Miracle-dz/UniFAR-FTUs huggingface dataset:
A New Matrix-Free Algorithm for the Large-Scale Trust-Region Subproblem

We present a new method for the large-scale trust-region subproblem. The method is matrix-free in the sense that only matrix-vector products are required. We recast the trust-region subproblem as a parameterized eigenvalue problem and compute an optimal value for the parameter. We then find the solution of the trust-region subproblem from the eigenvectors associated with two of the smallest eigenvalues of the parameterized eigenvalue problem corresponding to the optimal parameter. The new algorithm uses a different interpolating scheme than existing methods and introduces a unified iteration that naturally includes the so-called hard case. We show that the new iteration is well defined and convergent at a superlinear rate. We present computational results to illustrate convergence properties and robustness of the method.
Damage Detection in Composite Cylindrical Multilayered Shells with Delaminations

In this study, effective computational procedures are introduced and used to characterize the dynamic behavior of cylindrical panels with circular cross-section having the single delamination between laminate layers. Based on the computed results it is possible to determine the effect of delamination on the overall structural dynamic behavior. Those results are used to quantify the difference between the results of the relevant parameters in the cases of perfect and defected structures. Usually, the wave propagation can be observed with the use of piezoelectric sensors. Therefore, in the next step of our analysis we modeled delaminated structures with a finite number of PZT sensors to consider also their influence on the structural dynamic response. The numerical analysis have been conducted with the use of 3D finite elements. A lot of numerical results allow us to understand better the influence of various parameters on the form of wave propagation in cylindrical multilayered shells.
Morphogenesis of Simple and Compound Leaves: A Critical Review

The leaves of seed plants evolved from a primitive shoot system and are generated as determinate dorsiventral appendages at the flanks of radial indeterminate shoots. The remarkable variation of leaves has remained a constant source of fascination, and their developmental versatility has provided an advantageous platform to study genetic regulation of subtle, and sometimes transient, morphological changes. Here, we describe how eudicot plants recruited conserved shoot meristematic factors to regulate growth of the basic simple leaf blade and how subsets of these factors are subsequently re-employed to promote and maintain further organogenic potential. By comparing tractable genetic programs of species with different leaf types and evaluating the pros and cons of phylogenetic experimental procedures, we suggest that simple and compound leaves, and, by the same token, leaflets and serrations, are regulated by distinct ontogenetic programs. Finally, florigen, in its capacity as a general growth regulator, is presented as a new upper-tier systemic modulator in the patterning of compound leaves.
Protecting Data on Smartphones and Tablets from Memory Attacks

Smartphones and tablets are easily lost or stolen. This makes them susceptible to an inexpensive class of memory attacks, such as cold-boot attacks, using a bus monitor to observe the memory bus, and DMA attacks. This paper describes Sentry, a system that allows applications and OS components to store their code and data on the System-on-Chip (SoC) rather than in DRAM. We use ARM-specific mechanisms originally designed for embedded systems, but still present in today's mobile devices, to protect applications and OS subsystems from memory attacks.
Vascular endothelial growth factor (VEGF) serum levels are associated with survival in early stages of lung cancer patients.

AIM Evaluate the serum vascular endothelial growth factor (VEGF) levels in the prognosis of lung cancer patients. METHODS Fifty-four serum samples were analyzed for VEGF concentrations (79.3% nonsmall cell lung cancer (NSCLC) and 20.7% small cell lung cancer). RESULTS Patients with serum VEGF-A levels higher than the mean of the patients studied (434.93 pg/mL) presented a shorter median survival time than those with lower levels (p =.04), as in patients with NSCLC tumors (p =.04) and in those with stages I-II (p <.05), and high serum VEGF-A levels. CONCLUSION Elevated VEGF serum levels have a negative prognostic impact on survival in NSCLC and early stages of lung cancer patients.
Contribution of CD4+ and CD8+ T cells to graft-versus-host disease and graft-versus-leukemia reactivity after transplantation of MHC-compatible bone marrow.

A murine model of allogeneic bone marrow (BM) transplantation was used to determine the relative importance of CD4+ and CD8+ T cells in establishing donor T cell chimerism and in the development of graft-versus-host (GVH) and graft-versus-leukemia (GVL) reactivity. Mature donor T cells were essential for complete chimerism when host mice (AKR, H-2k) were conditioned with suboptimal irradiation (9 Gy = LD50). Transplantation of donor BM (B10.BR, H-2k) resulted in mixed chimerism, whereas mice given BM containing additional T cells developed into complete and stable chimeras. Depletion of T cell subsets was associated with an increase in the frequency of mixed chimerism. The incidence of lethal GVHD was dependent on the number of T cells added to the BM inoculum. Ex vivo depletion of CD4+ T cells eliminated GVH-associated mortality. Removal of CD8+ T cells had no effect on overall survival. In contrast to the GVH results, removal of either CD4+ or CD8+ T cells compromised GVL reactivity, indicating that an optimal GVL response required both CD4+ and CD8+ T cells. T cell-subset depletion did not interfere with the induction of donor-host tolerance in these chimeras and may have facilitated its development. The loss of GVH/GVL effector cells as a result of T cell depletion and the development of donor-host tolerance may act synergistically to prevent or suppress GVH and GVL reactivity.
Anomalous Decrease of Off-State Drain Leakage Current in GaN/AlGaN HEMTs With Dual Optical Excitation

We report an anomalous decrease of off-state drain leakage current (IOff-state) of GaN/AlGaN HEMTs upon dual optical excitation. The phenomenon was observed accidentally during dc characterization of devices when both fluorescent white room light and incandescent optical microscope light were turned on. A similar phenomenon was observed and verified through simultaneous optical excitation of both ultraviolet (UV ~350 nm) light and 532-nm green light. A spectrally resolved measurement revealed broad trap level centered ~2.27 eV. The decrease of IOff-state during dual excitation is owing to the optical quenching of photoconductivity in GaN buffer layer. This quenching effect is originated from enhanced light-defect interaction, where sub-band gap light reduces photoconductivity induced by above bandgap light. Observation of this phenomenon would provide us an alternative way to characterize GaN buffer layer quality for the development of GaN HEMTs.
Reviewers’ Ratings and Bibliometric Indicators: Hand in Hand When Assessing Over Research Proposals?

Background The peer review system has been traditionally challenged due to its many limitations especially for allocating funding. Bibliometric indicators may well present themselves as a complement. Objective We analyze the relationship between peers’ ratings and bibliometric indicators for Spanish researchers in the 2007 National R&D Plan for 23 research fields. Methods and Materials We analyze peers’ ratings for 2333 applications. We also gathered principal investigators’ research output and impact and studied the differences between accepted and rejected applications. We used the Web of Science database and focused on the 2002-2006 period. First, we analyzed the distribution of granted and rejected proposals considering a given set of bibliometric indicators to test if there are significant differences. Then, we applied a multiple logistic regression analysis to determine if bibliometric indicators can explain by themselves the concession of grant proposals. Results 63.4% of the applications were funded. Bibliometric indicators for accepted proposals showed a better previous performance than for those rejected; however the correlation between peer review and bibliometric indicators is very heterogeneous among most areas. The logistic regression analysis showed that the main bibliometric indicators that explain the granting of research proposals in most cases are the output (number of published articles) and the number of papers published in journals that belong to the first quartile ranking of the Journal Citations Report. Discussion Bibliometric indicators predict the concession of grant proposals at least as well as peer ratings. Social Sciences and Education are the only areas where no relation was found, although this may be due to the limitations of the Web of Science’s coverage. These findings encourage the use of bibliometric indicators as a complement to peer review in most of the analyzed areas.
Correlation of Osteopontin Protein Expression and Pathological Stage across a Wide Variety of Tumor Histologies

Purpose: Osteopontin (OPN) is an integrin-binding protein overexpressed in various experimental models of malignancy and appears to be involved in tumorigenesis and metastasis. Although various studies have assessed OPN protein levels in several tumor types, a broad survey of OPN expression in human neoplasia under the same experimental conditions has not been carried out. Experimental Design: We used immunohistochemistry to detect OPN in a selection of 350 human tumors and 113 normal tissues, from a variety of body sites, using stage-oriented human cancer tissue arrays. Tumors included malignancies from breast (26), ovary (22), endometrium (14), esophagus (10), stomach (11), pancreas (16), bile duct (1), liver (9), colon (20), kidney (53), bladder (33), prostate (28), head and neck (60), salivary glands (14), lung (17), skin (6), and brain (10). Results: High cytoplasmic OPN staining was observed in 100% of gastric carcinomas, 85% of colorectal carcinomas, 82% of transitional cell carcinomas of the renal pelvis, 81% of pancreatic carcinomas, 72% of renal cell carcinomas, 71% of lung and endometrial carcinomas, 70% of esophageal carcinomas, 58% of squamous cell carcinomas of the head and neck, and 59% of ovarian carcinomas. Although OPN expression was identified in a good number of bladder, prostate, and brain tumors, the majority of 6 skin cancers, 11 of 14 salivary gland cancers, 2 thyroid carcinomas, and 23 of 26 breast cancers revealed low OPN positivity or were negative. When considering all sites, OPN expression significantly correlated with tumor stage (Spearman’s correlation coefficient, P = 0.0002). OPN score and stage were also significantly correlated for specific cancer sites including bladder (P = 0.01), colon (P = 0.004), kidney (P = 0.0001), larynx (P = 0.035), mouth (P = 0.046), and salivary gland (P = 0.011). Conclusions: This study reports the broad distribution of OPN in human tumors from different body sites, suggesting involvement of this protein in tumor formation. The strong correlation between pathological stage and OPN across multiple tumor types suggests a role for OPN in tumor progression.
Directed differentiation of neural cells to hypothalamic dopaminergic neurons

Hypothalamic neurons play a key role in homeostasis, yet little is known about their differentiation. Here, we demonstrate that Shh and Bmp7 from the adjacent prechordal mesoderm govern hypothalamic neural fate, their sequential action controlling hypothalamic dopaminergic neuron generation in a Six3-dependent manner. Our data suggest a temporal distinction in the requirement for the two signals. Shh acts early to specify dopaminergic neurotransmitter phenotype. Subsequently, Bmp7 acts on cells that are ventralised by Shh, establishing aspects of hypothalamic regional identity in late-differentiating/postmitotic cells. The concerted actions of Shh and Bmp7 can direct mouse embryonic stem cell-derived neural progenitor cells to a hypothalamic dopaminergic fate ex vivo.
Naïve listeners' prominence and boundary perception

This paper examines how ordinary listeners, naive with respect to the phonetics and phonology of prosody, perceive the location of prosodic boundaries that demarcate speech “chunks” and prominences that serve a “highlighting” function, in spontaneous speech (Buckeye corpus). Over 70 naive listeners marked the locations of prominences and boundaries in a real-time transcription task. Fleiss’ multitranscribers’ reliability tests show that naive transcribers are consistent in their perception of prosodic boundaries and prominences. Specifically, we observe higher multi-transcriber agreement scores for boundary marking than for prominence marking. Variation between transcriptions of the same speech excerpt produced by different listeners reveals individual differences in the perception of prominences and boundaries. Variation in Fleiss’ multi-transcribers’ agreement scores for excerpts from different speakers suggests that speakers vary in how they structure an utterance prosodically and/or in how effectively they cue prosodic structure. We also find that nuclear prominences are more consistently perceived by naive listeners than prenuclear prominences. The finding that naive listeners agree well above chance on the location of prosodic events indicates that naive transcription is a valid method for prosody analysis which can augment analysis based solely on expert labeling.
Data Reprocessing and Assumption Representation in Signal Understanding Systems

A key issue in the development of next-generation intelligent systems is the ability to perceive and understand the complex environments in which they will operate. Complex environments are characterized by variable signal-to-noise ratios, unpredictable source behavior, and the simultaneous occurrence of target sources whose signal signatures can overlap, mask, or otherwise distort each other. This paper argues that traditional perceptual architectures have limited effectiveness in such environments and presents an alternative design that is a significant extension of the Integrated Processing and Understanding of Signals (IPUS) architecture. The IPUS philosophy emphasizes structured bidirectional interaction between numeric signal processing and symbolic interpretation processes. The interaction occurs as a result of search for signal processing control parameter values that produce evidence satisfying the interpretation processes'' goals. This search is constrained by formal signal processing theory and dynamically generated problem-solving assumptions. Within the overall goal of extending, generalizing, and validating the IPUS architecture, this research program will explore the utility and scalability of formally designing perceptual systems with three features to make their processing strategies more adaptive to complex environments'' demands: 1) Selective Processing Streams (the ability to selectively apply signal processing algorithms to portions of the environment''s signal data), 2) Multiple Views Synthesis (the ability to integrate results from several front-end processings each with its own processing parameter settings), and 3) Explicit Processing Assumptions (the ability to represent and revise environmental and problem-solving assumptions as first-class objects and to use such information in all system components). This paper presents the current status of the IPUS testbed, discusses issues to be addressed in extending its architecture to accommodate the new features, and describes how the new architecture should be evaluated. --Frank
Relational Reinforcement Learning via Sampling the Space of First-Order Conjunctive Features

We propose a novel method for reinforcement learning in domains that are best described using relational (“first-order”) features. Our approach is to rapidly sample a large space of such features, selecting a good subset to use as the basis for our Q-function. Our Q-function is created via a regression model that combines the collection of first-order features into a single prediction. To control the effect of the random predictions we use an ensemble approach for our predictions, generating multiple Q-function models and then combining the results of these models into a single prediction. Experiments with our technique on an interesting reinforcement learning problem, the Keep-Away subtask of RoboCup, suggest that our method can learn to effectively predict Q-values for a challenging reinforcement-learning task.
Engineering Mononucleosomes for Single-Pair FRET Experiments

In DNA nanotechnology, DNA is used as a structural material, rather than as an information carrier. The structural organization of the DNA itself determines accessibility to its underlying information content in vivo . Nucleosomes form the basic level of DNA com-paction in eukaryotic nuclei. Nucleosomes sterically hinder enzymes that must bind the nucleosomal DNA, and hence play an important role in gene regulation. In order to understand how accessibility to nucleosomal DNA is regulated, it is necessary to resolve the molecular mechanisms underlying conformational changes in the nucleosome. Exploiting bottom-up control, we designed and constructed nucleosomes with fluorescent labels at strategically cho-sen locations to study nucleosome structure and dynamics in molecular detail with single-pair Fluorescence Resonance Energy Transfer (spFRET) microscopy. Using widefield total internal reflection fluorescence (TIRF) microscopy on immobilized molecules, we observed and quantified DNA breathing dynamics on individual nucleosomes. Alternatively, fluorescence microscopy on freely diffusing molecules in a confocal detection volume allows a fast characterization of nucleosome conformational distributions.
Stretch force guides finger-like pattern of bone formation in suture

Mechanical tension is widely applied on the suture to modulate the growth of craniofacial bones. Deeply understanding the features of bone formation in expanding sutures could help us to improve the outcomes of clinical treatment and avoid some side effects. Although there are reports that have uncovered some biological characteristics, the regular pattern of sutural bone formation in response to expansion forces is still unknown. Our study was to investigate the shape, arrangement and orientation of new bone formation in expanding sutures and explore related clinical implications. The premaxillary sutures of rat, which histologically resembles the sutures of human beings, became wider progressively under stretch force. Micro-CT detected new bones at day 3. Morphologically, these bones were forming in a finger-like pattern, projecting from the maxillae into the expanded sutures. There were about 4 finger-like bones appearing on the selected micro-CT sections at day 3 and this number increased to about 18 at day 7. The average length of these projections increased from 0.14 mm at day 3 to 0.81 mm at day 7. The volume of these bony protuberances increased to the highest level of 0.12 mm3 at day 7. HE staining demonstrated that these finger-like bones had thick bases connecting with the maxillae and thin fronts stretching into the expanded suture. Nasal sections had a higher frequency of finger-like bones occuring than the oral sections at day 3 and day 5. Masson-stained sections showed stretched fibers embedding into maxillary margins. Osteocalcin-positive osteoblasts changed their shapes from cuboidal to spindle and covered the surfaces of finger-like bones continuously. Alizarin red S and calcein deposited in the inner and outer layers of finger-like bones respectively, which showed that longer and larger bones formed on the nasal side of expanded sutures compared with the oral side. Interestingly, these finger-like bones were almost paralleling with the direction of stretch force. Inclined force led to inclined finger-like bones formation and deflection of bilateral maxillae. Additionally, heavily compressive force caused fracture of finger-like bones in the sutures. These data together proposed the special finger-like pattern of bone formation in sutures guided by stretch force, providing important implications for maxillary expansion.
Correspondence between genet diversity and spatial distribution of above‐ and below‐ground populations of the ectomycorrhizal fungus Hebeloma cylindrosporum

Population studies of ectomycorrhizal fungal species have largely relied upon fruit body (the reproductive organ) sampling. Analysis of the fruit bodies alone supposes that they reflect the present and spatial organization of all below‐ground genets (mycorrhizas and extramatrical mycelia). The relation between fruit bodies and ectomycorrhizas was investigated for the basidiomycete agaric Hebeloma cylindrosporum in four Pinus pinaster stands in south‐west France. Genet identification was based on the comparison of polymorphisms within a hypervariable segment of the ribosomal intergenic spacer amplified by polymerase chain reaction (PCR) using a H. cylindrosporum species‐specific primer. Mycorrhizas were sorted from soil samples collected underneath patches of fruit bodies or patches where fruit bodies had or had not been observed during the years prior to mycorrhiza collection. On average 65% of the 1026 mycorrhizas collected underneath fruit bodies were formed by H. cylindrosporum, whereas only 2% of the 954 collected in places from where fruit bodies were absent were formed by this species. All genotypes identified above ground were also identified below ground. In patches where one genotype formed all or more than 90% of the fruit bodies, the same genotype formed all or a large majority of the mycorrhizas. In patches occupied by several different fruiting genotypes, additional nonfruiting ones could be present on the root systems. In all cases, the mycorrhizas of one genotype were found no more than 10–20 cm away from its corresponding fruit bodies, and fruit body disappearance at a given place was associated with the disappearance of the corresponding mycorrhizas within 1 year. Although there was not a strict coincidence between the total numbers of genets present below ground and of those forming fruit bodies, fruit body analysis for H. cylindrosporum appears to reflect both the genetic diversity and the spatial structure of its below‐ground populations. The results obtained also illustrate the rapid turnover of ectomycorrhizal fungal species on the root systems in the absence of any obvious major disturbance of the ecosystem.
Molecular Evolution of Catalytic Antibodies in Autoimmune Mice1

Catalytic Abs (catAbs) preferentially evolved in autoimmune MRL/MPJ-lpr/lpr (MRL/lpr) mice upon immunization with the phosphonate transition-state analogue (TSA), but this did not happen in normal BALB/c mice. The majority of the catAbs from MRL/lpr mice were from several independent clones of the same family. Most of them had a lysine at position 95 in the heavy chain (H95), which is at the junctional region. This residue, which interacts with the phosphonate moiety of the TSA and presumably is involved in the catalytic activity, was not changed even after expansive evolution following multiple mutations. By contrast, the majority that arose from BALB/c mice were the non-catAbs, which were quite different in the sequence from the catAbs from MRL/lpr mice, but they were clonally related to one another, so most of them were originated from a single clone. In the MRL/lpr mice, the catalytic subsets that existed in the initial repertoire were effectively captured by the phosphonyl oxygens in the TSA by interacting with the lysine at H95. In the BALB/c mice, however, another noncatalytic subset with only the binding capability directed to a moiety other than the phosphonate moiety was alternatively evolved, because of the lowest abundance or elimination of the catalytic subsets.