gebhart/patrepeval huggingface dataset:
Notch function in the vasculature: insights from zebrafish, mouse and man (2004)

Vascular development entails multiple cell-fate decisions to specify a diverse array of vascular structures. Notch proteins are signaling receptors that regulate cell-fate determination in a variety of cell types. The finding that Notch genes are robustly expressed in the vasculature suggests roles for Notch in guiding endothelial and associated mural cells through the myriad of cell-fate decisions needed to form the vasculature. In fact, mice with defects in genes encoding Notch, Notch ligands, and components of the Notch signaling cascade invariably display vascular defects. Human Notch genes are linked to Alagille's Syndrome, a developmental disorder with vascular defects, and CADASIL, a cerebral arteriopathy. Studies in zebrafish, mice and humans indicate that Notch works in conjunction with other angiogenic pathways to pattern and stabilize the vasculature. Here, we will focus on established functions for Notch in vascular remodeling and arterial/venous specification and more speculative roles in vascular homeostasis and organ-specific angiogenesis.
Parallel symbolic execution for automated real-world software testing (2011)

This paper introduces Cloud9, a platform for automated testing of real-world software. Our main contribution is the scalable parallelization of symbolic execution on clusters of commodity hardware, to help cope with path explosion. Cloud9 provides a systematic interface for writing "symbolic tests" that concisely specify entire families of inputs and behaviors to be tested, thus improving testing productivity. Cloud9 can handle not only single-threaded programs but also multi-threaded and distributed systems. It includes a new symbolic environment model that is the first to support all major aspects of the POSIX interface, such as processes, threads, synchronization, networking, IPC, and file I/O. We show that Cloud9 can automatically test real systems, like memcached, Apache httpd, lighttpd, the Python interpreter, rsync, and curl. We show how Cloud9 can use existing test suites to generate new test cases that capture untested corner cases (e.g., network stream fragmentation). Cloud9 can also diagnose incomplete bug fixes by analyzing the difference between buggy paths before and after a patch.
Digital halftoning by means of green-noise masks (1999)

We introduce a novel technique for generating green-noise halftones—stochastic dither patterns composed of homogeneously distributed pixel clusters. Although techniques employing error diffusion have been proposed previously, the technique here employs a dither array referred to as a green-noise mask, which greatly reduces the computational complexity formerly associated with green noise. Compared with those generated with blue-noise masks, halftones generated with green-noise masks are less susceptible to printer distortions. Because green noise constitutes patterns with widely varying cluster sizes and shapes, the technique introduced here for constructing these green-noise masks is tunable; that is, it allows for specific printer traits, with small clusters reserved for printers with low distortion and large clusters reserved for printers with high distortion. Given that blue noise is a limiting case of green noise, this new technique can even create blue-noise masks.
Sensing Caspase 3 Activity with Quantum Dot−Fluorescent Protein Assemblies (2009)

We demonstrate the use of a hybrid fluorescent protein semiconductor quantum dot (QD) sensor capable of specifically monitoring caspase 3 proteolytic activity. mCherry monomeric red fluorescent protein engineered to express an N-terminal caspase 3 cleavage site was ratiometrically self-assembled to the surface of QDs using metal-affinity coordination. The proximity of the fluorescent protein to the QD allows it to function as an efficient fluorescence resonance energy transfer acceptor. Addition of caspase 3 enzyme to the QD-mCherry conjugates specifically cleaved the engineered mCherry linker sequence, altering the energy transfer with the QD and allowing quantitative monitoring of proteolytic activity. Inherent advantages of this sensing approach include bacterial expression of the protease substrate in a fluorescently appended form, facile self-assembly to QDs, and the ability to recombinantly modify the substrate to target other proteases of interest.
The role of chemoattraction in cancer metastases (2001)

It has long been unclear as to why particular cancers preferentially metastasize to certain sites. The possibilities usually discussed involve differential survival and proliferation at these sites, or selective trapping with or without preferential homing. A recent report by Muller et al.(1) provides evidence for preferential homing of breast cancer to metastatic sites. The findings indicate that the chemokine receptors CXCR4 and CCR7 are found on breast cancer cells and their ligands are highly expressed at sites associated with breast cancer metastases. This results in chemotaxis, or directed migration of tumor cells from their primary site via the circulation to the preferential sites of metastases. The evidence for this model and its significance are reviewed here.
Binding of ZAP-70 to Phosphorylated T-Cell Receptor ζ and η Enhances Its Autophosphorylation and Generates Specific Binding Sites for SH2 Domain-Containing Proteins (1995)

ZAP-70 is a protein tyrosine kinase thought to play a critical role in T-cell receptor (TCR) signal transduction. During T-cell activation, ZAP-70 binds to a conserved signalling motif known as the immune receptor tyrosine activating motif (ITAM) and becomes tyrosine phosphorylated. To determine whether binding of ZAP-70 to the phosphorylated ITAM was able to activate its kinase activity, we measured the kinase activity of ZAP-70 both when it was bound and when it was unbound to phosphorylated TCR subunits. The ability of ZAP-70 to phosphorylate itself, but not exogenous substrates, was enhanced when it was bound to the tyrosine-phosphorylated TCR zeta and eta chains or to a construct that contained duplicated epsilon ITAMs. No enhanced ZAP-70 autophosphorylation was noted when it was bound to tyrosine-phosphorylated CD3 gamma or epsilon. In addition, autophosphorylation of ZAP-70 when bound to zeta or eta resulted in the generation of multiple distinct ZAP-70 phosphorylated tyrosine residues which had the capacity to bind the SH2 domains of fyn, lck, GAP, and abl. As the effect was noted only when ZAP-70 was bound to TCR subunits containing multiple ITAMs, we propose that one of the roles of the tandem ITAMs is to facilitate the autophosphorylation of ZAP-70. Tyrosine-phosphorylated ZAP-70 then mediates downstream signalling by recruiting SH2 domain-containing signalling proteins.
Fabrication of Temperature-Stable Multilayer Ceramic Capacitor in the (1 -x-y)PMN-xPT-yPNW Ternary System. (2003)

Multilayer ceramic capacitors (MLCCs) were fabricated by laminating layers with different Curie temperatures to improve the temperature coefficient of capacitance in the Pb(Mg1/3Nb2/3)O3-PbTiO3-Pb(Ni1/2W1/2)O3 ternary system. A green sheet was prepared by tape casting using a mixture of Pb(Mg1/3Nb2/3)O3, PbTiO3 and PbO, NiO, WO3. 80Ag-20Pd was attached on the green sheet as an internal electrode. The green sheets with the electrode were then laminated under 2.9×107 Pa at 70°C and sintered at 1000°C for 2h. MLCCs with 11 layers of 0.85PMN-0.05PT-0.1PNW, 2 layers of 0.7PMN-0.2PT-0.1PNW and 4 layers of 0.6PMN-0.3PT-0.1PNW showed an improved temperature coefficient of capacitance (ΔC/C; −13.26−3.85%) in the temperature range from −50 to 80°C.
A parametric error analysis of Goldschmidt's division algorithm (2004)

Back in the 60's Goldschmidt presented a variation of Newton-Raphson iterations for division that is well suited for pipelining. The problem in using Goldschmidt's division algorithm is to present an error analysis that enables one to save hardware by using just the right amount of precision for intermediate calculations while still providing correct rounding. Previous implementations relied on combining formal proof methods (that span thousands of lines) with millions of test vectors. These techniques yield correct designs but the analysis is hard to follow and is not quite tight. We present a simple parametric error analysis of Goldschmidt's division algorithm. This analysis sheds more light on the effect of the different parameters on the error. In addition, we derive closed error formulae that allow to determine optimal parameter choices in four practical settings. We apply our analysis to show that a few bits of precision can be saved in the floating-point division (FP-DIV) microarchitecture of the AMD-K7/spl trade/ microprocessor. These reductions in precision apply to the initial approximation and to the lengths of the multiplicands in the multiplier. When translated to cost, the reductions reflect a savings of 10.6% in the overall cost of the FP-DIV microarchitecture.
Registration of planar film radiographs with computed tomography (1996)

The authors describe a method to register computed tomography (CT) data with planar film radiographs. Previous methods applied to the problem of CT-radiograph registration rely on determining the correspondence between occluding contours of the 3D surface in the CT data with 2D contours in the projection image. These methods implicitly assume that the correspondence is accurate, ignoring fundamental nonlinear differences in the underlying measurements. In contrast, the authors' emphasis has been to directly exploit the relationship between imaging devices. This is performed by registering radiograph data with intensity-corrected simulated radiograph data derived from CT measurements. The authors show that by exploiting the physical relationship between CT and radiograph measurements one can significantly improve registration accuracy. Concomitantly, the authors detail the relationship between CT and radiograph measurements and the primary factors influencing discrepancies between simulated and real radiograph data.
Consequences of Cas9 cleavage in the chromosome ofEscherichia coli (2016)

The RNA-guided Cas9 nuclease from CRISPR-Cas systems has emerged as a powerful biotechnological tool. The specificity of Cas9 can be reprogrammed to cleave desired sequences in a cell's chromosome simply by changing the sequence of a small guide RNA. Unlike in most eukaryotes, Cas9 cleavage in the chromosome of bacteria has been reported to kill the cell. However, the mechanism of cell death remains to be investigated. Bacteria mainly rely on homologous recombination (HR) with sister chromosomes to repair double strand breaks. Here, we show that the simultaneous cleavage of all copies of the Escherichia coli chromosome at the same position cannot be repaired, leading to cell death. However, inefficient cleavage can be tolerated through continuous repair by the HR pathway. In order to kill cells reliably, HR can be blocked using the Mu phage Gam protein. Finally, the introduction of the non-homologous end joining (NHEJ) pathway from Mycobacterium tuberculosis was not able to rescue the cells from Cas9-mediated killing, but did introduce small deletions at a low frequency. This work provides a better understanding of the consequences of Cas9 cleavage in bacterial chromosomes which will be instrumental in the development of future CRISPR tools.
The Tapped-Inductor Boost Converter (2007)

In many emerging applications it is required a high boosting gain; in the literature has been proposed many topologies to make this possible, since the traditional dc-dc boost converter can not make the very high boosting function by itself. In this paper a different approach to obtain the high boosting gain is proposed: the tapped-inductor boost converter. This converter has few components and high efficiency, and also operates in a simple way. Analysis and experimental results are presented.
Cobweb cellular arrays (1965)

The cobweb cellular arrays are embellishments of the cutpoint cellular array that are made by complicating the cell-interconnection structure. This new class of arrays will allow for more economical and efficient logical designs than are possible in cutpoint arrays. As a background to the new arrays, the properties of the cutpoint array will be reviewed.
Fecal Microbiota Transplant for Treatment of Clostridium difficile Infection in Immunocompromised Patients (2014)

This series demonstrates the effective use of FMT for CDI in IC patients with few SAEs or related AEs. Importantly, there were no related infectious complications in these high-risk patients.
Inhibition of the Eighth Component of Complement (C8) by Ethylenediaminetetra-Acetate (Edta) (1970)

Abstract Functionally pure C8 from human or guinea pig serum was inactivated by 1 to 2 × 10-3 M EDTA. Native C8 in serum was partially inactivated by EDTA, but much longer periods of incubation at 37°C were required for this to be evident. The effect of EDTA on C8 was dependent upon time, temperature, and concentrations of both the chelating agent and C8. The inactivation of C8 by EDTA was partially or totally reversed by the addition of Ca2+ or by dialysis, but reversal was dependent upon the duration of exposure and the temperature. The process became irreversible within relatively short periods of time at 30°C and 37°C. EDTA had no apparent effect on the activity of cell-bound C8 or on the binding site of C8 for C9, but it did impair the binding site of C8 for C7. Neither EAC1–7 nor C9 was affected by EDTA.
Systematic comparison of RNA extraction techniques from frozen and fresh lung tissues: checkpoint towards gene expression studies (2009)

Our data demonstrated that although the GTC technique has yielded a higher amount of RNA, the SGC technique was much more superior with respect to the reliable generation of an intact RNA and effectively amplified longer products in fresh as well as in frozen tissues.
Bipolar disorder comorbidity in patients with a primary diagnosis of OCD (2016)

BD may not be as highly prevalent in OCD as reported in literature. Those with OCD seem to have only a marginally higher risk for developing BD than the general population. A diagnosis of BD seems to have a pathoplastic effect on the course of OCD. Patients with OCD-BD comorbidity have to be specifically assessed for suicide risk.
Design of 1.2 Gbps MIMO WLAN system for 4K digital cinema transmission (2009)

This paper deals with our work in designing a 1.2 Gbps WLAN system. It reaches 33 meter propagation distance by using 80 MHz bandwidth on 5 GHz band. The proposed preamble has backward compatibility with IEEE802.11n system, allows band sharing and avoids collision within 5 GHz band. The proposed preamble has comparable PAPR and preamble efficiency with IEEE802.11n system. The 4 × 5 MIMO configuration contributes 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> -order diversity gain and maintains both the throughput and performance. Run test for transmitting 90 frames of 4 K digital cinema under in-door channel model demonstrates the excellent performance of the proposed system.
NrCAM, a neuronal system cell-adhesion molecule, is induced in papillary thyroid carcinomas (2007)

NrCAM (neuron-glia-related cell-adhesion molecule) is primarily, although not solely, expressed in the nervous system. In the present study, NrCAM expression was analysed in a series (46) of papillary thyroid carcinomas (PTCs) and paired normal tissues (NT). Quantitative reverse transcriptase (QRT)-PCR revealed that NrCAM expression was upregulated in all PTCs compared to normal thyroid, whatever the stage or size of the primary tumour. NrCAM transcript levels were 1.3- to 30.7-fold higher in PTCs than in NT. Immunohistochemistry (IHC) confirmed that the expression of NrCAM was considerably higher in tumours (score 2+/3+) than in adjacent normal paratumoural thyroid tissue. The NrCAM protein was detected in all but three (93.3%) PTC samples, and it was mainly cytoplasmic; in some cases there was additional membranous localisation - basolateral and partly apical. In the normal thyroid and tissues surrounding tumours, focal NrCAM immunolabelling was seen only in follicles containing tall cells, where staining was restricted to the apical pole of thyrocytes. Western blot analysis corroborated the QRT-PCR and IHC results, showing higher NrCAM protein levels in PTCs than in paired NT. The level of overexpression of the NrCAM mRNA in tumourous tissue appeared to be independent of the primary tumour stage (pT) or the size of the PTC. These data provide the first evidence that NrCAM is overexpressed in human PTCs at the mRNA and protein levels, whatever the tumour stage. Thus, the induction and upregulation of NrCAM expression could be implicated in the pathogenesis and behaviour of papillary thyroid cancers.
AAM Derived Face Representations for Robust Facial Action Recognition (2006)

In this paper, we present results on experiments employing active appearance model (AAM) derived facial representations, for the task of facial action recognition. Experimental results demonstrate the benefit of AAM-derived representations on a spontaneous AU database containing "real-world" variation. Additionally, we explore a number of normalization methods for these representations which increase facial action recognition performance.
Improved Reservoir History Matching and Production Optimization with Tracer Data (2018)

Abstract Interwell tracers have been shown to provide invaluable information about reservoir dynamics, well connectivity, and fluid flow allocations. However, tracer tests are often applied sporadically because their immediate returns of investments are not readily apparent to a resource-holder. Here, we rigorously demonstrate that tracer data can indeed improve reservoir history matching, and, more importantly, improve future production, using reservoir simulations on benchmark problems. Sensitivity studies and the limitations of tracer data are also provided. The numerical experiments were divided in two sections. First, production data with or without tracer data from reference fields were collected for the first water flooding periods for history matching. Second, the history matched models from the first section were used for production optimization for the next water flooding periods. The ensemble smoother with multiple data assimilation (ES-MDA) was used for the history matching processes for the first part of the numerical experiments, and the modified robust ensemble-based optimization (EnOpt) was adopted to maximize the net present value (NPV) for the second part of the numerical experiments. The three-dimensional channelized "Egg Model" was chosen as the initial benchmark problem. From the first part of the numerical experiments, using the same hyper-parameters, it was observed that history matching including tracer data resulted in a better match of the field production rates with smaller standard deviations. In addition, history matching including tracer data resulted in more distinct geological features when observing the history matched permeability maps. From the second part of the numerical experiments, we observed that the geological models history matched including tracer data resulted in better production optimization with higher NPV produced. In the specific case of the Egg Model, +4.3% increase of the NPV was observed. To understand the sensitivity and the limitations of the tracer data, the same numerical experiments were performed on a library of reservoir models with different fracture patterns. After the history matching and production optimization simulations, we observed that including tracer data gave positive NPV increases ranging from +0.3% to +9.4% from 5 of the 7 test cases. It was observed that tracers were more effective for the non-homogeneously flooded reservoirs. To the best of our knowledge, this paper is the first study that quantifies the benefits of tracers in the context of the improved production, measured in NPV. In a broader perspective, we believe this is the best way to test any new history matching algorithms or reservoir surveillance methods. In this work, we show that tracers can result in positive NPV in most situations, and oil producers using large-scale water flooding operations would benefit from performing more tracer tests in their operations.
Tunable single-mode fiber reflective grating litter (1987)

By placing a periodic perturbation in the evanescent field of a side-pollshed single-mode fiber,1–4 a narrowband reflection filter can be constructed.2,3 These fiber-compatible devices offer the potential for high efficiency3 and low insertion loss, since the signal is not removed from the fiber. One limitation of these previously demonstrated devices2,3 Is that they operate at only one fixed wavelength which Is set by the spatial period of the evanescent perturbation. We describe a method which allows for tunable operation of a narrowband evanescent-field reflection filter.
An Optical Method for Evaluation of Geometric Fidelity for Anatomically Shaped Tissue-Engineered Constructs (2009)

Quantification of shape fidelity of complex geometries for tissue-engineered constructs has not been thoroughly investigated. The objective of this study was to quantitatively describe geometric fidelities of various approaches to the fabrication of anatomically shaped meniscal constructs. Ovine menisci (n = 4) were imaged using magnetic resonance imaging (MRI) and microcomputed tomography (microCT). Acrylonitrile butadiene styrene plastic molds were designed from each imaging modality and three-dimensional printed on a Stratasys FDM 3000. Silastic impression molds were fabricated directly from ovine menisci. These molds were used to generate shaped constructs using 2% alginate with 2% CaSO(4). Solid freeform fabrication was conducted on a custom open-architecture three-dimensional printing platform. Printed samples were made using 2% alginate with 0.75% CaSO(4). Hydrogel constructs were scanned via laser triangulation distance sensor. The point cloud images were analyzed to acquire computational measurements for key points of interest (e.g., height, width, and volume). Silastic molds were within + or - 10% error with respect to the native tissue for seven key measurements, microCT molds for six of seven, microCT prints for four of seven, MRI molds for five of seven, and MRI prints for four of seven. This work shows the ability to generate and quantify anatomically shaped meniscal constructs of high geometric fidelity and lends insight into the relative geometric fidelities of several tissue engineering techniques.
Nonlinear-optical amplifier based on a dual-core fiber (1996)

We propose a scheme for all-optical amplification based on a nonlinear-optical coupler in which one core is amplifying while another is attenuating. In this scheme the input signal is fed into the amplifying core, from where the output is also obtained. A weak input easily couples to the lossy core and gets dissipated in it, whereas a stronger signal stays and undergoes a nearly linear amplification in the active core. When it is used for reshaping pulses in a long transmission line, this scheme should allow the pulses to be amplified while simultaneously suppressing the noises between them. Simulating equations for the cw signal in this model, we are able to find a regime that provides for a strong contrast between the suppression of weak signals and amplification of strong ones as well as a steep transition from suppression to amplification at a certainthreshold.