bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying seasonal population fluxes driving rubella transmission dynamics using mobile phone data
Authors: Wesolowski Amy , Metcalf C. J. E. , Eagle Nathan , Kombich Janeth , Grenfell Bryan T. , Bjørnstad Ottar N. , Lessler Justin , Tatem Andrew J. , Buckee Caroline O. 
Published: August 2015

SignificanceChanging patterns of human mobility can drive seasonal outbreaks of infectious diseases, but limited data about travel behavior and population flux over time have made this idea difficult to quantify. Mobile phone data provide a unique source of information about human travel. Here we quantify seasonal travel patterns using mobile phone data from nearly 15 million anonymous subscribers in Kenya. Using a rich data source of rubella incidence, we show that patterns of population fluxes inferred from mobile phone data are predictive of disease transmission and improve significantly on standard school term time and weather covariates, showing for the first time to our knowledge that mobile phone data capture epidemiologically relevant patterns of movement.
Structural remodeling of bacteriophage T4 and host membranes during infection initiation
Authors: Hu Bo , Margolin William , Molineux Ian J. , Liu Jun 
Published: August 2015

Significance
The bacteriophage T4 tail is a complex nanomachine that undergoes a succession of structural changes as it infects a bacterium. We analyzed cryo-electron microscopic images of T4 at different stages of infection. Three-dimensional visualization of key intermediates revealed unprecedented structural details, allowing a better understanding of this fundamental and highly efficient process. Contrary to common descriptions, most long tail fibers are folded back against the virion before infection, and not all interact with the cell before the short tail fibers irreversibly bind. Sheath contraction drives the tail tube only into the periplasm where, unexpectedly, the cytoplasmic membrane bulges outwards to fuse with the tail tube. Fusion does not require the proton motive force, which only becomes necessary for genome translocation.
Temporal and spatial variation of the human microbiota during pregnancy
Authors: DiGiulio Daniel B. , Callahan Benjamin J. , McMurdie Paul J. , Costello Elizabeth K. , Lyell Deirdre J. , Robaczewska Anna , Sun Christine L. , Goltsman Daniela S. A. , Wong Ronald J. , Shaw Gary , Stevenson David K. , Holmes Susan P. , Relman David A. 
Published: August 2015

Significance
The human indigenous microbial communities (microbiota) play critical roles in health and may be especially important for mother and fetus during pregnancy. Using a case-control cohort of 40 women, we characterized weekly variation in the vaginal, gut, and oral microbiota during and after pregnancy. Microbiota membership remained relatively stable at each body site during pregnancy. An altered vaginal microbial community was associated with preterm birth; this finding was corroborated by an analysis of samples from an additional cohort of nine women. We also discovered an abrupt change in the vaginal microbiota at delivery that persisted in some cases for at least 1 y. Our findings suggest that pregnancy outcomes might be predicted by features of the microbiota early in gestation.
Transcription factors FOXA1 and FOXA2 maintain dopaminergic neuronal properties and control feeding behavior in adult mice
Authors: Pristerà Alessandro , Lin Wei , Kaufmann Anna-Kristin , Brimblecombe Katherine R. , Threlfell Sarah , Dodson Paul D. , Magill Peter J. , Fernandes Cathy , Cragg Stephanie J. , Ang Siew-Lan 
Published: August 2015

Significance
Dopaminergic neurons in the brain control voluntary movement and a variety of cognitive functions, including reward–motivation mechanisms, mood regulation, addiction, and memory. Understanding how dopaminergic neurons' phenotype and function are maintained throughout their life span is of great importance in the light of the diverse roles that they play. Transcription factors FOXA1/2 control dopaminergic neurons' development and then retain their expression in adult neurons. The role of these factors during development is well established, but the meaning of their expression in the adult is still not well understood. We demonstrate here that FOXA1/2 are crucial to maintain key cellular and functional features of dopaminergic neurons in the adult brain. We also show that FOXA1/2-mediated deficits ultimately affect feeding behavior.
Multiple component networks support working memory in prefrontal cortex
Authors: Markowitz David A. , Curtis Clayton E. , Pesaran Bijan 
Published: August 2015

Significance
Human cognition depends on the brain’s ability to remember and manipulate information about recent experience. Although this working memory ability has been linked with the persistent spiking activity of neurons in prefrontal cortex (PFC), the population-scale organization of working memory in this region remains poorly understood. Here we provide the first population-scale map, to our knowledge, of persistent activity across multiple depths and topographic regions of PFC in two monkeys performing a delayed eye movement task. We show that working memory is supported by three functionally specialized networks with different anatomical localizations, and not by a functionally homogeneous network, as commonly believed. These findings reveal specific circuit-level targets for studying the causes of working memory dysfunction in many psychiatric disorders.
The massacre mass grave of Schöneck-Kilianstädten reveals new insights into collective violence in Early Neolithic Central Europe
Authors: Meyer Christian , Lohr Christian , Gronenborn Detlef , Alt Kurt W. 
Published: August 2015

SignificanceThe Early Neolithic massacre-related mass grave of Schöneck-Kilianstädten presented here provides new data and insights for the ongoing discussions of prehistoric warfare in Central Europe. Although several characteristics gleaned from the analysis of the human skeletal remains support and strengthen previous hypotheses based on the few known massacre sites of this time, a pattern of intentional mutilation of violence victims identified here is of special significance. Adding another key site to the evidence for Early Neolithic warfare generally allows more robust and reliable reconstructions of the possible reasons for the extent and frequency of outbreaks of lethal mass violence and the general impact these events had on shaping the further development of the Central European Neolithic.
Amplifying the response of soft actuators by harnessing snap-through instabilities
Authors: Overvelde Johannes T. B. , Kloek Tamara , D’haen Jonas J. A. , Bertoldi Katia 
Published: August 2015

Significance
Although instabilities have traditionally been avoided as they often represent mechanical failure, here we embrace them to amplify the response of fluidic soft actuators. Besides presenting a robust strategy to trigger snap-through instabilities at constant volume in soft fluidic actuators, we also show that the energy released at the onset of the instabilities can be harnessed to trigger instantaneous and significant changes in internal pressure, extension, shape, and exerted force. Therefore, in stark contrast to previously studied soft fluidic actuators, we demonstrate that by harnessing snap-through instabilities it is possible to design and construct systems with highly controllable nonlinear behavior, in which small amounts of fluid suffice to generate large outputs.
Phytochemical diversity drives plant–insect community diversity
Authors: Richards Lora A. , Dyer Lee A. , Forister Matthew L. , Smilanich Angela M. , Dodson Craig D. , Leonard Michael D. , Jeffrey Christopher S. 
Published: August 2015

Significance
Phytochemical diversity is a key component of functional diversity. Challenges in quantifying phytochemical diversity have limited our understanding of the causes and consequences of variation in phytochemical diversity across plant species and families. Here we show that phytochemical diversity across dozens of plant species predicts herbivore diversity, herbivore specialization, phototoxicity, herbivory, and attack by natural enemies. Our approach and findings provide a framework for future investigations focused on uncovering chemical underpinnings of trophic interactions at realistic ecological, geographic, and taxonomic scales, and have implications for the conservation of functional and taxonomic diversity.
Dual allosteric activation mechanisms in monomeric human glucokinase
Authors: Whittington A. Carl , Larion Mioara , Bowler Joseph M. , Ramsey Kristen M. , Brüschweiler Rafael , Miller Brian G. 
Published: August 2015

Significance
Glucokinase (GCK), the body’s primary glucose sensor, displays a unique sigmoidal kinetic response that is a hallmark of allostery. Allostery in GCK is different from textbook models, because the enzyme is monomeric and contains only one glucose binding site. Previously, synthetic activators and activating disease mutations were thought to share a common mechanism of allosteric activation in which GCK is shifted toward a glucose-bound–like state. Using mutagenesis and genetic selection, we identify an activated variant that utilizes a different mechanism. Limited proteolysis and NMR reveal that activation is achieved by modulating the dynamic properties of an active-site loop without perturbing the ensemble structure. This previously undescribed activation mechanism is shown to operate in naturally occurring, hyperinsulinemia-associated disease variants.
Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe
Authors: Leff Jonathan W. , Jones Stuart E. , Prober Suzanne M. , Barberán Albert , Borer Elizabeth T. , Firn Jennifer L. , Harpole W. Stanley , Hobbie Sarah E. , Hofmockel Kirsten S. , Knops Johannes M. H. , McCulley Rebecca L. , La Pierre Kimberly , Risch Anita C. , Seabloom Eric W. , Schütz Martin , Steenbock Christopher , Stevens Carly J. , Fierer Noah 
Published: August 2015

Significance
Human activities have resulted in large increases in the availability of nutrients in terrestrial ecosystems worldwide. Although plant community responses to elevated nutrients have been well studied, soil microbial community responses remain poorly understood, despite their critical importance to ecosystem functioning. Using DNA-sequencing approaches, we assessed the response of soil microbial communities to experimentally added nitrogen and phosphorus at 25 grassland sites across the globe. Our results demonstrate that the composition of these communities shifts in consistent ways with elevated nutrient inputs and that there are corresponding shifts in the ecological attributes of the community members. This study represents an important step forward for understanding the connection between elevated nutrient inputs, shifts in soil microbial communities, and altered ecosystem functioning.
Plasma metabolomic profiles enhance precision medicine for volunteers of normal health
Authors: Guo Lining , Milburn Michael V. , Ryals John A. , Lonergan Shaun C. , Mitchell Matthew W. , Wulff Jacob E. , Alexander Danny C. , Evans Anne M. , Bridgewater Brandi , Miller Luke , Gonzalez-Garay Manuel L. , Caskey C. Thomas 
Published: August 2015

Significance
Metabolomics has been increasingly recognized as a powerful functional tool that integrates the impacts from genetics, environment, microbiota, and xenobiotics. We used a broad-spectrum metabolomics platform to analyze plasma samples from 80 adults of normal health. The comprehensive metabolic profiles provided a functional readout to assess the penetrance of gene mutations identified by whole-exome sequencing on these individuals. Conversely, metabolic abnormalities identified by statistical analysis uncovered potential damaging mutations that were previously unappreciated. Additionally, we found metabolic signatures consistent with early signs of disease conditions and drug effects associated with efficacy and toxicity. Our findings demonstrate that metabolomics could be an effective tool in precision medicine for disease risk assessment and customized drug therapy in clinics.
Screen for multi-SUMO–binding proteins reveals a multi-SIM–binding mechanism for recruitment of the transcriptional regulator ZMYM2 to chromatin
Authors: Aguilar-Martinez Elisa , Chen Xi , Webber Aaron , Mould A. Paul , Seifert Anne , Hay Ronald T. , Sharrocks Andrew D. 
Published: August 2015

SignificanceSmall ubiquitin-like modifier (SUMO) is thought to function by acting as a protein recruitment platform. To date, studies have focused on the role of mono-SUMO and poly-SUMO in the form of linear chains. However, recent findings suggested a role for multi-SUMOylation where several SUMO moieties are spread across numerous proteins found at sites of DNA damage. Here, we used a novel screen to identify dozens of multi-SUMO–binding proteins. We investigated one of these in detail and demonstrate that a multi-SIM–containing SUMO-binding module is required for recruitment of the transcriptional regulator ZMYM2 to chromatin. Because little is known about the function of multi-SUMOylation and multi-SIM–binding proteins, this represents an important conceptual advance in our thinking about how protein SUMOylation might exert its molecular effects.
Structure of BipA in GTP form bound to the ratcheted ribosome
Authors: Kumar Veerendra , Chen Yun , Ero Rya , Ahmed Tofayel , Tan Jackie , Li Zhe , Wong Andrew See Weng , Bhushan Shashi , Gao Yong-Gui 
Published: August 2015

Significance
The regulation of protein synthesis is a vital process in all cells. We have determined the structure of the BPI-inducible protein A (BipA), a GTPase involved in bacterial stress response, in various biologically relevant states, including bound to the ribosome in its active form. Our study provides the first structural basis to our knowedge for BipA working as a ribosome-dependent translational GTPase factor and serves as a crucial step for elucidating BipA functioning in vivo. Because no other stress response factor is known to interact with the A-site tRNA, our findings provide a novel mechanistic insight of translational regulation by BipA. Furthermore, the distinctive structural attributes of ribosome upon BipA binding can shed new light on the translational factor recruitment and GTPase activation mechanisms by the ribosome.
Electrochemically addressable trisradical rotaxanes organized within a metal–organic framework
Authors: McGonigal Paul R. , Deria Pravas , Hod Idan , Moghadam Peyman Z. , Avestro Alyssa-Jennifer , Horwitz Noah E. , Gibbs-Hall Ian C. , Blackburn Anthea K. , Chen Dongyang , Botros Youssry Y. , Wasielewski Michael R. , Snurr Randall Q. , Hupp Joseph T. , Farha Omar K. , Stoddart J. Fraser 
Published: August 2015

Significance
This research paper presents a strategy for the organization of artificial molecular switches based on mechanically interlocked molecules within a porous crystalline framework. Once arranged within the pores of the framework, the electronic state of the switches can be altered by the application of an electrochemical potential. This strategy is particularly useful when it comes to integrating dynamic, stimulus-responsive, mechanically interlocked molecules with the robustness and periodicity of porous solids. The findings of the research establish proof-of-concept for the application of postsynthetic transformations of porous crystalline frameworks in the creation of solid-state molecular switches and machines.
A fish-eye view on the new Arctic lightscape
Authors: Varpe Øystein , Daase Malin , Kristiansen Trond 
Published: August 2015

Abstract
A gigantic light experiment is taking place in the Arctic. Climate change has led to substantial reductions in sea ice extent and thickness in the Arctic Ocean. Sea ice, particularly when snow covered, acts as a lid hindering light to reach the waters underneath. Less ice will therefore mean more light entering the water column, with profound effects on pelagic and benthic ecosystems. Responses through primary production are so far well acknowledged. Here we argue that there is a need to broaden the view to include light-driven effects on fish, as they depend on light to locate prey. We used the Norwegian Earth System Model estimates of past and future sea ice area and thickness in the Arctic and applied attenuation coefficients for ice and snow to estimate light intensity. The results show a dramatic increase in the amount of light predicted to reach the future Arctic Ocean. We combined this insight with mechanistic understanding of how light modulates visual prey-detection and predict that fish will forage more efficiently as sea ice diminishes and that their populations will expand to higher latitudes, at least seasonally. Poleward shifts of boreal fish species have been predicted by many and to some extent observed, but a changing light environment has so far not been considered a driver. Expanding distributions and greater visual predation may restructure ecological relationships throughout the Arctic foodweb and lead to regime shifts. Research efforts should focus on the dynamics of how less sea ice will affect the feeding ecology and habitat usage of fish, particularly the northern limits of distributions. Mechanistic approaches to these topics offer insights beyond statistical correlations and extrapolations, and will help us understand how changing biophysical dynamics in the Arctic influence complex processes including production, predator–prey interactions, trait-evolution, and fisheries.
AGN flickering and chaotic accretion
Authors: King Andrew , Nixon Chris 
Published: August 2015

Abstract
Observational arguments suggest that the growth phases of the supermassive black holes in active galactic nuclei have a characteristic time-scale ∼105 yr. We show that this is the time-scale expected in the chaotic accretion picture of black hole feeding, because of the effect of self-gravity in limiting the mass of any accretion-disc feeding event.
Intubation Biomechanics
Authors: Hindman Bradley J. , From Robert P. , Fontes Ricardo B. , Traynelis Vincent C. , Todd Michael M. , Zimmerman M. Bridget , Puttlitz Christian M. , Santoni Brandon G. 
Published: August 2015

AbstractAbstract
Biomechanics during laryngoscopy revealed similarity of laryngoscope forces and cervical spine motion between humans and cadavers. Repeated intubation procedures changed biomechanics during laryngoscopy in cadavers. In cadavers with a type II odontoid fracture, cervical motion during intubation with either the Macintosh or the Airtraq (Airtraq LLC, USA) did not greatly exceed the range observed in intact cervical spines during the same procedures.
Supplemental Digital Content is available in the text.

Background
The aims of this study are to characterize (1) the cadaver intubation biomechanics, including the effect of repeated intubations, and (2) the relation between intubation force and the motion of an injured cervical segment.

Methods
Fourteen cadavers were serially intubated using force-sensing Macintosh and Airtraq laryngoscopes in random order, with simultaneous cervical spine motion recorded with lateral fluoroscopy. Motion of the C1-C2 segment was measured in the intact and injured state (type II odontoid fracture). Injured C1-C2 motion was proportionately corrected for changes in intubation forces that occurred with repeated intubations.

Results
Cadaver intubation biomechanics were comparable with those of patients in all parameters other than C2-C5 extension. In cadavers, intubation force (set 2/set 1 force ratio = 0.61; 95% CI, 0.46 to 0.81; P = 0.002) and Oc-C5 extension (set 2 − set 1 difference = −6.1 degrees; 95% CI, −11.4 to −0.9; P = 0.025) decreased with repeated intubations. In cadavers, C1-C2 extension did not differ (1) between intact and injured states; or (2) in the injured state, between laryngoscopes (with and without force correction). With force correction, in the injured state, C1-C2 subluxation was greater with the Airtraq (mean difference 2.8 mm; 95% CI, 0.7 to 4.9 mm; P = 0.004).

Conclusions
With limitations, cadavers may be clinically relevant models of intubation biomechanics and cervical spine motion. In the setting of a type II odontoid fracture, C1-C2 motion during intubation with either the Macintosh or the Airtraq does not appear to greatly exceed physiologic values or to have a high likelihood of hyperextension or direct cord compression.
A genomic region containingRNF212andCPLX1is associated with sexually-dimorphic recombination rate variation in Soay sheep (Ovis aries)
Authors: Johnston Susan E. , Bérénos Camillo , Slate Jon , Pemberton Josephine M. 
Published: August 2015

ABSTRACTMeiotic recombination breaks down linkage disequilibrium and forms new haplotypes, meaning thatit is an important driver of diversity in eukaryotic genomes. Understanding the causes of variation in recombination rate is important in interpreting and predicting evolutionary phenomena and forunderstanding the potential of a population to respond to selection. However, despite attention inmodel systems, there remains little data on how recombination rate varies at the individual level in natural populations. Here, we used extensive pedigree and high-density SNP information in a wild population of Soay sheep (Ovis aries) to investigate the genetic architecture of individual autosomal recombination rate. Individual rates were high relative to other mammal systems, and were higher in males than in females (autosomal map lengths of 3748 cM and 2860 cM, respectively). The heritability of autosomal recombination rate was low but significant in both sexes(h2= 0.16 & 0.12 in females and males, respectively). In females, 46.7% of the heritable variation was explained by a sub-telomeric region on chromosome 6; a genome-wide association study showed the strongest associations at the locusRNF212, with further associations observed at a nearby ~374kb region of complete linkage disequilibrium containing three additional candidate loci,CPLX1,GAKandPCGF3. A second region on chromosome 7 containingREC8andRNF212Bexplained 26.2% of the heritable variation in recombination rate in both sexes. Comparative analyses with 40 other sheep breeds showed that haplotypes associated with recombination rates are both old and globally distributed. Both regions have been implicated in rate variation in mice, cattle and humans, suggesting a common genetic architecture of recombination rate variation in mammals.AUTHOR SUMMARYRecombination offers an escape from genetic linkage by forming new combinations of alleles, increasing the potential for populations to respond to selection. Understanding the causes and consequences of individual recombination rates are important in studies of evolution and genetic improvement, yet little is known on how rates vary in natural systems. Using data from a wild population of Soay sheep, we show that individual recombination rate is heritable and differs between the sexes, with the majority of genetic variation in females explained by a genomic region containing thegenesRNF212andCPLX1.