bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional expression of a blood tolerant laccase in Pichia pastoris
Authors: Mate Diana M , Gonzalez-Perez David , Kittl Roman , Ludwig Roland , Alcalde Miguel 
Published: April 2013

Abstract

Background
Basidiomycete high-redox potential laccases (HRPLs) working in human physiological fluids (pH 7.4, 150 mM NaCl) arise great interest in the engineering of 3D-nanobiodevices for biomedical uses. In two previous reports, we described the directed evolution of a HRPL from basidiomycete PM1 strain CECT 2971: i) to be expressed in an active, soluble and stable form in Saccharomyces cerevisiae, and ii) to be active in human blood. In spite of the fact that S. cerevisiae is suited for the directed evolution of HRPLs, the secretion levels obtained in this host are not high enough for further research and exploitation. Thus, the search for an alternative host to over-express the evolved laccases is mandatory.

Results
A blood-active laccase (ChU-B mutant) fused to the native/evolved α-factor prepro-leader was cloned under the control of two different promoters (PAOX1 and PGAP) and expressed in Pichia pastoris. The most active construct, which contained the PAOX1 and the evolved prepro-leader, was fermented in a 42-L fed-batch bioreactor yielding production levels of 43 mg/L. The recombinant laccase was purified to homogeneity and thoroughly characterized. As happened in S. cerevisiae, the laccase produced by P. pastoris presented an extra N-terminal extension (ETEAEF) generated by an alternative processing of the α-factor pro-leader at the Golgi compartment. The laccase mutant secreted by P. pastoris showed the same improved properties acquired after several cycles of directed evolution in S. cerevisiae for blood-tolerance: a characteristic pH-activity profile shifted to the neutral-basic range and a greatly increased resistance against inhibition by halides. Slight biochemical differences between both expression systems were found in glycosylation, thermostability and turnover numbers.

Conclusions
The tandem-yeast system based on S. cerevisiae to perform directed evolution and P. pastoris to over-express the evolved laccases constitutes a promising approach for the in vitro evolution and production of these enzymes towards different biocatalytic and bioelectrochemical applications.
Anti-inflammatory effect of Prunus yedoensis through inhibition of nuclear factor-κB in macrophages
Authors: Lee Juyeong , Yang Gabsik , Lee Kyungjin , Lee Mi-Hwa , Eom Ji-Whan , Ham Inhye , Choi Ho-Young 
Published: April 2013

Abstract

Background

Prunus yedoensis (PY) is a traditional anti-allergy and anti-inflammatory herb medicine used in South Korea. However, until date, little is known regarding its mechanism of action.

Methods
In order to elucidate the mechanism of anti-inflammatory effect of PY, the constituents of PY were analysed by high performance liquid chromatography (HPLC), and nitric oxide (NO) and prostaglandin E2 (PGE2) production were measured enzyme-linked immuno sorbent assay (ELISA). The expression levels of inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2), and nuclear factor-κB (NF-κB) were also measured by western blotting in lipopolysaccharide (LPS)-induced RAW 264.7 macrophage cells treated with PY.

Results
The results indicate that (50, 100 μg/mL) methanol and ethyl acetate fractionation extracts of PY not only inhibited LPS-mediated NO production and iNOS expression, but also decreased LPS-induced PGE2 production and COX-2 expression. The anti-inflammatory effects of PY were also due to the attenuation of nuclear translocation of NF-κB, as evaluated by the use of anti-p50 on nuclear fractions. LPS-induced nuclear translocation of NF-κB decreased significantly by the methanol extract and ethyl acetate fraction of PY. High performance liquid chromatography (HPLC) analyses revealed that methanol extract and ethyl acetate fraction have similar patterns of retention time and peaks.

Conclusion
Our results demonstrate that methanol extracts and the ethyl acetate fraction of PY have anti-inflammatory properties, thus emphasizing the potential of PY as a natural health product.
Designing of inhibitors against drug tolerant Mycobacterium tuberculosis (H37Rv)
Authors: Singla Deepak , Tewari Rupinder , Kumar Ashwani , Raghava Gajendra PS ,   Open Source Drug Discovery Consortium
Published: April 2013

Abstract

Background

Mycobacterium tuberculosis (M.tb) is the causative agent of tuberculosis, killing ~1.7 million people annually. The remarkable capacity of this pathogen to escape the host immune system for decades and then to cause active tuberculosis disease, makes M.tb a successful pathogen. Currently available anti-mycobacterial therapy has poor compliance due to requirement of prolonged treatment resulting in accelerated emergence of drug resistant strains. Hence, there is an urgent need to identify new chemical entities with novel mechanism of action and potent activity against the drug resistant strains.

Results
This study describes novel computational models developed for predicting inhibitors against both replicative and non-replicative phase of drug-tolerant M.tb under carbon starvation stage. These models were trained on highly diverse dataset of 2135 compounds using four classes of binary fingerprint namely PubChem, MACCS, EState, SubStructure. We achieved the best performance Matthews correlation coefficient (MCC) of 0.45 using the model based on MACCS fingerprints for replicative phase inhibitor dataset. In case of non-replicative phase, Hybrid model based on PubChem, MACCS, EState, SubStructure fingerprints performed better with maximum MCC value of 0.28. In this study, we have shown that molecular weight, polar surface area and rotatable bond count of inhibitors (replicating and non-replicating phase) are significantly different from non-inhibitors. The fragment analysis suggests that substructures like hetero_N_nonbasic, heterocyclic, carboxylic_ester, and hetero_N_basic_no_H are predominant in replicating phase inhibitors while hetero_O, ketone, secondary_mixed_amine are preferred in the non-replicative phase inhibitors. It was observed that nitro, alkyne, and enamine are important for the molecules inhibiting bacilli residing in both the phases. In this study, we introduced a new algorithm based on Matthews correlation coefficient called MCCA for feature selection and found that this algorithm is better or comparable to frequency based approach.

Conclusion
In this study, we have developed computational models to predict phase specific inhibitors against drug resistant strains of M.tb grown under carbon starvation. Based on simple molecular properties, we have derived some rules, which would be useful in robust identification of tuberculosis inhibitors. Based on these observations, we have developed a webserver for predicting inhibitors against drug tolerant M.tb H37Rv available at http://crdd.osdd.net/oscadd/mdri/.
Treatment of Prostate Cancer With Intermittent Versus Continuous Androgen Deprivation: A Systematic Review of Randomized Trials
Authors: Niraula Saroj , Le Lisa W. , Tannock Ian F. 
Published: April 2013

Purpose Uncertainty exists regarding benefits of intermittent androgen deprivation (IAD) compared with continuous androgen deprivation (CAD) for treatment of prostate cancer. On the basis of a systematic review of evidence, our aim was to formulate a recommendation for either IAD or CAD to treat relapsing, locally advanced, or metastatic prostate cancer. Methods We searched literature published up to September 2012 from MEDLINE, EMBASE, the Cochrane Library, and major conference proceedings. We included randomized controlled trials comparing IAD and CAD if they reported overall survival (OS) or biochemical/radiologic time to disease progression. Results Nine studies with 5,508 patients met our criteria. There were no significant differences in time-to-event outcomes between the groups in any studies. The pooled hazard ratio (HR) for OS was 1.02 (95% CI, 0.94 to 1.11) for IAD compared with CAD, and the HR for progression-free survival was 0.96 (95% CI, 0.76 to 1.20). More prostate cancer–related deaths with IAD tended to be balanced by more deaths not related to prostate cancer with CAD. Superiority of IAD for sexual function, physical activity, and general well-being was observed in some trials. Median cost savings with IAD was estimated to be 48%. Conclusion There is fair evidence to recommend use of IAD instead of CAD for the treatment of men with relapsing, locally advanced, or metastatic prostate cancer who achieve a good initial response to androgen deprivation. This recommendation is based on evidence against superiority of either strategy for time-to-event outcomes and substantial decrease with IAD in exposure to androgen deprivation, resulting in less cost, inconvenience, and potential toxicity.
Next-Generation Sequencing Reveals High Concordance of Recurrent Somatic Alterations Between Primary Tumor and Metastases From Patients With Non–Small-Cell Lung Cancer
Authors: Vignot Stéphane , Frampton Garrett M. , Soria Jean-Charles , Yelensky Roman , Commo Frédéric , Brambilla Christian , Palmer Gary , Moro-Sibilot Denis , Ross Jeffrey S. , Cronin Maureen T. , André Fabrice , Stephens Philip J. , Lazar Vladimir , Miller Vincent A. , Brambilla Elisabeth 
Published: April 2013

Purpose Characterization of the genomic changes that drive an individual patient's disease is critical in management of many cancers. In patients with non–small-cell lung cancer (NSCLC), obtaining tumor samples of sufficient size for genomic profiling on recurrence is often challenging. We undertook this study to compare genomic alterations identified in archived primary tumors from patients with NSCLC with those identified in metachronous or synchronous metastases. Patients and Methods Primary and matched metastatic tumor pairs from 15 patients were analyzed by using a targeted next-generation sequencing assay in a Clinical Laboratory Improvement Amendments laboratory. Genomic libraries were captured for 3,230 exons in 182 cancer-related genes plus 37 introns from 14 genes often rearranged in cancer and sequenced to high coverage. Results Among 30 tumors, 311 genomic alterations were identified of which 63 were known recurrent (32 in primary tumor, 31 in metastasis) and 248 were nonrecurrent (likely passenger). TP53 mutations were the most frequently observed recurrent alterations (12 patients). Tumors harbored two or more (maximum four) recurrent alterations in 10 patients. Comparative analysis of recurrent alterations between primary tumor and matched metastasis revealed a concordance rate of 94% compared with 63% for likely passenger alterations. Conclusion This high concordance suggests that for the purposes of genomic profiling, use of archived primary tumor can identify the key recurrent somatic alterations present in matched NSCLC metastases and may provide much of the relevant genomic information required to guide treatment on recurrence.
Bone graft substitutes currently available in orthopaedic practice
Authors: Kurien T. , Pearson R. G. , Scammell B. E. 
Published: April 2013

We reviewed 59 bone graft substitutes marketed by 17 companies currently available for implantation in the United Kingdom, with the aim of assessing the peer-reviewed literature to facilitate informed decision-making regarding their use in clinical practice. After critical analysis of the literature, only 22 products (37%) had any clinical data. Norian SRS (Synthes), Vitoss (Orthovita), Cortoss (Orthovita) and Alpha-BSM (Etex) had Level I evidence. We question the need for so many different products, especially with limited published clinical evidence for their efficacy, and conclude that there is a considerable need for further prospective randomised trials to facilitate informed decision-making with regard to the use of current and future bone graft substitutes in clinical practice. Cite this article: Bone Joint J 2013;95-B:583–97.
The value of ultrasonic diagnosis in the management of vascular complications of supracondylar fractures of the humerus in children
Authors: Benedetti Valentini M. , Farsetti P. , Martinelli O. , Laurito A. , Ippolito E. 
Published: April 2013

Of 48 consecutive children with Gartland III supracondylar fractures, 11 (23%) had evidence of vascular injury, with an absent radial pulse. The hand was pink and warm in eight and white and cold in the other three patients. They underwent colour-coded duplex scanning (CCDS) and ultrasound velocimetry (UV) to investigate the patency of the brachial artery and arterial blood flow. In seven patients with a pink pulseless hand, CCDS showed a displaced, kinked and spastic brachial artery and a thrombosis was present in the other. In all cases UV showed reduced blood flow in the hand. In three patients with a white pulseless hand, scanning demonstrated a laceration in the brachial artery and/or thrombosis. In all cases, the fracture was reduced under general anaesthesia and fixed with Kirschner wires. Of the seven patients with a pink pulseless hand without thrombosis, the radial pulse returned after reduction in four cases. The remaining three underwent exploration, along with the patients with laceration in the brachial artery and/or thrombosis. We believe that the traditional strategy of watchful waiting in children in whom the radial pulse remains absent in spite of good peripheral perfusion should be revisited. Vascular investigation using these non-invasive techniques that are quick and reliable is recommended in the management of these patients. Cite this article: Bone Joint J 2013;95-B:694–98.
A comparison of hemiarthroplasty with a novel polycarbonate–urethane acetabular component for displaced intracapsular fractures of the femoral neck
Authors: Cadossi M. , Chiarello E. , Savarino L. , Tedesco G. , Baldini N. , Faldini C. , Giannini S. 
Published: April 2013

We undertook a randomised controlled trial to compare bipolar hemiarthroplasty (HA) with a novel total hip replacement (THR) comprising a polycarbonate–urethane (PCU) acetabular component coupled with a large-diameter metal femoral head for the treatment of displaced fractures of the femoral neck in elderly patients. Functional outcome, assessed with the Harris hip score (HHS) at three months and then annually after surgery, was the primary endpoint. Rates of revision and complication were secondary endpoints. Based on a power analysis, 96 consecutive patients aged > 70 years were randomised to receive either HA (49) or a PCU-THR (47). The mean follow-up was 30.1 months (23 to 50) and 28.6 months (22 to 52) for the HA and the PCU group, respectively. The HHS showed no statistically significant difference between the groups at every follow-up. Higher pain was recorded in the PCU group at one and two years’ follow-up (p = 0.006 and p = 0.019, respectively). In the HA group no revision was performed. In the PCU-THR group six patients underwent revision and one patient is currently awaiting re-operation. The three-year survival rate of the PCU-THR group was 0.841 (95% confidence interval 0.680 to 0.926). Based on our findings we do not recommend the use of the PCU acetabular component as part of the treatment of patients with fractures of the femoral neck. Cite this article: Bone Joint J 2013;95-B:609–15.
Association Between Changes in Electromyographic Signal Amplitude and Abdominal Muscle Thickness in Individuals With and Without Lumbopelvic Pain
Authors: Whittaker Jackie L. , McLean Linda , Hodder Joanne , Warner Martin B. , Stokes Maria J. 
Published: April 2013

Study Design Validation study. Objectives To investigate the association between changes in electromyographic (EMG) signal amplitude and sonographic measures of muscle thickness of 4 abdominal muscles, during 2 clinical tests, in adults with and without lumbopelvic pain. Background There is a trend in rehabilitation to use ultrasound imaging (USI) to determine the extent of abdominal muscle contraction. However, the literature investigating the relationship between abdominal muscle thickness change and level of activation is inconclusive and has not included clinically relevant tasks. Methods Simultaneous recording from fine-wire EMG and USI was performed for 4 abdominal muscles, in 7 adults with lumbopelvic pain (mean ± SD age, 29.7 ± 12.0 years) and 7 adults without lumbopelvic pain (32.0 ± 10.6 years), during an active straight leg raise (ASLR) test and an abdominal drawing-in maneuver (ADIM). Cross-correlation functions and linear regression analyses were used to describe the relationship between the 2 measures. Analyses of variance were used to compare individuals with and without lumbopelvic pain, with an alpha set at .05. Results Across all muscles, peak cross-correlation values were low (ASLR, r = 0.28 ± 0.09; ADIM, r = 0.35 ± 0.11), and there was large variability in associated time lags (ASLR, τ = 0.69 ± 2.56 seconds; ADIM, τ = 0.53 ± 3.75 seconds). Regression analyses did not detect a systematic pattern of association between EMG signal amplitude and USI measurements, and analyses of variance revealed no differences between cohorts. Conclusion These results suggest a weak relationship between EMG amplitude and abdominal muscle thickness change measured with USI during the ADIM and ASLR, and raise questions about thickness change derived from USI as a measure of muscular activity for the abdominal musculature. J Orthop Sports Phys Ther 2013;43(7):466–477. Epub 30 April 2013. doi:10.2519/jospt.2013.4440
La phonologie diachronique générative : du formalisme initial à la réappropriation de la tradition
Authors: Verleyen Stijn 
Published: April 2013

RÉSUMÉ: Cet article traite du modèle de phonologie diachronique, développé au sein de la grammaire générative au cours des années '60 et '70 du 20e s. (cf. Halle 1962, Kiparsky 1965, King 1969), et de l’évolution qu’a connue ce modèle après la publication du Sound Pattern of English (Chomsky -Halle 1968; désormais SPE).
Nous essayerons de montrer que le modèle 'formaliste’ initial, greffé entièrement sur la théorie synchronique proposée dans SPE,
évolue vers une conception plus 'réaliste’ du changement linguistique dans des publications ultérieures, et qu’on peut discerner une revalorisation des notions et de concepts explicatifs plus traditionnels en linguistique diachronique, reformulés dans le cadre formel propre à la grammaire générative. Nous esquissons d’abord les caractéristiques essentielles du modèle phonologique esquissé dans SPE [ 1.], et son application à la diachronie [ 2.], pour passer en revue ensuite l’essentiel des développements qui témoignent d’un retrait vers une position plus nuancée, réservant une place plus importante aux facteurs fonctionnels et aux facteurs liés à la substance phonique [ 3.].
Le statut du lexique dans la Grammaire de Laurent Chiflet et dans la Méthode de Claude Irson : 1656-1660
Authors: Delesalle Simone 
Published: April 2013

L’Essai de grammaire de Laurent Chiflet et la Méthode de Claude Irson, qui paraissent dans les mêmes années, au milieu du 17e s., traitent le domaine du lexique de manières très différentes. Chiflet (1598-1658), jésuite, s’inscrit dans la lignée des Remarqueurs, entre Vaugelas et Bouhours et fait des analyses fines de synonymes. Irson, qui est lié au groupe Janséniste, développe davantage l’étude du domaine lexical. La Méthode comprend deux listes commentées, formant dictionnaire : l’une traite les mots par rapport à l’usage, et la seconde, la plus importante, se préoccupe de l’origine des mots et de la formation du vocabulaire français, ce qui annonce la première édition du
Dictionnaire de l’Académie.
Disjunction and conjunction in Euclid's elements
Authors: Acerbi Fabio 
Published: April 2013

Nous présentons un aperçu des différentes façons dont les connecteurs disjonctifs et conjonctifs sont utilisés dans les
Éléments. La présence d’ētoi prépositif dans les disjonctions exclusives permet de situer l’emploi de ce connecteur dans la droite ligne des prescriptions stoïciennes. La conjonction, en revanche, est formulée d’une manière assez variée, permettant d’éviter toutes sortes d’ambiguïtés. Nous abordons aussi le problème qui consiste à évaluer dans quelle mesure les doctrines stoïciennes peuvent avoir été influencées par la systématisation linguistique démontrée par le style mathématique canonique.
Microsatellite primers identified by 454 sequencing in the floodplain tree species Eucalyptus victrix (Myrtaceae)
Authors: Nevill Paul G. , Bradbury Donna , Jørgensen Tina , Krauss Siegfried , Samaraweera Sunil , Gardner Michael G. 
Published: April 2013

• Premise of the study: Microsatellite primers were developed for Eucalyptus victrix (Myrtaceae) to evaluate the population and spatial genetic structure of this widespread northwestern Australian riparian tree species, which may be impacted by hydrological changes associated with mining activity.• Methods and Results: 454 GS‐FLX shotgun sequencing was used to obtain 1895 sequences containing putative microsatellite motifs. Ten polymorphic microsatellite loci were identified and screened for variation in individuals from two populations in the Pilbara region. Observed heterozygosities ranged from 0.44 to 0.91 (mean: 0.66) and the number of alleles per locus ranged from five to 25 (average: 11).• Conclusions: These microsatellite loci will be useful in future studies of population and spatial genetic structure in E. victrix, and inform the development of seed sourcing strategies for the species.
IL-6 Cooperates with G-CSF To Induce Protumor Function of Neutrophils in Bone Marrow by Enhancing STAT3 Activation
Authors: Yan Bin , Wei Jing-Jing , Yuan Ye , Sun Rui , Li Dong , Luo Jing , Liao Sheng-Jun , Zhou Yuan-Hong , Shu Yu , Wang Qi , Zhang Gui-Mei , Feng Zuo-Hua 
Published: April 2013

Abstract
Neutrophils are known to have antitumor potential. However, in recent years the tumor-promoting effect of neutrophils has been well demonstrated. So far, it remains unclear what causes the conversion of neutrophil function from tumor suppressive to tumor promoting. In this article, we report that the conversion of murine neutrophil function occurs in bone marrow, and that IL-6 cooperation with G-CSF is required for this conversion. IL-6 cooperated with G-CSF to modulate neutrophils in bone marrow, altering the activation potential of signaling pathways in neutrophils, especially that of STAT3. Costimulation with G-CSF and IL-6 induced a higher level of phospho-STAT3 in neutrophils, which was further increased by upregulation of STAT3 expression in neutrophils owing to downregulation of IFN-β expression in bone marrow macrophages by IL-6. Augmented STAT3 activation was crucial for upregulating the expression of Mmp9 and Bv8 genes and downregulating the expression of Trail and Rab27a genes in neutrophils. Moreover, G-CSF/IL-6–modulated neutrophils could not efficiently release azurophilic granules because of downregulation of Rab27a and inefficient activation of PI3K and p38 MAPK pathways. Because of premodulation by G-CSF and IL-6, neutrophils in response to complex stimuli in tumor released much less myeloperoxidase, neutrophil elastase, and TRAIL, but showed much higher expression of Mmp9 and Bv8 genes. Taken together, these results demonstrate that G-CSF and IL-6, despite their well-known physiological functions, could modulate the activation potential of signaling pathways in neutrophils, resulting in the production or release of the above-mentioned factors in a way that favors tumor angiogenesis and tumor growth.