bluuebunny/crossref_metadata_2025 huggingface dataset:
Aliifodinibius roseus gen. nov., sp. nov., and Aliifodinibius sediminis sp. nov., two moderately halophilic bacteria isolated from salt mine samples
Authors: Wang Yong-Xia , Liu Ji-Hui , Xiao Wei , Ma Xiao-Liang , Lai Yong-Hong , Li Zhi-Ying , Ji Kai-Yan , Wen Meng-Liang , Cui Xiao-Long
Published: January 2013

Two rod-shaped, non-motile bacteria were isolated from two separate salt mines in Yunnan, south-western China. These strains, designated YIM D15T and YIM J21T, were Gram-negative and moderately halophilic. The two strains required 6–10 % NaCl (w/v; optimal) for growth. The DNA G+C contents of strains YIM D15T and YIM J21T were 49.0 mol% and 48.4 mol%, respectively. The predominant isoprenoid quinone was MK-7. The polar lipid profiles of strains YIM D15T and YIM J21T were composed predominantly of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, three unknown polar lipids and one glycolipid. Minor amounts of other lipids were also detectable. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 1ω9c/10 methyl-C16 : 0 and C16 : 1ω7c/C16 : 1ω6c. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the two isolates formed a distinct clade with the genus

Fodinibius

(in the phylum

Bacteroidetes

) and were related to the species

Fodinibius salinus

, with sequence similarities of 91.9–92.4 %. Analyses of 16S rRNA gene sequences revealed that strains YIM D15T and YIM J21T were related to each other (97.3 % sequence similarity). The DNA–DNA hybridization relatedness between the two isolates was 34 %. On the basis of the phylogenetic analysis, DNA–DNA hybridization relatedness, phenotypic and chemotaxonomic characteristics, strains YIM D15T and YIM J21T should be classified as members of a novel genus and as two novel species, for which the names Aliifodinibius roseus gen. nov., sp. nov. (type strain YIM D15T = ACCC 10715T = KCTC 23442T) and Aliifodinibius sediminis sp. nov. (type strain YIM J21T = ACCC 10714T = DSM 21194T) are proposed.
‘ Candidatus Phytoplasma solani’, a novel taxon associated with stolbur- and bois noir-related diseases of plants
Authors: Quaglino Fabio , Zhao Yan , Casati Paola , Bulgari Daniela , Bianco Piero Attilio , Wei Wei , Davis Robert Edward
Published: January 2013

Phytoplasmas classified in group 16SrXII infect a wide range of plants and are transmitted by polyphagous planthoppers of the family Cixiidae. Based on 16S rRNA gene sequence identity and biological properties, group 16SrXII encompasses several species, including ‘CandidatusPhytoplasma australiense’, ‘CandidatusPhytoplasma japonicum’ and ‘CandidatusPhytoplasma fragariae’. Other group 16SrXII phytoplasma strains are associated with stolbur disease in wild and cultivated herbaceous and woody plants and with bois noir disease in grapevines (Vitis viniferaL.). Such latter strains have been informally proposed to represent a separate species, ‘CandidatusPhytoplasma solani’, but a formal description of this taxon has not previously been published. In the present work, stolbur disease strain STOL11 (STOL) was distinguished from reference strains of previously described species of the ‘CandidatusPhytoplasma’ genus based on 16S rRNA gene sequence similarity and a unique signature sequence in the 16S rRNA gene. Other stolbur- and bois noir-associated (‘Ca.Phytoplasma solani’) strains shared >99 % 16S rRNA gene sequence similarity with strain STOL11 and contained the signature sequence. ‘Ca.Phytoplasma solani’ is the only phytoplasma known to be transmitted byHyalesthes obsoletus. Insect vectorship and molecular characteristics are consistent with the concept that diverse ‘Ca.Phytoplasma solani’ strains share common properties and represent an ecologically distinct gene pool. Phylogenetic analyses of 16S rRNA,tuf,secYandrplV–rpsCgene sequences supported this view and yielded congruent trees in which ‘Ca.Phytoplasma solani’ strains formed, within the group 16SrXII clade, a monophyletic subclade that was most closely related to, but distinct from, that of ‘Ca.Phytoplasma australiense’-related strains. Based on distinct molecular and biological properties, stolbur- and bois noir-associated strains are proposed to represent a novel species level taxon, ‘Ca.Phytoplasma solani’; STOL11 is designated the reference strain.
Defluviimonas

aestuarii sp. nov., a marine bacterium isolated from a tidal flat, and emended description of the genus

Defluviimonas

Foesel et al. 2011
Authors: Math Renukaradhya K. , Jin Hyun Mi , Jeong Sang Hyeon , Jeon Che Ok
Published: January 2013

A novel Gram-staining-negative, strictly aerobic bacterium, designated BS14T, was isolated from a marine tidal flat of the South Sea in Korea. Colonies were opaque, white, smooth and circular on marine agar. Cells were moderately halophilic, non-motile rods showing catalase- and oxidase-positive reactions. Growth of strain BS14T was observed at 5–40 °C (optimum: 30 °C), pH 6.5–9.5 (optimum: 7.0–7.5) and 0–10 % (w/v) NaCl (optimum: 1–1.5 %). The G+C content of the genomic DNA was 61.6 mol%. Strain BS14T contained ubiquinone-10 (Q-10) as the sole respiratory quinone and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C18 : 0 3-OH, C10 : 0 3-OH and C18 : 0 as the major fatty acids. The polar lipid pattern comprised phosphatidylethanolamine, diphosphatidylglycerol, an unidentified aminolipid, an unidentified phospholipid and an unidentified polar lipid. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BS14T formed a tight phylogenetic lineage with

Defluviimonas denitrificans

D9-3T with a bootstrap value of 100 %. The 16S rRNA gene sequence similarity between strain BS14T and

D. denitrificans

D9-3T was 97.4 % and their DNA–DNA relatedness was 19.1±3.6 %. Based on the phenotypic and genotypic studies, strain BS14T represents a novel species of the genus

Defluviimonas

, for which the name

Defluviimonas

aestuarii sp. nov. is proposed. The type strain is BS14T ( = KACC 16442T = JCM 18630T). An emended description of the genus

Defluviimonas

Foesel et al. 2011 is also proposed.
Proposal for a new class within the phylum

Proteobacteria

, Acidithiobacillia classis nov., with the type order

Acidithiobacillales

, and emended description of the class

Gammaproteobacteria
Authors: Williams Kelly P. , Kelly Donovan P.
Published: January 2013

The order

Acidithiobacillales

was previously assigned to the class

Gammaproteobacteria

. Recent analyses have indicated that this order actually lies outside all the proteobacterial classes, as a sister group to the combined classes

Betaproteobacteria

and

Gammaproteobacteria

. We now confirm this result with multiprotein phylogenetic analysis of all the available genomes of members of the order

Acidithiobacillales

and representatives of all available bacterial orders, and propose the new proteobacterial class, Acidithiobacillia, with the type order

Acidithiobacillales

, comprising the families

Acidithiobacillaceae

and

Thermithiobacillaceae

with the type genus

Acidithiobacillus

.
Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation
Authors: Hausser Jean , Syed Afzal Pasha , Bilen Biter , Zavolan Mihaela
Published: January 2013

Most of what is presently known about how miRNAs regulate gene expression comes from studies that characterized the regulatory effect of miRNA binding sites located in the 3′ untranslated regions (UTR) of mRNAs. In recent years, there has been increasing evidence that miRNAs also bind in the coding region (CDS), but the implication of these interactions remains obscure because they have a smaller impact on mRNA stability compared with miRNA-target interactions that involve 3′ UTRs. Here we show that miRNA-complementary sites that are located in both CDS and 3′-UTRs are under selection pressure and share the same sequence and structure properties. Analyzing recently published data of ribosome-protected fragment profiles upon miRNA transfection from the perspective of the location of miRNA-complementary sites, we find that sites located in the CDS are most potent in inhibiting translation, while sites located in the 3′ UTR are more efficient at triggering mRNA degradation. Our study suggests that miRNAs may combine targeting of CDS and 3′ UTR to flexibly tune the time scale and magnitude of their post-transcriptional regulatory effects.
RootScape: A Landmark-Based System for Rapid Screening of Root Architecture in Arabidopsis
Authors: Ristova Daniela , Rosas Ulises , Krouk Gabriel , Ruffel Sandrine , Birnbaum Kenneth D. , Coruzzi Gloria M.
Published: January 2013

The architecture of plant roots affects essential functions including nutrient and water uptake, soil anchorage, and symbiotic interactions. Root architecture comprises many features that arise from the growth of the primary and lateral roots. These root features are dictated by the genetic background but are also highly responsive to the environment. Thus, root system architecture (RSA) represents an important and complex trait that is highly variable, affected by genotype × environment interactions, and relevant to survival/performance. Quantification of RSA in Arabidopsis (Arabidopsis thaliana) using plate-based tissue culture is a very common and relatively rapid assay, but quantifying RSA represents an experimental bottleneck when it comes to medium- or high-throughput approaches used in mutant or genotype screens. Here, we present RootScape, a landmark-based allometric method for rapid phenotyping of RSA using Arabidopsis as a case study. Using the software AAMToolbox, we created a 20-point landmark model that captures RSA as one integrated trait and used this model to quantify changes in the RSA of Arabidopsis (Columbia) wild-type plants grown under different hormone treatments. Principal component analysis was used to compare RootScape with conventional methods designed to measure root architecture. This analysis showed that RootScape efficiently captured nearly all the variation in root architecture detected by measuring individual root traits and is 5 to 10 times faster than conventional scoring. We validated RootScape by quantifying the plasticity of RSA in several mutant lines affected in hormone signaling. The RootScape analysis recapitulated previous results that described complex phenotypes in the mutants and identified novel gene × environment interactions.
Elevated Early Callose Deposition Results in Complete Penetration Resistance to Powdery Mildew in Arabidopsis
Authors: Ellinger Dorothea , Naumann Marcel , Falter Christian , Zwikowics Claudia , Jamrow Torsten , Manisseri Chithra , Somerville Shauna C. , Voigt Christian A.
Published: January 2013

A common response by plants to fungal attack is deposition of callose, a (1,3)-β-glucan polymer, in the form of cell wall thickenings called papillae, at site of wall penetration. While it has been generally believed that the papillae provide a structural barrier to slow fungal penetration, this idea has been challenged in recent studies of Arabidopsis (Arabidopsis thaliana), where fungal resistance was found to be independent of callose deposition. To the contrary, we show that callose can strongly support penetration resistance when deposited in elevated amounts at early time points of infection. We generated transgenic Arabidopsis lines that express POWDERY MILDEW RESISTANT4 (PMR4), which encodes a stress-induced callose synthase, under the control of the constitutive 35S promoter. In these lines, we detected callose synthase activity that was four times higher than that in wild-type plants 6 h post inoculation with the virulent powdery mildew Golovinomyces cichoracearum. The callose synthase activity was correlated with enlarged callose deposits and the focal accumulation of green fluorescent protein-tagged PMR4 at sites of attempted fungal penetration. We observed similar results from infection studies with the nonadapted powdery mildew Blumeria graminis f. sp. hordei. Haustoria formation was prevented in resistant transgenic lines during both types of powdery mildew infection, and neither the salicylic acid-dependent nor jasmonate-dependent pathways were induced. We present a schematic model that highlights the differences in callose deposition between the resistant transgenic lines and the susceptible wild-type plants during compatible and incompatible interactions between Arabidopsis and powdery mildew.
Cell-to-Cell Movement of Two Interacting AT-Hook Factors inArabidopsisRoot Vascular Tissue Patterning
Authors: Zhou Jing , Wang Xu , Lee Jung-Youn , Lee Ji-Young
Published: January 2013

The xylem and phloem, major conducting and supporting tissues in vascular plants, are established by cell division and cell-type specification in the procambium/cambium. The organization of the xylem, phloem, and procambium/cambium is tightly controlled. However, the underlying regulatory mechanisms remain largely unknown. In this study, we report the discovery of two transcription factors, AT-HOOK MOTIF NUCLEAR LOCALIZED PROTEIN 3 (AHL3) and AHL4, which regulate vascular tissue boundaries in Arabidopsis thaliana roots. In either of the knockout mutants of AHL3 and AHL4, encoding closely related AT-hook transcription factors, a misspecification of tissue boundaries between the xylem and procambium occurred and ectopic xylem developed in the procambium domain. In plants, specific types of transcription factors can serve as direct intercellular signals by moving from one cell to another, playing crucial roles in tissue patterning. Adding to this paradigm, AHL4 moves actively from the procambium to xylem in the root meristem to regulate the tissue boundaries. When the intercellular movement of AHL4 was impaired, AHL4 could not complement the xylem phenotype in the ahl4. Furthermore, AHL4 revealed unique characteristics in that it interacts with AHL3 in vivo and that this interaction facilitates their intercellular trafficking. Taken together, this study uncovered a novel mechanism in vascular tissue patterning that requires the intercellular trafficking of two interacting transcription factors.
Transcription Repressor HANABA TARANU Controls Flower Development by Integrating the Actions of Multiple Hormones, Floral Organ Specification Genes, and GATA3 Family Genes inArabidopsis
Authors: Zhang Xiaolan , Zhou Yun , Ding Lian , Wu Zhigang , Liu Renyi , Meyerowitz Elliot M.
Published: January 2013

Plant inflorescence meristems and floral meristems possess specific boundary domains that result in proper floral organ separation and specification. HANABA TARANU (HAN) encodes a boundary-expressed GATA3-type transcription factor that regulates shoot meristem organization and flower development in Arabidopsis thaliana, but the underlying mechanism remains unclear. Through time-course microarray analyses following transient overexpression of HAN, we found that HAN represses hundreds of genes, especially genes involved in hormone responses and floral organ specification. Transient overexpression of HAN also represses the expression of HAN and three other GATA3 family genes, HANL2 (HAN-LIKE 2), GNC (GATA, NITRATE-INDUCIBLE, CARBON-METABOLISM-INVOLVED), and GNL (GNC-LIKE), forming a negative regulatory feedback loop. Genetic analysis indicates that HAN and the three GATA3 family genes coordinately regulate floral development, and their expression patterns are partially overlapping. HAN can homodimerize and heterodimerize with the three proteins encoded by these genes, and HAN directly binds to its own promoter and the GNC promoter in vivo. These findings, along with the fact that constitutive overexpression of HAN produces an even stronger phenotype than the loss-of-function mutation, support the hypothesis that HAN functions as a key repressor that regulates floral development via regulatory networks involving genes in the GATA3 family, along with genes involved in hormone action and floral organ specification.
The Impact of Iron on the Bleaching Efficacy of Hydrogen Peroxide in Liquid Whey Systems
Authors: Jervis Suzanne M. , Drake MaryAnne
Published: January 2013

Whey is a value‐added product that is utilized in many food and beverage applications for its nutritional and functional properties. Whey and whey products are generally utilized in dried ingredient applications. One of the primary sources of whey is from colored Cheddar cheese manufacture that contains the pigment annatto resulting in a characteristic yellow colored Cheddar cheese. The colorant is also present in the liquid cheese whey and must be bleached so that it can be used in ingredient applications without imparting a color. Hydrogen peroxide and benzoyl peroxide are 2 commercially approved chemical bleaching agents for liquid whey. Concerns regarding bleaching efficacy, off‐flavor development, and functionality changes have been previously reported for whey bleached with hydrogen peroxide and benzoyl peroxide. It is very important for the dairy industry to understand how bleaching can impact flavor and functionality of dried ingredients. Currently, the precise mechanisms of off‐flavor development and functionality changes are not entirely understood. Iron reactions in a bleached liquid whey system may play a key role. Reactions between iron and hydrogen peroxide have been widely studied since the reaction between these 2 relatively stable species can cause great destruction in biological and chemical systems. The actual mechanism of the reaction of iron with hydrogen peroxide has been a controversy in the chemistry and biological community. The precise mechanism for a given reaction can vary greatly based upon the concentration of reactants, temperature, pH, and addition of biological material. In this review, some hypotheses for the mechanisms of iron reactions that may occur in fluid whey that may impact bleaching efficacy, off‐flavor development, and changes in functionality are presented.

Practical Application:  Cheese whey is bleached to remove residual carotenoid cheese colorant. Concerns regarding bleaching efficacy, off‐flavor development, and functionality changes have been reported for whey proteins bleached with hydrogen peroxide and benzoyl peroxide. It is very important for the dairy industry to understand how whey bleaching can impact flavor and functionality of dried ingredients. Proposed mechanisms of off‐flavor development and functionality changes are discussed in this hypothesis paper.
Prenatal diagnosis of abnormally invasive placenta reduces maternal peripartum hemorrhage and morbidity
Authors: Chantraine Frédéric , Braun Thorsten , Gonser Markus , Henrich Wolfgang , Tutschek Boris
Published: January 2013

Objective

Abnormally invasive placenta (AIP) poses diagnostic and therapeutic challenges. We analyzed clinical cases with confirmed placenta increta or percreta.

Design

Retrospective case series.

Setting

Multicenter study.

Population

Pregnant women with AIP.

Methods

Chart review.

Main outcome measures

Prenatal detection rates, treatment choices, morbidity, mortality and short‐term outcome.

Results

Sixty‐six cases were analyzed. All women and all but three fetuses survived; 57/64 women (89%) had previous uterine surgery. In 26 women (39%) the diagnosis was not known before delivery (Group 1), in the remaining 40 (61%) diagnosis had been made between 14 and 37 weeks of gestation (Group 2). Placenta previa was present in 36 women (54%). In Groups 1 and 2, 50% (13/26) and 62% (25/40) of the women required hysterectomy, respectively. In Group 1 (unknown at the time of delivery) 69% (9/13) required (emergency) hysterectomy for severe hemorrhage in the immediate peripartum period compared with only 12% (3/25) in Group 2 (p = 0.0004). Mass transfusions were more frequently required in Group 1 (46%, 12/26 vs. 20%, 8/40; p = 0.025). In 18/40 women (45%) from Group 2 the placenta was intentionally left in situ; secondary hysterectomies and infections were equally frequent (18%) among these differently treated women. Overall, postpartum infections occurred in 11% and 20% of women in Groups 1 and 2, respectively.

Conclusions

AIP was known before delivery in more than half of the cases. Unknown AIP led to significantly more emergency hysterectomies and mass transfusions during or immediately after delivery. Prenatal diagnosis of AIP reduces morbidity. Future studies should also address the selection criteria for cases appropriate for leaving the placenta in situ.
Hysteroscopic resection of abnormally invasive placenta residuals
Authors: Nisolle Michelle , Delbecque Katty , Perrier D'Hauterive Sophie , Firquet Anne , Chantraine Frédéric
Published: January 2013

Objective

To present our experience in hysteroscopic removal of abnormally invasive placenta (AIP) residuals using bipolar energy.

Design

Case series.

Setting

University hospital.

Population

Sixteen patients with AIP residuals after 17 pregnancies.

Methods

Cases were identified by ultrasound, treated with hysteroscopic bipolar electrosurgery and oral contraceptives, and followed up by ultrasound or hysteroscopy. Nine subsequent pregnancies were described.

Main outcome measures and Results

Complete removal of AIP residuals was achieved by hysteroscopic bipolar electrosurgery in all cases except one. No perioperative complications occurred. AIP residual recurred in one patient after a subsequent pregnancy and was successfully treated using the same procedure.

Conclusions

AIP residual is a rare condition. Management by hysteroscopic resection using bipolar energy is safe and feasible.
Relationship of Δ6‐desaturase and Δ5‐desaturase activities with thyroid hormone status in adolescents with eating disorders and weight loss
Authors: Swenne Ingemar , Vessby Bengt
Published: January 2013

Aim

In starvation, there is down‐regulation of metabolism and changes in essential fatty acid (FA) status, which could be related to alterations of desaturase activities. Presently, the relationship between thyroid hormones and desaturase activities has been investigated in adolescents with eating disorders and weight loss.

Methods

Serum triiodothyronine concentrations and proportions of polyunsaturated FA in plasma phospholipids were analysed in blood samples from 227 adolescents with ED. Δ6‐desaturase (D6D) activity was calculated as the FA ratio 20:3ω6/18:2ω6 and Δ5‐desaturase (D5D) activity as the ratio 20:4ω6/20:3ω6.

Results

Serum triiodothyronine concentrations were related to leanness and ongoing weight loss. The estimated D6D activity was positively correlated with serum triiodothyronine (R2 = 0.232; p < 0.001). D5D activity exhibited a strong inverse correlation with serum triiodothyronine (R2 = 0.410; p < 0.001).

Conclusion

Changes in desaturase activities during starvation cannot be explained by inhibition/disinhibition by essential FA only. It is possible that the effects of starvation on these enzyme activities, and hence on essential FA status, are mediated by triiodothyronine.
Impacts of an Invasive N2‐Fixing Tree on Hawaiian Stream Water Quality
Authors: Wiegner Tracy N. , Hughes Flint , Shizuma Lisa M. , Bishaw David K. , Manuel Mark E.
Published: January 2013

N2‐fixing trees can affect stream water quality. This has been documented in temperate streams, but not in tropical ones, even though N2‐fixing trees are prevalent in the tropics. We investigated the effects of the introduced, invasive tree, Falcataria moluccana (albizia) on water quality of Hawaiian streams. Nutrient concentrations were measured in reaches above and below F. moluccana‐dominated riparian zones of four streams over 14 mo, and benthic algal nutrient limitation was examined in one stream. NO3−+NO2− concentrations were up to 600 percent higher in reaches below F. moluccana stands than in ones above them. In contrast, dissolved organic nitrogen concentrations were 24 percent lower in most reaches below F. moluccana stands, and NH4+ and particulate nitrogen concentrations were similar above and below the stands. Dissolved organic carbon concentrations were up to 30 percent lower below F. moluccana stands, but particulate carbon concentrations were similar between reaches. Total dissolved phosphorus concentrations were similar above and below F. moluccana stands, whereas H4SiO4 concentrations were higher below the stands. In the stream where benthic chlorophyll a was measured, concentrations were three times higher below the F. moluccana stand than above it. Benthic algae were co‐limited by nitrogen and phosphorus above the F. moluccana stand, and limited by phosphorus below it. These results suggest that F. moluccana's presence relieved nitrogen‐limitation and caused the benthic algae to become solely phosphorus‐limited. Overall, our results demonstrate that F. moluccana can strongly affect the chemistry and primary producers of these tropical streams.
Optimal timing for solids introduction – why are the guidelines always changing?
Authors: Koplin J. J. , Allen K. J.
Published: January 2013

There have been dramatic changes in timing of first exposure to solid foods for children over the last 40 years, ranging from exposure prior to 4 months of age for most infants in the 1960s, to guidelines recommending delaying solids until after 6 months of age introduced in the 1990s. Infant diet, specifically age of weaning and age at introduction of allergenic foods, has long been thought to play a role food allergy. However, controversy surrounding the relationship between timing of introduction of foods and development of food allergy has lead to a plethora of inconsistent infant feeding guidelines both between and within countries. The aims of this article were to discuss the history of changing guidelines for optimal timing of introduction of solids in general and allergenic solids in particular and the evidence (or lack thereof) underpinning recommendations at each of these time‐points. We present the current clinical equipoise with regards to recently revised guidelines published almost simultaneously in the UK, US and Australia and argue that guideline modification about timing of introduction (both for high risk infants but also for the general population) will require careful review of emerging literature to provide a true evidence base to inform public health practice such as infant feeding guidelines.
Intra-articular nuclear factor-κB blockade ameliorates collagen-induced arthritis in mice by eliciting regulatory T cells and macrophages
Authors: Min S-Y , Yan M , Du Y , Wu T , Khobahy E , Kwon S-R , Taneja V , Bashmakov A , Nukala S , Ye Y , Orme J , Sajitharan D , Kim H-Y , Mohan C
Published: January 2013

Nuclear factor (NF)-κB is a transcription factor implicated in the pathogenesis of autoimmune disorders such as rheumatoid arthritis (RA). Here we have examined the effect of intra-articular administration of the IKK inhibitor, NEMO-binding domain peptide (NBD), on the severity of collagen-induced arthritis (CIA). NBD peptides were injected intra-articularly into the knee joints of DBA/1J mice after the onset of disease. Collagen-injected mice given a scrambled peptide served as controls. Arthritis severity was determined by visual examination of paws. Intra-articular NBD injection reduced the arthritis score and ameliorated morphological signs of bone destruction compared to the controls. Serum levels of type-II collagen-specific immunoglobulin (Ig)G2a antibodies were lower in NBD-treated mice versus the control mice, whereas the levels of type-II collagen-specific IgG1 antibodies were increased by NBD treatment. NBD treatment diminished the proinflammatory cytokines interleukin (IL)-17 and interferon (IFN)-γ in serum, but increased the regulatory cytokine IL-10. NBD-treated CIA mice exhibited significantly higher percentages and numbers of forkhead box protein 3 (FoxP3+)CD4+CD25+ regulatory T cells than controls. Immunofluorescence analysis of NBD-treated mice revealed that FoxP3 and Ym1, a marker of alternatively activated macrophages, were juxtaposed to each other within draining inguinal lymph nodes. Intra-articular administration of NBD peptide is effective as an experimental therapy in a murine model of RA. Nevertheless, the intra-articular treatment modality is still associated with systemic effects on the immune system.
Surgical management of rectovaginal fistula in a tertiary referral centre: many techniques are needed
Authors: Tozer P. J. , Balmforth D. , Kayani B. , Rahbour G. , Hart A. L. , Phillips R. K. S.
Published: January 2013

Aim

Surgery is the mainstay of treatment for rectovaginal fistula (RVF). Published success rates vary with initial success being around 50% rising to 80% with repeated surgery. Fistulae in Crohn's disease are more likely to recur.

Method

A retrospective study was performed of RVF repair carried out between 2003 and 2008 in a tertiary referral centre. Patients undergoing surgery for an RVF under the senior author during the study period were identified and their clinical notes were reviewed.

Results

Thirty‐five patients underwent 50 operations. The median age was 42 years and 83% were tertiary referrals. Two patients were lost to follow‐up. Healing occurred in 19 (58%) of 33 patients after a mean of 1.4 operations. The median time to success was 11 (2.5–48) months. The ‘curative’ group had an overall success of 73% (19 of 26). Seventy‐five per cent of non‐inflammatory bowel disease patients and 67% of those with Crohn's disease had successful treatment of the RVF. Twenty‐four of 35 patients (67%) underwent creation of a stoma. Sixteen of 24 (67%) were deemed fit for restoration of continuity. No demographic or disease related factors were found to influence healing.

Conclusion

Cure of RVF can be achieved by a range of surgical approaches including abdominal and anal. A variety of different anal techniques are necessary, depending on the integrity of the anal sphincter and the presence or absence of perineal descent/internal intussusception.
Altering the therapeutic paradigm towards a distal bowel margin of < 1 cm in patients with low‐lying rectal cancer: a systematic review and commentary
Authors: Pahlman L. , Bujko K. , Rutkowski A. , Michalski W.
Published: January 2013

Aim

The 1‐cm rule of distal bowel clearance in patients with low‐lying rectal cancer undergoing anterior resection is based mainly on pathological data showing distal intramural spread. Because clinical data are contradictory, a review that includes only cancers located ≤ 5 or ≤ 6 cm from the anal verge was carried out.

Method

A systematic review of the literature identified seven studies that presented results in relation to a margin of ≤ 1 cm (n = 293) vs > 1 cm (n = 315). In six studies, pre‐ or postoperative radiotherapy was implemented, and in one study patients were treated with surgery alone. Three studies, all implementing radiotherapy, reported results related to a margin of ≤ 5 mm (n = 51) vs > 5 mm (n = 125).

Results

In none of the studies were the differences in local recurrence rate between the small and large margin groups statistically significant. The pooled analysis of six studies, in which patients received perioperative radiotherapy, showed a 1.2% [95% confidence interval (Cl) −4.5–7.0%] higher local recurrence rate in the ≤ 1 cm margin group compared with the > 1 cm margin group (P = 0.6). The corresponding figures for the ≤ 5 mm cut‐off point were 0.5% (95% CI −7.6–8.7%, P = 0.9). The 5‐year local recurrence rate in the only study in which radiotherapy had not been used was 8.6% higher in the ≤ 1 cm margin group compared with the > 1 cm margin group (P = 0.09).

Conclusion

Clinical evidence does not support the 1‐cm rule in patients with low‐lying rectal cancer undergoing pre‐ or postoperative radiotherapy.
A systematic review of stercoral perforation
Authors: Chakravartty S. , Chang A. , Nunoo‐Mensah J.
Published: January 2013

Aim

Stercoral perforation is a rarely suspected life‐threatening condition. Early diagnosis is difficult but essential. A comprehensive systematic review was performed to evaluate its presentation, diagnosis and treatment.

Method

A systematic review was carried out of Embase, MEDLINE, PubMed and Cochrane databases for all articles published between 1998 and 2011. Only studies describing stercoral perforation were included.

Results

Twenty‐four relevant articles were found including 137 patients (median age = 62 years) with stercoral perforation, of whom 81% had chronic constipation. Stercoral perforation was diagnosed by CT scan in 90% of 31 patients, with the commonest findings being a combination of faecal impaction (84%) and subphrenic (90%) or extraluminal air (61%). The commonest site of perforation was the sigmoid colon (50%) followed by the rectosigmoid junction (24%). The overall mortality was 34%.

Conclusion

Stercoral perforation should be suspected in elderly and chronically constipated patients with unexplained abdominal pain and investigated appropriately with a CT scan to allow timely and optimal treatment.
A prospective study of early removal of the urethral catheter after colorectal surgery in patients having epidural analgesia as part of the Enhanced Recovery After Surgery programme
Authors: Stubbs B. M. , Badcock K. J. M. , Hyams C. , Rizal F. E. , Warren S. , Francis D.
Published: January 2013

Aim

Early removal of the urethral catheters is part of the enhanced postoperative recovery programme (ERAS). The effect of epidural anaesthesia on urinary retention was investigated in patients after colorectal resection.

Method

A prospective cohort study of all patients having colorectal surgery within an ERAS programme that included insertion of an epidural catheter over the last 5 years.

Results

Two‐hundred and ten patients had an epidural and a urethral catheter postoperatively. The duration of catheterization was not recorded in one patient who was therefore excluded from the study. One‐hundred and eighteen patients had a trial without catheter (TWOC) prior to stopping the epidural (early TWOC). Ninety‐one patients had TWOC after the epidural was stopped (late TWOC). Sixteen (7.6%) patients went into urinary retention (14 early TWOC and two late TWOC). The rate of urinary retention in the early TWOC group was significantly higher than that in the late TWOC group (11.9% vs 2.2%; χ2, P = 0.009). Those who underwent a laparoscopic resection were significantly more likely to have undergone an early TWOC (χ2, P = 0.001); however, there was no difference in retention rates between open and laparoscopic surgery (χ2, P = 0.402). Pelvic surgery was not significantly associated with an increased risk of postoperative urinary retention (χ2, P = 0.627). Male sex was not significantly associated with urinary retention (χ2, P = 0.087). In the early TWOC group 86% had the catheter removed within 24 hours of surgery.

Conclusion

Early TWOC with epidural analgesia running significantly increases the risk of urinary retention; however, it was still successful in 88% of patients.
The economic impact of anastomotic leakage after anterior resections in English NHS hospitals: are we adequately remunerating them?
Authors: Ashraf S. Q. , Burns E. M. , Jani A. , Altman S. , Young J. D. , Cunningham C. , Faiz O. , Mortensen N. J.
Published: January 2013

Aim

Our aim was to determine the frequency and economic impact of anastomotic leakage (AL) at local and national levels in England.

Method

All patients who underwent AR in Oxford between 2007 and 2009 were evaluated for AL. Hospital Episode Statistics (HES) data were used to determine reoperation rates after elective AR (n = 23 388) in England between 2000 and 2008. Hospital episode remuneration costs were calculated by the local commissioning department and compared with Department of Health (DH) reference index costs.

Results

The frequency of AL following anterior resection was 10.9% (31 out of 285) in Oxford. Laparotomy for leakage was performed in 5.6% of cases. The 30‐day hospital mortality rate for all ARs was 2.1%, compared with 3.2% after AL. The national relaparotomy rate (within 28 days) and 30‐day hospital mortality in English National Health Service (NHS) trusts following AR were 5.9% and 2.9%, respectively. Institutional remunerated tariffs (£6233 (SD ± 965)) were similar to DH reference costs (£6319 (SD ± 1830)) after uncomplicated AR. However, there was a significant (P = 0.008) discrepancy between the remunerated tariff for AL (£9605 (SD ± 6908)) and the actual cost (£17 220 (SD ± 9642)). AL resulted in an additional annual cost of approximately £1.1 million to £3.5 million when extrapolated nationally.

Conclusion

The estimated economic burden of anastomotic leakage following AR is approximately double that of the remunerated tariff.
In vivo measurement of human rectus femoris architecture by ultrasonography: validity and applicability
Authors: Ema Ryoichi , Wakahara Taku , Mogi Yasuyoshi , Miyamoto Naokazu , Komatsu Toshihiko , Kanehisa Hiroaki , Kawakami Yasuo
Published: January 2013

The architectural feature of the rectus femoris (RF) has been scarcely investigated despite its substantial contribution to knee extension torque and large plasticity in the muscularity. This study aimed to examine the reproducibility and validity of ultrasound measurements of RF architecture and interrelationships among the architectural parameters. After confirming the measurement accuracy of an examiner (measurement errors <1%), in vivo and cadaveric measurements of fascicle lengths and pennation angles of RF were performed. Day‐to‐day reproducibility of measurements was investigated in vivo including muscle thickness measurement. Validity of measurements was investigated by comparing the values between direct and ultrasound measurements for the cadaver. The intraclass correlation coefficients were 0·984, 0·960 and 0·932, and root mean square difference between measured values on 2 days was 0·8 mm, 3·1 mm and 1·4° for muscle thickness, fascicle length and pennation angle, respectively. The validity of measurements was similar or better than those of previous reports on other muscles. We also confirmed a positive correlation between the muscle thickness and the pennation angle as has been shown in other muscles. The current results warrant the use of B‐mode ultrasonography for examining the architectural characteristics of RF in vivo.
Pleomorphic fibroma and dermal atypical lipomatous tumor: are they related?
Authors: Al‐Zaid Tariq , Wang Wei‐Lien , Lopez‐Terrada Dolores , Lev Dina , Hornick Jason L. , Hafeez Diwan A. , Fletcher Christopher D. M. , Lazar Alexander J.
Published: January 2013

Pleomorphic fibromas represent dome‐shaped or polypoid cutaneous lesions characterized by a paucicellular and densely fibrotic background punctuated by scattered atypical to pleomorphic spindle and multinucleated giant cells. Some of these tumors will have incorporated adipose tissue, although these adipocytic areas lack distinct cytologic atypia and may represent entrapped normal periadnexal or subcutaneous adipose tissue. Nonetheless, owing to the similarity of some of the morphologic features of pleomorphic fibroma with cutaneous atypical lipomatous tumor, diagnostic confusion can ensue. The potential diagnostic challenges are further highlighted by a recent report of a lesion with histopathologic features of both. In response, we studied the presence of 12q15/ MDM2 amplification by fluorescence in situ hybridization and MDM2 expression by immunohistochemistry in a series of 15 pleomorphic fibromas to investigate whether these two entities share a common pathogenic origin. One case of cutaneous atypical lipomatous tumor was used as positive control for 12q15 amplification. All 15 cases were negative for MDM2 by immunohistochemistry with no demonstrable 12q15/MDM2 amplification by fluorescence in situ hybridization. Therefore, these two entities are best regarded as pathogenetically distinct. MDM2 immunohistochemistry or fluorescence in situ hybridization studies can be used to differentiate between the two if needed.
Biotic homogenization at the community scale: disentangling the roles of urbanization and plant invasion
Authors: Trentanovi Giovanni , von der Lippe Moritz , Sitzia Tommaso , Ziechmann Ulrike , Kowarik Ingo , Cierjacks Arne
Published: January 2013

Aim

Urbanization as a major global trend profoundly changes biodiversity patterns, and homogenization of urban biota due to expanding exotic species and declining native species is of increasing concern. Previous studies on this topic have mostly taken place at large scales that include high habitat heterogeneity. Here, we aimed at disentangling the effects of urbanization and plant invasion on species composition through the analysis of similarity patterns of urban plant assemblages at the community scale where species interact.

Location

Berlin, Germany.

Methods

We analysed how different levels of urbanization, specific components of the urban matrix and the dominance of a native (Betula pendula) versus an exotic tree species (Robinia pseudoacacia) affect alpha and beta diversity of urban woodland understorey vegetation in sixty‐eight 100‐m2 plots.

Results

Exotic dominance reduced alpha diversity, but not beta diversity of the total species pool. Comparing beta diversity among different species groups revealed significant but divergent effects of exotic dominance, habitat connectivity and levels of urbanization in native and non‐native species assemblages. In particular, urbanity proved to homogenize the native species pool, whereas the beta diversity of the non‐native species pool showed a more pronounced response to exotic dominance.

Main conclusions

Our data provide evidence that both the urban context and the dominance of exotic species can modify homogenization processes at the community level. These novel insights into the mechanisms of biotic homogenization of urban floras may contribute to mitigating the effects of urbanization on biodiversity.
On evaluating species distribution models with random background sites in place of absences when test presences disproportionately sample suitable habitat
Authors: Smith Adam B.
Published: January 2013

Modelling the distribution of rare and invasive species often occurs in situations where reliable absences for evaluating model performance are unavailable. However, predictions at randomly located sites, or ‘background’ sites, can stand in for true absences. The maximum value of the area under the receiver operator characteristic curve, AUC, calculated with background sites is believed to be 1 − a/2, where a is the typically unknown prevalence of the species on the landscape. Using a simple example of a species' range, I show how AUC can achieve values > 1 − a/2 when test presences do not represent each inhabited region of a species__ range in proportion to its area. Values of AUC that surpass 1 − a/2 are associated with higher model predictions in areas overrepresented in the test data set, even if they are less environmentally suitable than other regions the species occupies. Pursuit of high AUC values can encourage inclusion of spurious predictors in the final model if they help to differentiate areas with disproportionate representation in the test data. Choices made during modelling to increase AUC calculated with background sites on the assumption that higher scores connote more accurate models can decrease actual accuracy when test presences disproportionately represent inhabited areas.
Scaling species richness and endemism of tropical dry forests on oceanic islands
Authors: Gillespie Thomas W. , Keppel Gunnar , Pau Stephanie , Price Jonathan P. , Jaffré Tanguy , O'Neill Kristin
Published: January 2013

Aim

We examine variation in woody plant species richness and endemism within tropical dry forest on oceanic islands and determine what climatic and biogeographic metrics best explain native species richness and endemism across archipelagos, islands and plots.

Location

Oceanic islands in the Pacific.

Methods

Stand‐level sampling (0.1 ha) at 35 different dry forest sites across 16 islands, and five archipelagos (New Caledonia, Fiji, Marquesas, Marianas and Hawaii). Descriptors of native species richness and endemism were calculated at the plot, island and archipelago level. Biogeographic and climate metrics at the archipelago, island and plot level were drawn from the literature and computer databases. The effects of biogeographic and climate metrics were investigated using linear mixed‐effects models.

Results

Dry forests of New Caledonia and Fiji had the highest native species richness, while New Caledonia and Hawaii had the highest endemism. Native species richness and endemism within tropical dry forests on oceanic islands are primarily influenced by biogeographic metrics, especially isolation of the archipelago, and not climatic metrics. Most variance in native species richness and endemism (60% and 64%) is at the archipelago level compared with the island (8%, 16%) and plot (32%, 15%) level. At the island level, species richness in tropical dry forest is affected by precipitation, while island area significantly affects endemism. The area of forest fragments is an important predictor of native species richness and endemism in plots.

Main conclusions

Although dry forests in the Pacific have been exceptionally deforested and degraded, high native species richness and endemism remains in a number of forest fragments. Biogeographic metrics explain most of the variance in native species richness and endemism across scales, while climatic metrics are important at the island level. First‐order assessments of native richness and endemism at the archipelago, island and stand‐level are possible for forest types on oceanic archipelagos.
Integrating multiple scales in rarity assessments of invertebrate taxa
Authors: Leroy Boris , Canard Alain , Ysnel Frédéric
Published: January 2013

Aim

To provide a procedure for measuring the rarity of both invertebrate species and assemblages of species from multiple scales without the need for fine‐resolution datasets over broad areas.

Location

The western Palearctic (WP) and western France.

Methods

On the basis of different datasets from different geographical extents, we applied a multiscale rarity weight to species occurrence from multiple scales. Multiscale rarity weights were then averaged at an assemblage level in a multiscale index of relative rarity (IRR). These rarity weights were calculated using a flexible, scale‐dependent method that ensures equitable contributions of each scale to the final index. We provided a simple two‐scale example of the application, on spiders of western France, for which we obtained occurrence information from a regional‐extent dataset (regional scale) and a western Palearctic‐extent dataset (WP scale). Thus, we showed the necessity of a two‐scale approach by successively analysing species occurrence, multiscale rarity weights of species and multiscale indices of species assemblage. Finally, we presented a case study within a nature reserve.

Results

Species occurrences are not predictable from one scale to another, and rarity indices of assemblages are poorly congruent among scales, which supports the necessity of a two‐scale approach. Multiscale rarity weights accurately showed information on species rarity from both scales. Multiscale indices of assemblages were congruent but with additional information over each one‐scale index.

Main conclusions

The novelty of the multiscale method developed here is to accurately combine different datasets of varying extents and resolutions to provide multiscale rarity weights for species and indices for assemblages. Given the increasing availability of datasets for invertebrate taxa, this method represents a significant improvement for rarity and conservation studies on invertebrates.