gebhart/patrepeval huggingface dataset:
Genetically targeted cell disruption in Caenorhabditis elegans (1997)

The elimination of identified cells is a powerful tool for investigating development and system function. Here we report on genetically mediated cell disruption effected by the toxic Caenorhabditis elegans mec-4(d) allele. We found that ectopic expression of mec-4(d) in the nematode causes dysfunction of a wide range of nerve, muscle, and hypodermal cells. mec-4(d)-mediated toxicity is dependent on the activity of a second gene, mec-6, rendering cell disruption conditionally dependent on genetic background. We describe a set of mec-4(d) vectors that facilitate construction of cell-specific disruption reagents and note that genetic cell disruption can be used for functional analyses of specific neurons or neuronal classes, for confirmation of neuronal circuitry, for generation of nematode populations lacking defined classes of functional cells, and for genetic screens. We suggest that mec-4(d) and/or related genes may be effective general tools for cell inactivation that could be used toward similar purposes in higher organisms.
Thermal Inactivation of Uricase (Urate Oxidase): Mechanism and Effects of Additives (2012)

Uricase (Urc) is an oxidoreductase enzyme of both general and commercial interest, the former because of its lack of a cofactor and the latter because of its use in the treatment of hyperuricemic disorders. Results of fluorometry and circular dichroism (CD) spectroscopy indicate that the main phase of thermal Urc inactivation follows an irreversible two-state mechanism, with loss of ~20% of the helical structure, loss of the majority of the tertiary structure, and partial exposure of tryptophan residues to solution being approximately concurrent with activity loss. Results of size exclusion chromatography and 8-anilinonaphthalene-1-sulfonate binding studies confirm that this process results in the formation of aggregated molten globules. In addition to this process, CD studies indicate the presence of a rapid reversible denaturation phase that is not completely coupled to the main phase. Urc inactivation is inhibited by the presence of glycerol and trimethylamine oxide, stabilizers of hydrophobic interactions and backbone structure respectively, confirming that loss of hydrophobic bonding and loss of helical structure are key events in the loss of Urc activity. NaCl, however, destabilizes the enzyme at elevated temperature, emphasizing the importance of ionic interactions to Urc stability. A model is developed in which interfacial disruption, involving local loss of hydrophobic interactions, ionic bonds, and helical structure, leads to Urc inactivation and aggregation. Additional studies of Urc inactivation at a more ambient temperature indicate that the inactivation process followed under such conditions is different from that followed at higher temperatures, highlighting the limitations of high-temperature enzyme stability studies.
Discovering probiotic microorganisms: in vitro, in vivo, genetic and omics approaches (2015)

Over the past decades the food industry has been revolutionized toward the production of functional foods due to an increasing awareness of the consumers on the positive role of food in wellbeing and health. By definition probiotic foods must contain live microorganisms in adequate amounts so as to be beneficial for the consumer's health. There are numerous probiotic foods marketed today and many probiotic strains are commercially available. However, the question that arises is how to determine the real probiotic potential of microorganisms. This is becoming increasingly important, as even a superficial search of the relevant literature reveals that the number of proclaimed probiotics is growing fast. While the vast majority of probiotic microorganisms are food-related or commensal bacteria that are often regarded as safe, probiotics from other sources are increasingly being reported raising possible regulatory and safety issues. Potential probiotics are selected after in vitro or in vivo assays by evaluating simple traits such as resistance to the acidic conditions of the stomach or bile resistance, or by assessing their impact on complicated host functions such as immune development, metabolic function or gut-brain interaction. While final human clinical trials are considered mandatory for communicating health benefits, rather few strains with positive studies have been able to convince legal authorities with these health claims. Consequently, concern has been raised about the validity of the workflows currently used to characterize probiotics. In this review we will present an overview of the most common assays employed in screening for probiotics, highlighting the potential strengths and limitations of these approaches. Furthermore, we will focus on how the advent of omics technologies has reshaped our understanding of the biology of probiotics, allowing the exploration of novel routes for screening and studying such microorganisms.
Medical Imaging and Registration in Computer Assisted Surgery (1998)

Imaging, sensing, and computing technologies that are being introduced to aid in the planning and execution of surgical procedures are providing orthopaedic surgeons with a powerful new set of tools for improving clinical accuracy, reliability, and patient outcomes while reducing costs and operating times. Current computer assisted surgery systems typically include a measurement process for collecting patient specific medical data, a decision making process for generating a surgical plan, a registration process for aligning the surgical plan to the patient, and an action process for accurately achieving the goals specified in the plan. Some of the key concepts in computer assisted surgery applied to orthopaedics with a focus on the basic framework and underlying technologies is outlined. In addition, technical challenges and future trends in the field are discussed.
A survey of methods and strategies in character segmentation (1996)

Character segmentation has long been a critical area of the OCR process. The higher recognition rates for isolated characters vs. those obtained for words and connected character strings well illustrate this fact. A good part of recent progress in reading unconstrained printed and written text may be ascribed to more insightful handling of segmentation. This paper provides a review of these advances. The aim is to provide an appreciation for the range of techniques that have been developed, rather than to simply list sources. Segmentation methods are listed under four main headings. What may be termed the "classical" approach consists of methods that partition the input image into subimages, which are then classified. The operation of attempting to decompose the image into classifiable units is called "dissection." The second class of methods avoids dissection, and segments the image either explicitly, by classification of prespecified windows, or implicitly by classification of subsets of spatial features collected from the image as a whole. The third strategy is a hybrid of the first two, employing dissection together with recombination rules to define potential segments, but using classification to select from the range of admissible segmentation possibilities offered by these subimages. Finally, holistic approaches that avoid segmentation by recognizing entire character strings as units are described.
Anomalous threo-diastereoselectivity in allylic silane- or stannane–aldehyde condensation reactions: new interpretation of the antiperiplanar vs. synclinal problem on the transition-state conformations (1990)

Unusual threo-diastereoselectivity has been observed in the intermolecular reactions of β-substituted crotyl-silane or-stannane with 2-benzyloxypropanal under chelation conditions, which implies preference for the synclinal over the antiperiplanar transition state.
Injury to muscle fibres after single stretches of passive and maximally stimulated muscles in mice. (1995)

1. Our purpose was to investigate the initial mechanisms responsible for contraction‐induced injury. Most studies of mechanisms of contraction‐induced injury have been based on observations made either shortly after many repeated contractions at the peak of fatigue, or days after, at the peak of delayed onset injury. As a result, conclusions based on these studies are complicated by interactions of mechanical and biochemical events, as well as the passage of time. We studied the initial mechanical events associated with contraction‐induced injury immediately following single stretches of whole skeletal muscles of mice in situ. 2. We tested the hypothesis that immediately following a single stretch, the severity of contraction‐induced injury is a function of both strain and average force. Consequently, the work done to stretch the muscle would be the best predictor of the magnitude of injury. Extensor digitorum longus muscles were adjusted to optimum length for force (L(o)). Passive (not stimulated) and maximally activated muscles were exposed to single stretches of 10, 20, 30, 50 or 60% strain, relative to muscle fibre length (Lf), at a rate of 2 Lf s‐1. 3. The magnitude of injury was represented by the force deficit 1 min after the stretch expressed as a percentage of the maximum force prior to the stretch. The occurrence of injury was confirmed directly by electron microscopic analysis of the ultrastructure of muscle fibres that were fixed immediately following single stretches. 4. For active muscles, a single stretch of only 30% strain produced a significant force deficit, whereas for passive muscles, a larger strain was required. Stretches of greater than 50% strain resulted in greater force deficits for passive than for maximally activated muscles. For either condition, the work done to stretch the muscle was the best predictor of the magnitude of injury, accounting for 76% of the variability in the force deficit for maximally activated muscles, and 85% for passive muscles.
Applying Semantic Web Service Composition for Action Planning in Multi-robot Systems (2009)

In this paper we demonstrate how the Web services based solutions can be effectively utilized and integrated into robotic world. In particular, we consider robotic systems where overall control is not embedded into any of the robots and the local behavior of each robot is loosely dependent on behavior of other robots. We propose an architecture for swarm action planning based on Web services paradigm exploiting a problem ontology for service discovery, linear logic based service composition for action planning and a task allocation layer for finding the most suitable robot to perform an action. In our solution all entities in the system expose their functionalities as Web services and allow dynamic service discovery and selection.
Characteristics of a monoclonal antibody (WT-31) that recognizes a common epitope on the human T cell receptor for antigen. (1985)

We describe a monoclonal antibody, WT-31, that reacted with all human T lymphocytes. Electrophoretic analysis of the material reacting with WT-31 revealed that it precipitated predominantly an 80-kD disulfide-linked heterodimer from the cell surface-labeled T leukemic cell line HPB-ALL. This heterodimer was identical to the one precipitated with a recently described monoclonal reagent, T40/25, which recognizes a clonotypic structure on HPB-ALL. The target antigen of WT-31 comodulated with T3 after incubation of T cells with excess anti-T3 antibody, indicating that the WT-31 target antigen is associated with T3. We also found that anti-T3 reagents, but not the clonotypic reagent T40/25, blocked binding of FITC-labeled WT-31 to HPB-ALL cells. This indicates that the T cell receptor epitope recognized by WT-31 is located close to the epitopes recognized by the anti-T3 reagents anti-Leu-4 and SPV-T3b but distal from the clonotypic T40/25 epitope. Functional studies showed that WT-31 reacts similar to anti-T3 antibodies. It is mitogenic for resting T cells, blocks cytolysis mediated by alloantigen-specific CTL clones, and induces antigen-nonspecific cytolysis by CTL clones against Daudi target cells. WT-31 did not inhibit the formation of conjugates, but it blocked cytolysis just before or during the Ca2++-dependent programming for lysis. We conclude that WT-31 is an antibody that recognizes a common determinant on the T cell receptor for antigen. The present results support the notion that the two chains of the T cell receptor (alpha and beta) form a functional protein ensemble with the three invariable T3 polypeptide chains (T3-gamma-, delta-, epsilon).
Supply of Fatty Acid Is One Limiting Factor in the Accumulation of Triacylglycerol in Developing Embryos1 (1999)

Abstract The metabolic factors that determine oil yield in seeds are still not well understood. To begin to examine the limits on triacylglycerol (TAG) production, developingCuphea lanceolata, Ulmus carpinifolia, and Ulmus parvifolia embryos were incubated with factors whose availability might limit oil accumulation. The addition of glycerol or sucrose did not significantly influence the rate of TAG synthesis. However, the rate of 14C-TAG synthesis upon addition of 2.1 mm14C-decanoic acid (10:0) was approximately four times higher than the in vivo rate of TAG accumulation in C. lanceolata and two times higher than the in vivo rate in U. carpinifolia andU. parvifolia. In C. lanceolata embryos, the highest rate of 14C-TAG synthesis (14.3 nmol h−1 embryo−1) was achieved with the addition of 3.6 mm decanoic acid. 14C-Decanoic acid was incorporated equally well in all three acyl positions of TAG. The results suggest that C. lanceolata, U. carpinifolia, and U. parvifolia embryos have sufficient acyltransferase activities and glycerol-3-phosphate levels to support rates of TAG synthesis in excess of those found in vivo. Consequently, the amount of TAG synthesized in these oilseeds may be in part determined by the amount of fatty acid produced in plastids.
High-throughput DNA synthesis in a multichannel format (1995)

We describe an approach to high-throughput parallel DNA synthesis in which a multiwell format is used. The reactions are carried out in open wells using an argon ambient atmosphere to prevent reagent contamination. The controlled-pore glass beads which form the substrate for synthesis are held in individual wells with high-density polyethylene filter bottoms through which reagents are drawn into a vacuum manifold. The synthesis is carried out using direct reagent dispensing into the individual reaction wells. A computer controls the sequence in which reagents are dispensed and the timing of the periodic vacuum pulses required to synthesize the desired sequence. Experiments to date have demonstrated the viability of the approach for a variety of test sequences. Results obtained with HPLC analysis demonstrate coupling efficiencies as high as 99.5% under optimized conditions. Use of the oligomers for DNA sequencing templates and as PCR primers has been demonstrated in production applications. The current instrument design consists of a series of discrete reaction chambers in a 12 channel module which can be multiplexed in a 12 x n format where n can be 1-8, i.e. 96 wells. A projected time interval for 12 parallel syntheses is 2.5 h, with 96 syntheses in 3.5 h. Because of the reduced volume of reagents required in the open well format, significant cost savings are projected.
Extensive Association of Functionally and Cytotopically Related mRNAs with Puf Family RNA-Binding Proteins in Yeast (2004)

Genes encoding RNA-binding proteins are diverse and abundant in eukaryotic genomes. Although some have been shown to have roles in post-transcriptional regulation of the expression of specific genes, few of these proteins have been studied systematically. We have used an affinity tag to isolate each of the five members of the Puf family of RNA-binding proteins in Saccharomyces cerevisiae and DNA microarrays to comprehensively identify the associated mRNAs. Distinct groups of 40-220 different mRNAs with striking common themes in the functions and subcellular localization of the proteins they encode are associated with each of the five Puf proteins: Puf3p binds nearly exclusively to cytoplasmic mRNAs that encode mitochondrial proteins; Puf1p and Puf2p interact preferentially with mRNAs encoding membrane-associated proteins; Puf4p preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors; and Puf5p is associated with mRNAs encoding chromatin modifiers and components of the spindle pole body. We identified distinct sequence motifs in the 3'-untranslated regions of the mRNAs bound by Puf3p, Puf4p, and Puf5p. Three-hybrid assays confirmed the role of these motifs in specific RNA-protein interactions in vivo. The results suggest that combinatorial tagging of transcripts by specific RNA-binding proteins may be a general mechanism for coordinated control of the localization, translation, and decay of mRNAs and thus an integral part of the global gene expression program.
Advanced polymer systems for optoelectronic integrated circuit applications (1997)

An advanced versatile low-cost polymeric waveguide technology is proposed for optoelectronic integrated circuit applications. We have developed high-performance organic polymeric materials that can be readily made into both multimode and single-mode optical waveguide structures of controlled numerical aperture (NA) and geometry. These materials are formed from highly crosslinked acrylate monomers with specific linkages that determine properties such as flexibility, toughness, loss, and stability against yellowing and humidity. These monomers are intermiscible, providing for precise adjustment of the refractive index from 1.30 to 1.60. Waveguides are formed photolithographically, with the liquid monomer mixture polymerizing upon illumination in the UV via either mask exposure or laser direct-writing. A wide range of rigid and flexible substrates can be used, including glass, quartz, oxidized silicon, glass-filled epoxy printed circuit board substrate, and flexible polyimide film. We discuss the use of these materials on chips and on multi-chip modules (MCMs), specifically in transceivers where we adaptively produced waveguides on vertical-cavity surface-emitting lasers (VCSELs) embedded in transmitter MCMs and on high- speed photodetector chips in receiver MCMs. Light coupling from and to chips is achieved by cutting 45 degree mirrors using excimer laser ablation. The fabrication of our polymeric structures directly on the modules provides for stability, ruggedness, and hermeticity in packaging.
Bayesian analysis of signaling networks governing embryonic stem cell fate decisions (2004)

The Bayesian network modeling approach allows us to uncover previously reported signaling activities related to mouse ES cell self-renewal, such as the roles of LIF and STAT3 in maintaining undifferentiated ES cell populations. Furthermore, the network predicts novel influences such as between ERK phosphorylation and differentiation, or RAF phosphorylation and differentiated cell proliferation. Visualization of the influences detected by the Bayesian network provides intuition about the underlying physiology of the signaling pathways. We demonstrate that the Bayesian networks can capture the linear, nonlinear and multistate logic interactions that connect extracellular cues, intracellular signals and consequent cell functional responses.
Spread-Spectrum Mobile Radio with Variable-Bit-Rate Speech Transmission (1982)

We describe a digital mobile radio system in which users experiencing poor transmission reduce the number of bits per second used for speech coding from 32000 to 28000. They do so in a manner that greatly reduces the binary error rate. The reduced error rate more than compensates for increased quantization noise. We predict two statistics of user satisfaction in a mobile radio service area: POW, the percentage of users experiencing poor or worse transmission, and GOB, the percentage good or better. In a typical environment the maximum number of users that can operate within a 20 MHz band with POW ≤ 5 percent is 137, compared to 91 users when everyone transmits 32 kbits/s. The modulation technique is FH-FSK (frequency hopped, frequency shift keying) and the digital code is embedded ADPCM (adaptive differential pulse code modulation), in the mobile radio service area, signal strength depends on distance from mobile unit to a central base station. There is slow (shadow) fading due to terrain and building variations and rapid (Rayleigh) fading due to multipath propagation. To predict user satisfaction we have combined three different analyses: 1) a theory of FH-FSK, 2) a theory of the signal-to-noise ratio statistics in mobile radio service areas, and 3) a model, based on computer simulations and subjective testing data, of the dependence of subjective speech quality on ADPCM transmission rate and binary error rate.
Vision-based autonomous mapping and exploration using a quadrotor MAV (2012)

In this paper, we describe our autonomous vision-based quadrotor MAV system which maps and explores unknown environments. All algorithms necessary for autonomous mapping and exploration run on-board the MAV. Using a front-looking stereo camera as the main exteroceptive sensor, our quadrotor achieves these capabilities with both the Vector Field Histogram+ (VFH+) algorithm for local navigation, and the frontier-based exploration algorithm. In addition, we implement the Bug algorithm for autonomous wall-following which could optionally be selected as the substitute exploration algorithm in sparse environments where the frontier-based exploration under-performs. We incrementally build a 3D global occupancy map on-board the MAV. The map is used by the VFH+ and frontier-based exploration in dense environments, and the Bug algorithm for wall-following in sparse environments. During the exploration phase, images from the front-looking camera are transmitted over Wi-Fi to the ground station. These images are input to a large-scale visual SLAM process running off-board on the ground station. SLAM is carried out with pose-graph optimization and loop closure detection using a vocabulary tree. We improve the robustness of the pose estimation by fusing optical flow and visual odometry. Optical flow data is provided by a customized downward-looking camera integrated with a microcontroller while visual odometry measurements are derived from the front-looking stereo camera. We verify our approaches with experimental results.
Influence of Acellular Natural Lung Matrix on Murine Embryonic Stem Cell Differentiation and Tissue Formation (2010)

We report here the first attempt to produce and use whole acellular (AC) lung as a matrix to support development of engineered lung tissue from murine embryonic stem cells (mESCs). We compared the influence of AC lung, Gelfoam, Matrigel, and a collagen I hydrogel matrix on the mESC attachment, differentiation, and subsequent formation of complex tissue. We found that AC lung allowed for better retention of cells with more differentiation of mESCs into epithelial and endothelial lineages. In constructs produced on whole AC lung, we saw indications of organization of differentiating ESC into three-dimensional structures reminiscent of complex tissues. We also saw expression of thyroid transcription factor-1, an immature lung epithelial cell marker; pro-surfactant protein C, a type II pneumocyte marker; PECAM-1/CD31, an endothelial cell marker; cytokeratin 18; alpha-actin, a smooth muscle marker; CD140a or platelet-derived growth factor receptor-alpha; and Clara cell protein 10. There was also evidence of site-specific differentiation in the trachea with the formation of sheets of cytokeratin-positive cells and Clara cell protein 10-expressing Clara cells. Our findings support the utility of AC lung as a matrix for engineering lung tissue and highlight the critical role played by matrix or scaffold-associated cues in guiding ESC differentiation toward lung-specific lineages.