Miracle-dz/UniFAR-FTUs huggingface dataset:
Sulfurimonas gotlandica sp. nov., a chemoautotrophic and psychrotolerant epsilonproteobacterium isolated from a pelagic redoxcline, and an emended description of the genus Sulfurimonas

A psychro- and aerotolerant bacterium was isolated from the sulfidic water of a pelagic redox zone of the central Baltic Sea. The slightly curved rod- or spiral-shaped cells were motile by one polar flagellum or two bipolar flagella. Growth was chemolithoautotrophic, with nitrate or nitrite as electron acceptor and either a variety of sulfur species of different oxidation states or hydrogen as electron donor. Although the bacterium was able to utilize organic substances such as acetate, pyruvate, peptone and yeast extract for growth, these compounds yielded considerably lower cell numbers than obtained with reduced sulfur or hydrogen; in addition, bicarbonate supplementation was necessary. The cells also had an absolute requirement for NaCl. Optimal growth occurred at 15 °C and at pH 6.6–8.0. The predominant fatty acid of this organism was 16 : 1ω7c, with 3-OH 14 : 0, 16 : 0, 16 : 1ω5c+t and 18 : 1ω7c present in smaller amounts. The DNA G+C content was 33.6 mol%. As determined in 16S rRNA gene sequence phylogeny analysis, the isolate belongs to the genus Sulfurimonas, within the class Epsilonproteobacteria, with 93.7 to 94.2 % similarity to the other species of the genus Sulfurimonas, Sulfurimonas autotrophica, Sulfurimonas paralvinellae and Sulfurimonas denitrificans. However, the distinct physiological and genotypic differences from these previously described taxa support the description of a novel species, Sulfurimonas gotlandica sp. nov. The type strain is GD1T ( = DSM 19862T = JCM 16533T). Our results also justify an emended description of the genus Sulfurimonas.
Kaolin Foliar Application Has a Stimulatory Effect on Phenylpropanoid and Flavonoid Pathways in Grape Berries

Drought, elevated air temperature, and high evaporative demand are increasingly frequent during summer in grape growing areas like the Mediterranean basin, limiting grapevine productivity and berry quality. The foliar exogenous application of kaolin, a radiation-reflecting inert mineral, has proven effective in mitigating the negative impacts of these abiotic stresses in grapevine and other fruit crops, however, little is known about its influence on the composition of the grape berry and on key molecular mechanisms and metabolic pathways notably important for grape berry quality parameters. Here, we performed a thorough molecular and biochemical analysis to assess how foliar application of kaolin influences major secondary metabolism pathways associated with berry quality-traits, leading to biosynthesis of phenolics and anthocyanins, with a focus on the phenylpropanoid, flavonoid (both flavonol- and anthocyanin-biosynthetic) and stilbenoid pathways. In grape berries from different ripening stages, targeted transcriptional analysis by qPCR revealed that several genes involved in these pathways—VvPAL1, VvC4H1, VvSTSs, VvCHS1, VvFLS1, VvDFR, and VvUFGT—were more expressed in response to the foliar kaolin treatment, particularly in the latter maturation phases. In agreement, enzymatic activities of phenylalanine ammonia lyase (PAL), flavonol synthase (FLS), and UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT) were about two-fold higher in mature or fully mature berries from kaolin-treated plants, suggesting regulation also at a transcriptional level. The expression of the glutathione S-transferase VvGST4, and of the tonoplast anthocyanin transporters VvMATE1 and VvABCC1 were also all significantly increased at véraison and in mature berries, thus, when anthocyanins start to accumulate in the vacuole, in agreement with previously observed higher total concentrations of phenolics and anthocyanins in berries from kaolin-treated plants, especially at full maturity stage. Metabolomic analysis by reverse phase LC-QTOF-MS confirmed several kaolin-induced modifications including a significant increase in the quantities of several secondary metabolites including flavonoids and anthocyanins in the latter ripening stages, probably resulting from the general stimulation of the phenylpropanoid and flavonoid pathways.
Fivebranes wrapped on SLAG three-cycles and related geometry

We construct ten-dimensional supergravity solutions corresponding to the near horizon limit of IIB fivebranes wrapping special lagrangian three-cycles of constant curvature. The case of branes wrapping a three-sphere provides a gravity dual of pure = 2 super--Yang-Mills theory in D = 3. The non-trivial part of the solutions are seven manifolds that admit two G2 structures each of which is covariantly constant with respect to a different connection with torsion. We derive a formula for the generalised calibration for this general class of solutions. We discuss analogous aspects of the geometry that arises when fivebranes wrap other supersymmetric cycles which lead to Spin(7) and SU(N) structures. In some cases there are two covariantly constant structures and in others one.
Review of Trends in Soil Fertility Research (2007–2016) using Scopus Database

ABSTRACT A critical analysis of publications on soil fertility was carried out using data from Scopus database for the period of 2007–2016. A total of 16,612 articles were found relating to soil fertility. An exponential increase was evident from the review of published literature and scientists involved in the soil fertility research also increased over period of time. The journals Soil Science and Plant Nutrition and Acta Ecologica Sinica were major publishers of the soil fertility research. Giller K. E. from Wageningen University, The Netherlands was a major contributor followed by Salvati L. of Centro Per Lo Studio Delle Relazioni Piñata-Suolo, Italy. China was the most productive country with 3323 articles. Cluster analysis of author-supplied keywords showed five clusters, namely, desertification, soil organic carbon, plant nutrition, nitrogen, and geostatic. This work will be useful to researchers to know the trends in soil fertility research.
Review of the current state of whole slide imaging in pathology

Whole slide imaging (WSI), or "virtual" microscopy, involves the scanning (digitization) of glass slides to produce "digital slides". WSI has been advocated for diagnostic, educational and research purposes. When used for remote frozen section diagnosis, WSI requires a thorough implementation period coupled with trained support personnel. Adoption of WSI for rendering pathologic diagnoses on a routine basis has been shown to be successful in only a few "niche" applications. Wider adoption will most likely require full integration with the laboratory information system, continuous automated scanning, high-bandwidth connectivity, massive storage capacity, and more intuitive user interfaces. Nevertheless, WSI has been reported to enhance specific pathology practices, such as scanning slides received in consultation or of legal cases, of slides to be used for patient care conferences, for quality assurance purposes, to retain records of slides to be sent out or destroyed by ancillary testing, and for performing digital image analysis. In addition to technical issues, regulatory and validation requirements related to WSI have yet to be adequately addressed. Although limited validation studies have been published using WSI there are currently no standard guidelines for validating WSI for diagnostic use in the clinical laboratory. This review addresses the current status of WSI in pathology related to regulation and validation, the provision of remote and routine pathologic diagnoses, educational uses, implementation issues, and the cost-benefit analysis of adopting WSI in routine clinical practice.
Effects of Ginkgo Biloba Special Extract EGb 761® in Very Mild Cognitive Impairment (vMCI)

Objective: To assess effects of EGb 761 ® on cognition and quality of life in subjects with very mild cognitive impairment. Methods: We randomized 300 subjects aged 45 to 65 with cognitive complaints and low functioning (more than one standard deviation below appropriate norm) in at least one cognitive test to double-blind treatment with once daily 240 mg EGb 761 ® or placebo for 12 weeks. Results: The exploratory intention-to-treat analysis showed significant improvement (p < 0.025, one-sided) beyond practice effects for EGb 761 ® in a measure of attention (Vienna Test SystemWork Performance Series) and trends in favour of EGb 761 ® in measures of memory (Wechsler Memory Scale IIIFaces I, Appointments Test—delayed recall), and perceived physical health (SF36-factor score Physical Health). Cognitive effects were more pronounced and more consistent (p < 0.025 in 4 of 5 tests) in subjects with lower memory function at baseline. Specifically, practice effects in the more demanding tests were attenuated or absent in these subjects. Conclusion: Ginkgo biloba extract EGb 761 ® improved cognitive functioning and aspects of quality of life in subjects with very mild cognitive impairment.
CloudZombie: Launching and Detecting Slow-Read Distributed Denial of Service Attacks from the Cloud

As the Cloud is becoming more ubiquitous and less expensive to utilize, a new class of denial of service attacks is emerging. These attacks employ the Cloud to launch denial of service attacks against a target outside the Cloud. Slow-read denial of service can be one of those attacks. It is a new type of application-layer denial of service attacks that exploits vulnerabilities in the HTTP protocol in order to make services inaccessible for legitimate users on a target machine. This attack is difficult to detect by conventional intrusion detection systems, as it generates legitimate and complete packets in all networking layers and in a slow rate. The attack exhausts the target's resources such as Web server connection pool and generally needs much less bandwidth compared to traditional volumetric attacks. The Cloud is an ideal platform to launch slow-read attack, since virtual machines on the Cloud can be easily exploited as a botnet for the purpose of this attack. We show how this new phenomenon, CloudZombie, can happen by remotely launching slow-read attacks from the Cloud. We also present a new approach to detect slow-read attacks. Our method uses Random Forests to build classifiers based on which the incoming slow-read traffic can be detected at the destination. High performance and low error rates of our approach indicate its efficiency to detect the attack.
Enumerations, Forbidden Subgraph Characterizations, and the Split-Decomposition

Forbidden characterizations may sometimes be the most natural way to describe families of graphs, and yet these characterizations are usually very hard to exploit for enumerative purposes.By building on the work of Gioan and Paul (2012) and Chauve et al.(2014), we show a methodology by which we constrain a split-decomposition tree to avoid certain patterns, thereby avoiding the corresponding induced subgraphs in the original graph.We thus provide the grammars and full enumeration for a wide set of graph classes: ptolemaic, block, and variants of cactus graphs (2,3-cacti, 3-cacti and 4-cacti). In certain cases, no enumeration was known (ptolemaic, 4-cacti); in other cases, although the enumerations were known, an abundant potential is unlocked by the grammars we provide (in terms of asymptotic analysis, random generation, and parameter analyses, etc.). We believe this methodology here shows its potential; the natural next step to develop its reach would be to study split-decomposition trees which contain certain prime nodes. This will be the object of future work.
Development of abnormal recrossing retinotectal projections after superior colliculus lesions in newborn Syrian hamsters

The development of the retinal projections to the roof of the midbrain was studied in Syrian hamsters after right superior colliculus (SC) lesions on the day of birth, using both autoradiographic and degeneration techniques. The dead tissue resulting from the heat lesion is not completely removed until the eighth day after birth. Normally the midline of the SC is defined by a pia‐lined fissure separating the left and right colliculi, but in the animals with early unilateral lesions, the pia at the midline is damaged. When it regrows, together with vascular and other meningeal tissues, it forms a flat tissue bridge across the midline as early as two days after the lesion.
Robust 3D modeling from silhouette cues

We consider the problem of 3D modeling under the environments where colors of the foreground objects are similar to the background, which poses a difficult problem of foreground and background classification. A purely image-based algorithm is adopted in this paper, with no prior information about the foreground objects. We classify foreground and background by fusing the information at the pixel and region levels to obtain the similarity probability map, followed by a Bayesian sensor fusion framework to infer the space occupancy grid. The estimation of the occupancy allows incremental updating once a new observation is available, and the contribution of each observation can be adjusted according to its reliability. Finally, three parameters in the algorithm are analyzed in detail and experiments show the effectiveness of this method.
Design and performance comparison of a novel high Q coaxial resonator filter and compact waveguide filter for millimeter wave payload applications

A novel high‐performance high Q filter with ultra‐wide spurious‐free stopband and thermally stable performance is introduced using higher order mode of the coaxial resonator. The 7‐pole Chebyshev and a 5‐pole cross‐coupled filter are designed at Ka‐band to validate the concept. A compact cross‐coupled waveguide filter is introduced with a different approach to realize cross‐coupling makes the filter compact. The coaxial resonator and waveguide resonator filter have the same configuration, and their performances are compared at ambient and over the temperature. The high power analysis is done for both these filters to find their power handling capability. The high power performance of the coaxial resonator filter is superior, and it can handle 45.525 kW peak power. This filter is suitable to be used as pre‐select filter in millimeter wave payloads as well as for high power filtering applications.
Asynchrony in Quantum-Dot Cellular Automata Nanocomputation: Elixir or Poison?

Emerging computing technologies inherently exhibit high process and timing variation. Many researchers believe that an asynchronous approach is likely to play an enabling role in making these technologies feasible. This article compares the cost and performance of fully synchronous and mixed synchronous asynchronous implementations of quantum cellular automata, and makes the case that asynchrony is inevitable at the top levels of QCA designs.
Motion Estimation in Cardiac Fluorescence Imaging With Scale-Space Landmarks and Optical Flow: A Comparative Study

Motion artifacts are a major disadvantage of cardiac optical mapping studies. Pixel misalignment due to contraction is a main cause of the presence of gross motion artifacts in action potential recordings. This study is focused on methods for identifying landmarks and tracking the motion of cardiac tissue for preparations in optical mapping recordings. This is a first step toward our long-term goal to implement a landmark-based image registration technique to correct for pixel misalignment in cardiac optical mapping fluorescence videos and, hence, for gross motion artifacts. Preliminary results for the registration step are presented as an initial proof of concept. The characteristics of the optical mapping images are challenging, since their lack of contrast and well-defined features impose a limitation on the techniques than can be used for landmark selection and motion tracking. This paper compares results of motion estimation of the cardiac surface with two approaches that do not rely on high-contrast features: 1) Scale-invariant feature transform (SIFT) detected “keypoints,” to be used as landmarks for motion tracking, as well as 2) a classical global optical flow (OF) algorithm. Both are applied to low-contrast and low-resolution cardiac fluorescence images. We demonstrate that the performance of SIFT is superior to that of OF for pixel motion tracking in cardiac optical mapping images with simulated motion. Results for action potential recovery and action potential duration calculation after landmark-based image registration show that SIFT landmark-based registration yields superior performance in this regard as well.
Microkernel Architecture and Hardware Abstraction Layer of a Reliable Reconfigurable Real-Time Operating System (R3TOS)

This article presents a new solution for easing the development of reconfigurable applications using Field-Programable Gate Arrays (FPGAs). Namely, our Reliable Reconfigurable Real-Time Operating System (R3TOS) provides OS-like support for partially reconfigurable FPGAs. Unlike related works, R3TOS is founded on the basis of resource reusability and computation ephemerality. It makes intensive use of reconfiguration at very fine FPGA granularity, keeping the logic resources used only while performing computation and releasing them as soon as it is completed. To achieve this goal, R3TOS goes beyond the traditional approach of using reconfigurable slots with fixed boundaries interconnected by means of a static communication infrastructure. Instead, R3TOS approaches a static route-free system where nearly everything is reconfigurable. The tasks are concatenated to form a computation chain through which partial results naturally flow, and data are exchanged among remotely located tasks using FPGA’s reconfiguration mechanism or by means of “removable” routing circuits. In this article, we describe the R3TOS microkernel architecture as well as its hardware abstraction services and programming interface. Notably, the article presents a set of novel circuits and mechanisms to overcome the limitations and exploit the opportunities of Xilinx reconfigurable technology in the scope of hardware multitasking and dependability.
Impact of comorbidities and drug therapy on development of renal impairment in a predominantly African American and Hispanic HIV clinic population

Purpose Renal impairment in human immunodeficiency virus (HIV)-infected patients could potentially be caused by many factors. HIV-related renal impairment risks have been little studied in African Americans and Hispanics. We investigated the impact of HIV itself, highly active antiretroviral therapy (HAART), comorbidities, and non-HIV-related drug treatment on glomerular filtration rate in a predominantly African American/Hispanic HIV-infected population who had received HAART for at least one year. This study was a retrospective electronic medical record database evaluation of renal impairment risks in a largely African American/Hispanic HIV population obtaining medical care at an HIV clinic in Dallas, Texas. Methods Proportional hazards models were used to investigate an association between an estimated glomerular filtration rate decrease >25% from baseline (ie, renal impairment) and demographics, antiretroviral/nonantiretroviral medications, comorbidities (hypertension, diabetes mellitus, hepatitis C virus [HCV] infection, hepatitis B virus [HBV] infection), CD4+ counts, viral load, and duration patients were monitored at the clinic (time on study). Results In total, 323 patients were evaluated: 82% males; 61% African American/12% Hispanic/19% Caucasian; mean age 37.9 years (standard deviation [SD] 8.5); 6% HBV-positive; 34% HCV-positive; 29% hypertensive; 3% diabetic; 52% tenofovir-treated; mean weight 75.4 kg (SD, 15.4); mean estimated glomerular filtration 114.5 mL/min/1.73 m2 (SD, 36.7) using the Modification of Diet in Renal Disease (MDRD) calculation method; mean creatinine clearance (from which estimated glomerular filtration was extrapolated) by the Cockcroft-Gault calculation method 120.6 mL/min/1.73 m2 (SD, 41.2); mean time on study 2.7 years (SD, 1.0 year). An estimated glomerular filtration rate decrease of >25% from baseline was significantly associated with time on study (P = 0.0017; hazards ratio [HR] = 0.999) and hypertension (HR = 1.706; P = 0.0158) by the MDRD method, and with age (HR = 1.039; P = 0.0077), weight (HR = 0.987; P = 0.0023), and time on study (HR = 0.999; P = 0.0043) by extrapolation of Cockcroft-Gault creatinine clearance calculation. No specific HAART agent was associated with significant renal impairment risk by the definition used in this study. Conclusion This retrospective database study showed time on study, hypertension, weight, and age to be the only significant predictors of an estimated glomerular filtration rate decrease >25% from baseline.
Novel Nonlinear Knowledge-Based Mean Force Potentials Based on Machine Learning

The prediction of 3D structures of proteins from amino acid sequences is one of the most challenging problems in molecular biology. An essential task for solving this problem with coarse-grained models is to deduce effective interaction potentials. The development and evaluation of new energy functions is critical to accurately modeling the properties of biological macromolecules. Knowledge-based mean force potentials are derived from statistical analysis of proteins of known structures. Current knowledge-based potentials are almost in the form of weighted linear sum of interaction pairs. In this study, a class of novel nonlinear knowledge-based mean force potentials is presented. The potential parameters are obtained by nonlinear classifiers, instead of relative frequencies of interaction pairs against a reference state or linear classifiers. The support vector machine is used to derive the potential parameters on data sets that contain both native structures and decoy structures. Five knowledge-based mean force Boltzmann-based or linear potentials are introduced and their corresponding nonlinear potentials are implemented. They are the DIH potential (single-body residue-level Boltzmann-based potential), the DFIRE-SCM potential (two-body residue-level Boltzmann-based potential), the FS potential (two-body atom-level Boltzmann-based potential), the HR potential (two-body residue-level linear potential), and the T32S3 potential (two-body atom-level linear potential). Experiments are performed on well-established decoy sets, including the LKF data set, the CASP7 data set, and the Decoys “R”Us data set. The evaluation metrics include the energy Z score and the ability of each potential to discriminate native structures from a set of decoy structures. Experimental results show that all nonlinear potentials significantly outperform the corresponding Boltzmann-based or linear potentials, and the proposed discriminative framework is effective in developing knowledge-based mean force potentials. The nonlinear potentials can be widely used for ab initio protein structure prediction, model quality assessment, protein docking, and other challenging problems in computational biology.