Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Phylogeography of Two Crow Species: Jungle Crow Corvus macrorhynchos and Carrion Crow Corvus corone

The jungle crow Corvus macrorhynchos Wagler, 1827, and the carrion crow Corvus corone L. , 1758, are two closely related species with similar ecological requirements that occupy wide distribution ranges in the Palearctic. We studied patterns of their genetic variation by using sequences of the mitochondrial cytochrome b gene. Corvus macrorhynchos demonstrates a low level of variation and differentiation throughout its range, except for a highly diverged population of Cheju Island (Korea). The haplotype network shows two haplogroups. The island group comprises populations of Sakhalin, Hokkaido, Honshu, and Kyushu, while the haplotypes of Taiwan and Ryukyu Islands proved to be closer to the mainland group, which also includes populations from the Primorye, Khabarovsk, Amur, and Magadan regions in the Russian Far East. This pattern allowed us to develop a phylogeographic hypothesis regarding the two modes of settling of the island populations. Concerning C. corone, the presence of two distinct haplogroups was confirmed within the range of C. c. orientalis. Both haplogroups are found within the same populations in Kamchatka and North Sakhalin, which implies secondary contacts there. Populations of C. corone are found to be rather stable in the western parts of its range, while in the Far East populations experienced recent growth, as was observed for C. macrorhynchos in general. The two species appear to have passed through different evolutionary scenarios.
Automatic detection and correction of web application vulnerabilities using data mining to predict false positives

Web application security is an important problem in today's internet. A major cause of this status is that many programmers do not have adequate knowledge about secure coding, so they leave applications with vulnerabilities. An approach to solve this problem is to use source code static analysis to find these bugs, but these tools are known to report many false positives that make hard the task of correcting the application. This paper explores the use of a hybrid of methods to detect vulnerabilities with less false positives. After an initial step that uses taint analysis to flag candidate vulnerabilities, our approach uses data mining to predict the existence of false positives. This approach reaches a trade-off between two apparently opposite approaches: humans coding the knowledge about vulnerabilities (for taint analysis) versus automatically obtaining that knowledge (with machine learning, for data mining). Given this more precise form of detection, we do automatic code correction by inserting fixes in the source code. The approach was implemented in the WAP tool and an experimental evaluation was performed with a large set of open source PHP applications.
Livelihood decisions under the shadow of conflict in the Chittagong Hill Tracts of Bangladesh

We analyse rural household livelihood and children´s school enrollment decisions in a post-conflict setting in the Chittagong Hill Tracts region of Bangladesh. The innovation of the paper lies in the fact that we employ information about current subjective perceptions regarding the possibility of violence in the future and past actual experiences of violence to explain household economic decision-making. Preferences are endogenous in line with behavioural economics. Regression results show that heightened subjective perceptions of future violence and past actual experiences of conflict influences current consumption increases child enrollment, and encourages risky mixed crop cultivation. The trauma emanating from past experiences combined with current high perceptions of risk of violence may induce bolder and riskier behaviour in line with prospect theories of risk. Furthermore, a post-conflict household-level Phoenix or economic revival factor may be in operation, based in part on greater within group trust.
Structural Analysis of SHARPIN, a Subunit of a Large Multi-protein E3 Ubiquitin Ligase, Reveals a Novel Dimerization Function for the Pleckstrin Homology Superfold*

Background: SHARPIN is a subunit of the E3 ligase complex LUBAC and the gene that is mutated in chronic proliferative dermatitis mice. Results: The N-terminal portion of SHARPIN adopts the PH superfold and mediates homodimerization. Conclusion: The PH superfold can be used as a protein dimerization module. Significance: This study highlights the versatility of the PH superfold and its function as a protein interaction module. SHARPIN (SHANK-associated RH domain interacting protein) is part of a large multi-protein E3 ubiquitin ligase complex called LUBAC (linear ubiquitin chain assembly complex), which catalyzes the formation of linear ubiquitin chains and regulates immune and apoptopic signaling pathways. The C-terminal half of SHARPIN contains ubiquitin-like domain and Npl4-zinc finger domains that mediate the interaction with the LUBAC subunit HOIP and ubiquitin, respectively. In contrast, the N-terminal region does not show any homology with known protein interaction domains but has been suggested to be responsible for self-association of SHARPIN, presumably via a coiled-coil region. We have determined the crystal structure of the N-terminal portion of SHARPIN, which adopts the highly conserved pleckstrin homology superfold that is often used as a scaffold to create protein interaction modules. We show that in SHARPIN, this domain does not appear to be used as a ligand recognition domain because it lacks many of the surface properties that are present in other pleckstrin homology fold-based interaction modules. Instead, it acts as a dimerization module extending the functional applications of this superfold.
Development and Deployment of a Large-Scale Flower Recognition Mobile App

Today’s major image search engines, which focus on search-by-image-content, work by matching and retrieving of images that are already available on the web. With the proliferation of user generated content, especially from mobile devices, there is a need to develop applications which are more content-aware, i.e. can understand and recognize what is in the image, and which can handle the deteriorated quality inherent to user images uploaded from mobile devices. In this paper we describe a mobile phone application intended to automatically recognize ﬂower images taken by users and classify them into a set of ﬂower categories. The app is served by a web-scale image search engine and relies on computer vision recognition technology. The mobile phone app is available free to users, and as a web interface. We share experiences about designing, developing, and deploying such a system in practice. We discuss practical aspects of applying the object recognition technology, including runtime, scalability, and data collection which is crucial for such data-driven application. More speciﬁcally, we describe a large-scale dataset which was collected in a number of stages to be as close as possible to the data distribution the actual users of the app will encounter. We further describe our strategy for collecting user feedback, which we view as an opportunity to improve the server-side algorithms and datasets.
Contact of nominally flat surfaces

It is usually assumed that the real area of contact between two nominally flat metal surfaces is determined by the plastic deformation of their highest asperities. This leads at once to the result that the real area of contact is directly proportional to the load and independent of the apparent area—a result with many applications in the theories of electric contacts and friction. Archard pointed out that plastic deformation could not be the universal rule, and introduced a model which showed that, contrary to earlier ideas, the area of contact could be proportional to the load even with purely elastic contact. This paper describes a new theory of elastic contact, which is more closely related to real surfaces than earlier theories. We show how the contact deformation depends on the topography of the surface, and establish the criterion for distinguishing surfaces which touch elastically from those which touch plastically. The theory also indicates the existence of an ‘elastic contact hardness’, a composite quantity depending on the elastic properties and the topography, which plays the same role in elastic contact as the conventional hardness does in plastic contact. A new instrument for measuring surface topography has been built; with it the various parameters shown by the theory to govern surface contact can be measured experimentally. The typical radii of surface asperities have been measured. They were found, surprisingly, to be orders of magnitude larger than the heights of the asperities. More generally we have been able to study the distributions of asperity heights and of other surface features for a variety of surfaces prepared by standard techniques. Using these data we find that contact between surfaces is frequently plastic, as usually assumed, but that surfaces which touch elastically are by no means uncommon in engineering practice.
Functional magnetic resonance imaging: A review of methodological aspects and clinical applications

This paper gives an overview of the recent literature on methodological developments of functional magnetic resonance imaging (fMRI) and recent trends in clinical applications. With the recent introduction of high‐field systems and methodological developments leading to more robust signal behavior, fMRI is in a transition state from a research modality for use by experts to a standard procedure with useful applications in patient management. Compared to the use in neuroscientific research, which is often based on BOLD techniques alone, the application in patients is distinguished by a multiparametric characterization of the brain using a combination of several techniques. Neuronal fiber tracking based on diffusion anisotropy measurements, in particular, has already turned out to provide relevant supplementary information to the BOLD‐based cortical activation maps. J. Magn. Reson. Imaging 2003;18:1–15. © 2003 Wiley‐Liss, Inc.
ANTIBODY RESPONSE OF INBRED MOUSE STRAINS TO ORDERED TETRAPEPTIDES OF TYROSINE AND GLUTAMIC ACID ATTACHED TO MULTICHAIN POLYALANINE OR POLYPROLINE

Five inbred mouse strains which represent high and low responders to the random synthetic polypeptide poly(LTyr,LGlu)-polyDLAla--polyLLys, designated (T, G)-A--L, to which the immune response is controlled by an H-2-linked gene, were immunized with three ordered tetrapeptides composed of tyrosine and glutamic acid attached either to multichain poly-DL-alanine or to polyproline. Only one of the three antigenic determinants, namely tyrosyl-tyrosyl-glytamyl-glutamic acid (T-T-G-G), resembled the random peptide (T, G) in the pattern of immune responses elicited against it, and in the cross-reactivity of the specific antibodies with (T, G)-A--L. The immune response pattern to the other two ordered tetrapeptides, T-G-T-G and G-T-T-G, was different from that obtained with (T, G)-A--L, and no cross-reactivity was detected between the antibodies provoked with these peptides and (T, G)-A--L. Thus, it is suggested that T-T-G-G is a major determinant in the random (T, G)-A--L.
Capability determinants of information & communications technology services (ICTS) sector: a Malaysian policy perspective

This paper adopted the H-Model Framework to assess the organizational capability of the contemporary information and communications technology services (ICTS) sector. The ICTS sector needs to not only cope with new age forces that come in different technological shapes and shades, but also has to build up capabilities to provide efficient and effective ICT services that user communities demand today. Capability models like CMMI, PCMM, ITIL, ISO, eSCM-SP and Six Sigma provide a measurement framework together with accreditations and certifications for gauging capabilities at the organizational level. The proposed H-model provides a generic framework for measuring the sector capability pertaining to the provision of ICT Services. Under the eight broad categories entailing 40 study variables, the model investigated the capabilities of 271 ICTS companies in Malaysia. Factor Analysis was used in data reduction to four latent constructs, namely Government relations, Competency and Standards, Business Development Efficacy and Human Capital and Talents. The study revealed that Government relations was the weakest link, with the industry lacking awareness and knowledge about the incentives and facilities offered by mainstream Government agencies pertaining to innovation, R&D, commercialization and export services.
Inertial Sensor-Based Methods in Walking Speed Estimation: A Systematic Review

Self-selected walking speed is an important measure of ambulation ability used in various clinical gait experiments. Inertial sensors, i.e., accelerometers and gyroscopes, have been gradually introduced to estimate walking speed. This research area has attracted a lot of attention for the past two decades, and the trend is continuing due to the improvement of performance and decrease in cost of the miniature inertial sensors. With the intention of understanding the state of the art of current development in this area, a systematic review on the exiting methods was done in the following electronic engines/databases: PubMed, ISI Web of Knowledge, SportDiscus and IEEE Xplore. Sixteen journal articles and papers in proceedings focusing on inertial sensor based walking speed estimation were fully reviewed. The existing methods were categorized by sensor specification, sensor attachment location, experimental design, and walking speed estimation algorithm.
The prevalence and origin of exoprotease-producing cells in the Bacillus subtilis biofilm

Biofilm formation by the Gram-positive bacterium Bacillus subtilis is tightly controlled at the level of transcription. The biofilm contains specialized cell types that arise from controlled differentiation of the resident isogenic bacteria. DegU is a response regulator that controls several social behaviours exhibited by B. subtilis including swarming motility, biofilm formation and extracellular protease (exoprotease) production. Here, for the first time, we examine the prevalence and origin of exoprotease-producing cells within the biofilm. This was accomplished using single-cell analysis techniques including flow cytometry and fluorescence microscopy. We established that the number of exoprotease-producing cells increases as the biofilm matures. This is reflected by both an increase at the level of transcription and an increase in exoprotease activity over time. We go on to demonstrate that exoprotease-producing cells arise from more than one cell type, namely matrix-producing and non-matrix-producing cells. In toto these findings allow us to add exoprotease-producing cells to the list of specialized cell types that are derived during B. subtilis biofilm formation and furthermore the data highlight the plasticity in the origin of differentiated cells.
Direct Delivery of Low-Dose 7-Nitroindazole Into the Bronchial Artery Attenuates Pulmonary Pathophysiology After Smoke Inhalation and Burn Injury in an Ovine Model

ABSTRACT Bronchial circulation plays a critical role in the pathophysiology of burn and smoke inhalation–induced acute lung injury. A 10-fold increase in bronchial blood flow is associated with excessive production of nitric oxide (NO) following smoke inhalation and cutaneous burn. Because an increased release of neuropeptides from the airway has been implicated in smoke inhalation injury, we hypothesized that direct delivery into the bronchial artery of low-dose 7-nitroindazole (7-NI), a specific neuronal NO synthase inhibitor, would attenuate smoke/burn-induced acute lung injury. Eighteen adult female sheep were instrumented for chronic hemodynamic monitoring 5 to 7 days before the injury. The bronchial artery was cannulated via intercostal thoracotomy, while blood flow was preserved. Acute lung injury was induced by 40% total body surface area third-degree cutaneous burn and smoke inhalation (48 breaths of cotton smoke, <40°C) under deep anesthesia. Following injury, animals (35.4 ± 1.1 kg) were divided into three groups: (a) 7-NI group: 1 h after injury, 7-NI (0.01 mg · kg−1 · h−1, 2 mL · h−1) was continuously infused into the bronchial artery, n = 6; (b) control group: 1 h after injury, same amount of saline was injected into the bronchial artery, n = 6; (c) sham group: no injury, no treatment, same operation and anesthesia, n = 6. After injury, all animals were ventilated and fluid resuscitated according to an established protocol. The experiment was conducted for 24 h. Injury induced severe pulmonary dysfunction, which was associated with increases in lung edema formation, airway obstruction, malondialdehyde, and nitrate/nitrite. 7-Nitroindazole injection into the bronchial artery reduced the degree of lung edema formation and improved pulmonary gas exchange. The increase in malondialdehyde and nitrate/nitrite in lung tissue was attenuated by treatment. Our data strongly suggest that local airway production of NO contributes to pulmonary dysfunction following smoke inhalation and burn injury. Most mechanisms that drive this pathophysiology reside in the airway.
Toxicity of inhaled traffic related particulate matter

Traffic generated ultrafine particulates may play a major role in the development of adverse health effects. However, little is known about harmful effects caused by recurring exposure. We hypothesized that repeated exposure to particulate matter results in adverse pulmonary and systemic toxic effects. Exposure to diesel engine exhaust resulted in signs of oxidative stress in the lung, impaired coagulation, and changes in the immune system. Pro-inflammatory cytokine levels were decreased in some regions of the brain but increased in the striatum implying that exposure to diesel engine exhaust may selectively aggravate neurological impairment. Data from these three studies suggest that exposure to traffic related PM can mediate changes in the vasculature and brain of healthy rats. To what extent these changes may contribute to chronic neurodegenerative or vascular diseases is at present unclear.
Behavior understanding at railway station by postures and the pseud-trellis analysis of trajectories

Protection of critical transportation infrastructure such as railroad station is an important topic in these days. In this paper, we develop a new rule based approach to video surveillance system for detecting situations where pedestrians may be in peril, as well as suspicious action or interactions at railroad station. We analyze here two general types of pedestrian involved behaviors: (i) single pedestrian or no interaction, (ii) multiple pedestrian interactions. The behavior analysis is accomplished through the development of geometric and motion visual features for each pedestrian. The performance evaluation is carried out by using the video streams taken in the rail road stations. The results show that our algorithm is very simple and effective.
Exploiting Chunk-level Features to Improve Phrase Chunking

Most existing systems solved the phrase chunking task with the sequence labeling approaches, in which the chunk candidates cannot be treated as a whole during parsing process so that the chunk-level features cannot be exploited in a natural way. In this paper, we formulate phrase chunking as a joint segmentation and labeling task. We propose an efficient dynamic programming algorithm with pruning for decoding, which allows the direct use of the features describing the internal characteristics of chunk and the features capturing the correlations between adjacent chunks. A relaxed, online maximum margin training algorithm is used for learning. Within this framework, we explored a variety of effective feature representations for Chinese phrase chunking. The experimental results show that the use of chunk-level features can lead to significant performance improvement, and that our approach achieves state-of-the-art performance. In particular, our approach is much better at recognizing long and complicated phrases.
Contourlet-Based Feature Extraction on Texture Images

According to the directional property and coefficients energy feature in contourlet decomposition, we proposed a new algorithm which is adapted to extract the rotated texture¿s features. By using this algorithm, we can take good advantage of directional information in contourlet decomposition by different decomposition level. With the extracted feature vectors, we can easily distinguish different texture in standard Brodatz texture database with high classification accuracy.
A new polymorphic multicast routing protocol for MANET

We propose in this paper, a polymorphic, hybrid multicast routing protocol for MANET (mobile ad hoc networks). This new polymorphic protocol attempts to take benefit of the high efficiency of proactive behavior and the low cost of network traffic of the reactive behavior. The protocol is based on the principle of adaptability and multi-behavioral modes of operations. The proposed protocol is able to change behavior in different situations in order to improve certain metrics like the battery power. Extensive simulations demonstrated the effectiveness of the proposed protocol in improving performance and in extending battery power longevity.
Proposal for a Pancreatic Configuration Index for Determining Patients at High Risk of Pancreatic Fistula Following Pancreatoduodenectomy

Background/Aims: The pancreatic configuration is one of the most important factors that have an impact on the incidence of postoperative pancreatic fistula (POPF). This study sought to propose a new index, called the pancreatic configuration index (PCI), to categorize patients at a high risk for POPF. Methods: Two hundred and thirty-one patients who underwent pancreatoduodenectomies were subjected to the analysis. The pancreatic parenchymal thickness and the main pancreatic duct (MPD) diameter at the pancreatic neck were measured using axial computed tomography scan images. The PCI was calculated by dividing the axial thickness by the MPD diameter. Results: Sixty-two of the patients (26.8%) developed clinically significant POPF. Using a receiver operating characteristic curve analysis, the cut-off value of the PCI in predicting POPF was 5.3. The incidence of POFP increased depending on the PCI level. Using a multivariate analysis that included the various risk factors of POPF, a high PIC (≥5) was identified as an independent risk factor of POPF, with the highest OR at 6.50. Conclusion: The PCI is useful for stratifying patients at a high risk for POPFs. This index may be used to classify the patient population when evaluating other risk factors for POPF.
Bacterial Competition for Human Nasal Cavity Colonization: Role of Staphylococcal agr Alleles

ABSTRACT We examined the bacterial aerobic nasal flora of 216 healthy volunteers to identify potential competitive interactions among different species, with special emphasis on the influence of staphylococcal agr alleles. The Staphylococcus aureus colonization rate correlated negatively with the rate of colonization by Corynebacterium spp. and non-aureus staphylococci, especially S. epidermidis, suggesting that both Corynebacterium spp. and S. epidermidis antagonize S. aureus colonization. Most of the S. aureus and S. epidermidis isolates were agr typed by a PCR method. Only one S. aureus agr (agrSa) allele was detected in each carrier. Multiple logistic regression of the two most prevalent agrSa alleles (agr-1Sa and agr-2Sa) and the three S. epidermidis agr (agrSe) alleles showed a specific influence of the agr system. The results of this model did not support conclusions drawn from previous in vitro agr-specific cross-inhibition experiments. Our findings suggest that the agr alleles, which are strongly linked to the bacterial genetic background, may simply be associated with common biological properties—including mediators of bacterial interference—in the strains that bear them.