gebhart/patrepeval huggingface dataset:
Sox17 Promotes Cell Cycle Progression and Inhibits TGF-β/Smad3 Signaling to Initiate Progenitor Cell Behavior in the Respiratory Epithelium (2009)

The Sry-related high mobility group box transcription factor Sox17 is required for diverse developmental processes including endoderm formation, vascular development, and fetal hematopoietic stem cell maintenance. Expression of Sox17 in mature respiratory epithelial cells causes proliferation and lineage respecification, suggesting that Sox17 can alter adult lung progenitor cell fate. In this paper, we identify mechanisms by which Sox17 influences lung epithelial progenitor cell behavior and reprograms cell fate in the mature respiratory epithelium. Conditional expression of Sox17 in epithelial cells of the adult mouse lung demonstrated that cell cluster formation and respecification of alveolar progenitor cells toward proximal airway lineages were rapidly reversible processes. Prolonged expression of Sox17 caused the ectopic formation of bronchiolar-like structures with diverse respiratory epithelial cell characteristics in alveolar regions of lung. During initiation of progenitor cell behavior, Sox17 induced proliferation and increased the expression of the progenitor cell marker Sca-1 and genes involved in cell cycle progression. Notably, Sox17 enhanced cyclin D1 expression in vivo and activated cyclin D1 promoter activity in vitro. Sox17 decreased the expression of transforming growth factor-beta (TGF-beta)-responsive cell cycle inhibitors in the adult mouse lung, including p15, p21, and p57, and inhibited TGF-beta1-mediated transcriptional responses in vitro. Further, Sox17 interacted with Smad3 and blocked Smad3 DNA binding and transcriptional activity. Together, these data show that a subset of mature respiratory epithelial cells retains remarkable phenotypic plasticity and that Sox17, a gene required for early endoderm formation, activates the cell cycle and reinitiates multipotent progenitor cell behavior in mature lung cells.
Attenuation of sound in highly concentrated suspensions and emulsions (1979)

The absorption of sound in emulsions and suspensions is due to viscous and thermal transport processes occurring at the interface of the nonhomogeneities, as well as to the intrinsic absorption in the materials comprising the system. For highly concentrated mixtures, multiple scattering is shown to play an important role. Following the arguments of Waterman and Truell [J. Math. Phys. 2, 512 (1961)], the behavior of the scattering medium may be specified explicitly in terms of the number of scatterers per unit volume, and the farfield amplitude f (ϑ) obtained for a single scatterer. The coefficients of f (ϑ) for a single scatterer have been calculated by Allegra and Hawley [J. Acoust. Soc. Am. 51, 1545 (1972)] for systems of solid and fluid particles suspended in a fluid media.
Proof of Single-Molecule Sensitivity in Surface Enhanced Raman Scattering (SERS) by Means of a Two-Analyte Technique (2006)

A method is proposed to pin down unambiguous proof for single-molecule sensitivity in surface enhanced Raman spectroscopy (SERS). The simultaneous use of two analyte molecules enables a clear confirmation of the single (or few)-molecule nature of the signals. This method eliminates most of the uncertainties associated with low dye concentrations in previous experiments. It further shows that single- or few-molecule signals are very common in SERS, both in liquids and on dry substrates.
Geometric reasoning for machining features using convex decomposition (1993)

A convex decomposition called Alternating Sum of Volumes with Partitioning (ASVP) is a hierarchical volumetric representationof solid objects obtained fmm the bmmdaryinformation. Form features inrrinsic to the shape of solid objects can be recognized using ASVP decomposition.
Independence of logic database queries and update (1990)

A query is independent of an update if executing the update cannot change the result of evaluating the query. The theorems of this paper give methods for proving independence in concrete cases, taking into account integrity constraints, recursive rules, and arbitrary queries. First we define the notion of independence model-theoretically, and we prove basic properties of the concept. Then we provide proof-theoretic conditions for a conjunctive query to be independent of an update. Finally, we prove correct an induction scheme for showing that a recursive query is independent of an update.
Approximate fair dropping for variable length packets (2001)

The CHOKe router algorithm provides an approximately fair bandwidth allocation at a low implementation cost. The authors consider performance and implementation issues associated with CHOKe, with particular emphasis on variable-length packets.
Effects of L-5HTP With and Without Carbidopa on Plasma β-Endorphin and Pain Perception: Possible Implications in Migraine Prophylaxis (1986)

L-Tryptophan (L-TP) has been used in migraine and other pain conditions. The mechanism underlying the analgesic effect is still partly undefined. In this study the effects of subchronic administration of L-5-hydroxytryptophan (L-5HTP) (with and without carbidopa) on plasma beta-endorphin (beta-EP) levels and subjective pain threshold and tolerance were investigated in seven healthy volunteers. To measure also an objective indicator of pain, the nociceptive flexion reflex threshold was studied. L-5HTP treatment with and without carbidopa administration increased beta-EP levels significantly (p less than 0.05). L-5HTP plus carbidopa induced an increase in beta-EP significantly (p less than 0.05) greater than that induced by L-5HTP alone. Neither the subjective pain threshold and tolerance nor the RIII threshold was modified by either treatment. Our data seem to point to the existence of a complex linkage between plasma opioid levels and pain perception.
Virus-Like 30S RNA in Mouse Cells (1979)

Uninfected JLS-V9 mouse cells are known to express high levels of viral sequences that hybridize to complementary DNA made by the BrdU-induced virus of JLS-V9 cells. The genome in the BrdU-induced virus has been found to consist mainly of an RNA species that migrates as 30S RNA material during electrophoresis through agarose gels. This virus-like 30S RNA, designated VL30 RNA, apparently represents a new class of endogenous defective retroviruses that are not generally evident because of their defectiveness and lack of biological function. Fingerprint analysis and hybridization studies show that VL30 RNA does not have homology with the standard nondefective murine leukemia viruses. Upon superinfection with a nondefective murine leukemia virus, or upon induction of endogenous virus with BrdU, VL30 RNA is rescued into virions by phenotypic mixing. When VL30 RNA is rescued by BrdU induction, the VL30 RNA is mainly organized as a 50S complex, but when VL30 is rescued by superinfection, VL30 is also found in 70S RNA. Rescued VL30 RNA sequences can be reverse transcribed by the virion-associated DNA polymerase in an endogenous reaction. Many mouse cells express the sequences, whereas heterologous cells such as rat or rabbit cells do not contain them. By using hybridization of a complementary DNA probe to cellular RNA immobilized on paper, no subgenomic RNA related to the VL30 RNA could be found in cells expressing the VL30 sequences. From 20 to 50 copies of these sequences were found to be contained in the mouse genome. VL30 RNA is probably present in most stocks of leukemia and sarcoma viruses made in mouse cells.
Detection of Alzheimer Disease (AD)-Specific Tau Pathology in AD and NonAD Tauopathies by Immunohistochemistry With Novel Conformation-Selective Tau Antibodies (2018)

Aggregation of tau into fibrillar structures within the CNS is a pathological hallmark of a clinically heterogeneous set of neurodegenerative diseases termed tauopathies. Unique misfolded conformations of tau, referred to as strains, are hypothesized to underlie the distinct neuroanatomical and cellular distribution of pathological tau aggregates. Here, we report the identification of novel tau monoclonal antibodies (mAbs) that selectively bind to an Alzheimer disease (AD)-specific conformation of pathological tau. Immunohistochemical analysis of tissue from various AD and nonAD tauopathies demonstrate selective binding of mAbs GT-7 and GT-38 to AD tau pathologies and absence of immunoreactivity for tau aggregates that are diagnostic of corticobasal degenerations (CBD), progressive supranuclear palsy (PSP), and Pick's disease (PiD). In cases with co-occurring AD tauopathy, GT-7 and GT-38 distinguish comorbid AD tau from pathological tau in frontotemporal lobar degeneration characterized by tau inclusions (FTLD-Tau), as confirmed by the presence of both 3 versus 4 microtubule-binding repeat isoforms (3R and 4R tau isoforms, respectively), in AD neurofibrillary tangles but not in the tau aggregates of CBD, PSP, or PiD. These findings support the concept of an AD-specific tau strain. The mAbs described here enable the selective detection of AD tau pathology in nonAD tauopathies.
Hybrid Optimal Control Framework for Mission Planning (2005)

With the progressive sophistication of future missions, it has become increasingly apparent that a new framework is necessary for efficient planning, analysis, and optimization of various concepts of operations (CONOPS). In recognizing that CONOPS involve categorical variables, we propose a hybrid optimal control framework that mathematically formalizes such problems. Hybrid optimal control theory extends ordinary optimal control theory by including categorical variables in the problem formulation. The proposed formalism frees mission planners to focus on high-level decision making by automating and optimizing the details of the inner loops. The eventual goal of this formalism is to develop efficient tools and techniques to support the objective of increasing autonomy for future systems. In using the pseudospectral knotting method to solve hybrid optimal control problems, we generate a mixed-variable programming (MVP) problem. A simple, feasible integer programming subproblem is identified that reduces the combinatorial complexity of solving the MVP. In addition to developing the framework using various examples from aerospace engineering, we provide details for a two-agent benchmark problem associated with a multiagent launch system. The entire process is illustrated with a numerical example.
Plant Growth Promotion and Amelioration of Salinity Stress in Crop Plants by a Salt-Tolerant Bacterium (2011)

Out of a large number of bacteria isolated from the rhizosphere of Cynodon dactylon , a facultative halophyte, nine were found to be highly salt-tolerant, growing in nutrient agar medium supplemented with 10% NaCl. Morphological, biochemical, and molecular characterization of all the isolates was done. RAPD analysis to determine relatedness among the nine bacteria were carried out, which revealed that all nine isolates could be grouped into 2 main clusters. In order to determine whether the isolates possess plant growth promoting activities, in vitro tests were done initially. Â  Based on the in vitro tests the isolate â€˜S4â€™ was selected as a potential salt-tolerant PGPR. This bacterium was identified as Bacillus cereus. For in vivo tests, this bacterium was applied as an aqueous suspension to the rhizosphere of 3 plants- Vigna radiata, Cicer arietinum and Oryza sativa; a set of each plant was also applied with 200mM NaCl solution 3 times a week after 15 days of growth. Â  Results revealed that the bacterium could promote growth of the seedlings significantly which showed increased height, number and length of leaves, as well as root and shoot biomass. The ability of the bacterium to solubilize soil phosphate was also confirmed. B.cereus could also elicit antioxidant responses against salt stress in the plants, as evidenced by increased activities of enzymes such as superoxide dismutase, peroxidase, ascorbate peroxidase and catalase. Besides, it could also induce the activities of defense enzymes such as chitinase, I²-1, 3 glucanse and phenyl alanine ammonia lyase associated with induced systemic resistance. Results imply that the bacterium acts through a combination of direct and indirect mechanisms.
The OsNRAMP1 iron transporter is involved in Cd accumulation in rice (2011)

Cadmium (Cd) is a heavy metal toxic to humans and the accumulation of Cd in the rice grain is a major agricultural problem, particularly in Asia. The role of the iron transporter OsNRAMP1 in Cd uptake and transport in rice was investigated here. An OsNRAMP1:GFP fusion protein was localized to the plasma membrane in onion epidermal cells. The growth of yeast expressing OsNRAMP1 was impaired in the presence of Cd compared with yeast transformed with an empty vector. Moreover, the Cd content of OsNRAMP1-expressing yeast exceeded that of the vector control. The expression of OsNRAMP1 in the roots was higher in a high Cd-accumulating cultivar (Habataki) than a low Cd-accumulating cultivar (Sasanishiki) regardless of the presence of Cd, and the amino acid sequence of OsNRAMP1 showed 100% identity between Sasanishiki and Habataki. Over-expression of OsNRAMP1 in rice increased Cd accumulation in the leaves. These results suggest that OsNRAMP1 participates in cellular Cd uptake and Cd transport within plants, and the higher expression of OsNRAMP1 in the roots could lead to an increase in Cd accumulation in the shoots. Our results indicated that OsNRAMP1 is an important protein in high-level Cd accumulation in rice.
Dual Magnetic Probe System for Phase Measurements in Thermal Induction Plasmas (1972)

Previously reported measurements of rf magnetic field distributions in thermal induction plasmas by a water-cooled coil probe have been extended to phase measurements through the use of a second identical probe placed at a fixed position near the plasma boundary. From measurements of the vector sum and/or difference in addition to the individual signals from both probes, data for the variation of the phase angle with radius were obtained. The reliability of the method was checked with an electrolyte of known conductivity. Tests conducted at 2.6 MHz in a 14-cm-wide argon-plasma column at ambient pressure yielded a change in phase angle of 285 deg over the radius. The variations in phase and magnitude of the magnetic field were used to derive those of the induced electric field, the current density, the electrical conductivity, and the real part of the Poynting vector. From the latter a specific power input of about 1500 W/cm was obtained. A correlation of the conductivity data with temperatures derived from absolute line and continuum intensities is in good agreement with predictions from an equilibrium theory.
Wolfram syndrome: structural and functional analyses of mutant and wild-type wolframin, the WFS1 gene product (2003)

Mutations of the WFS1 gene are responsible for Wolfram syndrome, a rare, recessive disorder characterized by early-onset, non-autoimmune diabetes mellitus, optic atrophy and further neurological and endocrinological abnormalities. The WFS1 gene encodes wolframin, a putative multispanning membrane glycoprotein of the endoplasmic reticulum. The function of wolframin is completely unknown. In order to characterize wolframin, we have generated polyclonal antibodies against both hydrophilic termini of the protein. Wolframin was found to be ubiquitously expressed with highest levels in brain, pancreas, heart and insulinoma beta-cell lines. Analysis of the structural features provides experimental evidence that wolframin contains nine transmembrane segments and is embedded in the membrane in an N(cyt)/C(lum) topology. Wolframin assembles into higher molecular weight complexes of approximately 400 kDa in the membrane. Pulse-chase experiments demonstrate that during maturation wolframin is N-glycosylated but lacks proteolytical processing. Moreover, N-glycosylation appears to be essential for the biogenesis and stability of wolframin. Here we investigate, for the first time, the molecular mechanisms that cause loss-of-function of wolframin in affected individuals. In patients harboring nonsense mutations complete absence of the mutated wolframin is caused by instability and rapid decay of WFS1 nonsense transcripts. In a patient carrying a compound heterozygous missense mutation, R629W, we found markedly reduced steady-state levels of wolframin. Pulse-chase experiments of mutant wolframin expressed in COS-7 cells indicated that the R629W mutation leads to instability and strongly reduced half-life of wolframin. Thus, the Wolfram syndrome in patients investigated here is caused by reduced protein dosage rather than dysfunction of the mutant wolframin.
A voltage-tunable microfabricated accelerometer (1991)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1992.
Laboratory core flooding experimental systems for CO2geosequestration： An updated review over the past decade (2016)

Carbon dioxide （CO2） geosequestration in deep saline aquifers has been currently deemed as a preferableand practicable mitigation means for reducing anthropogenic greenhouse gases （GHGs） emissions to theatmosphere, as deep saline aquifers can offer the greatest potential from a capacity point of view. Hence,research on core-scale CO2/brine multiphase migration processes is of great significance for preciselyestimating storage efficiency, ensuring storage security, and predicting the long-term effects of thesequestered CO2 in subsurface saline aquifers. This review article initially presents a brief description ofthe essential aspects of CO2 subsurface transport and geological trapping mechanisms, and then outlinesthe state-of-the-art laboratory core flooding experimental apparatus that has been adopted for simulatingCO2 injection and migration processes in the literature over the past decade. Finally, a summary ofthe characteristics, components and applications of publicly reported core flooding equipment as well asmajor research gaps and areas in need of further study are given in relevance to laboratory-scale coreflooding experiments in CO2 geosequestration under reservoir conditions.
Cephalic expression and molecular characterization of <i>Xenopus En-2</i> (1991)

We have isolated and characterized cDNAs corresponding to the Xenopus En-2 gene. Comparison of amino acid sequences between the entire Xenopus En-2 and the Drosophila engrailed proteins confirms conservation of sequences inside as well as proximal to the homeobox and reveals a region of similarity towards the N terminus. Two transcripts encode the Xenopus En-2 protein. Both transcripts are regulated temporally in an identical fashion and are likely to be transcribed from two copies of the En-2 gene. We have also analyzed the distribution of the protein in the head tissue and in the dissected brain of tailbud stage embryos. In addition to the main band of expression at the midbrain-hindbrain boundary, we show that the protein is expressed in three novel areas: the mandibular arch, the optic tectum and the region of anterior pituitary.
Artificial fingerprint recognition by using optical coherence tomography with autocorrelation analysis (2006)

Fingerprint recognition is one of the most widely used methods of biometrics. This method relies on the surface topography of a finger and, thus, is potentially vulnerable for spoofing by artificial dummies with embedded fingerprints. In this study, we applied the optical coherence tomography (OCT) technique to distinguish artificial materials commonly used for spoofing fingerprint scanning systems from the real skin. Several artificial fingerprint dummies made from household cement and liquid silicone rubber were prepared and tested using a commercial fingerprint reader and an OCT system. While the artificial fingerprints easily spoofed the commercial fingerprint reader, OCT images revealed the presence of them at all times. We also demonstrated that an autocorrelation analysis of the OCT images could be potentially used in automatic recognition systems.
Supporting Diverse Dynamic Intent-based Policies using Janus (2017)

Existing network policy abstractions handle basic group based reachability and access control list based security policies. However, QoS policies as well as dynamic policies are also important and not representing them in the high level policy abstraction poses serious limitations. At the same time, efficiently configuring and composing group based QoS and dynamic policies present significant technical challenges, such as (a) maintaining group granularity during configuration, (b) dealing with network-bandwidth contention among policies from distinct writers and (c) dealing with multiple path changes corresponding to dynamically changing policies, group membership and end-point mobility. In this paper we propose Janus, a system which makes two major contributions. First, we extend the prior policy graph abstraction model to represent complex QoS and dynamic tateful/temporal policies. Second, we convert the policy configuration problem into an optimization problem with the goal of maximizing the number of satisfied and configured policies, and minimizing the number of path changes under dynamic environments. To solve this, Janus presents several novel heuristic algorithms. We evaluate our system using a diverse set of bandwidth policies and network topologies. Our experiments demonstrate that Janus can achieve near-optimal solutions in a reasonable amount of time.
The separation of micron‐size particles from air by diffusiophoresis (1971)

Abstract The continuous separation of micron‐size particles from air by diffusiophoresis in a parallel plate collector was studied theoretically. Two models for the particle behavior were considered. Model I was based on the assumption that the particles adopt the local fluid velocity whereas the Schmitt‐Waldmann equation was used to determine the diffusiophoretic velocity in Model II. The latter also included thermophoretic and gravitational effects. The two models yielded similar results when diffusiophoresis was predominant. The theoretical results were also used in the sizing of an experimental particle collector. The collector, which operated under laminar flow conditions, was capable of removing the particles effectively and its performance conformed with the theoretical work.
Dynamic Light Scattering Study on Reentrant Sol−Gel Transition of Poly(vinyl alcohol)−Congo Red Complex in Aqueous Media (2002)

The poly(vinyl alcohol)−Congo Red (PVA/CR) complex in aqueous solutions exhibited a reentrant sol−gel transition at ambient temperature by increasing the CR concentration, CCR, when the PVA concentration was near the chain overlap concentration (CPVA ≈ 455 mM). The system was in the sol state at CCR ≤ 1.0 mM and 10.0 ≤ CCR ≤ 30.0 mM, while it underwent gelation at two CCR regions: 1.5 ≤ CCR ≤ 9.0 mM and 35 mM ≤ CCR. This reentrant transition has been investigated microscopically by means of dynamic light scattering. Speckle patterns appeared exclusively in the gel phase. The reentrant sol−gel transition was also demonstrated by a shape change of the time−intensity correlation function (ICF), which varied from a stretched-exponential function for sol states to a power-law function for gel states. The variations of the correlation length ξ and the power-law exponent, n, in ICF have been extensively discussed.