gebhart/patrepeval huggingface dataset:
Experimental evaluation of behavior-based failure-detection schemes in real-time communication networks (1999)

Effective detection of failures is essential for reliable communication services. Traditionally, non-real-time computer networks have relied on behavior-based techniques for detecting communication failures. That is, each node uses heartbeats to detect the failure of its neighbors and the end-to-end transport protocol (e.g., TCP) achieves reliable communication by acknowledgment/retransmission. Recently, there has been a growing demand for reliable "real-time" communication, but little research has been done on the failure detection problem. In this paper, we present two behavior-based failure-detection schemes-neighbor detection and end-to-end detection-for reliable real-time communication services and experimentally evaluate their effectiveness. Specifically, we measure and analyze the coverage and latency of these detection schemes through fault-injection experiments. The experimental results have shown that nearly all failures can be detected very quickly by the neighbor detection scheme, while the end-to-end detection scheme uncovers the remaining failures with larger detection latencies.
Bits to BNNs: Reconstructing FPGA ML-IP with Joint Bitstream and Side-Channel Analysis (2023)

Energy-efficient hardware acceleration platforms for edge deployment of artificial intelligence (AI) and machine learning (ML) applications has been an ongoing research endeavor. Many efforts have focused on optimizing the algorithms and compute structures for use in resource-constrained hardware such as field-programmable gate arrays (FPGAs). Indeed, the difficult nature of crafting the best model makes the ML model itself a valuable intellectual property (IP) asset. This can be problematic, as the IP can now be exposed to an attacker through physical interfaces, enabling threats from side-channel analysis (SCA) attacks. One of the more devastating attacks is the model extraction attack, which threatens piracy and cloning of the valuable IP. While the problem of SCA-based model extraction on FPGA-deployed neural networks has been well-studied, it does not capture the full picture of what vulnerabilities may be present in those platforms. In this paper, we demonstrate how bitstream analysis can be used to obtain neural network parameters and connectivity information from block RAMs (BRAMs). We leverage the knowledge gleaned from the bitstream to mount a power SCA attack to further refine the network reconstruction effort. This is the first method that has approached the problem of ML-IP theft from the angle of FPGA bitstream analysis and suggests that further work is needed to improve security assurance for edge intelligence.
Site- and allele-specific polycomb dysregulation in T-cell leukaemia (2015)

T-cell acute lymphoblastic leukaemias (T-ALL) are aggressive malignant proliferations characterized by high relapse rates and great genetic heterogeneity. TAL1 is amongst the most frequently deregulated oncogenes. Yet, over half of the TAL1(+) cases lack TAL1 lesions, suggesting unrecognized (epi)genetic deregulation mechanisms. Here we show that TAL1 is normally silenced in the T-cell lineage, and that the polycomb H3K27me3-repressive mark is focally diminished in TAL1(+) T-ALLs. Sequencing reveals that >20% of monoallelic TAL1(+) patients without previously known alterations display microinsertions or RAG1/2-mediated episomal reintegration in a single site 5' to TAL1. Using 'allelic-ChIP' and CrispR assays, we demonstrate that such insertions induce a selective switch from H3K27me3 to H3K27ac at the inserted but not the germline allele. We also show that, despite a considerable mechanistic diversity, the mode of oncogenic TAL1 activation, rather than expression levels, impact on clinical outcome. Altogether, these studies establish site-specific epigenetic desilencing as a mechanism of oncogenic activation.
Vesicular Transport Systems in Fungi (2011)

Canonical and unconventional mechanisms of secretion in many eukaryotic cells are relatively well known. In contrast to the situation in animal cells, mechanisms of secretion in fungi must include the capacity for trans-cell wall passage of macromolecules to the extracellular space. Although these mechanisms remain somewhat elusive, several studies in recent years have suggested that vesicular transport is required for trans-cell wall secretion of large molecules. Several fungal molecules, including proteins, lipids, polysaccharides and pigments, are released to the extracellular space in vesicles. In pathogenic fungi, a number of these vesicular components are associated with fungal virulence. Indeed, extracellular vesicles produced by fungi can interfere with the immunomodulatory activity of host cells. Fungal vesicles share many functional aspects with mammalian exosomes and extracellular vesicles produced by bacteria, plants and protozoa, but their cellular origin remains unknown. Here, we discuss the involvement of vesicular transport systems in fungal physiology and pathogenesis, making parallels with the mammalian, bacterial, protozoan and plant cell literature.
Flexible one diode–one resistor resistive switching memory arrays on plastic substrates (2014)

Flexible one diode–one resistor resistive random access memory (RRAM) with 8 × 8 arrays composed of high-performance silicon diodes and a resistive change material for fully functional flexible memory operation.
Demethyl Mutactimycins, New Anthracycline Antibiotics from Nocardia and Streptomyces Strains. (1998)

New anthracycline antibiotics 3'-O-demethyl mutactimycin (3) and 4-O,3'-O-didemethyl mutactimycin (4) were isolated from two actinomycetes strains, Nocardia transvalensis and Streptomyces sp. GW 60/1571. The chemical structures were elucidated by mass spectrometry and NMR spectroscopy. Antibiotic 3 displayed moderate antimicrobial activity against Gram-positive bacteria and cytotoxicity against P388, L1210 and HeLa tumor cells (IC50; 9.6, >25 and 20 microg/ml, respectively).
<title>Aperiodic microscreen design using DBS and training</title> (1998)

With the advent of high resolution (1200+ dpi) desktop printers, the use of conventional 128 by 128 screens can produce a distinctive periodicity in the printed images. A new method for design of multiple 32 by 32 screens using direct binary search and training is proposed. The screens are seamless with each other; and a small number of these screens are randomly tiled over the entire support of the continuous- tone image. These are then used to threshold the image to create the halftone image. Due to the random tiling of the screens, the resulting halftones do not have any periodicity in them. The resulting screens also have lower memory requirements than 128 by 128 screens. Experimental results also show that the exact order of the screens is not crucial to the quality of the final halftone. Therefore, no additional information about the ordering of the multiple screens needs to be stored.
Distinct roles for talin-1 and kindlin-3 in LFA-1 extension and affinity regulation (2012)

In inflammation, neutrophils and other leukocytes roll along the microvascular endothelium before arresting and transmigrating into inflamed tissues. Arrest requires conformational activation of the integrin lymphocyte function-associated antigen-1 (LFA-1). Mutations of the FERMT3 gene encoding kindlin-3 underlie the human immune deficiency known as leukocyte adhesion deficiency-III. Both kindlin-3 and talin-1, another FERM domain-containing cytoskeletal protein, are required for integrin activation, but their individual roles in the induction of specific integrin conformers are unclear. Here, we induce differential LFA-1 activation in neutrophils through engagement of the selectin ligand P-selectin glycoprotein ligand-1 or the chemokine receptor CXCR2. We find that talin-1 is required for inducing LFA-1 extension, which corresponds to intermediate affinity and induces neutrophil slow rolling, whereas both talin-1 and kindlin-3 are required for induction of the high-affinity conformation of LFA-1 with an open headpiece, which results in neutrophil arrest. In vivo, both slow rolling and arrest are defective in talin-1-deficient neutrophils, whereas only arrest is defective in kindlin-3-deficient neutrophils. We conclude that talin-1 and kindlin-3 serve distinct functions in LFA-1 activation.
Full-mesh optical backplane with standard MM fiber ribbons (2016)

A new optical backplane solution is proposed for high-capacity ICT apparatus. A modular, scalable and full-mesh bandwidth-upgradable optical interconnection between optoelectronic boards is guaranteed thanks to an optimized layout of standard MM 12-fiber ribbons which divides the overall backplane into several independent optical sub-circuits. The novel automated assembly procedure of fiber ribbons inside sub-circuits with a robotic work-cell is described. System validation of the optical backplane performed with commercially available MM 12-fiber transceivers @10Gb/s proved the feasibility of the proposed solution for future optical interconnections with terabit overall capacity.
Lifetimes of intermediates in the β-sheet to α-helix transition of β-lactoglobulin by using a diffusional IR mixer (2001)

The extremely slow alpha-helix/beta-sheet transition of proteins is a crucial step in amylogenic diseases and represents an internal rearrangement of local contacts in an already folded protein. These internal structural rearrangements within an already folded protein are a critical aspect of biological action and are a product of conformational flow along unknown metastable local minima of the energy landscape of the compact protein. We use a diffusional IR mixer with time-resolved Fourier transform IR spectroscopy capable of 400-micros time resolution to show that the trifluoroethanol driven beta-sheet to alpha-helix transition of beta-lactoglobulin proceeds via a compact beta-sheet intermediate with a lifetime of 7 ms, small compared with the overall folding time of beta-lactoglobulin.
A Rugged Energy Landscape Mechanism for Trapping of Transmembrane Receptors during Endocytosis (2003)

Efficient clathrin-mediated endocytosis of transmembrane receptors requires that clathrin-coated pits retain the receptors long enough to allow vesicle formation and internalization. In many cases, however, the receptors can exhibit mean lifetimes in coated pits much shorter than the lifetime of the pit at the plasma membrane. A rugged energy landscape for binding, which produces a broad distribution of residence times, ensures a significant probability of times much greater than the mean and would allow efficient trapping of proteins in these cases. We used fluorescence correlation spectroscopy and total internal reflection microscopy to measure the kinetics of movement of a C5a receptor-yellow fluorescent protein fusion in living cells. These experiments demonstrate that clusters of trapped receptors exhibit fluctuations in fluorescence intensity that vary in time scale over 2 orders of magnitude. Most of the variation in intensity is likely due to the motion of the receptors in the plane of the plasma membrane, although it is not possible to rule out a small contribution from motion orthogonal to the plane of the membrane. The broad time scale distribution of the intensity fluctuations is consistent with a rugged energy landscape mechanism for trapping of the receptors. This mechanism, which allows efficient trapping to coexist with rapid exchange, may also be relevant to other biological processes involving binding in heterogeneous chemical environments.
AmbiPack: A systematic algorithm for packing of macromolecular structures with ambiguous distance constraints (1998)

The determination of structures of multimers presents interesting new challenges. The structure(s) of the individual monomers must be found and the transformations to produce the packing interfaces must be described. A substantial difficulty results from ambiguities in assigning intermolecular distance measurements (from nuclear magnetic resonance, for example) to particular intermolecular interfaces in the structure. Here we present a rapid and efficient method to solve the packing and the assignment problems simultaneously given rigid monomer structures and (potentially ambiguous) intermolecular distance measurements. A promising application of this algorithm is to couple it with a monomer searching protocol such that each monomer structure consistent with intramolecular constraints can be subsequently input to the current algorithm to check whether it is consistent with (potentially ambiguous) intermolecular constraints. The algorithm AmbiPack uses a hierarchical division of the search space and the branch-and-bound algorithm to eliminate infeasible regions of the space. Local search methods are then focused on the remaining space. The algorithm generally runs faster as more constraints are included because more regions of the search space can be eliminated. This is not the case for other methods, for which additional constraints increase the complexity of the search space. The algorithm presented is guaranteed to find all solutions to a predetermined resolution. This resolution can be chosen arbitrarily to produce outputs at various level of detail. Illustrative applications are presented for the P22 tailspike protein (a trimer) and portions of beta-amyloid (an ordered aggregate).
The BUCKY object-relational benchmark (1997)

According to various trade journals and corporate marketing machines, we are now on the verge of a revolution—the object-relational database revolution. Since we believe that no one should face a revolution without appropriate armaments, this paper presents BUCKY, a new benchmark for object-relational database systems. BUCKY is a query-oriented benchmark that tests many of the key features offered by object-relational systems, including row types and inheritance, references and path expressions, sets of atomic values and of references, methods and late binding, and user-defined abstract data types and their methods. To test the maturity of object-relational technology relative to relational technology, we provide both an object-relational version of BUCKY and a relational equivalent thereof (i.e., a relational BUCKY simulation). Finally, we briefly discuss the initial performance results and lessons that resulted from applying BUCKY to one of the early object-relational database system products.
Interleukin 1, interleukin 6, tumor necrosis factor, and transforming growth factor beta increase cell resistance to tumor necrosis factor cytotoxicity by growth arrest in the G1 phase of the cell cycle. (1991)

During infection, inflammation, immune responses, and neoplastic growth, various cytokines are produced affecting both susceptibility to and protection from cellular death. We have studied the protective effect of pretreatment of the L929 fibroblast cell line with interleukin 1 beta (IL-1 beta), IL-6, tumor necrosis factor alpha (TNF-alpha), or transforming growth factor beta 1 (TGF-beta) on subsequent TNF/actinomycin D-induced cytotoxicity. The protective effects of these cytokines on TNF cytotoxicity were time and concentration dependent. TGF-beta was the most effective cytokine, followed by TNF, IL-1 beta, and IL-6. Activators of protein kinase C also afforded protection, and TGF-beta acted synergistically with either phorbol 12-myristate 13-acetate or the calcium ionophore A-23187. TGF-beta-induced protection against TNF was observed in cells subjected to prolonged treatment with phorbol 12-myristate 13-acetate. Cells pretreated with prostaglandin E2 or cholera toxin amplified the sensitivity to TNF and inhibited TGF-beta-mediated resistance, whereas indomethacin enhanced the protective effect of TGF-beta. Cells cultured in the presence of IL-1 beta, IL-6, TNF-alpha, or TGF-beta for 6 h inhibited DNA synthesis, and this was associated with concomitant growth arrest in the G1 phase of the cell cycle. On the other hand, prostaglandin E2 or cholera toxin stimulated the progression of cells from G1 toward G2 + M which was associated with increased TNF sensitivity. We conclude that these cytokines protect against death by arresting growth in the G1 phase of the cell cycle.
Nanopatterning by Area‐Selective Atomic Layer Deposition (2011)

This chapter contains sections titled: Concept of Area-Selective Atomic Layer Deposition Change of Surface Properties Patterning Applications of AS-ALD Current Challenges References
Towards Internet-of-Things for Wearable Neurotechnology (2021)

This paper outlines the prevalent challenges for the emerging wearable neurotechnology in modern IoT systems. We underline the recent insights in neuroscience and the ability to decode the brain circuitry with high confidence. We address the imminent challenges of translating the advanced high-cost medical setup for neural activity recording to a commodity IoT system. Emphasis is placed on non-invasive wearable sensing technology and the advances in data analytic for neurosignals. In particular, we focus on human-in-the-loop IoT systems where privacy concerns of leaking private human state and energy limitations for local data processing lay significant constraints on such systems' architecture. Along the way, we envision applications that will reach their full potential and provide the promised functionality by embedding wearable neurotechnology in their design. We end the paper by highlighting the prominent research opportunities and challenges for designing and developing the next generation of low-cost, energy-efficient, privacy-aware, and ubiquitous wearable neurotechnology. Most of these research challenges need to be addressed from a multi-disciplinary approach. Researchers from various communities need to coordinate and collaborate to successfully advance the research, development, and standardization of such neurotechnologies for the larger benefit of society.
Stochastic simulations of DNA in flow: Dynamics and the effects of hydrodynamic interactions (2002)

We present a fully parametrized bead–spring chain model for stained λ-phage DNA. The model accounts for the finite extensibility of the molecule, excluded volume effects, and fluctuating hydrodynamic interactions (HI). Parameters are determined from equilibrium experimental data for 21 μm stained λ-phage DNA, and are shown to quantitatively predict the non-equilibrium behavior of the molecule. The model is then used to predict the equilibrium and nonequilibrium behavior of DNA molecules up to 126 μm. In particular, the HI model gives results that are in quantitative agreement with experimental diffusivity data over a wide range of molecular weights. When the bead friction coefficient is fit to the experimental relaxation time at a particular molecular weight, the stretch in shear and extensional flows is adequately predicted by either a free-draining or HI model at that molecular weight, although the fitted bead friction coefficients for the two models differ significantly. In shear flow, we find two regimes at high shear rate (γ̇) that follow different scaling behavior. In the first, the viscosity and first normal stress coefficient scale roughly as γ̇−6/11 and γ̇−14/11, respectively. At higher shear rates, these become γ̇−2/3 and γ̇−4/3. These regimes are found for both free-draining and HI models and can be understood based on scaling arguments for the diffusion of chain ends.
PDM-OFDM for upgrade scenarios: An investigation of OFDM-induced XPM on 42.8-Gb/s DPSK over SSMF and LEAF (2010)

We investigate the nonlinear tolerance of 42.8-Gb/s DPSK with PDM-OFDM neighbors. It is found that the XPM penalty scales with the OFDM-bandwidth and that for data rates up to 40-Gb/s delta powers are required.
Isolation and translation of calvaria procollagen messenger ribonucleic acids (1976)

Procollagen messenger ribonucleic acid (mRNA) was isolated from the calvaria of 15-day-old chick embryos by chromatographing total RNA over oligo(dT)-cellulose two times, and then fractionating the twice-bound RNA on 85% Me2SO/0-20% sucrose gradients. When analyzed on 99% formamide gels, the 27-30S fraction had three sharp fluorescent bands, one corresponding to 27S ribosomal RNA (rRNA), the others having mobilities lower than 27S corresponding to molecular weights of 1 700 000 and 1 800 000. In wheat-germ, cell-free extracts, the 27-30S fraction directed the synthesis of two prominent collagenase sensitive polypeptides with mobilities corresponding to the calvaria pro-alpha chain markers. Twelve percent of this [3H]proline-labeled, wheat-germ product could be hydroxylated with prolyl hydroxylase.
Thermomechanical Characterization of Nickel-Titanium Copper Shape Memory Alloy Films (2001)

In an effort to develop a more extensive model for the thermomechanical behavior of shape memory alloy (SMA) films, a novel characterization method has been developed. This automated test has been tailored to characterize films for use in micro-electromechanical system (MEMS) actuators. The shape memory effect in NiTiCu is seen in the solid-state phase transformation from an easily deformable low-temperature state to a “shape remembering” high-temperature state. The accurate determination of engineering properties for these films necessitates measurements of both stress and strain in microfabricated test structures over the full range of desired deformation. Our various experimental methods (uniaxial tensile tests, bimorph curvature tests, and diaphragm bulge tests) provide recoverable stress and strain data and the stress-strain relations for these films. Tests were performed over a range of temperatures by resistive heating or ambient heating. These measurements provide the results necessary for developing active SMA structural film design models
Neuroendocrine Protein 7B2 Can Be Inactivated by Phosphorylation within the Secretory Pathway (2005)

The prohormone convertases play important roles in the maturation of neuropeptides and peptide hormone precursors. Prohormone convertase-2 (PC2) is the only convertase that requires the expression of another neuroendocrine protein, 7B2, for expression of enzyme activity. In this study, we determined that 7B2 can be phosphorylated in Rin cells (a rat insulinoma cell line) and cultured chromaffin cells, but not in AtT-20 cells (derived from mouse anterior pituitary). Phosphoamino acid analysis of Rin cell 7B2 indicated the presence of phosphorylated serine and threonine. Phosphorylation of Ser115 (located within the minimally active 36-residue peptide) was confirmed by mutagenesis, although Ser115 did not represent the sole residue phosphorylated. Two independent assays were used to investigate the effect of phosphorylated 7B2 on PC2 activation: the ability of 7B2 to bind to pro-PC2 was assessed by co-immunoprecipitation, and activation of pro-PC2 was assessed in a cell-free assay. Phosphorylated 7B2 was unable to bind pro-PC2, and the phosphorylated 7B2 peptide (residues 86-121, known to be the minimally active peptide for pro-PC2 activation) was impaired in its ability to facilitate the generation of PC2 activity in membrane fractions containing pro-PC2. In vitro phosphorylation experiments using Golgi membrane fractions showed that 7B2 could be phosphorylated by endogenous Golgi kinases. Golgi kinase activity was strongly inhibited by the broad-range kinase inhibitor staurosporine and partially inhibited by the protein kinase C inhibitor bisindolylmaleimide I, but not by the other protein kinase A, Ca2+/calmodulin-dependent kinase II, myosin light chain kinase, and protein kinase G inhibitors tested. We conclude that phosphorylation of 7B2 functionally inactivates this protein and suggest that this may be analogous to the phosphorylating inactivation of BiP, which impairs its ability to bind substrate.