Miracle-dz/UniFAR-FTUs huggingface dataset:
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

Novel sequencing technologies permit the rapid production of large sequence data sets. These technologies are likely to revolutionize genetics and biomedical research, but a thorough characterization of the ultra-short read output is necessary. We generated and analyzed two Illumina 1G ultra-short read data sets, i.e. 2.8 million 27mer reads from a Beta vulgaris genomic clone and 12.3 million 36mers from the Helicobacter acinonychis genome. We found that error rates range from 0.3% at the beginning of reads to 3.8% at the end of reads. Wrong base calls are frequently preceded by base G. Base substitution error frequencies vary by 10- to 11-fold, with A > C transversion being among the most frequent and C > G transversions among the least frequent substitution errors. Insertions and deletions of single bases occur at very low rates. When simulating re-sequencing we found a 20-fold sequencing coverage to be sufficient to compensate errors by correct reads. The read coverage of the sequenced regions is biased; the highest read density was found in intervals with elevated GC content. High Solexa quality scores are over-optimistic and low scores underestimate the data quality. Our results show different types of biases and ways to detect them. Such biases have implications on the use and interpretation of Solexa data, for de novo sequencing, re-sequencing, the identification of single nucleotide polymorphisms and DNA methylation sites, as well as for transcriptome analysis.
Diversity patterns along and across the Chilean margin: A continental slope encompassing oxygen gradients and methane seep benthic habitats

In the present study we review datasets available for the Chilean margin to assess the relationship between environmental (or habitat) heterogeneity and benthic diversity. Several factors, such as the presence of different water masses, including the oxygen-deficient Equatorial Sub-surface Waters (ESSW) at the continental shelf and upper slope, and the Antarctic Intermediate Waters (AIW) at mid slope depths appear to control the bathymetric distribution of benthic communities. The presence of methane seeps and an extended oxygen minimum zone (OMZ) add complexity to the benthic distribution patterns observed. All these factors generate environmental heterogeneity, which is predicted to affect the diversity patterns both along and across the Chilean continental margin. The response to these factors differs among different faunal size groups: meio-, macro-, and megafauna. Physiological adaptations to oxygen deficiency and constraints related to body size of each group seem to explain the larger-scale patterns observed, while sediment ⁄habitat heterogeneity (e.g. at water mass boundaries, hardgrounds, biogeochemical patchiness, sediment organic content, grain size) may influence the local fauna diversity patterns. Marine Ecology. ISSN 0173-9565
Antrodia camphorata Increases Insulin Secretion and Protects from Apoptosis in MIN6 Cells

Antrodia camphorata is a Taiwanese-specific fungus which has been used clinically to treat hypertension, immune- and liver-related diseases and cancer; however, it has never been studied in type 2 diabetes mellitus (T2DM). Hyperglycemia in T2DM causes endoplasmic reticulum (ER) stress, leading to β-cell dysfunction. During chronic ER stress, misfolded proteins accumulate and initiate β-cell apoptosis. Moreover, β-cell dysfunction leads to defect in insulin secretion, which is the key process in the development and progression of T2DM. Therefore, the aim of the present study was to examine the effects of A. camphorata on insulin secretion and ER stress-induced apoptosis in a mouse β-cell line, MIN6, and their underlying mechanisms. We demonstrated that the ethanolic extract of A. camphorata increased glucose-induced insulin secretion dose-dependently through peroxisome proliferator-activated receptor-γ (PPAR-γ) pathway, and upregulated genes that were involved in insulin secretion, including PPAR-γ, glucose transporter-2 and glucokinase. Furthermore, A. camphorata slightly increased cell proliferation, as well as protected from ER stress-induced apoptosis in MIN6 cells. In conclusion, this study provided evidences that A. camphorata might have anti-diabetic effects and could be a novel drug for T2DM.
A Scalable and High-efficiency Discovery Service Using a New Storage

Discovery Service (DS), used to trace the movement of objects along supply chains, is an important component of the Internet of Things (IoT). DS is faced with the challenge of huge volume of data as well as large amount of parallel requests of discovery and publish. This paper proposes a new central-indexing DS system using distributed NOSQL database HBase to better support big data and parallel processing. A new storage schema of DS data is designed to optimize the discovery efficiency of DS records. The new storage schema uses object ID as row key, event timestamp as column identifier and event index content as cell value. The typical recursive discovery algorithm, which is needed in DS but often neglected in previous works, is specified to realize the full tracing of object's movement. A prototype of the DS system proposed is implemented. The experiments show that the number of concurrent discoveries the proposed DS can handle per second is about 200 times that of the DS based on RDBMS, and the number of concurrent publishes the proposed DS can process per second is about five times that of the DS based on RDBMS.
An Optimal and Cost Effective Key Management Scheme for Secure Multicast Communication

The recent growth, popularity and extensive need fo r the deployment of group oriented applications lik e multiparty video conferencing, multiplayer online g aming and real time push based delivery systems has triggered the demand for secure group communication . These applications require multicast to minimize the volume of network traffic they generate. Multip arty communications have recently become the focus f new developments in the area of applications. The g oal of this paper is to establish a secure group communication using multicast key distribution sche me. In general, to meet forward secrecy and backwar d secrecy, any change in the group membership will in duce group rekeying. Here, a novel key management scheme is proposed in which no redistribution of gr oup key (shared key) is required during the group dynamics there by reducing computation and communic ation complexities considerably.
PPAR Gamma in Neuroblastoma: The Translational Perspectives of Hypoglycemic Drugs

Neuroblastoma (NB) is the most common and aggressive pediatric cancer, characterized by a remarkable phenotypic diversity and high malignancy. The heterogeneous clinical behavior, ranging from spontaneous remission to fatal metastatic disease, is attributable to NB biology and genetics. Despite major advances in therapies, NB is still associated with a high morbidity and mortality. Thus, novel diagnostic, prognostic, and therapeutic approaches are required, mainly to improve treatment outcomes of high-risk NB patients. Among neuroepithelial cancers, NB is the most studied tumor as far as PPAR ligands are concerned. PPAR ligands are endowed with antitumoral effects, mainly acting on cancer stem cells, and constitute a possible add-on therapy to antiblastic drugs, in particular for NB with unfavourable prognosis. While discussing clinical background, this review will provide a synopsis of the major studies about PPAR expression in NB, focusing on the potential beneficial effects of hypoglycemic drugs, thiazolidinediones and metformin, to reduce the occurrence of relapses as well as tumor regrowth in NB patients.
Multi-sensor Fuzzy Stochastic Fusion Based on Genetic Algorithms

To establish a parallel fusion approach of processing high dimensional information, the model and criterion of multi-sensor fuzzy stochastic data fusion were presented. In order to design genetic algorithm fusion ( the fusion parameter coding ) initial population and fitness function establishing, and fuzzy logic controller designing for genetic operations and probability choosing were complete d. The discussion on the highly dimensional fusion was given. For a moving target with the division of 1.64 (velocity) and 1.75 (acceleration), the precision of fusion is 0.94 and 0.98 respectively. The fusion approach can improve the reliability and decision precision effectively.
Self-Measurement of Combinatorial Circuit Delays in FPGAs

This article proposes a Built-In Self-Test (BIST) method to accurately measure the combinatorial circuit delays on an FPGA. The flexibility of the on-chip clock generation capability found in modern FPGAs is employed to step through a range of frequencies until timing failure in the combinatorial circuit is detected. In this way, the delay of any combinatorial circuit can be determined with a timing resolution of the order of picoseconds. Parallel and optimized implementations of the method for self-characterization of the delay of all the LUTs on an FPGA are also proposed. The method was applied to Altera Cyclone II and III FPGAs . A complete self-characterization of LUTs on a Cyclone II was achieved in 2.5 seconds, utilizing only 13kbit of block RAM to store the results. More extensive tests were carried out on the Cyclone III and the delays of adder circuits and embedded multiplier blocks were successfully measured. This self-measurement method paves the way for matching timing requirements in designs to FPGAs as a means of combating the problem of process variations.
Chronic alcoholism alters systemic and pulmonary glutathione redox status.

RATIONALE Previous studies have linked the development and severity of acute respiratory distress syndrome with a history of alcohol abuse. In clinical studies, this association has been centered on depletion of pulmonary glutathione and subsequent chronic oxidant stress. OBJECTIVES The impact on redox potential of the plasma or pulmonary pools, however, has never been reported. METHODS Plasma and bronchoalveolar lavage fluid were collected from otherwise healthy alcohol-dependent subjects and control subjects matched by age, sex, and smoking history. MEASUREMENTS AND MAIN RESULTS Redox potential was calculated from measured reduced and oxidized glutathione in plasma and lavage. Among subjects who did and did not smoke, lavage fluid glutathione redox potential was more oxidized in alcohol abusers by approximately 40 mV, which was not altered by dilution. This oxidation of the airway lining fluid associated with chronic alcohol abuse was independent of smoking history. A shift by 20 mV in plasma glutathione redox potential, however, was noted only in subjects who both abused alcohol and smoked. CONCLUSIONS Chronic alcoholism was associated with alveolar oxidation and, with smoking, systemic oxidation. However, systemic oxidation did not accurately reflect the dramatic alcohol-induced oxidant stress in the alveolar space. Although there was compensation for the oxidant stress caused by smoking in control groups, the capacity to maintain a reduced environment in the alveolar space was overwhelmed in those who abused alcohol. The significant alcohol-induced chronic oxidant stress in the alveolar space and the subsequent ramifications may be an important modulator of the increased incidence and severity of acute respiratory distress syndrome in this vulnerable population.
A charge pump circuit by using voltage-doubler as clock scheme

A new charge pump circuit with a clock that shows an increased clock voltage as its stage is increased is proposed in the paper. The charge pump circuit utilizes the cross-connected NMOS, voltage doubler, as a pumping stage. Each stage of the voltage-doubler provides a pair of complementary clock voltages. The clock voltage also increases as the stage of voltage doubler is increased. It shows that a voltage up to 37.85V was obtained after eight-stage's pumping of the circuit, through the simulation of HSpice under 0.35 µm process with 2V of supply voltage and clock voltage.
Performance Analysis of Concurrency Control Mechanisms for OLTP Databases

—Concurrency control (CC) in distributed and multidimensional databases is becoming more important due to recent increase in high-volume data storage with increasing online transaction processing (OLTP) requirements for medium and large organisations. This paper examines three concurrency control mechanisms commonly adopted and analyses their performance in distributed databases for OLTP operational systems of enterprises. The three CC mechanisms investigated are, two phase locking (2PL), wait depth limited (WDL) and optimistic concurrency control. These CC mechanisms have been studied well in disk-based systems. However, with the recent advances of cost-effective main memory or in-memory storage that can support much higher transaction rates than disk-based systems, there is sufficient motivation to re-investigate the performance of such CC mechanisms in diverse processor configurations. This paper presents a comparison of their behaviour and performance in terms of throughput rates achieved with varying transaction size and contention. The outcome of this study has resulted in further research proposals for improving the performance of these CC mechanisms for OLTP databases.
Development of a brachiation robot with hook-shaped end effectors and realization of brachiation motion with a simple strategy

In this research we focus on locomotive robots that move to a target location. In particular, we developed a new brachiation robot with a simple mechanism. The robot uses a hook-shaped end effector for a grasping mechanism. We propose a motion principle and a control strategy for achieving brachiation motion. In particular, we propose a motion principle based on the pendulum motion of a rigid body. Finally, we conducted experiments to investigate the brachiation motion achieved by using the developed brachiation robot and the proposed motion strategy. The robot successfully achieved brachiation motion.
An energy- and performance-aware DRAM cache architecture for hybrid DRAM/PCM main memory systems

The last few years have witnessed the emergence of a promising new memory technology. Phase-Change Memory (PCM) is increasingly viewed as an attractive alternative for the memory sub-system of future microprocessor architectures, mainly because of its inherent ability to scale deeply into the nanoscale regime, and its low power consumption. However, PCM's write performance is its Achilles' heel, especially when compared to the prevalent DRAM technology. This weakness necessitates the deployment of hybridized solutions that fuse DRAM and PCM, in order to attain high overall system performance. In this paper, we set out to explore how various DRAM/PCM hybrid configurations affect system performance and energy consumption, and then proceed with the presentation of a novel architecture that maximizes performance without adversely affecting power efficiency. An energy-delay product improvement of 42.2%, on average, over conventional hybrid structures, is demonstrated.
Uneven Distribution of Hepatitis C Virus Quasispecies in Tissues from Subjects with End-Stage Liver Disease: Confounding Effect of Viral Adsorption and Mounting Evidence for the Presence of Low-Level Extrahepatic Replication

ABSTRACT We have found differences among the populations of hepatitis C virus sequences in serum, peripheral blood mononuclear cells (PBMCs), and various tissues in patients with chronic hepatitis C. These results are compatible with the existence of independent viral compartments in the infected host. Our results also suggest that PBMCs, and probably various tissues, can selectively adsorb viral subpopulations differing in the E2 region.
A Trajectory Optimization Based Analysis of the 3 Di Flight Efficiency Metric

As a means of measuring progress towards fuel and emissions reduction targets, the United Kingdom Air Navigation Service Provider NATS developed the 3Di flight efficiency metric. In principle the 3Di score of a flight is calculated by comparing a flown trajectory to a theoretical fuel/CO2 optimum trajectory. In response to a Eurocontrol review of the metric, the 3Di score has been analysed using a trajectory optimization method based on optimal control. The results suggest that further development of the metric is required to make it sensitive to vertical flight inefficiencies not related to periods of level flight. The results also show that the BADA trajectories used in the 3Di score to define the optimum fuel efficient operation of the aircraft are not optimal fuel efficient trajectories. Additionally, the results show that fuel inefficiencies introduced by flight planning restrictions need to be accounted for in any vertical flight inefficiency metric.
J un 2 00 1 Evolution of random networks

We review a recent fast progress in statistical physics of evolving networks. Interest focuses mainly on the structure properties of random hierarchically organized networks in communications, biology, social sciences and economics. A number of giant artificial networks of such a kind were created recently. This opens a wide field for research of their topology, evolution, and complex processes proceeding in them. Such networks possess a rich set of scaling properties. A number of them is scale-free and show striking resilience against random breakdowns. In spite of huge sizes of these networks, the distances between most of nodes of the networks are short – the " small-world " effect. Their features make them appropriate for numerous applications. We discuss how growing networks self-organize into scale-free structure and the role of the mechanism of preferential linking. We consider the topological and structural properties of evolving networks, and percolation in networks. We present a number of models demonstrating the main features of evolving networks and discuss existing approaches to their simulation and analytical study. Applications of the general results to the particular networks in Nature are discussed. We demonstrate the generic connections of the network growth processes with the general problems of non-equilibrium physics, econophysics, evolutionary biology, etc.
Diffusion Dynamics in Structured Online Social Networks with Push-Based Forwarding Mechanism

In this paper, we propose models to characterize diffusion dynamics in structured online social networks with push-based forwarding mechanism. We introduce the term user influence to characterize the average number of times that messages are browsed which is incurred by a given type user generating a message, and then propose a theoretical analysis approach to estimate it. We conduct simulations and provide simulation results, which are consistent with the theoretical analysis results perfectly.
Dementia due to Meningovascular Syphilis in Medial Temporal Lobe and Cognitive Rehabilitation

The temporal lobe is essential in saving declarative memory and plays an important role along with the cerebral neocortex in creating and maintaining long-term memory. Damage to the temporal lobe is expected to result in cognitive impairment or dementia, which has characteristic symptoms such as cognitive and behavioral dysfunction and decreasing self-reliance in activities of daily living. We report on a patient, who suffered from dementia due to meningovascular syphilis affecting the medial temporal lobe, and on the outcome of cognitive rehabilitation.
Robust control for a class of uncertain switched time delay systems using delta operator

This paper considers the problem of stability and robust stabilization for a class of uncertain time delay switched systems using the delta operator. Based on multiple Lyapunov-Krasovskii function in delta domain, a sufficient condition for the existence of stability of the delta operator time delay switched system is presented, and a new sampling period and delay dependent design approach to robust state feedback controller is addressed. The proposed controller can robustly stabilize the uncertain delta operator time delay switched system for all admissible parameter perturbations. The solution to the controller is formulated in the form of a set of linear matrix inequalities. A numerical example is provided to illustrate the effectiveness of the developed method.
Cross Polarization Discrimination of MIMO Antenna Configurations

The cross polarization discrimination (XPD) of multiple input multiple output (MIMO) array antenna at a mobile station in indoor propagation environments is studied. The novel closed-form expressions for cross polarization discrimination of angular spread, mean angle of arrival (AOA) and scatterer numbers are presented. It provides a deep understanding of the cross polarization system for different indoor environments and takes into account both azimuth and elevation spectrum. Furthermore, XPD values depend highly on the propagation path between the base station (BS) and mobile station (MS) due to line of sight (LOS) and nonline of sight (NLOS) situation. Finally, we consider antenna inclination at MS, which impact on MIMO array antenna performance because it results in receiving power difference.
Cross-Brain Neurofeedback: Scientific Concept and Experimental Platform

The present study described a new type of multi-person neurofeedback with the neural synchronization between two participants as the direct regulating target, termed as “cross-brain neurofeedback. ” As a first step to implement this concept, an experimental platform was built on the basis of functional near-infrared spectroscopy, and was validated with a two-person neurofeedback experiment. This novel concept as well as the experimental platform established a framework for investigation of the relationship between multiple participants' cross-brain neural synchronization and their social behaviors, which could provide new insight into the neural substrate of human social interactions.
Exact likelihood ratio tests for penalised splines

Penalised-spline-based additive models allow a simple mixed model representation where the variance components control departures from linear models. The smoothing parameter is the ratio of the random-coefficient and error variances and tests for linear regression reduce to tests for zero random-coefficient variances. We propose exactlikelihood and restricted likelihood ratio tests for testing polynomial regression versus a general alternative modelled by penalised splines. Their spectral decompositions are used as the basis of fast simulation algorithms. We derive the asymptotic local power properties of the tests under weak conditions. In particular we characterise the local alternatives that are detected with asymptotic probability one. Confidence intervals for the smoothing parameter are obtained by inverting the tests for a fixed smoothing parameter versus a general alternative. We discuss F and R tests and show that ignoring the variability in the smoothing parameter estimator can have a dramatic effect on their null distributions. The powers of several known tests are investigated and a small set of tests with good power properties is identified. The restricted likelihood ratio test is among the best in terms of power. Copyright 2005, Oxford University Press.