bluuebunny/crossref_metadata_2025_split huggingface dataset:
The genomics of wild yeast populations sheds light on the domestication of man's best (micro) friend
Authors: Eberlein Chris , Leducq Jean‐Baptiste , Landry Christian R. 
Published: October 2015

The domestication of plants, animals and microbes by humans are the longest artificial evolution experiments ever performed. The study of these long‐term experiments can teach us about the genomics of adaptation through the identification of the genetic bases underlying the traits favoured by humans. In laboratory evolution, the characterization of the molecular changes that evolved specifically in some lineages is straightforward because the ancestors are readily available, for instance in the freezer. However, in the case of domesticated species, the ancestor is often missing, which leads to the necessity of going back to nature in order to infer the most likely ancestral state. Significant and relatively recent examples of this approach include wolves as the closest wild relative to domestic dogs (Axelsson et al. 2013) and teosinte as the closest relative to maize (reviewed in Hake & Ross‐Ibarra 2015). In both cases, the joint analysis of domesticated lineages and their wild cousins has been key in reconstructing the molecular history of their domestication. While the identification of closest wild relatives has been done for many plants and animals, these comparisons represent challenges for micro‐organisms. This has been the case for the budding yeast Saccharomyces cerevisiae, whose natural ecological niche is particularly challenging to define. For centuries, this unicellular fungus has been the cellular factory for wine, beer and bread crafting, and currently for bioethanol and drug production. While the recent development of genomics has lead to the identification of many genetic elements associated with important wine characteristics, the historical origin of some of the domesticated wine strains has remained elusive due to the lack of knowledge of their close wild relatives. In this issue of Molecular Ecology, Almeida et al. (2015) identified what is to date the closest known wild population of the wine yeast. This population is found associated with oak trees in Europe, presumably its natural host. Using population genomics analyses, Almeida and colleagues discovered that the initial divergence between natural and domesticated wine yeasts in the Mediterranean region took place around the early days of wine production. Surprisingly, genomic regions that are key to wine production today appeared not to be derived from these natural populations but from genes gained from other yeast species.
Species turnover (β‐diversity) in ectomycorrhizal fungi linked to uptake capacity
Authors: Kranabetter J. M. , Hawkins B. J. , Jones M. D. , Robbins S. , Dyer T. , Li T. 
Published: October 2015

AbstractEctomycorrhizal (EcM) fungal communities may be shaped by both deterministic and stochastic processes, potentially influencing ecosystem development and function. We evaluated community assembly processes for EcM fungi of Pseudotsuga menziesii among 12 sites up to 400 km apart in southwest British Columbia (Canada) by investigating species turnover (β‐diversity) in relation to soil nitrogen (N) availability and physical distance. We then examined functional traits for an N‐related niche by quantifying net fluxes of , and protons on excised root tips from three contrasting sites using a microelectrode ion flux measurement system. EcM fungal communities were well aligned with soil N availability and pH, with no effect of site proximity (distance–decay curve) on species assemblages. Species turnover was significant (β1/2 = 1.48) along soil N gradients, with many more Tomentella species on high N than low N soils, in contrast to Cortinarius species. Ammonium uptake was greatest in the spring on the medium and rich sites and averaged over 190 nmol/m2/s for Tomentella species. The lowest uptake rates of were by nonmycorrhizal roots of axenically grown seedlings (10 nmol/m2/s), followed by Cortinarius species (60 nmol/m2/s). EcM roots from all sites displayed only marginal uptake of nitrate (8.3 nmol/m2/s). These results suggest uptake capacity is an important functional trait influencing the assembly of EcM fungal communities. The diversity of EcM fungal species across the region arguably provides critical belowground adaptations to organic and inorganic N supply that are integral to temperate rainforest ecology.
Regulation of CsrB/C sRNA decay by EIIAGlc of the phosphoenolpyruvate: carbohydrate phosphotransferase system
Authors: Leng Yuanyuan , Vakulskas Christopher A. , Zere Tesfalem R. , Pickering Bradley S. , Watnick Paula I. , Babitzke Paul , Romeo Tony 
Published: October 2015

SummaryCsr is a conserved global regulatory system, which uses the sequence‐specific RNA‐binding protein CsrA to activate or repress gene expression by binding to mRNA and altering translation, stability and/or transcript elongation. In Escherichia coli, CsrA activity is regulated by two sRNAs, CsrB and CsrC, which bind to multiple CsrA dimers, thereby sequestering this protein away from its mRNA targets. Turnover of CsrB/C sRNAs is tightly regulated by a GGDEF‐EAL domain protein, CsrD, which targets them for cleavage by RNase E. Here, we show that EIIAGlc of the glucose‐specific PTS system is also required for the normal decay of these sRNAs and that it acts by binding to the EAL domain of CsrD. Only the unphosphorylated form of EIIAGlc bound to CsrD in vitro and was capable of activating CsrB/C turnover in vivo. Genetic studies confirmed that this mechanism couples CsrB/C sRNA decay to the availability of a preferred carbon source. These findings reveal a new physiological influence on the workings of the Csr system, a novel function for the EAL domain, and an important new way in which EIIAGlc shapes global regulatory circuitry in response to nutritional status.
The nucleotide‐dependent interaction of FlaH and FlaI is essential for assembly and function of the archaellum motor
Authors: Chaudhury Paushali , Neiner Tomasz , D'Imprima Edoardo , Banerjee Ankan , Reindl Sophia , Ghosh Abhrajyoti , Arvai Andrew S. , Mills Deryck J. , van der Does Chris , Tainer John A. , Vonck Janet , Albers Sonja‐Verena 
Published: October 2015

SummaryThe motor of the membrane‐anchored archaeal motility structure, the archaellum, contains FlaX, FlaI and FlaH. FlaX forms a 30 nm ring structure that acts as a scaffold protein and was shown to interact with the bifunctional ATPase FlaI and FlaH. However, the structure and function of FlaH has been enigmatic. Here we present structural and functional analyses of isolated FlaH and archaellum motor subcomplexes. The FlaH crystal structure reveals a RecA/Rad51 family fold with an ATP bound on a conserved and exposed surface, which presumably forms an oligomerization interface. FlaH does not hydrolyze ATP in vitro, but ATP binding to FlaH is essential for its interaction with FlaI and for archaellum assembly. FlaH interacts with the C‐terminus of FlaX, which was earlier shown to be essential for FlaX ring formation and to mediate interaction with FlaI. Electron microscopy reveals that FlaH assembles as a second ring inside the FlaX ring in vitro. Collectively these data reveal central structural mechanisms for FlaH interactions in mediating archaellar assembly: FlaH binding within the FlaX ring and nucleotide‐regulated FlaH binding to FlaI form the archaellar basal body core.
Armigeres subalbatus colonization of damaged pit latrines: a nuisance and potential health risk to residents of resettlement villages in Laos
Authors: HISCOX A. , HIROOKA R. , VONGPHAYLOTH K. , HILL N. , LINDSAY S. W. , GRANDADAM M. , BREY P. T. 
Published: October 2015

AbstractDuring the resettlement of 6500 persons living around the Nam Theun 2 hydroelectric project in Laos, more than 1200 pour‐flush latrines were constructed. To assess the role of these latrines as productive larval habitats for mosquitoes, entomological investigations using Centers for Disease Control (CDC) light traps, visual inspection and emergence trapping were carried out in over 300 latrines during the rainy seasons of 2008–2010. Armigeres subalbatus (Diptera: Culicidae) were nine times more likely to be found in latrines (mean catch: 3.09) than in adjacent bedrooms (mean catch: 0.37) [odds ratio (OR) 9.08, 95% confidence interval (CI) 6.74–15.11] and mosquitoes were active in and around 59% of latrines at dusk. Armigeres subalbatus was strongly associated with latrines with damaged or improperly sealed septic tank covers (OR 5.44, 95% CI 2.02–14.67; P < 0.001). Armigeres subalbatus is a nuisance biter and a putative vector of Japanese encephalitis and dengue viruses. Dengue virus serotype 3 was identified from a single pool of non‐blood‐fed female A. subalbatus using reverse transcription polymerase chain reaction. Maintaining a good seal around septic tanks by covering them with a layer of soil is a simple intervention to block mosquito exit/entry and contribute to vector control in resettlement villages. The scale‐up of this simple, cheap intervention would have global impact in preventing the colonization of septic tanks by nuisance biting and disease‐transmitting mosquitoes.
CO‐EVOLUTIONARY DYNAMICS OF A SOCIAL PARASITE–HOST INTERACTION MODEL: OBLIGATE VERSUS FACULTATIVE SOCIAL PARASITISM
Authors: KANG YUN , FEWELL JENNIFER HARRISON 
Published: October 2015

AbstractHost–parasite co‐evolution can have profound impacts on a wide range of ecological and evolutionary processes, including population dynamics, the maintenance of genetic diversity, and the evolution of recombination. To examine the co‐evolution of quantitative traits in hosts and parasites, we present and study a co‐evolutionary model of a social parasite–host system that incorporates (i) ecological dynamics that feed back into their co‐evolutionary outcomes; (ii) variation in whether the social parasite is obligate or facultative; and (iii) Holling Type II functional responses between host and social parasite, which are particularly suitable for social parasites that face time costs for host location and its social manipulation. We perform local and global analyses for the co‐evolutionary model and the corresponding ecological model. In the absence of evolution, our ecological model analyses imply that an extremely small value of the death rate for facultative social parasites can drive a host extinct globally under certain conditions, while an extremely large value of the death rate can drive the parasite extinct globally. The facultative parasite system can have one, two, or three coexistence equilibria, while the obligate parasite system can have either one or three coexistence equilibria. Multiple coexistence equilibria result in rich dynamics with multiple attractors. The ecological system, in particular, can exhibit bi‐stability between the facultative parasite‐only equilibrium and the coexistence equilibrium when it has two coexistence equilibria. Our analysis on the co‐evolutionary model provides important insights on how co‐evolution can change the ecological and evolutionary outcomes of host–parasite interactions. Our findings suggest that: (i) The host and parasite can select different strategies that may result in local extinction of host or parasite. These strategies can have convergence stability (CS), but may not be evolutionary stable strategies (ESS); (ii) The host and its facultative (or obligate) parasite can have ESS that drive the host (or the obligate parasite) extinct locally; (iii) The dependence of vital rates on the phenotypic trait plays an important role in the CS of both exclusion and coexistence equilibria, as well as their ESS; and (iv) A small variance in the trait difference that measures parasitism efficiency can destabilize the co‐evolutionary system, and generate evolutionary arms‐race dynamics with different host–parasite fluctuating patterns.
Acute Raoultella planticola cystitis in a child with rhabdomyosarcoma of the bladder neck
Authors: Yoon Jong Hyung , Ahn Yo Han , Chun Jong In , Park Hyeon Jin , Park Byung‐Kiu 
Published: October 2015

AbstractRaoultella planticola is a Gram‐negative, non‐motile, aerobic bacillus. It is an environmental bacteria found in soil and water, and a very rare cause of local or systemic infection in humans. Although some adult cases of R. planticola infection have been reported, childhood local or systemic infection caused by R. planticola is very rare. Reported herein is a rare case of acute cystitis due to R. planticola in a 16‐month‐old boy with rhabdomyosarcoma of the bladder neck, and a review of the literature.
Pneumomediastinum, pneumorrhachis and subcutaneous emphysema associated with viral infections: Report of three cases
Authors: Emiralioğlu Nagehan , Ozcan H Nursun , Oğuz Berna , Yalçın Ebru , Doğru Deniz , Özçelik Uğur , Kiper Nural 
Published: October 2015

AbstractSpontaneous pneumomediastinum is usually secondary to alveolar rupture in the pulmonary interstitium, associated with subcutaneous emphysema and occasionally with pneumothorax, but is rarely associated with pneumorrhachis. The leaked air into the pulmonary perivascular interstitium follows the path of least resistance from the mediastinum to the fascial planes of the neck. Air freely communicates via the neural foramina and collects in the epidural space. Pneumorrhachis is defined as the presence of air in the spinal canal, either in the intradural and/or extradural spaces. It is a very rare clinical entity and mostly asymptomatic, hence most probably underdiagnosed. Many pathological and physiological events can lead to alveolar rupture, and these clinical findings can be related to various, mainly traumatic and iatrogenic etiologies. Herein we report three cases of pneumomediastinum, subcutaneous emphysema, interstitial emphysema and pneumorrhachis in two cases, which were related to rhinovirus, human bocavirus and respiratory syncytial virus infection.
Relieving pain and distress during venipuncture: Pilot study of the Japan Environment and Children's Study (JECS)
Authors: Yamamoto‐Hanada Kiwako , Futamura Masaki , Kitazawa Hiroshi , Ohya Yukihiro , Kobayashi Fumio , Kusuda Takeshi , Sanefuji Masafumi , Oda Masako , Mitsubuchi Hiroshi , Shibata Eiji , Tsuji Mayumi , Kayama Fujio , Nakano Yuko , Suda Eiko , Michikawa Takehiro , Katoh Takahiko , Saito Hirohisa 
Published: October 2015

AbstractPain management for needle‐related procedures is poor in Japan. In many countries the use of lidocaine/prilocaine cream for the relief of pain associated with venipuncture has been approved. In children, a psychological approach has also been shown to be effective in reducing pain with venipuncture. We developed a multidisciplinary procedure that combines a cream (2.5% lidocaine and 2.5% prilocaine) and pharmacological approaches such as preparation, education, positioning and distraction. We evaluated the feasibility and acceptability of the procedure for young children. Among 132 pediatric participants, 58.3% did not cry during venipuncture. According to caregiver questionnaire, 71.9% felt that the multidisciplinary procedure eliminated the fear of needle‐related procedures in the children; 90.9% were satisfied with it and 75.8% thought it should be applied to all children undergoing venipuncture. The present results suggest that the multidisciplinary procedure is feasible, acceptable and suitable for use in children undergoing venipuncture.
Making Climate Decisions
Authors: Bradley Richard , Steele Katie 
Published: October 2015

AbstractMany fine‐grained (if not bigger picture) decisions concerning climate change involve significant, even severe, uncertainty. Here, we focus on modelling the decisions of single agents, whether individual persons or groups perceived as corporate entities. We offer a taxonomy of the sources and kinds of uncertainty that arise in framing these decision problems, as well as strategies for making a choice in spite of uncertainty. The aim is to facilitate a more transparent and structured treatment of uncertainty in climate decision making.
Two new taxa of Achnanthidium and Encyonema (Bacillariophyceae) from the Yom River, Thailand, with special reference to the areolae occlusions implying ontogenetic relationship
Authors: Yana Ekkachai , Mayama Shigeki 
Published: October 2015

SummaryWe discovered two new taxa of Achnanthidium and Encyonema occurring with high abundance in the upstream of the Yom River, which is one of four major rivers in Northern Thailand. Achnanthidium pseudoconspicuum var. yomensis var. nov. closely resembles Achnanthidium pseudoconspicuum var. pseudoconspicuum in scanning electron microscopy (SEM), but has clearly different valve morphometry under the light microscopy (LM). Achnanthidium pseudoconspicuum var. yomensis is also similar to A. japonicum in valve morphology under LM, but differs to this species based on SEM observation. Encyonema yuwadeeanum sp. nov. shows similarities to Encyonema leei and Encyonema subkukenanum, but differs in valve shape and/or polar fissure shape. We discuss the possible valve ontogenetic relationship between Achnanthidium and Cymbellales based on the detailed areolae structures of these two new taxa.
Chronically Occluded Arteriovenous Fistula Salvaged by Sharp Needle Recanalization
Authors: Beathard Gerald A. , Eradat Jilbert 
Published: October 2015

AbstractSalvage of a failed arteriovenous access with occlusion of the venous outflow and no alternative for a secondary arteriovenous fistula that would provide for immediate dialysis is a difficult problem for which there is no ideal solution. The present report is such a patient. The patient had a radial‐cephalic fistula represented by only a very short segment, inadequate for effective dialysis. Salvage was accomplished using the sharp needle revascularization technique in order to avoid a prolonged period of central venous catheter use.
Clinical Importance of Intraoperative Cephalic Vein Distensibility as a Predictor of Radiocephalic Arteriovenous Fistula Maturation
Authors: Kim Mi‐Hyeong , Kim Young‐Kyun , Jun Kang‐Woong , Hwang Jeong‐Kye , Kim Sang‐Dong , Kim Jang‐Yong , Park Sun‐Cheol , Kim Yong‐Soo , Moon In‐Sung , Kim Ji‐Il 
Published: October 2015

AbstractRadiocephalic arteriovenous fistula (RCAVF) is the preferred vascular access, but the maturation failure rate is high. Poor vein distensibility is the main cause of maturation failure. There have been several studies regarding vein distensibility, but vein dilation protocol and the cut‐off value predicting maturation failure were inconsistent. We were doubtful that the vein distensibility had been appropriately evaluated, and sought to determine a more clinically applicable parameter. The cephalic vein was dilated via intraluminal hydrostatic pressure during the surgery and the vein size was measured. Maturation failure occurred in 30 patients (22.4%) and was more common in females and in patients who had a previous history of arteriovenous access formation (p = 0.0095 and p = 0.014). The intraoperative postdilation diameter, and the difference between pre and postdilation diameters differed between the two groups (p = 0.0004 and p = 0.0004). The cut‐off value of the postdilation diameter, which indicated a high probability of maturation success, was >4 mm, and the cut‐off value which indicated a higher probability of maturation failure; that is, the difference between the pre and postdilation diameter, was ≤2.2 mm. The degree of distensibility of the cephalic vein may be an important determinant of RCAVF maturation.
Race/Ethnicity and Stop‐and‐Frisk: Past, Present, Future
Authors: Torres Jose 
Published: October 2015

AbstractScholarly debates surrounding stop‐and‐frisk typically assess the effectiveness and lawfulness of stop‐and‐frisk. Notwithstanding these efforts, recent reviews have excluded some recent research that addresses its impact on racial and ethnic immigrants. Understanding how the practice of stop‐and‐frisk affects racial and ethnic immigrants is worth including in reviews of these policies, considering the recent growth of research involving crime and immigrants that largely finds that immigration does not result in higher levels of crime. This review includes recent work showing that overall enforcement – stops and arrests – is higher in immigrant communities despite their lower levels of criminal involvement and recent work exploring differences among first‐generation and second‐generation immigrants in perceptions of police stops. Finally, some suggestions for the future of stop‐and‐frisk research are considered.
On the Streets, Under Arrest: Policing Homelessness in the 21st Century
Authors: Stuart Forrest 
Published: October 2015

AbstractSince the earliest days of the discipline, sociologists have viewed homelessness as a premier index of inequality and poverty more generally. Sociologists have increasingly turned to the regulation and policing of homelessness as a lens for analyzing how a given society understands and interacts with those who exist at the bottom of the social hierarchy. Against this intellectual backdrop, this article traces recent developments in the policing of homelessness, as well as the corresponding academic attempts to make sense of this empirical phenomenon. Doing so demonstrates that a vast majority of analyses have focused narrowly on the punitive and exclusionary functions of policing and, as a result, have tended to overlook issues surrounding differentiated functions, organizational dynamics, spatial contingencies, and questions of agency. This article complicates existing approaches and thereby lays the foundation for a more accurate and nuanced rendering of the policing of homelessness.
Maternal Conflict Behavior Profiles and Child Social Skills
Authors: Boyer Brittany P. , Scott Justin K. , Nelson Jackie A. 
Published: October 2015

AbstractThe current study examined associations between mothers’ behavioral profiles during mother‐child conflict interactions and their children's social skills. This person‐centered approach classified 181 mothers according to their levels of emotional responsiveness, intrusiveness, negativity, and engagement facilitation behaviors during an eight‐minute conflict discussion task with their child. Three distinct classes of mothers were identified using latent profile analysis: sensitive/engaged, moderately sensitive/engaged, and insensitive/disengaged. An analysis of covariance indicated that children of mothers in the sensitive/engaged group had significantly higher social skills than children of mothers in the moderately sensitive/engaged and insensitive/disengaged groups. Results suggest that mother‐child conflict interactions may benefit children's social development when mothers facilitate their children's participation in a highly sensitive manner.