bluuebunny/crossref_metadata_2025_split huggingface dataset:
miR-625-3p regulates oxaliplatin resistance by targeting MAP2K6-p38 signalling in human colorectal adenocarcinoma cells
Authors: Rasmussen Mads Heilskov , Lyskjær Iben , Jersie-Christensen Rosa Rakownikow , Tarpgaard Line Schmidt , Primdal-Bengtson Bjarke , Nielsen Morten Muhlig , Pedersen Jakob Skou , Hansen Tine Plato , Hansen Flemming , Olsen Jesper Velgaard , Pfeiffer Per , Ørntoft Torben Falck , Andersen Claus Lindbjerg 
Published: August 2016

AbstractOxaliplatin resistance in colorectal cancers (CRC) is a major medical problem, and predictive markers are urgently needed. Recently, miR-625-3p was reported as a promising predictive marker. Herein, we show that miR-625-3p functionally induces oxaliplatin resistance in CRC cells, and identify the signalling networks affected by miR-625-3p. We show that the p38 MAPK activator MAP2K6 is a direct target of miR-625-3p, and, accordingly, is downregulated in non-responder patients of oxaliplatin therapy. miR-625-3p-mediated resistance is reversed by anti-miR-625-3p treatment and ectopic expression of a miR-625-3p insensitive MAP2K6 variant. In addition, reduction of p38 signalling by using siRNAs, chemical inhibitors or expression of a dominant-negative MAP2K6 protein induces resistance to oxaliplatin. Transcriptome, proteome and phosphoproteome profiles confirm inactivation of MAP2K6-p38 signalling as one likely mechanism of oxaliplatin resistance. Our study shows that miR-625-3p induces oxaliplatin resistance by abrogating MAP2K6-p38-regulated apoptosis and cell cycle control networks, and corroborates the predictive power of miR-625-3p.
Free-electron creation at the 60° twin boundary in Bi2Te3
Authors: Kim Kwang-Chon , Lee Joohwi , Kim Byung Kyu , Choi Won Young , Chang Hye Jung , Won Sung Ok , Kwon Beomjin , Kim Seong Keun , Hyun Dow-Bin , Kim Hyun Jae , Koo Hyun Cheol , Choi Jung-Hae , Kim Dong-Ik , Kim Jin-Sang , Baek Seung-Hyub 
Published: August 2016

AbstractInterfaces, such as grain boundaries in a solid material, are excellent regions to explore novel properties that emerge as the result of local symmetry-breaking. For instance, at the interface of a layered-chalcogenide material, the potential reconfiguration of the atoms at the boundaries can lead to a significant modification of the electronic properties because of their complex atomic bonding structure. Here, we report the experimental observation of an electron source at 60° twin boundaries in Bi2Te3, a representative layered-chalcogenide material. First-principles calculations reveal that the modification of the interatomic distance at the 60° twin boundary to accommodate structural misfits can alter the electronic structure of Bi2Te3. The change in the electronic structure generates occupied states within the original bandgap in a favourable condition to create carriers and enlarges the density-of-states near the conduction band minimum. The present work provides insight into the various transport behaviours of thermoelectrics and topological insulators.
Ovarian fluid allows directional cryptic female choice despite external fertilization
Authors: Alonzo Suzanne H. , Stiver Kelly A. , Marsh-Rollo Susan E. 
Published: August 2016

AbstractIn species with internal fertilization, females can favour certain males over others, not only before mating but also within the female’s reproductive tract after mating. Here, we ask whether such directional post-mating (that is, cryptic) female mate choice can also occur in species with external fertilization. Using an in vitro sperm competition experiment, we demonstrate that female ovarian fluid (ovarian fluid) changes the outcome of sperm competition by decreasing the importance of sperm number thereby increasing the relative importance of sperm velocity. We further show that ovarian fluid does not differentially affect sperm from alternative male phenotypes, but generally enhances sperm velocity, motility, straightness and chemoattraction. Under natural conditions, female ovarian fluid likely increases the paternity of the preferred parental male phenotype, as these males release fewer but faster sperm. These results imply females have greater control over fertilization and potential to exert selection on males in species with external fertilization than previously thought possible.
Fishing down nutrients on coral reefs
Authors: Allgeier Jacob E. , Valdivia Abel , Cox Courtney , Layman Craig A. 
Published: August 2016

AbstractFishing is widely considered a leading cause of biodiversity loss in marine environments, but the potential effect on ecosystem processes, such as nutrient fluxes, is less explored. Here, we test how fishing on Caribbean coral reefs influences biodiversity and ecosystem functions provided by the fish community, that is, fish-mediated nutrient capacity. Specifically, we modelled five processes of nutrient storage (in biomass) and supply (via excretion) of nutrients, as well as a measure of their multifunctionality, onto 143 species of coral reef fishes across 110 coral reef fish communities. These communities span a gradient from extreme fishing pressure to protected areas with little to no fishing. We find that in fished sites fish-mediated nutrient capacity is reduced almost 50%, despite no substantial changes in the number of species. Instead, changes in community size and trophic structure were the primary cause of shifts in ecosystem function. These findings suggest that a broader perspective that incorporates predictable impacts of fishing pressure on ecosystem function is imperative for effective coral reef conservation and management.
Predicting non-small cell lung cancer prognosis by fully automated microscopic pathology image features
Authors: Yu Kun-Hsing , Zhang Ce , Berry Gerald J. , Altman Russ B. , Ré Christopher , Rubin Daniel L. , Snyder Michael 
Published: August 2016

AbstractLung cancer is the most prevalent cancer worldwide, and histopathological assessment is indispensable for its diagnosis. However, human evaluation of pathology slides cannot accurately predict patients’ prognoses. In this study, we obtain 2,186 haematoxylin and eosin stained histopathology whole-slide images of lung adenocarcinoma and squamous cell carcinoma patients from The Cancer Genome Atlas (TCGA), and 294 additional images from Stanford Tissue Microarray (TMA) Database. We extract 9,879 quantitative image features and use regularized machine-learning methods to select the top features and to distinguish shorter-term survivors from longer-term survivors with stage I adenocarcinoma (P<0.003) or squamous cell carcinoma (P=0.023) in the TCGA data set. We validate the survival prediction framework with the TMA cohort (P<0.036 for both tumour types). Our results suggest that automatically derived image features can predict the prognosis of lung cancer patients and thereby contribute to precision oncology. Our methods are extensible to histopathology images of other organs.
Self-mapping the longitudinal field structure of a nonlinear plasma accelerator cavity
Authors: Clayton C. E. , Adli E. , Allen J. , An W. , Clarke C. I. , Corde S. , Frederico J. , Gessner S. , Green S. Z. , Hogan M. J. , Joshi C. , Litos M. , Lu W. , Marsh K. A. , Mori W. B. , Vafaei-Najafabadi N. , Xu X. , Yakimenko V. 
Published: August 2016

AbstractThe preservation of emittance of the accelerating beam is the next challenge for plasma-based accelerators envisioned for future light sources and colliders. The field structure of a highly nonlinear plasma wake is potentially suitable for this purpose but has not been yet measured. Here we show that the longitudinal variation of the fields in a nonlinear plasma wakefield accelerator cavity produced by a relativistic electron bunch can be mapped using the bunch itself as a probe. We find that, for much of the cavity that is devoid of plasma electrons, the transverse force is constant longitudinally to within ±3% (r.m.s.). Moreover, comparison of experimental data and simulations has resulted in mapping of the longitudinal electric field of the unloaded wake up to 83 GV m−1 to a similar degree of accuracy. These results bode well for high-gradient, high-efficiency acceleration of electron bunches while preserving their emittance in such a cavity.
Mohawk promotes the maintenance and regeneration of the outer annulus fibrosus of intervertebral discs
Authors: Nakamichi Ryo , Ito Yoshiaki , Inui Masafumi , Onizuka Naoko , Kayama Tomohiro , Kataoka Kensuke , Suzuki Hidetsugu , Mori Masaki , Inagawa Masayo , Ichinose Shizuko , Lotz Martin K. , Sakai Daisuke , Masuda Koichi , Ozaki Toshifumi , Asahara Hiroshi 
Published: August 2016

AbstractThe main pathogenesis of intervertebral disc (IVD) herniation involves disruption of the annulus fibrosus (AF) caused by ageing or excessive mechanical stress and the resulting prolapse of the nucleus pulposus. Owing to the avascular nature of the IVD and lack of understanding the mechanisms that maintain the IVD, current therapies do not lead to tissue regeneration. Here we show that homeobox protein Mohawk (Mkx) is a key transcription factor that regulates AF development, maintenance and regeneration. Mkx is mainly expressed in the outer AF (OAF) of humans and mice. In Mkx−/− mice, the OAF displays a deficiency of multiple tendon/ligament-related genes, a smaller OAF collagen fibril diameter and a more rapid progression of IVD degeneration compared with the wild type. Mesenchymal stem cells overexpressing Mkx promote functional AF regeneration in a mouse AF defect model, with abundant collagen fibril formation. Our results indicate a therapeutic strategy for AF regeneration.
Human TRAV1-2-negative MR1-restricted T cells detect S. pyogenes and alternatives to MAIT riboflavin-based antigens
Authors: Meermeier Erin W. , Laugel Bruno F. , Sewell Andrew K. , Corbett Alexandra J. , Rossjohn Jamie , McCluskey James , Harriff Melanie J. , Franks Tamera , Gold Marielle C. , Lewinsohn David M. 
Published: August 2016

AbstractMucosal-associated invariant T (MAIT) cells are thought to detect microbial antigens presented by the HLA-Ib molecule MR1 through the exclusive use of a TRAV1-2-containing TCRα. Here we use MR1 tetramer staining and ex vivo analysis with mycobacteria-infected MR1-deficient cells to demonstrate the presence of functional human MR1-restricted T cells that lack TRAV1-2. We characterize an MR1-restricted clone that expresses the TRAV12-2 TCRα, which lacks residues previously shown to be critical for MR1-antigen recognition. In contrast to TRAV1-2+ MAIT cells, this TRAV12-2-expressing clone displays a distinct pattern of microbial recognition by detecting infection with the riboflavin auxotroph Streptococcus pyogenes. As known MAIT antigens are derived from riboflavin metabolites, this suggests that TRAV12-2+ clone recognizes unique antigens. Thus, MR1-restricted T cells can discriminate between microbes in a TCR-dependent manner. We postulate that additional MR1-restricted T-cell subsets may play a unique role in defence against infection by broadening the recognition of microbial metabolites.
Selection of suitable reference genes for quantitative RT-PCR normalization in the halophyte Halostachys caspica under salt and drought stress
Authors: Zhang Suwei , Zeng Youling , Yi Xiaoya , Zhang Yufang 
Published: August 2016

AbstractThe plants are always subjected to various environmental stress, because of plant sessile growth. qRT-PCR is a sensitive and reliable technology and the normalization of target gene expression with suitable reference genes is very important for obtaining accurate data. Halostachys caspica is an extremely salt-tolerant halophyte belonging to Chenopodiaceae and a good candidate to explore the stress-physiological and molecular mechanism. To get truly the expression profiles of coding genes and miRNAs in H. caspica in response to salt and drought stress using qRT-PCR, suitable reference genes need to be confirmed. In this study, 10 candidate genes including ACT, UBC10, UBC13, TUB2, TUB3, EF1α, 5S rRNA, tRNA, U6 and miR1436 from H. caspica are chosen and among them, the former nine are commonly used as internal control genes and miR1436 with high sequence copies is no significant difference expression in high salinity-treated and untreated small RNA libraries of this species. The three softwares are used to analyze expression stability. The results showed that EF1α and TUB3 were the most stable under salt and drought stress, respectively and UBC10 was the most constant aross all the samples with the both stressed combination. This work will benefit deep studies on abiotic tolerance in H. caspica.
Predatory bacteria are nontoxic to the rabbit ocular surface
Authors: Romanowski Eric G. , Stella Nicholas A. , Brothers Kimberly M. , Yates Kathleen A. , Funderburgh Martha L. , Funderburgh James L. , Gupta Shilpi , Dharani Sonal , Kadouri Daniel E. , Shanks Robert M. Q. 
Published: August 2016

AbstractGiven the increasing emergence of antimicrobial resistant microbes and the near absent development of new antibiotic classes, innovative new therapeutic approaches to address this global problem are necessary. The use of predatory bacteria, bacteria that prey upon other bacteria, is gaining interest as an “out of the box” therapeutic treatment for multidrug resistant pathogenic bacterial infections. Before a new antimicrobial agent is used to treat infections, it must be tested for safety. The goal of this study was to test the tolerability of bacteria on the ocular surface using in vitro and in vivo models. Predatory bacteria Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus were found to be non-toxic to human corneal stromal keratocytes in vitro; however, they did induce production of the proinflammatory chemokine IL-8 but not IL-1β. Predatory bacteria did not induce inflammation on the ocular surface of rabbit eyes, with and without corneal epithelial abrasions. Unlike a standard of care antibiotic vancomycin, predatory bacteria did not inhibit corneal epithelial wound healing or increase clinical inflammatory signs in vivo. Together these data support the safety of predatory bacteria on the ocular surface, but future studies are warranted regarding the use predatory bacteria in deeper tissues of the eye.
Stacking orders induced direct band gap in bilayer MoSe2-WSe2 lateral heterostructures
Authors: Hu Xiaohui , Kou Liangzhi , Sun Litao 
Published: August 2016

AbstractThe direct band gap of monolayer semiconducting transition-metal dichalcogenides (STMDs) enables a host of new optical and electrical properties. However, bilayer STMDs are indirect band gap semiconductors, which limits its applicability for high-efficiency optoelectronic devices. Here, we report that the direct band gap can be achieved in bilayer MoSe2-WSe2 lateral heterostructures by alternating stacking orders. Specifically, when Se atoms from opposite layers are stacked directly on top of each other, AA and A’B stacked heterostructures show weaker interlayer coupling, larger interlayer distance and direct band gap. Whereas, when Se atoms from opposite layers are staggered, AA’, AB and AB’ stacked heterostructures exhibit stronger interlayer coupling, shorter interlayer distance and indirect band gap. Thus, the direct/indirect band gap can be controllable in bilayer MoSe2-WSe2 lateral heterostructures. In addition, the calculated sliding barriers indicate that the stacking orders of bilayer MoSe2-WSe2 lateral heterostructures can be easily formed by sliding one layer with respect to the other. The novel direct band gap in bilayer MoSe2-WSe2 lateral heterostructures provides possible application for high-efficiency optoelectronic devices. The results also show that the stacking order is an effective strategy to induce and tune the band gap of layered STMDs.
Stable carbon isotope as a signal index for monitoring grassland degradation
Authors: Yao Hongyun , Wilkes Andreas , Zhu Guodong , Zhang Hongdan , Liu Xiaojuan , Dan Ding  , Zhai Xiajie , Tang Shiming , Chen Qing , Zhang Yujuan , Huang Ding , Wang Chengjie 
Published: August 2016

AbstractGrassland degradation due to overgrazing is common in many areas of the world. This study analyzed the potential of the stable carbon isotope (δ13C) value as a structural microcosmic index to monitor processes of grassland degradation. The δ13C values of plant leaves, roots and soils in non-grazed (NG) and over-grazed (OG) grassland were measured from samples collected from the seven types of grassland in China. We found that the leaf δ13C values of palatable species (δ13Cleaf) and root δ13C values (δ13Croot) in OG grasslands were reduced compared with those from NG grasslands. Furthermore, the δ13Cleaf and δ13Csoil were positive correlation with elevation and latitude, δ13Croot was negative correlation with them at high altitude (3000~5000m) and δ13Croot and δ13Csoil were negative correlation with them at low altitude (0~2000m), respectively. Consequently, tracing of the δ13C variations in grassland ecosystem can provide a powerful tool to evaluate the degree of grassland degradation.
Polydopamine-Coated Manganese Complex/Graphene Nanocomposite for Enhanced Electrocatalytic Activity Towards Oxygen Reduction
Authors: Parnell Charlette M. , Chhetri Bijay , Brandt Andrew , Watanabe Fumiya , Nima Zeid A. , Mudalige Thilak K. , Biris Alexandru S. , Ghosh Anindya 
Published: August 2016

AbstractPlatinum electrodes are commonly used electrocatalysts for oxygen reduction reactions (ORR) in fuel cells. However, this material is not economical due to its high cost and scarcity. We prepared an Mn(III) catalyst supported on graphene and further coated with polydopamine, resulting in superior ORR activity compared to the uncoated PDA structures. During ORR, a peak potential at 0.433 V was recorded, which is a significant shift compared to the uncoated material’s −0.303 V (both versus SHE). All the materials reduced oxygen in a wide pH range via a four-electron pathway. Rotating disk electrode and rotating ring disk electrode studies of the polydopamine-coated material revealed ORR occurring via 4.14 and 4.00 electrons, respectively. A rate constant of 6.33 × 106 mol−1s−1was observed for the polydopamine-coated material–over 4.5 times greater than the uncoated nanocomposite and superior to those reported for similar carbon-supported metal catalysts. Simply integrating an inexpensive bioinspired polymer coating onto the Mn-graphene nanocomposite increased ORR performance significantly, with a peak potential shift of over +730 mV. This indicates that the material can reduce oxygen at a higher rate but with lower energy usage, revealing its excellent potential as an ORR electrocatalyst in fuel cells.
Understanding the molecular basis of substrate binding specificity of PTB domains
Authors: Sain Neetu , Tiwari Garima , Mohanty Debasisa 
Published: August 2016

AbstractProtein-protein interactions mediated by phosphotyrosine binding (PTB) domains play a crucial role in various cellular processes. In order to understand the structural basis of substrate recognition by PTB domains, multiple explicit solvent atomistic simulations of 100ns duration have been carried out on 6 PTB-peptide complexes with known binding affinities. MM/PBSA binding energy values calculated from these MD trajectories and residue based statistical pair potential score show good correlation with the experimental dissociation constants. Our analysis also shows that the modeled structures of PTB domains can be used to develop less compute intensive residue level statistical pair potential based approaches for predicting interaction partners of PTB domains.
Gravity driven deterministic lateral displacement for suspended particles in a 3D obstacle array
Authors: Du Siqi , Drazer German 
Published: August 2016

AbstractWe present a simple modification to enhance the separation ability of deterministic lateral displacement (DLD) systems by expanding the two-dimensional nature of these devices and driving the particles into size-dependent, fully three-dimensional trajectories. Specifically, we drive the particles through an array of long cylindrical posts, such that they not only move parallel to the basal plane of the posts as in traditional two-dimensional DLD systems (in-plane motion), but also along the axial direction of the solid posts (out-of-plane motion). We show that the (projected) in-plane motion of the particles is completely analogous to that observed in 2D-DLD systems. In fact, a theoretical model originally developed for force-driven, two-dimensional DLD systems accurately describes the experimental results. More importantly, we analyze the particles out-of-plane motion and observe, for certain orientations of the driving force, significant differences in the out-of-plane displacement depending on particle size. Therefore, taking advantage of both the in-plane and out-of-plane motion of the particles, it is possible to achieve the simultaneous fractionation of a polydisperse suspension into multiple streams.
Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability
Authors: Li Zhenhai , Kono Hidetoshi 
Published: August 2016

AbstractNucleosome breathing potentially increases the DNA exposure, which in turn recruits DNA-binding protein and regulates gene transcription. Numerous studies have shown the critical roles of N-terminal tails of histones H3 and H4 in gene expression; however, few studies have focused on the H2A C-terminal tail. Here we present thorough computational studies on a single nucleosome particle showing the linker DNA closing and opening, which is thought to be nucleosome breathing. With our simulation, the H2A C-terminal and H3 N-terminal tails were found to modulate the nucleosome conformation differently. The H2A C-terminal tail regulates nucleosome conformation by binding to linker DNA at different locations, whereas the H3 N-terminal tail regulates linker DNA by binding to it in different patterns. Further MD simulation on tail truncated structures corroborates this analysis. These findings replenish our understanding of the histone tail regulation mechanism on atomic level.
Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets
Authors: Li Lianwei , Ma Zhanshan 
Published: August 2016

AbstractThe human microbiome project (HMP) has made it possible to test important ecological theories for arguably the most important ecosystem to human health—the human microbiome. Existing limited number of studies have reported conflicting evidence in the case of the neutral theory; the present study aims to comprehensively test the neutral theory with extensive HMP datasets covering all five major body sites inhabited by the human microbiome. Utilizing 7437 datasets of bacterial community samples, we discovered that only 49 communities (less than 1%) satisfied the neutral theory, and concluded that human microbial communities are not neutral in general. The 49 positive cases, although only a tiny minority, do demonstrate the existence of neutral processes. We realize that the traditional doctrine of microbial biogeography “Everything is everywhere, but the environment selects” first proposed by Baas-Becking resolves the apparent contradiction. The first part of Baas-Becking doctrine states that microbes are not dispersal-limited and therefore are neutral prone, and the second part reiterates that the freely dispersed microbes must endure selection by the environment. Therefore, in most cases, it is the host environment that ultimately shapes the community assembly and tip the human microbiome to niche regime.