Miracle-dz/UniFAR-FTUs huggingface dataset:
Convex shape decomposition

In this paper, we propose a new shape decomposition method, called convex shape decomposition. We formalize the convex decomposition problem as an integer linear programming problem, and obtain approximate optimal solution by minimizing the total cost of decomposition under some concavity constraints. Our method is based on Morse theory and combines information from multiple Morse functions. The obtained decomposition provides a compact representation, both geometrical and topological, of original object. Our experiments show that such representation is very useful in many applications.
Exopolysaccharide Biosynthesis Enables Mature Biofilm Formation on Abiotic Surfaces by Herbaspirillum seropedicae

H. seropedicae associates endophytically and epiphytically with important poaceous crops and is capable of promoting their growth. The molecular mechanisms involved in plant colonization by this microrganism are not fully understood. Exopolysaccharides (EPS) are usually necessary for bacterial attachment to solid surfaces, to other bacteria, and to form biofilms. The role of H. seropedicae SmR1 exopolysaccharide in biofilm formation on both inert and plant substrates was assessed by characterization of a mutant in the espB gene which codes for a glucosyltransferase. The mutant strain was severely affected in EPS production and biofilm formation on glass wool. In contrast, the plant colonization capacity of the mutant strain was not altered when compared to the parental strain. The requirement of EPS for biofilm formation on inert surface was reinforced by the induction of eps genes in biofilms grown on glass and polypropylene. On the other hand, a strong repression of eps genes was observed in H. seropedicae cells adhered to maize roots. Our data suggest that H. seropedicae EPS is a structural component of mature biofilms, but this development stage of biofilm is not achieved during plant colonization.
A Biomechanical Analysis of the Crural Fascia in the Feline Hindlimb during Locomotion and Intra-muscular Stimulation

PURPOSE It has been shown that by carefully removing the crural fascias attachment to the calcaneus approximately half the torque produced by the posterior Biceps Femoris (pBF) was lost [1, 2, 3]. Therefore, our objective is to quantify and characterize the role of the crural fascia in transmitting forces from muscles across joints thereby exploring its role in intra-limb coordination and stability. We hypothesize that the crural fascia redirects some of the force produced by the hip extensors and knee flexors to the ankle joint. APPROACH The crural fascia in the feline hindlimb initiates from the hip flexor/knee extensor muscles, surrounds the triceps surae muscles as a sheath and inserts into the medial side of the calcaneus as two thickened bands. We investigated this anatomical connection in the decerebrate cat by systematically disrupting the crural fascia. In all experiments we recorded four conditions: 1, intact; 2, longitudinal split through the sheath; 3, randomized cut of the medial or lateral band; and 4, cutting of the remaining band. This was conducted in locomotion studies involving electromyography (EMG) and kinematic recordings, as well as intramuscular stimulation (IM Stim) experiments recording ground reaction forces in the x, y and z directions. RESULTS In the locomotion preparation we observed a decrease in EMG in the peroneus brevis muscle; and an increase in rotation of the tibia resulting in an eversion of the foot during swing phase. During IM Stim, the largest change in the force direction in the xy plane was seen when one band was disrupted in the gracilis, semimembranosis and posterior biceps femoris muscles. Upon disruption of both bands the end point force direction returned closer to the original direction. CONCLUSIONS The crural fascia contributes to the stability and constraining of the degrees of freedom at the ankle joint, as well as the transmission of force from hip extensors/knee flexors to the ankle joint. action of the hamstrings muscles at the feline ankle mediated by the crural fascia. torque produce by the cat hamstrings muscle about the andle as a function of hindlimb position.
A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.

Comparative analysis is one of the most powerful methods available for understanding the diverse and complex systems found in biology, but it is often limited by a lack of comprehensive taxonomic sampling. Despite the recent development of powerful genome technologies capable of producing sequence data in large quantities (witness the recently completed first draft of the human genome), there has been relatively little change in how evolutionary studies are conducted. The application of genomic methods to evolutionary biology is a challenge, in part because gene segments from different organisms are manipulated separately, requiring individual purification, cloning, and sequencing. We suggest that a feasible approach to collecting genome-scale data sets for evolutionary biology (i.e., evolutionary genomics) may consist of combination of DNA samples prior to cloning and sequencing, followed by computational reconstruction of the original sequences. This approach will allow the full benefit of automated protocols developed by genome projects to be realized; taxon sampling levels can easily increase to thousands for targeted genomes and genomic regions. Sequence diversity at this level will dramatically improve the quality and accuracy of phylogenetic inference, as well as the accuracy and resolution of comparative evolutionary studies. In particular, it will be possible to make accurate estimates of normal evolution in the context of constant structural and functional constraints (i.e., site-specific substitution probabilities), along with accurate estimates of changes in evolutionary patterns, including pairwise coevolution between sites, adaptive bursts, and changes in selective constraints. These estimates can then be used to understand and predict the effects of protein structure and function on sequence evolution and to predict unknown details of protein structure, function, and functional divergence. In order to demonstrate the practicality of these ideas and the potential benefit for functional genomic analysis, we describe a pilot project we are conducting to simultaneously sequence large numbers of vertebrate mitochondrial genomes.
1 2 3 A Hybrid MPI / OpenMP Parallel Algorithm and Performance Analysis for an Ensemble 4 Square Root Filter Designed for Multi-scale Observations 5 6

31 A hybrid parallel scheme for the ensemble square root filter (EnSRF) suitable for parallel 32 assimilation of multi-scale observations including those from dense observational networks such 33 as those of radar is developed based on the domain decomposition strategy. The scheme handles 34 inter-node communication through message passing interface (MPI), and the communication 35 within shared-memory nodes via Open Multi-Processing (OpenMP) threads; it also supports pure 36 MPI and pure OpenMP modes. The parallel framework can accommodate high-volume remote-37 sensed radar (or satellite) observations as well as conventional observations that usually have 38 larger covariance localization radii. 39 The performance of the parallel algorithm has been tested with simulated and real radar 40 data. The parallel program shows good scalability in pure MPI and hybrid MPI/OpenMP modes, 41 while pure OpenMP runs exhibit limited scalability on a symmetric shared-memory system. It is 42 found that in MPI mode, better parallel performance is achieved with domain decomposition 43 configurations in which the leading dimension of the state variable arrays is larger, because this 44 configuration allows for more efficient memory access. Given a fixed amount of computing 45 resources, the hybrid parallel mode is preferred to pure MPI mode on supercomputers with nodes 46 containing shared-memory cores. The overall performance is also affected by factors such as the 47 cache size, memory bandwidth, and the networking topology. Tests with a real data case with a 48 large number of radars confirm that the parallel data assimilation can be done on a multi-core 49 supercomputer with a significant speedup compared to the serial data assimilation algorithm.
Efficacy of Cox Maze IV Procedure Using Argon-Based Cryoablation: A Comparative Study with N2O-Based Cryoablation

Background We compared the mid-term results of the Cox maze IV procedure using argon-based cryoablation with a procedure using N2O-based cryoablation. Methods From May 2006 to June 2012, 138 patients (mean age, 58.2±11.0 years) underwent the Cox maze IV procedure. Eighty-five patients underwent the maze procedure using an N2O-based cryoprobe (group N), and 53 patients underwent the maze procedure using an argon-based cryoprobe (group A). Bipolar radiofrequency ablation was concomitantly used in 131 patients. The presence of atrial fibrillation immediately, 6 months, 1 year, and 2 years after surgery was compared. Results Early mortality occurred in 6 patients (4.3%). There were no differences in early mortality or postoperative complications between the two groups. Nineteen of 115 patients (16.5%) remained in atrial fibrillation at postoperative 12 months (14 of 80 patients (17.5%) in group N and 5 of 35 patients (14.3%) in group A, p=0.669). There were no differences in the number of patients who remained in atrial fibrillation at any of the time periods except in the immediate postoperative period. A multivariable analysis revealed that the energy source of cryoablation was not associated with the presence of atrial fibrillation at 1 year (p=0.862) and that a fine F wave (<0.1 mV) was the only risk factor predicting the presence of atrial fibrillation at 1 year (p<0.001, odds ratio=20.287). Conclusion The Cox maze IV procedure using an argon-based cryoprobe was safe and effective compared with the maze procedure using an N2O-based cryoprobe in terms of operative outcomes and the restoration of sinus rhythm for up to 2 years after surgery.
On the entropy of four-dimensional near-extremal N = 2 black holes with R2-terms

We consider the entropy of four-dimensional near-extremal N = 2 black holes. The Bekenstein-Hawking entropy formula has the structure of the extremal black holes entropy with a shift of the charges depending on the non-extremality parameter and the moduli at infinity. We construct a class of near-extremal horizon solutions with R2-terms, and show that the generalized Wald entropy formula exhibits the same property.
The Case for Partitioning Virtual Machines on Multicore Architectures

In this paper we argue that partitioning is required for attaining the best performance of scientific applications when running on virtual machines. Current memory management and I/O handling techniques introduce high overhead when running scientific applications. Using KVM, we quantify this impact on applications written in multiple paradigms: message passing, shared memory and partitioned global address spaces. Our analysis shows that on NUMA systems, current memory translation schemes cannot preserve the locality of access and introduce up to 82 percent slowdown. We discuss the interaction between contemporary OS and VM architectures and argue that partitioning is the best solution to enforce memory locality. Current I/O solutions using one assistant task cannot provide the level of I/O parallelism required by scientific applications and we observe an average 7.2 × application slowdown on a cluster with 16 cores per node. More specialized solutions that implement shared memory by-pass within the communication stack also do not scale well with cores and we observe an average 2.4 × application slowdown. Overall, our results indicate that using partitioning and direct inter-VM shared memory support is enough to provide close to native performance in multicore clusters.
Analysis and Comparing of the Complexity Distributions of Precipitation in Two Typical Regions in Changing Environment, China

The environment have varied sharply since 1980s in China owing to the influence of climate change and human activities, which makes precipitation process become more and more nonlinear and dynamic and hard to be described. The fractal dimension is a fit index to describe the complexity of the hydrologic series quantitatively and Wavelet Transform is a feasible method for the study of the nonlinear and dynamic process. Using the fractal dimension based on Continuous Wavelet Transform (CWT), the complexity distributions of different precipitation process of which is from 1980 to 2000 in Hand an and the other is from 1980 to 2009 in Qilijie basin, are illuminated respectively in this study. The result indicates that the precipitation process since 1980s in Qilijie basin is more complex than that in Hand an and the fractal dimension of the precipitation in urban area is lager than that in other areas both in two typical regions. This study can provide technical guidance for the research of hydrologic system and reference for water management in the local region.
Age-Related Differences in Associative Learning of Landmarks and Heading Directions in a Virtual Navigation Task

Previous studies have showed that spatial memory declines with age but have not clarified the relevance of different landmark cues for specifying heading directions among different age groups. This study examined differences between younger, middle-aged and older adults in route learning and memory tasks after they navigated a virtual maze that contained: (a) critical landmarks that were located at decision points (i.e., intersections) and (b) non-critical landmarks that were located at non-decision points (i.e., the sides of the route). Participants were given a recognition memory test for critical and non-critical landmarks and also given a landmark-direction associative learning task. Compared to younger adults, older adults committed more navigation errors during route learning and were poorer at associating the correct heading directions with both critical and non-critical landmarks. Notably, older adults exhibited a landmark-direction associative memory deficit at decision points; this was the first finding to show that an associative memory deficit exist among older adults in a navigational context for landmarks that are pertinent for reaching a goal, and suggest that older adults may expend more cognitive resources on the encoding of landmark/object features than on the binding of landmark and directional information. This study is also the first to show that older adults did not have a tendency to process non-critical landmarks, which were regarded as distractors/irrelevant cues for specifying the directions to reach the goal, to an equivalent or larger extent than younger adults. We explain this finding in view of the low number of non-critical cues in our virtual maze (relative to a real-world urban environment) that might not have evoked older adults’ usual tendency toward processing or encoding distractors. We explain the age differences in navigational and cognitive performance with regards to functional and structural changes in the hippocampus and parahippocampus, and recommend further investigations into the functional connectivity between the prefrontal cortex and hippocampus for a better understanding of the landmark-direction associative learning among the elderly. Finally, it is hoped that the current behavioral findings will facilitate efforts to identify the neural markers of Alzheimer’s disease, a disease that commonly involves navigational deficits.
Security models and information flow

A theory of information flow is developed that differs from that of nondeducibility, which is seen to be a theory of information sharing. The theory is used to develop a flow-based security model (FM) and to show that the proper treatment of security-relevant causal factors in such a framework is very tricky. Using FM as a standard for comparison, an examination is made of interference, generalized noninterference, and extensions to noninterference designed to protect high-level output, and it is seen that the proper treatment of causal factors in such models requires programs to be considered as explicit input to systems. This gives a new perspective on security levels. The model of D.E. Bell and L.J. LaPadula (1973), on the other hand, more successfully models security-relevant causal information, although this success is bought at the expense of the model being vague about its primitives. This vagueness is examined with respect to the claim that the Bell-LaPadula model and noninterference are equivalent. <<ETX>>
On Lyapunov sampling for event-driven controllers

This paper investigates an event condition for event-driven controllers based on Lyapunov functions. Considering that constant values of a Lyapunov function define contour curves that form closed regions around the equilibrium point, in this paper we present a sampling mechanism that enforces job executions (sampling, control algorithm computation and actuation) each time the system trajectory reaches a given contour curve. By construction, the sequence of generated samples is stable in the discrete Lyapunov sense. However, in order to ensure that the system trajectory will tend to zero as time tends to infinity, it must be ensured that the sequence of samples is infinite. We provide conditions to ensure this property. The approach is illustrated by simulated examples.
The adhesion molecule on glia (AMOG) incorporated into lipid vesicles binds to subpopulations of neurons

To investigate the functional role of the novel adhesion molecule on glia (AMOG) in cell surface interactions, immunoaffinity-purified AMOG was incorporated into liposomes and measured for its ability to bind to cells in monolayer cultures. AMOG could be incorporated into liposomes in functionally active form after solubilization from membranes in 1% cholate buffer containing soybean lecithin, elution from the AMOG monoclonal antibody column with 4 M MgCl2, containing 1% octylglucoside, and removal of detergent for liposome incorporation by gel filtration. AMOG-containing liposomes bound to neurons, but not to oligodendrocytes, astrocytes, or fibroblasts in early postnatal cerebellar cultures. AMOG-containing liposomes also bound to the pheochromocytoma cell line PC12, but not to neurons in cultures of spinal cord and dorsal root ganglia after various times in vitro. Fab fragments of monoclonal AMOG antibodies, but not of L3 monoclonal antibodies directed against a carbohydrate structure on AMOG, inhibited binding of liposomes. Liposome binding was not reduced by preincubation of cerebellar cells with antibodies to AMOG, to the neuron adhesion molecule L1, the neural cell adhesion molecule N-CAM, or the L3 carbohydrate structure, nor with 2 monoclonal antibodies reacting with neuronal cell surface glycoproteins related to the L2/HNK-1 family. These results show that AMOG is indeed a ligand in adhesion and binds to particular subpopulations of neurons in L1- and N-CAM-independent mechanisms.
Attenuation of Tick-Borne Encephalitis Virus by Structure-Based Site-Specific Mutagenesis of a Putative Flavivirus Receptor Binding Site

ABSTRACT The impact of a specific region of the envelope protein E of tick-borne encephalitis (TBE) virus on the biology of this virus was investigated by a site-directed mutagenesis approach. The four amino acid residues that were analyzed in detail (E308 to E311) are located on the upper-lateral surface of domain III according to the X-ray structure of the TBE virus protein E and are part of an area that is considered to be a potential receptor binding determinant of flaviviruses. Mutants containing single amino acid substitutions, as well as combinations of mutations, were constructed and analyzed for their virulence in mice, growth properties in cultured cells, and genetic stability. The most significant attenuation in mice was achieved by mutagenesis of threonine 310. Combining this mutation with deletion mutations in the 3′-noncoding region yielded mutants that were highly attenuated. The biological effects of mutation Thr 310 to Lys, however, could be reversed to a large degree by a mutation at a neighboring position (Lys 311 to Glu) that arose spontaneously during infection of a mouse. Mutagenesis of the other positions provided evidence for the functional importance of residue 308 (Asp) and its charge interaction with residue 311 (Lys), whereas residue 309 could be altered or even deleted without any notable consequences. Deletion of residue 309 was accompanied by a spontaneous second-site mutation (Phe to Tyr) at position 332, which in the three-dimensional structure of protein E is spatially close to residue 309. The information obtained in this study is relevant for the development of specific attenuated flavivirus strains that may serve as future live vaccines.
Using Immune Marker Panels to Evaluate the Role of Inflammation in Cancer: Summary of an NCI-Sponsored Workshop

Chronic inflammation is recognized to play a role in the development of several cancers. Past investigations of inflammation and cancer have typically been small, used varied assay platforms, and included a narrow range of analytes. Multiplex technologies have now been developed to measure larger numbers of inflammatory markers using small volumes of specimens. This has created an opportunity for systematic, large-scale epidemiologic studies to evaluate the role of inflammation in cancer. However, lack of consensus on the approach to these studies, the technologies/assays to be used, and the most adequate analysis/interpretation of findings have thus far hindered progress. In June 2014, the National Cancer Institute (Bethesda, MD) convened a workshop involving epidemiologists, immunologists, statisticians, and laboratory biologists to share their experiences with new inflammation marker technologies and findings from association studies using such methods and technologies (http://epi.grants.cancer.gov/workshops/). Consensus and gaps in our understanding of the role of chronic inflammation in cancer were identified and recommendations were made to improve future efforts in this area. These recommendations are summarized herein, along with specific suggestions for how they may be implemented. By facilitating discussions among various groups and encouraging interdisciplinary collaborations, we anticipate that the pace of research in this field will be accelerated and duplication of efforts can be minimized. Cancer Epidemiol Biomarkers Prev; 24(9); 1427–33. ©2015 AACR.