Brain Differently Changes Its Algorithms in Parallel Processing of Visual Information

Feedback from the visual cortex (Vl) to the Lateral Geniculate Nucleus (LGN) in macaque monkey increase contrast gain of LGN neurons for black and white (B&W) and for color (C) stimuli. LGN parvocellular cells responses to B&W gratings are enhanced by feedback multiplicatively and in contrast independent manner. However, in magnocellular neurons corticofugal pathways enhance cells responses in a contrast~dependent non-linear manner. For C stimuli cortical feedback enhances parvocellular neurons responses in a very strong contrast-dependent manner. Based on these results [13] we propose a model which includes excitatory and inhibitory effects on cells activity (shunting equations) in retina and LGN while taking into account the anatomy of cortical feedback connections. The main mechanisms related to different algorithms of the data processing in the visual brain are differences in feedback properties from Vl to parvocellular (PC) and to magnocellular (MC) neurons. Descending pathways from Vl change differently receptive field (RF) structure of PC and MC cells. For B&W stimuli, in PC cells feedback changes gain similarly in the RF center and in the RF surround, leaving PC RF structure invariant. However, feedback influence MC cells in two ways: directly and through LGN interneurons, which together changes gain and sizes of their RF center differently than gain and size of the RF surround. For C stimuli PC cells operate like MC cells for B&W. The first mechanism extracts from the stimulus an important features in a independent way from other stimulus parameters, whereas the second channel changes its tuning properties as a function of other stimulus attributes like contrast and/or spatial extension. The model suggests novel idea about the possible functional role of PC and MC pathways

Evolution of the Neckeraceae (Bryophyta): resolving the backbone phylogeny

Earlier phylogenetic studies, including species belonging to the Neckeraceae, have indicated that this pleurocarpous moss family shares a strongly supported sister group relationship with the Lembophyllaceae, but the family delimitation of the former needs adjustment. To test the monophyly of the Neckeraceae, as well as to redefine the family circumscription and to pinpoint its phylogenetic position in a larger context, a phylogenetic study based on molecular data was carried out. Sequence data were compiled, combining data from all three genomes: nuclear ITS1 and 2, plastid trnS-rps4-trnT-trnL-trnF and rpl16, and mitochondrial nad5 intron. The Neckeraceae have sometimes been divided into the two families, Neckeraceae and Thamnobryaceae, a division rejected here. Both parsimony and Bayesian analyses of molecular data revealed that the family concept of the Neckeraceae needs several further adjustments, such as the exclusion of some individual species and smaller genera as well as the inclusion of the Leptodontaceae. Within the family three well-supported clades (A, B and C) can be distinguished. Members of clade A are mainly non-Asiatic and nontropical. Most species have a weak costa and immersed capsules with reduced peristomes (mainly Neckera spp.) and the teeth at the leaf margins are usually unicellular. Clade B members are also mainly non-Asiatic. They are typically fairly robust, distinctly stipilate, having a single, at least relatively strong costa, long setae (capsules exserted), and the peristomes are well developed or only somewhat reduced. Members of clade C are essentially Asiatic and tropical. The species of this clade usually have a strong costa and a long seta, the seta often being mammillose in its upper part. The peristome types in this clade are mixed, since both reduced and unreduced types are found. Several neckeraceous genera that were recognised on a morphological basis are polyphyletic (e.g. Neckera, Homalia, Thamnobryum, Porotrichum). Ancestral state reconstructions revealed that currently used diagnostic traits, such as the leaf asymmetry and costa strength are highly homoplastic. Similarly, the reconstructions revealed that the 'reduced' sporophyte features have evolved independently in each of the three clades.Earlier phylogenetic studies, including species belonging to the Neckeraceae, have indicated that this pleurocarpous moss family shares a strongly supported sister group relationship with the Lembophyllaceae, but the family delimitation of the former needs adjustment. To test the monophyly of the Neckeraceae, as well as to redefine the family circumscription and to pinpoint its phylogenetic position in a larger context, a phylogenetic study based on molecular data was carried out. Sequence data were compiled, combining data from all three genomes: nuclear ITS1 and 2, plastid trnS-rps4-trnT-trnL-trnF and rpl16, and mitochondrial nad5 intron. The Neckeraceae have sometimes been divided into the two families, Neckeraceae and Thamnobryaceae, a division rejected here. Both parsimony and Bayesian analyses of molecular data revealed that the family concept of the Neckeraceae needs several further adjustments, such as the exclusion of some individual species and smaller genera as well as the inclusion of the Leptodontaceae. Within the family three well-supported clades (A, B and C) can be distinguished. Members of clade A are mainly non-Asiatic and nontropical. Most species have a weak costa and immersed capsules with reduced peristomes (mainly Neckera spp.) and the teeth at the leaf margins are usually unicellular. Clade B members are also mainly non-Asiatic. They are typically fairly robust, distinctly stipilate, having a single, at least relatively strong costa, long setae (capsules exserted), and the peristomes are well developed or only somewhat reduced. Members of clade C are essentially Asiatic and tropical. The species of this clade usually have a strong costa and a long seta, the seta often being mammillose in its upper part. The peristome types in this clade are mixed, since both reduced and unreduced types are found. Several neckeraceous genera that were recognised on a morphological basis are polyphyletic (e.g. Neckera, Homalia, Thamnobryum, Porotrichum). Ancestral state reconstructions revealed that currently used diagnostic traits, such as the leaf asymmetry and costa strength are highly homoplastic. Similarly, the reconstructions revealed that the 'reduced' sporophyte features have evolved independently in each of the three clades.Earlier phylogenetic studies, including species belonging to the Neckeraceae, have indicated that this pleurocarpous moss family shares a strongly supported sister group relationship with the Lembophyllaceae, but the family delimitation of the former needs adjustment. To test the monophyly of the Neckeraceae, as well as to redefine the family circumscription and to pinpoint its phylogenetic position in a larger context, a phylogenetic study based on molecular data was carried out. Sequence data were compiled, combining data from all three genomes: nuclear ITS1 and 2, plastid trnS-rps4-trnT-trnL-trnF and rpl16, and mitochondrial nad5 intron. The Neckeraceae have sometimes been divided into the two families, Neckeraceae and Thamnobryaceae, a division rejected here. Both parsimony and Bayesian analyses of molecular data revealed that the family concept of the Neckeraceae needs several further adjustments, such as the exclusion of some individual species and smaller genera as well as the inclusion of the Leptodontaceae. Within the family three well-supported clades (A, B and C) can be distinguished. Members of clade A are mainly non-Asiatic and nontropical. Most species have a weak costa and immersed capsules with reduced peristomes (mainly Neckera spp.) and the teeth at the leaf margins are usually unicellular. Clade B members are also mainly non-Asiatic. They are typically fairly robust, distinctly stipilate, having a single, at least relatively strong costa, long setae (capsules exserted), and the peristomes are well developed or only somewhat reduced. Members of clade C are essentially Asiatic and tropical. The species of this clade usually have a strong costa and a long seta, the seta often being mammillose in its upper part. The peristome types in this clade are mixed, since both reduced and unreduced types are found. Several neckeraceous genera that were recognised on a morphological basis are polyphyletic (e.g. Neckera, Homalia, Thamnobryum, Porotrichum). Ancestral state reconstructions revealed that currently used diagnostic traits, such as the leaf asymmetry and costa strength are highly homoplastic. Similarly, the reconstructions revealed that the 'reduced' sporophyte features have evolved independently in each of the three clades.Peer reviewe

An annotated checklist of the bryophytes of Taita Hills region, Kenya

Based on previous literature and our own collections, we list 288 bryophyte species (145 liverworts, 143 mosses) from the Taita Hills region (including Mt. Kasigau and Maktau Hill) in SE Kenya. New records for Kenya include the liverworts Archilejeunea elobulata Steph., Bazzania nitida (F. Weber) Grolle, Cololejeunea grossepapillosa (Horik.) N. Kitag., Diplasiolejeunea kraussiana (Lindenb.) Steph., D. villaumei Steph., Lejeunea amaniensis E.W. Jones, L. cyathearum E.W. Jones, Lopholejeunea laciniata E.W. Jones, Metzgeria crassipilis (Lindb.) A. Evans, M. nudifrons Steph., Plagiochila boryana (F. Weber) Nees, and P. moenkemeyeri Steph., and the mosses Leucophanes hildebrandtii Müll. Hal. and Neckeromnion lepineanum (Mont.) S. Olsson, Enroth, Huttunen & D. Quandt. A further 22 liverworts and 13 mosses previously known from other parts of Kenya are reported for the first time from the Taita Hills region.Peer reviewe

Characterization of three new condensation particle counters for sub-3 nm particle detection during the Helsinki CPC workshop : the ADI versatile water CPC, TSI 3777 nano enhancer and boosted TSI 3010

In this study we characterized the performance of three new particle counters able to detect particles smaller than 3 nm during the Helsinki condensation particle counter (CPC) workshop in summer 2016: the Aerosol Dynamics Inc. (ADI; Berkeley, USA) versatile water condensation particle counter (vWCPC), TSI 3777 nano enhancer (TSI Inc., Shoreview, USA) and modified and boosted TSI 3010-type CPC from Universite Blaise Pascal called a B3010. The performance of all CPCs was first measured with charged tungsten oxide test particles at temperature settings which resulted in supersaturation low enough to not detect any ions produced by a radioactive source. Due to similar measured detection efficiencies, additional comparison between the 3777 and vWCPC were conducted using electrically neutral tungsten oxide test particles and with positively charged tetradodecylammonium bromide. Furthermore, the detection efficiencies of the 3777 and vWCPC were measured with boosted temperature settings yielding supersaturation which was at the onset of homogeneous nucleation for the 3777 or confined within the range of liquid water for the ADI vWCPC. Finally, CPC-specific tests were conducted to probe the response of the 3777 to various inlet flow relative humidities, of the B3010 to various inlet flow rates and of the vWCPC to various particle concentrations. For the 3777 and vWCPC the measured 50% detection diameters (d50s) were in the range of 1.3-2.4 nm for the tungsten oxide particles, depending on the particle charging state and CPC temperature settings, between 2.5 and 3.3 nm for the organic test aerosol, and in the range of 3.2-3.4 nm for tungsten oxide for the B3010.Peer reviewe

Alleniella aegaea Blockeel & Hugonnot (Neckeraceae), a new moss species from the Aegean islands of Greece

A new moss species, Alleniella aegaea (Neckeraceae) is described and illustrated from the Greek islands of Crete, Samos and Evvia based on morphological and molecular evidence. According to phylogenetic analysis of nuclear ITS and plastid trnS-F sequences it is sister to A. complanata, which it also morphologically resembles, but it differs from that species e.g. in its distinctly flattened habit, lack of caducous branchlets, more rounded leaf apices, and shorter median laminal cells. Alleniella aegaea is dioicous and the sporophytes remain unknow

Ganglion Cell Adaptability: Does the Coupling of Horizontal Cells Play a Role?

Background: The visual system can adjust itself to different visual environments. One of the most well known examples of this is the shift in spatial tuning that occurs in retinal ganglion cells with the change from night to day vision. This shift is thought to be produced by a change in the ganglion cell receptive field surround, mediated by a decrease in the coupling of horizontal cells. Methodology/Principal Findings: To test this hypothesis, we used a transgenic mouse line, a connexin57-deficient line, in which horizontal cell coupling was abolished. Measurements, both at the ganglion cell level and the level of behavioral performance, showed no differences between wild-type retinas and retinas with decoupled horizontal cells from connexin57-deficient mice. Conclusion/Significance: This analysis showed that the coupling and uncoupling of horizontal cells does not play a dominant role in spatial tuning and its adjustability to night and day light conditions. Instead, our data suggest that anothe

SICTIN: Rapid footprinting of massively parallel sequencing data

BACKGROUND: Massively parallel sequencing allows for genome-wide hypothesis-free investigation of for instance transcription factor binding sites or histone modifications. Although nucleotide resolution detailed information can easily be generated, biological insight often requires a more general view of patterns (footprints) over distinct genomic features such as transcription start sites, exons or repetitive regions. The construction of these footprints is however a time consuming task. METHODS: The presented software generates a binary representation of the signals enabling fast and scalable lookup. This representation allows for footprint generation in mere minutes on a desktop computer. Several different input formats are accepted, e.g. the SAM format, bed-files and the UCSC wiggle track. CONCLUSIONS: Hypothesis-free investigation of genome wide interactions allows for biological data mining at a scale never before seen. Until recently, the main focus of analysis of sequencing data has been targeted on signal patterns around transcriptional start sites which are in manageable numbers. Today, focus is shifting to a wider perspective and numerous genomic features are being studied. To this end, we provide a system allowing for fast querying in the order of hundreds of thousands of features

An annotated checklist of bryophytes of Europe, Macaronesia and Cyprus

Introduction. Following on from work on the European bryophyte Red List, the taxonomically and nomenclaturally updated spreadsheets used for that project have been expanded into a new checklist for the bryophytes of Europe. Methods. A steering group of ten European bryologists was convened, and over the course of a year, the spreadsheets were compared with previous European checklists, and all changes noted. Recent literature was searched extensively. A taxonomic system was agreed, and the advice and expertise of many European bryologists sought. Key results. A new European checklist of bryophytes, comprising hornworts, liverworts and mosses, is presented. Fifteen new combinations are proposed. Conclusions. This checklist provides a snapshot of the current European bryophyte flora in 2019. It will already be out-of-date on publication, and further research, particularly molecular work, can be expected to result in many more changes over the next few years.Peer reviewe

Y-Like Retinal Ganglion Cells Innervate the Dorsal Raphe Nucleus in the Mongolian Gerbil (Meriones unguiculatus)

Background: The dorsal raphe nucleus (DRN) of the mesencephalon is a complex multi-functional and multi-transmitter nucleus involved in a wide range of behavioral and physiological processes. The DRN receives a direct input from the retina. However little is known regarding the type of retinal ganglion cell (RGC) that innervates the DRN. We examined morphological characteristics and physiological properties of these DRN projecting ganglion cells. Methodology/Principal Findings: The Mongolian gerbils are highly visual rodents with a diurnal/crepuscular activity rhythm. It has been widely used as experimental animals of various studies including seasonal affective disorders and depression. Young adult gerbils were used in the present study. DRN-projecting RGCs were identified following retrograde tracer injection into the DRN, characterized physiologically by extracellular recording and morphologically after intracellular filling. The result shows that DRN-projecting RGCs exhibit morphological characteristics typical of alpha RGCs and physiological response properties of Y-cells. Melanopsin was not detected in these RGCs and they show no evidence of intrinsic photosensitivity. Conclusions/Significance: These findings suggest that RGCs with alpha-like morphology and Y-like physiology appear to perform a non-imaging forming function and thus may participate in the modulation of DRN activity which includes regulation of sleep and mood