bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cerebral Corpora amylacea are dense membranous labyrinths containing structurally preserved cell organelles
Authors: Navarro Paula P. , Genoud Christel , Castaño-Díez Daniel , Graff-Meyer Alexandra , Lewis Amanda J. , de Gier Yvonne , Lauer Matthias E. , Britschgi Markus , Bohrmann Bernd , Frank Stephan , Hench Jürgen , Schweighauser Gabriel , Rozemuller Annemieke J. M. , van de Berg Wilma D. J. , Stahlberg Henning , Shahmoradian Sarah H. 
Published: December 2018

AbstractCorpora amylaceaare cell-derived structures that appear physiologically in the aged human brain. While their histological identification is straightforward, their ultrastructural composition and microenvironment at the nanoscale have remained unclear so far, as has their relevance to aging and certain disease states that involve the sequestration of toxic cellular metabolites. Here, we apply correlative serial block-face scanning electron microscopy and transmission electron tomography to gain three-dimensional insight into the ultrastructure and surrounding microenvironment of cerebralCorpora amylaceain the human brainstem and hippocampal region. We find that cerebralCorpora amylaceaare composed of dense labyrinth-like sheets of lipid membranes, contain vesicles as well as morphologically preserved mitochondria, and are in close proximity to blood vessels and the glymphatic system, primarily within the cytoplasm of perivascular glial cells. Our results clarify the nature of cerebralCorpora amylaceaand provide first hints on how they may arise and develop in the aging brain.
Legacies of domestication, trade and herder mobility shape extant male zebu cattle diversity in South Asia and Africa
Authors: Pérez-Pardal Lucía , Sánchez-Gracia Alejandro , Álvarez Isabel , Traoré Amadou , Ferraz J. Bento S. , Fernández Iván , Costa Vânia , Chen Shanyuan , Tapio Miika , Cantet Rodolfo J. C. , Patel Ajita , Meadow Richard H. , Marshall Fiona B. , Beja-Pereira Albano , Goyache Félix 
Published: December 2018

AbstractAll tropically adapted humped cattle (Bos indicusor “zebu”), descend from a domestication process that took place >8,000 years ago in South Asia. Here we present an intercontinental survey of Y-chromosome diversity and a comprehensive reconstruction of male-lineage zebu cattle history and diversity patterns. Phylogenetic analysis revealed that all the zebu Y-chromosome haplotypes in our dataset group within three different lineages: Y3A, the most predominant and cosmopolitan lineage; Y3B, only observed in West Africa; and Y3C, predominant in South and Northeast India. The divergence times estimated for these three Zebu-specific lineages predate domestication. Coalescent demographic models support eitherde novodomestication of genetically divergent paternal lineages or more complex process including gene flow between wild and domestic animals. Our data suggest export of varied zebu lineages from domestication centres through time. The almost exclusive presence of Y3Ahaplotypes in East Africa is consistent with recent cattle restocking in this area. The cryptic presence of Y3Bhaplotypes in West Africa, found nowhere else, suggests that these haplotypes might represent the oldest zebu lineage introduced to Africa ca. 3,000 B.P. and subsequently replaced in most of the world. The informative ability of Interspersed Multilocus Microsatellites and Y-specific microsatellites to identify genetic structuring in cattle populations is confirmed.
Bidirectional propagation of tilting domain walls in perpendicularly magnetized T shaped structure with the interfacial Dzyaloshinskii-Moriya interaction
Authors: Kwon Jaesuk , Hwang Hee-Kyeong , Hong Jung-Il , You Chun-Yeol 
Published: December 2018

AbstractUnderstanding of domain wall (DW) propagation in a complex structure is an essential first step toward the development of any magnetic-domain based devices including spin-based logic or magnetic memristors. Interfacial Dzyaloshinskii-Moriya interaction (iDMI) in the structure with broken inversion symmetry induces an asymmetrical DW configuration with respect to the direction of in-plane field. Dynamic behaviors of field-driven DW within the film with perpendicular magnetic anisotropy is influenced by DW tilt from the iDMI effect and the corners in the T-shaped structure of the DW path. Images from Kerr microscopy reveal that the iDMI effective field contributes to a tilted structure of DW configuration and evolution along its propagation. With the combination of iDMI and T-shaped structure, we observed two distinguished bidirectional DW propagations in two output branches and distinct arriving times at the destination pads with a uniform external field. Micromagnetic simulation results is compared with the observed dynamics of a DW configuration in the structure providing an additional confirmation of the interpreted results.
Lactoferrin and lactoferricin endocytosis halt Giardia cell growth and prevent infective cyst production
Authors: Frontera Lorena S. , Moyano Sofía , Quassollo Gonzalo , Lanfredi-Rangel Adriana , Rópolo Andrea S. , Touz María C. 
Published: December 2018

AbstractLactoferrin (LF) is an 80 KDa iron-binding glycoprotein that plays a significant role in the innate immune system and is considered to be an important microbicide molecule. It has been suggested to be effective in the treatment of giardiasis, an intestinal disease caused by the protozoan parasiteG. lamblia. However, the molecular mechanisms by which LF exerts its effect on this parasite are unknown. Most of the microbicidal activity of human or bovine LF (hLF or bLF) has been associated with the N-terminal region of the mature LF - lactoferricin (LFcin). LFcin is produced by pepsin cleavage of the native proteinin vitroand likelyin vivo. In this work, we analyse the participation of the endocytic machinery ofG. lambliain the internalization of bLF and bLFcin and their effects on cell homeostasis. Our results show that, when bLF or bLFcin are internalized by receptor-mediated endocytosis, cell growth stops, and morphological changes are produced in the trophozoites, which ultimately will produce immature cysts. Our findings contribute to disclose the fine mechanism by which bLF and bLFcin may function as an antigiardial molecule and why they have therapeutic potential to eradicate giardiasis.
Near infrared emission properties of Er doped cubic sesquioxides in the second/third biological windows
Authors: Avram Daniel , Tiseanu Ion , Vasile Bogdan S. , Florea Mihaela , Tiseanu Carmen 
Published: December 2018

AbstractIn the recent years, there is an extensive effort concentrated towards the development of nanoparticles with near-infrared emission within the so called second or third biological windows induced by excitation outside 800–1000 nm range corresponding to the traditional Nd (800 nm) and Yb (980 nm) sensitizers. Here, we present a first report on the near-infrared (900–1700 nm) emission of significant member of cubic sesquioxides, Er-Lu2O3 nanoparticles, measured under both near-infrared up-conversion and low energy X-ray excitations. The nanoparticle compositions are optimized by varying Er concentration and Li addition. It is found that, under ca. 1500 nm up-conversion excitation, the emission is almost monochromatic (>93%) and centered at 980 nm while over 80% of the X-ray induced emission is concentrated around 1500 nm. The mechanisms responsible for the up-conversion emission of Er - Lu2O3 are identified by help of the up-conversion emission and excitation spectra as well as emission decays considering multiple excitation/emission transitions across visible to near-infrared ranges. Comparison between the emission properties of Er-Lu2O3 and Er-Y2O3 induced by optical and X-ray excitation is also presented. Our results suggest that the further optimized Er-doped cubic sesquioxides represent promising candidates for bioimaging and photovoltaic applications.
Ethanol represses the expression of methanol-inducible genes via acetyl-CoA synthesis in the yeast Komagataella phaffii
Authors: Ohsawa Shin , Nishida Susumu , Oku Masahide , Sakai Yasuyoshi , Yurimoto Hiroya 
Published: December 2018

AbstractIn methylotrophic yeasts, the expression of methanol-inducible genes is repressed by ethanol even in the presence of methanol, a phenomenon called ethanol repression. The mechanism of ethanol repression in Komagataella phaffii (Pichia pastoris) was studied, and acetyl-CoA synthesis from ethanol by sequential reactions of alcohol dehydrogenase, aldehyde dehydrogenase and acetyl-CoA synthetase (ACS) was involved in ethanol repression. Molecular analysis of the ACS-encoding gene product KpAcs1 revealed that its N-terminal motif, which is conserved in methylotrophic yeasts, was required for ethanol repression. ACS activity was downregulated during methanol-induced gene expression, which partially depended on autophagy. In addition, acetyl-CoA synthesis and phosphorylation of a transcription factor KpMxr1 were found to contribute to ethanol repression in a synergistic manner.
A causal inference explanation for enhancement of multisensory integration by co-articulation
Authors: Magnotti John F. , Smith Kristen B. , Salinas Marcelo , Mays Jacqunae , Zhu Lin L. , Beauchamp Michael S. 
Published: December 2018

AbstractThe McGurk effect is a popular assay of multisensory integration in which participants report the illusory percept of “da” when presented with incongruent auditory “ba” and visual “ga” (AbaVga). While the original publication describing the effect found that 98% of participants perceived it, later studies reported much lower prevalence, ranging from 17% to 81%. Understanding the source of this variability is important for interpreting the panoply of studies that examine McGurk prevalence between groups, including clinical populations such as individuals with autism or schizophrenia. The original publication used stimuli consisting of multiple repetitions of a co-articulated syllable (three repetitions, AgagaVbaba). Later studies used stimuli without repetition or co-articulation (AbaVga) and used congruent syllables from the same talker as a control. In three experiments, we tested how stimulus repetition, co-articulation, and talker repetition affect McGurk prevalence. Repetition with co-articulation increased prevalence by 20%, while repetition without co-articulation and talker repetition had no effect. A fourth experiment compared the effect of the on-line testing used in the first three experiments with the in-person testing used in the original publication; no differences were observed. We interpret our results in the framework of causal inference: co-articulation increases the evidence that auditory and visual speech tokens arise from the same talker, increasing tolerance for content disparity and likelihood of integration. The results provide a principled explanation for how co-articulation aids multisensory integration and can explain the high prevalence of the McGurk effect in the initial publication.
Wearable Nail Deformation Sensing for Behavioral and Biomechanical Monitoring and Human-Computer Interaction
Authors: Sakuma Katsuyuki , Abrami Avner , Blumrosen Gaddi , Lukashov Stanislav , Narayanan Rajeev , Ligman Joseph W. , Caggiano Vittorio , Heisig Stephen J. 
Published: December 2018

AbstractThe dynamics of the human fingertip enable haptic sensing and the ability to manipulate objects in the environment. Here we describe a wearable strain sensor, associated electronics, and software to detect and interpret the kinematics of deformation in human fingernails. Differential forces exerted by fingertip pulp, rugged connections to the musculoskeletal system and physical contact with the free edge of the nail plate itself cause fingernail deformation. We quantify nail warpage on the order of microns in the longitudinal and lateral axes with a set of strain gauges attached to the nail. The wearable device transmits raw deformation data to an off-finger device for interpretation. Simple motions, gestures, finger-writing, grip strength, and activation time, as well as more complex idioms consisting of multiple grips, are identified and quantified. We demonstrate the use of this technology as a human-computer interface, clinical feature generator, and means to characterize workplace tasks.
Integration of genetic and epidemiological data to infer H5N8 HPAI virus transmission dynamics during the 2016-2017 epidemic in Italy
Authors: Mulatti P. , Fusaro A. , Scolamacchia F. , Zecchin B. , Azzolini A. , Zamperin G. , Terregino C. , Cunial G. , Monne I. , Marangon S. 
Published: December 2018

AbstractBetween October 2016 and December 2017, several European Countries had been involved in a massive Highly Pathogenic Avian Influenza (HPAI) epidemic sustained by H5N8 subtype virus. Starting on December 2016, also Italy was affected by H5N8 HPAI virus, with cases occurring in two epidemic waves: the first between December 2016 and May 2017, and the second in July-December 2017. Eighty-three outbreaks were recorded in poultry, 67 of which (80.72%) occurring in the second wave. A total of 14 cases were reported in wild birds. Epidemiological information and genetic analyses were conjointly used to get insight on the spread dynamics. Analyses indicated multiple introductions from wild birds to the poultry sector in the first epidemic wave, and noteworthy lateral spread from October 2017 in a limited geographical area with high poultry densities. Turkeys, layers and backyards were the mainly affected types of poultry production. Two genetic sub-groups were detected in the second wave in non-overlapping geographical areas, leading to speculate on the involvement of different wild bird populations. The integration of epidemiological data and genetic analyses allowed to unravel the transmission dynamics of H5N8 virus in Italy, and could be exploited to timely support in implementing tailored control measures.
The microRNA-183/96/182 Cluster is Essential for Stereociliary Bundle Formation and Function of Cochlear Sensory Hair Cells
Authors: Geng Ruishuang , Furness David N , Muraleedharan Chithra K , Zhang Jinsheng , Dabdoub Alain , Lin Vincent , Xu Shunbin 
Published: December 2018

AbstractThe microRNA (miR)-183/96/182 cluster plays important roles in the development and functions of sensory organs, including the inner ear. Point-mutations in the seed sequence of miR-96 result in non-syndromic hearing loss in both mice and humans. However, the lack of a functionally null mutant has hampered the evaluation of the cluster’s physiological functions. Here we have characterized a loss-of-function mutant mouse model (miR-183CGT/GT), in which the miR-183/96/182 cluster gene is inactivated by a gene-trap (GT) construct. The homozygous mutant mice show profound congenital hearing loss with severe defects in cochlear hair cell (HC) maturation, alignment, hair bundle formation and the checkboard-like pattern of the cochlear sensory epithelia. The stereociliary bundles retain an immature appearance throughout the cochlea at postnatal day (P) 3 and degenerate soon after. The organ of Corti of mutant newborn mice has no functional mechanoelectrical transduction. Several predicted target genes of the miR-183/96/182 cluster that are known to play important roles in HC development and function, including Clic5, Rdx, Ezr, Rac1, Myo1c, Pvrl3 and Sox2, are upregulated in the cochlea. These results suggest that the miR-183/96/182 cluster is essential for stereociliary bundle formation, morphogenesis and function of the cochlear HCs.
The impact of carbon addition on the organisation of rhizosheath of chickpea
Authors: Rabbi Sheikh M. F. , Tighe Matthew K. , Knox Oliver , Young Iain M. 
Published: December 2018

AbstractSpatio-temporal development of the rhizosheath during root elongation has the potential to modify the function of the rhizosphere under abiotic stress. We quantified the impact of carbon (i.e. glucose) addition on the development and function of rhizosheath of drought tolerant and sensitive chickpea (Cicer arietinum L.) by integrating soil pore volume obtained from X-ray microtomography (µCT), soil physical and microbial respiration measures, and measurements of root traits. Structural equation modelling indicated the feedback mechanisms between added carbon, root traits, pore geometry, and soil functions differed between the cultivars in a fashion congruent with the concept of soil as a self-organising system that interacts with an introduced root system. The drought tolerant cultivar partitioned more photosynthetically fixed carbon to the roots, had more root hairs and more porous rhizosheath, as compared with the sensitive cultivar.
Facile fabrication and mechanistic understanding of a transparent reversible superhydrophobic – superhydrophilic surface
Authors: Majhy B. , Iqbal R. , Sen A. K. 
Published: December 2018

AbstractWe report a simple, inexpensive and rapid method for fabrication of a stable and transparent superhydrophobic (TSHB) surface and its reversible transition to a transparent superhydrophilic (TSHL) surface. We provide a mechanistic understanding of the superhydrophobicity and superhydrophilicity and the reversible transition. The proposed TSHB surface was created by candle sooting a partially cured n-hexane + PDMS surface followed by washing with DI water. The nano/microscopic grooved structures created on the surface conforms Cassie – Baxter state and thus gives rise to superhydrophobicity (water contact angle (WCA) = 161° ± 1°). The TSHB surface when subjected to oxygen plasma develops -OH bonds on the surface thus gets transformed into a TSHL surface (WCA < 1°). Both surface chemistry and surface morphology play important roles for the superhydrophobic to superhydrophilic transition. In the Cassie – Baxter relation for a composite surface, due to the capillary spreading of liquid in the nano/micro grooves, bothθ1,θ2 = 0, thus giving rise to complete wetting. Rapid recovery of superhydrophobicity from superhydrophilicity was achieved by heating the TSHL surface at 150 °C for 30 min, due to a much faster adsorption of the -OH bonds into the PDMS. Thus it is possible to achieve reversible transition from TSHB to TSHL and vice versa by exposing to oxygen plasma and heat, respectively.
Representations of time in human frontoparietal cortex
Authors: Hayashi Masamichi J. , van der Zwaag Wietske , Bueti Domenica , Kanai Ryota 
Published: December 2018

AbstractPrecise time estimation is crucial in perception, action and social interaction. Previous neuroimaging studies in humans indicate that perceptual timing tasks involve multiple brain regions; however, whether the representation of time is localized or distributed in the brain remains elusive. Using ultra-high-field functional magnetic resonance imaging combined with multivariate pattern analyses, we show that duration information is decoded in multiple brain areas, including the bilateral parietal cortex, right inferior frontal gyrus and, albeit less clearly, the medial frontal cortex. Individual differences in the duration judgment accuracy were positively correlated with the decoding accuracy of duration in the right parietal cortex, suggesting that individuals with a better timing performance represent duration information in a more distinctive manner. Our study demonstrates that although time representation is widely distributed across frontoparietal regions, neural populations in the right parietal cortex play a crucial role in time estimation.
Engineering Arabidopsis long-chain acyl-CoA synthetase 9 variants with enhanced enzyme activity
Authors: Xu Yang , Caldo Kristian Mark P. , Holic Roman , Mietkiewska Elzbieta , Ozga Jocelyn , Rizvi Syed Masood , Chen Guanqun , Weselake Randall J. 
Published: December 2018

Abstract
Long-chain acyl-CoA synthetase (LACS, EC 6.2.1.3) catalyzes the ATP-dependent activation of free fatty acid to form acyl-CoA, which, in turn, serves as the major acyl donor for various lipid metabolic pathways. Increasing the size of acyl-CoA pool by enhancing LACS activity appears to be a useful approach to improve the production and modify the composition of fatty acid-derived compounds, such as triacylglycerol. In the present study, we aimed to improve the enzyme activity of Arabidopsis thaliana LACS9 (AtLACS9) by introducing random mutations into its cDNA using error-prone PCR. Two AtLACS9 variants containing multiple amino acid residue substitutions were identified with enhanced enzyme activity. To explore the effect of each amino acid residue substitution, single-site mutants were generated and the amino acid substitutions C207F and D238E were found to be primarily responsible for the increased activity of the two variants. Furthermore, evolutionary analysis revealed that the beneficial amino acid site C207 is conserved among LACS9 from plant eudicots, whereas the other beneficial amino acid site D238 might be under positive selection. Together, our results provide valuable information for the production of LACS variants for applications in the metabolic engineering of lipid biosynthesis in oleaginous organisms.
Small GTPase peripheral binding to membranes: molecular determinants and supramolecular organization
Authors: Peurois François , Peyroche Gérald , Cherfils Jacqueline 
Published: December 2018

Abstract
Small GTPases regulate many aspects of cell logistics by alternating between an inactive, GDP-bound form and an active, GTP-bound form. This nucleotide switch is coupled to a cytosol/membrane cycle, such that GTP-bound small GTPases carry out their functions at the periphery of endomembranes. A global understanding of the molecular determinants of the interaction of small GTPases with membranes and of the resulting supramolecular organization is beginning to emerge from studies of model systems. Recent studies highlighted that small GTPases establish multiple interactions with membranes involving their lipid anchor, their lipididated hypervariable region and elements in their GTPase domain, which combine to determine the strength, specificity and orientation of their association with lipids. Thereby, membrane association potentiates small GTPase interactions with GEFs, GAPs and effectors through colocalization and positional matching. Furthermore, it leads to small GTPase nanoclustering and to lipid demixing, which drives the assembly of molecular platforms in which proteins and lipids co-operate in producing high-fidelity signals through feedback and feedforward loops. Although still fragmentary, these observations point to an integrated model of signaling by membrane-attached small GTPases that involves a diversity of direct and indirect interactions, which can inspire new therapeutic strategies to block their activities in diseases.
Structural biology and structure–function relationships of membrane proteins
Authors: Reis Rosana , Moraes Isabel 
Published: December 2018

Abstract
The study of structure–function relationships of membrane proteins (MPs) has been one of the major goals in the field of structural biology. Many Noble Prizes regarding remarkable accomplishments in MP structure determination and biochemistry have been awarded over the last few decades. Mutations or improper folding of these proteins are associated with numerous serious illnesses. Therefore, as important drug targets, the study of their primary sequence and three-dimensional fold, combined with cell-based assays, provides vital information about their structure–function relationships. Today, this information is vital to drug discovery and medicine. In the last two decades, many have been the technical advances and breakthroughs in the field of MP structural biology that have contributed to an exponential growth in the number of unique MP structures in the Protein Data Bank. Nevertheless, given the medical importance and many unanswered questions, it will never be an excess of MP structures, regardless of the method used. Owing to the extension of the field, in this brief review, we will only focus on structure–function relationships of the three most significant pharmaceutical classes: G protein-coupled receptors, ion channels and transporters.