bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biofilm Formation Avoids Complement Immunity and Phagocytosis of Streptococcus pneumoniae
Authors: Domenech Mirian , Ramos-Sevillano Elisa , García Ernesto , Moscoso Miriam , Yuste Jose 
Published: May 2013

ABSTRACT

Streptococcus pneumoniae
is a frequent member of the microbiota of the human nasopharynx. Colonization of the nasopharyngeal tract is a first and necessary step in the infectious process and often involves the formation of sessile microbial communities by this human pathogen. The ability to grow and persist as biofilms is an advantage for many microorganisms, because biofilm-grown bacteria show reduced susceptibility to antimicrobial agents and hinder recognition by the immune system. The extent of host protection against biofilm-related pneumococcal disease has not been determined yet. Using pneumococcal strains growing as planktonic cultures or as biofilms, we have investigated the recognition of
S. pneumoniae
by the complement system and its interactions with human neutrophils. Deposition of C3b, the key complement component, was impaired on
S. pneumoniae
biofilms. In addition, binding of C-reactive protein and the complement component C1q to the pneumococcal surface was reduced in biofilm bacteria, demonstrating that pneumococcal biofilms avoid the activation of the classical complement pathway. In addition, recruitment of factor H, the downregulator of the alternative pathway, was enhanced by
S. pneumoniae
growing as biofilms. Our results also show that biofilm formation diverts the alternative complement pathway activation by a PspC-mediated mechanism. Furthermore, phagocytosis of pneumococcal biofilms was also impaired. The present study confirms that biofilm formation in
S. pneumoniae
is an efficient means of evading both the classical and the PspC-dependent alternative complement pathways the host immune system.
Selenium Status Alters the Immune Response and Expulsion of Adult Heligmosomoides bakeri Worms in Mice
Authors: Smith Allen D. , Cheung Lumei , Beshah Ethiopia , Shea-Donohue Terez , Urban Joseph F. 
Published: May 2013

ABSTRACTHeligmosomoides bakeriis a nematode with parasitic development exclusively in the small intestine of infected mice that induces a potent STAT6-dependent Th2 immune response. We previously demonstrated that host protective expulsion of adultH. bakeriworms from a challenge infection was delayed in selenium (Se)-deficient mice. In order to explore mechanisms associated with the delayed expulsion, 3-week-old female BALB/c mice were placed on a torula yeast-based diet with or without 0.2 ppm Se, and after 5 weeks, they were inoculated withH. bakeriinfective third-stage larvae (L3s). Two weeks after inoculation, the mice were treated with an anthelmintic and then rested, reinoculated with L3s, and evaluated at various times after reinoculation. Analysis of gene expression in parasite-induced cysts and surrounding tissue isolated from the intestine of infected mice showed that the local-tissue Th2 response was decreased in Se-deficient mice compared to that in Se-adequate mice. In addition, adult worms recovered from Se-deficient mice had higher ATP levels than worms from Se-adequate mice, indicating greater metabolic activity in the face of a suboptimal Se-dependent local immune response. Notably, the process of worm expulsion was restored within 2 to 4 days after feeding a Se-adequate diet to Se-deficient mice. Expulsion was associated with an increased local expression of Th2-associated genes in the small intestine, intestinal glutathione peroxidase activity, secreted Relm-β protein, anti-H. bakeriIgG1 production, and reduced worm fecundity and ATP-dependent metabolic activity.
Ophthalmic surgical training following modernising medical careers: regional variation in experience across the UK
Authors: Rodrigues Ian AS , Symes Richard J , Turner Stephen , Sinha Arti , Bowler Gordon , Chan Wai H 
Published: May 2013

ObjectivesTo evaluate surgical experience among current doctors appointed into ophthalmology training posts since the introduction of the Modernising Medical Careers programme. Additionally, to identify regional variations in surgical experience and training programme delivery.DesignA cross-sectional survey.SettingThe UK's four largest deaneries (Schools of Ophthalmology).ParticipantsTrainee ophthalmologists, all having completed three or more years of training, who were appointed to the new ophthalmic specialty training programme.Primary and secondary outcome measuresThe mean annual surgical rate for each deanery in phacoemulsification cataract extractions and experience in other common elective and emergency surgical operations. Second, to calculate the mean timetabled clinical activity.ResultsThe responses of 40 doctors were analysed, with a response rate of 83%. Overall, the phacoemulsification rate was 73.52±29.24 operations/year. This was significantly higher in the South Thames Deanery (99.69±26.16, p=0.0005) and significantly lower in the North Western Deanery (48.08±19.72, p=0.0008). The annual mean complex cataract rate was 5.21±4.38. Only 40% were confident in dealing with the most common complication of cataract surgery (vitreous loss). The mean trabeculectomy (surgery for glaucoma) rate was 0.47±1.16 and for squint surgery it was 3.54±2.82 operations/year. Regarding the common ocular trauma surgery, 42.5% had not sutured a corneal laceration and 60% a globe rupture. 50% thought the training programme would adequately prepare them surgically. The timetabled clinical activity was highest in the South Thames Deanery (48.17 h/week) and lowest in the North Western Deanery (40.82 h/week) due to variations in the European Working Time Directive implementation and on-call commitments.ConclusionsSignificant regional variations in surgical training experience exist between UK deaneries, particularly with respect to cataract surgery, and they appear to be correlated to timetabled activity. Experience and confidence levels in managing complex cataract surgery and complications were low and experience with previously commonly performed elective and emergency operations was minimal. Although doctors from all the regions surveyed were very likely to achieve the minimum cataract extractions required for specialist training completion, we have identified shortcomings of the current training programme that need attention.
The Steroid Receptor Coactivator-3 Is Required for the Development of Castration-Resistant Prostate Cancer
Authors: Tien Jean C-Y. , Liu Zhaoliang , Liao Lan , Wang Fen , Xu Yixiang , Wu Ye-Lin , Zhou Niya , Ittmann Michael , Xu Jianming 
Published: May 2013

Abstract
The transcriptional coactivator SRC-3 plays a key role in enhancing prostate cancer cell proliferation. Although SRC-3 is highly expressed in advanced prostate cancer, its role in castration-resistant prostate cancer (CRPC) driven by PTEN mutation is unknown. We documented elevated SRC-3 in human CRPC and in PTEN-negative human prostate cancer. Patients with high SRC-3 and undetectable PTEN exhibited decreased recurrence-free survival. To explore the causal relationship in these observations, we generated mice in which both Pten and SRC-3 were inactivated in prostate epithelial cells (Pten3CKO mice), comparing them with mice in which only Pten was inactivated in these cells (PtenCKO mice). SRC-3 deletion impaired cellular proliferation and reduced tumor size. Notably, while castration of PtenCKO control mice increased the aggressiveness of prostate tumors relative to noncastrated counterparts, deletion of SRC-3 in Pten3CKO mice reversed all these changes. In support of this finding, castrated Pten3CKO mice also exhibited decreased levels of phospho-Akt, S6 kinase (RPS6KB1), and phosphorylated S6 protein (RPS6), all of which mediate cell growth and proliferation. Moreover, these tumors appeared to be more differentiated as evidenced by higher levels of Fkbp5, an AR-responsive gene that inhibits Akt signaling. Lastly, these tumors also displayed lower levels of certain androgen-repressed genes such as cyclin E2 and MMP10. Together, our results show that SRC-3 drives CRPC formation and offer preclinical proof of concept for a transcriptional coactivator as a therapeutic target to abrogate CRPC progression. Cancer Res; 73(13); 3997–4008. ©2013 AACR.
Loss of ARF Sensitizes Transgenic BRAFV600E Mice to UV-Induced Melanoma via Suppression of XPC
Authors: Luo Chi , Sheng Jinghao , Hu Miaofen G. , Haluska Frank G. , Cui Rutao , Xu Zhengping , Tsichlis Philip N. , Hu Guo-Fu , Hinds Philip W. 
Published: May 2013

AbstractBoth genetic mutations and UV irradiation (UVR) can predispose individuals to melanoma. Although BRAFV600E is the most prevalent oncogene in melanoma, the BRAFV600E mutant is not sufficient to induce tumors in vivo. Mutation at the CDKN2A locus is another melanoma-predisposing event that can disrupt the function of both p16INK4a and ARF. Numerous studies have focused on the role of p16INK4a in melanoma, but the involvement of ARF, a well-known p53 activator, is still controversial. Using a transgenic BRAFV600E mouse model previously generated in our laboratory, we report that loss of ARF is able to enhance spontaneous melanoma formation and cause profound sensitivity to neonatal UVB exposure. Mechanistically, BRAFV600E and ARF deletion synergize to inhibit nucleotide excision repair by epigenetically repressing XPC and inhibiting the E2F4/DP1 complex. We suggest that the deletion of ARF promotes melanomagenesis not by abrogating p53 activation but by acting in concert with BRAFV600E to increase the load of DNA damage caused by UVR. Cancer Res; 73(14); 4337–48. ©2013 AACR.
Buccinator Myomucosal Flap for Reconstruction of Glossectomy Defects
Authors: Woo Seung Hoon , Jeong Han‐Sin , Kim Jin Pyeong , Park Jung Je , Ryu Junsun , Baek Chung‐Hwan 
Published: May 2013

ObjectiveThe use of the myomucosal flap from the buccinator muscle is a valuable reconstruction method for intraoral defects. We report the clinical advantages and pitfalls of using the buccinator myomucosal flap for tongue reconstruction after intraoral resection of tongue cancer.Study DesignProspective study.SettingUniversity hospital.Subjects and MethodsWe used buccal artery–based buccinator myomucosal flaps for tongue reconstruction in 11 partial or total edentulous patients who underwent resection of tongue cancer. The size and site of the tongue defect ranged from one‐third to one‐half of the tongue in the lateral border. We analyzed the clinical features and oncologic and functional outcomes to define adequate indications.ResultsAll flaps were successfully harvested and transposed, and the donor sites were primarily closed. The pedicles were safely divided 2 to 3 weeks postoperatively. In 8 of 11 patients, concurrent upper neck dissection was performed without compromising blood supply to the flap. The range of tongue motion and the volume of the reconstructed tongue were satisfactory, and the patients experienced no difficulties in swallowing or speech.ConclusionParticularly in edentulous patients, the buccal myomucosal flap can be a good option for reconstructing partial tongue defects after cancer surgery.
Cosmetic Rhinoseptoplasty in Acute Nasal Bone Fracture
Authors: Kim Ji Heui , Lee Jung Woo , Park Chan Hum 
Published: May 2013

ObjectiveTraditionally, rhinoseptoplasty for nasal bone fracture is only considered after an unsatisfactory outcome from initial closed reduction. However, better surgical outcomes may be achieved if rhinoseptoplasty is performed at the same time as the nasal bone fracture reduction. This study investigated the surgical outcomes of patients who underwent rhinoseptoplasty concomitantly with nasal bone fracture reduction according to their computed tomography image‐based nasal bone fracture classifications.Study DesignCase series with chart review.SettingAcademic tertiary care medical center.Subjects and MethodsFifty‐six patients who underwent rhinoseptoplasty concomitantly with nasal bone fracture reduction were enrolled in this study. Nasal bone fractures were classified into 6 types by computed tomography scans. Two independent facial plastic surgeons evaluated the outcomes 6 months postoperatively using a visual analog scale. The nasal tip projection and rotation were measured using the pre‐ and postoperative profile views.ResultsThe satisfaction scores of type I, IIo, and IIIo fractures without septal fracture were significantly higher than those of type II, III, and IV fractures with septal fractures. Among the patients, 82.1% underwent lower vault surgery. The nasal tip projection and rotation were increased after surgery in patients without septal fractures, whereas the tip rotation was elevated but the projection was unchanged postoperatively in patients with septal fractures.ConclusionRhinoseptoplasty for acute nasal bone fractures can be performed at the same time as nasal bone fracture reduction. However, nasal bone fracture with septal fracture should be managed carefully.
Is Montgomery Tracheal Safe‐T‐Tube Clinical Failure Induced by Biofilm?
Authors: Fusconi Massimo , Lo Vasco Vincenza Rita , Delfini Andrea , De Virgilio Armando , Taddei Anna Rita , Vassalli Carlo , Conte Michela , Del Sette Fausto , Benincasa Anna Teresa , de Vincentiis Marco 
Published: May 2013

ObjectivesMontgomery Safe‐T‐Tube deterioration and early biofilm colonization may explain the discomfort claimed by many patients and clinical failures. The aim of the study was to analyze the deterioration of Montgomery Safe‐T‐Tube morphological and mechanical properties in vivo in 16 patients by using microbiological methods, optical and electron microscopy, and engineering tests.Study DesignProspective controlled study at a single medical center.SettingUniversity hospital.Subjects and MethodsThe study, conducted from April 2007 to February 2012 at the “Sapienza” University of Rome, was designed to collect 2 Montgomery Safe‐T‐Tubes from each patient. The first was removed 3 to 15 days after insertion (group A) and the second at least 90 days after (group B). Specimens underwent microbiologic assays, electron microscopic analysis, immunocytologic analysis, and mechanical tests.ResultsMicroorganisms were not isolated in 2 group A cases (12%), whereas they were in all group B cases. Biofilm was identified in 11 of 16 (69%) group A samples and in 16 of 16 (100%) group B samples (P =. 0149) using scanning electron microscopy. Immunohistochemistry showed monocyte‐granulocyte line cells producing interleukin‐1β on the external surfaces of Montgomery Safe‐T‐Tubes. The tensile test showed that the wear related to the longer period of use makes Montgomery Safe‐T‐Tubes more rigid than newer ones.ConclusionEarly biofilm colonization takes place in Montgomery Safe‐T‐Tubes in most cases. The mechanical decay could be justified in part by the destructive biofilm activity and by the release of inflammatory effectors and enzymes.
Reconstituting protein interaction networks using parameter-dependent domain-domain interactions
Authors: Memišević Vesna , Wallqvist Anders , Reifman Jaques 
Published: May 2013

Abstract

Background
We can describe protein-protein interactions (PPIs) as sets of distinct domain-domain interactions (DDIs) that mediate the physical interactions between proteins. Experimental data confirm that DDIs are more consistent than their corresponding PPIs, lending support to the notion that analyses of DDIs may improve our understanding of PPIs and lead to further insights into cellular function, disease, and evolution. However, currently available experimental DDI data cover only a small fraction of all existing PPIs and, in the absence of structural data, determining which particular DDI mediates any given PPI is a challenge.

Results
We present two contributions to the field of domain interaction analysis. First, we introduce a novel computational strategy to merge domain annotation data from multiple databases. We show that when we merged yeast domain annotations from six annotation databases we increased the average number of domains per protein from 1.05 to 2.44, bringing it closer to the estimated average value of 3. Second, we introduce a novel computational method, parameter-dependent DDI selection (PADDS), which, given a set of PPIs, extracts a small set of domain pairs that can reconstruct the original set of protein interactions, while attempting to minimize false positives. Based on a set of PPIs from multiple organisms, our method extracted 27% more experimentally detected DDIs than existing computational approaches.

Conclusions
We have provided a method to merge domain annotation data from multiple sources, ensuring large and consistent domain annotation for any given organism. Moreover, we provided a method to extract a small set of DDIs from the underlying set of PPIs and we showed that, in contrast to existing approaches, our method was not biased towards DDIs with low or high occurrence counts. Finally, we used these two methods to highlight the influence of the underlying annotation density on the characteristics of extracted DDIs. Although increased annotations greatly expanded the possible DDIs, the lack of knowledge of the true biological false positive interactions still prevents an unambiguous assignment of domain interactions responsible for all protein network interactions.
Executable files and examples are given at: http://www.bhsai.org/downloads/padds/
Assessment of bacterial diversity during composting of agricultural byproducts
Authors: Chandna Piyush , Nain Lata , Singh Surender , Kuhad Ramesh Chander 
Published: May 2013

Abstract

Background
Composting is microbial decomposition of biodegradable materials and it is governed by physicochemical, physiological and microbiological factors. The importance of microbial communities (bacteria, actinomycetes and fungi) during composting is well established. However, the microbial diversity during composting may vary with the variety of composting materials and nutrient supplements. Therefore, it is necessary to study the diversity of microorganisms during composting of different agricultural byproducts like wheat bran, rice bran, rice husk, along with grass clippings and bulking agents. Here it has been attempted to assess the diversity of culturable bacteria during composting of agricultural byproducts.

Results
The culturable bacterial diversity was assessed during the process by isolating the most prominent bacteria. Bacterial population was found to be maximum during the mesophilic phase, but decreased during the thermophilic phase and declined further in the cooling and maturation phase of composting. The bacterial population ranged from 105 to 109 cfu g-1 compost. The predominant bacteria were characterized biochemically, followed by 16S rRNA gene sequencing. The isolated strains, both Gram-positive and Gram-negative groups belonged to the order Burkholderiales, Enterobacteriales, Actinobacteriales and Bacillales, which includes genera e.g. Staphylococcus, Serratia, Klebsiella, Enterobacter, Terribacillus, Lysinibacillus Kocuria, Microbacterium, Acidovorax and Comamonas. Genera like Kocuria, Microbacterium, Acidovorax, Comamonas and some new species of Bacillus were also identified for the first time from the compost made from agricultural byproducts.

Conclusion
The use of appropriate nitrogen amendments and bulking agents in composting resulted in good quality compost. The culture based strategy enabled us to isolate some novel bacterial isolates like Kocuria, Microbacterium, Acidovorax and Comamonas first time from agro-byproducts compost. These bacteria can be used as potential compost inoculants for accelerating composting process.
Effectiveness of national evidence-based medicine competition in Taiwan
Authors: Weng Yi-Hao , Kuo Ken N , Yang Chun-Yuh , Liao Hsun-Hsiang , Chen Chiehfeng , Lo Heng-Lien , Lee Wui-Chiang , Chiu Ya-Wen 
Published: May 2013

AbstractBackgroundCompetition and education are intimately related and can be combined in many ways. The role of competition in medical education of evidence-based medicine (EBM) has not been investigated. In order to enhance the dissemination and implementation of EBM in Taiwan, EBM competitions have been established among healthcare professionals. This study was to evaluate the impact of competition in EBM learning.MethodsThe EBM competition used PICO (patient, intervention, comparison, and outcome) queries to examine participants’ skills in framing an answerable question, literature search, critical appraisal and clinical application among interdisciplinary teams. A structured questionnaire survey was conducted to investigate EBM among participants in the years of 2009 and 2011. Participants completed a baseline questionnaire survey at three months prior to the competition and finished the same questionnaire right after the competition.ResultsValid questionnaires were collected from 358 participants, included 162 physicians, 71 nurses, 101 pharmacists, and 24 other allied healthcare professionals. There were significant increases in participants’ knowledge of and skills in EBM (p < 0.001). Their barriers to literature searching and forming answerable questions significantly decreased (p < 0.01). Furthermore, there were significant increases in their access to the evidence-based retrieval databases, including the Cochrane Library (p < 0.001), MD Consult (p < 0.001), ProQuest (p < 0.001), UpToDate (p = 0.001), CINAHL (p = 0.001), and MicroMedex (p = 0.024).ConclusionsThe current study demonstrates a method that successfully enhanced the knowledge of, skills in, and behavior of EBM. The data suggest competition using PICO queries may serve as an effective way to facilitate the learning of EBM.
Experimental evidence for direct insulator-quantum Hall transition in multi-layer graphene
Authors: Chuang Chiashain , Lin Li-Hung , Aoki Nobuyuki , Ouchi Takahiro , Mahjoub Akram M , Woo Tak-Pong , Bird Jonathan P , Ochiai Yuichi , Lo Shun-Tsung , Liang Chi-Te 
Published: May 2013

Abstract
We have performed magnetotransport measurements on a multi-layer graphene flake. At the crossing magnetic field B
c, an approximately temperature-independent point in the measured longitudinal resistivity ρ

xx
, which is ascribed to the direct insulator-quantum Hall (I-QH) transition, is observed. By analyzing the amplitudes of the magnetoresistivity oscillations, we are able to measure the quantum mobility μ
q of our device. It is found that at the direct I-QH transition, μ
q
B
c ≈ 0.37 which is considerably smaller than 1. In contrast, at B
c, ρ

xx
is close to the Hall resistivity ρ

xy
, i.e., the classical mobility μB
c is ≈ 1. Therefore, our results suggest that different mobilities need to be introduced for the direct I-QH transition observed in multi-layered graphene. Combined with existing experimental results obtained in various material systems, our data obtained on graphene suggest that the direct I-QH transition is a universal effect in 2D.