bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome analysis of Pseudoalteromonas flavipulchra JG1 reveals various survival advantages in marine environment
Authors: Yu Min , Tang Kaihao , Liu Jiwen , Shi Xiaochong , Gulder Tobias AM , Zhang Xiao-Hua 
Published: October 2013

Abstract

Background
Competition between bacteria for habitat and resources is very common in the natural environment and is considered to be a selective force for survival. Many strains of the genus Pseudoalteromonas were confirmed to produce bioactive compounds that provide those advantages over their competitors. In our previous study, P. flavipulchra JG1 was found to synthesize a Pseudoalteromonas flavipulchra antibacterial Protein (PfaP) with L-amino acid oxidase activity and five small chemical compounds, which were the main competitive agents of the strain. In addition, the genome of this bacterium has been previously sequenced as Whole Genome Shotgun project (PMID: 22740664). In this study, more extensive genomic analysis was performed to identify specific genes or gene clusters which related to its competitive feature, and further experiments were carried out to confirm the physiological roles of these genes when competing with other microorganisms in marine environment.

Results
The antibacterial protein PfaP may also participate in the biosynthesis of 6-bromoindolyl-3-acetic acid, indicating a synergistic effect between the antibacterial macromolecule and small molecules. Chitinases and quorum quenching enzymes present in P. flavipulchra, which coincide with great chitinase and acyl homoserine lactones degrading activities of strain JG1, suggest other potential mechanisms contribute to antibacterial/antifungal activities. Moreover, movability and rapid response mechanisms to phosphorus starvation and other stresses, such as antibiotic, oxidative and heavy metal stress, enable JG1 to adapt to deleterious, fluctuating and oligotrophic marine environments.

Conclusions
The genome of P. flavipulchra JG1 exhibits significant genetic advantages against other microorganisms, encoding antimicrobial agents as well as abilities to adapt to various adverse environments. Genes involved in synthesis of various antimicrobial substances enriches the antagonistic mechanisms of P. flavipulchra JG1 and affords several admissible biocontrol procedures in aquaculture. Furthermore, JG1 also evolves a range of mechanisms adapting the adverse marine environment or multidrug rearing conditions. The analysis of the genome of P. flavipulchra JG1 provides a better understanding of its competitive properties and also an extensive application prospect.
Systematic interrogation of the Conus marmoreus venom duct transcriptome with ConoSorter reveals 158 novel conotoxins and 13 new gene superfamilies
Authors: Lavergne Vincent , Dutertre Sébastien , Jin Ai-hua , Lewis Richard J , Taft Ryan J , Alewood Paul F 
Published: October 2013

Abstract

Background
Conopeptides, often generically referred to as conotoxins, are small neurotoxins found in the venom of predatory marine cone snails. These molecules are highly stable and are able to efficiently and selectively interact with a wide variety of heterologous receptors and channels, making them valuable pharmacological probes and potential drug leads. Recent advances in next-generation RNA sequencing and high-throughput proteomics have led to the generation of large data sets that require purpose-built and dedicated bioinformatics tools for efficient data mining.

Results
Here we describe ConoSorter, an algorithm that categorizes cDNA or protein sequences into conopeptide superfamilies and classes based on their signal, pro- and mature region sequence composition. ConoSorter also catalogues key sequence characteristics (including relative sequence frequency, length, number of cysteines, N-terminal hydrophobicity, sequence similarity score) and automatically searches the ConoServer database for known precursor sequences, facilitating identification of known and novel conopeptides. When applied to ConoServer and UniProtKB/Swiss-Prot databases, ConoSorter is able to recognize 100% of known conotoxin superfamilies and classes with a minimum species specificity of 99%. As a proof of concept, we performed a reanalysis of Conus marmoreus venom duct transcriptome and (i) correctly classified all sequences previously annotated, (ii) identified 158 novel precursor conopeptide transcripts, 106 of which were confirmed by protein mass spectrometry, and (iii) identified another 13 novel conotoxin gene superfamilies.

Conclusions
Taken together, these findings indicate that ConoSorter is not only capable of robust classification of known conopeptides from large RNA data sets, but can also facilitate de novo identification of conopeptides which may have pharmaceutical importance.
Frailty and falls among adult patients undergoing chronic hemodialysis: a prospective cohort study
Authors: McAdams-DeMarco Mara A , Suresh Sunitha , Law Andrew , Salter Megan L , Gimenez Luis F , Jaar Bernard G , Walston Jeremy D , Segev Dorry L 
Published: October 2013

Abstract

Background
Patients undergoing hemodialysis are at high risk of falls, with subsequent complications including fractures, loss of independence, hospitalization, and institutionalization. Factors associated with falls are poorly understood in this population. We hypothesized that insights derived from studies of the elderly might apply to adults of all ages undergoing hemodialysis; we focused on frailty, a phenotype of physiological decline strongly associated with falls in the elderly.

Methods
In this prospective, longitudinal study of 95 patients undergoing hemodialysis (1/2009-3/2010), the association of frailty with future falls was explored using adjusted Poisson regression. Frailty was classified using the criteria established by Fried et al., as a combination of five components: shrinking, weakness, exhaustion, low activity, and slowed walking speed.

Results
Over a median 6.7-month period of longitudinal follow-up, 28.3% of study participants (25.9% of those under 65, 29.3% of those 65 and older) experienced a fall. After adjusting for age, sex, race, comorbidity, disability, number of medications, marital status, and education, frailty independently predicted a 3.09-fold (95% CI: 1.38-6.90, P=0.006) higher number of falls. This relationship between frailty and falls did not differ for younger and older adults (P=0.57).

Conclusions
Frailty, a validated construct in the elderly, was a strong and independent predictor of falls in adults undergoing hemodialysis, regardless of age. Our results may aid in identifying frail hemodialysis patients who could be targeted for multidimensional fall prevention strategies.
Genetically engineered endostatin-lidamycin fusion proteins effectively inhibit tumor growth and metastasis
Authors: Jiang Wen-guo , Lu Xin-an , Shang Bo-yang , Fu Yan , Zhang Sheng-hua , Zhou Daifu , Li Liang , Li Yi , Luo Yongzhang , Zhen Yong-su 
Published: October 2013

AbstractBackgroundEndostatin (ES) inhibits endothelial cell proliferation, migration, invasion, and tube formation. It also shows antiangiogenesis and antitumor activities in several animal models. Endostatin specifically targets tumor vasculature to block tumor growth. Lidamycin (LDM), which consists of an active enediyne chromophore (AE) and a non-covalently bound apo-protein (LDP), is a member of chromoprotein family of antitumor antibiotics with extremely potent cytotoxicity to cancer cells. Therefore, we reasoned that endostatin-lidamycin (ES-LDM) fusion proteins upon energizing with enediyne chromophore may obtain the combined capability targeting tumor vasculature and tumor cell by respective ES and LDM moiety.MethodsIn this study, we designed and obtained two new endostatin-based fusion proteins, endostatin-LDP (ES-LDP) and LDP-endostatin (LDP-ES). In vitro, the antiangiogenic effect of fusion proteins was determined by the wound healing assay and tube formation assay and the cytotoxicity of their enediyne-energized analogs was evaluated by CCK-8 assay. Tissue microarray was used to analyze the binding affinity of LDP, ES or ES-LDP with specimens of human lung tissue and lung tumor. The in vivo efficacy of the fusion proteins was evaluated with human lung carcinoma PG-BE1 xenograft and the experimental metastasis model of 4T1-luc breast cancer.ResultsES-LDP and LDP-ES disrupted the formation of endothelial tube structures and inhibited endothelial cell migration. Evidently, ES-LDP accumulated in the tumor and suppressed tumor growth and metastasis. ES-LDP and ES show higher binding capability than LDP to lung carcinoma; in addition, ES-LDP and ES share similar binding capability. Furthermore, the enediyne-energized fusion protein ES-LDP-AE demonstrated significant efficacy against lung carcinoma xenograft in athymic mice.ConclusionsThe ES-based fusion protein therapy provides some fundamental information for further drug development. Targeting both tumor vasculature and tumor cells by endostatin-based fusion proteins and their enediyne-energized analogs probably provides a promising modality in cancer therapy.
In vivo confocal microscopy in goldenhar syndrome: a case report
Authors: Triolo Giacinto , Ferrari Giulio , Doglioni Claudio , Rama Paolo 
Published: October 2013

Abstract

Background
Goldenhar Syndrome is characterized by malformations of multiple anatomical districts. Between these, bulbar dermoids are common and represent a significant clinical problem as they can affect both ocular function and aesthetic comfort.
Histologic characterization of dermoids has been extensively performed; however, no reports exist describing in vivo confocal microscopy (IVCM) of these lesions. We aimed to (i) describe the in vivo confocal morphology of limbal dermoids in Goldenhar syndrome and (ii) compare these findings with standard light microscopy.

Case presentation
A 15-year-old Caucasian female affected by Goldenhar Syndrome showed a left, infero-temporal, limbal neoformation, with extension to the left orbital region. Prior to surgical removal, IVCM was performed with the Heidelberg Retina Tomograph II, Cornea Module, using the “section” modality. The IVCM sections showed structures resembling corneal epithelium and vascular structures. Surgical removal of the lesion was decided as it caused poor eyelid closure. After surgical removal, sectioning and standard optical microscopy were performed. The comparison between IVCM imaging and standard microscopy sections were highly correlated in the detection of the pilar and vascular structures.

Conclusions
This study showed that IVCM may be a useful technique to study limbal dermoids, given its ability to detect typical microscopic features and its comparability to optical microscopy, which is the current standard.
At the moment of occurrence of a fragility hip fracture, men have higher mechanical properties values in comparison with women
Authors: Vale Ana C , Aleixo Inês P , Lúcio Miguel , Saraiva André , Caetano-Lopes Joana , Rodrigues Ana , Amaral Pedro M , Rosa Luís G , Monteiro Jacinto , Fonseca João E , Vaz Maria F , Canhão Helena 
Published: October 2013

Abstract

Background
It is well established that males have lower fracture risk in comparison with females, which suggests a higher bone resistance in men. The aim of our study was to find out if in older patients with hip fragility fractures, gender has also an impact on trabecular bone material behaviour, specifically to determine whether trabecular mechanical properties under compressive loading differ between men and women who suffered a fragility hip fracture.

Methods
Femoral epiphyses were consecutively collected during hip replacement surgery due to proximal femur fragility fracture. Trabecular bone cylinders were drilled and submitted to uniaxial compression tests and mechanical properties were assessed.

Results
Seventy-three patients, 55 women (mean age 81 years and standard deviation of 7 years) and 18 men (mean age 81 years and standard deviation of 8 years) were evaluated. The ultimate stress of trabecular bone was significantly higher in men than in women: the median values and the interquartile range (IQR) were respectively 8.04(5.35-10.90) MPa vs. 4.46(3.02-7.73) MPa, (p-value = 0.005). The same difference between male and female was observed in the Young’s modulus: 293.68(166.67-538.18) MPa vs. 174.26(73.07-322.28) MPa, (p-value = 0.028), and also in the energy to failure: 0.25(0.07-0.42) MJ/m3 vs. 0.11(0.05-0.25) MJ/m3, (p-value = 0.058). These differences were also verified after adjusting the analysis for age in a multivariate model analysis.

Conclusions
Our observations demonstrated that, even in a population who suffered a fragility hip fracture, men still have higher trabecular bone mechanical properties in comparison with women.
Sacral nerve stimulation lead implantation using the o-arm
Authors: Hellström Pekka A , Katisko Jani , Finnilä Pertti , Vaarala Markku H 
Published: October 2013

Abstract

Background
Sacral neuromodulation operations have usually been performed based on 2D fluoro images. However, sacral nerve stimulation lead implantation may be challenging when the normal anatomy is confused by obesity or congenital anomalies. Thus the surgical navigation and intraoperative imaging methods could be helpful as those same methods have proven to be feasible methods for guiding other surgical operations. Our recent knowledge about the O-arm in trauma pelvic operations encouraged us to evaluate the usefulness of O-arm guided navigation in sacral neuromodulation. Similar navigation would be useful for complex sacral nerve stimulation lead implantations.

Methods
In this preliminary article we report our experience of utilizing the orthopedically optimized O-arm to implant the S3 stimulation electrode in a patient. The 3D O-arm imaging was performed intraoperatively under surgical navigation control. General anesthesia was used. The obtained 3D image dataset was registered automatically into the patient’s anatomy. The stimulation needle was guided and the tined lead electrode was implanted using navigation.

Results
The bony sacral structures were clearly visualized. Due to automatic registration, the navigation was practicable instantly after the O-arm scanning and operation could be performed successfully under navigation control.

Conclusions
To our knowledge, this is the first published tined lead implantation which was guided based on the surgical navigation and intraoperative O-arm images. In this case, the applied method was useful and helped the surgeon to demarcate the region of surgical interest. The method is slightly more invasive than the formal technique but could be an option in anatomically challenging cases and reoperations. However, further evaluation with larger patient series is required before definitive recommendations can be made.
Relationship between financial speculation and food prices or price volatility: applying the principles of evidence-based medicine to current debates in Germany
Authors: Bozorgmehr Kayvan , Gabrysch Sabine , Müller Olaf , Neuhann Florian , Jordan Irmgard , Knipper Michael , Razum Oliver 
Published: October 2013

Abstract
There is an unresolved debate about the potential effects of financial speculation on food prices and price volatility. Germany’s largest financial institution and leading global investment bank recently decided to continue investing in agricultural commodities, stating that there is little empirical evidence to support the notion that the growth of agricultural-based financial products has caused price increases or volatility. The statement is supported by a recently published literature review, which concludes that financial speculation does not have an adverse effect on the functioning of the agricultural commodities market. As public health professionals concerned with global food insecurity, we have appraised the methodological quality of the review using a validated and reliable appraisal tool. The appraisal revealed major shortcomings in the methodological quality of the review. These were particularly related to intransparencies in the search strategy and in the selection/presentation of studies and findings; the neglect of the possibility of publication bias; a lack of objective or rigorous criteria for assessing the scientific quality of included studies and for the formulation of conclusions. Based on the results of our appraisal, we conclude that it is not justified to reject the hypothesis that financial speculation might have adverse effects on food prices/price volatility. We hope to initiate reflections about scientific standards beyond the boundaries of disciplines and call for high quality, rigorous systematic reviews on the effects of financial speculation on food prices or price volatility.
Functional magnetic resonance imaging of the ascending stages of the auditory system in dogs
Authors: Bach Jan-Peter , Lüpke Matthias , Dziallas Peter , Wefstaedt Patrick , Uppenkamp Stefan , Seifert Hermann , Nolte Ingo 
Published: October 2013

Abstract

Background
Functional magnetic resonance imaging (fMRI) is a technique able to localize neural activity in the brain by detecting associated changes in blood flow. It is an essential tool for studying human functional neuroanatomy including the auditory system. There are only a few studies, however, using fMRI to study canine brain functions. In the current study ten anesthetized dogs were scanned during auditory stimulation. Two functional sequences, each in combination with a suitable stimulation paradigm, were used in each subject. Sequence 1 provided periods of silence during which acoustic stimuli could be presented unmasked by scanner noise (sparse temporal sampling) whereas in sequence 2 the scanner noise was present throughout the entire session (continuous imaging). The results obtained with the two different functional sequences were compared.

Results
This study shows that with the proper experimental setup it is possible to detect neural activity in the auditory system of dogs. In contrast to human fMRI studies the strongest activity was found in the subcortical parts of the auditory pathways. Especially sequence 1 showed a high reliability in detecting activated voxels in brain regions associated with the auditory system.

Conclusion
These results indicate that fMRI is applicable for studying the canine auditory system and could become an additional method for the clinical evaluation of the auditory function of dogs. Additionally, fMRI is an interesting technique for future studies concerned with canine functional neuroanatomy.
Neuroethics, confidentiality, and a cultural imperative in early onset Alzheimer disease: a case study with a First Nation population
Authors: Stevenson Shaun , Beattie B Lynn , Vedan Richard , Dwosh Emily , Bruce Lindsey , Illes Judy 
Published: October 2013

Abstract
The meaningful consideration of cultural practices, values and beliefs is a necessary component in the effective translation of advancements in neuroscience to clinical practice and public discourse. Society’s immense investment in biomedical science and technology, in conjunction with an increasingly diverse socio-cultural landscape, necessitates the study of how potential discoveries in neurodegenerative diseases such as Alzheimer disease are perceived and utilized across cultures. Building on the work of neuroscientists, ethicists and philosophers, we argue that the growing field of neuroethics provides a pragmatic and constructive pathway to guide advancements in neuroscience in a manner that is culturally nuanced and relevant. Here we review a case study of one issue in culturally oriented neuroscience research where it is evident that traditional research ethics must be broadened and the values and needs of diverse populations considered for meaningful and relevant research practices. A global approach to neuroethics has the potential to furnish critical engagement with cultural considerations of advancements in neuroscience.
A phase I study on combined therapy with proton-beam radiotherapy and in situ tumor vaccination for locally advanced recurrent hepatocellular carcinoma
Authors: Abei Masato , Okumura Toshiyuki , Fukuda Kuniaki , Hashimoto Takayuki , Araki Masahiro , Ishige Kazunori , Hyodo Ichinosuke , Kanemoto Ayae , Numajiri Haruko , Mizumoto Masashi , Sakae Takeji , Sakurai Hideyuki , Zenkoh Junko , Ariungerel Gerelchuluun , Sogo Yu , Ito Atsuo , Ohno Tadao , Tsuboi Koji 
Published: October 2013

AbstractBackgroundProton-beam radiotherapy (PBT) has been shown to be effective to hepatocellular carcinoma (HCC) as a nonsurgical local treatment option. However, HCC still remains as one of the most difficult cancers to be cured because of frequent recurrences. Thus, methods to inhibit the recurrence need to be explored. To prevent the HCC recurrence, we here report on a prospective phase I study of‘in situ’tumor vaccination using CalTUMP, a newly developed immunoadjuvant consisting of BCG extract bound to hydroxyapatite and microparticulated tuberculin, following local PBT for HCC.MethodsPatients with locally advanced recurrent HCC, which had been heavily pretreated with various treatments, were enrolled. PBT was performed with the conventional method to the target HCC. Subsequently, CalTUMP was injected into the same irradiated-tumor three times at one-week intervals. Three dose-levels of CalTUMP (1/10, 1/3, and 1/1) were administered to 3 patients each. Vital signs, blood samples, ultrasound, and computed tomographic scans were monitored to evaluate the safety.ResultsThree intratumoral injections of CalTUMP following PBT (median dose: 72.6 GyE) were accomplished in 9 patients. Transient low-grade fever and minor laboratory changes were observed in 7 patients after CalTUMP injections. No other treatment-related adverse events were observed. Median progression-free survival was 6.0 months (range: 2.1-14.2) and 4 patients were progression-free for more than 1 year.ConclusionsIntratumoral injection of CalTUMP following PBT was feasible and safe in patients with heavily pre-treated HCC. Further clinical studies to evaluate the efficacy of thisin situtumor vaccination are warranted.