gebhart/patrepeval huggingface dataset:
Efficient statistical analysis of large correlated multivariate datasets: a case study on brain connectivity matrices (2010)

In neuroimaging, a large number of correlated tests are routinely performed to detect active voxels in single-subject experiments or to detect regions that differ between individuals belonging to different groups. In order to bound the probability of a false discovery of pair-wise differences, a Bonferroni or other correction for multiplicity is necessary. These corrections greatly reduce the power of the comparisons which means that small signals (differences) remain hidden and therefore have been more or less successful depending on the application. We introduce a method that improves the power of a family of correlated statistical tests by reducing their number in an orderly fashion using our a-priori understanding of the problem . The tests are grouped by blocks that respect the data structure and only one or a few tests per group are performed. For each block we construct an appropriate summary statistic that characterizes a meaningful feature of the block. The comparisons are based on these summary statistics by a block-wise approach. We contrast this method with the one based on the individual measures in terms of power. Finally, we apply the method to compare brain connectivity matrices. Although the method is used in this study on the particular case of imaging, the proposed strategy can be applied to a large variety of problems that involves multiple comparisons when the tests can be grouped according to attributes that depend on the specific problem. Keywords and phrases: Multiple comparisons ; Family-wise error rate; False discovery rate; Bonferroni procedure; Human brain connectivity; Brain connectivity matrices.
Pancreatoblastoma in an elderly woman: A case report simulating a pancreatic neuroendocrine tumour with emphasis on cytomorphological features (2022)

Pancreatoblastoma (PB), a rare malignant epithelial neoplasm, is the most common pancreatic neoplasm of childhood. It is exceptionally rare in the adult population and its occurrence is limited to case reports. Although the neoplastic cells of PB can have a number of different directions of differentiation, PB is defined by the combination of neoplastic cells with acinar differentiation and squamoid morules. We report a case of a female patient in her 70s who presented with elevated creatinine level, concerning a kidney disorder, and was found to have an abdominal mass on CT scan. Fine needle aspiration (FNA) showed cellular smears with numerous 3-dimentional clusters of acinar cells and scattered squamoid morules. A cell block showed sheets of cells, some of which formed acini. Numerous squamoid morules were noted and were highlighted by nuclear labelling with antibodies to B-catenin in the cell block. The FNA diagnosis was rendered as "carcinoma with acinar differentiation, favour pancreatoblastoma." Subsequent histological findings confirmed the PB diagnosis. Next generation sequencing detected a CTNNB1 mutation. Given the wide usage of FNA in the preoperative diagnosis of pancreatic masses, the cytopathologist needs to be aware of the morphological features of PB and its cytological differential diagnosis, even in an elderly patient. The differential diagnosis includes acinar cell carcinoma, pancreatic neuroendocrine tumour, and solid pseudopapillary neoplasm. In conclusion, the cytological finding of neoplastic cells with acinar differentiation combined with squamous morules and/or mesenchymal elements in the smears and more commonly in the cell blocks appears to be the most specific finding for the diagnosis of PB.
Monochrome and Color Polarization Demosaicking Based on Intensity-Guided Residual Interpolation (2021)

A division-of-focal-plane or microgrid image polarimeter enables us to acquire a set of polarization images in one shot. Since the polarimeter consists of an image sensor equipped with a monochrome or color polarization filter array (MPFA or CPFA), the demosaicking process to interpolate missing pixel values plays a crucial role in obtaining high-quality polarization images. In this study, we proposed a novel MPFA demosaicking method based on intensity-guided residual interpolation (IGRI) and extended it to CPFA demosaicking. The key of IGRI is generating an effective intensity guide image, for which we proposed two methods considering four-directional intensity and polarization edge information. We also constructed a new full color-polarization image dataset captured using a 3-CCD RGB camera and a rotating polarizer. By using the constructed dataset, we experimentally validated that our IGRI-based methods outperform existing methods in MPFA and CPFA demosaicking.
Reduced Coating Diameter Fibers for High Density Cables (2022)

We review recent progress on reduced coating diameter fibers for increasing core density for optical interconnect applications. We discuss design considerations on microbending and mechanical reliability and present new experimental results.
Upper bounds on the rate of LDPC codes as a function of minimum distance (2005)

New upper bounds on the rate of low-density parity-check (LDPC) codes as a function of the minimum distance of the code are derived. These bounds are based on combinatorial arguments and linear programming. They improve on the previous bounds due to Burshtein et al. It is proved that at least for high rate LDPC codes have worse relative minimum distance than the one guaranteed by the Gilbert-Varshamov bound
Molecular characterization of the β chain of the murine interleukin 5 receptor (1991)

Interleukin 5 (IL-5) is a multifunctional cytokine that regulates the proliferation and differentiation of hematopoietic cells including B cells and eosinophils. The murine IL-5 acts on target cells via an IL-5 specific high-affinity receptor (Kd approximately 150 pM) that has been proposed to be composed of at least two membrane polypeptide chains. The p60 component recognized by anti-murine IL-5 receptor mAbs H7 and T21 binds IL-5 with low affinity (Kd approximately 10 nM). The other component is p130, detectable by following cross-linking experiments with IL-5. Using H7, T21, and R52.120 mAbs specific to murine IL-5 receptor, we characterized the molecular nature of the p130 of the high affinity receptor for murine IL-5. R52.120 mAb did not recognize the IL-5 binding recombinant p60 expressed on COS7 cells, but reacted with p130/140 on IL-5-dependent cell lines. R52.120 mAb showed partial inhibition of the IL-5-induced proliferation of the IL-5-dependent early B cell line Y16 at high IL-5 concentrations. Addition of R52.120 mAb together with H7 or T21 mAb caused more striking inhibition of the IL-5-dependent proliferation than that caused by either of them alone. R52.120 mAb down-regulated the number and dissociation constant of IL-5 binding sites with high affinity without affecting the levels of these with low-affinity. It also preferentially inhibited the formation of the cross-linked complex of p130 with radiolabeled IL-5. These results indicate that p130/p140, recognized by R52.120 mAb, is indispensable, together with p60, for the formation of high affinity IL-5 receptor. We propose to designate p60 and p130/p140 as the alpha and beta chain of IL-5 receptor, respectively.
Variable Reflection-Type Attenuators Based on Varactor Diodes (2012)

In this paper, variable reflection-type attenuators based on varactor diodes are introduced and described in detail. Their main components are 3-dB couplers, varactor diodes, and lumped elements. Initially, a simple varactor-based reflective load is introduced and its advantages and disadvantages in the circuit of reflection-type attenuators are discussed. Based on this, improvements and refinements to the simple varactor-based reflection-type attenuator are then discussed and a novel circuit of the varactor-based reflection load is proposed. This circuit offers high attenuation and controllable insertion losses. It is also shown that the intermodulation (IM) performance of the novel varactor-based reflection-type attenuator is controllable and that the reduction of insertion losses leads to an improvement of IM performance. As an experimental verification, varactor-based reflection-type attenuators operating at a center frequency of 2.5 GHz are fabricated and measured. It is shown in one reflection-type attenuator realization that insertion losses as low as 1.1 dB with a minimum third-order intercept point of 25.2 dBm are achievable, while in the second realization a dynamic range of over 36 dB is shown to be practically achievable. The results are discussed.
Preliminary Results on Adaptively Trained Neural Networks (1993)

Real world applications often involve time varying models. There is an intrinsic difficulty in dealing with this sort of models, specially when one is concerned with nonlinear syster. Layered neural networks have been successfully used in a variety of relevant problems when invariance assumptions can be properly made. On the other hand, very little can be found in the literature concerning time varying systems. We propose a new procedure to adjust weights in Neural Networks suitable for this type of models with no necessity of retraining. One of the main features of our approach concerns the designer flexibility to control a trade off problem between fitting new incoming data and causing minimum damage to the information related to the original data set. We desire to keep the error related to the late incoming data within a pre established tolerance, while maximizing the information incorporated by original training data. In this way, the designer is able to judge the relevance he or she wants to attribute to the latest data.
Synthesis and Characterization of Colloidal β-HgS Quantum Dots (2002)

High-quality colloidal mercury sulfide quantum dots (QDs) are synthesized at room temperature using a strategy combining the effects of strongly binding Hg(II) ligands and metal/chalcogen precursor phase separation. This combination prevents both the rapid precipitation of bulk HgS in preparations involving only weak Hg(II) ligands and the reduction of mercury that takes place when only strongly binding ligands are used to slow the growth kinetics. Both the linear absorption and complementary band edge emission of the synthesized HgS QDs exhibit narrow, size-dependent transitions between 500 and 800 nm for sizes ranging from 1 to 5 nm in diameter. The metastable zinc blende phase of HgS is verified by wide-angle X-ray diffraction experiments and suggests potentially large tunable band edges if larger HgS nanocrystals that approach the bulk (zero energy) gap can be made. Growth of HgS QDs can be arrested by subsequent addition of Cd or Zn to the surface, after which the QDs can be stabilized with long-chain thiols or amines.
Design of effectively single-mode air-core photonic bandgap fiber with improved transmission characteristics for the realization of ultimate low loss waveguide (2007)

In this paper, we study the novel propagation properties of an improved triangular-type air-core photonic bandgap fiber (PBGF) structured with an anti-resonant silica core surround, through a full-vector modal solver based on the finite-element method (FEM). At first, to realize a single-mode operation over a wide wavelength range, the fiber whose core is constructed by removing 1 air-hole and expanded is proposed and structurally-optimized. In particular, the structural parameters for the fiber that prevent the narrow-band transmission due to the existence of the surface modes and enhance the confinement of the power in the air-core are presented. For the realization of an ultimate low loss transmission, a 7-unit-cell PBGF is analyzed and we show that the 7-unit-cell PBGF can achieve not only lower confinement loss than that of regular-type 7-unit-cell PBGF, but also lower power fraction in the silica-ring when compared with the regular 19-unit-cell PBGF with an anti-resonant core surround, exhibiting an effectively single-mode operation.
Sum Rate Maximization for MU-MISO with Partial CSIT using Joint Multicasting and Broadcasting (2015)

In this paper, we consider a MU-MISO system where users have highly accurate Channel State Information (CSI), while the Base Station (BS) has partial CSI consisting of an imperfect channel estimate and statistical knowledge of the CSI error. With the objective of maximizing the Average Sum Rate (ASR) subject to a power constraint, a special transmission scheme is considered where the BS transmits a common symbol in a multicast fashion, in addition to the conventional private symbols. This scheme is termed Joint Multicasting and Broadcasting (JMB). The ASR problem is transformed into an augmented Average Weighted Sum Mean Square Error (AWSMSE) problem which is solved using Alternating Optimization (AO). The enhanced rate performance accompanied with the incorporation of the multicast part is demonstrated through simulations.
Model-Free Temporal Difference Learning for Non-Zero-Sum Games (2019)

In this paper, we consider the two-player nonzero-sum games problem for continuous-time linear dynamic systems. It is shown that the non-zero-sum games problem results in solving the coupled algebraic Riccati equations, which are nonlinear algebraic matrix equations. Compared with the algebraic Riccati equation of the linear dynamic systems with only one player, the coupled algebraic Riccati equations of nonzero-sum games with multi-player are more difficult to be solved directly. First, the policy iteration algorithm is introduced to find the Nash equilibrium of the non-zero-sum games, which is the sufficient and necessary condition to solve the coupled algebraic Riccati equations. However, the policy iteration algorithm is offline and requires complete knowledge of the system dynamics. To overcome the above issues, a novel online iterative algorithm, named integral temporal difference learning algorithm, is developed. Moreover, an equivalent compact form of the integral temporal difference learning algorithm is also presented. It is shown that the integral temporal difference learning algorithm can be implemented in an online fashion and requires only partial knowledge of the system dynamics. In addition, in each iteration step, the closed-loop stability using the integral temporal difference learning algorithm is analyzed. Finally, the simulation study shows the effectiveness of the presented algorithm.
Performance of a time-independent scattering wave packet technique using real operators and wave functions (1996)

We investigate the performance of a scattering algorithm which uses purely real algebra for the major part of the wave function calculation, while incorporating automatically the appropriate boundary conditions. The algorithm falls in the category of time-independent wave packet methods ([R. Kosloff, J. Phys. Chem. 92, 2087 (1988)], and, more specifically for scattering [Y. Huang, W. Zhu, D. J. Kouri, and D. K. Hoffman, Chem. Phys. Lett. 206, 96 (1993)]), and combines two previous approaches: A method [V. A. Mandelshtam and H. S. Taylor, J. Chem. Phys. 103, 2903 (1995)] in which the action of the absorbing potentials is implicitly inserted in a polynomial expansion of the Green’s function, and a real initial wave function approach, in which zero initial momenta are avoided. Compared to the conventional, multiple time-step Chebyshev method, the new algorithm required three times less Hamiltonian evaluations for a model problem involving direct scattering. The new method also showed faster convergence for a problem involving resonances. Both methods showed convergence problems in the vicinity of a very narrow resonance.
Pursuit of the Renal Mass. Is Ultrasound Enough? (1985)

No AccessJournal of UrologyRadiology, Nuclear Medicine and Sonography1 Jan 1985Pursuit of the Renal Mass. Is Ultrasound Enough? R.V. Clayman, V. Surya, R.P. Miller, D.B. Reinke, and E.E. Fraley R.V. ClaymanR.V. Clayman More articles by this author , V. SuryaV. Surya More articles by this author , R.P. MillerR.P. Miller More articles by this author , D.B. ReinkeD.B. Reinke More articles by this author , and E.E. FraleyE.E. Fraley More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)48858-6AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Pursuit of the Renal Mass. Is Ultrasound Enough?." The Journal of Urology, 133(1), pp. 154–155 © 1985 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 133Issue 1January 1985Page: 154-155 Advertisement Copyright & Permissions© 1985 by The American Urological Association Education and Research, Inc.MetricsAuthor Information R.V. Clayman More articles by this author V. Surya More articles by this author R.P. Miller More articles by this author D.B. Reinke More articles by this author E.E. Fraley More articles by this author Expand All Advertisement PDF DownloadLoading ...
Aging and Cancer: Telomeres, Telomerase and Radiation (2009)

The increased average age of astronauts (~45 years) suggests that diseases associated with increased age may be exacerbated by the space radiation environment. Aging can be defined as the gradual decline in performance and reserve capacity of organ systems leading to impaired responses to stress and increased risk of disease. Major diseases associated with aging include: Alzheimer’s disease, arthritis, cancer, diabetes, heart disease, osteoporosis and stroke. In addition, normal changes associated with aging include shortsightedness and deterioration of color vision, hearing, taste and smell loses, loss of skin elasticity, graying and loss of hair, musculoskeletal changes, loss of cartilage, decreased heart, lung, kidney and pancreas function, decreased immune function, and loss of neural cells. A central question that needs to be addressed is how does the space environment impact on these normal and disease associated aging processes? Over the last decade significant amounts of information about changes in astronaut health have been accumulating. For example, there are decreases in bone mineralization, decreases in muscle mass including cardiovascular changes, decreases in immune function which may correlate with increased risk for cancer, early appearance of cataracts, changes in thyroid function, and loss of neural cells. It is now important to discover the underlying causes of these changes to determine if we can slow down or reverse these changes. The major theories of aging include protein cross linking, DNA damage, free radical damage, mitochondrial DNA damage and cellular senescence. The presentation of slides accompanying this introduction covers many of the proposed causes of aging with a special focus on the telomere theory of aging. Telomeres (the ends of linear chromosomes) progressively shorten in most human tissues with each division and may become limiting in chronic diseases. Replicative senescence is a general stress-response program that restrains cellular proliferation. Under optimal growth conditions, the onset of senescence depends on telomere status, even though there are other factors that can induce a stress or senescence-like state when telomeres are not critically short. However, when telomeres are sufficiently short (or uncapped), a DNA damage response-induced growth arrest occurs. The senescence pathway involves the formation of telomere dysfunction induced foci that contain DNA damage response factors. Importantly, the DNA-damage response observed in
Biomimetic Synthesis of Insulin Enabled by Oxime Ligation and Traceless “C-Peptide” Chemical Excision (2017)

For decades, insulin has represented a preeminent synthetic target. Recently introduced "biomimetic" strategies based on convertible single-chain precursors require incorporation of a chemical linker or a unique proteolytic site, which limits their practicality. In this approach the A- and B-chains are linked by two sequential oxime ligations followed by disulfide bond formation under redox conditions and linker excision by diketopiperazine (DKP) formation and ester hydrolysis, yielding native two-chain insulin. The method is expected to be applicable to any member of the insulin superfamily.
Long-Term Function of Cryopreserved Rat Hepatocytes in a Coculture System (2004)

The goal of this study was to investigate postpreservation long-term function of cryopreserved primary rat hepatocytes using the hepatocyte/3T3-J2 fibroblast coculture system. The long-term function of thawed hepatocytes cocultured with fibroblasts was evaluated and compared with hepatocytes cultured without fibroblasts. Fresh isolated primary rat hepatocytes were frozen at a controlled rate (-1 degrees C/min) up to -80 degrees C, and then stored in liquid nitrogen for up to 90 days. Thawed hepatocytes were thereafter cocultured with 3T3-J2 murine fibroblasts and cocultivation was monitored for 14 days. The viability of fresh isolated hepatocytes was 91.4%, and that of cryopreserved hepatocytes was 82.1%. Cellular morphology and polarity, which were determined by the localization of actin filaments and connexin-32, were successfully maintained in cryopreserved hepatocytes following cryopreservation. Albumin and urea synthesis reached the maximum level and became stable after day 7 in coculture in both fresh and cryopreserved hepatocytes. Urea synthesis of cryopreserved hepatocytes was maintained 89.0% of nonfrozen fresh control, and albumin production of cryopreserved hepatocytes was 63.7% of control in coculture. Cytochrome P450 activity, which was measured by deethylation of ethoxyresorufin, was also maintained in cryopreserved hepatocytes at 88.6% of nonfrozen fresh control in coculture. The retention of synthetic and detoxification activities was verified to be well preserved during extended low-temperature storage (90 days). Both fresh control and cryopreserved hepatocytes cultured without fibroblast did not retain their synthetic and detoxification functions in long-term culture. These data illustrate that, through the utilization of our cryopreservation procedure, primary hepatocyte function was successfully maintained when placed into coculture configuration following thawing.
Binding Preferences, Surface Attachment, Diffusivity, and Orientation of a Family 1 Carbohydrate-binding Module on Cellulose (2012)

Cellulase enzymes often contain carbohydrate-binding modules (CBMs) for binding to cellulose. The mechanisms by which CBMs recognize specific surfaces of cellulose and aid in deconstruction are essential to understand cellulase action. The Family 1 CBM from the Trichoderma reesei Family 7 cellobiohydrolase, Cel7A, is known to selectively bind to hydrophobic surfaces of native cellulose. It is most commonly suggested that three aromatic residues identify the planar binding face of this CBM, but several recent studies have challenged this hypothesis. Here, we use molecular simulation to study the CBM binding orientation and affinity on hydrophilic and hydrophobic cellulose surfaces. Roughly 43 μs of molecular dynamics simulations were conducted, which enables statistically significant observations. We quantify the fractions of the CBMs that detach from crystal surfaces or diffuse to other surfaces, the diffusivity along the hydrophobic surface, and the overall orientation of the CBM on both hydrophobic and hydrophilic faces. The simulations demonstrate that there is a thermodynamic driving force for the Cel7A CBM to bind preferentially to the hydrophobic surface of cellulose relative to hydrophilic surfaces. In addition, the simulations demonstrate that the CBM can diffuse from hydrophilic surfaces to the hydrophobic surface, whereas the reverse transition is not observed. Lastly, our simulations suggest that the flat faces of Family 1 CBMs are the preferred binding surfaces. These results enhance our understanding of how Family 1 CBMs interact with and recognize specific cellulose surfaces and provide insights into the initial events of cellulase adsorption and diffusion on cellulose.