gebhart/patrepeval huggingface dataset:
The Molecular Nature of Stromal-Derived Inducing Activity in Dopaminergic Differentiation of Human Embryonic Stem Cells (2008)

The utilization of Stromal-Derived Inducing Activity (SDIA) is one of the most efficientmethods in generating dopaminergic (DA) neurons from embryonic stem cells (ESC).Neuronal and dopaminergic ind ...
Genes of the transforming growth factor-beta signalling pathway are associated with pre-implantation embryonic development in cattle (2012)

One of the main factors affecting cattle fertility is pre-implantation development of the bovine embryo, which is a complex process regulated by various signal-transduction pathways. The transforming growth factor-β (TGF-β) signalling system, which is responsible for many biological processes including cell proliferation, differentiation and apoptosis, also is involved in embryo development. We hypothesized that altered expression of TGF-β genes in pre-implantation bovine embryos is associated with morphological abnormalities of these embryos. To test this hypothesis, we produced embryos in vitro and classified them at the blastocyst stage as either normally developed blastocysts or degenerates (growth-arrested embryos). The expression patterns of 25 genes from the TGF-β pathway were assessed using quantitative real time PCR. Ten genes showed differential expression between the two embryo groups, four genes displayed similar expressional profiles, and 11 genes had no detectable expression. An altered expression profile was statistically significant for 10 of the 14 expressed genes, and all were up-regulated in degenerate embryos vs. blastocysts. Furthermore, genomic association analysis of the cows from which embryos were produced revealed a significant association of ID3 and BMP4 polymorphisms--two of the most significant differentially expressed genes--with fertilization rate and blastocyst rate, respectively. Taken together, we conclude that TGF-β pathway genes, especially BMP4 and ID3 play a vital function in the regulation of pre-implantation embryo development at both embryo and maternal levels. Hence, these genes may be suitable as genetic markers for embryo development and fertility in cattle.
Association of Genetic Variation to Healthfulness of Beef (2005)

The objective was to determine the natural variability in beef fatty acid composition and to identify single nucleotide polymorphisms (SNPs) in the stearoyl-CoA desaturase (SCD) gene to test the association of SNPs with fatty acid composition. We have used common gas chromatographic techniques to determine the fatty acid composition of phospholipids and triacylglycerols (TAGs) extracted from beef muscle (longissimus dorsi) from 800 sire-identified cattle originating from Iowa State University beef cattle breeding selection projects. Heritability of individual fatty acids and indexes of fatty acid desaturase and elongase systems were calculated by evaluating specific ratios of fatty acids (product/precursor). In general, we found that TAG composition is heritable, but phospholipid composition is not. The atherogenic index of TAGs as proposed by Ulbright and Southgate had a heritability estimate of 0.55 and 0.45 for the TAG and total lipids, respectively. Individual fatty acids of TAGs also had high heritability estimates. For example, the heritability estimates of 14:0 and 16:0 in TAG were 0.49 and 0.40, respectively. Monounsaturates 16:1 and 18:1 in TAGs both had heritability estimates greater than 0.5. Future research will focus on DNA sequencing of candidate genes from sires that are phenotypically divergent for a trait of interest. Ultimately, we plan to develop DNA markers for use in selecting breeding stock to improve healthfulness of fatty acids in beef. Three SNP candidates in the SCD gene were tested by using Iowa State University beef cattle. Two of the potential SNPs were homozygous in this population (n=123). We have classified 172 cattle into two genotypes, VA and VV, based on the third SNP. The ratio of palmitoleic acid (C16:1) concentration vs palmitic acid (C16:0) concentration of TAG is significantly associated with the SNP (P=0.02). There is no significant association of the SNP with the fatty acid composition of phospholipids.
Fabrication of thin-film LiMn2O4 cathodes for rechargeable microbatteries (1991)

We have fabricated thin-film cathodes of lithiated manganese oxide (LixMn2O4, where x≤1), which can reversibly intercalate nearly one Li atom per unit formula, at a steady potential of 4.1 V. This results in a theoretical energy density of about 600 Wh/kg. The polycrystalline films (thickness of 0.5–2 μm) show electrochemical performance exceeding that of bulk materials. This is attributed to the small grain size and the porosity within these LixMn2O4 three-dimensional spinel films, reducing the diffusion path length for Li+ ions. The films are tested as the cathodes in about 70 charging/discharging cycles, in a secondary lithium cell, at current rates of 10–100 μA cm−2. No measurable self-discharge over 12 h periods is observed. These thin-film cathodes with above electrochemical properties are very promising for a new generation thin-film secondary batteries.
A novel, compliant, four degree-of-freedom, robotic fingertip sensor (1990)

A novel, low-cost, compliant fingertip sensor for robotic gripper applications is presented. The fingertip sensor is intended for use in grippers where force feedback information is needed, such as in clean room or space applications where telerobotic operation is desired. The fingertip is approximately the size of the thumb of an adult male and is approximately as compliant as human flesh. The sensor was designed to optimize the sensitivity to four components of force/torque: the normal force, both tangential force terms, and the torque about the normal axis. Finite-element analysis was used to optimize the shape of the fingertip and the location/size of the polyvinylidene fluoride (PVDF) film piezoelectric sensing elements. The design analysis and the experimental results from evaluation of the prototype robot fingertip sensors are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Intra-Domain Group Key Management Protocol (2000)

This document describes a protocol for intra-domain group key
management for IP multicast security, based on the framework of
[HCD99]. In order to support multicast groups, the domain is divided
into a number of administratively-scoped A host-member of a
multicast group is defined to reside within one (and only one) of
these areas. The purpose of placing host-members in areas is to
achieve flexible and efficient key management, particularly in the
face of the problem of changes (joining, leaving, ejections) in the
membership of a multicast group. A separate administratively-scoped
area control-group is defined for each (data) multicast group, for the
express purpose of key management and other control-message delivery.
Current perpendicular to the plane spin-valves with CoFeGe magnetic layers (2008)

The magnetotransport properties of current perpendicular to the plane giant magnetoresistive spin-valves utilizing (CoFe)100−xGex alloys are investigated. The composition range of 21≤x≤32 at. % is determined to be the alloy composition that maximizes magnetoresistance. ΔRA values of 2.6 mΩ–μm2 are measured for spin-valves with CoFeGe in the free and reference layer resulting in magnetoresistance values of greater than 6%, which is almost twice the value of similar spin-valves with CoFeAl alloys. An analysis of the physical properties of the CoFeGe thin films in the range of interest is also presented.
Genetic mechanisms of <i>Rhesus box</i> variation (2005)

There is considerable variation of Rhesus box sequences associated with distinct RHD alleles. RHD zygosity diagnostics in African persons is best based on quantitative polymerase chain reaction or amplification of the full-length hybrid Rhesus box. Because aberrant Rhesus boxes were observed among European persons, use of more than one method for hybrid Rhesus box detection may even be advisable in European persons.
Sparseness Measures of Signals for Compressive Sampling (2007)

Recent theoretical developments in compressive sampling (or compressed sensing) show that if a signal has a sparse representation in some basis, then it is possible to capture the signal information via a small number of projections. Furthermore, the signal can be accurately reconstructed using low complexity algorithms. Although the information encoding process may be agnostic to signal type – random projections can capture the information with high probability – accurate reconstruction of the signal often depends on proper selection of a reconstruction basis. In this paper, we evaluate techniques for measuring sparseness, including some not traditionally used in signal processing, and apply them to compressive sampling with the goal of selecting the best basis for signal reconstruction.
Dynamic Temperature Management of Near-Sensor Processing for Energy-Efficient High-Fidelity Imaging (2021)

Vision processing on traditional architectures is inefficient due to energy-expensive off-chip data movement. Many researchers advocate pushing processing close to the sensor to substantially reduce data movement. However, continuous near-sensor processing raises sensor temperature, impairing imaging/vision fidelity. We characterize the thermal implications of using 3D stacked image sensors with near-sensor vision processing units. Our characterization reveals that near-sensor processing reduces system power but degrades image quality. For reasonable image fidelity, the sensor temperature needs to stay below a threshold, situationally determined by application needs. Fortunately, our characterization also identifies opportunities-unique to the needs of near-sensor processing-to regulate temperature based on dynamic visual task requirements and rapidly increase capture quality on demand. Based on our characterization, we propose and investigate two thermal management strategies-stop-capture-go and seasonal migration-for imaging-aware thermal management. For our evaluated tasks, our policies save up to 53% of system power with negligible performance impact and sustained image fidelity.
Scanning laser ophthalmoscope design with adaptive optics (2005)

A design for a high-resolution scanning instrument is presented for <i>in vivo</i> imaging of the human eye at the cellular scale. This system combines adaptive optics technology with a scanning laser ophthalmoscope (SLO) to image structures with high lateral (~2 μm) resolution. In this system, the ocular wavefront aberrations that reduce the resolution of conventional SLOs are detected by a Hartmann-Shack wavefront sensor, and compensated with two deformable mirrors in a closed-loop for dynamic correction and feedback control. A laser beam is scanned across the retina and the reflected light is captured by a photodiode, yielding a two-dimensional image of the retina at any depth. The quantity of back-scattered light from the retina is small (0.001% of reflection) and requires the elimination of all parasite reflections. As an <i>in vivo</i> measurement, faint cellular reflections must be detected with a low-energy source, a supraluminescent laser diode, and with brief exposures to avoid artifacts from eye movements. The current design attempts to optimize trade-offs between improved wavefront measurement and compensation of the optical aberrations by fractioning the light coming to the wavefront sensor, better sensitivity by increasing the input light energy or the exposure time and the response speed of the system. This instrument design is expected to provide sufficient resolution for visualizing photoreceptors and ganglion cells, and therefore, may be useful in diagnosing and monitoring the progression of retinal pathologies such as glaucoma or aged-related macular degeneration.
Preparation of Water-soluble PEGylated Semiconductor Nanocrystals (2004)

Abstract We describe the synthesis of water-soluble PEGylated semiconductor nanocrystals and the characterization of their optical properties and colloidal stability by fluorescence and UV spectrometers. The fluorescence intensity of PEGylated CdSe/ZnS in PBS buffer was observed to be 75% of the initial values of conventional CdSe/ZnS in chloroform. The PEGylated CdSe/ZnS exhibited higher fluorescence intensity than PEGylated CdSe and CdSe/CdS in PBS buffer. The colloidal stability of PEGylated QDs in PBS buffer was estimated by transmittance as a function of time at 37 °C. The PEGylated CdSe/ZnS showed a colloidal stable dispersion in PBS buffer during 24 h.
Calixarenes with diphenylphosphoryl acetamide functions at the upper rim. A new class of highly efficient extractants for lanthanides and actinides (1996)

Various calix[4]arene tetraalkyl ethers and a calix[5]arene pentaalkyl ether substituted at the upper rim by the CMPO-like functional group –NH–C(O)–CH2–P(O)Ph2 as well as some linear model compounds have been synthesized for the first time. Their ability to extract europium, thorium, neptunium, plutonium and americium from 1 mol dm–3 aqueous HNO3 into methylene chloride or o-nitrophenyl hexyl ether was studied under various conditions. All the new oligomeric ligands, but especially the calixarene derivatives, are tremendously strong extractants compared with the commonly used CMPO [(N,N-diisobutylcarbamoylmethyl)octylphenylphosphine oxide]. Also in transport studies through supported liquid membranes their efficiency is higher than that of CMPO which shows lower transport rates even at a 10-fold concentration.
In Vitro Assembly of Diverse Bacterial Microcompartment Shell Architectures (2018)

Bacterial microcompartments (BMCs) are organelles composed of a selectively permeable protein shell that encapsulates enzymes involved in CO<sub>2</sub> fixation (carboxysomes) or carbon catabolism (metabolosomes). Confinement of sequential reactions by the BMC shell presumably increases the efficiency of the pathway by reducing the crosstalk of metabolites, release of toxic intermediates, and accumulation of inhibitory products. Because BMCs are composed entirely of protein and self-assemble, they are an emerging platform for engineering nanoreactors and molecular scaffolds. However, testing designs for assembly and function through in vivo expression is labor-intensive and has limited the potential of BMCs in bioengineering. Here, we developed a new method for in vitro assembly of defined nanoscale BMC architectures: shells and nanotubes. By inserting a "protecting group", a short ubiquitin-like modifier (SUMO) domain, self-assembly of shell proteins in vivo was thwarted, enabling preparation of concentrates of shell building blocks. Addition of the cognate protease removes the SUMO domain and subsequent mixing of the constituent shell proteins in vitro results in the self-assembly of three types of supramolecular architectures: a metabolosome shell, a carboxysome shell, and a BMC protein-based nanotube. We next applied our method to generate a metabolosome shell engineered with a hyper-basic luminal surface, allowing for the encapsulation of biotic or abiotic cargos functionalized with an acidic accessory group. This is the first demonstration of using charge complementarity to encapsulate diverse cargos in BMC shells. Collectively, our work provides a generally applicable method for in vitro assembly of natural and engineered BMC-based architectures.
Detection of heavy metal ions using screen printed wireless LC sensor (2015)

This paper reports on the successful development of a fully printed wireless LC sensor for the detection of toxic heavy metal ions. The LC sensor, consisting of inductors and interdigitated electrodes (IDE) in planar form, was screen printed on flexible polyethylene-terephthalate (PET) substrate with silver (Ag) ink as metallization layer. Palladium nanoparticles (Pd NP) were drop casted onto the IDEs as sensing layer. The resonant frequency of the LC sensor was remotely monitored by measuring the reflection coefficient (S <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</inf> ) of a detection coil (planar inductor). The change in resonant frequency of the LC sensor towards varying concentrations of mercury (Hg <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> +) and lead (Pb <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> +) ions, revealed micro molar detection levels. The response of the printed wireless LC sensor is analyzed and presented.
Effect of Column Parameters on FRP-Confined Concrete (1998)

Confinement effectiveness of fiber reinforced plastic (FRP) jackets (shells) in concrete columns depends on several parameters, including concrete strength, types of fibers and resin, fiber volume and fiber orientation in the jacket, jacket thickness, shape of cross section, length-to-diameter (slenderness) ratio of the column, and the interface bond between the core and the jacket. In this paper effects of shape, length, and bond on FRP-confined concrete are studied. Square sections are shown to be less effective in confining concrete than their circular counterparts. Their effectiveness is measured by a modified confinement ratio that is a function of the corner radius and the jacket's hoop strength. Length effect in short columns of up to 5:1 is shown to be similar to ACI provisions for tied columns, i.e., 10% eccentricity and 20% strength reduction in pure compression. While chemical adhesive bond does not change the confinement effectiveness of the jacket, mechanical shear connectors can enhance the load-carrying capacity of the column by providing an effective load distribution mechanism.
Exploiting annotations for the rapid development of collaborative web applications (2013)

Web application frameworks are a proven means to accelerate the development of interactive web applications. However, implementing collaborative real-time applications like Google Docs requires specific concurrency control services (i.e. document synchronization and conflict resolution) that are not included in prevalent general-purpose frameworks like jQuery or Knockout. Hence, developers have to get familiar with specific collaboration frameworks (e.g. ShareJS) which substantially increases the development effort. To ease the development of collaborative web applications, we propose a set of source code annotations representing a lightweight mechanism to introduce concurrency control services into mature web frameworks. Those annotations are interpreted at runtime by a dedicated collaboration engine to sync documents and resolve conflicts. We enhanced the general-purpose framework Knockout with a collaboration engine and conducted a developer study comparing our approach to a traditional concurrency control library. The evaluation results show that the effort to incorporate collaboration capabilities into a web application can be reduced by up to 40 percent using the annotation-based solution.
Diversity coding for transparent self-healing and fault-tolerant communication networks (1993)

A channel coding approach called diversity coding is introduced for self-healing and fault-tolerance in digital communication networks for nearly instantaneous recovery from link failures. To achieve this goal, the problem of link failures is treated as an erasure channel problem. Implementation details of this technique in existing and future communication networks are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The high affinity choline transporter: topology and choline binding site as studied by site‐directed mutagenesis (2008)

The high affinity choline transporter (CHT1) is expressed in cholinergic neuron. CHT1 takes up choline and provides it for acetylcholine synthesis. CHT1 has two putative glycosylation sites (N69, N301). We found that N69Q mutant was glycosylated as well as wild type CHT1, but N301Q mutant was not glycosylated and not expressed on the cell surface. We have constructed a number of mutants substituted with cysteine and examined the accessibility of impermeable SH reagent to each cysteine residue in these mutants expressed in HEK293 cells. Obtained results indicated that CHT1 has the extracellular amino terminus and 13 transmembrane segments. Several acidic or basic amino acid residues in the putative third and 12th transmembrane segments were indicated to be involved in the choline uptake activity. In particular, the E451D mutant had approximately five times higher Km for choline uptake and five times lower Kd for HC3 binding as compared with wild type hCHT1, indicating that the E451 residue is involved in recognition of choline and HC3.
Bridging Centrality: Identifying Bridging Nodes in Scale-free Networks (2006)

Several centrality measures were introduced to identify essential components and compute components’ importance in networks. Majority of these centrality measures are dominated by components’ degree due to their nature of looking at networks’ topology. We propose a novel essential component identification model, bridging centrality, based on information flow and topological locality in scale-free networks. Bridging centrality provides an entirely new way of scrutinizing network structures and measuring components’ importance. We apply bridging centrality on real world networks, including one simulated network, two biological networks, two social networks, and one web network, and show that the nodes distinguished by bridging centrality are well located on the connecting positions between highly connected regions through analyzing the clustering coefficient and average path length of those networks. Bridging centrality can discriminate bridging nodes, the nodes with more information flowed through them and locations between highly connected regions, while other centrality measures can not.
Efficient framework for deformable 2D-3D registration (2008)

Using 2D-3D registration it is possible to extract the body transformation between the coordinate systems of X-ray and volumetric CT images. Our initial motivation is the improvement of accuracy of external beam radiation therapy, an effective method for treating cancer, where CT data play a central role in radiation treatment planning. Rigid body transformation is used to compute the correct patient setup. The drawback of such approaches is that the rigidity assumption on the imaged object is not valid for most of the patient cases, mainly due to respiratory motion. In the present work, we address this limitation by proposing a flexible framework for deformable 2D-3D registration consisting of a learning phase incorporating 4D CT data sets and hardware accelerated free form DRR generation, 2D motion computation, and 2D-3D back projection.