bluuebunny/crossref_metadata_2025 huggingface dataset:
Cohaesibacter haloalkalitolerans sp. nov., isolated from a soda lake, and emended description of the genus Cohaesibacter
Authors: Sultanpuram Vishnuvardhan Reddy , Lodha Tushar Dilipchand , Chintalapati Venkata Ramana , Chintalapati Sasikala
Published: June 2013

Two novel Gram-stain-negative, motile, catalase-negative and oxidase-positive strains of bacteria (JC131T and JC112) were isolated from Lonar, a soda lake in India. Based on 16S rRNA gene sequence similarity studies, strains JC131T and JC112 belong to the family

Cohaesibacteraceae

of the class

Alphaproteobacteria

and were most closely related to

Cohaesibacter marisflavi

DQHS21T (98.0 %) and

Cohaesibacter gelatinilyticus

CL-GR15T (96.0 %). Polar lipids of strains JC131T and JC112 include phosphatidylglycerol, phosphatidylethnolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol and two unidentified lipids (L1 and L2). Both strains have diplopterol, diploptene, an unidentified hopane (UH) and bacteriohopane derivatives (BHD1 and 2) as major hopanoids and an unidentified pigment (P1). The predominant isoprenoid quinone of both strains was ubiquinone-10 (Q10). Whole-cell fatty acid analysis of both strains revealed that C18 : 1ω7c was the predominant cellular fatty acid and significant proportions of C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), 11-methyl C18 : 1ω7c, C18 : 1ω9c, C18 : 0 and C20 : 1ω7c were also detected. The DNA G+C content of strains JC131T and JC112 was 54.6 and 53.8 mol%, respectively. The genome reassociation (based on DNA–DNA hybridization) of strains JC131T and JC112 with

Cohaesibacter marisflavi

NCCB 100300T ( = DQHS21T) was about 58 %, while between JC131T and JC112 it was about 87 %. On the basis of physiological, biochemical and chemotaxonomical properties, strains JC131T and JC112 are differentiated from the other two members of the genus

Cohaesibacter

. Strains JC131T and JC112 represent a novel species of the genus

Cohaesibacter

, for which the name Cohaesibacter haloalkalitolerans sp. nov. is proposed. The type strain is JC131T ( = KCTC 32038T = NBRC 109022T). An emended description of the genus

Cohaesibacter

is presented.
Spelaeicoccus albus gen. nov., sp. nov., an actinobacterium isolated from a natural cave
Authors: Lee Soon Dong
Published: June 2013

A novel Gram-stain-positive, non-endospore-forming, coccoid actinobacterium, designated strain D3-40T, was isolated from the soil of a natural cave and characterized by means of a polyphasic taxonomic analysis. 16S rRNA gene sequence analysis showed that strain D3-40T is a member of the suborder

Micrococcineae

and forms a distinct branch at the base of a

Brevibacteriaceae

cluster. Its closest relative is the type strain of

Brevibacterium samyangense

(95.7 % sequence similarity). The chemotaxonomic characteristics were as follows: the cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid; the major menaquinone was MK-9(H2); the polar lipids consisted of phosphatidylglycerol, phosphatidylinositol, an unknown glycolipid and an unknown phospholipid; the major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C16 : 0 and cyclohexyl-C17 : 0; mycolic acids were absent. The G+C content of the DNA was 64.3 mol%. On the basis of morphological, chemotaxonomic and phylogenetic data, it is suggested that the organism represents a novel species of a new genus within the family

Brevibacteriaceae

, for which the name Spelaeicoccus albus gen. nov., sp. nov. is proposed. The type strain of the type species is D3-40T ( = KCTC 29141T = DSM 26341T).
Halomonas zincidurans sp. nov., a heavy-metal-tolerant bacterium isolated from the deep-sea environment
Authors: Xu Lin , Xu Xue-Wei , Meng Fan-Xu , Huo Ying-Yi , Oren Aharon , Yang Jun-Yi , Wang Chun-Sheng
Published: June 2013

A Gram-stain-negative, aerobic, rod-like, motile by peritrichous flagella and moderately halophilic bacterium, designated strain B6T, was isolated a deep-sea sediment collected from the South Atlantic Ocean. The isolate grew with 0.5–15 % (w/v) NaCl, at 4–37 °C and pH 5.0–8.5 and showed a high tolerance to zinc, manganese, cobalt and copper ions. The major fatty acids were C16 : 0, C19 : 0 cyclo ω8c, C12 : 0 3-OH and C12 : 0. The predominant ubiquinone was Q-9. The genomic DNA G+C content was 61.1 mol%. Phylogenetic analysis based on 16S rRNA gene comparisons indicated that strain B6T belonged to the genus

Halomonas

, and the closest relative was

Halomonas xinjiangensis

TRM 0175T (96.1 %). Based upon the phenotypic, chemotaxonomic and genetic data, strain B6T represents a novel species from the genus

Halomonas

, for which the name Halomonas zincidurans sp. nov. is proposed. The type strain is B6T ( = CGMCC 1.12450T = JCM 18472T).
Isolation and characterization of Desulfocurvus thunnarius sp. nov., a sulfate-reducing bacterium isolated from an anaerobic sequencing batch reactor treating cooking wastewater
Authors: Hamdi Olfa , Ben Hania Wajdi , Postec Anne , Bartoli Manon , Hamdi Moktar , Bouallagui Hassib , Fauque Guy , Ollivier Bernard , Fardeau Marie-Laure
Published: June 2013

A novel anaerobic, chemo-organotrophic, sulfate-reducing bacterium, designated strain Olac 40T, was isolated from a Tunisian wastewater digestor. Cells were curved, motile rods or vibrios (5.0–7.0×0.5 µm). Strain Olac 40T grew at temperatures between 15 and 50 °C (optimum 40 °C), and between pH 5.0 and 9.0 (optimum pH 7.1). It did not require NaCl for growth but tolerated it up to 50 g l−1 (optimum 2 g l−1). In the presence of sulfate or thiosulfate, strain Olac 40T used lactate, pyruvate and formate as energy sources. Growth was observed on H2 only in the presence of acetate as carbon source. In the presence of sulfate or thiosulfate, the end products of lactate oxidation were acetate, sulfide and CO2. Sulfate, thiosulfate and sulfite were used as terminal electron acceptors, but not elemental sulfur, nitrate or nitrite. The genomic DNA G+C content of strain Olac 40T was 70 mol%. The profile of polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and four phospholipids. The main fatty acids were C16 : 0, anteiso-C15 : 0 and iso-C15 : 0. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Olac 40T was affiliated with the family
Desulfovibrionaceae
within the class
Deltaproteobacteria
. On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain Olac 40T is proposed to be assigned to a novel species of the genus
Desulfocurvus
, for which the name Desulfocurvus thunnarius is proposed. The type strain is Olac 40T ( = DSM 26129T = JCM 18546T).
Georgenia sediminis sp. nov., a moderately thermophilic actinobacterium isolated from sediment
Authors: You Zhi-Qing , Li Jie , Qin Sheng , Tian Xin-Peng , Wang Fa-Zuo , Zhang Si
Published: June 2013

A Gram-stain-positive actinobacterium, designated strain SCSIO 15020T, was isolated from sediment of the South China Sea, and characterized by using a polyphasic approach. The temperature range for growth was 24–60 °C, with optimal growth occurring at 50 °C. The pH range for growth was 6–10 (optimum pH 8–9). The NaCl concentration range for growth was 0–5 % (w/v). The peptidoglycan type was A4α. Polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unknown polar lipid. The major menaquinone was MK-8(H4); MK-7(H4) was present as a minor component. The major fatty acids (>5 %) were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0. The DNA G+C content of strain SCSIO 15020T was 73.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SCSIO 15020T belonged to the genus

Georgenia

, with the closest neighbours being

Georgenia muralis

1A-CT (96.3 % similarity),

Georgenia thermotolerans

TT02-04T (95.7 %) and

Georgenia ruanii

YIM 004T (95.6 %). Based on evidence from the present polyphasic study, strain SCSIO 15020T is considered to represent a novel species of the genus

Georgenia

, for which the name Georgenia sediminis sp. nov. is proposed. The type strain is SCSIO 15020T ( = DSM 25884T = NBRC 108941T).
Shimia haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai
Authors: Hyun Dong-Wook , Kim Min-Soo , Shin Na-Ri , Kim Joon Yong , Kim Pil Soo , Whon Tae Woong , Yun Ji-Hyun , Bae Jin-Woo
Published: June 2013

A novel Gram-stain-negative, motile, rod-shaped bacterium, designated strain WM35T, was isolated from the intestinal tract of an abalone, Haliotis discus hannai, which was collected from the northern coast of Jeju in Korea. The cells of the isolate grew optimally at 30 °C, pH 7, and with 3 % (w/v) NaCl. Based on 16S rRNA gene sequence similarity comparisons, strain WM35T was grouped in the genus

Shimia

and was closely related to the type strains of

Shimia isoporae

(98.7 % similarity) and

Shimia marina

(97.8 % similarity). The major cellular fatty acids were summed feature 8 and C16 : 0 2-OH. Ubiquinone Q-10 was the predominant respiratory quinone. The polar lipids of strain WM35T comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid and an unidentified lipid. The DNA G+C content of the isolate was 53.8 mol%. DNA–DNA hybridization values indicated <16 % genomic relatedness with members of the genus

Shimia

. The physiological, chemical and genotypic analyses indicated that strain WM35T represents a novel species of the genus

Shimia

, for which the name Shimia haliotis sp. nov. is proposed. The type strain is WM35T ( = KACC 17212T = JCM 18870T).
Allokutzneria multivorans sp. nov., an actinomycete isolated from soil
Authors: Cao Yan-Ru , Chen Xiu , Jiang Yi , Wang Li-Song , Jiang Cheng-Lin
Published: June 2013

An actinomycete with well-branched mycelia, designated strain YIM 120521T, was isolated from soil collected from the banks of the Nujiang River, Yunnan Province, south-west China. Both aerial and substrate mycelia were white and non-pigmented. Growth was observed at 4–40 °C (optimum 28 °C), pH 6.0–9.0 (optimum 7.0) and in 0–4 % (w/v) NaCl (optimum 0 %). Analysis of the 16S rRNA gene sequence revealed that strain YIM 120521T belongs to the genus

Allokutzneria

with the highest sequence similarity to

Allokutzneria albata

DSM 44149T (98.4 %). However, the mean DNA–DNA relatedness value between the two strains was below 70 %. Chemotaxonomic characteristics supported the inclusion of strain YIM 120521T in the genus

Allokutzneria

, with rhamnose, arabinose, glucose, galactose and mannose as the whole-cell sugars, meso-diaminopimelic acid as the cell-wall diamino acid and MK-9(H4) as the predominant menaquinone. On the basis of physiological, biochemical and chemotaxonomic characteristics, strain YIM 120521T is considered to represent a novel species of the genus

Allokutzneria

, for which the name Allokutzneria multivorans sp. nov. is proposed. The type strain is YIM 120521T ( = JCM 17342T = DSM 45532T).
Competition between virus-derived and endogenous small RNAs regulates gene expression inCaenorhabditis elegans
Authors: Sarkies Peter , Ashe Alyson , Le Pen Jérémie , McKie Mikel A. , Miska Eric A.
Published: June 2013

Positive-strand RNA viruses encompass more than one-third of known virus genera and include many medically and agriculturally relevant human, animal, and plant pathogens. The nematodeCaenorhabditis elegansand its natural pathogen, the positive-strand RNA virus Orsay, have recently emerged as a new animal model to understand the mechanisms and evolution of innate immune responses. In particular, the RNA interference (RNAi) pathway is required forC. elegansresistance to viral infection. Here we report the first genome-wide analyses of gene expression upon viral infection inC. elegans. Using the laboratory strain N2, we identify a novelC. elegansinnate immune response specific to viral infection. A subset of these changes is driven by the RNAi response to the virus, which redirects the Argonaute protein RDE-1 from its endogenous small RNA cofactors, leading to loss of repression of endogenous RDE-1 targets. Additionally, we show that aC. eleganswild isolate, JU1580, has a distinct gene expression signature in response to viral infection. This is associated with a reduction in microRNA (miRNA) levels and an up-regulation of their target genes. Intriguingly, alterations in miRNA levels upon JU1580 infection are associated with a transformation of the antiviral transcriptional response into an antibacterial-like response. Together our data support a model whereby antiviral RNAi competes with endogenous small RNA pathways, causing widespread transcriptional changes. This provides an elegant mechanism forC. elegansto orchestrate its antiviral response, which may have significance for the relationship between small RNA pathways and immune regulation in other organisms.
De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements
Authors: Schlesinger Felix , Smith Andrew D. , Gingeras Thomas R. , Hannon Gregory J. , Hodges Emily
Published: June 2013

Deep sequencing of mammalian DNA methylomes has uncovered a previously unpredicted number of discrete hypomethylated regions in intergenic space (iHMRs). Here, we combined whole-genome bisulfite sequencing data with extensive gene expression and chromatin-state data to define functional classes of iHMRs, and to reconstruct the dynamics of their establishment in a developmental setting. Comparing HMR profiles in embryonic stem and primary blood cells, we show that iHMRs mark an exclusive subset of active DNase hypersensitive sites (DHS), and that both developmentally constitutive and cell-type-specific iHMRs display chromatin states typical of distinct regulatory elements. We also observe that iHMR changes are more predictive of nearby gene activity than the promoter HMR itself, and that expression of noncoding RNAs within the iHMR accompanies full activation and complete demethylation of mature B cell enhancers. Conserved sequence features corresponding to iHMR transcript start sites, including a discernible TATA motif, suggest a conserved, functional role for transcription in these regions. Similarly, we explored both primate-specific and human population variation at iHMRs, finding that while enhancer iHMRs are more variable in sequence and methylation status than any other functional class, conservation of the TATA box is highly predictive of iHMR maintenance, reflecting the impact of sequence plasticity and transcriptional signals on iHMR establishment. Overall, our analysis allowed us to construct a three-step timeline in which (1) intergenic DHS are pre-established in the stem cell, (2) partial demethylation of blood-specific intergenic DHSs occurs in blood progenitors, and (3) complete iHMR formation and transcription coincide with enhancer activation in lymphoid-specified cells.
Live Cell Imaging of Cytoplasmic Ca2+ Dynamics in Arabidopsis Guard Cells
Authors: Behera Smrutisanjita , Kudla Jörg
Published: July 2013

This protocol describes a classical method for measuring cytoplasmic Ca2+ dynamics in Arabidopsis thaliana guard cells. The Förster (fluorescence) resonance energy transfer (FRET)-based genetically modified Ca2+ indicator Yellow Cameleon YC3.6, under the control of the guard cell-specific promoter GC1, is used for Ca2+ measurements.
Electrophoretic Mobility-Shift Assays
Authors: Carey Michael F. , Peterson Craig L. , Smale Stephen T.
Published: July 2013

In an electrophoretic mobility-shift assay (EMSA, or simply “gel shift”), a 32P-labeled DNA fragment containing a specific DNA site is incubated with a cognate DNA-binding protein. The protein–DNA complexes are separated from free (unbound) DNA by electrophoresis through a nondenaturing polyacrylamide gel. The protein retards the mobility of the DNA fragments to which it binds. Thus, the free DNA will migrate faster than the DNA–protein complex. An image of the gel is used to reveal the positions of the free and bound radiolabeled DNAs.
Counting and Measuring Ultrastructural Features of Biological Samples
Authors: West Mark J.
Published: July 2013

Ultrastructural features of cells can be fractions of a micrometer in diameter, and electron microscopy is needed to resolve them to a degree that is compatible with stereological techniques. Because the focal depth of transmission electron microscopy (TEM) images is thousands of times greater than the thickness of the sections used with TEM, virtual sectioning of sections suitable for TEM is not possible, as it is with light microscopy and the optical disector probe. With features the size of neuronal synapses, for example, this necessitates the use of physical sections and physical disectors. Regardless of how the imaging is performed, the design of stereological studies for quantifying ultrastructural features will be essentially the same as that used in the example described here, which uses physically separated ultrathin sections viewed with conventional TEM to estimate the number and size of synapses in a particular brain region.
RpoS and oxidative stress conditions regulate succinyl‐CoA: 3‐ketoacid‐coenzyme A transferase (SCOT) expression in Burkholderia pseudomallei
Authors: Chutoam Palatip , Charoensawan Varodom , Wongtrakoongate Patompon , Kum‐arth Apiratana , Buphamalai Pisanu , Tungpradabkul Sumalee
Published: June 2013

Burkholderia pseudomallei, a pathogenic gram‐negative bacterium, causes the severe human disease melioidosis. This organism can survive in eukaryotic host cells by escaping reactive oxygen species via the regulation of stress responsive sigma factors, including RpoS. In B. pseudomallei, RpoS has been reported to play a role in the oxidative stress response through enhanced activity of OxyR and catalase. In this study, the RpoS dependent oxidative stress responsive system was further characterized using comparative proteomic analysis. The proteomic profiles of wild‐type B. pseudomallei following exposure to H2O2 and between wild‐type and the rpoS mutant strains were analyzed. Using stringent criteria, 13 oxidative responsive proteins, eight of which are regulated by RpoS, were identified with high confidence. It was observed that ScoA, a subunit of the SCOT enzyme not previously shown to be involved directly in the oxidative stress response, is significantly down‐regulated after hydrogen peroxide treatment. ScoA and ScoB have been predicted to be organized in a single operon using computational methods: in this study it was confirmed by RT‐PCR that these genes are indeed co‐transcribed as a single mRNA. The present study is the first to report a role for RpoS in the down‐regulation of SCOT expression in response to oxidative stress in B. pseudomallei.
Stocks‐to‐use ratios and prices as indicators of vulnerability to spikes in global cereal markets
Authors: Bobenrieth Eugenio , Wright Brian , Zeng Di
Published: June 2013

We identify critical stocks‐to‐use ratios (SURs) for major grains and for an index of total calories from these grains. The latter appears to be a promising indicator of vulnerability to large price spikes when the current price shows no cause for concern. More generally, our results suggest that stocks data, though no doubt unreliable, can be valuable complements to price data as indicators of vulnerability to shortages and price spikes.
Prognostic impact of monocyte count at presentation in mantle cell lymphoma
Authors: Aprile von Hohenstaufen Kathrin , Conconi Annarita , de Campos Cassio Polpo , Franceschetti Silvia , Bertoni Francesco , Margiotta Casaluci Gloria , Stathis Anastasios , Ghielmini Michele , Stussi Georg , Cavalli Franco , Gaidano Gianluca , Zucca Emanuele
Published: June 2013

An increased number of circulating monocytes at presentation has recently been associated with shorter survival in Hodgkin lymphoma, follicular lymphoma and diffuse large B cell lymphoma. This study aimed to assess the prognostic impact of the absolute monocyte count (AMC) at diagnosis in mantle cell lymphoma (MCL). AMC at diagnosis was available in 97 MCL cases recorded in the databases of the Oncology Institute of Southern Switzerland in Bellinzona (Switzerland) and the Division of Haematology of the Amedeo Avogadro University of Eastern Piedmont in Novara (Italy). With a median follow up of 7 years, the 5‐year overall survival was 29% for patients with AMC >0·50 × 109/l and 62% for patients with AMC ≤0·50 × 109/l (P = 0·008). Elevated AMC and beta‐2 microglobulin at diagnosis remained independent outcome predictors at multivariate analysis, controlling for the MCL International Prognostic Index (MIPI), and have been used to build a simple prognostic scoring system. In this relatively small and heterogeneous series an increased AMC identified poor‐risk patients. Our results suggest that AMC together with the beta‐2 microglobulin level might provide an inexpensive way to stratify MCL patient risk as a complement to the MIPI, which was confirmed to be a very powerful prognostic tool.
Effective estimation of correct platelet counts in pseudothrombocytopenia using an alternative anticoagulant based on magnesium salt
Authors: Schuff‐Werner Peter , Steiner Michael , Fenger Sebastian , Gross Hans‐Jürgen , Bierlich Alexa , Dreissiger Katrin , Mannuß Steffen , Siegert Gabriele , Bachem Maximilian , Kohlschein Peter
Published: June 2013

Pseudothrombocytopenia remains a challenge in the haematological laboratory. The pre‐analytical problem that platelets tend to easily aggregate in vitro, giving rise to lower platelet counts, has been known since ethylenediamine‐tetra acetic acid EDTA and automated platelet counting procedures were introduced in the haematological laboratory. Different approaches to avoid the time and temperature dependent in vitro aggregation of platelets in the presence of EDTA were tested, but none of them proved optimal for routine purposes. Patients with unexpectedly low platelet counts or flagged for suspected aggregates, were selected and smears were examined for platelet aggregates. In these cases patients were asked to consent to the drawing of an additional sample of blood anti‐coagulated with a magnesium additive. Magnesium was used in the beginning of the last century as anticoagulant for microscopic platelet counts. Using this approach, we documented 44 patients with pseudothrombocytopenia. In all cases, platelet counts were markedly higher in samples anti‐coagulated with the magnesium containing anticoagulant when compared to EDTA‐anticoagulated blood samples. We conclude that in patients with known or suspected pseudothrombocytopenia the magnesium‐anticoagulant blood samples may be recommended for platelet counting.
VisRuption: Intuitive and Efficient Visualization of Temporal Airline Disruption Data
Authors: Rosenthal P. , Pfeiffer L. , Müller N. H. , Ohler P.
Published: July 2013

The operation of an airline is a very complex task and disruptions to the planned operation can occur on very short notice. Already a small disruption like a delay of some minutes can cost the airline a tremendous amount of money. Hence, it is crucial to proactively control all operations of the airline and efficiently prioritize and handle disruptions. Due to the complex setting and the need for ad hoc decisions this task can only be carried out by human operation controllers. In the field of airline operations control there exists already a vast variety of different software in productive use. We analyze the different approaches from two of the market leaders and identify problematic design choices. We take into account this analysis and develop a set of rules for an intuitive visualization of airline disruption data. Finally, we introduce our tool for visualizing such data which complies to these rules. The visualization enables the user to gain a fast overview over the current problem situation and to intuitively prioritize different problems and problem hierarchies. The efficiency of the design is evaluated with the help of a user study which shows that the new system significantly outperforms the current state of the art.
A Visual Approach to Investigating Shared and Global Memory Behavior of CUDA Kernels
Authors: Rosen Paul
Published: July 2013

We present an approach to investigate the memory behavior of a parallel kernel executing on thousands of threads simultaneously within the CUDA architecture. Our top‐down approach allows for quickly identifying any significant differences between the execution of the many blocks and warps. As interesting warps are identified, we allow further investigation of memory behavior by visualizing the shared memory bank conflicts and global memory coalescence, first with an overview of a single warp with many operations and, subsequently, with a detailed view of a single warp and a single operation. We demonstrate the strength of our approach in the context of a parallel matrix transpose kernel and a parallel 1D Haar Wavelet transform kernel.
Scale‐Stack Bar Charts
Authors: Hlawatsch M. , Sadlo F. , Burch M. , Weiskopf D.
Published: July 2013

It is difficult to create appropriate bar charts for data that cover large value ranges. The usual approach for these cases employs a logarithmic scale, which, however, suffers from issues inherent to its non‐linear mapping: for example, a quantitative comparison of different values is difficult. We present a new approach for bar charts that combines the advantages of linear and logarithmic scales, while avoiding their drawbacks. Our scale‐stack bar charts use multiple scales to cover a large value range, while the linear mapping within each scale preserves the ability to visually compare quantitative ratios. Scale‐stack bar charts can be used for the same applications as classic bar charts; in particular, they can readily handle stacked bar representations and negative values. Our visualization technique is demonstrated with results for three different application areas and is assessed by an expert review and a quantitative user study confirming advantages of our technique for quantitative comparisons.
Visualizing Robustness of Critical Points for 2D Time‐Varying Vector Fields
Authors: Wang B. , Rosen P. , Skraba P. , Bhatia H. , Pascucci V.
Published: July 2013

Analyzing critical points and their temporal evolutions plays a crucial role in understanding the behavior of vector fields. A key challenge is to quantify the stability of critical points: more stable points may represent more important phenomena or vice versa. The topological notion of robustness is a tool which allows us to quantify rigorously the stability of each critical point. Intuitively, the robustness of a critical point is the minimum amount of perturbation necessary to cancel it within a local neighborhood, measured under an appropriate metric. In this paper, we introduce a new analysis and visualization framework which enables interactive exploration of robustness of critical points for both stationary and time‐varying 2D vector fields. This framework allows the end‐users, for the first time, to investigate how the stability of a critical point evolves over time. We show that this depends heavily on the global properties of the vector field and that structural changes can correspond to interesting behavior. We demonstrate the practicality of our theories and techniques on several datasets involving combustion and oceanic eddy simulations and obtain some key insights regarding their stable and unstable features.
Spatially Efficient Design of Annotated Metro Maps
Authors: Wu Hsiang‐Yun , Takahashi Shigeo , Hirono Daichi , Arikawa Masatoshi , Lin Chun‐Cheng , Yen Hsu‐Chun
Published: July 2013

Annotating metro maps with thumbnail photographs is a commonly used technique for guiding travelers. However, conventional methods usually suffer from small labeling space around the metro stations especially when they are interchange stations served by two or more metro lines. This paper presents an approach for aesthetically designing schematic metro maps while ensuring effective placement of large annotation labels that are sufficiently close to their corresponding stations. Our idea is to distribute such labels in a well‐balanced manner to labeling regions around the metro network first and then adjust the lengths of metro line and leader line segments, which allows us to fully maximize the space coverage of the entire annotated map. This is accomplished by incorporating additional constraints into the conventional mixed‐integer programming formulation, while we devised a three‐step algorithm for accelerating the overall optimization process. We include several design examples to demonstrate the spatial efficiency of the map layout generated using the proposed approach through minimal user intervention.
Synthetic Brainbows
Authors: Wan Y. , Otsuna H. , Hansen C.
Published: July 2013

Brainbow is a genetic engineering technique that randomly colorizes cells. Biological samples processed with this technique and imaged with confocal microscopy have distinctive colors for individual cells. Complex cellular structures can then be easily visualized. However, the complexity of the Brainbow technique limits its applications. In practice, most confocal microscopy scans use different florescence staining with typically at most three distinct cellular structures. These structures are often packed and obscure each other in rendered images making analysis difficult. In this paper, we leverage a process known as GPU framebuffer feedback loops to synthesize Brainbow‐like images. In addition, we incorporate ID shuffling and Monte‐Carlo sampling into our technique, so that it can be applied to single‐channel confocal microscopy data. The synthesized Brainbow images are presented to domain experts with positive feedback. A user survey demonstrates that our synthetic Brainbow technique improves visualizations of volume data with complex structures for biologists.
Complications after laparoscopic and open subtotal colectomy for inflammatory colitis: a case‐matched comparison
Authors: Parnaby C. N. , Ramsay G. , Macleod C. S. , Hope N. R. , Jansen J. O. , McAdam T. K.
Published: July 2013

Aim

The aim of this study was to compare the early postoperative outcome of patients undergoing laparoscopic subtotal colectomy with those undergoing open subtotal colectomy for colitis refractory to medical treatment.

Method

A retrospective observational study was carried out of patients who underwent subtotal colectomy for refractory colitis, at a single centre, between 2006 and 2012. Patients were matched for age, gender, American Society of Anesthesiology (ASA) grade, urgency of operation and immunosuppressant/modulator treatment. The primary outcome measure was the number of postoperative complications, classified using the Clavien–Dindo scale. Secondary end‐points included procedure duration, laparoscopic conversion rates, blood loss, 30‐day readmission rates and length of hospital stay.

Results

Ninety‐six patients were included, 39 of whom had laparoscopic surgery. Thirty‐two of these were matched to similar patients who underwent an open procedure. The overall duration of the procedure was longer for laparoscopic surgery than for open surgery (median: 240 vs 150 min, P < 0.005) but estimated blood loss was less (median: 75 vs 400 ml, P < 0.005). In the laparoscopic group, 23 patients experienced 27 complications, and in the open surgery group, 23 patients experienced 30 complications. Most complications were minor (Grade I/II), and the distribution of complications, by grade, was similar between the two groups. There was no statistically significant difference in 30‐day readmission rates between the laparoscopic and open groups (five readmissions vs eight readmissions, P = 0.536). Length of hospital stay was 4 days shorter for laparoscopic surgery, but this difference was not statistically significant (median: 7 vs 11 days, P = 0.159).

Conclusion

In patients requiring colectomy for acute severe colitis, laparoscopic surgery reduced blood loss but increased operating time and was not associated with a reduction in early postoperative complications, length of hospital stay or readmission rates.
Interstitial cells of Cajal: crucial for the development of megacolon in human Chagas' disease?
Authors: Jabari S. , da Silveira A. B. M. , de Oliveira E. C. , Quint K. , Wirries A. , Neuhuber W. , Brehmer A.
Published: July 2013

Aim

Megacolon, chronic dilation of a colonic segment,is accompanied by extensive myenteric neuron loss. However, this fails to explain unequivocally the formation of megacolon. We aimed to study further enteric structures that are directly or indirectly involved in colonic motility.

Method

From surgically removed megacolon segments of seven Chagasic patients, three sets of cryosections from oral, megacolonic and anal zones were immunohistochemically quadruple‐stained for smooth‐muscle actin (SMA), synaptophysin (SYN, for nerve fibres), S100 (glia) and c‐Kit (interstitial cells of Cajal, ICCs). Values of area measurements were related to the appropriate muscle layer areas and these proportions were compared with those of seven non‐Chagasic control patients.

Results

Whereas nerve and glia profile proportions did not mirror unequivocally the changes of Chagasic colon calibre (nondilation/dilation/nondilation), the proportions of SMA (i.e. muscle tissue density) and c‐Kit (i.e. ICC density) did so: they decreased from the oral to the megacolonic segment but increased to the anal zones (muscle tissue density: control 68.3%, oral 54.3%, mega 42.1%, anal 47.6%; ICC‐density: control 1.8%, oral 1.1%, mega 0.4, anal 0.8%).

Conclusion

Of the parameters evaluated, muscle tissue and ICC densities may be involved in the formation of Chagasic megacolon, although the mechanism of destruction cannot be deduced.
Applying the Taguchi method to examine the optimal parameters of cotton fabric dyeing by biodegradable surfactant
Authors: Kuo Chung‐Feng Jeffery , Dong Min‐Yan , Lan Wei‐Lun
Published: June 2013

Wastewater from the cotton fabric dyeing process causes high levels of environmental pollution. In order to address this problem, this study used a series of biodegradable surfactants in cotton fabric dyeing and applied the Taguchi method to analyse the optimal parameters of cotton fabric dyeing by such surfactants. The test parameters included the hydrophobic group chain length of the surfactant, and surfactant concentration and the processing time. This study calculated the signal‐to‐noise ratio of the experimental results by the‐larger‐the‐better characteristic and applied analysis of variance to discuss its impact on the dyeing results. The results confirmed that the most important influential factor is processing time, followed by surfactant concentration. Moreover, the addition of surfactant could promote a dyeing effect during processing.
Biotransformation of CI Acid Blue 113 and other dyes by Shewanella sp. P6
Authors: Biala Sunil , Chauhan Priyanka , Chadha Bhupinder Singh , Singh Bikram , Saini Harvinder Singh
Published: June 2013

The isolate P6, an indigenous Shewanella sp., was able to decolorise 90% of CI Acid Blue 113 in just 30 min of incubation under anoxic conditions. The decolorisation potential of cells was not significantly affected even in the presence of 2% (w/v) sodium chloride and 8% (w/v) sodium sulphate. Mass spectrometric analysis detected the formation of aniline sodium salt, 1,4‐diaminonaphthalene, 5‐amino‐8‐(phenylamino)‐naphthalene‐1‐sulphonic acid sodium salt and 8‐(phenylamino)‐naphthalene‐1‐sulphonic acid sodium salt. Further, cells of P6 decolorised the raw effluent collected from the equalisation tank of a textile industry wastewater treatment plant. The water‐soluble dyes/intermediates present in the sludge, generated after chemical flocculation of raw effluent, were transformed by P6 cells within 24 h of incubation under anoxic conditions. Thus, isolate P6 has a potential application in the biological treatment of liquid and solid waste of textile processing plants because of its efficient decolorisation and transformation properties.
Recipient's unemployment restricts access to renal transplantation
Authors: Sandhu Gurprataap S. , Khattak Muhammad , Pavlakis Martha , Woodward Robert , Hanto Douglas W. , Wasilewski Marcy A. , Dimitri Noelle , Goldfarb‐Rumyantzev Alexander
Published: July 2013

Equitable distribution of a scarce resource such as kidneys for transplantation can be a challenging task for transplant centers. In this study, we evaluated the association between recipient's employment status and access to renal transplantation in patients with end‐stage renal disease (ESRD). We used data from the United States Renal Data System (USRDS). The primary variable of interest was employment status at ESRD onset. Two outcomes were analyzed in Cox model: (i) being placed on the waiting list for renal transplantation or being transplanted (whichever occurred first); and (ii) first transplant in patients who were placed on the waiting list. We analyzed 429 409 patients (age of ESRD onset 64.2 ± 15.2 yr, 55.0% males, 65.1% White). Compared with patients who were unemployed, patients working full time were more likely to be placed on the waiting list/transplanted (HR 2.24, p < 0.001) and to receive a transplant once on the waiting list (HR 1.65, p < 0.001). Results indicate that recipient's employment status is strongly associated with access to renal transplantation, with unemployed and partially employed patients at a disadvantage. Adding insurance status to the model reduces the effect size, but the association still remains significant, indicating additional contribution from other factors.
The survival outcomes following liver transplantation (SOFT) score: validation with contemporaneous data and stratification of high‐risk cohorts
Authors: Rana Abbas , Jie Tun , Porubsky Marian , Habib Shahid , Rilo Horacio , Kaplan Bruce , Gruessner Angelika , Gruessner Rainer
Published: July 2013

Models to project survival after liver transplantation are important to optimize outcomes. We introduced the survival outcomes following liver transplantation (SOFT) score in 2008 (1) and designed to predict survival in liver recipients at three months post‐transplant with a C statistic of 0.70. Our objective was to validate the SOFT score, with more contemporaneous data from the OPTN database. We also applied the SOFT score to cohorts of the sickest transplant candidates and the poorest‐quality allografts. Analysis included 21 949 patients transplanted from August 1, 2006, to October 1, 2010. Kaplan–Meier survival functions were used for time‐to‐event analysis. Model discrimination was assessed using the area under the receiver operating characteristic (ROC) curve. We validated the SOFT score in this cohort of 21 949 liver recipients. The C statistic was 0.70 (CI 0.68–0.71), identical to the original analysis. When applied to cohorts of high‐risk recipients and poor‐quality donor allografts, the SOFT score projected survival with a C statistic between 0.65 and 0.74. In this study, a validated SOFT score was informative among cohorts of the sickest transplant candidates and the poorest‐quality allografts.
A population study of fractures: what we can learn and what we cannot learn
Authors: Henderson Richard
Published: June 2013

This commentary is on the original article by Uddenfeldt Wort et al. on pages 821–826 of this issue.
Assessment of Mitral Annular and Velocity Vector Imaging in Acute Myopericarditis
Authors: Lynch Matthew , O'Donnell Robert , Weintraub Neal L. , López‐Candales Angel
Published: July 2013

A 25‐year‐old student presenting with pleuritic chest pain, elevated troponin levels and subtle electrocardiogram abnormalities was treated for presumptive myopericarditis. On echocardiography, a lower than expected mitral annular displacement and systolic velocity were identified along with abnormalities in left ventricular strain generation that matched areas of edema and necrosis by cardiac magnetic resonance imaging. The patient was treated with nonsteroidal antiinflammatory drugs and colchicine, and both the symptoms and echocardiographic abnormalities rapidly resolved. These novel findings suggest that changes in mitral annular displacement and systolic velocity occur in acute myopericarditis and may be useful in following the course of the disease
Molecular phylogeny and pathotyping of Fusarium solani: a causal agent of Dalbergia sissoo decline
Authors: Arif M. , Zaidi N. W. , Haq Q. M. R. , Singh Y. P. , Khan S. , Singh U. S.
Published: June 2013

Sissoo (Dalbergia sissoo), commonly known as shisham, is amongst the finest woods of South Asia, but ‘wilt’ disease has caused a rapid decline in this species. The cause of the disease remains uncertain. The aim of this study is to identify the causal agent of the disease and characterize isolates made from diseased trees, based on genomic data and variations in virulence. Samples of infected roots, stems and the ooze exuded from infected trees were obtained from plants showing symptoms in different geographical regions of India for the isolation of microorganisms. Isolates were used to inoculate healthy plants. Based on the morphological characteristics, genus‐ and species‐specific PCR, and in silico analysis of 5.8S rDNA‐ITS regions, of the 38 fungal isolates, 24 and 14 were identified as Fusarium solani and Fusarium sp., respectively. In a pathotyping study, eighteen F. solani isolates, isolated from roots and stem parts of symptomatic plants, induced typical wilt symptoms when inoculated through soil and roots on D. sissoo seedlings of 1–15 months in age. The population of F. solani was the highest in infected roots and the lowest in parts of stems, gradually decreasing with height, and was isolated constantly up to approximately 40% height of the seedling. F. solani isolates used in inoculations were successfully re‐isolated from the rhizosphere, infected roots and wilted stems, as confirmed using isolate‐specific DNA fingerprints. Molecular phylogenies based on rDNA‐ITS sequences showed that the 38 isolates fell into 2 groups. Group I comprised of F. solani isolates from D. sissoo and F. solani sequences in the NCBI GenBank database, whereas group II included Fusarium isolates other than F. solani. These results are helpful in developing integrated control measures for this highly variable pathogen and to establish a base for future population studies.
Children often present with infantile spasms after herpetic encephalitis
Authors: Aznar Laín Gemma , Dellatolas Georges , Eisermann Monika , Boddaert Nathalie , Chiron Catherine , Bulteau Christine , Monteiro José P. , An Isabelle , Pédespan Jean‐Michel , Cancès Claude , Peudenier Sylvianne , Barthez Marie‐Anne , Milh Mathieu , Dorfmuller Georges , Héron Bénédicte , Nabbout Rima , Grevent David , Dulac Olivier
Published: July 2013

Purpose

To determine what epilepsy types occur after herpetic encephalitis and what are the determinant factors for subsequent infantile spasms.

Methods

We analyzed retrospectively the clinical history of 22 patients, referred to Necker and Saint Vincent de Paul Hospitals (Paris) through the French pediatric epilepsy network from March 1986 to April 2010 and who developed epilepsy some months after herpetic encephalitis. We focused on seizure semiology with video–electroencephalography (EEG) recording, and on neuroradiology and epilepsy follow‐up.

Key Findings

Fourteen patients developed pharmacoresistant spasms, and eight developed focal epilepsy, but none had both. The patients who developed spasms were more frequently younger than 30 months at age of onset of epilepsy and had herpetic encephalitis earlier (mean 10.6 months of age) than those who developed focal epilepsy (mean 59.7 and 39.6 months, respectively). Epilepsy follow‐up was similar in both groups (8.5 and 11 years, respectively). We found 26 affected cerebral areas; none alone was related to the development of epileptic spasms.

Significance

Risk factors to develop epileptic spasms were to have had herpetic encephalitis early (mean 10 months); to be significantly younger at onset of epilepsy (mean 22.1 months); and to have cerebral lesions involving the insula, the hippocampus, and the temporal pole.
Different strains of Propionibacterium acnes modulate differently the cutaneous innate immunity
Authors: Jasson Fiona , Nagy Istvan , Knol Anne Chantal , Zuliani Thomas , Khammari Amir , Dréno Brigitte
Published: June 2013

Acne is a chronic inflammatory illness of the pilosebaceous follicle where innate immunity plays a central role. In acne, the density of Propionibacterium acnes is increased in the pilosebaceous unit. We hypothesized that the severity of acne is not only dependent on the proliferation of P. acnes but also dependent on the pro‐inflammatory potential of P. acnes strains and consequently constitutes potential triggering factor for acne scarring. We investigated pro‐inflammatory potential of five different strains of P. acnes and P. avidum in skin explants and the preventive effect of zinc gluconate. The expression of immune markers was studied by immunohistochemistry, RT‐qPCR and ELISA. P. acnes strains modulate differently the expression of immune markers both at gene and at protein levels. P. acnes type III had the highest pro‐inflammatory potential by up‐regulating the expression of PAR‐2, TNF‐alpha, MMP‐13 and TIMP‐2, whereas P. avidum had the weakest by up‐regulating only MMP‐13 and TIMP‐2. Preincubation of zinc gluconate, which is a modulator of innate immunity, down‐regulates the expression of most immune markers induced by P. acnes, PAR‐2, TIMP‐2, up‐regulates MMP‐1, TIMP‐1. Our results demonstrate that different P. acnes strains have different inflammatory potential targeting markers of cutaneous innate immunity, and that inflammatory potential can be down‐regulated by zinc gluconate. As such, the inflammatory potential of P. acnes strains on acne skin may influence the severity of inflammatory acne lesions and scars.
Spatial genetic analysis of two polyploid macrophytes reveals high connectivity in a modified wetland
Authors: James Elizabeth A. , Jordan Rebecca , Griffin Philippa C.
Published: July 2013

Modification of aquatic habitats by human activity changes physical and genetic connections and poses a risk to the ecological stability of wetlands. Altered water regimes and land use can change dispersal patterns due to altered landscape permeability that will vary with the dispersal vector.

We hypothesised that modifications to the Gippsland Lakes wetlands of south‐eastern Australia, affecting connectivity over many decades, would be reflected differently in the genetic structure of two widespread polyploid wetland plants, Phragmites australis and Triglochin procera due to different dispersal pathways.

We found that genetic connectivity over the region, assessed with microsatellite markers, was high for both species. Phragmites australis consisted of a single genetic cluster, supporting the notion that wind is its primary dispersal vector. Contrary to expectations, Triglochin procera also showed high genetic connectivity, despite some differentiation between two wetland regions (Lake King and Lake Wellington). Spatial genetic autocorrelation revealed a high incidence of local‐scale gene flow in both species.

We conclude that despite significant anthropogenic habitat modification, genetic connectivity remains high for both species. The current patterns may reflect historical connectivity, with plant longevity buffering the effect of disruptions to gene flow, or contemporary dispersal may be sufficient to overcome anthropogenic influences. Waterbirds are likely to be a more significant dispersal vector of T. procera than anticipated because water dispersal alone cannot explain connectivity across river systems. As wetland systems are put under increasing pressure, we need to ensure that natural dispersal mechanisms still operate to maintain connectivity.