Miracle-dz/UniFAR-FTUs huggingface dataset:
A Model Based Iterative Reconstruction Algorithm For High Angle Annular Dark Field-Scanning Transmission Electron Microscope (HAADF-STEM) Tomography

High angle annular dark field (HAADF)-scanning transmission electron microscope (STEM) data is increasingly being used in the physical sciences to research materials in 3D because it reduces the effects of Bragg diffraction seen in bright field TEM data. Typically, tomographic reconstructions are performed by directly applying either filtered back projection (FBP) or the simultaneous iterative reconstruction technique (SIRT) to the data. Since HAADF-STEM tomography is a limited angle tomography modality with low signal to noise ratio, these methods can result in significant artifacts in the reconstructed volume. In this paper, we develop a model based iterative reconstruction algorithm for HAADF-STEM tomography. We combine a model for image formation in HAADF-STEM tomography along with a prior model to formulate the tomographic reconstruction as a maximum a posteriori probability (MAP) estimation problem. Our formulation also accounts for certain missing measurements by treating them as nuisance parameters in the MAP estimation framework. We adapt the iterative coordinate descent algorithm to develop an efficient method to minimize the corresponding MAP cost function. Reconstructions of simulated as well as experimental data sets show results that are superior to FBP and SIRT reconstructions, significantly suppressing artifacts and enhancing contrast.
Why-Question Answering using Intra- and Inter-Sentential Causal Relations

In this paper, we explore the utility of intra- and inter-sentential causal relations between terms or clauses as evidence for answering why-questions. To the best of our knowledge, this is the first work that uses both intra- and inter-sentential causal relations for why-QA. We also propose a method for assessing the appropriateness of causal relations as answers to a given question using the semantic orientation of excitation proposed by Hashimoto et al. (2012). By applying these ideas to Japanese why-QA, we improved precision by 4.4% against all the questions in our test set over the current state-of-theart system for Japanese why-QA. In addition, unlike the state-of-the-art system, our system could achieve very high precision (83.2%) for 25% of all the questions in the test set by restricting its output to the confident answers only.
Bacterial Diversity and Community Structure in the Pine Wood Nematode Bursaphelenchus xylophilus and B. mucronatus with Different Virulence by High-Throughput Sequencing of the 16S rDNA

Bursaphelenchus xylophilus is the pathogen of pine wilt disease. Bursaphelenchus mucronatus is similar to B. xylophilus in morphology. Both species share a common niche, but they are quite different in pathogenicity. Presently, the role of bacteria in pine wilt disease development has been widely speculated. The diversity of bacteria associated with B. xylophilus and B. mucronatus with different virulence remains unclear. In this study, virulence of four B. xylophilus and four B. mucronatus strains were evaluated by inoculating Pinus thunbergii. High-throughput sequencing targeted 16S rDNA of different virulence nematode strains was carried out. The associated bacterial community structures of the eight strains were analyzed. The results showed that 634,051 high-quality sequences were obtained from the eight nematode strains. The number of OTUs of bacteria associated with B. mucronatus was generally greater than those of B. xylophilus. The richness of the community of bacteria associated with high virulent B. xylophilus ZL1 and AmA3 was higher than moderately virulent B. xylophilus AA3, HE2, and all B. mucronatus strains. While the diversity of bacteria associated with B. mucronatus was higher than B. xylophilus. Stenotrophomonas, Pseudomonadaceae_Unclassified or Rhizobiaceae_Unclassified were predominant in the nematode strains with different virulence. Oxalobacteraceae and Achromobacter were found more abundant in the low virulent B. xylophilus and non-virulent B. mucronatus strains.
Bmc Medical Research Methodology Open Access Multivariable Risk Prediction Can Greatly Enhance the Statistical Power of Clinical Trial Subgroup Analysis

Background: When subgroup analyses of a positive clinical trial are unrevealing, such findings are commonly used to argue that the treatment's benefits apply to the entire study population; however, such analyses are often limited by poor statistical power. Multivariable risk-stratified analysis has been proposed as an important advance in investigating heterogeneity in treatment benefits, yet no one has conducted a systematic statistical examination of circumstances influencing the relative merits of this approach vs. conventional subgroup analysis.
Regulation of the ventral tegmental area by the bed nucleus of the stria terminalis is required for expression of cocaine preference

Lateral hypothalamus (LH) orexin neurons are essential for the expression of a cocaine place preference. However, the afferents that regulate the activity of these orexin neurons during reward behaviors are not completely understood. Using tract tracing combined with Fos staining, we examined LH afferents for Fos induction during cocaine preference in rats. We found that the ventral bed nucleus of the stria terminalis (vBNST) was a major input to the LH orexin cell field that was significantly Fos‐activated during cocaine conditioned place preference (CPP). Inactivation of the vBNST with baclofen plus muscimol blocked expression of cocaine CPP. Surprisingly, such inactivation of the vBNST also increased Fos induction in LH orexin neurons; as activity in these cells is normally associated with increased preference, this result indicates that a vBNST–orexin connection is unlikely to be responsible for CPP that is dependent on vBNST activity. Because previous studies have revealed that vBNST regulates dopamine cells in the ventral tegmental area (VTA), which is known to be involved in CPP and other reward functions, we tested whether vBNST afferents to the VTA are necessary for cocaine CPP. We found that disconnection of the vBNST and VTA (using local microinjections of baclofen plus muscimol unilaterally into the vBNST and contralateral VTA) significantly attenuated expression of cocaine preference. However, blocking ionotropic glutamatergic afferents to the VTA from the vBNST did not significantly reduce cocaine preference. These results indicate that a non‐glutamatergic vBNST–VTA projection is involved in expression of cocaine preference.
SEMIPARAMETRIC EFFICIENCY BOUNDS FOR CONDITIONAL MOMENT RESTRICTION MODELS WITH DIFFERENT CONDITIONING VARIABLES

This paper addresses the problem of semiparametric efficiency bounds for conditional moment restriction models with different conditioning variables. We characterize such an efficiency bound, that in general is not explicit, as a limit of explicit efficiency bounds for a decreasing sequence of unconditional (marginal) moment restriction models. An iterative procedure for approximating the efficient score when this is not explicit is provided. Our theoretical results provide new insight for the theory of semiparametric efficiency bounds literature and open the door to new applications. In particular, we investigate a class of regression-like (mean regression, quantile regression,…) models with missing data, an example of a supply and demand simultaneous equations model and a generalized bivariate dichotomous model.
The Mass of the Black Hole in the Quasar PG 2130+099

We present the results of a recent reverberation-mapping campaign undertaken to improve measurements of the radius of the broad-line region and the central black hole mass of the quasar PG 2130+099. Cross-correlation of the 5100 Å continuum and Hβ emission-line light curves yields a time lag of 22.9−4.3+4.4 days, corresponding to a central black hole mass MBH = (3.8 ± 1.5) × 107 M☉. This value supports the notion that previous measurements yielded an incorrect lag. We reanalyze previous data sets to investigate the possible sources of the discrepancy and conclude that previous measurement errors were apparently caused by a combination of undersampling of the light curves and long-term secular changes in the Hβ emission-line equivalent width. With our new measurements, PG 2130+099 is no longer an outlier in either the RBLR-L or the MBH-σ* relationship.
CEO Narcissism and Earnings Management

This paper investigates the relation between CEO narcissism and a firm’s propensity to adopt earnings manipulation. There is growing evidence that narcissistic leaders over-identify themselves with the organizations they lead and expend considerable resources to achieve their goals, including engagements in unethical behaviour. We provide evidence that firms with more narcissistic CEOs are more likely to positively manage earnings. Our results highlight the importance of CEO personality to firms’ accounting decisions.
Detergent-Resistant Microdomains Determine the Localization of σ-1 Receptors to the Endoplasmic Reticulum-Mitochondria Junction

σ-1 receptors (Sig-1Rs) that bind diverse synthetic and endogenous compounds have been implicated in the pathophysiology of several human diseases such as drug addiction, depression, neurodegenerative disorders, pain-related disorders, and cancer. Sig-1Rs were identified recently as novel ligand-operated molecular chaperones. Although Sig-1Rs are predominantly expressed at endoplasmic reticulum (ER) subdomains apposing mitochondria [i.e., the mitochondria-associated ER membrane (MAM)], they dynamically change the cellular distribution, thus regulating both MAM-specific and plasma membrane proteins. However, what determines the location of Sig-1R at the MAM and how the receptor translocation is initiated is unknown. Here we report that the detergent-resistant membranes (DRMs) play an important role in anchoring Sig-1Rs to the MAM. The MAM, which is highly capable of accumulating ceramides, is enriched with both cholesterol and simple sphingolipids, thus forming Triton X-114-resistant DRMs. Sig-1Rs associate with MAM-derived DRMs but not with those from microsomes. A lipid overlay assay found that solubilized Sig-1Rs preferentially associate with simple sphingolipids such as ceramides. Disrupting DRMs by lowering cholesterol or inhibiting de novo synthesis of ceramides at the ER largely decreases Sig-1R at DRMs and causes translocation of Sig-1R from the MAM to ER cisternae. These findings suggest that the MAM, bearing cholesterol and ceramide-enriched microdomains at the ER, may use the microdomains to anchor Sig-1Rs to the location; thus, it serves to stage Sig-1R at ER-mitochondria junctions.
The visual (un)conscious and its (dis)contents : a microtemporal approach

Preface 1. Introduction 2. Conceptual and Methodological Issues 3. Microtemporal Analyses of Object Perception 4. Contours and Surfaces: Why visual consciousness is "superficial" 5. Functional Hierarchy of Unconscious Object Processing 6. The Dorsal Pathway's Contribution to Perception and Top-Down Influences on Processing in the Ventral Pathway 7. Visual Consciousness of Things Past 8. Consciousness and Attention: Partners but not equals 9. Some Psycho-Philosophic Assessments 10. Epilogue: Reflections on consciousness and realism References
Molecular Analysis of RNA-RNA Interactions between 5′ and 3′ Untranslated Regions during the Initiation of Translation of a Cardiovirulent and a Live-Attenuated Coxsackievirus B3 Strains

Coxsackievirus B3 (CVB3) is a causative agent of viral myocarditis, meningitis and pancreatitis. CVB3 overcome their host cells by usurping the translation machinery to benefit viral gene expression. This is accomplished through alternative translation initiation in a cap independent manner at the viral internal ribosomal entry site. The 5′ untranslated region (5′UTR) of CVB3 genomic RNA is highly structured. It is the site of multiple RNA-protein and RNA-RNA interactions and it plays a critical role during translation initiation. Similar to the 5′UTR, CVB3 3′ untranslated region (3′UTR) also contains secondary structural elements consisting of three stem-loops followed by a poly (A) tail sequence. Long-range RNA-RNA interactions between 5′ and 3′ ends of some viral genomes have been observed. Because of their dual role in translation and replication, the 5′ and 3′UTRs represent promising candidates for the study of CVB3 cardiovirulence. Taking into account that efficient initiation of mRNA translation depends on a temporally and spatially orchestrated sequence of protein-protein, protein-RNA and RNA-RNA interactions, and that, at present, little is known about RNA-RNA interactions between CVB3 5′ and 3′UTRs, we aimed in the present study, to assess a possible RNA-RNA interaction between 5′ and 3′UTRs during the initiation of translation of a wild-type and a previously characterized mutant (Sabin3-like) CVB3 strains and to investigate the effect of the Sabin3-like mutation on these potential interactions. For this purpose, “Electrophoretic Mobility Shift” assays were carried out. Data obtained did not show any RNA-RNA direct interactions between the 5′- and 3′- ends. Therefore, we can suggest that the possible mechanism by which 3′UTR enhances CVB3 IRES activity may be by bridging the 5′ to the 3′ end through RNA-protein interaction and not through RNA-RNA direct contact. However, these findings need to be confirmed by carrying out further experiments.
Singular Perturbation Method for Smart Building Temperature Control Using Occupant Feedback

In this work we propose a framework for incorporating occupant feedback towards temperature control of multi‐occupant spaces, and analyze it using singular perturbation theory. Such a system would typically have to accommodate occupants with different temperature preferences, and incorporate that with thermal correlation among multiple zones to obtain optimal control for minimization of occupant discomfort and energy cost. In current practice, an acceptable temperature set point for the occupancy level of the zone is estimated, and the control law is designed to maintain temperature at the corresponding set point irrespective of the changes in occupancy and the preferences of multiple occupants. Proposed algorithm incorporates active occupant feedback to minimize aggregate user discomfort and total energy cost. Occupant binary feedback in the form of hot/cold or thermal comfort preference input is used by the control algorithm. The control algorithm also takes the energy cost into account, trading it off optimally with the aggregate occupant discomfort. For convergence to the optimal, sufficient separation between the occupant feedback frequency and the temperature dynamics of system is necessary; in absence of which, the occupant feedback provided do not correctly reflect the effect of current control input value on occupant discomfort. Under sufficient time scale separation, using singular perturbation theory, we establish the stability condition of the system and show convergence of the proposed solution to the desired temperature that minimizes energy cost plus occupant discomfort. The occupants are only assumed to be rational in that they choose their own comfort range to minimize individual thermal discomfort. Optimization for a multi‐zone building also takes into account the thermal correlation among different zones. Simulation study with parameters based on our test facility, and experimental study conducted in the same building demonstrates performance of the algorithm under different occupancy and ambient conditions.
Institutional report - Thoracic oncologic Pneumonectomy for lung cancer over the age of 75 years: is it worthwhile?

The objective of the study was to evaluate the outcome in elderly patients ()75 years) submitted to pneumonectomy for lung cancer. Records of 40 elderly patients, who underwent pneumonectomy at our Institution from 1990 to 2008, were retrospectively reviewed. This group was compared with 289 younger patients submitted to pneumonectomy in the same period. In the older group median age was 77 years (range 75–84 years), 16 were right-side procedures. In the younger group median age was 62 years (range 24–74 years), 114 were right-sided procedures. The overall mortality rate was 7.5% and 6.2% in the older and younger groups, respectively (Ps0.75); morbidity rate was 35.1% and 17.7% (Ps0.01) and five-year survival rate was 32% and 30%, respectively (Ps0.85). Right-sided procedures (Ps0.0006) were associated with higher risk of mortality and age over 75 years (Ps0.01) with increased risk of morbidity; pathological stage was the only predictor of five-year survival. Pneumonectomy appears to be justified even in patients older than 75 years, because short- and longterm outcomes can be acceptable and comparable with those of younger patients. Advanced age alone does not justify denying curative resection of lung cancer, but right-sided procedures require a careful pre- and postoperative approach. 2010 Published by European Association for Cardio-Thoracic Surgery. All rights reserved.
8-Oxoguanine DNA Glycosylase (OGG1) Deficiency Increases Susceptibility to Obesity and Metabolic Dysfunction

Oxidative damage to DNA is mainly repaired via base excision repair, a pathway that is catalyzed by DNA glycosylases such as 8-oxoguanine DNA glycosylase (OGG1). While OGG1 has been implicated in maintaining genomic integrity and preventing tumorigenesis, we report a novel role for OGG1 in altering cellular and whole body energy homeostasis. OGG1-deficient (Ogg1−/−) mice have increased adiposity and hepatic steatosis following exposure to a high-fat diet (HFD), compared to wild-type (WT) animals. Ogg1−/− animals also have higher plasma insulin levels and impaired glucose tolerance upon HFD feeding, relative to WT counterparts. Analysis of energy expenditure revealed that HFD-fed Ogg1−/− mice have a higher resting VCO2 and consequently, an increased respiratory quotient during the resting phase, indicating a preference for carbohydrate metabolism over fat oxidation in these mice. Additionally, microarray and quantitative PCR analyses revealed that key genes of fatty acid oxidation, including carnitine palmitoyl transferase-1, and the integral transcriptional co-activator Pgc-1α were significantly downregulated in Ogg1−/− livers. Multiple genes involved in TCA cycle metabolism were also significantly reduced in livers of Ogg1−/− mice. Furthermore, hepatic glycogen stores were diminished, and fasting plasma ketones were significantly reduced in Ogg1−/− mice. Collectively, these data indicate that OGG1 deficiency alters cellular substrate metabolism, favoring a fat sparing phenotype, that results in increased susceptibility to obesity and related pathologies in Ogg1−/− mice.
Patterns of Trauma Induced by Motorboat and Ferry Propellers as Illustrated by Three Known Cases from Rhode Island *

Abstract: Understanding patterns of trauma is important to determining cause and manner of death. A thorough evaluation of taphonomy, trauma, and bone fracture mechanisms is necessary to reconstruct the circumstances of the death. This study examines the skeletal trauma caused by boat propeller strikes in terms of wound characteristics and location based on three cases from Rhode Island. These case studies review the traumatic characteristics caused by propeller injuries and highlight the anatomic regions most likely to sustain skeletal trauma. With this information, investigators may be able to identify propeller trauma even in severely decomposed remains. The discussion of boat propeller trauma also raises issues regarding how forensic anthropologists and forensic pathologists classify trauma (specifically blunt force vs. sharp) and highlights semantic issues arising in trauma classification. The study also discusses why these propeller cases should be classified as blunt trauma rather than sharp or chop/hack trauma. Ultimately, the authors urge consistency and communication between pathologist and forensic anthropologists performing trauma analyses.
An Efficient Implementation of the Non Restoring Square Root Algorithm in Gate Level

This paper proposes an efficient strategy to implement modified non restoring algorithm based on FPGA in gate level abstraction of VHDL, which adopt fully pipelined architecture. A new basic building block is called controlled subtract-multiplex (CSM) is introduced. The main principle of the proposed method is similar with conventional non-restoring algorithm, but it only uses subtract operation and append 01, while add operation and append 11 is not used. The proposed strategy has conducted to implement FPGA successfully, and it is offer an efficient in hardware resource.
Melatonin Reduces Angiogenesis in Serous Papillary Ovarian Carcinoma of Ethanol-Preferring Rats

Angiogenesis is a hallmark of ovarian cancer (OC); the ingrowth of blood vessels promotes rapid cell growth and the associated metastasis. Melatonin is a well-characterized indoleamine that possesses important anti-angiogenic properties in a set of aggressive solid tumors. Herein, we evaluated the role of melatonin therapy on the angiogenic signaling pathway in OC of an ethanol-preferring rat model that mimics the same pathophysiological conditions occurring in women. OC was chemically induced with a single injection of 7,12-dimethylbenz(a)anthracene (DMBA) under the ovarian bursa. After the rats developed serous papillary OC, half of the animals received intraperitoneal injections of melatonin (200 µg/100 g body weight/day) for 60 days. Melatonin-treated animals showed a significant reduction in OC size and microvessel density. Serum levels of melatonin were higher following therapy, and the expression of its receptor MT1 was significantly increased in OC-bearing rats, regardless of ethanol intake. TGFβ1, a transforming growth factor-beta1, was reduced only after melatonin treatment. Importantly, vascular endothelial growth factor (VEGF) was severely reduced after melatonin therapy in animals given or not given ethanol. Conversely, the levels of VEGF receptor 1 (VEGFR1) was diminished after ethanol consumption, regardless of melatonin therapy, and VEGFR2 was only reduced following melatonin. Hypoxia-inducible factor (HIF)-1α was augmented with ethanol consumption, and, notably, melatonin significantly reduced their levels. Collectively, our results suggest that melatonin attenuates angiogenesis in OC in an animal model of ethanol consumption; this provides a possible complementary therapeutic opportunity for concurrent OC chemotherapy.
TORC1 and TORC2 Coactivators Are Required for Tax Activation of the Human T-Cell Leukemia Virus Type 1 Long Terminal Repeats

ABSTRACT Human T-cell leukemia virus type 1 (HTLV-1) Tax protein activates viral transcription from the long terminal repeats (LTR). Mechanisms through which Tax activates LTR have been established, but coactivators of this process remain to be identified and characterized. Here we show that all three members of the TORC family of transcriptional regulators are coactivators of Tax for LTR-driven expression. TORC coactivation requires CREB, but not ATF4 or other bZIP factors. Tax physically interacts with TORC1, TORC2, and TORC3 (TORC1/2/3), and the depletion of TORC1/2/3 inhibited Tax activity. TORC coactivation can be further enhanced by transcriptional coactivator p300. In addition, coactivators in the p300 family are required for full activity of Tax independently of TORC1/2/3. Thus, both TORC and p300 families of coactivators are essential for optimal activation of HTLV-1 transcription by Tax.