gebhart/patrepeval huggingface dataset:
Compact Leakage-Free Support for Integrity and Reliability (2020)

The memory system is vulnerable to a number of security breaches, e.g., an attacker can interfere with program execution by disrupting values stored in memory. Modern Intel® Software Guard Extension (SGX) systems already support integrity trees to detect such malicious behavior. However, in spite of recent innovations, the bandwidth overhead of integrity+replay protection is non-trivial; state-of-the-art solutions like Synergy introduce average slowdowns of 2.3× for memory-intensive benchmarks. Prior work also implements a tree that is shared by multiple applications, thus introducing a potential side channel. In this work, we build on the Synergy and SGX baselines, and introduce three new techniques. First, we isolate each application by implementing a separate integrity tree and metadata cache for each application; this improves metadata cache efficiency and improves performance by 39%, while eliminating the potential side channel. Second, we reduce the footprint of the metadata. Synergy uses a combination of integrity and error correction metadata to provide low-overhead support for both. We share error correction metadata across multiple blocks, thus lowering its footprint (by 16×) while preventing error correction only in rare corner cases. However, we discover that shared error correction metadata, even with caching, does not improve performance. Third, we observe that thanks to its lower footprint, the error correction metadata can be embedded into the integrity tree. This reduces the metadata blocks that must be accessed to support both integrity verification and chipkill reliability. The proposed Isolated Tree with Embedded Shared Parity (ITESP) yields an overall performance improvement of 64%, relative to baseline Synergy.
Bisbenzimidazoles: Anticancer Vacuolar (H+)-ATPase Inhibitors (2019)

Small molecule chemotherapeutic agents such as Imatinib, Gefitinib, and Erlotinib have played a significant role in the treatment of cancer. Although the unprecedented progress has been achieved in cancer treatment with these targeted agents, there is a strong demand for the development of selective and highly efficacious cancer drugs. V-ATPases are emerging as important target for the identification of novel therapeutic agents for cancer. Our screening and drug discovery processes have identified the bisbenzimidazole derivative (RP-15) as a potent anticancer V-ATPase inhibitor. In the present study, bisbenzimidazoles (compound-25, RP-11 and RP-15) have been tested for proton-pump inhibition activity in human hepatoma cell line (Huh7.5). RP-15 displayed comparable proton-pump inhibition activity to the standard Bafilomycin A1. We examined the antiproliferative activity of these analogs in two highly invasive and metastatic inflammatory breast cancer (IBC) cell lines (SUM 149PT and SUM190PT) along with Huh7.5. The compound-25 (SUM190PT: IC 50 = 0.430.11 M) and its structural analog RP-11 (SUM190PT: IC 50 = 0.490.09 M) have shown significant inhibition toward IBC cell lines. Additionally, RP-11 and RP-15 have demonstrated very good cytotoxicity toward the majority of cancer cell lines in the NCI 60 cell line panel.
Performance evaluation of the mobile peer-to-peer service (2004)

The utilization of peer-to-peer (P2P) overlay networks on mobile ad hoc networks (MANET) introduces new services and possibilities such as content based routing and location based services (LBS). A simple layering of both networks is inefficient and does not scale well because the virtual P2P overlay network does not match the frequently changing physical network topology of the MANET. The mobile peer-to-peer (MPP) protocol stack offers a very promising concept by introducing a cross-layer communication channel between the physical network layer and the virtual P2P network layer. This reduces significantly the messaging overhead and increases the search success rate, as we can prove in this work. Therefore, we describe an implementation of the MPP protocol stack in the Network Simulator 2 (ns-2). With this implementation, we prove the significant performance improvements which can be achieved with MPP, to allow P2P networking in mobile ad hoc environments.
Clock Generation and Distribution Using Traveling-Wave Oscillators with Reflection and Regeneration (2006)

We propose a novel traveling-wave oscillator (R <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> TWO) that uses reflection and regeneration of waves on a transmission line to generate multi-GHz square wave signals. We also propose a scalable, low-power, low-skew and low-jitter clock distribution network by tiling the basic R <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> TWO s in a regular fashion. Measurement results of a TSMC 0.18mum CMOS test chip show that it can generate and distribute near full-swing 6.5GHz global clock signals with power saving of more than 75% (compared with a traditional ring oscillator). The measured jitter is less than 0.84ps, and the skew less than 1.3ps
How patient migration in bed affects the sacral soft tissue loading and thereby the risk for a hospital‐acquired pressure injury (2020)

Head-of-bed (HOB) elevation is a common clinical practice in hospitals causing the patient's body to slide down in bed because of gravity. This migration effect likely results in tissue shearing between the sacrum and the support surface, which increases the risk for pressure injuries. StayInPlace (HillRom Inc.) is a commercial migration-reduction technology (MRT) incorporated in intensive care bedframes. Yet, the effects of migration-reduction on tissue shear stresses during HOB elevation are unknown. We analysed relationships between migration and resulting sacral soft tissue stresses by combining motion analysis and three-dimensional finite element modelling of the buttocks. Migration data were collected for 10 subjects, lying supine on two bedframe types with and without MRT, and at HOB elevations of 45°/65°. Migration data were used as displacement boundary conditions for the modelling to calculate tissue stress exposures. Migration values for the conventional bed were 1.75- and 1.6-times greater than those for the migration-reduction bed, for elevations of 45° and 65°, respectively (P < .001). The modelling showed that the farther the migration, the greater the tissue stress exposures. Internal stresses were 1.8-fold greater than respective skin stresses. Our results, based on the novel integrated experimental-computational method, point to clear biomechanical benefits in minimising migration using MRT.
Heparin/Heparan Sulfate N-Sulfamidase from Flavobacterium heparinum (2009)

Sulfated polysaccharides such as heparin and heparan sulfate glycosaminoglycans (HSGAGs) are chemically and structurally heterogeneous biopolymers that that function as key regulators of numerous biological functions. The elucidation of HSGAG fine structure is fundamental to understanding their functional diversity, and this is facilitated by the use of select degrading enzymes of defined substrate specificity. Our previous studies have reported the cloning, characterization, recombinant expression, and structure-function analysis in Escherichia coli of the Flavobacterium heparinum 2-O-sulfatase and 6-O-sulfatase enzymes that cleave O-sulfate groups from specific locations of the HSGAG polymer. Building on these preceding studies, we report here the molecular cloning and recombinant expression in Escherichia coli of an N-sulfamidase, specific for HSGAGs. In addition, we examine the basic enzymology of this enzyme through molecular modeling studies and structure-function analysis of substrate specificity and basic biochemistry. We use the results from these studies to propose a novel mechanism for nitrogen-sulfur bond cleavage by the N-sulfamidase. Taken together, our structural and biochemical studies indicate that N-sulfamidase is a predominantly exolytic enzyme that specifically acts on N-sulfated and 6-O-desulfated glucosamines present as monosaccharides or at the nonreducing end of odd-numbered oligosaccharide substrates. In conjunction with the previously reported specificities for the F. heparinum 2-O-sulfatase, 6-O-sulfatase, and unsaturated glucuronyl hydrolase, we are able to now reconstruct in vitro the defined exolytic sequence for the heparin and heparan sulfate degradation pathway of F. heparinum and apply these enzymes in tandem toward the exo-sequencing of heparin-derived oligosaccharides.
Serial 13C-Based Flux Analysis of an L-Phenylalanine-Producing E. coli Strain Using the Sensor Reactor (2004)

With the aid of the recently developed Sensor reactor system, a series of three subsequent (13)C labeling experiments was performed mirroring the l-phenylalanine (l-Phe) production phase of a recombinant E. coli strain that was cultivated under industry-like conditions in a 300 L bioreactor. On the basis of the data from NMR labeling analysis, three subsequent flux patterns were successfully derived monitoring the l-Phe formation during an observation window from 14 to 23.3 h process time. Linear programming was performed to identify optimal flux patterns for l-Phe formation. Additionally, flux sensitivity analysis was used to identify the most promising metabolic engineering target. As a result, high rates of phosphoenolpyruvate (PEP) to pyruvate (PYR) conversion were identified as the most important reason for deterioration of the l-Phe/glucose yield from 20 to finally 11 mol %. Considering the characteristics of the enzyme kinetics involved, the working hypothesis was formulated that phosphoenolpyruvate synthase activity was increasingly hampered by rising oxaloacetate and 2-oxoglutarate concentrations, while at the same time pyruvate kinase activity arose due to activation by fructose 1,6-diphosphate. Hence, pps overexpression should be performed to optimize the existing production strain.
Dynamical Electrical Complexity Is Reduced during Neuronal Differentiation in Autism Spectrum Disorder (2019)

Neuronal activity can be modeled as a nonlinear dynamical system to yield measures of neuronal state and dysfunction. The electrical recordings of stem cell-derived neurons from individuals with autism spectrum disorder (ASD) and controls were analyzed using minimum embedding dimension (MED) analysis to characterize their dynamical complexity. MED analysis revealed a significant reduction in dynamical complexity in ASD neurons during differentiation, which was correlated to bursting and spike interval measures. MED was associated with clinical endpoints, such as nonverbal intelligence, and was correlated with 53 differentially expressed genes, which were overrepresented with ASD risk genes related to neurodevelopment, cell morphology, and cell migration. Spatiotemporal analysis also showed a prenatal temporal enrichment in cortical and deep brain structures. Together, we present dynamical analysis as a paradigm that can be used to distinguish disease-associated cellular electrophysiological and transcriptional signatures, while taking into account patient variability in neuropsychiatric disorders.
Distributed stochastic optimization with gradient tracking over strongly-connected networks (2019)

In this paper, we study distributed stochastic optimization to minimize a sum of smooth and strongly-convex local cost functions over a network of agents, communicating over a strongly-connected graph. Assuming that each agent has access to a stochastic first-order oracle ($\mathcal{SFO}$), we propose a novel distributed method, called $\mathcal{S}$-$\mathcal{AB}$, where each agent uses an auxiliary variable to asymptotically track the gradient of the global cost in expectation. The $\mathcal{S}$-$\mathcal{AB}$ algorithm employs row- and column-stochastic weights simultaneously to ensure both consensus and optimality. Since doubly-stochastic weights are not used, $\mathcal{S}$-$\mathcal{AB}$ is applicable to arbitrary strongly-connected graphs. We show that under a sufficiently small constant step-size, $\mathcal{S}$-$\mathcal{AB}$ converges linearly (in expected mean-square sense) to a neighborhood of the global minimizer. We present numerical simulations based on real-world data sets to illustrate the theoretical results.
Optical Fiber-Tip Monolithic Silicon Pressure Sensors (2019)

Fiber-tip interferometric pressure sensors offer high resolution over broad frequency and dynamic ranges with minimal device footprint. We fabricate a 100 μm wide monolithic silicon pressure-sensing-diaphragm and reference cavity as a unit on the wafer-scale, simplifying the packaging. The 1.0 μm thick diaphragm and 1 μm thick cavity form a pressure-sensitive optical resonator which we interrogate over an optical fiber with a polished turning mirror. Our sensors function at pressures up to 3.5 atm, and have tunable dynamic ranges and sensitivities through choice of operational wavelength. We demonstrate 0.002 atm resolution over a 0.9 atm dynamic range using 1544 nm light for atmospheric pressure testing. We introduce an optical model for fiber-tip Fabry-Pérot sensors with diffraction-loss and show good agreement with experimental results. We test the devices in a wind-tunnel environment and demonstrate broad-bandwidth operation and resolution competitive with standard microelectromechanical sensors.
Optimal charging of electric vehicles taking distribution network constraints into account (2017)

The increasing uptake of electric vehicles suggests that vehicle charging will have a significant impact on the electricity grid. Finding ways to shift this charging to off-peak periods has been recognized as a key challenge for integration of electric vehicles into the electricity grid on a large scale. In this paper, electric vehicle charging is formulated as a receding horizon optimization problem that takes into account the present and anticipated constraints of the distribution network over a finite charging horizon. The constraint set includes transformer and line limitations, phase unbalance, and voltage stability within the network. By using a linear approximation of voltage drop within the network, the problem solution may be computed repeatedly in near real time, and thereby take into account the dynamic nature of changing demand and vehicle arrival and departure. It is shown that this linear approximation of the network constraints is quick to compute, while still ensuring that network constraints are respected. The approach is demonstrated on a validated model of a real network via simulations that use real vehicle travel profiles and real demand data. Using the optimal charging method, high percentages of vehicle uptake can be sustained in existing networks without requiring any further network upgrades, leading to more efficient use of existing assets and savings for the consumer.
Blocking the FAM19A5-LRRC4B complex enhances neurite growth and synapse assembly. (2023)

Abstract Disruption in dynamic balance of synapse build-and-removal process is a major cause of neurological diseases, although the mechanisms underlying the brain fine-tunes and balances this process remain poorly understood. Here, we show that FAM19A5 binds to the postsynaptic adhesion molecule LRRC4B via the FAM19A5 binding (FB) domain, suppressing the interaction of LRRC4B with a presynaptic adhesion molecule PTPRF. Decoys with the FB domain bind to FAM19A5 and redirect it away from the FAM19A5-LRRC4B complex, promoting neurite growth and synapse formation of neurons. The anti-FAM19A5 monoclonal antibody NS101 breaks apart the FAM19A5-LRRC4B complex and enables the transfer of FAM19A5 from the brain into the bloodstream, leading to the restoration of synaptic integrity and improve cognitive function in mouse models of Alzheimer’s disease. Together, our findings suggest that blocking the complex with NS101 may offer therapeutic strategy for treating neurodegenerative diseases requiring regeneration of neurites and formation of new synapses.
Dynamics of exciton diffusion in poly(p-phenylene vinylene)/fullerene heterostructures (2005)

The exciton diffusion process in a poly($p$-phenylene vinylene)- (PPV-)based derivative is investigated using time-resolved photoluminescence in conjugated polymer/fullerene heterostructures. The decay of the luminescence in the polymer/fullerene heterostructures is governed by exciton diffusion and subsequent dissociation at the polymer/fullerene interface. The decay curves of polymer layers with varying thickness are consistently modeled using an exciton diffusion constant of $3\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}4}\phantom{\rule{0.3em}{0ex}}{\mathrm{cm}}^{2}∕\mathrm{s}$. The resulting exciton migration radius amounts to $6\phantom{\rule{0.3em}{0ex}}\mathrm{nm}$, which is a measure for the active part of the PPV/fullerene heterojunction for photovoltaic applications.
PAIR Technology: Exon-Specific RNA-Binding Protein Isolation in Live Cells (2010)

RNA-binding proteins (RBPs) are fundamental regulatory proteins for all forms of transcriptional and posttranscriptional control of gene expression. However, isolating RBPs is technically challenging for investigators. Currently, the most widely used techniques to isolate RBPs are in vitro biochemical approaches. Although these approaches have been useful, they have several limitations. One key limitation to using in vitro biochemical approaches is that RBP-RNA interactions are isolated under nonbiological conditions. Here we review a novel experimental approach to identify RBPs called peptide nucleic acid (PNA)-assisted identification of RBPs (PAIR) technology (Zielinski et al., Proc Natl Acad Sci USA 103:1557-1562, 2006). This technology has two significant advantages over traditional approaches. (1) It overcomes the in vitro limitation of biochemical approaches by allowing investigators to isolate RBP-RNA interactions under in vivo conditions. (2) This technology is highly mRNA specific; it isolates RBPs in an exon-specific manner. By selectively targeting alternatively spliced exons with PAIR technology, investigators can isolate splice variant-specific and mRNA region-specific (5-UTR and 3-UTR) RBP complexes for any mRNA of interest.
Ultrabroadband phase-matched optical parametric generation in the ultraviolet by use of guided waves (1997)

We present what is believed to be the first experimental demonstration of guided-wave phase-matched frequency mixing and harmonic conversion in gases. Broad-bandwidth ultrafast pulses, tunable around 270 nm, were generated from an ultrafast Ti:sapphire amplifier system using 2? + 2? - ? parametric wave mixing in a capillary waveguide. We achieved nonresonant phase matching by coupling both the fundamental and the second-harmonic light into the lowest-order mode. The output 3? pulses have an energy of >4muJ at a 1-kHz repetition rate. Simple extensions of this method can generate higher-energy 10-20-fs pulses tunable throughout the vacuum ultraviolet.
Real-time In Vivo Tissue Raman Spectroscopy for Early Cancer Detection (2016)

A platform technology for real-time in vivo tissue Raman spectroscopy was developed that takes 1-2 seconds to obtain a spectrum. The system was tested over 900 skin patients and 80 lung patients, achieved high diagnostic sensitivity (90%) and good specificities (73%, 65%) for skin cancer and lung cancer detection.
Next-Generation Human Cerebral Organoids as Powerful Tools To Advance NeuroHIV Research (2021)

Long-term effective use of antiretroviral therapy (ART) among people with HIV (PWH) has significantly reduced the burden of disease, yet a cure for HIV has not been universally achieved, likely due to the persistence of an HIV reservoir. The central nervous system (CNS) is an understudied HIV sanctuary. Importantly, due to viral persistence in the brain, cognitive disturbances persist to various degrees at high rates in PWH despite suppressive ART. Given the complexity and accessibility of the CNS compartment and that it is a physiologically and anatomically unique immune site, human studies to reveal molecular mechanisms of viral entry, reservoir establishment, and the cellular and structural interactions leading to viral persistence and brain injury to advance a cure and either prevent or limit cognitive impairments in PWH remain challenging. Recent advances in human brain organoids show that they can mimic the intercellular dynamics of the human brain and may recapitulate many of the events involved in HIV infection of the brain (neuroHIV). Human brain organoids can be produced, spontaneously or with addition of growth factors and at immature or mature states, and have become stronger models to study neurovirulent viral infections of the CNS. While organoids provide opportunities to study neuroHIV, obstacles such as the need to incorporate microglia need to be overcome to fully utilize this model. Here, we review the current achievements in brain organoid biology and their relevance to neuroHIV research efforts.
Conductance modulation techniques in switched-capacitor DC-DC converter for maximum-efficiency tracking and ripple mitigation in 22nm Tri-gate CMOS (2014)

Active conduction modulation techniques are demonstrated in a fully integrated multi-ratio switched-capacitor voltage regulator with hysteretic control, implemented in 22nm tri-gate CMOS with high-density MIM capacitor. We present (i) an adaptive switching frequency and switch-size scaling scheme for maximum efficiency tracking across a wide range voltages and currents, governed by a frequency-based control law that is experimentally validated across multiple dies and temperatures, and (ii) a simple active ripple mitigation technique to modulate gate drive of select MOSFET switches effectively in all conversion modes. Efficiency boosts upto 15% at light loads are measured under light load conditions. Load-independent output ripple of <50mV is achieved, enabling fewer interleaving. Testchip implementations and measurements demonstrate ease of integration in SoC designs, power efficiency benefits and EMI/RFI improvements.
Optimal Sampling Strategies for Minimum Latency Routing with Imperfect Link State (2012)

Abstract—Since dynamic wireless networks evolve over time, optimal routing computations need to be performed frequently on time-varying network topologies. However, it is often infeasible or expensive to gather the current state of links for the entire network all the time. We provide a thorough analytical charac-terization of the effect of various link-state sampling strategies operating under a limited sampling budget on the performance of the minimum-latency routing policy in a special class of dynamic networks. We show that for a two-state Markov link-dynamics model parameterized by probabilities p, q, if links are more likely to turn on than off at each time instant (p&amp;gt; q), a “depth-first” sampling strategy is optimal, whereas a “breadth-first ” sampling strategy is optimal if links are more likely to turn off than on (p &amp;lt; q)—under the Cut Through (CuT) latency model, i.e., when the packet-forwarding latency is negligible compared to the time scale of the link dynamics. We precisely characterize the optimal-latency spatial-sampling schedules for one-shot interrogation. We also present numerical simulation results on comparing various spatio-temporal sampling schedules under an overall sampling rate constraint, and initial results on comparisons of optimal schedules under a Store-and-Advance (SoA) packet-forwarding latency model. I.
ChemInform Abstract: Synthesis of Methyl (.+‐.)‐2,3‐O‐Isopropylideneglycerate by Electrochemical Oxidation of (.+‐.)‐1,2‐O‐Isopropylideneglycerol. (1991)

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.