bluuebunny/crossref_metadata_2025_split huggingface dataset:
The potential HLA Class I-restricted epitopes derived from LeIF and TSA of Leishmania donovani evoke anti-leishmania CD8+ T lymphocyte response
Authors: Dikhit Manas Ranjan , Das Sushmita , Mahantesh Vijaya , Kumar Akhilesh , Singh Ashish Kumar , Dehury Budheswar , Rout Ajaya Kumar , Ali Vahab , Sahoo Ganesh Chandra , Topno Roshan Kamal , Pandey Krishna , Das V. N. R. , Bimal Sanjiva , Das Pradeep 
Published: September 2018

AbstractTo explore new protective measure against visceral leishmaniasis, reverse vaccinology approach was employed to identify key immunogenic regions which can mediate long-term immunity. In-depth computational analysis revealed nine promiscuous epitopes which can possibly be presented by 46 human leukocyte antigen, thereby broadening the worldwide population up to 94.16%. This is of reasonable significance that most of the epitopes shared 100% sequence homology with otherLeishmaniaspecies and could evoke a common pattern of protective immune response. Transporter associated with antigen processing binding affinity, molecular docking approach followed by dynamics simulation and human leukocyte antigen stabilization assay suggested that the best five optimal set of epitopes bind in between α1 and α2 binding groove with sufficient affinity and stability which allows the translocation of intact epitope to the cell surface. Fascinatingly, the human leukocyte antigen stabilization assay exhibited a modest correlation with the positive immunogenicity score predicted by class I pMHC immunogenicity predictor. A support for this notion came from ELISA and FACS analysis where the epitopes as a cocktail induced CD8+ IFN-γ and Granzyme B levels significantly in treated visceral leishmaniasis subject which suggests the immunogenic ability of the selected epitopes.
Genome-wide analysis of polymorphism × sodium interaction effect on blood pressure identifies a novel 3′-BCL11B gene desert locus
Authors: Hachiya Tsuyoshi , Narita Akira , Ohmomo Hideki , Sutoh Yoichi , Komaki Shohei , Tanno Kozo , Satoh Mamoru , Sakata Kiyomi , Hitomi Jiro , Nakamura Motoyuki , Ogasawara Kuniaki , Yamamoto Masayuki , Sasaki Makoto , Hozawa Atsushi , Shimizu Atsushi 
Published: September 2018

AbstractExcessive sodium intake is a global risk factor for hypertension. Sodium effects on blood pressure vary from person to person; hence, high-risk group targeting based on personal genetic information can play a complementary role to ongoing population preventive approaches to reduce sodium consumption. To identify genetic factors that modulate sodium effects on blood pressure, we conducted a population-based genome-wide interaction analysis in 8,768 Japanese subjects, which was >3 times larger than a similar previous study. We tested 7,135,436 polymorphisms in the discovery cohort, and loci that met suggestive significance were further examined in an independent replication cohort. We found that an interaction between a novel 3′-BCL11B gene desert locus and daily sodium consumption was significantly associated with systolic blood pressure in both discovery and replication cohorts under the recessive model. Further statistical analysis of rs8022678, the sentinel variant of the 3′-BCL11B gene desert locus, showed that differences in mean systolic blood pressure between high and low sodium consumption subgroups were 5.9 mm Hg (P = 8.8 × 10−12) in rs8022678 A carriers and −0.3 mm Hg (P = 0.27) in rs8022678 A non-carriers, suggesting that the rs8022678 genotype can classify persons into sodium-sensitive (A carriers) and sodium-insensitive (A non-carriers) subgroups. Our results implied that rs8022678 A carriers may receive a greater benefit from sodium-lowering interventions than non-carriers.
Validation of the Sleep Regularity Index in Older Adults and Associations with Cardiometabolic Risk
Authors: Lunsford-Avery Jessica R. , Engelhard Matthew M. , Navar Ann Marie , Kollins Scott H. 
Published: September 2018

AbstractSleep disturbances, including insufficient sleep duration and circadian misalignment, confer risk for cardiometabolic disease. Less is known about the association between the regularity of sleep/wake schedules and cardiometabolic risk. This study evaluated the external validity of a new metric, the Sleep Regularity Index (SRI), among older adults (n = 1978; mean age 68.7 ± 9.2), as well as relationships between the SRI and cardiometabolic risk using data from the Multi-Ethnic Study of Atherosclerosis (MESA). Results indicated that sleep irregularity was associated with delayed sleep timing, increased daytime sleep and sleepiness, and reduced light exposure, but was independent of sleep duration. Greater sleep irregularity was also correlated with 10-year risk of cardiovascular disease and greater obesity, hypertension, fasting glucose, hemoglobin A1C, and diabetes status. Finally, greater sleep irregularity was associated with increased perceived stress and depression, psychiatric factors integrally tied to cardiometabolic disease. These results suggest that the SRI is a useful measure of sleep regularity in older adults. Additionally, sleep irregularity may represent a target for early identification and prevention of cardiometabolic disease. Future studies may clarify the causal direction of these effects, mechanisms underlying links between sleep irregularity and cardiometabolic risk, and the utility of sleep interventions in reducing cardiometabolic risk.
Application of a mechanobiological algorithm to investigate mechanical mediation of heterotopic bone in trans-femoral amputees
Authors: Rosenberg Naomi M. , Bull Anthony M. J. 
Published: September 2018

AbstractHeterotopic ossification (HO) is the process of bone formation in tissues that are not usually osseous. It occurs in 60% of those with blast-related amputations. HO can result in reduced range of motion, pain, nerve impingement and can affect prosthesis fitting and is caused by a combination of mechanical, biological, local and systemic factors. As with normal bone formation and remodelling, it is expected that heterotopic bone responds to mechanical stimuli and understanding this relationship can give insight into the pathology. The objective of this research was to investigate whether a physiological 2D computational model that considers both mechanical and biological factors can be used to simulate HO in the residual limb of a trans-femoral amputee. The study found that characteristic morphologies of HO were reproduced by adjusting the loading environment. Significant effects were produced by changing the loading direction on the femur; this is potentially associated with different initial surgical interventions such as muscle myodesis. Also, initial treatment such as negative pressure through a dressing was found to change the shape of heterotopic bone.
Helicobacter pylori infection is not related to increased carotid intima-media thickness in general population
Authors: Feng Yunfei , Zhou Weibin , Luo Luo , Xu Weiwei 
Published: September 2018

AbstractThe aim is to determine whether there is an independent association between Hp infection and carotid intima-media thickness (CIMT) in a cross-section observational study. Among of 14588 routine health check-up participants, 13770 subjects underwent the 13C-urea breath test (13C-UBT) and ultrasound measurement of CIMT. Traditional atherosclerotic risk factors were also recorded. The ratio of increased CIMT in Hp positive group (28.6%) was not significant difference compared with Hp negative group (29.7%) (p = 0.164). The HP infection rates was no significant difference between increased CIMT (38.4%) and non- increased CIMT (39.7%) patients. However, all the traditional atherosclerotic risk factors including age, gender, BMI, waistline, total cholesterol, low density lipoprotein cholesterol, very low density lipoprotein cholesterol, high density lipoprotein cholesterol, triglycerides, free fatty acid, homocysteine, systolic and diastolic blood pressure, fasting plasma glucose and C reactive protein were different between increased CIMT and non- increased CIMT participants. The odds of Hp infection for CIMT risk (OR 0.948; 95% CI 0.879–1.022; P = 0.164) was not higher in binary logistic regression analysis even after adjustment for traditional risk factors (OR 1.118; 95% CI 0.958–1.306; P = 0.157). Our study found no evidence of association between CIMT and HP infection.
Agricultural landscapes and the Loire River influence the genetic structure of the marbled newt in Western France
Authors: Costanzi Jean-Marc , Mège Pascal , Boissinot Alexandre , Isselin-Nondedeu Francis , Guérin Sandra , Lourdais Olivier , Trochet Audrey , Le Petitcorps Quentin , Legrand Agathe , Varenne François , Grillet Pierre , Morin-Pinaud Sophie , Picard Damien 
Published: September 2018

AbstractAmphibians are particularly sensitive to landscape fragmentation. Potential barriers between breeding sites can negatively influence the dispersal of individuals and increase genetic structure between populations. In this study, we genotyped 10 microsatellites for 334 marbled newts (Triturus marmoratus) at 11 different locations in Western France. Samples were collected in different regions with contrasting agricultural landscapes (low and high proportion of arable land in the north and south, respectively). We found a strong genetic structure between the northern and southern sampling sites. Isolation by distance was recorded after 62 km, but within the northern region, little or no genetic structure was detected over large distances (up to 114 km). Genetic structure at shorter distance (43 km) was found between sites situated in landscapes with larger amounts of arable lands. A significant positive relationship was found between the pairwise genetic distance (Fst) between sites and the amount of arable land together with the distance between sites. Our results suggest that the Loire River might act as a corridor for the marbled newt, while arable land might act as a barrier. Finally, although a large city is located between sampling sites, no effect was detected on population structure.
The Cytotoxic Necrotizing Factor of Yersinia pseudotuberculosis (CNFy) is Carried on Extracellular Membrane Vesicles to Host Cells
Authors: Monnappa Ajay K. , Bari Wasimul , Seo Jeong Kon , Mitchell Robert J. 
Published: September 2018

AbstractIn this study we show Yersinia pseudotuberculosis secretes membrane vesicles (MVs) that contain different proteins and virulence factors depending on the strain. Although MVs from Y. pseudotuberculosis YPIII and ATCC 29833 had many proteins in common (68.8% of all the proteins identified), those located in the outer membrane fraction differed significantly. For instance, the MVs from Y. pseudotuberculosis YPIII harbored numerous Yersinia outer proteins (Yops) while they were absent in the ATCC 29833 MVs. Another virulence factor found solely in the YPIII MVs was the cytotoxic necrotizing factor (CNFy), a toxin that leads to multinucleation of host cells. The ability of YPIII MVs to transport this toxin and its activity to host cells was verified using HeLa cells, which responded in a dose-dependent manner; nearly 70% of the culture was multinucleated after addition of 5 µg/ml of the purified YPIII MVs. In contrast, less than 10% were multinucleated when the ATCC 29833 MVs were added. Semi-quantification of CNFy within the YPIII MVs found this toxin is present at concentrations of 5 ~ 10 ng per µg of total MV protein, a concentration that accounts for the cellular responses seen.
Heterogeneity of material structure determines the stationary surface topography and friction
Authors: Li Qiang , Voll Lars , Starcevic Jasminka , Popov Valentin L. 
Published: September 2018

AbstractThe character of surface roughness and the force of friction in the stationary state after a sufficiently long run-in process are of key importance for numerous applications, e.g. for friction between road and tire. In the present paper, we study theoretically and experimentally the asymptotic worn state of a bi-phasic material that is arbitrarily heterogeneous in the contact plane, but homogeneous in the direction of the surface normal. Under the assumption of Archard’s wear law in its local formulation, the asymptotic shape is found in the closed integral form. Given the surface profile, the coefficient of friction can be estimated, since the coefficient of friction is known to be strongly correlated with the mean square root value of the surface slope. The limiting surface profiles and the corresponding coefficient of friction are determined as functions of size, relative concentration and wear ratio of the phases. The results of numerical calculations are compared to and validated by experiments carried out on simplified model systems. The main conclusion is that the rms value of the surface slope is not influenced by the characteristic linear size of inclusions and depends solely on the relative concentration of phases, as well as the ratio of their wear coefficients.
Development of zebrafish paired and median fin musculature: basis for comparative, developmental, and macroevolutionary studies
Authors: Siomava Natalia , Shkil Fedor , Voronezhskaya Elena , Diogo Rui 
Published: September 2018

AbstractThe model organism Dario rerio (zebrafish) is widely used in evo-devo and comparative studies. Nevertheless, little is known about the development and differentiation of the appendicular musculature in this fish. In this study, we examined the development of the muscles of all five zebrafish fin types (pectoral, pelvic, anal, dorsal and caudal). We describe the development of the muscles of these fins, including some muscles that were never mentioned in the literature, such as the interhypurales of the caudal fin. Interestingly, these caudal muscles are present in early stages but absent in adult zebrafishes. We also compare various stages of zebrafish fin muscle development with the configuration found in other extant fishes, including non-teleostean actinopterygians as well as cartilaginous fishes. The present work thus provides a basis for future developmental, comparative, evolutionary and evo-devo studies and emphasizes the importance of developmental works on muscles for a more comprehensive understanding of the origin, development and evolution of the appendicular appendages of vertebrate animals.
Respiratory Syncytial Virus induces the classical ROS-dependent NETosis through PAD-4 and necroptosis pathways activation
Authors: Muraro Stéfanie P. , De Souza Gabriela F. , Gallo Stephanie W. , Da Silva Bruna K. , De Oliveira Sílvia D. , Vinolo Marco Aurélio R. , Saraiva Elvira M. , Porto Bárbara N. 
Published: September 2018

AbstractRespiratory syncytial virus (RSV) is a major cause of diseases of the respiratory tract in young children and babies, being mainly associated with bronchiolitis. RSV infection occurs primarily in pulmonary epithelial cells and, once infection is established, an immune response is triggered and neutrophils are recruited. In this study, we investigated the mechanisms underlying NET production induced by RSV. We show that RSV induced the classical ROS-dependent NETosis in human neutrophils and that RSV was trapped in DNA lattices coated with NE and MPO. NETosis induction by RSV was dependent on signaling by PI3K/AKT, ERK and p38 MAPK and required histone citrullination by PAD-4. In addition, RIPK1, RIPK3 and MLKL were essential to RSV-induced NETosis. MLKL was also necessary to neutrophil necrosis triggered by the virus, likely promoting membrane-disrupting pores, leading to neutrophil lysis and NET extrusion. Finally, we found that RSV infection of alveolar epithelial cells or lung fibroblasts triggers NET-DNA release by neutrophils, indicating that neutrophils can identify RSV-infected cells and respond to them by releasing NETs. The identification of the mechanisms responsible to mediate RSV-induced NETosis may prove valuable to the design of new therapeutic approaches to treat the inflammatory consequences of RSV bronchiolitis in young children.
Tuning magnetocrystalline anisotropy by cobalt alloying in hexagonal Fe3Ge1
Authors: McGuire Michael A. , Shanavas K. V. , Kesler Michael S. , Parker David S. 
Published: September 2018

AbstractWe show using both experimental and theoretical methods that cobalt substitution in the hexagonal ferromagnet Fe3Ge suppresses the planar magnetic anisotropy and favors a uniaxial state. Uniaxial ferromagnetism is observed at room temperature for cobalt concentrations of only a few percent, and 10% substitution fully suppresses the planar magnetic structure at least down to 5 K, with only a small effect on the magnetization and Curie temperature. First principles calculations predict strong uniaxial magnetocrystalline anisotropy and promising permanent magnet properties for higher cobalt concentrations. Although these high Co concentrations were not realized experimentally, this work suggests that the rare-earth-free Fe3Ge structure supports intrinsic magnetic properties that may enable promising permanent magnet performance.
Impaired wound healing in type 1 diabetes is dependent on 5-lipoxygenase products
Authors: Ramalho Theresa , Filgueiras Luciano , Silva-Jr Ildefonso Alves , Pessoa Ana Flavia Marçal , Jancar Sonia 
Published: September 2018

AbstractType 1 diabetes is associated with systemic low grade inflammation (LGI). We have previously shown that LGI in diabetic mice depends on systemic circulation of leukotriene (LTB4) which potentiates the toll-like/IL1β receptors response in macrophages. Impaired wound healing is an important co-morbidity in diabetes, and macrophages play a key role in this process. Here, we investigated the role of leukotrienes on monocytes and macrophages phenotype and in the impaired wound healing in diabetic mice. Type 1 diabetes was induced with streptozotocin in 129SvE wild-type (WT) and leukotrienes-deficient 5LO−/− (5-lipoxygenase knockout) mice. In diabetics, the systemic levels of LTB4, TNF-α, IL-6, IL-10, IL-12 and IFNγ were increased as well as the frequency of pro-inflammatory monocytes (CD11b+Ly6ChighLy6G−) compared to healthy mice. In diabetic 5LO−/− mice, these parameters were similar to those in healthy mice. Resident peritoneal macrophages from diabetic WT mice showed a classically activated M1-like phenotype (high Nos2, Stat and Il12 expression, and nitrite levels). Macrophages from diabetic 5LO−/− mice presented alternatively activated M2-macrophages markers (high Arg1 and Chi3l3 expression and arginase activity) and when stimulated with IL4, enhanced phosphorylated-STAT6. Cutaneous wound healing in diabetic WT mice was impaired, which correlated with the decreased frequency of M2-macrophages (CD45+F4/80+CD206+) in the lesions. In diabetic 5LO−/− mice, the frequency of M2-macrophages in the wound was similar to that in healthy mice, suggesting that the impaired healing of diabetic mice depends on 5LO products. The inhibition of leukotrienes or antagonism of its receptors could be a therapeutic alternative for diabetic patients with impaired healing.
Light sintering of ultra-smooth and robust silver nanowire networks embedded in poly(vinyl-butyral) for flexible OLED
Authors: Lee Dong Jun , Oh Youngsu , Hong Jae-Min , Park Young Wook , Ju Byeong-Kwon 
Published: September 2018

AbstractA conductive, uniform, and ultra-smooth flexible transparent composite film is produced by embedding silver nanowires (AgNWs) into poly(vinyl-butyral) (PVB) without pressure or high-temperature annealing. The adhesion of AgNWs was greatly improved by embedding them in PVB, and surface roughness and sheet resistance (Rs) improvements were achieved through the use of the intense pulsed light (IPL) method, which welds the interconnections among AgNWs in a short time without heat or pressure treatment. The sheet resistance of PVB/AgNWs with the IPL(PAI) composite film reaches 12.6 ohm/sq with a transmittance of 85.7% (at 550 nm); no clear changes in the sheet resistance are observed after a substrate bending and tape test, suggesting excellent flexibility. In the case of PAI, the change in sheet resistance was only 2.6% after a 2,000-bend test, and the resulting bending radius was less than 1 mm. When IPL was exposed to PVB/AgNWs, the figure of merit was 2.36 times higher than that without exposure. Finally, flexible OLEDs using PAI exhibited comparable or higher electroluminescent characteristics than other devices with well-known flexible electrodes—including indium-zinc-oxide on polymer plastic—which is a promising discovery for flexible optoelectronic applications.
Magnetic Force-driven in Situ Selective Intracellular Delivery
Authors: Wang Ran , Chow Yu Ting , Chen Shuxun , Ma Dongce , Luo Tao , Tan Youhua , Sun Dong 
Published: September 2018

AbstractIntracellular delivery of functional materials holds great promise in biologic research and therapeutic applications but poses challenges to existing techniques, including the reliance on exogenous vectors and lack of selectivity. To address these problems, we propose a vector-free approach that utilizes millimeter-sized iron rods or spheres driven by magnetic forces to selectively deform targeted cells, which in turn generates transient disruption in cell membranes and enables the delivery of foreign materials into cytosols. A range of functional materials with the size from a few nanometers to hundreds of nanometers have been successfully delivered into various types of mammalian cells in situ with high efficiency and viability and minimal undesired effects. Mechanistically, material delivery is mediated by force-induced transient membrane disruption and restoration, which depend on actin cytoskeleton and calcium signaling. When used for siRNA delivery, CXCR4 is effectively silenced and cell migration and proliferation are significantly inhibited. Remarkably, cell patterns with various complexities are generated, demonstrating the unique ability of our approach in selectively delivering materials into targeted cells in situ. In summary, we have developed a magnetic force-driven intracellular delivery method with in situ selectivity, which may have tremendous applications in biology and medicine.
Pleistocene climate cycling and host plant association shaped the demographic history of the bark beetle Pityogenes chalcographus
Authors: Schebeck Martin , Dowle Eddy J. , Schuler Hannes , Avtzis Dimitrios N. , Bertheau Coralie , Feder Jeffrey L. , Ragland Gregory J. , Stauffer Christian 
Published: September 2018

AbstractHistorical climatic oscillations and co-evolutionary dependencies were key evolutionary drivers shaping the current population structure of numerous organisms. Here, we present a genome-wide study on the biogeography of the bark beetle Pityogenes chalcographus, a common and widespread insect in Eurasia. Using Restriction Associated DNA Sequencing, we studied the population structure of this beetle across a wide part of its western Palaearctic range with the goal of elucidating the role of Pleistocene glacial-interglacial cycling and its close relationship to its main host plant Norway spruce. Genetic distance among geographic sites was generally low, but clustering analysis revealed three genetically distinct groups, that is, southern, central/south-eastern, and north-eastern locations. Thus, three key P. chalcographus glacial refugia were identified: in the Italian-Dinaric region, the Carpathians, and the Russian plain, shared with its main host. The current phylogeographic signal was affected by genetic divergence among geographically isolated refugia during glacial periods and postglacial re-establishment of genetic exchange through secondary contact, reflected by admixture among genetic groups. Additionally, certain life history traits, like the beetle’s dispersal and reproductive behaviour, considerably influenced its demographic history. Our results will help to understand the biogeography of other scolytine beetles, especially species with similar life history traits.