bluuebunny/crossref_metadata_2025 huggingface dataset:
Oxytocin reactivity during intergroup conflict in wild chimpanzees
Authors: Samuni Liran , Preis Anna , Mundry Roger , Deschner Tobias , Crockford Catherine , Wittig Roman M.
Published: December 2016

Significance

Warfare is one of the most pervasive problems among human societies, and understanding mechanisms involved in in-group cooperation and favoritism is of paramount importance. Wild chimpanzees share key features of humans’ intergroup conflict, in terms of in-group coordination, coalitionary support, and out-group hostility. The hormone oxytocin may regulate humans’ intergroup conflict, although tests in natural settings are lacking. We found strong evidence that, like in humans, oxytocin is involved in chimpanzee intergroup conflict. Both intergroup conflict anticipation and participation involved high urinary oxytocin levels, irrespective of intragroup affiliations or potential threat by rivals. These results are indicative of similar physiological processes involved in intergroup violence and intragroup support in both species, likely supporting behavior that is adaptive during intergroup conflicts.
Influenza A surface glycosylation and vaccine design
Authors: Wu Chung-Yi , Lin Chih-Wei , Tsai Tsung-I , Lee Chang-Chun David , Chuang Hong-Yang , Chen Jhih-Bin , Tsai Ming-Hung , Chen Bo-Rui , Lo Pei-Wen , Liu Chiu-Ping , Shivatare Vidya S. , Wong Chi-Huey
Published: December 2016

Significance

Influenza A virus (IAV) is a major threat to global public health, and so understanding the biology of IAV is essential to develop antiflu vaccines and therapeutics. Here, we show the links between viral surface glycosylation and IAV function. The glycosylation of HA modulates virus infectivity, and host immune response; the glycosylation of NA affects its structure, activity, specificity, and thermostability to regulate virus release and virulence. In addition, using live attenuated IAV without the stalk and catalytic domains of NA as vaccine can strongly induce IAV-specific CD8
+
T-cell responses to various virus strains. Therefore, our findings have clarified the role of glycosylation in IAV and provided a new direction for the development of universal flu vaccines.
Transparent amorphous oxide semiconductors for organic electronics: Application to inverted OLEDs
Authors: Hosono Hideo , Kim Junghwan , Toda Yoshitake , Kamiya Toshio , Watanabe Satoru
Published: December 2016

Significance

Organic electronics have vast potential due to the huge space for molecular design and the soft nature of organics. If the intrinsic advantages of inorganic semiconductors could be complementarily combined with organic semiconductors, exciting new avenues to practical applications would be opened. A key issue is how to realize efficient electron transfer between the cathode and the active organic layers. It is thus a challenge to develop excellent materials for electron injection and transport layers. This paper reports unique transparent amorphous oxide semiconductors for this purpose and successful fabrication of inverted organic light-emitting diode devices with high performance as an application.
Large-scale heterochromatin remodeling linked to overreplication-associated DNA damage
Authors: Feng Wei , Hale Christopher J. , Over Ryan S. , Cokus Shawn J. , Jacobsen Steven E. , Michaels Scott D.
Published: December 2016

Significance

Heterochromatin is a challenging environment in which to repair DNA damage. In addition to dense packaging, heterochromatin often contains repetitive DNA that can lead to errors in homologous recombination-based repair. One strategy to address this problem has been reported in animals. In Drosophila, heterochromatic double-strand breaks are translocated out of the heterochromatin into nearby euchromatin for repair. Here, we show that ARABIDOPSIS TRITHORAX-RELATED 5,6 (
atxr5,6
) mutants use an interesting variation of the approach used by animals. Rather than translocating heterochromatic breaks into euchromatin, heterochromatic aggregations, called “chromocenters,” are remodeled to create specialized compartments with reduced chromatin density. These compartments contain double-strand breaks and DNA-repair enzymes and therefore are likely to play a role in facilitating heterochromatic DNA repair.
Lanthanide-dependent cross-feeding of methane-derived carbon is linked by microbial community interactions
Authors: Krause Sascha M. B. , Johnson Timothy , Samadhi Karunaratne Yasodara , Fu Yanfen , Beck David A. C. , Chistoserdova Ludmila , Lidstrom Mary E.
Published: December 2016

Significance

A great challenge in microbial ecology lies in determining the underlying mechanisms that drive interactions in complex natural communities. In this study we used bacterial isolates from Lake Washington sediment that are important for the utilization of the greenhouse gas methane. We show how simple cocultures can be used to identify mechanisms involved in cross-feeding in microbial communities; these mechanisms cannot be deduced from pure cultures alone. We demonstrate that the presence of one species alters gene expression and metabolism in another species such that the second species excretes a carbon and energy source to sustain the cross-fed species. This mode of cross-feeding based on partner-induced altered gene expression may have important implications for microbial interactions in the environment.
Towards Superlogic
Authors: Bar-Lev Zev
Published: December 2016

This article argues for a semantic theory of discourse structure, with a strong cross-linguistic focus. Its argument starts with analysis of two phenomena related to discourse and cognition : conjunction; and categorization. After this initial justification, claims are developed within a specific research model for discourse, but also drawing on the rich field of data available in intercultural environments. Specific results include the claim that 'Mediterranean' discourse-types differ from Anglo AND 'Oriental ' types in preferring a different form of 'framing' device for discourse, namely a particularizing rather than generalizing form. There is also discussion of the implications of the approach for linguistic methodology and cognitive theory.
A Rationale for the Cloze Procedure
Authors: Foley J.A.
Published: December 2016

This article attempts to answer two questions : firstly, the question of what cloze actually is. Explanations using the principle of 'redundancy1 in the text and the 'grammar expectancy' of the decoder seem to be more satisfactory than theories based on gestalt psychology or the 'information theory'.

Secondly, the question of what cloze actually does. This would appear to be only satisfactorily answered by reference to the syntactic, semantic and rhetorical elements of language. Comprehension assessment for which cloze is often used is normally understood as getting at the conceptual world of the encoder. This cannot be directly tapped by cloze as it would involve skills over and above those accessible by cloze, such as skimming, scanning, reorganization, inference and evaluation.
Is Morphology used to encode Derivations when Learning a Foreign Language?
Authors: Sandra Dominiek
Published: December 2016

Derived words suggest a very efficient mnemonic when they have to be learnt as items in a foreign language (FL). They could be remembered by tagging in semantic memory the property that is lexicalized by the stem and storing the particular affix. A learning experiment was designed to find out whether students make spontaneous use of this encoding strategy. The results indicated that subjects' recall performance was better for derived words than underived ones, even when the presence of stems was not pointed out to them by the experimenter. The error data were compatible with the use of the proposed mnemonic. Surprisingly, subjects who were given only native language translations did better on the derivations than those who were provided additional comment on the morphological structure of these words. This finding proves that the method of giving translations for FL words is not so bad after ail and that the memory representations subjects form in such conditions are not necessarily of the paired-associate type.
Bedenkingen rond juridische terminografie of de term woonplaats op zijn plaats gezet
Authors: vd Bulcke Patricia
Published: December 2016

Aan de hand van een terminografische aanpak van de term "woonplaats" en de bijbehorende begripsanalyse, werd gepoogd de specificiteit van juridische terminografie wat duidelijker te stellen.

In de eerste plaats wijzen we op het pragmatisch karakter van wetteksten, wat voor de juridische termen meebrengt dat ze heel vaak een "dubbele" inhoud hebben: een begripsomschrijving en een juridische toepassing. Het is o.i. dan ook wenselijk dat de terminograaf beide aspecten probeert te benaderen.

Anderzijds wijzen we op het prescriptief karakter van de wetteksten waardoor de termen automatisch genormaliseerd zijn. Als nu voorkomt - en het gebeurt vaak - dat de wetgever eenzelfde term hanteert maar met een gewijzigde begripsinhoud, dan ziet de doctrine zich verplicht nieuwe termen te creëren om de synonimie te verduidelijken en zal de terminograaf op zijn hoede moeten zijn voor termen die in ruime en in strikte zin kunnen gedefinieerd worden.

On the basis of a terminography approach of the term "woonplaats" (domicile) and a companion analysis of the concept, a tentative outline is given of the specificity of juridical terminography.

On the one hand, we give evidence of the pragmatic character of law texts, often resulting in their juridical terms having a doublelayered content: a definition of concept and a juridical application respectively. We find it advisable that a terminographer try and combine both aspects.

On the other hand, we draw attention to the prescriptive nature of law texts, which automatically normalizes them. When the legislator - as is often the case - uses a term with an altered meaning, doctrine has to create new terms so as to make clear synonymy and the terminographer will have to beware of terms that could be defined in both a broad and a narrow sense.
Opioid Overdose Prevention Training with Naloxone, An Adjunct to Basic Life Support Training for First-Year Medical Students
Authors: Berland Noah , Fox Aaron , Tofighi Babak , Hanley Kathleen
Published: December 2016

Background: Opioid overdose deaths have reached epidemic proportions in the United States. This problem stems from both licit and illicit opioid use. Prescribing opioids, recognizing risky use, and initiating prevention, including opioid overdose prevention training (OOPT), are key roles physicians play. The American Heart Association (AHA) modified their basic life support (BLS) algorithms to consider naloxone in high-risk populations and when a pulse is appreciated; however, the AHA did not provide OOPT. The authors’ intervention filled this training deficiency by teaching medical students opioid overdose resuscitation with a Train-the-Trainer model as part of mandatory BLS training. Methods: The authors introduced OOPT, following a Train-the-Trainer model, into the required basic life support (BLS) training for first-year medical students at a single medical school in a large urban area. The authors administered pre- and post-evaluations to assess the effects of the training on opioid overdose knowledge, self-reported preparedness to respond to opioid overdoses, and attitudes towards patients with substance use disorders (SUDs). Results: In the fall 2014, 120 first-year medical students received OOPT. Seventy-three students completed both pre- and posttraining evaluations. Improvements in knowledge about and preparedness to respond to opioid overdoses were statistically significant ( P < .01) and large (Cohen's D = 2.70 and Cohen's D = 2.10, respectively). There was no statistically significant change in attitudes toward patients with SUDs. Conclusions: The authors demonstrated the effectiveness of OOPT as an adjunct to BLS in increasing knowledge about and preparedness to respond to opioid overdoses; improving attitudes toward patients with SUDs likely requires additional intervention. The authors will characterize knowledge and preparedness durability, program sustainability, and long-term changes in attitudes in future evaluations. These results support dissemination of OOPT as a part of BLS training for all medical students, and potentially all BLS providers.
5-hydroxytryptamine synthesized in the aorta-gonad-mesonephros regulates hematopoietic stem and progenitor cell survival
Authors: Lv Junhua , Wang Lu , Gao Ya , Ding Yu-Qiang , Liu Feng
Published: December 2016

The in vitro or ex vivo production of transplantable hematopoietic stem cells (HSCs) holds great promise for the treatment of hematological diseases in the clinic. However, HSCs have not been produced from either embryonic or induced pluripotent stem cells. In this study, we report that 5-hydroxytryptamine (5-HT; also called serotonin) can enhance the generation of hematopoietic stem and progenitor cells (HSPCs) in vitro and is essential for the survival of HSPCs in vivo during embryogenesis. In tryptophan hydroxylase 2–deficient embryos, a decrease in 5-HT synthesized in the aorta-gonad-mesonephros leads to apoptosis of nascent HSPCs. Mechanistically, 5-HT inhibits the AKT-Foxo1 signaling cascade to protect the earliest HSPCs in intraaortic hematopoietic clusters from excessive apoptosis. Collectively, our results reveal an unexpected role of 5-HT in HSPC development and suggest that 5-HT signaling may be a potential therapeutic target for promoting HSPC survival.
Infectious Disease (ID) Learning Unit: What the ID Clinician Needs to Know About Buprenorphine Treatment for Opioid Use Disorder
Authors: Westlake Amanda A. , Eisenberg Mark P.
Published: December 2016

In the context of an escalating opioid epidemic, infectious disease clinicians increasingly treat the infectious complications of injection drug use. In this learning unit, we review the history, pharmacology, and clinical use of buprenorphine as maintenance therapy for opioid use disorder, and we describe the process by which clinicians can obtain a buprenorphine waiver.
Characteristics of Resistance to Phytophthora Root and Crown Rot inCucurbita pepo
Authors: Krasnow Charles S. , Hammerschmidt Raymond , Hausbeck Mary K.
Published: December 2016

Root and crown rot incited by Phytophthora capsici causes considerable annual losses in squash-producing regions in the United States. ‘Spineless Perfection’ zucchini and ‘Cougar’ straightneck squash (Cucurbita pepo L.), partially resistant and susceptible to root and crown rot, respectively, were investigated for differences in root and crown physical factors and the histology of crown infection by P. capsici. The pH and titratable acidity of healthy root and crown tissue from tissue extracts were not significantly different between cultivars (P = 0.05). Crude fiber content (%) of blended and oven-dried root and crown tissue from healthy plants was similar between cultivars. However, dry matter (%) was highest for Cougar (P = 0.05). Colonies of P. capsici grown from mycelial plugs in root exudates collected from each cultivar were similar in diameter. Whole mounts and histological sections of healthy and infected crown tissue revealed that vascular bundles and metaxylem vessels were more abundant in crowns of Spineless Perfection than Cougar. Twelve to 48 h post inoculation (hpi), mycelia in the crown of each cultivar was limited to the cortex and hypodermal tissue. By 72 hpi, hyphae were observed in the cortex and endodermal tissue of Cougar and were concentrated in the phloem and parenchyma cells surrounding vascular bundles. Mycelia were limited to the outer cortex in Spineless Perfection. Mycelia and occluding material were present in the majority of metaxylem vessels of Cougar but not Spineless Perfection at 92 hpi; dissolution of parenchyma cells surrounding vascular bundles was apparent in Cougar. The vascular occlusions observed in Cougar may be responsible for plant wilting, a common disease symptom. Additional straightneck, crookneck, scallop, and acorn squash (C. pepo ssp. ovifera), and zucchini, marrow, and pumpkin (C. pepo ssp. pepo) cultivars were evaluated in a greenhouse study for resistance to root and crown rot. Cucurbita pepo ssp. ovifera cultivars were significantly more susceptible than C. pepo ssp. pepo to root and crown rot (P < 0.0001). Growing C. pepo ssp. pepo cultivars may be beneficial in an integrated Phytophthora management program.
Baseline Sensitivity of Fusarium virguliforme to Fluopyram Fungicide
Authors: Wang Jie , Bradley Carl A. , Stenzel Olivia , Pedersen Dianne K. , Reuter-Carlson Ursula , Chilvers Martin I.
Published: December 2016

Fluopyram, a succinate dehydrogenase inhibitor (SDHI) fungicide, was recently registered for use as a soybean seed treatment for management of sudden death syndrome (SDS) caused by Fusarium virguliforme. Although registered and now used commercially, in vitro baseline fungicide sensitivity of F. virguliforme to fluopyram has not yet been established. In this study, the baseline sensitivity of F. virguliforme to fluopyram was determined using in vitro growth of mycelium and germination of conidia assays with two collections of F. virguliforme isolates. A total of 130 and 75 F. virguliforme isolates were tested using the mycelial growth and conidia germination assays, respectively, including a core set of isolates that were tested with both assays. In the mycelial growth inhibition assay, 113 out of 130 isolates (86.9%) were inhibited 50% by effective concentrations (EC50) less than 5 µg/ml with a mean EC50 of 3.35 µg/ml. For the conidia germination assay, 73 out of 75 isolates (97%) were determined to have an estimated EC50 of less than 5 µg/ml with a mean EC50 value of 2.28 µg/ml. In a subset of 20 common isolates that were phenotyped with both assays, conidia germination of F. virguliforme was determined to be more sensitive to fluopyram (mean EC50 = 2.28 µg/ml) than mycelial growth (mean EC50 = 3.35 µg/ml). Hormetic effects were observed in the mycelial growth inhibition assay as 22% of the isolates demonstrated more growth on medium amended with the lowest fluopyram concentration (1 µg/ml), as compared with the nonfluopyram amended control. It was not possible to determine EC50 values for nine out of 185 isolates (4.8%), as those isolates were not inhibited by 50% even at the highest fluopyram concentrations of 100 µg/ml for mycelial growth and 20 µg/ml for conidia germination inhibition assays. On the whole, the F. virguliforme population appears to be sensitive to fluopyram, and this study enables future monitoring of fungicide sensitivity.
Molecular and Biological Characterization of Tomato mottle mosaic virus and Development of RT-PCR Detection
Authors: Sui Xuelian , Zheng Yi , Li Rugang , Padmanabhan Chellappan , Tian Tongyan , Groth-Helms Deborah , Keinath Anthony P. , Fei Zhangjun , Wu Zujian , Ling Kai-Shu
Published: December 2016

Tomato mottle mosaic virus (ToMMV) was first identified in 2013 as a novel tobamovirus infecting tomatoes in Mexico. In just a few years, ToMMV has been identified in several countries around the world, including the United States. In the present study, we characterized the molecular, serological, and biological properties of ToMMV and developed a species-specific RT-PCR to detect three tomato-infecting tobamoviruses: Tobacco mosaic virus (TMV), Tomato mosaic virus (ToMV), and ToMMV. Previously, ToMMV has been reported in Florida and New York. In this study, we made two new reports on the occurrences of ToMMV on tomatoes in California and South Carolina. Their complete genome sequences were obtained and their genetic relationships to other tobamoviruses evaluated. In host range studies, some differential responses in host plants were also identified between ToMMV and ToMV. To alleviate cross-serological reactivity among the tomato-infecting tobamoviruses, a new multiplex RT-PCR was developed to allow for species-specific detection and identification of TMV, ToMV, and ToMMV. In addition, we observed resistance breaking by ToMMV on selected tomato cultivars that were resistant to ToMV. This has caused serious concerns to tomato growers worldwide. In conclusion, the characterization in molecular and biological properties of ToMMV would provide us with fundamental knowledge to manage this emerging virus on tomato and other solanaceous crops in the U.S. and around the world.
Opportune cell culture conditions permit transfer of the neurosphere paradigm to cells of the cerebellar granule cell lineage by being permissive to sonic hedgehog signaling
Authors: Heil Constantin
Published: December 2016

Thein vitrostudy of neural progenitors is based around the idea that defined culture conditions can emulate an environment which maintains an undifferentiated state and self-renewal capability of explanted progenitor cells, culminating in the growth of neurospheres. Neurosphere culture systems are used to study cells of physiological origin as well as transformed cells. In the case of the cerebellar granule cell lineage, neurosphere cultures have been produced from medulloblastoma tumors, while non-transformed granule progenitors are reported to be transientin vitro.SHH signaling is a key signaling pathway with roles in morphogenesis and cell proliferation in the central nervous system, in particular, involved in mitogenic signaling within the context of postnatal cerebellar granule cell expansion. In this paper, I demonstrate that in addition to commonly used mitogens such as EGF and bFGF, the SHH pathway agonist SAG, as well as genetic activation of SHH signaling by PTCH1 deletion, can lead to the growth of neurospheres from postnatal day 7 (p7) cerebellar explants.

I also show that these neurosphere adhere to the cerebellar GCP lineage.. Strikingly, mSS cells can be maintained indefinitely in culture, as demonstrated by extensive clonogenic capability, assayed over a period of 10 weeks. In the context of self-renewal, I assay gene expression of POU3f2, POU5f1, NANOG, and SOX2, genes associated with neural progenitors, which I find expressed in mSS cells. Importantly, mSS cultures are continuously dependent on SAG for their clonogenic potential and SHH pathway activation, assayed by expression of GLI1, PTCH1 and NMYC. In addition to the aforementioned extensive self-renewal capability, mSS neurosphere cultures also maintain the ability to differentiate.In vitrodifferentiation leads to formation of cells with typical granule cell morphology and which are positive for beta3-tubulin and express GABRA6.

Overall, my work demonstrates that by applying culture conditions which are tailored towards biological characteristics of specific regions of the central nervous system the paradigm of the neurosphere can be expanded to include lineages not previously studied in this way. In particular, I apply this principle to unmask the property of cells from the GCP lineage as having extensive self-renewal capabilityin vitro.
DNAlogo: a smart mini application for generating DNA sequence logos
Authors: Guo Yabin
Published: December 2016

Sequence logos are frequently used for presenting consensus sequences and motifs of nucleic acids and proteins. WebLogo of UC Berkeley is the most popular tool for creating sequence logos, whereas, it is often restricted by the internet speed in some developing countries and no graphic interface for its stand-alone version. Here, the author generated an application, DNAlogo, using VB.net, which runs in Windows system. DNAlogo is small and convenient. It creates both bitmap and vector map. Beside the classic sequence logo function, DNAlogo introduced compensated logo to generate consensus sequences considering different GC contents of different genomes. DNAlogo provides a simple way for researchers without programming knowledge to create DNA sequence logos.
Super-resolution Imaging of Synaptic and Extra-synaptic Pools of AMPA Receptors with Different-sized Fluorescent Probes
Authors: Lee Sang Hak , Jin Chaoyi , Cai En , Ge Pinghua , Ishitsuka Yuji , Teng Kai Wen , Thomaz Andre A. de , Nall Duncan , Baday Murat , Jeyifous Okunola , Demonte Daniel , Dundas Christopher M. , Park Sheldon , Green William N. , Selvin Paul R.
Published: December 2016

Whether AMPA receptors (AMPARs) enter into neuronal synapses, by exocytosis from an internal pool, or by diffusion from an external membrane-bound pool, is hotly contested. 3D super-resolution fluorescent nanoscopy to measure the dynamics and placement of AMPAR is a powerful method for addressing this issue. However, probe size and accessibility to tightly packed spaces can be limiting. We have therefore labeled AMPARs with differently sized fluorophores: small organic fluorescent dyes (~ 4 nm), small quantum dots (sQD, ~10 nm in diameter), or big (commercial) quantum dots (bQD, ~ 20 nm in diameter). We then compared their diffusion rate, trajectories, and placement with respect to a postsynaptic density (PSD) protein, Homer 1c. Labeled with the small probes of sQDs or organic fluorophores, we find that AMPARs are located largely within PSDs (~73-93%), and generally reside in “nanodomains” with constrained diffusion. In contrast, when labeled with bQDs, only 5-10% of AMPARs are within PSDs. The results can be explained by relatively free access, or lack thereof, to synaptic clefts of the AMPARs when labeled with small or big probes, respectively. This implies that AMPARs primarily enter PSDs soon after their exocytosis and not from a large diffusive pool of extrasynaptic AMPARs.
Dealing with many correlated covariates in capture-recapture models
Authors: Gimenez Olivier , Barbraud Christophe
Published: December 2016

Capture-recapture models for estimating demographic parameters allow covariates to be incorporated to better understand population dynamics. However, high-dimensionality and multicollinearity can hamper estimation and inference. Principal component analysis is incorporated within capture-recapture models and used to reduce the number of predictors into uncorrelated synthetic new variables. Principal components are selected by sequentially assessing their statistical significance. We provide an example on seabird survival to illustrate our approach. Our method requires standard statistical tools, which permits an efficient and easy implementation using standard software.
Frequency‐ and angle‐dependent poroelastic seismic analysis for highly attenuating reservoirs
Authors: Zhao Luanxiao , Yao Qiuliang , Han De‐hua , Zhou Rui , Geng Jianhua , Li Hui
Published: December 2016

We extend the frequency‐ and angle‐dependent poroelastic reflectivity to systematically analyse the characteristic of seismic waveforms for highly attenuating reservoir rocks. It is found that the mesoscopic fluid pressure diffusion can significantly affect the root‐mean‐square amplitude, frequency content, and phase signatures of seismic waveforms. We loosely group the seismic amplitude‐versus‐angle and ‐frequency characteristics into three classes under different geological circumstances: (i) for Class‐I amplitude‐versus‐angle and ‐frequency, which corresponds to well‐compacted reservoirs having Class‐I amplitude‐versus‐offset characteristic, the root‐mean‐square amplitude at near offset is boosted at high frequency, whereas seismic energy at far offset is concentrated at low frequency; (ii) for Class‐II amplitude‐versus‐angle and ‐frequency, which corresponds to moderately compacted reservoirs having Class‐II amplitude‐versus‐offset characteristic, the weak seismic amplitude might exhibit a phase‐reversal trend, hence distorting both the seismic waveform and energy distribution; (iii) for Class‐III amplitude‐versus‐angle and ‐frequency, which corresponds to unconsolidated reservoir having Class‐III amplitude‐versus‐offset characteristic, the mesoscopic fluid flow does not exercise an appreciable effect on the seismic waveforms, but there exists a non‐negligible amplitude decay compared with the elastic seismic responses based on the Zoeppritz equation.
Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers
Authors: Lindh Markus V. , Sjöstedt Johanna , Ekstam Börje , Casini Michele , Lundin Daniel , Hugerth Luisa W. , Hu Yue O. O. , Andersson Anders F. , Andersson Agneta , Legrand Catherine , Pinhassi Jarone
Published: December 2016

Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations. Notably, the occupancy‐frequency distributions were significantly bimodal with a satellite mode of rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Temporal changes in population distributions supported several theoretical frameworks. Still, bimodality was found among bacterioplankton communities across the entire Baltic Sea, and was also frequent in globally distributed datasets. Datasets spanning waters with widely different physicochemical characteristics or environmental gradients typically lacked significant bimodal patterns. When such datasets were divided into subsets with coherent environmental conditions, bimodal patterns emerged, highlighting the importance of positive feedbacks between local abundance and occupancy within specific biomes. Thus, metapopulation theory applied to microbial biogeography can provide novel insights into the mechanisms governing shifts in biodiversity resulting from natural or anthropogenically induced changes in the environment.
The molecular response of the white‐rot fungus Dichomitus squalens to wood and non‐woody biomass as examined by transcriptome and exoproteome analyses
Authors: Rytioja Johanna , Hildén Kristiina , Di Falco Marcos , Zhou Miaomiao , Aguilar‐Pontes Maria Victoria , Sietiö Outi‐Maaria , Tsang Adrian , de Vries Ronald P. , Mäkelä Miia R.
Published: December 2016

The ability to obtain carbon and energy is a major requirement to exist in any environment. For several ascomycete fungi, (post‐)genomic analyses have shown that species that occupy a large variety of habitats possess a diverse enzymatic machinery, while species with a specific habitat have a more focused enzyme repertoire that is well‐adapted to the prevailing substrate. White‐rot basidiomycete fungi also live in a specific habitat, as they are found exclusively in wood. In this study, we evaluated how well the enzymatic machinery of the white‐rot fungus Dichomitus squalens is tailored to degrade its natural wood substrate. The transcriptome and exoproteome of D. squalens were analyzed after cultivation on two natural substrates, aspen and spruce wood, and two non‐woody substrates, wheat bran and cotton seed hulls. D. squalens produced ligninolytic enzymes mainly at the early time point of the wood cultures, indicating the need to degrade lignin to get access to wood polysaccharides. Surprisingly, the response of the fungus to the non‐woody polysaccharides was nearly as good a match to the substrate composition as observed for the wood polysaccharides. This indicates that D. squalens has preserved its ability to efficiently degrade plant biomass types not present in its natural habitat.
Oscillospira and related bacteria – From metagenomic species to metabolic features
Authors: Gophna Uri , Konikoff Tom , Nielsen Henrik Bjørn
Published: December 2016

Oscillospira is an under‐studied anaerobic bacterial genus from Clostridial cluster IV that has resisted cultivation for over a century since the first time it was observed. In recent years its 16S rRNA gene was identified in several human gut microbiota studies where it was often associated with interesting traits, especially leanness. However, very little is known about its metabolism or physiology. Here we used nearly complete genomes derived from shot‐gun metagenomic data from the human gut to analyze Oscillospira and related bacteria. We used sequence similarity, gene neighbourhood information and manual metabolic pathway curation to decipher key metabolic features of this intriguing bacterial genus. We infer that Oscillospira species are butyrate producers, and at least some of them have the ability to utilize glucuronate, a common animal‐derived sugar that is both produced by the human host and consumed by that host in diets rich in animal products. These findings could help explain diet‐related inter‐individual variation in faecal Oscillospira levels as well as the observation that the presence of this genus is reduced in diseases that involve inflammation.
Gestational diabetes alters the fetal heart rate variability during an oral glucose tolerance test: a fetal magnetocardiography study
Authors: Fehlert E , Willmann K , Fritsche L , Linder K , Mat‐Husin H , Schleger F , Weiss M , Kiefer‐Schmidt I , Brucker S , Häring H‐U , Preissl H , Fritsche A
Published: December 2016

Objective

Gestational diabetes mellitus (GDM) potentially harms the child before birth. We previously found GDM to be associated with developmental changes in the central nervous system. We now hypothesise that GDM may also impact on the fetal autonomic nervous system under metabolic stress like an oral glucose tolerance test (OGTT).

Design

We measured heart rate variability (HRV) of mothers and fetuses during a three‐point OGTT using fetal magnetocardiography (fMCG).

Setting

Measurements were performed in the fMEG Centre in Tübingen.

Population

After exclusion of 23 participants, 13 pregnant women with GDM and 36 pregnant women with normal glucose tolerance were examined.

Methods

All women underwent the same examination setting with OGTT during which fMCG was recorded three times.

Main outcome measure(s)

Parameters of heart rate variability were measured.

Results

Compared with mothers with normal glucose regulation, mothers with GDM showed increased heart rate but no significant differences of maternal HRV. In contrast, HRV in fetuses of mothers with GDM differed from those in the metabolically healthy group regarding standard deviation normal to normal beat (SDNN) (P = 0.012), low‐frequency band (P = 0.008) and high‐frequency band (P = 0.031). These HRV parameters exhibit a decrease only in GDM fetuses during the second hour of the OGTT.

Conclusions

These results show an altered response of the fetal autonomic nervous system to metabolic stress in GDM‐complicated pregnancies. Hence, disturbances in maternal glucose metabolism might not only impact on the central nervous system of the fetus but may also affect the fetal autonomic nervous system.

Tweetable abstract

Metabolic stress reveals a different response of fetal autonomic nervous system in GDM‐complicated pregnancies.
Decreasing mortality during pregnancy and for a year after while mortality after termination of pregnancy remains high: a population‐based register study of pregnancy‐associated deaths in Finland 2001–2012
Authors: Karalis E , Ulander V‐M , Tapper A‐M , Gissler M
Published: December 2016

Objective

To investigate mortality in the non‐pregnant fertile female population, and mortality during pregnancy and up to 1 year after the end of pregnancy, in Finland from 2001 to 2012 and compare the results with those of 1987–2000.

Design

Retrospective cohort study.

Setting

Finland.

Population

10 427 deceased women of reproductive age (15–49).

Methods

Pregnancy outcomes were categorised into: ongoing pregnancy or birth, miscarriage or ectopic pregnancy and termination of pregnancy. Mortality was calculated per 100 000 pregnancies. The mortality rate of the non‐pregnant female population of fertile age was calculated per 100 000 person‐years, and the results were compared with those of 1987–2000.

Main outcome measures

Pregnancy‐associated mortality during pregnancy and up to 1 year after the end of pregnancy. Mortality of non‐pregnant, fertile‐age, female population.

Results

The age‐adjusted mortality rate during pregnancy and within 1 year after the end of pregnancy was 28.4/100 000 pregnancies, and it had significantly decreased compared with the period 1987–2000 [risk ratio (RR) 0.75 (95% CI, 0.65–0.88)]. Mortality in non‐pregnant fertile‐age females was 48.1/100 000 person‐years. Mortality for diseases and medical conditions during and after pregnancy decreased by 26% [RR 0.74 (95% CI, 0.59–0.92)] and for external causes by 23% [RR 0.77 (95% CI, 0.62–0.95)]. The mortality rate for suicides was 3.3/100 000 in ongoing pregnancies and pregnancies ending in birth while it was 21.8/100 000 after termination of pregnancy and 10.2/100 000 among non‐pregnant women.

Conclusions

In comparison with earlier decades, pregnancy‐associated mortality has decreased in Finland.

Tweetable abstract

Mortality decreases among pregnant women and within 1 year after pregnancy in Finland.
Sex‐ and Size‐Related Patterns of Carrion Visitation inNecrodes littoralis(Coleoptera: Silphidae) andCreophilus maxillosus(Coleoptera: Staphylinidae)
Authors: Mądra‐Bielewicz Anna , Frątczak‐Łagiewska Katarzyna , Matuszewski Szymon
Published: December 2016

The estimation of postmortem interval (PMI) based on successional patterns of adult insects is largely limited, due to the lack of potentialPMImarkers. Sex and size of adult insects could be easily used for such estimation. In this study, sex‐ and size‐related patterns of carrion attendance by adult insects were analyzed inNecrodes littoralis(Coleoptera: Silphidae) andCreophilus maxillosus(Coleoptera: Staphylinidae). For both species, abundance of males and females changed similarly during decomposition. A slightly female‐biased sex ratio was recorded inN. littoralis. Females ofN. littoralisstarted visiting carcasses, on average, one day earlier than males. There was a rise in size of males ofN. littoralisat the end of decomposition, whereas for females of both species and males ofC. maxillosus, no size‐related patterns of carrion visitation were found. Current results demonstrate that size and sex of adult carrion beetles are poor indicators ofPMI.
How do groups of red imported fire ants (Hymenoptera: Formicidae) feed on a droplet of sugar water?
Authors: Wang Cai , Chen Xuan , Hooper‐Bùi Linda M. , Strecker Rachel , Wen Yu‐Zhen , Qin Wen‐Quan , Ma Tao , Sun Zhao‐Hui , Chen Xiao‐Yang , Wen Xiu‐Jun
Published: December 2016

Many previous studies have focused on the foraging behaviors and strategies of the red imported fire ants, Solenopsis invicta Buren on solid food or granular bait; little attention has been paid to how liquid sugar is fed upon. In the present study, behavioral responses of S. invicta to 25% sucrose water droplets were observed. Five foraging patterns were identified in S. invicta colonies under laboratory conditions: (i) no feeding, no sucrose water feeding was observed; (ii) surround feeding, ants surrounded and fed along the edge of the sucrose droplet; (iii) stacked feeding, ants stacked and fed along the edge of the sucrose droplet; (iv) droplet‐break feeding, ants broke the liquid droplet and sucked sucrose water that spread on surface of the substance or soil particles previously transported by ants; and (v) cover feeding, whole surface of the sucrose droplet was covered by layers of feeding ants. This is the first time cover feeding in S. invicta has been reported, which obviously requires more ants compared to the other patterns. In addition, individual ants were tracked in videos under laboratory conditions, and behavioral repertoires that led to stacking, covering and droplet‐breaking were identified and described. The field investigation showed that surround feeding was most frequently performed by S. invicta foragers; however, cover feeding was not observed under field conditions during this study. Both laboratory and field studies showed colony‐level variations in sugar‐water feeding.
Recurrence of Helicobacter pylori infection and the affecting factors: A follow‐up study
Authors: Zhou Li Ya , Song Zhi Qiang , Xue Yan , Li Xiao , Li Yan Qing , Qian Jia Ming
Published: December 2016

Objective

Recurrence of Helicobacter pylori (H. pylori) infection weakens the protective effect and long‐term prognosis of eradication. With the widespread therapies, decreasing prevalence of H. pylori infection and improvement in living conditions, the recurrence of H. pylori infection may present with new features. We conducted this prospective, large‐scale, multicenter follow‐up study to determine the recurrence rate of H. pylori infection and its affecting factors.

Methods

A total of 827 patients receiving successful H. pylori eradication in our previous randomized controlled trial were enrolled. 13
C‐urea breath test (UBT) was repeated one year after the eradication therapy to determine its recurrence. Moreover, a questionnaire survey was performed to explore the potential factors affecting the recurrence.

Results

A total of 743 patients completed 13C‐UBT (follow‐up rate 89.8%), and the result was positive in 13 patients one year after eradication therapy, with an annual recurrence rate of 1.75% (95% confidence interval [CI] 0.81–2.69%). Six hundred and ninety‐two patients (13 with recurrence and 679 without recurrence) returned their questionnaires, with a response rate of >80%. Multivariate analysis revealed that peptic ulcer (odds ratio [OR] 3.385, 95% CI 1.016–11.274), close contact with individuals having H. pylori infection (OR 4.231, 95% CI 1.201–14.911), and hospitalization (OR 9.302, 95% CI 2.441–35.440) were independent risk factors of H. pylori infection recurrence.

Conclusions

The recurrence of H. pylori infection one year after eradication therapy is low in urban population of China. Peptic ulcer, contact history with individuals having H. pylori infection and hospitalization are risk factors.
RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al. (2016)
Authors: McKinney Garrett J. , Larson Wesley A. , Seeb Lisa W. , Seeb James E.
Published: December 2016

In their recently corrected manuscript, “Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing for genome scans of adaptation”, Lowry et al. argue that genome scans using RADseq will miss many loci under selection due to a combination of sparse marker density and low levels of linkage disequilibrium in most species. We agree that marker density and levels of LD are important considerations when designing a RADseq study; however, we dispute that RAD‐based genome scans are as prone to failure as Lowry et al. suggest. Their arguments ignore the flexible nature of RADseq; the availability of different restriction enzymes and capacity for combining restriction enzymes ensures that a well‐designed study should be able to generate enough markers for efficient genome coverage. We further believe that simplifying assumptions about linkage disequilibrium in their simulations are invalid in many species. Finally, it is important to note that the alternative methods proposed by Lowry et al. have limitations equal to or greater than RADseq. The wealth of studies with positive impactful findings that have used RAD genome scans instead supports the argument that properly conducted RAD genome scans are an effective method for gaining insight into ecology and evolution, particularly for non‐model organisms and those with large or complex genomes.
How to measure mitochondrial function in birds using red blood cells: a case study in the king penguin and perspectives in ecology and evolution
Authors: Stier Antoine , Romestaing Caroline , Schull Quentin , Lefol Emilie , Robin Jean‐Patrice , Roussel Damien , Bize Pierre
Published: December 2016

Mitochondria are the powerhouse of animal cells. They produce through oxidative phosphorylation more than 90% of the cellular energy (ATP) required for organism's growth, reproduction, and maintenance. Hence, information on mitochondrial function is expected to bring important insights in animal ecology and evolution. Unfortunately, the invasiveness of the procedures required to measure mitochondrial function (e.g. sampling of liver or muscles) has limited its study in wild vertebrate populations so far. Here, we capitalize on the fact that bird red blood cells (RBCs) possess functional mitochondria to describe a minimally invasive approach to study mitochondrial function, using blood samples.

In the king penguin, we present a protocol, using a high‐resolution respirometry system and specific agonists and antagonists enabling the assessment of mitochondrial function in RBCs. We evaluated the inter‐assay repeatability of our measures of mitochondrial function, and tested the influence of sample storage and bird handling time on these measures. We also compared measures of mitochondrial function in RBCs and in the pectoral muscle obtained from the same individuals.

Mitochondria from RBCs showed the expected responses to mitochondrial agonists and antagonists, and therefore the protocol presented allows computing effective measures of mitochondrial function. The different measures of RBC mitochondrial function were significantly repeatable, were not affected by the handling time of the bird prior to blood sampling (i.e. stress response), and only minimally affected by the storage time of the sample at 4 °C up to 24 h. Most notably, we showed that mitochondrial parameters measured in RBCs moderately correlated to those measured in the pectoral muscle.

This study sheds light on the use of RBCs in birds as a valuable and minimally invasive source of information on mitochondrial function. This approach opens new opportunities to study mitochondrial function in free‐living animals and could bring knowledge gains in ecology and evolution. Fish, amphibians and reptiles also possess mitochondria in their RBCs, and the approach presented here could also be applicable to these taxa.
A SMART data analysis method for constructing adaptive treatment strategies for substance use disorders
Authors: Nahum‐Shani Inbal , Ertefaie Ashkan , Lu Xi (Lucy) , Lynch Kevin G. , McKay James R. , Oslin David W. , Almirall Daniel
Published: December 2016

Aims

To demonstrate how Q‐learning, a novel data analysis method, can be used with data from a sequential, multiple assignment, randomized trial (SMART) to construct empirically an adaptive treatment strategy (ATS) that is more tailored than the ATSs already embedded in a SMART.

Method

We use Q‐learning with data from the Extending Treatment Effectiveness of Naltrexone (ExTENd) SMART (N = 250) to construct empirically an ATS employing naltrexone, behavioral intervention, and telephone disease management to reduce alcohol consumption over 24 weeks in alcohol dependent individuals.

Results

Q‐learning helped to identify a subset of individuals who, despite showing early signs of response to naltrexone, require additional treatment to maintain progress.

Conclusions

Q‐learning can inform the development of more cost‐effective, adaptive treatment strategies for treating substance use disorders.
Chinese National Income, ca. 1661–1933
Authors: Xu Yi , Shi Zhihong , van Leeuwen Bas , Ni Yuping , Zhang Zipeng , Ma Ye
Published: December 2016

In recent decades, national income has become increasingly important as a measure of a nation's economic health. In this study, we used a wide array of primary and secondary sources to arrive at values of the Chinese per capita gross domestic product during the period of 1661–1933. We found a persistent decline in the per capita gross domestic product between the seventeenth and nineteenth centuries, followed by a period of stagnation. This pattern, which shows up in many Asian countries, with the exception of Japan, provides a basis for improving our understanding of the patterns of global economic convergence and divergence.