bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lactobacillus crispatus inhibits the infectivity of Chlamydia trachomatis elementary bodies, in vitro study
Authors: Nardini Paola , Ñahui Palomino Rogers Alberto , Parolin Carola , Laghi Luca , Foschi Claudio , Cevenini Roberto , Vitali Beatrice , Marangoni Antonella 
Published: June 2016

AbstractLactobacillus species dominate the vaginal microbiota of healthy reproductive-age women and protect the genitourinary tract from the attack of several infectious agents. Chlamydia trachomatis, a leading cause of sexually transmitted disease worldwide, can induce severe sequelae, i.e. pelvic inflammatory disease, infertility and ectopic pregnancy. In the present study we investigated the interference of Lactobacillus crispatus, L. gasseri and L. vaginalis, known to be dominant species in the vaginal microbiome, with the infection process of C. trachomatis. Lactobacilli exerted a strong inhibitory effect on Chlamydia infectivity mainly through the action of secreted metabolites in a concentration/pH dependent mode. Short contact times were the most effective in the inhibition, suggesting a protective role of lactobacilli in the early steps of Chlamydia infection. The best anti-Chlamydia profile was shown by L. crispatus species. In order to delineate metabolic profiles related to anti-Chlamydia activity, Lactobacillus supernatants were analysed by 1H-NMR. Production of lactate and acidification of the vaginal environment seemed to be crucial for the activity, in addition to the consumption of the carbonate source represented by glucose. The main conclusion of this study is that high concentrations of L. crispatus inhibit infectivity of C. trachomatis in vitro.
Soot Combustion over Nanostructured Ceria with Different Morphologies
Authors: Zhang Wen , Niu Xiaoyu , Chen Liqiang , Yuan Fulong , Zhu Yujun 
Published: June 2016

AbstractIn this study, nano-structure ceria with three different morphologies (nanorod, nanoparticle and flake) have been prepared by hydrothermal and solvothermal methods. The ceria samples were deeply characterized by XRD, SEM, TEM, H2-TPR, XPS and in-situ DRIFTS, and tested for soot combustion in absence/presence NO atmospheres under loose and tight contact conditions. The prepared ceria samples exhibit excellent catalytic activities, especially, the CeO2 with nanorod (Ce-R) shows the best catalytic activity, for which the peak temperature of soot combustion (Tm) is about 500 and 368 °C in loose and tight contact conditions, respectively. The catalytic activity for Ce-R is higher than that of the reported CeO2 catalysts and reaches a level that of precious metals. The characterization results reveal that the maximal amounts of adsorbed oxygen species on the surface of the nanostructure Ce-R catalyst should be the crucial role to decide the catalytic soot performance. High BET surface area may also be a positive effect on soot oxidation activity under loose contact conditions.
Super-oscillatory focusing of circularly polarized light by ultra-long focal length planar lens based on binary amplitude-phase modulation
Authors: Chen Gang , Li Yuyan , Yu Anping , Wen Zhongquan , Dai Luru , Chen Li , Zhang Zhihai , Jiang Senlin , Zhang Kun , Wang Xianyou , Lin Feng 
Published: June 2016

AbstractIn traditional optics, the focal spot size of a conventional lens is restricted to the diffraction limit 0.5λ/NA, where λ is the wavelength in vacuum and NA is the numerical aperture of the lens. Recently, various sub-diffraction focusing optical devices have been demonstrated, but they usually have short focal length and high numerical aperture. Moreover, they always suffer the problem of huge sidelobes near the focal spot and small field of view, especially when the focal spot size is less than the super-oscillation criteria 0.38λ/NA. To address the problem, here, we reported a far-field sub-diffraction point-focusing lens based on binary phase and amplitude modulation with ultra-long focal length 252.8 μm (399.5λ) and small numerical aperture 0.78 and experimentally demonstrated a super-oscillatory focusing of circularly polarized light with spot size 287 nm (0.454λ), smaller than the diffraction limit 0.64λ and the super-oscillation criterion 0.487λ. What’s more, on the focal plane, in the measured area within the radius of 142λ, the largest sidelobe intensity is less than 26% of the central lobe intensity. Such ultra-long distance super-oscillatory focusing with small sidelobes and large field of view has great potential applications in far-field super-resolution microscopy, ultra-high-density optical storage and nano-fabrication.
Multifunction Sr, Co and F co-doped microporous coating on titanium of antibacterial, angiogenic and osteogenic activities
Authors: Zhou Jianhong , Zhao Lingzhou 
Published: June 2016

AbstractAdvanced multifunction titanium (Ti) based bone implant with antibacterial, angiogenic and osteogenic activities is stringently needed in clinic, which may be accomplished via incorporation of proper inorganic bioactive elements. In this work, microporous TiO2/calcium-phosphate coating on Ti doped with strontium, cobalt and fluorine (SCF-TiCP) was developed, which had a hierarchical micro/nano-structure with a microporous structure evenly covered with nano-grains. SCF-TiCP greatly inhibited the colonization and growth of both gram-positive and gram-negative bacteria. No cytotoxicity appeared for SCF-TiCP. Furthermore, SCF-TiCP stimulated the expression of key angiogenic factors in rat bone marrow stem cells (MSCs) and dramatically enhanced MSC osteogenic differentiation. The in vivo animal test displayed that SCF-TiCP induced more new bone and tighter implant/bone bonding. In conclusion, multifunction SCF-TiCP of antibacterial, angiogenic and osteogenic activities is a promising orthopedic and dental Ti implant coating for improved clinical performance.
Hydrocephalus and Papilledema in Spinal Cord Tumors: A Report of Two Cases
Authors: Marzban Ahmad , Saxena Ankur , Bhattacharyya Dev , Ivanov Marcel 
Published: June 2016

Background The association between spinal cord tumors and hydrocephalus is a rarely reported phenomenon. Diagnosis in this group of patients is difficult as they present with findings of an intracranial pathology and the symptoms of a spinal lesion may be absent.
Case Report We report two cases of spinal cord tumors presenting with visual disturbance and findings of increased intracranial pressure.
Discussions Mechanisms describing the relationship between spinal cord tumors and increased intracranial pressure have been explained. Most of the literature reported marked regression of these manifestations after tumor excision.
Conclusions Spinal cord tumors associated with hydrocephalus and papilledema are rare conditions. The diagnosis of these conditions may be difficult or confusing because the symptoms referable to the spinal lesion may be minimal. Meticulous history taking, examination, and investigations are mandatory to diagnose this entity.
A face-selective ventral occipito-temporal map of the human brain with intracerebral potentials
Authors: Jonas Jacques , Jacques Corentin , Liu-Shuang Joan , Brissart Hélène , Colnat-Coulbois Sophie , Maillard Louis , Rossion Bruno 
Published: June 2016

SignificanceUnderstanding the neural basis of face perception, arguably the most important visual function for human social ecology, is of the utmost importance. With an original fast periodic visual stimulation approach, we provide a comprehensive quantification of selective brain responses to faces throughout the ventral visual stream with direct recordings in the gray matter. Selective responses to faces are distributed in the whole ventral occipito-temporal cortex, with a right hemispheric and regional specialization supporting two decades of indirect recordings of human brain activity in neuroimaging. We also disclose three distinct face-selective regions in the anterior temporal lobe, an undersampled region in neuroimaging, and reveal exclusive responses to faces at the neural population level in these regions.
Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair
Authors: Zhu Chenxu , Lu Lining , Zhang Jun , Yue Zongwei , Song Jinghui , Zong Shuai , Liu Menghao , Stovicek Olivia , Gao Yi Qin , Yi Chengqi 
Published: June 2016

Significance
Oxidative DNA damage can be cytotoxic or mutagenic to cells. NEIL1 (Nei-like 1) is a DNA repair glycosylase guarding the mammalian genome against various oxidized DNA bases; yet how NEIL1 recognizes and catalyzes the removal of its substrates remains poorly understood. Here we integrate crystal structures of a NEIL1/double-stranded DNA complex, computational simulations, and biochemical analyses and show that NEIL1 promotes tautomerization of thymine glycol—a cognate substrate—for efficient substrate recognition and excision. Such tautomerism-dependent substrate recognition and catalysis is, to the best of our knowledge, reported for the first time in an enzyme-catalyzed reaction.
Biomechanics of red blood cells in human spleen and consequences for physiology and disease
Authors: Pivkin Igor V. , Peng Zhangli , Karniadakis George E. , Buffet Pierre A. , Dao Ming , Suresh Subra 
Published: June 2016

SignificanceThe 3D opening of the interendothelial slit in human spleen creates a physical fitness test for red blood cells (RBCs) and clears them from circulation if their geometry and deformability are altered. We present a unique computational framework for the development of prognostic markers for diseases that alter RBC physical characteristics and identify quantitative limits for splenic slit clearance. Our work shows how the splenic slit determines distributions of size and shape of healthy RBCs. Our work lays the groundwork for systematic reconstruction of RBC navigation in the human spleen with consequences for a variety of acute and chronic medical conditions associated with hereditary alterations of RBCs, infectious diseases, and cancers.
Human antibody responses after dengue virus infection are highly cross-reactive to Zika virus
Authors: Priyamvada Lalita , Quicke Kendra M. , Hudson William H. , Onlamoon Nattawat , Sewatanon Jaturong , Edupuganti Srilatha , Pattanapanyasat Kovit , Chokephaibulkit Kulkanya , Mulligan Mark J. , Wilson Patrick C. , Ahmed Rafi , Suthar Mehul S. , Wrammert Jens 
Published: June 2016

Significance
In this study, we address the issue of cross-reactivity between dengue virus (DENV) and Zika virus (ZIKV) by testing sera and plasmablast-derived monoclonal antibodies from dengue patients against ZIKV. We show that both acute and convalescent dengue sera potently bind and neutralize ZIKV and that this cross-reactivity is also evident at the monoclonal level. We also demonstrate in vitro antibody-dependent enhancement of ZIKV infection in the presence of dengue-induced antibodies. Our findings strongly suggest that preexisting dengue antibodies may modulate immune responses to ZIKV infection. These data are timely and highly relevant from a public health standpoint given that a majority of regions currently experiencing Zika virus epidemics are endemic for dengue.
Protestant Pioneers in Sanskrit Studies in the Early 18th Century
Authors: Van Hal Toon 
Published: June 2016

SummarySanskrit has played a notable role in the history of the language sciences. Its intensive study at the turn of the 19th century went hand in hand with the institutionalization of linguistics as an independent academic discipline. This paper endeavours to trace the earliest Sanskrit studies conducted by Protestant missionaries in Tranquebar (present-day Tharangambadi in Tamil Nadu) under the auspices of theDänisch-Hallesche Missionfrom 1706 onwards. In contrast to some of their Jesuit colleagues, the Protestant missionaries did not leave us full-blown manuscript grammars. However, this does not imply that the Tranquebar missionaries had no interest in the sacred language of the Hindus. It was, of course, the primary concern of all missionaries to spread the word of Christ among the indigenous people. Hence, they placed an extremely high value on a firm command of the local vernacular languages. In the case of the Tranquebar missionaries, the study of both Portuguese and Tamil was, therefore, prioritized. In a second stage, however, many of the Tranquebar missionaries, once they had mastered the local vernaculars, gained interest in Sanskrit, which they frequently styled ‘Malabaric Latin’. Partly on the basis of unpublished manuscript sources, this paper (a) investigates why the Tranquebar missionaries were interested in Sanskrit in the first place, (b) surveys the numerous problems they had to overcome, and (c) studies their interaction with scholars working in Europe, from whom they received many incentives. In so doing, the paper investigates to what extent this 18th-century interest in Sanskrit reflects a fascination with the original traditional culture and religion of South India. In conjunction with this, the paper also examines to what extent this largely overlooked chapter in early Sanskrit philology may shed an indirect light on the specific role of Sanskrit in the institutionalization of linguistics.
Comparison of Visual Survey and Mark–Recapture Population Estimates of a Benthic Fish in Hawaii
Authors: Hain Ernie F. , Lamphere Bradley A. , Blum Michael J. , McIntyre Peter B. , Nelson Stacy A.C. , Gilliam James F. 
Published: June 2016

AbstractVisual surveys are conducted to rapidly estimate population densities of stream fishes, often without calibration against more established or more widely used methods to determine precision and accuracy or to correct for potential biases. We compared population density estimates from a visual survey (VS) point quadrat method widely used in Hawaii with estimates from “in hand” individual and batch mark–recapture (BMR) methods. Visual survey sampling and individual mark–recapture (IMR) sampling were conducted in three watersheds that represent gradients of land use and prevalence of nonnative poeciliid fishes on the Island of Hawaii. Focusing on adult O‘opu Nākea Awaous stamineus, VSs were conducted prior to IMR events to allow direct comparisons of results independent of location and time. Density estimates of O‘opu Nākea from VS and IMR samplings were strongly correlated, although VS estimates were generally higher and underrepresented exceptionally large fish. Batch mark–recapture estimates of O‘opu Nākea densities were conducted for comparison with VSs at 13 sites across the archipelago. Estimates of VSs were not significantly different from BMR estimates. Estimates of VSs also exhibited less variance than did BMR estimates across sites. General linear models showed that the relationship between VS and IMR estimates varied significantly among watersheds but not seasons and that land use was associated with a greater mismatch between VS and BMR estimates of population density. These findings indicate that visual surveys using a point quadrat method are an efficient and accurate approach for estimating the abundance of small benthic fishes, such as O‘opu Nākea, in wadeable streams and that obtaining absolute densities or size distributions from VS methods would benefit from a calibration with IMR not BMR estimates.Received July 15, 2015; accepted February 23, 2016 Published online June 29, 2016
Scale‐Dependent Seasonal Pool Habitat Use by Sympatric Wild Brook Trout and Brown Trout Populations
Authors: Davis Lori A. , Wagner Tyler 
Published: June 2016

AbstractSympatric populations of native Brook Trout Salvelinus fontinalis and naturalized Brown Trout Salmo trutta exist throughout the eastern USA. An understanding of habitat use by sympatric populations is of importance for fisheries management agencies because of the close association between habitat and population dynamics. Moreover, habitat use by stream‐dwelling salmonids may be further complicated by several factors, including the potential for fish to display scale‐dependent habitat use. Discrete‐choice models were used to (1) evaluate fall and early winter daytime habitat use by sympatric Brook Trout and Brown Trout populations based on available residual pool habitat within a stream network and (2) assess the sensitivity of inferred habitat use to changes in the spatial scale of the assumed available habitat. Trout exhibited an overall preference for pool habitats over nonpool habitats; however, the use of pools was nonlinear over time. Brook Trout displayed a greater preference for deep residual pool habitats than for shallow pool and nonpool habitats, whereas Brown Trout selected for all pool habitat categories similarly. Habitat use by both species was found to be scale dependent. At the smallest spatial scale (50 m), habitat use was primarily related to the time of year and fish weight. However, at larger spatial scales (250 and 450 m), habitat use varied over time according to the study stream in which a fish was located. Scale‐dependent relationships in seasonal habitat use by Brook Trout and Brown Trout highlight the importance of considering scale when attempting to make inferences about habitat use; fisheries managers may want to consider identifying the appropriate spatial scale when devising actions to restore and protect Brook Trout populations and their habitats.Received December 11, 2015; accepted March 2, 2016 Published online June 29, 2016
Reproductive traits affect the rescue of valuable and endangered multipurpose tropical trees
Authors: Sinébou Viviane , Quinet Muriel , Ahohuendo Bonaventure C. , Jacquemart Anne-Laure 
Published: June 2016

Abstract
Conservation strategies are urgently needed in Tropical areas for widely used tree species. Increasing numbers of species are threatened by overexploitation and their recovery might be poor due to low reproductive success and poor regeneration rates. One of the first steps in developing any conservation policy should be an assessment of the reproductive biology of species that are threatened by overexploitation. This work aimed to study the flowering biology, pollination and breeding system of V. doniana , a multipurpose threatened African tree, as one step in assessing the development of successful conservation strategies. To this end, we studied (1) traits directly involved in pollinator attraction like flowering phenology, flower numbers and morphology, and floral rewards; (2) abundance, diversity and efficiency of flower visitors; (3) breeding system, through controlled hand-pollination experiments involving exclusion of pollinators and pollen from different sources; and (4) optimal conditions for seed germination. The flowering phenology was asynchronous among inflorescences, trees and sites. The flowers produced a large quantity of pollen and nectar with high sugar content. Flowers attracted diverse and abundant visitors, counting both insects and birds, and efficient pollinators included several Hymenoptera species. We detected no spontaneous self-pollination, indicating a total dependence on pollen vectors. Vitex doniana is self-compatible and no inbreeding depression occurred in the first developmental stages. After extraction of the seed from the fruit, seed germination did not require any particular conditions or pre-treatments and the seeds showed high germination rates. These pollination and breeding characteristics as well as germination potential offer the required conditions to develop successful conservation strategies. Protection, cultivation and integration in agroforestry systems are required to improve the regeneration of the tree.
AutoSite: an automated approach for pseudo-ligands prediction—from ligand-binding sites identification to predicting key ligand atoms
Authors: Ravindranath Pradeep Anand , Sanner Michel F. 
Published: June 2016

AbstractMotivation: The identification of ligand-binding sites from a protein structure facilitates computational drug design and optimization, and protein function assignment. We introduce AutoSite: an efficient software tool for identifying ligand-binding sites and predicting pseudo ligand corresponding to each binding site identified. Binding sites are reported as clusters of 3D points called fills in which every point is labelled as hydrophobic or as hydrogen bond donor or acceptor. From these fills AutoSite derives feature points: a set of putative positions of hydrophobic-, and hydrogen-bond forming ligand atoms.Results: We show that AutoSite identifies ligand-binding sites with higher accuracy than other leading methods, and produces fills that better matches the ligand shape and properties, than the fills obtained with a software program with similar capabilities, AutoLigand. In addition, we demonstrate that for the Astex Diverse Set, the feature points identify 79% of hydrophobic ligand atoms, and 81% and 62% of the hydrogen acceptor and donor hydrogen ligand atoms interacting with the receptor, and predict 81.2% of water molecules mediating interactions between ligand and receptor. Finally, we illustrate potential uses of the predicted feature points in the context of lead optimization in drug discovery projects.Availability and Implementation: http://adfr.scripps.edu/AutoDockFR/autosite.htmlContact: sanner@scripps.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Inheritance-mode specific pathogenicity prioritization (ISPP) for human protein coding genes
Authors: Hsu Jacob Shujui , Kwan Johnny S.H. , Pan Zhicheng , Garcia-Barcelo Maria-Mercè , Sham Pak Chung , Li Miaoxin 
Published: June 2016

Abstract
Motivation: Exome sequencing studies have facilitated the detection of causal genetic variants in yet-unsolved Mendelian diseases. However, the identification of disease causal genes among a list of candidates in an exome sequencing study is still not fully settled, and it is often difficult to prioritize candidate genes for follow-up studies. The inheritance mode provides crucial information for understanding Mendelian diseases, but none of the existing gene prioritization tools fully utilize this information.
Results: We examined the characteristics of Mendelian disease genes under different inheritance modes. The results suggest that Mendelian disease genes with autosomal dominant (AD) inheritance mode are more haploinsufficiency and de novo mutation sensitive, whereas those autosomal recessive (AR) genes have significantly more non-synonymous variants and regulatory transcript isoforms. In addition, the X-linked (XL) Mendelian disease genes have fewer non-synonymous and synonymous variants. As a result, we derived a new scoring system for prioritizing candidate genes for Mendelian diseases according to the inheritance mode. Our scoring system assigned to each annotated protein-coding gene (N = 18 859) three pathogenic scores according to the inheritance mode (AD, AR and XL). This inheritance mode-specific framework achieved higher accuracy (area under curve  = 0.84) in XL mode.
Conclusion: The inheritance-mode specific pathogenicity prioritization (ISPP) outperformed other well-known methods including Haploinsufficiency, Recessive, Network centrality, Genic Intolerance, Gene Damage Index and Gene Constraint scores. This systematic study suggests that genes manifesting disease inheritance modes tend to have unique characteristics.
Availability and implementation: ISPP is included in KGGSeq v1.0 (http://grass.cgs.hku.hk/limx/kggseq/), and source code is available from (https://github.com/jacobhsu35/ISPP.git).
Contact: mxli@hku.hk
Supplementary information: Supplementary data are available at Bioinformatics online.