bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primary giant cell carcinomas of the lung: a clinicopathological and immunohistochemical analysis of seven cases
Authors: Weissferdt Annikka , Moran Cesar A 
Published: August 2015

AimsSeven cases of primary giant cell carcinomas of the lung are presented.Methods and resultsThe patients were five women and two men between the ages of 48 and 72 years (average: 63 years). Clinically, the patients presented with symptoms of cough, chest pain, dyspnoea and general malaise. Diagnostic imaging revealed the presence of intrapulmonary masses; five tumours were located in the right lung and two in the left, with a general predilection for the upper lobes. All patients underwent surgical resection and staging of their tumours. Five patients were staged as T2 and T3 with nodal metastasis, while two patients in stages T1 and T3, respectively, had no nodal disease. Histologically, the giant cells were typed as syncytiotrophoblast‐like or ‘null type’, according to the expression of β‐human chorionic gonadotrophin or expression of cytokeratin alone. Follow‐up information revealed that five patients died within a period of 1–3 years, while two patients remain alive between 1 and 3 years.ConclusionsThe cases presented herein highlight the importance of separating these tumours from the group of sarcomatoid carcinomas and analysing them carefully by immumohistochemical means, as we believe that these neoplasms represent a specific tumour entity.
Television advertising, not viewing, is associated with negative dietary patterns in children
Authors: Kelly B. , Freeman B. , King L. , Chapman K. , Baur L. A. , Gill T. 
Published: August 2015

SummaryBackgroundChildren's exposure to unhealthy food marketing is a contributor to poor diets and weight gain. Television food advertising, in particular, has been the focus of research and policy discussions.ObjectivesWe aimed to quantify the specific impact of television advertising, as distinct from television viewing generally, on children's usual diet. Methods Four hundred seventeen Australian children aged 10–16 participated in an online survey, which assessed television viewing habits and consumption of 12 frequently advertised unhealthy foods/drinks. Consumption of these foods/drinks was dichotomized (less weekly, weekly or more) and summed (1 point for each item consumed weekly or more) to give cumulative consumption scores.ResultsAfter adjusting for age and socioeconomic status, there was strong evidence of an increase in unhealthy food score (P < 0.001), drink score (P = 0.002) and food/drink combined score (P < 0.001), with increasing commercial television viewing.ConclusionsThe link between television viewing and poor diet was strongest for children who watched the most commercial television, and those who were actually exposed to advertisements embedded within programs. This association between advertisement exposure and poor diet emphasizes the need for public policy intervention to reduce children's food advertising exposures.
Taxonomic revision of oil‐producing green algae, Chlorococcum oleofaciens (Volvocales, Chlorophyceae), and its relatives
Authors: Kawasaki Yuriko , Nakada Takashi , Tomita Masaru 
Published: August 2015

Historically, species in Volvocales were classified based primarily on morphology. Although the taxonomy of Chlamydomonas has been re‐examined using a polyphasic approach including molecular phylogeny, that of Chlorococcum (Cc.), the largest coccoid genus in Volvocales, has yet to be reexamined. Six species thought to be synonymous with the oil‐producing alga Cc. oleofaciens were previously not confirmed by molecular phylogeny. In this study, seven authentic strains of Cc. oleofaciens and its putative synonyms, along with 11 relatives, were examined based on the phylogeny of the 18S ribosomal RNA (rRNA) gene, comparisons of secondary structures of internal transcribed spacer 1 (ITS1) and ITS2 rDNA, and morphological observations by light microscopy. Seven 18S rRNA types were recognized among these strains and three were distantly related to Cc. oleofaciens. Comparisons of ITS rDNA structures suggested possible separation of the remaining four types into different species. Shapes of vegetative cells, thickness of the cell walls in old cultures, the size of cells in old cultures, and stigma morphology of zoospores also supported the 18S rRNA grouping. Based on these results, the 18 strains examined were reclassified into seven species. Among the putative synonyms, synonymy of Cc. oleofaciens, Cc. croceum, and Cc. granulosum was confirmed, and Cc. microstigmatum, Cc. rugosum, Cc. aquaticum, and Cc. nivale were distinguished from Cc. oleofaciens. Furthermore, another related strain is described as a new species, Macrochloris rubrioleum sp. nov.
PfeT, a P1B4‐type ATPase, effluxes ferrous iron and protects Bacillus subtilis against iron intoxication
Authors: Guan Guohua , Pinochet‐Barros Azul , Gaballa Ahmed , Patel Sarju J. , Argüello José M. , Helmann John D. 
Published: August 2015

SummaryIron is an essential element for nearly all cells and limited iron availability often restricts growth. However, excess iron can also be deleterious, particularly when cells expressing high affinity iron uptake systems transition to iron rich environments. Bacillus subtilis expresses numerous iron importers, but iron efflux has not been reported. Here, we describe the B. subtilis PfeT protein (formerly YkvW/ZosA) as a P1B4‐type ATPase in the PerR regulon that serves as an Fe(II) efflux pump and protects cells against iron intoxication. Iron and manganese homeostasis in B. subtilis are closely intertwined: a pfeT mutant is iron sensitive, and this sensitivity can be suppressed by low levels of Mn(II). Conversely, a pfeT mutant is more resistant to Mn(II) overload. In vitro, the PfeT ATPase is activated by both Fe(II) and Co(II), although only Fe(II) efflux is physiologically relevant in wild‐type cells, and null mutants accumulate elevated levels of intracellular iron. Genetic studies indicate that PfeT together with the ferric uptake repressor (Fur) cooperate to prevent iron intoxication, with iron sequestration by the MrgA mini‐ferritin playing a secondary role. Protection against iron toxicity may also be a key role for related P1B4‐type ATPases previously implicated in bacterial pathogenesis.
Serum club cell protein 16 is associated with asymptomatic airway responsiveness in adults: Findings from the French epidemiological study on the genetics and environment of asthma
Authors: Rava Marta , Le Moual Nicole , Dumont Xavier , Guerra Stefano , Siroux Valerie , Jacquemin Benedicte , Kauffmann Francine , Bernard Alfred , Nadif Rachel 
Published: August 2015

AbstractBackground and objectiveClub cell secretory protein (CC‐16) is a sensitive biomarker of airways epithelium integrity. It has gained interest as a biological marker in chronic lung diseases because of its presumed relationship to inflammation. Little is known about the association between CC‐16 serum level and asthma, lung function and airway responsiveness (AR).MethodsSerum CC‐16 level was determined by latex immunoassay in 1298 participants from the French Epidemiological case‐control and family‐based study on Genetics and Environment of Asthma (EGEA) (mean age 43 years; 49% men, 38% with asthma). Pre‐bronchodilator lung function (forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC) and degree of AR, expressed as a function of the dose–response slope to methacholine test were measured. Standardized residuals CC‐16 z‐scores were obtained by regressing CC‐16 level on the glomerular filtration rate. CC‐16 z‐scores were correlated with asthma, lung function and AR in participants with and without asthma.ResultsCC‐16 geometric mean level was 12.4 μg/L (range: 2.2–70.6 μg/L). In participants without asthma, lower CC‐16 z‐scores was associated with impaired FEV1/FVC% (β = 0.50 (95% CI: 0.06, 0.95) and with higher degree of AR (β = 0.24 (95% CI: 0.09, 0.39)). CC‐16 was not associated with impaired lung function or AR in participants with asthma.ConclusionsLower CC‐16 serum level was associated with impaired lung function and AR, suggesting that serum CC‐16 level may reflect early damages to the lung epithelium in adults without asthma.
Simulating cardiac ultrasound image based on MR diffusion tensor imaging
Authors: Qin Xulei , Wang Silun , Shen Ming , Lu Guolan , Zhang Xiaodong , Wagner Mary B. , Fei Baowei 
Published: August 2015

Purpose:Cardiac ultrasound simulation can have important applications in the design of ultrasound systems, understanding the interaction effect between ultrasound and tissue and setting the ground truth for validating quantification methods. Current ultrasound simulation methods fail to simulate the myocardial intensity anisotropies. New simulation methods are needed in order to simulate realistic ultrasound images of the heart.Methods:The proposed cardiac ultrasound image simulation method is based on diffusion tensor imaging (DTI) data of the heart. The method utilizes both the cardiac geometry and the fiber orientation information to simulate the anisotropic intensities in B‐mode ultrasound images. Before the simulation procedure, the geometry and fiber orientations of the heart are obtained from high‐resolution structural MRI and DTI data, respectively. The simulation includes two important steps. First, the backscatter coefficients of the point scatterers inside the myocardium are processed according to the fiber orientations using an anisotropic model. Second, the cardiac ultrasound images are simulated with anisotropic myocardial intensities. The proposed method was also compared with two other nonanisotropic intensity methods using 50 B‐mode ultrasound image volumes of five different rat hearts. The simulated images were also compared with the ultrasound images of a diseased rat heart in vivo. A new segmental evaluation method is proposed to validate the simulation results. The average relative errors (AREs) of five parameters, i.e., mean intensity, Rayleigh distribution parameter σ, and first, second, and third quartiles, were utilized as the evaluation metrics. The simulated images were quantitatively compared with real ultrasound images in both ex vivo and in vivo experiments.Results:The proposed ultrasound image simulation method can realistically simulate cardiac ultrasound images of the heart using high‐resolution MR‐DTI data. The AREs of their proposed method are 19% for the mean intensity, 17.7% for the scale parameter of Rayleigh distribution, 36.8% for the first quartile of the image intensities, 25.2% for the second quartile, and 19.9% for the third quartile. In contrast, the errors of the other two methods are generally five times more than those of their proposed method.Conclusions:The proposed simulation method uses MR‐DTI data and realistically generates cardiac ultrasound images with anisotropic intensities inside the myocardium. The ultrasound simulation method could provide a tool for many potential research and clinical applications in cardiac ultrasound imaging.
Carbapenems and Rifampin Exhibit Synergy against Mycobacterium tuberculosis and Mycobacterium abscessus
Authors: Kaushik Amit , Makkar Nayani , Pandey Pooja , Parrish Nicole , Singh Urvashi , Lamichhane Gyanu 
Published: August 2015

ABSTRACT

An effective regimen for treatment of tuberculosis (TB) is comprised of multiple drugs that inhibit a range of essential cellular activities in
Mycobacterium tuberculosis
. The effectiveness of a regimen is further enhanced if constituent drugs act with synergy. Here, we report that faropenem (a penem) or biapenem, doripenem, or meropenem (carbapenems), which belong to the β-lactam class of antibiotics, and rifampin, one of the drugs that forms the backbone of TB treatment, act with synergy when combined. One of the reasons (carba)penems are seldom used for treatment of TB is the high dosage levels required, often at the therapeutic limits. The synergistic combination of rifampin and these (carba)penems indicates that (carba)penems can be administered at dosages that are therapeutically relevant. The combination of faropenem and rifampin also limits the frequency of resistant mutants, as we were unable to obtain spontaneous mutants in the presence of these two drugs. The combinations of rifampin and (carba)penems were effective not only against drug-sensitive
Mycobacterium tuberculosis
but also against drug-resistant clinical isolates that are otherwise resistant to rifampin. A combination of doripenem or biapenem and rifampin also exhibited synergistic activity against
Mycobacterium abscessus
. Although the MICs of these three drugs alone against
M. abscessus
are too high to be of clinical relevance, their concentrations in combinations are therapeutically relevant; therefore, they warrant further evaluation for clinical utility to treat
Mycobacterium abscessus
infection, especially in cystic fibrosis patients.
Dps and DpsL Mediate SurvivalIn VitroandIn Vivoduring the Prolonged Oxidative Stress Response in Bacteroides fragilis
Authors: Betteken Michael I. , Rocha Edson R. , Smith C. Jeffrey 
Published: August 2015

ABSTRACTBacteroides fragilisis a Gram-negative anaerobe and member of the human intestinal tract microbiome, where it plays many beneficial roles. However, translocation of the organism to the peritoneal cavity can lead to peritonitis, intra-abdominal abscess formation, bacteremia, and sepsis. During translocation,B. fragilisis exposed to increased oxidative stress from the oxygenated tissues of the peritoneal cavity and the immune response. In order to survive,B. fragilismounts a robust oxidative stress response consisting of an acute and a prolonged oxidative stress (POST) response. This report demonstrates that the ability to induce high levels of resistance totert-butyl hydroperoxide (tBOOH) after extended exposure to air can be linked to the POST response. Disk diffusion assays comparing the wild type to a Δdpsmutant and a ΔdpsΔbfrmutant showed greater sensitivity of the mutants to tBOOH after exposure to air, suggesting that Dps and DpsL play a role in the resistance phenotype. Complementation studies withdpsorbfr(encoding DpsL) restored tBOOH resistance, suggesting a role for both of these ferritin-family proteins in the response. Additionally, cultures treated with the iron chelator dipyridyl were not killed by tBOOH, indicating Dps and DpsL function by sequestering iron to prevent cellular damage. Anin vivoanimal model showed that the ΔdpsΔbfrmutant was attenuated, indicating that management of iron is important for survival within the abscess. Together, these data demonstrate a role for Dps and DpsL in the POST response which mediates survivalin vitroandin vivo.IMPORTANCEB. fragilisis the anaerobe most frequently isolated from extraintestinal opportunistic infections, but there is a paucity of information about the factors that allow this organism to survive outside its normal intestinal environment. This report demonstrates that the iron storage proteins Dps and DpsL protect against oxidative stress and that they contribute to survival bothin vitroandin vivo. Additionally, this work demonstrates an important role for the POST response inB. fragilissurvival and provides insight into the complex regulation of this response.
Inferring the Origin of Metastases from Cancer Phylogenies
Authors: Hong Woo Suk , Shpak Max , Townsend Jeffrey P. 
Published: August 2015

Abstract
Determining the evolutionary history of metastases is a key problem in cancer biology. Several recent studies have presented inferences regarding the origin of metastases based on phylogenies of cancer lineages. Many of these studies have concluded that the observed monophyly of metastatic subclones favored metastasis-to-metastasis spread (“a metastatic cascade” rather than parallel metastases from the primary tumor). In this article, we argue that identifying a monophyletic clade of metastatic subclones does not provide sufficient evidence to unequivocally establish a history of metastatic cascades. In the absence of a complete phylogeny of the subclones within the primary tumor, a scenario of parallel metastatic events from the primary tumor is an equally plausible interpretation. Future phylogenetic studies on the origin of metastases should obtain a complete phylogeny of subclones within the primary tumor. This complete phylogeny may be obtainable by ultra-deep sequencing and phasing of large sections or by targeted sequencing of many small, spatially heterogeneous sections, followed by phylogenetic reconstruction using well-established molecular evolutionary models. In addition to resolving the evolutionary history of metastases, a complete phylogeny of subclones within the primary tumor facilitates the identification of driver mutations by application of phylogeny-based tests of natural selection. Cancer Res; 75(19); 4021–5. ©2015 AACR.
How Well Do the CMIP5 Models Simulate the Antarctic Atmospheric Energy Budget?
Authors: Previdi Michael , Smith Karen L. , Polvani Lorenzo M. 
Published: August 2015

Abstract
The authors evaluate 23 coupled atmosphere–ocean general circulation models from phase 5 of CMIP (CMIP5) in terms of their ability to simulate the observed climatological mean energy budget of the Antarctic atmosphere. While the models are shown to capture the gross features of the energy budget well [e.g., the observed two-way balance between the top-of-atmosphere (TOA) net radiation and horizontal convergence of atmospheric energy transport], the simulated TOA absorbed shortwave (SW) radiation is too large during austral summer. In the multimodel mean, this excessive absorption reaches approximately 10 W m−2, with even larger biases (up to 25–30 W m−2) in individual models. Previous studies have identified similar climate model biases in the TOA net SW radiation at Southern Hemisphere midlatitudes and have attributed these biases to errors in the simulated cloud cover. Over the Antarctic, though, model cloud errors are of secondary importance, and biases in the simulated TOA net SW flux are instead driven mainly by biases in the clear-sky SW reflection. The latter are likely related in part to the models’ underestimation of the observed annual minimum in Antarctic sea ice extent, thus underscoring the importance of sea ice in the Antarctic energy budget. Finally, substantial differences in the climatological surface energy fluxes between existing observational datasets preclude any meaningful assessment of model skill in simulating these fluxes.
Continuous Loop Double Endobutton Reconstruction for Acromioclavicular Joint Dislocation
Authors: Struhl Steven , Wolfson Theodore S. 
Published: August 2015

Background: Current anatomic methods for reconstruction of the dislocated acromioclavicular (AC) joint show improved clinical results but continue to be associated with significant rates of fixation loss and complications, limiting more widespread use. Purpose: To determine the long-term clinical and radiologic outcomes of a novel surgical technique using a closed-loop double Endobutton device to reconstruct both acute and chronic dislocations. Study Design: Case series; Level of evidence, 4. Methods: Between 2003 and 2012, a total of 35 patients (31 men, 4 women) at a mean age of 42 years (range, 25-70 years) were surgically treated for a Rockwood type III or greater AC joint dislocation with the described technique (26 chronic, 9 acute). Imbrication of the AC joint capsule and deltotrapezial fascia was performed in all patients. Biological bridging across the coracoclavicular (CC) interval was performed in all patients by use of coracoacromial (CA) ligament transfer in 28 patients and primary repair of the CC ligament in 7 patients. Complete follow-up information was obtained for 31 of 35 patients. Results: At a mean follow-up of 5.2 years (range, 27-144 months), the construct remained stable in all but 1 patient. The mean CC interval difference was 1.1 mm (range, –2.5 to 4.0 mm) and was <2 mm in 87% of patients. The mean Constant score was 98; the mean University of California, Los Angeles Shoulder Rating Scale score was 34; and the mean American Shoulder and Elbow Surgeons Shoulder Score was 98. Follow-up MRI evaluation in 10 patients consistently demonstrated a wide band of dense scar tissue between the coracoid and clavicle. No infections, fractures, or perioperative complications occurred. Conclusion: Excellent results were obtained and maintained over long-term follow-up. The continuous loop device eliminated the possibility of knot slippage or breakage. MRI confirmed a robust healing response. The described technique resulted in outcomes that were significantly superior to historical reports of nonsurgical outcomes, and the technique can be recommended both for acute and chronic dislocations.
Streptococcal Diversity of Human Milk and Comparison of Different Methods for the Taxonomic Identification of Streptococci
Authors: Martín Virginia , Mediano Pilar , del Campo Rosa , Rodríguez Juan M. , Marín María 
Published: August 2015

Background: The genus Streptococcus is 1 of the dominant bacterial groups in human milk, but the taxonomic identification of some species remains difficult. Objective: The objective of this study was to investigate the discriminatory ability of different methods to identify streptococcal species in order to perform an assessment of the streptococcal diversity of human milk microbiota as accurately as possible. Methods: The identification of 105 streptococcal strains from human milk was performed by 16S rRNA, tuf, and sodA gene sequencing, phylogenetic analysis, and Matrix Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) mass spectrometry. Results: Streptococcus salivarius, Streptococcus mitis, and Streptococcus parasanguinis were the streptococcal dominant species in the human milk microbiota. Sequencing of housekeeping genes allowed the classification of 96.2% (16S rRNA), 84.8% ( sodA), and 88.6% ( tuf) of the isolates. Phylogenetic analysis showed 3 main streptococcal clusters corresponding with the mitis (73 isolates), salivarius (29), mutans (1)-pyogenic (2) groups, but many of the mitis group isolates (36) could not be assigned to any species. The application of the MALDI-TOF Bruker Biotyper system resulted in the identification of 56 isolates (53.33%) at the species level, but it could not discriminate between S pneumoniae and S mitis isolates, in contrast to the Vitek-MS system. Conclusion: There was a good agreement among the different methods assessed in this study to identify those isolates of the salivarius, mutans, and pyogenic groups, whereas unambiguous discrimination could not be achieved concerning some species of the mitis group ( S mitis, S pneumoniae, S pseudopneumoniae, S oralis).