bluuebunny/crossref_metadata_2025 huggingface dataset:
Uncovering challenges to sustainability of AZA Animal Programs by evaluating the outcomes of breeding and transfer recommendations with PMCTrack
Authors: Faust Lisa J. , Long Sarah T. , Perišin Kaitlyn , Simonis Juniper L.
Published: January 2019

The Association of Zoos and Aquariums (AZA) cooperatively manages Species Survival Plans® to create demographically and genetically viable populations. SSPs issue animal‐specific recommendations to participating institutions via Breeding and Transfer Plans (BTPs). Fulfillment of recommendations is a crucial step in maintaining viable populations, but there have been no comprehensive evaluations of the system. Using PMCTrack, a database of over 110,000 breeding and transfer recommendations issued from over 200 SSPs from 1999 to 2013, we analyzed fulfillment of recommendations. Action‐based recommendations had lower rates: Breed With recommendations were fulfilled at a rate of 20.0% before the next BTP, Send To at 56.8%, Do Not Breed at 95.7%, and Hold at 92.9%. We used generalized (logistic) mixed‐effects model regressions to evaluate the impact of biological, management, and programmatic factors on fulfillment rates. For all recommendation types, there was significant variation in fulfillment among Programs and within Programs among BTPs. Out of 80 potential hypothesized fixed effects (20 factors * 4 recommendation types), only 20 effects (25%) were statistically significant. Rates were strongly influenced by temporal variables, generally increasing over time and as programs get older. Notably, the amount of time between BTPs was the only variable that significantly predicted fulfillment of all recommendation types. Many additional factors at the individual animal and institutional level may effect fulfillment rates and should be the subject of future analysis. Our results illustrate the utility of PMCTrack and indicate that improvements to the viability of SSPs will need to address multiple biological and management challenges.
Topological defect lines and renormalization group flows in two dimensions
Authors: Chang Chi-Ming , Lin Ying-Hsuan , Shao Shu-Heng , Wang Yifan , Yin Xi
Published: January 2019

Abstract

We consider topological defect lines (TDLs) in two-dimensional conformal field theories. Generalizing and encompassing both global symmetries and Verlinde lines, TDLs together with their attached defect operators provide models of fusion categories without braiding. We study the crossing relations of TDLs, discuss their relation to the ’t Hooft anomaly, and use them to constrain renormalization group flows to either conformal critical points or topological quantum field theories (TQFTs). We show that if certain non-invertible TDLs are preserved along a RG flow, then the vacuum cannot be a non-degenerate gapped state. For various massive flows, we determine the infrared TQFTs completely from the consideration of TDLs together with modular invariance.
Four-dimensional black hole entropy from F-theory
Authors: Grimm Thomas W. , het Lam Huibert , Mayer Kilian , Vandoren Stefan
Published: January 2019

Abstract

We study the central charges and levels of a two-dimensional N = (0, 4) superconformal field theory describing four-dimensional BPS black holes in F-theory. These arise from D3-branes wrapping a curve in the base of an elliptically fibered Calabi-Yau threefold times a circle, and probe a transverse Taub-NUT space. The near horizon geometry of these D3-branes is AdS3 × S3
/ℤ
m
, where m is the NUT charge. Starting from a six-dimensional supergravity effective action we compute three-dimensional Chern-Simons terms to deduce the central charges and levels. We find that it is crucial to integrate out an infinite tower of massive Kaluza-Klein states on S3
/ℤ
m
to match the expected microscopic results. The induced corrections turn out to contribute at leading order to the central charges and levels, which in turn determine the black hole entropy.
Perturbative four-point functions in planar $$ \mathcal{N}=4 $$ SYM From hexagonalization
Authors: Coronado Frank
Published: January 2019

Abstract

We use hexagonalization to compute four-point correlation functions of long BPS operators with special R-charge polarizations. We perform the computation at weak coupling and show that at any loop order our correlators can be expressed in terms of single value polylogarithms with uniform and maximal transcendentality. As a check of our computation we extract nine-loop OPE data and compare it against sum rules of (squared) structures constants of non-protected exchanged operators described by hundreds of Bethe solutions.
Negative effects of acorns on the wood mouse Apodemus speciosus
Authors: Shimada Takuya , Saitoh Takashi
Published: January 2019

Antinutritional effects of acorns and tannic acid on the Japanese wood mouse Apodemus speciosus were examined in the laboratory. The first feeding experiment was conducted for 15 days using three types of diet: control diet (laboratory chow for mice), acorns of Quercus serrata (QS), and acorns of Q. mongolica var. grosseserrata (QM), which differ in tannin content (control, tannin free; QS, 2.7% tannic acid equivalent; QM, 8.5%). Six and one of eight mice died in the QM and QS groups, respectively, whereas all mice survived in good health in the control group. Body weight in the QM and QS groups decreased as much as 23.6% and 16.8% in the first 5 days, respectively, whereas that in the control group did not change significantly. Dry matter intake in the QM group was 50.0% and 38.7% less than that in the control and QS, respectively. Apparent dry matter digestibility was not different among the diets, but apparent nitrogen digestibility did differ between the two acorn groups (QM, −17.5%; QS, 12.0%). The logistic regression analyses revealed that the survival of mice was synergistically influenced by both dry matter intake and apparent nitrogen digestibility. In the second experiment, wood mice fed the tannin‐free formula diet, which is nutritionally matched to QS and QM acorns except for the tannin, did not suffer antinutritional effects, whereas mice fed the tannin‐supplemented formula diets suffered body weight loss and negative nitrogen digestibility. These results indicate that the tannins in acorns could cause serious damage to the wood mouse, which may rely on acorns as a usual diet. Plausible hypotheses explaining how the wood mice could overcome the deleterious effects of the acorns are discussed.
The role of gravity in the prediction of the circular hydraulic jump radius for high-viscosity liquids
Authors: Wang Yunpeng , Khayat Roger E.
Published: January 2019

The free-surface flow formed by a circular jet impinging on a stationary disk is analysed theoretically. We develop a simple and coherent model to predict the location and height of the jump for high-viscosity liquids. The study explores the effect of gravity in the supercritical flow. The formulation reduces to a problem, involving only one parameter: $\unicode[STIX]{x1D6FC}=Re^{1/3}Fr^{2}$, where $Re$ and $Fr$ are the Reynolds and Froude numbers based on the flow rate and the jet radius. We show that the jump location coincides with the singularity in the thin-film equation when gravity is included, suggesting that the jump location can be determined without the knowledge of downstream flow conditions such as the jump height, the radius of the disk, which corroborates earlier observations in the case of type I circular hydraulic jumps. Consequently, there is no need for a boundary condition downstream to determine the jump radius. Our results corroborate well existing measurements and numerical simulation. Our predictions also confirm the constancy of the Froude number $Fr_{J}$ based on the jump radius and height as suggested by the measurements of Duchesne et al. (Europhys. Lett., vol. 107, 2014, 54002). We establish theoretically the conditions for $Fr_{J}$ to remain independent of the flow rate. The subcritical flow and the height of the hydraulic jump are sought subject to the thickness at the edge of the disk, comprising contributions based on the capillary length and minimum flow energy. The thickness at the edge of the disk appears to be negligibly small for high-viscosity liquids.
Drag reduction in turbulent flows along a cylinder by streamwise-travelling waves of circumferential wall velocity
Authors: Zhao Ming-Xiang , Huang Wei-Xi , Xu Chun-Xiao
Published: January 2019

Drag reduction at the external surface of a cylinder in turbulent flows along the axial direction by circumferential wall motion is studied by direct numerical simulations. The circumferential wall oscillation can lead to drag reduction due to the formation of a Stokes layer, but it may also result in centrifugal instability, which can enhance turbulence and increase drag. In the present work, the Reynolds number based on the reference friction velocity and the nominal thickness of the boundary layer is 272. A map describing the relationship between the drag-reduction rate and the control parameters, namely, the angular frequency $\unicode[STIX]{x1D714}^{+}=\unicode[STIX]{x1D714}\unicode[STIX]{x1D708}/u_{\unicode[STIX]{x1D70F}0}^{2}$ and the streamwise wavenumber $k_{x}^{+}=k_{x}\unicode[STIX]{x1D708}/u_{\unicode[STIX]{x1D70F}0}$, is obtained at the oscillation amplitude of ${A^{+}=A/u}_{\unicode[STIX]{x1D70F}0}=16$, where $u_{\unicode[STIX]{x1D70F}0}$ is the friction velocity of the uncontrolled flow and $\unicode[STIX]{x1D708}$ is the kinematic viscosity of the fluid. The maximum drag-reduction rate and the maximum drag-increase rate are both approximately 48 %, which are respectively attained at $(\unicode[STIX]{x1D714}^{+},k_{x}^{+})=$ (0.0126, 0.0148) and (0.0246, 0.0018). The drag-reduction rate can be scaled well with the help of the effective thickness of the Stokes layer. The drag increase is observed in a narrow triangular region in the frequency–wavenumber plane. The vortices induced by the centrifugal instability become the primary coherent structure in the near-wall region, and they are closely correlated with the high skin friction. In these drag-increase cases, the effective control frequency or wavenumber is crucial in scaling the drag-increase rate. As the wall curvature normalised by the boundary layer thickness becomes larger, the drag-increase region in the $(\unicode[STIX]{x1D714}^{+},k_{x}^{+})$ plane as well as the maximum drag-increase rate also become larger. Net energy saving with a considerable drag-reduction rate is possible when reducing the oscillation amplitude. At $A^{+}=4$, a net energy saving of 18 % can be achieved with a drag-reduction rate of 25 % if only the power dissipation due to viscous stress is taken into account in an ideal actuation system.
Rhizomatic Influence: The Antigenealogy of Glissant and Deleuze
Authors: Allar Neal A.
Published: January 2019

To identify literary influences is, conventionally, to build a genealogy—to, in Salman Rushdie’s words, “name one’s parents.” But can this family-tree view of literary influence hold up in postcolonial literature—a body of work that has so thoroughly deconstructed concepts of genealogy? This article turns to a pivotal case of “influence” in postcolonial Francophone literature and philosophy: among Édouard Glissant and Gilles Deleuze and Félix Guattari. The latter two writers are thought to have influenced Glissant’s thinking with their concept of the “rhizome,” but the rhizome directly counters such genealogizing as this “influence” would imply. In fact, this article shows, Glissant develops his own version of the rhizome from his very earliest writings, particularly his first poems. An analysis of them alongside Glissant’s subsequent essays and Deleuze and Guattari’s own writing, allows for a more complicated, multidirectional—that is, rhizomatic—theory of postcolonial influence.
Justification, Conformity, and the Norm of Belief
Authors: Fassio Davide
Published: January 2019

According to a popular view in contemporary epistemology, a belief is justified if, and only if, it amounts to knowledge. Upholders of this view also hold that knowledge is the fundamental norm governing belief and that conforming to this norm is both necessary and sufficient for justification. I argue against the claim that mere norm conformity is sufficient for justification. Rather, justification requires norm conformity for sufficient undefeated reasons. An important consequence is the rejection of the claim that conformity to the norm of belief is necessary and sufficient for epistemic justification. I illustrate some interesting consequences of this result.
Trichomonas vaginalisandMycoplasma hominis: new tales of two old friends
Authors: Dessì Daniele , Margarita Valentina , Cocco Anna Rita , Marongiu Alessandra , Fiori Pier Luigi , Rappelli Paola
Published: January 2019

Trichomonas vaginalisis an anaerobic protist, responsible for the most prevalent non-viral sexually transmitted infection in humans. One of the most intriguing aspects ofT. vaginalispathobiology is the complex relationship with intracellular microbial symbionts: a group of dsRNA viruses belonging to family ofTotiviridae(T. vaginalisvirus), and eubacteria belonging to theMycoplasmagenus, in particularMycoplasma hominis. Both microorganisms seem to strongly influence the lifestyle ofT. vaginalis, suggesting a role of the symbiosis in the high variability of clinical presentation and sequelae during trichomoniasis. In the last few years many aspects of this unique symbiotic relationship have been investigated:M. hominisresides and replicates in the protozoan cell, andT. vaginalisis able to pass the bacterial infection to both mycoplasma-free protozoan isolates and human epithelial cells;M. hominissynergistically upregulates the proinflammatory response of human monocytes toT. vaginalis. Furthermore, the influence ofM. hominisoverT. vaginalismetabolism and physiology has been characterized. The identification of a novel species belonging to the class ofMollicutes(CandidatusMycoplasma girerdii) exclusively associated toT. vaginalisopens new perspectives in the research of the complex series of events taking place in the multifaceted world of the vaginal microbiota, both under normal and pathological conditions.
WHERE DID ALL THE PAGANS GO? THE NON-CHRISTIAN SARCOPHAGI OF FOURTH-CENTURY ROME
Authors: Couzin Robert
Published: January 2019

The number of Roman sarcophagi without explicit Christian iconography conventionally dated to the fourth century is not commensurate with any reasonable estimate of the number of well-to-do pagans. This article explores several possible explanations for the anomaly. One approach would be to attempt to correct the archaeological record by finding errors in the religious classification of monuments that exaggerate the Christian corpus, adding non-Christian sarcophagi that have escaped published inventories, or establishing a systematic misdating of pagan sarcophagi. Alternatively, the preserved monuments could be taken as an accurate reflection of original production, the shortfall implying some change in commemorative habits specific to non-Christians. The author concludes that neither of these theories is likely to reduce the pagan sarcophagus deficit substantially. Instead, the shortfall is ascribed mainly to differential rates of preservation. This hypothesis is consistent with certain medieval practices of reuse that suggest a higher probability of survival for antique sarcophagi bearing Christian imagery.
Jobb�gy, Lopes, and Reddy Receive 2018 Ambassador Awards
Authors:   AGU
Published: January 2019

Esteban Jobb�gy, Rosaly M. C. Lopes, and Christopher Reddy received the 2018 Ambassador Award at the AGU Fall Meeting Honors Ceremony, held 12 December 2018 in Washington, D. C. The award is in recognition of “outstanding contributions to one or more of the following area(s): societal impact, service to the Earth and space community, scientific leadership, and promotion of talent/career pool.”
Allometric scaling of weight to height and resulting body mass index thresholds in two Asian populations
Authors: Hood Karoline , Ashcraft Jacob , Watts Krista , Hong Sangmo , Choi Woong , Heymsfield Steven B. , Gautam Rajesh K. , Thomas Diana
Published: January 2019

Background

Body mass index (BMI) represents a normalization of weight to height and is used to classify adiposity. While the capacity of BMI as an adiposity index has been experimentally validated in Caucasians, but there has been little testing Asian populations.

Methods

To determine whether weight scales to height squared in Asian Indians across the general population and in Asian Indian tribes an allometric analysis on the power law model, W = αHβ, where W is weight (kg) and H is height (m) was performed on cross-sectional weight and height data from India (N = 43,880) collected through the Anthropological Survey of India. The database contained males 18–84 years of age spanning 161 districts of 14 states and including 33 different tribes (N = 5,549). Models were developed that were unadjusted and adjusted for tribe membership. The Korean National Health and Nutrition Examination Survey (KNHANES) was used to compare to height–weight data from the Anthropological Survey of India and to calculate BMI thresholds for obesity status using a receiver operating characteristic.

Results

The unadjusted power was β = 2.08 (s = 0.02). The power for the general population (non-tribal) was β = 2.11 (s = 0.02). Powers when adjusted for tribe ranged from 1.87 to 2.35 with 24 of the 33 tribes resulting in statistically significant (p < 0.05) differences in powers from the general population. The coefficients of the adjusted terms ranged from −0.22 to 0.26 and therefore the scaling exponent does not deviate far from 2. Thresholds for BMI classification of overweight in the KNHANES database were BMI = 21 kg/m2 (AUC = 0.89) for males 18 kg/m2 (AUC = 0.97) for females. Obesity classification was calculated as BMI = 26 kg/m2 (AUC = 0.81) and 23 kg/m2 (AUC = 0.83) for females.

Conclusions

Our study confirms that weight scales to height squared in Asian Indian males even after adjusting for tribe membership. We also demonstrate that optimal BMI thresholds are lower in a Korean population in comparison to currently used BMI thresholds. These results support the application of BMI in Asian populations with potentially lower thresholds.
Flat acoustics with soft gradient-index metasurfaces
Authors: Jin Yabin , Kumar Raj , Poncelet Olivier , Mondain-Monval Olivier , Brunet Thomas
Published: January 2019

Recently, metasurfaces have been proven to be effective and compact devices for the design of arbitrary wavefronts. Metasurfaces are planar metamaterials with a subwavelength thickness that allows wavefront shaping by introducing in-plane variations, namely, gradients, in the spatial wave response of these flat structures. Here we report a new class of acoustic gradient-index (GRIN) metasurfaces engineered from soft graded-porous silicone rubber with a high acoustic index for broadband ultrasonic three-dimensional wavefront shaping in water. The functionalities of these soft flat lenses are illustrated through various experiments, which demonstrate beam steering and beam focusing, as well as vortex beam generation in free space. These new GRIN metasurfaces may have important applications in various domains using designed ultrasonic fields (biomedical imaging, industrial non-destructive testing, contactless particle manipulation), since their fabrication is very straightforward with common polymer science engineering.
Excitation to defect-bound band edge states in two-dimensional semiconductors and its effect on carrier transport
Authors: Wang Dan , Han Dong , West Damien , Chen Nian-Ke , Xie Sheng-Yi , Tian Wei Quan , Meunier Vincent , Zhang Shengbai , Li Xian-Bin
Published: January 2019

The ionization of dopants is a crucial process for electronics, yet it can be unexpectedly difficult in two-dimensional materials due to reduced screening and dimensionality. Using first-principles calculations, here we propose a dopant ionization process for two-dimensional semiconductors where charge carriers are only excited to a set of defect-bound band edge states, rather than to the true band edge states, as is the case in three-dimensions. These defect-bound states have small enough ionization energies but large enough spatial delocalization. With a modest defect density, carriers can transport through band by such states.
Biodiversity in remnants of natural mountain forests under conservation-oriented management
Authors: Horák Jakub , Materna Jan , Halda Josef P. , Mladenović Strahinja , Bogusch Petr , Pech Pavel
Published: January 2019

The structure of forests is an important stabilizing factor regarding ongoing global climate and land use change. Biodiverse mountain forests with natural structure are one of the ecosystems most endangered by these problems. We focused on the mountain forest islands of European beech (Fagus sylvatica) and their role in the natural distribution of organisms. The study area was situated in the oldest Czech national park, Krkonoše (385 km2), which is the highest mountain ridge in the country. We studied multi-taxa (lichens, beetles and hymenopterans) responses to three hierarchical spatial levels of the environment: the topography was described by the elevation gradient; the patch structure was described by canopy openness, dead wood amounts, and Norway spruce (Picea abies) cover; and the tree level was described by species of the sampled tree and its diameter. Lichens preferred higher elevations, while insect groups responded conversely. Furthermore, insect groups were mainly influenced by the inner patch structure of beech islands. Lichens may be jeopardized due to the predicted future increase in temperatures, since they would need to shift toward higher altitudes. Insects may be mainly threatened in the future by land use changes (i.e., forest management) – as indicated by an interconnection of canopy openness and the amount of dead wood.
SOX2 participates in spermatogenesis of Zhikong scallop Chlamys farreri
Authors: Liang Shaoshuai , Liu Danwen , Li Xixi , Wei Maokai , Yu Xiaohan , Li Qi , Ma Huixin , Zhang Zhifeng , Qin Zhenkui
Published: January 2019

As an important transcription factor, SOX2 involves in embryogenesis, maintenance of stem cells and proliferation of primordial germ cell (PGC). However, little was known about its function in mature gonads. Herein, we investigated theSOX2gene profiles in testis of scallop,Chlamys farreri. The level ofC.farreri SOX2(Cf-SOX2) mRNA increased gradually along with gonadal development and reached the peak at mature stage, and was located in all germ cells, including spermatogonia, spermatocytes, spermatids and spermatozoa. Knockdown ofCf-SOX2using RNAi leaded to a mass of germ cells lost, and only a few spermatogonia retained in the nearly empty testicular acini after 21 days. TUNEL assay showed that apoptosis occurred in spermatocytes. Furthermore, transcriptome profiles of the testes were compared betweenCf-SOX2knockdown and normal scallops, 131,340 unigenes were obtained and 2,067 differential expression genes (DEGs) were identified. GO and KEGG analysis showed that most DEGs were related to cell apoptosis (casp2,casp3,casp8), cell proliferation (samd9,crebzf,iqsec1) and spermatogenesis (htt,tusc3,zmynd10,nipbl,mfge8), and enriched in p53, TNF and apoptosis pathways. Our study revealedCf-SOX2is essential in spermatogenesis and testis development ofC.farreriand provided important clues for better understanding ofSOX2regulatory mechanisms in bivalve testis.
Deducing Mucosal Pharmacokinetics and Pharmacodynamics of the Anti-HIV Molecule Tenofovir from Measurements in Blood
Authors: Govil Sachin , Katz David F.
Published: January 2019

Microbicide pharmacokinetic (PK) studies typically sample drug in luminal fluid, mucosal tissue, and blood. Blood measurements can be conducted most frequently, serially within subjects. Antiretroviral drugs, however, act against HIV in mucosal tissue/cells. We computationally modeled the extent measurements in blood can predict concentrations in tissue, focusing on the antiretroviral drug tenofovir delivered by a vaginal gel. Deterministic PK models input host and product factors and output spatiotemporal drug concentrations in luminal fluid, epithelium, stroma/host cells, and blood. Pharmacodynamic (PD) analysis referenced stroma/host cell concentrations to prophylactic values; summary metrics were time from product insertion to protection (tlag) and degree of protection (PPmax). Results incorporated host factors characteristic of population variability. Neural nets (NN) linked simulated blood PK metrics (Cmax, tmax, AUC, C24) to mucosal PK/PD metrics. The NNs delivered high-performance mapping of these multiparametric relationships. Given multi-log variability typical of biopsy data for tenofovir and other topical microbicides, results suggest downstream but higher fidelity measurements in blood could help improve determination of PK and create inferences about PD. Analysis here is for a tenofovir gel, but this approach offers promise for application to other microbicide modalities and to topical drug delivery to vaginal mucosa more generally.
Behaviors of Glioblastoma Cells in in Vitro Microenvironments
Authors: Diao Wenwen , Tong Xuezhi , Yang Cheng , Zhang Fengrong , Bao Chun , Chen Hao , Liu Liyu , Li Ming , Ye Fangfu , Fan Qihui , Wang Jiangfei , Ou-Yang Zhong-Can
Published: January 2019

Glioblastoma (GBM) is the most malignant and highly aggressive brain tumor. In this study, four types of typical GBM cell lines (LN229, SNB19, U87, U251) were cultured in a microfabricated 3-D model to study their in vitro behaviors. The 3-D in vitro model provides hollow micro-chamber arrays containing a natural collagen interface and thus allows the GBM cells to grow in the 3-D chambers. The GBM cells in this model showed specific properties on the aspects of cell morphology, proliferation, migration, and invasion, some of which were rarely observed before. Furthermore, how the cells invaded into the surrounding ECM and the corresponding specific invasion patterns were observed in details, implying that the four types of cells have different features during their development in cancer. This complex in vitro model, if applied to patient derived cells, possesses the potential of becoming a clinically relevant predictive model.
Functional and morphologic study of retinal hypoperfusion injury induced by bilateral common carotid artery occlusion in rats
Authors: Qin Yali , Ji Meiqi , Deng Tingting , Luo Dan , Zi Yingxin , Pan Lin , Wang Zhijun , Jin Ming
Published: January 2019

Retinal hypoperfusion injury is the pathophysiologic basis of ocular ischemic syndrome (OIS) which often leads to severe visual loss. In this study, we aimed to establish a rat model of retinal chronic hypoperfusion by bilateral common carotid artery occlusion (BCCAO) and observe changes in the retinal function and morphology. We found that model rats showed retinal arteriosclerosis, slight dilated retinal vein, small hemangiomas, hemorrhages, vascular segmental filling, and nonperfused areas after 2 weeks of BCCAO. In the model rats, the retinal circulation time was significantly prolonged by fluorescein fundus angiography (FFA), the latency of a and b waves was delayed and the amplitude was decreased significantly at each time point by electroretinogram (ERG), and the perfusion of the eyes continued to reduced. Morphologic and ultrastructural changes covered that the retinal ganglion cells (RGCs) presented obvious apoptosis and the thickness in the retinal layers were significantly thinner. Collectively, these findings suggested that BCCAO induced retinal hypoperfusion injury in the model rats, thus providing an ideal animal model for the study of OIS.
Memory effect of arsenic-induced cellular response and its influences on toxicity of titanium dioxide nanoparticle
Authors: Liu Su , Wu Bing , Yu Yue , Shen Zhuoyan
Published: January 2019

Toxicity of arsenic (As) has been widely characterized. However, few studies focus on whether cell responses induced by As at nontoxic concentration could be inherited and further change cell tolerance to another pollutant. In this study, human A549 and HeLa cells were exposed to As at nontoxic concentrations for 10 or 15 passages, then the cells were recovered in the cell medium without As. At 25th passage, residual As in both type of cells was completely removed through the recovery process. And no abnormity in cell viability was identified in both type of cells between control and As-treated groups. Above results indicated that As exposure-recovery treatment had limited influence on phenotype of the cells. However, gene expression profiles determined by high-throughput sequencing showed that As exposure-recovery treatment induced similar expression modification of genes related to inflammation, oxidative stress and epigenetic modulation in the A549 and HeLa cells after recovery of 10 or 15 passages, indicating that As-induced cellular responses have been partially memorized at transcriptional level. The memory effect might play key roles in increased tolerance of the A549 and HeLa cells to adverse effects (cell viability, intracellular reactive oxygen species (ROS) generation and plasma membrane damage) induced by titanium dioxide nanoparticles (as representative pollutant). This study shed new lights on toxic effects induced by As at nontoxic concentration, which is useful for risk assessment of combined effects of As and other pollutants.
Astrocytoma progression scoring system based on the WHO 2016 criteria
Authors: Li Zhen-Hang , Guan Yan-Lei , Liu Qiang , Wang Yao , Cui Run , Wang Yun-Jie
Published: January 2019

Diffuse astrocytoma (including glioblastoma) is morbid with a worse prognosis than other types of glioma. Therefore, we sought to build a progression-associated score to improve malignancy and prognostic predictions for astrocytoma. The astrocytoma progression (AP) score was constructed through bioinformatics analyses of the training cohort (TCGA RNA-seq) and included 18 genes representing distinct aspects of regulation during astrocytoma progression. This classifier could successfully discriminate patients with distinct prognoses in the training and validation (REMBRANDT, GSE16011 and TCGA-GBM Microarray) cohorts (P < 0.05 in all cohorts) and in different clinicopathological subgroups. Distinct patterns of somatic mutations and copy number variation were also observed. The bioinformatics analyses suggested that genes associated with a higher AP score were significantly involved in cancer progression-related biological processes, such as the cell cycle and immune/inflammatory responses, whereas genes associated with a lower AP score were associated with relatively normal nervous system biological processes. The analyses indicated that the AP score was a robust predictor of patient survival, and its ability to predict astrocytoma malignancy was well elucidated. Therefore, this bioinformatics-based scoring system suggested that astrocytoma progression could distinguish patients with different underlying biological processes and clinical outcomes, facilitate more precise tumour grading and possibly shed light on future classification strategies and therapeutics for astrocytoma patients.
In vivo effects of single or combined topical neuroprotective and regenerative agents on degeneration of retinal ganglion cells in rat optic nerve crush model
Authors: Kitamura Yuta , Bikbova Guzel , Baba Takayuki , Yamamoto Shuichi , Oshitari Toshiyuki
Published: January 2019

To determine the effectiveness of a single or a combination of topical neurotrophic factors (NFs) in protecting retinal ganglion cells (RGCs) in the rat optic nerve crush (ONC) model, the left ONC was performed to induce the death of the RGCs in adult Sprague-Dawley rats. The NFs studied were tauroursodeoxycholic acid (TUDCA), citicoline, neurotrophin-4 (NT-4), combined TUDCA/citicoline (Doublet-1), combined TUDCA/NT-4 (Doublet-2), combined TUDCA/citicoline/NT-4 (Triplet), and PBS. After 2 weeks, the number of RGCs was determined by Brn3a immunostaining. The optic nerves were immunostained for anti-Growth Associated Protein-43(GAP-43) and -200kD neurofilament heavy antibody to study optic nerve regeneration. Two weeks after the ONC, the densities of RGCs in all treated eyes were significantly higher than that of the PBS treated eyes. In the Triplet group, the number of RGC axons after ONC was significantly higher than that in all of the single treatment groups and the number of TUNEL positive cells was significantly reduced and the number of GAP-43 immunopositive axons was significantly greater than those in the PBS group. Neovascularization was observed only in the Doublet-1 group. We conclude that the combination of the three NFs was the most effective way to protect RGCs after the ONC.
POGLUT1, the putative effector gene driven by rs2293370 in primary biliary cholangitis susceptibility locus chromosome 3q13.33
Authors: Hitomi Yuki , Ueno Kazuko , Kawai Yosuke , Nishida Nao , Kojima Kaname , Kawashima Minae , Aiba Yoshihiro , Nakamura Hitomi , Kouno Hiroshi , Kouno Hirotaka , Ohta Hajime , Sugi Kazuhiro , Nikami Toshiki , Yamashita Tsutomu , Katsushima Shinji , Komeda Toshiki , Ario Keisuke , Naganuma Atsushi , Shimada Masaaki , Hirashima Noboru , Yoshizawa Kaname , Makita Fujio , Furuta Kiyoshi , Kikuchi Masahiro , Naeshiro Noriaki , Takahashi Hironao , Mano Yutaka , Yamashita Haruhiro , Matsushita Kouki , Tsunematsu Seiji , Yabuuchi Iwao , Nishimura Hideo , Shimada Yusuke , Yamauchi Kazuhiko , Komatsu Tatsuji , Sugimoto Rie , Sakai Hironori , Mita Eiji , Koda Masaharu , Nakamura Yoko , Kamitsukasa Hiroshi , Sato Takeaki , Nakamuta Makoto , Masaki Naohiko , Takikawa Hajime , Tanaka Atsushi , Ohira Hiromasa , Zeniya Mikio , Abe Masanori , Kaneko Shuichi , Honda Masao , Arai Kuniaki , Arinaga-Hino Teruko , Hashimoto Etsuko , Taniai Makiko , Umemura Takeji , Joshita Satoru , Nakao Kazuhiko , Ichikawa Tatsuki , Shibata Hidetaka , Takaki Akinobu , Yamagiwa Satoshi , Seike Masataka , Sakisaka Shotaro , Takeyama Yasuaki , Harada Masaru , Senju Michio , Yokosuka Osamu , Kanda Tatsuo , Ueno Yoshiyuki , Ebinuma Hirotoshi , Himoto Takashi , Murata Kazumoto , Shimoda Shinji , Nagaoka Shinya , Abiru Seigo , Komori Atsumasa , Migita Kiyoshi , Ito Masahiro , Yatsuhashi Hiroshi , Maehara Yoshihiko , Uemoto Shinji , Kokudo Norihiro , Nagasaki Masao , Tokunaga Katsushi , Nakamura Minoru
Published: January 2019

Primary biliary cholangitis (PBC) is a chronic and cholestatic autoimmune liver disease caused by the destruction of intrahepatic small bile ducts. Our previous genome-wide association study (GWAS) identified six susceptibility loci for PBC. Here, in order to further elucidate the genetic architecture of PBC, a GWAS was performed on an additional independent sample set, then a genome-wide meta-analysis with our previous GWAS was performed based on a whole-genome single nucleotide polymorphism (SNP) imputation analysis of a total of 4,045 Japanese individuals (2,060 cases and 1,985 healthy controls). A susceptibility locus on chromosome 3q13.33 (including ARHGAP31, TMEM39A, POGLUT1, TIMMDC1, and CD80) was previously identified both in the European and Chinese populations and was replicated in the Japanese population (OR = 0.7241, P = 3.5 × 10−9). Subsequent in silico and in vitro functional analyses identified rs2293370, previously reported as the top-hit SNP in this locus in the European population, as the primary functional SNP. Moreover, e-QTL analysis indicated that the effector gene of rs2293370 was Protein O-Glucosyltransferase 1 (POGLUT1) (P = 3.4 × 10−8). This is the first study to demonstrate that POGLUT1 and not CD80 is the effector gene regulated by the primary functional SNP rs2293370, and that increased expression of POGLUT1 might be involved in the pathogenesis of PBC.
Slow insertion of silicon probes improves the quality of acute neuronal recordings
Authors: Fiáth Richárd , Márton Adrienn Lilla , Mátyás Ferenc , Pinke Domonkos , Márton Gergely , Tóth Kinga , Ulbert István
Published: January 2019

Neural probes designed for extracellular recording of brain electrical activity are traditionally implanted with an insertion speed between 1 µm/s and 1 mm/s into the brain tissue. Although the physical effects of insertion speed on the tissue are well studied, there is a lack of research investigating how the quality of the acquired electrophysiological signal depends on the speed of probe insertion. In this study, we used four different insertion speeds (0.002 mm/s, 0.02 mm/s, 0.1 mm/s, 1 mm/s) to implant high-density silicon probes into deep layers of the somatosensory cortex of ketamine/xylazine anesthetized rats. After implantation, various qualitative and quantitative properties of the recorded cortical activity were compared across different speeds in an acute manner. Our results demonstrate that after the slowest insertion both the signal-to-noise ratio and the number of separable single units were significantly higher compared with those measured after inserting probes at faster speeds. Furthermore, the amplitude of recorded spikes as well as the quality of single unit clusters showed similar speed-dependent differences. Post hoc quantification of the neuronal density around the probe track showed a significantly higher number of NeuN-labelled cells after the slowest insertion compared with the fastest insertion. Our findings suggest that advancing rigid probes slowly (~1 µm/s) into the brain tissue might result in less tissue damage, and thus in neuronal recordings of improved quality compared with measurements obtained after inserting probes with higher speeds.
Measuring Tumor Mutational Burden (TMB) in Plasma from mCRPC Patients Using Two Commercial NGS Assays
Authors: Qiu Ping , Poehlein Christian H. , Marton Matthew J. , Laterza Omar F. , Levitan Diane
Published: January 2019

Tumor tissue mutational burden (TMB) has emerged as a promising predictive biomarker for immune checkpoint therapy. Measuring TMB from circulating tumor DNA (ctDNA) found in plasma is attractive in tissue-constrained indications. We compared the performance of two plasma-based commercial TMB assays including the effect of two different collection methods. Our findings suggest that the two plasma based TMB assays are highly correlated and they are also both correlated with a tissue-based TMB assay for relatively high TMB samples. The two collection methods are also found to be very comparable. Plasma-based TMB assays may be mature enough to be clinically useful in mCRPC and potentially other indications.
A Nervous System-Specific Model of Creatine Transporter Deficiency Recapitulates the Cognitive Endophenotype of the Disease: a Longitudinal Study
Authors: Molinaro Angelo , Alessandrì Maria Grazia , Putignano Elena , Leuzzi Vincenzo , Cioni Giovanni , Baroncelli Laura , Pizzorusso Tommaso
Published: January 2019

Mutations in creatine (Cr) transporter (CrT) gene lead to cerebral creatine deficiency syndrome-1 (CTD), an orphan neurodevelopmental disorder presenting with brain Cr deficiency, intellectual disability, seizures, movement and autistic-like behavioral disturbances, language and speech impairment. We have recently generated a murine model of CTD obtained by ubiquitous deletion of 5–7 exons in the CrT gene. These mice showed a marked Cr depletion, associated to early and progressive cognitive impairment, and autistic-like defects, thus resembling the key features of human CTD. Given the importance of extraneural dysfunctions in neurodevelopmental disorders, here we analyzed the specific role of neural Cr in the CTD phenotype. We induced the conditional deletion of Slc6a8 gene in neuronal and glial cells by crossing CrT floxed mice with the Nestin::Cre recombinase Tg (Nes-cre) 1Kln mouse. We report that nervous system-specific Cr depletion leads to a progressive cognitive regression starting in the adult age. No autistic-like features, including repetitive and stereotyped movements, routines and rituals, are present in this model. These results indicate that Cr depletion in the nervous system is a pivotal cause of the CTD pathological phenotype, in particular with regard to the cognitive domain, but extraneural actors also play a role.
The downed and dead wood inventory of forests in the United States
Authors: Woodall Christopher W. , Monleon Vicente J. , Fraver Shawn , Russell Matthew B. , Hatfield Mark H. , Campbell John L. , Domke Grant M.
Published: January 2019

The quantity and condition of downed dead wood (DDW) is emerging as a major factor governing forest ecosystem processes such as carbon cycling, fire behavior, and tree regeneration. Despite this, systematic inventories of DDW are sparse if not absent across major forest biomes. The Forest Inventory and Analysis program of the United States (US) Forest Service has conducted an annual DDW inventory on all coterminous US forest land since 2002 (~1 plot per 38,850 ha), with a sample intensification occurring since 2012 (~1 plot per 19,425 ha). The data are organized according to DDW components and by sampling information which can all be linked to a multitude of auxiliary information in the national database. As the sampling of DDW is conducted using field efficient line-intersect approaches, several assumptions are adopted during population estimation that serve to identify critical knowledge gaps. The plot- and population-level DDW datasets and estimates provide the first insights into an understudied but critical ecosystem component of temperate forests of North America with global application.
Rheological Properties of Tomato Products
Authors: Kubo Miriam T. K. , Rojas Meliza L. , Miano Alberto C. , Augusto Pedro E. D.
Published: January 2019

This chapter provides an overview of the rheological characterization of tomato-based products, the importance of which is related to processing design, quality control, and sensory acceptance. First, we present some general principles of rheology, covering the fundamental concepts and rheological classification of fluid foods. Then, we discuss steady-state shear, time-dependent, and viscoelastic properties. Each of these is discussed separately, focusing on tomato products and presenting the equations generally used to model rheological behaviour and their respective parameters. In addition, some factors that influence rheological characteristics are presented, including the composition and characteristics of the product and the processing conditions.
New Approaches for Rapid Tomato Quality Control
Authors: Rodriguez-Saona Luis E. , Aykas Didem Peren
Published: January 2019

Monitoring quality traits is very important for the tomato industry at different stages of the production cycle including agricultural production, harvesting, and processing. The most important tomato quality traits include color, consistency, sugars, and acids, in addition to other components that are important contributors to the flavor of the product. Consumer acceptance and behaviour when buying tomato products are influenced by nutritional value, sensory characteristics (flavor, color, aroma), consistency, acidity, and serum separation, which correspond to quality parameters that are commonly monitored in tomato production. Cutting-edge sensor technologies can provide a valuable window into in-process food manufacturing to permit optimization of production rate and quality of tomato products. The new generation of optical systems incorporate the analytical precision for chemical identification and quantitation with a spectral resolution equivalent to that of benchtop instruments. In this chapter the current state of technologies that provide rapid assessment of tomato quality is presented. Advances in microelectro-mechanical systems (MEMS), semiconductors, lasers, computing capabilities, and chemometrics have allowed the miniaturization of systems for field and online applications. Technologies such as spectrophotometers, colorimeters, hyperspectral imaging, and vibrational spectroscopy (NIR, mid-IR, and Raman) have benefited from these innovations with commercial micro- and nanoscale devices that have found applications in quality assurance. Technologies that reveal early quality problems can provide a competitive edge to the industry by providing real-time information, thus preventing consequences of increased costs (recall, liability, withdrawals), lost revenue or market share, and damaged brand.
Chinese Consumers’ Willingness to Pay for Safety-certified Tomatoes: Evidence from Random nth-Price Auctions
Authors: Yin Shijiu , Han Fei , Wang Yiqin , Lv Shanshan
Published: January 2019

The food safety certification system in China has multiple levels including organic, green, and hazard-free certifications. This study assessed consumer preferences for tomatoes that carry these different labels. Data were collected from 286 randomly selected consumers in Shandong Province, China, using the random nth-price auction experiment. The authors used the multivariate probit (MVP) model to analyse the factors that influence consumer preferences for tomatoes that carry different certification labels. Results indicated that consumers’ willingness to pay (WTP) for tomatoes that carry the green or organic label was significantly higher than their WTP for conventional tomatoes (CTs). However, consumers’ WTP for tomatoes that carry a hazard-free label was slightly higher than their WTP for CTs. Results of the MVP model analysis demonstrated that consumers with different individual characteristics have heterogeneous preferences for food certification labels. Food safety consciousness has positive effects on consumers’ WTP. Environmental awareness can help promote consumers’ WTP for safe food, but the environmental benefits of green and organic certifications are not likely to undergo significant growth. This research is of value to academia and to policymakers and suppliers. Governments and manufacturers should consider consumer preferences for different certification labels in their strategy development to satisfy diverse market requirements.
Traditional Tomato Products and the Need for Innovation
Authors: Porretta Sebastiano
Published: January 2019

In this chapter some innovative experimental approaches to the development of new tomato products and/or the performance of existing products are discussed. In particular, results of studies on the processing of genetically modified tomatoes are presented. The addition of calcium chloride to diced tomatoes, its optimization using a surface response technique, and its effects on important physicochemical and sensory parameters are also reported. Finally, some proposals for innovative packaging in order to make tomato products more competitive in today's markets are presented.
Study of peak capacities generated by a porous layered radially elongated pillar array column coupled to a nano-LC system
Authors: Futagami Shunta , Hara Takeshi , Ottevaere Heidi , Terryn Herman , Baron Gino V. , Desmet Gert , De Malsche Wim
Published: January 2019

The performance of a porous-layered radially elongated pillar (PLREP) array column in a commercial nano-LC system was examined by performing separation of alkylphenones and peptides.
A multiplex droplet digital PCR assay for non-invasive prenatal testing of fetal aneuploidies
Authors: Tan Chianru , Chen Xihua , Wang Fang , Wang Dong , Cao Zongfu , Zhu Xiurui , Lu Chao , Yang Wenjun , Gao Na , Gao Huafang , Guo Yong , Zhu Lingxiang
Published: January 2019

Using universal locked nucleic acid probes, a high multiplexing ddPCR-based NIPT was developed to reliably identify fetal aneuploidies.
A dimanganese(iii) porphyrin dication diradical and its transformation to a μ-hydroxo porphyrin–oxophlorin heterodimer
Authors: Kumar Amit , Sil Debangsu , Usman Mohammad , Rath Sankar Prasad
Published: January 2019

Spin coupling models are different between iron and manganese in their dication diradical complexes, which is reflected in their reactivity as shown.
Visible light intensity dependent negative photochromism of a binaphthyl-bridged phenoxyl-imidazolyl radical complex
Authors: Yonekawa Izumi , Mutoh Katsuya , Abe Jiro
Published: January 2019

We herein report a novel biphotochromic molecule composed of two fast negative photochromic phenoxyl-imidazolyl radical complex units showing incident light intensity dependence of the photochemical reaction.