gebhart/patrepeval huggingface dataset:
Full-duplex spectrum sensing in cognitive radios using optical self-interference cancellation (2015)

We propose and experimentally demonstrate an optical self-interference cancellation system to realize full-duplex spectrum sensing in cognitive radios. The optical system is an analog radio-frequency front-end module, which cancels in-band self-interference, enabling a radio to simultaneously transmit and receive signals. The system achieves 83 dB of narrowband interference cancellation, and 60 dB of cancellation of a 50 MHz frequency-modulated signal. The center frequency of the optical canceler is freely tunable across the radio frequency spectrum, limited only by the bandwidth of the photodetector and the electro-optic modulators to 10 GHz. The system is modulation-format independent and requires only one piece of hardware to operate across a wide radio-frequency bandwidth. By reducing self-interference to acceptably low powers, a cognitive radio can continuously sense its radio-frequency environment to detect the presence of a licensed user or scan for spectrum white spaces even while transmitting simultaneously.
Population of 224 realistic human subject-based computational breast phantoms (2015)

This work provides a new population of 224 breast phantoms based on in vivo bCT data for imaging research. Compared to previous studies based on only a few prototype cases, this dataset provides a rich source of new cases spanning a wide range of breast types, volumes, densities, and parenchymal patterns.
Iterative helical cone-beam CT reconstruction using graphics hardware: a simulation study (2011)

This paper presents a simulation study on iterative reconstruction methods for helical cone-beam CT using graphics hardware. While analytic methods have been proposed to achieve an exact reconstruction for helical cone-beam CT, these methods may not perform well for projection noise and imaging geometry variations, especially for spiral variations. Iterative methods such as SART are advantageous in this aspect. Since SART is computationally intense, graphics hardware (GPU) may be utilized to handle the computations and increase the efficiency of SART. GPU SART reconstruction results are presented for spiral cone-beam CT, and these results are compared with the Katsevich reconstructions in presence of projection noise and spiral variations. The comparison shows that SART is accurate, efficient, and more robust to projection noise and spiral variations than the Katsevich method.
Method of an enhanced self-amplified spontaneous emission for x-ray free electron lasers (2005)

We describe a technique by which an energy modulation of electrons via interaction with a laser pulse in a wiggler magnet is used for a significant increase of the electron peak current prior to entering a long self-amplified spontaneous emission (SASE) free electron laser undulator. This results in a reduction of the gain length for the SASE process and a modification of the structure of the output x-ray radiation. It also temporally links the output x-ray pulse to the initial laser pulse, thus providing an opportunity for accurate synchronization between the laser pump pulse and x-ray probe pulse for pump-probe experiments.
The Protein Coded by a Short Open Reading Frame, Not by the Annotated Coding Sequence, Is the Main Gene Product of the Dual-Coding Gene MIEF1 (2018)

Proteogenomics and ribosome profiling concurrently show that genes may code for both a large and one or more small proteins translated from annotated coding sequences (CDSs) and unannotated alternative open reading frames (named alternative ORFs or altORFs), respectively, but the stoichiometry between large and small proteins translated from a same gene is unknown. <i>MIEF1</i>, a gene recently identified as a dual-coding gene, harbors a CDS and a newly annotated and actively translated altORF located in the 5'UTR. Here, we use absolute quantification with stable isotope-labeled peptides and parallel reaction monitoring to determine levels of both proteins in two human cells lines and in human colon. We report that the main <i>MIEF1</i> translational product is not the canonical 463 amino acid MiD51 protein but the small 70 amino acid alternative MiD51 protein (altMiD51). These results demonstrate the inadequacy of the single CDS concept and provide a strong argument for incorporating altORFs and small proteins in functional annotations.
Power Allocation for Cognitive Radio Networks under Channel Uncertainty (2011)

Cognitive radio (CR) networks can re-use the RF spectrum licensed to the primary user (PU) network by carefully controlling the interference to the PUs. However, due to lack of explicit support from the PU system, CR sensing algorithms often face difficulty in acquiring CR-to-PU channels accurately. Moreover, the sensing algorithms cannot detect silent PU receivers, which nevertheless have to be protected. In order to achieve aggressive spectrum re-use even in such challenging scenarios, a CR power control problem with probabilistic interference constraints is formulated. Both log-normal shadowing and small-scale fading uncertainties are taken into account through suitable approximations. In particular, a weighted sum-rate maximization problem is considered, whose Karush-Kuhn-Tucker points are obtained via sequential geometric programming. Numerical tests verify the performance of our novel approach.
ChemInform Abstract: Dipodazine, a Diketopiperazine from Penicillium dipodomyis. (1999)

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.
Preparation and Characterization of Nano‐Crystalline LiNi <sub>0.5</sub> Mn <sub>1.5</sub> O <sub>4</sub> Cathode Material by the Soft Combustion Reaction Method (2009)

This chapter discusses Nano-crystalline LiNi0.5Mn1.5O4 with a unique powder characterization has been successfully synthesized by a soft combustion reaction method, using lithium nitrate, manganese nitrate, and nickel nitrate as the starting materials, and no organic materials being introduced in the whole process. The LiNi0.5Mn1.5O4 powders synthesized by the soft combustion reaction method are investigated by differential thermal analysis and thermogravime-try, X-ray diffractometer, and transmission electron microscopy. The resultant product was a pure phase of LiNi0.5Mn1.5O4 without any other impurities. Electrochemical measurements are also performed. The electrochemical properties of the as-prepared LiNi0.5Mn1.5O4 are initially characterized in the voltage range of 3.5-4.9 V.
Sources of stress in the competition environment: comparison of elite and non-elite athletes (2011)

Changes in the temporary hearing threshold ( TTS2 ) and heart rate (HR) were examined in subjects exposed to stable noise, whole body vibration and dynamic muscular work at a dry-bulb temperature of 30 degrees C. The exposure combinations consisted of three categories of dynamic muscular work with varying loads ( 2W , 4W , 8W ), of two categories of noise and of three categories of vibration. The noise categories were: (1) no noise, and (2) stable, broadband (bandwidth 0.2-16.0 kHz) A-weighted noise with an intensity of 90 dB. The vibration categories were: (1) no vibration, (2) sinusoidal whole body vibration (Z-axis) with a frequency of 5 Hz, and (3) stochastic broadband (bandwidth 2.8-11.2 Hz) whole body vibration. A single test consisted of a control period of 30 min, three consecutive exposure periods of 16 min, each followed by a 4-min post-exposure interval and a recovery period of 15 min. The results of the variance analyses indicated that noise had the most notable effect on the TTS2 values at the hearing frequencies of both 4 and 6 kHz. Of the paired combinations, noise plus vibration and noise plus dynamic muscular work caused the most obvious combined effects. The combined effect of all three factors (noise, vibration and work) on the TTS2 values after three consecutive exposure periods was significant at the 2.5% level at the 4 kHz hearing frequency and at the 5% level at the 6 kHz hearing frequency. The added effect of vibration on enhanced TTS2 values was particularly clear when the vibration was stochastic and when the subjects had a low ( 2W ) working efficiency. Increasing the working efficiency, on the other hand, seemed to retard increases in the hearing threshold. Thus TTS2 values seemed to reflect the changes in HR values. It is as if the low rate of cardiovascular activity during light dynamic muscular work had enabled the manifestation of the cardiovascular effects of noise and vibration; during strenuous dynamic muscular work, however, the high rate of cardiovascular activity aimed in some way at compensating for the effects of noise and vibration on blood circulation.
Drug-induced mitochondrial dysfunction in cardiac and skeletal muscle injury (2008)

Mitochondrial function is important in the context of muscle survival, hence, the requirement to identify novel mitochondrial targets and develop new therapies to counteract chemical-induced degeneration of mitochondrial function and muscle performance.
A method for the selective isolation ofMyxococcus directly from soil (1996)

A new method is described for the selective isolation of species of Myxococcus directly from soil by dilution plating. The method involves suppression of competing microorganisms with antibiotics combined with air drying and wet heat treatment of soils. Fungi were eliminated by supplementing the plating medium with cycloheximide and nystatin. Non-sporulating bacteria were controlled by air drying soils and then heating aqueous soil dilutions for 10 min at 56 degrees C. The predominant sporulating bacteria in soil, Streptomyces and Bacillus, were suppressed by adding either tiacumicin B, ristocetin or vancomycin to the medium. Swarming of Myxococcus colonies was controlled with a casein digest-yeast extract plating medium (CY-C10 agar). Ultrasound treatment of soil suspensions gave the highest number of Myxococcus colonies in the soils studied, but these cultures could be recovered without ultrasound. Strains of Myxococcus fulvus, M. xanthus, M. coralloides, M. stipitatus and M. virescens were isolated from soil using this technique. Soils examined yielded one or two Myxococcus species per sample.
Visualization of looping involving the immunoglobulin heavy-chain locus in developing B cells (2005)

The immunoglobulin heavy-chain (IgH) locus undergoes large-scale contraction in B cells poised to undergo IgH V(D)J recombination. We considered the possibility that looping of distinct IgH V regions plays a role in promoting long-range interactions. Here, we simultaneously visualize three subregions of the IgH locus, using three-dimensional fluorescence in situ hybridization. Looping within the IgH locus was observed in both B- and T-lineage cells. However, monoallelic looping of IgH V regions into close proximity of the IgH DJ cluster was detected in developing B cells with significantly higher frequency when compared with hematopoietic progenitor or CD8+ T-lineage cells. Looping of a subset of IgH V regions, albeit at lower frequency, was also observed in RAG-deficient pro-B cells. Based on these observations, we propose that Ig loci are repositioned by a looping mechanism prior to IgH V(D)J rearrangement to facilitate the joining of Ig variable, diversity, and joining segments.
Identification of compositionally distinct regions in genomes using the centroid method (2007)

Supplementary data are available at Bioinformatics online.
2085 Strain encoded magnetic resonance imaging (SENC) assessment of regional ventricular function in pulmonary arterial hypertension – initial results (2008)

Introduction Evaluation of right ventricular (RV) function is an important prognostic factor in many cardiac and/or pulmonary conditions. Pulmonary arterial hypertension (PAH) is a major cause of RV dysfunction and failure, which in turn affects left ventricular performance due to ventricular interdependence. Cardiac MRI is a reproducible three dimensional tomographic tool providing accurate measurements of global right ventricular function. For the RV, measuring regional strain using MRI (e.g., using tagging) is limited by thin wall. Strain encoded MRI (SENC), however, enables the quantification of RV strain (1) in the longitudinal direction (Ell), which is the main contributor to RV contractile function. On the other hand, fast strain encoded MRI (fSENC) allows for single heartbeat, non breath hold, acquisitions; thus providing an alternative to patients experiencing difficulty in breath holding (2).
A nucleolar targeting signal in PML-I addresses PML to nucleolar caps in stressed or senescent cells (2007)

The promyelocytic leukemia (PML) tumour suppressor is the organiser of PML nuclear bodies, which are domains the precise functions of which are still disputed. We show that upon several types of stress, endogenous PML proteins form nucleolar caps and eventually engulf nucleolar components. Only two specific PML splice variants (PML-I and PML-IV) are efficiently targeted to the nucleolus and the abundant PML-I isoform is required for the targeting of endogenous PML proteins to this organelle. We identified a nucleolar targeting domain within the evolutionarily conserved C-terminus of PML-I. This domain contains a predicted exonuclease III fold essential for the targeting of the PML-I C-terminus to nucleolar fibrillar centres. Furthermore, spontaneous or oncogene retrieval-induced senescence is associated with the formation of very large PML nuclear bodies that initially contain nucleolar components. Later, poly-ubiquitin conjugates are found on the outer shell or within most of these senescence-associated PML bodies. Thus, unexpectedly, the scarcely studied PML-I isoform links PML bodies, nucleolus, senescence and proteolysis.
Observation of Spin Dynamics in MAMMOS media by Femtosecond Laser (2004)

This paper describes results of a time-resolved study of the ultrafast magnetic response of Gd23.1Fe71.9Co5.0 MAMMOS structures under conditions near actual read temperature. An all-optical pump and probe method was used, in which an intense (pump) light beam excited a medium due to ultrafast laser heating and a less intense (probe) beam monitored this photo-excited state through the magnetooptical Kerr effect. Our experiment clearly demonstrates that the photo-excitation effectively excites coherent spin waves in the magnetic material. Precession frequencies of several GHz and relaxation times in the nanosecond range were observed.
Statistical timing analysis under spatial correlations (2005)

Process variations are of increasing concern in today's technologies, and they can significantly affect circuit performance. An efficient statistical timing analysis algorithm that predicts the probability distribution of the circuit delay considering both inter-die and intra-die variations, while accounting for the effects of spatial correlations of intra-die parameter variations, is presented. The procedure uses a first-order Taylor series expansion to approximate the gate and interconnect delays. Next, principal component analysis (PCA) techniques are employed to transform the set of correlated parameters into an uncorrelated set. The statistical timing computation is then easily performed with a program evaluation and review technique (PERT)-like circuit graph traversal. The run time of this algorithm is linear in the number of gates and interconnects, as well as the number of varying parameters and grid partitions that are used to model spatial correlations. The accuracy of the method is verified with Monte Carlo (MC) simulation. On average, for the 100 nm technology, the errors of mean and standard deviation (SD) values computed by the proposed method are 1.06% and -4.34%, respectively, and the errors of predicting the 99% and 1% confidence point are -2.46% and -0.99%, respectively. A testcase with about 17 800 gates was solved in about 500 s, with high accuracy as compared to an MC simulation that required more than 15 h.
PCSPOOF: Compromising the Safety of Time-Triggered Ethernet (2023)

Designers are increasingly using mixed-criticality networks in embedded systems to reduce size, weight, power, and cost. Perhaps the most successful of these technologies is Time-Triggered Ethernet (TTE), which lets critical time-triggered (TT) traffic and non-critical best-effort (BE) traffic share the same switches and cabling. A key aspect of TTE is that the TT part of the system is isolated from the BE part, and thus BE devices have no way to disrupt the operation of the TTE devices. This isolation allows designers to: (1) use untrusted, but low cost, BE hardware, (2) lower BE security requirements, and (3) ignore BE devices during safety reviews and certification procedures.We present PCSPOOF, the first attack to break TTE’s isolation guarantees. PCSPOOF is based on two key observations. First, it is possible for a BE device to infer private information about the TT part of the network that can be used to craft malicious synchronization messages. Second, by injecting electrical noise into a TTE switch over an Ethernet cable, a BE device can trick the switch into sending these malicious synchronization messages to other TTE devices. Our evaluation shows that successful attacks are possible in seconds, and that each successful attack can cause TTE devices to lose synchronization for up to a second and drop tens of TT messages — both of which can result in the failure of critical systems like aircraft or automobiles. We also show that, in a simulated spaceflight mission, PCSPOOF causes uncontrolled maneuvers that threaten safety and mission success. We disclosed PCSPOOF to aerospace companies using TTE, and several are implementing mitigations from this paper.
Silicon nanowire pirani sensor fabricated using FIB lithography (2013)

As radio frequency microelectromechanical systems (RF-MEMS) mature as a manufacturable technology, packaging of the devices becomes increasingly important. Devices such as aluminum nitride (AlN) RF-filters require packaging which is either hermetic or under vacuum to protect the devices [1]. It then becomes critical to have a measurement of pressure inside the packaged chamber. Typically for this need, Pirani gauges are fabricated using poly silicon or metal patterned on suspended membranes [2]. These type of devices increase die area, add complexity to fabrication flows, and difficulty when attempting to suspend the membranes. In this work we fabricate and characterize a suspended silicon nanowire for use as Pirani gauge by utilizing Ga lithography and plasma reactive ion etching for defining the nanowire geometry and simultaneously releasing the wire. This method benefits from the high surface to volume ratio inherent in the nano regime, decreased thermal conductivity of amorphous silicon (from implantation) and increased electrical conductivity of Ga doping to reduce device area and fabrication complexity of a Pirani gauge.
Generation of Human Ventral Midbrain Organoids Derived from Pluripotent Stem Cells (2022)

Parkinson's disease (PD) is the second most common neurodegenerative disorder worldwide and is caused by the degeneration and loss of dopamine (DA) neurons in the ventral midbrain (VM). The focal and progressive degeneration of DA neurons in the VM makes PD a particularly attractive target for cell-based therapies. Human pluripotent stem cells (hPSCs) offer unprecedented opportunities to model the development and functional properties of human DA neurons in a dish. The use of human in vitro models based on hPSCs has empowered studies of VM development and provided access to neurons expressing a particular disease-specific phenotype. Currently, hPSC differentiation is most routinely carried out in monolayer cultures, which do not properly recapitulate cell-cell interactions and the structural complexity of the brain. Moreover, 2D cultures are challenging to maintain long term, as the cells tend to detach from the plate and lose their functional characteristics. This precludes the possibility of mimicking later phases of DA neurogenesis and recreating the complexity of functional neural circuitries. Here, we describe protocols showing how to maintain hPSCs in an undifferentiated state and how to then drive these hPSCs into 3D regionalized VM organoids. After long-term culture, these VM organoids exhibit mature and post-mitotic molecular features, including neuromelanin pigments similar to those released in primate VMs. We also report a protocol describing how to efficiently perform immunohistochemistry and how to detect neuromelanin-containing DA neurons in VM organoids. Together, these protocols provide a 3D in vitro platform that can be used to better understand the molecular mechanisms underlying DA neuron function and disease and may serve as a powerful tool for designing more targeted disease-modifying therapies. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Human pluripotent stem cell culture Basic Protocol 2: hPS cell differentiation for the generation of human ventral midbrain organoids Basic Protocol 3: Characterization of ventral midbrain organoids.
Intratumoral oxygen gradients mediate sarcoma cell invasion (2016)

Significance Previous works demonstrated the role of hypoxia in tumor development and metastasis. However, the understanding how oxygen (O 2 ) gradients regulate early stages of tumor metastasis is lacking. Leveraging our O 2 -controlling hydrogel, we generated a 3D in vitro model that enables us to analyze cancer cell responses to O 2 gradients and small-molecule inhibitors. Using this approach, we present a previously unidentified concept in which O 2 acts as a 3D physicotactic agent during sarcoma tumor invasion, findings that are important for the understanding of the metastatic process. Through this concept, we also establish the 3D in vitro model as a platform for testing therapeutic targets and interventions for the treatment of sarcoma and potentially other cancers.
Biological effect of radiotherapy on cancer cells (2019)

Radiation therapy is a mainstay for curative treatment of many types of tumours. The cure rate of radiation therapy depends on its ability to induce non-repairable DNA damage leading to cellular death or loss of proliferative capacity. In addition to clinical factors, efficacy of radiation therapy has been explained by the radiobiological concept of 4R parameters summarized by Rodney Withers in 1975, which include Repair of DNA damage, Repopulation, Redistribution of tumour cells in the cell cycle, and Reoxygenation. This chapter reviews the direct and indirect effects of irradiation on cancer cells, mechanisms of DNA repair and radiation-induced cell death, and also discusses implementation of the cancer stem cell model for the radiobiological concept of tumour radioresistance.
Influence of Molecular Weight on the Performance of Organic Solar Cells Based on a Fluorene Derivative (2010)

Abstract The performance of organic photovoltaic (OPV) bulk‐heterojunction blends comprising a liquid‐crystalline fluorene derivative and a small‐molecular fullerene is found to increase asymptotically with the degree of polymerization of the former. Similar to various thermodynamic transition temperatures as well as the light absorbance of the fluorene moiety, the photocurrent extracted from OPV devices is found to strongly vary with increasing oligomer size up to a number average molecular weight, M n ≈ 10 kg mol −1 , but is rendered less chain‐length dependent for higher M n as the fluorene derivative gradually adopts polymeric behavior.