bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lytic phages obscure the cost of antibiotic resistance in Escherichia coli
Authors: Tazzyman Samuel J , Hall Alex R 
Published: September 2014

Abstract
The long-term persistence of antibiotic-resistant bacteria depends on their fitness relative to other genotypes in the absence of drugs. Outside the laboratory, viruses that parasitize bacteria (phages) are ubiquitous, but costs of antibiotic resistance are typically studied in phage-free experimental conditions. We used a mathematical model and experiments with Escherichia coli to show that lytic phages strongly affect the incidence of antibiotic resistance in drug-free conditions. Under phage parasitism, the likelihood that antibiotic-resistant genetic backgrounds spread depends on their initial frequency, mutation rate and intrinsic growth rate relative to drug-susceptible genotypes, because these parameters determine relative rates of phage-resistance evolution on different genetic backgrounds. Moreover, the average cost of antibiotic resistance in terms of intrinsic growth in the antibiotic-free experimental environment was small relative to the benefits of an increased mutation rate in the presence of phages. This is consistent with our theoretical work indicating that, under phage selection, typical costs of antibiotic resistance can be outweighed by realistic increases in mutability if drug resistance and hypermutability are genetically linked, as is frequently observed in clinical isolates. This suggests the long-term distribution of antibiotic resistance depends on the relative rates at which different lineages adapt to other types of selection, which in the case of phage parasitism is probably extremely common, as well as costs of resistance inferred by classical in vitro methods.
Emissions of methane from offshore oil and gas platforms in Southeast Asia
Authors: Nara Hideki , Tanimoto Hiroshi , Tohjima Yasunori , Mukai Hitoshi , Nojiri Yukihiro , Machida Toshinobu 
Published: September 2014

AbstractMethane is a substantial contributor to climate change. It also contributes to maintaining the background levels of tropospheric ozone. Among a variety of CH4 sources, current estimates suggest that CH4 emissions from oil and gas processes account for approximately 20% of worldwide anthropogenic emissions. Here, we report on observational evidence of CH4 emissions from offshore oil and gas platforms in Southeast Asia, detected by a highly time-resolved spectroscopic monitoring technique deployed onboard cargo ships of opportunity. We often encountered CH4 plumes originating from operational flaring/venting and fugitive emissions off the coast of the Malay Peninsula and Borneo. Using night-light imagery from satellites, we discovered more offshore platforms in this region than are accounted for in the emission inventory. Our results demonstrate that current knowledge regarding CH4 emissions from offshore platforms in Southeast Asia has considerable uncertainty and therefore, emission inventories used for modeling and assessment need to be re-examined.
Behavior of bats at wind turbines
Authors: Cryan Paul. M. , Gorresen P. Marcos , Hein Cris D. , Schirmacher Michael R. , Diehl Robert H. , Huso Manuela M. , Hayman David T. S. , Fricker Paul D. , Bonaccorso Frank J. , Johnson Douglas H. , Heist Kevin , Dalton David C. 
Published: September 2014

Significance
Bats are dying in unprecedented numbers at wind turbines, but causes of their susceptibility are unknown. Fatalities peak during low-wind conditions in late summer and autumn and primarily involve species that evolved to roost in trees. Common behaviors of “tree bats” might put them at risk, yet the difficulty of observing high-flying nocturnal animals has limited our understanding of their behaviors around tall structures. We used thermal surveillance cameras for, to our knowledge, the first time to observe behaviors of bats at experimentally manipulated wind turbines over several months. We discovered previously undescribed patterns in the ways bats approach and interact with turbines, suggesting behaviors that evolved at tall trees might be the reason why many bats die at wind turbines.
Structural basis of cellular dNTP regulation by SAMHD1
Authors: Ji Xiaoyun , Tang Chenxiang , Zhao Qi , Wang Wei , Xiong Yong 
Published: September 2014

Significance
SAMHD1 is a dNTPase that depletes the cellular dNTP pool to inhibit the replication of retroviruses, including HIV-1. The dNTPase activity of SAMHD1 also enables the enzyme to be a major regulator of cellular dNTP levels in mammalian cells, in addition to be implicated in the pathogenesis of chronic lymphocytic leukemia (CLL) and Aicardi Goutières syndrome (AGS). Here we present extensive structural and enzymatic data to reveal how SAMHD1 is activated and regulated via the combined actions of GTP and all cellular dNTPs. Our work establishes a complete spectrum of nucleotide binding and the exquisite regulatory mechanism of SAMHD1 in cellular dNTP metabolism, retrovirus restriction, and the pathogenesis of CLL and AGS.
Marine algae and land plants share conserved phytochrome signaling systems
Authors: Duanmu Deqiang , Bachy Charles , Sudek Sebastian , Wong Chee-Hong , Jiménez Valeria , Rockwell Nathan C. , Martin Shelley S. , Ngan Chew Yee , Reistetter Emily N. , van Baren Marijke J. , Price Dana C. , Wei Chia-Lin , Reyes-Prieto Adrian , Lagarias J. Clark , Worden Alexandra Z. 
Published: September 2014

Significance
Phytochromes are photosensory signaling proteins widely distributed in unicellular organisms and multicellular land plants. Best known for their global regulatory roles in photomorphogenesis, plant phytochromes are often assumed to have arisen via gene transfer from the cyanobacterial endosymbiont that gave rise to photosynthetic chloroplast organelles. Our analyses support the scenario that phytochromes were acquired prior to diversification of the Archaeplastida, possibly before the endosymbiosis event. We show that plant phytochromes are structurally and functionally related to those discovered in prasinophytes, an ecologically important group of marine green algae. Based on our studies, we propose that these phytochromes share light-mediated signaling mechanisms with those of plants. Phytochromes presumably perform critical acclimative roles for unicellular marine algae living in fluctuating light environments.
Autoreactive T cells specific for insulin B:11-23 recognize a low-affinity peptide register in human subjects with autoimmune diabetes
Authors: Yang Junbao , Chow I-Ting , Sosinowski Tomasz , Torres-Chinn Nadia , Greenbaum Carla J. , James Eddie A. , Kappler John W. , Davidson Howard W. , Kwok William W. 
Published: September 2014

Significance
The importance of antigenic peptides with low-affinity HLA binding in human autoimmune disease remains unclear. Studies in the nonobese diabetic mouse demonstrate recognition of a crucial insulin epitope presented in a weakly bound register. This work details a direct study of responses to this insulin B-chain peptide in humans. Responses were readily detected in subjects with type 1 diabetes. Furthermore, T-cell clones were shown to recognize the peptide presented in a weakly bound alternative register. These findings confirm the relevance of immune recognition of this segment of the insulin B-chain in human disease and highlight a mechanism shared by mouse and man through which T cells that recognize a weakly bound peptide can circumvent tolerance mechanisms.
The multifunctionality offiiin Gulf Pidgin Arabic
Authors: Bakir Murtadha J. 
Published: September 2014

The paper is a descriptive account of the various grammatical functions of the particlefiiin the grammar of Gulf Pidgin Arabic, the contact system that has developed in the Arab countries of the Arabian Gulf for use between the Arabic-speaking native citizens and the expatriate workforce in these countries. It aims at discussing the grammatical multifunctionality of this element and the factors behind the expansion of its grammatical functions, when it was adopted from the lexifier Gulf Arabic.In Gulf Arabic,fiiis used as a preposition and as an existential predicate. When it was adopted into GPA,fiialso assumed the role of a possession marker and predication marker in non-verbal subject-predicate sentences and sentences with verbal predicates. A similar expansion in grammatical roles has affected its negative counterpartmaafii, which is used as a negative offiiin its role as an existential predicate in Gulf Arabic. In GPA the use ofmaafiihas also been expanded so that it is now used as a universal negator in the language, regardless of the predicate or sentence type. The paper investigates the factors that motivated this extension in the uses offii/maafiiand argues that it is not transfer-induced. Rather, language-internal motivation and universal tendencies are more legitimate candidates for the forces lying behind this process.
Influence of Habitat Characteristics on Shore‐Spawning Kokanee
Authors: Whitlock Steven L. , Quist Michael C. , Dux Andrew M. 
Published: September 2014

AbstractSockeye Salmon Oncorhynchus nerka and kokanee (lacustrine Sockeye Salmon) commonly spawn in both lentic and lotic environments; however, the habitat requirements of shore spawners are virtually unknown relative to those of stream spawners. A laboratory experiment and an in situ incubation study were conducted to better understand the influence of habitat characteristics on the shoreline incubation success of kokanee. The laboratory experiment assessed kokanee intragravel survival, fry emergence, and fry condition in response to eight substrate treatments. The in situ study, conducted at three major shoreline spawning sites in Lake Pend Oreille, Idaho, evaluated the effect of depth, substrate composition, dissolved oxygen, shoreline slope, and groundwater on intragravel survival. Substrate size composition was generally a poor predictor of survival in both the laboratory experiment and in situ study; although, fry condition and counts of emerged fry in the laboratory were lowest for the substrate treatment that had the highest proportion of fine sediment. Results of the in situ study suggest that groundwater flow plays an important role in enhancing intragravel survival in habitats generally considered unsuitable for spawning.Received January 7, 2014; accepted May 28, 2014
Matching Bacteriological and Medico-Administrative Databases Is Efficient for a Computer-Enhanced Surveillance of Surgical Site Infections: Retrospective Analysis of 4,400 Surgical Procedures in a French University Hospital
Authors: Leclère Brice , Lasserre Camille , Bourigault Céline , Juvin Marie-Emmanuelle , Chaillet Marie-Pierre , Mauduit Nicolas , Caillon Jocelyne , Hanf Matthieu ,   SSI Study Group
Published: September 2014

Objective.Our goal was to estimate the performance statistics of an electronic surveillance system for surgical site infections (SSIs), generally applicable in French hospitalsMethods.Three detection algorithms using 2 different data sources were tested retrospectively on 9 types of surgical procedures performed between January 2010 and December 2011 in the University Hospital of Nantes. The first algorithm was based on administrative codes, the second was based on bacteriological data, and the third used both data sources. For each algorithm, sensitivity, specificity, and positive and negative predictive values (PPV and NPV) were calculated. The reference method was the hospital’s routine surveillance: a comprehensive review of the computerized medical charts of the patients who underwent one of the targeted procedures during the study period.Setting.A 3,000-bed teaching hospital in western France.Population.We analyzed 4,400 targeted surgical procedures.Results.Sensitivity results varied significantly between the three algorithms, from 25% (95% confidence interval, 17–33) when using only administrative codes to 87% (80%–93%) with the bacteriological data and 90% (85%–96%) with the combined algorithm. Fewer variations were observed for specificity (91%–98%), PPV (21%–25%), and NPV (98% to nearly 100%). Overall, performance statistics were higher for deep SSIs than for superficial infections.Conclusions.A reliable computer-enhanced SSI surveillance can easily be implemented in French hospitals using common data sources. This should allow infection control professionals to spend more time on prevention and education duties. However, a multicenter study should be conducted to assess the generalizability of this method.Infect Control Hosp Epidemiol 2014;35(11):1330–1335
Domestic Architecture, Ancient Israel
Authors: Meyers Carol 
Published: September 2014

Since the advent of agriculture, all humans have lived in built environments, and traditional societies typically produce living spaces that exhibit considerable uniformity. Domestic architecture, ancient Israel refers to the typical structures that housed most Israelite families in the Iron Age (c. 1200–587 bce). Although some house forms that existed in the pre-Israelite periods continued into the Iron Age, mainly in enclaves of non-Israelites, one house form came to dominate in settlements identified as Israelite. This type is called by various names. It was first identified as a rectangular space divided into three longitudinal spaces and, at the back, one horizontal space, creating four rooms; it was thus designated a “four-room house” (and more recently a “longitudinal four-space house”). However, as more excavated examples became known, it became clear that this house type had many variations, some having fewer than four rooms and many, especially when second stories are taken into account, having considerably more. Thus, because a row of pillars typically separates two of the longitudinal spaces, they are sometimes called “pillared” houses or “pillar-courtyard” houses. Either way, the location of courtyard space in these buildings is not clear. The function of these structures was not only to provide shelter from the elements or from enemies; it was also the workspace for many of the activities that were essential for the survival of the agriculturalists who comprised the great majority of the Israelite population. Houses served as places to sleep and eat and also to carry out basic economic functions: preparing food, making and using essential household items (e.g., textiles, pottery, baskets), and storing provisions and implements. They also were the settings for religious activities and local social and political as well as familial interactions. In addition, the organization of space in a dwelling probably embodied and communicated cultural values.
Charles Darwin
Authors: Radick Gregory 
Published: September 2014

Anyone beginning to learn about Charles Darwin (b. 1809–d. 1882) will sooner or later need to reckon with the vast body of writings by him and about him. This bibliographic guide aims to help newcomers find their way to the best of classic and recent scholarship. As the major episodes and achievements of Darwin’s life organize the main part of this guide, it is well to start with a brief biographical sketch. Born and educated in the English town of Shrewsbury, Darwin attended Edinburgh University medical school and then Cambridge University, where he received clerical-scientific training. Next came five years traveling around the world aboard HMS Beagle (1831–1836), followed by several years of intense geological publishing and private theorizing from a base in London. It was in this period that Darwin developed many of his distinctive ideas about the evolution or, to use the vocabulary of the day, “transmutation” of species, including the two most important: that living and fossil species belong to a branching “tree of life;” and that much of the evolutionary change propelling the gradual growth of this tree is due to a process that Darwin called “natural selection.” The decades from 1842 to 1882, spent largely at Down House in Kent with his wife Emma and their ever more numerous children, were immensely productive, domestically contented, physically trying (due to a mysterious illness), and—after the publication of the Origin of Species in 1859—scientifically controversial. From start to finish, it was a life of great privilege. Darwin’s grandfathers were the pottery magnate Josiah Wedgwood and the physician, poet, and scientific (indeed evolutionary) thinker Erasmus Darwin. In an era when no one in Britain could study for a university science degree, young Charles received the best scientific education available, especially from the naturalist Robert Grant at Edinburgh and the geologist Adam Sedgwick and botanist John Stevens Henslow at Cambridge. Darwin’s costs on the Beagle voyage were covered courtesy of his wealthy father, Robert. On returning from the voyage, Darwin moved easily among the London scientific elite, becoming close with Charles Lyell, whose books on gradualist geology Darwin had absorbed. Nor did it hurt that, between Darwin family money and the Wedgwood family money that came with marriage to Emma (his first cousin), Darwin was very rich, leaving him free—when not undone by illness—to devote himself fully to his scientific pursuits.
Pediatric Urology Patients With Megaureter May Have a Risk of Contracting Crohn Disease
Authors: Kolho Kaija‐Leena , Taskinen Seppo , Rintala Risto J. 
Published: September 2014

ABSTRACTCrohn disease (CD) may develop at any age, but is most typically diagnosed in late adolescence and early adulthood. To the best of our knowledge, there are no reports showing that congenital urological abnormalities may be associated to CD. We describe 5 pediatric patients who had ureteral/urethral abnormalities in their infancy and developed CD during subsequent years. The occurrence of CD in these patients constitutes a novel potential association.
Eating Behaviors and Quality of Life in Preadolescents at Risk for Obesity With and Without Abdominal Pain
Authors: Crowell Michael D. , Murphy Tasha B. , Levy Rona L. , Langer Shelby L. , Kunin‐Batson Alicia , Seburg Elisabeth M. , Senso Meghan , Sherwood Nancy E. 
Published: September 2014

ABSTRACTObjectives:We evaluated eating behaviors and quality of life (QOL) in preadolescent children at risk for obesity, with and without abdominal pain (AP).Methods:Participants were parent–child dyads enrolled in a randomized, controlled obesity prevention trial. The children were between 5 and 10 years of age and at risk for obesity (70th–95th percentile of body mass index, n = 420). Parents completed measures of their child's eating behaviors, QOL, AP, and bowel function and their own depression status, concern about child weight, and feeding practices. Children's height and weight were also measured.Results:Children with frequent AP (≥2/month, n = 103) were compared with children reporting infrequent AP (<2/month, n = 312). Age and body mass index did not differ between groups, but AP was more prevalent in girls. Child emotional overeating and parental depression scores were higher in the frequent AP group (P < 0.01), and child QOL was lower (P < 0.01). In multivariable analysis, female gender (odds ratio [OR] 2.18, 95% confidence interval [CI] 1.20–3.97), emotional overeating (OR 2.28, 95% CI 1.37–3.81), and parental depression (OR 1.23, 95% CI 1.12–1.35) were associated with more frequent AP. Secondary analyses were completed for children who met Rome III criteria for irritable bowel syndrome.Conclusions:Clinicians working with children with AP at risk for obesity should consider assessing for and, when appropriate, addressing parent and child factors that could exacerbate AP.
Intestinal Failure–Associated Liver Disease
Authors: Lacaille Florence , Gupte Girish , Colomb Virginie , D'Antiga Lorenzo , Hartman Corina , Hojsak Iva , Kolacek Sanja , Puntis John , Shamir Raanan 
Published: September 2014

ABSTRACTIntestinal failure–associated liver disease is the most prevalent complication affecting children with intestinal failure receiving long‐term parenteral nutrition. This paper reviews the definition, diagnostic criteria, pathogenesis, and risk factors. The authors discuss the role of enteral nutrition, parenteral nutrition, and its components, especially lipid emulsions. The authors also discuss the surgical treatment, including intestinal transplantation, its indications, technique, and results, and emphasise the importance of specialised intestinal failure centres.
The Role of Plasma Membrane Aquaporins in Regulating the Bundle Sheath-Mesophyll Continuum and Leaf Hydraulics
Authors: Sade Nir , Shatil-Cohen Arava , Attia Ziv , Maurel Christophe , Boursiac Yann , Kelly Gilor , Granot David , Yaaran Adi , Lerner Stephen , Moshelion Menachem 
Published: September 2014

AbstractOur understanding of the cellular role of aquaporins (AQPs) in the regulation of whole-plant hydraulics, in general, and extravascular, radial hydraulic conductance in leaves (Kleaf), in particular, is still fairly limited. We hypothesized that the AQPs of the vascular bundle sheath (BS) cells regulate Kleaf. To examine this hypothesis, AQP genes were silenced using artificial microRNAs that were expressed constitutively or specifically targeted to the BS. MicroRNA sequences were designed to target all five AQP genes from the PLASMA MEMBRANE-INTRINSIC PROTEIN1 (PIP1) subfamily. Our results show that the constitutively silenced PIP1 (35S promoter) plants had decreased PIP1 transcript and protein levels and decreased mesophyll and BS osmotic water permeability (Pf), mesophyll conductance of CO2, photosynthesis, Kleaf, transpiration, and shoot biomass. Plants in which the PIP1 subfamily was silenced only in the BS (SCARECROW:microRNA plants) exhibited decreased mesophyll and BS Pf and decreased Kleaf but no decreases in the rest of the parameters listed above, with the net result of increased shoot biomass. We excluded the possibility of SCARECROW promoter activity in the mesophyll. Hence, the fact that SCARECROW:microRNA mesophyll exhibited reduced Pf, but not reduced mesophyll conductance of CO2, suggests that the BS-mesophyll hydraulic continuum acts as a feed-forward control signal. The role of AQPs in the hierarchy of the hydraulic signal pathway controlling leaf water status under normal and limited-water conditions is discussed.