gebhart/patrepeval huggingface dataset:
575. High Content Analysis of CRISPR-Cas9 Gene-Edited Human Embryonic Stem Cells (2016)

Gene-edited human cells are important resources for drug target identification, regulatory science, regenerative medicine and basic biology. Recently, use of the CRISPR-Cas9 system drastically cut the time required to produce gene-edited cell lines down to a few months. Targeted gene disruption in a population of human cells followed by selection and next-generation sequencing can identify drug targets, however many of these methods destroy all mutant clones, so a subsequent gene-editing experiment is required to obtain living mutant cells for downstream analysis. Overall, there is a need to increase the speed, multiplexing and precision in generating CRISPR-Cas9 mutants. ArrayEdit, a simple approach utilizing surface-modified multiwell plates containing one-pot transcribed single-guide RNAs (see Figure), separates thousands of edited cell populations for automated, live, high-content imaging and analysis. The approach lowers the time and cost of gene editing and produces edited human embryonic stem cells at high efficiencies. Edited genes can be expressed in both pluripotent stem cells and differentiated cells from all three major germ layers. This allows for the real-time observation of mutations causing phenotypic differences that can be measured in in vitro tissues and organoids during culture as opposed to defined end points. The live cell and tissue assays on ArrayEdit are compatible with standard screening platforms and a variety of human cell types, thus permitting robust and sensitive detection of differences in proliferation, differentiation and other downstream effects of gene editing. This preclinical platform adds important capabilities to observe editing and selection in situ within complex structures generated by human cells, ultimately enabling optical and other molecular perturbations in the editing workflow that could refine the specificity and versatility of gene editing.
Anticipatory Optimization of Traffic Control (2000)

Traffic control and travelers’ behavior are two mutually influential processes with different objectives. Decisions made in traffic control influence travelers’ possibilities in choosing their preferred mode, route, and time of departure; and the choices made by travelers influence the optimization possibilities for traffic control. This research presents the results of simulation studies and a mathematical analysis of this bilevel optimization problem. Under certain conditions, multiple stable situations are possible, but some of these situations are sensitive to small disturbances by which the system moves away from the original equilibrium state. There appears to be a nonlinear relationship between system parameters and the character and location of the equilibrium situations. The details of the travel time model appear to have a large influence. If road authorities want to optimize traffic control, they have to anticipate the reaction of travelers. This makes the optimization process much more complicated. Iterative optimization, where traffic control is adjusted as soon as traffic conditions change, generally does not lead to a system optimum. Methods are therefore necessary that allow for the optimization of traffic control while taking into account that traffic flows will change as a result of traffic control.
ChemInform Abstract: Crystal Structure and Magnetic Properties of Di‐μ‐aqua‐bis[μ‐[N,N′‐bis(2‐hydroxyethyl)dithiooxamidato(2‐)‐N,O,S :N′,O′,S′]]bis[aquacopper(II)sulfatocopper(II)]. A New Example of Very Strong Antiferromagnetic Coupling Between Copper(II)Ions Far Away from Each Other. (1980)

Abstract Die 3:1‐molare Umsetzung von Cu(II)‐sulfatpentahydrat mit N,N′‐Bis‐[2‐hydroxyethyl]‐dithiooxamid in Methanol, die anschließende Zugabe von konz. H 2 SO 4 und Behandlung mit Ammoniumsulfat enthaltenem Wasser führen zu einem kristallinen Niederschlag, dem aufgrund einer Röntgenanalyse und magnetischer Untersuchungen die Struktur (I) zuerkannt wird.
Consolidation of Interacting BPEL Process Models with Fault Handlers. (2013)

Abstract The interaction behavior between processes of organizations and their suppliers can be modeled by using choreographies. When an organization decides to gain more control about their suppliers and to minimize transaction costs they may decide to insource these companies. This also requires the integration of the partner processes into the organization. In previous work we proposed an approach to merge (consolidate) interacting BPEL process models of different partners into a single process model by deriving control flow links between the process models from their interaction specification. In this work we are detailing this consolidation approach. Thereby, special attention is turned on extending the consolidation operations in a way that process models with fault handlers can be merged. 1
Studies on Acylase Activity and Microorganisms. XX. Isolation of Soil Bacteria Capable of Resolving Tryptophan by their Acylase on N-Acetyl-DL-tryptophan (1962)

Two strains (KT 251 and KT 253) of bacteria capable of resolving tryptophan by their acylase on N-acetyl-DL-tryptophan were isolated from soil samples by using a synthetic medium containing N-acetyl-DL-tryptophan as the sole source of carbon. Both. KT 251 and KT 253 could be cultivated in various synthetic media.
Characterising the association of latency with α1-antitrypsin polymerisation using a novel monoclonal antibody (2014)

α1-Antitrypsin is primarily synthesised in the liver, circulates to the lung and protects pulmonary tissues from proteolytic damage. The Z mutant (Glu342Lys) undergoes inactivating conformational change and polymerises. Polymers are retained within the hepatocyte endoplasmic reticulum (ER) in homozygous (PiZZ) individuals, predisposing the individuals to hepatic cirrhosis and emphysema. Latency is an analogous process of inactivating, intra-molecular conformational change and may co-occur with polymerisation. However, the relationship between latency and polymerisation remained unexplored in the absence of a suitable probe. We have developed a novel monoclonal antibody specific for latent α1-antitrypsin and used it in combination with a polymer-specific antibody, to assess the association of both conformers in vitro, in disease and during augmentation therapy. In vitro kinetics analysis showed polymerisation dominated the pathway but latency could be promoted by stabilising monomeric α1-antitrypsin. Polymers were extensively produced in hepatocytes and a cell line expressing Z α1-antitrypsin but the latent protein was not detected despite manipulation of the secretory pathway. However, α1-antitrypsin augmentation therapy contains latent α1-antitrypsin, as did the plasma of 63/274 PiZZ individuals treated with augmentation therapy but 0/264 who were not receiving this medication (p<10(-14)). We conclude that latent α1-antitrypsin is a by-product of the polymerisation pathway, that the intracellular folding environment is resistant to formation of the latent conformer but that augmentation therapy introduces latent α1-antitrypsin into the circulation. A suite of monoclonal antibodies and methodologies developed in this study can characterise α1-antitrypsin folding and conformational transitions, and screen methods to improve augmentation therapy.
Optical Response of Photonic Crystals Requiring High Precision Band Calculation in the Form of<b>k</b>(ω) Including Evanescent Waves (2005)

We give a general method to calculate photonic band structure in the form of wave number k as a function of frequency ω, which is required whenever we want to calculate signal intensity related with photonic band structure. This method is based on the fact that the elements of the coefficient matrix for the plane wave expansion of the Maxwell equations contain wave number up to the second order, which allows us to rewrite the original eigenvalue equation for ω 2 into that for wave number. This method is much better, especially for complex wave numbers, than the transfer matrix method of Pendry, which gives the eigenvalues in the form of exp [i k d ]. The present method leads to a good improvement in the calculation of reflectivity spectrum by eliminating unphysical part due to insufficient precision of numerical results, showing the cross-section dependence of a surface of given Miller index more precisely.
Mammalian blastocyst: transport functions in a developing epithelium (1988)

This article reviews the current state of knowledge concerning morphological and physiological mechanisms important to growth and differentiation of the mammalian blastocyst between compaction and implantation. Morphological processes occur in conjunction with major changes in transport systems that control the movement of substances into and out of the embryo. Compaction is a morphological development that is associated with the formation of an outer squamous epithelium, the trophectoderm, which regulates the composition of the medium bathing the presumptive embryo (the inner cell mass). Implantation involves the interaction of two epithelia, the adhesion between the trophectoderm and the maternal endometrium. Before adhesion, the blastocyst lies free in the uterine fluid and exchanges occur between this fluid and the embryo. Apposition of these epithelia is brought about in part by expansion of the blastocyst and removal of the uterine fluid. Blastocyst physiology is an inherently important field because vectorial transport system development and the genes that regulate it can be studied.
Evolution of the Pseudogap State of High-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi>T</mml:mi></mml:mrow><mml:mrow><mml:mi>c</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math>Superconductors with Doping (1996)

We report on a study of the infrared properties of ${\mathrm{Bi}}_{2}{\mathrm{Sr}}_{2}{\mathrm{CaCu}}_{2}{\mathrm{O}}_{8+\ensuremath{\delta}}$, ${\mathrm{Bi}}_{1.66}{\mathrm{Pb}}_{0.34}{\mathrm{Sr}}_{2}{\mathrm{CaCu}}_{2}{\mathrm{O}}_{8+\ensuremath{\delta}}$, and ${\mathrm{Tl}}_{2}{\mathrm{Ba}}_{2}{\mathrm{CuO}}_{6+\ensuremath{\delta}}$ crystals at doping levels from underdoped to strongly overdoped. We calculate the frequency-dependent scattering rate $1/\ensuremath{\tau}(\ensuremath{\omega},T)$ and study its doping dependence. While we observe a normal-state gaplike depression in $1/\ensuremath{\tau}(\ensuremath{\omega},T)$ in the underdoped regime, it is not observed in the overdoped regime. While the high-frequency $1/\ensuremath{\tau}(\ensuremath{\omega},T)$ is temperature independent in the underdoped regime, it scales with temperature in the overdoped regime.
Lieu-temps [Of time and place] (2007) (Ricordiamo Forlì, 2005 - 53'30", Arrivederci, 2005 - 15'40") DVD-A (digital audio media), Empreintes digitales iMED0787, Montréal, 2007 (2007)

Two related works make up this publication, created with the assistance of an AHRC research leave award (2004-5): Ricordiamo Forlì (digital audio work) and Arrivederci (ensemble and electroacoustic sounds).\n\nPremieres: Ricordiamo Forlì: Cultural Exchanges, De Montfort University, Leicester, 2 March 2006 (Premiere broadcast: Radio New Zealand ConcertFM, 24 July 2006); Arrivederci, Ilott Concert Chamber, Wellington Town Hall, New Zealand, 20 July 2006, by ensemble STROMA)\n\nPublished: Empreintes Digitales, Montréal, 2007.\n\nAward: Ricordiamo Forlì was awarded first prize in the programme music category of the 34th Concours Internationaux de Musique et d’Art Sonore Électroacoustiques de Bourges, 2007.\n\nResearch summary: This disc contains the results of a practice-led research project investigating the potentials of natural sound sources to support the creation of musical structures. The two works share common material in the form of cathedral bells from the Italian city of Forlì, and a more generally poetic theme of emotional response to the passage of time and the sense of ‘place’ as experienced through the contemplation of a specific soundscape. Ricordiamo Forlì is a hybrid work that integrates elements of documentary, radiophonic and electroacoustic music in relating the story of one family and one Allied soldier in Italy in WWII, largely in and around the town of Forlì. The work integrates original present-day field recordings made there, the soldier’s recollections of events, and original war correspondence and actuality recordings found in BBC and Radio New Zealand sound archives. Arrivederci takes a Forlì ‘soundmark’ (the bell of the city’s Duomo) and uses spectral deconstruction and mixing techniques to shape the harmonic structure, fusing the imagery of a sound drawn from a real environment with abstract spectral/harmonic development. A report on the methods used in these works was given in ‘Sound, Sign and Sense’ a paper presented at the 2005 Sonoimágenes conference, Buenos Aires.
Effect of Precipitates on Fatigue Strength (1971)

Many high-strength alloys, such as Cu-Be alloy, Al-Cu-Mg-Zn alloy (duralumin), 17-7 PH stainless steel and maraging steel are strengthened by dispersing fine precipitates into a matrix. However, the increase of fatigue strength by precipitation hardening is usually smaller than the values expected from other mechanical properties. For example, carbon steel has a value σw⁄σB=0.4∼0.5 (σw: fatigue limit, σB: tensile strength), but as for duralumin, σw⁄σB=0.2∼0.3. These properties paticular to fatigue strength of precipitation-hardening alloys are assumed to be mainly due to the generation of lattice vacancies or interstitials during fatigue process. So, the effect of excess vacancies on ageing process during fatigue is very interesting.Then the effects of point defects generated by fatigue during the ageing process and the influence of fine precipitates on fatigue strength were investigated for Cu-Be alloy, Fe-Ni-Ti alloy, and Fe-Cr-Mo alloy which have relatively high recrystallization temperatures.As a result of experiments, the fatigue strength of these alloys was found to increase by precipitating fine particles in the matrix. The precipitating process is accelerated by the generation of lattice vacancies and interstitials during fatigue. When precipitation-hardening alloys are aged isothermally, the increase rate of fatigue strength is larger than that of other mechanical properties. However, the absolute value for the increase of fatigue strength is small as compared with other mechanical properties. The influence of the size and distribution of fine precipitate on fatigue strength was investigated using a transmission electron microscope.
Equilibrium concentration of singlet oxygen in photoreaction of reaction center/carbon nanotube bionanocomposites (2015)

The reaction center protein is the unit in the photosynthetic organisms in which the primary events of the photoelectric energy conversion take place during photosynthesis. When the photochemistry following the excitation of the reaction center by light is oversaturated there is a large probability to form reactive oxygen species (ROS, e.g., singlet oxygen (1O2)). Because the ROS components decrease the overall yield of the photochemical energy conversion there is a considerable effort in many laboratories to find conditions to reduce these harmful compounds. The aim of our work is to create a system by using carbon nanotubes (CNTs) and RCs for efficient light-energy conversion. The role of the 1O2 that destroys the RC structure is discussed. 1,3-Diphenylisobenzofuran was used to detect the concentration of the 1O2. Although, 1O2 can be sensitized by CNTs in certain conditions, in our experiments the main sources of the 1O2 are the RCs. The concentration of the 1O2 in the equilibrium is determined by the forward sensitization and the backward deactivation processes of the components and functions of the CNT/RC composite.
Studies of the anti–platelet factor 4/heparin immune response: adapting the enzyme‐linked immunosorbent spot assay for detection of memory B cells against complex antigens (2009)

HIT lacks a strong memory B-cell response, perhaps explaining transience and lack of anamnesis of the anti-PF4/heparin immune response. The technical modifications we describe for the ELISPOT assay, which permit detection of B-cell reactions to complex antigens, could be useful for studying other immunohematologic disorders, for example, drug-dependent thrombocytopenia and acquired hemophilia.
The Phase of Iron Catalyst Nanoparticles during Carbon Nanotube Growth (2012)

We study the Fe-catalyzed chemical vapor deposition of carbon nanotubes by complementary in situ grazing-incidence X-ray diffraction, in situ X-ray reflectivity, and environmental transmission electron microscopy. We find that typical oxide supported Fe catalyst films form widely varying mixtures of bcc and fcc phased Fe nanoparticles upon reduction, which we ascribe to variations in minor commonly present carbon contamination levels. Depending on the as-formed phase composition, different growth modes occur upon hydrocarbon exposure: For γ-rich Fe nanoparticle distributions, metallic Fe is the active catalyst phase, implying that carbide formation is not a prerequisite for nanotube growth. For α-rich catalyst mixtures, Fe3C formation more readily occurs and constitutes part of the nanotube growth process. We propose that this behavior can be rationalized in terms of kinetically accessible pathways, which we discuss in the context of the bulk iron–carbon phase diagram with the inclusion of phase equilibrium lines for metastable Fe3C. Our results indicate that kinetic effects dominate the complex catalyst phase evolution during realistic CNT growth recipes.
Specialty fibers for discrete and distributed sensing application (2009)

Over the past decades, discrete or distributed Fiber Optic Sensing (FOS) applications have seen an increased acceptance in many areas. High level optical and mechanical reliability of optical fiber is necessary to guarantee reliable performance of FOS. In this paper, we review recent research and development activities on new specialty fibers. The main approaches to enhancing fiber attributes include new refractive index profile design and fiber coating modification.
Identifying Deep Contrasting Networks from Time Series Data: Application to Brain Network Analysis (2017)

The analysis of multiple time series data, which are generated from a networked system, has attracted much attention recently. This technique has been used in a wide range of applications including functional brain network analysis of neuroimaging data and social influence analysis. In functional brain network analysis, the activity of different brain regions can be represented as multiple time series. An important task in the analysis is to identify the latent network from the observed time series data. In this network, the edges (functional connectivity) capture the correlation between different time series (brain regions). Conventional network extraction approaches usually focus on capturing the connectivity through linear measures under unsupervised settings. In this paper, we study the problem of identifying deep nonlinear connections under group-contrasting settings, where we have two groups of time series samples, and the goal is to identify nonlinear connections that are discriminative across the two groups. We propose a method called GCC (Graph Construction CNN) which is based on deep convolutional neural networks for the task of network construction. The CNN in our model learns a nonlinear edge-weighting function to assign discriminative values to the edges of a network. Experiments on a real-world ADHD dataset show that our proposed method can effectively identify the nonlinear connections among different brain regions. We also demonstrate the extensibility of our proposed framework by combining it with an autoencoder to capture subgraph patterns from the constructed networks.
ChemInform Abstract: SILBERION‐INDUZIERTE RINGOEFFNUNG VON CHLOR‐FLUOR‐CYCLOPROPANEN (1974)

Abstract 1‐Chlor‐1‐fluor‐cyclopropane (I) werden durch Behandlung mit Silberacetat in Essigsäure in Gegenwart geringer Mengen Silbertetrafluoroborat unter Ringöffnung in 2‐Fluor‐allylacetate (II) übergeführt, die sich sehr leicht zu den entsprechenden Allylalkoholen(III) verseifen lassen.
Parental History of Diabetes in an Insulin‐treated Diabetes Registry (1997)

To confirm observations of an excess maternal transmission of Type 2 (non-insulin dependent) diabetes mellitus in a setting which minimizes potential biases and confounders, we explored the patterns of maternal and paternal diabetes in a cohort (n = 1775) of subjects with insulin-treated diabetes mellitus (ITDM) in Tasmania, Australia. In order to identify individuals with Type 1 diabetes or insulin-treated Type 2 diabetes, cases were classified into groups based on their age at diagnosis and subsequent time to commencement of insulin. Individuals initially diagnosed younger than age 30 (predominantly Type 1 diabetes cases) reported a similar percentage of mothers and fathers with diabetes, but individuals diagnosed at age 30 or older (predominantly insulin-treated Type 2 diabetes) reported a maternal excess of diabetes. Having an elevated body mass index was associated with a higher frequency of maternal diabetes, but not of paternal diabetes. Because both childhood-onset Type 1 diabetes and adult-onset insulin-treated Type 2 diabetes cases were subject to the same potential study biases, these results offer support for an excess maternal role in Type 2 diabetes transmission. © 1997 by John Wiley & Sons, Ltd.
A severe case of Puumala hantavirus infection successfully treated with bradykinin receptor antagonist icatibant (2013)

A patient with severe capillary leakage syndrome caused by a Puumala hantavirus infection was treated with a single dose of icatibant, a bradykinin receptor antagonist, with a dramatic positive response. We suggest that this drug should be tested in a larger number of patients with severe hantavirus infection.
Computer‐Aided Concrete‐Placement Optimization (1990)

This paper describes an enumeration method that considers both material costs and time‐delay penalties to minimize the total cost of a concrete pour subject to quality and time constraints. A wide variety of placement alternatives can be considered for each pour. The method uses the concrete‐maturity method to determine if particular concrete mix and placement combinations are feasible. The method was implemented in conjunction with a commercially available concrete strength and maturity development monitoring and simulation program. This software implementation is called the Economic Optimization Module (EOM). The EOM finds the most desirable combination of concrete mixes, concrete starting temperatures, formwork types, and curing/insulation materials for a variety of pour characteristics, weather conditions, and time requirements. Cost minimization is performed subject to quality and time constraints provided by the user. The system uses a data base of concrete mixes, concrete starting temperatures, soil types, soil temperatures, formwork types, and curing/insulation types.
Battle Analysis: The Battle of Monte la Difensa. Deliberate Assault, Mountains, Winter, 2-8 December 1943 (1984)

From 2-8 Dec 1943, a composite US-Canadian elite force of highly trained soldiers attacked German Forces on one of the mountains in the Camino hill mass, a key terrain feature on the route to Rome. The battle analysis provides valuable information on mountain warfare and small unit factors.