Miracle-dz/UniFAR-FTUs huggingface dataset:
The one-way unlocalizable quantum discord

We present the in-plane optical reflectance measurement on single crystals of URu2Si2. The study revealed a strong temperature-dependent spectral evolution. Above 50 K, the low frequency optical conductivity is rather flat without a clear Drude-like response, indicating a very short transport lifetime of the free carriers. Well below thecoherence temperature, there appears an abrupt spectral weight suppression below 400 cm(-1), yielding evidence for the formation of a hybridization energy gap arising from the mixing of the conduction electron and narrow f-electron bands. A small part of the suppressed spectral weight was transferred to the low frequency side, leading to a narrow Drude component, while the majority of the suppressed spectral weight was transferred to the high frequency side centered near 3500 cm(-1). Below the hidden order temperature, another very prominent energy gap structure was observed, which leads to the removal of a large part of the Drude component and a sharp reduction of the carrier scattering rate. The study revealed that the hybridization gap and the hidden order gap are distinctly different: they occur at different energy scales and exhibit completely different spectral characteristics.
A comparison of BWT approaches to string pattern matching

Recently a number of algorithms have been developed to search files compressed with the Burrows‐Wheeler Transform (BWT) without the need for full decompression first. This allows the storage requirement of data to be reduced through the exceptionally good compression offered by BWT, while allowing fast access to the information for searching by taking advantage of the sorted nature of BWT files. We provide a detailed description of five of these algorithms: BWT‐based Boyer‐Moore, Binary Search, Suffix Arrays, q‐grams and the FM‐index, and also present results from a set of extensive experiments that were performed to evaluate and compare the algorithms. Furthermore, we introduce a technique to improve the search times of Binary Search, Suffix Arrays and q‐grams by 22% on average, as well as reduce the memory requirement of the latter two by 40% and 31%, respectively. Our results indicate that, while the compressed files of the FM‐index are larger than those of the other approaches, it is able to perform searches with considerably less memory. Additionally, when only counting the occurrences of a pattern, or when locating the positions of a small number of matches, it is the fastest algorithm. For larger searches, Binary Search provides the fastest results. Comparative results with non‐BWT based search methods are also included. Copyright © 2005 John Wiley & Sons, Ltd.
THE EFFECT OF VARIABLE FREQUENCY OF SEXUAL REPRODUCTION ON THE GENETIC STRUCTURE OF NATURAL POPULATIONS OF A CYCLICAL PARTHENOGEN

Cyclical parthenogens are a valuable system in which to empirically test theoretical predictions as to the genetic consequences of sexual reproduction in natural populations, particularly if the frequency of sexual relative to asexual reproduction can be quantified. In this study, we used a series of lake populations of the cyclical parthenogen, Daphnia pulicaria, that vary consistently in their investment in sexual reproduction, to address the questions of whether the ecological variation in investment in sex is detectable at the genetic level, and if so, whether the genetic patterns seen are consistent with theoretical predictions. We show that there is variation in the genetic structure of these populations in a manner consistent with their investment in sexual reproduction. Populations engaging in a high frequency of sex were in Hardy–Weinberg and gametic phase equilibrium, and showed little genotypic differentiation across sampled years. In contrast, populations with a lower frequency of sex deviated widely from equilibrium, had reduced multilocus clonal diversity, and showed significant temporal genotypic deviation.
In vitro optimization of 2′-OMe-4′-thioribonucleoside–modified anti-microRNA oligonucleotides and its targeting delivery to mouse liver using a liposomal nanoparticle

MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression post-transcriptionally. Previous studies, which characterized miRNA function, revealed their involvement in fundamental biological processes. Importantly, miRNA expression is deregulated in many human diseases. Specific inhibition of miRNAs using chemically modified anti-miRNA oligonucleotides (AMOs) can be a potential therapeutic strategy for diseases in which a specific miRNA is overexpressed. 2′-O-Methyl (2′-OMe)-4′-thioRNA is a hybrid type of chemically modified oligonucleotide, exhibiting high binding affinity to complementary RNAs and high resistance to nuclease degradation. Here, we evaluate 2′-OMe-4′-thioribonucleosides for chemical modification on AMOs. Optimization of the modification pattern using a variety of chemically modified AMOs that are perfectly complementary to mature miR-21 revealed that the uniformly 2′-OMe-4′-thioribonucleoside–modified AMO was most potent. Further investigation showed that phosphorothioate modification contributed to long-term miR-122 inhibition by the 2′-OMe-4′-thioribonucleoside–modified AMO. Moreover, systemically administrated AMOs to mouse using a liposomal delivery system, YSK05-MEND, showed delivery to the liver and efficient inhibition of miR-122 activity at a low dose in vivo.
A distinct tethering step is vital for vacuole membrane fusion

Past experiments with reconstituted proteoliposomes, employing assays that infer membrane fusion from fluorescent lipid dequenching, have suggested that vacuolar SNAREs alone suffice to catalyze membrane fusion in vitro. While we could replicate these results, we detected very little fusion with the more rigorous assay of lumenal compartment mixing. Exploring the discrepancies between lipid-dequenching and content-mixing assays, we surprisingly found that the disposition of the fluorescent lipids with respect to SNAREs had a striking effect. Without other proteins, the association of SNAREs in trans causes lipid dequenching that cannot be ascribed to fusion or hemifusion. Tethering of the SNARE-bearing proteoliposomes was required for efficient lumenal compartment mixing. While the physiological HOPS tethering complex caused a few-fold increase of trans-SNARE association, the rate of content mixing increased more than 100-fold. Thus tethering has a role in promoting membrane fusion that extends beyond simply increasing the amount of total trans-SNARE complex. DOI: http://dx.doi. org/10.7554/eLife.03251. 001
An Analysis Architecture for Communications in Multi-agent Systems

Evaluation tools are significant from the Agent Oriented Software Engineering (AOSE) point of view. Defective designs of communications in Multi-agent Systems (MAS) may overload one or several agents, causing a bullying effect on them. Bullying communications have avoidable consequences, as high response times and low quality of service (QoS). Architectures that perform evaluation functionality must include features to measure the bullying activity and QoS, but it is also recommendable that they have reusability and scalability features. Evaluation tools with these features can be applied to a wide range of MAS, while minimizing designer�s effort. This work describes the design of an architecture for communication analysis, and its evolution to a modular version, that can be applied to different types of MAS. Experimentation of both versions shows differences between its executions.
Design and development of a hand rehabilitation robot for patient-cooperative therapy following stroke

Stroke is very common and always leads to severe hand impairment. Traditional robotic systems have been introduced to assist therapy for a long time and already achieved certain effect. However, with further development of therapy strategies in the last few years, higher request to the rehabilitation robot has been put forward. Thus, we are developing a novel hand rehabilitation robot named HIT-glove to provide patient-cooperative therapy for hand-impaired post-stroke patients. In this paper, the mechanical design of the actuated hand exoskeleton is detailed and the control strategy for patient-cooperative therapy is introduced. The actuated hand exoskeleton, which can be applied to hands in different sizes and shapes, is able to bilaterally actuate every joint of the fingers. The patient-cooperative control strategy, based on the sensing system and an interactive interface, is well designed to let the patient actively participate into the therapy. Besides, to get a better effect of functional rehabilitation of the hand, our robot is expected to provide the following two categories of therapy: motor function exercise for joints and movement coordination training for fingers.
Inactivation of Uropathogenic Escherichia coli in Ground Chicken Meat Using High Pressure Processing and Gamma Radiation, and in Purge and Chicken Meat Surfaces by Ultraviolet Light

Extraintestinal pathogenic Escherichia coli, including uropathogenic E. coli (UPEC), are common contaminants in poultry meat and may cause urinary tract infections after colonization of the gastrointestinal tract and transfer of contaminated feces to the urethra. Three non-thermal processing technologies used to improve the safety and shelf-life of both human and pet foods include high pressure processing (HPP), ionizing (gamma) radiation (GR), and ultraviolet light (UV-C). Multi-isolate cocktails of UPEC were inoculated into ground chicken which was then treated with HPP (4°C, 0–25 min) at 300, 400, or 500 MPa. HPP D10, the processing conditions needed to inactivate 1 log of UPEC, was 30.6, 8.37, and 4.43 min at 300, 400, and 500 MPa, respectively. When the UPEC was inoculated into ground chicken and gamma irradiated (4 and -20°C) the GR D10 were 0.28 and 0.36 kGy, respectively. The UV-C D10 of UPEC in chicken suspended in exudate and placed on stainless steel and plastic food contact surfaces ranged from 11.4 to 12.9 mJ/cm2. UV-C inactivated ca. 0.6 log of UPEC on chicken breast meat. These results indicate that existing non-thermal processing technologies such as HPP, GR, and UV-C can significantly reduce UPEC levels in poultry meat or exudate and provide safer poultry products for at-risk consumers.
Progressive damage of randomly oriented short fiber reinforced composites

Recently, short fiber reinforced composites are widely utilized in many structural parts in automobile, infrastructure and electric equipment applications due to their high specific strength, high specific stiffness, long fatigue life and high impact resistance as well as cost effective capability of production. If these parts are exposed to low-velocity impact, significant damages may develop inside the composite parts. These damages may cause reduction of mechanical performances of composite parts. Therefore, predictive analytical or numerical tools are required to evaluate and analyze the integrity of composite parts with impact damages. In this study, a user-defined material subroutine incorporating damage mechanisms of short fiber reinforced composites was developed adopting and modifying various damage models. Then, the subroutine is implemented into ABAQUS to conduct analysis of short fiber reinforced composites parts. The results were compared with those without considering damage mechanism.
Multidimensional Simulations of the Accretion-induced Collapse of White Dwarfs to Neutron Stars

We present 2.5-dimensional radiation-hydrodynamics simulations of the accretion-induced collapse (AIC) of white dwarfs, starting from two-dimensional rotational equilibrium configurations, thereby accounting consistently for the effects of rotation prior to and after core collapse. We focus our study on a 1.46 and a 1.92 M☉ a model. Electron capture leads to the collapse to nuclear densities of these cores a few tens of milliseconds after the start of the simulations. The shock generated at bounce moves slowly, but steadily, outward. Within 50-100 ms, the stalled shock breaks out of the white dwarf along the poles. The blast is followed by a neutrino-driven wind that develops within the white dwarf, in a cone of ~40° opening angle about the poles, with a mass loss rate of (5-8) × 10-3 M☉ s-1. The ejecta have an entropy on the order of (20-50)kB baryon-1 and an electron fraction that is bimodal. By the end of the simulations, at ≳600 ms after bounce, the explosion energy has reached (3-4) × 1049 ergs and the mass has reached a few times 10-3 M☉. We estimate the asymptotic explosion energies to be lower than 1050 ergs, significantly lower than those inferred for standard core collapse. The AIC of white dwarfs thus represents one instance where a neutrino mechanism leads undoubtedly to a successful, albeit weak, explosion. We document in detail the numerous effects of the fast rotation of the progenitors: the neutron stars are aspherical; the ``νμ'' and e neutrino luminosities are reduced compared to the νe neutrino luminosity; the deleptonized region has a butterfly shape; the neutrino flux and electron fraction depends strongly upon latitude (a la von Zeipel); and a quasi-Keplerian 0.1-0.5 M☉ accretion disk is formed.
Finite size scaling investigations in the quantum φ 4-model with long-range interaction

In this paper, we study in details the critical behavior of the O(n) quantum ϕ 4 model with long-range interaction decaying with the distances r by a power law as r −d−σ in the large n-limit. The zero-temperature critical behavior is discussed. Its alteration by the finite temperature and/or finite sizes in the space is studied. The scaling behaviours are studied in different regimes depending upon whether the finite temperature or the finite sizes of the system is leading. A number of results for the correlation length, critical amplitudes and the finite size shift, for different dimensionalities between the lower d < = σ/2 and the upper d > = 3σ/2 critical dimensions, are calculated.
Potential Search: A Bounded-Cost Search Algorithm

In this paper we address the following search task: find a goal with cost smaller than or equal to a given fixed constant. This task is relevant in scenarios where a fixed budget is available to execute a plan and we would like to find such a plan with minimum search effort. We introduce an algorithm called Potential search (PTS) which is specifically designed to solve this problem. PTS is a best-first search that expands nodes according to the probability that they will be part of a plan whose cost is less than or equal to the given budget. We show that it is possible to implement PTS even without explicitly calculating these probabilities, when a heuristic function and knowledge about the error of this heuristic function are given. In addition, we also show that PTS can be modified to an anytime search algorithm. Experimental results show that PTS outperforms other relevant algorithms in most cases, and is more robust.
′ / ε at O ( p 4 ) in the Chiral Expansion

After updating the determination of the combination of Kobayashi-Maskawa elements Im V ∗ tsVtd according to a new estimate of the parameter B̂K , we study the CP -violating ratio ε/ε by means of hadronic matrix elements computed to O(p4) in the chiral expansion and NLO Wilson coefficients. It is the first time that this order in chiral perturbation theory is included in the analysis. The most important effect of this improved study is the substantial reduction of the contribution of the electroweak penguin operator 〈Q8〉2 and accordingly a reduced cancellation between the latter and the gluonic penguin operator 〈Q6〉0. The ratio ε/ε is thus larger than previously estimated and its predicted value enjoys a smaller uncertainty. Values positive and of the order of 1× 10 are preferred even though a vanishingly small value cannot be excluded: we find ε/ε = 1.5 +1.9 −1.0 × 10 and ε/ε = 1.2 +1.8 −0.8 × 10 for the CP violating phase in the first and second quadrants respectively. They give the averaged value 1.3 +1.9 −1.0 × 10.
Enhancement of HIF 1 mediated Tumor Radiosensitization via Vascular Normalization

In this proposal, the combination of vascular normalization with HIF­1 blockade is sug­ gested as a possible means to radiosensitizing tumors. Research has shown that, after ad­ ministering antiangiogenic agents, there is window of vascular normalization in which tumor hypoxia is alleviated, and tumor radiosensitivity is increased. Recent research also shows that HIF­1 blockade after fractionated radiotherapy causes significant tumor vascular radiosen­ sitization. The careful combination of vascular normalization with post­irradiative HIF­1 blockade has the potential to further increase tumor radiosensitivity through the interplay of the effects of both therapies. It is hypothesized that the partial tumor reoxygenation, due to vascular normalization, will restrict the radioprotective effects that HIF­1 inhibition has on distal tumor cells. It is also hypothesized that partial tumor reoxygenation might allow a greater magnitude of HIF­1 activation upon irradiation. This would make the administration of HIF­1 inhibition following the irradiation of a vasculature­normalized tumor a promising method of further radiosensitizing tumors.
EEG dynamic source localization using constrained particle filtering

We consider the dynamic EEG source localization problem with additional constraints on the expected value of the state. In dynamic EEG source localization, the brain sources, also called dipoles, are not stationary but vary over time. Moreover, given our specific EEG experiment, we expect the dipoles to be located within a certain area of the brain (here, the visual cortex). We formulate this constrained dynamic source localization problem as a constrained non-linear state-estimation problem. Particle filters (PFs) are nowadays the state-of-the-art in optimal non-linear and non-Gaussian state estimation. However, PFs cannot handle additional constraints on the state that cannot be incorporated within the system model. In this case, the additional constraint is on the mean of the state, which means that realizations of the state, also called particles within the PF framework, may or may not satisfy the constraint. However, the state must satisfy the constraint on average. This is indeed the case when tracking brain dipoles from EEG experiments that try to target a specific cortex of the brain. Such constraints on the mean of the state are hard to deal with because they reflect global constraints on the posterior density of the state. The popular solution of constraining every particle in the PF may lead either to a stronger condition or to a different (unrelated) condition; both of which result in incorrect estimation of the state. We propose the Iterative Mean Density Truncation (IMeDeT) algorithm, which inductively samples particles that are guaranteed to satisfy the constraint on the mean. Application of IMeDeT on synthetic and real EEG data shows that incorporating a priori constraints on the state improves the tracking accuracy as well as the convergence rate of the tracker.
Racial Differences in the Use of Adjuvant Chemotherapy for Breast Cancer in a Large Urban Integrated Health System

Background. Racial differences in breast cancer survival may be in part due to variation in patterns of care. To better understand factors influencing survival disparities, we evaluated patterns of receipt of adjuvant chemotherapy among 2,234 women with invasive, nonmetastatic breast cancer treated at the Henry Ford Health System (HFHS) from 1996 through 2005. Methods. Sociodemographic and clinical information were obtained from linked datasets from the HFHS, Metropolitan Detroit Cancer Surveillance Systems, and U.S. Census. Comorbidity was measured using the Charlson comorbidity index (CCI), and economic deprivation was categorized using a neighborhood deprivation index. Results. African American (AA) women were more likely than whites to have advanced tumors with more aggressive clinical features, to have more comorbidity and to be socioeconomically deprived. While in the unadjusted model, AAs were more likely to receive chemotherapy (odds ratio (OR) 1.22, 95% confidence interval (CI) 1.02–1.46) and to have a delay in receipt of chemotherapy beyond 60 days (OR 1.68, 95% CI, 1.26–1.48), after multivariable adjustment there were no racial differences in receipt (odds ratio (OR) 1.02, 95% confidence interval (CI) 0.73–1.43), or timing of chemotherapy (OR 1.18, 95 CI, 0.8–1.74). Conclusions. Societal factors and not race appear to have an impact on treatment delay among African American women with early breast cancer.
Trichostatin A-Mediated Epigenetic Transformation of Adult Bone Marrow-Derived Mesenchymal Stem Cells Biases the In Vitro Developmental Capability, Quality, and Pluripotency Extent of Porcine Cloned Embryos

The current research was conducted to explore the in vitro developmental outcome and cytological/molecular quality of porcine nuclear-transferred (NT) embryos reconstituted with adult bone marrow-derived mesenchymal stem cells (ABM-MSCs) that were epigenetically transformed by treatment with nonspecific inhibitor of histone deacetylases, known as trichostatin A (TSA). The cytological quality of cloned blastocysts was assessed by estimation of the total cells number (TCN) and apoptotic index. Their molecular quality was evaluated by real-time PCR-mediated quantification of gene transcripts for pluripotency- and multipotent stemness-related markers (Oct4, Nanog, and Nestin). The morula and blastocyst formation rates of NT embryos derived from ABM-MSCs undergoing TSA treatment were significantly higher than in the TSA-unexposed group. Moreover, the NT blastocysts generated using TSA-treated ABM-MSCs exhibited significantly higher TCN and increased pluripotency extent measured with relative abundance of Oct4 and Nanog mRNAs as compared to the TSA-untreated group. Altogether, the improvements in morula/blastocyst yields and quality of cloned pig embryos seem to arise from enhanced abilities for promotion of correct epigenetic reprogramming of TSA-exposed ABM-MSC nuclei in a cytoplasm of reconstructed oocytes. To our knowledge, we are the first to report the successful production of mammalian high-quality NT blastocysts using TSA-dependent epigenomic modulation of ABM-MSCs.
β-Amyloid Regulation of Presynaptic Nicotinic Receptors in Rat Hippocampus and Neocortex

Alteration by β-amyloid (Aβ) of signaling via nicotinic acetylcholine receptors (nAChRs) has been implicated in the early stages of Alzheimer's disease. nAChRs function both post- and presynaptically in the nervous system; however, little is known about the functional consequence of the interaction of Aβ with these receptors, particularly those on presynaptic nerve terminals. In view of the strong correlation between loss of synaptic terminals and dementia, together with the reduction in nAChRs in Alzheimer's disease, the possibility exists that presynaptic nAChRs may be targets for Aβ. To explore this possibility, we assessed the effect of Aβ peptides on nicotine-evoked changes in presynaptic Ca2+ level via confocal imaging of isolated presynaptic nerve endings from rat hippocampus and neocortex. Aβ1-42 appeared to inhibit presynaptic nAChR activation by nicotine. Surprisingly, picomolar Aβ1-42 was found to directly evoke sustained increases in presynaptic Ca2+ via nAChRs, revealing that the apparent inhibitory action of Aβ1-42 was the result of an occlusion of nicotine to further stimulate the receptors. The direct effect of Aβ was found to be sensitive to α-bungarotoxin, mecamylamine, and dihydro-β-erythroidine, indicating involvement of α7-containing nAChRs and non-α7-containing nAChRs. Prior depolarization strongly attenuated subsequent Aβ-evoked responses in a manner dependent on the amplitude of the initial presynaptic Ca2+ increase, suggesting that nerve activity or Ca2+ channel density may control the impact of Aβ on presynaptic nerve terminal function. Together, these results suggest that the sustained increases in presynaptic Ca2+ evoked by Aβ may underlie disruptions in neuronal signaling via nAChRs in the early stages of Alzheimer's disease.