Miracle-dz/UniFAR-FTUs huggingface dataset:
Stream Scare: Riparian Species Richness and Fish Diversity as Indicators of Stream Health

Stream health is a major concern for communities that utilize its resources for freshwater or recreational activities, and for a diverse range of wildlife and vegetation. The distribution and diversity of fish and aquatic plants within freshwater streams can act as indicators of lotic ecosystem health. This study looks at two separate stream ecosystems within the same drainage basin. Kickapoo Stream is a small, slow moving headwater stream with minimal coverage. Here, riparian species richness and percent coverage of submergent, emergent, and floating vegetation was observed at various 27 distances flowing out of Kickapoo Lake (Figure 3). The West Branch Ontonagon River was the second study site. Here, fish diversity was sampled at four sites of varying distance from its main source (Cisco Lake; Figure 4). Riffle, run, and pool habitat type was sampled at each site. Length and mass of Redtail Chub, an abundant species of the West Branch Ontonagon River, was also taken at habitat type within each site. In Kickapoo, riparian species richness increased with increasing distance from Kickapoo Lake, but the percent coverage of vegetation was not affected with changes in distance. In the West Branch Ontonagon River, fish species richness and diversity did not differ with site (distance from mainsource lake) or habitat type (riffle, pool, or run). However, Redtail Chub mass and length differed with both site and habitat. Introduction Freshwater streams are important for various reasons ranging from a hometown communities’ drinking water and recreational getaway to a habitat for diverse fish and wildlife. Maintaining stream health is essential in providing a sustainable ecosystem to provide these resources. Both fish diversity and riparian species richness can be important metrics of stream health. There are often similar responses to stream condition across trophic levels (Mazeika et al., 2008), and insight into these responses can give researchers key information into the effects of human influences (Mazeika et al., 2008) and natural disturbances (Montgomery, 1999) on stream ecosystems. Vannote et al. (1980) developed a frequently used framework to describe the structure and function of communities along healthy river systems known as the “River Continuum Concept” or the RCC (Figure 1). This framework looks at how the gradient of physical factors within drainage networks affects living organisms in fresh running water. Since
A new adaptive image sequence coding scheme using Kohonen's SOFM

This paper presents a novel adaptive vector quantisation scheme based on the SOFM neural network. All adaptation is performed directly from the quantised image with no explicit adaptation information transmitted or stored. Thus the network learns an input distribution it has never actually seen. Training sets are generated from the received image by scaling the image to approximate the statistics of the original image and selecting blocks in such a way as to capture edges and other image features. This data is fed to a SOFM neural network to update the codebook. A new method is also presented for ensuring that all neurons are well used, by estimating directly from the quantised image how much distortion each neuron introduces. The ability of this scheme to adapt successfully is verified by simulation.
Positive cascade effects of forest fragmentation on acorn weevils mediated by seed size enlargement

Abstract. 1. Today, forest fragmentation is one of the major threats to biodiversity worldwide. In this context, fragmented populations of specialised forest organisms face an increasing risk of extinction because of factors such as local food scarcity. Nonetheless, the role of food availability may differ depending on organism size, which is expected to determine the energy requirements and mobility between fragments.
Rigid body mechanics in Galilean spacetimes

An observer-independent formulation of rigid body dynamics is provided in the general setting of a Galilean spacetime. The equations governing the motion of a rigid body undergoing a rigid motion in a Galilean spacetime are derived on the basis of the principle of conservation of spatial momentum. The formulation of rigid body dynamics is then studied in the presence of an observer. It is seen that an observer defines a connection such that there exist rigid motions that are horizontal with respect to this connection that give the same physical motion of the rigid body, and for which the general equations of motion are exactly the usual Euler equations for a rigid body undergoing rigid motion.
APPRAISAL OF THE ENTIRE MITOCHONDRIAL GENOME FOR DNA BARCODING IN BIRDS

DNA barcoding based on a standardized region of 648 base pairs of mitochondrial DNAsequences from Cytochrome C Oxidase 1 (COX1) is proposed for animal species identification.Recent studies suggested that DNA barcoding has been effective for identifying 94% of birdspecies. The proposed threshold of 10 times the average intraspecific variation could be used forthe identification and delimitation of new species. As a different part of the mitochondrial DNAevolves at various mutation rates, they show a variety of capabilities to distinguish taxa tospecies level. In order to compare the efficiency of protein-coding genes (PCGs) in birds, thecomplete genome of 310 birds, including 12 mitochondrial genes (except ND6) and barcodingthe region of COX1, were examined. We concentrated on the intra- and inter-specific variationsand the degree of mutational saturation as criteria for our evaluations. Some genes like ATP8,ND2 and ND5 showed the greatest divergence in intra- and inter-specific variations. Theoverlap between intra- and inter-specific variability for all genes is still troublesome. Our resultsmay have been influenced by the sample size because our data were not representative of allbird species. More additional taxa may shed light more on DNA barcoding candidate genes.
Load-deflection Analysis of CFRP Strengthened RC Slab Using Focused Feed-forward Time Delay Neural Network

In this paper, the load-deflection analysis of the Carbon Fiber Reinforced Polymer (CFRP) strengthened Reinforced Concrete (RC) slab using Focused Feed-forward Time Delay Neural Network (FFTDNN) is investigated. S ix reinforced concrete slabs having dimension 1800×400×120 mm with similar steel bar of 2T10 and strengthened using different length and width of CFRP were tested and compared with similar samples without CFRP. The experimental load-deflection results were uploaded, normalized, and converted to a time sequence parameter in MATLAB software. Loading, time, and the effect of the different CFRP strip lengths on the slab moment of inertia were as neurons in input layer and mid-span deflection was as neuron in output layer. The network was generated using feed-forward network and a tapped delay line at the input layer to memorize the input data while training process. From 122 load-deflection data, 111 data utilized for network generation and 11 data for the network testing. The results of model on the testing stage showed that the generated FFTDNN predicted the load-deflection analysis of the slabs in acceptable technique with a correlation of determination of 0.98. The ratio between predicted deflection by FFTDNN and experimental output was in the range of 0.92 to 1.23.
The Influence of Plant Population Spatial Arrangement on Individual Plant Yield

Two greenhouse experiments were conducted to evaluate the performance of individual oat (Avena sativa) target plants as influenced by neighbor oat plants with different spatial arrangements. Crop spatial arrangement was separated into three com- ponents: (1) population density, (2) distance between plants (distance dispersion, DD), and (3) angular arrangement of plants about one another (angular dispersion, AD). Distance dispersion was quantified using a weighted mean distance from a target individual to its neighbors. Angular dispersion of neighbors around the target was quantified using a measure of circular variance. DD and AD were combined to create a dispersion index (DI). At constant density, distance dispersion treatments were combined with angular dispersion treatments in a randomized-block factorial design. Target plant biomass production was predicted using a rectangular hyperbola equation including population density, DD, AD, and DI as independent variables. Fifty-five and 44% of the residual variation (the variation not accounted for by density alone) in individual plant yield was accounted for when spatial arrangement (DI) was added to the regression. The approach can be used to compare the intensity of competition among different crop planting patterns.
Second-harmonic generation imaging analysis can help distinguish sarcoidosis from tuberculoid leprosy

Abstract. Sarcoidosis and tuberculoid leprosy (TL) are prototypes of granulomatous inflammation in dermatology, which embody one of the histopathology limitations in distinguishing some diseases. Recent advances in the use of nonlinear optical microscopy in skin have enabled techniques, such as second-harmonic generation (SHG), to become powerful tools to study the physical and biochemical properties of skin. We use SHG images to analyze the collagen network, to distinguish differences between sarcoidosis and TL granulomas. SHG images obtained from skin biopsies of 33 patients with TL and 24 with sarcoidosis retrospectively were analyzed using first-order statistics (FOS) and second-order statistics, such as gray-level co-occurrence matrix (GLCM). Among the four parameters evaluated (optical density, entropy, contrast, and second angular moment), only contrast demonstrated statistical significance, being higher in sarcoidosis (p = 0.02; 4908.31 versus 2822.17). The results may indicate insufficient differentiating power for most tested FOS and GLCM parameters in classifying sarcoidosis and TL granulomas, when used individually. But in combination with histopathology (H&E and complementary stains, such as silver and fast acid stains), SHG analysis, like contrast, can contribute to distinguishing between these diseases. This study can provide a way to evaluate collagen distribution in granulomatous diseases.
Preserved Microarrays for Simultaneous Detection and Identification of Six Fungal Potato Pathogens with the Use of Real-Time PCR in Matrix Format

Fungal diseases of plants are of great economic importance causing 70–80% of crop losses associated with microbial plant pathogens. Advanced on-site disease diagnostics is very important to maximize crop productivity. In this study, diagnostic systems have been developed for simultaneous detection and identification of six fungal pathogens using 48-well microarrays (micromatrices) for qPCR. All oligonucleotide sets were tested for their specificity using 59 strains of target and non-target species. Detection limit of the developed test systems varied from 0.6 to 43.5 pg of DNA depending on target species with reproducibility within 0.3−0.7% (standard deviation). Diagnostic efficiency of test systems with stabilized and freeze-dried PCR master-mixes did not significantly differ from that of freshly prepared microarrays, though detection limit increased. Validation of test systems on 30 field samples of potato plants showed perfect correspondence with the results of morphological identification of pathogens. Due to the simplicity of the analysis and the automated data interpretation, the developed microarrays have good potential for on-site use by technician-level personnel, as well as for high-throughput monitoring of fungal potato pathogens.
A 6D interferometric inertial isolation system

We present the conceptual design and noise analysis of a novel inertial-isolation scheme based on six degree-of-freedom (6D) interferometric sensing of a single reference mass. It is capable of reducing inertial motion by more than two orders of magnitude at 100 mHz compared with what is achievable with state-of-the-art seismometers. This will enable substantial improvements in the low-frequency sensitivity of gravitational-wave detectors. The scheme is inherently two-stage, the reference mass is softly suspended within the platform to be isolated, which is itself suspended from the ground. The platform is held constant relative to the reference mass and this closed-loop control effectively transfers the low acceleration-noise of the reference mass to the platform. The loop gain also reduces non-linear couplings and dynamic range requirements in the soft-suspension mechanics and the interferometric sensing.
SNARE Proteins: One to Fuse and Three to Keep the Nascent Fusion Pore Open

Facilitating Fusion and Release For neurotransmitters to be released from a neuron, a synaptic vesicle must fuse with the plasma membrane and form a fusion pore. Soluble N-ethylmaleimide–sensitive factor attachment protein receptor (SNARE) complexes are the core protein machinery involved in fusion; however, there has been debate regarding the mechanism. While in vitro studies have found that a single SNARE can cause fusion of two bilayers, in vivo studies have shown that a minimum of three SNAREs are required for neurotransmitter release. The apparently contradictory results are explained by Shi et al. (p. 1355), who monitored fusion of vesicles to membrane nanodiscs. While a single SNARE complex was sufficient to fuse bilayers, a minimum of three SNARE complexes were required to open a pore large enough for neurotransmitter release. Whereas one fusion protein complex can fuse a vesicle with a bilayer, three are needed for efficient content release. Neurotransmitters are released through nascent fusion pores, which ordinarily dilate after bilayer fusion, preventing consistent biochemical studies. We used lipid bilayer nanodiscs as fusion partners; their rigid protein framework prevents dilation and reveals properties of the fusion pore induced by SNARE (soluble N-ethylmaleimide–sensitive factor attachment protein receptor). We found that although only one SNARE per nanodisc is required for maximum rates of bilayer fusion, efficient release of content on the physiologically relevant time scale of synaptic transmission apparently requires three or more SNARE complexes (SNAREpins) and the native transmembrane domain of vesicle-associated membrane protein 2 (VAMP2). We suggest that several SNAREpins simultaneously zippering their SNARE transmembrane helices within the freshly fused bilayers provide a radial force that prevents the nascent pore from resealing during synchronous neurotransmitter release.
Lipolysis of semi-hard cheese made with a lacticin 481-producing Lactococcus lactis strain and a Lactobacillus helveticus strain

Free fatty acids (FFA) liberated from milk fat by lipases and esterases during cheese ripening affect flavour, by themselves or as precursors for the synthesis of other volatile compounds. The effect of the lacticin 481-producing strain Lactococcus lactis subsp. lactis INIA 639 (BP) on the release of intracellular esterases from a Lactobacillus helveticus strain used as adjunct culture and FFA levels during ripening of semi-hard cheese was investigated. Cheeses were manufactured using either L. lactis subsp. lactis INIA 639, the bacteriocin non-producing strain L. lactis subsp. lactis INIA 437, or a combination of both strains, as mesophilic starter cultures. The Lb. helveticus strain, sensitive to lacticin 481, was added to all vats. Cheeses made with the BP strain exhibited on day 50 esterase activity values up to 29% higher than those of cheese made without the BP strain. Levels of most individual FFA in cheese were increased by milk inoculation with the BP strain. On day 50, total (C4:0-C18:2) FFA were 628 to 638 mg·kg −1 in cheeses made with the BP strain, and 576 mg·kg −1 in cheese made without the BP strain, mostly due to the higher accumulation of FFA from day 25 to day 50 in the former cheeses. Bacteriocin-mediated lysis of the Lb. helveticus strain and subsequent release of its esterases appeared to be responsible for accelerated lipolysis in cheese. lacticin 481 / lipolysis / cheese / Lactobacillus helveticus
Distribution of carbonate in surface sediments of the Pacific Ocean

The distribution of carbonate on the floor of the Pacific has been remapped on the basis of 1313 points from 80 references stored in the World Ocean Sediment Data Bank of Scripps Institution of Oceanography. Percent distribution maps and carbonate versus depth diagrams generally agree with previously published information and reflect the major controlling factors of carbonate sedimentation (depth, hydrography, fertility, and sedimentary processes). While carbonate distributions are of limited use in attempting to construct dissolution profiles, major trends are identifiable. In particular, the degree of lowering of the equatorial calcite compensation depth (CCD) together with an estimate of the differences in supply rates between the equator and the subtropical gyre can be used to estimate dissolution rate increase below the lysocline. There is considerable variation in the sharpness of the ‘CCD transition’ a concept defined here. This variation is thought to reflect both geographic differences in dissolution rate gradients and redeposition processes (carbonate, deep-sea sediments, calcite, and compensation depth).
Quantification of lattice images: the contribution from diffuse scattering (Eighth Conference on Frontiers of Electron Microscopy in Materials Science)

At present, quantitative comparisons of experimental and simulated high- resolution images show that the contrast in experimental images is usually much less than is predicted by simulations, typically by a factor of around three. Investigations of this contrast discrepancy in images of amorphous carbon have shown that the contrast in experimental images is lower than in simulations by the same factor for a wide range of spatial frequencies, suggesting the possibility that the contrast loss is due to the addition of a constant background to the experimental images. The source of this con- stant background is investigated using convergent-beam diffraction pat- terns as a function of thickness and lattice images from an (001)-oriented crystal of GaAs. The diffuse background is measured in the convergent- beam patterns and found to contribute about 33% of the total intensity at 25 nm thickness. However, at this thickness the experimental lattice image contrast is only about half that of a simulated lattice image. Thus, although the measured diffuse scattering produces a significant contrast reduction in lattice images, the diffuse scattering from phonons and amorphous car- bon is not sufficient to explain why lattice images have such low contrast.
Chemogenetic silencing of hippocampal neurons suppresses epileptic neural circuits

We investigated how pathological changes in newborn hippocampal dentate granule cells (DGCs) lead to epilepsy. Using a rabies virus–mediated retrograde tracing system and a designer receptors exclusively activated by designer drugs (DREADD) chemogenetic method, we demonstrated that newborn hippocampal DGCs are required for the formation of epileptic neural circuits and the induction of spontaneous recurrent seizures (SRS). A rabies virus–mediated mapping study revealed that aberrant circuit integration of hippocampal newborn DGCs formed excessive de novo excitatory connections as well as recurrent excitatory loops, allowing the hippocampus to produce, amplify, and propagate excessive recurrent excitatory signals. In epileptic mice, DREADD-mediated–specific suppression of hippocampal newborn DGCs dramatically reduced epileptic spikes and SRS in an inducible and reversible manner. Conversely, specific activation of hippocampal newborn DGCs increased both epileptic spikes and SRS. Our study reveals an essential role for hippocampal newborn DGCs in the formation and function of epileptic neural circuits, providing critical insights into DGCs as a potential therapeutic target for treating epilepsy.
Safety and efficacy of nivolumab applied at different dosage in the patients with relapsing Hodgkin lymphoma after allogeneic hematopoietic stem cell transplantation

Kirill V. Lepik, Andrey V. Kozlov, Evgeniya S. Borzenkova, Marina O. Popova, Ivan S. Moiseev, Elena I. Darskaya, Asmik G. Gevorgyan, Luibov A. Tsvetkova, Sergey N. Bondarenko, Alexander L. Alyanskiy, Elena V. Kondakova, Natalya B. Mikhailova, Boris V. Afanasyev R. M. Gorbacheva Memorial Institute of Children Oncology, Hematology and Transplantation, Chair of Hematology, Transfusiology and Transplantology, The First St. Petersburg State I. P. Pavlov Medical University, Roentgen St. 12; 197022, St. Petersburg, Russia Safety and efficacy of nivolumab applied at different dosage in the patients with relapsing Hodgkin lymphoma after allogeneic hematopoietic stem cell transplantation Cellular Therapy and Transplantation (CTT). Vol. 7, No. 2(23), 2018 doi: 10.18620/ctt-1866-8836-2018-7-2-28-35 Submitted: 03 May 2018, accepted: 29 June 2018
Comparative studies on growth and physiological responses to saline and alkaline stresses of Foxtail millet ('Setaria italica' L.) and Proso millet ('Panicum miliaceum' L.)

Soil salinization and alkalization are widespread environmental problems. To compare the growth and physiological responses under saline stress (SS) and alkaline stress (AS), Foxtail millet (Setaria italic L) and Proso millet (Panicum miliaceum L) were tested under saline and alkaline conditions by mixing the two neutral salts (NaCl and Na2SO4) and the two alkaline salts (NaHCO3 and Na2CO3). Compared to SS, AS inhibited in greater extent plant dry weight, relative growth rate (RGR), net assimilation rate (NAR), leaf area ratio (LAR) and relative water content (RWC) and the rates of reduction were more pronounced in Foxtail millet, indicating that tolerance to AS was higher in Proso millet than in Foxtail millet. Sodium concentration in leaves was enhanced at double by AS than in SS. Foxtail millet accumulated more Na in the leaves and stem but the roots of Proso millet contained a higher concentration of Na, indicating that Proso millet inhibited the transportation of Na from roots to shoots which resulted in less of a decrease in plant growth. The N content markedly decreased under AS in leaves, stems and roots of both species. The proline content in leaves increased under both treatments and it was higher in SS than in AS. These results suggest that the potential extent of stress-induced injuries was higher in Foxtail millet than in Proso millet and thus Proso millet may have a higher capacity to tolerate saline and alkaline conditions, especially the more deleterious alkaline condition.
Study of association between body composition and anthropometric dimensions in a population of Indian Army

Objectives: To investigate the association of various anthropometric measures with body composition parameters such as percentage of body fat (PBF), fat mass (FM) and fat free mass (FFM). Material and method: This study was carried out on randomly selected 373 Gorkha soldiers (age range was 20-48 years) of Indian army. All anthropometric parameters were measured using calibrated anthropometer, sliding caliper, skin fold calipers and inelastic steel measuring tape. Body composition variables were recorded using BIA model TANITA, TBF-310. Result: Result indicate that waist circumference (WC) showed the strongest correlations (p=0.000) with FM (r=0.802) and PBF(r=0.758). The highest amount of variation of PBF (57.4%) and FM (64.3%) was explained by WC while hip circumference (HC) explained 37.6% and 52.6% variation of PBF and FM respectively and HC also explained 52.6% variation of FFM. Conicity index (CI) explained low variation of PBF and FM compared to WC and WHR. Conclusion: Present study showed that WC has a better association with body fat than rest anthropometric parameters including WHR and CI. Hence the use of WC instead of WHR and CI could be advantageous in study of central adiposity with PBF and FM.