Miracle-dz/UniFAR-FTUs huggingface dataset:
Image formation principles in coded-aperture based x-ray phase contrast imaging

A novel x-ray phase contrast imaging technique based on coded apertures was recently developed at University College London. This technique removes most limitations of previous phase contrast methods and provides image improvements comparable to those obtained with synchrotron radiation with conventional x-ray sources. Unlike other phase contrast approaches, the technique does not impose restrictive wavelength and/or angular filtering on the beam emitted by the source, meaning that the beam can be exploited in full thus minimizing exposure times. As a consequence, the method provides, for the first time, a concrete opportunity to transfer x-ray phase contrast imaging into real medical applications. This paper discusses the image formation principles, analyses the shape and nature of the phase contrast profiles obtained and draws a significant conclusion on the role of convolution integrals in the acquisition of phase contrast patterns, applicable also to other phase contrast imaging approaches.
Subchronic Toxicities of HZ1006, a Hydroxamate-Based Histone Deacetylase Inhibitor, in Beagle Dogs and Sprague-Dawley Rats

Histone deacetylase inhibitors (HDACIs), such as vorinostat and panobinostat, have been shown to have active effects on many hematologic malignancies, including multiple myeloma and cutaneous T-cell lymphoma. Hydroxamate-based (Hb) HDACIs have very good toxicity profiles and are currently being tested in phases I and II clinical trials with promising results in selected neoplasms, such as bladder carcinoma. One of the Hb-HDACIs, HZ1006, has been demonstrated to be a promising drug for clinical use. The aim of our study was to determine the possible target of toxicity and to identify a non-toxic dose of HZ1006 for clinical use. In our studies, the repeated dosage toxicity of HZ1006 in Beagle dogs and Sprague Dawley (SD) rats was identified. Dogs and rats received HZ1006 orally (0–80 and 0–120 mg/kg/day, respectively) on a continuous daily dosing agenda for 28 days following a 14-day dosage-free period. HZ1006’s NOAEL (No Observed Adverse Effect Level) by daily oral administration for dogs and rats was 5 mg/kg and 60 mg/kg, respectively, and the minimum toxic dose was 20 and 120 mg/kg, respectively. All the side effects indicated that the digestive tract, the male reproductive tract, the respiratory tract and the hematological systems might be HZ1006 toxic targets in humans. HZ1006 could be a good candidate or a safe succedaneum to other existing HDACIs for the treatment of some solid tumor and hematologic malignancies.
Comparison of mRNA features affecting translation initiation and reinitiation

Regulation of gene expression at the level of translation accounts for up to three orders of magnitude in its efficiency. We systematically compared the impact of several mRNA features on translation initiation at the first gene in an operon with those for the second gene. Experiments were done in a system with internal control based on dual cerulean and red (CER/RFP) fluorescent proteins. We demonstrated significant differences in the efficiency of Shine Dalgarno sequences acting at the leading gene and at the following genes in an operon. The majority of frequent intercistronic arrangements possess medium SD dependence, medium dependence on the preceding cistron translation and efficient stimulation by A/U-rich sequences. The second cistron starting immediately after preceding cistron stop codon displays unusually high dependence on the SD sequence.
The influence of menopause on the development of hepatic fibrosis in nonobese women with nonalcoholic fatty liver disease

We read the article by Yang et al. with great interest concerning the effect of postmenopausal status on the development of hepatic fibrosis. There is mounting evidence that menopause accelerates the progression and severity of nonalcoholic steatohepatitis. In their article, Yang et al. concluded that postmenopausal women are at higher risk of severe fibrosis, when compared to premenopausal women, and they concluded that this additional risk was attributable to the decrease in estrogen levels. In this study, the mean body mass index (BMI) was 44.6 and 39.2 for preand postmenopausal woman, respectively. These BMIs are also categorized as class III and II obesity, respectively, according to the World Health Organization. It is well known that estrogen is produced from fat cells in addition to the ovaries, which are the primary source of this hormone. This secondary source of estrogen is especially important in postmenopausal women. Indeed, postmenopausal obese women have higher estrogen levels than their nonobese postmenopausal counterparts. Because of these facts, reconfirmation of the results reported by Yang et al. in nonobese postmenopausal women may be needed. Therefore, we limited our target population to women with nonalcoholic fatty liver disease (NAFLD) whose BMI was less than 30 and compared the severity of hepatic fibrosis after menopause within this cohort. Utilizing the Japan Study Group of NAFLD (JSG-NAFLD) database, 419 women with biopsy-proven NAFLD were included and comprised 90 premenopausal and 329 postmenopausal patients. As expected, even in nonobese NAFLD patients, postmenopausal women still had more severe fibrosis, when compared to the premenopausal subjects (P 5 0.0266; odds ratio [OR]: 2.173), after adjusting for hepatic inflammation, ballooning hepatocytes, BMI, impaired glucose tolerance/diabetes, and hypertension. Furthermore, this OR may be higher than that found in Yang et al.’s study. Our results reconfirm that postmenopausal women are more susceptible to development of hepatic fibrosis, and this may be caused by decreased levels of estrogen. With the increased incidence of obesity and diabetes globally, Yang et al.’s findings will become of increasing importance. However, the effects of estrogen on hepatic fibrosis may also need to be put in the context of the increasing age of the subjects, because this is a known factor in the development of liver disease. In conclusion, we hope the contents of this letter are useful for validation of the influence of menopause on the development of hepatic fibrosis. MASATO YONEDA, M.D., PH.D. EMMANUEL THOMAS, M.D., PH.D. YOSHIO SUMIDA, M.D., PH.D. YUICHIRO EGUCHI, M.D., PH.D. EUGENE R. SCHIFF, M.D. Schiff Center for Liver Diseases University of Miami Miller School of Medicine Miami, FL Department of Gastroenterology and Hepatology Kyoto Prefectural University of Medicine Kyoto, Japan Liver Center Saga Medical School Saga, Japan
High mass of the type IIP supernova 2004et inferred from hydrodynamic modeling

Context. Previous studies of type IIP supernovae have inferred that progenitor masses recovered from hydrodynamic models are higher than 15 M� . Aims. To verify the progenitor mass of this supernova category, we attempt a parameter determination of the well-observed luminous type IIP supernova 2004et. Methods. We model the bolometric light curve and the photospheric velocities of SN 2004et by means of hydrodynamic simulations in an extended parameter space. Results. From hydrodynamic simulations and observational data, we infer a presupernova radius of 1500 ± 140 R� , an ejecta mass of 24.5 ± 1 M� , an explosion energy of (2.3 ± 0.3) × 10 51 erg, and a radioactive 56 Ni mass of 0.068 ± 0.009 M� . The estimated progenitor mass on the main sequence is in the range of 25−29 M� . In addition, we find clear signatures of the explosion asymmetry in the nebular spectra of SN 2004et. Conclusions. The measured progenitor mass of SN 2004et is significantly higher than the progenitor mass suggested by the preexplosion images. We speculate that the mass inferred from hydrodynamic modeling is overestimated and crucial missing factors are multi-dimensional effects.
Multidetector CT scan for acute pulmonary embolism: embolic burden and clinical outcome.

BACKGROUND In patients with acute pulmonary embolism (PE), the correlation between the embolic burden assessed by multidetector CT (MDCT) scan and clinical outcomes remains unclear. Patients with symptomatic acute PE diagnosed based on MDCT angiography were included in a multicenter study aimed at assessing the prognostic role of the embolic burden evaluated with MDCT scan. METHODS Embolic burden was assessed as (1) localization of the emboli as central (saddle or at least one main pulmonary artery), lobar, or distal (segmental or subsegmental arteries) and (2) the obstruction index by the scoring system of Qanadli. The primary outcome was 30-day all-cause death or clinical deterioration. Predictors of all-cause death or clinical deterioration were identified by Cox regression statistics. RESULTS Overall, 579 patients were included in the study; 60 (10.4%) died or had clinical deterioration at 30 days. Central localization of emboli was not associated with all-cause death or clinical deterioration (hazard ratio [HR], 2.42; 95% CI, 0.77-7.59; P 5 .13). However, in 516 hemodynamically stable patients, central localization of emboli (HR, 8.3; 95% CI, 1.0-67; P 5 .047) was an independent predictor of all-cause death or clinical deterioration, whereas distal emboli were inversely associated with these outcome events (HR, 0.12; 95% CI, 0.015-0.97; P 5 .047). No correlation was found between obstruction index (evaluated in 448 patients) and all-cause death or clinical deterioration in the overall study population and in the hemodynamically stable patients. CONCLUSIONS In hemodynamically stable patients with acute PE, central emboli are associated with an increased risk for all-cause death or clinical deterioration. This risk is low in patients with segmental or subsegmental PE.
Branched-Chain Amino Acid Supplementation in Combination with Voluntary Running Improves Body Composition in Female C57BL/6 Mice

ABSTRACT Exercise is an inexpensive intervention that may be used to reduce obesity and its consequences. In addition, many individuals who regularly exercise utilize dietary supplements to enhance their exercise routine and to accelerate fat loss or increase lean mass. Branched-chain amino acids (BCAAs) are a popular supplement and have been shown to produce a number of beneficial effects in rodent models and humans. Therefore, we hypothesized that BCAA supplementation would protect against high fat diet (HFD)-induced glucose intolerance and obesity in mice with and without access to exercise. We subjected 80 female C57BL/6 mice to a paradigm of HFD feeding, exercise in the form of voluntary wheel running, and BCAA supplementation in the drinking water for 16 weeks (n = 10 per group). Body weight was monitored weekly, while food and water consumption were recorded twice weekly. During the 5th, 10th, and 15th weeks of treatment, glucose tolerance and body composition were analyzed. Exercise significantly improved glucose tolerance in both control-fed and HFD-fed mice. BCAA supplementation, however, did not significantly alter glucose tolerance in any treatment group. While BCAA supplements did not improve lean to fat mass ratio in sedentary mice, it significantly augmented the effects of exercise on this parameter.
Improved approximation algorithms for network design problems

1 Introduction We consider a class of network design problems in which one needs to find a minimum-cost network satisfying cer-tam connectivity requirements. For example, in the snr-vivable network design problem, the requirements specify that there should be at least r(v, UJ) edge-disjoint paths between each pair of vertices v and w. We present an approximation algorithm with a performance guarantee of 2TH(fmax) = 2(1 + $ + g +. . + &) where fmax is the maximum requirement. This improves upon the best previously known performance guarantee of 2fmax. We also show that our analysis is tight, up to a constant factor. In addition , we present approximation algorithms for two natural variations of the problem involving capacities. Our algorithms are based on a primal-dual approximation method for approximating a class of integer linear programs. Network design problems have a wide range of practical applications, ranging from telecommunications to transportation problems [lo]. In this paper, we will investigate approximation algorithms for several basic network design problems. In a network design problem, the input consists of an undirected graph G = (V, E), where each edge e E E has a nonneg-ative cost c(e), and we wish to select a minimum-cost subgraph that satisfies certain specified connec-tivity requirements. A general way to specify these constraints is to require, for each S c V, that the subgraph must contain at least f(S) edges in the cut 6(S) = {(v, w) E E : v E S, w $! S}, where we assume that there is a polynomial-time subroutine to compute f. Young Investigator Grant CC%8858097 with matching funds from AT&T, DEC, and 3M, and a grant from Powell Foundation. There has been a great deal of recent attention on the design and analysis of approximation algorithms for network design problems. There are two primary variants of these problems: one in which a solution may include multiple copies of each edge, and one in which this is forbidden. We first focus on the latter case. Extending work of Klein & Ravi [9] for proper function with range {0,2}, Williamson, Goemans, Mihail, & Vazirani [14] gave a polynomial-time 2fmax-approximation algorithm when the function f is proper, where fmax = maxscv f(S) and a p-approximation algorithm is an algorithm that always delivers a solution of cost at most p times the optimum. We shall defer the definition of proper functions , but we note …
Evolutionary neural network prediction for software reliability modeling

Software Reliability is a key concern of many users and developers of softwares. Demand for high software reliability requires robust modeling techniques for software quality prediction. This paper presents a new approach to software reliability assessment by using neural network. The neural network model has been applied to three different applications and normalized root mean of the square of error as an evaluation criterion. Results show that the neural network model adopted has good predictive capability.
Influence of Microstructural Features on the Plastic Deformation Behavior of Metallic Nanoglasses

Abstract We investigate the influence of microstructural properties on the plastic deformation behavior of Cu64 Zr36 nanoglasses by means of molecular dynamics simulations. Two different setups are used to prepare nanoglasses. One sample type is a nanoglass obtained by cold-compaction of chemically homogenous and inhomogenous nanoparticles. The second type is generated by assembling pre-shaped polyhedral cuts from the bulk phase. A detailed analysis of both types of microstructures shows that the volume fraction of interfaces in the particle-derived nanoglasses is significantly higher than in the bulk-derived nanoglasses with the same average grain size. The simulations also reveal a clearly distinct plastic response on uniaxial loading: The particle derived samples do not show a stress drop upon yielding, very little strain localization and no strain softening, whereas the bulk-derived samples exhibit a stress drop, strain softening and large strain localization upon loading. These findings are explained in terms of the different glass-glass interfaces present in both structure types. Our results therefore show that the macroscopic deformation behavior of metallic nanoglasses is intimately linked to the structure and topology of the glass-glass interfaces which in turn depend on the processing route.
Flow cytometric analysis of reticulocyte maturation after erythropoietin administration in rats

We have proposed a technique for transforming reticulocyte (RET) flow cytometry count into the age distribution allowing for a quantitative characterization of RETs dynamics. This technique was evaluated in homeostatic and erythropoietically stimulated rats. We administered a single intravenous dose (4,050 IU/kg) of recombinant human erythropoietin to Wistar rats, then stained their RETs with thiazole orange, and measured the distribution of the fluorescent signal using flow cytometry. The RET age distribution was determined assuming an exponential decline of RET RNA. The RET distribution over time was characterized by median age, production rate of mature red blood cell in the blood, bone marrow and blood maturation times, and RET loss from the blood. Erythropoietin was found to cause complex changes not only in RET count but also in age distribution. Generally, an increase in RET count was accompanied by the presence of young RETs and a decrease with the presence of old RETs. The rate at which RETs were removed from the blood was affected considerably by erythropoietin administration, and their death was attributed to it. Flow cytometric analysis of RET age distribution expands our understanding of erythropoiesis and augments the information we can obtain from RET measurements. © 2009 International Society for Advancement of Cytometry
Design and Practical Implementation of External Consensus Protocol for Networked Multiagent Systems With Communication Delays

This paper discusses the design and practical implementation of solving an external consensus problem for inhomogeneous networked multiagent systems with constant network delay in the output feedback. Based on the recursive equation, a novel prediction strategy is proposed using the transfer function form to overcome the effects of the network delay. By considering a single-input single-output linear system for each agent, the proposed strategy is simulated, demonstrated, and validated through a test-rig application. Concurrently, the stability of the control scheme and the criterion to determine the appropriate coupling gains value for the proposed consensus protocol are also studied.
Link prediction approach to collaborative filtering

Recommender systems can provide valuable services in a digital library environment, as demonstrated by its commercial success in book, movie, and music industries. One of the most commonly-used and successful recommendation algorithms is collaborative filtering, which explores the correlations within user-item interactions to infer user interests and preferences. However, the recommendation quality of collaborative filtering approaches is greatly limited by the data sparsity problem. To alleviate this problem we have previously proposed graph-based algorithms to explore transitive user-item associations. In this paper, we extend the idea of analyzing user-item interactions as graphs and employ link prediction approaches proposed in the recent network modeling literature for making collaborative filtering recommendations. We have adapted a wide range of linkage measures for making recommendations. Our preliminary experimental results based on a book recommendation dataset show that some of these measures achieved significantly better performance than standard collaborative filtering algorithms
Different Scales of Spatial Segregation of Two Species of Feather Mites on the Wings of a Passerine Bird

Abstract The “condition-specific competition hypothesis” proposes that coexistence of 2 species is possible when spatial or temporal variations in environmental conditions exist and each species responds differently to those conditions. The distribution of different species of feather mites on their hosts is known to be affected by intrinsic host factors such as structure of feathers and friction among feathers during flight, but there is also evidence that external factors such as humidity and temperature can affect mite distribution. Some feather mites have the capacity to move through the plumage rather rapidly, and within-host variation in intensity of sunlight could be one of the cues involved in these active displacements. We analyzed both the within- and between-feather spatial distribution of 2 mite species, Trouessartia bifurcata and Dolichodectes edwardsi, that coexist in flight feathers of the moustached warbler Acrocephalus melanopogon. A complex spatial segregation between the 2 species was observed at 3 spatial levels, i.e., “feather surfaces,” “between feathers,” and “within feathers. ” Despite certain overlapping distribution among feathers, T. bifurcata dominated proximal and medial regions on dorsal faces, while D. edwardsi preferred disto-ventral feather areas. An experiment to check the behavioral response of T. bifurcata to sunlight showed that mites responded to light exposure by approaching the feather bases and even leaving its dorsal face. Spatial heterogeneity across the 3 analyzed levels, together with response to light and other particular species adaptations, may have played a role in the coexistence and segregation of feather mites competing for space and food in passerine birds.
Modeling Human Reading with Neural Attention

When humans read text, they fixate some words and skip others. However, there have been few attempts to explain skipping behavior with computational models, as most existing work has focused on predicting reading times (e.g.,~using surprisal). In this paper, we propose a novel approach that models both skipping and reading, using an unsupervised architecture that combines a neural attention with autoencoding, trained on raw text using reinforcement learning. Our model explains human reading behavior as a tradeoff between precision of language understanding (encoding the input accurately) and economy of attention (fixating as few words as possible). We evaluate the model on the Dundee eye-tracking corpus, showing that it accurately predicts skipping behavior and reading times, is competitive with surprisal, and captures known qualitative features of human reading.
Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding

Vertex clustering in a stochastic blockmodel graph has wide applicability and has been the subject of extensive research. In thispaper, we provide a short proof that the adjacency spectral embedding can be used to obtain perfect clustering for the stochastic blockmodel and the degree-corrected stochastic blockmodel. We also show an analogous result for the more general random dot product graph model.
Resistance to single‐agent chemotherapy and its risk factors in low‐risk gestational trophoblastic neoplasms

Gestational trophoblastic neoplasm (GTN) is a rare disease which is classified into high‐ and low‐risk groups. While the high‐risk patients require combination therapy, the low‐risk groups respond to single‐agent chemotherapy. We studied resistance to single‐agent chemotherapy and its risk factors among the low‐risk GTN patients in Iran.