Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell Inhibition by HLA-Bw4 Ligand KIR3DL1 Polymorphisms That Affect NK

The killer cell Ig-like receptor ( KIR ) gene family encodes MHC class I receptors expressed by NK cells and several T cell subpopulations. Factors contributing to human KIR haplotype diversity are differences in gene number, gene content, and allelic polymorphism. Whereas functional and clinical consequences of the ﬁrst two factors are established, knowledge of the effects of KIR gene polymorphism is limited to special cases in which signaling function is reversed or cell surface expression lost. In this study we use retrovirally transduced human cell lines to show that 3DL1*002 is a stronger inhibitory receptor for HLA-Bw4 ligands than 3DL1*007. Analysis of mutant 3DL1*002 and 3DL1*007 molecules demonstrates that residue 238 in the D2 domain and 320 in the transmembrane region contribute to the difference in receptor strength. Neither position 238 nor 320 is predicted to interact directly with HLA-Bw4 ligand. This study also revealed that KIR3DL1 and LILRB1 both contribute to developing an inhibitory response to HLA-Bw4 ligands. The Journal of Immunology, 2005, 175: 5222–5229.
Multi-task Neural Networks for QSAR Predictions

Although artificial neural networks have occasionally been used for Quantitative Structure-Activity/Property Relationship (QSAR/QSPR) studies in the past, the literature has of late been dominated by other machine learning techniques such as random forests. However, a variety of new neural net techniques along with successful applications in other domains have renewed interest in network approaches. In this work, inspired by the winning team's use of neural networks in a recent QSAR competition, we used an artificial neural network to learn a function that predicts activities of compounds for multiple assays at the same time. We conducted experiments leveraging recent methods for dealing with overfitting in neural networks as well as other tricks from the neural networks literature. We compared our methods to alternative methods reported to perform well on these tasks and found that our neural net methods provided superior performance.
Structural Models of Credit Risk are Useful: Evidence from Hedge Ratios on Corporate Bonds

It is well known that structural models of credit risk provide poor predictions of bond prices. We show that they may perform much better as a predictor of debt return sensitivities to equity. This is important since it gives us an opportunity to identify much better the reasons for model failure. The main result of this paper is that even the simplest of the structural models (Merton (1974)) produces hedge ratios that are in line with those observed empirically. As well as providing insight into the determinants of corporate bond prices our results are also useful to practitioners who wish to hedge their positions in corporate debt. The paper also shows that corporate bond prices are sensitive to some variables - e.g., VIX - in a way that appears unrelated to credit risk.
Effect of synchronization errors on the performance of multicarrier CDMA systems

A synchronous multicarrier (MC) code-division multiple access (CDMA) system using inverse fast Fourier transform (IFFT) and fast Fourier transform (FFT) for the downlink mobile communication system operating in a frequency selective Rayleigh fading channel is analyzed. Both carrier frequency offset and timing offset are considered in the analysis. Bit error rate performance of the system with both equal gain combining and maximum ratio combining are obtained. The performance is compared to that of the conventional system using correlation receiver. It is shown that when subcarrier number is large, the system using IFFT/FFT has nearly the same performance as the conventional one, while when the subcarrier number is small, the system using IFFT/FFT will suffer slightly worse performance in the presence of carrier frequency offset.
Good syndrome: an adult-onset immunodeficiency remarkable for its high incidence of invasive infections and autoimmune complications.

BACKGROUND Good syndrome (GS) is a rare condition in which thymoma is associated with hypogammaglobulinemia. It is characterized by increased susceptibility to bacterial, viral, and fungal infections, as well as autoimmunity. Most patients have no circulating B cells. METHODS The French DEFicit Immunitaire de l'adulte cohort provides detailed clinical and immunological descriptions of 690 adults with primary hypogammaglobulinemia. Comparisons between patients with GS, those with common variable immunodeficiency (CVID), and those with B(-) CVID (circulating B cells <1%) were performed. RESULTS Twenty-one patients had GS and 440 had CVID, including 39 B(-) CVID, with a median age at diagnosis of 60, 35, and 34 years, respectively. Invasive bacterial infections were observed in 90.5% of GS, 54% of CVID, and 72% of B(-) CVID patients. Eight patients with GS had opportunistic infections, despite normal peripheral CD4(+) T-cell numbers. Autoimmune complications were demonstrated in 76% of GS, 29% of CVID, and 26% of B(-) CVID patients. The spectrum of autoimmunity in GS was uncommon, consisting of oral lichen planus, graft-vs-host disease-like colitis, and pure red cell aplasia, different from the pattern observed in CVID patients. GS patients did not display lymphoid hyperplasia nor lymphoma, unlike those with CVID or B(-) CVID. CONCLUSIONS GS differs notably from CVID and B(-) CVID: very late onset, no familial cases, and absence of lymphoid hyperplasia. The key observation is the very high frequency of invasive bacterial infections in GS, an issue that physicians should be aware of.
The Resolved Properties of Extragalactic Giant Molecular Clouds

We use high spatial resolution observations of CO to systematically measure the resolved size-line width, luminosity-line width, luminosity-size, and mass-luminosity relations of GMCs in a variety of extragalactic systems. Although the data are heterogeneous, we analyze them in a consistent manner to remove the biases introduced by limited sensitivity and resolution, thus obtaining reliable sizes, velocity dispersions, and luminosities. We compare the results obtained in dwarf galaxies with those from the Local Group spiral galaxies. We find that extragalactic GMC properties measured across a wide range of environments are very much compatible with those in the Galaxy. The property that shows the largest variability is their resolved brightness temperature, although even that is similar to the average Galactic value in most sources. We use these results to investigate metallicity trends in the cloud average column density and virial CO-to-H2 factor. We find that these measurements do not accord with simple predictions from photoionization-regulated star formation theory, although this could be due to the fact that we do not sample small enough spatial scales or the full gravitational potential of the molecular cloud. We also find that the virial CO-to-H2 conversion factor in CO-bright GMCs is very similar to Galactic and that the excursions do not show a measurable metallicity trend. We contrast these results with estimates of molecular mass based on far-infrared measurements obtained for the Small Magellanic Cloud, which systematically yield larger masses, and interpret this discrepancy as arising from large H2 envelopes that surround the CO-bright cores. We conclude that GMCs identified on the basis of their CO emission are a unique class of objects that exhibit a remarkably uniform set of properties from galaxy to galaxy.
Reformulating Space Syntax: The Automatic Definition and Generation of Axial Lines and Axial Maps

Space syntax is a technique for measuring the relative accessibility of different locations in a spatial system which has been loosely partitioned into convex spaces.These spaces are approximated by straight lines, called axial lines, and the topological graph associated with their intersection is used to generate indices of distance, called integration, which are then used as proxies for accessibility. The most controversial problem in applying the technique involves the definition of these lines. There is no unique method for their generation, hence different users generate different sets of lines for the same application. In this paper, we explore this problem, arguing that to make progress, there need to be unambiguous, agreed procedures for generating such maps. The methods we suggest for generating such lines depend on defining viewsheds, called isovists, which can be approximated by their maximum diameters,these lengths being used to form axial maps similar to those used in space syntax. We propose a generic algorithm for sorting isovists according to various measures,approximating them by their diameters and using the axial map as a summary of the extent to which isovists overlap (intersect) and are accessible to one another. We examine the fields created by these viewsheds and the statistical properties of the maps created. We demonstrate our techniques for the small French town of Gassin used originally by Hillier and Hanson (1984) to illustrate the theory, exploring different criteria for sorting isovists, and different axial maps generated by changing the scale of resolution. This paper throws up as many problems as it solves but we believe it points the way to firmer foundations for space syntax.
FÖRSTER TRANSFER CALCULATIONS BASED ON CRYSTAL STRUCTURE DATA FROM Agmenellum quadruplicatum C‐PHYCOCYANIN

Excitation energy transfer in C‐phycocyanin is modeled using the Forster inductive resonance mechanism. Detailed calculations are carried out using coordinates and orientations of the chromophores derived from X‐ray crystallographic studies of C‐phycocyanin from two different species (Schirmer et al, J. Mol. Biol.184, 257–277 (1985) and ibid., 188, 651‐677 (1986)). Spectral overlap integrals are estimated from absorption and fluorescence spectra of C‐phycocyanin of Mastigocladus laminosus and its separated subunits. Calculations are carried out for the β‐subunit, αβ‐monomer, (αβ)3‐trimer and (αβ)0‐hexamer species with the following chromophore assignments: β155 = 's’(sensitizer), β84 =‘f (fluorescer) and α84 =‘m’(intermediate):]:. The calculations show that excitation transfer relaxation occurs to 3=98% within 200 ps in nearly every case; however, the rates increase as much as 10‐fold for the higher aggregates. Comparison with experimental data on fluorescence decay and depolarization kinetics from the literature shows qualitative agreement with these calculations. We conclude that Forster transfer is sufficient to account for all of the observed fluorescence properties of C‐phycocyanin in aggregation states up to the hexamer and in the absence of linker polypeptides.
A wavelet approach on energy distribution of eye movement potential towards direction

This study presents an investigation in classification of Electrooculography (EOG) signals of eye movement potentials. In recent years, the classification of EOG signals by using the FFT is computationally efficient in means and has been a good considerable in research effort. In the quest to improve the accuracy of the EOG signals classification, a method of time-frequency based analysis is proposed. The EOG signals are captured using electrodes placed on the forehead around the eyes to record the eye movements. The wavelet features are used to determine the characteristic of eye movement waveform. EOG signals are captured using the Neurofax EEG-9200. The recorded data is composed of an eye movement toward four directions (upward, downward, left and right). The proposed analysis for each eyes signal is analyzed by using Wavelet Transform (WT) by comparing the energy distribution with the change of time and frequency of a signal. A wavelet scalogram is plotted to display the different percentages of energy for each wavelet coefficient towards different movement. From the result, it is proved that the different EOG signals exhibit differences in signals energy with their corresponding level such as left with level 6 (8–16Hz), right with level 8 (2–4Hz), downward with level 7 (4–8Hz) and upward with level 9 (1–2Hz).
IMAGE DECOMPOSITION AND RESTORATION USING TOTAL VARIATION MINIMIZATION AND THE H−1 NORM∗

Abstract. In this paper, we propose a new model for image restoration and image decomposition into cartoon and texture, based on the total variation minimization of Rudin, Osher, and Fatemi [Phys. D, 60 (1992), pp. 259–268], and on oscillatory functions, which follows results of Meyer [Oscillating Patterns in Image Processing and Nonlinear Evolution Equations, Univ. Lecture Ser. 22, AMS, Providence, RI, 2002]. This paper also continues the ideas introduced by the authors in a previous work on image decomposition models into cartoon and texture [L. Vese and S. Osher, J. Sci. Comput. , to appear]. Indeed, by an alternative formulation, an initial image f is decomposed here into a cartoon part u and a texture or noise part v. The u component is modeled by a function of bounded variation, while the v component is modeled by an oscillatory function, bounded in the norm dual to | · |H1 0 . After some transformation, the resulting PDE is of fourth order, envolving the
Functional analysis of the rice vacuolar zinc transporter OsMTP1

Heavy metal homeostasis is maintained in plant cells by specialized transporters which compartmentalize or efflux metal ions, maintaining cytosolic concentrations within a narrow range. OsMTP1 is a member of the cation diffusion facilitator (CDF)/metal tolerance protein (MTP) family of metal cation transporters in Oryza sativa, which is closely related to Arabidopsis thaliana MTP1. Functional complementation of the Arabidopsis T-DNA insertion mutant mtp1-1 demonstrates that OsMTP1 transports Zn in planta and localizes at the tonoplast. When heterologously expressed in the yeast mutant zrc1 cot1, OsMTP1 complemented its Zn hypersensitivity and was also localized to the vacuole. OsMTP1 alleviated, to some extent, the Co sensitivity of this mutant, rescued the Fe hypersensitivity of the ccc1 mutant at low Fe concentrations, and restored growth of the Cd-hypersensitive mutant ycf1 at low Cd concentrations. These results suggest that OsMTP1 transports Zn but also Co, Fe, and Cd, possibly with lower affinity. Site-directed mutagenesis studies revealed two substitutions in OsMTP1 that alter the transport function of this protein. OsMTP1 harbouring a substitution of Leu82 to a phenylalanine can still transport low levels of Zn, with an enhanced affinity for Fe and Co, and a gain of function for Mn. A substitution of His90 with an aspartic acid completely abolishes Zn transport but improves Fe transport in OsMTP1. These amino acid residues are important in determining substrate specificity and may be a starting point for refining transporter activity in possible biotechnological applications, such as biofortification and phytoremediation.
New strategy for in vitro activation of primordial follicles with mTOR and PI3K stimulators

It had been known for decades that primordial follicles in mammalian ovaries are assembled with definite numbers and represent the ovarian reserve throughout the reproductive life. Intra-oocyte PI3K/mTOR pathways have been indicated to play a central role on the activation of primordial follicles. Genetic modified mouse models with chronic activation of PI3K/mTOR signals in primordial oocytes showed premature activation of all primordial follicles and eventually their exhaustion. On the other hand, this may suggest that, unlike chronic activation of PI3K/mTOR, its acute activation in infertility would activate primordial follicles, permitting fertility during the treatment. Previously, PI3K stimulators were reported as a temporary measure to accelerate primordial follicle activation and follicular development in both mouse and human, and were applied in the treatment of infertility in premature ovarian failure (POF) patients. To address whether mTOR stimulators could play similar role in the process, we transiently treated neonatal and aged mouse ovaries with mTOR stimulators-phosphatidic acid (PA) and propranolol. Our results demonstrated the stimulators increased activation of primordial follicles and the production of progeny. Human ovarian cortex cubes were also treated with mTOR or/and PI3K stimulators in vitro. When they were used separately, both of them showed similar promotive effects on primordial follicles. Surprisingly, after joint-treatment with the 2 kinds of stimulators together, synergistic effects on follicular development were observed. Based on increased efficiency of follicular activation in humans, here we propose in vitro transient treatment with mTOR and PI3K stimulators as an optimized protocol for the application in different clinical conditions with limited follicle reserve.
Prototyping 'clasp': implications for designing digital technology for and with adults with autism

This paper presents Clasp, a novel tactile anxiety management, communication and peer support tool developed with, by and for adults diagnosed with High Functioning Autism (HFA). Clasp connects a tactile anxiety coping device to a smartphone, which records and communicates anxiety levels for self-feedback and reflection. By adopting an iterative prototyping approach, we gained a deep insight into anxiety experienced by adults with HFA and evaluated the role of digital technology in its management. The paper describes our development approach, which we argue is unique to this multidisciplinary and multiorganizational design context involving hard-to-reach and vulnerable groups. Finally, we reflect on lessons learned from this process and share a set of design implications for the future development of digital tools that, like Clasp, are specifically designed with, by and for adults with HFA.
Effect of Herbicides on Narrow Leaved Weeds and Yield of Wheat (Triticum aestivum L.)

─This study was conducted to investigate the efficacy of five herbicides on narrow leaved weeds and growth and yield of wheat. An experiment was conducted at Agronomic Research Farm, University of Agriculture Faisalabad. The experiment was laid out in randomized complete block designee (RCBD) with three replications. Treatments studied were clodinafop (Topic-15 WG) at 37 g a.i. ha, clodinafop (Topaz-15 WG) at 45 g a.i. ha, fenoxaprop-p-ethyl (Puma Super-75 EW) at 45 g a.i. ha, fenoxaprop-p-ethyl (Gramicide-6.9 EW) at 85 g a.i. ha, fenoxaprop-p-ethyl (Chinlima-6.9 EW) at 85 g a.i. ha and weedy check. Plots treated with fenoxaprop-p-ethyl (Puma Super-75 EW) at 45 g a.i. ha produced relatively less weed biomass, more plant height, number of spike bearing tillers, number of grains per spike, 1000-grain weight and grain yield (4.20 t ha). Keywords─clodinafop, fenoxaprop-p-ethyl, weeds, wheat
On the Environmental Dependence of Galaxy Properties Established by the Initial Cosmological Conditions

We study theoretically how the initial cosmological conditions establish the dependence of galaxy properties on the environment. First we adopt the linear tidal torque theory, according to which the angular momentum of a protogalaxy is generated to first order by the misalignment between the protogalaxy's inertia tensor and the local tidal tensor. Then we quantify analytically the degree of misalignment between the two tensors and show quantitatively that it increases as the density of the environment decreases. This implies that protogalaxies forming in lower density regions should end up with higher angular momentum than those in higher density regions, which is consistent with the recent numerical finding that void and field galaxies have higher spin parameters than do cluster galaxies. Since the galaxy angular momentum plays a role in developing a disklike structure and hindering star formation, our theoretical insight provides an answer to such a fundamental observational question as why the large void galaxies have young stellar populations and high specific star formation rates, which was not explained by the previous morphology-density relation.
The Dynamical Equilibrium of Galaxy Clusters

If a galaxy cluster is effectively in dynamical equilibrium, then all galaxy populations within the cluster must have distributions in velocity and position that individually reflect the same underlying mass distribution, although the derived virial masses can be quite different. Specifically, within the Canadian Network for Observational Cosmology cluster sample, the virial radius of the red galaxy population is, on the average, a factor of 2.05 ± 0.34 smaller than that of the blue population. The red galaxies also have a smaller rms velocity dispersion, a factor of 1.31 ± 0.13 within our sample. Consequently, the virial mass calculated from the blue galaxies is 3.5 ± 1.3 times larger than from the red galaxies. However, applying the Jeans equation of stellar hydrodynamic equilibrium to the red and blue subsamples separately gives statistically identical cluster mass profiles. This is strong evidence that these clusters are effectively equilibrium systems and therefore demonstrates empirically that the masses in the virialized region are reliably estimated using dynamical techniques.
Temporal Relationship and Prognostic Significance of Atrial Fibrillation in Heart Failure Patients With Preserved Ejection Fraction: A Community-Based Study

Background— In patients with heart failure and preserved ejection fraction (HFpEF), atrial fibrillation (AF) may predate, concur with, or develop after HFpEF diagnosis. We sought to define the temporal relationship between AF and HFpEF, to identify factors associated with AF, and to determine the prognostic impact of prevalent and incident AF in HFpEF. Method and Results— From 1983 to 2010, 939 Olmsted County, Minnesota, residents (age, 77±12 years; 61% female) newly diagnosed with HFpEF (EF ≥0.50) were evaluated. Baseline rhythm classification included prior AF (>3 months before HFpEF diagnosis), concurrent AF (±3 months), or sinus rhythm. Incident AF (>3 months after HFpEF diagnosis) and all-cause mortality were ascertained through February 2012. Prior AF (29%) and concurrent AF (23%) were associated with older age, higher brain-type natriuretic peptide, and larger left atrial volume index at HFpEF diagnosis compared with sinus rhythm. Of HFpEF patients in sinus rhythm at diagnosis, 32% developed AF over a median follow-up of 3.7 years (interquartile range, 1.5–6.7 years; 69 events per 1000 person-years). Age and diastolic dysfunction were positively and statin use was inversely associated with incident AF. With no AF used as the referent, prior or concurrent AF (combined hazard ratio, 1.3; 95% confidence interval, 1.0–1.6; P=0.03) and incident AF, modeled as a time-dependent covariate (hazard ratio, 2.1; 95% confidence interval, 1.4–3.0; P<0.001), were independently associated with death after adjustment for pertinent covariates. Conclusions— AF occurs in two thirds of HFpEF patients at some point in the natural history and confers a poor prognosis. Further study is required to determine whether intervention for AF may improve outcomes or if statin use can prevent AF in HFpEF.
Using click-evoked auditory brainstem response waveforms to measure hearing loss in the bottlenose dolphin (Tursiops truncatus)

Developing an improved methodology for efficient and informative hearing assessment in marine mammals would prove insightful in expanding current knowledge regarding marine mammal hearing sensitivity, particularly in studying the effects of anthropogenic noise. This study examines the click-evoked auditory brainstem response in relation to upper frequency limit of hearing in the bottlenose dolphin (Tursiops truncatus) as a proxy for hearing capacity. 2016 This work is intended for review only. It is not intended for citation, quotation, or other use in any form.