bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of vitamin D status with liver and kidney disease: A systematic review of clinical trials, and cross-sectional and cohort studies
Authors: Parizadeh Seyed Mostafa , Rezayi Majid , Jafarzadeh-Esfehani Reza , Avan Amir , Ghazizadeh Hamideh , Emadzadeh Maryam , Sahebi Reza , Ferns Gordon A. , Ghayour-Mobarhan Majid 
Published: February 2019

Abstract. Background: Vitamin D deficiency (VDD) is a major public health problem. There are few comprehensive systematic reviews about the relationship between Vitamin D status and liver and renal disease in Iran. Methods: We systemically searched the following databases: Web of Science; PubMed; Cochrane Library; Scopus; Science Direct; Google Scholar and two Iranian databases (Scientific Information Database (SID) and IranMedex) up until November 2017 to identify all randomized control trials (RCTs), case control, cross-sectional and cohort studies investigating the association between vitamin D and any form of liver or kidney disease. Results: Vitamin D insufficiency, or deficiency (VDD), is highly prevalent in Iran, reports varying between 44.4% in Isfahan to 98% in Gorgan. There is also a high prevalence of VDD among patients with liver or kidney disease, and the administration of vitamin D supplements may have beneficial effects on lipid profile, blood glucose, liver function and fatty liver disease, and bone health. Low serum vitamin D levels are related with abnormalities in these laboratory and clinical parameters. Conclusion: VDD is prevalent in patients with chronic liver or renal disease in Iran. There appear to be several beneficial effects of vitamin D supplementation in vitamin D deficient patients with liver or kidney disease.
Precursory Stress Changes and Fault Dilation Lead to Fault Rupture: Insights From Discrete Element Simulations
Authors: Blank D. G. , Morgan J. K. 
Published: February 2019

AbstractWe use the discrete element method to create numerical analogs to subduction megathrusts with natural roughness and heterogeneous fault friction. Boundary conditions simulate tectonic loading, inducing fault slip. Intermittently, slip develops into complex rupture events that include foreshocks, mainshocks, and aftershocks. We probe the kinematics and stress evolution of the fault zone to gain insight into the physical processes that govern these phenomena. Prolonged, localized differential stress drops precede dynamic failure, a phenomenon we attribute to the gradual unlocking of contacts as the fault dilates prior to rupture. Slip stability in our system appears to be governed primarily by geometrical phenomena, which allow both slow and fast slip to take place at the same areas along the fault. Similarities in slip behavior between simulated faults and real subduction zones affirm that modeled physical processes are also at work in nature.
The mesopelagic anoxic Black Sea as an unexpected habitat for Synechococcus challenges our understanding of global “deep red fluorescence”
Authors: Callieri Cristiana , Slabakova Violeta , Dzhembekova Nina , Slabakova Nataliya , Peneva Elisaveta , Cabello-Yeves Pedro J , Di Cesare Andrea , Eckert Ester M , Bertoni Roberto , Corno Gianluca , Salcher Michaela M , Kamburska Lyudmila , Bertoni Filippo , Moncheva Snejana 
Published: February 2019

Abstract
The Black Sea is the largest meromictic sea with a reservoir of anoxic water extending from 100 to 1000 m depth. These deeper layers are characterised by a poorly understood fluorescence signal called “deep red fluorescence”, a chlorophyll a- (Chl a) like signal found in deep dark oceanic waters. In two cruises, we repeatedly found up to 103 cells ml−1 of picocyanobacteria at 750 m depth in these waters and isolated two phycoerythrin-rich Synechococcus sp. strains (BS55D and BS56D). Tests on BS56D revealed its high adaptability, involving the accumulation of Chl a in anoxic/dark conditions and its capacity to photosynthesise when re-exposed to light. Whole-genome sequencing of the two strains showed the presence of genes that confirms the putative ability of our strains to survive in harsh mesopelagic environments. This discovery provides new evidence to support early speculations associating the “deep red fluorescence” signal to viable picocyanobacteria populations in the deep oxygen-depleted oceans, suggesting a reconsideration of the ecological role of a viable stock of Synechococcus in dark deep waters.
Leveraging brain cortex-derived molecular data to elucidate epigenetic and transcriptomic drivers of complex traits and disease
Authors: Hatcher Charlie , Relton Caroline L. , Gaunt Tom R. , Richardson Tom G. 
Published: February 2019

AbstractIntegrative approaches that harness large-scale molecular datasets can help develop mechanistic insight into findings from genome-wide association studies (GWAS). We have performed extensive analyses to uncover transcriptional and epigenetic processes which may play a role in complex trait variation. This was undertaken by applying Bayesian multiple-trait colocalization systematically across the genome to identify genetic variants responsible for influencing intermediate molecular phenotypes as well as complex traits. In this analysis, we leveraged high-dimensional quantitative trait loci data derived from the prefrontal cortex tissue (concerning gene expression, DNA methylation and histone acetylation) and GWAS findings for five complex traits (Neuroticism, Schizophrenia, Educational Attainment, Insomnia and Alzheimer’s disease). There was evidence of colocalization for 118 associations, suggesting that the same underlying genetic variant influenced both nearby gene expression as well as complex trait variation. Of these, 73 associations provided evidence that the genetic variant also influenced proximal DNA methylation and/or histone acetylation. These findings support previous evidence at loci where epigenetic mechanisms may putatively mediate effects of genetic variants on traits, such as KLC1 and schizophrenia. We also uncovered evidence implicating novel loci in disease susceptibility, including genes expressed predominantly in the brain tissue, such as MDGA1, KIRREL3 and SLC12A5. An inverse relationship between DNA methylation and gene expression was observed more than can be accounted for by chance, supporting previous findings implicating DNA methylation as a transcriptional repressor. Our study should prove valuable in helping future studies prioritize candidate genes and epigenetic mechanisms for in-depth functional follow-up analyses.
Quantitative analysis of plant ER architecture and dynamics
Authors: Pain Charlotte , Kriechbaumer Verena , Kittelmann Maike , Hawes Chris , Fricker Mark 
Published: February 2019

AbstractThe endoplasmic reticulum (ER) is a highly dynamic polygonal membrane network composed of interconnected tubules and sheets (cisternae) that forms the first compartment in the secretory pathway involved in protein translocation, folding, glycosylation, quality control, lipid synthesis, calcium signalling, and metabolon formation. Despite its central role in this plethora of biosynthetic, metabolic and physiological processes, there is little quantitative information on ER structure, morphology or dynamics. Here we describe a software package (AnalyzER) to automatically extract ER tubules and cisternae from multi-dimensional fluorescence images of plant ER. The structure, topology, protein-localisation patterns, and dynamics are automatically quantified using spatial, intensity and graph-theoretic metrics. We validate the method against manually-traced ground-truth networks, and calibrate the sub-resolution width estimates against ER profiles identified in serial block-face SEM images. We apply the approach to quantify the effects on ER morphology of drug treatments, abiotic stress and over-expression of ER tubule-shaping and cisternal-modifying proteins.
Continuous wave amplified spontaneous emission in phase-stable lead halide perovskites
Authors: Brenner Philipp , Bar-On Ofer , Jakoby Marius , Allegro Isabel , Richards Bryce S. , Paetzold Ulrich W. , Howard Ian A. , Scheuer Jacob , Lemmer Uli 
Published: February 2019

AbstractSustained stimulated emission under continuous-wave (CW) excitation is a prerequisite for new semiconductor materials being developed for laser gain media. Although hybrid organic-inorganic lead-halide perovskites have attracted much attention as optical gain media, the demonstration of room-temperature CW lasing has still not been realized. Here, we present a critical step towards this goal by demonstrating CW amplified spontaneous emission (ASE) in a phase-stable perovskite at temperatures up to 120 K. The phase-stable perovskite maintains its room-temperature phase while undergoing cryogenic cooling and can potentially support CW lasing also at higher temperatures. We find the threshold level for CW ASE to be 387 W cm-2 at 80 K. These results indicate that easily-fabricated single-phase perovskite thin films can sustain CW stimulated emission, potential at higher temperatures as well, by further optimization of the material quality in order to extend the carrier lifetimes.
Coherent spin-wave processor of stored optical pulses
Authors: Mazelanik Mateusz , Parniak Michał , Leszczyński Adam , Lipka Michał , Wasilewski Wojciech 
Published: February 2019

AbstractA device being a pinnacle of development of an optical quantum memory should combine the capabilities of storage, inter-communication, and processing of stored information. In particular, the ability to capture a train of optical pulses, interfere them in an arbitrary way and finally, perform on-demand release could realize arbitrary optical computation. Here we demonstrate the operation of a coherent optical memory being able to store optical pulses in the form of collective spin-wave excitations in a two-dimensional wavevector space. During storage, we perform complex beamsplitter operations and demonstrate a variety of protocols implemented at the processing stage, including real-time controlled interference of a pair of spin-wave modes with 95% visibility. The highly multimode structure of the presented memory lends itself to enhancing classical optical telecommunication, as well as parallel processing of optical qubits at the single-photon level.
ImmtorLig_DB: repertoire of virtually screened small molecules against immune receptors to bolster host immunity
Authors: Chatterjee Deepyan , Kaur Gurkirat , Muradia Shilpa , Singh Balvinder , Agrewala Javed N. 
Published: February 2019

AbstractHost directed therapies to boost immunity against infection are gaining considerable impetus following the observation that use of antibiotics has become a continuous source for the emergence of drug resistant strains of pathogens. Receptors expressed by the cells of immune system play a cardinal role in initiating sequence of events necessary to ameliorate many morbid conditions. Although, ligands for the immune receptors are available; but their use is limited due to complex structure, synthesis and cost-effectiveness. Virtual screening (VS) is an integral part of chemoinformatics and computer-aided drug design (CADD) and aims to streamline the process of drug discovery. ImmtorLig_DB is a repertoire of 5000 novel small molecules, screened from ZINC database and ranked using structure based virtual screening (SBVS) against 25 immune receptors which play a pivotal role in defending and initiating the activation of immune system. Consequently, in the current study, small molecules were screened by docking on the essential domains present on the receptors expressed by cells of immune system. The screened molecules exhibited efficacious binding to immune receptors, and indicated a possibility of discovering novel small molecules. Other features of ImmtorLig_DB include information about availability, clustering analysis, and estimation of absorption, distribution, metabolism, and excretion (ADME) properties of the screened small molecules. Structural comparisons indicate that predicted small molecules may be considered novel. Further, this repertoire is available via a searchable graphical user interface (GUI) throughhttp://bioinfo.imtech.res.in/bvs/immtor/.
Curvilinear MetaSurfaces for Surface Wave Manipulation
Authors: La Spada Luigi , Spooner Chris , Haq Sajad , Hao Yang 
Published: February 2019

AbstractArtificial sheet materials, known as MetaSurfaces, have been applied to fully control both space and surface waves due to their exceptional abilities to dynamically tailor wave fronts and polarization states, while maintaining small footprints. However, previous and current designs and manufactured MetaSurfaces are limited to specific types of surfaces. There exists no general but rigorous design methodology for MetaSurfaces with generic curvature. The aim of this paper is to develop an analytical approach to characterize the wave behavior over arbitrary curvilinear MetaSurfaces. The proposed method allows us to fully characterize all propagating and evanescent wave modes from the MetaSurfaces. We will validate the proposed technique by designing, realizing and testing an ultrathin MetaSurface cloak for surface waves. Good results are obtained in terms of bandwidth, polarization independence and fabrication simplicity.
Adaptation reveals multi-stage coding of visual duration
Authors: Heron James , Fulcher Corinne , Collins Howard , Whitaker David , Roach Neil W. 
Published: February 2019

AbstractIn conflict with historically dominant models of time perception, recent evidence suggests that the encoding of our environment’s temporal properties may not require a separate class of neurons whose raison d'être is the dedicated processing of temporal information. If true, it follows that temporal processing should be imbued with the known selectivity found within non-temporal neurons. In the current study, we tested this hypothesis for the processing of a poorly understood stimulus parameter: visual event duration. We used sensory adaptation techniques to generate duration aftereffects: bidirectional distortions of perceived duration. Presenting adapting and test durations to the same vs different eyes utilises the visual system’s anatomical progression from monocular, pre-cortical neurons to their binocular, cortical counterparts. Duration aftereffects exhibited robust inter-ocular transfer alongside a small but significant contribution from monocular mechanisms. We then used novel stimuli which provided duration information that was invisible to monocular neurons. These stimuli generated robust duration aftereffects which showed partial selectivity for adapt-test changes in retinal disparity. Our findings reveal distinct duration encoding mechanisms at monocular, depth-selective and depth-invariant stages of the visual hierarchy.
Ex Vivo 1H NMR study of pituitary adenomas to differentiate various immunohistochemical subtypes
Authors: Ijare Omkar B. , Baskin David S. , Pichumani Kumar 
Published: February 2019

AbstractPituitary adenomas (PAs) are benign growths arising from epithelial cells in the adenohypophysis of the pituitary gland. To date, there has been no detailed metabolic characterization of PAs of various subtypes. In this study, we report nuclear magnetic resonance (NMR) based metabolomic analysis of surgically resected tumors from forty five pituitary tumor patients [gonadotropic (LH/FSH-secreting) = 17; prolactinomas (PRL-secreting) = 11, Cushing’s disease (ACTH-secreting) = 4, non-functional = 5, and mixed = 8] who underwent transsphenoidal selective adenomectomy. Compared to LH/FSH-secreting tumors, PRL-secreting tumors showed statistically significant decrease in the levels of N-acetylaspartate (NAA), myo-inositol (mI), scyllo-inositol (sI), glycine, taurine, phosphoethanolamine (PE) and increase in the levels of glutamine. When compared with LH/FSH-secreting tumors, ACTH-secreting tumors showed statistically significant decrease in the levels of sI, glycine, PE and increase in the levels of aspartate. Although lipid extracts of PAs showed the presence of many common lipid molecules, only glycerophosphoethanolamine (GPE) showed statistically significant decrease in PRL, ACTH and non-functional subtypes when compared to LH/FSH-secreting tumors. Changes observed in these metabolite concentrations among various subtypes of PAs reflect metabolic heterogeneity in these tumors and may pave the way towards the development of metabolic markers to distinguish various immunohistochemical subtypes of PAs.
Complement-dependent outer membrane perturbation sensitizes Gram-negative bacteria to Gram-positive specific antibiotics
Authors: Heesterbeek D. A. C. , Martin N. I. , Velthuizen A. , Duijst M. , Ruyken M. , Wubbolts R. , Rooijakkers S. H. M. , Bardoel B. W. 
Published: February 2019

AbstractGram-negative bacteria are refractory to the action of many antibiotics due to their impermeable outer membrane. An important player of the immune system is the complement system, a protein network in serum that directly kills Gram-negative bacteria through pore-formation by the Membrane Attack Complexes (MAC). We here show that the MAC rapidly perforates the outer membrane but that inner membrane damage, which is essential for killing, is relatively slow. Importantly, we demonstrate that MAC-induced outer membrane damage sensitizes Gram-negative bacteria to otherwise ineffective, Gram-positive-specific, antimicrobials. Synergy between serum and nisin was observed for 22 out of 53 tested Gram-negative clinical isolates and for multi-drug resistant (MDR) blood isolates. The in vivo relevance of this process is further highlighted by the fact that blood sensitizes a MDR K. pneumoniae strain to vancomycin. Altogether, these data imply that antibiotics that are considered ineffective to treat infections with Gram-negatives may have different functional outcomes in patients, due to the presence of the complement system.
Neonatal outcomes following different ovarian stimulation protocols in fresh single embryo transfer
Authors: Jwa Seung Chik , Nakashima Akira , Kuwahara Akira , Saito Kazuki , Irahara Minoru , Sakumoto Tetsuro , Ishihara Osamu , Saito Hidekazu 
Published: February 2019

AbstractPrevious studies suggested ovarian stimulation was associated with lower birth weight and higher risk of preterm delivery (PTD) from fresh embryo transfers (ETs). However, whether the increased risk differs between distinct ovarian stimulation protocols remains unknown. A retrospective cohort study of 38,220 singleton deliveries after fresh single ETs from 2007 to 2013 was conducted. Main outcomes were birth weight and gestational length. Compared with the natural cycle, all ovarian stimulation protocols were associated with a significantly increased risk for PTD, low birth weight (LBW) and small for gestational age (SGA). In subgroup analysis of maternal age under 35 years, luteal support using progesterone, and early cleavage ETs, the significant associations remained for LBW and SGA in gonadotropin-releasing hormone (GnRH) antagonist protocol and for LBW in GnRH agonist protocol. Ovarian stimulation using clomiphene citrate (CC) had the highest increased risks for LBW (Adjusted odds ratio [AOR], 1.58, 95% confidence interval [95% CI], 1.43−1.73) and SGA (AOR, 1.65, 95% CI, 1.50−1.82) compared with natural cycles, and was further associated with PTD and cesarean section. These findings suggest ovarian stimulation was associated with lower birth weight, and CC may have adverse effect on neonatal outcomes in fresh cycles.
An efficient and cost-effective method for primer-induced nucleotide labeling for massive sequencing on next-generation sequencing platforms
Authors: Guo Junjie , Cheng Tao , Xu Han , Li Yide , Zeng Jie 
Published: February 2019

AbstractNext generation sequencing (NGS) technologies play a powerful role in the preparation of large DNA databases such as DNA barcoding since it can produce a large number of sequence reads. Here we demonstrate a primer-induced sample labeling method aiming at sequencing a large number of samples simultaneously on NGS platforms. The strategy is to label samples with a unique oligo attached to the 5′-ends of primers. As a case study, 894 unique pentanucleotide oligoes were attached to the 5′-ends of three pairs of primers (for amplifying ITS, matK and rbcL) to label 894 samples. All PCR products of three barcodes of 894 samples were mixed together and sequenced on a high throughput sequencing platform. The results showed that 87.02%, 89.15% and 95.53% of the samples were successfully sequenced for rbcL, matK and ITS, respectively. The mean ratio of label mismatches for the three barcodes was 5.68%, and a sequencing depth of 30 ×to 40× was enough to obtain reliable sequences. It is flexible to label any number of samples simply by adjusting the length of oligoes. This easy, reliable and cost efficient method is useful in sequencing a large number of samples for construction of reference libraries for DNA barcoding, population biology and community phylogenetics.
Bone-inspired enhanced fracture toughness of de novo fiber reinforced composites
Authors: Libonati Flavia , Vellwock Andre E. , Ielmini Francesco , Abliz Dilmurat , Ziegmann Gerhard , Vergani Laura 
Published: February 2019

AbstractAmplification in toughness and balance with stiffness and strength are fundamental characteristics of biological structural composites, and a long sought-after objective for engineering design. Nature achieves these properties through a combination of multiscale key features. Yet, emulating all these features into synthetic de novo materials is rather challenging. Here, we fine-tune manual lamination, to implement a newly designed bone-inspired structure into fiber-reinforced composites. An integrated approach, combining numerical simulations, ad hoc manufacturing techniques, and testing, yields a novel composite with enhanced fracture toughness and balance with stiffness and strength, offering an optimal lightweight material solution with better performance than conventional materials such as metals and alloys. The results also show how the new design significantly boosts the fracture toughness compared to a classic laminated composite, made of the same building blocks, also offering an optimal tradeoff with stiffness and strength. The predominant mechanism, responsible for the enhancement of fracture toughness in the new material, is the continuous deviation of the crack from a straight path, promoting large energy dissipation and preventing a catastrophic failure. The new insights resulting from this study can guide the design of de novo fiber-reinforced composites toward better mechanical performance to reach the level of synergy of their natural counterparts.