Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution of MLH1 Foci in Horse Male Synaptonemal Complex

Advances in molecular cytogenetics have provided the opportunity to study events during prophase I of meiosis. Immunofluorescent localization of different meiotic protein components were used to characterize the early stages of the first meiotic division in horse spermatocytes. The frequency and distribution of recombination events during prophase I were investigated using the mutL homolog 1 (MLH1) protein that is known to be associated with these events. The frequency and distribution of MLH1 foci were investigated in pachytene nuclei of 6 fertile stallions, and the average relative synaptonemal complex length was found to be highly correlated with the average number of MLH1 foci. The frequency and distribution of MLH1 foci were found to closely correspond to the frequency and distribution of chiasmata on metaphase I chromosomes, and genetic length, calculated from MLH1 foci data, for the whole genome was 2,505.5 cM.
Systematic tendencies in scene viewing

While many current models of scene perception debate the relative roles of low- and highlevel factors in eye guidance, systematic tendencies in how the eyes move may be informative. We consider how each saccade and fixation is influenced by that which preceded or followed it, during free inspection of images of natural scenes. We find evidence to suggest periods of localized scanning separated by ‘global’ relocations to new regions of the scene. We also find evidence to support the existence of small amplitude ‘corrective’ saccades in natural image viewing. Our data reveal statistical dependencies between successive eye movements, which may be informative in furthering our understanding of eye guidance.
The role of RgpA in the pathogenicity of Porphyromonas gingivalis in the murine periodontitis model.

AIM To investigate the in vivo role of gingipains in Porphyromonas gingivalis' virulence, and suggest a possible host mechanisms through which the bacteria cause alveolar bone loss. MATERIALS AND METHODS Mice were orally infected with P. gingivalis wild type, or the gingipains mutants (RgpA⁻, Kgp⁻, RgpA⁻/Kgp⁻). Mice were analysed for alveolar bone loss using micro-computed tomography. The molecular effects of the proteases were evaluated using the subcutaneous chamber model. Mice were infected with P. gingivalis wild type or mutants. Exudates were analysed for cytokine and leukocytes levels, in vivo phagocytosis, P. gingivalis survival and serum anti-P. gingivalis IgG titres. RESULTS Only RgpA-expressing bacteria induced significantly alveolar bone loss, and suppressed phagocytosis resulting in increased survival of P. gingivalis in the chamber exudates. In addition, RgpA-expressing bacteria induced higher levels of leukocytes and cytokines 2 h post-infection, and reduced levels of serum anti-P. gingivalis IgG titres 7 days post-infection. CONCLUSIONS Our findings showed that elimination of RgpA from P. gingivalis diminished inflammation, but augmented phagocytosis and antibody titres, coincidental with reduced alveolar bone loss. These findings support the hypothesis that RgpA is a critical virulence factor in the pathogenesis of experimental periodontitis in mice.
Activation of ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) by rubisco activase : effects of some sugar phosphates.

The activation of purified ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) has been studied in the presence of sugar phosphates, and the effect of rubisco activase on this process determined. During an 11-minute time course at pH 7.7 and 11 micromolar CO(2), the activation of rubisco was strongly inhibited by ribulose-1,5-bisphosphate (4 millimolar), fructose-1,6-bisphosphate (1 millimolar) and ribose 5-phosphate (5 millimolar), but this inhibition was overcome by the addition of rubisco activase and activation then proceeded to a greater extent than spontaneous activation of rubisco. Glycerate 3-phosphate (20 millomolar) slowed the initial rate but not the extent of activation and rubisco activase had no effect on this. The activation of rubisco was shown to be affected by phosphoenolpyruvate (3 millimolar) but not by creatine phosphate (3 millimolar) or ATP (3 millimolar), and the creatine-phosphate/creatine phosphokinase system was used to generate the high ATP/ADP quotients required for rubisco activase to function. ATP was shown to be required for the rubisco activase-dependent rubisco activation in the presence of fructose-1,6-bisphosphate (1 millimolar). It is concluded that rubisco activase has a mixed specificity for some sugar phosphate-bound forms of rubisco, but has low or no activity with others. Some possible bases for these differences among sugar phosphates are discussed but remain to be established.
AN ANALYTICAL FRAMEWORK FOR PREDICTING THE PERFORMANCE OF AUTONOMOUS UNDERWATER VEHICLE POSITIONING

In this paper we present a set of simple models to predict the performance of underwater positioning solutions for autonomous underwater vehicles (AUVs). Improvements in underwater navigation continue to contribute to the expansion of our capability for exploration, scientific discovery and environmental monitoring. Despite the diversity instruments and algorithms employed to improve performance, the fundamental trade-offs involved in estimating position can be understood with a few general stochastic observation models and informationcentric analysis. We present models for the most common oceanographic navigation observations: absolute reference solutions such as long-baseline (LBL) acoustic positioning, relative positioning solutions such as Doppler velocity log (DVL) dead-reckoning and accurate heading such as a fiber optic gyro (FOG) reference. We combine these simple models using the Cramér Rao lower bound to predict both the precision and accuracy of common AUV positioning solutions. To demonstrate the utility of such predictions, we model the uncertainty of current solutions and proposed future implementations. Many current solutions use a combination of LBL positioning and DVL odometry. We show how this approach can predict the performance of such a configuration. Finally, we substantiate the use of this framework by comparing model-based performance predictions to experimental evidence. The field experiment we present is a controlled evaluation of DVL dead-reckoning, using the Jason remotely operated vehicle (ROV). We observe a total error growth that can be approximated as 0.04% of distance traveled.
Second order optimization of kernel parameters

In kernel methods such as SVMs, the data representation, implicitly chosen through the so-called kernel K(x,x′), strongly influences the performances. Recent applications [3] and developments based on SVMs have shown that using multiple kernels instead of a single one can enhance interpretability of the decision function and improve classifier performance. In such cases, a common approach is to consider that the kernel K(x,x′) is actually a convex linear combination of other basis kernels:
Dynamic Min-Cut Clustering for Energy Savings in Ultra-Dense Networks

Femtocells are envisioned as a key solution to embrace the ever-increasing high data rate and thus are extensively deployed. Given that numerous femtocell access points (FAPs) deployed in ultra- dense networks (UDNs) lead to significant energy consumption, boosting their energy efficiency (EE) becomes an important issue to be addressed. However, most existing works either focus on homogeneous networks or assume that FAPs are equally distributed, which is not realistic in a dense network as random deployments cause severe interference. This paper explores the realistic scenario of randomly distributed FAPs in heterogeneous networks and proposes a clustering approach combined with an active FAP selection algorithm to boost both spectral and energy efficiency without manual configuration. Taking into account traffic load and interference, the paper reduces the complexity from the Bell Number to polynomial time by exploiting a graph-based Min-Cut strategy to cluster FAPs and allocate orthogonal resources in one cluster to mitigate interference that in turn improves EE. Simulation results confirm the effectiveness of the framework.
Teaching social determinants of child health in a pediatric advocacy rotation: Small intervention, big impact

Background: Traditionally, medical education does not specifically address the social determinants of health or how to advocate for families’ cultural, social or economic needs in spite of our increasingly diverse society. Aim: This article describes a new social–legal curriculum added to a Pediatric Resident's Advocacy course. Methods: Pediatric interns completed ‘Memos To Myself’ after the Advocacy rotation. Results: The curriculum impacted residents’ (1) realization regarding family circumstances; (2) reflections regarding self and personal practice; and (3) knowledge about advocacy issues and community partnerships for solutions. Conclusions: This curriculum raised awareness about topics that are traditionally not covered in medical education.
Concurrent Object-Oriented Programming and Anomalies

The concepts of object-oriented programming and concurrency are well established. However, the formal definitions about the both are weak. The framework becomes more prone to errors when the behaviour of objects is made concurrent. In this thesis, an effort is made to establish the formal framework modeling the concurrent object-oriented programming paradigm. In addition, it is shown that in such a system the mechanism of inheritance and object synchronization may produce anomalous results, if not carefully modeled.
Indoor positioning by distributed machine-learning based data analytics on smart gateway network

Real-time data analysis on sensor nodes is challenging due to limited computing resources. A changing environment where received signal strength (RSSI) varies with time makes it more complex to update position predictors for real-time indoor positioning. Based on the distributed collection and analytics of RSSI values in a gateway network, a time-efficient workload-based (WL) distributed support vector machine (WL-DSVM) algorithm is introduced in this paper to perform the indoor positioning. Experimental results show that with 5 distributed sensor nodes running in parallel, the proposed WL-DSVM can achieve a performance improvement in run time up to 3.2× with a stable positioning accuracy.
A supervised solution for redundant feature detection depending on instances

As a high dimensional problem, analysis of microarray data sets is a challenging task, where many weakly relevant or redundant features hurt generalization performance of classifiers. The previous works used redundant feature detection methods to select discriminative compact gene set, which only considered the relationship among features, not the redundancy of classification ability among features. Here, we propose a novel algorithm named RESI (Redundant fEature Selection depending on Instance), which considers label information in the measure of feature subset redundancy. Experimental results on benchmark data sets show that RESI performs better than the previous state-of-arts algorithms on redundant feature selection methods like mRMR.
A putative new domain target for anti‐hepatitis B virus: Residues flanking hepatitis B virus reverse transcriptase residue 306 (rtP306)

Previous work showed that conservation of proline at residue 306 (rtP306) of hepatitis B virus (HBV) reverse transcriptase (RT) is crucial for virus replication and encapsidation of pregenomic RNA (pgRNA). In this study, the functions of residues flanking rtP306 in HBV RT (rtG304, rtY305, rtA307, rtL308 and rtL311) are presented. Alanine or phenylalanine was used to substitute these residues by constructing site‐directed mutants which were used to transfect Huh‐7 cells. Replication competencies and encapsidation efficiencies were compared between the mutants and the parental viral strain. Substitutions at these residues resulted in marked decrease of replication competency, which was confirmed by Southern blot hybridization of HBV DNA isolated from intracytoplasmic core particles, and trans‐complementation between a non‐replicative defective mutant and corresponding RT mutants. Impaired pgRNA encapsidation efficiency of these mutants was shown as the major mechanism for decreased replication efficiency. Since residues from rt304 to rt311 are highly conserved among genotypes A–H HBV strains, results suggest that rt304 to rt311 in HBV RT may serve as a putative anti‐HBV new target domain. J. Med. Virol. 79: 676–682, 2007. © 2007 Wiley‐Liss, Inc.
Recherche locale de politique dans un espace convexe

En apprentissage par renforcement, la recherche locale de politique est une approche classique permettant de prendre en compte de grands espaces d'etat. Formellement, elle consiste a chercher localement dans un espace de politiques parametrees la solution qui va maximiser la fonction de valeur associee, moyennee selon une loi predefinie sur les etats. La premiere contribution de cet article montre que si l'espace de politiques est convexe, \emph{tout optimum local} (approche) presente une \emph{garantie globale de performance}. Malheureusement, supposer la convexite de l'espace de recherche est une hypothese forte : elle n'est pas satisfaite par les representations usuelles des politiques et definir une parametrisation non triviale qui satisfasse cette propriete est difficile. Une solution naturelle pour palier ce probleme est d'optimiser la fonction objectif associee grâce a une montee de gradient fonctionnel, la recherche etant contrainte a l'enveloppe convexe de l'espace de politiques. Il s'avere que l'algorithme resultant est une legere generalisation du schema d'iteration conservative de la politique. Ainsi, notre seconde contribution consiste a souligner cette connexion originale entre recherche locale de politique et programmation dynamique approchee.
A Mathematical Cache Miss Analysis for Pointer Data Structures

As the gap between processor and memory performance widens, careful analyses and optimizations of cache memory behavior become increasingly important. While analysis of regular loop-based scientific programs has made significant progress, the analysis of less regular reference patterns has lagged somewhat. This paper presents basic analytic expressions for cache miss behavior in fundamental types of irregular programs: linked list traversals and binary tree searches. We compare our analytic expressions to simulation-based results. Although quite elementary, these simple expressions will form the foundation for our planned work in analyzing the behavior of database and other applications which have linked lists, trees, and other pointer data structures at their core.
Handprinted character/digit recognition using a multiple feature/resolution philos-ophy

tb prpcr outli4es the philosophy, desrgn and implementation of the Gradient, Structural, bvily (GSC) recognition algorithm, which has been used successfully in several aGG"d rcading applications at CEDAR. The GSC algorithm takes a quasi multi-dio approach to feature generation. This philosophy coupled with the appropriaie *tf,aatim function results in a recognizer which has both high accuracy and good-'et-cc behavior. This allows it to be used in higher level digit string and word ggliti@ algorithms which search for digit/character boundaries. Tests of the GSC Ner oD standard digit, character and non-character databases are reported. L htroduction lfuy different approaches have been used by researchers to solve the problem of machine qn end character recognition [Suen92]. These approaches have included investigations of: t&re seb [Srik93] Man86], classifier algorithms, multiple combinations of classifrers tltogSl and novel statistical methods [Klein93]. There can be much overlap between Cftreot methods and a precise taxonomy can prove difficutt. It would be safe to say that thc pecise classification of an algorithm has much to do with the perspective of the Lrwstigator during the design of the algorithm. lvtany different algorithms have been explored by the researchers at CEDAR tlee93l. These algorithms have encompassed a wide range of feature and classifier t1pes. Brcry algorithm has characteristics, such as high speed, high accuracy, good thresholding rbility, and generalization, which are useful for specific applications. Examplas of classifiers &veloped at CEDAR are listed in Table 1. This paper will outline the philosophical and Fcticsl deta'ls of one these classifiers: the Gradient, structural, concavity (GSC) cl'sifier. 2" Philosophy Tbe approach used in designing the GSC was based on the observation that feature sets can be designed to extact certain tlpes of information from the image. Feature detectors can be built to detect the local, intermediate and global feaares of an image. The basic unit of an image is the pixel and we are interested in both is location (x,y coordinate) and the relationship of the pixel to its neighbors at different ranges from locally and globally. This
Efficient counting of models for boolean formulas represented by embedded cycles

To compute the number of models of a 2-CF (conjunction of clauses with two literals at most), the well-known problem as #2-SAT, is a classical #P-complete problem. We show here an extensive class of instances of 2CF’s where to compute the number of models can be done
Etiology and pathogenesis of traumatic dental injuries. A clinical study of 1,298 cases.

Abstract— The etiology and pathogenesis of traumatic dental injuries were studied on the basis of a hospital material of 1,298 patients (908 males and 390 females). A total number of 3,026 injured teeth were treated, including 787 primary and 2,239 permanent teeth. Repeated dental injuries were found in 24 % of the cases. All traumas were classified according to the type of injury affecting the lips, oral mucosa, tooth-supporting structures, and hard dental tissues. The type of injury seems to be related to the dentition, with traumas predominantly involving the tooth supporting structures in the primary dentition. The origin of trauma was allotted into 9 groups, partly on the basis of a presumed difference in energy of the impact as well as a difference in the resiliency of the impact. A statistical analysis revealed significant differences in the injury pattern between the different trauma groups. The relation between lip injuries and injuries to tooth or tooth-supporting structures was analyzed separately. It appeared from this analysis that the lips may act as an impact absorber reducing the chance of brown fracture and increasing the risk of luxation and alveolar fracture.
Quantitative Immobilization of Phthalocyanine onto Bacterial Cellulose for Construction of a High-Performance Catalytic Membrane Reactor

We report the fabrication of a tetra-amino cobalt (II) phthalocyanine (CoPc)-immobilized bacterial cellulose (BC) functional nanocomposite, CoPc@BC, by quantitative immobilization of CoPc onto a BC membrane. Lab-cultured BC was oxidized by NaIO4 to generate aldehyde groups on BC for the subsequent CoPc immobilization, the processing conditions were optimized by monitoring both the generated aldehyde content and the resulting CoPc loading. X-ray photoelectron spectroscopy (XPS) was employed to characterize the change of the element bonding environment during the functionalization processes. The CoPc@BC functional nanocomposite was utilized for the treatment of reactive red X-3B dye wastewater. The CoPc molecules in the CoPc@BC nanocomposite can function as an “antenna” to adsorb the target anionic dye molecules, the adsorption takes place both on the surface and in the interior of CoPc@BC. A catalytic membrane reactor (CMR) was assembled with the CoPc@BC nanocomposite, the performance of CMR was evaluated based on the catalytic oxidation behavior of reactive red X-3B, with H2O2 as an oxidant. Highly-reactive hydroxyl radical (OH) was involved in the catalytic oxidation process, as detected by electron paramagnetic resonance (EPR). Under optimal operating conditions of a flow rate of 6 mL/min, a reaction temperature of 50 °C, and an H2O2 concentration of 10 mmol/L, the decoloration rate of CMR was as high as 50 μmol⋅min−1⋅g−1.
The Domination Heuristic for LP-type Problems

Certain geometric optimization problems, for example finding the smallest enclosing ellipse of a set of points, can be solved in linear time by simple randomized (or complicated deterministic) combinatorial algorithms. In practice, these algorithms are enhanced or replaced with heuristic variants that are faster but do not come with a theoretical runtime guarantee. In this paper, we introduce a new speed-up heuristic that can easily be integrated into the known linear-time algorithms, without decreasing their worst-case performance. The heuristic can actually be defined for every problem in the well-known abstract class of LP-type problems; its effectiveness in practice depends on whether and how fast the heuristic can be implemented for the specific problem at hand, and on whether the input distribution is favorable. We provide test results showing that for two concrete problems, the new heuristic may lead to significant speedups compared to state-of-the-art implementations that are available in the Computational Geometry Algorithms Library CGAL.
Intercellular Communication Within the Rat Anterior Pituitary: XIV Electron Microscopic and Immunohistochemical Study on the Relationship Between the Agranular Cells and GnRH Neurons in the Dorsal Pars Tuberalis of the Pituitary Gland

Although numerous investigators in 1970s to 1980s have reported the distribution of LH‐RH nerve fibers in the median eminence, a few LH‐RH fibers have been shown to be present in the pars tuberalis. The significance of the finding remains to be elucidated, and there are few studies on the distribution of LH‐RH neurons in the pars tuberalis, especially in the dorsal pars tuberalis (DPT). Adult male Wistar‐Imamichi rats were separated into two groups: one for electron microscopy and the other for immunohistochemistry to observe LH‐RH and neurofilaments. Pituitary glands attached to the brain were fixed by perfusion, and the sections were prepared parallel to the sagittal plane. The typical glandular structure of the pars tuberalis was evident beneath the bottom floor of the third ventricle, and the thick glandular structure was present in the foremost region. Closer to the anterior lobe, the glandular structure changed to be a thin layer, and it was again observed at the posterior portion. Then the pituitary stalk was surrounded with the dorsal, lateral, and ventral pars tuberalis. LH‐RH and neurofilaments fibers were noted in the bottom floor, and some of them vertically descended to the gland. Adjacent to the glandular folliculostellate cells in the pars tuberalis, Herring bodies with numerous dense granules invading into the gland were present between the pituitary stalk and DPT. It was postulated that the “message” carried by LH‐RH might have been transmitted to the cells in the DPT to aid in the modulation of LH release. Anat Rec, 290:1388–1398, 2007. © 2007 Wiley‐Liss, Inc.
Improving broadcast news transcription by lightly supervised discriminative training

We present our experiments on lightly supervised discriminative training with large amounts of broadcast news data for which only closed caption transcriptions are available (TDT data). In particular, we use language models biased to the closed-caption transcripts to recognise the audio data, and the recognised transcripts are then used as the training transcriptions for acoustic model training. A range of experiments that use maximum likelihood (ML) training as well as discriminative training based on either maximum mutual information (MMI) or minimum phone error (MPE) are presented. In a 5xRT broadcast news transcription system that includes adaptation, it is shown that reductions in word error rate (WER) in the range of 1% absolute can be achieved. Finally, some experiments on training data selection are presented to compare different methods of "filtering" the transcripts.