bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning of Active Binocular Vision in a Biomechanical Model of the Oculomotor System
Authors: Klimmasch Lukas , Lelais Alexander , Lichtenstein Alexander , Shi Bertram E. , Triesch Jochen 
Published: July 2017

AbstractWe present a model for the autonomous learning of active binocular vision using a recently developed biome-chanical model of the human oculomotor system. The model is formulated in the Active Efficient Coding (AEC) framework, a recent generalization of classic efficient coding theories to active perception. The model simultaneously learns how to efficiently encode binocular images and how to generate accurate vergence eye movements that facilitate efficient encoding of the visual input. In order to resolve the redundancy problem arising from the actuation of the eyes through antagonistic muscle pairs, we consider the metabolic costs associated with eye movements. We show that the model successfully learns to trade off vergence accuracy against the associated metabolic costs, producing high fidelity vergence eye movements obeying Sherrington’s law of reciprocal innervation.
Pavement cells and the topology puzzle
Authors: Carter Ross , Sánchez-Corrales Yara E. , Grieneisen Verônica A. , Marée Athanasius F. M. 
Published: July 2017

AbstractD’Arcy Thompson emphasised the importance of surface tension as a potential driving force in establishing cell shape and topology within tissues. Leaf epidermal pavement cells grow into jigsaw-piece shapes, highly deviating from such classical forms. We investigate the topology of developingArabidopsisleaves composed solely of pavement cells. Image analysis of around 50,000 cells reveals a clear and unique topological signature, deviating from previously studied epidermal tissues. This topological distribution is however established early during leaf development, already before the typical pavement cell shapes emerge, with topological homestasis maintained throughout growth and unaltered between division and maturation zones. Simulating graph models, we identify a heuristic cellular division rule that reproduces the observed topology. Our parsimonious model predicts how and when cells effectively place their division plane with respect to their neighbours. We verify the predicted dynamics through in vivo tracking of 800 mitotic events, and conclude that the distinct topology is not a direct consequence of the jigsaw-like shape of the cells, but rather owes itself to a strongly life-history-driven process, with limited impact from cell surface mechanics.Summary statementDevelopment of theArabidopsisleaf epidermis topology is driven by deceptively simple rules of cell division, independent of surface tension, cell size and, often complex, cell shape.
Combining multiple functional annotation tools increases coverage of metabolic annotation
Authors: Griesemer Marc , Kimbrel Jeffrey , Zhou Carol , Navid Ali , D’haeseleer Patrik 
Published: July 2017

ABSTRACTGenome-scale metabolic modeling is a cornerstone of systems biology analysis of microbial organisms and communities, yet these genome-scale modeling efforts are invariably based on incomplete functional annotations. Annotated genomes typically contain 30-50% of genes without functional annotation, severely limiting our knowledge of the “parts lists” that the organisms have at their disposal. These incomplete annotations may be sufficient to derive a model of a core set of well-studied metabolic pathways that support growth in pure culture. However, pathways important for growth on unusual metabolites exchanged in complex microbial communities are often less understood, resulting in missing functional annotations in newly sequenced genomes. Here, we present results on a comprehensive reannotation of 27 bacterial reference genomes, focusing on enzymes with EC numbers annotated by KEGG, RAST, EFICAz, and the BRENDA enzyme database, and on membrane transport annotations by TransportDB, KEGG and RAST. Our analysis shows that annotation using multiple tools can result in a drastically larger metabolic network reconstruction, adding on average 40% more EC numbers, 3-8 times more substrate-specific transporters, and 37% more metabolic genes. These results are even more pronounced for bacterial species that are more phylogenetically distant from well-studied model organisms such as E. coli.
Adipose‐derived mesenchymal stem cells therapy for acute kidney injury induced by ischemia‐reperfusion in a rat model
Authors: Zhang Jian‐Bo , Wang Xiao‐Qiao , Lu Guo‐Lin , Huang Huan‐Sen , Xu Shi‐Yuan 
Published: July 2017

SummaryAcute kidney injury (AKI) represents a group of complicated syndromes with a high mortality rate. The administration of adipose‐derived mesenchymal stem cells (ADMSCs) has been tested as a possible treatment method for AKI. The long‐term evaluation of AKI induced by ischemia/reperfusion (IR) and the probable renal protection of ADMSCs are limited. In this study we have established a rat AKI model induced by IR and investigated the possible protective effects of ADMSCs. Adult Sprague‐Dawley (SD) rats were divided into three groups (n = 6/each group). The MOCK group was as the normal control. Rats in the IR‐AKI and IR‐AKI+ADMSCs groups were subjected to IR injury by clamping both renal pedicles for 40 minutes. Rats in the MOCK and IR‐AKI groups were injected with PBS via the tail vein as negative treatment controls. Rats in the IR‐AKI+ADMSCs group received ADMSCs therapy (2 × 106 cells were injected into the rats via the tail vein). We found that ADMSC transplantation restored the pathologic morphology induced by IR‐AKI to normal compared with the MOCK group, suggesting the reparative function of ADMSCs in kidney tissues. Compared with IR‐induced AKI alone, ADMSC treatment significantly decreased the number of apoptotic cells, the level of total urinary protein and serum creatinine, the expression of pro‐inflammatory cytokines (IL‐6, TNF‐α, IL‐1β, IFN‐γ, TNF‐α, IFN‐γ, and TGF‐β), and the inflammation‐associated proteins (HGF and SDF1), but increased the expression of the anti‐inflammatory cytokine, IL‐10, and the anti‐apoptotic regulator, Bcl‐2. Our data have indicated that ADMSC transplantation may protect against IR‐induced AKI by anti‐apoptotic and anti‐inflammatory effects.
AQP4‐knockout aggravation of isoprenaline‐induced myocardial injury is mediated by p66Shc and endoplasmic reticulum stress
Authors: Cheng Yusi , Chao Jie , Dai Dezai , Dai Yin , Zhu Dongdong , Liu Bicheng 
Published: July 2017

SummaryAquaporin 4 (AQP4) is a type of water channel protein that maintains the water balance of cardiomyocytes. However, the physiological role of AQP4 in cardiovascular disease is poorly understood. We wanted to explore whether p66Shc and endoplasmic reticulum stress participates in AQP4 knockout (KO)‐mediated cardiac injury. There were two types of mice: AQP4 knockout and wild‐type mice. Each type was randomly divided into three groups: Control group, isoprenaline stimulation group (ISO, 1 mg/kg, s.c., 5 days), and apocynin treatment group (APO, 100 mg/kg, p.o., 3 days). H9c2 rat cardiomyocytes were cultured for RNA interference of AQP4. Results showed increased left ventricular weight index and more severe myocardial inflammation were induced in AQP4 knockout mice relative to wild‐type mice, accompanied by significantly increased levels of the oxidative stress biomarkers MDA and NOX4. In addition, the expressions of p66Shc, ER stress markers PERK, GRP78 and CHOP and proinflammatory factors such as ETA, IL6 and TNFα were upregulated in the myocardium of AQP4 knockout mice or AQP4 siRNA treated cardiomyocytes, whereas CASQ2 was downregulated. ISO stimulation aggravated these abnormalities, which were significantly attenuated by apocynin. This study showed that AQP4 knockout mice were susceptible to cardiac injury induced by ISO. The mechanism was closely connected with p66Shc and proinflammatory factors. Endoplasmic reticulum stress was also involved in the pathological process.
‘Hidden identities’: perceptions of sexual identity in Beijing
Authors: Miles‐Johnson Toby , Wang Yurong 
Published: July 2017

AbstractThis article draws upon responses given by volunteers who work in the Beijing LGBT Centre regarding perceptions of sexual identity, and how Chinese culture affects hidden or open sexual identities of Chinese lesbian and gay people in this region. The insights gained from those working carefully to create social change offers an important and original contribution to the field of gay and lesbian studies in China. The findings indicate the volunteers at the Beijing LGBT Centre are frustrated by the lack of acceptance of non‐heterosexual relationships among Chinese culture and society, and by the disregard of lesbian gay and bisexual (LGB) people by the Chinese government. The findings also illustrate stigmatization of homosexuality in China is enacted in structural terms (such as in the lack of policy, legislation and positive endorsement by governmental and socio‐political organizations), public expression (such as negative attitudes, beliefs or reactions towards LGB people) and internalized repression (through fear of stigmatization, and subsequent abuse due to negative societal attitudes and discrimination). Influenced by the Chinese tradition of conforming to group values, the findings from this study show that volunteers at the Beijing LGBT Centre believe LGB people in China are generally hesitant to disclose their sexual identities, and reject the idea that there had been a collective shift in Chinese culture regarding increased acceptance of LGB people. It also finds volunteers at the LGBT Centre in Beijing blame Chinese culture for its lack of acceptance of non‐heterosexual relationships, and state stigmatization of homosexuality in China is due to deep‐rooted cultural homophobia.
Does scatter‐hoarding of seeds benefit cache owners or pilferers?
Authors: GU Haifeng , ZHAO Qingjian , ZHANG Zhibin 
Published: July 2017

AbstractThe scatter‐hoarding behavior of granivorous rodents plays an important role in seed dispersal and seedling regeneration of trees, as well as the evolution of several well‐known mutualisms between trees and rodents in forest ecosystems. Because it is difficult to identify seed hoarders and pilferers under field conditions by traditional methods, the full costs incurred and benefits accrued by scatter‐hoarding have not been fully evaluated in most systems. By using infrared radiation camera tracking and seed tagging, we investigated the benefits and losses of scatter‐hoarded seeds (Camellia oleifera) for 3 sympatric rodent species (Apodemus draco, Niviventer confucianus and Leopoldamys edwardsi) in a subtropical forest of Southwest China during 2013 to 2015. We established the relationships between the rodents and the seeds at the individual level. For each rodent species, we calculated the cache recovery rate of cache owners, as well as conspecific and interspecific pilferage rates. We found that all 3 sympatric rodent species had a cache recovery advantage with rates that far exceeded average pilferage rates over a 30‐day tracking period. The smallest species (A. draco) showed the highest rate of scatter‐hoarding and the highest recovery advantage compared with the other 2 larger species (N. confucianus and L. edwardsi). Our results suggest that scatter‐hoarding benefits cache owners in food competition, supporting the pilferage avoidance hypothesis. Therefore, scatter‐hoarding behavior should be favored by natural selection, and plays a significant role in species coexistence of rodent community and in the formation of mutualism between seeds and rodents in forest ecosystems.
Insular mammalian fauna dynamics and paleogeography: A lesson from the Western Mediterranean islands
Authors: PALOMBO Maria Rita 
Published: July 2017

AbstractSince the time of Darwin (1859) and Wallace (1869), islands have been regarded by scientists as a prime target for scrutinizing the forces that may influence evolution and diversification and important elements in biogeographic studies. This research aims to scrutinize whether and to what extent the composition and structure of past mammal insular faunas and their changes through time may provide sound clues for inferring the paleogeographical evolution of a region. As a case study, I critically analyzed the dynamics shown by the Plio–Pleistocene mammalian fauna of 3 Western Mediterranean insular districts, the Balearic Islands, Sardinia and Sicily, each characterized by its own peculiar paleobiogeographical evolutionary history. The revision of faunas and the critical analysis of the dispersal ability of the ancestors of island settlers have allowed hypothesizing on the time and mode of island colonization. The results obtained confirm that the early isolation of the Balearic Islands from the mainland led to the establishment of an endemic fauna since the pre‐Messinian Miocene (?Astaracian European Land Mammal Age, MN7/8), and that Sardinia has definitely been isolated since the Pliocene, although dispersal events led to some faunal turnovers during the Pleistocene. In addition, the results suggest for Sicily a complex, still imperfectly disentangled history of alternate phases of complete separation and sporadic, more or less difficult connections with southern Italy.
A physiologically based pharmacokinetic modelling approach to predict buprenorphine pharmacokinetics following intravenous and sublingual administration
Authors: Kalluri Hari V. , Zhang Hongfei , Caritis Steve N. , Venkataramanan Raman 
Published: July 2017

AimsOpioid dependence is associated with high morbidity and mortality. Buprenorphine (BUP) is approved by the Food and Drug Administration to treat opioid dependence. There is a lack of clear consensus on the appropriate dosing of BUP due to interpatient physiological differences in absorption/disposition, subjective response assessment and other patient comorbidities. The objective of the present study was to build and validate robust physiologically based pharmacokinetic (PBPK) models for intravenous (IV) and sublingual (SL) BUP as a first step to optimizing BUP pharmacotherapy.MethodsBUP‐PBPK modelling and simulations were performed using SimCyp® by incorporating the physiochemical properties of BUP, establishing intersystem extrapolation factors‐based in vitro–in‐vivo extrapolation (IVIVE) methods to extrapolate in vitro enzyme activity data, and using tissue‐specific plasma partition coefficient estimations. Published data on IV and SL‐BUP in opioid‐dependent and non‐opioid‐dependent patients were used to build the models. Fourteen model‐naïve BUP‐PK datasets were used for inter‐ and intrastudy validations.ResultsThe IV and SL‐BUP‐PBPK models developed were robust in predicting the multicompartment disposition of BUP over a dosing range of 0.3–32 mg. Predicted plasma concentration–time profiles in virtual patients were consistent with reported data across five single‐dose IV, five single‐dose SL and four multiple dose SL studies. All PK parameter predictions were within 75–137% of the corresponding observed data. The model developed predicted the brain exposure of BUP to be about four times higher than that of BUP in plasma.ConclusionThe validated PBPK models will be used in future studies to predict BUP plasma and brain concentrations based on the varying demographic, physiological and pathological characteristics of patients.
Diminazene aceturate prevents nephropathy by increasing glomerular ACE2 and AT2 receptor expression in a rat model of type1 diabetes
Authors: Goru Santosh Kumar , Kadakol Almesh , Malek Vajir , Pandey Anuradha , Sharma Nisha , Gaikwad Anil Bhanudas 
Published: July 2017

Background and PurposeOne of the protective actions of angiotensin converting enzyme‐2 (ACE2) is the inactivation of angiotensin II. Expression and activity of ACE2 was reduced in glomeruli of diabetic patients and in animal models of diabetes. Recently the potential role of recombinant ACE2 administration in preventing diabetic nephropathy (DN) has been shown. Here we have tested the effects of the ACE2 activator, diminazene aceturate (DIZE), in a model of DN.Experimental ApproachMale Wistar rats were rendered diabetic using a single dose of streptozotocin (55 mg·kg−1, i.p.). After 4 weeks, diabetic animals were divided into experimental groups and treated with DIZE, at a low dose (5 mg·kg−1·day−1), a high dose (15 mg·kg−1·day−1) and the high dose with of the AT2 receptor antagonist PD123319 (10 mg·kg−1·day−1). At the end of the treatment , kidneys from all the groups were collected and processed separately for glomerular isolation, protein isolation, mRNA extraction and for immunohistochemical studies.Key ResultsTreatment with DIZE restored ACE2 expression in glomeruli and increased expression of AT2 receptors in whole kidney and isolated glomeruli of diabetic animals. DIZE administration reduced angiotensin II levels and increased angiotensin‐(1–7) levels in diabetic kidney. However, PD123319 treatment reversed all these actions of DIZE.Conclusions and ImplicationsDIZE treatment reduced diabetes‐induced renal damage as shown by reduction of fibrosis and apoptosis. These protective actions of DIZE were blocked by the AT2 receptor antagonist. Taken together, these results suggest that DIZE protected against DN through the ACE2/angiotensin‐(1–7)/ AT2 receptor axis.
Inhibition of hyaluronan synthesis attenuates pulmonary hypertension associated with lung fibrosis
Authors: Collum Scott D , Chen Ning‐Yuan , Hernandez Adriana M , Hanmandlu Ankit , Sweeney Heather , Mertens Tinne C J , Weng Tingting , Luo Fayong , Molina Jose G , Davies Jonathan , Horan Ian P , Morrell Nick W , Amione‐Guerra Javier , Al‐Jabbari Odeaa , Youker Keith , Sun Wenchao , Rajadas Jayakumar , Bollyky Paul L , Akkanti Bindu H , Jyothula Soma , Sinha Neeraj , Guha Ashrith , Karmouty‐Quintana Harry 
Published: July 2017

Background and PurposeGroup III pulmonary hypertension (PH) is a highly lethal and widespread lung disorder that is a common complication in idiopathic pulmonary fibrosis (IPF) where it is considered to be the single most significant predictor of mortality. While increased levels of hyaluronan have been observed in IPF patients, hyaluronan‐mediated vascular remodelling and the hyaluronan‐mediated mechanisms promoting PH associated with IPF are not fully understood.Experimental ApproachExplanted lung tissue from patients with IPF with and without a diagnosis of PH was used to identify increased levels of hyaluronan. In addition, an experimental model of lung fibrosis and PH was used to test the capacity of 4‐methylumbeliferone (4MU), a hyaluronan synthase inhibitor to attenuate PH. Human pulmonary artery smooth muscle cells (PASMC) were used to identify the hyaluronan‐specific mechanisms that lead to the development of PH associated with lung fibrosis.Key ResultsIn patients with IPF and PH, increased levels of hyaluronan and expression of hyaluronan synthase genes are present. Interestingly, we also report increased levels of hyaluronidases in patients with IPF and IPF with PH. Remarkably, our data also show that 4MU is able to inhibit PH in our model either prophylactically or therapeutically, without affecting fibrosis. Studies to determine the hyaluronan‐specific mechanisms revealed that hyaluronan fragments result in increased PASMC stiffness and proliferation but reduced cell motility in a RhoA‐dependent manner.Conclusions and ImplicationsTaken together, our results show evidence of a unique mechanism contributing to PH in the context of lung fibrosis.
Response of unconfined turbidity current to relay‐ramp topography: insights from process‐based numerical modelling
Authors: Ge Zhiyuan , Nemec Wojciech , Gawthorpe Rob L. , Rotevatn Atle , Hansen Ernst W. M. 
Published: July 2017

AbstractThis natural‐scale experimental study combines structural modelling of soft‐linked normal‐fault relays with a CFD (computational fluid dynamics) numerical simulation of a range of unconfined turbidity currents overrunning the relay‐system topography. The flow, released from an upslope inlet gate 2000‐m wide and 50‐m to 100‐m high, rapidly expands and adjusts its thickness, velocity and sediment load to the substrate slope of 1.5°. A lower initial sediment concentration or smaller thickness renders the quasi‐steady flow slower and its sediment‐transport capacity lower. A 3D pattern of large interfering Kelvin‐Helmholtz waves causes fluctuations of the local flow velocity magnitude and sediment concentration. Four zones of preferential sediment deposition are recognized: a near‐gate zone of abrupt flow expansion and self‐regulation; a flow‐transverse zone on the counter‐slope of fault footwall edges; a flow‐transverse zone at the fault‐scarp toes and a similar transverse zone near the crest of the hanging wall counter‐slopes. The sand deposited on the counter‐slope tends to be re‐entrained and fed back to the current by a secondary reverse underflow. The spatial extent and sediment accumulation capacity of depozones depend upon the released current volume. The impact of relay system on an overrunning current depends upon the fault separation distance and stage of tectonic evolution. An early‐stage relay system, with small vertical displacement and little overlap of faults, is bypassed by the current with minimum flow disturbance and no pronounced deposition. An advanced‐stage system, with greater fault displacement and overlap, gives a similar hydraulic effect as a single fault segment if the fault separation is small. If the separation is relatively large, the flow tends to be internally redirected sideways from the ramp into the hanging wall synclinal depressions. Since normal‐fault relays are common features in extensional basins, the study bears important implications for turbiditic slope‐fan models and for the spatial sand prediction in subsurface exploration of faulted submarine slopes.
Assessment of colorectal length using the electromagnetic capsule tracking system: a comparative validation study in healthy subjects
Authors: Mark E. B. , Poulsen J. L. , Haase A. M. , Frøkjær J. B. , Schlageter V. , Scott S. M. , Krogh K. , Drewes A. M. 
Published: July 2017

AbstractAimWe aimed to determine colorectal length with the 3D‐Transit system by describing a ‘centreline’ of capsule movement and comparing it with known anatomy, as determined by magnetic resonance imaging (MRI). Further, we aimed to test the day‐to‐day variation of colorectal length assessed with the system.MethodThe 3D‐Transit system consists of electromagnetic capsules that can be tracked as they traverse the gastrointestinal tract. Twenty‐five healthy subjects were examined with both 3D‐Transit and MRI. Another 21 healthy subjects were examined with 3D‐Transit on two consecutive days.ResultsComputation of colorectal length from capsule passage was possible for 60 of the 67 3D‐Transit recordings. The length of the colorectum measured with MRI and 3D‐Transit was 95 (75–153) cm and 99 (77–147) cm, respectively (P = 0.15). The coefficient of variation (CV) between MRI and 3D‐Transit was 7.8%. Apart from the caecum/ascending colon being 26% (P = 0.002) shorter on MRI, there were no other differences in total or segmental colorectal lengths between methods (all P > 0.05). The length of the colorectum measured with 3D‐Transit on two consecutive days was 102 (73–119) cm and 103 (75–123) cm (P = 0.67). The CV between days was 7.3%.ConclusionThe 3D‐Transit system allows accurate and reliable determination of colorectal length compared with MRI‐derived colorectal length and between days. Antegrade or retrograde capsule movement relative to this centreline, as well as the length and speed of movements, may be determined by future studies to allow better classification and treatment in patients with dysmotility.