Miracle-dz/UniFAR-FTUs huggingface dataset:
Parallel Optimal Pairwise Biological Sequence Comparison

Many bioinformatics applications, such as the optimal pairwise biological sequence comparison, demand a great quantity of computing resource, thus are excellent candidates to run in high-performance computing (HPC) platforms. In the last two decades, a large number of HPC-based solutions were proposed for this problem that run in different platforms, targeting different types of comparisons with slightly different algorithms and making the comparative analysis of these approaches very difficult. This article proposes a classification of parallel optimal pairwise sequence comparison solutions, in order to highlight their main characteristics in a unified way. We then discuss several HPC-based solutions, including clusters of multicores and accelerators such as Cell Broadband Engines (CellBEs), Field-Programmable Gate Arrays (FPGAs), Graphics Processing Units (GPUs) and Intel Xeon Phi, as well as hybrid solutions, which combine two or more platforms, providing the actual landscape of the main proposals in this area. Finally, we present open questions and perspectives in this research field.
Fluorodeoxyglucose uptake in human cancer cell lines is increased by hypoxia.

UNLABELLED Malignant neoplasms commonly have increased rates of glucose utilization, poor perfusion and areas of low oxygenation. Autoradiographic studies of excised tumors have shown increased FDG uptake in viable cells near necrotic portions of tumor. We evaluated in vitro whether tumor cell FDG uptake increased with hypoxia. METHODS The uptake of 3H-FDG into two human tumor cell lines (HTB 63 melanoma and HTB 77 IP3 ovarian carcinoma) was determined after exposure to differing oxygen atmospheres ranging from 0% to 20% O2 for varying time periods. Glucose transport was independently determined as well as estimates of the level of Glut-1 glucose transporter membrane protein. RESULTS FDG uptake in both the melanoma and the ovarian carcinoma cell lines increased significantly (39.6% +/- 6.7% and 36.7% +/- 9%, respectively) over basal (20% O2) conditions when cells were exposed to a mild hypoxic environment (5% O2) for 1.5 hr. With a 4-hr exposure to 1.5% O2, the increase in FDG uptake was greater at 52.3% +/- 8.9% and 43.5% +/- 19%, respectively. With 4 hr of anoxia, the increase in FDG uptake over basal conditions was 42.7% +/- 10% and 63.3% +/- 13.7% for melanoma and ovarian carcinoma cells, respectively. Membrane transport of 3-O-methylglucose (3-OMG) was increased by hypoxia for melanoma and ovarian carcinoma. Immunochemical assays for Glut-1 showed an increase in the membrane expression of the Glut-1 transporter in cells exposed to hypoxia. CONCLUSION Hypoxia increases cellular uptake of FDG in two different malignant human cell lines. Increased glucose transport, in part due to increased membrane expression of the Glut-1 glucose transporter, contributes to this phenomenon. Increased FDG uptake in tumors visualized during PET imaging may be partly reflective of tumor hypoxia.
Experiments on the preference-based organization interface in recommender systems

As e-commerce has evolved into its second generation, where the available products are becoming more complex and their abundance is almost unlimited, the task of locating a desired choice has become too difficult for the average user. Therefore, more effort has been made in recent years to develop recommender systems that recommend products or services to users so as to assist in their decision-making process. In this article, we describe crucial experimental results about a novel recommender technology, called the preference-based organization (Pref-ORG), which generates critique suggestions in addition to recommendations according to users' preferences. The critique is a form of feedback (“I would like something cheaper than this one”) that users can provide to the currently displayed product, with which the system may better predict what the user truly wants. We compare the preference-based organization technique with related approaches, including the ones that also produce critique candidates, but without the consideration of user preferences. A simulation setup is first presented, that identified Pref-ORG's significantly higher algorithm accuracy in predicting critiques and choices that users should intend to make, followed by a real-user evaluation which practically verified its significant impact on saving users' decision effort.
Abnormal Admission Chest X-Ray and MEWS as ICU Outcome Predictors in a Sub-Saharan Tertiary Hospital: A Prospective Observational Study

Background. Critical care in Uganda is a neglected speciality and deemed costly with limited funding/prioritization. We studied admission X-ray and MEWS as mortality predictors of ICU patients requiring mechanical ventilation. Materials and Methods. We did a cross-sectional study in Mulago Hospital ICU and 87 patients for mechanical ventilation were recruited with mortality as the outcome of interest. Chest X-ray results were the main independent variable and MEWS was also gotten for all patients. Results. We recruited 87 patients; most were males (60.92%), aged between 16 and 45 years (59.77%), and most admissions for mechanical ventilation were from the Trauma Unit (30.77%). Forty-one (47.13%) of the 87 patients died and of these 34 (53.13%) had an abnormal CXR with an insignificant IRR = 1.75 (0.90–3.38) (p = 0.062). Patients with MEWS ≥ 5 (p values = 0.018) and/or having an abnormal superior mediastinum (p values = 0.013) showed a positive association with mortality while having a MEWS ≥ 5 had an incidence risk ratio = 3.29 (1.00–12.02) (p = 0.018). MEWS was a good predictor of mortality (predictive value = 0.6739). Conclusion. Trauma (31%) caused most ICU admissions, having an abnormal admission chest X-rays positively associated with mortality and a high MEWS was also a good predictor of mortality.
Effects of RNAi-Mediated Knockdown of Histone Methyltransferases on the Sex-Specific mRNA Expression of Imp in the Silkworm Bombyx mori

Sexual differentiation in Bombyx mori is controlled by sex-specific splicing of Bmdsx, which results in the omission of exons 3 and 4 in a male-specific manner. In B. mori, insulin-like growth factor II mRNA-binding protein (Imp) is a male-specific factor involved in male-specific splicing of Bmdsx. Male-specific Imp mRNA results from the male-specific inclusion of exon 8. To verify the link between histone methylation and alternative RNA processing in Imp, we examined the effects of RNAi-mediated knockdown of several histone methyltransferases on the sex-specific mRNA expression of Imp. As a result, male-specific expression of Imp mRNA was completely abolished when expression of the H3K79 methyltransferase DOT1L was repressed to <10% of that in control males. Chromatin immunoprecipitation-quantitative PCR analysis revealed a higher distribution of H3K79me2 in normal males than in normal females across Imp. RNA polymerase II (RNAP II) processivity assays indicated that RNAi knockdown of DOT1L in males caused a twofold decrease in RNAP II processivity compared to that in control males, with almost equivalent levels to those observed in normal females. Inhibition of RNAP II-mediated elongation in male cells repressed the male-specific splicing of Imp. Our data suggest the possibility that H3K79me2 accumulation along Imp is associated with the male-specific alternative processing of Imp mRNA that results from increased RNAP II processivity.
Properties of Certain Families of 2k-Cycle-Free Graphs

Let v = v(G) and e = e(G) denote the order and size of a simple graph G, respectively. Let G = {Gi}i? 1, be a family of simple graphs of magnitude r > 1 and constant ? > 0, i.e., e(Gi) = (? + o(1))v(Gi)r, i ? ∞. For any such family G, whose members are bipartite and of girth at least 2k + 2, and every integer t, 2 ? t ? k ? 1, we construct a family G? t of graphs of the same magnitude r, of constant greater than ? , and all of whose members contain each of the cycles C4, C6, . , C2t, but none of the cycles C2t + 2, . , C2k. We also prove that for every family of 2k-cycle-free extremal graphs (i.e., graphs having the greatest size among all 2k-cycle-free graphs of the same order), all but finitely many such graphs must be either non-bipartite or have girth at most 2k ? 2. In particular, we show that the best known lower bound on the size of 2k-cycle-free extremal graphs for k = 3, 5, namely (2 ? (k + 1)/k + o(1))v(k + 1)/k, can be improved to ((k ? 1)·k? (k + 1)/k + o(1))v(k + 1)/k.
Systolic FFT Processors: Past, Present and Future

This paper reviews developments in the implementation of systolic fast Fourier transform processors over two decades (early 1980s to early 2000s) and identifies positive and negative lessons learned. The modular transform processor was developed at TRW in 1983-84. It is a set of 6 large circuit boards that computes 4096 point FFTs using 22-bit floating-point arithmetic at sustained data rates of 40 MSPS. A single chip systolic FFT developed by the Mayo Foundation in 2001-02 computes 4096 point FFTs using 16-bit fixed-point arithmetic at sustained data rates of 200 MSPS. Some thoughts on the future directions of systolic FFT processor development are offered. Future systems will compute larger FFTs at higher data rates, will employ IEEE standard floating point arithmetic and will consume less power
Design of Solar Powered Airplanes for Continuous Flight

This thesis deals with airplanes using solar energy as their only source of energy for more than 24 hours flight. Using solar panels, they collect it during the day for immediate use but also store the remaining part for the night flight. This work presents a new analytical methodology for the conceptual design of such airplane. Its major advantage lies in the fact that it is simple and versatile, which makes it applicable to a large range of airplanes of different wingspans, from the small MAV to the large manned aircraft. The design methodology is based on power and mass balances occurring during level flight. An extensive study was done on the mathematical modeling of the subparts, for example concerning electric motors the question being to know how their mass and their efficiency vary with power. Empirical data over a large range were used in this study. Finally, the analytical method contains 5 mission parameters and 25 others linked to the various technologies involved that the user can vary in order to see on a graph the dependencies between the 3 layout variables (aspect ratio, wingspan and total mass) for all the feasible solutions. The final selection can then be easily made. Sky-Sailor, a 3.2 meters wingspan solar powered airplane, was then designed using this methodology. A prototype, with an ultra lightweight structure covered by silicon solar cells was built in order to validate the process. We also developed in this framework dedicated electronics for the autonomous navigation and the efficient solar power management. The final 2.44 kg airplane was tested with success during several autonomous flights, showing capabilities that were very close to the one calculated in theory. The longest flight achieved lasted more than 27 hours within a circuit length of more than 874 kilometers and proved the feasibility of solar powered continuous flight. In addition to the first application example on Sky-Sailor, other designs are presented and discussed, like the case of a 70 cm solar UAV but also a 60 m manned solar airplane. It is then very interesting to see how things evolve with scaling. In fact, going in each direction removes and adds its batch of
Chapter 2 What Difference Does it Make? An Institutional Perspective on Actors and Types Thereof

Abstract While some institutionalists have highlighted the explanatory power of organizational actors, others stress their social construction. In line with the latter perspective, the author states in the first part that, except from meta-theoretical reflections, the social sciences tend to utilize actor concepts without further reflection. The author also shows how actors are reproduced in social practice, excessively in media semantics and more rigid in legal affairs, and that experts and professional helpers constantly reproduce actor images and identities. The second part focuses on the differences between the three dominant types of actors: states, organizations, and individuals. Although rationalization constructs the three different types of actors, which share much in common as institutionally derived entities, each type – still – has its own distinctive qualities: welfare issues are crucial for states; emotional qualities are a characteristic feature of individuals; and stakeholder sensitivity is paramount for organizational actors.
Composite and Nanocomposite Metal Foams

Open-cell and closed-cell metal foams have been reinforced with different kinds of micro- and nano-sized reinforcements to enhance their mechanical properties of the metallic matrix. The idea behind this is that the reinforcement will strengthen the matrix of the cell edges and cell walls and provide high strength and stiffness. This manuscript provides an updated overview of the different manufacturing processes of composite and nanocomposite metal foams.
Wavelet estimation of the derivatives of an unknown function from a convolution model

We observe a stochastic process where a convolution product of an unknown function $f$ and a known function $g$ is corrupted by Gaussian noise. We wish to estimate the $d$-th derivatives of $f$ from the observations. To reach this goal, we develop an adaptive estimator based on wavelet block thresholding. We prove that it achieves near optimal rates of convergence under the mean integrated squared error (MISE) over a wide range of smoothness classes.
Control of Multi-Input Integrated Buck-Boost Converter

The analysis and control of multi-input integrated DC-DC converter is presented in this paper. The integrated converter is essentially a combination of buck and buck-boost converters. However, on account of integration only one inductor is sufficient enough for performing the power conversion. In order to have simple control strategy as well as simpler compensator design a single loop control scheme, voltage-mode and current-limit control, are proposed here for the power distribution. Closed-loop converter performance of this converter is simulated and compared with the theoretical predictions. Experimental measurements are provided for validating the control concept.
Young Children in Institutional Care at Risk of Harm

A recent survey has revealed a large number of young children in institutional care across Europe. Young children placed in institutional care without parents may be at risk of harm. This review considers systematically the research evidence on the impact of institutional care on brain growth, attachment, social behavior, and cognitive development. Analytical epidemiological study designs (i.e., including a control/comparison group) show that young children placed in institutional care are at risk of harm in terms of attachment disorder and developmental delays in social, behavioral, and cognitive domains. Delays in physical growth, neural atrophy, and abnormal brain development have also been implicated. The findings suggest that the lack of a one-to-one relationship with a primary caregiver is a major cause of harm to children in residential care. Evidence indicates that infants who are placed in institutional care will suffer harm to their development if they are not moved to family-based care by the age of 6 months. The neglect and damage caused by early privation and deprivation is equivalent to violence and policy makers should work to ensure that every child has the opportunity to grow up in a family environment.
NuMA: an unusually long coiled-coil related protein in the mammalian nucleus

A bank of 892 autoimmune sera was screened by indirect immunofluorescence on mammalian cells. Six sera were identified that recognize an antigen(s) with a cell cycle-dependent localization pattern. In interphase cells, the antibodies stained the nucleus and in mitotic cells the spindle apparatus was recognized. Immunological criteria indicate that the antigen recognized by at least one of these sera corresponds to a previously identified protein called the nuclear mitotic apparatus protein (NuMA). A cDNA which partially encodes NuMA was cloned from a lambda gt11 human placental cDNA expression library, and overlapping cDNA clones that encode the entire gene were isolated. DNA sequence analysis of the clones has identified a long open reading frame capable of encoding a protein of 238 kD. Analysis of the predicted protein sequence suggests that NuMA contains an unusually large central alpha-helical domain of 1,485 amino acids flanked by nonhelical terminal domains. The central domain is similar to coiled- coil regions in structural proteins such as myosin heavy chains, cytokeratins, and nuclear lamins which are capable of forming filaments. Double immunofluorescence experiments performed with anti- NuMA and antilamin antibodies indicate that NuMA dissociates from condensing chromosomes during early prophase, before the complete disintegration of the nuclear lamina. As mitosis progresses, NuMA reassociates with telophase chromosomes very early during nuclear reformation, before substantial accumulation of lamins on chromosomal surfaces is evident. These results indicate that the NuMA proteins may be a structural component of the nucleus and may be involved in the early steps of nuclear reformation during telophase.
BLASTING through the information theoretic barrier with FUSION TREES

The information theoretic bound asserts that sorting N numbers requires NlogN comparisons in the worst case. The degree of universality of this bound has not been fully resolved. Paul and Simon [4] have established that any unit cost random access machine algorithm whose operations include addition, subtraction, multiplication, and comparison with 0 (but not division or bit-wise Boolean operations) requires £2 (NlogN) time to sort N numbers in the worst case. On the other hand, with the inclusion of division and Boolean operations, they obtain a linear time algorithm. This linear time algorithm, however, suffers from an abuse of the unit cost assumption. In particular, the algorithm generates operands during the course of its computation whose individual lengths are N 2 times the length of the largest of the N numbers to be sorted.
RouteSpray: A multiple-copy routing algorithm based on transit routes

Vehicular networks represent a special type of wireless network that has gained the attention of researchers over the past few years. Routing protocols for this type of network must face several challenges, such as high mobility, high speeds and frequent network disconnections. This paper proposes a vehicular routing algorithm called RouteSpray that in addition to using vehicular routes to help make routing decisions, uses controlled spraying to forward multiple copies of messages, thus ensuring better delivery rates without overloading the network. The results of experiments performed in this study indicate that the RouteSpray algorithm delivered 13.46% more messages than other algorithms reported in the literature. In addition, the RouteSpray algorithm kept the buffer occupation 73.38% lower. Keywords: wireless networks, vehicular networks, routing protocols.
Increasing the precision of mobile sensing sy stems through super-sampling

Sensors integrated into mobile phones have the advantage of mobility, co-location with people, pre-built network and power infrastructure, and potentially, ubiquity. These characteristics, however, also present significant challenges. Mobility means non-uniform sampling in space, and also constrains the size and weight of the sensors. In this paper, we focus on non-uniform sampling, and imprecision. We investigate the question, “Assuming well calibrated sensors, what precision can we expect from a network of sensors embedded in location aware cell phones? ” We briefly describe some results that suggest that a Gaussian process based model is appropriate. I. Introduction With increased public focus on environmental conditions and increasing industrialization of developing countries, the need for environmental monitoring has increased significantly. Current air pollution monitoring systems typically consist of highly sensitive, bulky equipment placed in a few strategic locations. These systems, such as the California Air Resource Board (CARB) monitoring system mostly monitor ambient levels over large geographic areas [1]. Not only do systems like CARB have very coarse granularity, but they also only measure the human and environmental health impacts of pollution indirectly. The Networked Suite of Mobile Atmospheric Real-Time Sensors (N-SMARTS) project [2] aims to radically improve the geographic coverage and granularity of environmental monitoring by integrating pollution (and other environmental) sensors into location-aware mobile phones. Our current sensor devices connect to the phone via Bluetooth, and will eventually fit into a modified battery pack, for tight ergonomic integration. Sensors integrated into mobile phones have the advantage of mobility, co-location with people, pre-built network and power infrastructure, and potentially, ubiquity. These characteristics, however, also present significant challenges. Mobility means nonuniform sampling in space, and also constrains the size and weight of the sensors. Although co-location with people means that samples will often be taken near a particular person, hence providing a good approximation of a person’s exposure to pollution, co-location also means that a person’s behavior (putting their phone in their pockets, riding in cars, remaining indoors vs. outdoors) will impact the readings of the sensors. Tracking a person’s location also has enormous
Design of Pneumatic Drive and Its Control System for A SkilMate Hand

In this paper, we focus on linear modeling and design of a self-tuning PID controller for a pneumatic cylinder system for applicable to a SkilMate hand for astronauts ’ Extra-vehicular activity (EVA). For the purpose of giving the initial values to the PID controller, we develop linear modeling by applying first-order Taylor series expansion, and design a self -tuning PID controller with applying real-time system identification capability utilizing fuzzy curve fitting. Finally, we verified the validity of the controller by simulation the system behavior.
Decentralised Data Fusion And Control In Active Sensor Networks

The paper presents an algorithm for Bayesian decentralized data fusion (BDDF) and its extension to informationtheoretic control. The algorithm is stated for a feature represented by a general probability density function. Several specific representations are then considered – Gaussian, discrete, Certainty Grid, and hybrid. Well known algorithms for these representations are shown to fit the general BDDF pattern. Stating the algorithms in Bayesian terms has a practical advantage of allowing a generic software implementation. It is also hoped that a clear general formulation will stimulate extensions to efficient non-parametric representations of arbitrary distributions. The algorithms are described in the context of the Active Sensor Network architecture – a modular framework for decentralized cooperative data fusion and control. The approach is illustrated with the results of two deployment scenarios with an indoor sensor network.