gebhart/patrepeval huggingface dataset:
Antagonistic Effects of BACE1 and APH1B-γ-Secretase Control Axonal Guidance by Regulating Growth Cone Collapse (2015)

ΒACE1 is the major drug target for Alzheimer's disease, but we know surprisingly little about its normal function in the CNS. Here, we show that this protease is critically involved in semaphorin 3A (Sema3A)-mediated axonal guidance processes in thalamic and hippocampal neurons. An active membrane-bound proteolytic CHL1 fragment is generated by BACE1 upon Sema3A binding. This fragment relays the Sema3A signal via ezrin-radixin-moesin (ERM) proteins to the neuronal cytoskeleton. APH1B-γ-secretase-mediated degradation of this fragment stops the Sema3A-induced collapse and sensitizes the growth cone for the next axonal guidance cue. Thus, we reveal a cycle of proteolytic activity underlying growth cone collapse and restoration used by axons to find their correct trajectory in the brain. Our data also suggest that BACE1 and γ-secretase inhibition have physiologically opposite effects in this process, supporting the idea that combination therapy might attenuate some of the side effects associated with these drugs.
Pleiotropic morphological and antibiotic deficiencies result from mutations in a gene encoding a tRNA-like product in Streptomyces coelicolor A3(2). (1987)

In Streptomyces coelicolor, bldA mutants are defective in antibiotic production and the development of aerial hyphae and spores. Subcloning analysis showed that sequences spanning an NcoI site in cloned bldA+ DNA were needed to allow complementation of a bldA mutant. Nucleotide sequencing revealed a tRNA-like sequence 9 bp downstream from the NcoI site. Five independent bldA mutations all fell in a 16-bp region in the tRNA-like sequence, one of them changing the putative anticodon. In RNA dot-blot analysis, hybridization was detected with a probe specific for the tRNA-like transcript but not with a probe for "anti-tRNA-like" transcripts. The transcripts detected were all in the salt-soluble RNA fraction and accumulated relatively late in growth. It is postulated that bldA specifies a tRNA that would recognize the codon UUA (for leucine). This codon is very rare in Streptomyces genes [which generally contain greater than 70 mole% (G + C)], suggesting a possible role for bldA in translational control of development.
Fast vehicle detection based on evolving convolutional neural network (2017)

With the rapid development of pattern recognition, computer vision and artificial intelligence technology, vehicle detection, traffic, and public safety, are core areas to extract direct benefits. To identify and locate a fast-moving vehicle, with high positional accuracy an evolving algorithm, based on convolutional neural networks, is proposed. Enhanced feature extraction is achieved by embedding our framework with a computationally cost-efficient proposal network to generate initial anchor boxes as well as to discard unlikely regions; feature fusion technology was used to extract hyper features, refine the identification and locate the vehicle, as well as improve the quality and accuracy of vehicle detection. Finally, we evaluated our network performance against the recent DETRAC benchmark <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">[1]</sup> as well as using vehicle data sets collected by ourselves. The outcome of this study indicates a significant improvement over the state-of-the-art Faster RCNN by 9.61%, which fully highlights the effectiveness of the proposed algorithm.
Real-Time Enhancement of Defects in Periodic Patterns Using Photoinduced Anisotropy of a Bacteriorhodopsin Film (1997)

We propose a defect-enhancement system for periodic patterns using a nonlinear spatial filter that uses photoinduced anisotropy of a bacteriorhodopsin film. The nonlinear filter passes low-intensity beams while blocking high-intensity beams. The system enhances the defects in real time because the anisotropy induced on the bacteriorhodopsin film by the first sample does not have to be rewritten if subsequent samples have the same periodic structure. It can also be applied to moving samples due to the shift invariance of the Fourier pattern. In the experiments we detected 10 µm defects in a photomask for a liquid crystal display. The dependence of the contrast ratio of the enhanced defect to the background on the intensity of the probe beam is also measured.
Knockin of mutant PIK3CA activates multiple oncogenic pathways (2009)

The phosphatidylinositol 3-kinase subunit PIK3CA is frequently mutated in human cancers. Here we used gene targeting to "knock in" PIK3CA mutations into human breast epithelial cells to identify new therapeutic targets associated with oncogenic PIK3CA. Mutant PIK3CA knockin cells were capable of epidermal growth factor and mTOR-independent cell proliferation that was associated with AKT, ERK, and GSK3beta phosphorylation. Paradoxically, the GSK3beta inhibitors lithium chloride and SB216763 selectively decreased the proliferation of human breast and colorectal cancer cell lines with oncogenic PIK3CA mutations and led to a decrease in the GSK3beta target gene CYCLIN D1. Oral treatment with lithium preferentially inhibited the growth of nude mouse xenografts of HCT-116 colon cancer cells with mutant PIK3CA compared with isogenic HCT-116 knockout cells containing only wild-type PIK3CA. Our findings suggest GSK3beta is an important effector of mutant PIK3CA, and that lithium, an FDA-approved therapy for bipolar disorders, has selective antineoplastic properties against cancers that harbor these mutations.
Tensile properties of the human glenoid labrum (2007)

Human fresh-frozen cadaveric glenoid labrae from 16 donors were harvested and ten of these had no gross degeneration. These ten were divided into eight equal circumferential sections. Each section was cut to produce test-samples from the core layer with a cross-section of 1 x 1 mm. Tensile testing was performed within a controlled environment unit at 37 +/- 1 degrees C and 100% relative humidity. Each test-sample was precycled to a quasi-static state to alleviate the effects of deep-freezing, prior to final testing. The tangent modulus was calculated for each test-sample before and after a 5-min period of stress relaxation and at yield. The mean elastic modulus and yield stress of the glenoid labrum were 22.8 +/- 11.4 and 2.5 +/- 2.1 MPa, respectively. The anterosuperior portion had a lower elastic modulus and lower yield stress than the inferior portion (both P < 0.02). The pre-stress relaxation tangent modulus was significantly lower than the post-stress relaxation tangent modulus for all portions of the labrum. The glenoid labrum has similar tensile material properties to articular cartilage. Its elastic modulus varies around its circumference. This suggests that the labrum may encounter different forces at different positions.
D-NeRF: neural radiance fields for dynamic scenes (2021)

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Anatomy and function relation in the coronary tree: from bifurcations to myocardial flow and mass (2015)

The study of the structure-function relation of coronary bifurcations is necessary not only to understand the design of the vasculature but also to use this understanding to restore structure and hence function. The objective of this review is to provide quantitative relations between bifurcation anatomy or geometry, flow distribution in the bifurcation and degree of perfused myocardial mass in order to establish practical rules to guide optimal treatment of bifurcations including side branches (SB). We use the scaling law between flow and diameter, conservation of mass and the scaling law between myocardial mass and diameter to provide geometric relations between the segment diameters of a bifurcation, flow fraction distribution in the SB, and the percentage of myocardial mass perfused by the SB. We demonstrate that the assessment of the functional significance of an SB for intervention should not only be based on the diameter of the SB but also on the diameter of the mother vessel as well as the diameter of the proximal main artery, as these dictate the flow fraction distribution and perfused myocardial mass, respectively. The geometric and flow rules for a bifurcation are extended to a trifurcation to ensure optimal therapy scaling rules for any branching pattern.
Charged-particle pseudorapidity density at mid-rapidity in p–Pb collisions at $$\pmb {\sqrt{s_{\scriptscriptstyle {\mathrm{NN}}}}}$$ s NN = 8.16 TeV (2019)

The pseudorapidity density of charged particles, dN ch /d, in p-Pb collisions has been measured at a centreof-mass energy per nucleon-nucleon pair of s NN = 8.16 TeV at mid-pseudorapidity for non-single-diffractive events. The results cover 3.6 units of pseudorapidity, || < 1.8. The dN ch /d value is 19.1 0.7 at || < 0.5. This quantity divided by N part /2 is 4.73 0.20, where N part is the average number of participating nucleons, is 9.5% higher than the corresponding value for p-Pb collisions at s NN = 5.02 TeV. Measurements are compared with models based on different mechanisms for particle production. All models agree within uncertainties with data in the Pb-going side, while HIJING overestimates, showing a symmetric behaviour, and EPOS underestimates the p-going side of the dN ch /d distribution. Saturation-based models reproduce the distributions well for > -1.3. The dN ch /d is also measured for different centrality estimators, based both on the chargedparticle multiplicity and on the energy deposited in the Zero-Degree Calorimeters. A study of the implications of the large multiplicity fluctuations due to the small number of participants for systems like p-Pb in the centrality calculation for multiplicity-based estimators is discussed, demonstrating the advantages of determining the centrality with energy deposited near beam rapidity.
New Trends in (heterogeneous) Catalysis for the Fine Chemicals Industry (2014)

New catalytic methods and modern trends for the synthesis of fine chemicals, especially vitamins, carotenoids, flavoring and fragrance compounds are presented. In particular the application of heterogeneous catalysis in the formation and production on industrial scale of these classes of organic compounds will be highlighted and its use in the replacement of former stoichiometric processes.
Fabrication of quantum wires in thermally etched V-grooves by molecular beam epitaxy (1997)

Quasi-one-dimensional quantum wires have been formed in V-grooves on GaAs substrates. A new fabrication technique based on in situ thermal etching of masked substrates and subsequent overgrowth by molecular beam epitaxy has been developed. The device geometries enabled formation of low-resistance ohmic contacts. Two-terminal magnetoresistance measurements of single-wire devices show transport qualities previously not witnessed in growth on non-planar substrates. Illumination has been used to modulate the carrier density and lateral potential profile of the wires.
Warped Input Gaussian Processes for Time Series Forecasting (2019)

We introduce a Gaussian process-based model for handling of non-stationarity. The warping is achieved non-parametrically, through imposing a prior on the relative change of distance between subsequent observation inputs. The model allows the use of general gradient optimization algorithms for training and incurs only a small computational overhead on training and prediction. The model finds its applications in forecasting in non-stationary time series with either gradually varying volatility, presence of change points, or a combination thereof. We evaluate the model on synthetic and real-world time series data comparing against both baseline and known state-of-the-art approaches and show that the model exhibits state-of-the-art forecasting performance at a lower implementation and computation cost.
Causes of incorrect carrier-type identification in van der Pauw–Hall measurements (2008)

The impact of macroscopic sample inhomogeneity and contact placement on the measured carrier type and concentration in the widely used van der Pauw–Hall method is investigated using finite-element analysis of the electrostatics. A variety of likely macroscopic inhomogeneities in mobility or carrier concentration across a square-shaped sample are considered. Inhomogeneities in mobilities do not affect the measured carrier type and concentration, as long as the carrier concentration remains homogeneous. Inhomogeneities in carrier concentrations can result in an incorrect assignment of the carrier type. However, when contacts are placed at the sample corners and not inside the sample area, the correct carrier type is recovered. Our calculations provide an explanation for recent measurements on ZnO [Ohgaki et al., J. Mater. Res. 23, 2293 (2008)]. Guidelines for avoiding incorrect interpretation of van der Pauw–Hall measurements are provided.
Multifunctional photo-crosslinked polymeric ionic hydrogel films (2014)

The crosslinked ionic hydrogel films prepared by photopolymerization have multiple applications as magnetic, catalytic, antibiotic, and fluorescent materials.
Data from microRNA-205 Regulates HER3 in Human Breast Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;An increasing amount of experimental evidence shows that microRNAs can have a causal role in breast cancer tumorigenesis as a novel class of oncogenes or tumor suppressor genes, depending on the targets they regulate. HER2 overexpression is a hallmark of a particularly aggressive subset of breast tumors, and its activation is strictly dependent on the &lt;i&gt;trans&lt;/i&gt;-interaction with other members of HER family; in particular, the activation of the PI3K/Akt survival pathway, so critically important in tumorigenesis, is predominantly driven through phosphorylation of the kinase-inactive member HER3. Here, we show that miR-205, down-modulated in breast tumors compared with normal breast tissue, directly targets HER3 receptor, and inhibits the activation of the downstream mediator Akt. The reintroduction of miR-205 in SKBr3 cells inhibits their clonogenic potential and increases the responsiveness to tyrosine-kinase inhibitors Gefitinib and Lapatinib, abrogating the HER3-mediated resistance and restoring a potent proapoptotic activity. Our data describe miR-205 as a new oncosuppressor gene in breast cancer, able to interfere with the proliferative pathway mediated by HER receptor family. Our study also provides experimental evidence suggesting that miR-205 can improve the responsiveness to specific anticancer therapies. [Cancer Res 2009;69(6):2195–200]&lt;/p&gt;&lt;/div&gt;
An Analysis of Likely Scalants in the Treatment of Produced Water from Nova Scotia (2014)

A significant barrier to further use of hydraulic fracturing to recover shale oil and/or gas is the treatment and/or disposal of hypersaline produced water. This work is an analysis of produced water from Nova Scotia, with the aim of understanding how scale impacts the choice of desalination system used in its treatment. Four water samples are presented, and for a representative case, the supersaturation of some likely scalants is estimated as a function of temperature, recovery ratio, and pH. This supersaturation map is then compared to conditions representative of common desalination systems, allowing the identification of limitations imposed by the water's composition. In contrast to many natural waters, it is found that sodium chloride is the most likely first solid to form at high recovery ratios, and that the top temperature of thermal desalination systems is unlikely to be scale-limited in the treatment of these waters.
Hybrid Text Summarization Method based on the TF Method and the Lead Method. (2001)

This paper describes a hybrid text summarization method based on a TF-based sentence extraction method and a LEAD sentence extraction method. The LEAD method is known to be effective than other methods for document summarization of newspapers in lower summarization (output-to-input) ratio. In order to combine the LEAD method with the TF method, we used a rectangular distribution function that determines the importance of sentences according to their position in a document. With our method, the importance of a sentence is determined by multiplying the TF-based score and the distribution function. We conducted open test evaluation using the formal run test data of sentence extraction sub-task in NTCIR-2 Workshop TSC task (30 newspaper articles). The proposed method was tested by the average values of F-measure for 10%, 30%, and 50% summaries, and proved 34.1% for TF method, 39.1% for LEAD method, and 42.4% for the proposed method. Keywords: TF, LEAD, headline, hybrid, position, distribution. 1
Gradual Phenotypic Conversion Associated with Immortalization of Cultured Human Mammary Epithelial Cells (1997)

Examination of the process of immortal transformation in early passages of two human mammary epithelial cell (HMEC) lines suggests the involvement of an epigenetic step. These lines, 184A1 and 184B5, arose after in vitro exposure of finite lifespan 184 HMEC to a chemical carcinogen, and both are clonally derived. Although early-passage mass cultures of 184A1 and 184B5 maintained continuous slow growth, most individual cells lost proliferative ability. Uniform good growth did not occur until 20-30 passages after the lines first appeared. Early-passage cultures expressed little or no telomerase activity and telomeres continued to shorten with increasing passage. Telomerase activity was first detected when the telomeres became critically short, and activity levels gradually increased thereafter. Early-passage cultures had little or no ability to maintain growth in transforming growth factor-beta (TGFbeta); however, both mass cultures and clonal isolates showed a very gradual increase in the number of cells displaying progressively increased ability to maintain growth in TGFbeta. A strong correlation between capacity to maintain growth in the presence of TGFbeta and expression of telomerase activity was observed. We have used the term "conversion" to describe this process of gradual acquisition of increased growth capacity in the absence or presence of TGFbeta and reactivation of telomerase. We speculate that the development of extremely short telomeres may result in gradual, epigenetic-based changes in gene expression. Understanding the underlying mechanisms of HMEC conversion in vitro may provide new insight into the process of carcinogenic progression in vivo and offer novel modes for therapeutic intervention.
In vivo fluorescence imaging of β-amyloid plaques with push–pull dimethylaminothiophene derivatives (2015)

In vivo fluorescence imaging of β-amyloid (Aβ) plaques in the brain is expected to be used as a new method for detecting Alzheimer's disease (AD). We synthesized novel push-pull dimethylaminothiophenyl (DTM) derivatives and evaluated their utility as in vivo fluorescence imaging probes targeting Aβ plaques. As a result, we found that DTM-2 is a promising fluorescent probe for Aβ plaques in the AD brains.
Growth of the collection (2014)

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Authentication and traceability of food products through the supply chain using NQR spectroscopy (2017)

Maintaining the security and integrity of our food supply chain has emerged as a critical need. In this paper, we describe a novel authentication approach that can significantly improve the security of the food supply chain. It relies on applying nuclear quadrupole resonance (NQR) spectroscopy to authenticate the contents of packaged food products. NQR is a non-invasive, non-destructive, and quantitative radio frequency (RF) spectroscopic technique. It is sensitive to subtle features of the solid-state chemical environment such that signal properties are influenced by the manufacturing process, thus generating a manufacturer-specific watermark or intrinsic tag for the product. Such tags enable us to uniquely characterize and authenticate products of identical composition but from different manufacturers based on their NQR signal parameters. These intrinsic tags can be used to verify the integrity of a product and trace it through the supply chain. We apply a support vector machine (SVM)-based classification approach that trains the SVM with measured NQR parameters and then authenticates food products by checking their test responses. Measurement on an example substance using semi-custom hardware shows promising results (95% classification accuracy) which can be further improved with improved instrumentation.
SAW Chemical Sensors: An Expanding Role with Global Impact (1994)

Chemical microsensors have growing roles in applications with significant global impact, including environmental cleanup and monitoring, industrial process control, automotive and industrial emissions monitoring, aeronautical and space systems, planetary exploration, screening for explosives, worker safety, and health care.
Relationship between Functional Profile of HIV-1 Specific CD8 T Cells and Epitope Variability with the Selection of Escape Mutants in Acute HIV-1 Infection (2011)

In the present study, we analyzed the functional profile of CD8+ T-cell responses directed against autologous transmitted/founder HIV-1 isolates during acute and early infection, and examined whether multifunctionality is required for selection of virus escape mutations. Seven anti-retroviral therapy-naïve subjects were studied in detail between 1 and 87 weeks following onset of symptoms of acute HIV-1 infection. Synthetic peptides representing the autologous transmitted/founder HIV-1 sequences were used in multiparameter flow cytometry assays to determine the functionality of HIV-1-specific CD8+ T memory cells. In all seven patients, the earliest T cell responses were predominantly oligofunctional, although the relative contribution of multifunctional cell responses increased significantly with time from infection. Interestingly, only the magnitude of the total and not of the poly-functional T-cell responses was significantly associated with the selection of escape mutants. However, the high contribution of MIP-1β-producing CD8+ T-cells to the total response suggests that mechanisms not limited to cytotoxicity could be exerting immune pressure during acute infection. Lastly, we show that epitope entropy, reflecting the capacity of the epitope to tolerate mutational change and defined as the diversity of epitope sequences at the population level, was also correlated with rate of emergence of escape mutants.
Interfacing Carbon Nanotubes with Living Cells (2006)

We developed a polymer coating for carbon nanotubes (CNTs) that mimics the mucin glycoprotein coating of mammalian cells. CNTs coated with these mucin mimic polymers have two novel properties: they can bind to carbohydrate receptors, providing a means for biomimetic interactions with cell surfaces, and, importantly, they are rendered nontoxic to cells.
Photoconductivity in highly tetrahedral diamondlike amorphous carbon (1993)

A photoconductive effect is observed in tetrahedral amorphous carbon (ta-C) or amorphous diamond films with a high proportion of sp3 bonding and a structure analogous to amorphous silicon. The spectral response is shown to peak at around 750–800 nm and extend into the near UV region. The maximum photoresponse coincides with the optical absorption edge. The quantum efficiency of 300 nm thick films with interdigitated electrodes is over 10% in the wavelength range 450–800 nm.