gebhart/patrepeval huggingface dataset:
Modulation of NCAM/FGFR1 signaling suppresses EMT program in human proximal tubular epithelial cells (2018)

Neural cell adhesion molecule (NCAM) and fibroblast growth factor receptor 1 (FGFR1) cross-talk have been involved in epithelial-to-mesenchymal transition (EMT) process during carcinogenesis. Since EMT also contributes to maladaptive repair and parenchymal damage during renal fibrosis, we became encouraged to explore the role of NCAM/FGFR1 signaling as initiating or driving forces of EMT program in cultured human proximal tubular epithelial cells (TECs). TECs stimulated with TGF-β1 (10ng/mL) was used as an established in vitro EMT model. TGF-β1 downstream effectors were detected in vitro, as well as in 50 biopsies of different human kidney diseases to explore their in vivo correlation. NCAM/FGFR1 signaling and its modulation by FGFR1 inhibitor PD173074 (100nM) were analyzed by light microscopy, immunolabeling, qRT-PCR and scratch assays. Morphological changes associated with EMT appeared 48h after TGF-ß1 treatment and was clearly apparent after 72 hours, followed by loss of CDH1 (encoding E-Cadherin) and transcriptional induction of SNAI1 (SNAIL), SNAI2 (SLUG), TWIST1, MMP2, MMP9, CDH2 (N-Cadherin), ITGA5 (integrin-α5), ITGB1 (integrin-β1), ACTA2 (α-SMA) and S100A4 (FSP1). Moreover, at the early stage of EMT program (24 hours upon TGF-β1 exposure), transcriptional induction of several NCAM isoforms along with FGFR1 was observed, implicating a mechanistic link between NCAM/FGFR1 signaling and induction of EMT. These assumptions were further supported by the inhibition of the EMT program after specific blocking of FGFR1 signaling by PD173074. Finally, there was evidence for an in vivo TGF-β1 pathway activation in diseased human kidneys and correlation with impaired renal excretory functions. Collectively, NCAM/FGFR1 signaling appears to be involved in the initial phase of TGF-ß1 initiated EMT which can be effectively suppressed by application of FGFR inhibitor.
Design of a magneto-optic residual current device using aqueous ferrofluid as the sensing material (2004)

The paper presents a design for a Magneto-Optic Residual Current Device (MORCD) using ferrofluid as the sensing material. As the selection of suitable magneto-optic material was seen as the critical phase in the design, a novel Magneto-Optical performance Indicator is proposed and verified using known optical materials. It was experimentally established that the designed MORCD is sufficiently fast and capable of detecting residual current as low as 1.51 mA.
Breeding at higher latitude is associated with higher photoperiod threshold and delayed reproductive development in a songbird (2020)

Many organisms time reproduction to photoperiod, a constant from year to year. Predicting how anthropogenic change will influence future timing demands greater knowledge of the current role of photoperiod. We held two closely related bird populations in a common environment. One population is resident; the other winters in sympatry with the resident population but migrates north prior to reproducing. We increased photoperiod gradually and measured preparation for migration and reproduction, using feather stable isotopes to estimate breeding latitude. We predicted population differences in the minimum stimulatory day length to elicit a response (CPP, critical photoperiod) and co-variation between CPP and distance migrated. We found clear population differences in CPP and greater CPP in longer distance migrants. We conclude that current geographic variation in reproductive timing has a genetic or early developmental basis and recommends that future research focus on how anthropogenic changes will interact with CPP to adjust the timing of reproduction and migration.
Catalysis by chymotrypsinogen. Demonstration of an acyl-zymogen intermediate (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleCatalysis by chymotrypsinogen. Demonstration of an acyl-zymogen intermediateArieh Gertler, Kenneth A. Walsh, and Hans NeurathCite this: Biochemistry 1974, 13, 6, 1302–1310Publication Date (Print):March 1, 1974Publication History Published online1 May 2002Published inissue 1 March 1974https://doi.org/10.1021/bi00703a038RIGHTS & PERMISSIONSArticle Views62Altmetric-Citations77LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (971 KB) Get e-Alertsclose Get e-Alerts
A Weighted Late Fusion Framework for Recognizing Human Activity from Wearable Sensors (2019)

Following the technological advancement and the constantly emerging assisted living applications, sensor-based activity recognition research receives great attention. Until recently, the majority of relevant research involved extracting knowledge out of single modalities, however, when individual sensors performances are not satisfactory, combining information from multiple sensors can be of use and improve the activity recognition rate. Early and late fusion classifier strategies are usually employed to successfully merge multiple sensors. This paper proposes a novel framework for combining accelerometers and gyroscopes at decision level, in order to recognize human activity. More specifically, we propose a weighted late fusion framework that utilizes the detection rate of a classifier. Furthermore, we propose the modification of an already existing class-based weighted late fusion framework. Experimental results on a publicly available and widely used dataset demonstrated that the combination of accelerometer and gyroscope under the proposed frameworks improves the classification performance.
The effects of neutralized particles on the sampling efficiency of polyurethane foam used to estimate the extrathoracic deposition fraction (2015)

In addition to chemical composition, the site of deposition of inhaled particles is important for determining the potential health effects from an exposure. As a result, the International Organization for Standardization adopted a particle deposition sampling convention. This includes extrathoracic particle deposition sampling conventions for the anterior nasal passages (ET1) and the posterior nasal and oral passages (ET2). This study assessed how well a polyurethane foam insert placed in an Institute of Occupational Medicine (IOM) sampler can match an extrathoracic deposition sampling convention, while accounting for possible static buildup in the test particles. In this way, the study aimed to assess whether neutralized particles affected the performance of this sampler for estimating extrathoracic particle deposition. A total of three different particle sizes (4.9, 9.5, and 12.8 µm) were used. For each trial, one particle size was introduced into a low-speed wind tunnel with a wind speed set a 0.2 m/s (∼40 ft/min). This wind speed was chosen to closely match the conditions of most indoor working environments. Each particle size was tested twice either neutralized, using a high voltage neutralizer, or left in its normal (non neutralized) state as standard particles. IOM samplers were fitted with a polyurethane foam insert and placed on a rotating mannequin inside the wind tunnel. Foam sampling efficiencies were calculated for all trials to compare against the normalized ET1 sampling deposition convention. The foam sampling efficiencies matched well to the ET1 deposition convention for the larger particle sizes, but had a general trend of underestimating for all three particle sizes. The results of a Wilcoxon Rank Sum Test also showed that only at 4.9 µm was there a statistically significant difference (p-value = 0.03) between the foam sampling efficiency using the standard particles and the neutralized particles. This is interpreted to mean that static buildup may be occurring and neutralizing the particles that are 4.9 µm diameter in size did affect the performance of the foam sampler when estimating extrathoracic particle deposition.
Function Discovery and Structural Characterization of a Methylphosphonate Esterase (2015)

Pmi1525, an enzyme of unknown function from Proteus mirabilis HI4320 and the amidohydrolase superfamily, was cloned, purified to homogeneity, and functionally characterized. The three-dimensional structure of Pmi1525 was determined with zinc and cacodylate bound in the active site (PDB id: 3RHG ). The structure was also determined with manganese and butyrate in the active site (PDB id: 4QSF ). Pmi1525 folds as a distorted (β/α)8-barrel that is typical for members of the amidohydrolase superfamily and cog1735. The substrate profile for Pmi1525 was determined via a strategy that marshaled the utilization of bioinformatics, structural characterization, and focused library screening. The protein was found to efficiently catalyze the hydrolysis of organophosphonate and carboxylate esters. The best substrates identified for Pmi1525 are ethyl 4-nitrophenylmethyl phosphonate (kcat and kcat/Km values of 580 s(-1) and 1.2 × 10(5) M(-1) s(-1), respectively) and 4-nitrophenyl butyrate (kcat and kcat/Km values of 140 s(-1) and 1.4 × 10(5) M(-1) s(-1), respectively). Pmi1525 is stereoselective for the hydrolysis of chiral methylphosphonate esters. The enzyme hydrolyzes the (SP)-enantiomer of isobutyl 4-nitrophenyl methylphosphonate 14 times faster than the corresponding (RP)-enantiomer. The catalytic properties of this enzyme make it an attractive template for the evolution of novel enzymes for the detection, destruction, and detoxification of organophosphonate nerve agents.
High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis (2016)

The High-performance Integrated Virtual Environment (HIVE) is a distributed storage and compute environment designed primarily to handle next-generation sequencing (NGS) data. This multicomponent cloud infrastructure provides secure web access for authorized users to deposit, retrieve, annotate and compute on NGS data, and to analyse the outcomes using web interface visual environments appropriately built in collaboration with research and regulatory scientists and other end users. Unlike many massively parallel computing environments, HIVE uses a cloud control server which virtualizes services, not processes. It is both very robust and flexible due to the abstraction layer introduced between computational requests and operating system processes. The novel paradigm of moving computations to the data, instead of moving data to computational nodes, has proven to be significantly less taxing for both hardware and network infrastructure.The honeycomb data model developed for HIVE integrates metadata into an object-oriented model. Its distinction from other object-oriented databases is in the additional implementation of a unified application program interface to search, view and manipulate data of all types. This model simplifies the introduction of new data types, thereby minimizing the need for database restructuring and streamlining the development of new integrated information systems. The honeycomb model employs a highly secure hierarchical access control and permission system, allowing determination of data access privileges in a finely granular manner without flooding the security subsystem with a multiplicity of rules. HIVE infrastructure will allow engineers and scientists to perform NGS analysis in a manner that is both efficient and secure. HIVE is actively supported in public and private domains, and project collaborations are welcomed. Database URL: https://hive.biochemistry.gwu.edu.
Theory and Application of Parallel-T Resistance-Capacitance Frequency-Selective Networks (1946)

This paper deals with the theory and application of the parallel-T resistance-capacitance network, and gives a more general treatment of this network than that found in earlier papers. Using wye-delta conversion methods, the parallel-T resistance-capacitance network is represented by a single equivalent pi circuit. By introducing symbols corresponding to frequency and component values, simple expressions are derived for the impedance of the pi arms, as well as the network transmission, at any frequency. Since no arbitrary relationships are assumed between component values, the derived expressions are general. The practical application of the network is also considered. Three versatile circuit embodiments are described, and the effects of deviating from specified component values investigated. A calculation is made to illustrate the application of the network to a negative-feedback circuit using a single stage of voltage amplification.
At-speed interconnect test and diagnosis of external memories on a system (2005)

This work presents a built-in self test (BIST) implementation for external memories like DDR (double data rate), double DDR, QDR (quad data rate) SRAM, DDR FCRAM (fast cycle RAM), and RLDRAM (reduced latency DRAM). We utilize the memory controller in the functional block to design the BIST so that the BIST design can be simplified and executed at the functional speed. However, there are many different types of the memory controllers depending on the types of external memories, functional interface protocols, and implementation methodologies. In order to support the various memory controllers, we defined the latency of the memory controllers and classified them into three different categories: fixed latency, handshake, and both fixed latency, and handshake memory controllers. With these three models, we developed a general BIST architecture to support different types of memory controllers. During the boundary-scan driven BIST operation in the board and the system-level test and diagnosis, system clock, system hard reset, soft reset, and other programmable features were considered carefully to make the BIST operate properly. This work also presents a unique way of utilizing special BIST functions during the board and system level test, and also during the system mission operation.
Bis deficiency results in early lethality with metabolic deterioration and involution of spleen and thymus (2008)

Bcl-2 interacting cell death suppressor (Bis), also known as Bag3 or CAIR-1, is involved in antistress and antiapoptotic pathways. In addition to Bcl-2, Bis binds to several proteins, suggesting it has diverse functions in normal and pathological conditions. To better define the physiological function of Bis in vivo, we developed bis-deficient mice with a cre-loxP system. Targeted disruption of exon 4 of the bis gene was demonstrated by Southern blotting and PCR, and Western blotting showed that no intact or truncated Bis protein was synthesized in bis(-/-) mice. While heterozygotes were fertile and appeared normal, Bis-deficient mice showed growth retardation and died by 3 wk after birth. The relative weight of the thymus and spleen was reduced and the total numbers of white blood cells, splenocytes, and thymocytes were significantly reduced compared with wild-type littermates. Serum profiles indicated significant hypoglycemia as well as decrease in triglyceride and cholesterol levels. Expression profiles of metabolic genes indicated that gluconeogenesis and beta-oxidation are activated in the liver of bis(-/-) mice. This activation, as well as a decrease in peripheral fat and an induction of fatty liver, appears to be an adaptive response to hypoglycemia. Our study reveals that the absence of Bis has considerable influences on postnatal growth and survival, possibly due to a nutritional impairment.
Methodology of modeling of the internal activity of a FPGA for conducted emission prediction purpose (2017)

International audience
Crystal structure of (η5-pentamethylcyclopentadienyl)(η5-1-(2,2-dimethylpropyl) cyclopentadienyl)(hydroxy)titaniumchloride, C20H31ClOTi (2002)

Article Crystal structure of (η5-pentamethylcyclopentadienyl)(η5-1-(2,2-dimethylpropyl) cyclopentadienyl)(hydroxy)titaniumchloride, C20H31ClOTi was published on December 1, 2002 in the journal Zeitschrift für Kristallographie - New Crystal Structures (volume 217, issue 1).
Mathematical modeling for predicting betamethasone profile and burst release from in situ forming systems based on PLGA (2014)

This paper examines the application of mathematical modeling to a novel drug delivery system using artificial neural networks. For this purpose, a Feed-Forward back propagation network was trained by two different concepts and the behavior of this drug delivery system was analyzed based on the simulated results. The network also successfully determined the most accurate release profiles under specific formulation parameters. The simulated results showed a high correlation with the real data in this study. Furthermore, a new method was proposed in order to predict the burst release point in Poly Lactic-co-Glycolic Acid (PLGA) based drug delivery systems. This paper reveals that the mathematical modeling of novel drug delivery systems not only significantly decreases time and cost, but also facilitates the design of new pharmaceutical formulations.
Chronic obstructive pulmonary disease: current burden and future projections (2006)

Information about the comparative magnitude of the burden from various diseases and injuries is a critical input into building the evidence base for health policies and programmes. Such information should be based on a critical evaluation of all available epidemiological data using standard and comparable procedures across diseases and injuries, including information on the age at death and the incidence, duration and severity of cases who do not die prematurely from the disease. A summary measure, disability-adjusted life yrs (DALYs), has been developed to simultaneously measure the amount of disease burden due to premature mortality and the amount due to the nonfatal consequences of disease.
Optimizing exact genetic linkage computations (2003)

Genetic linkage analysis is a challenging application which requires Bayesian networks consisting of thousands of vertices. Consequently, computing the likelihood of data, which is needed for learning linkage parameters, using exact inference procedures calls for an extremely efficient implementation that carefully optimizes the order of conditioning and summation operations. In this paper we present the use of stochastic greedy algorithms for optimizing this order. Our algorithm has been incorporated into the newest version of superlink, which is currently the fastest genetic linkage program for exact likelihood computations in general pedigrees. We demonstrate an order of magnitude improvement in run times of likelihood computations using our new optimization algorithm, and hence enlarge the class of problems that can be handled effectively by exact computations.
Growth hormone as an amplifier of insulin-like growth factor-I action: potentiated oestradiol accumulation (1997)

The interaction between GH and IGF-I in modulating oestradiol biosynthetic capacity was examined in cultured porcine granulosa cells. Granulosa cells (2 x 10(6) viable cells/culture) were initially cultured for 96 h (treatment period) in an androstenedione-free medium in the absence or presence of IGF-I (0 or 50 ng/ml), with or without GH at 100 ng/ml. At the conclusion of this period, culture media were discarded and the cells were washed twice with the androstenedione-free medium and reincubated for an additional 24 h (test interval) in an androstenedione (10(-7) M)-supplemented medium for oestradiol accumulation. GH alone induced no stimulation (P > 0.05) of basal oestradiol accumulation. In contrast, concurrent treatment with IGF-I produced a 4.3-fold increase (26 vs 112 ng/ 2 x 10(6) cells per 24 h, P < 0.001) in oestradiol accumulation. GH amplified IGF-I-induced oestradiol production in a dose (minimal dose requirement of 0.3 ng/ml)- and time (minimal time requirement of 24-48 h)-dependent manner. Studies on the site(s) of action indicated that GH exerts its amplifying effects on IGF-I-induced oestradiol production both proximal and distal to cAMP generation. As the specificity study and the inhibitory study indicated, GH amplification of IGF-I-induced oestradiol production is a process involving gene transcription and/or translation and the synergism is not solely specific to IGF-I as IGF-II-induced oestradiol production was also amplified in the presence of GH.
The equivalent circuit model in solid-state electronics—Part I: The single energy level defect centers (1967)

The equivalent circuit model is developed in this series of papers and applied to solid-state junction devices. In this paper, the exact equivalent circuit of a single energy level defect center in a semiconductor is developed based on the Shockley-Read-Hall model. It is then applied to the calculation of the steady-state lifetimes of electrons and holes and to the transient decay time constants. The transient decay time constants are obtained for arbitrary nonequilibrium, but steady-state, conditions and are presented as a function of the steady-state electron and hole concentrations by means of contour maps. Simple examples and gold in silicon are used for the construction of these maps. The general criteria of trapping, recombination, and generation are also obtained using the single energy level defect center model which divides the carrier concentration plane log <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10</inf> N versus log <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10</inf> P into four quadrants centered at the equality carrier concentrations p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">*</sup> and n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">*</sup> . At this equality point, the four rates of electron or hole capture or emission at the defect center are equal and the four quadrants represent regions where recombination, generation, electron trapping, or hole trapping dominates.