gebhart/patrepeval huggingface dataset:
Autophagy in Neuroprotection and Neurodegeneration: A Question of Balance (2008)

A central issue in developing therapies for neurodegenerative diseases involves understanding why adaptive responses to stress or injury fail to prevent synaptic dysfunction and neuronal cell death. Macroautophagy is a major, evolutionarily conserved response to nutrient and bioenergetic stresses, which has the capacity to remove aggregated proteins and damaged organelles such as mitochondria. This has prompted intense interest in autophagy-related therapies for Huntington's, Alzheimer's, Parkinson's, stroke and other neurological diseases. However, excessive or imbalanced induction of autophagic recycling can actively contribute to neuronal atrophy, neurite degeneration and cell death. Oxidative-, aging- and disease-related increase in demand for autophagy, coupled with declining axonal trafficking, lysosomal degradation or biosynthetic efficiencies promote increased susceptibility to a harmful state of autophagic stress. A more complete understanding of dysfunction along the entire spectrum of autophagic recycling, from autophagosome formation through clearance and regeneration of new cellular components is necessary to restore balance to the system, promote neuronal health and maximize therapeutic potentials.
History of the Acetone-Butanol-Ethanol Fermentation Industry in China: Development of Continuous Production Technology (2007)

The acetone-butanol-ethanol (ABE) fermentation industry in China was started in the early 1950s in Shanghai and expanded rapidly thereafter. At its peak, there were about 30 plants all over the country and the total annual production of solvents reached 170,000 tons. This large enterprise was compelled to complete shutdown at the end of the 20th century due to the rapid increase of petrochemicals. The success of the ABE industry in China had special features like the development of a continuous fermentation technology. Its main strategic considerations were as follows: maintaining maximal growth and acid production phase, adoption of multiple stages in the solvent phase to allow gradual adaptation to increasing solvent, and the incorporation of stillage to offer enough nutrients to delay cell degeneration. Due to the tremendous national demand for solvents, China has begun a new round of ABE fermentation research. It is expected that a new era in the ABE industry is on the horizon.
Solid state: Fast electron-beam lithography: High blanking speeds may make this new system a serious challenger in producing submicrometer ICs (1981)

Electron-beam lithography may become competitive with optical methods for making integrated circuits. The step that could make this possible is an electron-beam lithography system developed at Hewlett-Packard that is potentially many times faster than previous machines for making ICs through direct writing on wafers or generating high-precision masks. The Hewlett-Packard system has a beam spot-corresponding to the smallest pixel that can be written-with a diameter that can be varied from 0.5 to 0.25 μm.
Dynamic programming parsing for context-free grammars in continuous speech recognition (1991)

The use of context-free grammars in automatic speech recognition is discussed. A dynamic programming algorithm for recognizing and parsing spoken word strings of a context-free grammar is presented. The time alignment is incorporated in to the parsing algorithm. The algorithm performs all functions simultaneously, namely, time alignment, work boundary detection, recognition, and parsing. As a result, no postprocessing is required. From the probabilistic point of view, the algorithm finds the most likely explanation or derivation for the observed input string, which amounts to Viterbi scoring rather than Baum-Welch scoring in the case of regular or finite-state languages. The algorithm provides a closed-form solution. The computational complexity of the algorithm is studied. Details of the implementation and experimental tests are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Both hPTH(1–34) and bFGF Increase Trabecular Bone Mass in Osteopenic Rats but They Have Different Effects on Trabecular Bone Architecture (2003)

Both hPTH(1-34) and bFGF are anabolic agents in the osteopenic female rat. However, hPTH(1-34) increases trabecular bone volume primarily by thickening existing trabeculae, whereas bFGF adds trabecular bone mass through increasing trabecular number and trabecular connectivity. These results suggest the possibility of sequential treatment paradigms for severe osteoporosis.
Characterization of dermonecrotic toxin produced by serotype D strains of Pasteurella multocida (1984)

Dermonecrotic toxin (DNT) produced by serotype D strains of Pasteurella multocida, isolated from pigs, was characterized and compared with DNT produced by Bordetella bronchiseptica. The DNT prepared by sonication from P multocida or B bronchiseptica had dermonecrotic activity and lethal toxicity for guinea pigs and mice, and also induced marked atrophy of spleens in the mice. Toxicity of P multocida or B bronchiseptica DNT was completely inactivated by heating at 70 C for 30 minutes, and was reduced by treatment with trypsin, formalin, or glutaraldehyde, indicating that the DNT may be a protein. Although biologic and toxic properties of P multocida DNT were similar to those of B bronchiseptica DNT, cross-neutralization tests between P multocida and B bronchiseptica indicated that DNT from the 2 bacterial species were serologically distinct.
Tuning principal component weights to individualize HRTFs (2012)

Prior research has investigated development of virtual auditory displays (VADs) using low-dimensional models of head related transfer functions (HRTFs) as a function of a finite number of principal components (PCs) and associated weights (PCWs). This paper investigates the effect of PCWs on horizontal plane HRTFs derived from a database of HRIRs through analytical optimization experiments. The experiments investigate whether average HRTFs can be tuned to match individual HRTFs. Results provide insight on the effect of tuning PCWs on spectral features of the HRTF. A reduced order modeling technique is used to compactly represent each HRTF. Subject testing results are provided, showing that a human can conduct the tuning procedure and reduce localization errors.
Common themes in microbial pathogenicity (1989)

A bacterial pathogen is a highly adapted microorganism which has the capacity to cause disease. The mechanisms used by pathogenic bacteria to cause infection and disease usually include an interactive group of virulence determinants, sometimes coregulated, which are suited for the interaction of a particular microorganism with a specific host. Because pathogens must overcome similar host barriers, common themes in microbial pathogenesis have evolved. However, these mechanisms are diverse between species and not necessarily conserved; instead, convergent evolution has developed several different mechanisms to overcome host barriers. The success of a bacterial pathogen can be measured by the degree with which it replicates after entering the host and reaching its specific niche. Successful microbial infection reflects persistence within a host and avoidance or neutralization of the specific and nonspecific defense mechanisms of the host. The degree of success of a pathogen is dependent upon the status of the host. As pathogens pass through a host, they are exposed to new environments. Highly adapted pathogenic organisms have developed biochemical sensors exquisitely designed to measure and respond to such environmental stimuli and accordingly to regulate a cascade of virulence determinants essential for life within the host. The pathogenic state is the product of dynamic selective pressures on microbial populations.
Revisiting Principal-Axes Aligned conies: A unified algebraic constraint and geometric interpretation for camera calibration (2012)

In this paper, we present a novel viewpoint of treating conks-based calibration as the algebraic and geometric constraints. From this viewpoint, we use four intersection points correspondence to conduct a unified algebraic constraint of Principal-Axes Aligned (PAA) conies which is a necessary and sufficient condition to recover the 2D Euclidean structure (ES). Under this unified constraint, we can establish the link to other existing approaches (such as concentric circles, confocal conies) and find some novel patterns. Meanwhile, the geometric interpretation that the quadrangle formed by PAA conies is actually a rectangle with one degree of freedom is shown. Then a framework is introduced to deal with various situations of PAA conies. Finally, we propose an optimization procedure to estimate the lens distortion which is discarded by previous methods. The experiments with linear method and optimization method show the good performance of our camera calibration algorithms.
On the integration of IR and Databases (1999)

Integration of information retrieval (IR) in database management systems (DBMSs) has proven difficult. Previous attempts to integration suffered from inherent performance problems, or lacked desirable separation between logical and physical data models. To overcome these problems, we discuss a database approach based on structural object-orientation. We implement of IR techniques using extensions in an object algebra called MOA. MOA has been implemented on top of the database backend Monet, a state-ofthe-art high-performance database kernel with a binary relational interface. Our prototype implementation of the inference network retrieval model using MOA and Monet demonstrates the feasibility of this approach. We evaluate the benefits of the resulting system. We conclude with a discussion of the topic of query optimization in the context of extending an object algebra.
Muscle and tendon: properties, models, scaling, and application to biomechanics and motor control. (1989)

Skeletal muscles transform neural control signals into forces that act upon the body segments to effect a coordinated motor task. This transformation is complex, not only because the properties of muscles are complex, but because the tendon affects the transmission of muscle force to the skeleton. This review focuses on how to synthesize basic properties of muscle and tendon to construct models applicable to studies of coordination. After a review of the properties of muscle and tendon, their integrated ability to generate force statically and dynamically is studied by formulating a generic model of the "musculotendon actuator", which has only one parameter, the ratio of tendon length at rest to muscle fiber length at rest. To illustrate the utility of the model, it is analyzed to show how this one parameter specifies whether excitation-contraction or musculotendon contraction is the rate-limiting process of force generation, whether elastic energy is stored in tendon or muscle, and whether hip- and knee-extensor actuators function as springs or dashpots during walking.
Upscaling of Geocellular Models for Flow Simulation (2004)

Geocellular reservoir descriptions are generally much too detailed for direct use in reservoir flow simulations. Upscaling procedures are required to coarsen these detailed reservoir models to scales more suitable for flow calculations. In this talk, a number of different upscaling techniques, appropriate for both moderate and high degrees of coarsening, will be described and illustrated. Upscaling of single-phase parameters (permeability) will be considered first. The approaches discussed include upscaling and grid generation techniques for unstructured models, upscaling in the near-well region, and an efficient local-global procedure for the calculation of upscaled transmissibilities that depend on the global flow field. The high level of accuracy of these methods will be illustrated for different types of permeability characterizations and global flows.
A universal, fault-tolerant, non-linear analytic network for modeling and fault detection (1992)

The similarities and differences of a universal network to normal neural networks are outlined. The description and application of a universal network is discussed by showing how a simple linear system is modeled by normal techniques and by universal network techniques. A full implementation of the universal network as universal process modeling software on a dedicated computer system at EBR-II is described and example results are presented. It is concluded that the universal network provides different feature recognition capabilities than a neural network and that the universal network can provide extremely fast, accurate, and fault-tolerant estimation, validation, and replacement of signals in a real system.
Role of Co-stimulation in Leishmaniasis (2011)

Leishmania are obligate intracellular parasites that cause a wide spectrum of diseases ranging from cutaneous, mucocutaneous and the visceral kind. Persistence or resolution of leishmaniasis is governed by host immune response. Co-stimulation is an important secondary signal that governs the extent, strength and direction of the immune response that follows. Co-stimulation by CD40, B7 and OX40 family has been shown to influence the outcome following Leishmania infection and manipulation of these pathways has shown promise for use in immune therapy of leishmaniasis. In this review, we discuss the roles of CD40, B7 and OX40 co-stimulatory pathways in regulating immunity to Leishmania and their implications in the treatment of this disease.
Global food demand and the sustainable intensification of agriculture (2011)

Global food demand is increasing rapidly, as are the environmental impacts of agricultural expansion. Here, we project global demand for crop production in 2050 and evaluate the environmental impacts of alternative ways that this demand might be met. We find that per capita demand for crops, when measured as caloric or protein content of all crops combined, has been a similarly increasing function of per capita real income since 1960. This relationship forecasts a 100-110% increase in global crop demand from 2005 to 2050. Quantitative assessments show that the environmental impacts of meeting this demand depend on how global agriculture expands. If current trends of greater agricultural intensification in richer nations and greater land clearing (extensification) in poorer nations were to continue, ~1 billion ha of land would be cleared globally by 2050, with CO(2)-C equivalent greenhouse gas emissions reaching ~3 Gt y(-1) and N use ~250 Mt y(-1) by then. In contrast, if 2050 crop demand was met by moderate intensification focused on existing croplands of underyielding nations, adaptation and transfer of high-yielding technologies to these croplands, and global technological improvements, our analyses forecast land clearing of only ~0.2 billion ha, greenhouse gas emissions of ~1 Gt y(-1), and global N use of ~225 Mt y(-1). Efficient management practices could substantially lower nitrogen use. Attainment of high yields on existing croplands of underyielding nations is of great importance if global crop demand is to be met with minimal environmental impacts.
Hierarchical Density Estimates for Data Clustering, Visualization, and Outlier Detection (2015)

An integrated framework for density-based cluster analysis, outlier detection, and data visualization is introduced in this article. The main module consists of an algorithm to compute hierarchical estimates of the level sets of a density, following Hartigan’s classic model of density-contour clusters and trees. Such an algorithm generalizes and improves existing density-based clustering techniques with respect to different aspects. It provides as a result a complete clustering hierarchy composed of all possible density-based clusters following the nonparametric model adopted, for an infinite range of density thresholds. The resulting hierarchy can be easily processed so as to provide multiple ways for data visualization and exploration. It can also be further postprocessed so that: (i) a normalized score of “outlierness” can be assigned to each data object, which unifies both the global and local perspectives of outliers into a single definition; and (ii) a “flat” (i.e., nonhierarchical) clustering solution composed of clusters extracted from local cuts through the cluster tree (possibly corresponding to different density thresholds) can be obtained, either in an unsupervised or in a semisupervised way. In the unsupervised scenario, the algorithm corresponding to this postprocessing module provides a global, optimal solution to the formal problem of maximizing the overall stability of the extracted clusters. If partially labeled objects or instance-level constraints are provided by the user, the algorithm can solve the problem by considering both constraints violations/satisfactions and cluster stability criteria. An asymptotic complexity analysis, both in terms of running time and memory space, is described. Experiments are reported that involve a variety of synthetic and real datasets, including comparisons with state-of-the-art, density-based clustering and (global and local) outlier detection methods.
Overexpression ofE2F3promotes proliferation of functional human β cells without induction of apoptosis (2013)

The mechanisms that control proliferation, or lack thereof, in adult human β cells are poorly understood. Controlled induction of proliferation could dramatically expand the clinical application of islet cell transplantation and represents an important component of regenerative approaches to a functional cure of diabetes. Adult human β cells are particularly resistant to common proliferative targets and often dedifferentiate during proliferation. Here we show that expression of the transcription factor E2F3 has a role in regulating β-cell quiescence and proliferation. We found human islets have virtually no expression of the pro-proliferative G 1/S transcription factors E2F1-3, but an abundance of inhibitory E2Fs 4-6. In proliferative human insulinomas, inhibitory E2Fs were absent, while E2F3 is expressed. Using this pattern as a "roadmap" for proliferation, we demonstrated that ectopic expression of nuclear E2F3 induced significant expansion of insulin-positive cells in both rat and human islets. These cells did not undergo apoptosis and retained their glucose-responsive insulin secretion, showing the ability to reverse diabetes in mice. Our results suggest that E2F4-6 may help maintain quiescence in human β cells and identify E2F3 as a novel target to induce proliferation of functional β cells. Refinement of this approach may increase the islets available for cell-based therapies and research and could provide important cues for understanding in vivo proliferation of β cells.
Supplementation With Human Milk Protein Improves Growth of Small Premature Infants Fed Human Milk (1986)

We investigated the influence of human milk protein and medium-chain triglyceride supplementations of human milk feedings on the growth of very low birth weight infants during their first weeks of life. A group of 44 preterm infants with birth weights of less than 1,520 g and a mean gestational age of 30.3 weeks was randomly divided into four groups to receive plain human milk or human milk supplemented with human milk protein (0.9 g/dL), with medium-chain triglycerides (1 g/dL), or with both. The medium-chain triglyceride oil supplementation did not influence the growth of these infants. The infants given supplementary protein gained weight faster during weeks 4 to 6 than those without (18.5 ± 0.7 v 15.1 ± 0.6 g/kg/d; mean ± SEM; P = .001). After 4 weeks of age the infants given supplementary protein had a mean weight gain equal to the mean intra-uterine rate, in contrast to the infants of the other groups, who grew more slowly until age 6 weeks. Furthermore, we found a correlation between serum albumin concentration and weight gain during the seventh week of life (P = .018). The length growth velocity for the infants with protein supplementation was 0.99 ± 0.06 cm/wk (mean ± SEM) and for those without 0.83 ± 0.05 cm/wk (P = .043). There was no difference in growth of head circumference between the groups. We conclude that human milk protein supplementation improves the growth of small premature infants fed human milk, and that the protein concentration of bank milk is insufficient for their adequate growth.
Tumour stromal cells derived from paediatric malignancies display MSC-like properties and impair NK cell cytotoxicity (2010)

Our data show that TStrC and MSC share important phenotypic and functional characteristics. The inhibitory effect of TStrC on PBMC and especially on NK cells may facilitate the immune evasion of paediatric tumours.
The amount of secreted IgA may not determine the secretory IgA coating ratio of gastrointestinal bacteria (2009)

It is reported that some, but not all, bacteria in human faeces are coated with secretory immunoglobulin A (S-IgA). We evaluated the proportion of S-IgA-coated bacteria to total intestinal bacteria (S-IgA coating ratio) in the gastrointestinal tract of two different strains of mice supplied by two different suppliers. The S-IgA coating ratio was significantly different in each gastrointestinal segment and between mouse suppliers. The amount of non-bacteria-bound IgA (free IgA) in each gastrointestinal segment indicated that this difference in the S-IgA coating ratio might not be due to the amount of secreted IgA. Furthermore, immunoblotting analysis revealed that only a small amount of IgA (<5% to free-IgA) was used for the coating. This indicates that, although sufficient S-IgA was secreted to coat the entire intestinal population of bacteria, only some part of the bacteria were coated with S-IgA. This study suggests that the amount of luminal S-IgA may not determine the S-IgA coating ratio, and that the amount of IgA coating intestinal commensal bacteria is very small.
Effect of virgin olive oil phenolic compounds on in vitro oxidation of human low density lipoproteins. (1999)

The beneficial effects of a Mediterranean diet may be ascribable not only to the high unsaturated/saturated fatty acid ratio characteristic of olive oil, but also to the unique antioxidant properties of its phenolic compounds.
Observation of large multimers in the electrospray ionization mass spectrometry of peptides (1994)

Large multimeric ions were detected from electrospray ionization (ESI) mass spectrometry of peptides, using a quadrupole mass spectrometer of standard mass range. Multimers, up to heptamers, were seen for angiotensin I; and multimers, up to pentamers, were observed for renin substrate. The appearance of the multimeric species could be controlled by manipulation of sampling conditions in the ESI interface. The relevance of the observation of large multimers to proposed mechanisms of ESI is discussed. Implications of the observation of large multimers to efforts to deduce higher order structure of biomolecules from ESI mass spectrometric experiments are also noted.
Light-dependent RNA interference with nucleobase-caged siRNAs (2007)

Within the past years RNA interference (RNAi) has become one of the most valuable tools for post-transcriptional gene silencing. Making RNAi temporally and/or spatially controllable would even enlarge its scope of application. Attaching a light-removable protection group to siRNAs is a very promising approach to achieve this control over RNAi. It has been reported that modifying siRNA nucleobases surrounding the mRNA cleavage site between the 10th and 11th nucleotides successfully suppresses RNAi. We investigated the influence of photolabile protection groups at these and the adjacent nucleobases on siRNA activity and chose to incorporate caged deoxynucleotides instead of ribonucleotides. The siRNAs designed by these means were shown to be completely inactive. By irradiation with UV light (366 nm) they could be fully reactivated and showed the same activity as their unmodified siRNA counterparts.