bluuebunny/crossref_metadata_2025 huggingface dataset:
The basal chorionic trophoblast cell layer: An emerging coordinator of placenta development
Authors: Walentin Katharina , Hinze Christian , Schmidt‐Ott Kai M.
Published: January 2016

During gestation, fetomaternal exchange occurs in the villous tree (labyrinth) of the placenta. Development of this structure depends on tightly coordinated cellular processes of branching morphogenesis and differentiation of specialized trophoblast cells. The basal chorionic trophoblast (BCT) cell layer that localizes next to the chorioallantoic interface is of critical importance for labyrinth morphogenesis in rodents. Gcm1‐positive cell clusters within this layer initiate branching morphogenesis thereby guiding allantoic fetal blood vessels towards maternal blood sinuses. Later these cells differentiate and contribute to the syncytiotrophoblast of the fetomaternal barrier. Additional cells within the BCT layer sustain continued morphogenesis, possibly through a repopulating progenitor population. Several mouse mutants highlight the importance of a structurally intact BCT epithelium, and a growing number of studies addresses its patterning and epithelial architecture. Here, we review and discuss emerging concepts in labyrinth development focussing on the biology of the BCT cell layer.
Targeting MYC in cancer therapy: RNA processing offers new opportunities
Authors: Koh Cheryl M. , Sabò Arianna , Guccione Ernesto
Published: January 2016

MYC is a transcription factor, which not only directly modulates multiple aspects of transcription and co‐transcriptional processing (e.g. RNA‐Polymerase II initiation, elongation, and mRNA capping), but also indirectly influences several steps of RNA metabolism, including both constitutive and alternative splicing, mRNA stability, and translation efficiency. As MYC is an oncoprotein whose expression is deregulated in multiple human cancers, identifying its critical downstream activities in tumors is of key importance for designing effective therapeutic strategies. With this knowledge and recent technological advances, we now have multiple angles to reach the goal of targeting MYC in tumors, ranging from the direct reduction of MYC levels, to the dampening of selected house‐keeping functions in MYC‐overexpressing cells, to more targeted approaches based on MYC‐induced secondary effects.
Nomogram for prediction of prognosis in patients with initially unresectable colorectal liver metastases
Authors: Imai K , Allard M-A , Castro Benitez C , Vibert E , Sa Cunha A , Cherqui D , Castaing D , Bismuth H , Baba H , Adam R
Published: January 2016

Background

Although recent advances in surgery and chemotherapy have increasingly enabled hepatectomy in patients with initially unresectable colorectal liver metastases (CRLM), not all such patients benefit from surgery. The aim of this study was to develop a nomogram to predict survival after hepatectomy for initially unresectable CRLM.

Methods

Patients with initially unresectable CRLM treated with chemotherapy followed by hepatectomy between 1990 and 2012 were included in the study. A nomogram to predict survival was developed based on a multivariable Cox model. The predictive performance of the model was assessed according to the C-statistic, Kaplan–Meier curve and calibration plots.

Results

Of a total of 439 patients, liver and globally completed surgery was achieved in 380 (86·6 per cent) and 335 (76·3 per cent) patients respectively. The 5-year overall and disease-free survival rates were 39·9 and 10·0 per cent respectively. Based on the Cox model, the following five factors were selected for the nomogram and assigned specific scores: node-positive primary, 5; more than six metastases at hepatectomy, 7; carbohydrate antigen 19–9 level at hepatectomy above 37 units/ml, 10; disease progression during first-line chemotherapy, 9; and presence of extrahepatic disease, 4. The model achieved relatively good discrimination and calibration, with a C-statistic of 0·66. The overall survival rate for patients with a score greater than 16 was significantly worse than that for patients with a score of 16 or less (5-year survival rate 4 versus 46·3 per cent respectively; P < 0·001).

Conclusion

The nomogram facilitates personalized assessment of prognosis for patients with initially unresectable CRLM treated with chemotherapy and with planned resection.
Restoration of normal colonic motor patterns and meal responses after distal colorectal resection
Authors: Vather R , O'Grady G , Arkwright J W , Rowbotham D S , Cheng L K , Dinning P G , Bissett I P
Published: January 2016

Background

Colorectal resections alter colonic motility, including disruption of control by neural or bioelectrical cell networks. The long-term impact of surgical resections and anastomoses on colonic motor patterns has, however, never been assessed accurately. Fibreoptic high-resolution colonic manometry was employed to define motility in patients who had undergone distal colorectal resection.

Methods

Recruited patients had undergone distal colorectal resections more than 12 months previously, and had normal bowel function. Manometry was performed in the distal colon (36 sensors; 1-cm intervals), with 2-h recordings taken before and after a meal, with comparison to controls. Analysis quantified all propagating events and frequencies (cyclical, short single, and long single motor patterns), including across anastomoses.

Results

Fifteen patients and 12 controls were recruited into the study. Coordinated propagating events directly traversed the healed anastomoses in nine of 12 patients with available data, including antegrade and retrograde cyclical, short single and long single patterns. Dominant frequencies in the distal colon were similar in patients and controls (2–3 cycles/min) (antegrade P = 0·482; retrograde P = 0·178). Compared with values before the meal, the mean(s.d.) number of dominant cyclical retrograde motor patterns increased in patients after the meal (2·1(2·7) versus 32·6(31·8) in 2 h respectively; P < 0·001), similar to controls (P = 0·178), although the extent of propagation was 41 per cent shorter in patients, by a mean of 3·4 cm (P = 0·003). Short and long single propagating motor patterns were comparable between groups in terms of frequency, velocity, extent and amplitude.

Conclusion

Motility patterns and meal responses are restored after distal colorectal resection in patients with normal bowel function. Coordinated propagation across healed anastomoses may indicate regeneration of underlying cellular networks.
Variation in the oxytocin receptor gene moderates the protective effects of a family‐based prevention program on telomere length
Authors: Smearman Erica L. , Yu Tianyi , Brody Gene H.
Published: January 2016

Introduction

Parent–child relationships with high conflict and low warmth and support are associated with later adverse behavioral and physiological child outcomes. These outcomes include shorter telomere lengths, the repetitive sequences at the ends of chromosomes that have been utilized as a biomarker for chronic stress. Our research group furthered this by exploring telomere length outcomes following a family‐based prevention program and identified reduced telomere shortening 5 years post intervention among those originally exposed to nonsupportive parenting and randomized to the intervention condition. However, not all individuals respond equally, and a growing literature suggests genetic sensitivity to one's environment, with variations in the oxytocin receptor gene (OXTR) potentially influencing this sensitivity.

Methods

We utilized data from African American youths (mean age 17) randomized to intervention (n = 100) or control condition (n = 91) with baseline assessments of genetic status and nonsupportive parenting, and 5‐year follow‐up assessments of telomere length.

Results

We found a significant three‐way interaction between nonsupportive parenting, intervention condition, and OXTR rs53576 genotype. OXTR GG individuals, who are suggested to be more sensitive to their social environment, exhibited significantly more variability, evidencing the shortest telomeres when exposed to nonsupportive parenting and randomized to the control condition, and similar telomere lengths to non at‐risk groups when randomized to the intervention. In contrast, those with the A allele showed no statistical difference in telomere lengths across parental and intervention conditions. Subsequent analyses suggest that these findings may be mediated through chronic anger, whereby GG individuals exposed to nonsupportive parenting and randomized to the control condition had a greater increase in chronic anger by study follow‐up, compared to those in the intervention, and this change associated with greater telomere shortening.

Conclusions

These findings highlight the importance of individual differences and potential role of genetic status in moderating the relationship between environmental contexts and biological outcomes.
Variations in the origin of the deep femoral artery: A meta‐analysis
Authors: Tomaszewski Krzysztof A. , Henry Brandon Michael , Vikse Jens , Pękala Przemysław , Roy Joyeeta , Svensen Maren , Guay Daniel , Hsieh Wan Chin , Loukas Marios , Walocha Jerzy A.
Published: January 2016

The deep femoral artery (DFA) is the largest branch of the femoral artery (FA) and is responsible for vascularization of the thigh muscles. Knowledge of the anatomical variations in its origin point is important for surgeons and interventional radiologists. The aim of our study was to provide a comprehensive evidence‐based assessment of its anatomical properties. An extensive search through the major electronic databases was conducted to find all articles reporting data on the anatomical characteristics of the DFA. No date limits or language restrictions were imposed. A total of 25 articles (n = 2,502 lower limbs) were included in the meta‐analysis. Six different patterns of origin of the DFA from the FA were identified, the most common type being a posterior origin (38.8%, 95% CI 22.8–49.5%). The DFA most commonly branched off in the proximal third of the thigh, with a prevalence of 47.6% (95% CI 35.8–59.2%). The pooled mean distance of the DFA from its point of origin to the mid‐inguinal point was 41.15 mm (95% CI 32.39–53.73). The point and level of origin of the DFA from the FA varies widely in the general population. Owing to this variability, accurate anatomical knowledge regarding the DFA is crucial for clinicians if iatrogenic injuries are to be avoided during procedures in the femoral region. Clin. Anat. 30:106–113, 2017. © 2016 Wiley Periodicals, Inc.
Expression of aurora kinase A correlates with the Wnt‐modulator RACGAP1 in gastric cancer
Authors: Bornschein Jan , Nielitz Jessica , Drozdov Ignat , Selgrad Michael , Wex Thomas , Jechorek Doerthe , Link Alexander , Vieth Michael , Malfertheiner Peter
Published: January 2016

Canonical Wnt signaling is involved in gastric carcinogenesis. The aim of this study was to identify the link between Wnt signaling and aurora kinase A (AURKA), a target for the treatment of gastrointestinal cancers. Publicly available microarray data were used to identify phenotype‐specific protein–protein interaction (PPI) subnetworks. The in silico analysis revealed a gastric cancer‐specific PPI subnetwork consisting of 2745 proteins and 50,935 interactions. We focused on the link of AURKA to a Wnt‐specific interaction module consisting of 92 proteins. There was a direct association of AURKA with Rac GTPase‐activating protein 1 (RACGAP1), as well as with CTNBB1 (β‐catenin) and CDKN1A as second‐order interactors. Differential expression analysis revealed a significant downregulation of both AURKA and RACGAP1 in gastric cancer compared to noncancer controls. Biopsies from a prospective cohort of 56 patients with gastric cancer (32 intestinal type, 24 diffuse type) and 20 noncancer controls were used for validation of the identified targets. The RT‐PCR data confirmed a strong correlation of AURKA and RACGAP1 gene expression both in the tumor, the tumor‐adjacent and the tumor‐distant mucosa. RACGAP1 in the tumor was also associated with CTNBB1 expression, and inversely associated with CDKN1A gene expression. Immunohistochemistry confirmed expression of the RACGAP1 protein in gastric cancer and the tumor‐adjacent mucosa. RACGAP1 expression was not associated with tumor stage, grading, Lauren type, Helicobacter pylori infection, or age. In conclusion, AURKA is directly associated with the expression of RACGAP1, a modulator of the canonical Wnt signaling pathway.
Nimotuzumab enhances temozolomide‐induced growth suppression of glioma cells expressing mutant EGFR in vivo
Authors: Nitta Yusuke , Shimizu Saki , Shishido‐Hara Yukiko , Suzuki Kaori , Shiokawa Yoshiaki , Nagane Motoo
Published: January 2016

A mutant form of epidermal growth factor receptor (EGFR), EGFRvIII, is common in glioblastoma (GBM) and confers enhanced tumorigenic activity and drug resistance. Nimotuzumab, an anti‐EGFR antibody, has shown preclinical and clinical activity to GBM, but its specific activity against EGFRvIII has not been fully investigated. Human glioma U87MG or LNZ308 cells overexpressing either wild‐type (wt) EGFR or EGFRvIII were treated with nimotuzumab, temozolomide, or both. Expression and phosphorylation status of molecules were determined by Western blot analysis. Methylation status of promoter region of O6‐methylguanine‐DNA methyltransferase (MGMT) was detected by methylation‐specific PCR. Antitumor activity was tested using nude mice bearing either subcutaneous or intracerebral xenografts along with analyses of EGFR phosphorylation status, proliferation, apoptosis, and vessel density. Nimotuzumab treatment resulted in reduction of EGFRvIII tyrosine phosphorylation with a decrease in Akt phosphorylation that was greater than that of wtEGFR. Correspondingly, antitumor effects, growth suppression and survival elongation, were more significant in mice bearing either subcutaneous or intracerebral tumor expressing EGFRvIII than in those expressing wtEGFR. These effects were markedly increased when temozolomide was combined with nimotuzumab. The post‐treatment recurrent brain tumors exhibited a decrease in expression of the mismatch repair (MMR) proteins, MSH6 and MLH1, but their methylated MGMT status did not changed. Nimotuzumab has in vivo antitumor activity against GBM, especially those expressing EGFRvIII, when combined with temozolomide. This could provide a basis for preselection of patients with GBM by EGFR status who might benefit from the nimotuzumab and temozolomide combination therapy.
Development and characterization of two human triple‐negative breast cancer cell lines with highly tumorigenic and metastatic capabilities
Authors: Su Yanrong , Pogash Thomas J. , Nguyen Theresa D. , Russo Jose
Published: January 2016

Triple‐negative breast cancer (TNBC) is a group of cancer with high diversity, limited therapies, and poor prognosis. TNBC cell lines and animal models provide effective tools for studies and drug discovery. Here, we report the development of two TNBC cell lines (XtMCF and LmMCF) based on our existing cell model that consists of normal breast epithelial cell line MCF10F, estradiol‐transformed cells trMCF, and Boyden chamber‐selected tumorigenic cells bsMCF. The XtMCF and LmMCF cell line were derived from xenograft and lung metastasis of bsMCF cells, respectively. The bsMCF, XtMCF, and LmMCF cells have undergone epithelial–mesenchymal transition (EMT), exhibiting a mesenchymal‐like feature. In vivo studies showed XtMCF and LmMCF cells were highly tumorigenic and metastatic. The injection of 5 × 104 cells to CB17/SCID mice mammary fat pad produced xenografts in 9/9 mice and tumors reached 10 millimeters in diameter in 5 weeks. The injection of 1 × 106 XtMCF or 8 × 104 LmMCF cells into the mice tail vein was sufficient to form extensive lung metastases in 4 weeks. The two new cell lines exhibited CD44+/CD49f+ and CD44+/EpCAM+ cancer stem cell (CSC) characteristics, and the EGF‐like domain of EpCAM was cleaved off. Together with the normal and early transformed counterparts, herein we provide a complete cancer model for the study of initiation, evolution, and identification of new therapeutics for TNBC. The finding that EGF‐like domain of EpCAM was cleaved off in cells which have undergone EMT suggests this cleavage may be involved in the EMT process and the cancer stem cell properties of these cells.
Cell culture density affects the proliferation activity of human adipose tissue stem cells
Authors: Kim Dae Seong , Lee Myoung Woo , Ko Young Jong , Chun Yong Hoon , Kim Hyung Joon , Sung Ki Woong , Koo Hong Hoe , Yoo Keon Hee
Published: January 2016

In this study, we investigated the effect of cell density on the proliferation activity of human mesenchymal stem cells (MSCs) derived from adipose tissue (AT‐MSCs) over time in culture. Passage #4 (P4) and #12 (P12) AT‐MSCs from two donors were plated at a density of 200 (culture condition 1, CC1) or 5000 (culture condition 2, CC2) cells cm−2. After 7 days of incubation, P4 and P12 AT‐MSCs cultured in CC1 were thin and spindle‐shaped, whereas those cultured in CC2 had extensive cell‐to‐cell contacts and an expanded cell volume. In addition, P4 and P12 AT‐MSCs in CC1 divided more than three times, while those in CC2 divided less than once on average. Flow cytometric analysis using 5(6)‐carboxyfluorescein diacetate N‐succinimidyl ester dye showed that the fluorescence intensity of AT‐MSCs was lower in CC1 than in CC2. Furthermore, expression of proliferation‐associated genes, such as CDC45L, CDC20A and KIF20A, in P4 AT‐MSCs was higher in CC1 than in CC2, and this difference was also observed in P12 AT‐MSCs. These data demonstrated that cell culture density affects the proliferation activity of MSCs, suggesting that it is feasible to design a strategy to prepare suitable MSCs using specific culture conditions. Copyright © 2016 John Wiley & Sons, Ltd.
Location of Framework Al Atoms in the Channels of ZSM‐5: Effect of the (Hydrothermal) Synthesis
Authors: Pashkova Veronika , Sklenak Stepan , Klein Petr , Urbanova Martina , Dědeček Jiří
Published: January 2016

27Al 3Q MAS NMR and UV/Vis spectroscopy with bare CoII ions as probes of Al pairs in the zeolite framework were employed to analyze the location of framework Al atoms in the channel system of zeolite ZSM‐5. Furthermore, the effect of Na+ ions together with tetrapropylammonium cation (TPA+) in the ZSM‐5 synthesis gel on the location of Al in the channel system was investigated. Zeolites prepared using exclusively TPA+ as a structure‐directing agent (i.e., in the absence of Na+ ions) led to 55–90 % of Al atoms located at the channel intersection, regardless the presence or absence of Al pairs [Al−O−(Si−O)2−Al sequences in one ring] in the zeolite framework. The presence of Na+ ions in the synthesis gel did not modify the Al location at the channel intersection (55–95 % of Al atoms) and led only to changes in i) the distribution of framework Al atoms between Al pairs (decrease) and single isolated Al atoms (increase), and ii) the siting of Al in distinguishable framework tetrahedral sites.
Can Non‐Kramers TmIII Mononuclear Molecules be Single‐Molecule Magnets (SMMs)?
Authors: Meng Yin‐Shan , Qiao Yu‐Sen , Zhang Yi‐Quan , Jiang Shang‐Da , Meng Zhao‐Sha , Wang Bing‐Wu , Wang Zhe‐Ming , Gao Song
Published: January 2016

In recent years, plentiful lanthanide‐based (TbIII, DyIII, and ErIII) single‐molecule magnets (SMMs) were studied, while examples of other lanthanides, for example, TmIII are still unknown. Herein, for the first time, we show that by rationally manipulating the coordination sphere, two thulium compounds, 1[(Tp)Tm(COT)] and 2[(Tp*)Tm(COT)] (Tp=hydrotris(1‐pyrazolyl)borate; COT=cyclooctatetraenide; Tp*=hydrotris(3,5‐dimethyl‐1‐pyrazolyl)borate), can adopt the structure of non‐Kramers SMMs and exhibit their behaviors. Dynamic magnetic studies indicated that both compounds showed slow magnetic relaxation under dc field and a relatively high effective energy barrier (111 K for 1, 46 K for 2). Magnetic diluted 1 a[(Tp)Tm0.05Y0.95(COT)] and 2 a[(Tp*)Tm0.05Y0.95(COT)] even exhibited magnetic relaxation under zero dc field. Relativistic ab initio calculations combined with single‐crystal angular‐resolved magnetometry measurements revealed the strong easy axis anisotropy and nearly degenerated ground doublet states. The comparison of 1 and 2 highlights the importance of local symmetry for obtaining Tm SMMs.
Water‐ and Temperature‐Triggered Reversible Structural Transformation of Tetranuclear Cobalt(II) Cores Sandwiched by Polyoxometalates
Authors: Kuriyama Yosuke , Kikukawa Yuji , Suzuki Kosuke , Yamaguchi Kazuya , Mizuno Noritaka
Published: January 2016

Although stimuli‐responsive structural transformations of inorganic materials have attracted considerable attention because of their potential use as functional switchable materials, multinuclear metal cores frequently suffer from unexpected dissociation of metal cations and/or irreversible transformations into infinite structures. In this study, we describe the successful demonstration of the water‐ and temperature‐triggered reversible structural transformation between cubane‐ and planar‐type tetranuclear CoII cores sandwiched by polyoxometalates. The arrangements and coordination geometries of the CoII cations were interconverted by simple hydration and dehydration, resulting in the manipulation of the magnetic and optical properties of these compounds. Moreover, this system showed unique thermochromism through temperature‐dependent reversible structural interconversion.
Jackknife empirical likelihood for comparing two Gini indices
Authors: Wang Dongliang , Zhao Yichuan
Published: January 2016

The focus of this paper is to derive the jackknife empirical likelihood for the difference of two Gini indices. For independent data we propose a novel U‐statistic, which allows direct utilization of the jackknife empirical likelihood without involving a nuisance parameter. For paired data we established Wilks’ theorem for the profile likelihood after maximization over the nuisance parameter. Simulation studies show that our method is comparable to existing empirical likelihood methods in terms of coverage accuracy, but obtains much shorter intervals. The proposed methods are illustrated via analyzing a real data set.The Canadian Journal of Statistics44: 102–119; 2016 © 2016 Statistical Society of Canada
Development of early‐born γ‐Aminobutyric acid hub neurons in mouse hippocampus from embryogenesis to adulthood
Authors: Villette Vincent , Guigue Philippe , Picardo Michel Aimé , Sousa Vitor Hugo , Leprince Erwan , Lachamp Philippe , Malvache Arnaud , Tressard Thomas , Cossart Rosa , Baude Agnès
Published: January 2016

Early‐born γ‐aminobutyric acid (GABA) neurons (EBGNs) are major components of the hippocampal circuit because at early postnatal stages they form a subpopulation of “hub cells” transiently supporting CA3 network synchronization (Picardo et al. [2011] Neuron 71:695–709). It is therefore essential to determine when these cells acquire the remarkable morphofunctional attributes supporting their network function and whether they develop into a specific subtype of interneuron into adulthood. Inducible genetic fate mapping conveniently allows for the labeling of EBGNs throughout their life. EBGNs were first analyzed during the perinatal week. We observed that EBGNs acquired mature characteristics at the time when the first synapse‐driven synchronous activities appeared in the form of giant depolarizing potentials. The fate of EBGNs was next analyzed in the adult hippocampus by using anatomical characterization. Adult EBGNs included a significant proportion of cells projecting selectively to the septum; in turn, EBGNs were targeted by septal and entorhinal inputs. In addition, most EBGNs were strongly targeted by cholinergic and monoaminergic terminals, suggesting significant subcortical innervation. Finally, we found that some EBGNs located in the septum or the entorhinal cortex also displayed a long‐range projection that we traced to the hippocampus. Therefore, this study shows that the maturation of the morphophysiological properties of EBGNs mirrors the evolution of early network dynamics, suggesting that both phenomena may be causally linked. We propose that a subpopulation of EBGNs forms into adulthood a scaffold of GABAergic projection neurons linking the hippocampus to distant structures. J. Comp. Neurol. 524:2440–2461, 2016. © 2016 Wiley Periodicals, Inc.
Sex and laterality differences in medial amygdala neurons and astrocytes of adult mice
Authors: Pfau Daniel R. , Hobbs Nicholas J. , Breedlove S. Marc , Jordan Cynthia L.
Published: January 2016

The posterodorsal aspect of the medial amygdala (MePD) in rats is sexually dimorphic, being larger and containing more and larger neurons in males than in females. It is also highly lateralized, with the right MePD larger than the left in both sexes, but with the smaller left MePD actually containing more and larger neurons than the larger right. Astrocytes are also strikingly sexually differentiated, with male‐biased numbers and lateralized favoring the right in the rat MePD. However, comparable information is scant for mice where genetic tools offer greater experimental power. Hence, we examined the MePD from adult male and female C57Bl/6J mice. We now report that the MePD is larger in males than in females, with the MePD in males containing more astrocytes and neurons than in females. However, we did not find sex differences in astrocyte complexity or overall glial number nor effects of laterality in either measure. While the mouse MePD is generally less lateralized than in rats, we did find that the sex difference in astrocyte number is only on the right because of a significant lateralization in females, with significantly fewer astrocytes on the right than the left but only in females. A sex difference in neuronal soma size favoring males was also evident, but only on the left. Sex differences in the number of neurons and astrocytes common to both rodent species may represent core morphological features that critically underlie the expression of sex‐specific behaviors that depend on the MePD. J. Comp. Neurol. 524:2492–2502, 2016. © 2016 Wiley Periodicals, Inc.
Extracellular matrix protein expression is brain region dependent
Authors: Dauth Stephanie , Grevesse Thomas , Pantazopoulos Harry , Campbell Patrick H. , Maoz Ben M. , Berretta Sabina , Parker Kevin Kit
Published: January 2016

In the brain, extracellular matrix (ECM) components form networks that contribute to structural and functional diversity. Maladaptive remodeling of ECM networks has been reported in neurodegenerative and psychiatric disorders, suggesting that the brain microenvironment is a dynamic structure. A lack of quantitative information about ECM distribution in the brain hinders an understanding of region‐specific ECM functions and the role of ECM in health and disease. We hypothesized that each ECM protein as well as specific ECM structures, such as perineuronal nets (PNNs) and interstitial matrix, are differentially distributed throughout the brain, contributing to the unique structure and function in the various regions of the brain. To test our hypothesis, we quantitatively analyzed the distribution, colocalization, and protein expression of aggrecan, brevican, and tenascin‐R throughout the rat brain utilizing immunohistochemistry and mass spectrometry analysis and assessed the effect of aggrecan, brevican, and/or tenascin‐R on neurite outgrowth in vitro. We focused on aggrecan, brevican, and tenascin‐R as they are especially expressed in the mature brain, and have established roles in brain development, plasticity, and neurite outgrowth. The results revealed a differentiated distribution of all three proteins throughout the brain and indicated that their presence significantly reduces neurite outgrowth in a 3D in vitro environment. These results underline the importance of a unique and complex ECM distribution for brain physiology and suggest that encoding the distribution of distinct ECM proteins throughout the brain will aid in understanding their function in physiology and in turn assist in identifying their role in disease. J. Comp. Neurol. 524:1309–1336, 2016. © 2016 Wiley Periodicals, Inc.
A Liquid Crystalline Oligomer Exhibiting Nematic and Twist‐Bend Nematic Mesophases
Authors: Mandle Richard J. , Goodby John W.
Published: January 2016

The twist‐bend nematic phase (NTB) has been described as the structural link between the untilted uniaxial nematic phase (N) and the helical chiral nematic phase (N*). The NTB phase exhibits phenomena of fundamental importance to science, that is, 1) the spontaneous formation of a helical pitch on the nanometer scale in a fluid and 2) the spontaneous breaking of mirror symmetry, leading to the emergence of chiral domains in an achiral system. In this Communication, we present a study on T49 [bis(4‐(9‐(4‐((4‐cyanobenzoyl)oxy)phenyl)nonyl)phenyl) 4,4′‐(nonane‐1,9‐diyl)dibenzoate], a liquid‐crystalline oligomer exhibiting the twist‐bend nematic phase, which has a molecular length that is of comparable dimensions to the sub‐10 nm pitch determined for CB9CB, and provide new insights into the differentiation between the nano‐ and macro‐science for self‐assembling supermolecular systems.
Maximizing the adequacy of Hologic® Cervista® HPV HR results on ThinPrep® Pap samples treated with glacial acetic acid
Authors: Mahajan Aparna , Kucher Erek , Hoefle Wanda , Engelhardt Shawna , Accola Molly , Barasch Samuel , Rehrauer William , Selvaggi Suzanne M.
Published: January 2016

Background

Although glacial acetic acid (GAA) treatment of bloody cervical samples has reduced the rate of unsatisfactory Pap Tests, recent studies suggest that it may negatively impact high‐risk (hr)‐HPV test results. The objectives of this study were to compare the levels of genomic DNA between GAA treated and nontreated ThinPrep® samples using the Hologic® Cervista® HPV‐HR assay and to compare the adequacy of the ThinPrep® Pap Test between aliquoted and nonaliquoted samples.

Methods

Prior to GAA treatment, 2.5 ml of the cervical sample was prealiquoted from 102 bloody ThinPrep® vials. Both GAA treated and nontreated samples were analyzed for hr‐HPV using the Cervista® HPV HR assay. The levels of genomic DNA were measured and compared between these samples. In addition, ThinPrep® Pap Test adequacy rates were calculated and compared on aliquoted and nonaliquoted cervical samples.

Results

Of the 102 cervical samples, 95 (93%) nontreated aliquots contained satisfactory levels of genomic DNA as compared to 36 (35%) GAA‐treated samples (p < 0.00001). Ninety‐nine (97%) aliquoted cervical samples were satisfactory for cytologic evaluation as compared to 1,326 (96%) GAA treated samples from 2013 (nonaliquoted); not statistically significant (p = 0.7968).

Conclusion

The levels of genomic DNA were significantly decreased in GAA treated vs non‐treated TP samples. Aliquoting from the TP sample prior to treatment with GAA enables accurate measurement of DNA without affecting the adequacy of the TP cytology slide. Diagn. Cytopathol. 2016;44:215–219. © 2016 Wiley Periodicals, Inc.
Doing more with less: New markers for sarcoma diagnosis and their applicability to cytology specimens
Authors: Dodd Leslie G , Ware Patrick , Duncan Daniel , Hertel Johann
Published: January 2016

Sarcomas are a rare and extremely diverse set of neoplasms that are often a challenge to diagnose for pathologists. For a number of reasons, primary diagnosis of soft tissue neoplasms is increasingly being performed on small biopsy specimens including fine needle aspiration (FNA) and core needle biopsy (CNB). In the last several years, there has been a significant increase in our understanding of the molecular pathogenesis of this group of tumors. New insights into the genetic mechanisms of tumor formation have been exploited to create a new generation of diagnostic markers that are accessible to most laboratories. This review describes a number of new ancillary markers, and how they can facilitate accurate diagnosis of soft tissue neoplasms on FNA/CNB. Diagn. Cytopathol. 2016;44:351–360. © 2016 Wiley Periodicals, Inc.
Timing and location of reproduction in African waterfowl: an overview of >100 years of nest records
Authors: Cumming Graeme S. , Harebottle Douglas M. , Mundava Josphine , Otieno Nickson , Tyler Stephanie J.
Published: January 2016

The timing and location of reproduction are fundamental elements of reproductive success for all organisms. Understanding why animals choose to reproduce at particular times and in particular places is also important for our understanding of other aspects of organismal ecology, such as their habitat requirements, movement strategies, and biogeography. Although breeding patterns in waterfowl are relatively well documented, most studies are from northern temperate regions and the influences of location and time of year on breeding in Afrotropical ducks (Anatidae) are poorly understood. We outline six alternative (but not mutually exclusive) hypotheses that might explain where and when Afrotropical ducks choose to breed. To explore these hypotheses, we assembled and analyzed a new database of c. 22,000 breeding records for 16 Afrotropical ducks and one introduced Palearctic species (the Mallard Anas platyrhynchos). The full database is available on line as an appendix to this article. We identified five distinct breeding strategies as well as two outliers. Peak breeding for 9 of 16 indigenous duck species occurs during the dry season. We found no evidence for spatial synchrony or spatial autocorrelation in breeding, suggesting a high level of flexibility in waterfowl responses to prevailing conditions in any given year. More intensive analyses of alternative hypotheses are needed, but our initial analysis suggests that the timing of breeding for the majority of Afrotropical ducks is driven by a combination of resource availability and predation risk.
Within species support for the expensive tissue hypothesis: a negative association between brain size and visceral fat storage in females of the Pacific seaweed pipefish
Authors: Tsuboi Masahito , Shoji Jun , Sogabe Atsushi , Ahnesjö Ingrid , Kolm Niclas
Published: January 2016

The brain is one of the most energetically expensive organs in the vertebrate body. Consequently, the high cost of brain development and maintenance is predicted to constrain adaptive brain size evolution (the expensive tissue hypothesis, ETH). Here, we test the ETH in a teleost fish with predominant female mating competition (reversed sex roles) and male pregnancy, the pacific seaweed pipefish Syngnathus schlegeli. The relative size of the brain and other energetically expensive organs (kidney, liver, heart, gut, visceral fat, and ovary/testis) was compared among three groups: pregnant males, nonpregnant males and egg producing females. Brood size in pregnant males was unrelated to brain size or the size of any other organ, whereas positive relationships were found between ovary size, kidney size, and liver size in females. Moreover, we found that the size of energetically expensive organs (brain, heart, gut, kidney, and liver) as well as the amount of visceral fat did not differ between pregnant and nonpregnant males. However, we found marked differences in relative size of the expensive organs between sexes. Females had larger liver and kidney than males, whereas males stored more visceral fat than females. Furthermore, in females we found a negative correlation between brain size and the amount of visceral fat, whereas in males, a positive trend between brain size and both liver and heart size was found. These results suggest that, while the majority of variation in the size of various expensive organs in this species likely reflects that individuals in good condition can afford to allocate resources to several organs, the cost of the expensive brain was visible in the visceral fat content of females, possibly due to the high costs associated with female egg production.
Photographic identification of individuals of a free‐ranging, small terrestrial vertebrate
Authors: Treilibs Claire E. , Pavey Chris R. , Hutchinson Mark N. , Bull C. Michael
Published: January 2016

Recognition of individuals within an animal population is central to a range of estimates about population structure and dynamics. However, traditional methods of distinguishing individuals, by some form of physical marking, often rely on capture and handling which may affect aspects of normal behavior. Photographic identification has been used as a less‐invasive alternative, but limitations in both manual and computer‐automated recognition of individuals are particularly problematic for smaller taxa (<500 g). In this study, we explored the use of photographic identification for individuals of a free‐ranging, small terrestrial reptile using (a) independent observers, and (b) automated matching with the Interactive Individual Identification System (I3S Pattern) computer algorithm. We tested the technique on individuals of an Australian skink in the Egernia group, Slater's skink Liopholis slateri, whose natural history and varied scale markings make it a potentially suitable candidate for photo‐identification. From ‘photographic captures’ of skink head profiles, we designed a multi‐choice key based on alternate character states and tested the abilities of observers — with or without experience in wildlife survey — to identify individuals using categorized test photos. We also used the I3S Pattern algorithm to match the same set of test photos against a database of 30 individuals. Experienced observers identified a significantly higher proportion of photos correctly (74%) than those with no experience (63%) while the I3S software correctly matched 67% as the first ranked match and 83% of images in the top five ranks. This study is one of the first to investigate photo identification with a free‐ranging small vertebrate. The method demonstrated here has the potential to be applied to the developing field of camera‐traps for wildlife survey and thus a wide range of survey and monitoring applications.
Evolution of tail fork depth in genusHirundo
Authors: Hasegawa Masaru , Arai Emi , Kutsukake Nobuyuki
Published: January 2016

A classic example of a sexually selected trait, the deep fork tail of the barn swallowHirundo rusticais now claimed to have evolved and be maintained mainly via aerodynamic advantage rather than sexually selected advantage. However, this aerodynamic advantage hypothesis does not clarify which flight habits select for/against deep fork tails, causing diversity of tail fork depth in hirundines. Here, by focusing on the genusHirundo, we investigated whether the large variation in tail fork depth could be explained by the differential flight habits. Using a phylogenetic comparative approach, we found that migrant species had deeper fork tails, but less colorful plumage, than the other species, indicating that migration favors a specific trait, deep fork tails. At the same time, tail fork depth but not plumage coloration decreased with increasing bill size – a proxy of prey size, suggesting that foraging on larger prey items favors shallower fork tails. Variation of tail fork depth in the genusHirundomay be explained by differential flight habits, even without assuming sexual selection.
Influence of arbuscular mycorrhizal colonization on whole‐plant respiration and thermal acclimation of tropical tree seedlings
Authors: Fahey Catherine , Winter Klaus , Slot Martijn , Kitajima Kaoru
Published: January 2016

Symbiotic arbuscular mycorrhizal fungi (AMF) are ubiquitous in tropical forests. AMF play a role in the forest carbon cycle because they can increase nutrient acquisition and biomass of host plants, but also incur a carbon cost to the plant. Through their interactions with their host plants they have the potential to affect how plants respond to environmental perturbation such as global warming. Our objective was to experimentally determine how plant respiration rates and responses to warmer environment are affected by AMF colonization in seedlings of five tropical tree species at the whole plant level. We evaluated the interaction between AMF colonization and temperature on plant respiration against four possible outcomes; acclimation does or does not occur regardless of AMF, or AMF can increase or decrease respiratory acclimation. Seedlings were inoculated with AMF spores or sterilized inoculum and grown at ambient or elevated nighttime temperature. We measured whole plant and belowground respiration rates, as well as plant growth and biomass allocation. There was an overall increase in whole plant, root, and shoot respiration rate with AMF colonization, whereas temperature acclimation varied among species, showing support for three of the four possible responses. The influence of AMF colonization on growth and allocation also varied among plant species. This study shows that the effect of AMF colonization on acclimation differs among plant species. Given the cosmopolitan nature of AMF and the importance of plant acclimation for predicting climate feedbacks a better understanding of the patterns and mechanisms of acclimation is essential for improving predictions of how climate warming may influence vegetation feedbacks.
Gillespie eco‐evolutionary models (GEMs) reveal the role of heritable trait variation in eco‐evolutionary dynamics
Authors: DeLong John P. , Gibert Jean P.
Published: January 2016

Heritable trait variation is a central and necessary ingredient of evolution. Trait variation also directly affects ecological processes, generating a clear link between evolutionary and ecological dynamics. Despite the changes in variation that occur through selection, drift, mutation, and recombination, current eco‐evolutionary models usually fail to track how variation changes through time. Moreover, eco‐evolutionary models assume fitness functions for each trait and each ecological context, which often do not have empirical validation. We introduce a new type of model, Gillespie eco‐evolutionary models (GEMs), that resolves these concerns by tracking distributions of traits through time as eco‐evolutionary dynamics progress. This is done by allowing change to be driven by the direct fitness consequences of model parameters within the context of the underlying ecological model, without having to assume a particular fitness function. GEMs work by adding a trait distribution component to the standard Gillespie algorithm – an approach that models stochastic systems in nature that are typically approximated through ordinary differential equations. We illustrate GEMs with the Rosenzweig–MacArthur consumer–resource model. We show not only how heritable trait variation fuels trait evolution and influences eco‐evolutionary dynamics, but also how the erosion of variation through time may hinder eco‐evolutionary dynamics in the long run. GEMs can be developed for any parameter in any ordinary differential equation model and, furthermore, can enable modeling of multiple interacting traits at the same time. We expect GEMs will open the door to a new direction in eco‐evolutionary and evolutionary modeling by removing long‐standing modeling barriers, simplifying the link between traits, fitness, and dynamics, and expanding eco‐evolutionary treatment of a greater diversity of ecological interactions. These factors make GEMs much more than a modeling advance, but an important conceptual advance that bridges ecology and evolution through the central concept of heritable trait variation.
Dispersal, niche, and isolation processes jointly explain species turnover patterns of nonvolant small mammals in a large mountainous region of China
Authors: Wen Zhixin , Quan Qing , Du Yuanbao , Xia Lin , Ge Deyan , Yang Qisen
Published: January 2016

Understanding the mechanisms that govern the spatial patterns of species turnover (beta diversity) has been one of the fundamental issues in biogeography. Species turnover is generally recognized as strong in mountainous regions, but the way in which different processes (dispersal, niche, and isolation) have shaped the spatial turnover patterns in mountainous regions remains largely unexplored. Here, we explore the directional and elevational patterns of species turnover for nonvolant small mammals in the Hengduan Mountains of southwest China and distinguish the relative roles of geographic distance, environmental distance, and geographic isolation on the patterns. The spatial turnover was assessed using the halving distance (km), which was the geographic distance that halved the similarity (Jaccard similarity) from its initial value. The halving distance was calculated for the linear, logarithmic, and exponential regression models between Jaccard similarity and geographic distance. We found that the east–west turnover is generally faster than the south–north turnover for high‐latitudinal regions in the Hengduan Mountains and that this pattern corresponds to the geographic structure of the major mountain ranges and rivers that mainly extend in a south–north direction. There is an increasing trend of turnover toward the higher‐elevation zones. Most of the variation in the Jaccard similarity could be explained by the pure effect of geographic distance and the joint effects of geographic distance, environmental distance, and average elevation difference. Our study indicates that dispersal, niche, and isolation processes are all important determinants of the spatial turnover patterns of nonvolant small mammals in the Hengduan Mountains. The spatial configuration of the landscape and geographic isolation can strongly influence the rate of species turnover in mountainous regions at multiple spatial scales.
Mixture EMOS model for calibrating ensemble forecasts of wind speed
Authors: Baran S. , Lerch S.
Published: January 2016

Ensemble model output statistics (EMOS) is a statistical tool for post‐processing forecast ensembles of weather variables obtained from multiple runs of numerical weather prediction models in order to produce calibrated predictive probability density functions. The EMOS predictive probability density function is given by a parametric distribution with parameters depending on the ensemble forecasts. We propose an EMOS model for calibrating wind speed forecasts based on weighted mixtures of truncated normal (TN) and log‐normal (LN) distributions where model parameters and component weights are estimated by optimizing the values of proper scoring rules over a rolling training period. The new model is tested on wind speed forecasts of the 50 member European Centre for Medium‐range Weather Forecasts ensemble, the 11 member Aire Limitée Adaptation dynamique Développement International‐Hungary Ensemble Prediction System ensemble of the Hungarian Meteorological Service, and the eight‐member University of Washington mesoscale ensemble, and its predictive performance is compared with that of various benchmark EMOS models based on single parametric families and combinations thereof. The results indicate improved calibration of probabilistic and accuracy of point forecasts in comparison with the raw ensemble and climatological forecasts. The mixture EMOS model significantly outperforms the TN and LN EMOS methods; moreover, it provides better calibrated forecasts than the TN–LN combination model and offers an increased flexibility while avoiding covariate selection problems. © 2016 The Authors Environmetrics Published by JohnWiley & Sons Ltd.