gebhart/patrepeval huggingface dataset:
Genomic Epidemiology of a Protracted Hospital Outbreak Caused by a Toxin A-Negative Clostridium difficile Sublineage PCR Ribotype 017 Strain in London, England (2015)

Clostridium difficile remains the leading cause of nosocomial diarrhea worldwide, which is largely considered to be due to the production of two potent toxins: TcdA and TcdB. However, PCR ribotype (RT) 017, one of five clonal lineages of human virulent C. difficile, lacks TcdA expression but causes widespread disease. Whole-genome sequencing was applied to 35 isolates from hospitalized patients with C. difficile infection (CDI) and two environmental ward isolates in London, England. The phylogenetic analysis of single nucleotide polymorphisms (SNPs) revealed a clonal cluster of temporally variable isolates from a single hospital ward at University Hospital Lewisham (UHL) that were distinct from other London hospital isolates. De novo assembled genomes revealed a 49-kbp putative conjugative transposon exclusive to this hospital clonal cluster which would not be revealed by current typing methodologies. This study identified three sublineages of C. difficile RT017 that are circulating in London. Similar to the notorious RT027 lineage, which has caused global outbreaks of CDI since 2001, the lineage of toxin-defective RT017 strains appears to be continually evolving. By utilization of WGS technologies to identify SNPs and the evolution of clonal strains, the transmission of outbreaks caused by near-identical isolates can be retraced and identified.
Improved Lossy Image Compression with Priming and Spatially Adaptive Bit\n Rates for Recurrent Networks (2017)

We propose a method for lossy image compression based on recurrent,\nconvolutional neural networks that outperforms BPG (4:2:0 ), WebP, JPEG2000,\nand JPEG as measured by MS-SSIM. We introduce three improvements over previous\nresearch that lead to this state-of-the-art result. First, we show that\ntraining with a pixel-wise loss weighted by SSIM increases reconstruction\nquality according to several metrics. Second, we modify the recurrent\narchitecture to improve spatial diffusion, which allows the network to more\neffectively capture and propagate image information through the network's\nhidden state. Finally, in addition to lossless entropy coding, we use a\nspatially adaptive bit allocation algorithm to more efficiently use the limited\nnumber of bits to encode visually complex image regions. We evaluate our method\non the Kodak and Tecnick image sets and compare against standard codecs as well\nrecently published methods based on deep neural networks.\n
Perspective on the future of silicon photonics and electronics (2021)

Silicon photonics is advancing rapidly in performance and capability with multiple fabrication facilities and foundries having advanced passive and active devices, including modulators, photodetectors, and lasers. Integration of photonics with electronics has been key to increasing the speed and aggregate bandwidth of silicon photonics based assemblies, with multiple approaches to achieving transceivers with capacities of 1.6 Tbps and higher. Progress in electronics has been rapid as well, with state-of-the-art chips including switches having many tens of billions of transistors. However, the electronic system performance is often limited by the input/output (I/O) and the power required to drive connections at a speed of tens of Gbps. Fortunately, the convergence of progress in silicon photonics and electronics means that co-packaged silicon photonics and electronics enable the continued progress of both fields and propel further innovation in both.
Administration of Drugs, Transdermal Route (2016)

This Glossary of Terms Related to Pharmaceutics is needed by practitioners in the field of pharmaceutics as this field fulfills an important and crucial role, different from the roles of other scientific disciplines involved in the drugmaking process. The glossary contains 168 definitions used in pharmaceutics. These are related to various aspects of this discipline, such as: (1) physicochemical characterization of pharmaceutical preparations and the active ingredients they contain; (2) unit operations used in the practice of pharmaceutics; (3) terms related to the various dosage forms; (4) terms related to the various modes and routes of drug delivery; (5) terms used in pharmacokinetics and biopharmaceutics in general; and additional miscellaneous terms. The field of pharmaceutics itself is of a multidisciplinary nature as its practitioners come from a variety of disciplines, such as chemistry or various biological sciences, thus a glossary containing authoritative definitions would be useful for them. The terms used in pharmaceutics are rarely covered by existing glossaries, and in the cases they are, their definitions are often inappropriate for the field of pharmaceutics and require new or modified definitions to better fit the new context.
Optimum Codebook Design and Average SEP Loss Analysis of Spatially Independent and Correlated Feedback Based MISO Systems With Rectangular QAM Constellation (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> In this correspondence, we present an optimum codebook design algorithm that minimizes the loss in average symbol error probability (SEP) of a spatially correlated multiple-input single-output (MISO) system with finite-rate feedback under both perfect and imperfect channel estimate assumptions. Towards the goal of designing an optimum codebook that minimizes average SEP (ASEP) loss due to finite-rate channel quantization, we derive the distortion function as a first order approximation of the instantaneous SEP loss. Utilizing high resolution quantization theory and assuming perfect channel estimation at the receiver, we analyze the loss in ASEP for spatially independent and correlated finite-rate feedback transmit beamforming MISO systems with <formula formulatype="inline"> <tex Notation="TeX">$M_{1} \times M_{2}$</tex></formula>-QAM constellation. We then consider the high-SNR regime and show that the loss associated with quantizing the spatially independent channels is related to the loss associated with quantizing the spatially correlated channels by a scaling constant given by the determinant of the correlation matrix. We also present simulation results that illustrate the effectiveness of the new codebook design and validate the derived analytical expressions for ASEP loss. </para>
325 Fabrication of sandwich panel consisting of A6061-ADC12 functionally graded porous Al and A1050 Al plate (2015)

Porous aluminum has lightweight and high energy absorption properties. Therefore, it is expected to be used as structural materials. In this study, sandwich panel consisting of A6061-ADC12 functionally graded porous Al and A1050 Al plate was fabricated by friction stir processing (FSP) route. It was shown that obtained sandwich panel has different pore structures by a difference of holding time during foaming process.
Fabrication and evaluation of sapphire fiber cladding via magnesium aluminate spinel sol-gel based approaches (2019)

The absence of an effective and stable cladding has been a major hurdle in utilizing single crystal fibers for harsh environment sensing applications despite the promise of sapphire for temperatures as high as 1800&deg;C. This work discusses the development of a high temperature cladding for sapphire fibers using wet chemical methods. Magnesium aluminate spinel has been chosen as the material for the cladding as it has a lower refractive index compared to sapphire and does not undergo significant interdiffusion with sapphire at temperatures below approximately 1200&deg;C. Different sol-gel based approaches have been pursued to develop polycrystalline cladding layers with thicknesses greater than a micron, as required to ensure adequate confinement of the guided electromagnetic radiation within the fiber core. For sapphire fibers, high temperature stability of the cladded fibers as well as the effect of the cladding layer on optical characteristics under different application relevant gas environments at elevated temperatures has been investigated.
Temperature behavior of sound velocity of fluorine-doped vitreous silica thin films studied by picosecond ultrasonics (2015)

Temperature behavior of sound velocity of fluorine-
Effective Bipyridine and Pyrazine‐Based Polysulfide Dissolution Resistant Complex Framework Material Systems for High Capacity Rechargeable Lithium–Sulfur Batteries (2019)

Lithium–sulfur (Li–S) batteries with high theoretical capacity (≈1650 mAh g −1 ) and specific energy density (≈2567 Wh g −1 ) have not achieved commercialization status due to low cycling stability arising from lithium polysulfide dissolution. Herein, sulfur infiltrated noncarbonized noncarbonate containing metal organic complex framework material (CFM) systems; sulfur‐copper‐bipyridine‐CFM (S‐Cu‐bpy‐CFM) and sulfur‐copper‐pyrazine‐CFM (S‐Cu‐pyz‐CFM) are developed as sulfur cathodes for the first time. The S‐Cu‐bpy‐CFM and S‐Cu‐pyz‐CFM show an initial capacity of 1626 and 1565 mAh g −1 with stable capacities of 1063 and 1025 mAh g −1 , respectively, after 150 cycles. An X‐ray photoelectron spectroscopy (XPS) analysis after sulfur infiltration reveals the presence of —C—S— bonds arising from the Lewis acid–base interaction of the CFMs with sulfur. The battery separators cycled with the CMF cathodes display complete absence of polysulfides after 150 cycles. These CFM cathodes exhibit an initial fade in capacity during the first ≈25 cycles attributed to the irreversible reaction of nitrogen with sulfur (—N—S—) during cycling. A clear understanding of this chemical interaction between sulfur and nitrogen present in the sulfur‐infiltrated CFMs is essential for engineering nitrogen containing hosts for trapping polysulfides effectively. Understanding reported here will lead to new materials for achieving the high specific energy densities characteristic to Li–S batteries.
Liver surgery in the multidisciplinary management of gastrointestinal stromal tumour (2014)

R0 resection and clinical response to TKI are predictors of survival. Surgical resection should be performed as soon as feasible in responder patients. In poor responders, surgery may not add any survival benefit, except in localized progressive disease. In resectable metastatic liver disease, preoperative TKIs or upfront surgery followed by adjuvant therapy could be considered. Larger studies are needed to determine the optimum approach in patients with metastatic GIST.
Expression of DISC1-Interactome Members Correlates with Cognitive Phenotypes Related to Schizophrenia (2014)

Cognitive dysfunction is central to the schizophrenia phenotype. Genetic and functional studies have implicated Disrupted-in-Schizophrenia 1 (DISC1), a leading candidate gene for schizophrenia and related psychiatric conditions, in cognitive function. Altered expression of DISC1 and DISC1-interactors has been identified in schizophrenia. Dysregulated expression of DISC1-interactome genes might, therefore, contribute to schizophrenia susceptibility via disruption of molecular systems required for normal cognitive function. Here, the blood RNA expression levels of DISC1 and DISC1-interacting proteins were measured in 63 control subjects. Cognitive function was assessed using neuropsychiatric tests and functional magnetic resonance imaging was used to assess the activity of prefrontal cortical regions during the N-back working memory task, which is abnormal in schizophrenia. Pairwise correlations between gene expression levels and the relationship between gene expression levels and cognitive function and N-back-elicited brain activity were assessed. Finally, the expression levels of DISC1, AKAP9, FEZ1, NDEL1 and PCM1 were compared between 63 controls and 69 schizophrenic subjects. We found that DISC1-interactome genes showed correlated expression in the blood of healthy individuals. The expression levels of several interactome members were correlated with cognitive performance and N-back-elicited activity in the prefrontal cortex. In addition, DISC1 and NDEL1 showed decreased expression in schizophrenic subjects compared to healthy controls. Our findings highlight the importance of the coordinated expression of DISC1-interactome genes for normal cognitive function and suggest that dysregulated DISC1 and NDEL1 expression might, in part, contribute to susceptibility for schizophrenia via disruption of prefrontal cortex-dependent cognitive functions.
Empowering parameter-efficient transfer learning by recognizing the kernel structure in self-attention (2022)

The massive amount of trainable parameters in the pre-trained language models (PLMs) makes them hard to be deployed to multiple downstream tasks. To address this issue, parameter-efficient transfer learning methods have been proposed to tune only a few parameters during fine-tuning while freezing the rest. This paper looks at existing methods along this line through the kernel lens. Motivated by the connection between self-attention in transformer-based PLMs and kernel learning, we propose kernel-wise adapters, namely Kernel-mix, that utilize the kernel structure in self-attention to guide the assignment of the tunable parameters. These adapters use guidelines found in classical kernel learning and enable separate parameter tuning for each attention head. Our empirical results, over a diverse set of natural language generation and understanding tasks, show that our proposed adapters can attain or improve the strong performance of existing baselines.
Ethanol infusion for Marshall bundle epicardial connections in Marshall bundle‐related atrial tachycardias following atrial fibrillation ablation: The accessibility and success rate of ethanol infusion by using a femoral approach (2019)

The present study demonstrated that the VOM was highly accessible and MB-AT was amenable to treatment by ethanol infusion by using a femoral approach.
Field emission properties of carbon nanohorn films (2002)

Self-supporting carbon films were prepared from a carbonaceous material, nanohorns. Nanohorns are spherical particles built of sharp cones of a single graphene sheet. The films show good field emission characteristics due to the sharp horn-like structures, in particular a low turn-on field and good long-term stability.
Role of Cyclic Adenosine 3′,5′-Monophosphate and the Cyclic Adenosine 3′,5′-Monophosphate Receptor Protein in the Initiation of lac Transcription (1971)

Abstract Optimal transcription of the lac operon in a defined purified in vitro system is dependent upon the concentrations of cyclic adenosine 3',5'-monophosphate (cyclic AMP), the cyclic AMP-binding protein (CRP) and RNA polymerase. The concentration of CRP required for maximal lac transcription varies proportionately with the concentration of lac DNA used as template. Maximal lac transcription is obtained with less CRP when lac ps DNA is used as template than with wild type lac DNA. Both in vivo and in vitro the lac ps mutation appears to result in a more efficient lac promoter. The formation of a preinitiation complex which will synthesize lac mRNA upon addition of nucleoside triphosphates requires preincubation of λh80dlac DNA, RNA polymerase, CRP, and cyclic AMP. The formation of this preinitiation complex is both time and temperature dependent. A lag period of about 2 min is observed between the binding of RNA polymerase to lac DNA and the appearance of detectable lac specific hybridizable RNA. This lag period is possibly due to a slow transition occurring between the formation of the lac preinitiation complex and the onset of extensive polymerization. Our experiments provide further evidence that CRP and cyclic AMP act on lac DNA to stimulate an early step in the initiation of lac transcription by RNA polymerase.
The involvement of glial cell-derived reactive oxygen and nitrogen species in Alzheimer’s disease (2001)

Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by adult-onset progressive dementia and mainly affects the elderly. Pathologically, the brains of AD patients are characterized by the presence of neurofibrillary tangles (NFTs), amyloid β peptide (Aβ)-containing senile plaques (SPs) and synaptic and neuronal cell loss. Most research on AD has focused on the mechanisms that result in the formation of these insoluble NFTs and SPs [1 2]. NFTs represent the insoluble filamentous remnants of the cytoskeleton of affected neurons, with a major component being phosphorylated forms of the microtubule-associated protein tau. SPs primarily contain aggregated Aβ peptide fragments derived from the amyloid precursor protein (APP). In AD brains, both SPs and NFTs, as well as vulnerable neurons, have been shown to undergo a number of modifications indicative of ongoing oxidative stress [3-12].
Integrated optical fiber shape sensor modules based on twisted multicore fiber grating arrays (2014)

In this paper we report on the development of a complete integrated optical fiber assembly suitable for shape sensing. Our shape sensor module consists of a length (&gt;1m) of twisted multicore optical fiber with fiber Bragg gratings inscribed along its length. Our fiber has a compact 180 micron coated diameter, a twist of 50 turns per meter and grating reflectivities greater than 0.01% per cm of array, suitable for high efficiency scatter measurements over many meters of fiber. Single core to multicore fanouts and low reflectivity fiber termination are used to terminate the end of the array.
Lebein, a Snake Venom Disintegrin, Induces Apoptosis in Human Melanoma Cells (2016)

Melanoma, the most threatening form of skin cancer, has a very poor prognosis and is characterized by its very invasive and chemoresistant properties. Despite the recent promising news from the field of immunotherapy, there is an urgent need for new therapeutic approaches that are free of resistance mechanisms and side effects. Anti-neoplasic properties have been highlighted for different disintegrins from snake venom including Lebein; however, the exact effect of Lebein on melanoma has not yet been defined. In this study, we showed that Lebein blocks melanoma cell proliferation and induces a more differentiated phenotype with inhibition of extracellular signal-regulated kinase (ERK) phosphorylation and microphthalmia-associated transcription factor (MITF) overexpression. Melanoma cells became detached but were less invasive with upregulation of E-cadherin after Lebein exposure. Lebein induced a caspase-independent apoptotic program with apoptosis inducing factor (AIF), BCL-2-associated X protein (BAX) and Bim overexpression together with downregulation of B-cell lymphoma-2 (BCL-2). It generated a distinct response in reactive oxygen species (ROS) generation and p53 levels depending on the p53 cell line status (wild type or mutant). Therefore, we propose Lebein as a new candidate for development of potential therapies for melanoma.
Modeling Complementary Products and Customer Preferences with Context Knowledge for Online Recommendation. (2019)

Modeling item complementariness and user preferences from purchase data is essential for learning good representations of products and customers, which empowers the modern personalized recommender system for Walmart's e-commerce platform. The intrinsic complementary relationship among products captures the buy-also-buy patterns and provides great sources for recommendations. Product complementary patterns, though often reflected by population purchase behaviors, are not separable from customer-specific bias in purchase data. We propose a unified model with Bayesian network structure that takes account of both factors. In the meantime, we merge the contextual knowledge of both products and customers into their representations. We also use the dual product embeddings to capture the intrinsic properties of complementariness, such as asymmetry. The separating hyperplane theory sheds light on the geometric interpretation of using the additional embedding. We conduct extensive evaluations on our model before final production, and propose a novel ranking criterion based on product and customer embeddings. Our method compares favorably to existing approaches in various offline and online testings, and case studies demonstrate the advantage and usefulness of the dual product embeddings as well as the user embeddings.
10 Gbit s−1 Free Space Data Transmission at 9 µm Wavelength With Unipolar Quantum Optoelectronics (2021)

Abstract Free space optics data transmission with bitrate in excess of 10 Gbit s −1 is demonstrated at 9 µm wavelength by using a unipolar quantum optoelectronic system at room temperature, composed of a quantum cascade laser, a modulator, and a quantum cascade detector. The large frequency bandwidth of the system is set by the detector and the modulator that are both high frequency devices, while the laser emits in continuous wave. The amplitude modulator relies on the Stark shift of an absorbing optical transition in and out of the laser frequency. This device is designed to avoid charge displacement, and therefore it is characterized by an intrinsically large bandwidth and very low electrical power consumption. This demonstration of high‐bitrate data transmission sets unipolar quantum devices as the most performing platform for the development of optoelectronic systems operating at very high frequency in the mid‐infrared for several applications, such as digital communications and high‐resolution spectroscopy.
Shape Memory Alloys in Continuum and Soft Robotic Applications (2019)

Abstract Continuum robots are inspired by biological trunks, snakes and tentacles. Unlike conventional robot manipulators, there are no rigid structures or joints. Advantageous is the ease of miniaturization combined with high dexterity, since limiting components such as bearings or gears can be omitted. Most currently used actuation elements in continuum robots require a large drive unit with electric motors or similar mechanisms. Contrarily, shape memory alloys (SMAs) can be integrated into the actual robot. The actuation is realized by applying current to the wires, which eliminates the need of an additional outside drive unit. In the presented study, SMA actuator wires are used in variously scaled continuum robots. Diameters vary from 1 to 60 mm and the lengths of the SMA driven tentacles range from 75 to 220 mm. The SMAs are arranged on an annulus in a defined distance to the neutral fiber, whereby the used cores vary from superelastic NiTi rods to complex structures and also function as restoring unit. After outlining the theoretical basics for the design of an SMA actuated continuum robot, the design process is demonstrated exemplarily using a guidewire for cardiac catheterizations. Results regarding dynamics and bending angle are shown for the presented guidewire.
Concerning “Maximum Power Point Tracking for Photovoltaic Optimization Using Ripple-Based Extremum Seeking Control” (2011)

This paper highlights key contributions in extremum seeking (ES) control and ripple correlation control (RCC). Maximum power point tracking (MPPT) utilizing the 120-Hz inherent inverter ripple is shown to be developed in the early 1980s. Even though that specific MPPT development did not explicitly mention ES control, the analysis presented there shows otherwise. RCC stability and operating properties are also addressed where the fundamental difference between RCC and popular ES control methods is the perturbation source. Since RCC utilizes inherent switching ripple in power electronics, the high ripple frequency leads to fast RCC convergence.