gebhart/patrepeval huggingface dataset:
alpha-Galactosidases of Penicillium simplicissimum: production, purification and characterization of the gene encoding AGLI. (1998)

Production of extracellular a-galactosidases by the filamentous fungus Penicillium simplicissimum (previously P. janthinellum) VTT-D-78090 was studied on different carbon sources. Steam-exploded oat husks were chosen as the best carbon source for enzyme production. Three a-galactosidases (AGL) were purified from the culture filtrate using ion-exchange chromatography, hydrophobic interaction chromatography and gel filtration. The isoelectric points of AGLI, AGLII and AGLIII were 5.2, 4.4 and 7.0, and the molecular masses as determined by SDS/PAGE were 61, 84 and 61 kDa, respectively. All enzymes were glycosylated. The optimum pH for the activity of AGLI and AGLIII was between 3.0 and 4.5 and that of AGLII was between 4.0 and 5.0. AGLII was more stable and more resistant to product inhibition by galactose than the other two enzymes. AGLI and AGLIII were also inhibited by p-nitrophenol-a-D-galactopyranoside, the substrate used for enzyme activity assay. The gene encoding AGLI was cloned and sequenced. The gene, agl1, encodes 435 amino acids including the signal sequence. It showed similarity with the other a-galactosidases belonging to the glycosyl hydrolase family 27. The N-terminal amino acid sequence of AGLIII was also similar to the sequences of other members of family 27, whereas the N-terminus of AGLII was completely different from the sequences of other reported hydrolases.
Early Detection of the Aflatoxin B₁ Mutational Fingerprint: A Diagnostic Tool for Liver Cancer (2017)

Using duplex-consensus sequencing technology, we recently identified the characteristic high-resolution mutational spectrum of the liver carcinogen aflatoxin B₁ in a mouse model, many months before aflatoxin-induced tumors are detectable. The diagnostic power of this spectrum is then demonstrated by accurately identifying, among the sequenced human liver tumors, the subset of cancers associated with aflatoxin B₁ exposure. Keywords: Duplex sequencing; HCC; hepatocellular carcinoma; mutagenesis; mutational signature; mycotoxins
Nanoparticle-based drug delivery systems: a commercial and regulatory outlook as the field matures (2016)

Nanomedicine has emerged as a major field of academic research with direct impact on human health. While a first generation of products has been successfully commercialized and has significantly contributed to enhance patient's life, recent advances in material design and the emergence of new therapeutics are contributing to the development of more sophisticated systems. As the field matures, it is important to comprehend the challenges related to nanoparticle commercial development for a more efficient and predictable path to the clinic. Areas covered: The review provides an overview of nanoparticle-based delivery systems currently on the market and in clinical trials, and discuss the principal challenges for their commercial development, both from a manufacturing and regulatory perspective, to help gain understanding of the translational path for these systems. Expert opinion: Clinical translation of nanoparticle-based delivery systems remains challenging on account of their 3D nanostructure and requires robust nano-manufacturing process along with adequate analytical tools and methodologies. By identifying early enough in the development the product critical attributes and understanding their impact on the therapeutic performance, the developers of nanopharmaceuticals will be better equipped to develop efficient product pipelines. Second-generation products are expected to broaden nanopharmaceutical global market in the upcoming years.
A comparative multinational epidemiological study of adolescent outpatient clinics (1998)

SEC62. Child psychiatry (-)Pindolol is a IS-HTIA antagonist. With the group of F. Artigas, we have shown that pindolol in the rat can block the somatodendritic S-HTIA autoreceptor in the dorsal raphe without affecting the responsiveness of postsynaptic S-HTlA receptors in the dorsal hippocampus.
Shuhai: A Tool for Benchmarking High Bandwidth Memory on FPGAs (2021)

FPGAs are starting to incorporate High Bandwidth Memory (HBM) to both reduce the memory bandwidth bottleneck encountered in some applications and to provide more capacity to store application state. However, the overall performance characteristics of HBMs are still not well understood, especially in the context of FPGAs, making it difficult to optimize designs relying on HBM. In this article, we bridge the gap between nominal specifications and actual performance by characterizing HBM on a state-of-the-art FPGA, i.e., a Xilinx Alveo U280 featuring a two-stack HBM subsystem. To this end, we have developed Shuhai, a benchmarking tool that throws light on all the subtle details of the performance and usage of HBMs on an FPGA. FPGA-based benchmarking should also provide a more accurate picture of HBM than measuring performance on CPUs/GPUs, since CPUs/GPUs are noisier systems due to their complex control logic and cache hierarchy. Since the memory itself is complex, leveraging custom hardware logic to benchmark it directly from an FPGA provides more details as well as more accurate and deterministic measurements. We observe that 1) HBM is able to provide up to 425 GB/s memory bandwidth, and 2) how HBM is used has a significant impact on the achievable throughput, which in turn demonstrates the importance of unveiling the performance characteristics of HBM so as to use HBM in the right manner. To demonstrate the generality of Shuhai, we also show results for other types of memory, e.g., DDR4, and DDR3, and quantitatively compare the performance characteristics of HBM with those of DDR4 and DDR3.
The Comprehensive Assessment of Neurodegeneration and Dementia: Canadian Cohort Study (2019)

Availability of data from the COMPASS-ND study will provide a major stimulus for dementia research in Canada in the coming years.
[The road to treating chronic active Epstein-Barr viral infection]. (2021)

Chronic active Epstein-Barr virus (CAEBV) infection is a progressive disease characterized by persistent inflammatory symptoms accompanied by clonally proliferating EBV-positive T or NK cells. The optimal medical treatment for CAEBV to eradicate EBV-infected T or NK cells has not yet been established, with allogeneic hematopoietic stem cell transplantation as the only strategy currently available. Patients with CAEBV have been reported mainly from limited area of Japan and East Asia. However, CAEBV is drawing a global attention, and the number of reports is increasing worldwide after its definition was added to the EBV-positive T- or NK-cell neoplasms in the 2017 World Health Organization classification. We had previously discovered that STAT3 was constitutively activated in EBV-infected tumor cells in CAEBV inducing the immortalization and production of inflammatory cytokines. Based on these findings, an investigator-initiated clinical research of a JAK1/2 inhibitor ruxolitinib for CAEBV infection was initiated in January 2019. Japanese researchers have been expected to elucidate pathological mechanisms and to establish an effective treatment.
A Link-Directionality-Based Dual Channel MAC Protocol with a Power Exchange Algorithm for IEEE 802.11 Ad-Hoc Networks (2006)

When an IEEE 802.11 ad-hoc network achieves capacity C by using a single channel, the targeted capacity by using two channels should be <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2middotC</sub> . However, most or the multi-channel 802.11 protocols proposed in the literature only appear to be able to achieve less than 60% or the 2middotC targeted capacity. In our paper (2006), we proposed a link-directionality-based dual channel MAC protocol (DCP) to boost the network capacities up to 78% of our targeted capacities, 78%*2middotC = 1.56middotC. However, DCP still failed to reach the 2middotC capacity target due to the overheads incurred by the protocol. In this paper, we implement a power exchange algorithm on top of the DCP in an attempt to double the capacities of networks using the single-channel 802.11 protocol. This algorithm incurs relatively small overheads and can further release the protocol constraints imposed by DCP. Simulations show that the proposed scheme (DCPwPEA) can achieve more than 132% of our targeted capacities, 132%* 2middotC = 2.64middotC. We believe this protocol can be extended to allow multi-link simultaneous transmissions which can multiply the network capacities of ad-hoc networks by using only two channels
Segmenting multi-intent queries for spoken language understanding (2019)

With the rising popularity of voice assistants, automatic speech recognition (ASR) systems play a crucial role in translating speech to text in order to enablenatural language understanding (NLU) models to process human commands. However, NLU models lack the proper resources to handle certain natural human speechcharacteristics, such as dividing or segmenting several intents expressed in one spo-ken sentence. This study presents an innovative approach to sentence boundarysegmentation from ASR output using a neural network model. We improve on previous attempts by removing the need for complex model output postprocessing, aswell as reporting higher accuracy than previous studies on the subject.
Ultradense Silicon Photonic Interface for Optical Interconnection (2015)

A scalable ultradense silicon photonic interface with 61 compact vertical grating couplers on a pitch of 42.3 μm is designed and fabricated to match a pitch reducing optical fiber array (PROFA) hexagonal channel pattern. Experimental results show that the designed grating couplers with a minimum insertion loss of 4.5 dB and a 3-dB bandwidth of 50 nm are obtained. The crosstalk between different channels is less than -50 dB and the maximum loss difference across the PROFA interface is ~0.7 dB. High-speed data transmission indicates that a bandwidth density as large as 27 Tb/s/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> could be achieved within a footprint of 0.096 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , demonstrating the potential of silicon photonics for broadband optical interconnection.
Lactivibrio alcoholicus gen. nov., sp. nov., an anaerobic, mesophilic, lactate-, alcohol-, carbohydrate- and amino-acid-degrading bacterium in the phylum Synergistetes (2014)

A mesophilic, obligately anaerobic, lactate-, alcohol-, carbohydrate- and amino-acid- degrading bacterium, designated strain 7WAY-8-7(T), was isolated from an upflow anaerobic sludge blanket reactor treating high-strength organic wastewater from isomerized sugar production processes. Cells of strain 7WAY-8-7(T) were motile, curved rods (0.7-1.0×5.0-8.0 µm). Spore formation was not observed. The strain grew optimally at 37 °C (range for growth was 25-40 °C) and pH 7.0 (pH 6.0-7.5), and could grow fermentatively on yeast extract, glucose, ribose, xylose, malate, tryptone, pyruvate, fumarate, Casamino acids, serine and cysteine. The main end-products of glucose fermentation were acetate and hydrogen. In co-culture with the hydrogenotrophic methanogen Methanospirillum hungatei DSM 864(T), strain 7WAY-8-7(T) could utilize lactate, glycerol, ethanol, 1-propanol, 1-butanol, L-glutamate, alanine, leucine, isoleucine, valine, histidine, asparagine, glutamine, arginine, lysine, threonine, 2-oxoglutarate, aspartate and methionine. A Stickland reaction was not observed with some pairs of amino acids. Yeast extract was required for growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite and Fe (III) were not used as terminal electron acceptors. The G+C content of the genomic DNA was 61.4 mol%. 16S rRNA gene sequence analysis revealed that the isolate belongs to the uncultured environmental clone clade (called 'PD-UASB-13' in the Greengenes database) in the bacterial phylum Synergistetes, showing less than 90% sequence similarity with closely related described species such as Aminivibrio pyruvatiphilus and Aminobacterium colombiense (89.7% and 88.7%, respectively). The major cellular fatty acids were iso-C(13 : 0), iso-C(15 : 0), anteiso-C(15 : 0), C(18 : 1), C(19 : 1), C(20 : 1) and C(21 : 1). A novel genus and species, Lactivibrio alcoholicus gen. nov., sp. nov. is proposed to accommodate strain 7WAY-8-7(T) ( = JCM 17151(T) = DSM 24196(T) = CGMCC 1.5159(T)).
ANALYTICAL METHOD FOR 1-METHYL-4-AMINO-PIPERAZINE IN AN ACTIVE PHARMACEUTICAL INGREDIENT USING CHEMICAL DERIVATIZATION AND HPLC-UV (2010)

Abstract A method to form a UV-active derivative of 1-methyl-4-amino-piperazine (AMP) was developed. The method was based on the reaction of AMP with benzaldehyde, forming a stable derivative, which was UV-active. The method was used to analyze samples of an active pharmaceutical ingredient (API) for trace amounts of AMP. The derivatization approach allowed detection of AMP at low levels, using readily available HPLC-UV instrumentation. The method was validated in the range of about 30 to 190 ppm (on a mass to mass basis relative to API). It was shown through spiked recovery tests that the derivatization reaction occurred smoothly without interference from the API. The results suggest that other organohydrazine compounds may be amenable to the same derivatization technique. Keywords: benzaldehydebenzylidenederivatizationhydrazinehydrazoneorganohydrazine
Liver fibrosis and fatty liver in Asian HIV‐infected patients (2016)

HIV-monoinfected patients are at risk for liver fibrosis and cirrhosis. HIV-related mechanisms and fatty liver disease may play important roles. Screening and intervention to prevent severe outcomes should be considered.
Context-Patch Face Hallucination Based on Thresholding Locality-constrained Representation and Reproducing Learning (2018)

Face hallucination is a technique that reconstruct high-resolution (HR) faces from low-resolution (LR) faces, by using the prior knowledge learned from HR/LR face pairs. Most state-of-the-arts leverage position-patch prior knowledge of human face to estimate the optimal representation coefficients for each image patch. However, they focus only the position information and usually ignore the context information of image patch. In addition, when they are confronted with misalignment or the Small Sample Size (SSS) problem, the hallucination performance is very poor. To this end, this study incorporates the contextual information of image patch and proposes a powerful and efficient context-patch based face hallucination approach, namely Thresholding Locality-constrained Representation and Reproducing learning (TLcR-RL). Under the context-patch based framework, we advance a thresholding based representation method to enhance the reconstruction accuracy and reduce the computational complexity. To further improve the performance of the proposed algorithm, we propose a promotion strategy called reproducing learning. By adding the estimated HR face to the training set, which can simulates the case that the HR version of the input LR face is present in the training set, thus iteratively enhancing the final hallucination result. Experiments demonstrate that the proposed TLcR-RL method achieves a substantial increase in the hallucinated results, both subjectively and objectively. Additionally, the proposed framework is more robust to face misalignment and the SSS problem, and its hallucinated HR face is still very good when the LR test face is from the real-world. The MATLAB source code is available at https://github.com/junjun-jiang/TLcR-RL
Low-stress silicon carbonitride for the machining of high-frequency nanomechanical resonators (2006)

The synthesis of silicon carbonitride by low-temperature plasma-enhanced chemical vapor deposition and the machining of nanomechanical resonators in this material are reported. Films with thickness of 1μm, 200nm, and 50nm were deposited using ammonia, nitrogen, and diethylsilane as precursors. X-ray photoelectron spectroscopy indicated that usage of higher NH3:DES gas flow ratios results in higher nitrogen and low carbon contents in the deposited films. In addition, annealing of the material enabled the full tunability of its residual stress from the compressive to the tensile range. Infrared spectroscopy indicated that desorption of incorporated hydrogen was responsible for those changes. Assaying of resonant cantilevers fabricated from 200-nm-thick films yielded root-modulus-over-density values as high as √(E∕ρ)=8.35×103m∕s, comparable to those of silicon. Doubly clamped beams were also fabricated from 50-nm-thick films of low (σ=80MPa) and high (σ=220MPa) tensile stresses. Beam resonators fabricated in the lower stress material showed resonance qualities ranging between 3000 and 5000, and resonant frequencies between f=6.1MHz and f=16MHz. Beam resonators machined in the higher stress material experienced quality factors between 8000 and 23 000 and frequencies between f=7.6 and 24MHz. These values correspond to fQ products as high as of 1.5×1011s−1, exceeding the performance of previously reported silicon resonators.
BEOL-Embedded 3D Polylithic Integration: Thermal and Interconnection Considerations (2020)

In this paper, a BEOL-embedded chiplet integration scheme is proposed for dense 3D integration. This scheme represents a system with multiple device tiers (primary and embedded tiers) where custom chiplets, such as voltage regulator modules, I/O drivers, RF front-end chips, etc. are embedded into the BEOL of an application processor tier with a monolithic memory device tier, such as resistive RAM. The proposed integration scheme is thermally evaluated to investigate the effects of design parameters on the thermal operation of the primary and embedded tiers, along with transient analysis to estimate the extent of inter-tier thermal coupling. Results for steady-state operation suggest the thermal viability of such an integration approach. Considerable reduction in inter-tier thermal coupling for transient operation was achieved with dual-sided cooling (tier 1 to tier 3 coupling: 85% for air-cooling, reduced to 65% for dual-sided cooling). We also propose and demonstrate metal electroless plating in addition to mechanical self-alignment as an enabling technology for BEOL-embedded integration to facilitate low-temperature, low-pressure, and high interconnect density inter-die bonding. Post assembly Ni electroless deposited bonding was verified across all inspected diagonal pillars in an area array of 50×50 copper pillars.
Cladding Pumped Erbium-Doped Multicore Fiber Amplifiers for Space Division Multiplexing (2014)

We report on recent development of multicore fiber amplifiers for applications in space division multiplexed systems. Amplification and noise properties of cladding pumped multicore erbium doped fiber amplifiers employing end- and side-pumping, are presented.
Digital Control Of Repetitive Errors In Disk Drive Systems (1989)

Tracking errors in disk drive systems have a significant repetitive component that is not explicitly taken into account in conventional servo controllers. Three specialized digital controllers applied as plug-in modules to a winchester disk drive with a pre-existing analog feedback controller to demonstrate their efficacy in the reduction of this periodic component. These controllers include the discrete time repetitive controller which is based on the internal model principle and feedforward cancellation controllers based on an adaptive prediction algorithm and on input and output measurements of the system.
Influence of tacticity and sorbed water on the material properties of poly(N,N'‐dimethylacrylamide) (1981)

Abstract The effects of variation in tacticity on the thermal, morphological, stress–strain and stress–relaxation properties (both in the dry state and 140°C, and at a RH of 72% and ambient temperature) were evaluated for a series of homopolymers of poly( N,N ‐dimethylacrylamide). In the range of 19 to 23% tacticity (isotactic content), a fundamental change in the level of crystallinity and morphology occurs for this series of polymers which in turn greatly affects the above‐mentioned properties. Below 19% tacticity, the polymers are amorphous, but above 23% they are distinctly semicrystalline. Sorbed water plasticizes all these polymers, but the influences of the water on the stress–strain properties is greatest for the amorphous polymers, where the relative sorption of water is also highest.
Applications of liquid‐based separation in conjunction with mass spectrometry to the analysis of forensic evidence (2018)

In the past few years, there has been a significant effort by the forensic science community to develop new scientific techniques for the analysis of forensic evidence. Forensic chemists have been spearheaded to develop information-rich confirmatory technologies and techniques and apply them to a broad array of forensic challenges. The purpose of these confirmatory techniques is to provide alternatives to presumptive techniques that rely on data such as color changes, pattern matching, or retention time alone, which are prone to more false positives. To this end, the application of separation techniques in conjunction with mass spectrometry has played an important role in the analysis of forensic evidence. Moreover, in the past few years the role of liquid separation techniques, such as liquid chromatography and capillary electrophoresis in conjunction with mass spectrometry, has gained significant tractions and have been applied to a wide range of chemicals, from small molecules such as drugs and explosives, to large molecules such as proteins. For example, proteomics and peptidomics have been used for identification of humans, organs, and bodily fluids. A wide range of HPLC techniques including reversed phase, hydrophilic interaction, mixed-mode, supercritical fluid, multidimensional chromatography, and nanoLC, as well as several modes of capillary electrophoresis mass spectrometry, including capillary zone electrophoresis, partial filling, full filling, and micellar electrokenetic chromatography have been applied to the analysis drugs, explosives, and questioned documents. In this article, we review recent (2015-2017) applications of liquid separation in conjunction with mass spectrometry to the analysis of forensic evidence.
A computational approach for time-optimal planning of high-rise elevators (2002)

An important issue in elevatoring is to transport passengers in near-minimum time while satisfying the elevator's intrinsic dynamic constraints, such as allowable hoist torque/power, and extrinsically imposed comfort constraints, such as allowable acceleration and deceleration. Furthermore, a solution is sought in near-real-time using concurrently sensed data of passenger load and destination. In this paper, a new approach for minimum-time trajectory generation for high-rise elevators is presented. It is shown that, for systems characterized by linear differential equations, subject to linear or nonlinear inequality constraints, the time-optimal trajectory possesses the special property that at least one constraint is always active. This property is exploited to build an efficient algorithm to compute minimum-time solutions.