Miracle-dz/UniFAR-FTUs huggingface dataset:
Test-Retest Reliability of “High-Order” Functional Connectivity in Young Healthy Adults

Functional connectivity (FC) has become a leading method for resting-state functional magnetic resonance imaging (rs-fMRI) analysis. However, the majority of the previous studies utilized pairwise, temporal synchronization-based FC. Recently, high-order FC (HOFC) methods were proposed with the idea of computing “correlation of correlations” to capture high-level, more complex associations among the brain regions. There are two types of HOFC. The first type is topographical profile similarity-based HOFC (tHOFC) and its variant, associated HOFC (aHOFC), for capturing different levels of HOFC. Instead of measuring the similarity of the original rs-fMRI signals with the traditional FC (low-order FC, or LOFC), tHOFC measures the similarity of LOFC profiles (i.e., a set of LOFC values between a region and all other regions) between each pair of brain regions. The second type is dynamics-based HOFC (dHOFC) which defines the quadruple relationship among every four brain regions by first calculating two pairwise dynamic LOFC “time series” and then measuring their temporal synchronization (i.e., temporal correlation of the LOFC fluctuations, not the BOLD fluctuations). Applications have shown the superiority of HOFC in both disease biomarker detection and individualized diagnosis than LOFC. However, no study has been carried out for the assessment of test-retest reliability of different HOFC metrics. In this paper, we systematically evaluate the reliability of the two types of HOFC methods using test-retest rs-fMRI data from 25 (12 females, age 24.48 ± 2.55 years) young healthy adults with seven repeated scans (with interval = 3–8 days). We found that all HOFC metrics have satisfactory reliability, specifically (1) fair-to-good for tHOFC and aHOFC, and (2) fair-to-moderate for dHOFC with relatively strong connectivity strength. We further give an in-depth analysis of the biological meanings of each HOFC metric and highlight their differences compared to the LOFC from the aspects of cross-level information exchanges, within-/between-network connectivity, and modulatory connectivity. In addition, how the dynamic analysis parameter (i.e., sliding window length) affects dHOFC reliability is also investigated. Our study reveals unique functional associations characterized by the HOFC metrics. Guidance and recommendations for future applications and clinical research using HOFC are provided. This study has made a further step toward unveiling more complex human brain connectome.
Secure and trustworthy file sharing over cloud storage using eID tokens

This paper presents a multi-platform, open-source application that aims to protect data stored and shared in existing cloud storage services. The access to the cryptographic material used to protect data is implemented using the identification and authentication functionalities of national electronic identity (eID) tokens. All peer to peer dialogs to exchange cryptographic material is implemented using the cloud storage facilities. Furthermore, we have included a set of mechanisms to prevent files from being permanently lost or damaged due to concurrent modification, deletion and malicious tampering. We have implemented a prototype in Java that is agnostic relatively to cloud storage providers; it only manages local folders, one of them being the local image of a cloud folder. We have successfully tested our prototype in Windows, Mac OS X and Linux, with Dropbox, OneDrive, Google Drive and SugarSync.
Biomechanical Characterization of Human Soft Tissues Using Indentation and Tensile Testing

Regenerative medicine aims to engineer materials to replace or restore damaged or diseased organs. The mechanical properties of such materials should mimic the human tissues they are aiming to replace; to provide the required anatomical shape, the materials must be able to sustain the mechanical forces they will experience when implanted at the defect site. Although the mechanical properties of tissue-engineered scaffolds are of great importance, many human tissues that undergo restoration with engineered materials have not been fully biomechanically characterized. Several compressive and tensile protocols are reported for evaluating materials, but with large variability it is difficult to compare results between studies. Further complicating the studies is the often destructive nature of mechanical testing. Whilst an understanding of tissue failure is important, it is also important to have knowledge of the elastic and viscoelastic properties under more physiological loading conditions. This report aims to provide a minimally destructive protocol to evaluate the compressive and tensile properties of human soft tissues. As examples of this technique, the tensile testing of skin and the compressive testing of cartilage are described. These protocols can also be directly applied to synthetic materials to ensure that the mechanical properties are similar to the native tissue. Protocols to assess the mechanical properties of human native tissue will allow a benchmark by which to create suitable tissue-engineered substitutes.
The potential hazardous effect of exposure to iron dust in Egyptian smoking and nonsmoking welders

ABSTRACT Exposure to iron dust and welding fumes is widespread and may increase the risk of lung inflammation. The aim of this study was to identify associations between exposure to iron/welding fumes and the levels of inflammatory parameters and allergic mediators among 120 Egyptian men. Forty nonsmoking and 40 smoking Egyptian welders as well as 40 healthy volunteers who were never exposed to welding fumes and were nonsmoking were enrolled in the study. Peak expiratory flow rates (PEFR) assessed at the end of the shift of work on working days revealed an impairment in lung function, with the smoking workers showing the worse results, followed by nonsmoking workers, as compared to healthy volunteers. Moreover, the results of the present study showed a significant increase in serum iron and immunoglobulin E, as well as plasma thiobarbaturic acid reactive substances, C-reactive protein, tumor necrosis factor-alpha, haptoglobin, interleukin-2, interleukin-6 and interleukin-23 histamine, lactate dehydrogenase isoenzyme-3, and calcitonin. In addition, the results revealed significant decrease in plasma α-1-antitrypsin and serum transferrin, as well as blood activities of antioxidant enzymes: catalase, superoxide dismutase, glutathione peroxidase, and glutathione reductase (as compared with control group). However, there was a nonsignificant change in arginase and α-L-fucosidase in smoking and nonsmoking welders exposed to iron dust and welding fumes. In conclusion, occupational exposure to iron dust and welding fumes increases lung inflammation risk among Egyptian blacksmith workers, a condition that worsens with smoking.
UniVSE: Robust Visual Semantic Embeddings via Structured Semantic Representations

We propose Unified Visual-Semantic Embeddings (UniVSE) for learning a joint space of visual and textual concepts. The space unifies the concepts at different levels, including objects, attributes, relations, and full scenes. A contrastive learning approach is proposed for the fine-grained alignment from only image-caption pairs. Moreover, we present an effective approach for enforcing the coverage of semantic components that appear in the sentence. We demonstrate the robustness of Unified VSE in defending text-domain adversarial attacks on cross-modal retrieval tasks. Such robustness also empowers the use of visual cues to resolve word dependencies in novel sentences.
An Indoor Localization Algorithm Based on Continuous Feature Scaling and Outlier Deleting

In this paper, a received signal strength indicator (RSSI) based indoor localization system is implemented employing Wi-Fi infrastructure. In the light of the feature-scaling-based <inline-formula> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula>-nearest neighbor (FS-<inline-formula> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula>NN) algorithm, a new continuous-feature-scaling model is proposed, which uses continuous weights instead of the discrete weights used in the FS-<inline-formula> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula>NN, and needs not divide the entire RSSI space into the intervals. This gridless scheme avoids the difficulty of the weight selection at the common boundary of the adjacent intervals that could meet in the grid-based method of FS-<inline-formula> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula>NN, which needs to divide the RSSI space into the intervals, ahead. An outlier deleting procedure is further used to improve the accuracy of the localization system. Experimental results indicate that the proposed method can be with a small localization error and is superior to some previous methods. One of the experiments achieves 1.34 m of the indoor localization error in a 12 m <inline-formula> <tex-math notation="LaTeX">$\times 8\,\,{\mathrm{m}}$ </tex-math></inline-formula> area. The other is with 1.72 m of the indoor localization error in a 30 m <inline-formula> <tex-math notation="LaTeX">$\times 25\,\,{\mathrm{m}}$ </tex-math></inline-formula> area. The proposed method performances best among the counterparts in the experiments.
Designing values in an adaptive learning platform

To a certain extent, the process of design is always driven by guiding values. An ethical analysis, as it has been argued, can help in making such a process more reflexive, highlighting existing conflicts and discussing desirable solutions. These premises guide approaches like Value Sensitive Design or Privacy by Design. This paper discusses the issues of values in technology design in the context of a platform for adaptive learning. To what extent can principles of privacy by design be operationalized in design practices? Using the case of an adaptive learning platform, we describe how values have originally driven developers’ decisions and design choices and show how clashes between values are unavoidable. We claim that including a collaboration between ethicists and designers at an early stage of the design process may foster a reflection on the ethical considerations at stake.
The International Journal of Biostatistics Likelihood Estimation of Conjugacy Relationships in Linear Models with Applications to High-Throughput Genomics

In the simultaneous estimation of a large number of related quantities, multilevel models provide a formal mechanism for efficiently making use of the ensemble of information for deriving individual estimates. In this article we investigate the ability of the likelihood to identify the relationship between signal and noise in multilevel linear mixed models. Specifically, we consider the ability of the likelihood to diagnose conjugacy or independence between the signals and noises. Our work was motivated by the analysis of data from high-throughput experiments in genomics. The proposed model leads to a more flexible family. However, we further demonstrate that adequately capitalizing on the benefits of a well fitting fully-specified likelihood in the terms of gene ranking is difficult.
Training machine translation for human acceptability

Discriminative training, a.k. a. tuning, is an important part of Statistical Machine Translation. This step optimises weights for the several statistical models and heuristics used in a machine translation system, in order to balance their relative effect on the translation output. Different weights lead to significant changes in the quality of translation outputs, and thus selecting appropriate weights is of key importance. This thesis addresses three major problems with current discriminative training methods in order to improve translation quality. First, we design more accurate automatic machine translation evaluation metrics that have better correlation with human judgements. An automatic evaluation metric is used in the loss function in most discriminative training methods, however what the best metric is for this purpose is still an open question. In this thesis we propose two novel evaluation metrics that achieve better correlation with human judgements than the current de facto standard, the BLEU metric. We show that these metrics can improve translation quality when used in discriminative training. Second, we design an algorithm to select sentence pairs for training the discriminative learner from large pools of freely available parallel sentences. These resources tend to be noisy and include translations of varying degrees of quality and suitability for the translation task at hand, especially if obtained using crowdsourcing methods. Nevertheless, they are crucial when professionally created training data is scarce or unavailable. There is very little previous research on the data selection for discriminative training. Our novel data selection algorithm does not require knowledge of the test set nor uses decoding outputs, and is thus more generally useful and efficient. Our experiments show that with this data selection algorithm, translation quality consistently improves over strong baselines. Finally, the third component of the thesis is a novel weighted ranking-based optimisation algorithm for discriminative training. In contrast to previous approaches, this technique assigns a different weight to each training instance according to its reachability and its relationship to test sentence being decoded, a form of transductive learning. Our experimental results show improvements over a modern state-of-the-art method across different language pairs. Overall, the proposed approaches lead to better translation quality when compared strong baselines in our experiments, both in isolation and when combined, and can be easily applied to most existing statistical machine translation approaches.
Affective recommendation system for tourists by using Emotion Generating Calculations

An emotion orientated intelligent interface consists of Emotion Generating Calculations (EGC) and Mental State Transition Network (MSTN). We have developed the Android EGC application software which the agent works to evaluate the feelings in the conversation. In this paper, we develop the tourist information system which can estimate the user's feelings at the sightseeing spot. The system can recommend the sightseeing spot and the local food corresponded to the user's feeling. The system calculates the recommendation list by the estimate function which consists of Google search results, the important degree of a term at the sightseeing website, and the the aroused emotion by EGC. In order to show the effectiveness, this paper describes the experimental results for some situations during Hiroshima sightseeing.
Adaptive demand‐aware work‐stealing in multi‐programmed multi‐core architectures

Modern multi‐core computers often execute multiple programs concurrently, but traditional work‐stealing schedulers assume that only a single program executes at a time. If multiple work‐stealing programs run on a multi‐core computer concurrently, the performance of these co‐located programs is poor and unbalanced due to the interference among their workers. To relieve this problem, this paper proposes demand‐aware work‐stealing (DWS) for a single work‐stealing program. If multiple programs that adopt DWS run simultaneously on a multi‐core system, the computation resources are evenly allocated to the co‐located programs at the beginning. At runtime, if a program does not need all its allocated cores, it donates its free cores. Otherwise, if a program needs more cores, it steals the free cores donated by its co‐located programs. In addition, each program that adopts DWS dynamically puts its workers to sleep and wakes them up according to the number of its queued tasks. Experimental results show that DWS can improve the co‐located programs' performance up to 42.6% and can also balance the performance of the co‐located programs compared with traditional work‐stealing. Copyright © 2015 John Wiley & Sons, Ltd.
Antibiotic stress selects against cooperation in the pathogenic bacterium Pseudomonas aeruginosa

Significance The evolution of cooperation is a central issue in biology and the social sciences. Study of model systems of social microbes has focused on how “cooperators” and “cheats” interact but rarely accounts for the surrounding environment. We demonstrate how environmental stress in the form of antibiotics alters the evolution of public goods cooperation in a bacterium. Antibiotics accentuate the costs to cooperators, resulting in their rapid demise relative to cheats. In a more applied vein, antibiotic resistance was maximal in the presence of both producers and cheats, suggesting that knowledge about social strategies can be used to improve therapies. Our work emphasizes ecoevolutionary feedback in social evolution and demonstrates that social interactions may be considerably modified in natural, stressful environments. Cheats are a pervasive threat to public goods production in natural and human communities, as they benefit from the commons without contributing to it. Although ecological antagonisms such as predation, parasitism, competition, and abiotic environmental stress play key roles in shaping population biology, it is unknown how such stresses generally affect the ability of cheats to undermine cooperation. We used theory and experiments to address this question in the pathogenic bacterium, Pseudomonas aeruginosa. Although public goods producers were selected against in all populations, our competition experiments showed that antibiotics significantly increased the advantage of nonproducers. Moreover, the dominance of nonproducers in mixed cultures was associated with higher resistance to antibiotics than in either monoculture. Mathematical modeling indicates that accentuated costs to producer phenotypes underlie the observed patterns. Mathematical analysis further shows how these patterns should generalize to other taxa with public goods behaviors. Our findings suggest that explaining the maintenance of cooperative public goods behaviors in certain natural systems will be more challenging than previously thought. Our results also have specific implications for the control of pathogenic bacteria using antibiotics and for understanding natural bacterial ecosystems, where subinhibitory concentrations of antimicrobials frequently occur.
ICE 1 promotes the link between splicing and nonsense-mediated mRNA decay

The nonsense-mediated mRNA decay (NMD) pathway detects aberrant transcripts containing premature termination codons (PTCs) and regulates expression of 5–10% of nonaberrant human mRNAs. To date, most proteins involved in NMD have been identified by genetic screens in model organisms; however, the increased complexity of gene expression regulation in human cells suggests that additional proteins may participate in the human NMD pathway. To identify proteins required for NMD, we performed a genome-wide RNAi screen against >21,000 genes. Canonical members of the NMD pathway were highly enriched as top hits in the siRNA screen, along with numerous candidate NMD factors, including the conserved ICE1/KIAA0947 protein. RNAseq studies reveal that depletion of ICE1 globally enhances accumulation and stability of NMD-target mRNAs. Further, our data suggest that ICE1 uses a putative MIF4G domain to interact with exon junction complex (EJC) proteins and promotes the association of the NMD protein UPF3B with the EJC. DOI: https://doi.org/10.7554/eLife.33178. 001
A staging table for the embryonic development of the brownbanded bamboo shark (Chiloscyllium punctatum)

Background: Studying cartilaginous fishes (chondrichthyans) has helped us understand vertebrate evolution and diversity. However, resources such as genome sequences, embryos, and detailed staging tables are limited for species within this clade. To overcome these limitations, we have focused on a species, the brownbanded bamboo shark (Chiloscyllium punctatum), which is a relatively common aquarium species that lays eggs continuously throughout the year. In addition, because of its relatively small genome size, this species is promising for molecular studies. Results: To enhance biological studies of cartilaginous fishes, we establish a normal staging table for the embryonic development of the brownbanded bamboo shark. Bamboo shark embryos take around 118 days to reach the hatching period at 25°C, which is approximately 1.5 times as fast as the small‐spotted catshark (Scyliorhinus canicula) takes. Our staging table divides the embryonic period into 38 stages. Furthermore, we found culture conditions that allow early embryos to grow in partially opened egg cases. Conclusions: In addition to the embryonic staging table, we show that bamboo shark embryos exhibit relatively fast embryonic growth and are amenable to culture, key characteristics that enhance their experimental utility. Therefore, the present study is a foundation for cartilaginous fish research. Developmental Dynamics 247:712–723, 2018. © 2017 Wiley Periodicals, Inc.
Comparison of the Tight Rope Technique and Clavicular Hook Plate for the Treatment of Rockwood Type III Acromioclavicular Joint Dislocation

ABSTRACT Aim: Acromioclavicular joint dislocation is one of the most common shoulder problems and may lead to instability or degenerative changes. The aim of this study was to compare the clinical outcomes of the Tight Rope system and clavicular hook plate for Rockwood type III acromioclavicular joint dislocation in adults. Materials and Methods: This was a prospective, randomized study in a hospital setting. From January 2012 to December 2014, 69 patients with type III injury were reviewed. Patients were randomly divided into two groups: Group A was treated using the TightRope system and Group B with the clavicular hook plate. All participants were followed up for 12 months. Clinical outcomes, radiological results and postoperative complications were recorded. Results: The length of incision was significantly shorter in Goup A than that in Group B. The blood loss of surgery was significantly less in the Group A. Significant difference could be found between the two groups regarding the Visual Analogue Scale scores one day after surgery, at the 3 and 12 months follow-up. There were no differences according to the improvement of the Constant–Murley score and the coracoclavicular distance between the groups. Conclusions: The two groups have similar clinical and radiological outcomes. Both treatments could relieve the pain of dislocation, improve the function of Acromioclavicular joint and rectify the coracoclavicular distance measured in plain films. However, the TightRope system exhibited some advantages in terms of length of incision, blood loss of surgery, the pain postoperatively and no need for a second surgery.
A Practical q -Gram Index for Text Retrieval Allowing Errors

We propose an indexing technique for approximate text searching, which is practical and powerful, and especially optimized for natural language text. Unlike other indices of this kind, it is able to retrieve any string that approximately matches the search pattern, not only words. Every text substring of a fixed length q is stored in the index, together with pointers to all the text positions where it appears. The search pattern is partitioned into pieces which are searched in the index, and all their occurrences in the text are verified for a complete match. To reduce space requirements, pointers to blocks instead of exact positions can be used, which increases querying costs. We design an algorithm to optimize the pattern partition into pieces so that the total number of verifications is minimized. This is especially well suited for natural language texts, and allows to know in advance the expected cost of the search and the expected relevance of the query to the user. We show experimentally the building time, space requirements and querying time of our index, finding that it is a practical alternative for text retrieval. The retrieval times are reduced from 10% to 60% of the best on-line algorithm.