bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequence of the Sponge-Associated Strain Bacillus atrophaeus C89, a Potential Producer of Marine Drugs
Authors: Liu Fang , Sun Wei , Su Fei , Zhou Kang , Li Zhiyong 
Published: July 2012

ABSTRACT

Bacillus atrophaeus
C89, isolated from the marine sponge
Dysidea avara
, is a potential producer of bioactive compounds, such as neobacillamide A and bacillamide C. Here, we present a 4.2-Mb assembly of its genome. The nonribosomal peptide synthetases (NRPSs) make it possible to produce the bioactive compounds.
Construction and validation of a questionnaire distinguishing a chronic abdominal wall pain syndrome from irritable bowel syndrome
Authors: van Assen Tijmen , Boelens Oliver B , Kamphuis Jan T , Scheltinga Marc R , Roumen Rudi M 
Published: July 2012

ObjectiveThe irritable bowel syndrome (IBS) population is heterogeneous, harbouring a variety of abdominal symptoms. Therefore, IBS is often termed a ‘diagnosis of exclusion’. Chronic abdominal wall pain (CAWP) is a poorly recognized entity, frequently caused by the anterior cutaneous nerve entrapment syndrome (ACNES). Some patients may be misdiagnosed because IBS and CAWP share symptoms. Aim of this study was to construct and validate a questionnaire to distinguish patients with CAWP (including ACNES) patients with IBS.DesignA questionnaire was designed of 17 ACNES characteristic items obtained from ACNES patients (n=33) and expert opinion of two specialized surgeons. Eleven IBS-related items (‘Rome III’ criteria) were added leading to a questionnaire containing 28 items. This was validated in a ‘gold standard’ ACNES group (successfully operated ACNES patients, n=68) and a ‘prospective’ IBS group (n=64) as well as in a ‘prospective’ ACNES group (n=47). Distinctive power of individual items was analyzed by χ2. Reliability was tested with Crohnbach's α. ROC curve was used to determine cut-off values.ResultsEighteen of 28 items were significantly distinctive (p<0.01) between ACNES and IBS patients leading to an 18-point ACNES score with good internal consistency (α=0.85). Cut-off value of 10 points resulted in 94% sensitivity, 92% specificity and areas under the curve (AUC) of 0.98. Evaluation of the prospective ACNES group led to 85% sensitivity, 92% specificity and AUC 0.95 indicating high discriminative properties of the questionnaire.ConclusionsThis novel questionnaire may be useful and valid as a simple tool distinguishing patients harbouring a CAWP syndrome from those having IBS.
Candida krusei: biotechnological potentials and concerns about its safety
Authors: Yadav Jay Shankar Singh , Bezawada Jyothi , Yan Song , Tyagi R.D. , Surampalli R.Y. 
Published: July 2012

Yeasts have a tradition in biotechnological applications, and Saccharomyces species are the most dominating representatives. Among the yeast species, Candida krusei has been isolated from different habitats, and in recent years, it has gained increased interest because of its diverse biotechnological role. It is found in many fermented food items and dairy products and has also been exploited for production of biochemicals and enzymes. However, because of its opportunistic pathogenic nature, it draws scientific attention regarding the safety of its industrial exploitation. Candida krusei generally causes infections in immunocompromised patients, such as those suffering from Human immunodeficiency virus – acquired immune deficiency syndrome, and also in cancer patients. The recent increase in the use of immunosuppressive drugs has increased the chances of C. krusei infections. Candida krusei possesses an intrinsic resistance to many triazole antifungal drugs, especially fluconazole, which is a main drug used in antifungal therapy; therefore, there is serious concern regarding its safe industrial use.
VopB1 and VopD1 are essential for translocation of type III secretion system 1 effectors of Vibrio parahaemolyticus
Authors: Shimohata Takaaki , Mawatari Kazuaki , Iba Hitomi , Hamano Masakazu , Negoro Sachie , Asada Shoko , Aihara Mutsumi , Hirata Akiko , Su Zehong , Takahashi Akira 
Published: July 2012

Vibrio parahaemolyticus is a pathogenic Vibrio species that causes food-borne acute gastroenteritis, often related to the consumption of raw or undercooked seafood. Vibrio parahaemolyticus has 2 type III secretion systems (T3SS1 and T3SS2). Here, we demonstrate that VP1657 (VopB1) and VP1656 (VopD1), which share sequence similarity with Pseudomonas genes popB (38%) and popD (36%), respectively, are essential for translocation of T3SS1 effectors into host cells. A VP1680CyaA fusion reporter system was constructed to observe effector translocation. Using this reporter assay we showed that the VopB1 and VopD1 deletion strains were unable to translocate VP1680 to host cell but that the secretion of VP1680 into the culture medium was not affected. VopB1 or VopD1 deletion strains did not enhance cytotoxicity and failed to activate mitogen-activated protein kinases and secretion of interleukin-8, which depend on VP1680. Thus, we conclude that VopB1 and VopD1 are essential components of the translocon. To target VopB1 and VopD1 may have therapeutic potential for the treatment or prevention in V. parahaemolyticus infection.
A Genome-Wide Association Study Identifies Novel Loci for Paclitaxel-Induced Sensory Peripheral Neuropathy in CALGB 40101
Authors: Baldwin R. Michael , Owzar Kouros , Zembutsu Hitoshi , Chhibber Aparna , Kubo Michiaki , Jiang Chen , Watson Dorothy , Eclov Rachel J. , Mefford Joel , McLeod Howard L. , Friedman Paula N. , Hudis Clifford A. , Winer Eric P. , Jorgenson Eric M. , Witte John S. , Shulman Lawrence N. , Nakamura Yusuke , Ratain Mark J. , Kroetz Deanna L. 
Published: July 2012

AbstractPurpose: Sensory peripheral neuropathy is a common and sometimes debilitating toxicity associated with paclitaxel therapy. This study aims to identify genetic risk factors for the development of this toxicity.Experimental Design: A prospective pharmacogenetic analysis of patients with primary breast cancer, randomized to the paclitaxel arm of CALGB 40101, was used to identify genetic predictors of the onset and severity of sensory peripheral neuropathy. A genome-wide association study in 855 subjects of European ancestry was conducted and findings were replicated in additional European (n = 154) and African American (n = 117) subjects.Results: A single nucleotide polymorphism in FGD4 was associated with the onset of sensory peripheral neuropathy in the discovery cohort [rs10771973; HR, 1.57; 95% confidence interval (CI), 1.30–1.91; P = 2.6 × 10−6] and in a European (HR, 1.72; 95% CI, 1.06–2.80; P = 0.013) and African American (HR, 1.93; 95% CI, 1.13–3.28; P = 6.7 × 10−3) replication cohort. There is also evidence that markers in additional genes, including EPHA5 (rs7349683) and FZD3 (rs10771973), were associated with the onset or severity of paclitaxel-induced sensory peripheral neuropathy.Conclusions: A genome-wide association study has identified novel genetic markers of paclitaxel-induced sensory peripheral neuropathy, including a common polymorphism in FGD4, a congenital peripheral neuropathy gene. These findings suggest that genetic variation may contribute to variation in development of this toxicity. Validation of these findings may allow for the identification of patients at increased risk of peripheral neuropathy and inform the use of an alternative to paclitaxel and/or the clinical management of this toxicity. Clin Cancer Res; 18(18); 5099–109. ©2012 AACR.
Progressive muscle relaxation in persons with schizophrenia: a systematic review of randomized controlled trials
Authors: Vancampfort Davy , Correll Christoph U , Scheewe Thomas W , Probst Michel , De Herdt Amber , Knapen Jan , De Hert Marc 
Published: July 2012

Objective: The aim of this systematic review was to assess the effectiveness of progressive muscle relaxation on psychological distress and anxiety symptoms and on response/remission for people with schizophrenia. Methods: Randomized controlled trials were considered if they investigated progressive muscle relaxation in patients with schizophrenia. EMBASE, PsycINFO, PubMed, ISI Web of Science, CINAHL, PEDro and Cochrane Library were searched. The selection of studies, data extraction and quality assessment were performed independently by two reviewers. Results: Three randomized controlled trials involving 146 patients met the inclusion criteria. Progressive muscle relaxation can acutely reduce state anxiety and psychological distress and improve subjective well-being. No studies investigated the evidence for progressive muscle relaxation as an add-on treatment for general psychopathology and for positive or negative symptoms. Also, no studies assessed the value of progressive muscle relaxation in longer-term treatment and for relapse prevention. There were no data to draw any conclusions about progressive muscle relaxation in comparison with other treatment modalities. None of the studies encountered adverse events. Dose-response relationships could not be determined. Conclusion: Progressive muscle relaxation might be a useful add-on treatment to reduce state anxiety and psychological distress and improve subjective well-being in persons with schizophrenia.
Effect of body mass index on the location of the right adrenal vein in patients with primary aldosteronism
Authors: Iwasaki Toshitaka , Kurisu Satoshi , Mitsuba Naoya , Ishibashi Ken , Dohi Yoshihiro , Nishioka Kenji , Kihara Yasuki 
Published: July 2012

Background: Variable location of the orifice of the right adrenal vein appears to be associated with a poor success rate of sampling, especially in less experienced hands. We described the spectrum of the location of the right adrenal vein, and identified the relation of its location to body mass index in patients with primary aldosteronism. Methods and results: The study population consisted of 95 patients with primary aldosteronism who underwent adrenal venous sampling. On the basis of the anterior view of the right adrenal venogram, the cranio-caudal level of the orifice of right adrenal vein was determined relative to vertebral bodies and disks. In 93 (98%) of the 95 patients, the orifice was located at a level ranging from the upper segment of T11 to the upper segment of L1. In the remaining two patients, it was located at the level of the lower segment of T10. High body mass index was associated with the higher level of the orifice of right adrenal vein. Conclusion: Our data suggested that the location of the orifice of right adrenal vein was largely related to body mass index in patients with primary aldosteronism.
Evolution of specifier proteins in glucosinolate-containing plants
Authors: Kuchernig Jennifer C , Burow Meike , Wittstock Ute 
Published: July 2012

Abstract

Background
The glucosinolate-myrosinase system is an activated chemical defense system found in plants of the Brassicales order. Glucosinolates are stored separately from their hydrolytic enzymes, the myrosinases, in plant tissues. Upon tissue damage, e.g. by herbivory, glucosinolates and myrosinases get mixed and glucosinolates are broken down to an array of biologically active compounds of which isothiocyanates are toxic to a wide range of organisms. Specifier proteins occur in some, but not all glucosinolate-containing plants and promote the formation of biologically active non-isothiocyanate products upon myrosinase-catalyzed glucosinolate breakdown.

Results
Based on a phytochemical screening among representatives of the Brassicales order, we selected candidate species for identification of specifier protein cDNAs. We identified ten specifier proteins from a range of species of the Brassicaceae and assigned each of them to one of the three specifier protein types (NSP, nitrile-specifier protein, ESP, epithiospecifier protein, TFP, thiocyanate-forming protein) after heterologous expression in Escherichia coli. Together with nine known specifier proteins and three putative specifier proteins found in databases, we subjected the newly identified specifier proteins to phylogenetic analyses. Specifier proteins formed three major clusters, named AtNSP5-cluster, AtNSP1-cluster, and ESP/TFP cluster. Within the ESP/TFP cluster, specifier proteins grouped according to the Brassicaceae lineage they were identified from. Non-synonymous vs. synonymous substitution rate ratios suggested purifying selection to act on specifier protein genes.

Conclusions
Among specifier proteins, NSPs represent the ancestral activity. The data support a monophyletic origin of ESPs from NSPs. The split between NSPs and ESPs/TFPs happened before the radiation of the core Brassicaceae. Future analyses have to show if TFP activity evolved from ESPs at least twice independently in different Brassicaceae lineages as suggested by the phylogeny. The ability to form non-isothiocyanate products by specifier protein activity may provide plants with a selective advantage. The evolution of specifier proteins in the Brassicaceae demonstrates the plasticity of secondary metabolism within an activated plant defense system.
Presence of S100A9-positive inflammatory cells in cancer tissues correlates with an early stage cancer and a better prognosis in patients with gastric cancer
Authors: Fan Biao , Zhang Lian-Hai , Jia Yong-ning , Zhong Xi-Yao , Liu Yi-Qiang , Cheng Xiao-Jing , Wang Xiao-Hong , Xing Xiao-Fang , Hu Ying , Li Ying-Ai , Du Hong , Zhao Wei , Niu Zhao-Jian , Lu Ai-Ping , Li Ji-You , Ji Jia-Fu 
Published: July 2012

Abstract

Background
S100A9 was originally discovered as a factor secreted by inflammatory cells. Recently, S100A9 was found to be associated with several human malignancies. The purpose of this study is to investigate S100A9 expression in gastric cancer and explore its role in cancer progression.

Methods
S100A9 expression in gastric tissue samples from 177 gastric cancer patients was assessed by immunohistochemistry. The expression of its dimerization partner S100A8 and the S100A8/A9 heterodimer were also assessed by the same method. The effect of exogenous S100A9 on motility of gastric cancer cells AGS and BGC-823 was then investigated.

Results
S100A9 was specifically expressed by inflammatory cells such as macrophages and neutrophils in human gastric cancer and gastritis tissues. Statistical analysis showed that a high S100A9 cell count (> = 200) per 200x magnification microscopic field in cancer tissues was predictive of early stage gastric cancer. High S100A9-positive cell count was negatively correlated with lymph node metastasis (P = 0.009) and tumor invasion (P = 0.011). S100A9 was identified as an independent prognostic predictor of overall survival of patients with gastric cancer (P = 0.04). Patients with high S100A9 cell count were with favorable prognosis (P = 0.021). Further investigation found that S100A8 distribution in human gastric cancer tissues was similar to S100A9. However, the number of S100A8-positive cells did not positively correlate with patient survival. The inflammatory cells infiltrating cancer were S100A8/A9 negative, while those in gastritis were positive. Furthermore, exogenous S100A9 protein inhibited migration and invasion of gastric cancer cells.

Conclusions
Our results suggested S100A9-positive inflammatory cells in gastric cancer tissues are associated with early stage of gastric cancer and good prognosis.
Severe vitamin B12 deficiency in an exclusively breastfed 5-month-old Italian infant born to a mother receiving multivitamin supplementation during pregnancy
Authors: Guez Sophie , Chiarelli Gabriella , Menni Francesca , Salera Simona , Principi Nicola , Esposito Susanna 
Published: July 2012

Abstract

Background
In infants, vitamin B12 deficiency may be due to an inborn error of absorption and metabolism, or nutritional problems.

Case presentation
An exclusively breastfed 5-month-old Italian male infant, who was born after a normal full-term pregnancy to a vegan mother who was apparently daily treated with a multivitamin oral preparation during the second and third trimester, was hospitalised because of poor weight gain, feeding difficulties, severe pallor, muscle hypotonia and somnolence. Upon admission, his weight, length and head circumference were below the third percentile, he had an enlarged liver and spleen, and showed a significant delay in developmental milestones and communicative reactions. He had a hemoglobin level of 4.7 g/dL with an MCV of 84.2 fL, a white blood cell count of 4,680/mm3, and a platelet count of 45,000/mm3. His serum vitamin B12 level was 57 pg/mL (normal value 180–500 pg/mL) and serum folate level 12.8 ng/mL (normal value >3 ng/mL). The results of metabolic examinations excluded a cobalamin C disorder, whereas nutritional screening showed a serum iron concentration of 9 μg/dL and serum ferritin of 4 ng/mL. Magnetic resonance imaging of the brain showed mild dilatation of the lateral ventricles with diffuse delayed myelination. The child was diagnosed as having vitamin B12 and iron deficiency due to nutritional inadequacy and was immediately treated with packed red blood cells, intramuscular vitamin B12 injections, and iron supplementation. A few days after the start of therapy, his hemoglobin levels and other hematological parameters rapidly improved, and a clinical improvement was observed within few weeks. There was an increase in his achievement of developmental milestones, but his development was still retarded seven months after the start of therapy.

Conclusion
This case underlines the importance of adequately controlling maternal vitamin B12 intake during pregnancy by means of supplementation which, in the case of vegan mothers, should be significantly greater than that usually given. Moreover, the supplementation should be continued during lactation in order to avoid the development of signs of deficiency that may be associated with persistent neurological problems in infants. The case also highlights the need to consider vitamin B12 deficiency in infants with severe anemia even if their hematological parameters do not indicate megaloblastic anemia because the concomitant presence of substantial iron deficiency may modify the characteristics of the anemia.
A summary index of infant and child feeding practices is associated with child growth in urban Shanghai
Authors: Ma Jing-Qiu , Zhou Li-Li , Hu Yan-Qi , Liu Jin-Rong , Liu Shan-Shan , Zhang Jie , Sheng Xiao-Yang 
Published: July 2012

Abstract

Background
Recently, an infant and child feeding index (ICFI) constructed on brief recalls of breastfeeding, feeding frequency and food diversification was assumed to provide long-term prediction about child feeding practices. The aim of this study was to investigate the association between the cross-sectional ICFI (CS-ICFI) or longitudinal ICFI (L-ICFI) and child anthropometric indices in downtown Shanghai, China.

Methods
The prospective cohort study included 180 infants aged 5-7 mo with their main caregivers who were visited 3 times every 6 months over 12 months. A CS-ICFI was constructed for each visit by using data on feeding practices based on 24-h and 7-d recalls. An L-ICFI was constructed with use of the 3 CS-ICFIs. The associations between ICFI and length-for-age z score (LAZ), weight-for-age z score (WAZ), and weight-for-length z score (WLZ) were examined. The stability of the CS-ICFI was assessed by using repeatability coefficient (RC).

Results
The L-ICFI was positively associated with LAZ and WAZ at Visit 3(beta = 0.151, P = 0.040 and beta = 0.173, P = 0.024, respectively). Moreover, the CS-ICFI at Visit 1 was positively associated with LAZ, WAZ and WLZ (beta = 0.160, P = 0.029; beta = 0.191, P = 0.009; beta = 0.176, P = 0.020) at Visit 3, and the CS-ICFI at Visit 3 was also positively associated with LAZ (beta = 0.176, P = 0.016). Stability of the CS-ICFI was shown by the value of 0.14 (95% CI: 0.07, 0.31) of the RC, which differed significantly from 0 (P < 0.05).

Conclusions
The ICFI constructed on brief recalls based on cross-sectional studies can be used to evaluate the effects of child feeding practice on child growth.
IL-3 and TNFα increase Thymic Stromal Lymphopoietin Receptor (TSLPR) expression on eosinophils and enhance TSLP-stimulated degranulation
Authors: Cook Ellen B , Stahl James L , Schwantes Elizabeth A , Fox Kristen E , Mathur Sameer K 
Published: July 2012

AbstractBackgroundThymic stromal lymphopoietin (TSLP) and eosinophils are prominent components of allergic inflammation. Therefore, we sought to determine whether TSLP could activate eosinophils, focusing on measuring the regulation of TSLPR expression on eosinophils and degranulation in response to TSLP, as well as other eosinophil activation responses.MethodsEosinophil mRNA expression of TSLPR and IL-7Rα was examined by real-time quantitative PCR of human eosinophils treated with TNFα and IL-5 family cytokines, and TSLPR surface expression on eosinophils was analyzed by flow cytometry. Eosinophils were stimulated with TSLP (with and without pre-activation with TNFα and IL-3) and evaluated for release of eosinophil derived neurotoxin (EDN), phosphorylation of STAT5, and survival by trypan blue exclusion. A blocking antibody for TSLPR was used to confirm the specificity of TSLP mediated signaling on eosinophil degranulation.ResultsEosinophil expression of cell surface TSLPR and TSLPR mRNA was upregulated by stimulation with TNFα and IL-3. TSLP stimulation resulted in release of EDN, phosphorylation of STAT5 as well as promotion of viability and survival. TSLP-stimulated eosinophil degranulation was inhibited by a functional blocking antibody to TSLPR. Pre-activation of eosinophils with TNFα and IL-3 promoted eosinophil degranulation at lower concentrations of TSLP stimulation.ConclusionsThis study demonstrates that eosinophils are activated by TSLP and that eosinophil degranulation in response to TSLP may be enhanced on exposure to cytokines present in allergic inflammation, indicating that the eosinophil has the capacity to participate in TSLP-driven allergic responses.