bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbiota organization is a distinct feature of proximal colorectal cancers
Authors: Dejea Christine M. , Wick Elizabeth C. , Hechenbleikner Elizabeth M. , White James R. , Mark Welch Jessica L. , Rossetti Blair J. , Peterson Scott N. , Snesrud Erik C. , Borisy Gary G. , Lazarev Mark , Stein Ellen , Vadivelu Jamuna , Roslani April C. , Malik Ausuma A. , Wanyiri Jane W. , Goh Khean L. , Thevambiga Iyadorai , Fu Kai , Wan Fengyi , Llosa Nicolas , Housseau Franck , Romans Katharine , Wu XinQun , McAllister Florencia M. , Wu Shaoguang , Vogelstein Bert , Kinzler Kenneth W. , Pardoll Drew M. , Sears Cynthia L. 
Published: December 2014

Significance
We demonstrate, to our knowledge for the first time, that bacterial biofilms are associated with colorectal cancers, one of the leading malignancies in the United States and abroad. Colon biofilms, dense communities of bacteria encased in a likely complex matrix that contact the colon epithelial cells, are nearly universal on right colon tumors. Most remarkably, biofilm presence correlates with bacterial tissue invasion and changes in tissue biology with enhanced cellular proliferation, a basic feature of oncogenic transformation occurring even in colons without evidence of cancer. Microbiome profiling revealed that biofilm communities on paired normal mucosa cluster with tumor microbiomes but lack distinct taxa differences. This work introduces a previously unidentified concept whereby microbial community structural organization exhibits the potential to contribute to disease progression.
Direct measurements of methane emissions from abandoned oil and gas wells in Pennsylvania
Authors: Kang Mary , Kanno Cynthia M. , Reid Matthew C. , Zhang Xin , Mauzerall Denise L. , Celia Michael A. , Chen Yuheng , Onstott Tullis C. 
Published: December 2014

Significance
Recent studies indicate that greenhouse gas emission inventories are likely missing methane emission sources. We conducted the first methane emission measurements from abandoned oil and gas wells and found substantial emissions, particularly from high-emitting abandoned wells. These emissions are not currently considered in any emissions inventory. We scaled methane emissions from our direct measurements of abandoned wells in Pennsylvania and calculate that they represent 4–7% of current total anthropogenic methane emissions in Pennsylvania. Millions of abandoned wells exist across the country and some are likely to be high emitters. Additional measurements of methane emissions from abandoned wells and their inclusion in greenhouse gas inventories will aid in developing and implementing appropriate greenhouse gas emission reduction strategies.
Scalable detection of statistically significant communities and hierarchies, using message passing for modularity
Authors: Zhang Pan , Moore Cristopher 
Published: December 2014

Significance
Most work on community detection does not address the issue of statistical significance, and many algorithms are prone to overfitting. We address this using tools from statistical physics. Rather than trying to find the partition of a network that maximizes the modularity, our approach seeks the consensus of many high-modularity partitions. We do this with a scalable message-passing algorithm, derived by treating the modularity as a Hamiltonian and applying the cavity method. We show analytically that our algorithm succeeds all the way down to the detectability transition in the stochastic block model; it also performs well on real-world networks. It also provides a principled method for determining the number of groups or hierarchies of communities and subcommunities.
Fire responses to postglacial climate change and human impact in northern Patagonia (41–43°S)
Authors: Iglesias Virginia , Whitlock Cathy 
Published: December 2014

SignificanceFire is a key ecological process affecting ecosystem dynamics and services. Fire frequency, intensity, and size reflect complex climate–vegetation–human interactions and their evolution through time. The long-term history of these interactions provides insights into the variability of the ecosystem and a context for future environmental change. We use paleoenvironmental data from the Patagonian forest/steppe border and introduce generalized additive models as trend-detection tools in paleoecology to assess the relative influence of climate, vegetation, and humans in shaping the fire regime. Our results suggest that for the last 18,000 y, fires have been predominantly limited by fuel discontinuity rather than by suitable climate conditions. In contrast to extensive present-day anthropogenic impact, Patagonian ecosystems evolved with minimal human influence prior to European settlement.
Structural basis and dynamics of multidrug recognition in a minimal bacterial multidrug resistance system
Authors: Habazettl Judith , Allan Martin , Jensen Pernille Rose , Sass Hans-Jürgen , Thompson Charles J. , Grzesiek Stephan 
Published: December 2014

Significance
Multidrug recognition is an important phenomenon that is not well understood. TipA, a bacterial transcriptional regulator, constitutes a minimal multidrug resistance system against numerous thiopeptide antibiotics. We show that motions in the millisecond to microsecond time range form the basis of the TipA multidrug recognition mechanism. This may be common to many multidrug recognition systems. The discovery that the structural antibiotic motifs essential for binding to TipA and to the ribosome are identical makes the multidrug recognition mechanism of TipA a useful model for ribosomal thiopeptide binding and current antibiotic drug development.
Structural and functional studies of Bud23–Trm112 reveal 18S rRNA
N
7
-G1575 methylation occurs on late 40S precursor ribosomes
Authors: Létoquart Juliette , Huvelle Emmeline , Wacheul Ludivine , Bourgeois Gabrielle , Zorbas Christiane , Graille Marc , Heurgué-Hamard Valérie , Lafontaine Denis L. J. 
Published: December 2014

Significance
Ribosomes are essential cellular nanomachines responsible for all protein synthesis in vivo. Efficient and faithful ribosome biogenesis requires a plethora of assembly factors whose precise role and timing of action remains to be established. Here we determined the crystal structure of Bud23–Trm112, which is required for efficient pre-rRNA processing steps leading to 18S rRNA synthesis and methylation of 18S rRNA at position G1575. For the first time, to our knowledge, we identified where on Bud23–Trm112 the contacts with precursor ribosomes occur. We further report that the essential helicase Dhr1 interacts directly with Bud23–Trm112, proposing a concerted action of these proteins in ribosome assembly. Finally, we reveal that the methyltransferase activity of Bud23–Trm112 and its requirement for pre-rRNA processing are disconnected in time.
Robust scaling of strength and elastic constants and universal cooperativity in disordered colloidal micropillars
Authors: Strickland Daniel J. , Huang Yun-Ru , Lee Daeyeon , Gianola Daniel S. 
Published: December 2014

Significance
The mechanical response of glassy materials is important in numerous technological and natural processes, yet the link between the embryonic stages of plastic deformation and macroscopic mechanical failure remains elusive. The incipient inelastic rearrangements are believed to be highly cooperative and characterized by a scaling of yield strength and elastic constants. Whether this behavior transcends the nature of bonding is still an open question. Here, we show that disordered colloidal micropillars spanning the spectrum of glassy packing also demonstrate a robust scaling of elastic and plastic properties. Our measured relationship and deduced cooperative rearrangement strains bear striking resemblance to other glassy systems with disparate bonding, implying a universal building block for macroscopic flow.
Wireless gas detection with a smartphone via rf communication
Authors: Azzarelli Joseph M. , Mirica Katherine A. , Ravnsbæk Jens B. , Swager Timothy M. 
Published: December 2014

Significance
This paper describes the first example of an adaption of near-field communication (NFC) technology—in 0.5 billion modern smartphones and mobile devices installed in 2014—toward portable, wireless, non-line-of-sight gas phase chemical sensing. We demonstrate the ability to convert inexpensive commercial NFC tags into chemical sensors that detect and discriminate analytes at part-per-thousand and part-per-million concentrations. This effort merges rational design of conductive nanostructured materials for selective chemical sensing with portable and widely distributed NFC technology to deliver a new method of acquiring chemical information about an NFC tag’s local environment. This paper introduces a concept for distributed chemical sensing by the growing number of people that carry NFC-enabled smartphones, tablets, and other smart devices.
Impact of an immune modulator fingolimod on acute ischemic stroke
Authors: Fu Ying , Zhang Ningnannan , Ren Li , Yan Yaping , Sun Na , Li Yu-Jing , Han Wei , Xue Rong , Liu Qiang , Hao Junwei , Yu Chunshui , Shi Fu-Dong 
Published: December 2014

Significance
In patients with acute ischemic stroke (AIS), the abrupt and massive influx of lymphocytes from the periphery to the ischemic region orchestrates focal inflammatory responses, catalyzes tissue death, and worsens clinical outcomes. In this early phase clinical study, we reduced lymphocyte migration to the brain during the first 72 h of AIS via oral administration of three doses of fingolimod. This administration led to a significant reduction of secondary lesion enlargement, microvascular permeability, and better clinical outcomes during the acute phase and 3-mo follow-up visit. This study will provoke new investigations on the efficacy of modulation of brain inflammation in AIS.
Fibroblasts secrete Slit2 to inhibit fibrocyte differentiation and fibrosis
Authors: Pilling Darrell , Zheng Zhichao , Vakil Varsha , Gomer Richard H. 
Published: December 2014

Significance
A key question in fibrosing diseases is why monocytes do not become fibrocytes in healthy tissues but can become fibrocytes in fibrotic lesions. We show that fibroblasts secrete a signal that inhibits the differentiation of monocytes into fibrocytes. We identify the signal as Slit2 and show that Slit2 levels are low in fibrotic lesions. We also show that injection of Slit2 prevents fibrosis in a mouse model of lung fibrosis. The identification of Slit2 as a key signal in normal tissues that prevents entering monocytes from becoming fibrocytes represents a major advance in our understanding of the regulation of the innate immune system and how fibrosis propagates, as well as a potential novel therapeutic for fibrosis.
Context-dependent incremental timing cells in the primate hippocampus
Authors: Sakon John J. , Naya Yuji , Wirth Sylvia , Suzuki Wendy A. 
Published: December 2014

Significance
Episodic memory refers to the ability to recall specifics of past events in our lives. An essential aspect of events is timing when things occur during an episode. A number of recent studies have shown that the hippocampus, a structure known to be essential to form episodic memories, possesses neurons that explicitly mark moments in time. We add a previously unidentified finding to this work by showing that individual primate hippocampal neurons not only track time, but do so only when specific contextual information (e.g., object identity/location) is cued. These time context-sensitive neurons represent a novel way in which the brain unites disparate streams that comprise an episode and will aid in our understanding of how we store and retrieve episodic memories.
Impact of Antarctic mixed-phase clouds on climate
Authors: Lawson R. Paul , Gettelman Andrew 
Published: December 2014

Significance
Polar regions are foci of climate change, because of more-than-expected warming, problematic remote-sensing retrievals, and large uncertainties about cloud effects on radiation budgets. Antarctica is the world’s most remote, coldest, and driest location. Until recently, researchers have assumed that low-level clouds over the frozen Antarctic Plateau consist mainly of ice crystals. Now, measurements with a unique tethered balloon system and a ground-based lidar show that nearly 50% of clouds in the austral summer contain supercooled water which has a significant impact on the radiative properties of Antarctic clouds. Modifying a global climate model to relax the freezing below −20 °C results in a strong simulated radiative (cooling) effect, affecting the entire Antarctic Continent and extending out into the Southern Ocean.
αCGRP is essential for algesic exocytotic mobilization of TRPV1 channels in peptidergic nociceptors
Authors: Devesa Isabel , Ferrándiz-Huertas Clotilde , Mathivanan Sakthikumar , Wolf Christoph , Luján Rafael , Changeux Jean-Pierre , Ferrer-Montiel Antonio 
Published: December 2014

Significance
Pain is a societal burden with enormous economic and social costs. More than 50% of pain patients find current therapies unsatisfactory. A major reason for this pharmacological failure is our limited understanding of the cellular processes underlying pain. Algesic sensitization of nociceptors is a complex event in pain transduction that involves the potentiation of thermosensory channels. The molecular mechanisms remain controversial because of nociceptor heterogeneity that suggests the existence of cell-type–specific strategies. We show that algesic sensitization of transient receptor potential vanilloid 1 (TRPV1) involves the exocytotic recruitment of new receptors in peptidergic nociceptors and the modulation of channel gating in nonpeptidergic sensory neurons. Furthermore, algesic delivery of TRPV1 channels is concomitant with pro-inflammatory neuropeptide secretion, ensuring rapid modulation of pain transduction.
Overexpression of Q-rich prion-like proteins suppresses polyQ cytotoxicity and alters the polyQ interactome
Authors: Ripaud Leslie , Chumakova Victoria , Antonin Matthias , Hastie Alex R. , Pinkert Stefan , Körner Roman , Ruff Kiersten M. , Pappu Rohit V. , Hornburg Daniel , Mann Matthias , Hartl F. Ulrich , Hipp Mark S. 
Published: December 2014

Significance
Expansion of a poly-glutamine (polyQ) repeat is the causal mutation of several inherited neurological disorders, including Huntington’s disease. In a yeast genetic screen, we identified several proteins with Q-rich, prion-like domains that reduce the toxicity of mutant polyQ proteins when overexpressed. One of these, glycine threonine serine repeat protein (Gts1p), was characterized in more detail. Association with Gts1p did not prevent aggregation but altered the physical properties and the interactome of the aggregates. Specifically, Gts1p expression reduced the sequestration of other prion-like proteins into the polyQ aggregates. These findings link polyQ toxicity in yeast with the coaggregation of prion proteins and show that short Q-rich peptides are able to shield toxic forms of polyQ proteins, directing them into nontoxic aggregates.
GATA2 facilitates steroid receptor coactivator recruitment to the androgen receptor complex
Authors: He Bin , Lanz Rainer B. , Fiskus Warren , Geng Chuandong , Yi Ping , Hartig Sean M. , Rajapakshe Kimal , Shou John , Wei Liping , Shah Shrijal S. , Foley Christopher , Chew Sue Anne , Eedunuri Vijay K. , Bedoya Diego J. , Feng Qin , Minami Takashi , Mitsiades Constantine S. , Frolov Anna , Weigel Nancy L. , Hilsenbeck Susan G. , Rosen Daniel G. , Palzkill Timothy , Ittmann Michael M. , Song Yongcheng , Coarfa Cristian , O’Malley Bert W. , Mitsiades Nicholas 
Published: December 2014

Significance
Androgen receptor (AR) signaling is a key driver of prostate cancer (PC), even in the context of resistance to current therapies, creating an unmet need for novel approaches to inhibit AR. We demonstrate that the transcription factor GATA-binding protein 2 (GATA2) is critical for both AR expression and optimal transcriptional activity. GATA2 colocalizes with AR and Forkhead box protein A1 on chromatin to enhance recruitment of steroid receptor coactivators and formation of the transcriptional holocomplex. A GATA2 inhibitor suppressed the expression and transcriptional function of AR (including the constitutively active splice variants) and exerted potent anticancer activity against PC cells. We propose GATA2 inhibition as a previously unexplored approach to extinguish both ligand-dependent and ligand-independent AR transcriptional activity and to improve clinical outcomes for PC patients.
Antagonist of GH-releasing hormone receptors alleviates experimental ocular inflammation
Authors: Qin Yong Jie , Chan Sun On , Chong Kelvin Kam Lung , Li Benjamin Fuk Loi , Ng Tsz Kin , Yip Yolanda Wong Ying , Chen Haoyu , Zhang Mingzhi , Block Norman L. , Cheung Herman S. , Schally Andrew V. , Pang Chi Pui 
Published: December 2014

Significance
We have shown that the growth hormone-releasing hormone–growth hormone–insulin-like growth factor-1 (GHRH–GH–IGF1) axis is involved in experimentally induced acute inflammation in the iris and ciliary body, where its activation is associated with inflammatory responses. Blocking GHRH–GH–IGF1 axis activity by the GHRH receptor (GHRH-R) antagonist is effective in alleviating inflammatory responses. These findings demonstrate a novel activity of GHRH–GH–IGF1 axis signaling in ocular inflammation and suggest a potential therapeutic application of GHRH-R antagonist.
The influence of playing surface on physiological and performance responses during and after soccer simulation
Authors: Stone Keeron J. , Hughes Michael G. , Stembridge Michael R. , Meyers Robert W. , Newcombe Daniel J. , Oliver Jon L. 
Published: December 2014

AbstractThe aim of this study was to investigate the effect of playing surface on physiological and performance responses during and in the 48 h after simulated soccer match play. Blood lactate, single‐sprint, repeated‐sprint and agility of eight amateur soccer players were assessed throughout a 90‐min soccer‐simulation protocol (SSP) completed on natural turf (NT) and artificial turf. Counter‐movement jump, multiple‐rebound jump, sprint (10 m, 60 m), L‐agility run (L‐AR), creatine kinase (CK) and perception of muscle soreness (PMS) were measured before, immediately after, 24 h and 48 h after exercise. Analyses revealed significant changes in blood lactate and single‐sprint performance (both P < 0.05) during the SSP but with no significant differences between surfaces. Conversely, repeated‐sprint performance demonstrated an interaction effect, with reductions in performance evident on NT only (P < 0.05). Whilst L‐AR and 10‐m sprint performance remained unchanged, 60‐m sprint and multiple‐rebound jump performance were impaired, and PMS and CK were elevated immediately following the SSP (all P < 0.05) but with no surface effects. Although performance, CK and PMS were negatively affected to some degree in the 48 h after the SSP, there was no surface effect. For the artificial and natural surfaces used in the present study, physiological and performance responses to simulated soccer match play appear to be similar. Whilst a potential for small differences in performance response exists during activity, surface type does not affect the pattern of recovery following simulated match play.
The development and validation of the Interpersonal Support in Physical Activity Consultations Observational Tool
Authors: Rouse Peter C. , Duda Joan L. , Ntoumanis Nikos , Jolly Kate , Williams Geoffrey C. 
Published: December 2014

AbstractThis study describes the development and psychometric characteristics of an observational instrument that examines four aspects of interpersonal support (or lack of) provided during physical activity (PA) promotion consultations (i.e., Autonomy Support, Involvement, Structure and Interpersonal Control), as identified by Self‐determination Theory (SDT). The reliability and validity of the Interpersonal Support in Physical Activity Consultations Observational Tool (ISPACOT) were examined within an exploratory randomised control trial. Recorded consultations (N = 42) conducted by qualified PA advisors (N = 14) at 13 leisure centres across the West Midlands (UK) were rated. Intra‐class correlation coefficients (ICC) indicated moderate to high inter‐rater reliability for overall interpersonal support (0.80), and the Autonomy Support (0.74), Involvement (0.73) and Structure (0.91) dimensions, but low reliability for Interpersonal Control (0.35). The advisors, who conducted PA promotion consultations that were rated as low in their interpersonally supportive features, were perceived by their clients as being less supportive (F(1,10) = 5.0, p <.05). Ratings on the ISPACOT differentiated advisors who were trained in SDT principles and those who were not. Overall, the findings provided preliminary evidence for the reliability and convergent validity of the ISPACOT.
Prokinetics Prescribing in Paediatrics
Authors: Mt‐Isa Shahrul , Tomlin Stephen , Sutcliffe Alastair , Underwood Martin , Williamson Paula , Croft Nicholas M. , Ashby Deborah 
Published: December 2014

AbstractObjectives:Domperidone and metoclopramide are prokinetics commonly prescribed off‐label to infants and younger children in an attempt to treat gastro‐oesophageal reflux symptoms. Another prokinetic drug, cisapride, was used but withdrawn in 2000 in the United Kingdom because of serious arrhythmic adverse events. Medicines and Healthcare Products Regulatory Agency issued safety warnings for domperidone in May 2012 and restricted its indications. We report here national primary care prescribing trends and safety signals of these drugs in children.Methods:We used data from the General Practice Research Database between 1990 and 2006 for children <18 years. Descriptive statistics and Poisson regressions were performed to characterise prescribing trends. We examined safety signals in nested case–control studies.Results:The proportion of children <2 years old being prescribed one of the medications doubled during the study period. Prescriptions of domperidone increased 10‐fold, mainly following the withdrawal of cisapride in 2000. Prescriptions of metoclopramide did not change significantly. Despite the increase in prescriptions of domperidone, no new safety signals were identified.Conclusions:These data showed dramatic changes in prescribing of cisapride and domperidone despite the lack of good‐quality supporting evidence. It is possible that these prescribing trends were influenced by published guidelines. Even if produced without robust efficacy and safety evidence, published guidelines can influence clinicians and consequently affect prescribing. Therefore, improving the evidence base on prokinetics to inform future guidelines is vital. The lack of new safety signals during this period would support the development of suitable powered clinical studies.