Miracle-dz/UniFAR-FTUs huggingface dataset:
River network architecture, genetic effective size and distributional patterns predict differences in genetic structure across species in a dryland stream fish community

Dendritic ecological network (DEN) architecture can be a strong predictor of spatial genetic patterns in theoretical and simulation studies. Yet, interspecific differences in dispersal capabilities and distribution within the network may equally affect species’ genetic structuring. We characterized patterns of genetic variation from up to ten microsatellite loci for nine numerically dominant members of the upper Gila River fish community, New Mexico, USA. Using comparative landscape genetics, we evaluated the role of network architecture for structuring populations within species (pairwise FST) while explicitly accounting for intraspecific demographic influences on effective population size (Ne). Five species exhibited patterns of connectivity and/or genetic diversity gradients that were predicted by network structure. These species were generally considered to be small‐bodied or habitat specialists. Spatial variation of Ne was a strong predictor of pairwise FST for two species, suggesting patterns of connectivity may also be influenced by genetic drift independent of network properties. Finally, two study species exhibited genetic patterns that were unexplained by network properties and appeared to be related to nonequilibrium processes. Properties of DENs shape community‐wide genetic structure but effects are modified by intrinsic traits and nonequilibrium processes. Further theoretical development of the DEN framework should account for such cases.
Signatures of local adaptation in lowland and highland teosintes from whole‐genome sequencing of pooled samples

Spatially varying selection triggers differential adaptation of local populations. Here, we mined the determinants of local adaptation at the genomewide scale in the two closest maize wild relatives, the teosintes Zea mays ssp parviglumis and ssp. mexicana. We sequenced 120 individuals from six populations: two lowland, two intermediate and two highland populations sampled along two altitudinal gradients. We detected 8 479 581 single nucleotide polymorphisms (SNPs) covered in the six populations with an average sequencing depth per site per population ranging from 17.0× to 32.2×. Population diversity varied from 0.10 to 0.15, and linkage disequilibrium decayed very rapidly. We combined two differentiation‐based methods, and correlation of allele frequencies with environmental variables to detect outlier SNPs. Outlier SNPs displayed significant clustering. From clusters, we identified 47 candidate regions. We further modified a haplotype‐based method to incorporate genotype uncertainties in haplotype calling, and applied it to candidate regions. We retrieved evidence for selection at the haplotype level in 53% of our candidate regions, and in 70% of the cases the same haplotype was selected in the two lowland or the two highland populations. We recovered a candidate region located within a previously characterized inversion on chromosome 1. We found evidence of a soft sweep at a locus involved in leaf macrohair variation. Finally, our results revealed frequent colocalization between our candidate regions and loci involved in the variation of traits associated with plant–soil interactions such as root morphology, aluminium and low phosphorus tolerance. Soil therefore appears to be a major driver of local adaptation in teosintes.
Asexual queen succession mediates an accelerated colony life cycle in the termite Silvestritermes minutus

Mixed modes of reproduction, combining sexual processes with thelytokous parthenogenesis, occur in all major clades of social insects. In several species of termites, queens maximize their genetic input into nondispersing replacement queens through parthenogenesis, while maintaining genetically diverse sterile offspring and dispersing reproductives via sexual reproduction. This so‐called asexual queen succession (AQS) has multiple independent origins and its presumed advantages are diverse as well, ranging from multiplication of colony reproductive potential to extension of its lifespan beyond that of the foundress. However, how AQS shapes colony life cycles under natural conditions remains poorly known. The neotropical termite Silvestritermes minutus inhabits small but conspicuous nests, offering a unique opportunity to investigate the impact of AQS on life history. We report on its breeding system, life cycle and sex allocation using social structure census in 137 nests and genotyping of 12 colonies at 12 microsatellite loci. We show that colonies are established by an outbred pair of primary reproductives. In less than 2 years, the foundress is replaced by multiple neotenic queens, arising mostly through automixis with central fusion. Sterile castes, male and most (93%) female dispersers are produced sexually. Colony reproduction is usually restricted to a single dispersal of alates with unbiased sex ratio, taking place after 3 years. We conclude that S. minutus benefits from AQS to maximize colony growth rate and alate production within a very short life cycle rather than to extend colony lifespan. This highlights the versatile role of AQS in different cases of its polyphyletic origin.
The Synaptic Organization of the Brain

The first edition of this book reconciled new findings in synaptic physiology with classic neuron theory. For each of several brain regions such as hippocampus or cerebellum, Shepherd described the major neurons, illustrated their synaptic interrelationships, and diagramed a "basic circuit. " This second edition expands to include other brain regions such as the basal ganglia and to communicate new findings, especially regarding neurotransmitter substances. For some brain regions, contrary to the classic view, the dendrite rather than the entire neuron is the basic information-processing unit. The dendrite summates synaptic influences on it and, by way of dendrodendritic synapses, transfers this processed input to another dendrite, without necessarily affecting the potential on the neuronal cell body or axonal membrane. In fact, for the granule cell of the olfactory bulb and the amacrine cell of the retina, dendrodendritic action is the only neuronal communication that can occur; these cells have no axons.
Zooplankton community structure along a pollution gradient at fine geographical scales in river ecosystems: The importance of species sorting over dispersal

The release of anthropogenic pollution into freshwater ecosystems has largely transformed biodiversity and its geographical distribution patterns globally. However, for many communities including ecologically crucial ones such as zooplankton, it is largely unknown how different communities respond to environmental pollution. Collectively, dispersal and species sorting are two competing processes in determining the structure and geographical distribution of zooplankton communities in running water ecosystems such as rivers. At fine geographical scales, dispersal is usually considered as the dominant factor; however, the relative role of species sorting has not been evaluated well, mainly because significant environmental gradients rarely exist along continuously flowing rivers. The Chaobai River in northern China represents a rare system, where a significant environmental gradient exists at fine scales. Here, we employed high‐throughput sequencing to characterize complex zooplankton communities collected from the Chaobai River, and tested the relative roles of dispersal and species sorting in determining zooplankton community structure along the pollution gradient. Our results showed distinct patterns of zooplankton communities along the environmental gradient, and chemical pollutant‐related factors such as total phosphorus and chlorophyll‐a were identified as the major drivers for the observed patterns. Further partial redundancy analyses showed that species sorting overrode the effect of dispersal to shape local zooplankton community structure. Thus, our results reject the dispersal hypothesis and support the concept that species sorting caused by local pollution can largely determine the zooplankton community structure when significant environmental gradients exist at fine geographical scales in highly polluted running water ecosystems.
Inbreeding and inbreeding avoidance in wild giant pandas

Inbreeding can have negative consequences on population and individual fitness, which could be counteracted by inbreeding avoidance mechanisms. However, the inbreeding risk and inbreeding avoidance mechanisms in endangered species are less studied. The giant panda, a solitary and threatened species, lives in many small populations and suffers from habitat fragmentation, which may aggravate the risk of inbreeding. Here, we performed long‐term observations of reproductive behaviour, sampling of mother–cub pairs and large‐scale genetic analyses on wild giant pandas. Moderate levels of inbreeding were found in 21.1% of mating pairs, 9.1% of parent pairs and 7.7% of panda cubs, but no high‐level inbreeding occurred. More significant levels of inbreeding may be avoided passively by female‐biased natal dispersal rather than by breeding dispersal or active relatedness‐based mate choice mechanisms. The level of inbreeding in giant pandas is greater than expected for a solitary mammal and thus warrants concern for potential inbreeding depression, particularly in small populations isolated by continuing habitat fragmentation, which will reduce female dispersal and increase the risk of inbreeding.
Surgical Treatment of Pediatric Peripheral Giant Cell Granuloma: A Case Report

Ozet Periferal dev hucreli granuloma dis etinde ortaya cikan reaktif bir lezyondur. Dental plak, dis tasi, uygun olmayan restorasyonlar ve mikrotravma hikayesi gibi lokal faktorlerin periferal dev hucreli granuloma olusumunda rol oynadiklari dusunulmektedir. Periferal dev hucreli granuloma her yasta gorulmesine ragmen cocukluk caginda goreceli olarak daha az gorulmektedir. Bu olgu raporunda bir pediatrik periferal dev hucreli granulomanin cerrahi tedavisi sunulmus ve histopatolojik ozellikleri incelenmistir. Anahtar Kelimeler: Periferal dev hucreli granuloma, pediatrik, dev hucre, reaktif Abstract Peripheral giant cell granuloma (PGCG) is a reactive lesion which occurs on gingiva. Local factors such as inappropriate dental restorations, dental plaque and microtraumas are considered to be responsible for the occurrence of the lesion. Although PGCG may be seen in all decades of life, pediatric form is relatively rare. In this case report, a pediatric PGCG is presented with histopathological features. Key words: Peripheral giant cell granuloma, pediatric, giant cell, reactive lesion
Transcriptomics in the wild: Hibernation physiology in free‐ranging dwarf lemurs

Hibernation is an adaptive strategy some mammals use to survive highly seasonal or unpredictable environments. We present the first investigation on the transcriptomics of hibernation in a natural population of primate hibernators: Crossley's dwarf lemurs (Cheirogaleus crossleyi). Using capture–mark–recapture techniques to track the same animals over a period of 7 months in Madagascar, we used RNA‐seq to compare gene expression profiles in white adipose tissue (WAT) during three distinct physiological states. We focus on pathway analysis to assess the biological significance of transcriptional changes in dwarf lemur WAT and, by comparing and contrasting what is known in other model hibernating species, contribute to a broader understanding of genomic contributions of hibernation across Mammalia. The hibernation signature is characterized by a suppression of lipid biosynthesis, pyruvate metabolism and mitochondrial‐associated functions, and an accumulation of transcripts encoding ribosomal components and iron‐storage proteins. The data support a key role of pyruvate dehydrogenase kinase isoenzyme 4 (PDK4) in regulating the shift in fuel economy during periods of severe food deprivation. This pattern of PDK4 holds true across representative hibernating species from disparate mammalian groups, suggesting that the genetic underpinnings of hibernation may be ancestral to mammals.
Hybridization in Trypanosoma congolense does not challenge the predominant clonal evolution model. A comment on Tihon et al., 2017, Mol. Ecol.

Tihon et al. have just published in Mol. Ecol. a fine genomic study on Trypanosoma congolense, agent of Animal African Trypanosomiasis. They present very convincing evidence that T. congolense underwent several hybridization events between distinct genetic lines in Zambia. They claim that their data challenge our predominant clonal evolution model (PCE) of micropathogens. We point out the main tenets of our model and show that Tihon et al.'s claim is based on a misinterpretation of the PCE model. Actually, their data strongly support PCE in T. congolense at a microevolutionary level.
Local directional mask maximum edge patterns for image retrieval and face recognition

This study proposes a new feature descriptor, local directional mask maximum edge pattern, for image retrieval and face recognition applications. Local binary pattern (LBP) and LBP variants collect the relationship between the centre pixel and its surrounding neighbours in an image. Thus, LBP based features are very sensitive to the noise variations in an image. Whereas the proposed method collects the maximum edge patterns (MEP) and maximum edge position patterns (MEPP) from the magnitude directional edges of face/image. These directional edges are computed with the aid of directional masks. Once the directional edges (DE) are computed, the MEP and MEPP are coded based on the magnitude of DE and position of maximum DE. Further, the robustness of the proposed method is increased by integrating it with the multiresolution Gaussian filters. The performance of the proposed method is tested by conducting four experiments onopen access series of imaging studies-magnetic resonance imaging, Brodatz, MIT VisTex and Extended Yale B databases for biomedical image retrieval, texture retrieval and face recognition applications. The results after being investigated the proposed method shows a significant improvement as compared with LBP and LBP variant features in terms of their evaluation measures on respective databases.
THE LIMITS OF PRIVACY

When George Orwell looked ahead at mid-century to predict the rise of totalitarian regimes, he saw the complete abrogation of personal privacy as their crowning achievement. Nothing about our personal lives could be kept from centralized governments in the year 1984 as it followed us with the new technology of television. Citizens would be forced to watch government-mandated programs, and government agents would watch them back through personal video cameras. Every move of every person could be tracked and recorded. The image was terrifying. How trivial the capacity of television to intrude on our lives has now become in comparison to that of a personal computer connected to the Internet. How inconsequentia l a video image of our daily activities soon may seem in comparison to a genetic pro le that de nes our very being. Vast amounts of personal information are fed into networks of computers to be processed, analyzed, and sent around the country and around the world, often to be combined with other data stored on other computers. Much of this information we readily enter ourselves from the comfort of our homes when we make purchases, seek medical advice, or check  nancial records over the Internet. The result is a detailed picture of us that can be kept as a permanent record by entities of which we are not even aware. America was founded on a tradition of rebellion against government power and of resistance to government control over our lives. Historically, nothing has threatened the spirit of America more than unchecked centralized government authority in a world like that of Orwell’s 1984. When the spirit
Effect of glitches against masked AES S-box implementation and countermeasure

Masking of gates is one of the most popular techniques to prevent differential power analysis (DPA) of AES algorithm. It has been shown that the logic circuits used in the implementation of cryptographic algorithms leak side-channel information inspite of masking, which can be exploited, in differential power attacks. The phenomenon in CMOS circuits responsible for the leakage of masked circuits is known as glitching. Motivated by this fact, the authors analyse the effect of glitches in CMOS circuits against masked implementation of the AES S-box. The authors explicitly demonstrate that glitches do not affect always. There exists a relation between combinational path delay of the circuit and timing difference of input vectors to the circuit, which has a bearance on the amount of information leaked by the masked gates. A balanced masked S-box circuit is proposed where the inputs are synchronised by sequential components. Detailed SPICE results are shown to support the claim that the modifications indeed reduce the vulnerability of the masked AES S-box against DPA attacks.
Non-inferiority of pulsed xenon UV light versus bleach for reducing environmental Clostridium difficile contamination on high-touch surfaces in Clostridium difficile infection isolation rooms.

The standard for Clostridium difficile surface decontamination is bleach solution at a concentration of 10 % of sodium hypochlorite. Pulsed xenon UV light (PX-UV) is a means of quickly producing germicidal UV that has been shown to be effective in reducing environmental contamination by C. difficile spores. The purpose of this study was to investigate whether PX-UV was equivalent to bleach for decontamination of surfaces in C. difficile infection isolation rooms. High-touch surfaces in rooms previously occupied by C. difficile infected patients were sampled after discharge but before and after cleaning using either bleach or non-bleach cleaning followed by 15 min of PX-UV treatment. A total of 298 samples were collected by using a moistened wipe specifically designed for the removal of spores. Prior to disinfection, the mean contamination level was 2.39 c.f. u. for bleach rooms and 22.97 for UV rooms. After disinfection, the mean level of contamination for bleach was 0.71 c.f. u. (P = 0.1380), and 1.19 c.f. u. (P = 0.0017) for PX-UV disinfected rooms. The difference in final contamination levels between the two cleaning protocols was not significantly different (P = 0.9838). PX-UV disinfection appears to be at least equivalent to bleach in the ability to decrease environmental contamination with C. difficile spores. Larger studies are needed to validate this conclusion.
Simultaneous determination of 7-O-succinyl macrolactin A and its active major metabolite, macrolactin A in dog plasma using high-performance liquid chromatography with UV detection.

We developed a method for the simultaneous quantification of 7-O-succinyl macrolactin A and its active metabolite, macrolactin A, in dog plasma. After protein precipitation with acetonitrile including flufenamic acid as an internal standard, 7-O-succinyl macrolactin A, macrolactin A, and flufenamic acid were chromatographed on a reverse-phase C18 analytical column. The mobile phase, consisting of 20 mM acetate buffer and acetonitrile, was eluted using a gradient program at 1 mL/min, and the UV absorbance was measured at 230 nm. The retention times of 7-O-succinyl macrolactin A, flufenamic acid, and macrolactin A were 3.4, 4.8, and 6.9 min, respectively. The coefficient of variation in the assay precision for both substances was less than 6%, and the accuracy ranged from 96 to 105%. This method was used to measure the concentrations of 7-O-succinyl macrolactin A and macrolactin A in dog plasma following an intravenous administration of a single dose (25 mg/kg) of 7-O-succinyl macrolactin A salt.
Content-based image retrieval in dermatology using intelligent technique

This study proposes a content-based image retrieval system for skin lesion images as a diagnostic aid. Effectiveness is measured by the rate of correct retrieval of images from skin lesions. The proposed architecture is used to retrieve digital images and the name of the disease category from an image data repository by the contents in the image, such as shape, texture and colour that is extracted from the image. The author's proposed algorithm used feature vector, classification and regression tree to retrieve comprehensive reference sources for diagnostic purpose. The results proved using a receiver operating characteristic curve that the proposed architecture has high contribute to computer-aided diagnosis of skin lesions. Experiments on a set of 1210 images yielded a specificity of 97.25% and a sensitivity of 91.24%. Their empirical evaluation has a superior retrieval and diagnosis performance when compared to the performance of other works. The authors present explicit combinations of feature vectors corresponding to healthy and lesion skin.
Detection of single nucleotide polymorphisms based on the multilocus sequence typing database of Staphylococcus aureus using locked nucleic acid oligonucleotides.

Meticillin-resistant Staphylococcus aureus (MRSA) remains an important pathogen in the nosocomial setting and is being seen with increasing frequency within the community on a global basis (Fluit et al., 2001; Chambers, 2001). In recent years, there have been a considerable number of studies attempting to address the requirement for a rapid and economical method for determining strain relatedness in both local outbreak investigations and global epidemiological studies. Methods which span the entire genome, such as amplified fragment length polymorphism and PFGE, offer very high resolution and are used for distinguishing strains isolated over short periods of time (Melles et al., 2007), but do not lend themselves to the study of genetic relatedness or evolution. PFGE (the current ‘gold standard’) is criticized for being technically demanding and time-consuming, with difficulty in making interlaboratory comparisons (Sabat et al., 2006). Multilocus sequence typing (MLST), which assigns a strain to a sequence type (ST) based on the sequences of seven housekeeping genes, is often used for global studies (Robinson & Enright, 2004). However, the workload and expense associated with MLST mean that it is often limited to well-resourced facilities.
Congenital deficiency of the pericardium associated with a bronchogenic cyst

BRAILSFORD, JAMES F. (1943), Brit. 3. Radiol. , May, borne out by radiographic evidence, for the dead fragment sequestrated by inflammatory changes retains its hardness and sharpness of outline, whereas the fragments tolerated tend to undergo progressive decalcification and softening, and (1943)~ 3. Bone Jt. Surg. , April, 249. 2’. (1944), The Radiology of Bones and Joints, 3rd ed. London : 3. & A. Churchill. (1936)) Brit. med. J., 2, 657. (1941), Brit. 3. Radiol. , Oct., 320.