bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thirty-two essential questions for understanding the social–ecological system of forage fish: the case of pacific herring
Authors: Levin Phillip S. , Francis Tessa B. , Taylor Nathan G. 
Published: May 2016

Abstract
Forage fishes are ecologically and economically important low trophic level species, and in recent years interest in their biology and management has intensified. Pacific Herring are emblematic of the management issues facing forage species—they are central components of the Northeast Pacific pelagic food web and support important commercial fisheries. In addition, the importance of Herring to indigenous peoples have made them cultural keystone species. We employed a participatory process to promote collaborative priority-setting for this critical forage species. Working with managers, the fisheries industry, indigenous peoples, and scientists, we co-constructed a conceptual model of the Pacific Herring social–ecological system () in the Northeast Pacific. We then identified a set of questions, that, if answered, would significantly increase our ability to sustainably manage the Herring . Our objective was to generate a road map for scientists who wish to conduct useful forage fish research, for resource managers who wish to develop new research efforts that could fill critical gaps, and for public agencies and private foundations seeking to prioritize funding on forage fish issues in the Pacific. With this socio-cultural centrality comes complexity for fisheries management. Our participatory process highlighted the value of conceptualizing the full SES, overcame disciplinary differences in scientific approaches, research philosophy, and language, and charted a path forward for future research and management for forage species.
Simulation of water content distributions in degenerated human intervertebral discs
Authors: Zhu Qiaoqiao , Gao Xin , Brown Mark D. , Temple H. Thomas , Gu Weiyong 
Published: May 2016

ABSTRACTThe objective of this study was to investigate the spatial and temporal variations of water content in intervertebral discs during degeneration and repair processes. We hypothesized that the patterns of water content distribution in the discs are related to the intensity patterns observed in T2‐weighted MRI images. Water content distributions in the mildly (e.g., 80% viable cells in the disc, 2.3% decrease in disc height) and moderately (e.g., 40% viable cells in the disc, 9.3% decrease in disc height) degenerated discs were predicted using a finite element model. The variation of water content in the degenerated discs treated with three biological therapies (i.e., increasing the cell density in the nucleus pulposus [Case I], increasing glycosaminoglycan synthesis rate in the nucleus pulposus [Case II], and decreasing glycosaminoglycan degradation rate in the nucleus pulposus [Case III]) were also predicted. It was found that two patterns of water content distributions, a horizontal region with lower water content at the mid‐axial plane of nucleus pulposus and a spot with higher water content at the posterior region, were shown during the degeneration progress for the disc simulated in this study. These two patterns disappeared after treatment in Case I, but in Case II and Case III. The implication of these patterns for the horizontal gray band and high intensity zone in T2‐weighted MRI images was discussed. This study provided new guidance to develop a novel method for diagnosing disc degeneration and assessing outcomes of biological therapies with MRI techniques. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:147–153, 2017.
The impact of damage accumulation on the kinetics of network strength recovery for a physical polymer gel subjected to shear deformation
Authors: Thornell Travis L. , Subramaniam Krithika , Erk Kendra A. 
Published: May 2016

ABSTRACTShear rheophysical experiments were used to quantify the kinetics of strength recovery of model thermoreversible polymer gels that were fractured and ultimately sheared to different total magnitudes of strain (700 and 4000%) before resting for set periods of time. Relationships between the amount of strength recovered and the normalized ratio of resting times to characteristic relaxation times were developed. It was found that gels displayed fully healed networks within timescales that were 2–3 orders of magnitude greater than the gel's characteristic relaxation time. Gels deformed to 700% applied strain either healed slower at lower gel concentrations as compared to experiments at larger applied strains due to possible viscous heating, or healed faster from incomplete fracture propagation for higher gel concentrations. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys.2016,54, 1693–1701
It takes a team: reflections on insecticide discoveries, toxicological problems and enjoying the unexpected
Authors: Wing Keith D 
Published: May 2016

AbstractAbsorption/distribution/metabolism/excretion (ADME)‐related studies are mandatory in agrochemical development/registration, but can also play a valuable role in the discovery process. In combination with target‐site potency, bioavailability/ADME characteristics determine agrochemical bioactivity and selectivity, and these concerns can dictate the fate of a discovery lead area. Bioavailability/ADME research was critical to the eventual commercialization of three different insecticide chemistries examined in this paper. In one situation, improved systemicity in anthranilic diamides was required to expand pest spectrum. In another, ADME tools were needed to improve the selective toxicity and non‐target safety of sodium channel blocker insecticides. Finally, differential ADME characteristics of two classes of hormone agonists dictated differential insecticidal activity, and were useful in optimizing the dibenzoylhydrazine ecdysone agonists. ADME discovery research will help companies to advance novel, efficacious and selective agrochemicals, but organizational patience and a desire to understand lead areas in depth are required. © 2016 Society of Chemical Industry
Modelling the effects of malaria infection on mosquito biting behaviour and attractiveness of humans
Authors: Abboubakar H. , Buonomo B. , Chitnis N. 
Published: May 2016

Abstract
We develop and analyse a deterministic population-based ordinary differential equation of malaria transmission to consider the impact of three common assumptions of malaria models: (1) malaria infection does not change the attractiveness of humans to mosquitoes; (2) exposed mosquitoes (infected with malaria but not yet infectious to humans) have the same biting rate as susceptible mosquitoes; and (3) mosquitoes infectious to humans have the same biting rate as susceptible mosquitoes. We calculate the basic reproductive number,

$$R_0$$

R
0

, for this model and show the existence of a transcritical bifurcation at

$$R_0=1$$

R
0

=
1

, in common with most epidemiological models. We further show that for some sets of parameter values, this bifurcation can be backward (subcritical). We show with numerical simulations that increasing the relative attractiveness of infectious humans, increases

$$R_0$$

R
0

but reduces the equilibrium prevalence of infectious humans; decreasing the biting rate of exposed mosquitoes increases

$$R_0$$

R
0

and the equilibrium prevalence of infectious humans and mosquitoes; and increasing the biting rate of infectious mosquitoes has no impact on

$$R_0$$

R
0

or the equilibrium prevalence of infectious humans, but decreases the infectious prevalence of infectious mosquitoes. These analyses of a simple malaria model show that common assumptions around the relative attractiveness of infectious humans and the relative biting rates of exposed and infectious mosquitoes can have substantial and counter-intuitive effects on malaria transmission dynamics.
Alcoholysis of Starch to Produce Alkyl Polyglycosides with Sub‐Critical Isooctyl Alcohol
Authors: Zou Mihua , Chen Jinyang , Wang Yingdi , Li Mingli , Zhang Chao , Yang Xuanyu 
Published: May 2016

AbstractAlkyl polyglycosides are a type of green non‐ionic surfactants, and are synthesized from starch and isooctyl alcohol with a new eco‐friendly one‐step sub‐critical alcoholysis with the temperature ranging from 240 to 320 °C and autogenous pressure. Yellow alkyl polyglycosides were obtained through the oxidative decoloration of alcoholysis products at a temperature 80 °C for 2 h with a 5 % weight content of hydrogen peroxide. The alkyl polyglycoside product was determined to be isooctyl glucoside with HPLC, IR and NMR. The CMC and HLB of the produced isooctyl glucoside were 2.5 g/L and 17, respectively. With the weight ratio of isooctyl alcohol to starch at 10, a temperature of 260 °C and a reaction time of 2 h, the yield of isooctyl glucoside can attain 132.21 % versus a theoretical yield (defined as the final mass of isooctyl glycoside/initial mass of starch) of 183 %.
Cavitation structures formed during the collision of a sphere with an ultra-viscous wetted surface
Authors: Mansoor M. M. , Marston J. O. , Uddin J. , Christopher G. , Zhang Z. , Thoroddsen S. T. 
Published: May 2016

We investigate the inception of cavitation and resulting structures when a sphere collides with a solid surface covered with a layer of non-Newtonian liquid having a kinematic viscosity of up to${\it\nu}_{0}=20\,000\,000$cSt. We show the existence of shear-stress-induced cavitation during sphere approach towards the base wall (i.e. the pressurization stage) in ultra-viscous films using a synchronized dual-view high-speed imaging system. For the experimental parameters employed, liquids having viscoelastic properties of$De\geqslant O(1)$are shown to enable sphere rebound without any prior contact with the solid wall. Cavitation by depressurization (i.e. during rebound) in such non-contact cases is observed to onset after a noticeable delay from when the minimum gap distance is reached. Also, the cavities created originate from remnant bubbles, being the remains of the primary bubble entrapment formed by the lubrication pressure of the air during film entry. Cases where physical contact occurs (contact cases) in 10 000 cSt${\leqslant}{\it\nu}_{0}\leqslant 1000\,000$cSt films produce cavities attached to the base wall, which extend into an hourglass shape. In contrast, strikingly different structures occur in the most viscous liquids due to the disproportionality in radial expansion and longitudinal extension along the cavity length. Horizontal shear rates calculated using particle image velocimetry (PIV) measurements show the apparent fluid viscosity to vary substantially as the sphere approaches and rebounds away from the base wall. A theoretical model based on the lubrication assumption is solved for the squeeze flow in the regime identified for shear-induced cavity events, to investigate the criterion for cavity inception in further detail.
On a conservative Bayesian method of inferring extinction
Authors: Alroy John 
Published: May 2016

AbstractFew methods exist that put a posterior probability on the hypothesis that a thing is gone forever given its sighting history. A recently proposed Bayesian method is highly accurate but aggressive, generating many near-zero or near-one probabilities of extinction. Here I explore a Bayesian method called the agnostic equation that makes radically different assumptions and is much more conservative. The method assumes that the overall prior probability of extinction is 50% and that slices of the prior are exponentially distributed across the time series. The conditional probability of the data given survival is based on a simple, long-known combinatorial expression that captures the chance all presences would fall at random before or within the last sighting’s interval (L) given that they could fall anywhere. The same equation is used to compute the conditional probability given extinction at the start of each intervali, that is, the chance that all sightings would fall before or withinLgiven that none could equal or postdatei. The conditional probability is zero for all hypothesized extinction intervals throughL. Bayes’s theorem is then used to compute the posterior extinction probability. It is noted that recycling the mean posterior for a population as a prior improves the method’s accuracy. The agnostic equation differs from an earlier, related one, because it explicitly includes a term to represent the hypothesis of survival, and it therefore does not assume that the species has necessarily gone extinct within the sampling window. Simulations demonstrate that the posterior extinction probabilities are highly accurate when considered as a suite but individually indecisive, rarely approaching one. This property is advantageous whenever inferring extinction would have dangerous consequences. The agnostic method is therefore advocated in cases where conservative estimates are desired.
Regular-equivalence of 2-knot diagrams and sphere eversions
Authors: TAKASE MASAMICHI , TANAKA KOKORO 
Published: May 2016

AbstractFor each diagramDof a 2-knot, we provide a way to construct a new diagramD′ of the same knot such that any sequence of Roseman moves betweenDandD′ necessarily involves branch points. The proof is done by developing the observation that no sphere eversion can be lifted to an isotopy in 4-space.
Type-specific photoreceptor loss in pigeons after disruption of parasympathetic control of choroidal blood flow by the medial subdivision of the nucleus of Edinger–Westphal
Authors: REINER A. , WONG T.T. , NAZOR C.C. , DEL MAR N. , FITZGERALD M.E.C. 
Published: May 2016

AbstractThe medial part of the nucleus of Edinger–Westphal (EWM) in birds mediates light-regulated adaptive increases in choroidal blood flow (ChBF). We sought to characterize the effect of loss of EWM-mediated ChBF regulation on photoreceptor health in pigeons housed in either moderate intensity diurnal or constant light (CL). Photoreceptor abundance following complete EWM destruction was compared to that following a lesion in the pupil control circuit (as a control for spread of EWM lesions to the nearby pupil-controlling lateral EW) or following no EW damage. Birds were housed post-lesion in a 12 h 400 lux light/12 h dark light cycle for up to 16.5 months, or in constant 400 lux light for up to 3 weeks. Paraformaldehyde–glutaraldehyde fixed eyes were embedded in plastic, sectioned, slide-mounted, and stained with toluidine blue/azure II. Blinded analysis of photoreceptor outer segment abundance was performed, with outer segment types distinguished by oil droplet tint and laminar position. Brains were examined histologically to assess lesion accuracy. Disruption of pupil control had no adverse effect on photoreceptor outer segment abundance in either diurnal light or CL, but EWM destruction led to 50–60% loss of blue/violet cone outer segments in both light conditions, and a 42% loss of principal cone outer segments in CL. The findings indicate that adaptive regulation of ChBF by the EWM circuit plays a role in maintaining photoreceptor health and mitigates the harmful effect of light on photoreceptors, especially short wavelength-sensitive cone photoreceptors.
Magnetic field controlled charge density wave coupling in underdoped YBa2Cu3O6+x
Authors: Chang J. , Blackburn E. , Ivashko O. , Holmes A. T. , Christensen N. B. , Hücker M. , Liang Ruixing , Bonn D. A. , Hardy W. N. , Rütt U. , Zimmermann M. v. , Forgan E. M. , Hayden S M 
Published: May 2016

AbstractThe application of magnetic fields to layered cuprates suppresses their high-temperature superconducting behaviour and reveals competing ground states. In widely studied underdoped YBa2Cu3O6+x (YBCO), the microscopic nature of field-induced electronic and structural changes at low temperatures remains unclear. Here we report an X-ray study of the high-field charge density wave (CDW) in YBCO. For hole dopings ∼0.123, we find that a field (B∼10 T) induces additional CDW correlations along the CuO chain (b-direction) only, leading to a three-dimensional (3D) ordered state along this direction at B∼15 T. The CDW signal along the a-direction is also enhanced by field, but does not develop an additional pattern of correlations. Magnetic field modifies the coupling between the CuO2 bilayers in the YBCO structure, and causes the sudden appearance of the 3D CDW order. The mirror symmetry of individual bilayers is broken by the CDW at low and high fields, allowing Fermi surface reconstruction, as recently suggested.
Marginal zone B cells exacerbate endotoxic shock via interleukin-6 secretion induced by Fcα/μR-coupled TLR4 signalling
Authors: Honda Shin-ichiro , Sato Kazuki , Totsuka Naoya , Fujiyama Satoshi , Fujimoto Manabu , Miyake Kensuke , Nakahashi-Oda Chigusa , Tahara-Hanaoka Satoko , Shibuya Kazuko , Shibuya Akira 
Published: May 2016

AbstractMarginal zone (MZ) B cells produce a first wave of antibodies for protection from blood-borne pathogens. However, the role of MZ B cells in inflammatory responses has not been elucidated. Here we show that MZ B cells produce pro-inflammatory cytokines, such as interleukin-6 (IL-6), and exacerbate systemic inflammatory responses to lipopolysaccharide (LPS). After intravenous injection of LPS or E. coli, mice deficient in MZ B cells or IL-6 only in MZ B cells have attenuated systemic inflammatory responses and prolonged survival compared with wild-type mice. LPS directly stimulates MZ B cells via Toll-like receptor 4 (TLR4) and MyD88 pathways for IL-6 production. Furthermore, TLR4 requires physical and functional association with Fcα/μR (CD351) for its oligomer formation, NF-κB signalling and IL-6 production from MZ B cells; this association is responsible for systemic inflammatory responses and endotoxic shock. These results reveal a pro-inflammatory role of MZ B cells in endotoxic shock.
Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota
Authors: Audebert Christophe , Even Gaël , Cian Amandine ,   The Blastocystis Investigation Group, Safadi Dima El , Certad Gabriela , Delhaes Laurence , Pereira Bruno , Nourrisson Céline , Poirier Philippe , Wawrzyniak Ivan , Delbac Frédéric , Morelle Christelle , Bastien Patrick , Lachaud Laurence , Bellanger Anne-Pauline , Botterel Françoise , Candolfi Ermanno , Desoubeaux Guillaume , Morio Florent , Pomares Christelle , Rabodonirina Meja , Loywick Alexandre , Merlin Sophie , Viscogliosi Eric , Chabé Magali 
Published: May 2016

AbstractAlterations in the composition of commensal bacterial populations, a phenomenon known as dysbiosis, are linked to multiple gastrointestinal disorders, such as inflammatory bowel disease and irritable bowel syndrome, or to infections by diverse enteric pathogens. Blastocystis is one of the most common single-celled eukaryotes detected in human faecal samples. However, the clinical significance of this widespread colonization remains unclear, and its pathogenic potential is controversial. To address the issue of Blastocystis pathogenicity, we investigated the impact of colonization by this protist on the composition of the human gut microbiota. For that purpose, we conducted a cross-sectional study including 48 Blastocystis-colonized patients and 48 Blastocystis-free subjects and performed an Ion Torrent 16S rDNA gene sequencing to decipher the Blastocystis-associated gut microbiota. Here, we report a higher bacterial diversity in faecal microbiota of Blastocystis colonized patients, a higher abundance of Clostridia as well as a lower abundance of Enterobacteriaceae. Our results contribute to suggesting that Blastocystis colonization is usually associated with a healthy gut microbiota, rather than with gut dysbiosis generally observed in metabolic or infectious inflammatory diseases of the lower gastrointestinal tract.
HIV-1 Infection-Induced Suppression of the Let-7i/IL-2 Axis Contributes to CD4+ T Cell Death
Authors: Zhang Yijun , Yin Yue , Zhang Shaoying , Luo Haihua , Zhang Hui 
Published: May 2016

AbstractThe mechanisms underlying HIV-1-mediated CD4+ T cell depletion are highly complicated. Interleukin-2 (IL-2) is a key cytokine that maintains the survival and proliferation of activated CD4+ T cells. IL-2 levels are disturbed during HIV-1 infection, but the underlying mechanism(s) requires further investigation. We have reported that cellular microRNA (miRNA) let-7i upregulates IL-2 expression by targeting the promoter TATA-box region, which functions as a positive regulator. In this study, we found that HIV-1 infection decreases the expression of let-7i in CD4+ T cells by attenuating its promoter activity. The reduced let-7i miRNA expression led to a decline in IL-2 levels. A let-7i mimic increased IL-2 expression and subsequently enhanced the resistance of CD4+ T cells to HIV-1-induced apoptosis. By contrast, the blockage of let-7i with a specific inhibitor resulted in elevated CD4+ T cell apoptosis during HIV-1 infection. Furthermore, by knocking down the expression of IL-2, we found that the let-7i-mediated CD4+ T cell resistance to apoptosis during HIV-1 infection was dependent on IL-2 signaling rather than an alternative CD95-mediated cell-death pathway. Taken together, our findings reveal a novel pathway for HIV-1-induced dysregulation of IL-2 cytokines and depletion of CD4+ T-lymphocytes.
Colorectal cancer risk genes are functionally enriched in regulatory pathways
Authors: Lu Xi , Cao Mingming , Han Su , Yang Youlin , Zhou Jin 
Published: May 2016

AbstractColorectal cancer (CRC) is a common complex disease caused by the combination of genetic variants and environmental factors. Genome-wide association studies (GWAS) have been performed and reported some novel CRC susceptibility variants. However, the potential genetic mechanisms for newly identified CRC susceptibility variants are still unclear. Here, we selected 85 CRC susceptibility variants with suggestive association P < 1.00E-05 from the National Human Genome Research Institute GWAS catalog. To investigate the underlying genetic pathways where these newly identified CRC susceptibility genes are significantly enriched, we conducted a functional annotation. Using two kinds of SNP to gene mapping methods including the nearest upstream and downstream gene method and the ProxyGeneLD, we got 128 unique CRC susceptibility genes. We then conducted a pathway analysis in GO database using the corresponding 128 genes. We identified 44 GO categories, 17 of which are regulatory pathways. We believe that our results may provide further insight into the underlying genetic mechanisms for these newly identified CRC susceptibility variants.