Miracle-dz/UniFAR-FTUs huggingface dataset:
The ARTS web server for aligning RNA tertiary structures

RNA molecules with common structural features may share similar functional properties. Structural comparison of RNAs and detection of common substructures is, thus, a highly important task. Nevertheless, the current available tools in the RNA community provide only a partial solution, since they either work at the 2D level or are suitable for detecting predefined or local contiguous tertiary motifs only. Here, we describe a web server built around ARTS, a method for aligning tertiary structures of nucleic acids (both RNA and DNA). ARTS receives a pair of 3D nucleic acid structures and searches for a priori unknown common substructures. The search is truly 3D and irrespective of the order of the nucleotides on the chain. The identified common substructures can be large global folds with hundreds and even thousands of nucleotides as well as small local motifs with at least two successive base pairs. The method is highly efficient and has been used to conduct an all-against-all comparison of all the RNA structures in the Protein Data Bank. The web server together with a software package for download are freely accessible at .
A Factorial Space for a System-Based Detection of Botcloud Activity

Today, beyond a legitimate usage, the numerous advantages of cloud computing are exploited by attackers, and Botnets supporting DDoS attacks are among the greatest beneficiaries of this malicious use. Such a phenomena is a major issue since it strongly increases the power of distributed massive attacks while involving the responsibility of cloud service providers that do not own appropriate solutions. In this paper, we present an original approach that enables a source-based de- tection of UDP-flood DDoS attacks based on a distributed system behavior analysis. Based on a principal component analysis, our contribution consists in: (1) defining the involvement of system metrics in a botcoud's behavior, (2) showing the invariability of the factorial space that defines a botcloud activity and (3) among several legitimate activities, using this factorial space to enable a botcloud detection.
Emerging Concepts in Transesophageal Echocardiography

Introduced in 1977, transesophageal echocardiography (TEE) offered imaging through a new acoustic window sitting directly behind the heart, allowing improved evaluation of many cardiac conditions. Shortly thereafter, TEE was applied to the intraoperative environment, as investigators quickly recognized that continuous cardiac evaluation and monitoring during surgery, particularly cardiac operations, were now possible. Among the many applications for perioperative TEE, this review will focus on four recent advances: three-dimensional TEE imaging, continuous TEE monitoring in the intensive care unit, strain imaging, and assessment of diastolic ventricular function.
Light paths in retinal vessel oximetry

The oxygen utilization and, therefore, the metabolic state, of a distinctive area of the retina may be calculated from the diameter of the supplying artery and vein, the haemoglobin oxygenation, and the velocity of the blood. The first two parameters can be determined by imaging spectrometry at the patients ocular fundus. However the reflected light emerging from a vessel followed different pathways through the ocular fundus layers and the vessel embedded in the retina. The contribution of the single pathways to the vessel reflection profile is investigated by a Monte Carlo simulation. Considering retinal vessels with diameters of 25-200 /spl mu/m we found the reflection from a thin vessel to be determined by the single and double transmission of light at 560 nm. The backscattering from the blood column determines the reflectance in the case of a thick vessel. However, both components are in the same order of magnitude. This has to be considered in the calculation of the oxygen saturation of blood in retinal vessels from their reflection spectra.
Subcortical Deep Gray Matter Pathology in Patients with Multiple Sclerosis Is Associated with White Matter Lesion Burden and Atrophy but Not with Cortical Atrophy: A Diffusion Tensor MRI Study

BACKGROUND AND PURPOSE: The association between subcortical deep gray matter, white matter, and cortical pathology is not well understood in MS. The aim of this study was to use DTI to investigate the subcortical deep gray matter alterations and their relationship with lesion burden, white matter, and cortical atrophy in patients with MS and healthy control patients. MATERIALS AND METHODS: A total of 210 patients with relapsing-remitting MS, 75 patients with progressive MS, and 110 healthy control patients were included in the study. DTI metrics in whole brain, normal-appearing white matter, normal-appearing gray matter, and subcortical deep gray matter structures were compared. The association between DTI metrics of the subcortical deep gray matter structures with lesion burden, normalized white matter volume, and normalized cortical volume was investigated. RESULTS: DTI measures were significantly different in whole brain, normal-appearing white matter, and normal-appearing gray matter among the groups (P < .01). Significant differences in DTI diffusivity of total subcortical deep gray matter, caudate, thalamus, and hippocampus (P < .001) were found. DTI diffusivity of total subcortical deep gray matter was significantly associated with normalized white matter volume (P < .001) and normalized cortical volume (P = .033) in healthy control patients. In both relapsing and progressive MS groups, the DTI subcortical deep gray matter measures were associated with the lesion burden and with normalized white matter volume (P < .001), but not with normalized cortical volume. CONCLUSIONS: These findings suggest that subcortical deep gray matter abnormalities are associated with white matter lesion burden and atrophy, whereas cortical atrophy is not associated with microstructural alterations of subcortical deep gray matter structures in patients with MS.
Helicobacter pylori babA2 Positivity Predicts Risk of Gastric Cancer in Ardabil, a Very High-Risk Area in Iran.

BACKGROUND Ardabil, a Northwestern province of Iran, was found to have the highest rate of gastric cancer (GC) in the country (ASRs = 51.8/100,000 for males and 24.9/100,000 for females) and one of the highest gastric cardia cancer rates in the world. The aim of the present study was to assess the associations of the cagA and babA2 status of Helicobacter pylori with GC in the Ardabil population. MATERIALS AND METHODS A total of 103 patients with non-atrophic gastritis (56) and GC (47), who underwent endoscopy at the Imam Khomeini Hospital in Ardabil, were assessed. The status of 16S rDNA, cagA and babA2 genes was determined using PCR and histopathological assessment was performed. RESULTS The following genotypic frequency was observed: cagA+ (50.6%), cagA- (49.4%), babA2+ (26.5%), babA2- (73.5%) cagA+/babA2+ (19.3%), cagA-/babA2+ (7.2%), cagA+/babA2- (31.3%), cagA-/babA2- (42.2%). Although the frequency of the cagA+, cagA+/babA2+ and cagA-/ babA2+ genotypes in patients with GC (55.6%, 25.9%, and 14.8%, respectively) was higher than in those with NAG (48.2%, 16.1%, and 3.6%, respectively), the difference did not reach significance. In contrast, the presence of the babA2 gene (40.7% vs 19.6%) significantly increased the risk of GC; the age-sex-adjusted odds ratio (95% confidence interval) was 5.068 (1.506-17.058; P=0.009), by multiple logistic regression. CONCLUSIONS It is proposed that the H. pylori babA2 positivity might be considered as an important determinant of GC risk in Ardabil.
Auxin Influx Carrier AUX1 Confers Acid Resistance for Arabidopsis Root Elongation Through the Regulation of Plasma Membrane H+-ATPase

Abstract The plant plasma membrane (PM) H+-ATPase regulates pH homeostasis and cell elongation in roots through the formation of an electrochemical H+ gradient across the PM and a decrease in apoplastic pH; however, the detailed signaling for the regulation of PM H+-ATPases remains unclear. Here, we show that an auxin influx carrier, AUXIN RESISTANT1 (AUX1), is required for the maintenance of PM H+-ATPase activity and proper root elongation. We isolated a low pH-hypersensitive 1 (loph1) mutant by a genetic screen of Arabidopsis thaliana on low pH agar plates. The loph1 mutant is a loss-of-function mutant of the AUX1 gene and exhibits a root growth retardation restricted to the low pH condition. The ATP hydrolysis and H+ extrusion activities of the PM H+-ATPase were reduced in loph1 roots. Furthermore, the phosphorylation of the penultimate threonine of the PM H+-ATPase was reduced in loph1 roots under both normal and low pH conditions without reduction of the amount of PM H+-ATPase. Expression of the DR5:GUS reporter gene and auxin-responsive genes suggested that endogenous auxin levels were lower in loph1 roots than in the wild type. The aux1-7 mutant roots also exhibited root growth retardation in the low pH condition like the loph1 roots. These results indicate that AUX1 positively regulates the PM H+-ATPase activity through maintenance of the auxin accumulation in root tips, and this process may serve to maintain root elongation especially under low pH conditions.
Security Analysis of the Lightweight Cryptosystem TWINE in the Internet of Things

The TWINE is a new Generalized Feistel Structure (GFS) lightweight cryptosystem in the Internet of Things. It has 36 rounds and the key lengths support 80 bits and 128 bits, which are flexible to provide security for the RFID, smart cards and other highly-constrained devices. Due to the strong attacking ability, fast speed, simple implementation and other characteristics, the differential fault analysis has become an important method to evaluate the security of lightweight cryptosystems. On the basis of the 4-bit fault model and the differential analysis, we propose an effective differential fault attack on the TWINE cryptosystem. Mathematical analysis and simulating experiments show that the attack could recover its 80-bit and 128-bit secret keys by introducing 8 faulty ciphertexts and 18 faulty ciphertexts on average, respectively. The result in this study describes that the TWINE is vulnerable to differential fault analysis. It will be beneficial to the analysis of the same type of other iterated lightweight cryptosystems in the Internet of Things.
Violent Video Games and Children’s Aggressive Behaviors

The literature provides some evidence that the use of violent video games increases the risk for young people to develop aggressive cognitions and even behaviors. We aimed to verify whether exposure to violent video games is linked to problems of aggression in a sample of Italian children. Four questionnaires were administered to 346 children between 7 and 14 years of age, attending primary and secondary schools in Northern Italy. Variables measured were externalization, quality of interpersonal relationships, aggression, quality of coping strategies, and parental stress. Participants who preferred violent games showed higher scores for externalization and aggression. The use of violent video games and age were linked to higher levels of aggression, coping strategies, and the habitual video game weekly consumption of participants. Our data confirm the role of violent video games as risk factors for problems of aggressive behavior and of externalization in childhood and early adolescence.
Usefulness of Myocardial Contrast Echocardiography Early After Acute Myocardial Infarction

Objectives: (1) Evaluate wall motion and perfusion abnormalities after reperfusion therapy of the culprit lesion, (2) delineate the ability of myocardial contrast echocardiography (MCE) to evaluate the microvasculature after reperfusion, in order to distinguish between stunning and necrosis in the risk area. Methods: We analyzed 446 segments from 28 patients, 10 normal controls (160 segments), and 18 with a first AMI (286 segments). MCE was obtained with Optison and a two‐dimensional echocardiography was performed at 3 months post acute myocardial infarction (AMI). Results: In the group with AMI, we analyzed 286 segments, of which 107 had wall motion abnormalities (WMA) related to the culprit artery. Two subgroups were identified: Group I with WMA and normal perfusion (50 segments, 47%) and Group II with WMA and perfusion defects (57 segments, 53%). According to the 2D echocardiogram at 3 months, they were further subdivided into: Group IA: with wall motion improvement (stunning): 18 segments, 36%, Group IB: without wall motion improvement: 32 segments, 64%, Group IIA: with wall motion improvement: 12 segments, 21%, Group IIB: without wall motion improvement (necrosis): 45 segments, 79%. Conclusions: (1) The presence of myocardial perfusion in segments with WMA immediately after AMI reperfusion therapy predicts viability in most patients. Conversely, the lack of perfusion is not an absolute indicator of the presence of necrosis. (2) Perfusion defects allow to detect patients with thrombolysis in myocardial infarction (TIMI) 3 flow and “no‐reflow” phenomenon who will not show improved wall motion in the 2D echocardiogram. However, some patients with initial no‐reflow could have microvascular stunning and their regional contractile function will normalize after a recovery period.
Transition of Children With Autism From Intensive Behavioural Intervention Programs Into the School System

This study concerns the issue of the transition of children with autism from intensive behavioural intervention (IBI) programs to school. Literature on the transition of children with autism is sparse, and anecdotal evidence suggests there are significant challenges. The current study used survey methodology to examine the beliefs of IBI program and school system staff about this transition, and the similarities and differences between their beliefs and experiences. It was found that, in some respects, the transition beliefs of the two groups were similar. However, there were notable differences between the ideal views of transition processes and actual experiences of participants in both groups, as well as some barriers to the process. Directions for future research and implications for practice are discussed. This study concerned the issue of transition of children with autism from Intensive Behavioural Intervention (IBI) programs into the school system. Transition to school is a significant event for all children and their families. Studies have shown that some children may experience increased stress levels and somatic and psychological symptoms during the transition to school. This time is also stressful for parents as this is often the first time that a large part of their child's day is organized without their input (Pianta & Kraft-Sayre, 2003). For children with developmental disabilities (DD) and their parents, this transition can be even more stressful. In addition to the concerns cited above, these parents and their children are faced with additional challenges, such as navigating the Individualized Placement and Review Process of the Ontario education system and ensuring appropriate services within the school system (Hundert, 2004). In light of these challenges, the Ministry of Education in Ontario has specific
Stochastic-Deterministic Multipath Model for Time-Delay Estimation

Line-of-sight (LOS) delay estimation in multipath scenarios is a central problem in global navigation satellite systems (GNSS). Deterministic channel models can be used to describe the multipath environment, but this usually requires the estimation of several nuisance parameters. In order to avoid this effort, stochastic channel models can be used. In this case the multipath statistics have to be estimated. The correlated path (CP) model combines the two approaches, dividing the multipath signal into a part correlated with the LOS signal, and the rest as uncorrelated multipath interference. In an earlier version of the CP model the multipath interference was modeled as temporally white noise. This is not an accurate assumption however, especially in the case when a bank of correlators is used for signal compression. In this paper we derive the temporal covariance matrix of the multipath interference and show how the temporal multipath correlation can incorporated into the maximum-likelihood (ML) estimator of the CP model. Simulation results show that this new approach leads to better LOS timedelay estimation performance.
Bind: a Partitioned Global Workflow Parallel Programming Model

High Performance Computing is notorious for its long and expensive software development cycle. To address this challenge, we present Bind: a "partitioned global workflow" parallel programming model for C++ applications that enables quick prototyping and agile development cycles for high performance computing software targeting heterogeneous distributed many-core architectures. We present applications of Bind to Linear Algebra and MapReduce algorithms alongside with performance results.
Navigation function of mobile robots for formation driving

This paper investigates a vehicle formation control based on the following of a leader by nonholonomic mobile robots with two driving wheels. In this research, we propose a method for creating continuous and non-differentiable navigation functions, from which we derive a formation control law for each robot. The non-differentiability of the proposed navigation function removes the singularity encountered by conventional methods. The stability condition of a formation based on leader-following has been demonstrated by Tanner et al. as “Leader-to-Formation Stability” (LFS) [1]. In this paper, we assess the LFS property by regarding the navigation function as a LFS Lyapunov function.
Modified RECIST criteria for assessment of response in malignant pleural mesothelioma.

BACKGROUND The growth pattern of malignant pleural mesothelioma makes the use of RECIST (response evaluation criteria in solid tumours) response criteria difficult. We have developed and validated Modified RECIST criteria adapted to the growth pattern of malignant pleural mesothelioma. PATIENTS AND METHODS We evaluated 73 patients from two clinical trials of cisplatin/gemcitabine chemotherapy in malignant pleural mesothelioma. Tumour thickness perpendicular to the chest wall or mediastinum was measured in two positions at three separate levels on thoracic CT scans. The sum of the six measurements defined a pleural unidimensional measure. Bidimensionally measureable lesions were measured unidimensionally as for RECIST. All measurements were added to obtain the total tumour measurement. A reduction of at least 30% on two occasions 4 weeks apart defined a partial response; an increase of 20% over the nadir measurement, progressive disease. The validity of the modified criteria was gauged by evaluating survival and pulmonary function. RESULTS Response according to these criteria predicted for superior survival (15.1 versus 8.9 months; P = 0.03) and forced vital capacity (FVC) increase during treatment (P <0.0001). A significant correlation between change in linear tumour measurement and FVC was seen (R = 0.63; P = 0.0001). CONCLUSION These Modified RECIST criteria for tumour response correlate with survival and lung function and can be used to measure outcome in pleural mesothelioma.
A simulation platform for smart microgrids in university campuses

In this paper, a simulation platform for a smart microgrid configuration in a university campus is presented. The microgrid units include a photovoltaic installation, a battery energy storage system and an electricity energy management system. Sensitivity analysis is performed considering the impact of the developed model inputs, using as a test case one campus of the Democritus University of Thrace (DUTH) in Greece. The proposed platform can facilitate the analysis of crucial energy calculations in order to minimize electricity costs, optimize the size of the microgrid components, design of the campus energy management and load control operations. Additionally, it can be used as an educational tool, raising awareness among users on energy saving issues, the application of sustainable technologies and the incorporation of smart technologies in buildings. Finally, the developed campus model can be incorporated in studies of active distribution networks topologies, including demand response strategies, etc.
Resolving Bovine viral diarrhea virus subtypes from persistently infected U.S. beef calves with complete genome sequence

Bovine viral diarrhea virus (BVDV) is classified into 2 genotypes, BVDV-1 and BVDV-2, each of which contains distinct subtypes with genetic and antigenic variation. To effectively control BVDV by vaccination, it is important to know which subtypes of the virus are circulating and how their prevalence is changing over time. Accordingly, the purpose of our study was to estimate the current prevalence and diversity of BVDV subtypes from persistently infected (PI) beef calves in the central United States. Phylogenetic analysis of the 5′-UTR (5′ untranslated region) for 119 virus strains revealed that a majority (82%) belonged to genotype 1b, and the remaining strains were distributed between genotypes 1a (9%) and 2 (8%); however, BVDV-2 subtypes could not be confidently resolved. Therefore, to better define the variability of U.S. BVDV isolates and further investigate the division of BVDV-2 isolates into subtypes, complete genome sequences were obtained for these isolates as well as representatives of BVDV-1a and -1b. Phylogenetic analyses of the complete coding sequence provided more conclusive genetic classification and revealed that U.S. BVDV-2 isolates belong to at least 3 distinct genetic groups that are statistically supported by both complete and individual coding gene analyses. These results show that a more complex set of BVDV-2 subtypes has been circulating in this region than was previously thought.
Improving Effectiveness Through Strategic Planning

Nolen Ellison (1987) notes that community colleges have now entered the third stage of their development where the need is to develop a strategic agenda to deal with such critical issues as education for minority citizens, articulation between public schools and two-year colleges, economic and human resource development and literacy education. During the second stage community colleges pursued increases in enrollment both as a means of enhancing their visibility and importance within the educational world and as a means of increasing revenues, since their funding was closely tied to enrollments. In the 1 980s community colleges faced with threatened or actual reductions in enrollments, caps on funding and increasing pressures for accountability, have begun to examine questions of effectiveness. Such efforts have been strongly influenced by the concern with quality that has increasingly captured the public imagination as the nation has moved from an era whose primary concern was access into a time when there is a growing consensus that providing everyone with an opportunity to attend some form of postsecondary institution is no longer good enough. The questions of the 80s are: "Access to what? " and "With what outcomes? " This paper begins by reviewing concepts of effectiveness that appear in the literature to establish a context for a discussion of the changes that may be necessary as community colleges move from a focus on the number of students enrolled to increasing concern with institutional outcomes. The notion of organizational culture is then described as a way of defining the alternatives open to community colleges interested in improving their effectiveness. Finally, the paper describes a way of translating these concepts into institutional practice through identifying five strategies used by community colleges in their pursuit of increased effectiveness. In particular, the paper dwells upon strategic planning as a process that seems particularly well attuned to the types of changes institutions seek to make in the present environment.