bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developing 3D SEM in a broad biological context
Authors: KREMER A. , LIPPENS S. , BARTUNKOVA S. , ASSELBERGH B. , BLANPAIN C. , FENDRYCH M. , GOOSSENS A. , HOLT M. , JANSSENS S. , KROLS M. , LARSIMONT J.‐C. , Mc GUIRE C. , NOWACK M.K. , SAELENS X. , SCHERTEL A. , SCHEPENS B. , SLEZAK M. , TIMMERMAN V. , THEUNIS C. , VAN BREMPT R. , VISSER Y. , GUÉRIN C.J. 
Published: January 2015

SummaryWhen electron microscopy (EM) was introduced in the 1930s it gave scientists their first look into the nanoworld of cells. Over the last 80 years EM has vastly increased our understanding of the complex cellular structures that underlie the diverse functions that cells need to maintain life. One drawback that has been difficult to overcome was the inherent lack of volume information, mainly due to the limit on the thickness of sections that could be viewed in a transmission electron microscope (TEM). For many years scientists struggled to achieve three‐dimensional (3D) EM using serial section reconstructions, TEM tomography, and scanning EM (SEM) techniques such as freeze‐fracture. Although each technique yielded some special information, they required a significant amount of time and specialist expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and subsequently robotic ultramicrotomes (serial block‐face, SBF‐SEM) microscopists were able to collect large volumes of 3D EM information at resolutions that could address many important biological questions, and do so in an efficient manner. We present here some examples of 3D EM taken from the many diverse specimens that have been imaged in our core facility. We propose that the next major step forward will be to efficiently correlate functional information obtained using light microscopy (LM) with 3D EM datasets to more completely investigate the important links between cell structures and their functions.
Toward structural/chemical cotailoring of phase‐change Ge–Sb–Te in a transmission electron microscope
Authors: ZHANG W , KIM J.‐G. , ZHENG W.T. , CUI X.Q. , KIM Y.‐J. , SONG S.A. 
Published: January 2015

SummaryGe2Sb2Te5, as the prototype material for phase‐change memory, can be transformed from amorphous phase into nanoscale rocksalt‐type GeTe provided with an electron irradiation assisted by heating to 520°C in a 1250 kV transmission electron microscope. This sheds a new light into structural and chemical cotailoring of materials through coupling of thermal and electrical fields.
Clonal expansion of hepatocytes with a selective advantage occurs during all stages of chronic hepatitis B virus infection
Authors: Tu T. , Mason W. S. , Clouston A. D. , Shackel N. A. , McCaughan G. W. , Yeh M. M. , Schiff E. R. , Ruszkiewicz A. R. , Chen J. W. , Harley H. A. J. , Stroeher U. H. , Jilbert A. R. 
Published: January 2015

SummaryHepatocyte clone size was measured in liver samples of 21 patients in various stages of chronic hepatitis B virus (HBV) infection and from 21 to 76 years of age. Hepatocyte clones containing unique virus–cell DNA junctions formed by the integration of HBV DNA were detected using inverse nested PCR. The maximum hepatocyte clone size tended to increase with age, although there was considerable patient‐to‐patient variation in each age group. There was an upward trend in maximum clone size with increasing fibrosis, inflammatory activity and with seroconversion from HBV e‐antigen (HBeAg)‐positive to HBeAg‐negative, but these differences did not reach statistical significance. Maximum hepatocyte clone size did not differ between patients with and without a coexisting hepatocellular carcinoma. Thus, large hepatocyte clones containing integrated HBV DNA were detected during all stages of chronic HBV infection. Using laser microdissection, no significant difference in clone size was observed between foci of HBV surface antigen (HBsAg)‐positive and HBsAg‐negative hepatocytes, suggesting that expression of HBsAg is not a significant factor in clonal expansion. Laser microdissection also revealed that hepatocytes with normal‐appearing histology make up a major fraction of the cells undergoing clonal expansion. Thus, preneoplasia does not appear to be a factor in the clonal expansion detected in our assays. Computer simulations suggest that the large hepatocyte clones are not produced by random hepatocyte turnover but have an as‐yet‐unknown selective advantage that drives increased clonal expansion in the HBV‐infected liver.
Single‐molecule tracking and super‐resolution imaging shed light on cholera toxin transcription activation
Authors: Landes Christy F. 
Published: January 2015

SummaryBecause of their small size, bacterial cells have long kept details about their inner workings a secret. We are starting to decipher their mechanistic secrets, in no small part due to the development of single‐molecule and super‐resolution fluorescence imaging, the subject of the 2014 Nobel Prize in Chemistry. These new methods have yielded a surge of discoveries about the subcellular organization and dynamics inside microbes. One example is an increased understanding of the virulence pathway within the cholera‐causing microbe, Vibrio cholerae. Here, expression of the cholera toxin is regulated by an unusual step: transcription is activated by two inner‐membrane proteins. Relating potential cooperative mechanisms between these two membrane‐bound proteins and transcription activation is difficult using ensemble methods, which could obfuscate any underlying heterogeneity. Recent efforts using single‐molecule tracking and super‐resolution imaging have begun to unravel the heterogeneity. The results support a mechanism in which one membrane protein recruits the other in order to activate transcription. The study helps to explain the relationship between the two proteins in cholera replication and also sheds light on the broader process of membrane‐bound transcription activation which, although uncommon, has been observed in other organisms.
Conservation of fungal and animal nicotinamide adenine dinucleotide phosphate oxidase complexes
Authors: Scott Barry 
Published: January 2015

SummaryNicotinamide adenine dinucleotide phosphate (NADPH) oxidases (Nox) are a group of eukaryotic flavoenzymes that catalyse the reduction of dioxygen to the superoxide anion using electrons provided by NADPH. An integral membrane flavocytochrome b558 heterodimer, composed of the catalytic subunit gp91phox and the adaptor protein p22phox, is essential for catalytic activity of the mammalian Nox2 complex. Two homologues of the mammalian gp91phox, NoxA and NoxB, have been identified in fungi and shown to be crucial for distinct fungal cell differentiation and developmental processes, but to date, no homologue of the p22phox adaptor protein has been identified. Isolation of a mutant from Podospora anserina with a phenotype identical to a previously characterised PaNox1 mutant, combined with phylogenetic analysis, identified a fungal homologue of p22phox called PaNoxD. The same adaptor protein was shown to be a component of the Botrytis cinerea NoxA complex as supported by the identical phenotypes of the bcnoxA and bcnoxD mutants and direct physical interaction between BcNoxA and BcNoxD. These results suggest that NoxA/NoxD is the fungal equivalent of the mammalian gp91phox/p22phox flavocytochrome complex. Tetraspanin (Pls1) mutants of P. anserina and B. cinerea have identical phenotypes to noxB mutants, suggesting that Pls1 is the corresponding integral membrane adaptor for assembly of the NoxB complex.
Ratio of urine and blood urea nitrogen concentration predicts the response of tolvaptan in congestive heart failure
Authors: Shimizu Keisuke , Doi Kent , Imamura Teruhiko , Noiri Eisei , Yahagi Naoki , Nangaku Masaomi , Kinugawa Koichiro 
Published: January 2015

AbstractAimThis study was conducted to evaluate the performance of the ratio of urine and blood urea nitrogen concentration (UUN/BUN) as a new predictive factor for the response of an arginine vasopressin receptor 2 antagonist tolvaptan (TLV) in decompensated heart failure patients.MethodsThis study enrolled 70 decompensated heart failure patients who were administered TLV at University of Tokyo Hospital. We collected the data of clinical parameters including UUN/BUN before administering TLV. Two different outcomes were defined as follows: having over 300 mL increase in urine volume on the first day (immediate urine output response) and having any decrease in body weight within one week after starting TLV treatment (subsequent clinical response).ResultsAmong the 70 enrolled patients, 37 patients (52.9%) showed immediate urine output response; 51 patients (72.9%) showed a subsequent clinical response of body weight decrease. Receiver operating characteristics (ROC) analysis showed good prediction by UUN/BUN for the immediate response (AUC‐ROC 0.86 [0.75–0.93]) and a significantly better prediction by UUN/BUN for the subsequent clinical response compared with urinary osmolality (AUC‐ROC 0.78 [0.63–0.88] vs. 0.68 [0.52–0.80], P < 0.05).ConclusionsWe demonstrated that a clinical parameter of UUN/BUN can predict the response of TLV even when measured before TLV administration. UUN/BUN might enable identification of good responders for this new drug.
Towards a quantitative model of kidney morphogenesis
Authors: Combes Alexander N 
Published: January 2015

AbstractKidney growth is dependent on functional interactions between mesenchymal nephron progenitors, the ureteric epithelium and surrounding stroma, which together make up the nephrogenic niche. Signalling between these populations regulates nephron progenitor maintenance, branching morphogenesis and nephron induction. Nephron endowment is sensitive to changes in the size of the nephron progenitor pool and to decreases in factors that promote branching morphogenesis. However, determining the morphogenic consequences of these disruptions in vivo has been challenging as quantitating kidney morphogenesis is hampered by the size, opacity and three‐dimensional complexity of the tissue. The recent application of whole mount immunofluorescence and tissue clearing, coupled with multiscale imaging and quantitative analysis, has begun to give insights into the dynamics of kidney formation. This review focuses on how the quantitative nature of this approach has enabled mathematical modelling of cell cycle lengths, growth rates, cell number and branching rates and is advancing our understanding of kidney organogenesis.
Extending the generality of leaf economic design principles in the cycads, an ancient lineage
Authors: Zhang Yong‐Jiang , Cao Kun‐Fang , Sack Lawren , Li Nan , Wei Xue‐Mei , Goldstein Guillermo 
Published: January 2015

Summary

Cycads are the most ancient lineage of living seed plants, but the design of their leaves has received little study. We tested whether cycad leaves are governed by the same fundamental design principles previously established for ferns, conifers and angiosperms, and characterized the uniqueness of this relict lineage in foliar trait relationships.

Leaf structure, photosynthesis, hydraulics and nutrient composition were studied in 33 cycad species from nine genera and three families growing in two botanical gardens.

Cycads varied greatly in leaf structure and physiology. Similarly to other lineages, light‐saturated photosynthetic rate per mass (Am) was related negatively to leaf mass per area and positively to foliar concentrations of chlorophyll, nitrogen (N), phosphorus and iron, but unlike angiosperms, leaf photosynthetic rate was not associated with leaf hydraulic conductance. Cycads had lower photosynthetic N use efficiency and higher photosynthetic performance relative to hydraulic capacity compared with other lineages.

These findings extend the relationships shown for foliar traits in angiosperms to the cycads. This functional convergence supports the modern synthetic understanding of leaf design, with common constraints operating across lineages, even as they highlight exceptional aspects of the biology of this key relict lineage.
Host–microbe and microbe–microbe interactions in the evolution of obligate plant parasitism
Authors: Kemen Ariane C. , Agler Matthew T. , Kemen Eric 
Published: January 2015

SummaryResearch on obligate biotrophic plant parasites, which reproduce only on living hosts, has revealed a broad diversity of filamentous microbes that have independently acquired complex morphological structures, such as haustoria. Genome studies have also demonstrated a concerted loss of genes for metabolism and lytic enzymes, and gain of diversity of genes coding for effectors involved in host defense suppression. So far, these traits converge in all known obligate biotrophic parasites, but unexpected genome plasticity remains. This plasticity is manifested as transposable element (TE)‐driven increases in genome size, observed to be associated with the diversification of virulence genes under selection pressure. Genome expansion could result from the governing of the pathogen response to ecological selection pressures, such as host or nutrient availability, or to microbial interactions, such as competition, hyperparasitism and beneficial cooperations. Expansion is balanced by alternating sexual and asexual cycles, as well as selfing and outcrossing, which operate to control transposon activity in populations. In turn, the prevalence of these balancing mechanisms seems to be correlated with external biotic factors, suggesting a complex, interconnected evolutionary network in host–pathogen–microbe interactions. Therefore, the next phase of obligate biotrophic pathogen research will need to uncover how this network, including multitrophic interactions, shapes the evolution and diversity of pathogens.

Contents

Summary
1207

I.
Introduction
1208

II.
Mechanisms of convergent evolution in obligate plant parasitism
1209

III.
Obligate biotrophy does not constrain genome size
1211

IV.
Sexual and asexual cycles balance genome size variation
1217

V.
Haploid or diploid: which phase dominates?
1218

VI.
Comparative genomics and effector evolution: what have we learned?
1219

VII.
Obligate biotrophy and the microbiome
1221

VIII.
Conclusions and research needs: biotrophic pathogens are a dynamic threat to food security and unpredictable without the understanding of their evolutionary and ecological networks
1224

Acknowledgements
1224

References
1224
Ectomycorrhizal fungal maladaptation and growth reductions associated with assisted migration ofDouglas‐fir
Authors: Kranabetter J. Marty , Stoehr Michael , O'Neill Greg A. 
Published: January 2015

SummaryClimatic adaptations are the foundation of conifer genecology, but populations also display variation in traits for nitrogen (N) utilization, along with some heritable specificity for ectomycorrhizal fungi (EMF). We examined soil andEMFinfluences on assisted migration of Douglas‐fir (Pseudotsuga menziesiivar.menziesii) by comparing two contrasting maritime populations planted up to 400 km northward in southwestern British Columbia.Soil N availability and host N status (via δ15N) were assessed across 12 maritime test sites, whereasEMFon local and introduced hosts were quantified by morphotyping with molecular analysis.Climatic transfer effects were only significant with soil N concentrations of test sites as a covariate, and illustrated how height growth was compromised for populations originating from relatively dry or cool maritime environments. We also found evidence forEMFmaladaptation, where height declined by up to 15% with the extent of dissimilarity inEMFcommunities of southern populations relative to local hosts.The results demonstrate how geographic structure in belowground environments can contribute to conifer genecology. Differences in the inherent growth potential of conifers may be partly related to nutritional adaptations arising under native soil fertility, and optimization of this growth potential likely requires close affiliation with localEMFcommunities.
Aging in Medieval Japanese Buddhism
Authors: Drott Edward R. 
Published: January 2015

AbstractIn medieval Japan (ca. 1185–1603), Buddhist practices and concepts contributed substantively to the ways in which old age was defined and understood. The widespread custom of lay ordination at the onset of old age rendered a large proportion of the elderly population Buddhist home‐leavers (shukke). Many medieval literati adopted the persona of the aged Buddhist recluse when composing poetry or essays that touched on Buddhist themes. On the other hand, didactic texts and illustrations used the miseries incumbent on the aged body as a means of leading auditors and readers to an appreciation of Buddhist truth. Buddhist legends utilized the figure of the mysterious, enigmatic old man (okina) as a stand‐in for local gods or as avatars of buddhas or bodhisattvas. The aged female body, however, was most often employed to represent demonic beings.
Exploring soil databases: a self‐organizing map approach
Authors: Rivera D. , Sandoval M. , Godoy A. 
Published: January 2015

AbstractA soil quality database (SQDB) is a collection of soil samples described by a given set of parameters, allowing farmers, scientists and other stakeholders to make informed decisions about practices, processes and policies for soil use and management. If each parameter is considered as a dimension of the space spanned by the SQDB, extracting information becomes a difficult task when the number of parameters is >3. A widely used approach to explore multidimensional data sets is the self‐organizing map (SOM) method, which is suitable for clustering, visualization and extraction of information from multidimensional data. We applied the SOM method as an exploratory technique to an unlabelled SQDB to extract knowledge – data patterns and data associations – from the data set (the time and location of each sample were unknown). The SQDB used in this study is a set of 1240 unlabelled samples within the Central Valley of Chile, covering ca 7500 km2. The predominant soils are Andisols with a large organic matter content (7–12%), small bulk densities (0.6–1.0 g/cm3) and large water‐holding capacity. We identified three patterns: (i) isolated region within the map with close neurons (smooth transitions), (ii) two or more regions with predominantly large or small values and (iii) homogeneous map with small values with an isolated region of large values. These patterns show that the data set represented more than two groups that were not necessarily related. For pH, no important associations with other investigated parameters were observed. Previous studies carried out by the local agricultural research station showed that pH values below 5.5 constrain nutrient uptake. Thus, locations presenting pH<5,5 should be subject to seasonal monitoring to assess management practices that mitigate soil acidity. The component plane for organic matter indicates that ca. 50% of the soil samples had contents <8% related to soil series characteristics and management practices. As the k‐means is initialized by random partitions, the two‐step approach (clustering the map representing the input data) is less sensitive to variations in the input data (subsamples) than is the direct application of k‐means to the input data, but it also reduces the computational cost. The ability of SOMs to visualize multidimensional data sets helps gain an understanding of the data in the exploratory phase, such as the association and integration of physical, chemical and biological parameters.
Comparison of doxorubicin–cyclophosphamide with doxorubicin–dacarbazine for the adjuvant treatment of canine hemangiosarcoma
Authors: Finotello R. , Stefanello D. , Zini E. , Marconato L. 
Published: January 2015

AbstractCanine hemangiosarcoma (HSA) is a neoplasm of vascular endothelial origin that has an aggressive biological behaviour, with less than 10% of dogs alive at 12‐months postdiagnosis. Treatment of choice consists of surgery followed by adjuvant doxorubicin‐based chemotherapy. We prospectively compared adjuvant doxorubicin and dacarbazine (ADTIC) to a traditional doxorubicin and cyclophosphamide (AC) treatment, aiming at determining safety and assessing whether this regimen prolongs survival and time to metastasis (TTM). Twenty‐seven dogs were enrolled; following staging work‐up, 18 were treated with AC and 9 with ADTIC. Median TTM and survival time were longer for dogs treated with ADTIC compared with those receiving AC (>550 versus 112 days, P = 0.021 and >550 versus 142 days, P = 0.011, respectively). Both protocols were well tolerated, without need for dose reduction or increased interval between treatments. A protocol consisting of combined doxorubicin and dacarbazine is safe in dogs with HSA and prolongs TTM and survival time.
Proton‐induced x‐ray fluorescence CT imaging
Authors: Bazalova‐Carter Magdalena , Ahmad Moiz , Matsuura Taeko , Takao Seishin , Matsuo Yuto , Fahrig Rebecca , Shirato Hiroki , Umegaki Kikuo , Xing Lei 
Published: January 2015

Purpose:To demonstrate the feasibility of proton‐induced x‐ray fluorescence CT (pXFCT) imaging of gold in a small animal sized object by means of experiments and Monte Carlo (MC) simulations.Methods:First, proton‐induced gold x‐ray fluorescence (pXRF) was measured as a function of gold concentration. Vials of 2.2 cm in diameter filled with 0%–5% Au solutions were irradiated with a 220 MeV proton beam and x‐ray fluorescence induced by the interaction of protons, and Au was detected with a 3 × 3 mm2 CdTe detector placed at 90° with respect to the incident proton beam at a distance of 45 cm from the vials. Second, a 7‐cm diameter water phantom containing three 2.2‐diameter vials with 3%–5% Au solutions was imaged with a 7‐mm FWHM 220 MeV proton beam in a first generation CT scanning geometry. X‐rays scattered perpendicular to the incident proton beam were acquired with the CdTe detector placed at 45 cm from the phantom positioned on a translation/rotation stage. Twenty one translational steps spaced by 3 mm at each of 36 projection angles spaced by 10° were acquired, and pXFCT images of the phantom were reconstructed with filtered back projection. A simplified geometry of the experimental data acquisition setup was modeled with the MC TOPAS code, and simulation results were compared to the experimental data.Results:A linear relationship between gold pXRF and gold concentration was observed in both experimental and MC simulation data (R2 > 0.99). All Au vials were apparent in the experimental and simulated pXFCT images. Specifically, the 3% Au vial was detectable in the experimental [contrast‐to‐noise ratio (CNR) = 5.8] and simulated (CNR = 11.5) pXFCT image. Due to fluorescence x‐ray attenuation in the higher concentration vials, the 4% and 5% Au contrast were underestimated by 10% and 15%, respectively, in both the experimental and simulated pXFCT images.Conclusions:Proton‐induced x‐ray fluorescence CT imaging of 3%–5% gold solutions in a small animal sized water phantom has been demonstrated for the first time by means of experiments and MC simulations.