bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global testing of shifts in metabolic phenotype
Authors: Fazelzadeh Parastoo , Hoefsloot Huub C. J. , Hankemeier Thomas , Most Jasper , Kersten Sander , Blaak Ellen E. , Boekschoten Mark , van Duynhoven John 
Published: October 2018

Abstract
Introduction
Current metabolomics approaches to unravel impact of diet- or lifestyle induced phenotype variation and shifts predominantly deploy univariate or multivariate approaches, with a posteriori interpretation at pathway level. This however often provides only a fragmented view on the involved metabolic pathways.

Objectives
To demonstrate the feasibility of using Goeman’s global test (GGT) for assessment of variation and shifts in metabolic phenotype at the level of a priori defined pathways.

Methods
Two intervention studies with identified phenotype variations and shifts were examined. In a weight loss (WL) intervention study obese subjects received a mixed meal challenge before and after WL. In a polyphenol (PP) intervention study obese subjects received a high fat mixed meal challenge (61E% fat) before and after a PP intervention. Plasma samples were obtained at fasting and during the postprandial response. Besides WL- and PP-induced phenotype shifts, also correlation of plasma metabolome with phenotype descriptors was assessed at pathway level. The plasma metabolome covered organic acids, amino acids, biogenic amines, acylcarnitines and oxylipins.

Results
For the population of the WL study, GGT revealed that HOMA correlated with the fasting levels of the TCA cycle, BCAA catabolism, the lactate, arginine–proline and phenylalanine–tyrosine pathways. For the population of the PP study, HOMA correlated with fasting metabolite levels of TCA cycle, fatty acid oxidation and phenylalanine–tyrosine pathways. These correlations were more pronounced for metabolic pathways in the fasting state, than during the postprandial response. The effect of the WL and PP intervention on a priori defined metabolic pathways, and correlation of pathways with insulin sensitivity as described by HOMA was in line with previous studies.

Conclusion
GGT confirmed earlier biological findings in a hypothesis led approach. A main advantage of GGT is that it provides a direct view on involvement of a priori defined pathways in phenotype shifts.
Absorbed Residue Evidence for PrehistoricDaturaUse in the American Southeast and Western Mexico
Authors: King Adam , Powis Terry G. , Cheong Kong F. , Deere Bobi , Pickering Robert B. , Singleton Eric , Gaikwad Nilesh W. 
Published: October 2018

ABSTRACTAbsorbed residue studies have been used in subsistence research for decades. Only more recently have the chemical methods employed been used to explore the consumption of ritual concoctions such as those including cacao, yaupon holly, and alcohol. In this article we use mass spectrometry to identifyDaturaresidues in prehistoric contexts from western Mexico and the American Southeast.Daturais a genus of flowering plants that contain hallucinogenic alkaloids. Their use in both regions is known historically and still continues today. This study sampled 55 pottery vessels and 18 shell vessels using both a traditional burr method and a water-based sonicator sampling method.Daturaresidues were found in 13 pottery vessels and 14 shell vessels using both sampling approaches. These results demonstrate that it is possible to identifyDaturaresidue in pottery and shell vessels and that the use ofDaturaextends back into prehistory in both regions. The form and decoration of pottery vessels withDaturaresidues show correlations with specific motifs and themes. Historically, shell vessels were used in the Southeast for the consumption of another ritual beverage, called the Black Drink. The presence ofDaturashows that those vessels were used for other kinds of beverages as well.
Whole-genome sequencing for methicillin-resistant Staphylococcus aureus (MRSA) outbreak investigation in a neonatal intensive care unit
Authors: Madigan Theresa , Cunningham Scott A. , Patel Robin , Greenwood-Quaintance Kerryl E. , Barth Jean E. , Sampathkumar Priya , Cole Nicolynn C. , Kohner Peggy C. , Colby Christopher E. , Asay Garth F. , Fang Jennifer L. , Baker Christine A. , Heinrich Angela L. , Fjerstad Kelly A. , Lujero Maria J. , Chia Nicholas , Jeraldo Patricio R. , Nelson Heidi , Huskins W. Charles 
Published: October 2018

AbstractObjectiveTo evaluate whole-genome sequencing (WGS) as a molecular typing tool for MRSA outbreak investigation.DesignInvestigation of MRSA colonization/infection in a neonatal intensive care unit (NICU) over 3 years (2014–2017).SettingSingle-center level IV NICU.PatientsNICU infants and healthcare workers (HCWs).MethodsInfants were screened for MRSA using a swab of the anterior nares, axilla, and groin, initially by targeted (ring) screening, and later by universal weekly screening. Clinical cultures were collected as indicated. HCWs were screened once using swabs of the anterior nares. MRSA isolates were typed using WGS with core-genome multilocus sequence typing (cgMLST) analysis and by pulsed-field gel electrophoresis (PFGE). Colonized and infected infants and HCWs were decolonized. Control strategies included reinforcement of hand hygiene, use of contact precautions, cohorting, enhanced environmental cleaning, and remodeling of the NICU.ResultsWe identified 64 MRSA-positive infants: 53 (83%) by screening and 11 (17%) by clinical cultures. Of 85 screened HCWs, 5 (6%) were MRSA positive. WGS of MRSA isolates identified 2 large clusters (WGS groups 1 and 2), 1 small cluster (WGS group 3), and 8 unrelated isolates. PFGE failed to distinguish WGS group 2 and 3 isolates. WGS groups 1 and 2 were codistributed over time. HCW MRSA isolates were primarily in WGS group 1. New infant MRSA cases declined after implementation of the control interventions.ConclusionWe identified 2 contemporaneous MRSA outbreaks alongside sporadic cases in a NICU. WGS was used to determine strain relatedness at a higher resolution than PFGE and was useful in guiding efforts to control MRSA transmission.
Overview of the oxygen isotope systematics of land snails from North America
Authors: Yanes Yurena , Al-Qattan Nasser M. , Rech Jason A. , Pigati Jeffrey S. , Dodd Justin P. , Nekola Jeffrey C. 
Published: October 2018

AbstractContinental paleoclimate proxies with near-global coverage are rare. Land snail δ18O is one of the few proxies abundant in Quaternary sediments ranging from the tropics to the high Arctic tundra. However, its application in paleoclimatology remains difficult, attributable in part to limitations in published calibration studies. Here we present shell δ18O of modern small (<10 mm) snails across North America, from Florida (30°N) to Manitoba (58°N), to examine the main climatic controls on shell δ18O at a coarse scale. This transect is augmented by published δ18O values, which expand our coverage from Jamaica (18°N) to Alaska (64°N). Results indicate that shell δ18O primarily tracks the average annual precipitation δ18O. Shell δ18O increases 0.5–0.7‰ for every 1‰ increase in precipitation δ18O, and 0.3–0.7‰ for every 1°C increase in temperature. These relationships hold true when all taxa are included regardless of body size (ranging from ~1.6 to ~58 mm), ecology (herbivores, omnivores, and carnivores), or behavior (variable seasonal active periods and mobility habits). Future isotopic investigations should include calibration studies in tropical and high-latitude settings, arid environments, and along altitudinal gradients to test if the near linear relationship between shell and meteoric precipitation δ18O observed on a continental scale remains significant.
Quantification of dissolved organic14C-containing compounds by accelerator mass spectrometry in a corrosion experiment with irradiated steel
Authors: Cvetković Benjamin Z , Salazar Gary , Kunz Dominik , Tits Jan , Szidat Sönke , Wieland Erich 
Published: October 2018

ABSTRACTLow- and intermediate-level (L/ILW) radioactive waste produced in Switzerland consists of large amounts of14C-containing irradiated steel.14C will be released during the anoxic corrosion of the steel in the cementitious near field of an L/ILW repository. In this study, a corrosion experiment with irradiated steel was carried out to determine the speciation of14C released during the corrosion process in conditions similar to those anticipated in the near field of a cement-based repository. The development of the experimental setup, including installation of the reactor and development of suitable analytical methods based on compound-specific14C analysis with accelerator mass spectrometry (CSRA AMS) is reported. Time-dependent increase in the total content of14C-bearing organic compounds in solution (TO14C) was determined by AMS and the main organic corrosion products that are14C-bearing formate, acetate and lactate were identified by CSRA AMS after a pre-concentration step. The concentration of the14C-bearing organic compounds was found to be very low (fmol to pmol14C/L). Stable carbon compounds were identified and quantified while the source of stable carbon in the system has not yet been identified and the temporal evolution of the concentration of these carbon species is presently not understood.
Bringing sustainable seafood back to the table: exploring chefs’ knowledge, attitudes and practices in Peru
Authors: López De La Lama Rocio , De La Puente Santiago , Valdés-Velásquez Armando 
Published: October 2018

AbstractConservation organizations promoting sustainable seafood have had greater success when chefs are empowered as agents of change in favour of sustainable seafood. Peru is experiencing a gastronomic revolution with seafood at its core, and Peruvian top chefs are being approached by conservation organizations to become environmental advocates. Within this context we characterize the factors that influence chefs’ behaviours regarding sustainable seafood. A total of 52 Peruvian top chefs were surveyed using the Knowledge, Attitudes and Practices Framework, complemented by a focus group with a subset of the surveyed population. Our results suggest that, regardless of their age or academic background, chefs are aware of the negative consequences that human activities have on the ocean and believe that restaurants have an obligation to become part of the solution by promoting the use of sustainable seafood. Nonetheless, three factors limit chefs’ understanding of key concepts and prevent them from fully internalizing the environmental consequences of their actions in restaurants: (1) sustainability is a new topic for them, particularly for older chefs; (2) the fish species commonly used at restaurants are poorly regulated, and (3) chefs are risk averse to actions that could result in profit loss. Additionally, the structure of the seafood supply chain further limits chefs’ capacity to act sustainably, even if they are aware of the need to change their behaviour. Recommendations are provided for future conservation campaigns advocating use of sustainable seafood, some of which have now been implemented.
Uqsuqtuurmiut inuita tuktumi qaujimaningit(Inuit knowledge of caribou from Gjoa Haven, Nunavut): Collaborative research contributions to co-management efforts
Authors: Ljubicic Gita , Okpakok Simon , Robertson Sean , Mearns Rebecca 
Published: October 2018

AbstractCaribou (tuktuit) are embedded in northern life, and have been part of Inuit culture and seasonal rounds for generations. InInuit Nunangat(Inuit homelands),tuktuitare the most prevalent of country foods consumed, and remain interconnected with Inuit values, beliefs and practices. Despite co-management mandates to consider Inuit and scientific knowledge equally, the intertwined colonial legacies of research and wildlife management render this challenging. In Uqsuqtuuq (Gjoa Haven, Nunavut), community members identified the importance of documenting Inuit knowledge in order to be taken more seriously by researchers and government managers. To address this priority we worked with Uqsuqtuurmiut (people of Uqsuqtuuq) to articulate which types oftuktuitare found on or near Qikiqtaq (King William Island), provide a historical perspective oftuktuitpresence/absence in the region, and describe seasonal movements oftuktuiton and off the island. In reflecting on potential intersections of our work with the Government of Nunavut strategy “Working Together for Caribou”, we identify several considerations in support ofQanuqtuurniq(information and knowledge acquisition): defining information needs, recognising and valuing Inuit knowledge, and developing and implementing credible research. By sharing lessons from our collaborative process we aim to contribute to broader cross-cultural research and co-management efforts in Nunavut.
Repeated Chlamydia trachomatis infections are associated with lower bacterial loads
Authors: Gupta K. , Bakshi R. K. , Van Der Pol B. , Daniel G. , Brown L. , Press C. G. , Gorwitz R. , Papp J. , Lee J. Y. , Geisler W. M. 
Published: October 2018

Abstract
Chlamydia trachomatis (CT) infections remain highly prevalent. CT reinfection occurs frequently within months after treatment, likely contributing to sustaining the high CT infection prevalence. Sparse studies have suggested CT reinfection is associated with a lower organism load, but it is unclear whether CT load at the time of treatment influences CT reinfection risk. In this study, women presenting for treatment of a positive CT screening test were enrolled, treated and returned for 3- and 6-month follow-up visits. CT organism loads were quantified at each visit. We evaluated for an association of CT bacterial load at initial infection with reinfection risk and investigated factors influencing the CT load at baseline and follow-up in those with CT reinfection. We found no association of initial CT load with reinfection risk. We found a significant decrease in the median log10 CT load from baseline to follow-up in those with reinfection (5.6 CT/ml vs. 4.5 CT/ml; P = 0.015). Upon stratification of reinfected subjects based upon presence or absence of a history of CT infections prior to their infection at the baseline visit, we found a significant decline in the CT load from baseline to follow-up (5.7 CT/ml vs. 4.3 CT/ml; P = 0.021) exclusively in patients with a history of CT infections prior to our study. Our findings suggest repeated CT infections may lead to possible development of partial immunity against CT.
Advancing the assessment of cultural orientation: A developmental and contextual framework of multiple psychological dimensions and social identities
Authors: Knight George P. , Safa M. Dalal , White Rebecca M. B. 
Published: October 2018

AbstractThis paper aims to advance the scientific understanding of the role of culture, particularly cultural orientation, in development and psychopathology. We advance a theoretical framework that conceptualizes cultural orientation as a developmental construct represented by multiple psychological dimensions and social identities, and influenced by the contexts in which individuals are embedded. This perspective suggests that cultural orientation changes within individuals over time as a function of their experiences with and memberships in multiple groups, including the mainstream and ethnic culture groups, as well as a function of their normative developmental changes (i.e., the development of cognitive, social, and emotional capabilities). In addition, this framework places the development of an ethnic culture social identity (e.g., an ethnic identity) and a mainstream culture social identity in broader developmental perspectives that recognize these as two of the many social identities that are simultaneously embedded within the individual's self-concept and that simultaneously influence one's cultural orientation. To support the successful integration of culture into the study of development and psychopathology, we describe how highly reliable and valid measures of cultural orientation, indexed by individuals’ social identities, are essential for generating a scientifically credible understanding of the role of cultural orientation in development and psychopathology. Further, we detail some best research practices associated with our developmental and contextual framework, and note some important considerations for researchers interested in studying cultural orientation, development, and psychopathology.
Podcast-based pronunciation training: Enhancing FL learners’ perception and production of fossilised segmental features
Authors: Fouz-González Jonás 
Published: October 2018

AbstractThis study investigates the potential of a podcast-based approach aimed at helping foreign language learners improve their pronunciation of features that tend to be fossilised in their interlanguage. Training took place over a period of three weeks in which podcasts were used for perceptual and productive practice as well as for peer evaluation. Participants in this study (N=47) were randomly assigned to two groups that acted as control and experimental at the same time. One group received training on the English /s – z/ contrast and the other one was trained on the pronunciation of English /b d g/ as stops in intervocalic position. Pre- and post-tests were used to measure the participants’ perception and production of the target features. The results show that training had a positive impact on the participants’ perception and production of the target sounds. Even though the differences between groups did not reach statistical significance for every sound in every task, the data reveal that the approach adopted could foster substantial improvements in the participants’ pronunciation of features that tend to be fossilised, even after short periods of training.
Additive negative effects of Philornis nest parasitism on small and declining Neotropical bird populations
Authors: BULGARELLA MARIANA , QUIROGA MARTÍN A. , HEIMPEL GEORGE E. 
Published: October 2018

SummaryThe declining-population paradigm holds that small populations are particularly vulnerable to anthropogenic influences such as habitat destruction, pollution and species introductions. While the effects of particular stressors, such as parasitism, may be unimportant in a large, healthy population, they can be serious and even devastating in situations characterised by a restricted geographic range, or by fragmented or reduced population sizes. We apply this idea to nest parasitism of threatened Neotropical bird species that exist in small populations, focusing on dipteran nest parasites in the genusPhilornis. We review the literature onPhilornisparasitism exerting negative pressure on bird populations that have become small and isolated due to human actions and present a new case ofPhilornisparasitism of a threatened hummingbird species. Our aim is to raise awareness about the exacerbating effect that nest parasites can have on small and declining bird populations; especially when biological information is scarce. The five reviewed cases involve two species of Darwin’s Finches in the Galápagos Islands attacked by the invasiveP. downsi, two species of hawks on islands in the Caribbean attacked by the nativeP. piciandP. obscura, and the Yellow CardinalGubernatrix cristatain southern South America attacked by an unknownPhilornisspecies. We also present new documentation of parasitism of a threatened hummingbird species in mainland Ecuador by an unidentifiedPhilornisspecies. We recommend more field studies to determine the presence of nest parasites in bird populations worldwide to improve understanding how nest parasites affect bird fitness and population viability and to allow time to act in advance if needed. Parasitism byPhilornismay represent a severe mortality factor in most already threatened bird species, putting them at greater risk of extinction. Therefore, parasitism management should be included in all threatened species recovery plans.
Prevalence and predictors of malnutrition in elderly Chinese adults: results from the China Health and Retirement Longitudinal Study
Authors: Wei Jun-Min , Li Shirley , Claytor Ling , Partridge Jamie , Goates Scott 
Published: October 2018

AbstractObjectiveChina has the largest population of elderly citizens in the world, with 177 million adults aged 60 years or older. However, no national estimate of malnutrition in elderly Chinese adults exists. We estimated the prevalence and predictors of malnutrition in this population.DesignData from the second wave of the Chinese Health and Retirement Longitudinal Study (CHARLS) include interview and biomarker data for 6450 subjects aged 60 years or older from 448 different communities in twenty-eight provinces, allowing for nationally representative results. Malnutrition was identified based on the ESPEN (European Society of Parenteral and Enteral Nutrition and Metabolism) criteria. We used multivariable regression to investigate the predictors of malnutrition, including demographic factors, marital status, self-reported health status, self-reported standard of living, health insurance status and education.SettingChina.SubjectsCommunity-dwelling Chinese adults aged 60 years or older.ResultsThe prevalence of malnutrition in elderly Chinese adults was 12·6 %. Malnutrition was most common among those who were older (OR=1·09; 95 % CI 1·07, 1·10), male (OR=1·41; 95 % CI 1·10, 1·79), lived in rural areas (v. urban: OR=0·75; 95 % CI 0·57, 1·00) or lacked health insurance (P<0·01).ConclusionsThe burden of malnutrition on elderly Chinese adults is significant. Based on current population estimates, up to 20 million are malnourished. Malnutrition is strongly associated with demographic factors, shows a trend to association with health status and is not strongly associated with standard of living or education. A coordinated effort is needed to address malnutrition in this population.
Wideband isolation-improved substrate-integrated waveguide power dividers/combiners
Authors: Huang Yong Mao , Jin Haiyan , Zhou Yuliang , Leng Supeng , Bozzi Maurizio 
Published: October 2018

AbstractIn this paper, a 3 dB H-plane substrate-integrated waveguide (SIW) power divider/combiner with improved isolation is reported. By adding two isolated ports into the Y-junction, it will perform like a multi-port coupler, so that the isolation between its dividing ports can be effectively improved as the newly-added ports are properly matched. To verify the availability and effectiveness of this concept, two prototypes, one is terminated by coaxial terminations and the other is loaded with lumped resistors, are developed. Their measured results are separately in good agreement with their corresponding simulations. Meanwhile, isolations better than 16 dB with fractional bandwidth (FBW) of 35 and 25% are achieved, respectively, as well as low phase and amplitude imbalances. Compared with some reported similar SIW power dividers, the proposed ones exhibit wider FBW with similar isolation, insertion loss, phase, and amplitude balance performance.
‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets
Authors: Kuntal Bhusan K , Chandrakar Pranjal , Sadhu Sudipta , Mande Sharmila S 
Published: October 2018

Abstract
The combined effect of mutual association within the co-inhabiting microbes in human body is known to play a major role in determining health status of individuals. The differential taxonomic abundance between healthy and disease are often used to identify microbial markers. However, in order to make a microbial community based inference, it is important not only to consider microbial abundances, but also to quantify the changes observed among inter microbial associations. In the present study, we introduce a method called ‘NetShift’ to quantify rewiring and community changes in microbial association networks between healthy and disease. Additionally, we devise a score to identify important microbial taxa which serve as ‘drivers’ from the healthy to disease. We demonstrate the validity of our score on a number of scenarios and apply our methodology on two real world metagenomic datasets. The ‘NetShift’ methodology is also implemented as a web-based application available at https://web.rniapps.net/netshift