Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic, physiological and biotechnological assessment of microorganisms for renewable and sustainable energy resource production

The term "algae" defines variety of photosynthetic organisms found throughout the world in various environmental conditions. Algae species are estimated to number in the tens of thousands. Because algae are photosynthetic, naturally able to replicate rapidly and produce high amount of oils, alcohols, and biomass, they have attracted the attention of researchers and industrial producers seeking alternatives to currently used fossil fuels. Algae thrive on organic carbon or CO2, nutrients such as nitrogen, phosphorus and other inorganic substances which enables algae to be used in bioremediation. Growth conditions, nutrients such as carbon and nitrogen, and many other factors affect the algal cell metabolism. Thus, manipulation of different cultivation conditions have been shown successful in increasing algal biomass and lipid productivity in order to substitute petroleum use. Algae biotechnology research goals especially include finding ways to increase the reproductive rate, improve metabolism of inputs, and enhance the production of desired oils, fuel-grade alcohols in useful species. In this thesis, newly isolated halophilic unicellular green algae species are assessed for potential renewable energy resource. Novel strategies for increasing cellular lipid production were established. Exogenous application of oxidative stress by hydrogen peroxide treatment was shown as a novel lipid accumulation inducer. Moreover, increased lipid accumulation response was also observed in heavy metal induced oxidative stress which makes combination of heavy metal bioremediation and oil production possible as a novel algae cultivation strategy. Directed evolution and natural selection strategies were applied to model organism Saccharomyces cerevisiae and Dunaliella salina for revealing underlying biochemical, genetic factors of increased cellular lipid production in order to provide useful strategies for future biofuel production.
Color Lens: Adaptive Color Scale Optimization for Visual Exploration

Visualization applications routinely map quantitative attributes to color using color scales. Although color is an effective visualization channel, it is limited by both display hardware and the human visual system. We propose a new interaction technique that overcomes these limitations by dynamically optimizing color scales based on a set of sampling lenses. The technique inspects the lens contents in data space, optimizes the initial color scale, and then renders the contents of the lens to the screen using the modified color scale. We present two prototype implementations of this pipeline and describe several case studies involving both information visualization and image inspection applications. We validate our approach with two mutually linked and complementary user studies comparing the Color Lens with explicit contrast control for visual search.
Monotone Submodular Maximization over a Matroid via Non-Oblivious Local Search

We present an optimal, combinatorial $1-1/e$ approximation algorithm for monotone submodular optimization over a matroid constraint. Compared to the continuous greedy algorithm [G. Calinescu et al., IPCO, Springer, Berlin, 2007, pp. 182--196] our algorithm is extremely simple and requires no rounding. It consists of the greedy algorithm followed by a local search. Both phases are run not on the actual objective function, but on a related auxiliary potential function, which is also monotone and submodular. In our previous work on maximum coverage [Y. Filmus and J. Ward, FOCS, IEEE, Piscataway, NJ, 2012, pp. 659--668], the potential function gives more weight to elements covered multiple times. We generalize this approach from coverage functions to arbitrary monotone submodular functions. When the objective function is a coverage function, both definitions of the potential function coincide. Our approach generalizes to the case where the monotone submodular function has restricted curvature. For any curvatu.
Telemedicine: Its Effects on Health Communication

This article analyzes telemedicine, the use of distant communication technologies within the context of clinical health care, and the effects it has on health communication. The main effect is that telemedicine has the capacity to substantially transform health care in both positive and negative ways and to radically modify personal face-to-face communication (Turner, 2003). This has tremendous implications for health communication scholars in that they can extend the telemedicine debate by integrating fresh insights into more acceptable approaches that will refine and humanize mediated channels of health communication. There are several key areas of telemedicine that need to be discussed (i.e., e-health services, clinical encounters, etc.), all of which are identified in this article. In addition to describing the past and current applications of telemedicine, this article provides a better understanding of unique needs, resources, problems, and opportunities germane to telemedicine services.
Cyanobacterial harmful algal blooms are a biological disturbance to Western Lake Erie bacterial communities

Human activities are causing a global proliferation of cyanobacterial harmful algal blooms (CHABs), yet we have limited understanding of how these events affect freshwater bacterial communities. Using weekly data from western Lake Erie in 2014, we investigated how the cyanobacterial community varied over space and time, and whether the bloom affected non-cyanobacterial (nc-bacterial) diversity and composition. Cyanobacterial community composition fluctuated dynamically during the bloom, but was dominated by Microcystis and Synechococcus OTUs. The bloom's progression revealed potential impacts to nc-bacterial diversity. Nc-bacterial evenness displayed linear, unimodal, or no response to algal pigment levels, depending on the taxonomic group. In addition, the bloom coincided with a large shift in nc-bacterial community composition. These shifts could be partitioned into components predicted by pH, chlorophyll a, temperature, and water mass movements. Actinobacteria OTUs showed particularly strong correlations to bloom dynamics. AcI-C OTUs became more abundant, while acI-A and acI-B OTUs declined during the bloom, providing evidence of niche partitioning at the sub-clade level. Thus, our observations in western Lake Erie support a link between CHABs and disturbances to bacterial community diversity and composition. Additionally, the short recovery of many taxa after the bloom indicates that bacterial communities may exhibit resilience to CHABs.
Synthesizing manipulation sequences for under-specified tasks using unrolled Markov Random Fields

Many tasks in human environments require performing a sequence of navigation and manipulation steps involving objects. In unstructured human environments, the location and configuration of the objects involved often change in unpredictable ways. This requires a high-level planning strategy that is robust and flexible in an uncertain environment. We propose a novel dynamic planning strategy, which can be trained from a set of example sequences. High level tasks are expressed as a sequence of primitive actions or controllers (with appropriate parameters). Our score function, based on Markov Random Field (MRF), captures the relations between environment, controllers, and their arguments. By expressing the environment using sets of attributes, the approach generalizes well to unseen scenarios. We train the parameters of our MRF using a maximum margin learning method. We provide a detailed empirical validation of our overall framework demonstrating successful plan strategies for a variety of tasks.
Title: Mars: a Metamodel Recovery System Using Grammar Inference Author 1 (corresponding Author)

100 words): Domain-specific modeling (DSM) assists subject matter experts in describing the essential characteristics of a problem in their domain. When a metamodel is lost, repositories of domain models can become orphaned from their defining metamodel. Within the purview of model-driven engineering, the ability to recover the design knowledge in a repository of legacy models is needed. In this paper we describe MARS, a semi-automatic grammar-centric system that leverages grammar inference techniques to solve the metamodel recovery problem. The paper also contains an applicative case study, as well as experimental results from the recovery of several metamodels in diverse domains.
Fluorescent In Situ Hybridization on Isolated Tumor Cell Nuclei: A Sensitive Method for 1p and 19q Deletion Analysis in Paraffin-Embedded Oligodendroglial Tumor Specimens

In oligodendroglial neoplasms, losses of chromosomal material at 1p and 19q associate with chemosensitivity and prolonged survival. Thus, 1p/19q testing is increasingly proposed for use in brain tumor diagnosis and prognostic assessment. Fluorescent in situ hybridization (FISH) is a classic technique for investigation of 1p/19q status in paraffin-embedded tissues. A major limitation of this method is truncation of tumor cell nuclei complicating assessment of hybridization results. In our study, we analyzed 1p and 19q status in a series of 79 oligodendroglial neoplasms (49 oligodendrogliomas, 30 oligoastrocytomas, WHO: 57 Grade II, 22 Grade III tumors) and controls (gliotic brain tissue: n = 4, diffuse low-grade astrocytoma: n = 4) using FISH on isolated whole tumor cell nuclei, prepared as cytospin preparations, thus bypassing the problem of nuclear truncation. For interpretation of FISH results, we used consensus criteria as defined by the SIOP—Europe Neuroblastoma Study Group for analysis of peripheral neuroblastic tumors. FISH yielded interpretable results in 98.7% for 1p and 92.1% for 19q. Chromosome 1p/19q alterations comprised deletions (1p: 79.5%, 19q: 80%) and imbalances (1p: 11.5%, 19q: 12.9%). 1p aberrations were more frequent in oligodendroglioma than in oligoastrocytoma (100% versus 75.9%, P = .001). The frequency of 1p/19q alterations was not significantly different in WHO Grade II or Grade III tumors or in primary and recurrent tumors. We conclude that FISH on isolated cell nuclei, with application of the SIOP Europe Neuroblastoma consensus criteria, is a sensitive method for detection and interpretation of 1p and 19q aberrations in paraffin-embedded tissue specimens of oligodendroglial neoplasms.
How Much Up-Front? A Grounded theory of Agile Architecture

The tension between software architecture and agility is not well understood by agile practitioners or researchers. If an agile software team spends too little time designing architecture up-front then the team faces increased risk and higher chance of failure, if the team spends too much time the delivery of value to the customer is delayed, and responding to change can become extremely difficult. This paper presents a grounded theory of agile architecture that describes how agile software teams answer the question of how much upfront architecture design effort is enough. This theory, based on grounded theory research involving 44 participants, presents six forces that affect the team's context and five strategies that teams use to help them determine how much effort they should put into up-front design.
Complex Regional Pain Syndrome and Acute Carpal Tunnel Syndrome Following Radial Artery Cannulation

AbstractComplex regional pain syndrome (CRPS) associated with acute carpal tunnel syndrome (aCTS) developed in a 38-year-old right-handed man following radial artery cannulation (RAC) during the course of lumbar spine surgery. Inciting events and risk factors that might have led to these complications included: multiple arterial punctures and subsequent hematoma formation, radial artery spasm compounded by aggressive hemostasis, anatomical changes in the wrists related to repetitive manual activities in the workplace, and possible protracted hyperextension of the wrists during perioperative and operative procedure. Although CRPS is considered a rare complication of RAC, the condition is disabling and debilitating, especially when associated with aCTS.
Implementation and experiment of multi-modal transmission system for stable communication

Recently, there have been large numbers of research related to ITS (Intelligent Transport System). The major specification to realize ITS network is RC-005 using band frequency 5.8GHz. However it is difficult to connect if something disturbs Line-of-Sight (LOS) between communication devices due to characteristic of radio. In this paper, we propose a communication system based on approaches of temporal backup and frequency backup to increase communication stability and to cover wider area. We implement the prototype system and conduct some experiment using them. The result shows that temporal backup and frequency backup are effective in terms of data arrival rate and stable communication. We conclude in case of Non Line-of-Sight (NLOS) communication, temporal backup and frequency backup are efficient.
3D nanorobotic manipulations of multi-walled carbon nanotubes

Multi-walled carbon nanotubes (MWNTs) are manipulated in 3D space with a 10-DOF nanorobotic manipulator, which is actuated with PZTs and Picomotors/sup TM/ (New Focus Inc.) and operated inside a scanning electronic microscope (SEM). The coarse linear resolutions of the manipulator are better than 30 nm (X, Y, Z stages actuated by Picomotors) and the rotary one 2 mrad, while the resolutions of fine motions (actuated by PZTs) are within nano-order. AFM cantilevers are used as the end-effector. Several kinds of manipulations of MWNTs are performed with the developed manipulators with the assistance of dielectrophoresis and van der Waals forces. A single MWNT with estimated dimensions of /spl phi/ 40 nm /spl times/7 /spl mu/m has been picked up on an AFM cantilever. Another /spl phi/ 50 nm /spl times/6 /spl mu/m MWNT is placed between two cantilevers, and still another /spl phi/ 40 nm /spl times/8 /spl mu/m MWNT is bent between a cantilever and sample substrate. Carbon nanotube (CNT) junctions are basic building blocks for more complex devices based on CNTs. A cross-junction was constructed with two MWNTs of dimensions of /spl sim//spl phi/ 40 nm /spl times/6 /spl mu/m and /spl sim//spl phi/ 50 nm /spl times/7 /spl mu/m, and a T-junction was made of two MWNTs with the dimensions of /spl sim//spl phi/ 40 nm /spl times/3 /spl mu/m and /spl sim//spl phi/ 50 nm /spl times/2 /spl mu/m. Force measurements are performed and the flexural rigidity and Young's modulus of an /spl sim//spl phi/ 30 nm /spl times/7 /spl mu/m MWNT are estimated to be 8.641/spl times/10/sup -20/ Nm/sup 2/ and 2.17 TPa respectively. Such manipulations are essential for both the property research of CNTs and the fabrication of CNT-based NEMS.
Paired-End Sequencing of Long-Range DNA Fragments for De Novo Assembly of Large, Complex Mammalian Genomes by Direct Intra-Molecule Ligation

Background The relatively short read lengths from next generation sequencing (NGS) technologies still pose a challenge for de novo assembly of complex mammal genomes. One important solution is to use paired-end (PE) sequence information experimentally obtained from long-range DNA fragments (>1 kb). Here, we characterize and extend a long-range PE library construction method based on direct intra-molecule ligation (or molecular linker-free circularization) for NGS. Results We found that the method performs stably for PE sequencing of 2- to 5- kb DNA fragments, and can be extended to 10–20 kb (and even in extremes, up to ∼35 kb). We also characterized the impact of low quality input DNA on the method, and develop a whole-genome amplification (WGA) based protocol using limited input DNA (<1 µg). Using this PE dataset, we accurately assembled the YanHuang (YH) genome, the first sequenced Asian genome, into a scaffold N50 size of >2 Mb, which is over100-times greater than the initial size produced with only small insert PE reads(17 kb). In addition, we mapped two 7- to 8- kb insertions in the YH genome using the larger insert sizes of the long-range PE data. Conclusions In conclusion, we demonstrate here the effectiveness of this long-range PE sequencing method and its use for the de novo assembly of a large, complex genome using NGS short reads.
INFLUENCE OF BODY POSITION ON CARDIOVASCULAR CHANGES DURING ISOMETRIC EXERCISE

A group of seven male participants [aged 22,9 (SD = 0,9) years] twice performed, a two-leg extension effort lasting a total of 4 minutes with a 30% intensity of maximal voluntary contraction (MVC), in the sitting (ST) and two days later in the supine position (SU). At rest, during each minute of exercise and the 4 minute recovery period the following variables were measured: heart rate (HR), stroke volume (SV), cardiac output (CO) by impedance cardiography system, systolic (SP) and diastolic blood pressures (DP) by the Korotkof method. Mean arterial blood pressure (MP) and total peripherial resistance (TPR) were also calculated. It was observed that at rest the SV was significantly higher, but HR, DP and MP were lower in SU when compared to ST (p < 0,05). Moreover during exercise these indices decreased more in the SU than in ST position when compared to the resting values. HR, DP and MP were enhanced in both the tested positions, but CO and SP were significantly higher in both positions as compared to the resting values. From our study it was concluded that the adaptability of the cardiovascular system during isometric exercise is based on changes in the left ventricular afterload, different in various body position with simultaneous suppressed baroreceptor reflexes.
Fused Smart Sensor Network for Multi-Axis Forward Kinematics Estimation in Industrial Robots

Flexible manipulator robots have a wide industrial application. Robot performance requires sensing its position and orientation adequately, known as forward kinematics. Commercially available, motion controllers use high-resolution optical encoders to sense the position of each joint which cannot detect some mechanical deformations that decrease the accuracy of the robot position and orientation. To overcome those problems, several sensor fusion methods have been proposed but at expenses of high-computational load, which avoids the online measurement of the joint’s angular position and the online forward kinematics estimation. The contribution of this work is to propose a fused smart sensor network to estimate the forward kinematics of an industrial robot. The developed smart processor uses Kalman filters to filter and to fuse the information of the sensor network. Two primary sensors are used: an optical encoder, and a 3-axis accelerometer. In order to obtain the position and orientation of each joint online a field-programmable gate array (FPGA) is used in the hardware implementation taking advantage of the parallel computation capabilities and reconfigurability of this device. With the aim of evaluating the smart sensor network performance, three real-operation-oriented paths are executed and monitored in a 6-degree of freedom robot.
M2 and M3 Muscarinic Receptor Activation of Urinary Bladder Contractile Signal Transduction. II. Denervated Rat Bladder

Normal rat bladder contractions are mediated by the M3 muscarinic receptor subtype. The M2 receptor subtype mediates contractions of the denervated, hypertrophied bladder. This study determined signal transduction mechanisms mediating contraction of the denervated rat bladder. Denervated bladder muscle strips were exposed to inhibitors of enzymes thought to be involved in signal transduction in vitro followed by a cumulative carbachol concentration-response curve. Outcome measures were the maximal contraction, the potency of carbachol, and the affinity of darifenacin for inhibition of contraction. Inhibition of phosphoinositide-specific phospholipase C (PI-PLC) with 1-O-octadecyl-2-O-methyl-sn-glycero-3-phosphorylcholine (ET-18-OCH3) has no effect on denervated bladder contractions, whereas inhibition of phosphatidyl choline-specific phospholipase C (PC-PLC) with O-tricyclo[5.2. 1.02,6]dec-9-yl dithiocarbonate potassium salt (D609) attenuates the carbachol maximum and potency. Inhibition of rho kinase with (R)-(+)-trans-4-(1-aminoethyl)-N-(4-pyridyl)cyclohexanecarboxamide dihydrochloride (Y-27632) reduces carbachol maximum, carbachol potency, and increases darifenacin affinity. Inhibition of rho kinase, protein kinase A (PKA), and protein kinase G (PKG) with 1-(5-isoquinolinesulfonyl)-homopiperazine·HCl (HA-1077) reduces the carbachol maximum and potency. Inhibition of PKC with chelerythrine increases darifenacin affinity, whereas inhibition of rho kinase, PKA, PKG, and protein kinase C (PKC) with 1-(5-isoquinolinesulfonyl)-2-methylpiperazine·2HCl (H7) reduces the carbachol potency while increasing darifenacin affinity. Inhibition of rho kinase, PKA, and PKG with N-[2-(p-bromocinnamylamino)ethyl]-5-isoquinolinesulfonamide·2HCl (H89) increases darifenacin affinity. This study demonstrates that different signal transduction mechanisms mediate the contractile response in the denervated rat bladder than in normal rat bladder. In normal rat bladder, PI-PLC and PC-PLC mediate the contraction, but in denervated bladder only PC-PLC is involved. In the denervated bladder, the rho kinase pathway is more dominant than in normal bladders. PKA seems to mediate a contractile response in normal bladders, whereas it seems to inhibit contraction in denervated bladders.
Afferent influences on the development of the brain stem auditory nuclei of the chicken: Otocyst ablation

The effects of embryonic deafferentation on the morphological development of the avian cochlear nuclei, n. angularis (NA) and n. magnocellularis (NM), were investigated. The right otocyst was surgically removed from chick embryos at 55 to 60 hours of incubation and the subsequent development of total volume, neuron number, and neuron cross‐sectional area were studied with quantitative methods in animals sacrificed at 2‐day intervals between embryonic days 9 and 19 and at 28 days posthatching. The development of NA and NM is severely affected by otocyst ablation. Between embryonic days 9 and 19, a large group of NA neurons in the medioventral portion of the nucleus on the perated side moves to an ectopic ventromedial position, while the remainder of this nucleus stays in its normal dorsolateral position. Beginning about day 13 of incubation, the normal increase in the volume of NA and the size of its neurons becomes progressively retarded and 40% of its neurons are lost. The growth of NM is also retarded after day 11 of incubation and the growth of mean neuron size is retarded after day 15. There is a 30% loss of neurons in NM which begins after embronic day 11.
Data-Core-Based Fuzzy Min–Max Neural Network for Pattern Classification

A fuzzy min-max neural network based on data core (DCFMN) is proposed for pattern classification. A new membership function for classifying the neuron of DCFMN is defined in which the noise, the geometric center of the hyperbox, and the data core are considered. Instead of using the contraction process of the FMNN described by Simpson, a kind of overlapped neuron with new membership function based on the data core is proposed and added to neural network to represent the overlapping area of hyperboxes belonging to different classes. Furthermore, some algorithms of online learning and classification are presented according to the structure of DCFMN. DCFMN has strong robustness and high accuracy in classification taking onto account the effect of data core and noise. The performance of DCFMN is checked by some benchmark datasets and compared with some traditional fuzzy neural networks, such as the fuzzy min-max neural network (FMNN), the general FMNN, and the FMNN with compensatory neuron. Finally the pattern classification of a pipeline is evaluated using DCFMN and other classifiers. All the results indicate that the performance of DCFMN is excellent.