bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic diversity of the unicellular nitrogen‐fixing cyanobacteria UCYN‐A and its prymnesiophyte host
Authors: Thompson Anne , Carter Brandon J. , Turk‐Kubo Kendra , Malfatti Francesca , Azam Farooq , Zehr Jonathan P. 
Published: April 2014

SummarySymbiotic interactions between nitrogen‐fixing prokaryotes and photosynthetic eukaryotes are an integral part of biological nitrogen fixation at a global scale. One of these partnerships involves the cyanobacterium UCYN‐A, which has been found in partnership with an uncultivated unicellular prymnesiophyte alga in open‐ocean and coastal environments. Phylogenetic analysis of the UCYN‐A nitrogenase gene (nifH) showed that the UCYN‐A lineage is represented by three distinct clades, referred to herein as UCYN‐A1, UCYN‐A2 and UCYN‐A3, which appear to have overlapping and distinct geographic distributions. The relevance of UCYN‐A's genetic diversity to its symbiosis and ecology was explored through combining flow cytometric cell sorting and molecular techniques to determine the host identity, nifH expression patterns and host cell size of one newly discovered clade, UCYN‐A2, at a coastal site. UCYN‐A2 nifH expression peaked during daylight hours, which is consistent with expression patterns of the UCYN‐A1 clade in the open ocean. However, the cell size of the UCYN‐A2 host was significantly larger than UCYN‐A1 and host, suggesting adaptation to different environmental conditions. Like the UCYN‐A1 host, the UCYN‐A2 host was closely related to the genus Braarudosphaera; however, the UCYN‐A1 and UCYN‐A2 host rRNA sequences clustered into two distinct clades suggesting co‐evolution of symbiont and host.
Freeing Pseudomonas putida KT2440 of its proviral load strengthens endurance to environmental stresses
Authors: Martínez‐García Esteban , Jatsenko Tatjana , Kivisaar Maia , de Lorenzo Víctor 
Published: April 2014

Summary2.6% of the genome of the soil bacterium Pseudomonas putida KT2440 encodes phage‐related functions, but the burden of such opportunistic DNA on the host physiology is unknown. Each of the four apparently complete prophages borne by this strain was tested for stability, spontaneous excision and ability to cause lysis under various stressing conditions. While prophages P3 (PP2266–PP2297) and P4 (PP1532–1584) were discharged from the genome at a detectable rate, their induction failed otherwise to yield infective viruses. Isogenic P. putida KT2440 derivatives bearing single and multiple deletions of each of the prophages were then subjected to thorough phenotypic analyses, which generally associated the loss of proviral DNA with an increase of physiological vigour. The most conspicuous benefit acquired by prophage‐less cells was a remarkable improvement in tolerance to UV light and other insults to DNA. This was not accompanied, however, with an upgrade of recA‐mediated homologous recombination. The range of tolerance to DNA damage gained by the prophage‐free strain was equivalent to the UV resistance endowed by the TOL plasmid pWW0 to the wild‐type bacterium. While the P. putida's prophages are therefore genuinely parasitic, their detrimental effects can be offset by acquisition of compensatory traits through horizontal gene transfer.
A novel mode of lactate metabolism in strictly anaerobic bacteria
Authors: Weghoff Marie Charlotte , Bertsch Johannes , Müller Volker 
Published: April 2014

SummaryLactate is a common substrate for major groups of strictly anaerobic bacteria, but the biochemistry and bioenergetics of lactate oxidation is obscure. The high redox potential of the pyruvate/lactate pair of E0′ = −190 mV excludes direct NAD+ reduction (E0′ = −320 mV). To identify the hitherto unknown electron acceptor, we have purified the lactate dehydrogenase (LDH) from the strictly anaerobic, acetogenic bacterium Acetobacterium woodii. The LDH forms a stable complex with an electron‐transferring flavoprotein (Etf) that exhibited NAD+ reduction only when reduced ferredoxin (Fd2−) was present. Biochemical analyses revealed that the LDH/Etf complex of A. woodii uses flavin‐based electron confurcation to drive endergonic lactate oxidation with NAD+ as oxidant at the expense of simultaneous exergonic electron flow from reduced ferredoxin (E0′ ≈ –500 mV) to NAD+ according to: lactate + Fd2− + 2 NAD+ → pyruvate + Fd + 2 NADH. The reduced Fd2− is regenerated from NADH by a sequence of events that involves conversion of chemical (ATP) to electrochemical and finally redox energy (Fd2− from NADH) via reversed electron transport catalysed by the Rnf complex. Inspection of genomes revealed that this metabolic scenario for lactate oxidation may also apply to many other anaerobes.
Loving Diversity/Controlling Diversity: Exploring the Ambivalent Mobilization of Upper‐Middle‐Class Gentrifiers, South End, Boston
Authors: Tissot Sylvie 
Published: April 2014

AbstractThis article centers on a group of upper‐middle‐class gentrifiers living in a neighborhood in theSouthEnd ofBoston, and their complex attitude towards diversity. I use data from my fieldwork in theSouthEnd, based on ethnographic observation and 77 interviews with residents active in local organizations, such as neighborhood associations. These residents explicitly stress their endorsement of diversity, in terms of class, race, but also sexual orientation, and their commitment to maintaining it. I examine the meaning they give to this principle, the actions they take in its name and the kind of relations they establish with those ‘others’ who embody such diversity. I argue that the gentrifiers' love of diversity, which cannot be reduced to sheer hypocrisy, is intrinsically linked to their capacity to control it, thus shedding light on the changing definition of social distinction in upper‐middle‐class culture.
Neither ‘Deepest, Darkest Peckham’ nor ‘Run‐of‐the‐Mill’ East Dulwich: The Middle Classes and their ‘Others’ in an Inner‐London Neighbourhood
Authors: Jackson Emma , Benson Michaela 
Published: April 2014

AbstractThis article examines how middle‐class residents of an inner‐London neighbourhood draw up socio‐spatial and symbolic boundaries between themselves and their ‘others’. Through a discussion of accounts of two very different boundaries — the boundary of a multi‐ethnic high street and a less clearly defined boundary of a neighbouring middle‐class area — we argue that the production of middle‐class identities is bound up with processes of disaffiliation not only from proximate stigmatized areas, but also from more upmarket areas and the people who populate them. Against this background it becomes clear that middle‐class claims to belonging are made through (1) the asymmetric processes by which the middle classes create and maintain spatial boundaries between themselves and racialized/classed others, and (2) the subtle processes of distinction that go on within the middle classes. Nevertheless, relationships to place remain ambivalent, and as neighbourhoods undergo change, physical boundaries separating one area from another refuse to stay put. We argue that the re‐inscription of such boundaries in the accounts of middle‐class respondents are attempts to create a stable identity on the shifting ground of the contemporary global city.
Variation of urinary protein to creatinine ratio during the day in women with suspected pre‐eclampsia
Authors: Verdonk K , Niemeijer IC , Hop WCJ , de Rijke YB , Steegers EAP , van den Meiracker AH , Visser W 
Published: April 2014

ObjectiveTo investigate the stability throughout the day of the protein to creatinine ratio (PCR) in spot urine, to demonstrate whether the PCR is a valid alternative for 24‐hour protein investigation in pregnant women.DesignProspective study.SettingTertiary referral university centre.PopulationWomen suspected of having pre‐eclampsia, admitted to the Erasmus Medical Centre.MethodsTwenty‐four‐hour urine collections and simultaneously three single voided 5‐ml aliquots were obtained at 8 a.m., 12 a.m. (noon) and 5 p.m. A PCR was measured in each specimen and compared with the 24‐hour protein excretion.Main outcome measuresThe 24‐hour proteinuria and PCR measured in spontaneous voids.ResultsThe PCRs correlated strongly with each other and with the 24‐hour protein excretion but did show variation throughout the day (mean coefficient of variation 36%; 95% confidence interval 31–40%). The coefficient of variation was unrelated to the degree of 24‐hour proteinuria. Receiver operating characteristics curves to discriminate between values below and greater than or equal to the threshold of 0.3 g protein per 24‐hour had an area under the curve of respectively 0.94 (8 a.m.), 0.96 (noon) and 0.97 (5 p.m.). Sensitivities at 8 a.m., noon and 5 p.m. were respectively 89%, 96% and 94%; specificities were 75%, 78% and 78% with the proposed PCR cut‐off of 30 mg/mmol (0.26 g/g) (National Institute for Health and Care Excellence guidelines).There is no evidence of a difference between the three measurement times regarding the sensitivities and specificities.ConclusionThe PCR determined in spot urine varies throughout the day but is a valid alternative for 24‐hour urine collections in pregnant women. It is especially useful to rapidly identify clinically relevant proteinuria.
Fetal Age Determination Through Biparietal Diameter: A Simple Method of Cranial Reconstruction Using Multipurpose Silicone
Authors: Aromatario Mariarosaria , Fiore Paola A. , Cappelletti Simone , Bottoni Edoardo , Ciallella Costantino 
Published: April 2014

AbstractIn forensic medicine, gestational age of fetal remains is a crucial information in several contests, but the classic methods are inadequate when early gestational age needs to be assessed. In the author's experience, the measurement of the biparietal diameter provides more accurate information for this purpose. The status of the fetal head is therefore critical. This work describes an easy technique that allows to reconstruct the cranial volume of the fetus using multipurpose silicone given both the flexibility of the fetal head structure and the inorganic nature of the silicone itself. In conclusion, the determination of the biparietal diameter achieved through the above‐described technique permitted a more accurate estimation of the dating of pregnancy in judicial cases where the fetal remains were incomplete and disrupted.
Hyperoxia affects the regional pulmonary ventilation/perfusion ratio: an electrical impedance tomography study
Authors: LI Y. , TESSELAAR E. , BORGES J. B. , BÖHM S. H. , SJÖBERG F. , JANEROT‐SJÖBERG B. 
Published: April 2014

BackgroundThe way in which hyperoxia affects pulmonary ventilation and perfusion is not fully understood. We investigated how an increase in oxygen partial pressure in healthy young volunteers affects pulmonary ventilation and perfusion measured by thoracic electrical impedance tomography (EIT).MethodsTwelve semi‐supine healthy male volunteers aged 21–36 years were studied while breathing room air and air–oxygen mixtures (FiO2) that resulted in predetermined transcutaneous oxygen partial pressures (tcPO2) of 20, 40 and 60 kPa. The magnitude of ventilation (ΔZv) and perfusion (ΔZQ)‐related changes in cyclic impedance variations, were determined using an EIT prototype equipped with 32 electrodes around the thorax. Regional changes in ventral and dorsal right lung ventilation (V) and perfusion (Q) were estimated, and V/Q ratios calculated.ResultsThere were no significant changes in ΔZv with increasing tcPO2 levels. ΔZQ in the dorsal lung increased with increasing tcPO2 (P = 0.01), whereas no such change was seen in the ventral lung. There was a simultaneous decrease in V/Q ratio in the dorsal region during hyperoxia (P = 0.04). Two subjects did not reach a tcPO2 of 60 kPa despite breathing 100% oxygen.ConclusionThese results indicate that breathing increased concentrations of oxygen induces pulmonary vasodilatation in the dorsal lung even at small increases in FiO2. Ventilation remains unchanged. Local mismatch of ventilation and perfusion occurs in young healthy men, and the change in ventilation/perfusion ratio can be determined non‐invasively by EIT.
A low‐cost, yet simple and highly repeatable system for acoustically surveying cryptic species
Authors: Lambert Kathryn T. A. , McDonald Paul G. 
Published: April 2014

AbstractAccurate determination of the population density of key focal species is necessary for monitoring the success of management programs and ecosystem health across a wide range of contexts. Unfortunately, many key taxa are visually cryptic and thus difficult to count using traditional observation‐based techniques. Bell miners (Manorina melanophrys), are just such a species. They are widespread throughout south‐eastern Australia, yet they are critical to monitor given their association and potential causal link to spreading vegetative dieback in this region. A new passive acoustic monitoring technique was trialled by testing its ability to determine population densities of bell miner colonies via counting the distinctive ‘tink’ vocalization of this species. This call was given at a constant rate per individual, and at a common amplitude across 10 colonies throughout the entire geographic range of the species. Theoretical sound transmission and playback trials through typical habitat determined that any bird within a 50‐m radius of the recorders used would be louder than 70 dB, enabling this threshold amplitude to be used to determine the number of birds in a 50 m radius of the recorder. Field trials of the acoustic protocol versus human observers using traditional visual surveys found that passive acoustic monitoring was able to detect more individuals, using a less expensive protocol that drastically reduced the need for observer training or expertise. Sound therefore offers a reliable method for determining the density of this vocal, but visually cryptic species. We present methods for calibrating recording devices and detecting calls louder than species‐specific thresholds using readily available freeware, enabling our methods to be easily adapted to census a variety of acoustically distinctive species, offering a more effective, yet lower cost and in our case more efficient census technique for surveying difficult species.
It is time to introduce ST analysis for fetal monitoring in the labor ward?
Authors: Visser Gerard H.A. , Kessler Jørg 
Published: April 2014

AbstractFive randomized controlled trials have been published on intrapartum fetal heart rate monitoring with ST analysis of the fetal electrocardiogram, but the debate on its usefulness has not yet been ended. We consider ST analysis a useful and cost‐effective addition to conventional fetal heart rate monitoring. We will provide support for this opinion by discussing the pathophysiology of ST changes in relation to fetal asphyxia, the results of the randomized controlled trials and numerous meta‐analyses of these randomized controlled trials and trends in fetal outcome in hospitals in different countries following the introduction of the ST technology in the labor ward.
Acute response and subcellular movement of HSP27, αB‐crystallin and HSP70 in human skeletal muscle after blood‐flow‐restricted low‐load resistance exercise
Authors: Cumming K. T. , Paulsen G. , Wernbom M. , Ugelstad I. , Raastad T. 
Published: April 2014

AbstractAimHeat‐shock proteins (HSP) are important chaperones for stressed and damaged proteins. Low‐load blood‐flow‐restricted resistance exercise (BFRE) is generally believed not to induce significant muscle damage, but is hitherto unverified with intracellular markers. Consequently, the aim of this study was to investigate the HSP response after BFRE in human skeletal muscle.MethodsNine healthy volunteers performed five sets to failure of unilateral knee extension at 30% of 1RM with partial blood‐flow restriction. The contralateral leg performed the same work with free blood flow. Muscle biopsies were collected before exercise, 1, 24 and 48 h after exercise and analysed for HSP27, αB‐crystallin, HSP70, desmin, glycogen content and myosin heavy chain by immunohistochemistry, ELISA and western blotting.ResultsOne hour after exercise, HSP27 and αB‐crystallin levels were reduced in the cytosolic and increased in the cytoskeletal fraction in the BFRE leg. HSP70 showed a delayed response and was increased over 48 h in the BFRE leg. Immunohistochemical analyses showed higher staining intensity of HSP70 in type 1 fibres in the BFRE leg at 24 and 48 h post‐exercise. PAS staining showed decreased glycogen levels after BFRE, and interestingly, glycogen was still depleted 48 h after exercise in the same fibres displaying high HSP70 staining (type 1 fibres).ConclusionTranslocation of HSP27 and αB‐crystallin from cytosol to cytoskeletal structures indicates that cytoskeletal proteins are stressed during BFRE. However, overt signs of myofibrillar disruptions were not observed. Interestingly, the stress response was more pronounced in type 1 than in type 2 fibres and coincided with low glycogen levels.
Integrative analysis of prognosis data on multiple cancer subtypes
Authors: Liu Jin , Huang Jian , Zhang Yawei , Lan Qing , Rothman Nathaniel , Zheng Tongzhang , Ma Shuangge 
Published: April 2014

SummaryIn cancer research, profiling studies have been extensively conducted, searching for genes/SNPs associated with prognosis. Cancer is diverse. Examining the similarity and difference in the genetic basis of multiple subtypes of the same cancer can lead to a better understanding of their connections and distinctions. Classic meta‐analysis methods analyze each subtype separately and then compare analysis results across subtypes. Integrative analysis methods, in contrast, analyze the raw data on multiple subtypes simultaneously and can outperform meta‐analysis methods. In this study, prognosis data on multiple subtypes of the same cancer are analyzed. An AFT (accelerated failure time) model is adopted to describe survival. The genetic basis of multiple subtypes is described using the heterogeneity model, which allows a gene/SNP to be associated with prognosis of some subtypes but not others. A compound penalization method is developed to identify genes that contain important SNPs associated with prognosis. The proposed method has an intuitive formulation and is realized using an iterative algorithm. Asymptotic properties are rigorously established. Simulation shows that the proposed method has satisfactory performance and outperforms a penalization‐based meta‐analysis method and a regularized thresholding method. An NHL (non‐Hodgkin lymphoma) prognosis study with SNP measurements is analyzed. Genes associated with the three major subtypes, namely DLBCL, FL, and CLL/SLL, are identified. The proposed method identifies genes that are different from alternatives and have important implications and satisfactory prediction performance.
Outcomes in patients with relapsed or refractory multiple myeloma in a phase I study of everolimus in combination with lenalidomide
Authors: Yee Andrew J. , Hari Parameswaran , Marcheselli Raffaella , Mahindra Anuj K. , Cirstea Diana D. , Scullen Tyler A. , Burke Jill N. , Rodig Scott J. , Hideshima Teru , Laubach Jacob P. , Ghobrial Irene M. , Schlossman Robert L. , Munshi Nikhil C. , Anderson Kenneth C. , Weller Edie A. , Richardson Paul G. , Raje Noopur S. 
Published: April 2014

SummaryEverolimus, an oral mammalian target of rapamycin (mTOR) inhibitor, has been studied in multiple myeloma (MM) but lacks significant single agent activity. Based on preclinical studies showing synergistic activity of mTOR inhibitors with lenalidomide, we studied the combination of lenalidomide and everolimus in relapsed or refractory MM in a phase I clinical trial. We assessed patient samples using gene expression, Western blotting and immunohistochemistry to probe the mTOR pathway. Twenty‐six patients were evaluable for toxicity. Dose‐limiting toxicities included grade 4 neutropenia and thrombocytopenia. The maximum tolerated dose was lenalidomide 15 mg and everolimus 5 mg for 21 d with a 7 d rest period. Grade 3/4 adverse events included thrombocytopenia (35%) and neutropenia (42%). The overall response rate was 65% (1 complete response + 4 partial response + 10 minimal response). The median progression‐free survival was 5·5 months and median overall survival was 29·5 months. Biomarker data demonstrated downregulation of phosphorylated p70S6K. Gene expression profiling suggested activation of mTOR in responders versus non‐responders. The combination of lenalidomide and everolimus was well tolerated with predictable toxicities and showed responses in a heavily pretreated population. When confirmed with larger patient numbers, this analysis may guide patient selection for future clinical trials of mTOR inhibition in MM.
Frontline bortezomib and rituximab for the treatment of newly diagnosed high tumour burden indolent non‐Hodgkin lymphoma: a multicentre phase II study
Authors: Evens Andrew M. , Smith Mitchell R. , Lossos Izidore S. , Helenowski Irene , Millenson Michael , Winter Jane N. , Rosen Steve T. , Gordon Leo I. 
Published: April 2014

SummaryThere is a lack of published data examining non‐cytotoxic options for the frontline treatment of patients with high‐tumour burden (HTB) indolent non‐Hodgkin lymphoma (iNHL). We completed a multicentre phase II study for patients with untreated HTB iNHL (NCT00369707) consisting of three induction cycles of weekly bortezomib and rituximab followed by an abbreviated consolidation. Forty‐two patients were treated and all were evaluable; the most common histology was follicular lymphoma (FL) (n = 33, 79%). Patient characteristics included median age 62 years (40–86); 38% bulky disease; 19% malignant effusions; 91% advanced‐stage disease; and median FL International Prognostic Index (FLIPI) score was 3. Therapy was well tolerated with few grade 3/4 toxicities including minimal neurotoxicity. On intent‐to‐treat, the overall response rate (ORR) at end of therapy was 70% with a complete remission (CR) rate of 40% (FL: ORR 76%, CR 44%). With 50‐month median follow‐up, 4‐year progression‐free survival (PFS) was 44% with 4‐year overall survival (OS) of 87% (FL: 44% and 97%, respectively). Four‐year PFS for FLIPI 0–2 vs. 3–5 was 60% vs. 26% respectively (P = 0·02), with corresponding OS rates of 92% and 81% respectively (P = 0·16). Collectively, bortezomib/rituximab is a non‐cytotoxic therapeutic regimen that was well tolerated and resulted in long‐term survival rates approximating prior rituximab/cytotoxic chemotherapy series for untreated HTB FL.