Miracle-dz/UniFAR-FTUs huggingface dataset:
Oxidative Stress in Mammalian Cells Impinges on the Cysteines Redox State of Human XRCC3 Protein and on Its Cellular Localization

In vertebrates, XRCC3 is one of the five Rad51 paralogs that plays a central role in homologous recombination (HR), a key pathway for maintaining genomic stability. While investigating the potential role of human XRCC3 (hXRCC3) in the inhibition of DNA replication induced by UVA radiation, we discovered that hXRCC3 cysteine residues are oxidized following photosensitization by UVA. Our in silico prediction of the hXRCC3 structure suggests that 6 out of 8 cysteines are potentially accessible to the solvent and therefore potentially exposed to ROS attack. By non-reducing SDS-PAGE we show that many different oxidants induce hXRCC3 oxidation that is monitored in Chinese hamster ovarian (CHO) cells by increased electrophoretic mobility of the protein and in human cells by a slight decrease of its immunodetection. In both cell types, hXRCC3 oxidation was reversed in few minutes by cellular reducing systems. Depletion of intracellular glutathione prevents hXRCC3 oxidation only after UVA exposure though depending on the type of photosensitizer. In addition, we show that hXRCC3 expressed in CHO cells localizes both in the cytoplasm and in the nucleus. Mutating all hXRCC3 cysteines to serines (XR3/S protein) does not affect the subcellular localization of the protein even after exposure to camptothecin (CPT), which typically induces DNA damages that require HR to be repaired. However, cells expressing mutated XR3/S protein are sensitive to CPT, thus highlighting a defect of the mutant protein in HR. In marked contrast to CPT treatment, oxidative stress induces relocalization at the chromatin fraction of both wild-type and mutated protein, even though survival is not affected. Collectively, our results demonstrate that the DNA repair protein hXRCC3 is a target of ROS induced by environmental factors and raise the possibility that the redox environment might participate in regulating the HR pathway.
Optimizing annotation efforts to build reliable annotated corpora for training statistical models

Creating high-quality manual annotations on text corpus is time-consuming and often requires the work of experts. In order to explore methods for optimizing annotation efforts, we study three key time burdens of the annotation process: (i) multiple annotations, (ii) consensus annotations, and (iii) careful annotations. Through a series of experiments using a corpus of clinical documents annotated for personally identifiable information written in French, we address each of these aspects and draw conclusions on how to make the most of an annotation effort.
The structure of plant photosystem I super-complex at 2.8 Å resolution

Most life forms on Earth are supported by solar energy harnessed by oxygenic photosynthesis. In eukaryotes, photosynthesis is achieved by large membrane-embedded super-complexes, containing reaction centers and connected antennae. Here, we report the structure of the higher plant PSI-LHCI super-complex determined at 2.8 Å resolution. The structure includes 16 subunits and more than 200 prosthetic groups, which are mostly light harvesting pigments. The complete structures of the four LhcA subunits of LHCI include 52 chlorophyll a and 9 chlorophyll b molecules, as well as 10 carotenoids and 4 lipids. The structure of PSI-LHCI includes detailed protein pigments and pigment–pigment interactions, essential for the mechanism of excitation energy transfer and its modulation in one of nature's most efficient photochemical machines. DOI: http://dx.doi. org/10.7554/eLife.07433. 001
A Hierarchical Internet Object Cache

This paper discusses the design and performance of a hierarchical proxy-cache designed to make Internet information systems scale better. The design was motivated by our earlier trace-driven simulation study of Internet traffic. We challenge the conventional wisdom that the benefits of hierarchical file caching do not merit the costs, and believe the issue merits reconsideration in the Internet environment. The cache implementation supports a highly concurrent stream of requests. We present performance measurements that show that our cache outperforms other popular Internet cache implementations by an order of magnitude under concurrent load. These measurements indicate that hierarchy does not measurably increase access latency. Our software can also be configured as a Web-server accelerator; we present data that our httpd-accelerator is ten times faster than Netscape's Netsite and NCSA 1.4 servers. Finally, we relate our experience fitting the cache into the increasingly complex and operational world of Internet information systems, including issues related to security, transparency to cache-unaware clients, and the role of file systems in support of ubiquitous wide-area information systems.
A Health and Usage Monitoring System for ROS-based service robots

This paper presents a multi-core processing solution for ROS-based service robots. The power management together with the control and availability of the processing resources are supervised by a custom-made Power Management Board (PMB) based on a Digital Signal Processor (DSP) micro controller, implementing a Health and Usage Monitoring System (HUMS). The proposed architecture also allows for the PMB to control the most critical robot functions in case of low battery conditions or impossibility of performing energy harvesting, thus extending the lifespan of the robot. All PMB data is recorded on a SD card so as to allow offline analyses of the robotic mission and, thus, support subsequent maintenance activities. Two different implementations of the proposed system have been fielded in two Multi-Robot Systems (MRS) for environmental monitoring, covering aerial, water surface, and wheeled ground vehicles. An additional implementation of the architecture is currently being deployed on an industrial autonomous logistics robot. These three implementations are presented and discussed.
An improved 2D cost aggregation method for advanced driver assistance systems

In advanced driver assistance systems, the stereo matching algorithm is the key resource to obtain depth information of outdoor scenes. Semi-Global Matching (SGM) is currently the most efficient stereo matching algorithm for outdoor environments. However, because the number of pixels is large, SGM uses only a subset of them when estimating the disparity of a pixel. To overcome this limitation, Cost Aggregation Table (CAT) was proposed which uses two-dimensional cost aggregation so as to utilize whole image information. In this paper, we propose improved global 2D cost aggregation methods by loosening aggregation constraints. It aggregates every cost in the whole image to estimate each disparity. Although our method aggregates every cost in the image, the computational complexity is the same as that of SGM and CAT. The proposed cost aggregation method achieves superior disparity accuracy compared to the SGM.
Traffic-and thermal-aware routing for throttled three-dimensional Network-on-Chip systems

Thermal issue is one of the major challenges in the research field of three-dimensional (3D) IC. Network-on-Chip (NoC) has been viewed as a practical communication infrastructure in 3D IC. In this paper, we proposed an adaptive routing algorithm, Traffic- and Throttling-Awareness Routing (TTAR), to address the traffic congestion due to throttling of transient-temperature control. TTAR can balance the network traffic and detour the throttled tiles. The experimental results show that TTAR does not influence the ability of heat dissipation seriously and can achieve 8% ∼ 680% throughput improvements than the previous routing algorithms at 50-cycle average latency.
On the Security of Software Systems and Services

This work investigates new methods for facing the security issues and threats arising from the composition of software. This task has been carried out through the formal modelling of both the software composition scenarios and the security properties, i.e., policies, to be guaranteed. Our research moves across three different modalities of software composition which are of main interest for some of the most sensitive aspects of the modern information society. They are mobile applications, trust-based composition and service orchestration. Mobile applications are programs designed for being deployable on remote platforms. Basically, they are the main channel for the distribution and commercialisation of software for mobile devices, e.g., smart phones and tablets. Here we study the security threats that affect the application providers and the hosting platforms. In particular, we present a programming framework for the development of applications with a static and dynamic security support. Also, we implemented an enforcement mechanism for applying fine-grained security controls on the execution of possibly malicious applications. In addition to security, trust represents a pragmatic and intuitive way for managing the interactions among systems. Currently, trust is one of the main factors that human beings keep into account when deciding whether to accept a transaction or not. In our work we investigate the possibility of defining a fully integrated environment for security policies and trust including a runtime monitor. Finally, Service-Oriented Computing (SOC) is the leading technology for business applications distributed over a network. The security issues related to the service networks are many and multi-faceted. We mainly deal with the static verification of secure composition plans of web services. Moreover, we introduce the synthesis of dynamic security checks for protecting the services against illegal invocations.
PREDICTORS OF VICARIOUS TRAUMATIZATION AMONG TRAUMA CLINICIANS AND GENERAL MENTAL HEALTH PROVIDERS: A COMPARISON

viii Predictors of Vicarious Traumatization among Trauma Clinicians and General Mental Health Providers: A Comparison. 1 Literature Review. 2 Vicarious Traumatization. 2 Differentiating Vicarious Traumatization from Other Effects of Trauma Work. 8 Correlates of Vicarious Traumatization. 10 Therapist Factors. 10 Organizational Factors. 18 Aims and Hypotheses. 29 Method. 33 Participants. 34 Procedure. 35 Measures. 36 Data Analytic Strategy. 45 Results. 47 Sample Characteristics. 47 Prevalence and Severity of Occupational Stress Constructs. 55 Descriptives for Therapist Variables. 58 Supervision Experiences. 61 Hypotheses. 63 Discussion. 93 Therapist Factors Affecting Vicarious Traumatization. 97 Occupational Factors Affecting Vicarious Traumatization. 103 Constructs Related to Vicarious Traumatization. 107 Secondary Traumatic Stress. 107 Burnout. 110 Differentiation of Vicarious Trauma. 114 Limitations. 116
Evaluating Structure of Complex Networks by Navigation Entropy

Complex networks are extensively studied in various areas such as social networks, biological networks, Internet and WWW. Those networks have many characters such as small-diameter, higher cluster and power-law degree distribution. Small-world is evolved for efficient information transformation and navigation. Thus, navigation is an important functional character of networks. Previous researches mostly focus on understanding the navigability of small-world networks by analyzing the diameter and the routing efficiency. In this paper, we use the navigability to model the basic structural complexity of a network. That is, given a network topology, we need a model to evaluate how complex the topology is. Some network complexity models have been proposed but none of them consider the navigability factor of the network systems. We believe that using the navigability factor to evaluate the network structural complexity is a feasible and reasonable way. We use the adjacent matrix to build a navigation transition matrix and evaluate the randomness of random walks on the transition matrix by defining navigation entropy on it. We use the iteration of the random walk matrix to evaluate the navigability of a network and the complexity of network. That is, the higher the navigation entropy, the higher the randomness of a network. The lower the navigation entropy, the higher the structure of a network. We apply the navigation entropy model on a set of structural and random network topologies to show how the model can show the different complexity of networks.
HRIR~: modulating range in headphone-reproduced spatial audio

HRIR~, a new software audio filter for Head-Related Impulse Response (HRIR) convolution is presented. The filter, implemented as a Pure-Data object, allows dynamic modification of a sound source's apparent location by modulating its virtual azimuth, elevation, and range in realtime, the last attribute being missing in surveyed similar applications. With hrir~ users can virtually localize monophonic sources around a listener's head in a region delimited by elevations between [--40, 90]°, and ranges between [20, 160] cm from the center of the virtual listener's head. An application based on hrir~ is presented to illustrate its benefits.
Combining Q-Learning with Artificial Neural Networks in an Adaptive Light Seeking Robot

Q-learning is a reinforcement learning technique that works by learning an action-value function that gives the expected utility of performing a given action in a given state and following a fixed policy thereafter. The basic implementation uses a q-table to store the data. With increasing complexity in the environment and the agent, this approach fails to scale well as the space requirements become prohibitive. In this paper, we investigate an alternative implementation in which we use an artificial neural network as a function approximator and eliminate the need for an explicit table.
Subcutaneous Adipose Tissue–Derived Stem Cell Utility Is Independent of Anatomical Harvest Site

Abstract One of the challenges for tissue engineering and regenerative medicine is to obtain suitably large cell numbers for therapy. Mesenchymal stem cells (MSCs) can easily be expanded in vitro to obtain large numbers of cells, but this approach may induce cellular senescence. The characteristics of cells are dependent on variables like age, body mass index (BMI), and disease conditions, however, and in the case of adipose tissue–derived stem cells (ASCs), anatomical harvest site is also an important variable that can affect the regenerative potential of isolated cells. We therefore had kept the parameters (age, BMI, disease conditions) constant in this study to specifically assess influence of anatomical sites of individual donors on utility of ASCs. Adipose tissue was obtained from multiple anatomical sites in individual donors, and viability and nucleated cell yield were determined. MSC frequency was enumerated using colony forming unit assay and cells were characterized by flow cytometry. Growth characteristics were determined by long-term population doubling analysis of each sample. Finally, MSCs were induced to undergo adipogenic, osteogenic, and chondrogenic differentiation. To validate the findings, these results were compared with similar single harvest sites from multiple individual patients. The results of the current study indicated that MSCs obtained from multiple harvest sites in a single donor have similar morphology and phenotype. All adipose depots in a single donor exhibited similar MSC yield, viability, frequency, and growth characteristics. Equivalent differentiation capacity into osteocytes, adipocytes, and chondrocytes was also observed. On the basis of results, we conclude that it is acceptable to combine MSCs obtained from various anatomical locations in a single donor to obtain suitably large cell numbers required for therapy, avoiding in vitro senescence and lengthy and expensive in vitro culturing and expansion steps.
Key Confirmation in Key Exchange: A Formal Treatment and Implications for TLS 1.3

Key exchange protocols allow two parties at remote locations to compute a shared secret key. The common security notions for such protocols are secrecy and authenticity, but many widely deployed protocols and standards name another property, called key confirmation, as a major design goal. This property should guarantee that a party in the key exchange protocol is assured that another party also holds the shared key. Remarkably, while secrecy and authenticity definitions have been studied extensively, key confirmation has been treated rather informally so far. In this work, we provide the first rigorous formalization of key confirmation, leveraging the game-based security framework well-established for secrecy and authentication notions for key exchange. We define two flavors of key confirmation, full and almost-full key confirmation, taking into account the inevitable asymmetry of the roles of the parties with respect to the transmission of the final protocol message. These notions capture the strongest level of key confirmation reasonably expectable for the two communication partners of the key exchange. We demonstrate the benefits of having precise security definitions for key-confirmation by applying them to the next version of the Transport Layer Security (TLS) protocol, version 1.3, currently developed by the Internet Engineering Task Force (IETF). Our analysis shows that the full handshake as specified in the TLS 1.3 draft draft-ietf-tls-tls13-10 achieves desirable notions of key confirmation for both clients and servers. While key confirmation is generally understood and in the TLS 1.3 draft described as being obtained from the Finished messages exchanged, interestingly we can show that the full TLS 1.3 handshake provides key confirmation even without those messages, shedding a formal light on the security properties different handshake messages entail. We further demonstrate the usefulness of rigorous definition by revisiting a folklore approach to establish key confirmation (as discussed for example in SP 800-56A of NIST). We provide a formalization as a generic protocol transformation and show that the resulting protocols enjoy strong key confirmation guarantees, thus confirming its beneficial use in both theoretical and practical protocol designs.
The effect of soymilk intake on the fecal microbiota, particularly Bifidobacterium species, and intestinal environment of healthy adults: a pilot study

The influence of soymilk on the fecal microbiota, particularly Bifidobacterium species, and metabolic activities were investigated in eight healthy adult humans. During the soymilk intake period, the number of bifidobacteria in feces was significantly higher (p<0.05) on day 14 of the soymilk intake period than before the intake period, whereas that of Enterobacteriaceae was significantly lower (p<0.05) on days 7 and 14 of the soymilk intake period than before the intake period. In an investigation of Bifidobacterium at the species or group level, the numbers of all species and groups studied slightly increased during the soymilk intake period. These results show that the intake of soymilk may contribute to improving the intestinal environment.
Design guidelines to achieve minimum energy operation for ultra low voltage tunneling FET logic circuits

A tunneling field effect transistor (TFET) attracts attention, because TFET circuits can achieve better energy efficiency than conventional MOSFET circuits. Although design issues in ultra low voltage logic circuits, such as the minimum operatable voltage (VDDmin), have been investigated for MOSFET’s, VDDmin for TFET’s have not been discussed. In this paper, VDDmin of TFET logic circuits is evaluated for the first time and a closed-form expression of VDDmin is derived, which indicates that the within-die threshold voltage variation (σVT) strongly affects VDDmin. In addition, since it is not clear how much the energy of the logic circuits is quantitatively reduced when both the subthreshold swing (S) and the power supply voltage are reduced, an analytical equation of the minimum energy of TFET logic circuits is also derived. From the derived equations, the design guideline is presented for the device engineers of TFET’s that σVT should be reduced as S decreases.
Thioredoxin-1 Protects against Neutrophilic Inflammation and Emphysema Progression in a Mouse Model of Chronic Obstructive Pulmonary Disease Exacerbation

Background Exacerbations of chronic obstructive pulmonary disease (COPD) are characterized by acute enhancement of airway neutrophilic inflammation under oxidative stress and can be involved in emphysema progression. However, pharmacotherapy against the neutrophilic inflammation and emphysema progression associated with exacerbation has not been established. Thioredoxin-1 has anti-oxidative and anti-inflammatory properties and it can ameliorate neutrophilic inflammation through anti-chemotactic effects and prevent cigarette smoke (CS)-induced emphysema. We aimed to determine whether thioredoxin-1 can suppress neutrophilic inflammation and emphysema progression in a mouse model of COPD exacerbation and if so, to reveal the underlying mechanisms. Results Mice were exposed to CS and then challenged with polyinosine-polycytidylic acid [poly(I:C)], an agonist for virus-induced innate immunity. Airway neutrophilic inflammation, oxidative stress and lung apoptosis were enhanced in smoke-sensitive C57Bl/6, but not in smoke-resistant NZW mice. Exposure to CS and poly(I:C) challenge accelerated emphysema progression in C57Bl/6 mice. Thioredoxin-1 suppressed neutrophilic inflammation and emphysema progression. Poly(I:C) caused early neutrophilic inflammation through keratinocyte-derived chemokine and granulocyte-macrophage colony-stimulating factor (GM-CSF) release in the lung exposed to CS. Late neutrophilic inflammation was caused by persistent GM-CSF release, which thioredoxin-1 ameliorated. Thioredoxin-1 enhanced pulmonary mRNA expression of MAP kinase phosphatase 1 (MKP-1), and the suppressive effects of thioredoxin-1 on prolonged GM-CSF release and late neutrophilic inflammation disappeared by inhibiting MKP-1. Conclusion Using a mouse model of COPD exacerbation, we demonstrated that thioredoxin-1 ameliorated neutrophilic inflammation by suppressing GM-CSF release, which prevented emphysema progression. Our findings deepen understanding of the mechanisms underlying the regulation of neutrophilic inflammation by thioredoxin-1 and indicate that thioredoxin-1 could have potential as a drug to counteract COPD exacerbation.