Miracle-dz/UniFAR-FTUs huggingface dataset:
Reconstruction de surfaces d'objets courbes en vision par ordinateur. (Reconstruction of curved object surfaces in computer vision)

De par les recents progres de l'informatique dans le domaine de l'imagerie, il est dorenavant possible de manipuler des surfaces d'objets reels a partir des ordinateurs. Un des besoins qui en decoule concerne l'acquisition de ces surfaces. Dans ce document, nous nous penchons sur le probleme de la reconstruction de surfaces d'objets courbes a partir de sequences d'images. Les contours images de ce type d'objets, les contours occultants, constituent une riche source d'informations sur la geometrie de la surface de l'objet. Il est en particulier possible d'estimer les proprietes locales de la surface lorsqu'une sequence d'au moins trois contours est disponible. Nous presentons dans ce cadre une methodologie de reconstruction de surfaces. Celle-ci permet de passer d'une sequence de contours occultant a une description de la partie de la surface observee correspondante, sous la forme de facettes triangulaires. Plusieurs aspects de la reconstruction lies aux contours occultants sont par ailleurs pris en compte pour ameliorer les resultats: la correction des effets dus au bruit present dans l'ensemble du processus d'acquisition ainsi que la detection des parties non-visibles de la surface par les contours, les concavites par exemple. Les differentes etapes de la methodologie sont illustrees tout au long du document par de nombreuses experimentations sur des donnees reelles et synthetiques
The objective structured clinical examination revisited for postgraduate trainees in general practice

Objectives: To investigate if the psychometric qualities of an OSCE consisting of more complex simulated patient encounters remain valid and reliable in the assessment of postgraduate trainees in general practice. Methods: In this intervention study without control group, the traditional OSCE was formally replaced by the new, complex version. The study population was composed by all postgraduate trainees (second and third phase) in general practice during the ongoing academic year. Data were handled and collected as part of the formal assessment program. Univariate analyses, the variance of scores and multivariate analyses were performed to assess the test qualities. Results: A total of 340 students participated. Average final scores were slightly higher for third-phase students (t-test, p=0.05). Overall test scores were equally distributed on station level, circuit level and phase level. A multiple regression analysis revealed that test scores were dependent on the stations and circuits, but not on the master phase. Conclusions: In a changing learning environment, assessment and evaluation strategies require reorientation. The reliability and validity of the OSCE remain subject to discussion. In particular, when it comes to content and design, the traditional OSCE might underestimate the performance level of postgraduate trainees in general practice. A reshaping of this OSCE to a more sophisticated design with more complex patient encounters appears to restore the validity of the test results.
The dynamics of Ku70/80 and DNA-PKcs at DSBs induced by ionizing radiation is dependent on the complexity of damage

DNA double-strand breaks (DSBs) are biologically one of the most important cellular lesions and possess varying degrees of chemical complexity. The notion that the repairability of more chemically complex DSBs is inefficient led to the concept that the extent of DSB complexity underlies the severity of the biological consequences. The repair of DSBs by non-homologous end joining (NHEJ) has been extensively studied but it remains unknown whether more complex DSBs require a different sub-set of NHEJ protein for their repair compared with simple DSBs. To address this, we have induced DSBs in fluorescently tagged mammalian cells (Ku80-EGFP, DNA-PKcs-YFP or XRCC4-GFP, key proteins in NHEJ) using ultra-soft X-rays (USX) or multi-photon near infrared (NIR) laser irradiation. We have shown in real-time that simple DSBs, induced by USX or NIR microbeam irradiation, are repaired rapidly involving Ku70/80 and XRCC4/Ligase IV/XLF. In contrast, DSBs with greater chemical complexity are repaired slowly involving not only Ku70/80 and XRCC4/Ligase IV/XLF but also DNA-PKcs. Ataxia telangiectasia-mutated inhibition only retards repair of the more chemically complex DSBs which require DNA-PKcs. In summary, the repair of DSBs by NHEJ is highly regulated with pathway choice and kinetics of repair dependent on the chemical complexity of the DSB.
Engineered Aptamers to Probe Molecular Interactions on the Cell Surface

Significant progress has been made in understanding the nature of molecular interactions on the cell membrane. To decipher such interactions, molecular scaffolds can be engineered as a tool to modulate these events as they occur on the cell membrane. To guarantee reliability, scaffolds that function as modulators of cell membrane events must be coupled to a targeting moiety with superior chemical versatility. In this regard, nucleic acid aptamers are a suitable class of targeting moieties. Aptamers are inherently chemical in nature, allowing extensive site-specific chemical modification to engineer sensing molecules. Aptamers can be easily selected using a simple laboratory-based in vitro evolution method enabling the design and development of aptamer-based functional molecular scaffolds against wide range of cell surface molecules. This article reviews the application of aptamers as monitors and modulators of molecular interactions on the mammalian cell surface with the aim of increasing our understanding of cell-surface receptor response to external stimuli. The information gained from these types of studies could eventually prove useful in engineering improved medical diagnostics and therapeutics.
An opportunistic network-coded cooperative uplink transmission scheme for wireless multi-relay networks

In this paper, a feedback-based opportunistic network-coded cooperative scheme is proposed to be combined with cooperative communication in wireless uplink multi-relay networks. Different from previous network-coded schemes that conduct network coding all the time, we propose a scheme that conducts network coding and direct transmission alternately according to the quality of the channels. The outage probability is analyzed theoretically and the approximate expression of outage probability is derived. Compared with the previous schemes, the proposed scheme achieves a performance gain in terms of outage probability. The validity of the proposed scheme is verified by theoretical analysis and simulation results.
A More Accurate Model for Finding Tutorial Segments Explaining APIs

Developers prefer to utilize third-party libraries when they implement some functionalities and Application Programming Interfaces (APIs) are frequently used by them. Facing an unfamiliar API, developers tend to consult tutorials as learning resources. Unfortunately, the segments explaining a specific API scatter across tutorials. Hence, it remains a challenging issue to find the relevant segments. In this study, we propose a more accurate model to find the exact tutorial fragments explaining APIs. This new model consists of a text classifier with domain specific features. More specifically, we discover two important indicators to complement traditional text based features, namely co-occurrence APIs and knowledge based API extensions. In addition, we incorporate Word2Vec, a semantic similarity metric to enhance the new model. Extensive experiments over two publicly available tutorial datasets show that our new model could find up to 90% fragments explaining APIs and improve the state-of-the-art model by up to 30% in terms of F-measure.
The Price of Privacy in Untrusted Recommender Systems

Recent increase in online privacy concerns prompts the following question: can a recommender system be accurate if users do not entrust it with their private data? To answer this, we study the problem of learning item-clusters under local differential privacy, a powerful, formal notion of data privacy. We develop bounds on the sample-complexity of learning item-clusters from privatized user inputs. Significantly, our results identify a sample-complexity separation between learning in an information-rich and an information-scarce regime, thereby highlighting the interaction between privacy and the amount of information (ratings) available to each user. In the information-rich regime, where each user rates at least a constant fraction of items, a spectral clustering approach is shown to achieve a sample-complexity lower bound derived from a simple information-theoretic argument based on Fano's inequality. However, the information-scarce regime, where each user rates only a vanishing fraction of items, is found to require a fundamentally different approach both for lower bounds and algorithms. To this end, we develop new techniques for bounding mutual information under a notion of channel-mismatch. These techniques may be of broader interest, and we illustrate this by applying them to (i) learning based on 1-bit sketches, and (ii) adaptive learning. Finally, we propose a new algorithm, MaxSense, and show that it achieves optimal sample-complexity in the information-scarce regime.
Iterative Learning Control for varying tasks: Achieving optimality for rational basis functions

Iterative Learning Control (ILC) can achieve superior tracking performance for systems that perform repeating tasks. However, the performance of standard ILC deteriorates dramatically when the task is varied. In this paper ILC is extended with rational basis functions to obtain excellent extrapolation properties. A new approach for rational basis functions is proposed where the iterative solution algorithm is of the form used in instrumental variable system identification algorithms. The optimal solution is expressed in terms of learning filters similar as in standard ILC. The proposed approach is shown to be superior over existing approaches in terms of performance by a simulation example.
A unified framework for link and rating prediction in multi-modal social networks

Multi-modal social networks (MSNs) allow users to form explicit (by adding new friends in their network) or implicit (by similarly co-rating items) social networks. Previous research work was limited either to the prediction of new relationships among users (i.e., link prediction problem) or to the prediction of item ratings (i.e., rating prediction problem and item recommendations). In this paper, we develop a framework to incorporate both research directions into a unified model. Our social-union algorithm combines similarity matrices derived from heterogeneous (unipartite and bipartite) explicit or implicit MSNs. We perform an extensive experimental comparison of the proposed method against existing link and rating prediction algorithms, using synthetic and two real data sets (Epinions and Flixter). Our experimental results show that our social-union framework is more effective in both rating and link prediction.
p22phox C242T Single-Nucleotide Polymorphism Inhibits Inflammatory Oxidative Damage to Endothelial Cells and Vessels

Background— The NADPH oxidase, by generating reactive oxygen species, is involved in the pathophysiology of many cardiovascular diseases and represents a therapeutic target for the development of novel drugs. A single-nucleotide polymorphism, C242T of the p22phox subunit of NADPH oxidase, has been reported to be negatively associated with coronary heart disease and may predict disease prevalence. However, the underlying mechanisms remain unknown. Methods and Results— With the use of computer molecular modeling, we discovered that C242T single-nucleotide polymorphism causes significant structural changes in the extracellular loop of p22phox and reduces its interaction stability with Nox2 subunit. Gene transfection of human pulmonary microvascular endothelial cells showed that C242T p22phox significantly reduced Nox2 expression but had no significant effect on basal endothelial O2 . – production or the expression of Nox1 and Nox4. When cells were stimulated with tumor necrosis factor-&agr; (or high glucose), C242T p22phox significantly inhibited tumor necrosis factor-&agr;–induced Nox2 maturation, O2 . – production, mitogen-activated protein kinases and nuclear factor &kgr;B activation, and inflammation (all P<0.05). These C242T effects were further confirmed using p22phox short-hairpin RNA–engineered HeLa cells and Nox2–/– coronary microvascular endothelial cells. Clinical significance was investigated by using saphenous vein segments from non–coronary heart disease subjects after phlebotomies. TT (C242T) allele was common (prevalence of ≈22%) and, in comparison with CC, veins bearing TT allele had significantly lower levels of Nox2 expression and O2 . – generation in response to high-glucose challenge. Conclusions— C242T single-nucleotide polymorphism causes p22phox structural changes that inhibit endothelial Nox2 activation and oxidative response to tumor necrosis factor-&agr; or high-glucose stimulation. C242T single-nucleotide polymorphism may represent a natural protective mechanism against inflammatory cardiovascular diseases.
The Price of Play: Self-Organized Infant Mortality Cycles in Chimpanzees

Chimpanzees have been used extensively as a model system for laboratory research on infectious diseases. Ironically, we know next to nothing about disease dynamics in wild chimpanzee populations. Here, we analyze long-term demographic and behavioral data from two habituated chimpanzee communities in Taï National Park, Côte d'Ivoire, where previous work has shown respiratory pathogens to be an important source of infant mortality. In this paper we trace the effect of social connectivity on infant mortality dynamics. We focus on social play which, as the primary context of contact between young chimpanzees, may serve as a key venue for pathogen transmission. Infant abundance and mortality rates at Taï cycled regularly and in a way that was not well explained in terms of environmental forcing. Rather, infant mortality cycles appeared to self-organize in response to the ontogeny of social play. Each cycle started when the death of multiple infants in an outbreak synchronized the reproductive cycles of their mothers. A pulse of births predictably arrived about twelve months later, with social connectivity increasing over the following two years as the large birth cohort approached the peak of social play. The high social connectivity at this play peak then appeared to facilitate further outbreaks. Our results provide the first evidence that social play has a strong role in determining chimpanzee disease transmission risk and the first record of chimpanzee disease cycles similar to those seen in human children. They also lend more support to the view that infectious diseases are a major threat to the survival of remaining chimpanzee populations.
The Peierls-Nabarro model revisited

We re-examine two important issues within the Peierls-Nabarro model, which are critical in obtaining accurate values for the Peierls stress. The first is related to the sampling scheme (double versus single counting) of the misfit energy across the glide plane and the second is the effect of atomic relaxation on the Peierls stress. We argue that the double-counting scheme is physically more appropriate. An analytical formula is derived for the Peierls stress of dislocations in alternating lattices. The atomic relaxation is shown to play an important role on the Peierls stress for narrow dislocations.
Contextualizing nativity status, Latino social ties, and ethnic enclaves: an examination of the ‘immigrant social ties hypothesis’

Objectives Researchers have posited that one potential explanation for the better-than-expected health outcomes observed among some Latino immigrants, vis-à-vis their US-born counterparts, may be the strength of social ties and social support among immigrants. Methods We examined the association between nativity status and social ties using data from the Chicago Community Adult Health Study's Latino subsample, which includes Mexicans, Puerto Ricans, and other Latinos. First, we used ordinary least squares (OLS) regression methods to model the effect of nativity status on five outcomes: informal social integration; social network diversity; network size; instrumental support; and informational support. Using multilevel mixed-effects regression models, we estimated the association between Latino/immigrant neighborhood composition and our outcomes, and whether these relationships varied by nativity status. Lastly, we examined the relationship between social ties and immigrants' length of time in the USA. Results After controlling for individual-level characteristics, immigrant Latinos had significantly lower levels of social ties than their US-born counterparts for all the outcomes, except informational support. Latino/immigrant neighborhood composition was positively associated with being socially integrated and having larger and more diverse social networks. The associations between two of our outcomes (informal social integration and network size) and living in a neighborhood with greater concentrations of Latinos and immigrants were stronger for US-born Latinos than for immigrant Latinos. US-born Latinos maintained a significant social ties advantage over immigrants – regardless of length of time in the USA – for informal social integration, network diversity, and network size. Conclusion At the individual level, our findings challenge the assumption that Latino immigrants would have larger networks and/or higher levels of support and social integration than their US-born counterparts. Our study underscores the importance of understanding the contexts that promote the development of social ties. We discuss the implications of these findings for understanding Latino and immigrant social ties and health outcomes.
Significance of lung biopsy for the definitive diagnosis of lung nodules in breast cancer patients

The aim of the present study was to evaluate the significance of lung biopsy for the modification of the treatment strategy in breast cancer patients who develop lung nodules during follow-up after breast surgery. Of 53 consecutive patients who underwent lung biopsies in two institutions (Hiroshima University Hospital and Hiroshima Prefectural Hospital, Hiroshima, Japan) between 1997 and 2014, 45 underwent lung surgery and 8 underwent percutaneous or transbronchial tumor biopsy for lung nodules developing after curative surgery for breast cancer. The indications for lung biopsy included lung nodules for which a definitive diagnosis was difficult to achieve, and those for which the treatment strategy depended on the pathological diagnosis. The lung nodules were pathologically diagnosed as primary breast cancer metastases to the lungs in 25 (47%), primary malignant lung tumors in 21 (40%) and benign disease in 7 (13%) patients. Among the 25 metastatic patients confirmed by lung biopsy, phenotype discordance was observed in 6 patients (24%). A total of 3 patients with lung metastasis proven to have estrogen or progesterone receptor upregulation by lung biopsy received endocrine therapy. Univariate analysis revealed that patients with metastatic breast cancer confirmed by lung biopsy were significantly younger and had more locally advanced primary cancers diagnosed via clinical and pathological assessment compared with patients with other diseases. Therefore, mastectomy and axillary lymph node dissection were performed more frequently in the metastasis group compared with the others group. Multivariate analysis revealed that mastectomy (P<0.001) and axillary dissection (P<0.001) were independent factors predicting that the lung nodules would be metastases from breast cancer. Lung biopsy in breast cancer patients who developed lung nodules during the follow-up period after breast cancer surgery was crucial for making a definitive diagnosis and modifying the treatment strategy, which may improve the prognosis of breast cancer patients.
Quantum dot PbS0.9Se0.1/TiO2 heterojunction solar cells

We report on photovoltaic cells based on ternary PbS0.9Se0. 1 quantum dots utilizing a heterojunction type device configuration. The best device shows an AM 1.5 power conversion efficiency of 4.25%. Furthermore, this ternary PbSxSe1−x quantum dot heterojunction device has a peak external quantum efficiency above 100% at 2.76 eV, approximately 2.7 × the bandgap energy. The ternary quantum dots combine the higher short circuit currents of the binary PbSe system with the higher open circuit voltages of the binary PbS system.
Dual Effects of TRAIL in Suppression of Autoimmunity: The Inhibition of Th1 Cells and the Promotion of Regulatory T Cells

TRAIL is known to play a pivotal role in the inhibition of autoimmune disease. We previously demonstrated that administration of dendritic cells engineered to express TRAIL and myelin-oligodendrocyte glycoprotein reduced the severity of experimental autoimmune encephalomyelitis and suggested that CD4+CD25+ regulatory T cells (Tregs) were involved in mediating this preventive effect. In the current study, we investigated the effect of TRAIL on Tregs, as well as conventional T cells, using TRAIL-deficient mice. Upon induction of experimental autoimmune encephalomyelitis, TRAIL-deficient mice showed more severe clinical symptoms, a greater frequency of IFN-γ–producing CD4+ T (Th1) cells, and a lower frequency of CD4+Foxp3+ Tregs than did wild-type mice. In vitro, conventional T cells stimulated by bone marrow-derived dendritic cells (BM-DCs) from TRAIL-deficient mice showed a greater magnitude of proliferation than did those stimulated by BM-DCs from wild-type mice. In contrast, TRAIL expressed on the stimulator BM-DCs enhanced the proliferative response of CD4+CD25+ Tregs in the culture. The functional TRAILR, mouse death receptor 5 (mDR5), was expressed in conventional T cells and Tregs upon stimulation. In contrast, the decoy receptor, mDc-TRAILR1, was slightly expressed only on CD4+CD25+ Tregs. Therefore, the distinct effects of TRAIL may be due to differences in the mDc-TRAILR1 expression or the signaling pathways downstream of mouse death receptor 5 between the two T cell subsets. Our data suggest that TRAIL suppresses autoimmunity by two mechanisms: the inhibition of Th1 cells and the promotion of Tregs.
Insights into anti-termination regulation of the hut operon in Bacillus subtilis: importance of the dual RNA-binding surfaces of HutP

The anti-termination protein, HutP, regulates the gene expression of the hut (histidine utilization) operon of Bacillus subtilis, by destabilizing the hut terminator RNA located upstream of the coding region encoding l-histidine degradation enzymes. On the basis of biochemical, in vivo and X-ray structural analyses, we now report that HutP uses its dual RNA-binding surfaces to access two XAG-rich regions (sites I and II) within the terminator RNA to mediate the destabilization process. In this process, HutP initiates destabilization at the 5'-end of its mRNA by binding to the first XAG-rich region (site I) and then accesses the second XAG-rich region (site II), located downstream of the stable G-C-rich segment of the terminator stem. By this action, HutP appears to disrupt the G-C-rich terminator stem, and thus prevents premature termination of transcription in the RNA segment preceding the regions encoding for the histidine degradation enzymes.