bluuebunny/crossref_metadata_2025 huggingface dataset:
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.
Conformational cycle and ion-coupling mechanism of the Na
+
/hydantoin transporter Mhp1
Authors: Kazmier Kelli , Sharma Shruti , Islam Shahidul M. , Roux Benoît , Mchaourab Hassane S.
Published: September 2014

Significance

Na
+
-coupled symporters use the cellular Na
+
gradient to power transport of physiologically important molecules across the lipid membrane. However, the mechanism by which binding and dissociation of Na
+
drive transport remains undefined. This work investigated the Na
+
/hydantoin transporter Mhp1, a member of the LeuT-fold class of transporters, to describe the conformations sampled during its transport cycle and elucidate the ligand-induced shifts in its conformational equilibrium. The results of this study suggest that Mhp1 isomerization between inward- and outward-facing conformations are Na
+
-independent and that coupling to the Na
+
gradient occurs through modulation of substrate affinity by Na
+
coordination. A previously unidentified model of Mhp1 transport defined by ligand-independent equilibrium fluctuations emerges from this work, offering a new perspective on Na
+
-coupled symport in the LeuT-fold.
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 morphosyntax and prosody of topic and focus in Juba Arabic
Authors: Manfredi Stefano , Tosco Mauro
Published: September 2014

The article discusses the information structure of Juba Arabic, an Arabic-based pidgincreole of South Sudan, showing how the expression of topic and focus is the result of a complex interaction of morphosyntactic and prosodic means. While the lexical elements used in the expression of topic and focus are Arabic-derived, no such influence can be found in the prosody. Both topic- and focus-marked utterances can be opposed to neutral ones. Topics are marked syntactically through left dislocation as well as prosodically. Morphosyntactic means include the use of the ‘almost-dedicated’ markerzátufor marking contrastive focus and the two dedicated particlesyáwuandyawú, both derived from the multifunctional elementya. The articles further explores the grammaticalization path leading to the dedicated focus particles of Juba Arabic.
Juba Arabic as a written language
Authors: Miller Catherine
Published: September 2014

This paper deals with the issue of Juba Arabic (JA) as a written language and investigates various written materials produced from early 20th century up to the early 21st century. The investigated writings are presented in their socio-historical context in order to determine in which ways genres and contexts impact writing practices, particularly regarding orthographic and grammatical choices. These choices are analyzed following the notions of sameness and distance used for evaluating literacy processes in non-standard languages. The paper highlights the key moments and key agents of the codification of JA as a written language and the new developments led by the use of the internet.
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.
Functive phrases in typological and diachronic perspective
Authors: Creissels Denis
Published: September 2014

This paper is concerned with a particular semantic type of noun phrases in secondary predicate function, illustrated byas a negotiatorinHe was sent as a negotiator. It explores the cross-linguistic regularities in the polysemy patterns characteristic of the markers and constructions having the expression of this meaning as one of their possible uses, and discusses the grammaticalization paths in which they are involved.
Influence of Habitat Characteristics on Shore‐Spawning Kokanee
Authors: Whitlock Steven L. , Quist Michael C. , Dux Andrew M.
Published: September 2014

Sockeye 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
Immunoglobulin E plays an immunoregulatory role in lupus
Authors: Dema Barbara , Charles Nicolas , Pellefigues Christophe , Ricks Tiffany K. , Suzuki Ryo , Jiang Chao , Scheffel Jorg , Hasni Sarfaraz , Hoffman Victoria , Jablonski Mathieu , Sacré Karim , Gobert Delphine , Papo Thomas , Daugas Eric , Crampton Steve , Bolland Silvia , Rivera Juan
Published: September 2014

The (patho)physiological role of IgE in nonallergic inflammatory diseases is not well understood. Here, we explored the effect of IgE deficiency on the inflammatory response in FcγRIIB-deficient mice as well as in mice carrying both a deletion of FcγRIIB and the chromosomal translocation of Y-linked autoimmune acceleration (Yaa) that hastens and results in a more aggressive lupuslike disease in these mice. The findings show that deficiency of IgE delays disease development and severity as demonstrated by reduced autoantibody production and amelioration of organ pathologies. This was associated with decreased numbers of plasma cells and reduced levels of IgG2b and IgG3. Unexpectedly, the loss of IgE also caused a striking decrease of immune cell infiltration in secondary lymphoid organs with a marked effect on the presence of dendritic cells, monocytes, neutrophils, and eosinophils in these organs and decreased activation of basophils. The presence of autoreactive IgE in human systemic lupus erythematosus subjects was also associated with increased basophil activation and enhanced disease activity. These findings argue that IgE facilitates the amplification of autoimmune inflammation.
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 hospitals

Methods.

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.
Risk Communication
Authors: Ruhrmann Georg , Guenther Lars
Published: September 2014

Many natural disasters and industrial accidents are not unforeseen; in many cases, scientists and other experts have conducted analyses and communicated the potential risks in advance. When a disaster does occur, journalists and the media react immediately. Politicians and administrators, spurred by this media coverage, then begin to work to change laws and regulations. Finally, representatives from the business sector not only change production processes and products but also invest in new research and public relations: this is done to shape media coverage in the event of another accident or disaster and to inform the public and reach acceptance of risks and uncertainty. A theory of risk communication, however, is only beginning to develop. The term risk communication appeared for the first time in the mid-1980s, as an interdisciplinary field bringing together a wide array of disciplines: economics, sociology, psychology, and communication research (Jungermann, et al. 1988; Lundgreen and McKaien 2013, cited under Communication about Risks). Analyses dealing with risk communication describe and explain (1) what persons communicate in what ways about risks, (2) how the mass media covers risks, and (3) what influences the way the general public receives, understands, and uses risk-related information. Based in the United States and beginning in the late 1960s—and supported by several major industrial accidents (e.g., the Bhopal gas leak and the Chernobyl [see Chernousenko 1991] and the Three Mile Island nuclear meltdowns)—a scientific and political controversy was ignited. Key issues were (1) how experts perceive and assess risks; (2) how journalists, the media, and the general public perceive and evaluate risks based on expert opinion; and (3) if a dialogue between experts and non-experts would result in more acceptance toward the undesirable but inevitable consequences of risks. Risk communication research explores the general public’s concerns regarding important scientific findings, technological innovations, and their social consequences, as well as the skepticism of experts, journalists, and information recipients toward uncertain consequences of technological innovations. These forces can be seen both in media coverage about science and in public-relations materials. Risk communication research emphasizes that basic research and innovations are associated with risks but that these risks are necessary to increase wealth and knowledge.
The Kibbutz
Authors: Getz Shlomo
Published: September 2014

The first kibbutz was founded in 1910 and since then more and more kibbutzim were established, first in Palestine under Turkish rule, followed by British control and then in Israel. Today a total of 270 kibbutzim (plural of “kibbutz”) are found with a population of about 140,000, less than 2 percent of the total population of Israel. The size of kibbutzim varies from small kibbutzim with less than 100 members to larger ones with about 800 members and a total population of more than 1,200 inhabitants. The main values upon which the kibbutz were originally based are: (1) equality among members, creating an environment in which members receive their needs from the community and in which each contributes to it according to their ability; (2) common ownership, involving common ownership of the means of production and consumption; (3) mutual responsibility; (4) direct democracy in local governance and the practice of rotation of all officeholders; (5) Self-labor (i.e., without hired labor), deriving from the socialist ideal not to exploit hired labor. Kibbutz members had to supply all the demands of running a community with their own labor; in practice, kibbutz members receive equal budgets and special additions for individual needs, members own and operate kibbutz assets in common, working together in kibbutz-owned economic ventures, eating their meals in central dining halls, raising their children in communal centers for children that serve also as dormitories, and living in kibbutz-owned housing. The commune and the settlement are one entity: the geographical-municipal entity and the social community, the kibbutz, are congruent. Variations among kibbutzim (e.g., some of the first established kibbutzim had familial sleeping arrangements) are found. The kibbutz has never been static and has always been in a state of change. The economy of the kibbutzim was originally based on agriculture; today kibbutzim rely mostly on industry and many members (an average of 30 percent) work outside the kibbutz. The communal sleeping arrangement of children has been abolished and children stay in the homes of their parents. The method of distributing goods to members has slowly changed. Thus in the 1970s, when the economic situation of the kibbutzim was thriving, the “all-inclusive budget” replaced the small “personal budget.” Later, in many kibbutzim during the 1980s, a lump sum of money was given to members. But the most fundamental changes took place at the end of the 1980s, following an economic crisis that produced demographic and ideological crises. Changes took a new direction, leading to a deep transformation in most of the kibbutzim. The new type of kibbutz, called “renewed kibbutz,” is based on differential salaries, private ownership of kibbutz assets, and private ownership of housing. Consequently, “is the kibbutz still a kibbutz?” is a question asked by many kibbutz members and scholars.
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.
Creationism
Authors: Ruse Michael
Published: September 2014

Creationism in the broadest sense refers to God as Creator. It is an essential element in the beliefs of the so-called Abrahamic religions (Judaism, Christianity, and Islam) and centers on the claim that God made the physical world out of nothing. However, more recently “creationism” has been appropriated for an idiosyncratic version of Protestant Christianity, American made, and dating from the early 19th century. At the beginning of the 20th century a series of pamphlets, known as the “Fundamentals,” gave a name to the overall position of a literal reading of the Bible, and this was followed by legal efforts in parts of the United States to enforce exclusion of nonbiblical ideas (first and foremost, evolution) from the state-supported schools of the Union. In 1925 in Tennessee a young schoolteacher named John Thomas Scopes was prosecuted for teaching that humans have natural origins. Although he was found guilty, the conviction was overturned on a technicality. Then some thirty years later, thanks to the book Genesis Flood (1961), written by biblical scholar John C. Whitcomb and hydraulic engineer Henry M. Morris, the modern creationism movement was born. Matters came to a climax in 1981 when an Arkansas state law mandated “balanced treatment” between evolution and creationism (now often known as “creation science” or “scientific creationism”). A challenge was mounted, and the teaching of creationism was judged unconstitutional. In the early 1990s, the shift was made to arguing that the problem with much science, especially science that challenges a literalistic reading of the Bible, is that it is overly reliant on the materialistic atheistic doctrine of “naturalism.” Backed later in the decade by the writings of both those trained in the sciences and those trained in the humanities, and backed financially by the Discovery Institute in Seattle, so-called intelligent design theory (IDT) elbowed aside the more traditional creationism. In 2005 after a court case in Dover, Pennsylvania, it was ruled that IDT violated the First Amendment separation of church and state no less than scientific creationism did.
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

Crohn 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

Objectives:

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

Intestinal 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.
On the challenges and mechanisms of embodied decisions
Authors: Cisek Paul , Pastor-Bernier Alexandre
Published: September 2014

Neurophysiological studies of decision-making have focused primarily on elucidating the mechanisms of classic economic decisions, for which the relevant variables are the values of expected outcomes and action is simply the means of reporting the selected choice. By contrast, here we focus on the particular challenges of embodied decision-making faced by animals interacting with their environment in real time. In such scenarios, the choices themselves as well as their relative costs and benefits are defined by the momentary geometry of the immediate environment and change continuously during ongoing activity. To deal with the demands of embodied activity, animals require an architecture in which the sensorimotor specification of potential actions, their valuation, selection and even execution can all take place in parallel. Here, we review behavioural and neurophysiological data supporting a proposed brain architecture for dealing with such scenarios, which we argue set the evolutionary foundation for the organization of the mammalian brain.
Pantoea coffeiphila sp. nov., cause of the ‘potato taste’ of Arabica coffee from the African Great Lakes region
Authors: Gueule Dominique , Fourny Gérard , Ageron Elisabeth , Le Flèche-Matéos Anne , Vandenbogaert Mathias , Grimont Patrick A. D. , Cilas Christian
Published: September 2014

Six isolates recovered from coffee seeds giving off a potato-like flavour were studied. Gene sequencing (rrs and rpoB) showed they belong to the genus

Pantoea

. By DNA–DNA hybridization, the isolates constituted a genomic species with less than 17 % relatedness to 96 strains representing enterobacterial species. Multilocus sequence analysis (gyrB, rpoB, atpD and infB genes) showed the isolates to represent a discrete species of the genus

Pantoea

. Nutritional versatility of the novel species was poor. The novel species is proposed as Pantoea coffeiphila sp.nov. and its type strain is Ca04T ( = CIP 110718T = DSM 28482T).
Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures
Authors: Sytnikova Yuliya A. , Rahman Reazur , Chirn Gung-wei , Clark Josef P. , Lau Nelson C.
Published: September 2014

Piwi proteins and Piwi-interacting RNAs (piRNAs) repress transposable elements (TEs) from mobilizing in gonadal cells. To determine the spectrum of piRNA-regulated targets that may extend beyond TEs, we conducted a genome-wide survey for transcripts associated with PIWI and for transcripts affected by PIWI knockdown in Drosophila ovarian somatic sheet (OSS) cells, a follicle cell line expressing the Piwi pathway. Despite the immense sequence diversity among OSS cell piRNAs, our analysis indicates that TE transcripts are the major transcripts associated with and directly regulated by PIWI. However, several coding genes were indirectly regulated by PIWI via an adjacent de novo TE insertion that generated a nascent TE transcript. Interestingly, we noticed that PIWI-regulated genes in OSS cells greatly differed from genes affected in a related follicle cell culture, ovarian somatic cells (OSCs). Therefore, we characterized the distinct genomic TE insertions across four OSS and OSC lines and discovered dynamic TE landscapes in gonadal cultures that were defined by a subset of active TEs. Particular de novo TEs appeared to stimulate the expression of novel candidate long noncoding RNAs (lncRNAs) in a cell lineage-specific manner, and some of these TE-associated lncRNAs were associated with PIWI and overlapped PIWI-regulated genes. Our analyses of OSCs and OSS cells demonstrate that despite having a Piwi pathway to suppress endogenous mobile elements, gonadal cell TE landscapes can still dramatically change and create transcriptome diversity.
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

Our 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.
Experiences with making diffraction image data available: what metadata do we need to archive?
Authors: Kroon-Batenburg Loes M. J. , Helliwell John R.
Published: September 2014

Recently, the IUCr (International Union of Crystallography) initiated the formation of a Diffraction Data Deposition Working Group with the aim of developing standards for the representation of raw diffraction data associated with the publication of structural papers. Archiving of raw data serves several goals: to improve the record of science, to verify the reproducibility and to allow detailed checks of scientific data, safeguarding against fraud and to allow reanalysis with future improved techniques. A means of studying this issue is to submit exemplar publications with associated raw data and metadata. In a recent study of the binding of cisplatin and carboplatin to histidine in lysozyme crystals under several conditions, the possible effects of the equipment and X-ray diffraction data-processing software on the occupancies andBfactors of the bound Pt compounds were compared. Initially, 35.3 GB of data were transferred from Manchester to Utrecht to be processed withEVAL. A detailed description and discussion of the availability of metadata was published in a paper that was linked to a local raw data archive at Utrecht University and also mirrored at the TARDIS raw diffraction data archive in Australia. By making these raw diffraction data sets available with the article, it is possible for the diffraction community to make their own evaluation. This led to one of the authors ofXDS(K. Diederichs) to re-integrate the data from crystals that supposedly solely contained bound carboplatin, resulting in the analysis of partially occupied chlorine anomalous electron densities near the Pt-binding sites and the use of several criteria to more carefully assess the diffraction resolution limit. General arguments for archiving raw data, the possibilities of doing so and the requirement of resources are discussed. The problems associated with a partially unknown experimental setup, which preferably should be available as metadata, is discussed. Current thoughts on data compression are summarized, which could be a solution especially for pixel-device data sets with fine slicing that may otherwise present an unmanageable amount of data.
Multi-crystal native SAD analysis at 6 keV
Authors: Liu Qun , Guo Youzhong , Chang Yanqi , Cai Zheng , Assur Zahra , Mancia Filippo , Greene Mark I. , Hendrickson Wayne A.
Published: September 2014

Anomalous diffraction signals from typical native macromolecules are very weak, frustrating their use inde novostructure determination. Here, native SAD procedures are described to enhance signal to noise in anomalous diffraction by using multiple crystals in combination with synchrotron X-rays at 6 keV. Increased anomalous signals were obtained at 6 keV compared with 7 keV X-ray energy, which was used for previous native SAD analyses. A feasibility test of multi-crystal-based native SAD phasing was performed at 3.2 Å resolution for a known tyrosine protein kinase domain, and real-life applications were made to two novel membrane proteins at about 3.0 Å resolution. The three applications collectively serve to validate the robust feasibility of native SAD phasing at lower energy.
Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data
Authors: Terwilliger Thomas C. , Bricogne Gerard
Published: September 2014

Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.
Archiving raw crystallographic data
Authors: Terwilliger Thomas C.
Published: September 2014

This article describes some of the activities of the IUCr Diffraction Data Deposition Working Group and introduces a collection of articles discussing the archiving of diffraction images.
Crystal structure of 2-bromobenzoic acid at 120 K: a redetermination
Authors: Kowalska Kornelia , Trzybiński Damian , Sikorski Artur
Published: September 2014

The crystal structure of the title compound, C7H5BrO2, was originally studied using photographic data at room temperature with Cu Kα radiation [Ferguson & Sim (1962).Acta Cryst.15, 346–350]. The present study was undertaken at 120 K with a CCD diffractometer using Cu Kα radiation, and resulted in improved geometrical parameters. In the molecule, the carboxy group is inclined to the benzene ring by 18.7 (2)° and there is a close intramolecular Br...O contact of 3.009 (3) Å. In the crystal, molecules are linked by pairs of O—H...O hydrogen bonds, forming inversion dimers with the classicalR22(8) ring motif for carboxylic acids. Neighbouring dimers are linked by weak C—H...O hydrogen bonds, forming tapes propagating in [1-10]. Adjacent tapes interact by slipped parallel π–π interactions [inter-centroid distance = 3.991 (2), interplanar distance = 3.509 (2) Å, slippage = 1.900 Å] to form columns approximately along theb-axis direction. Neighbouring columns interact dispersively, forming a three-dimensional framework structure.
Crystal structure of (4Z)-1-(3,4-dichlorophenyl)-4-[hydroxy(4-methylphenyl)methylidene]-3-methyl-4,5-dihydro-1H-pyrazol-5-one
Authors: Sharma Naresh , Parihar Sanjay , Jadeja R. N. , Kant Rajni , Gupta Vivek K.
Published: September 2014

The title compound, C18H14Cl2N2O2, crystallizes with two molecules,AandB, in the asymmetric unit. In moleculeA, the dihedral angles between the central pyrazole ring and pendant dichlorobenzene andp-tolyl rings are 2.18 (16) and 46.78 (16)°, respectively. In moleculeB, the equivalent angles are 27.45 (16) and 40.45 (18)°, respectively. Each molecule features an intramolecular O—H...O hydrogen bond, which closes anS(6) ring and moleculeAalso features a C—H...O interaction. In the crystal, weak C—H...π interactions and aromatic π–π stacking [shortest centroid–centroid separation = 3.707 (2) Å] generate a three-dimensional network.
Cu3Sn – understanding the systematic absences
Authors: Müller Carola J. , Lidin Sven
Published: September 2014

The intermetallic compound Cu3Sn has previously been described as a long-period antiphase boundary superstructure of the Cu3Ti structure type. While the compound itself has been reported as a tenfold and an eightfold superstructure, ternary doped alloys show shorter repetitions. Interestingly, the diffraction patterns of these compounds show non-crystallographic absences that cannot be explained using the superstructure models. Since the compound exhibits phase broadening, these models are not satisfactory because the paucity of observed data does not allow for a refinement of the composition. Here, an alternative, superspace model in the orthorhombic space groupXmcm(0β0)000 is proposed, with the centering vectors (0,0,0,0) and (½,0,0,½). The presence of the non-crystallographic absences is explained as a result of a dominating occupational modulation that is accompanied by a weaker displacive modulation. In consistency with the EDXS results, the composition has been refined to Cu3 + xSn from single-crystal X-ray diffraction data. It is further demonstrated that by varying the length and the direction of the modulation wavevector in the superspace model, the ternary Cu3Sn compounds and other colored hexagonal close packing (h.c.p.) structures can be produced.
Peg-bush alignment under elastic vibrations
Authors: Sadauskas Edvardas , Baksys Bronius
Published: September 2014

Purpose

– The paper aims to theoretically and experimentally investigate vibratory peg-bush alignment using elastic vibrations of the peg, when the peg is axially excited by a pressed piezoelectric vibrator on the upper end.

Design/methodology/approach

– Experimental research of part alignment using elastic vibrations was performed and dependencies of alignment duration on excitation signal parameters and initial pressing force were defined for rectangular and circular cross-section parts. Mathematical model of two-mass dynamic systems with elastic contact model representing alignment process was created. Dependencies of system parameters on the alignment duration were obtained by numerically solving systems differential equations.

Findings

– Theoretical and experimental investigation approved the usage of elastic vibrations for alignment of chamferless circular and rectangular cross-section parts. This novel method of part alignment compensates axial misalignment between mating parts by directional displacement of movably based bush.

Research limitations/implications

– Impact and non-impact interaction between bush and peg is possible; however, only non-impact regime was investigated. Static and dynamic coefficients of friction between the parts are equivalent and do not depend on relative velocity of parts.

Practical implications

– The results are useful in designing reliable and effective assembly equipment with vibratory assistance alignment for peg-bush operations, which do not require auxiliary sensors and feedback systems. Use of a piezoelectric resonator for peg excitation makes this system easily adaptable to the existing automated assembly equipment.

Originality/value

– The proposed method is a new approach to vibratory alignment. The data obtained during investigation expand the insight of the physical processes that drive bush to the axial alignment direction.
What future for humans in assembly?
Authors: Bogue Robert
Published: September 2014

Purpose

– This paper aims to investigate the predicted expansion of robotic and three-dimensional (3D) printing technologies and its impact on the global assembly and manufacturing workforce.

Design/methodology/approach

– Following an introduction, this paper first considers the anticipated proliferation of industrial robots and then discusses 3D printing. It concludes with a discussion of the impact of these technologies on employment.

Findings

– This paper shows that a major expansion in the use of robotics is imminent and that 3D printing is emerging as a major manufacturing technology. These trends will considerably reduce the size of the assembly and manufacturing workforce.

Originality/value

– This paper provides a timely review of the impact of advanced robotics and 3D printing on employment in assembly and manufacture.