bluuebunny/crossref_metadata_2025 huggingface dataset:
Site-Specific Targeting of Platelet-Rich Plasma via Superparamagnetic Nanoparticles
Authors: Talaie Tara , Pratt Stephen J.P. , Vanegas Camilo , Xu Su , Henn R. Frank , Yarowsky Paul , Lovering Richard M.
Published: January 2015

Background:

Muscle strains are one of the most common injuries treated by physicians. Standard conservative therapy for acute muscle strains usually involves short-term rest, ice, and nonsteroidal anti-inflammatory medications, but there is no clear consensus regarding treatments to accelerate recovery. Recently, clinical use of platelet-rich plasma (PRP) has gained momentum as an option for therapy and is appealing for many reasons, most notably because it provides growth factors in physiological proportions and it is autologous, safe, easily accessible, and potentially beneficial. Local delivery of PRP to injured muscles can hasten recovery of function. However, specific targeting of PRP to sites of tissue damage in vivo is a major challenge that can limit its efficacy.

Hypothesis:

Location of PRP delivery can be monitored and controlled in vivo with noninvasive tools.

Study Design:

Controlled laboratory study.

Methods:

Superparamagnetic iron oxide nanoparticles (SPIONs) can be visualized by both magnetic resonance imaging (MRI) (in vivo) and fluorescence microscopy (after tissue harvesting). PRP was labeled with SPIONs and administered by intramuscular injections of SPION-containing platelets. MRI was used to monitor the ability to manipulate and retain the location of PRP in vivo by placement of an external magnet. Platelets were isolated from whole blood and incubated with SPIONs. Following SPION incubation with PRP, a magnetic field was used to manipulate platelet location in culture dishes. In vivo, the tibialis anterior (TA) muscles of anesthetized Sprague-Dawley rats were injected with SPION-containing platelets, and MRI was used to track platelet position with and without a magnet worn over the TA muscles for 4 days.

Results:

The method used to isolate PRP yielded a high concentration (almost 4-fold increase) of platelets. In vitro experiments showed that the platelets successfully took up SPIONs and then rapidly responded to an applied magnetic field. Platelets without SPIONs did not respond to the magnetic field. In vivo experiments showed that the SPION-containing platelets can be noninvasively maintained at a specific site with the application of a magnetic field.

Conclusion:

PRP may be a useful product in the clinical treatment of muscle injuries, but one problem with using it as a therapeutic tool is retaining PRP at the site of injury. This study proposes a potential solution, with findings that support this method at the cell, whole muscle, and in vivo levels. Controlling the location of PRP will allow the clustering of PRP to enrich the target area with growth factors and will prevent loss of platelets over time at the site of injury.
Autologous Hamstring Anterior Cruciate Ligament Graft Failure Using the Anteromedial Portal Technique With Suspensory Femoral Fixation
Authors: Galdi Balazs , Reyes Allan , Brabston Eugene W. , Levine William N.
Published: January 2015

Background:

The anteromedial portal technique for drilling of the femoral tunnel during anterior cruciate ligament (ACL) reconstruction has been advocated by many surgeons as allowing improved access to the anatomical footprint. Furthermore, suspensory fixation of soft tissue grafts has become popularized because of complications associated with cross-pin fixation. Concerns regarding the use of both have recently arisen.

Purpose:

To raise awareness of the increased risk of graft failure when using the anteromedial portal technique with suspensory femoral fixation during ACL reconstruction.

Study Design:

Cohort study; Level of evidence, 3.

Methods:

From November 1998 to August 2012, a total of 465 primary ACL reconstructions were performed using quadrupled hamstring autograft tendons, with drilling of the femoral tunnel performed via the transtibial portal. Graft fixation on the femur was achieved with cross-pin fixation, while interference screw fixation was used on the tibia. From September 2012 to October 2013, there were 69 reconstructions performed through an anteromedial portal. While there was no change in graft choice, a change was made to using suspensory femoral fixation. No other surgical or postoperative rehabilitation changes were made.

Results:

During the 14-year period in which ACL reconstructions were performed via the transtibial portal and with cross-pin fixation, 2 graft failures (0.4% failure rate) were reported. After switching to the anteromedial portal with suspensory fixation, 7 graft failures (10.1% failure rate) were reported over a 13-month period. These were 5 male and 2 female patients, with a mean age of 18.8 years—all elite athletes. The same surgical technique was used in all patients, and all patients had at least an 8 mm–diameter graft. Patients were cleared to return to sport at an average of 8.4 months postoperatively, after completing functional performance tests. Of the 7 patients, 6 sustained a rerupture of the graft within 2 weeks of returning to full competition. The final patient sustained a rerupture 10 months after being cleared to play.

Conclusion:

Compared with the transtibial technique with cross-pin graft fixation, there is an increased risk of graft failure when performing autologous hamstring ACL reconstructions using the anteromedial portal technique with cortical suspensory fixation.
Mindful Music Listening Instruction Increases Listening Sensitivity and Enjoyment
Authors: Anderson William Todd
Published: January 2015

The purpose of this study was to examine the effect of mindful listening instruction on music listening sensitivity and music listening enjoyment. A pretest–posttest control group design was used. Participants, fourth-grade students ( N = 42) from an elementary school in a large city in the Northeastern United States, were randomly assigned to two groups, Mindful Listening and Control. Both groups received instruction using the same lessons. Students in the Mindful Listening group received slightly different listening instructions designed to promote mindful listening. Results indicated that mindful listening instruction yielded higher scores ( p < .05) for music listening sensitivity and music listening enjoyment. Suggestions for designing mindful listening activities are presented.
Exploring the Use of Sonographic Evaluation of the Glenohumeral Labrum
Authors: Volz Kevin R. , Dashottar Amitabh , Evans Kevin D.
Published: January 2015

Glenohumeral (GH) dislocations of the shoulder are prevalent in young male subjects and appear to be increasing in incidence. The classic diagnostic evaluation of labral injuries such as this involves the use of clinical testing as well as imaging modalities such as computed tomography, magnetic resonance imaging, and radiography, none of which provides a dynamic evaluation. This study was done to replicate sonographic evaluation of the glenoid labrum in a preclinical model and use the axillary scanning approach to specifically assess the integrity of the anterior inferior labrum. Using sonographic guidance, minimal amounts of differently colored dyes were injected into regions of the glenoid labrum. This replication was able to image only the posterior superior, posterior inferior, and anterior inferior aspects of the GH labrum. Bankart lesions were identified in two shoulders, confirmed on dissection. The presence of dyes in the target areas within and around the labrum was visually confirmed. These findings suggest that the concept of using an axillary scanning approach for detecting labral tears and Bankart lesions in patients with acute and chronic shoulder dislocation may be worthwhile to incorporate into a shoulder-scanning protocol.
Application of RF discharge in oxygen to create highly oxidized metal layers
Authors: Stadnichenko A. I. , Kibis L. S. , Svintsitskiy D. A. , Koshcheev S. V. , Boronin A. I.
Published: January 2015

The radio frequency (RF) discharge in an oxygen atmosphere was used to produce metal oxide films. The high efficiency of the RF discharge technique for metal oxidation at room temperature was demonstrated for gold, silver and copper foils. Oxide films up to 10 nm in thickness were obtained. The produced oxide films were studied by X-ray photoelectron spectroscopy (XPS). The XPS data showed the formation of oxidised species: Cu2+, Ag1+ and Au3+. Analysis of the oxygen species was performed using O1s spectra. For copper and silver foils, the formation of additional oxygen species apart from oxygen in the structure of oxides was shown. The reaction probability toward oxidation of carbon monoxide (CO) was estimated for all oxidised layers. It was established that gold and silver oxide films interacted with CO at room temperature, while cupric oxide showed high activity at temperature >353 K.
Nanostructured CeO2 coating for high temperature oxidation protection
Authors: Ghosh D. , Roy H. , Das S. , Mitra S. K.
Published: January 2015

This paper investigates the influence of nanostructured ceria (CeO2) coating on high temperature oxidation behaviour of 2·25 Cr-1 Mo steel. The isothermal corrosion study of the micrometre size and nanostructured CeO2 coated specimens was conducted in air oxidation environment at 973 K for 8 h. The corrosion rate and reaction kinetics were studied, and the post-corroded scales were characterised by field emission scanning electron microscopy and X-ray diffraction. The results clearly indicate that the nanostructured CeO2 coated specimen improves the oxidation resistance in comparison to the micrometre size CeO2 coated specimen. The improvement of oxidation resistance in the case of nanostructured CeO2 coating can be attributed to the formation of semimolten zone, which consists of nanostructured CeO2 particle. On the other hand, in the absence of semimolten nanostructured zone, the micrometre size CeO2 coated specimen shows higher corrosion rate in comparison to the nanostructured CeO2 powder coated specimen.
Statistical optimisation of trivalent chromium bath and characterisation of coating defects
Authors: Katırcı R.
Published: January 2015

The influences of chemicals used in the Cr electrodeposition bath on the brightness and efficiency of Cr coating were studied using fractional factorial design of experimental method. Cr coating defects that emerged during the coating were investigated using a scanning electron microscope (SEM). Analysis of variance test was performed to check the accuracy of each effect in the statistical studies. The statistical results show that boric acid enhances the efficiency and thickness of Cr coating the most. The stability of Cr coating is dependent on two parameters: pH and Cr+3 ion concentration in the Cr III bath. SEM images and energy dispersive spectroscopy measurements showed that the blackness and dullness defects on Cr coating are due to the emergence of chromium (III) sulphide (Cr2S3) and fast hydrogen evolution on Cr coating.
The mouse NKR-P1B:Clr-b recognition system is a negative regulator of innate immune responses
Authors: Rahim Mir Munir A. , Chen Peter , Mottashed Amelia N. , Mahmoud Ahmad Bakur , Thomas Midhun J. , Zhu Qinzhang , Brooks Colin G. , Kartsogiannis Vicky , Gillespie Matthew T. , Carlyle James R. , Makrigiannis Andrew P.
Published: January 2015

Key Points

NKR-P1B is involved in NK cell tolerance and MHC-I-independent missing-self recognition of Clr-b-deficient target cells. The NKR-P1B:Clr-b system plays a role in tumor surveillance and immune escape in the Eμ-myc transgenic mouse model of B-cell lymphoma.
Receptor-type tyrosine-protein phosphatase κ directly targets STAT3 activation for tumor suppression in nasal NK/T-cell lymphoma
Authors: Chen Yun-Wen , Guo Tianhuan , Shen Lijun , Wong Kai-Yau , Tao Qian , Choi William W. L. , Au-Yeung Rex K. H. , Chan Yuen-Piu , Wong Michelle L. Y. , Tang Johnny C. O. , Liu Wei-Ping , Li Gan-Di , Shimizu Norio , Loong Florence , Tse Eric , Kwong Yok-Lam , Srivastava Gopesh
Published: January 2015

Key Points

PTPRK binds to STAT3 and directly dephosphorylates phospho-STAT3 at Tyr705. Loss of PTPRK, located in the deleted 6q region, leads to STAT3 activation and contributes to nasal-type NK/T-cell lymphoma pathogenesis.
γδ T-cell reconstitution after HLA-haploidentical hematopoietic transplantation depleted of TCR-αβ+/CD19+ lymphocytes
Authors: Airoldi Irma , Bertaina Alice , Prigione Ignazia , Zorzoli Alessia , Pagliara Daria , Cocco Claudia , Meazza Raffaella , Loiacono Fabrizio , Lucarelli Barbarella , Bernardo Maria Ester , Barbarito Giulia , Pende Daniela , Moretta Alessandro , Pistoia Vito , Moretta Lorenzo , Locatelli Franco
Published: January 2015

Key Points

Vδ1 and Vδ2 T cells promptly reconstitute in children given haploidentical stem cell transplantation depleted of αβ+ T and CD19+ B cells. Vδ1 cells are expanded in patients experiencing cytomegalovirus reactivation; ZOL potentiates Vδ2 killing against leukemia blasts.
Airway wall thickness associated with forced expiratory volume in 1 second decline and development of airflow limitation
Authors: Mohamed Hoesein Firdaus A.A. , de Jong Pim A. , Lammers Jan-Willem J. , Mali Willem P.T.M. , Schmidt Michael , de Koning Harry J. , van der Aalst Carlijn , Oudkerk Matthijs , Vliegenthart Rozemarijn , Groen Harry J.M. , van Ginneken Bram , van Rikxoort Eva M. , Zanen Pieter
Published: January 2015

Airway wall thickness and emphysema contribute to airflow limitation.

We examined their association with lung function decline and development of airflow limitation in 2021 male smokers with and without airflow limitation. Airway wall thickness and emphysema were quantified on chest computed tomography and expressed as the square root of wall area of a 10-mm lumen perimeter (Pi10) and the 15th percentile method (Perc15), respectively. Baseline and follow-up (median (interquartile range) 3 (2.9–3.1) years) spirometry was available.

Pi10 and Perc15 correlated with baseline forced expiratory volume in 1 s (FEV1) (r= −0.49 and 0.11, respectively (p<0.001)). Multiple linear regression showed that Pi10 and Perc15 at baseline were associated with a lower FEV1 after follow-up (p<0.05). For eachsdincrease in Pi10 and decrease in Perc15 the FEV1 decreased by 20 mL and 30.2 mL, respectively. The odds ratio for developing airflow limitation after 3 years was 2.45 for a 1-mm higher Pi10 and 1.46 for a 10-HU lower Perc15 (p<0.001).

A greater degree of airway wall thickness and emphysema was associated with a higher FEV1 decline and development of airflow limitation after 3 years of follow-up.
Pulmonary manifestations in adult patients with chronic granulomatous disease
Authors: Salvator Hélène , Mahlaoui Nizar , Catherinot Emilie , Rivaud Elisabeth , Pilmis Benoit , Borie Raphael , Crestani Bruno , Tcherakian Colas , Suarez Felipe , Dunogue Bertrand , Gougerot-Pocidalo Marie-Anne , Hurtado-Nedelec Margarita , Dreyfus Jean-François , Durieu Isabelle , Fouyssac Fanny , Hermine Olivier , Lortholary Olivier , Fischer Alain , Couderc Louis-Jean
Published: January 2015

Chronic granulomatous disease (CGD) is a primary immunodeficiency caused by failure of superoxide production in phagocytic cells. The disease is characterised by recurrent infections and inflammatory events, frequently affecting the lungs. Improvement of life expectancy now allows most patients to reach adulthood. We aimed to describe the pattern of pulmonary manifestations occurring during adulthood in CGD patients.

This was a retrospective study of the French national cohort of adult patients (≥16 years old) with CGD.

Medical data were obtained for 67 adult patients. Pulmonary manifestations affected two-thirds of adult patients. Their incidence was significantly higher than in childhood (mean annual rate 0.22versus0.07, p=0.01). Infectious risk persisted despite anti-infectious prophylaxis. Invasive fungal infections were frequent (0.11 per year per patient) and asymptomatic in 37% of the cases. They often required lung biopsy for diagnosis (10 out of 30). Noninfectious respiratory events concerned 28% of adult patients, frequently associated with a concomitant fungal infection (40%). They were more frequent in patients with the X-linked form of CGD. Immune-modulator therapies were required in most cases (70%).

Respiratory manifestations are major complications of CGD in adulthood. Noninfectious pulmonary manifestations are as deleterious as infectious pneumonia. A specific respiratory monitoring is necessary.
Plasma pro-surfactant protein B and lung function decline in smokers
Authors: Leung Janice M. , Mayo John , Tan Wan , Tammemagi C. Martin , Liu Geoffrey , Peacock Stuart , Shepherd Frances A. , Goffin John , Goss Glenwood , Nicholas Garth , Tremblay Alain , Johnston Michael , Martel Simon , Laberge Francis , Bhatia Rick , Roberts Heidi , Burrowes Paul , Manos Daria , Stewart Lori , Seely Jean M. , Gingras Michel , Pasian Sergio , Tsao Ming-Sound , Lam Stephen , Sin Don D.
Published: January 2015

Plasma pro-surfactant protein B (pro-SFTPB) levels have recently been shown to predict the development of lung cancer in current and ex-smokers, but the ability of pro-SFTPB to predict measures of chronic obstructive pulmonary disease (COPD) severity is unknown. We evaluated the performance characteristics of pro-SFTPB as a biomarker of lung function decline in a population of current and ex-smokers.

Plasma pro-SFTPB levels were measured in 2503 current and ex-smokers enrolled in the Pan-Canadian Early Detection of Lung Cancer Study. Linear regression was performed to determine the relationship of pro-SFTPB levels to changes in forced expiratory volume in 1 s (FEV1) over a 2-year period as well as to baseline FEV1 and the burden of emphysema observed in computed tomography (CT) scans.

Plasma pro-SFTPB levels were inversely related to both FEV1 % predicted (p=0.024) and FEV1/forced vital capacity (FVC) (p<0.001), and were positively related to the burden of emphysema on CT scans (p<0.001). Higher plasma pro-SFTPB levels were also associated with a more rapid decline in FEV1 at 1 year (p=0.024) and over 2 years of follow-up (p=0.004).

Higher plasma pro-SFTPB levels are associated with increased severity of airflow limitation and accelerated decline in lung function. Pro-SFTPB is a promising biomarker for COPD severity and progression.
Efficacy of short-term prednisolone treatment in patients with chronic eosinophilic pneumonia
Authors: Oyama Yoshiyuki , Fujisawa Tomoyuki , Hashimoto Dai , Enomoto Noriyuki , Nakamura Yutaro , Inui Naoki , Kuroishi Shigeki , Yokomura Koshi , Toyoshima Mikio , Yamada Takashi , Shirai Toshihiro , Masuda Masafumi , Yasuda Kazumasa , Hayakawa Hiroshi , Chida Kingo , Suda Takafumi
Published: January 2015

In patients with chronic eosinophilic pneumonia (CEP), dramatic improvements are seen in response to corticosteroid therapy; however, relapse is common after treatment has ceased. The optimal duration of corticosteroid therapy remains unclear.

In a randomised, open-label, parallel group study, eligible patients with CEP received oral prednisolone for either 3 months (3-month group) or 6 months (6-month group), followed by 2 years observation. All patients were treated with an initial dose of prednisolone of 0.5 mg·kg−1·day−1, which was then tapered and discontinued at either 3 or 6 months. The primary end-point was relapse during the follow-up period.

In the final analysis, there were 23 patients in the 3-month group and 21 patients in the 6-month group. All patients showed a good response to prednisolone treatment. There were 12 (52.1%) relapses in the 3-month group and 13 (61.9%) relapses in the 6-month group. No significant difference was found in the cumulative rate of relapse (p=0.56). All relapse cases showed improvement upon resumption of prednisolone treatment.

No difference was observed in the rate of relapse between the 3- and 6-month prednisolone treatment groups for patients with CEP.
Exploratory use of docetaxel loaded acid-prepared mesoporous spheres for the treatment of malignant melanoma
Authors: Kaiser Sameer , MacPherson Maximilian B , James Ted A , Emery Albert , Spiess Page , van der Vliet Albert , Landry Christopher C , Shukla Arti
Published: January 2015

Introduction

Five year survival for metastatic melanoma (MM) is very low at <10%. Therapeutic options have been limited secondary to systemic toxicity. As a result there has been a growing movement towards developing targeted drug delivery models. Prior research of this group has demonstrated the effectiveness of acid-prepared mesoporous spheres (APMS-TEG) in delivering chemotherapeutic agents at a lower effective dose than systemic administration. This study aims to assess the ability of the previously developed APMS-TEG particles to deliver therapeutic doses of docetaxel for the treatment of melanoma.

Methods

In vitro experiments were performed to assess docetaxel loading onto APMS-TEG particles and release kinetics. Toxicity experiments were performed using docetaxel and docetaxel loaded APMS-TEG. The effect on cell growth was assessed using the MelJuSo, UACC903, and WM1205 melanoma cell lines.

Results

Docetaxel demonstrated statistically significant dose dependent reduction in growth of melanoma cells. In all three cell lines, doses of 1 nM were sufficient to produce statistically significant reduction in cell growth. Scanning electron micrographs demonstrate increased uptake of APMS-TEG particles by melanoma cells in the first 24 hours, with the majority within the first 4 hours. Unloaded APMS particles had no effect on the melanoma cells, demonstrating that the particles themselves are not toxic. APMS-TEG particles had a peak release of drug within the first hour, with equilibration thereafter. The 5, 10, and 20 nM loaded particles all had statistically significant reduction in cell growth than the control groups.

Discussion

The high potency against melanoma cells makes docetaxel a suitable choice for loading into APMS-TEG particles. Docetaxel loaded APMS-TEG particles demonstrate significant activity against malignant melanoma and thus offer an innovative approach to the treatment of metastatic melanoma.
Low-dose hydrocortisone reduces norepinephrine duration in severe burn patients: a randomized clinical trial
Authors: Venet Fabienne , Plassais Jonathan , Textoris Julien , Cazalis Marie-Angélique , Pachot Alexandre , Bertin-Maghit Marc , Magnin Christophe , Rimmelé Thomas , Monneret Guillaume , Tissot Sylvie
Published: January 2015

Introduction

The aim of this study was to assess the effect of low-dose corticosteroid therapy in reducing shock duration after severe burn.

Methods

A placebo-controlled, double-blind, randomized clinical trial (RCT) was performed on two parallel groups in the burn intensive care unit (ICU). Patients were randomized to receive either low-dose corticosteroid therapy or placebo for seven days. A corticotropin test was performed at the time of randomization, before the administration of the treatment dose. Thirty-two severely burned patients with refractory shock (>0.5 μg/kg/min of norepinephrine) were prospectively included in the study.

Results

We included 12 patients in the hydrocortisone-treated group and 15 patients in the placebo group in the final analysis. Among these patients, 21 were nonresponders to the corticotropin test. Median norepinephrine treatment duration (primary objective) was significantly lower in the corticosteroid-treated versus the placebo group (57 hours versus 120 hours, P = 0.035). The number of patients without norepinephrine 72 hours after inclusion was significantly lower in the treated group (P = 0.003, log-rank test analysis). The total quantities of norepinephrine administered to patients were lower in the hydrocortisone-treated versus the placebo group (1,205 μg/kg (1,079 to 2,167) versus 1,971 μg/kg (1,535 to 3,893), P = 0.067). There was no difference in terms of ICU or hospital length of stay, sepsis incidence, cicatrization or mortality.

Conclusions

In this placebo-controlled, randomized, double-blind clinical trial, we show for the first time that the administration of low-dose hydrocortisone in burn patients with severe shock reduces vasopressor administration.

Trial registration

Clinicaltrial.gov NCT00149123. Registered 6 September 2005.
Causes and consequences of crossing-over evidenced via a high-resolution recombinational landscape of the honey bee
Authors: Liu Haoxuan , Zhang Xiaohui , Huang Ju , Chen Jian-Qun , Tian Dacheng , Hurst Laurence D , Yang Sihai
Published: January 2015

Background

Social hymenoptera, the honey bee (Apis mellifera) in particular, have ultra-high crossover rates and a large degree of intra-genomic variation in crossover rates. Aligned with haploid genomics of males, this makes them a potential model for examining the causes and consequences of crossing over. To address why social insects have such high crossing-over rates and the consequences of this, we constructed a high-resolution recombination atlas by sequencing 55 individuals from three colonies with an average marker density of 314 bp/marker.

Results

We find crossing over to be especially high in proximity to genes upregulated in worker brains, but see no evidence for a coupling with immune-related functioning. We detect only a low rate of non-crossover gene conversion, contrary to current evidence. This is in striking contrast to the ultrahigh crossing-over rate, almost double that previously estimated from lower resolution data. We robustly recover the predicted intragenomic correlations between crossing over and both population level diversity and GC content, which could be best explained as indirect and direct consequences of crossing over, respectively.

Conclusions

Our data are consistent with the view that diversification of worker behavior, but not immune function, is a driver of the high crossing-over rate in bees. While we see both high diversity and high GC content associated with high crossing-over rates, our estimate of the low non-crossover rate demonstrates that high non-crossover rates are not a necessary consequence of high recombination rates.
Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements
Authors: Zhang Weiwei , Spector Tim D , Deloukas Panos , Bell Jordana T , Engelhardt Barbara E
Published: January 2015

Background

Recent assays for individual-specific genome-wide DNA methylation profiles have enabled epigenome-wide association studies to identify specific CpG sites associated with a phenotype. Computational prediction of CpG site-specific methylation levels is critical to enable genome-wide analyses, but current approaches tackle average methylation within a locus and are often limited to specific genomic regions.

Results

We characterize genome-wide DNA methylation patterns, and show that correlation among CpG sites decays rapidly, making predictions solely based on neighboring sites challenging. We built a random forest classifier to predict methylation levels at CpG site resolution using features including neighboring CpG site methylation levels and genomic distance, co-localization with coding regions, CpG islands (CGIs), and regulatory elements from the ENCODE project. Our approach achieves 92% prediction accuracy of genome-wide methylation levels at single-CpG-site precision. The accuracy increases to 98% when restricted to CpG sites within CGIs and is robust across platform and cell-type heterogeneity. Our classifier outperforms other types of classifiers and identifies features that contribute to prediction accuracy: neighboring CpG site methylation, CGIs, co-localized DNase I hypersensitive sites, transcription factor binding sites, and histone modifications were found to be most predictive of methylation levels.

Conclusions

Our observations of DNA methylation patterns led us to develop a classifier to predict DNA methylation levels at CpG site resolution with high accuracy. Furthermore, our method identified genomic features that interact with DNA methylation, suggesting mechanisms involved in DNA methylation modification and regulation, and linking diverse epigenetic processes.
Exoproteome analysis of Clostridium cellulovorans in natural soft-biomass degradation
Authors: Esaka Kohei , Aburaya Shunsuke , Morisaka Hironobu , Kuroda Kouichi , Ueda Mitsuyoshi
Published: January 2015

Clostridium cellulovorans is an anaerobic, cellulolytic bacterium, capable of effectively degrading various types of soft biomass. Its excellent capacity for degradation results from optimization of the composition of the protein complex (cellulosome) and production of non-cellulosomal proteins according to the type of substrates. In this study, we performed a quantitative proteome analysis to determine changes in the extracellular proteins produced by C. cellulovorans for degradation of several types of natural soft biomass. C. cellulovorans was cultured in media containing bagasse, corn germ, rice straw (natural soft biomass), or cellobiose (control). Using an isobaric tag method and a liquid chromatograph equipped with a long monolithic silica capillary column/mass spectrometer, we identified 372 proteins in the culture supernatant. Of these, we focused on 77 saccharification-related proteins of both cellulosomal and non-cellulosomal origins. Statistical analysis showed that 18 of the proteins were specifically produced during degradation of types of natural soft biomass. Interestingly, the protein Clocel_3197 was found and commonly involved in the degradation of every natural soft biomass studied. This protein may perform functions, in addition to its known metabolic functions, that contribute to effective degradation of natural soft biomass.
Fungal strain matters: colony growth and bioactivity of the European medicinal polypores Fomes fomentarius, Fomitopsis pinicola and Piptoporus betulinus
Authors: Dresch Philipp , D´Aguanno Maria Nives , Rosam Katharina , Grienke Ulrike , Rollinger Judith Maria , Peintner Ursula
Published: January 2015

Polypores have been applied in traditional Chinese medicine up to the present day, and are becoming more and more popular worldwide. They show a wide range of bioactivities including anti-cancer, anti-inflammatory, antiviral and immuno-enhancing effects. Their secondary metabolites have been the focus of many studies, but the importance of fungal strain for bioactivity and metabolite production has not been investigated so far for these Basidiomycetes. Therefore, we screened several strains from three medicinal polypore species from traditional European medicine: Fomes fomentarius, Fomitopsis pinicola and Piptoporus betulinus. A total of 22 strains were compared concerning their growth rates, optimum growth temperatures, as well as antimicrobial and antifungal properties of ethanolic fruit body extracts. The morphological identification of strains was confirmed based on rDNA ITS phylogenetic analyses. Our results showed that species delimitation is critical due to the presence of several distinct lineages, e.g. within the Fomes fomentarius species complex. Fungal strains within one lineage showed distinct differences in optimum growth temperatures, in secondary metabolite production, and accordingly, in their bioactivities. In general, F. pinicola and P. betulinus extracts exerted distinct antibiotic activities against Bacillus subtilis and Staphylococcus aureus at minimum inhibitory concentrations (MIC) ranging from 31-125 μg mL−1; The antifungal activities of all three polypores against Aspergillus flavus, A. fumigatus, Absidia orchidis and Candida krusei were often strain-specific, ranging from 125-1000 μg mL−1. Our results highlight that a reliable species identification, followed by an extensive screening for a ‘best strain’ is an essential prerequisite for the proper identification of bioactive material.
Feasibility study of an alkaline-based chemical treatment for the purification of polyhydroxybutyrate produced by a mixed enriched culture
Authors: Jiang Yang , Mikova Gizela , Kleerebezem Robbert , van der Wielen Luuk AM , Cuellar Maria C
Published: January 2015

This study focused on investigating the feasibility of purifying polyhydroxybutyrate (PHB) from mixed culture biomass by alkaline-based chemical treatment. The PHB-containing biomass was enriched on acetate under non-sterile conditions. Alkaline treatment (0.2 M NaOH) together with surfactant SDS (0.2 w/v% SDS) could reach 99% purity, with more than 90% recovery. The lost PHB could be mostly attributed to PHB hydrolysis during the alkaline treatment. PHB hydrolysis could be moderated by increasing the crystallinity of the PHB granules, for example, by biomass pretreatment (e.g. freezing or lyophilization) or by effective cell lysis (e.g. adjusting alkali concentration). The suitability of the purified PHB by alkaline treatment for polymer applications was evaluated by molecular weight and thermal stability. A solvent based purification method was also performed for comparison purposes. As result, PHB produced by mixed enriched cultures was found suitable for thermoplastic applications when purified by the solvent method. While the alkaline method resulted in purity, recovery yield and molecular weight comparable to values reported in literature for PHB produced by pure cultures, it was found unsuitable for thermoplastic applications. Given the potential low cost and favorable environmental impact of this method, it is expected that PHB purified by alkaline method may be suitable for other non-thermal polymer applications, and as a platform chemical.
An iterative algorithm for fixed point problem and convex minimization problem with applications
Authors: Cai Gang , Shehu Yekini
Published: January 2015

In this paper we prove the strong convergence of an iterative sequence for finding a common element of the fixed points set of a strictly pseudocontractive mapping and the solution set of the constrained convex minimization problem for a convex and continuously Fréchet differentiable functional in a real Hilbert space. We apply our result to solving the split feasibility problem and the convexly constrained linear inverse problem involving the fixed point problem for a strictly pseudocontractive mapping in a real Hilbert space.
Bioavailability and bioaccumulation characterization of essential and heavy metals contents in R. acetosa, S. oleracea and U. dioica from copper polluted and referent areas
Authors: Balabanova Biljana , Stafilov Trajče , Bačeva Katerina
Published: January 2015

Background

Bioavailability of metals occurring in soil is the basic source of its accumulation in vegetables and herbs. The impact of soil pollution (due to urban and mining areas) on the food chain presents a challenge for many investigations. Availability of metals in a potentially polluted soil and their possible transfer and bioaccumulation in sorrel (Rumex acetosa), spinach (Spinacia oleracea) and common nettle (Urtica dioica), were examined.

Methods

Microwave digestion was applied for total digestion of the plant tissues, while on the soil samples open wet digestion with a mixture of acids was applied. Three extraction methods were implemented for the bioavailable metals in the soil. Atomic emission spectrometry with inductively coupled plasma was used for determination of the total contents of 21 elements.

Results

Significant enrichments in agricultural soil for As, Pb and Zn (in urban area), Cd, Cu and Ni (in a copper mine area), compared with the respective values from European standards were detected. On the basis of three different extraction methods, higher availability was assumed for both lithogenic and anthropogenic elements. Translocation values >1 were obtained for As, Cd, Cu, Ni, Pb and Zn. Higher bioconcentrating value was obtained only for Cd, while the bioaccumulation values vary from 0.17 for Cd to 0.82 for Zn.

Conclusions

The potential availability of hazardous metals in urban and mining soils is examined using DTPA-TEA-CaCl2(urban) and HCl (Cu-mines areas). Our results suggested thatS. oleraceaandR. acetosahave a phytostabilization potential for Cd, Cu, Ni and Pb, whileU. dioicaonly for Cu.R. acetosahas a potential for phytoextraction of Cd in urban and copper polluted areas.
X-ray tomography of a soil block: a useful tool for the restoration of archaeological finds
Authors: Re Alessandro , Corsi Jacopo , Demmelbauer Marco , Martini Margherita , Mila Giorgia , Ricci Chiara
Published: January 2015

Introduction

X-ray imaging is a very powerful tool which can be exploited in several fields. In the last few years, its use in archaeology has grown consistently. One of the most recent and interesting applications of computed X-ray tomography (CT) is the analysis of soil blocks, coming from excavations, in order to seek for finds of different kinds and materials possibly contained therein. For this purpose, both medical and industrial CT scanners have been employed. In this paper, the application of a CT instrument specifically designed and developed for the analysis of Cultural Heritage materials is presented. We analysed a soil block extracted from a necropolis in the Italian region of Abruzzo and probably dating back to the VI-IV century B.C., which was found to contain a bronze belt.

Results

Thanks to the versatility of the CT equipment we designed, a complete scan has been obtained in less than four hours and has delivered extremely useful information in a completely non-invasive way. The CT dataset and images allowed a virtual extraction of the find to be performed before the actual stratigraphic recovery that, in this case, was simplified thanks to the merging of the archaeological evidences and with information coming from scientific analyses. The information provided by the tomography consisted in: the distribution, shape and dimensions of fragments composing the artefact; indications about its general conditions; the recognition of repairs done in the past and the presence of different materials (although not precisely identified).

Conclusions

The use of CT has great potential for the work of both archaeologists and restorers. The indirect extraction of an artefact from an archaeological excavation, which entailed moving a soil block to the laboratory, allowed one to reconstruct almost all its parts and to collect information about materials. CT analysis has been particularly useful for determining both its conditions and its repairs before the actual recovery, thereby facilitating the restoration process.

The recovery and conservation of an historical piece like the one presented here can help archaeological and conservation studies, enrich a museum collection and contribute to the dissemination of acquired cultural information.
Guanaco abundance and monitoring in Southern Patagonia: distance sampling reveals substantially greater numbers than previously reported
Authors: Travaini Alejandro , Zapata Sonia C , Bustamante Javier , Pedrana Julieta , Zanón Juan I , Rodríguez Alejandro
Published: January 2015

Background

Guanacos (Lama guanicoe) are thought to have declined in Patagonia mainly as a result of hunting and sheep ranching. Currently accepted estimates of total population size are extrapolated from densities obtained through strip transects in local studies. We used road surveys (8,141 km) and distance sampling to estimate guanaco density and population size over major environmental gradients of Santa Cruz, a large region in southern Patagonia. We also calculated the survey effort required to detect population trends in Santa Cruz.

Results

We found considerable spatial variation in density (1.1 to 7.4 ind/km2), with a mean value of 4.8 ind/km2, which is more than twice the mean value guessed for central and northern Patagonia. Consequently, guanaco numbers in Santa Cruz were estimated at 1.1 million individuals (95% CI 0.7 to 1.6), which almost doubles current estimates of guanaco population size in South America. High guanaco abundance was found in arid lands, overgrazed and unable to support profitable sheep stocks. Detecting a 50% change in guanaco population size over a 10-year period requires substantial monitoring effort: the annual survey of between 40 and 80 30-km transects, which becomes up to 120 transects if trends are to be detected over 5 years.

Conclusions

Regional patterns in guanaco density can only be detected through large-scale surveys. Coupling these surveys with distance sampling techniques produce robust estimates of density and its variation. Figures so obtained improve currently available estimates of guanaco population size across its geographic range, which seem to be extrapolated from strip counts over small areas. In arid lands degraded by sheep overgrazing, sustainable use of guanaco populations would help harmonize guanaco conservation, socio-economic progress of rural areas, and eventually the restoration of shrub-steppes.
Comparative evaluation of biphasic calcium phosphate and biphasic calcium phosphate collagen composite on osteoconductive potency in rabbit calvarial defect
Authors: Lee Eun-Ung , Kim Dong-Ju , Lim Hyun-Chang , Lee Jung-Seok , Jung Ui-Won , Choi Seong-Ho
Published: January 2015

Background

The aim of this study was to determine the osteoconductivity of biphasic calcium phosphate collagen composite (BCPC) in rabbit calvarial defect model by comparing with biphasic calcium phosphate (BCP). Four 8 mm diameter bicortical calvarial defects were made in ten rabbits. Each of the defects was randomly assigned and filled with 1) collagen sponge, 2) BCP, 3) BCPC, and 4) nothing as control. The animals were sacrificed at either 2 weeks (n = 5) or 8 weeks (n = 5) healing period.

Results

All groups showed wedge shaped new bone formation limited to the area of the defect margin at both healing periods. The amounts of new bone and defect closure were similar among all groups. In the control and collagen sponge group, the center of the defect was depressed by surrounding tissues. In contrast, in BCP and BCPC group, the center of the defect did not depressed and the grafted materials maintained the space. And the augmented area was significantly higher in BCP and BCPC group compared to the control and collagen sponge group at both healing periods (p < 0.05).

Conclusions

The BCPC and BCP demonstrated proper space maintaining capacity and osteoconductive property, suggesting BCPC can be efficiently utilized in various clinical situations.
The Postsecular Turn and Muslim American Literature
Authors: Haque Danielle
Published: January 2015

This essay argues that contemporary discourses around postsecularism in literature do not adequately express the concerns of Muslim American writers who are reimaging how they can practice their religion within the specificity of the US secular context. It examines the ways Mohja Kahf’s bildungsroman, The Girl in the Tangerine Scarf, challenges the contemporary notion of postsecular literature, which takes a weakened, hybridized, liberal spirituality as its starting point. Although the bildungsroman conventionally plots an individual’s modernization in line with the nation’s, Kahf uses the formal strategies of the bildungsroman to contest the moral superiority of secular feminism and to assert an Islamic feminism that works in tandem with American identity. She situates her protagonist’s ultimate independence from the family fold, patriarchal Islam, and mainstream US society in explicitly gendered and religious acts of claiming control over her body. While Kahf illuminates the limits of secularism, she also sees its potential, and the novel ultimately envisions the secular context as a place in which to foster the umma—the global, transnational community to which every Muslim belongs.
9 Thermidor: Cinderella among Revolutionary Journées
Authors: Jones Colin
Published: January 2015

Following the overthrow of Robespierre in the journée of 9 Thermidor II (July 27, 1794), the Convention set about establishing an official version of the events of the day. The principal protagonists had been Robespierre’s fellow Montagnards and the Parisian sections, which responded positively to the Convention’s call for armed support against Robespierre and the Paris Commune during the night of 9–10 Thermidor. Yet by the time the moderate deputy Edme-Bonaventure Courtois presented the official report to the assembly on 8 Thermidor Year III (July 26, 1795), a thorough reconceptualization of the day had occurred. The role of the Montagnards and of the people of Paris was simply erased. This rewriting of history was congruent with the general direction of Thermidorian policies toward popular involvement in the revolutionary process. It was also to prove influential in subsequent historiography of the events of 9 Thermidor.

Après le renversement de Robespierre pendant la journée du 9 thermidor II (27 juillet 1794), la Convention se mit à établir une version officielle des événements de la journée. Les principaux protagonistes avaient été les Montagnards, anciens compagnons de Robespierre, et les sections parisiennes. Celles-ci ont répondu positivement à l’appel de la Convention qui réclamait leur appui contre Robespierre et la Commune de Paris dans la nuit du 9–10 thermidor. Pourtant, au moment où le député modéré, Edme-Bonaventure Courtois, a présenté le rapport officiel à l’assemblée le 8 thermidor an III (26 juillet 1795), une conceptualisation complètement nouvelle de la journée avait eu lieu. Le rôle des Montagnards et du peuple de Paris a été tout simplement effacé. Cette réécriture de l’histoire s’accordait avec la tendance générale des politiques thermidoriennes à nier la participation populaire dans le processus révolutionnaire. Elle a également eu une grande influence sur l’historiographie ultérieure du 9 thermidor.
A Second Terror: The Purges of French Revolutionary Legislators after Thermidor
Authors: Harder Mette
Published: January 2015

French revolutionary legislators faced assassins, violent insurrections, and the risk of being injured or killed while on mission. Statistically, however, the most dangerous place for them was their own legislative assembly. As full-scale parliamentary warfare erupted between different political “factions” in the founding year of the republic, the safeguards of parliamentary immunity were removed and hundreds of legislators were purged. Much research has been done on the famous parliamentary purges of the Terror. The practice continued, however, long after Robespierre’s fall as the Thermidorian Reaction experienced a second Terror in the legislature. Little is known about these later purges, and few comparisons have been made to the higher-profile cases of Year II. This article investigates why the Thermidorians failed to halt the cycle of parliamentary violence in the post-Terror era, arguing that the purging of legislators had by then become a destructive, long-term political habit with dangerous consequences for French representative democracy.

Les conventionnels couraient souvent le risque d’être assassinés, de se faire agresser pendant les journées ou d’être blessés en mission. Le lieu le plus dangereux pour eux était, pourtant, leur propre assemblée : entre 1792 et 1794, la Convention nationale expulse 149 de ses membres de son sein. Accusés de crimes politiques, des députés girondins, dantonistes et robespierristes sont arrêtés, mis en prison et souvent condamnés à mort. Les épurations de la Convention sous la Terreur sont si bien étudiées qu’elles ont longtemps obscurci la continuation de la même politique épuratoire après la chute de Robespierre. La réaction thermidorienne, pourtant, commence une seconde Terreur contre les députés. Les historiens de la Révolution, en traitant ces incidents comme de simples résultats de la dynamique réactionnaire, niaient la possibilité d’un rapport plus direct entre les épurations de la Terreur et celles de la période thermidorienne. Le but de cet article sera d’identifier, premièrement, les continuités entre les épurations successives des conventionnels sous la Terreur et ses suites, et, deuxièmement, les conséquences pour la démocratie révolutionnaire de cette habitude politique d’épurer la législature.