Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-invasive biomarkers of oxidative stress: reproducibility and methodological issues

Abstract Oxidative stress is the hallmark of various chronic inflammatory lung diseases. Increased concentrations of reactive oxygen species (ROS) in the lungs of such patients are reflected by elevated concentrations of oxidative stress markers in the breath, airways, lung tissue and blood. Traditionally, the measurement of these biomarkers has involved invasive procedures to procure the samples or to examine the affected compartments, to the patient's discomfort. As a consequence, there is a need for less or non-invasive approaches to measure oxidative stress. The collection of exhaled breath condensate (EBC) has recently emerged as a non-invasive sampling method for real-time analysis and evaluation of oxidative stress biomarkers in the lower respiratory tract airways. The biomarkers of oxidative stress such as H2O2, F2-isoprostanes, malondialdehyde, 4-hydroxy-2-nonenal, antioxidants, glutathione and nitrosative stress such as nitrate/nitrite and nitrosated species have been successfully measured in EBC. The reproducibility, sensitivity and specificity of the methodologies used in the measurements of EBC oxidative stress biomarkers are discussed. Oxidative stress biomarkers also have been measured for various antioxidants in disease prognosis. EBC is currently used as a research and diagnostic tool in free radical research, yielding information on redox disturbance and the degree and type of inflammation in the lung. It is expected that EBC can be exploited to detect specific levels of biomarkers and monitor disease severity in response to appropriate prescribed therapy/treatment.
Measuring genome conservation across taxa: divided strains and united kingdoms

Species evolutionary relationships have traditionally been defined by sequence similarities of phylogenetic marker molecules, recently followed by whole-genome phylogenies based on gene order, average ortholog similarity or gene content. Here, we introduce genome conservation—a novel metric of evolutionary distances between species that simultaneously takes into account, both gene content and sequence similarity at the whole-genome level. Genome conservation represents a robust distance measure, as demonstrated by accurate phylogenetic reconstructions. The genome conservation matrix for all presently sequenced organisms exhibits a remarkable ability to define evolutionary relationships across all taxonomic ranges. An assessment of taxonomic ranks with genome conservation shows that certain ranks are inadequately described and raises the possibility for a more precise and quantitative taxonomy in the future. All phylogenetic reconstructions are available at the genome phylogeny server: <>.
The Storage and Use of Biological Tissue Samples from Minors for Research: A Focus Group Study

Genetic research on pediatric stored tissue samples raises specific ethical questions that differ from those raised when adults are the donors. To investigate opinions on this matter, we conducted 10 focus group discussions. Five focus groups were conducted with adult participants and 5 had teenage participants between 15 and 19 years old. The discussions were analyzed with NVIVO 8 (qualitative research software). We found the following recurrent categories: the requirement that research should not pose any burden on children and that it should benefit other children, the trust people had in the role of parents, the need for information and the growth towards autonomy. Both the adults and teenagers we interviewed thought that the inclusion of tissue samples from minors in research had ethical implications. A major concern was that nontherapeutic research would pose no extra burden on children, which would assume the use of nonintrusive methods of gathering samples and the use of samples that were gathered in a diagnostic context. Participants, however, also understood the necessity of such research. The overall impression was that parents would be the best persons to make decisions on behalf of a small child and that the same parents would engage their children in the decision-making when they grew older. People thought that there was a duty to recontact minors when they reached the age of competence but on a best-effort basis.
Labile Fe(II) concentrations in the Atlantic sector of the Southern Ocean along a transect from the subtropical domain to the Weddell Sea Gyre

Abstract. Labile Fe(II) distributions were investigated in the Sub-Tropical South Atlantic and the Southern Ocean during the BONUS-GoodHope cruise from 34 to 57° S (February–March 2008). Concentrations ranged from below the detection limit (0.009 nM) to values as high as 0.125 nM. In the surface mixed layer, labile Fe(II) concentrations were always higher than the detection limit, with values higher than 0.060 nM south of 47° S, representing between 39 % and 63 % of dissolved Fe (DFe). Apparent biological production of Fe(II) was evidenced. At intermediate depth, local maxima were observed, with the highest values in the Sub-Tropical domain at around 200 m, and represented more than 70 % of DFe. Remineralization processes were likely responsible for those sub-surface maxima. Below 1500 m, concentrations were close to or below the detection limit, except at two stations (at the vicinity of the Agulhas ridge and in the north of the Weddell Sea Gyre) where values remained as high as ~0.030–0.050 nM. Hydrothermal or sediment inputs may provide Fe(II) to these deep waters. Fe(II) half life times (t1/2) at 4°C were measured in the upper and deep waters and ranged from 2.9 to 11.3 min, and from 10.0 to 72.3 min, respectively. Measured values compared quite well in the upper waters with theoretical values from two published models, but not in the deep waters. This may be due to the lack of knowledge for some parameters in the models and/or to organic complexation of Fe(II) that impact its oxidation rates. This study helped to considerably increase the Fe(II) data set in the Ocean and to better understand the Fe redox cycle.
Endothelial AMP-Activated Protein Kinase Regulates Blood Pressure and Coronary Flow Responses Through Hyperpolarization Mechanism in Mice

Objective—Vascular endothelium plays an important role to maintain cardiovascular homeostasis through several mechanisms, including endothelium-dependent hyperpolarization (EDH). We have recently demonstrated that EDH is involved in endothelial metabolic regulation in mice. However, it remains to be examined whether AMP-activated protein kinase (AMPK), an important metabolic regulator, is involved in EDH and if so, whether endothelial AMPK (eAMPK) plays a role for circulatory regulation. Approach and Results—We examined the role of eAMPK in EDH, using mice with endothelium-specific deficiency of &agr;-catalytic subunit of AMPK, either &agr;1 (eAMPK&agr;1−/−&agr;2+/+) or &agr;2 (eAMPK&agr;1+/+&agr;2−/−) alone or both of them (eAMPK&agr;1−/−&agr;2−/−). We performed telemetry, organ chamber, electrophysiological, and Langendorff experiments to examine blood pressure, vascular responses, hyperpolarization of membrane potential, and coronary flow responses, respectively. Hypertension was noted throughout the day in eAMPK&agr;1−/−&agr;2−/− and eAMPK&agr;1−/−&agr;2+/+ but not in eAMPK&agr;1+/+&agr;2−/− mice when compared with respective control. Importantly, endothelium-dependent relaxations, EDH, and coronary flow increase were all significantly reduced in eAMPK&agr;1−/−&agr;2−/− and eAMPK&agr;1−/−&agr;2+/+ but not in eAMPK&agr;1+/+&agr;2−/− mice. In contrast, endothelium-independent relaxations to sodium nitroprusside (a NO donor), NS-1619 (a Ca2+-activated K+ channel opener), and exogenous H2O2 were almost comparable among the groups. In eAMPK&agr;1−/−&agr;2−/− mice, antihypertensive treatment with hydralazine or long-term treatment with metformin (a stimulator of AMPK) failed to restore EDH-mediated responses. Conclusions—These results provide the first direct evidence that &agr;1 subunit of eAMPK substantially mediates EDH responses of microvessels and regulates blood pressure and coronary flow responses in mice in vivo, demonstrating the novel role of eAMPK in cardiovascular homeostasis.
Distinct Affinity of Binding Sites for S-Layer Homologous Domains in Clostridium thermocellum and Bacillus anthracis Cell Envelopes

ABSTRACT Binding parameters were determined for the SLH (S-layer homologous) domains from the Clostridium thermocellum outer layer protein OlpB, from the C. thermocellum S-layer protein SlpA, and from the Bacillus anthracis S-layer proteins EA1 and Sap, using cell walls from C. thermocellum and B. anthracis. Each SLH domain bound to C. thermocellumand B. anthracis cell walls with a differentKD, ranging between 7.1 × 10−7 and 1.8 × 10−8 M. Cell wall binding sites for SLH domains displayed different binding specificities in C. thermocellum and B. anthracis. SLH-binding sites were not detected in cell walls of Bacillus subtilis. Cell walls of C. thermocellum lost their affinity for SLH domains after treatment with 48% hydrofluoric acid but not after treatment with formamide or dilute acid. A soluble component, extracted from C. thermocellum cells by sodium dodecyl sulfate treatment, bound the SLH domains from C. thermocellum but not those from B. anthracisproteins. A corresponding component was not found in B. anthracis.
Ultra-Low Power Nanomagnet-Based Computing: A System-Level Perspective

MOSFET scaling is facing overwhelming challenges with increased parameter variations, exponentially higher leakage current, and higher power density. Thus, researchers have started looking at alternative switching devices and spintronics-based computing paradigms. Nanomagnet-based computing is one such paradigm with intrinsic switching energy close to thermal limits and scalability down to 5 nm. In this paper, we explore the possibility of nanomagnet-based design using nonmajority gates. The design approach can offer significant area, delay, and energy advantages compared to majority-gate-based designs. Moreover, new clock technologies and architectures are developed to improve computation robustness and power dissipation of nanomagnet systems. We also developed a comprehensive device/circuit/system compatible simulation framework to evaluate the functionality and architecture of a nanomagnet system and conducted a feasibility/comparison study to determine the effectiveness of the technology compared to standard digital electronics. Performance results from a nanomagnet-based 16-point discrete cosine transform (DCT) with enhanced clock architecture, narrow gap cladding of nanomagnets, or embedding nanomagnets in solenoid with steel core, together with near neighbor system architecture, show up to 10 × improvement over subthreshold 15 nm CMOS (Vdd = 90 mV) design, using “energy-delay0.5-area product (ED0.5 A)” as comparison metric. Finally, we explored the scalability of nanomagnets and the effectiveness of field-based switching.
Protective effect of augmenter of liver regeneration on hydrogen peroxide-induced apoptosis in SH-SY5Y human neuroblastoma cells.

BACKGROUND Hydrogen peroxide, as other reactive oxygen species (ROS) produced during redox processes, induces lipid membrane peroxidation and protein degeneration causing cell apoptosis. ROS are recently considered as messengers in cell signalling processes, which, through reversible protein disulphide bridges formation, activate regulatory factors of cell proliferation and apoptosis. Disulphide bridges formation is catalysed by sulphydryl oxidase enzymes. AIM The neuroprotective effect of ALR protein (Alrp), a sulphydryl oxidase enzyme, on H(2)O(2)-induced apoptosis in SH-SY5Y cells has been evaluated. METHODS Cell viability, flow cytometric evaluation of apoptotic cells, fluorescent changes of nuclear morphology, immunocytochemistry Alrp detection, Western blot evaluation of mitochondrial cyt c release and mitochondrial swelling were determined. RESULTS Alrp prevents the H(2)O(2)-induced cell viability loss, apoptotic cell death and mitochondrial swelling in SH-SY5Y cells in culture. CONCLUSIONS The data demonstrate that Alrp improves SH-SY5Y cells survival in H(2)O(2)-induced apoptosis. It is speculated that this effect could be related to the Alrp enzymatic activity.
The age of the Oughterard Granite, Connemara, Ireland

Despite a wide latitude for interpretation of previous Rb–Sr isotopic data on the Oughterard Granite the age of this intrusion has been regarded as a critical time-marker in resolving the Caledonian evolution of Connemara. New isotopic data suggest that the age of the intrusion be revised from c. 460 Ma to c. 400 Ma, thus making the Oughterard Granite one among the many Newer Caledonian Granites in Ireland. The preferred age is 407 ± 23 Ma, and the initial 87 Sr/86Sr ratio is 0·7076 ± 1. Heterogeneity within the granite is demonstrated, which explains the difficulty in obtaining reliable isotopic ages from this intrusion.
Contextual mail (CXM): an e-mail system for enabling dynamic information-based destination control

There is a fact that, when people send messages, the destinations are not always deterministic; people sometimes want to send a message to someone who are just interested in the content of the message. However, e-mail services, which have been recognized as the de-facto standard for years, do not have such capability though a couple of emerging messaging applications like micro-blogging have it. Problems happen particularly when people use the e-mail system to make an announcement regarding an official event, which would be easily received even by people who are not likely interested in it. This paper proposes a new e-mail system that has the capability of dynamically controlling recipients of messages according to the context.
Receding horizon control and scheduling of quantized control systems with communication constraints

This paper investigates the problem of joint design of a receding horizon control and the medium access scheduling for quantized control systems over limited bandwidth networks, in which only a limited number of actuators are allowed to communicate with the controller at each time instant. By introducing a communication scheduling matrix to describe the medium access status and considering the influence of quantizers, we can model the control system as a switched model with structured norm-bounded uncertainties. The stabilizing channels with guaranteed stability are chosen first. Based on the stabilizing channels, a receding horizon control strategy with optimal dynamic resource allocation is proposed by minimizing the upper bound on a finite-horizon quadratic performance index. Simulation results show the effectiveness of the developed method finally.
The Mitochondrial Protein Import Motor

Abstract Mitochondrial proteins are synthesized as precursor proteins in the cytosol and are posttranslationally imported into the organelle. A complex system of translocation machineries recognizes and transports the precursor polypeptide across the mitochondrial membranes. Energy for the translocation process is mainly supplied by the mitochondrial membrane potential (∆ψ) and the hydrolysis of ATP. Mitochondrial Hsp70 (mtHsp70) has been identified as the major ATPase driving the membrane transport of the precursor polypeptides into the mitochondrial matrix. Together with the partner proteins Tim44 and Mge1, mtHsp70 forms an import motor complex interacting with the incoming preproteins at the inner face of the inner membrane. This import motor complex drives the movement of the polypeptides in the translocation channel and the unfolding of carboxy-terminal parts of the preproteins on the outside of the outer membrane. Two models of the molecular mechanism of mtHsp70 during polypeptide translocation are discussed. In the ‘trapping’ model, precursor movement is generated by Brownian movement of the polypeptide chain in the translocation pore. This random movement is made vectorial by the interaction with mtHsp70 in the matrix. The detailed characterization of conditional mutants of the import motor complex provides the basis for an extended model. In this ‘pulling’ model, the attachment of mtHsp70 at the inner membrane via Tim44 and a conformational change induced by ATP results in the generation of an inward-directed force on the bound precursor polypeptide. This active role of the import motor complex is necessary for the translocation of proteins containing tightly folded domains. We suggest that both mechanisms complement each other to reach a high efficiency of preprotein import.
Skewed Compressed Caches

Cache compression seeks the benefits of a larger cache with the area and power of a smaller cache. Ideally, a compressed cache increases effective capacity by tightly compacting compressed blocks, has low tag and metadata overheads, and allows fast lookups. Previous compressed cache designs, however, fail to achieve all these goals. In this paper, we propose the Skewed Compressed Cache (SCC), a new hardware compressed cache that lowers overheads and increases performance. SCC tracks super blocks to reduce tag overhead, compacts blocks into a variable number of sub-blocks to reduce internal fragmentation, but retains a direct tag-data mapping to find blocks quickly and eliminate extra metadata (i.e., No backward pointers). Saccades this using novel sparse super-block tags and a skewed associative mapping that takes compressed size into account. In our experiments, SCC provides on average 8% (up to 22%) higher performance, and on average 6% (up to 20%) lower total energy, achieving the benefits of the recent Decoupled Compressed Cache [26] with a factor of 4 lower area overhead and lower design complexity.
Study of relative quantitation of Tc-99m annexin localization in pulmonary nodules using an anthropomorphic phantom

In current clinical oncology practice, it often takes weeks or months of cancer therapy until a response to treatment can be identified by evaluation of tumor size in images. It is hypothesized that changes in relative localization of the apoptosis imaging agent Tc-99m Annexin before and after the administration of chemotherapy may be useful as an early indicator of the success of therapy. The objective of this study was to determine the minimum relative change in tumor localization that could be confidently determined as an increased localization. A modified version of the Data Spectrum Anthropomorphic Torso phantom, in which four spheres could be positioned in the lung region, was filled with organ concentrations of Tc-99m representative of those observed in clinical imaging of Tc-99m Annexin. Five acquisitions of an initial sphere to lung concentration, and at concentrations of 1.1, 1.2, 1.3, and 1.4 times the initial concentration, were acquired at clinically realistic count levels. The acquisitions were reconstructed by filtered backprojection, ordered subset expectation maximization (OSEM) without attenuation compensation (AC), and OSEM with AC. Permutation methodology was used to create multiple region-of-interest count ratios from the five noise realizations at each concentration and between the elevated and initial concentrations. The resulting distributions were approximated by Gaussians, which were then used to estimate the likelihood of Type 1 and Type 2 Errors. It was determined that for the cases investigated, greater than a 20% to 30% or more increase was needed to confidently determine that an increase in localization had occurred depending on sphere size and reconstruction strategy.
The mechanosensory lateral line is used to assess opponents and mediate aggressive behaviors during territorial interactions in an African cichlid fish

ABSTRACT Fish must integrate information from multiple sensory systems to mediate adaptive behaviors. Visual, acoustic and chemosensory cues provide contextual information during social interactions, but the role of mechanosensory signals detected by the lateral line system during aggressive behaviors is unknown. The aim of this study was first to characterize the lateral line system of the African cichlid fish Astatotilapia burtoni and second to determine the role of mechanoreception during agonistic interactions. The A. burtoni lateral line system is similar to that of many other cichlid fishes, containing lines of superficial neuromasts on the head, trunk and caudal fin, and narrow canals. Astatotilapia burtoni males defend their territories from other males using aggressive behaviors that we classified as non-contact or contact. By chemically and physically ablating the lateral line system prior to forced territorial interactions, we showed that the lateral line system is necessary for mutual assessment of opponents and the use of non-contact fight behaviors. Our data suggest that the lateral line system facilitates the use of non-contact assessment and fight behaviors as a protective mechanism against physical damage. In addition to a role in prey detection, the diversity of lateral line morphology in cichlids may have also enabled the expansion of their social behavioral repertoire. To our knowledge, this is the first study to implicate the lateral line system as a mode of social communication necessary for assessment during agonistic interactions. Highlighted Article: Hydrodynamic cues are needed for assessment and non-contact fight behaviors during territorial interactions in an African cichlid fish.
Types of Gas Hydrates in Marine Environments and Their Thermodynamic Characteristics

The hydrates in marine environment can be grouped into two categories, diffusion gas hydrates and vent gas hydrates. The diffusion gas hydrates occur widely in an area where bottom simulation reflector (BSR) was recorded in seismic profiles, and is a thermodynamic equilibrium system of hydrates and water with dissolved methane within gas hydrate stability zone (GHSZ). The hydrates are buried in a distance apart from the seafloor and are characterized by low concentrations. The vent gas hydrates occur in an area where gas vents out of the seafloor. It is a thermodynamic disequilibrium system of hydrate, water and free gas, occurs in a zone that extends from the base of GHSZ to the seafloor, and is characterized by high concentration. Reported evidences show that these two types of hydrates are possibly occurring in the South China Sea.
Detection of Mobile Botnet Using VPN

As most applications in wired networks become available on mobile devices and mobile networks are well integrated with Internet, Botnet becomes the most significant threat to mobile devices. We propose a mobile Botnet detection scheme that detects "pull" style C&C channel. Our network-based scheme detects Botnet by inspecting abnormal flow features of C&C traffic traveling through VPN which provides a shared path for both 3/4G and WiFi. Through the verification analysis under real Botnet attacks, we show that our proposed scheme provides high detection rate by using abnormal models as well as low FP rate by adding white list and signatures.