bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environment and evolutionary history determine the global biogeography of phytoplankton temperature traits
Authors: Thomas Mridul K. , Kremer Colin T. , Litchman Elena 
Published: October 2015

AbstractAimEcological and evolutionary forces shape the functional traits of species within and across environments, generating biogeographical patterns in traits. We aimed to: (1) determine the extent to which temperature traits of phytoplankton are adapted to their local environment, and (2) detect and explain differences in patterns of adaptation between functional groups (reflecting evolutionary history) and across ecosystems (freshwater versus marine).LocationWe used laboratory‐measured data on phytoplankton strains isolated from marine (76° N to 75° S) and freshwater ecosystems (80° N to 78° S).MethodsWe studied variation in five temperature traits: optimum temperature for growth (Topt), maximum and minimum persistence temperature (Tmax, Tmin), temperature niche width and maximum growth rate, estimated in 439 strains from over 200 species. We tested whether these traits change along environmental temperature gradients (across latitude and ecosystems) and also investigated differences in trait–environment relationships related to evolutionary history (functional group identity). We used mixed models to evaluate our hypotheses while accounting for intraspecific variation.ResultsWe identified three patterns caused by adaptation and community assembly: (1) Topt, Tmax and Tmin decline sharply with latitude; (2) Topt, Tmax and Tmin are similar across all functional groups at the equator, where temperature variation is low; and (3) Topt and Tmax are higher in freshwater locations than marine locations at similar latitudes. Additionally, evolutionary history explained substantial variation in all traits: functional groups differ strongly in their niche widths and maximum growth rates, as well as their Topt, Tmax, and Tmin relationships with latitude.Main conclusionsGlobally, phytoplankton temperature traits are well adapted to local conditions, changing across ecosystems and latitude. Functional groups differ strongly in their patterns of adaptation: traits are similar in hot tropical environments, but diverge at temperate latitudes. These differences reflect two possible evolutionary constraints: cyanobacterial inability to adapt to low temperatures and differences in nutrient requirements between groups.
Perceived poor health is positively associated with physical limitations and chronic diseases in Brazilian nonagenarians and centenarians
Authors: Sebastião Emerson 
Published: October 2015

AimThe oldest old are in most need of help. The present study examined the association between perceived health, physical functioning and diagnosed chronic disease in a sample of Brazilian nonagenarians and centenarians.MethodsThe 2008 Brazilian Household Survey dataset was used. The 2008 Brazilian Household Survey interviewed 292 553 individuals aged 14 years and older from the 26 Brazilian states plus the Federal District, selected in a multistage procedure. Our analytical sample focused on those aged 90 years and older. This yielded a final sample of 819 individuals. Logistic regression was used to examine the association between self‐reported health and health conditions.ResultsNearly 7% (n = 56) of the total sample were centenarians. High rates of physical limitations and chronic disease were reported by the participants. Participants reporting their health as poor were, on average, twofold more likely to report limitations in activities of daily living, and 1.7‐fold more likely to report a chronic disease.ConclusionsPerceived poor health was positively associated with physical limitations and chronic disease in Brazilian oldest‐old. These findings highlight the need for feasible interventions aiming to improve health and quality of life in this population, especially because this is the fastest growing age group worldwide. Geriatr Gerontol Int 2016; 16: 1196–1203.
Groundwater Protection and Unconventional Gas Extraction: The Critical Need for Field‐Based Hydrogeological Research
Authors: Jackson R.E. , Gorody A.W. , Mayer B. , Roy J.W. , Ryan M.C. , Van Stempvoort D.R. 
Published: October 2015

AbstractUnconventional natural gas extraction from tight sandstones, shales, and some coal‐beds is typically accomplished by horizontal drilling and hydraulic fracturing that is necessary for economic development of these new hydrocarbon resources. Concerns have been raised regarding the potential for contamination of shallow groundwater by stray gases, formation waters, and fracturing chemicals associated with unconventional gas exploration. A lack of sound scientific hydrogeological field observations and a scarcity of published peer‐reviewed articles on the effects of both conventional and unconventional oil and gas activities on shallow groundwater make it difficult to address these issues. Here, we discuss several case studies related to both conventional and unconventional oil and gas activities illustrating how under some circumstances stray or fugitive gas from deep gas‐rich formations has migrated from the subsurface into shallow aquifers and how it has affected groundwater quality. Examples include impacts of uncemented well annuli in areas of historic drilling operations, effects related to poor cement bonding in both new and old hydrocarbon wells, and ineffective cementing practices. We also summarize studies describing how structural features influence the role of natural and induced fractures as contaminant fluid migration pathways. On the basis of these studies, we identify two areas where field‐focused research is urgently needed to fill current science gaps related to unconventional gas extraction: (1) baseline geochemical mapping (with time series sampling from a sufficient network of groundwater monitoring wells) and (2) field testing of potential mechanisms and pathways by which hydrocarbon gases, reservoir fluids, and fracturing chemicals might potentially invade and contaminate useable groundwater.
Polymerase chain reaction–miniexon: a promising diagnostic method for mucocutaneous leishmaniasis
Authors: Ovalle‐Bracho Clemencia , Díaz‐Toro Yira Rosalba , Muvdi‐Arenas Sandra 
Published: October 2015

AbstractBackgroundMucocutaneous leishmaniasis is a chronic disease caused mainly by Leishmania species that belong to Viannia subgenus. It affects upper respiratory airways and may lead to deformity, dysphagia, and even death in severe cases. Diagnosis is a challenge because clinical and histopathologic changes are easily confused with other diseases, and conventional methods for parasite identification and culture have a low sensitivity. Molecular methods have been used in the last two decades. In 2007, we published a validation study using internal transcript spacers and kinetoplast DNA as molecular targets with satisfactory results. In this research, we tested miniexon gene as the target.MethodsMucosal tissue samples from 60 Colombian patients with clinical signs of mucocutaneous leishmaniasis were included. A composite reference standard defined 30 cases and 30 controls. Two blind observers performed patient classification and test application independently. Miniexon gene amplification generated: 226–230 bp fragment for subgenus Viannia; 308 bp fragment for L. amazonensis; 340 bp fragment for L. mexicana; and 418 bp fragment for L. infantum‐chagasi.ResultsPolymerase chain reaction (PCR) sensitivity for fresh samples was 87.5% (95% confidence interval [CI] 72.2–100), specificity, 95% (95% CI 83.0–100), and positive likelihood ratio was 17.5 (95% CI 2.58–118.93), similar to results obtained with paraffin‐embedded samples. Agreement between observers was 96% (kappa = 0.912; 95% CI 0.815–1.000) for both subgenus Viannia and Leishmania.ConclusionsWe consider PCR–miniexon as a diagnostic method of first choice for mucocutaneous leishmaniasis due to its excellent diagnostic performance and its ability to discriminate between Leishmania and Viannia subgenera as well as between species belonging to Leishmania subgenus.
16th IHIW : Review of HLA typing by NGS
Authors: De Santis D. , Dinauer D. , Duke J. , Erlich H. A. , Holcomb C. L. , Lind C. , Mackiewicz K. , Monos D. , Moudgil A. , Norman P. , Parham P. , Sasson A. , Allcock R. J. N. 
Published: October 2015

SummaryHuman leucocyte antigen (HLA) genes play an important role in the success of organ transplantation and are associated with autoimmune and infectious diseases. Current DNA‐based genotyping methods, including Sanger sequence‐based typing (SSBT), have identified a high degree of polymorphism. This level of polymorphism makes high‐resolution HLA genotyping challenging, resulting in ambiguous typing results due to an inability to resolve phase and/or defining polymorphisms lying outside the region amplified. Next‐generation sequencing (NGS) may resolve the issue through the combination of clonal amplification, which provides phase information, and the ability to sequence larger regions of genes, including introns, without the additional effort or cost associated with current methods. The NGS HLA sequencing project of the 16IHIW aimed to discuss the different approaches to (i) template preparation including short‐ and long‐range PCR amplicons, exome capture and whole genome; (ii) sequencing platforms, including GS 454 FLX, Ion Torrent PGM, Illumina MiSeq/HiSeq and Pacific Biosciences SMRT; (iii) data analysis, specifically allele‐calling software. The pilot studies presented at the workshop demonstrated that although individual sequencers have very different performance characteristics, all produced sequence data suitable for the resolution of HLA genotyping ambiguities. The developments presented at this workshop clearly highlight the potential benefits of NGS in the HLA laboratory.
16th IHIW: Global distribution of extended HLA haplotypes
Authors: Askar M. , Daghstani J. , Thomas D. , Leahy N. , Dunn P. , Claas F. , Doran S. , Saji H. , Kanangat S. , Karoichane M. , Tambur A. , Monos D. , El‐Khalifa M. , Turner V. , Kamoun M. , Mustafa M. , Ramon D. , Gandhi M. , Vernaza A. , Gorodezky C. , Wagenknecht D. , Gautreaux M. , Hajeer A. , Kashi Z. , Fernandez‐Vina M. 
Published: October 2015

SummaryThis report describes the project to identify the global distribution of extended HLA haplotypes, a component of 16th International HLA and Immunogenetics Workshop (IHIW), and summarizes the initial analyses of data collected. The project aims to investigate extended HLA haplotypes, compare their distribution among different populations, assess their frequency in hematopoietic stem cell unrelated donor registries and initiate an international family studies database and DNA repository to be made publicly available. HLA haplotypes compiled in immunogenetics laboratories during the evaluation of transplant candidates and related potential donors were analysed. Haplotypes were determined using the pedigree analysis tool publicly available from the National Marrow Donor Program (NMDP) website. Nineteen laboratories from 10 countries (11 laboratories from North America, five from Asia, two from Latin America and one from Australia) contributed data on a total of 1719 families comprised of 7474 individuals. We identified 10 393 HLA haplotypes, of which 1682 haplotypes included high‐resolution typing at HLA‐A, B, C, DRB1 and DQB1 loci. We also present haplotypes containing MICA and other HLA loci and haplotypes containing rare alleles seen in these families. The project will be extended through the 17th IHIW, and investigators interested in joining the project may communicate with the first author.
A Catholic Missiological and Ecumenical Appreciation of Together towards Life
Authors: Nnyombi Richard 
Published: October 2015

AbstractThe new mission statement Together towards Life does not so much propose new teachings about mission as point out pertinent reminders and reconfirmations of some of our beliefs and convictions about God's mission (missio Dei) in and for the world. The author suggests that among the many challenges expressed in the statement, three merit special attention: (1) the proposal to shift the mission concept from “mission to the margins” to “mission from the margins”; (2) the necessity to underline the intrinsic link between humanity and creation; and (3) the temptation to consider “mission” as at the service of the interests and aggrandizement of individual churches instead of the contrary. He concludes that this statement is an invitation to walk “together towards life” for the benefit of both humanity and the whole of God's creation, and that the urgent challenge is to forge concrete means to make this dream a reality, even in the face of paying the “cost of discipleship.”
Comparison of gastro‐oesophageal junction carcinomas in Chinese versus American patients
Authors: Huang Qin , Fan Xiangshan , Agoston Agoston T , Feng Anning , Yu Huiping , Lauwers Gregory , Zhang Lihua , Odze Robert D 
Published: October 2015

Huang Q, Fan X, Agoston A T, Feng A, Yu H, Lauwers G, Zhang L & Odze R D  (2011) Histopathology59, 188–197Comparison of gastro‐oesophageal junction carcinomas in Chinese versus American patientsAims:  To compare the clinical and pathological features of gastro‐oesophageal junction (GEJ) carcinomas in Chinese and American patients.Methods and results:  Eighty consecutive patients with a GEJ carcinoma (43 from mainland China, and 37 from the USA) were evaluated for association with Barrett oesophagus (BO), chronic Helicobacter pylori gastritis, intestinal metaplasia, and outcome. GEJ carcinomas were defined as tumours that were located within 20 mm of, and crossed, the GEJ. Overall, GEJ carcinomas from Chinese patients revealed significantly more frequent location in the proximal stomach, higher pathological stage, larger size, younger patient age, and association with chronic H. pylori gastritis. In contrast, GEJ cancers from American patients showed a strong association with distal oesophageal location, BO, and associated intestinal metaplasia and dysplasia. Pathologically, GEJ carcinomas from American patients were predominantly adenocarcinomas, whereas Chinese patients showed a higher proportion of mucinous, adenosquamous, acinar or neuroendocrine tumours. Overall, 3‐ and 5‐year survival rates were statistically similar between both patient groups, but upon multivariate analysis, Chinese patients showed statistically better survival rates for stage III tumours.Conclusions:  Most GEJ carcinomas in patients from China represent proximal gastric cancers associated with chronic H. pylori gastritis, and BO‐associated carcinomas are rare among this patient population.
Malignant potential of oral and labial chronic discoid lupus erythematosus: a clinicopathological study of 87 cases
Authors: Liu Wei , Shen Zheng‐Yu , Wang Li‐Jia , Hu Yu‐Hua , Shen Xue‐Ming , Zhou Zeng‐Tong , Li Jiang 
Published: October 2015

Liu W, Shen Z‐Y, Wang L‐J, Hu Y‐H, Shen X‐M, Zhou Z‐T & Li J  (2011) Histopathology59, 292–298Malignant potential of oral and labial chronic discoid lupus erythematosus: a clinicopathological study of 87 casesAims:  To investigate clinicopathological features and identify clinicopathological risk factors for the malignant transformation of oral and labial chronic discoid lupus erythematosus (DLE) in a relatively large number of patients from China.Methods and results:  A total of 87 patients with clinical and histopathological diagnosis of DLE between 1993 and 2009 were reviewed retrospectively in our hospital. The average age at diagnosis was 51.7 years, with a male:female ratio of 1:1.8. The lower lip was the most common site (71.3%). We documented six DLE patients with malignant transformation. On univariate analysis, patients with high‐risk dysplasia (P = 0.002) or aged >60 (P = 0.045) were associated with DLE malignant transformation, but gender, lesion site, smoking and alcohol intake were not risk factors. On multivariate analysis, high‐risk dysplasia was a significant indicator for DLE malignant transformation. High‐risk dysplasia was associated with a 14.24‐fold [95% confidence interval (95% CI), 1.97–102.88; P = 0.008] increased risk of malignant transformation, compared with non/low‐risk dysplasia.Conclusions:  The utilization of high‐risk dysplasia as a significant indicator for evaluating malignant transformation risk in patients with DLE is suggested, which may be helpful to guide treatment selection.
A microsatellite marker linkage map of the housefly, Musca domestica: evidence for male recombination
Authors: Feldmeyer B. , Pen I. , Beukeboom L. W. 
Published: October 2015

AbstractWe present the first molecular marker linkage map for Musca domestica containing 35 microsatellite plus six visible markers. We report the development of 33 new microsatellite markers of which 19 are included in the linkage map. Two hundred and thirty‐six F2 individuals were genotyped from three crosses yielding a linkage map consisting of five linkage groups that represent the five autosomes of the housefly. The map covers a total of 229.6 cM with an average marker spacing of 4.4 cM spanning approximately 80.2% of the genome. We found up to 29% recombination in male houseflies in contrast to most previous studies. The linkage map will add to genetic studies of the housefly.
Murine pulmonary infection and inflammation induced by inhalation of Burkholderia pseudomallei
Authors: West T. Eoin , Myers Nicolle D. , Liggitt H. Denny , Skerrett Shawn J. 
Published: October 2015

SummaryMelioidosis is a tropical disease caused by ingestion, percutaneous inoculation or inhalation of the Gram‐negative soil saprophyte Burkholderia pseudomallei. We developed a reproducible experimental murine model of pneumonic melioidosis induced by inhalation of aerosolized B. pseudomallei 1026b. In a series of experiments performed to bracket the lethal dose, we found that C57BL/6 mice were modestly more resistant than BALB/c mice (median lethal dose 334 CFU/lung vs 204 CFU/lung). We further characterized infection and pulmonary inflammation in C57BL/6 mice infected with a sublethal dose. We observed pulmonary replication and dissemination of bacteria to distant organs in the first days after infection, followed by bacterial containment by day 4 and no evidence of recrudescent infection for up to 2 months. We measured a robust host inflammatory response notable for a neutrophilic bronchoalveolar lavage fluid profile, elevated cytokines and chemokines in the lung and serum and scattered foci of neutrophilic infiltrates in the alveoli and in a perivascular distribution on histological analysis. We previously noted a similar pattern of inflammation in mice infected with aerosolized B. thailandensis. This report builds on the limited literature describing experimental murine pneumonic melioidosis induced by aerosol and characterizes pulmonary infection and resultant inflammation in C57BL/6 mice infected with aerosolized B. pseudomallei. This model has utility for the study of bacterial and host factors that contribute to the virulence of melioidosis.
Study of the retrogradation behaviour of rice cake using rapid visco analyser, Fourier transform infrared spectroscopy and X‐ray analysis
Authors: Ji Ying , Zhu Kexue , Zhou Huiming , Qian Haifeng 
Published: October 2015

SummaryRetrogradation of gelatinised starch is the main phenomenon that influences the texture of MiGao (rice cake). The hardness of the MiGao increased during stored at 25 °C for 5 days. Rapid visco analyser (RVA), Fourier transform infrared (FT‐IR) spectroscopy and X‐ray were quantified to analysis the retrogradation behaviour of MiGao. The most significant change in the pasting curve was the increase in peak viscosity over time measured with an RVA. FT‐IR indicated changes in crystallinity of the MiGao crumb. The X‐ray diffraction patterns could be classified as typical of A‐type starch for the fresh MiGao. With aging, the B‐type structure increases, while the A‐type structure remains virtually unchanged. All the results suggested that the main mechanism underlying the changes in properties is suggested to be slow amylopectin crystallisation.
Combined use of bacteriocin‐producing strains to control Listeria monocytogenes regrowth in raw pork meat
Authors: Kouakou Privat , Ghalfi Hakim , Dortu Carine , Evrard Pol , Thonart Philippe 
Published: October 2015

SummaryAvoiding the presence of Listeria in meat and dairy products is a major challenge for the food industry. In this work, a Lactobacillus curvatus strain producing the bacteriocin sakacin P and a Pediococcus acidilactici strain producing another bacteriocin, pediocin AcH, were used as starter cultures under laboratory conditions in a Listeria‐seeded raw‐pork‐meat matrix, which was then stored for 6 weeks at 4 °C. At 1 week intervals during the storage period, the antilisterial activity was evaluated. When either strain was added alone, the Listeria monocytogenes cfu count initially dropped from 102 cfu g−1 to an undetectable level by the end of week 1 or 2, but this was followed by a rebound (regrowth) 1 week later. When both strains were added together to the meat matrix, rebound was delayed, Listeria remaining undetected from the end of week 1 to the end of week 5. A rebound was observed 6 weeks post‐inoculation, but fewer than 10 cfu g−1 were counted. The use of more than one bacteriocin‐producing strain may thus overcome some of the problems limiting the effectiveness of bacteriocins in food systems.
Volatile compounds characterising Tunisian virgin olive oils: the influence of cultivar
Authors: Krichene Dhouha , Haddada Faouzia Mahjoub , Fernandez Xavier , Cuvelier Luisette Lizzani , Zarrouk Mokhtar 
Published: October 2015

SummaryIn this work, the volatile profiles of four Tunisian virgin olive oils were established by headspace‐solid phase microextraction and gas chromatography, using flame ionisation and mass spectrometer detectors. More than eighty compounds were isolated and characterised, representing 97–99% of the total GC area. The main volatile compounds present in the oil samples were determined quantitatively, the major constituents were often aldehydes, particularly (E)‐2‐hexenal (48–90%). Significant differences in the content of volatile constituents were observed. These quantitative differences were used to distinguish between virgin olive oils from different varieties.
Effects of low‐dose irradiation and electrical stimulation on quality parameters of beef longissimus from Bos indicus × Bos taurus bulls
Authors: Kuttinarayanan Palat , Ramanathan Ranjith 
Published: October 2015

SummaryOur objectives were to assess the effects of low‐dose irradiation and electrical stimulation on quality parameters of beef from Bos indicus × Bos taurus bulls. Loins from six animals were assigned to either irradiation (2.5 kGy) or electric stimulation (150 V, 50 Hz for 2 min), resulting in four treatments. From each treatment, 2.54‐cm‐thick steaks were cut, packaged in LDPE pouches, and stored at 4 °C for 28 days. Irradiated samples had shelf‐life of 28 days compared with non‐irradiated samples (P < 0.05). However, TBARS values were greater in irradiated samples compared with non‐irradiated samples. Electrically stimulated samples were tender, but had lower water holding capacity and greater redness and drip loss compared with non‐electric stimulated (P < 0.05). Thus, a combination of irradiation and electric stimulation can improve tenderness and reduce aerobic plate count of meat obtained from old and undernourished bulls of Bos indicus×Bos taurus origin.