnmt3a), histone deacetylation (Hdac2), growth factor signaling, and imprinting (Igf2, Igf2r) and apoptosis (Bax, Bcl2) regulation were observed in NT embryos. The expression of transcripts in MSC-NT embryos more closely followed that of the in vivo derived embryos compared with FF-NT embryos. In conclusion, MSCs with a relatively undifferentiated genome might serve as suitable donors that could be more efficiently reprogrammed to re-activate expression of early embryonic genes in porcine NT.
Gait spectral index (GSI): a new quantification method for assessing human gait (2010)

This paper introduces a simple, quantitative as-sessment tool to follow up the recovery of gait. Today, micro-electro-mechanical systems (MEMS) technology provides with small, simple, low-pow- er consuming and easy to don and doff sensors. In our approach we have selected an accelerome- ter and introduced a new quantity that charac-terizes the gait pattern in the frequency domain, we term it Gait Spectral Index (GSI). GSI allows assessing gait quality and closely relates to the speed and cadence of gait (dynamics). We have tested the GSI approach to quantify the quality of the gait of healthy young and elderly, and post- stroke hemiplegic individuals. We investigated the repeatability and coherence of GSI in healthy individuals (young and elderly) and contrasted this to the post-stroke hemiplegic individuals. We found that high correlation of the GSI with conventional gait parameters. This suggests that GSI, which needs only data from one acceler-ometer, could be an objective quantitative mea- sure of the quality of the walking thereby a sim- ple yet reliable measure of the recovery of func-tion during neuronrehabilitation.
High-precision measurement of a fiber connector end face by use of a Mirau interferometer (2006)

What we believe to be a new instrument for measuring the end-face geometrical parameters of fiber connectors is described. In this apparatus, a Mirau-type interferometric objective is employed to measure a small area of the connector end face and generate an interferogram corresponding to the surface profile. Various new technologies are used to ensure excellent performance and high measurement repeatability. A multipoint method is proposed to adjust the inclination of the physical contact sample stage. The physical contact angle of the sample stage is adjusted directly on the instrument by use of a special tool whose angle is calibrated with the reversal method. Measurement results of important parameters of the fiber connector end face are compared with those inspected by a commercial profiler or with a standard sample. Optical insertion losses of connectors inspected by the developed system are also evaluated.
Single-mode regime of 19-cell Yb-doped double-cladding photonic crystal fibers (2011)

The single-mode regime of 19-cell Yb-doped double-cladding photonic crystal fibers, successfully exploited for high-power applications due to their large mode area, has been studied. The first higher-order mode cut-off wavelength has been evaluated taking into account the crossing between its dispersion curve, obtained with a full-vector modal solver based on the finite element method, and the one of the fundamental space-filling mode, calculated for an infinite cladding. Moreover, the overlap integral on the doped core of the higher-order mode at cut-off condition has been calculated, in order to investigate its effective suppression in the gain competition with the fundamental mode, by applying a spatial and spectral amplifier model. 19-cell double-cladding photonic crystal fibers with different core diameter and refractive index values have been considered. Simulation results have shown that the approach based on the fundamental space-filling mode effective index is not suitable for the cut-off analysis of large core fibers with a finite cladding dimension.
Attack and Improvement of a Secure S-Box Calculation Based on the Fourier Transform (2008)

peer reviewed
FLoc: Dependable Link Access for Legitimate Traffic in Flooding Attacks (CMU-CyLab-11-019) (2018)

Malware-contaminated hosts organized as a "bot network" can target and flood network links (e.g., routers). Yet, none of the countermeasures to link flooding proposed to date have provided dependable link access (i.e., bandwidth guarantees) for legitimate traffic during such attacks. In this paper, we present a router subsystem called FLoc (Flow Localization) that confines attack effects and provides differential bandwidth guarantees at a congested link: (1) packet flows of uncontaminated domains (i.e., Autonomous Systems) receive better bandwidth guarantees than packet flows of contaminated ones; and (2) legitimate flows of contaminated domains are guaranteed substantially higher bandwidth than attack flows. FLoc employs new preferential packet-drop and traffic-aggregation policies that limit "collateral damage" and protect legitimate flows from a wide variety of flooding attacks. We present FLoc’s analytical model for dependable link access, a router design based on it, and illustrate FLoc’s effectiveness using simulations of different flooding strategies and comparisons with other flooding defense schemes. Internet-scale simulation results corroborate FLoc’s effectiveness in the face of large-scale attacks in the real Internet.
Human Antibody against Shiga Toxin 2 Administered to Piglets after the Onset of Diarrhea Due to Escherichia coli O157:H7 Prevents Fatal Systemic Complications (2005)

Infection of children with Shiga toxin (Stx)-producing Escherichia coli (STEC) can lead to hemolytic-uremic syndrome (HUS) in 5 to 10% of patients. Stx2, one of two toxins liberated by the bacterium, is directly linked with HUS. We have previously shown that Stx-specific human monoclonal antibodies protect STEC-infected animals from fatal systemic complications. The present study defines the protective antibody dose in relation to the time of treatment after the onset of diarrhea in infected gnotobiotic piglets. Using the mouse toxicity model, we selected 5C12, an antibody specific for the A subunit, as the most effective Stx2 antibody for further characterization in the piglet model in which piglets developed diarrhea 16 to 40 h after bacterial challenge, followed by fatal neurological symptoms at 48 to 96 h. Seven groups of piglets received doses of 5C12 ranging from 6.0 mg/kg to 0.05 mg/kg of body weight, administered parenterally 48 h after bacterial challenge. The minimum fully protective antibody dose was 0.4 mg/kg, and the corresponding serum antibody concentration in these piglets was 0.7 mug (+/-0.5)/ml, measured 7 to 14 days after administration. Of 40 infected animals which received Stx2 antibody treatment of > or =0.4 mg/kg, 34 (85%) survived, while only 1 (2.5%) of 39 placebo-treated animals survived. We conclude that the administration of the Stx2-specific antibody was protective against fatal systemic complications even when it was administered well after the onset of diarrhea. These findings suggest that children treated with this antibody, even after the onset of bloody diarrhea, may be equally protected against the risk of developing HUS.
Identification of metastasis-associated microRNAs in serum from rectal cancer patients (2017)

MicroRNAs (miRNAs) are promising prognostic and diagnostic biomarkers due to their high stability in blood. Here we investigate the expression of miRNAs and other noncoding (nc) RNAs in serum of rectal cancer patients. Serum from 96 rectal cancer patients was profiled using small RNA sequencing and expression of small RNAs was correlated with the clinicopathological characteristics of the patients. Multiple classes of RNAs were detected, including miRNAs and fragments of tRNAs, snoRNAs, long ncRNAs, and other classes of RNAs. Several miRNAs, miRNA variants (isomiRs) and other ncRNAs were differentially expressed between Stage IV and Stage I-III rectal cancer patients, including several members of the miR-320 family. Furthermore, we show that high expression of miR-320d as well as one tRNA fragment is associated with poor survival. We also show that several miRNAs and isomiRs are differentially expressed between patients receiving preoperative chemoradiotherapy and patients who did not receive any treatment before serum collection. In summary, our study shows that the expression of miRNAs and other small ncRNAs in serum may be used to predict distant metastasis and survival in rectal cancer.