bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclear expression of S‐phase kinase–associated protein 2 predicts poor prognosis of hepatocellular carcinoma
Authors: SHIN EUN , KIM SOO‐HEE , JEONG HAE‐YEON , JANG JA‐JUNE , LEE KYUNGBUN 
Published: November 2011

Shin E, Kim S‐H, Jeong H‐Y, Jang J‐J, Lee K. Nuclear expression of S‐phase kinase–associated protein 2 predicts poor prognosis of hepatocellular carcinoma. APMIS 2012; 120: 349–57.The S‐phase kinase–associated protein 2 (Skp2), which ubiquitinates the cell cycle inhibitor p27Kip1 and targets it for degradation, is commonly overexpressed in human cancers and is associated with poor prognosis in several cancers. The aim of this study was to investigate Skp2 expression and its clinicopathologic significance in surgically resected hepatocellular carcinomas. We collected 359 hepatocellular carcinoma samples and evaluated Skp2 protein expression in cytoplasmic and nuclear fractions by immunohistochemistry using a tissue microarray method. Among the 359 patients, nuclear expression of Skp2 was observed in 41 (10.38%), and cytoplasmic expression of Skp2 was observed in 195 (49.37%). Of the several clinicopathologic variables examined, high Edmonson‐Steiner grade and early recurrence correlated with nuclear expression of Skp2 (p = 0.000 and 0.022, respectively). Cytoplasmic expression of Skp2 correlated negatively with microvascular and macrovascular invasion, tumor size, histologic grade, and overall survival. Multivariate analysis revealed that nuclear expression of Skp2 correlated with short disease‐free survival. Our findings suggest that nuclear expression of Skp2 may be used as an independent predictor of poor prognosis for hepatocellular carcinoma, whereas cytoplasmic expression of Skp2 may indicate less aggressive disease.
Sebaceous hyperplasia within epidermis after scald
Authors: Yin ZhiQiang , Xu JiaLi , Luo Dan , Zhang MeiHua 
Published: November 2011

A 16‐year‐old girl with polycystic ovarian syndrome presented with numerous rufous papules arising within a large depigmented macule that developed following a severe scald injury on the back. Histopathology revealed that many mature sebaceous glands were growing in the middle and bottom of the epidermis with slight acanthosis. On the basis of patient history, clinical manifestation and histopathology, we suggested that this patient's skin lesion be diagnosed as ‘sebaceous hyperplasia within epidermis after scald’.Yin Z, Xu J, Luo D, Zhang M. Sebaceous hyperplasia within epidermis after scald.
Actinic granuloma occurring in an unusual association with cutaneous B‐cell chronic lymphocytic leukemia
Authors: Kauffman Julia A. , Ivan Doina , Cutlan Jonathan E. , Hymes Sharon R. 
Published: November 2011

Granulomatous cutaneous reactions are well described in association with T‐cell non‐Hodgkin lymphoma and Hodgkin lymphoma, but are rarely seen in association with B‐cell non‐Hodgkin lymphoma or leukemia. We report a case of a 65‐year‐old woman with B‐cell chronic lymphocytic leukemia (CLL)/small lymphocytic lymphoma (SLL) who presented with multiple, tender, firm pink papules on the face, upper trunk and upper extremities 6 years after diagnosis of CLL. Biopsy revealed both palisading granulomatous dermatitis consistent with actinic granuloma and a dense perivascular lymphocytic infiltrate consistent with the patient's known history of leukemia. This is an unusual manifestation of cutaneous B‐cell CLL that is rarely seen.Kauffman JA, Ivan DS, Cutlan JE, Hymes SR. Actinic granuloma occurring in an unusual association with cutaneous B‐cell chronic lymphocytic leukemia.
Herpes simplex virus‐induced plasmacytic atypia
Authors: Boyd Alan S. , Zwerner Jeffrey P. , Miller Jami L. 
Published: November 2011

The clinical and histopathological features of cutaneous herpes simplex virus (HSV) infection have been well described. Genital herpetic infections are largely induced by HSV type 2, but 30% of cases can be caused by HSV type 1. Immunocompromised patients are known to exhibit atypical patterns of clinical presentation with variable lesion morphology and anatomic location. A subset of patients may show morphology such as nodules or verrucous lesions. Analogously, some biopsy specimens may show unusual microscopical features, such as a lack of keratinocyte cytopathology, lymphocyte infiltration or vasculopathic changes that are expected irrespective of the patient's immune status. We present the case of a patient carrying a previous diagnosis of pemphigus vulgaris, status posttreatment with methotrexate and prednisone, who developed a perineal ulcer exhibiting significant numbers of plasma cells, many of which were cytologically atypical. This morphology was suggestive of a hematopoietic malignancy. Immunoperoxidase staining for HSV decorated a focal collection of keratinocytes that lacked appreciable viral changes expected of HSV infection.Boyd AS, Zwerner JP, Miller JL. Herpes simplex virus‐induced plasmacytic atypia.
Exploitation of Fallen Diaspores by Ants: Are there Ant–Plant Partner Choices?
Authors: Christianini Alexander V. , Mayhé‐Nunes Antônio J. , Oliveira Paulo S. 
Published: November 2011

AbstractAnts frequently interact with fleshy fallen diaspores (fruits or seeds) not adapted for ant‐dispersal. Such interactions are usually considered as opportunistic, but recent evidence has indicated that these ants may differ in their effects on diaspore survival and plant recruitment. We investigated if partner choices are recognizable among genera of ants and plants, and if ant and plant traits may influence such preferences in cerrado (savanna‐like vegetation) from southeast Brazil. During a 2‐yr period, 521 ant–diaspore interactions were recorded through various methods, yielding 71 ant species and 38 plant species. Exploitation of fallen diaspores was common among several ant genera, and included carnivorous, omnivorous, and fungivorous ants. Contrary to others areas around the world, where true myrmecochory (seed dispersal by ants) is common among shrubs, ants also exploited diaspores from several cerrado trees. Plant life form, diaspore size, and ant body size did not seem to explain the pattern of interactions observed. Two subsets of preferential interactions, however, segregated fungivorous ants from another group composed of carnivorous and omnivorous ants, probably influenced by the chemical composition of the plant diaspores. Omnivorous ants usually remove the fleshy portion of diaspores on spot and probably provide limited benefits to plants. Carnivorous and fungivorous ants usually remove the whole diaspore to the nest. As each of these ant groups may influence the fitness of diaspores in different ways, there are possible subtle pathways for the evolution of partner choices between ants and these non‐myrmecochorous diaspores.
Nitrogen Addition Shapes Soil Phosphorus Availability in Two Reforested Tropical Forests in Southern China
Authors: Lu Xiankai , Mo Jiangming , Gilliam Frank S. , Fang Hua , Zhu Feifei , Fang Yunting , Zhang Wei , Huang Juan 
Published: November 2011

AbstractScant information is available on how soil phosphorus (P) availability responds to atmospheric nitrogen (N) deposition, especially in the tropical zones. This study examined the effect of N addition on soil P availability, and compared this effect between forest sites of contrasting land‐use history. Effects of N addition on soil properties, litterfall production, P release from decomposing litter, and soil P availability were studied in a disturbed (reforested pine forest with previous understory vegetation and litter harvesting) and a rehabilitated (reforested mixed pine/broadleaf forest with no understory vegetation and litter harvesting) tropical forest in southern China. Experimental N‐treatments (above ambient) were the following: Control (no N addition), N50 (50 kg N ha−1 yr−1), and N100 (100 kg N ha−1 yr−1). Results indicated that N addition significantly decreased soil P availability in the disturbed forest. In the rehabilitated forest, however, soil P availability was significantly increased by N addition. Decreases in soil P availability may be correlated with decreases in rates of P release from decomposing litter in the N‐treated plots, whereas the increase in soil P availability was correlated with an increase in litterfall production. Our results suggest that response of soil P availability to N deposition in the reforested tropical forests in southern China may vary greatly with temporal changes in tree species composition and soil nutrient status, caused by different land‐use practices.
Photocatalytic Synthesis of Urea from in situ Generated Ammonia and Carbon Dioxide
Authors: Srinivas Basavaraju , Kumari Valluri Durga , Sadanandam Gullapelli , Hymavathi Chilumula , Subrahmanyam Machiraju , De Bhudev Ranjan 
Published: November 2011

AbstractTiO2 and Fe‐titanate (different wt%) supported on zeolite were prepared by sol‐gel and solid‐state dispersion methods. The photocatalysts prepared were characterized by X‐ray diffraction, scanning electron microscopy and ultraviolet (UV)–visible diffuse reflectance spectroscopy techniques. Photocatalytic reduction of nitrate in water and isopropanol/oxalic acid as hole scavengers are investigated in a batch reactor under UV illumination. The yield of urea increased notably when the catalysts were supported on zeolite. The Fe‐titanate supported catalyst promotes the charge separation that contributes to an increase in selective formation of urea. The product formation is because of the high adsorption of in situ generated CO2 and NH3 over shape‐selective property of the zeolite in the composite photocatalyst. The maximum yield of urea is found to be 18 ppm while 1% isopropanol containing solution over 10 wt% Fe‐titanate/HZSM‐5 photocatalyst was used.
Spatial analysis by distance indices: an alternative local clustering index for studying spatial patterns
Authors: Li Baohua , Madden Laurence V. , Xu Xiangming 
Published: November 2011

Summary1. The spatial analysis by distance indices (SADIE) methodology for data analysis is valuable for quantifying spatial patterns of organisms in terms of patches and gaps. Previous research showed that the calculation of the local clustering indices, key SADIE statistics, does not adequately adjust for the absolute location or the magnitude of the counts.2. We present a new definition of a local clustering index, which overcomes the problem associated with the original cluster indices related to sampling position and count size. The new index is calculated without breaking the link between the observed count and its original position and quantifies the contribution of an observed count at this particular position to the local gaps or patches for the observed pattern relative to the expected under the assumption of spatial independence amongst observed counts. Randomisation‐based testing for statistical significance of an individual local clustering index follows naturally from the definition of the new index.3. New indices, calculated for several simulated and observed data sets, showed that the original indices overestimated the number of points (sites, locations) contributing to the gaps/patches in a spatial grid. Results indicate that the significance (or interpretation) of individual local clustering indices cannot be made based on its magnitude only and needs to be supported by statistical testing.4. The newly developed index will provide a valuable tool for quantifying the local pattern and testing for its significance and enhance the value of SADIE methodology in analysing spatial patterns. It can also be used in conjunction with other approaches that test for global clustering.
Community Composition, Toxigenicity, and Environmental Conditions during a Cyanobacterial Bloom Occurring along 1,100 Kilometers of the Murray River
Authors: Al-Tebrineh Jamal , Merrick Chester , Ryan David , Humpage Andrew , Bowling Lee , Neilan Brett A. 
Published: November 2011

ABSTRACTA cyanobacterial bloom impacted over 1,100 km of the Murray River, Australia, and its tributaries in 2009. Physicochemical conditions in the river were optimal to support a bloom at the time. The data suggest that at least three blooms occurred concurrently in different sections of the river, with each having a different community composition and associated cyanotoxin profile. Microscopic and genetic analyses suggested the presence of potentially toxicAnabaena circinalis,Microcystis flos-aquae, andCylindrospermopsis raciborskiiat many locations. Low concentrations of saxitoxins and cylindrospermopsin were detected inAnabaenaandCylindrospermopsispopulations. A multiplex quantitative PCR was used, employing novel oligonucleotide primers and fluorescent TaqMan probes, to examine bloom toxigenicity. This single reaction method identified the presence of the major cyanotoxin-producing species present in these environmental samples and also quantified the various toxin biosynthesis genes. A large number of cells present throughout the bloom were not potential toxin producers or were present in numbers below the limit of detection of the assay and therefore not an immediate health risk. Potential toxin-producing cells, possessing the cylindrospermopsin biosynthesis gene (cyrA), predominated early in the bloom, while those possessing the saxitoxin biosynthesis gene (sxtA) were more common toward its decline. In this study, the concentrations of cyanotoxins measured via enzyme-linked immunosorbent assay (ELISA) correlated positively with the respective toxin gene copy numbers, indicating that the molecular method may be used as a proxy for bloom risk assessment.
Methicillin-Resistant Coagulase-Negative Staphylococci on Pig Farms as a Reservoir of Heterogeneous Staphylococcal Cassette Chromosome
mec
Elements
Authors: Tulinski Pawel , Fluit Ad C. , Wagenaar Jaap A. , Mevius Dik , van de Vijver Lucy , Duim Birgitta 
Published: November 2011

ABSTRACT

Methicillin-resistant
Staphylococcus aureus
(MRSA) likely originated by acquisition of the staphylococcal cassette chromosome
mec
(SCC
mec
) from coagulase-negative staphylococci (CNS). However, it is unknown whether the same SCC
mec
types are present in MRSA and CNS that reside in the same niche. Here we describe a study to determine the presence of a potential
mecA
reservoir among CNS recovered from 10 pig farms. The 44 strains belonged to 10 different
Staphylococcus
species. All
S. aureus
strains belonged to sequence type 398 (ST398), with SCC
mec
types V and IVa. Type IVc, as well as types III and VI, novel subtypes of type IV, and not-typeable types, were found in CNS.
S. aureus
,
S. epidermidis
, and
S. haemolyticus
shared SCC
mec
type V. The presence of SCC
mec
type IVc in several staphylococcal species isolated from one pig farm is noteworthy, suggesting exchange of this SCC
mec
type in CNS, but the general distribution of this SCC
mec
type still has to be established. In conclusion, this study shows that SCC
mec
types among staphylococcal species on pig farms are heterogeneous. On two farms, more than one recovered staphylococcal species harbored the same SCC
mec
type. We conclude that staphylococci on pig farms act as a reservoir of heterogeneous SCC
mec
elements. These staphylococci may act as a source for transfer of SCC
mec
to
S. aureus
.
Characterization of Phascolarctobacterium succinatutens sp. nov., an Asaccharolytic, Succinate-Utilizing Bacterium Isolated from Human Feces
Authors: Watanabe Yohei , Nagai Fumiko , Morotomi Masami 
Published: November 2011

ABSTRACT

Isolation, cultivation, and characterization of the intestinal microorganisms are important for understanding the comprehensive physiology of the human gastrointestinal (GI) tract microbiota. Here, we isolated two novel bacterial strains, YIT 12067
T
and YIT 12068, from the feces of healthy human adults. Phylogenetic analysis indicated that they belonged to the same species and were most closely related to
Phascolarctobacterium faecium
ACM 3679
T
, with 91.4% to 91.5% 16S rRNA gene sequence similarities, respectively. Substrate availability tests revealed that the isolates used only succinate; they did not ferment any other short-chain fatty acids or carbohydrates tested. When these strains were cocultured with the xylan-utilizing and succinate-producing bacterium
Paraprevotella xylaniphila
YIT 11841
T
, in medium supplemented with xylan but not succinate, their cell numbers became 2 to 3 orders of magnitude higher than those of the monoculture; succinate became undetectable, and propionate was formed. Database analysis revealed that over 200 uncultured bacterial clones from the feces of humans and other mammals showed high sequence identity (>98.7%) to YIT 12067
T
. Real-time PCR analysis also revealed that YIT 12067
T
-like bacteria were present in 21% of human fecal samples, at an average level of 3.34 × 10
8
cells/g feces. These results indicate that YIT 12067
T
-like bacteria are distributed broadly in the GI tract as subdominant members that may adapt to the intestinal environment by specializing to utilize the succinate generated by other bacterial species. The phylogenetic and physiological properties of YIT 12067
T
and YIT 12068 suggest that these strains represent a novel species, which we have designated
Phascolarctobacterium succinatutens
sp. nov.
Isolation of Bacteria Capable of Growth with 2-Methylisoborneol and Geosmin as the Sole Carbon and Energy Sources
Authors: Guttman Lior , van Rijn Jaap 
Published: November 2011

ABSTRACT

Using a relatively simple enrichment technique, geosmin and 2-methylisoborneol (MIB)-biodegrading bacteria were isolated from a digestion basin in an aquaculture unit. Comparison of 16S rRNA gene sequences affiliated one of the three isolates with the Gram-positive genus
Rhodococcus
, while the other two isolates were found to be closely related to the Gram-negative family
Comamonadaceae
(
Variovorax
and
Comamonas
). Growth rates and geosmin and MIB removal rates by the isolates were determined under aerated and nonaerated conditions in mineral medium containing either of the two compounds as the sole carbon and energy source. All isolates exhibited their fastest growth under aerobic conditions, with generation times ranging from 3.1 to 5.7 h, compared to generation times of up to 19.1 h in the nonaerated flasks. Incubation of the isolates with additional carbon sources caused a significant increase in their growth rates, while removal rates of geosmin and MIB were significantly lower than those for incubation with only geosmin or MIB. By fluorescence
in situ
hybridization, members of the genera
Rhodococcus
and
Comamonas
were detected in geosmin- and MIB-enriched sludge from the digestion basin.
Characterization and Functional Analyses of
R
-Specific Enoyl Coenzyme A Hydratases in Polyhydroxyalkanoate-Producing Ralstonia eutropha
Authors: Kawashima Yui , Cheng Wen , Mifune Jun , Orita Izumi , Nakamura Satoshi , Fukui Toshiaki 
Published: November 2011

ABSTRACT

A genome survey of polyhydroxyalkanoate (PHA)-producing
Ralstonia eutropha
H16 detected the presence of 16 orthologs of
R
-specific enoyl coenzyme A (enoyl-CoA) hydratase, among which three proteins shared high homologies with the enzyme specific to enoyl-CoAs of medium chain length encoded by
phaJ4
from
Pseudomonas aeruginosa
(

phaJ4
Pa

). The recombinant forms of the three proteins, termed PhaJ4a

Re

to PhaJ4c

Re

, actually showed enoyl-CoA hydratase activity with
R
specificity, and the catalytic efficiencies were elevated as the substrate chain length increased from C
4
to C
8
. PhaJ4a

Re

and PhaJ4b

Re

showed >10-fold-higher catalytic efficiency than PhaJ4c

Re

. The functions of the new PhaJ4 proteins were investigated using previously engineered
R. eutropha
strains as host strains; these strains are capable of synthesizing poly((
R
)-3-hydroxybutyrate-
co
-(
R
)-3-hydroxyhexanoate) [P(3HB-
co
-3HHx)] from soybean oil. Deletion of

phaJ4a
Re

from the chromosome resulted in significant decrease of 3HHx composition in the accumulated copolyester, whereas no change was observed with deletion of

phaJ4b
Re

or

phaJ4c
Re

, indicating that only PhaJ4a

Re

was one of the major enzymes supplying the (
R
)-3HHx-CoA monomer through β-oxidation. Introduction of

phaJ4a
Re

or

phaJ4b
Re

into the
R. eutropha
strains using a broad-host-range vector enhanced the 3HHx composition of the copolyesters, but the introduction of

phaJ4c
Re

did not. The two genes were then inserted into the
pha
operon on chromosome 1 of the engineered
R. eutropha
by homologous recombination. These modifications enabled the biosynthesis of P(3HB-
co
-3HHx) composed of a larger 3HHx fraction without a negative impact on cell growth and PHA production on soybean oil, especially when

phaJ4a
Re

or

phaJ4b
Re

was tandemly introduced with

phaJ
Ac

from
Aeromonas caviae
.
Cj1386 Is an Ankyrin-Containing Protein Involved in Heme Trafficking to Catalase in Campylobacter jejuni
Authors: Flint Annika , Sun Yi-Qian , Stintzi Alain 
Published: November 2011

ABSTRACT

Campylobacter jejuni
, a microaerophilic bacterium, is the most frequent cause of human bacterial gastroenteritis.
C. jejuni
is exposed to harmful reactive oxygen species (ROS) produced during its own normal metabolic processes and during infection from the host immune system and from host intestinal microbiota. These ROS will damage DNA and proteins and cause peroxidation of lipids. Consequently, identifying ROS defense mechanisms is important for understanding how
Campylobacter
survives this environmental stress during infection. Construction of a ΔCj1386 isogenic deletion mutant and phenotypic assays led to its discovery as a novel oxidative stress defense gene. The ΔCj1386 mutant has an increased sensitivity toward hydrogen peroxide. The Cj1386 gene is located directly downstream from
katA
(catalase) in the
C. jejuni
genome. A Δ
katA
Δ Cj1386 double deletion mutant was constructed and exhibited a sensitivity to hydrogen peroxide similar to that seen in the ΔCj1386 and Δ
katA
single deletion mutants. This observation suggests that Cj1386 may be involved in the same detoxification pathway as catalase. Despite identical KatA abundances, catalase activity assays showed that the
Δ
Cj1386 mutant had a reduced catalase activity relative to that of wild-type
C. jejuni
. Heme quantification of KatA protein from the ΔCj1386 mutant revealed a significant decrease in heme concentration. This indicates an important role for Cj1386 in heme trafficking to KatA within
C. jejuni
. Interestingly, the ΔCj1386 mutant had a reduced ability to colonize the ceca of chicks and was outcompeted by the wild-type strain for colonization of the gastrointestinal tract of neonate piglets. These results indicate an important role for Cj1386 in
Campylobacter
colonization and pathogenesis.