gebhart/patrepeval huggingface dataset:
Targeted Radiosensitization of ETS Fusion-Positive Prostate Cancer through PARP1 Inhibition (2013)

ETS gene fusions, which result in overexpression of an ETS transcription factor, are considered driving mutations in approximately half of all prostate cancers. Dysregulation of ETS transcription factors is also known to exist in Ewing's sarcoma, breast cancer, and acute lymphoblastic leukemia. We previously discovered that ERG, the predominant ETS family member in prostate cancer, interacts with the DNA damage response protein poly (ADP-ribose) polymerase 1 (PARP1) in human prostate cancer specimens. Therefore, we hypothesized that the ERG-PARP1 interaction may confer radiation resistance by increasing DNA repair efficiency and that this radio-resistance could be reversed through PARP1 inhibition. Using lentiviral approaches, we established isogenic models of ERG overexpression in PC3 and DU145 prostate cancer cell lines. In both cell lines, ERG overexpression increased clonogenic survival following radiation by 1.25 (±0.07) fold (mean ± SEM) and also resulted in increased PARP1 activity. PARP1 inhibition with olaparib preferentially radiosensitized ERG-positive cells by a factor of 1.52 (±0.03) relative to ERG-negative cells (P < .05). Neutral and alkaline COMET assays and immunofluorescence microscopy assessing γ-H2AX foci showed increased short- and long-term efficiencies of DNA repair, respectively, following radiation that was preferentially reversed by PARP1 inhibition. These findings were verified in an in vivo xenograft model. Our findings demonstrate that ERG overexpression confers radiation resistance through increased efficiency of DNA repair following radiation that can be reversed through inhibition of PARP1. These results motivate the use of PARP1 inhibitors as radiosensitizers in patients with localized ETS fusion-positive cancers.
Characterization of an atypical <i>Actinobacillus pleuropneumoniae</i> serovar 2 isolate with a rough-type lipopolysaccharide (2022)

We describe phenotypic and genetic characterization of an atypical Japanese Actinobacillus pleuropneumoniae isolate OT761. Nucleotide sequence analysis revealed that gene clusters involved in capsular polysaccharide and O-polysaccharide (O-PS) biosynthesis of the isolate were nearly identical to those of serovar 2 reference strain. The main difference found between the O-PS loci is the shortening of 31 amino acids from the C terminus of WcaJ in the atypical isolate due to a 93 bp deletion at the 3' end of wcaJ gene. Immunoblot analysis revealed that this isolate could not produce O-PS. Taken together, our results showed that the C-terminal domain of the A. pleuropneumoniae WcaJ plays a critical role in enzyme function of WcaJ involved in the biosynthesis of O-PS.
Impedance measurements in the ear canal (1989)

The objective of the present work is to make accurate impedance estimates at the eardrum Ztm (ω). This is done by measuring the thevenin parameters of an earphone using a four-cavity calibration method [J. B. Allen, “Measurement of eardrum acoustic impedance,” in Peripheral Auditory Mechanisms, edited by J. B. Allen et al. (1985)] for frequencies up to 15 kHz. The calibrated earphone is then used to measure the ear canal impedance Ze (ω) near the ear canal entrance. To transform Ze to Ztm, the ear canal cavity has been modeled. The following effects were accounted for by the model: (a) the jump in area from the earphone calibration cavity to that of the ear canal, (b) the distance to the eardrum, (c) variations in cross-sectional ear canal area, and (d) effects due to ear canal wall impedances. It is desirable that parameters of the ear canal be derivable from Ze. Preliminary results isolating each of these effects first in tubes and then in real ear canals are presented.
Spinal cord disease: clinical presentations and pathology (2005)

Abstract Although the clinical manifestations of myelopathy are not encountered as frequently as those of neuropathy and dementia, the spinal cord is commonly affected during HIV infection. The most common cause of spinal cord disease in the course of HIV infection is AIDS-associated vacuolar myelopathy (VM; Snider et al. 1983; Simpson and Tagliati 1994; Petito et al. 1985). Although VM is strictly a pathological diagnosis, the term VM is used at large to indicate the clinical manifestation of primary myelopathy associated with AIDS. VM has fairly typical clinical features and is potentially disabling, but its symptoms often overlap with those of neuropathy or other neurological disorders associated with late stage AIDS. This may explain, at least in part, why VM tends to be clinically underrecognized.
Multimodal magnetic resonance imaging to identify stroke onset within 6 h in patients with large vessel occlusions (2018)

In patients with large vessel occlusion and unknown time of stroke onset an automated multivariate imaging model is able to select patients who are likely within the 6 h time-window.
Conidia of the tomato powdery mildew <i>Oidium neolycopersici</i> initiate germ tubes at a predetermined site (2011)

The emergence of germ tubes from the conidia of powdery mildew fungi is the first morphological event of the infection process, preceding appressoria formation, peg penetration and primary haustoria formation. Germination patterns of the conidia are specific in powdery mildew fungi and therefore considered useful for identification. In the present study, we examined conidial germination of the tomato powdery mildew Oidium neolycopersici KTP-01 in order to clarify whether germ tube emergence site in KTP-01 conidia is determined by the first contact of the conidia to leaves (as found for the conidia of barley powdery mildew), or alternatively is predetermined and is unrelated to contact stimulus. Highly germinative conidia of KTP-01 were collected from conidial pseudochains on conidiophores in colonies on tomato leaves using two methods involving an electrostatic spore attractor and a blower. In the electrostatic spore attraction method, the conidia were attracted to the electrified insulator probe of the spore collector—this being the first contact stimulus for the conidia. In addition, the blowing method was used as a model of natural infection; pseudochain conidia were transferred to detached leaves by air (1 m/s) from a blower. Thus, landing on the leaves was the first contact for the conidia. Furthermore, conidia were also blown onto an artificial membrane (Parafilm-coated glass slides forming a hydrophobic surface) or solidified agar plates in Petri dishes (hydrophilic surface). Eventually, almost all conidia on the probe and on tomato leaves or artificial hydrophobic and hydrophilic surfaces synchronously germinated within 6 h of incubation, indicating that the first contact of the conidia with any of the aforementioned substrata was an effective germination induction signal. Germ tube emergence sites were exclusively subterminal on the conidia. Moreover, the germ tubes emerged without any relation to the sites touched first on the conidia. Thus, the present study strongly indicates that conidia of O. neolycopersici produce germ tubes at a predetermined site.
Formation of ilmenite-type single-crystalline MgTiO3 thin films by pulsed-laser deposition (2021)

Ilmenite structure is a good playground to explore magnetism in honeycomb lattices owing to the existence of an intriguing variety of magnetism in 3d transition metal compounds. Because of the absence of magnetic ions, ilmenite-type MgTiO3 is a promising candidate for d0 transparent insulators to reveal general features of TiO6 honeycomb layers. In this study, we found an optimum growth condition to synthesize ilmenite-type single-crystalline MgTiO3 thin films on Al2O3(0001) substrates by pulsed-laser deposition. By increasing oxygen pressure from roughly 10−6 to 10−1 Torr, we obtained (0001)-oriented MgTiO3 thin films with suppression of segregation of a Mg2TiO4 phase. On the triangular lattice of Al2O3, twin-domain formation is suppressed with decreasing deposition rate, resulting in the synthesis of single-crystalline MgTiO3 thin films. The bandgap of the MgTiO3 film was evaluated to be about 4.4 eV by optical absorption spectra, which implies d0 transparent insulator.
Effect of a p-type ZnO insertion layer on the external quantum efficiency of GaInN light-emitting diodes (2015)

The external quantum efficiency (EQE) of a GaInN green light-emitting diode (LED) is improved by inserting a p-type ZnO layer between the indium tin oxide electrode and the p-type GaN layer. Several hypotheses are discussed to explain the EQE improvement in the LED with the ZnO layer. It is concluded that higher hole injection efficiency and better electron confinement explain the EQE improvement, which is supported by the results of device simulations showing that the EQE is sensitive to the polarization sheet charge density at the interface between the last quantum barrier and electron-blocking layer. (C) 2015 The Japan Society of Applied Physics
Shifts of Core-level Electron Binding Energies for SrBi2Ta2O9 Nano-particles (2000)

Abstract The electron binding energies of Ta 4d5/2 and Sr 3p3/2 levels of SrBi2Ta2O9 nano-particles were larger by 1.2 eV than these of bulk SrBi2Ta2O9, while the Bi 4d5/2 electron binding energy was smaller by 1.4 eV than the bulk. Charge distribution in the unit cell of the nano-particles differs from that of the bulk.
Getting insights into hepatocellular carcinoma tumour heterogeneity by multiomics dissection (2019)

Malignant tumours are composed of a heterogeneous collection of single cells with different molecular and phenotypic features, a phenomenon termed intratumoural heterogeneity (ITH) that is involved in tumour growth, progression, invasion and metastasis. This multilesion scenario represents a serious hurdle to accurate diagnoses and effective treatments that should be urgently circumvented to improve the clinical management of oncologic patients. To this end, many efforts have been devoted to investigate the morphological, environmental and molecular principles of ITH, specifically in hepatocellular carcinoma (HCC).1 Understanding tumour immunogenicity is a central topic in cancer therapy as immune microenvironment, human leucocyte antigen heterogeneity and tumour-specific neoantigens may lead to next-generation vaccination strategies.2 Genetic variation has been appointed as a source of ITH in HCC with pharmacological implication, although caution should be taken in the interpretation of mutational signatures3 that should be subjected to further validation. In this regard, orthogonal analyses combining complementary approaches to analyse different layers of biological information are currently providing a more precise phenotypic description to the molecular complexity resulting from ITH. The study of ITH by integrating different sources of information was already proposed in 1983 and in recent years the use of genome-wide exploration technologies is emerging as a resource with unprecedented capabilities …
Large Hysteresis during Lithium Insertion into and Extraction from High‐Capacity Disordered Carbons (1998)

Perylene‐based disordered carbon (PBDC) heat‐treated at 550 °C for anodes in Li‐ion cells showed large hysteresis and a high reversible capacity of 800 mAh/g. The hysteresis was analyzed by polarization and impedance measurements. The overpotential during lithium extraction increased markedly in the range of open‐circuit potential, 0.5–1 V vs . The impedance spectra of PBDC during lithium insertion were significantly different from those during extraction. The charge‐transfer resistance for lithiated PBDC during extraction above 0.5 V was much larger than that for the PBDC during insertion. The chemical diffusion coefficient of lithium, DLi, of PBDC during lithium insertion decreased almost linearly from with increasing lithium storage capacity. The values of DLi during lithium extraction above 0.5 V were much smaller than those during insertion. The large hysteresis was due to the large charge‐transfer resistance and the slow diffusion of lithium during lithium extraction from the fully lithiated PBDC. The large charge‐transfer resistance during lithium extraction has been interpreted as the rectification of lithiated PBDC, which is similar to that of n‐type semiconductors under anodic polarization.
Nonlinear optical waveguides made of thin films of glass doped with semiconductor microcrystallites (1988)

The rf sputtering technique was used to deposit thin films of CdS microcrystallite-doped glass onto standard glass substrates. The presence of the microcrystallites in the films was verified by using Raman spectroscopy. A sharp cutoff below 500 nm was visible on the transmission spectra of the semiconductor microcrystallite-doped films. The evidence of size effects was visible on both Raman and transmission spectra of the films. Power-dependent prism coupling of light into the waveguides was investigated under cw-illumination conditions. The angular variation in decoupled power becomes more asymmetric with increasing input power until switching occurs on one side of the characteristic. The nonlinearity involved is presumably of thermal origin.
Interplay between large materials databases, semi-empirical approaches, neuro-computing and first principle calculations (1999)

Analyzing the conditions that make it possible to search for materials science concepts, it is shown that it was the amassing of a critical volume of experimentally-determined data in the literature that permitted an individual with deep insight to perceive an underlying pattern not previously apparent. Extending these facts to a new area of materials design leads to the following four key-points: 1) creation and use of huge, critically evaluated materials databases; 2) computer-aided reduction of elemental parameters and systematic combinations of them to find the relevant feature sets which can link materials properties qualitatively with the chemical species present; 3) refinement and optimisation of qualitatively-obtained results under (2) with the help of neurocomputing leading to more explicit quantitative results; and 4) focusing on predicted, most-promising materials systems with the aim to reduce the experimental work for verification, as well as trying to create a theoretically-based explanation for such quantitative results.
Prediction of the Radiated Emission(RE)s due to the PCB Power-Bus' Resonance Modes and Mitigation of the RE Levels (2007)

PCB Power-Bus (comprising power/ground planes) impedance and fields are evaluated by an efficient series expansion method that is suggested in this paper. It is used to investigate the structure's radiated emission(RE) levels and find acceptable ways of loading the power/ground planes such as decoupling capcitor(DeCap)s, balanced feeding and slits, in order to reduce the interferences. Also, the calculations and measurements of a proposed geometry are verified by vector fitting as a analysis model to check the behavior of the slit.
Passive Presence Detection Algorithm for Wi-Fi Sensing (2020)

In this paper, we derive a signal processing algorithm that enables a Wi-Fi station to passively detect the presence of a potential user in its vicinity. It is assumed that the potential user either doesn't carry a Wi-Fi device or, if it does, that its device does not participate in the detection procedure. Passive presence detection is performed by the station by means of tracking over time channel estimates obtained with packets transmitted by one or more stations in the Wi-Fi network, and determining when the user presence impacts the received signals. The proposed algorithm performs binary hypothesis testing and decides if a potential user is in the vicinity of the Wi-Fi station. It uses an estimate of the dynamic channel component power as the test statistic and compares it to a predefined threshold. As formulated in the paper, to increase the detection reliability, the power of the dynamic channel component is maximized by using an optimization procedure. Experimental results obtained with off-the-shelf Wi-Fi devices and with the proposed algorithm are presented which demonstrate the validity of the analytical formulation, as well as the feasibility of performing passive presence detection using a Wi-Fi network. In controlled residential and enterprise settings, the proposed algorithm provided a detection rate of 99.7% for a false alarm rate of less than 1%.
The Oxytocin–Bone Axis (2013)

We recently demonstrated a direct action of oxytocin (OT) on skeletal homeostasis, mainly mediated through stimulation of osteoblasts (OBs) formation and through the reciprocal modulation of osteoclast (OCs) formation and function. Thus, mice lacking the hormone or its receptor develop a low turnover osteoporosis that worsens with age in both sexes. The skeletons of OT (Ot) and OT receptor (Oxtr) null mice display a pronounced decrease in vertebral and femoral trabecular volume. At the cellular level, OBs from Ot KO and Oxtr KO mice exhibit lower mineralization activity and, at the mRNA level, all master genes for osteoblast differentiation are down-regulated. Moreover, OT has dual effects on OCs: it increases osteoclast formation both directly, by activating nuclear factor kB (NFkB) and mitogen-activated protein kinase (MAPK) signalling and, indirectly, through the up-regulation of receptor activator nuclear factor-kappaB ligand synthesis by OBs. On the other hand, it inhibits bone resorption by triggering cytosolic Ca(2+) release and nitric oxide synthesis in mature OCs. OT is locally produced by osteoblasts acting as paracrine-autocrine regulators of bone formation modulated by oestrogens. The oestrogen signal involved in this feedforward circuit is nongenomic because it requires an intact MAPK kinase signal transduction pathway, instead of the classical nuclear translocation of oestrogen receptor. The ability of oestrogen to increase bone mass in vivo is to some extent OXTR-dependent. Thus, Oxtr KO mice injected 17β-oestradiol did not show any effects on bone formation parameters, whereas the same treatment increases trabecular and cortical bone in wild-type mice. An intact OT autocrine-paracrine circuit appears to be essential for optimal skeletal remodelling.
Probabilistic quorum systems (1997)

Article Free Access Share on Probabilistic quorum systems Authors: Dahlia Malkhi AT&T Labs--Research, 180 Park Avenue, Florham Park, NJ AT&T Labs--Research, 180 Park Avenue, Florham Park, NJView Profile , Michael Reiter AT&T Labs--Research, 180 Park Avenue, Florham Park, NJ AT&T Labs--Research, 180 Park Avenue, Florham Park, NJView Profile , Rebecca Wright AT&T Labs--Research, 180 Park Avenue, Florham Park, NJ AT&T Labs--Research, 180 Park Avenue, Florham Park, NJView Profile Authors Info & Claims PODC '97: Proceedings of the sixteenth annual ACM symposium on Principles of distributed computingAugust 1997 Pages 267–273https://doi.org/10.1145/259380.259458Published:01 August 1997Publication History 55citation594DownloadsMetricsTotal Citations55Total Downloads594Last 12 Months24Last 6 weeks4 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Use of a novel approach, termed island probing, identifies the Shigella flexneri she pathogenicity island which encodes a homolog of the immunoglobulin A protease-like family of proteins (1997)

The she gene of Shigella flexneri 2a, which also harbors the internal enterotoxin genes set1A and set1B (F. R. Noriega, GenBank accession no. U35656, 1995) encodes a homolog of the virulence-related immunoglobulin A (IgA) protease-like family of secreted proteins, Tsh, EspC, SepA, and Hap, from an avian pathogenic Escherichia coli, an enteropathogenic E. coli, S. flexneri 5, and Haemophilus influenzae, respectively. To investigate the possibility that this locus was carried on a larger deletable element, the S. flexneri 2a YSH6000T she gene was insertionally disrupted by allelic exchange using a Tn10-derived tetAR(B) cassette. Then, to detect loss of the she locus, the tetracycline-resistant derivative was plated onto fusaric acid medium to select for tetracycline-sensitive revertants, which were observed to arise at a frequency of 10(-5) to 10(-6). PCR and pulsed-field gel electrophoresis analysis confirmed loss of the she::tetAR(B) locus in six independent tetracycline-sensitive isolates. Sample sequencing over a 25-kb region flanking she identified four insertion sequence-like elements, the group II intron-like sequence Sf.IntA, and the 3' end of a second IgA protease-like homolog, sigA, lying 3.6 kb downstream and in an orientation inverted with respect to she. The deletion was mapped to chromosomal NotI fragment A and determined to have a size of 51 kb. Hybridization with flanking probes confirmed that at least 17.7 kb of the 51-kb deletable element was unique to the seven she+ strains investigated, supporting the conclusion that she lay within a large pathogenicity island. The method described in this study, termed island probing, provides a useful tool to further the study of pathogenicity islands in general. Importantly, this approach could also be of value in constructing safer live attenuated bacterial vaccines.
Electrical detection SPR sensor with grating coupled backside illumination (2019)

A current detection surface plasmon resonance (SPR) sensor with an Au grating on an n-Si wafer was proposed. SPR excitation light is illuminated from the backside of the device and diffracted by the grating. Since the diffraction provides matching conditions, SPR can be coupled to the Au/analyte interface. Since the coupled SPR excites free electrons on the Au surface, the SPR can be detected as a current signal by a Schottky barrier diode formed on the Au/n-Si interface. The obtained angular current spectrum showed clear agreement with SPR coupling theory, thereby confirming that the sample on the Au surface can be electrically detected using the proposed sensor.
Multiclass G/M/1 queueing system with self-similar input and nonpreemptive priority (2007)

The Internet domains are tied together by service level agreements which are based on various QoS parameters such as delay, jitter, packet-loss rate, throughput and availability. To offer tighter and more comprehensive service level agreements, accurate modeling of IP traffic and its queuing behavior over the entire network domain is necessary. We present a novel analytical model of a single router which takes into account multiple classes of self-similar traffic based on G=M=1 queueing system with non-preemptive priority. Our long-range dependent traffic model is generated by infinitely many sources governed by a Poisson random measure. We derive exact expressions for the transition probabilities of the embedded Markov chain of G=M=1 by first deriving the interarrival distribution of the incoming traffic. Closed form expressions for the expected waiting time of multiple classes have been derived. The queuing system is evaluated numerically for a typical router to show the effect of the Hurst parameter on several performance measures. Such work forms a basis for modeling the behavior of self-similar traffic accurately through heterogenous network domains, eventually leading to the formation of realistic service level agreements.