gebhart/patrepeval huggingface dataset:
Enhancement of Alpha 1-antitrypsin Production in Pichia pastoris by Designing and Optimizing Medium Using Elemental Analysis (2017)

<b>Background:</b> Human alpha 1-antitrypsin (AAT) is a monomeric glycosylated protein; it is the potent inhibitor of a whole range of serine proteases and protects tissues against their destructive effects. The human plasma-derived AAT, which is currently used to augment the AAT level in patients, is limited due to high cost and source limitation. Recombinant production of AAT can be considered as a potential alternative. <b>Objectives:</b> This study aims to develop and optimize a new chemically defi ned medium based on an elemental analysis of the yeast <i>Pichia pastoris</i> for an effi cient culture of the recombinant yeast-producing secretory AAT. <b>Materials and Methods:</b> An elemental analysis of Carbon (C), Hydrogen (H), Nitrogen (N), Sulfur (S); CHNS in its abbreviated form, and metallic elements was performed to determine the exact molecular constituent of the <i>P. pastoris</i>. The medium components were selected according to the obtained formula; they were optimized by the response surface methodology (RSM). The grown yeast cell was measured at the end of 18 h glycerol batch culture. The amounts of AAT production and elastase inhibitory capacity (EIC) were measured at the end of three days' methanol feeding. <b>Results:</b> The optimized medium compositions consist of glycerol (40 g.L<sup>-1</sup>), KH<sub>2</sub>PO<sub>4</sub> (24.78 g.L<sup>-1</sup>), NaCl, (0.88 g.L<sup>-1</sup>), MgSO<sub>4</sub> .7H<sub>2</sub> O (1.95 g.L<sup>-1</sup>), (NH<sub>4</sub> )<sub>2</sub> SO<sub>4</sub> (22.76 g.L<sup>-1</sup>), and trace elements (20 mL.L<sup>-1</sup>). The presented quadratic models show that KH<sub>2</sub> PO<sub>4</sub> and (NH4)<sub>2</sub> SO<sub>4</sub>, are the most abundant ones in the <i>P. pastoris</i> biomass and have the greatest effect on the cell growth, EIC, and AAT protein production responses. <b>Conclusions:</b> According to the results of this study, it can be concluded that the characterizing cell composition formula could be considered as an appropriate method to design culture media in order to improve cell growth and productivity. Compared to the common <i>P. pastoris</i> chemically defi ned media, FM22 and BSM, production of AAT protein increased by 1.5 and 1.4 times, respectively, in this new medium.
On regular quasi-cyclic LDPC codes from binomials (2004)

In the past, several authors have considered quasicyclic LDPC codes whose circulant matrices in the parity-check matrix are cyclically shifted identity matrices. By composing a parity-check matrix not only with such matrices but also with sums of two cyclically shifted identity matrices and with zero matrices, one can increase the minimum distance while keeping the same regularity. Specifically, whereas for (3, 4)-regular codes in the first class the best minimum distance is 24, the best minimum distance in the second class is 32. We give examples of codes that achieve these bounds.
Syntheses and characterizations of allyl cellulose and glycidyl cellulose (1992)

Abstract Allyl cellulose was synthesized by reacting cellulose with allyl bromide in homogeneous LiCl/DMAc solution containing NaOH powder. The degree of substitution (DS) per anhydroglucose (AHG) unit was determined by titrating the allyl cellulose with bromine in chloroform solution, and an allyl DS of 2.80 was found. Glycidyl cellulose was then prepared by reacting this allyl cellulose with peracetic acid in methylene chloride at ambient temperature for 6 days. The measured reaction rate constant was 1.33 × 10 −3 min −1 . The glycidyl cellulose thus obtained with a glycidyl DS of 2.58 was determined by titrating the product with perchloric acid in conjunction with tetrabutylammonium iodide. The 2.58 of glycidyl DS was also confirmed by 1 H‐NMR integration. Both allyl cellulose and glycidyl cellulose were analyzed and characterized with FTIR, 1 H‐NMR, 13 C‐NMR, TGA, and GPC. During epoxidation of allyl cellulose, possible side reaction leading to ester formation was evidenced from the continuous increase of v CO at 1735 cm −1 in FTIR analyses. In addition, a bimodal distribution and a decreased molecular weight for glycidyl cellulose were found from GPC data, which might suggest a possible chain scission at the cellulosic ether linkage. © 1992 John Wiley & Sons, Inc.
Following the Shadow: Agile 3-D Beam-Steering for 60 GHz Wireless Networks (2018)

60 GHz networks, with multi-Gbps bitrate, are considered as the enabling technology for emerging applications such as wireless Virtual Reality (VR) and 4K/8K real-time Miracast. However, user motion, and even orientation change, can cause mis-alignment between 60 GHz transceivers' directional beams, thus causing severe link outage. Within the practical 3D spaces, the combination of location and orientation dynamics leads to exponential growth of beam searching complexity, which substantially exacerbates the outage and hinders fast recovery. In this paper, we first conduct an extensive measurement to analyze the impact of 3D motion on 60 GHz link performance, in the context of VR and Miracast applications. We find that 3D motion exhibits inherent non-predictability, so conventional beam steering solutions, which targets 2D scenarios with lower search space and short-term motion coherence, fail in practical 3D setup. Motivated by these observations, we propose a model-driven 3D beam-steering mechanism called Orthogonal Scanner (OScan), which can maintain high performance for mobile 60 GHz links in 3D space. OScan discovers and leverages a hidden interaction between 3D beams and the spatial channel profile of 60 GHz radios, and strategically scans the 3D space so as to reduce the search latency by more than one order of magnitude. Experiment results based on a custom-built 60 GHz platform along with a trace-driven emulator demonstrate OScan's remarkable throughput gain, up to 5×, compared with the state-of-the-art.
Overview of methods for image reconstruction from projections in emission computed tomography (2003)

Emission computed tomography (ECT) is a technology for medical imaging whose importance is increasing rapidly. There is a growing appreciation for the value of the functional (as opposed to anatomical) information that is provided by ECT and there are significant advancements taking place, both in the instrumentation for data collection, and in the computer methods for generating images from the measured data. These computer methods are designed to solve the inverse problem known as "image reconstruction from projections". This paper uses the various models of the data collection process as the framework for presenting an overview of the wide variety of methods that have been developed for image reconstruction in the major subfields of ECT, which are positron emission tomography (PET) and single-photon emission computed tomography (SPECT). The overall sequence of the major sections in the paper, and the presentation within each major section, both proceed from the more realistic and general models to those that are idealized and application specific. For most of the topics, the description proceeds from the three-dimensional case to the two-dimensional case. The paper presents a broad overview of algorithms for PET and SPECT, giving references to the literature where these algorithms and their applications are described in more detail.
Transcriptome Profiling, Molecular Biological, and Physiological Studies Reveal a Major Role for Ethylene in Cotton Fiber Cell Elongation (2006)

Upland cotton (Gossypium hirsutum) produces the most widely used natural fibers, yet the regulatory mechanisms governing fiber cell elongation are not well understood. Through sequencing of a cotton fiber cDNA library and subsequent microarray analysis, we found that ethylene biosynthesis is one of the most significantly upregulated biochemical pathways during fiber elongation. The 1-Aminocyclopropane-1-Carboxylic Acid Oxidase1-3 (ACO1-3) genes responsible for ethylene production were expressed at significantly higher levels during this growth stage. The amount of ethylene released from cultured ovules correlated with ACO expression and the rate of fiber growth. Exogenously applied ethylene promoted robust fiber cell expansion, whereas its biosynthetic inhibitor l-(2-aminoethoxyvinyl)-glycine (AVG) specifically suppressed fiber growth. The brassinosteroid (BR) biosynthetic pathway was modestly upregulated during this growth stage, and treatment with BR or its biosynthetic inhibitor brassinazole (BRZ) also promoted or inhibited, respectively, fiber growth. However, the effect of ethylene treatment was much stronger than that of BR, and the inhibitory effect of BRZ on fiber cells could be overcome by ethylene, but the AVG effect was much less reversed by BR. These results indicate that ethylene plays a major role in promoting cotton fiber elongation. Furthermore, ethylene may promote cell elongation by increasing the expression of sucrose synthase, tubulin, and expansin genes.
Wafer fabrication scheduling using flow rate control strategy (2003)

The authors present a strategy for shop-level scheduling in a semiconductor wafer fabrication facility, which reduces WIP (work in process) and improves on-time ship performance. Algorithms for lot-release and lot-dispatch are defined on the basis of dynamic programming techniques. The strategy is called flow rate control because it treats the production rates according to certain rules. The most important rule is the two-boundary rule that consists of a simple inventory control policy and a simple surplus control policy. Development of the strategy was motivated by three features of the wafer manufacturing process: job re-entry, the large number of machines and products, and random events such as machine failures and yield fluctuations. Two-boundary control works by first forming a virtual job shop corresponding to the manufacturing process flow. Inventory and surplus levels are calculated for each job step and compared with predetermined values. These predetermined values are calculated from the failure rates and yield fluctuations of wafer fabrication. The loading rate at each job step in the wafer fabrication process is determined by the result of the comparison. An event-driven simulator designed for job shop production simulation was used to compare the flow rate control strategy with other scheduling strategies. The results showed marked improvement in WIP levels and ship performance over these other approaches.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Network perspective of science and technology policy research community in Taiwan (2010)

This study proposes a way of mapping Sci-Tech policy research community by quantitatively analyzing Sci-Tech policy research projects funded by Taiwan government in recent thirty years. Taiwans Sci-Tech policy rsearch networks composed by research community and knowledge distribution are quantitatively investigated by the use of network theory and Taiwans Sci-Tech policy research map is created to obtain the purpose of two-dimensional visualization. The 3-dimensional networks and two-dimensional knowledge maps on the basis of the Taiwans Sci-Tech policy research projects can be depicted differently by choosing different information as network actor, e.g. institute, project investigator or keyword, to reflect Sci-Tech policy research structures in micro, meso, and macro-levels, respectively. Sci-Tech policy research projects are retrieved from GRB (Government Research Bulletin) database which archives research projects sponsored by Taiwan government. A total of 143 projects are retrieved in this study, most of research projects (59%) belong to the field of management, economics, and other (social). It can be observed that more Sci-Tech policy research projects in the field of technology management have been funded, and also the coverage of fields has been increased since 2000. This indicates not only the emergence but also the interdisciplinary phenomenon of Sci-Tech policy research in Taiwan.
Studies on pyruvate decarboxylase: acyloin formation from aliphatic, aromatic and heterocyclic aldehydes (1991)

D. H. G. Crout, H. Dalton, D. W. Hutchinson and M. Miyagoshi, J. Chem. Soc., Perkin Trans. 1, 1991, 1329 DOI: 10.1039/P19910001329
Pathogenesis and immune response of vaccinated and unvaccinated rhesus monkeys to tick-borne encephalitis virus (1983)

The rhesus monkey was used as a model for diseases caused by viruses of the tick-borne encephalitis virus complex to study the efficacy and safety of a commercial killed vaccine. Animals infected intravenously developed a subclinical infection with no histopathological lesions but with transient clinical chemical changes that included elevated transaminase, dehydrogenase, and creatine kinase activities and that declined as an immune response developed. The immune response was detected as neutralizing antibody in serum and serum antibody to several viral proteins. Antibodies to viral envelope protein and two other infected cell-specific polypeptides were also detected. Intranasal infection resulted in a disease resembling that in humans, except that no pyrexia was observed. Clinical chemical changes similar to those in intravenously infected monkeys developed, but most animals died before an immune response was mounted. Using this model, we have demonstrated that a commercial vaccine protects animals against a wild-type virus isolate and that it elicits an effective immune reaction without any evidence of an immune enhancement phenomenon or adverse side effects as judged by clinical observation, clinical chemistry, and histopathology.
Confinement of Transmembrane Cell Receptors in Tunable Stripe Micropatterns (2005)

We report a simple method to confine transmembrane cell receptors in stripe micropatterns of a lipid/lipopolymer monolayer, which are formed as result of the transfer onto a solid substrate. The stripes are aligned perpendicular to the meniscus, whose periodicity can systematically be tuned by the transfer velocity. This strongly suggests the dominant role of the cooperative interaction between the film and substrate. Selective fluorescence labeling of lipids and lipopolymers confirms that the observed patterns coincide with the demixing of two species. Covalent coupling of polymer headgroups enables us to use the stripe patterns as a support for a lipid bilayer membrane. Spreading of lipid vesicles with platelet integrin alphaIIbbeta3 on a self-assembled membrane micropattern demonstrates that cell adhesion receptors are selectively incorporated into the lipopolymer-rich region. The method established here provides us with a tunable template for the confinement of receptor proteins to geometrically control the cell adhesion.
Automatic determination of pedicle screw size, length, and trajectory from patient data (2005)

Pedicle screw insertion is an orthopaedic spinal fixation procedure involving the placement of screws through individual spine pedicles and secured in spinal vertebrae. Pedicle anatomy varies widely within and across the patient population, and many complications have been reported with the surgical technique. To reduce complications, an automated procedure was developed that utilizes patient-specific medical imaging data to predetermine optimum pedicle screw size, length, and trajectory. The procedure involves importing medical imaging scans into the software, creating uniform voxel data for algorithm simplicity, segmenting the bony anatomy of the spine and defining its boundary, and identifying the pedicle using a search algorithm. The operations are performed in two-dimensions in the coordinate system of the medical imaging data. For each image slice, the minimum pedicle width is identified, and examining all slices identifies the overall minimum pedicle width. The optimum trajectory is determined using a 3D linear least squares fit to the array of minimum pedicle width midpoints. With the optimum trajectory determined, the maximum screw size and length are determined.
Electron paramagnetic resonance of transition ions (1970)

This book is a reissue of a classic Oxford text, and provides a comprehensive treatment of electron paramagnetic resonance of ions of the transition groups. The emphasis is on basic principles, with numerous references to publications containing further experimental results and more detailed developments of the theory. An introductory survey gives a general understanding, and a general survey presents such topics as the classical and quantum resonance equations, thespin-Hamiltonian, Endor, spin-spin and spin-lattice interactions, together with an outline of the known behaviour of ions of each
Antitumor effect of systemic administration of novel recombinant tumor necrosis factor (rTNF-S) with less toxicity than conventional rTNF-alpha in vivo. (1989)

This study reported that acute toxicity (expressed as the LD50 value) of rTNF-SAM1 and rTNF-SAM2 which we constructed was considerably lower than that of rTNF-alpha (1). Following this finding, the antitumor effects of systemic administration of these novel recombinant tumor necrosis factors (TNF-S) (named rTNF-SAM1 and rTNF-SAM2) were examined in vivo on murine tumors (Meth A fibrosarcoma, MH134 hepatoma, and B16 melanoma). Both rTNF-SAM1 and rTNF-SAM2 could be administered systemically to tumor-bearing mice at doses up to 3 X 10(4) to 10(5) U. Growth of all tumors was significantly inhibited by systemic administration of rTNF-SAM1 or rTNF-SAM2 at a dose of greater than 3 X 10(4) U; at this dosage conventional rTNF-alpha could not be administered systemically to any of the mice strains due to its toxicity. These results confirm our previous finding that the rTNF-SAM group can be administered with safety at higher doses than rTNF-alpha, and revealed that these novel rTNF-S could be more promising antitumor drugs than rTNF-alpha in view of their lower toxicity compared with antitumor effect.
Antibodies to granulocytic ehrlichiae in cattle from Connecticut (2002)

Enzyme-linked immunosorbent assays (ELISA) with a purified recombinant 44-kDa protein and indirect fluorescent antibody (IFA) staining methods incorporating whole-cell antigens of the human granulocytic ehrlichiosis (HGE) agent were used to detect antibodies to Ehrlichia phagocytophila genogroup organisms in cattle sera. The cattle lived in tick-infested areas of Connecticut, USA and were healthy at the times blood samples were collected in 1990, 1999 and 2000. Of the 339 serum samples analysed, 40 (12%) and 15 (4%) were positive by ELISA and IFA, respectively. Western immunoblots of a subset of sera verified antibody reactivity of six serum samples, positive by ELISA with titres of 640-2,560, to a protein with a molecular mass of c. 44 kDa. Although seroprevalence rates were low, cattle were exposed to the HGE agent at different sites and should be monitored for anaemia, leukopenia or thrombocytopenia, especially if there is evidence of unexplained decreased milk production. Different serological testing methods should be used to detect immunoglobulins.
An Empirical Evaluation of Ten Depth Cameras: Bias, Precision, Lateral Noise, Different Lighting Conditions and Materials, and Multiple Sensor Setups in Indoor Environments (2018)

Over the last few years, novel color and depth sensors have pushed the boundaries of robot perception significantly. Today, several new depth-sensing products are replacing the earlier, well-examined red-green-blue-depth (RGBD) sensors, which have reached the end of their product life cycle and are no longer available. The properties of the new sensors have not yet been investigated, and it is unclear how they will compare to earlier RGBD sensors.
Zero-Knowledge Accumulators and Set Operations (2015)

Abstract. Accumulators provide a way to succinctly represent a set with elements drawn from a given domain, us-ing an accumulation value. Subsequently, short proofs for the set-membership (or non-membership) of any element from the domain can be constructed and efficiently verified with respect to this accumulation value. Accumula-tors have been widely studied in the literature, primarily, as an authentication primitive: a malicious prover (e.g., an untrusted server) should not be able to provide convincing proofs on false statements (e.g., successfully prove membership for a value not in the set) to a verifier that issues membership queries (of course, having no access to set itself). In essence, in existing constructions the accumulation value acts as a (honestly generated) “commitment” to the set that allows selective “opening ” as specified by membership queries—but with no “hiding ” properties. In this paper we revisit this primitive and propose a privacy-preserving enhancement. We define the notion of a zero-knowledge accumulator that provides the following very strong privacy notion: Accumulation values and proofs constructed during the protocol execution leak nothing about the set itself, or any subsequent updates to it (i.e., via element insertions/deletions). We formalize this property by a standard real/ideal execution game. An adversarial party that is allowed to choose the set and is given access to query and update oracles, cannot distinguish whether this interaction takes place with respect to the honestly executed algorithms of the scheme or with a simulator that is not given access to the set itself (and for updates, it does not even learn the type of update
Modeling and Analyzing Real-Time Data Streams (2011)

Achieving situation awareness is especially challenging for real-time data stream applications because they i) operate on continuous unbounded streams of data, and ii) have inherent real-time requirements. In this paper we show how formal data stream modeling and analysis can be used to better understand stream behavior, evaluate query costs, and improve application performance. We use MEDAL, a formal specification language based on Petri nets, to model the data stream queries and the Quality-of-Service (QoS) management mechanisms in a data stream system. MEDAL's ability to combine query logic and data admission control in one model allows us to design a single comprehensive model of the system. This model can be used to perform a large set of analyses to help improve the application's performance and QoS.
Conjugation of Duplexed siRNN Oligonucleotides with DD-HyNic Peptides for Cellular Delivery of RNAi Triggers (2016)

Despite the great promise that short interfering RNA (siRNA) induced RNAi responses hold as a therapeutic modality, due to their size (~15 kDa) and high negative charge (Bumcrot et al., 2006), siRNAs have no bioavailability and require a delivery agent to enter cells (Figure 1). TAT peptide transduction domain (PTD) has been developed as an agent that mediates cellular delivery of macromolecular therapeutics that otherwise lack bioavailability, making it a tantalizing candidate for siRNA delivery (Farkhani et al., 2014). Unfortunately, when conjugated to TAT PTD, the presence of 40 negative phosphodiester backbone charges on siRNA neutralizes the cationic PTD resulting in aggregation and poor cellular delivery (Meade and Dowdy, 2007). In light of this, we synthesized a neutral RNAi trigger, termed siRiboNucleic Neutrals, for conjugation to TAT PTD (Meade et al., 2014). In brief, the negatively charged phosphodiester backbone was neutralized by synthesis with bio-reversible phosphotriester protecting groups which are specifically converted into charged phosphodiester bonds inside of cells by the action of cytoplasmic restricted thioesterases resulting in a wild type siRNA that can induce RNAi responses. Here we describe the conjugation and cellular delivery of siRNN oligonucleotides with TAT PTD delivery domain (DD) HyNic peptides.