bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of Bacterial DNA Packaging in Early Stationary Phase by Competitive DNA Binding of Dps and IHF
Authors: Lee Sin Yi , Lim Ci Ji , Dröge Peter , Yan Jie 
Published: December 2015

AbstractThe bacterial nucleoid, a bacterial genome packed by nucleoid binding proteins, forms the physical basis for cellular processes such as gene transcription and DNA replication. Bacteria need to dynamically modulate their nucleoid structures at different growth phases and in response to environmental changes. At the nutrients deficient stationary phase, DNA-binding proteins from starved cells (Dps) and Integration host factors (IHF) are the two most abundant nucleoid associated proteins in E. coli. Yet, it remains unclear how the nucleoid architecture is controlled by the interplay between these two proteins, as well as the nucleoid’s response to environmental changes. This question is addressed here using single DNA manipulation approach. Our results reveal that the two proteins are differentially selected for DNA binding, which can be tuned by changing environmental factors over physiological ranges including KCl (50–300 mM), MgCl2 (0–10 mM), pH (6.5–8.5) and temperature (23–37 °C). Increasing pH and MgCl2 concentrations switch from Dps-binding to IHF-binding. Stable Dps-DNA and IHF-DNA complexes are insensitive to temperature changes for the range tested. The environment dependent selection between IHF and Dps results in different physical organizations of DNA. Overall, our findings provide important insights into E. coli nucleoid architecture.
High contrast microstructural visualization of natural acellular matrices by means of phase-based x-ray tomography
Authors: Hagen Charlotte K. , Maghsoudlou Panagiotis , Totonelli Giorgia , Diemoz Paul C. , Endrizzi Marco , Rigon Luigi , Menk Ralf-Hendrik , Arfelli Fulvia , Dreossi Diego , Brun Emmanuel , Coan Paola , Bravin Alberto , De Coppi Paolo , Olivo Alessandro 
Published: December 2015

AbstractAcellular scaffolds obtained via decellularization are a key instrument in regenerative medicine both per se and to drive the development of future-generation synthetic scaffolds that could become available off-the-shelf. In this framework, imaging is key to the understanding of the scaffolds’ internal structure as well as their interaction with cells and other organs, including ideally post-implantation. Scaffolds of a wide range of intricate organs (esophagus, lung, liver and small intestine) were imaged with x-ray phase contrast computed tomography (PC-CT). Image quality was sufficiently high to visualize scaffold microarchitecture and to detect major anatomical features, such as the esophageal mucosal-submucosal separation, pulmonary alveoli and intestinal villi. These results are a long-sought step for the field of regenerative medicine; until now, histology and scanning electron microscopy have been the gold standard to study the scaffold structure. However, they are both destructive: hence, they are not suitable for imaging scaffolds prior to transplantation and have no prospect for post-transplantation use. PC-CT, on the other hand, is non-destructive, 3D and fully quantitative. Importantly, not only do we demonstrate achievement of high image quality at two different synchrotron facilities, but also with commercial x-ray equipment, which makes the method available to any research laboratory.
Disassembly of the self-assembled, double-ring structure of proteasome α7 homo-tetradecamer by α6
Authors: Ishii Kentaro , Noda Masanori , Yagi Hirokazu , Thammaporn Ratsupa , Seetaha Supaporn , Satoh Tadashi , Kato Koichi , Uchiyama Susumu 
Published: December 2015

AbstractThe 20S core particle of the eukaryotic proteasome is composed of two α- and two β-rings, each of which is a hetero-heptamer composed of seven homologous but distinct subunits. Although formation of the eukaryotic proteasome is a highly ordered process assisted by assembly chaperones, α7, an α-ring component, has the unique property of self-assembling into a homo-tetradecamer. We used biophysical methods to characterize the oligomeric states of this proteasome subunit and its interaction with α6, which makes direct contacts with α7 in the proteasome α-ring. We determined a crystal structure of the α7 tetradecamer, which has a double-ring structure. Sedimentation velocity analytical ultracentrifugation and mass spectrometric analysis under non-denaturing conditions revealed that α7 exclusively exists as homo-tetradecamer in solution and that its double-ring structure is disassembled upon the addition of α6, resulting in a 1:7 hetero-octameric α6–α7 complex. Our findings suggest that proteasome formation involves the disassembly of non-native oligomers, which are assembly intermediates.
RNA-mediated paternal heredity of diet-induced obesity and metabolic disorders
Authors: Grandjean Valérie , Fourré Sandra , De Abreu Diana Andrea Fernandes , Derieppe Marie-Alix , Remy Jean-Jacques , Rassoulzadegan Minoo 
Published: December 2015

AbstractThe paternal heredity of obesity and diabetes induced by a high-fat and/or high-sugar diet (Western-like diet) has been demonstrated through epidemiological analysis of human cohorts and experimental analysis, but the nature of the hereditary vector inducing this newly acquired phenotype is not yet well defined. Here, we show that microinjection of either testis or sperm RNA of male mice fed a Western-like diet into naive one-cell embryos leads to the establishment of the Western-like diet-induced metabolic phenotype in the resulting progenies, whereas RNAs prepared from healthy controls did not. Among multiple sequence differences between the testis transcriptomes of the sick and healthy fathers, we noted that several microRNAs had increased expression, which was of interest because this class of noncoding RNA is known to be involved in epigenetic control of gene expression. When microinjected into naive one-cell embryos, one of these small RNA, i.e., the microRNA miR19b, induced metabolic alterations that are similar to the diet-induced phenotype. Furthermore, this pathological phenotype was inherited by the offspring after crosses with healthy partners. Our results indicate that acquired food-induced trait inheritance might be enacted by RNA signalling.
Novel Flower-like Nickel Sulfide as an Efficient Electrocatalyst for Non-aqueous Lithium-Air Batteries
Authors: Ma Zhong , Yuan Xianxia , Zhang Zhenlin , Mei Delong , Li Lin , Ma Zi-Feng , Zhang Lei , Yang Jun , Zhang Jiujun 
Published: December 2015

AbstractIn this paper, metal sulfide materials have been explored for the first time as a new choice of bifunctional cathode electrocatalyst materials for non-aqueous lithium-air batteries (LABs). Nickel sulfides with two different morphologies of flower-like (f-NiS) and rod-like (r-NiS) are successfully synthesized using a hydrothermal method with and without the assistance of cetyltrimethyl ammonium bromide. As LAB cathode catalysts, both f-NiS and r-NiS demonstrate excellent catalytic activities towards the formation and decomposition of Li2O2, resulting in improved specific capacity, reduced overpotentials and enhanced cycling performance when compared to those of pure Super P based electrode. Moreover, the morphology of NiS materials can greatly affect LAB performance. Particularly, the f-NiS is more favorable than r-NiS in terms of their application in LABs. When compared to both r-NiS and pure super P materials as LAB cathode materials, this f-NiS catalyst material can give the highest capacity of 6733 mA h g−1 and the lowest charge voltage of 4.24 V at the current density of 75 mA g−1 and also exhibit an quite stable cycling performance.
Landau damping effects in the synchronization of conformist and contrarian oscillators
Authors: Qiu Tian , Zhang Yue , Liu Jie , Bi Hongjie , Boccaletti S. , Liu Zonghua , Guan Shuguang 
Published: December 2015

AbstractTwo decades ago, a phenomenon resembling Landau damping was described in the synchronization of globally coupled oscillators: the evidence of a regime where the order parameter decays when linear theory predicts neutral stability for the incoherent state. We here show that such an effect is far more generic, as soon as phase oscillators couple to their mean field according to their natural frequencies, being then grouped into two distinct populations of conformists and contrarians. We report the analytical solution of this latter situation, which allows determining the critical coupling strength and the stability of the incoherent state, together with extensive numerical simulations that fully support all theoretical predictions. The relevance of our results is discussed in relationship to collective phenomena occurring in social and economical systems.
Impact of oil spills on coral reefs can be reduced by bioremediation using probiotic microbiota
Authors: Fragoso ados Santos Henrique , Duarte Gustavo Adolpho Santos , Rachid Caio TavoraCoelho da Costa , Chaloub Ricardo Moreira , Calderon Emiliano Nicolas , Marangoni Laura Fernandes de Barros , Bianchini Adalto , Nudi Adriana Haddad , do Carmo Flávia Lima , van Elsas Jan Dirk , Rosado Alexandre Soares , Castro Clovis Barreira e , Peixoto Raquel Silva 
Published: December 2015

AbstractSeveral anthropogenic factors, including contamination by oil spills, constitute a threat to coral reef health. Current methodologies to remediate polluted marine environments are based on the use of chemical dispersants; however, these can be toxic to the coral holobiont. In this study, a probiotic bacterial consortium was produced from the coral Mussismilia harttii and was trained to degrade water-soluble oil fractions (WSFs). Additionally, we assessed the effect of WSFs on the health of M. harttii in tanks and evaluated the bacterial consortium as a bioremediation agent. The consortium was responsible for the highly efficient degradation of petroleum hydrocarbons and it minimised the effects of WSFs on coral health, as indicated by raised photosynthetic efficiencies. Moreover, the impact of WSFs on the coral microbiome was diminished by the introduced bacterial consortium. Following introduction, the bacterial consortium thus had a dual function, i.e promoting oil WSF degradation and improving coral health with its probiotic features.
Developmental validation of an X-Insertion/Deletion polymorphism panel and application in HAN population of China
Authors: Zhang Suhua , Sun Kuan , Bian Yingnan , Zhao Qi , Wang Zheng , Ji Chaoneng , Li Chengtao 
Published: December 2015

AbstractInDels are short-length polymorphisms characterized by low mutation rates, high inter-population diversity, short amplicon strategy and simplicity of laboratory analysis. This work describes the developmental validation of an X-InDels panel amplifying 18 bi-allelic markers and Amelogenin in one single PCR system. Developmental validation indicated that this novel panel was reproducible, accurate, sensitive and robust for forensic application. Sensitivity testing of the panel was such that a full profile was obtainable even with 125 pg of human DNA with intra-locus balance above 70%. Specificity testing was demonstrated by the lack of cross-reactivity with a variety of commonly encountered animal species and microorganisms. For the stability testing in cases of PCR inhibition, full profiles have been obtained with hematin (≤1000 μM) and humic acid (≤150 ng/μL). For the forensic investigation of the 18 X-InDels in the HAN population of China, no locus deviated from the Hardy–Weinberg equilibrium and linkage disequilibrium. Since they are independent from each other, the CDPfemale was 0.999999726 and CDPmale was 0.999934223. The forensic parameters suggested that this X-Indel panel is polymorphic and informative, which provides valuable X-linked information for deficient relationship cases where autosomal markers are uninformative.
Perceptual Classification Images from Vernier Acuity Masked by Noise
Authors: Ahumada A J 
Published: December 2015

Letting external noise rather than internal noise limit discrimination performance allows information to be extracted about the observer's stimulus classification rule. A perceptual classification image is the correlation over trials between the noise amplitude at a spatial location and the observer's responses. If, for example, the observer followed the rule of the ideal observer, the response correlation image would be an estimate of the ideal observer filter, the difference between the two unmasked images being discriminated. Perceptual classification images were estimated for a Vernier discrimination task. The display screen had 48 pixels deg−1 horizontally and vertically. The no-offset image had a dark horizontal line of 4 pixels, a 1 pixel space, and 4 more dark pixels. Classification images were based on 1600 discrimination trials with the line contrast adjusted to keep the error rate near 25%. In the offset image, the second line was one pixel higher. Unlike the ideal observer filter (a horizontal dipole), the observer perceptual classification images are strongly oriented. Fourier transforms of the classification images had a peak amplitude near 1 cycle deg−1 and an orientation near 25 deg. The spatial spread is much more than image blur predicts, and probably indicates the spatial position uncertainty in the task.
Depth Illusion by Delayed 3-D Perception (‘Delayed Stereopsis Illusion’): A Novel Way to Determine Computation Times in Human Vision by Depth Reversal in Partially Occluded Moving Objects
Authors: Wolf R , Schuchardt M , Rosenzweig R 
Published: December 2015

Viewed through depth-reversing spectacles, nontransparent objects appear to cut ‘gaps’ into a patterned background. In moving objects this gap is seen to extend beyond the occluded area (‘delayed stereopsis illusion’, DSI): Its trailing border appears to lag behind by a precisely measurable distance, indicating a processing time of approximately 0.13 s to accomplish stereopsis [cf Morgan and Castet, 1995 Nature (London)378 380 – 383]. Other than in thigmaesthesia, there is no correction by antedating. Why is this delay not perceived in normal stereopsis? If an object is moving before some background, the background usually maintains its position; it may be occluded, or not. Depth information thus might be extrapolated to the continuously uncovered regions of the patterned background. Depth reversal demands that the occluded region of the background must jump behind the moving, occluding object. As this object is perceived to retain its distance, the background, as it is getting uncovered, must jump back into the foreground, where it can be perceived only after renewed calculation of binocular depth. The dependence of DSI on eye movements, disparity, velocity, motion direction, surface texture, illuminance, spatial frequency, and fractal dimension of the objects involved is currently being investigated in model systems which allow us to determine processing times of human stereopsis under well-defined conditions.
The Development of Multisensory Integration in the Brain
Authors: Wallace M T 
Published: December 2015

Multisensory integration in the superior colliculus (SC) of the cat requires a protracted postnatal developmental time course. Kittens 3 – 135 days postnatal (dpn) were examined and the first neuron capable of responding to two different sensory inputs (auditory and somatosensory) was not seen until 12 dpn. Visually responsive multisensory neurons were not encountered until 20 dpn. These early multisensory neurons responded weakly to sensory stimuli, had long response latencies, large receptive fields, and poorly developed response selectivities. Most striking, however, was their inability to integrate cross-modality cues in order to produce the significant response enhancement or depression characteristic of these neurons in adults. The incidence of multisensory neurons increased gradually over the next 10 – 12 weeks. During this period, sensory responses became more robust, latencies shortened, receptive fields decreased in size, and unimodal selectivities matured. The first neurons capable of cross-modality integration were seen at 28 dpn. For the following two months, the incidence of such integrative neurons rose gradually until adult-like values were achieved. Surprisingly, however, as soon as a multisensory neuron exhibited this capacity, most of its integrative features were indistinguishable from those in adults. Given what is known about the requirements for multisensory integration in adult animals, this observation suggests that the appearance of multisensory integration reflects the onset of functional corticotectal inputs.
Organisation and Interrelationships of Functional Maps in Cat and Monkey Striate Cortex
Authors: Shoham D , Hübener M , Bonhoeffer T , Grinvald A 
Published: December 2015

Optical imaging of intrinsic signals allows mapping of the cortical functional architecture in vivo at high spatial resolution. The ability to image activity patterns evoked by many different stimuli in the same piece of cortex can provide information on the spatial relationships between different functional maps. Our findings on the organisation of multiple functional maps in cat and monkey striate cortex are reviewed. The main focus is on the recent finding in cat of two subsystems differing in their response to spatiotemporal aspects of the stimulus. We used grating stimuli of different spatial frequencies in an attempt to verify the existence of spatial frequency columns in cat area 17. Rather than observing a map of continuously changing spatial frequency across the cortical surface we found two distinct sets of domains, one preferring low and one preferring high spatial frequencies. By using different drift velocities we also found that the low-spatial-frequency domains preferred higher speeds than the high-spatial-frequency domains. Comparison of these spatiotemporal frequency domains with the cytochrome oxidase staining pattern revealed that the cytochrome oxidase blobs in cat striate cortex coincide with domains devoted to the processing of the low-spatial-frequency and high-temporal-frequency contents of the visual scene. Together with recent anatomical results these data suggest that spatiotemporal frequency domains are the manifestation of parallel streams in cat visual cortex with distinct patterns of thalamic inputs and extrastriate projections. In the same experiments we also imaged the orientation preference and ocular dominance maps. We investigated the relationships between these three columnar systems, and compared them to an earlier study of orientation, ocular dominance, and blobs in macaque striate cortex. We found systematic relationships between the three systems. While some of these relationships were much weaker than those found in monkey, the organisational principles are similar.
Effects of Gaze Direction in Vision and Audition
Authors: Ehrenstein W H , Lewald J , Schlykowa L 
Published: December 2015

We asked to what extent the respective gaze direction influences (i) the spatial congruence of perceived direction of auditory and visual cues, and (ii) the discrimination of the direction of target motion. With fixed head position, subjects directed their gaze in various positions and localised auditory targets (band-pass noise, 2 kHz) presented at one of nine positions (straight ahead, or four symmetric positions to the left or right separated by 2.75 deg, respectively). Forced-choice judgements, whether the sound was perceived to the left or right of a visual reference light, show that the azimuth of the sound was perceived as slightly shifted to the left of a visual reference when the gaze was directed to the left, and vice versa. The maximum of this relative auditory - visual shift was 4.7 deg over a range of 45 deg (left or right) of gaze directions. In (ii), a spot of light started at the centre of a monitor and moved at 2 or 12 deg s−1 leftward or rightward. Subjects reported the direction by pressing a key; their gaze was directed at 0, 8, or 16 deg to the left or right. Mean choice-reaction times increased with increasing gaze eccentricity, but differently depending on stimulus direction and speed: with left fixation they were shorter for leftward than rightward motion; with right fixation they were shorter for rightward motion. This effect was stronger for the slow than for the fast stimulus speed. Thus, facilitation occurs when stimuli move with moderate velocity toward the direction of gaze. While the auditory-visual shift in (i) may reflect an incomplete transformation of spatial (craniocentric and oculocentric) coordinates as suggested by recordings in the primate midbrain, the results in (ii) conform with reports of specialised units in the posterior parietal cortex (areas LIP, 7a, MST) that, in registering oculomotor position, modulate visual sensitivity.
The LEO-Reading Test: A Set of Nine Reading Charts with M-Units
Authors: Kooijman A C , Beerthuizen J J G 
Published: December 2015

Visual acuity, near-distance visual acuity, and reading ability all depend on the minimal angle of resolution. Visual acuity is defined as the inverse of the minimal angle of resolution, measured at a distance of 4 – 6 m, and expressed in units of (min arc)−1. Near visual acuity and reading ability are measured at reading distance. The preferred reading distance is not the same for every subject. A practical way to combine character size and reading distance is to use the ‘M-unit’ for text size and ‘Dioptre’ for the reading distance. For example, a character size of 1 M at a viewing distance of 1 m corresponds to a visual acuity of 1. A character size of 0.20 M at a viewing distance of 25 cm (=4 D) corresponds to a visual acuity of 1/(0.2 × 4)=1.25. In the rehabilitation institute we had a need for reading charts with different text blocks for repeated testing (OD, OS, OU, and at various illumination levels). Furthermore we wanted text blocks with a comparable layout and reading difficulty. Such reading charts exist in other languages and we preferred to adopt a similar design, together with the M-unit and Dioptre notation. We composed the text and tested the equivalence of text blocks by measuring the reading speed of young (aged 18 – 27 years) and old (aged 60 – 69 years) subjects. We present the resulting set of nine reading charts with a plea for general use of the M-unit and Dioptre notation for near-distance visual acuity and reading ability assessment in visually impaired people.
Does Inverting Text Improve Reading Performance in Homonymous Hemianopes?
Authors: Baker M R , Henderson J , Hill A 
Published: December 2015

Anecdotal information from rehabilitation practice of reading performance and low-vision practice suggests that where right homonymous parafoveal field loss impairs reading at the visual-sensory level, an improvement in reading speed can be achieved by inverting the text. This is because whilst left-field loss is considered to impair return eye movements to the beginning of a line, right-field loss is considered to reduce the spatial size of the perceptual window and increase its temporal extent by prolonging fixations times, reducing the amplitudes of saccades to the right, and introducing frequent regressive saccades. Inverting the text was thought to reverse these effects as the leading edge of the perceptual window is ‘returned’ to the sighted field so that in-line saccades can be visually guided. Here we report that this does not appear to be the case. In our study we measured the eye movements of patients with right homonymous hemianopia and others with peripheral loss due to retinitis pigmentosa as well as normal controls using an infrared video eye-tracker. All groups display a similar proportional prolongation of fixations times, reduction of saccadic amplitude, and proportion of regressive saccades when asked to read inverted text, which suggests a cognitive component of impairment independent of visual field loss in right homonymous hemianopes.