bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling the evolution of transcription factor binding preferences in complex eukaryotes
Authors: Rosanova Antonio , Colliva Alberto , Osella Matteo , Caselle Michele 
Published: August 2017

AbstractTranscription factors (TFs) exert their regulatory action by binding to DNA with specific sequence preferences. However, different TFs can partially share their binding sequences due to their common evolutionary origin. This “redundancy” of binding defines a way of organizing TFs in “motif families” by grouping TFs with similar binding preferences. Since these ultimately define the TF target genes, the motif family organization entails information about the structure of transcriptional regulation as it has been shaped by evolution. Focusing on the human TF repertoire, we show that a one-parameter evolutionary model of the Birth-Death-Innovation type can explain the TF empirical repartition in motif families, and allows to highlight the relevant evolutionary forces at the origin of this organization. Moreover, the model allows to pinpoint few deviations from the neutral scenario it assumes: three over-expanded families (including HOX and FOX genes), a set of “singleton” TFs for which duplication seems to be selected against, and a higher-than-average rate of diversification of the binding preferences of TFs with a Zinc Finger DNA binding domain. Finally, a comparison of the TF motif family organization in different eukaryotic species suggests an increase of redundancy of binding with organism complexity.
A Neural Marker of Obsessive-Compulsive Disorder from Whole-Brain Functional Connectivity
Authors: Takagi Yu , Sakai Yuki , Lisi Giuseppe , Yahata Noriaki , Abe Yoshinari , Nishida Seiji , Nakamae Takashi , Morimoto Jun , Kawato Mitsuo , Narumoto Jin , Tanaka Saori C 
Published: August 2017

AbstractObsessive-compulsive disorder (OCD) is a common psychiatric disorder with a lifetime prevalence of 2–3%. Recently, brain activity in the resting state is gathering attention for exploring altered functional connectivity in psychiatric disorders. Although previous resting-state functional magnetic resonance imaging studies investigated the neurobiological abnormalities of patients with OCD, there are concerns that should be addressed. One concern is the validity of the hypothesis employed. Most studies used seed-based analysis of the fronto-striatal circuit, despite the potential for abnormalities in other regions. A hypothesis-free study is a promising approach in such a case, while it requires researchers to handle a dataset with large dimensions. Another concern is the reliability of biomarkers derived from a single dataset, which may be influenced by cohort-specific features. Here, our machine learning algorithm identified an OCD biomarker that achieves high accuracy for an internal dataset (AUC = 0.81; N = 108) and demonstrates generalizability to an external dataset (AUC = 0.70; N = 28). Our biomarker was unaffected by medication status, and the functional networks contributing to the biomarker were distributed widely, including the frontoparietal and default mode networks. Our biomarker has the potential to deepen our understanding of OCD and to be applied clinically.
Diversity, distribution and different habitat use among the tropical freshwater eels of genus Anguilla
Authors: Arai Takaomi , Abdul Kadir Siti Raudah 
Published: August 2017

AbstractAlong with the mysteries of their ecology, freshwater eels have fascinated biologists for centuries. However, information concerning species diversity, geographic distribution, and life histories of the tropical anguillid eels in the Indo-Pacific region are highly limited. Comprehensive research on the species composition, distribution and habitat use among tropical anguillid eels in the Peninsular Malaysia were conducted for four years. A total of 463 specimens were collected in the northwestern peninsular area. The dominant species was A. bicolor bicolor constituting of 88.1% of the total eels, the second one was A. bengalensis bengalensis at 11.7%, while A. marmorata was the least abundant at 0.2%. A. bicolor bicolor was widely distributed from upstream to downstream areas of the rivers. In comparison, A. bengalensis bengalensis preferred to reside from the upstream to midstream areas with no tidal zones, cooler water temperatures and higher elevation areas. The habitat preference might be different between sites due to inter-species interactions and intra-specific plasticity to local environmental conditions. These results suggest that habitat use in the tropical anguillid eels might be more influenced by ambient environmental factors, such as salinity, temperature, elevation, river size and carrying capacity, than ecological competition, such as interspecific competition.
An unusual role for the phytyl chains in the photoprotection of the chlorophylls bound to Water-Soluble Chlorophyll-binding Proteins
Authors: Agostini Alessandro , Palm Daniel M. , Schmitt Franz-Josef , Albertini Marco , Valentin Marilena Di , Paulsen Harald , Carbonera Donatella 
Published: August 2017

AbstractWater-Soluble Chlorophyll Proteins (WSCPs) fromBrassicaceaeare non-photosynthetic proteins which tetramerize upon binding four chlorophyll (Chl) molecules. The bound Chls are highly photostable, despite the lack of bound carotenoids known, in Chl-containing photosynthetic proteins, to act as singlet oxygen and Chl triplet (3Chl) quenchers. Although the physiological function of WSCPs is still unclear, it is likely to be related to their biochemical stability and their resistance to photodegradation. To get insight into the origin of this photostability, the properties of the3Chl generated in WSCPs upon illumination were investigated. We found that, unlike the excited singlet states, which are excitonic states, the triplet state is localized on a single Chl molecule. Moreover, the lifetime of the3Chl generated in WSCPs is comparable to that observed in other Chl-containing systems and is reduced in presence of oxygen. In contrast to previous observations, we found that WSCP actually photosensitizes singlet oxygen with an efficiency comparable to that of Chl in organic solvent. We demonstrated that the observed resistance to photooxidation depends on the conformation of the phytyl moieties, which in WSCP are interposed between the rings of Chl dimers, hindering the access of singlet oxygen to the oxidizable sites of the pigments.
Environmental concern-based site screening of carbon dioxide geological storage in China
Authors: Cai Bofeng , Li Qi , Liu Guizhen , Liu Lancui , Jin Taotao , Shi Hui 
Published: August 2017

AbstractEnvironmental impacts and risks related to carbon dioxide (CO2) capture and storage (CCS) projects may have direct effects on the decision-making process during CCS site selection. This paper proposes a novel method of environmental optimization for CCS site selection using China’s ecological red line approach. Moreover, this paper established a GIS based spatial analysis model of environmental optimization during CCS site selection by a large database. The comprehensive data coverage of environmental elements and fine 1 km spatial resolution were used in the database. The quartile method was used for value assignment for specific indicators including the prohibited index and restricted index. The screening results show that areas classified as having high environmental suitability (classes III and IV) in China account for 620,800 km2 and 156,600 km2, respectively, and are mainly distributed in Inner Mongolia, Qinghai and Xinjiang. The environmental suitability class IV areas of Bayingol Mongolian Autonomous Prefecture, Hotan Prefecture, Aksu Prefecture, Hulunbuir, Xilingol League and other prefecture-level regions not only cover large land areas, but also form a continuous area in the three provincial-level administrative units. This study may benefit the national macro-strategic deployment and implementation of CCS spatial layout and environmental management in China.
TRPC6 counteracts TRPC3-Nox2 protein complex leading to attenuation of hyperglycemia-induced heart failure in mice
Authors: Oda Sayaka , Numaga-Tomita Takuro , Kitajima Naoyuki , Toyama Takashi , Harada Eri , Shimauchi Tsukasa , Nishimura Akiyuki , Ishikawa Tatsuya , Kumagai Yoshito , Birnbaumer Lutz , Nishida Motohiro 
Published: August 2017

AbstractExcess production of reactive oxygen species (ROS) caused by hyperglycemia is a major risk factor for heart failure. We previously reported that transient receptor potential canonical 3 (TRPC3) channel mediates pressure overload-induced maladaptive cardiac fibrosis by forming stably functional complex with NADPH oxidase 2 (Nox2). Although TRPC3 has been long suggested to form hetero-multimer channels with TRPC6 and function as diacylglycerol-activated cation channels coordinately, the role of TRPC6 in heart is still obscure. We here demonstrated that deletion of TRPC6 had no impact on pressure overload-induced heart failure despite inhibiting interstitial fibrosis in mice. TRPC6-deficient mouse hearts 1 week after transverse aortic constriction showed comparable increases in fibrotic gene expressions and ROS production but promoted inductions of inflammatory cytokines, compared to wild type hearts. Treatment of TRPC6-deficient mice with streptozotocin caused severe reduction of cardiac contractility with enhancing urinary and cardiac lipid peroxide levels, compared to wild type and TRPC3-deficient mice. Knockdown of TRPC6, but not TRPC3, enhanced basal expression levels of cytokines in rat cardiomyocytes. TRPC6 could interact with Nox2, but the abundance of TRPC6 was inversely correlated with that of Nox2. These results strongly suggest that Nox2 destabilization through disrupting TRPC3-Nox2 complex underlies attenuation of hyperglycemia-induced heart failure by TRPC6.
Red-edge position of habitable exoplanets around M-dwarfs
Authors: Takizawa Kenji , Minagawa Jun , Tamura Motohide , Kusakabe Nobuhiko , Narita Norio 
Published: August 2017

AbstractOne of the possible signs of life on distant habitable exoplanets is the red-edge, which is a rise in the reflectivity of planets between visible and near-infrared (NIR) wavelengths. Previous studies suggested the possibility that the red-edge position for habitable exoplanets around M-dwarfs may be shifted to a longer wavelength than that for Earth. We investigated plausible red-edge position in terms of the light environment during the course of the evolution of phototrophs. We show that phototrophs on M-dwarf habitable exoplanets may use visible light when they first evolve in the ocean and when they first colonize the land. The adaptive evolution of oxygenic photosynthesis may eventually also use NIR radiation, by one of two photochemical reaction centers, with the other center continuing to use visible light. These “two-color” reaction centers can absorb more photons, but they will encounter difficulty in adapting to drastically changing light conditions at the boundary between land and water. NIR photosynthesis can be more productive on land, though its evolution would be preceded by the Earth-type vegetation. Thus, the red-edge position caused by photosynthetic organisms on habitable M-dwarf exoplanets could initially be similar to that on Earth and later move to a longer wavelength.
A simple quantum voting scheme with multi-qubit entanglement
Authors: Xue Peng , Zhang Xin 
Published: August 2017

AbstractWe propose a simple quantum voting scenario with a set of pairs of particles in a multi-particle entangled state. This scenario is suitable for large scale general votings. We also provide a proof of security of our scheme against the most general type of attack by generalizing Shor and Preskill’s proof of security of the other schemes.
Endocannabinoid tone is higher in healthy lean South Asian than white Caucasian men
Authors: Kantae Vasudev , Nahon Kimberly J. , Straat Maaike E. , Bakker Leontine E. H. , Harms Amy C. , van der Stelt Mario , Hankemeier Thomas , Jazet Ingrid M. , Boon Mariëtte R. , Rensen Patrick C. N. 
Published: August 2017

AbstractSouth Asians have a higher risk to develop obesity and related disorders compared to white Caucasians. This is likely in part due to their lower resting energy expenditure (REE) as related with less energy-combusting brown adipose tissue (BAT). Since overactivation of the endocannabinoid system is associated with obesity and low BAT activity, we hypothesized that South Asians have a higher endocannabinoid tone. Healthy lean white Caucasian (n = 10) and South Asian (n = 10) men were cold-exposed to activate BAT. Before and after cooling, REE was assessed and plasma was collected for analysis of endocannabinoids and lipids. At thermoneutrality, South Asians had higher plasma levels of 2-arachidonoylglycerol (2-AG; 11.36 vs 8.19 pmol/mL, p < 0.05), N-arachidonylethanolamine (AEA; 1.04 vs 0.89 pmol/mL, p = 0.05) and arachidonic acid (AA; 23.24 vs 18.22 nmol/mL, p < 0.001). After pooling of both ethnicities, plasma 2-AG but not AEA positively correlated with triglycerides (R2 = 0.32, p < 0.05) and body fat percentage (R2 = 0.18, p < 0.05). Interestingly, AA negative correlated with REE (R2 = 0.46, p < 0.001) and positively with body fat percentage (R2 = 0.33, p < 0.01). Cooling increased endocannabinoids. In conclusion, South Asian compared to white Caucasian men have higher endocannabinoid tone. This suggests that endocannabinoids may, at least in part, underlie the disadvantageous metabolic phenotype of South Asians later in life.
Comprehensive validation of T- and B-cell deficiency in rag1-null zebrafish: Implication for the robust innate defense mechanisms of teleosts
Authors: Tokunaga Yumie , Shirouzu Masamichi , Sugahara Ryota , Yoshiura Yasutoshi , Kiryu Ikunari , Ototake Mitsuru , Nagasawa Takahiro , Somamoto Tomonori , Nakao Miki 
Published: August 2017

Abstractrag1−/− zebrafish have been employed in immunological research as a useful immunodeficient vertebrate model, but with only fragmentary evidence for the lack of functional adaptive immunity. rag1-null zebrafish exhibit differences from their human and murine counterparts in that they can be maintained without any specific pathogen-free conditions. To define the immunodeficient status of rag1−/− zebrafish, we obtained further functional evidence on T- and B-cell deficiency in the fish at the protein, cellular, and organism levels. Our developed microscale assays provided evidence that rag1−/− fish do not possess serum IgM protein, that they do not achieve specific protection even after vaccination, and that they cannot induce antigen-specific CTL activity. The mortality rate in non-vaccinated fish suggests that rag1−/− fish possess innate protection equivalent to that of rag1+/− fish. Furthermore, poly(I:C)-induced immune responses revealed that the organ that controls anti-viral immunity is shifted from the spleen to the hepatopancreas due to the absence of T- and B-cell function, implying that immune homeostasis may change to an underside mode in rag-null fish. These findings suggest that the teleost relies heavily on innate immunity. Thus, this model could better highlight innate immunity in animals that lack adaptive immunity than mouse models.
Decoupling between the response of coral calcifying fluid pH and calcification to ocean acidification
Authors: Comeau S. , Cornwall C. E. , McCulloch M. T. 
Published: August 2017

AbstractEvaluating the factors responsible for differing species-specific sensitivities to declining seawater pH is central to understanding the mechanisms via which ocean acidification (OA) affects coral calcification. We report here the results of an experiment comparing the responses of the coral Acropora yongei and Pocillopora damicornis to differing pH levels (8.09, 7.81, and 7.63) over an 8-week period. Calcification of A. youngei was reduced by 35% at pH 7.63, while calcification of P. damicornis was unaffected. The pH in the calcifying fluid (pHcf) was determined using δ11B systematics, and for both species pHcf declined slightly with seawater pH, with the decrease being more pronounced in P. damicornis. The dissolved inorganic carbon concentration at the site of calcification (DICcf) was estimated using geochemical proxies (B/Ca and δ11B) and found to be double that of seawater DIC, and increased in both species as seawater pH decreased. As a consequence, the decline of the saturation state at the site of calcification (Ωcf) with OA was partially moderated by the DICcf increase. These results highlight that while pHcf, DICcf and Ωcf are important in the mineralization process, some corals are able to maintain their calcification rates despite shifts in their calcifying fluid carbonate chemistry.
Cross-buckled structures for stretchable and compressible thin film silicon solar cells
Authors: Nam Jiyoon , Seo Bowook , Lee Youngjoo , Kim Dong-Ho , Jo Sungjin 
Published: August 2017

AbstractIncreasing interests in stretchable electronic devices have resulted in vigorous research activities, most of which are focused on structural configurations. Diverse structural configurations are available for stretchability, including stiff-island, serpentine, and buckled structures. With easily deformable shapes and simple fabrication processes, buckled structures have the potential to realize stretchability. However, conventional buckled structures exhibit stretchability only in a single-axis direction. In the present study, a new type of cross-buckled structure, which can overcome the limitations of conventional buckled structures is developed. The stretchable thin film solar cells with the cross-buckled structure showed stable mechanical and electrical characteristics under both stretching and compressing conditions. The cross-buckled structure for stretchable electronic devices is expected to broaden the fields of wearable electronics, stretchable displays, and biocompatible applications.
Polarization invariant plasmonic nanostructures for sensing applications
Authors: Tobing Landobasa Y. M. , Goh Geat-Yee , Mueller Aaron D. , Ke Lin , Luo Yu , Zhang Dao-Hua 
Published: August 2017

AbstractOptics-based sensing platform working under unpolarized light illumination is of practical importance in the sensing applications. For this reason, sensing platforms based on localized surface plasmons are preferred to their integrated optics counterparts for their simple mode excitation and inexpensive implementation. However, their optical response under unpolarized light excitation is typically weak due to their strong polarization dependence. Herein, the role of rotational symmetry for realizing robust sensing platform exhibiting strong optical contrast and high sensitivity is explored. Specifically, gammadion and star-shaped gold nanostructures with different internal and external rotational symmetries are fabricated and studied in detail, from which their mode characteristics are demonstrated as superposition of their constituent longitudinal plasmons that are in conductive coupling with each other. We demonstrate that introducing and increasing internal rotational symmetry would lead to the enhancement in optical contrast up to ~3x under unpolarized light illumination. Finally, we compare the sensing performances of rotationally symmetric gold nanostructures with a more rigorous figure-of-merit based on sensitivity, Q-factor, and spectral contrast.
Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form
Authors: Seok Jong Hyeon , Kim Jeongwon , Lee Dan Bi , Cho Ki Joon , Lee Ji-Hye , Bae Garam , Chung Mi Sook , Kim Kyung Hyun 
Published: August 2017

AbstractMutational changes that mostly occur at the head region of hemagglutinin (HA) lead to the emergence of new epidemic influenza viruses, whereas HA antigens have been modified to generate broadly neutralizing antibodies toward highly conserved epitopes in the HA stem. Interestingly, a recent analysis of serum antibody repertoires showed that broadly neutralizing antibodies bind to HA monomer at a conserved region occluded at the intermonomer interface of HA trimer and confer protection in animal models. We showed previously that the recombinant HA ectodomain from a pandemic strain A/Korea/01/2009 was monomeric in solution and crystal structure. In order to examine the potential antigenicity of a monomeric form, we designed HA monomer that incorporates mutations to destabilize trimer conformations. Starting with the HA trimer from a seasonal strain A/Thailand/CU44/2006, mutations were introduced at the intermonomer interface, Ser199 of HA1 and Gly47, Arg75, Phe88, Val91, and Arg106 of HA2. Two mutants, F88E and V91W, were characterized to form a monomer and their double mutant F88E/V91W monomer was selected as an antigen. Animal studies showed that the HA monomer induced protective immunity in vivo, comparable to the trimer, albeit low antibody titers in sera.
Meniscal Ossicles as micro-CT Imaging Biomarker in a Rodent Model of Antigen-Induced Arthritis: a Synchrotron-Based X-ray Pilot Study
Authors: Donato Sandro , Pacilè Serena , Colombo Federico , Garrovo Chiara , Monego Simeone Dal , Macor Paolo , Tromba Giuliana , Biffi Stefania 
Published: August 2017

AbstractIt is increasingly recognized that early detection of bone erosion plays an important role in the overall evaluation of rheumatoid arthritis and in the choice of the correct treatment approach. Since an appropriate use of imaging biomarkers in preclinical settings offers the prospect of smaller and optimized sample size, in the present study we define an anatomical imaging biomarker that could be objectively measured from micro-CT imaging data as an indicator of bone erosion in arthritis process. The well-characterized antigen-induced arthritis (AIA) model in rats was used. The animals were divided into 2 groups: arthritic disease control and arthritic having been administrated with the tumor necrosis factor alpha-blocking agent (Humira). Rats were sacrificed in the acute phase of AIA; peripheral blood and synovial tissue were collected for assessment of arthritis.Ex vivomicro-CT tomography of knee joints was performed at the Elettra synchrotron light source (Trieste, Italy). Overall, results from this study suggest that use of high-resolution micro-CT analysis coupled with meniscal ossicles bone parameters quantification provide a powerful combination to enhance data interpretation and assessment of disease-modifying drugs in an animal model of arthritis.
Trophic isotopic carbon variation increases with pond’s hydroperiod: Evidence from an Austral ephemeral ecosystem
Authors: Dalu Tatenda , Wasserman Ryan J. , Froneman P. William , Weyl Olaf L. F. 
Published: August 2017

AbstractTrophic variation in food web structure occurs among and within ecosystems. The magnitude of variation, however, differs from system to system. In ephemeral pond ecosystems, temporal dynamics are relatively more important than in many systems given that hydroperiod is the ultimate factor determining the presence of an aquatic state. Here, using stable isotopes we tested for changes in trophic chain length and shape over time in these dynamic aquatic ecosystems. We found that lower and intermediate trophic level structure increased over time. We discuss these findings within the context of temporal environmental stability. The dynamic nature of these ephemeral systems seems to be conducive to greater levels of intermediate and lower trophic level diversity, with omnivorous traits likely being advantageous.