gebhart/patrepeval huggingface dataset:
Generative Probabilistic Novelty Detection with Adversarial Autoencoders (2018)

Novelty detection is the problem of identifying whether a new data point is considered to be an inlier or an outlier. We assume that training data is available to describe only the inlier distribution. Recent approaches primarily leverage deep encoder-decoder network architectures to compute a reconstruction error that is used to either compute a novelty score or to train a one-class classifier. While we too leverage a novel network of that kind, we take a probabilistic approach and effectively compute how likely is that a sample was generated by the inlier distribution. We achieve this with two main contributions. First, we make the computation of the novelty probability feasible because we linearize the parameterized manifold capturing the underlying structure of the inlier distribution, and show how the probability factorizes and can be computed with respect to local coordinates of the manifold tangent space. Second, we improved the training of the autoencoder network. An extensive set of results show that the approach achieves state-of-the-art results on several benchmark datasets.
Electroencephalogram spindle activity during dexmedetomidine sedation and physiological sleep (2007)

Analysis of sleep spindles shows that dexmedetomidine produces a state closely resembling physiological S2 sleep in humans, which gives further support to earlier experimental evidence for activation of normal non-rapid eye movement sleep-promoting pathways by this sedative agent.
Warehouse-scale video acceleration: co-design and deployment in the wild (2021)

Video sharing (e.g., YouTube, Vimeo, Facebook, TikTok) accounts for the majority of internet traffic, and video processing is also foundational to several other key workloads (video conferencing, virtual/augmented reality, cloud gaming, video in Internet-of-Things devices, etc.). The importance of these workloads motivates larger video processing infrastructures and – with the slowing of Moore’s law – specialized hardware accelerators to deliver more computing at higher efficiencies. This paper describes the design and deployment, at scale, of a new accelerator targeted at warehouse-scale video transcoding. We present our hardware design including a new accelerator building block – the video coding unit (VCU) – and discuss key design trade-offs for balanced systems at data center scale and co-designing accelerators with large-scale distributed software systems. We evaluate these accelerators “in the wild" serving live data center jobs, demonstrating 20-33x improved efficiency over our prior well-tuned non-accelerated baseline. Our design also enables effective adaptation to changing bottlenecks and improved failure management, and new workload capabilities not otherwise possible with prior systems. To the best of our knowledge, this is the first work to discuss video acceleration at scale in large warehouse-scale environments.
Uncoupling the ATPase Activity of the N-Ethylmaleimide Sensitive Factor (NSF) from 20S Complex Disassembly (2001)

The N-ethylmaleimide sensitive factor (NSF) plays a critical role in intracellular trafficking by disassembling soluble NSF attachment protein receptor (SNARE ) complexes. The NSF protomer consists of three domains (NSF-N, NSF-D1, and NSF-D2). Two domains (NSF-D1 and NSF-D2) contain a conserved ∼230 amino acid cassette, which includes a distinctive motif termed the second region of homology (SRH) common to all ATPases associated with various cellular activities (AAA). In hexameric NSF, several SRH residues become trans elements of the ATP binding pocket. Mutation of two conserved arginine residues in the NSF-D1 SRH (R385A and R388A) did not effect basal or soluble NSF attachment protein (SNAP)-stimulated ATPase activity; however, neither mutant underwent ATP-dependent release from SNAP−SNARE complexes. A trans element of the NSF-D2 ATP binding site (K631) has been proposed to limit the ATPase activity of NSF-D2, but a K631D mutant retained wild-type activity. A mutation of the equivalent residue in NSF-D1 (D359K) also did not affect nucleotide hydrolysis activity but did limit NSF release from SNAP−SNARE complexes. These trans elements of the NSF-D1 ATP binding site (R385, R388, and D359) are not required for nucleotide hydrolysis but are important as nucleotide-state sensors. NSF-N mediates binding to the SNAP−SNARE complex. To identify the structural features required for binding, three conserved residues (R67, S73, and Q76) on the surface of NSF-N were mutated. R67E completely eliminated binding, while S73R and Q76E showed limited effect. This suggests that the surface important for SNAP binding site lies in the cleft between the NSF-N subdomains adjacent to a conserved, positively charged surface.
Faster Cryptococcus melanization increases virulence in experimental and human cryptococcosis (2020)

Abstract Cryptococcus spp. are important human pathogens responsible for about 180,000 deaths per year. Studying their virulence attributes can lead to better cryptococcosis prevention and treatment. In this work, we systematically investigated virulence attributes of Cryptococcus spp. clinical isolates and correlated them with patient data. We collected 66 C. neoformans and 19 C. gattii isolates from Brazilian patients and analyzed multiple phenotypes related with their capsule, production of laccase, melanin and extracellular vesicles. We also tested their virulence in Galleria mellonella and ability to evade macrophage LC3-associated phagocytosis (LAP). All phenotypes analyzed varied widely among the isolates, but C. neoformans isolates tended to melanize faster and more intensely and produce thinner capsules in comparison with C. gattii . We also observed correlations that match previous studies, such as that between secreted laccase – but not total melanin production – and disease outcome in patients. The most striking results, though, came from our measurements of Cryptococcus colony melanization kinetics, which followed a sigmoidal curve for most isolates. Faster melanization correlated positively with LAP evasion, virulence in G. mellonella and worse prognosis in humans. These results suggest that the speed of melanization, more than the total amount of melanin Cryptococcus spp. produces, is crucial for virulence. Graphical abstract
SDR based multi-band subsampling receivers for GNSS applications (2014)

The advent in analog to digital converter technology and the available processing power of today's digital signal processors and general purpose processors as well as the available high speed FPGAs enables the design of radio receivers to move a step closer toward the ideal software defined radio (SDR) architecture. This paper presents some of the possibilities offered by the SDR by taking the example of a subsampling multi-standard GNSS receiver. The main differences between a superheterodyne and a subsampling receiver are presented and the sampling frequency selection procedure is detailed. Finally a test setup for the GNSS receiver as well as the frequency conversion results are shown.
Bulk Liquid Phase Processes Using Ionic Liquids — Success Factors and Recent Examples (2018)

This presentation highlights two recent developments of our group using ionic liquids as bulk liquid phase in industrially relevant, new process concepts. The first part of the presentation is dedicated to the role of an IL sorbent during the catalytic hydrogenation of CO2 to methanol. This reaction is limited under stoichiometric conditions to around 20 % methanol yield by the equilibrium (75 bar total pressure, 250 °C). However, in the presence of an IL that absorbs both methanol and water under reaction conditions, significantly higher overall MeOH yields can be realized. This new application of IL sorbents has been demonstrated on a 5 L reactor scale with a continuous methanol production rate of more than 50 g per hour. 

The second part of the presentation deals with a novel liquid-phase technology to convert lactic acid from fermentation to bio-acrylic acid. Acrylic acid is a major industrial chemical that is so far exclusively produced by a two-step oxidation process from propene. Selective conversion from biomass via lactic acid promises a strong reduction of the CO2 footprint, but also higher productivity under much milder conditions. The new process applies a bromide ionic liquid reaction medium to realize a nucleophile assisted dehydration process in hitherto unreached selectivity and yield.[2, 3]
A New Prediction Model on the Luminance of OLEDs Subjected to Different Reverse Biases for Alleviating Degradation in AMOLED Displays (2014)

Organic light-emitting diodes (OLEDs) have drawn much attention in areas of displays and varied illumination devices due to multiple advantages, such as high brightness, high efficiency, wide viewing angle, and simple structure. However, the long-time degradation of OLED emission is a serious drawback. This degradation was investigated by past works, which pointed out that the degradation was induced by high-density currents through OLED component under the long-time operation [1][2]. Proposed by a past work [3], different reverse biases was imposed on OLED components in display frames to alleviate the long-time degradation on OLEDs. Most recently, along with the reverse bias, new pixel circuits [4][5] for AMOLED displays are designed to alleviate OLED degradation, thus successfully extending OLED life time. However, since emission luminances in different frame times during AMOLED displaying differs significantly for displaying varied images, the OLED degradation evolves in a highly unpredictable fashion. In this study, based on valid theories, the voltage across the OLED is first used as indicator for OLED degradation. Then the relation between the level of OLED degradation, in terms of OLED’s cross voltage, and the history of imposing reverse biases are precisely modeled. With the model, the degradation of the OLED under reverse bias to extend lifetime can be successfully predicted. Based on this model, engineers can then optimize the applied reverse bias on OLEDs to maximize the OLED lifetime for varied display requirement.
Fabrication of a Beam Shaping Lens for Chip Scale Packaged LEDs (2010)

In this paper, we demonstrated the machining process of a novel Light Emitting Diodes (LED) beam shaping lens, called TIR Fresnel lens, for GaN-based blue Chip Scale Packaged (CSP) LEDs. Upon achieving a precise alignment of the tool and identifying the best manufacturing condition, we have successfully fabricated a prototype of this lens on poly methyl methacrylate (PMMA) plate. The form error of the central aspheric lens was less than 1 μm deviation, and surface quality of the Fresnel facets were sufficient for Total Internal refraction without any burr or adhesion of the machined chip. Fabricated TIR Fresnel lens reduced the viewing angle of the testing CSP LED from 140° to 17.4° in FWHM. The proposed lens produced extreme compactness as well as high collimation efficiency, thereby applicable to an ultra-thin optical system.
Simplifying RAM Forensics: A GUI and Extensions for the Volatility Framework (2012)

The Volatility Framework is a collection of tools for the analysis of computer RAM. The framework offers a multitude of analysis options and is used by many investigators worldwide. Volatility currently comes with a command line interface only, which might be a hinderer for some investigators to use the tool. In this paper we present a GUI and extensions for the Volatility Framework, which on the one hand simplify the usage of the tool and on the other hand offer additional functionality like storage of results in a database, shortcuts for long Volatility Framework command sequences, and entirely new commands based on correlation of data stored in the database.
P2‐321: Active vaccination of old Alzheimer's disease transgenic animals with oligomeric polymerized pbri and CpG ODN can reverse preexisting Alzheimer's disease pathology (2015)

We have previously demonstrated that immuno-intervention in AD animal models can lead to prevention of some pathology through innate immune system stimulation via TLR9 induced by CpG ODN (Scholtzova et al 2014) or the modulation of the adaptive immune system through active vaccination with the β-sheet oligomeric form of the polymerized Bri peptide (Goni et al 2014). A challenge to therapeutic immune stimulation of old AD Tg animals, with preexisting extensive pathology, is senescence of the immune system. We have now vaccinated old 3xTg AD animals with both Aβ and tau pathology, with the pBri as a conformational antigen and CpG ODN as an immune stimulator. Two groups of at least 15 months old 3xTg AD animals were inoculated four times over a period of two months with either vehicle or oligomeric pBri in Alum as previously described. Another group was inoculated from 12 to 17 month old with five doses of pBri or CpG ODN in alternate weeks as reported. Behavioral and locomotor tests were performed after the 17 month of age. The animals were then euthanized, followed by histological and biochemical analyses. We show that old animals still could mount a conformational immune response that results in diminished pathology, as well as rescue of cognitive function. Both groups vaccinated with pBri and pBri-CpG ODN showed behavioral rescue when compared to age matched controls. Biochemistry and immuno-histology showed improvements of some pathological features; importantly including diminished oligomeric Aβ and tau. The active immunomodulation using polymerized β-sheet oligomeric pBri can elicit a conformational antibody response even in old animals. These antibodies directed to β-sheet conformation can retard the progression and reverse some preexisting pathology. The use of CpG ODN can help to boost the innate immune system, in senescent animals, to help establish the subsequent adaptive conformational response.
Minimally Intrusive Single-Chip Recession/Temperature Sensors for Spacecraft Thermal Protection Systems (2023)

We report the initial results of ongoing development of minimally intrusive, single-chip integrated capacitive recession/temperature sensors that would provide real-time monitoring of ablation recession of heatshield thermal protection systems (TPS) during spacecraft atmospheric entry. This work, which was performed using Phenolic Impregnated Carbon Ablator (PICA), is also to demonstrate the ease of sensor insertion during TPS manufacturing, thereby resulting in faster, low-cost, uniform sensor assembly, and spatial distribution, without compromising TPS structural integrity. Using oxy-acetylene flame at 500 W-cm-<sup>2</sup> heat flux for 16 seconds, the average recession depth of 0.325 cm was obtained. While some measurement challenges were encountered in this first attempt, the initial results obtained were in relatively good agreement with published data, which offer promise of future improvement based on lessons learned.
Isolation and purification of L-methionine-alpha-deamino-gamma-mercaptomethane-lyase (L-methioninase) from Clostridium sporogenes. (1973)

Summary In an attempt irreversibly to deplete biological systems of the essential amino acid l-methionine, l-methionine-α-deamino-γ-mercaptomethane-lyase was isolated from Clostridium sporogenes (ATCC 7955), highly purified, and characterized. All the investigations undertaken indicate a double function: release of the α-amino- and the γ-methanethiol group by a single protein unit. It is possible that this bifunctional activity is brought about by gene fusion.
Epithermal and Thermal Alpha-Particle Transport and Control (1990)

Alpha-particle ash accumulation in tokamaks and two possible ash control techniques are discussed. The effect of thermal alpha-particle ash accumulation on plasma performance is examined using a zero-dimensional analysis with profile corrections. Alpha-particle accumulation is shown to have serious effects on ignition requirements. An analytical model developed to predict the effect of sawtooth disruption on ash accumulation is discussed. The analytical results indicate that the sawtooth is effective when the temperature profile is parabolic or flatter. Alpha-particle ejection by a fishbone oscillation is envisaged to be helpful in ash control, and a model of the physics in a large-aspect-ratio approximation is discussed using an extended version of a Chen et al. formalism. The trapped particle destabilization of the internal kinks due to the alpha particles and a second hot-particle species is considered, and the expected oscillation frequency and growth rates are derived.
Influence of Kernel Shape and Size on the Packing Ratio and Compressibility of Hard Red Winter Wheat (2018)

Abstract. Grain compaction occurs during bin storage, and its determination is important for the grain mass estimation needed for inventory and auditing. The degree of compaction is dependent on grain type, bin type, moisture content, amount of grain, initial grain bulk density, coefficients of friction, lateral-to-vertical pressure coefficient, and variation in kernel size. Previous studies have correlated several of these parameters, such as bulk density and grain packing, with moisture content. This study investigated the influence of wheat kernel shape and size distribution on packing ratio and compressibility. Two dockage-free hard red winter (HRW) wheat samples, with no shrunken or broken kernels, were sieved using U.S. Tyler sieves #6, #7, #8, and #10, and the kernels retained on the sieves were used in the experiments. The kernel dimensional parameters and bulk sample parameters were measured, and additional derived parameters were calculated for each size fraction and variety. Packing ratio and compressibility of the size fractions and of binary and ternary mixtures of the size fractions were also determined for each variety. Packing ratio increased with larger kernel size, while compressibility decreased. Sphericity and flatness shape factor had strong positive linear relationships with packing ratio and strong negative relationships with compressibility, while elongation shape factor behaved the opposite way with packing ratio and compressibility. The higher the percentage mass of the larger kernel fraction in a mixture, the higher was its packing ratio and the lower its compressibility. The two tested varieties of wheat did not significantly differ in packing ratio and compressibility. These findings can be used in developing models for more accurate estimation of grain pack factor and to determine the mass of grain inside bins and other storage structures. Keywords: Compressibility, Packing, Shape, Size, Wheat.
23S ribosomal ribonucleic acid of macrolide-producing streptomycetes contains methylated adenine (1979)

Coresistance to macrolide, lincosamide, and streptogramin B-type (MLS) antibiotics by a common biochemical mechanism characterizes clinically resistant pathogens. Of 10 streptomycetes tested for resistance to macrolide, lincosamide, and streptogramin B-type antibiotics, only 1, Streptomyces erythreus, the organism used for production of erythromycin, was found resistant to all three classes; moreover, it was the only streptomycete in the series tested found to contain N6-dimethyladenine (m62A) in 23S ribosomal ribonucleic acid, the structural alteration of ribosomal ribonucleic acid associated with clinical resistance. Of the seven streptomycetes tested for the presence of m62A and N6-methyladenine (m6A), two, S. fradiae and S. cirratus, which produce the macrolide antibiotics tylosin and cirramycin, respectively, were found to contain m6A, but not m62A. The remaining strains tested, including strains which produce lincomycin and streptogramins, contained neither m6A nor m62A.
Molecular characterization of the safracin biosynthetic pathway from Pseudomonas fluorescens A2‐2: designing new cytotoxic compounds (2005)

Safracin is an antibiotic with anti-tumour activity produced by Pseudomonas fluorescens A2-2. The entire safracin synthetic gene cluster spanning 17.5 kb has been identified, cloned and sequenced. The safracin cluster comprises 10 open reading frames (ORFs) encoding proteins for three non-ribosomal peptide synthetases (NRPS), three safracin precursor biosynthetic enzymes, two safracin tailoring enzymes, a safracin resistance protein and a small hypothetical protein of unknown function. These genes are organized in two divergent operons of eight and two genes respectively. This pathway exhibits unusual features when compared with other NRPS systems. We have demonstrated by heterologous expression of the cluster that it is able to direct the synthesis of safracin in other strains. Cross-feeding experiments have confirmed that 3-hydroxy-5-methyl-O-methyltyrosine is the precursor of two amino acids of the molecule. Genetic analyses have allowed us to demonstrate that the bicistronic operon encodes the hydroxylation and N-methylation activities of the pathway. The cloning and expression of the safracin cluster has settled the basis for the in vivo and in vitro production of a wide variety of compounds, such as the promising ecteinascidins anti-cancer compounds.
Stimulation of electron transport as potential novel therapy in Parkinson's disease with mitochondrial dysfunction (2015)

Parkinson's disease (PD) is a neurodegenerative motor disorder characterized by the loss of dopaminergic neurons. This loss of dopaminergic neurons is the pathological hallmark of the disease that results in the characteristic motor syndrome. Restoration of dopamine levels is the basis of current therapy; however, this does not tackle the cause of the disease. While the aetiology of PD remains mostly elusive, mitochondrial dysfunction has been linked to (at least) part of the PD cases. In this review we discuss recent findings in Drosophila melanogaster showing that stimulation of the electron transport chain is beneficial for PD fly models showing Complex I defects and discuss the possible clinical applications of these findings.