Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating Adaptation Methods for Cloud Applications: An Empirical Study

Web software systems generally reside in highly volatile environments, their incoming traffic may be subject to sharp fluctuations from reasons that cannot always be captured or predicted. Cloud computing provides a solution to this problem by offering flexible resources, like containers, which can be quickly and easily scaled according to the current workload needs. Automating this process is a key aspect for the management of modern web software systems, and there is a plethora of methods to implement autonomic management systems. In this work, we review three of these methods, a threshold-based approach, a control-based approach and a model-based approach. We design and run a number of experiments for all three systems with different workloads to evaluate their ability to manage the software system and how well they do so. Our experiments were conducted on the Amazon EC2 cloud with Docker containers.
Contributing factors for therapeutic diet adherence in patients receiving haemodialysis treatment: an integrative review

AIMS AND OBJECTIVES The objective of this integrative review is to identify the factors that contribute to diet adherence in people suffering from kidney disease who are receiving haemodialysis treatment. BACKGROUND Adherence to the therapeutic regimen determines therapeutic success, quality of life and survival in patients on haemodialysis. Lack of diet adherence ranges from 25%-86% in patients receiving haemodialysis treatment and affects patient morbidity and mortality. DESIGN An integrative literature review was conducted based on the criteria of Whittemore & Knafl. METHODS A literature review was performed by two members of the team using twelve databases including PubMed, CUIDEN, CINAHL, The Cochrane Library and ScienceDirect. RESULTS The main issues identified after analysing the results were as follows: the intrinsic barriers (age, dialysis time, motivation, perceived benefit, distorted perception of adherence) and facilitators (self-efficacy, perception of disease, perception of control), extrinsic barriers (family dysfunction, lack of social support, cultural patterns of consumption of food) and facilitators (social support, relationship with healthcare providers), and interventions to encourage diet adherence, such as the use of motivational interviewing in educational interventions, and the training and education of relevant professionals in communication skills. CONCLUSIONS Diet nonadherence remains a serious health problem and suffers from a lack of solid criteria to identify this condition. The onset of depression signs and the level of social support available to the patient should be assessed, because these are important factors that determine adherence to treatment. RELEVANCE TO CLINICAL PRACTICE Professionals should be trained in health education and communication techniques to contribute to the patient's self-management and motivation for diet adherence. Controlled and randomised clinical studies involving predialysis stages should be performed to investigate the impact of the assessment and control of barriers to diet adherence.
Notch and Aryl Hydrocarbon Receptor Signaling Impact Definitive Hematopoiesis from Human Pluripotent Stem Cells

Induced pluripotent stem cells (iPSCs) stand to revolutionize the way we study human development, model disease, and eventually, treat patients. However, these cell sources produce progeny that retain embryonic and/or fetal characteristics. The failure to mature to definitive, adult‐type cells is a major barrier for iPSC‐based disease modeling and drug discovery. To directly address these concerns, we have developed a chemically defined, serum and feeder‐free–directed differentiation platform to generate hematopoietic stem‐progenitor cells (HSPCs) and resultant adult‐type progeny from iPSCs. This system allows for strict control of signaling pathways over time through growth factor and/or small molecule modulation. Through direct comparison with our previously described protocol for the production of primitive wave hematopoietic cells, we demonstrate that induced HSPCs are enhanced for erythroid and myeloid colony forming potential, and strikingly, resultant erythroid‐lineage cells display enhanced expression of adult β globin indicating definitive pathway patterning. Using this system, we demonstrate the stage‐specific roles of two key signaling pathways, Notch and the aryl hydrocarbon receptor (AHR), in the derivation of definitive hematopoietic cells. We illustrate the stage‐specific necessity of Notch signaling in the emergence of hematopoietic progenitors and downstream definitive, adult‐type erythroblasts. We also show that genetic or small molecule inhibition of the AHR results in the increased production of CD34+CD45+ HSPCs while conversely, activation of the same receptor results in a block of hematopoietic cell emergence. Results presented here should have broad implications for hematopoietic stem cell transplantation and future clinical translation of iPSC‐derived blood cells. Stem Cells 2018;36:1004–1019
Path Selection under Budget Constraints in Multihop Cognitive Radio Networks

Cognitive radio (CR) technology opens the licensed spectrum bands for opportunistic usage and initiates spectrum trading to improve the spectrum utilization. In this paper, we investigate the path selection problem in multihop cognitive radio networks (CRNs) under constraints on flow routing, link scheduling and CR source's budget. We extend the per-user-based spectrum trading in prior work to CR session-based spectrum trading, and effectively develop the spectrum trading mechanisms based on the cross-layer optimization in multihop CRNs. We introduce a new service provider, called secondary service provider (SSP), to help CR sessions to select the paths for packet delivery. Considering the price of bands and the potential returning of primary services at different CR links, the SSP purchases the licensed spectrum and jointly conducts flow routing and link scheduling under the budget constraints. We also propose a 4D conflict graph to characterize the conflict relationship among CR links and mathematically formulate the path selection problem under multiple constraints into an optimization problem with the objective of maximizing the end-to-end throughput. Due to the NP-hardness of the problem, we have also developed a heuristic algorithm to find the approximate solution.
Effect of pore size on performance of monolithic tube chromatography of large biomolecules

Effect of pore size on the performance of ion‐exchange monolith tube chromatography of large biomolecules was investigated. Radial flow 1 mL polymer based monolith tubes of different pore sizes (1.5, 2, and 6 μm) were tested with model samples such as 20 mer poly T‐DNA, basic proteins, and acidic proteins (molecular weight 14 000–670 000). Pressure drop, pH transient, the number of binding site, dynamic binding capacity, and peak width were examined. Pressure drop–flow rate curves and dynamic binding capacity values were well correlated with the nominal pore size. While duration of the pH transient curves depends on the pore size, it was found that pH duration normalized on estimated surface area was constant, indicating that the ligand density is the same. This was also confirmed by the constant number of binding site values being independent of pore size. The peak width values were similar to those for axial flow monolith chromatography. These results showed that it is easy to scale up axial flow monolith chromatography to radial flow monolith tube chromatography by choosing the right pore size in terms of the pressure drop and capacity.
Syntrophomonas wolfei Uses an NADH-Dependent, Ferredoxin-Independent [FeFe]-Hydrogenase To Reoxidize NADH

ABSTRACT Syntrophomonas wolfei syntrophically oxidizes short-chain fatty acids (four to eight carbons in length) when grown in coculture with a hydrogen- and/or formate-using methanogen. The oxidation of 3-hydroxybutyryl-coenzyme A (CoA), formed during butyrate metabolism, results in the production of NADH. The enzyme systems involved in NADH reoxidation in S. wolfei are not well understood. The genome of S. wolfei contains a multimeric [FeFe]-hydrogenase that may be a mechanism for NADH reoxidation. The S. wolfei genes for the multimeric [FeFe]-hydrogenase (hyd1ABC; SWOL_RS05165, SWOL_RS05170, SWOL_RS05175) and [FeFe]-hydrogenase maturation proteins (SWOL_RS05180, SWOL_RS05190, SWOL_RS01625) were coexpressed in Escherichia coli, and the recombinant Hyd1ABC was purified and characterized. The purified recombinant Hyd1ABC was a heterotrimer with an αβγ configuration and a molecular mass of 115 kDa. Hyd1ABC contained 29.2 ± 1.49 mol of Fe and 0.7 mol of flavin mononucleotide (FMN) per mole enzyme. The purified, recombinant Hyd1ABC reduced NAD+ and oxidized NADH without the presence of ferredoxin. The HydB subunit of the S. wolfei multimeric [FeFe]-hydrogenase lacks two iron-sulfur centers that are present in known confurcating NADH- and ferredoxin-dependent [FeFe]-hydrogenases. Hyd1ABC is a NADH-dependent hydrogenase that produces hydrogen from NADH without the need of reduced ferredoxin, which differs from confurcating [FeFe]-hydrogenases. Hyd1ABC provides a mechanism by which S. wolfei can reoxidize NADH produced during syntrophic butyrate oxidation when low hydrogen partial pressures are maintained by a hydrogen-consuming microorganism. IMPORTANCE Our work provides mechanistic understanding of the obligate metabolic coupling that occurs between hydrogen-producing fatty and aromatic acid-degrading microorganisms and their hydrogen-consuming partners in the process called syntrophy (feeding together). The multimeric [FeFe]-hydrogenase used NADH without the involvement of reduced ferredoxin. The multimeric [FeFe]-hydrogenase would produce hydrogen from NADH only when hydrogen concentrations were low. Hydrogen production from NADH by Syntrophomonas wolfei would likely cease before any detectable amount of cell growth occurred. Thus, continual hydrogen production requires the presence of a hydrogen-consuming partner to keep hydrogen concentrations low and explains, in part, the obligate requirement that S. wolfei has for a hydrogen-consuming partner organism during growth on butyrate. We have successfully expressed genes encoding a multimeric [FeFe]-hydrogenase in E. coli, demonstrating that such an approach can be advantageous to characterize complex redox proteins from difficult-to-culture microorganisms.
Effect of the CCL5-Releasing Fibrin Gel for Intervertebral Disc Regeneration

Objective To explore if chemokine (C-C motif) ligand 5 (CCL5) delivery could recruit annulus fibrosus (AF) cells to the injury sites and facilitate the repair of ruptured AF. Design The effects of CCL5 on bovine AF cells in vitro were tested by transwell assay and quantitative real-time polymerase chain reaction. Fibrin gel containing CCL5 was used to treat annulotomized bovine caudal discs cultured under dynamic loading conditions. After 14 days of loading, the samples were collected for histological examination. A pilot animal study was performed using sheep cervical discs to investigate the effect of fibrin gel encapsulated with CCL5 for the treatment of ruptured AF. After 14 weeks, the animals were sacrificed, and the discs were scanned with magnetic resonance imaging before histopathological examination. Results CCL5 showed a chemotactic effect on AF cells in a dose-dependent manner. AF cells cultured with CCL5 in vitro did not show any change of the gene expression of CCL5 receptors, catabolic and proinflammatory markers. In vitro release study showed that CCL5 exhibited sustained release from the fibrin gel into the culture media; however, in the organ culture study CCL5 did not stimulate homing of AF cells toward the defect sites. The pilot animal study did not show any repair effect of CCL5. Conclusions CCL5 has a chemotactic effect on AF cells in vitro, but no ex vivo or in vivo regenerative effect when delivered within fibrin gel. Further study with a stronger chemotactic agent and/or an alternate biomaterial that is more conductive of cell migration is warranted.
Redox Regulation of Heme Oxygenase-2 and the Transcription Factor, Rev-Erb, Through Heme Regulatory Motifs.

SIGNIFICANCE Heme binds to and serves as a cofactor for a myriad of proteins that are involved in diverse biological processes. Hemoproteins also exhibit varying modes of heme binding, suggesting that the protein environment contributes to the functional versatility of this prosthetic group. The subject of this review is a subset of hemoproteins that contain at least one heme regulatory motif (HRM), which is a short sequence containing a Cys-Pro core that, in many cases, binds heme with the Cys acting as an axial ligand. Recent Advances: As more details about HRM-containing proteins are uncovered, some underlying commonalities are emerging, including a role in regulating protein stability. Further, the cysteines of some HRMs have been shown to form disulfide bonds. Because the cysteines must be in the reduced, dithiol form to act as a heme axial ligand, heme binds at these sites in a redox-regulated manner, as demonstrated for heme oxygenase-2 (HO2) and Rev-erbβ. CRITICAL ISSUES HRM-containing proteins have wide variations in heme affinity, utilize different axial ligand schemes, and exhibit differences in the ability to act as a redox sensor-all while having a wide variety of biological functions. Here, we highlight HO2 and Rev-erbβ to illustrate the similarities and differences between two hemoproteins that contain HRMs acting as redox sensors. FUTURE DIRECTIONS HRMs acting as redox sensors may be applicable to other HRM-containing proteins as many contain multiple HRMs and/or other cysteine residues, which may become more evident as the functional significance of HRMs is probed in additional proteins.
Gold nanorods with higher aspect ratio as potential contrast agent in optical coherence tomography and for photothermal applications around 1300 nm imaging window

Over the past few years, plasmon-resonant nanorods of gold (AuNRs) have been used as the contrast agent in optical imaging and for photothermal applications. However, most of these studies were limited to AuNRs whose spectral peaks fall below 1000 nm. Recently, optical coherence tomography (OCT) imaging around 1300 nm has become one of the niche research areas due to its potential for many diagnostics imaging applications. In this paper, we have investigated plasmon-resonant AuNRs with higher aspect ratio as a potential contrast agent in OCT and for photothermal applications around the 1300 nm window. The AuNRs with an aspect ratio of 8.8, and longitudinal plasmon-resonance peak at 1320 nm have been used for the study. The AuNR used in the study has an average dimension of 88 nm (length) × 10 nm (diameter), and an effective size (Reff) of 11.8 nm. The optical extinction of plasmon-resonant AuNRs has been characterized by OCT using a new cross-correlation approach. The extinction cross-section estimated using the OCT method is in good agreement with the values obtained via finite difference time domain-method and UV–vis–NIR spectroscopy. Both the simulation and phantom based experimental studies have shown that AuNRs exhibit a large absorption to scattering cross-section ratio, making them ideal for absorption based contrast enhancement in OCT imaging around 1300 nm. Ex vivo studies on the pig adipose tissue also illustrate the efficiency of AuNRs with identified aspect ratio as a potential photothermal agent around 1300 nm.
An Intramolecular Salt Bridge in Bacillus thuringiensis Cry4Ba Toxin Is Involved in the Stability of Helix α-3, Which Is Needed for Oligomerization and Insecticidal Activity

ABSTRACT Bacillus thuringiensis three-domain Cry toxins kill insects by forming pores in the apical membrane of larval midgut cells. Oligomerization of the toxin is an important step for pore formation. Domain I helix α-3 participates in toxin oligomerization. Here we identify an intramolecular salt bridge within helix α-3 of Cry4Ba (D111-K115) that is conserved in many members of the family of three-domain Cry toxins. Single point mutations such as D111K or K115D resulted in proteins severely affected in toxicity. These mutants were also altered in oligomerization, and the mutant K115D was more sensitive to protease digestion. The double point mutant with reversed charges, D111K-K115D, recovered both oligomerization and toxicity, suggesting that this salt bridge is highly important for conservation of the structure of helix α-3 and necessary to promote the correct oligomerization of the toxin. IMPORTANCE Domain I has been shown to be involved in oligomerization through helix α-3 in different Cry toxins, and mutations affecting oligomerization also elicit changes in toxicity. The three-dimensional structure of the Cry4Ba toxin reveals an intramolecular salt bridge in helix α-3 of domain I. Mutations that disrupt this salt bridge resulted in changes in Cry4Ba oligomerization and toxicity, while a double point reciprocal mutation that restored the salt bridge resulted in recovery of toxin oligomerization and toxicity. These data highlight the role of oligomer formation as a key step in Cry4Ba toxicity.
An Iterative Refinement Framework for Image Document Binarization with Bhattacharyya Similarity Measure

Background noise and illumination condition are two primary factors degrading the performance of document image binarization. In this paper, we propose an iterative refinement framework to support robust binarization. Initially, an input image is transformed into a Bhattacharyya similarity matrix with Gaussian kernel, which is subsequently converted into a binary image using maximum entropy classifier. Then, we adopt the run-length histogram to estimate the character stroke width, an important indicator to determine the length of filter window. After noise elimination, the output image is used for the next round of refinement and the process terminates when the estimated stroke width is stable. Extensive experiments were conducted on the standard DIBCO datasets as well as a new benchmark harvested from our user query log. Results show that our proposed method outperforms state-of-the-art methods and is more robust to handle low-quality images.
Comparison of Cepheid Xpert Flu/RSV XC and BioFire FilmArray for Detection of Influenza A, Influenza B, and Respiratory Syncytial Virus

ABSTRACT The Xpert Flu/RSV XC was compared to the FilmArray respiratory panel for detection of influenza (Flu) A, Flu B, and respiratory syncytial virus (RSV), using 128 nasopharyngeal swabs. Positive agreements were 100% for Flu A and RSV and 92.3% for Flu B. The Xpert may be useful in clinical situations when extensive testing is not required and may serve an important role in laboratories already performing broader respiratory panel testing.
Contribution of the Salmonella enterica KdgR Regulon to Persistence of the Pathogen in Vegetable Soft Rots

ABSTRACT During their colonization of plants, human enteric pathogens, such as Salmonella enterica, are known to benefit from interactions with phytopathogens. At least in part, benefits derived by Salmonella from the association with a soft rot caused by Pectobacterium carotovorum were shown to be dependent on Salmonella KdgR, a regulator of genes involved in the uptake and utilization of carbon sources derived from the degradation of plant polymers. A Salmonella kdgR mutant was more fit in soft rots but not in the lesions caused by Xanthomonas spp. and Pseudomonas spp. Bioinformatic, phenotypic, and gene expression analyses demonstrated that the KdgR regulon included genes involved in uptake and metabolism of molecules resulting from pectin degradation as well as those central to the utilization of a number of other carbon sources. Mutant analyses indicated that the Entner-Doudoroff pathway, in part controlled by KdgR, was critical for the persistence within soft rots and likely was responsible for the kdgR phenotype.
The Effect of Locomotion on Early Visual Contrast Processing in Humans

Most of our knowledge about vision comes from experiments in which stimuli are presented to immobile human subjects or animals. In the case of human subjects, movement during psychophysical, electrophysiological, or neuroimaging experiments is considered to be a source of noise to be eliminated. Animals used in visual neuroscience experiments are typically restrained and, in many cases, anesthetized. In reality, however, vision is often used to guide the motion of awake, ambulating organisms. Recent work in mice has shown that locomotion elevates visual neuronal response amplitudes (Niell and Stryker, 2010; Erisken et al., 2014; Fu et al., 2014; Lee et al., 2014; Mineault et al., 2016) and reduces long-range gain control (Ayaz et al., 2013). Here, we used both psychophysics and steady-state electrophysiology to investigate whether similar effects of locomotion on early visual processing can be measured in humans. Our psychophysical results show that brisk walking has little effect on subjects' ability to detect briefly presented contrast changes and that co-oriented flankers are, if anything, more effective masks when subjects are walking. Our electrophysiological data were consistent with the psychophysics indicating no increase in stimulus-driven neuronal responses while walking and no reduction in surround suppression. In summary, we have found evidence that early contrast processing is altered by locomotion in humans but in a manner that differs from that reported in mice. The effects of locomotion on very low-level visual processing may differ on a species-by-species basis and may reflect important differences in the levels of arousal associated with locomotion. SIGNIFICANCE STATEMENT Mice are the current model of choice for studying low-level visual processing. Recent studies have shown that mouse visual cortex is modulated by behavioral state: primary visual cortex neurons in locomoting mice tend to be more sensitive and less influenced by long-range gain control. Here, we tested these effects in humans by measuring psychophysical detection thresholds and electroencephalography (EEG) responses while subjects walked on a treadmill. We found no evidence of increased contrast sensitivity or reduced surround suppression in walking humans. Our data show that fundamental measurements of early visual processing differ between humans and mice and this has important implications for recent work on the links among arousal, behavior, and vision in these two species.
The emerging role of GSK‐3β in the pathobiology of classical Hodgkin lymphoma

Glycogen synthase kinase‐3 beta (GSK‐3β) is a serine/threonine kinase involved in glycogen metabolism, cell cycle progression, differentiation, embryogenesis, migration, metabolism, survival and cellular senescence. Its main biological function is to inhibit β‐catenin by sequestration and promotion of its proteasomal degradation in the Wnt canonical pathway; however, GSK‐3β interacts with multiple signalling pathways, and aberrant expression of the enzyme was reported in many solid neoplasms. This study aimed to investigate the biological relevance of GSK‐3β in classical Hodgkin lymphomas (cHL).
A Genetic Approach for Joint Link Scheduling and Power Control in SIC-enable Wireless Networks

Successive interference cancellation (SIC) is an effective means of multi-packet reception to combat interference at the physical layer. We investigate the joint optimization issue of channel access and power control for capacity maximization in SIC-enabled wireless networks. We propose a new interference model to characterize the sequential detection nature of SIC. Afterward, we formulize the joint optimization problem, prove it to be a nondeterministic polynomial-time-hard problem, and propose a novel approximation approach based on the genetic algorithm (GA). Finally, we discuss the design and parameter setting of the GA approach and validate its performance through extensive simulations.