gebhart/patrepeval huggingface dataset:
Retroviral transduction efficiency of G-CSF+SCF–mobilized peripheral blood CD34+ cells is superior to G-CSF or G-CSF+Flt3-L–mobilized cells in nonhuman primates (2003)

Gene transfer experiments in nonhuman primates have been shown to be predictive of success in human clinical gene therapy trials. In most nonhuman primate studies, hematopoietic stem cells (HSCs) collected from the peripheral blood or bone marrow after administration of granulocyte colony-stimulating factor (G-CSF) + stem cell factor (SCF) have been used as targets, but this cytokine combination is not generally available for clinical use, and the optimum target cell population has not been systematically studied. In our current study we tested the retroviral transduction efficiency of rhesus macaque peripheral blood CD34(+) cells collected after administration of different cytokine mobilization regimens, directly comparing G-CSF+SCF versus G-CSF alone or G-CSF+Flt3-L in competitive repopulation assays. Vector supernatant was added daily for 96 hours in the presence of stimulatory cytokines. The transduction efficiency of HSCs as assessed by in vitro colony-forming assays was equivalent in all 5 animals tested, but the in vivo levels of mononuclear cell and granulocyte marking was higher at all time points derived from target CD34(+) cells collected after G-CSF+SCF mobilization compared with target cells collected after G-CSF (n = 3) or G-CSF+Flt3-L (n = 2) mobilization. In 3 of the animals long-term marking levels of 5% to 25% were achieved, but originating only from the G-CSF+SCF-mobilized target cells. Transduction efficiency of HSCs collected by different mobilization regimens can vary significantly and is superior with G-CSF+SCF administration. The difference in transduction efficiency of HSCs collected from different sources should be considered whenever planning clinical gene therapy trials and should preferably be tested directly in comparative studies.
SAIL-APPROX: An Efficient On-Line Algorithm for Approximate Pattern Matching with Wildcards and Length Constraints (2007)

Finding patterns in biological sequences owns a significant impact on many real-world applications such as biological sequence analysis, text indexing, stream data mining, and sensor networking. The problem of Pattern Matching with Wildcards and Length Constraints is to find all locations of occurrences of a pattern P in a text T, which can be a biological sequence, text string, etc. The user can specify a varying range for the number of wildcards between every two consecutive letters in P and also the length constraints of P. Another constraint is the one-off condition, where every literal in T can only be used once for matching with P. The on-line version of this problem is to find out an occurrence of the given pattern that satisfies all constraints as soon as the occurrence appears in the input of T so far. There is an algorithm SAIL to find the optimal solution for the on-line version of this problem. However, SAIL only handles exact pattern matching. In this paper, we propose an efficient on-line algorithm for approximate pattern matching with wildcards and length constraints, which is a more general problem than exact matching. We apply dynamic programming in our algorithm and prove that our algorithm is correct.
Aluminum Activation in Ionic Liquids (2015)

Aluminum (Al) is the third most abundant element (after oxygen and silicon) and the most abundant metal in Earth's crust. Al is quite remarkable as it holds a low density and it has the ability to resist corrosion due to surface passivation. This passivation layer protects Al from corrosion in a relatively wide range of pH and potentials. Nevertheless, in aqueous media, the layer is vulnerable in both highly acidic and basic environments, leading to rapid corrosion reactions. As an anodic material, Al has a theoretical gravimetric capacity of 2.98 Ah/gr and its volumetric capacity is as high as 8.1 Ah/cm 3 . For the sake of comparison, Li metal holds capacities of 3.86 Ah/g and 2.06 Ah/cm 3 , respectively. In non-aqueous media electrochemical dissolution of Al is partly hampered due to inefficient and thus insufficient passivation layer removal prior to any current application. Similar issues pertain when the non- aqueous solutions employed are Room Temperature Ionic Liquids (RTIL). In the present work an activation of Al was studied in EMIm(HF) 2.3 F RTIL. For this specific electrolyte it was already established that electrochemical dissolution of Al occurs, in considerable rates, sufficient for application in Al-Air batteries [1] . The alteration of the surface, as detected by FTIR, XPS and STEM, suggests on the formation of passivating Al-O-F compounds on the surface, instead of native oxide passivation. The source of this specific activation is established in this work, and the surface of Al prior to and following activation was identified. The applied methodology was also used for identification and study of Al activation in other family of RTILs. The preliminary results of this specific electrochemical system will be also presented. [1] D. Gelman, B. Shvartsev, Y. Ein-Eli, J. Mater. Chem. A. 2.47 (2014) 20237-20242.
Computerized simulation of color appearance for dichromats (1997)

We propose an algorithm that transforms a digitized color image so as to simulate for normal observers the appearance of the image for people who have dichromatic forms of color blindness. The dichromat's color confusions are deduced from colorimetry, and the residual hues in the transformed image are derived from the reports of unilateral dichromats described in the literature. We represent color stimuli as vectors in a three-dimensional LMS space, and the simulation algorithm is expressed in terms of transformations of this space. The algorithm replaces each stimulus by its projection onto a reduced stimulus surface. This surface is defined by a neutral axis and by the LMS locations of those monochromatic stimuli that are perceived as the same hue by normal trichromats and a given type of dichromat. These monochromatic stimuli were a yellow of 575 nm and a blue of 475 nm for the protan and deutan simulations, and a red of 660 nm and a blue–green of 485 nm for the tritan simulation. The operation of the algorithm is demonstrated with a mosaic of square color patches. A protanope and a deuteranope accepted the match between the original and the appropriate image, confirming that the reduction is colorimetrically accurate. Although we can never be certain of another's sensations, the simulation provides a means of quantifying and illustrating the residual color information available to dichromats in any digitized image.
Understanding code architectures via interactive exploration and layout of layered diagrams (2008)

Visualization tools that target helping developers understand software have typically had visual scalability limitations, requiring significant input before providing useful results. In contrast, we present Strata, which has been designed to actively help users by providing layered diagrams. The defaults used are based on the package structure, and user interactions can allow for overriding these defaults and focusing on relevant parts of the codebase.
The costs of sugar production from different feedstocks and processing technologies (2019)

Abstract Sugar production is essential for the production of foods, biochemicals, and biofuels via biochemical or catalytic routes. Sugar‐containing crops, and starch‐based and cellulosic feedstocks are resources for sugar production via juice extraction, starch saccharification, and pretreatment and hydrolysis, respectively. Technologies have been developed to attain a high sugar yield; however, production costs are a major consideration in commercializing newly developed approaches to the production of sugars. In this review, the fixed capital and production costs of sugar produced from first‐ and second‐generation crops are summarized. As expected, first‐generation crops provide the lowest fixed capital costs, ranging from 0.01 to 0.13 $ kg −1 feedstock, and have production costs ranging from 0.22 to 0.55 $ kg −1 sugar. For cellulosic crops, because of their recalcitrant structure and complex processing, the fixed capital and production costs are higher, ranging from 0.02 to 1.10 $ kg −1 feedstock and 0.10 to 3.37 $ kg −1 sugar, respectively. © 2019 Society of Chemical Industry and John Wiley &amp; Sons, Ltd.
Ultrahigh laser pulse energy and power generation at 10 kHz (2012)

This Letter presents results from a new master-oscillator, power-amplifier pulse-burst laser system demonstrating ultrahigh pulse energies greater than 2.0 J/pulse at 1064 nm with interpulse separations of 100 μs (10 kHz) for burst durations of 100 pulses. Each pulse generates peak powers exceeding 130 MW and an average power of approximately 20 kW is generated over a 100-pulse-burst. Pulse energies decrease by less than 10% over a 100 sequential pulses, demonstrating negligible "droop" over long-duration pulse trains. Second-harmonic generation of 532 nm with conversion efficiency greater than 50% is demonstrated for 100-pulse-burst durations.
Effect of Age and Anatomical Site on Density of Sensory Innervation in Human Epidermis (2002)

Epidermal nerve density variations could explain the different sensitivity threshold in different parts of the body. Decreased spatial discrimination with aging may be associated with decreased epidermal nerve density.
Measuring current by counting electrons in a nanowire quantum dot (2008)

We measure current by counting single electrons tunneling through an InAs nanowire quantum dot (QD). The charge detector is realized by fabricating a quantum point contact in close vicinity to the nanowire. The results based on electron counting compare well to a direct measurements of the QD current, when taking the finite bandwidth of the detector into account. The ability to detect single electrons also opens up possibilities for manipulating and detecting individual spins in nanowire QDs.
On Spatial Attention in Object Tracking using a Synthetic Aperture Camera Array (2011)

S.443-449
Automatic Detection and Neurotransmitter Prediction of Synapses in Electron Microscopy (2021)

Abstract This paper presents a deep-learning based workflow to detect synapses and predict their neurotransmitter type in the primitive chordate Ciona intestinalis ( Ciona ) EM images. Identifying synapses from electron microscopy (EM) images to build a full map of connections between neurons is a labor-intensive process and requires significant domain expertise. Automation of synapse detection and classification would hasten the generation and analysis of connectomes. Furthermore, inferences concerning neuron type and function from synapse features are in many cases difficult to make. Finding the connection between synapse structure and function is an important step in fully understanding a connectome. Activation maps derived from the convolutional neural network provide insights on important features of synapses based on cell type and function. The main contribution of this work is in the differentiation of synapses by neurotransmitter type through the structural information in their EM images. This enables prediction of neurotransmitter types for neurons in Ciona which were previously unknown. The prediction model with code is available on Github.
Network Coding Aware Queue Management in Multi-Rate Wireless Networks (2012)

While network coding can potentially provide significant throughput benefits by combining packets prior to forwarding them, the achievable gains are directly related to the coding opportunities at a relay that performs encoding. If the relay does not have packets destined for distinct destinations, that can be encoded together, the network coding gains could be marginal. Towards increasing the opportunities for network coding, in this paper we propose a queue management scheme, that arbitrates the rate at which distinct transmitters send packets to a common relay which applies network coding. Our queue management approach prioritizes the channel access of nodes that do not have enough enqueued packets at the common relay, thereby essentially attempting to balance the number of packets from the distinct senders at the relay. We perform extensive simulations of our approach (built as a wrapper on top of the popular network coding approach COPE) in multi-rate scenarios. We find that our approach yields throughput gains of up to 57% compared to COPE due to enhanced opportunities towards encoding packets.
Upravljanje pravnim rizicima kao element korporativne bezbednosne politike (2017)

Management as an interdisciplinary field requires multidimensional approach and the engagement of different academic disciplines. The significance of Risk Management studies is rising since the end of the last century, along with technological development and corporate responsibility. However, the concept of risk has various definitions in the literature, international standards and business practice. One of the common concepts of risk determines it as relation between probability and the consequence, or level of possibility that an action or activity will lead to lead to a loss or to an undesired outcome (an action taken in spite of uncertainty with its consequence). The Legal Risk is a fresh concept that has not yet been unanimously determined and accepted in legal studies. Although legal science lacks relevant studies about Legal Risk, international associations and other entities are trying to define them and also to establish the principles of its management. The authors present and analyse theoretical approaches to this concept and also relevant international documents, such as Basel II and International Bar Association Discussion Paper. Also, legal risk are analysed by considering literature that covers different backgrounds – from legal risk in EU legal framework to standard corporate legal risk issues. The authors adopt two definitions of Legal Risk, based on its nature and the origin, and discuss that this definitions do not contradict each other and can well stand alongside, depending on the sort of Legal Risk as a complex phenomenon. The basic principles and rules of Legal Risk Management are recognised as a part of the Corporate Risk Management and Security Policy, where authors demonstrate the fact that reducing, transferring or otherwise controlling Legal Risk consequently result in the reducing of other corporate risks, especially in the security field. Corporate Security and Safety depend and administrative measures can be a powerful tool for improving the state of Corporate Security and Safety. The authors conclude the Legal Risk Management should be the focus of future empirical studies and state that its significance can be recognised in various fields.
Discrete Ridgelet Transforms for Image Representation (2001)

The ridgelet transform (Candes and Donoho, 1999) was introduced as a new multiscale representation for functions on continuous spaces that are smooth away from discontinuities along lines. In this paper, we present several discrete versions of the ridgelet transform that lead to algorithmic implementations. The resulting transforms are invertible, non-redundant and computed via fast algorithms. Furthermore, this construction leads to a family of directional orthonormal bases for digital images. Numerical results show that the new transforms are more e ective than the wavelet transform in approximating and denoising images with straight edges.
Recombinant tropomyosin from <i>Penaeus aztecus</i> (rPen a 1) for measurement of specific immuno‐ globulin E antibodies relevant in food allergy to crustaceans and other invertebrates (2004)

Immunoglobulin E (IgE)-mediated food allergy to crustaceans and mollusks is relatively common and affected individuals typically react to a range of different species. The only known major allergen of shrimp was first described over 20 years ago and later identified as the muscle protein tropomyosin. This protein may be useful as a defined and relevant diagnostic marker for allergic sensitization to invertebrate foods. In order to generate an assay reagent suitable for this purpose, tropomyosin from the shrimp Penaeus aztecus (Pen a 1) was produced as a recombinant protein in Escherichia coli and characterized with respect to IgE antibody binding properties in comparison to natural shrimp tropomyosin. Hexahistidine-tagged rPen a 1 accumulated as a predominantly soluble protein in the E. coli expression host and a two-step chromatographic procedure provided a high yield of pure and homogeneous protein. rPen a 1 displayed chromatographic and folding characteristics similar to those of purified natural shrimp tropomyosin. Serum preincubation with serial protein dilutions revealed similar capacity of recombinant and natural tropomyosin to compete with immobilized shrimp extract for IgE binding. rPen a 1 was further shown to extensively and specifically compete for IgE binding to extracts of other crustacean species, house dust mite and German cockroach.
The effects of early inlet valve closing and cylinder disablement on fuel economy and emissions of a direct injection diesel engine (2014)

The influence of EIVC (early inlet valve closure) on emissions, fuel economy and exhaust gas temperature of a turbocharged, 4 cylinder common rail direct injection diesel engine has been investigated and compared with the influence of deactivating two cylinders. IVC (inlet valve closing) timings were set at up to 60 CA (crank angle) degrees earlier than the production setting of 37° ABDC for the engine. At the earliest timing, effective compression ratio was reduced from 15.2:1 to 13.7:1. The effects on emissions were significant only for EIVC settings at least 40 CA degrees earlier than the production setting, and were sensitive to engine load. At 2 bar BMEP (brake mean effective pressure) and fixed levels of NOx, soot emissions were reduced but CO (carbon monoxide) and HC (hydrocarbon) increased unless fuel rail pressure was reduced. With increasing load, soot reduction diminished and was negligible at 6 bar BMEP; CO and HC emissions deteriorated further. At all conditions, EIVC raised exhaust gas temperature by >50 °C; the effect on fuel economy was negligible or a fuel economy penalty. Comparisons indicate cylinder deactivation is the more effective strategy for reducing engine-out emissions of HC and CO and raising exhaust gas temperature under light load operating conditions.
Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator (2021)

Long non-coding RNAs (lncRNAs) can be important components in gene-regulatory networks<sup>1</sup>, but the exact nature and extent of their involvement in human Mendelian disease is largely unknown. Here we show that genetic ablation of a lncRNA locus on human chromosome 2 causes a severe congenital limb malformation. We identified homozygous 27-63-kilobase deletions located 300 kilobases upstream of the engrailed-1 gene (EN1) in patients with a complex limb malformation featuring mesomelic shortening, syndactyly and ventral nails (dorsal dimelia). Re-engineering of the human deletions in mice resulted in a complete loss of En1 expression in the limb and a double dorsal-limb phenotype that recapitulates the human disease phenotype. Genome-wide transcriptome analysis in the developing mouse limb revealed a four-exon-long non-coding transcript within the deleted region, which we named Maenli. Functional dissection of the Maenli locus showed that its transcriptional activity is required for limb-specific En1 activation in cis, thereby fine-tuning the gene-regulatory networks controlling dorso-ventral polarity in the developing limb bud. Its loss results in the En1-related dorsal ventral limb phenotype, a subset of the full En1-associated phenotype. Our findings demonstrate that mutations involving lncRNA loci can result in human Mendelian disease.
Customers and Investors: A Framework for Understanding Financial Institutions (2015)

Financial institutions have both investors and customers. Investors, such as those who invest in stocks and bonds or private/public-sector guarantors of institutions, expect an appropriate risk-adjusted return in exchange for the financing and risk-bearing that they provide. Customers of a financial intermediary, in contrast, provide financing in exchange for a specific set of services, and do not want the fulfillment of these services to be contingent on the credit risk of the intermediary, even when they are not small, uninformed agents lacking in sophistication. This paper develops a framework that defines the roles of customers and investors in intermediaries, and uses the framework to provide an economic foundation for the aversion to intermediary credit risk on the part of its customers. This customer-investor nexus has implications for a host of issues related to how contracts between financial intermediaries and their customers are structured and how risks are shared between them, as well as the consequences of (unanticipated) deviations from the ex ante efficient contractual arrangement for institutional design, regulatory practices, and financial crises. Moreover, customers and investors are often intertwined in practice, and so this intertwining provides insights into the adoption of “too-big-to-fail” policies and bailouts by regulators in general.
Development of high temperature electrodeposited LIGA MEMS materials (2009)

In the current work, new electrodeposited materials including Ni-W alloys, Ni-Al 2 O 3 nanocomposites and Ni based superalloys were developed for use in high temperature MEMS applications. Ni-W alloys with different compositions (Ni 5 at% W and Ni 15 at% W) were electrodeposited from an alkaline ammonia citrate electrolyte in the form of compact thick (> 100 μm) layers and LIGA microspecimens. The mechanical investigations demonstrated in the as-deposited state higher strength and a brittle behaviour compared to pure nickel; while in the annealed state (300 - 700 °C), the strength remained high and additional plasticity was noticed. Higher W content resulted in higher strength up to a 700 °C annealing temperature, whereas lower W content led to more softening after annealing. These properties were confirmed by the nanocrystalline microstructure showing grains smaller than 100 nm in the as-deposited state that slightly increased in size after annealing but still remaining in the submicron range. This microstructural stability can be explained by the effect of W atoms impeding the boundaries' movements. In order to incorporate Al 2 O 3 into compact and thick layers and microspecimens, an electrolyte was developed and optimized based on an alkaline ammonia citrate sulfate solution containing hydrophilic nanoparticles electrostatically dispersed. The incorporation of the particles was evidenced by the detected nanosized agglomerates presenting an Al 2 O 3 content of about 3 wt% and 1.3 wt% for the layers and the microspecimens, respectively, and the increase in strength and brittleness in the as-deposited state compared to pure nickel. After annealing, Ni-Al 2 O 3 remained strong, which was in agreement with the slight increase in grain size showing microstructural stability till an annealing temperature of 600 °C. This may be due to the pinning effect of the particles on the grain boundaries. For use in the formation of superalloys, Ni-Al composites were electrodeposited from a similar solution as Ni-Al 2 O 3 at a neutral pH and containing metallic aluminum particles. It has been shown that the size of the particles affects the structure of the electrodeposited layer that was non-compact when incorporating microparticles, in contrast to nanoparticles resulting in defect free material. Moreover, the electrolyte was unstable even after a short aging time (24h). A first model, based on the determination of the diffusion distance of aluminum in nickel, was presented predicting the annealing parameters necessary for the formation of the high temperature resistant y' phase.