bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pervasive domestication of defective prophages by bacteria
Authors: Bobay Louis-Marie , Touchon Marie , Rocha Eduardo P. C. 
Published: August 2014

Significance
Several molecular systems with important adaptive roles have originated from the domestication of integrated phages (prophages). However, the evolutionary mechanisms and extent of prophage domestication remain poorly understood. In this work, we detected several hundred prophages originating from common integration events and described their dynamics of degradation within their hosts. Surprisingly, we observed strong conservation of the sequence of most vertically inherited prophages, including selection for genes encoding phage-specific functions. These results suggest pervasive domestication of parasites by the bacterial hosts. Because prophages account for a large fraction of bacterial genomes, phage domestication may drive bacterial adaptation.
Large sulfur-isotope anomaly in nonvolcanic sulfate aerosol and its implications for the Archean atmosphere
Authors: Shaheen Robina , Abaunza Mariana M. , Jackson Teresa L. , McCabe Justin , Savarino Joël , Thiemens Mark H. 
Published: August 2014

SignificanceThe highest S-isotope anomaly is observed in a nonvolcanic period, and the magnitude of anomaly is similar to the largest volcanic eruptions of the 20th century. S-quadruple isotope data provided the first evidence of how super El Niño Southern Oscillation (ENSO) events (1997–1998) have affected the transport and transformation of aerosols to the stratosphere; thus, record of paleo-ENSO events of this magnitude can be traced with the S-isotopic anomaly. High-resolution and high-precision S-isotopic fingerprinting also revealed that the tropospheric sulfate produced during fossil-fuel and biomass burning contributes to the stratospheric sulfate aerosol layer, a contribution previously unrecognized. The distribution of sulfur anomalies mimics the Archean isotope record, which is used to track the origin and evolution of oxygen on earth.
Transient Darwinian selection in
Salmonella enterica
serovar Paratyphi A during 450 years of global spread of enteric fever
Authors: Zhou Zhemin , McCann Angela , Weill François-Xavier , Blin Camille , Nair Satheesh , Wain John , Dougan Gordon , Achtman Mark 
Published: August 2014

Significance
The most recent common ancestor of Paratyphi A, one of the most common causes of enteric fever, existed approximately 450 y ago, centuries before that disease was clinically recognized. Subsequent changes in the genomic sequences included multiple mutations and acquisitions or losses of genes, including bacteriophages and genomic islands. Some of those evolutionary changes were reliably attributed to Darwinian selection, but that selection was only transient, and many genetic changes were subsequently lost because they rendered the bacteria less fit (purifying selection). We interpret the history of Paratyphi A as reflecting drift rather than progressive evolution and suggest that most recent increases in frequencies of bacterial diseases are due to environmental changes rather than the novel evolution of pathogenic bacteria.
Socially responsive effects of brain oxidative metabolism on aggression
Authors: Li-Byarlay Hongmei , Rittschof Clare C. , Massey Jonathan H. , Pittendrigh Barry R. , Robinson Gene E. 
Published: August 2014

Significance
Despite high energetic demands in the brain, glucose is not always metabolized to produce maximum energy. Aerobic glycolysis, that is, high levels of glucose consumption relative to oxygen use, is connected to cognition and disease, but metabolic plasticity remains challenging to study in vivo owing to the brain’s complexity. We show that decreased oxidative phosphorylation activity, a pattern that resembles aerobic glycolysis, causes increased aggression in honey bees and fruit flies. This effect is specific to neurons and not glia, and the social environment modulates the relationship between metabolism and aggression. The fly–bee system, linking variation in brain metabolism to a natural behavior, could be used to further study the function of brain metabolic plasticity.
Prion-like proteins sequester and suppress the toxicity of huntingtin exon 1
Authors: Kayatekin Can , Matlack Kent E. S. , Hesse William R. , Guan Yinghua , Chakrabortee Sohini , Russ Jenny , Wanker Erich E. , Shah Jagesh V. , Lindquist Susan 
Published: August 2014

Significance
Expansion of polyglutamine tracts in at least nine proteins causes neurodegeneration. Although the pathology caused by each protein is different, there must be common features of the polyglutamine expansion that contribute to toxicity. We modeled polyglutamine toxicity in yeast by expressing a 103-glutamine expanded fragment of huntingtin (Htt103Q) and screened the yeast genome to identify proteins that alter this toxicity. Surprisingly, our suppressors were proteins containing glutamine- and asparagine-rich segments typical of prion proteins. When we expressed just these segments with Htt103Q, the two proteins formed large, coaggregated particles, and smaller, more toxic aggregated forms were absent. Proteins with such segments may interact with polyQ-expanded proteins and thereby modulate their toxicity. These interaction partners provide targets for therapeutic intervention.
Modeling host interactions with hepatitis B virus using primary and induced pluripotent stem cell-derived hepatocellular systems
Authors: Shlomai Amir , Schwartz Robert E. , Ramanan Vyas , Bhatta Ankit , de Jong Ype P. , Bhatia Sangeeta N. , Rice Charles M. 
Published: August 2014

Significance
Major obstacles for using human hepatocytes to study hepatitis B virus (HBV) pathobiology are rapid loss of hepatocyte function after plating and the variability between hepatocyte donors. We show that micropatterning and coculturing of primary human hepatocytes with fibroblasts (MPCC format) maintains prolonged infection that is restricted by the innate immune response, and can be further boosted by suppression of this response. To address the problem of donor variability, we show that induced pluripotent stem cells (iPSC) differentiated into hepatocyte-like cells support HBV infection in a differentiation-dependent manner. Our study opens an avenue for using these systems to study virus–host interactions and test antiviral drugs, and suggests HBV permissiveness as a surrogate reporter to assess the degree of differentiation of candidate iPSC-derived hepatocyte-like cells.
Fibroblastic reticular cells of the lymph node are required for retention of resting but not activated CD8
+
T cells
Authors: Denton Alice E. , Roberts Edward W. , Linterman Michelle A. , Fearon Douglas T. 
Published: August 2014

Significance
The balance between the retention of lymphocytes in lymph nodes and their exit is a key factor determining clonal burst size, differentiation, and the efficacy of pathogen clearance. Currently, it is understood that naïve and activated T cells regulate their migration using a similar system, that is, balancing CC chemokine receptor (CCR)7-mediated retention signals against Sphingosine-1 phosphate receptor-1 (S1PR1)-mediated exit signals. This study utilizes a mouse model to selectively deplete the cellular source of CCR7 ligands, the fibroblastic reticular cells, before or during viral infection. The study concludes that while retention of naïve lymphocytes does depend on the fibroblastic reticular cell, it may be a cell-autonomous response of activated T cells that allows them to determine in a cell-intrinsic manner the magnitude of clonal expansion.
Patterns of cohesion in spoken text
Authors: Thompson Susan , Thompson Geoff 
Published: August 2014

Editors’ introduction
The article by Susan & Geoff Thompson, like several others in this volume, relates to the issue of text chunks and linkages, but in their case the text is a corpus of television advertisements where viewers (and analysts) have to deal with information at various levels simultaneously: written text, voice-over, moving images. In the case of television advertisements, there is great coherence between these three.

However, the strength of the paper lies essentially in the combination of two modes of analysis, of “soundings” and “wordings” (we must look elsewhere for an analysis of “imagings”), an analysis which finds that the two modes operate not only in complement with each other but also with points of contrast.
The chief problem they address is that of cohesion: how do chunks relate to each other? What makes the advert a single audiovisual unit, a text, as opposed to a set of elements? To answer this, they draw upon the notions of repetition and replacement (Winter 1974, 1979). In this view, repetition operates within a text “frame” with “slots”, typically a fairly narrow phrasal context, and serves to signal continuity of aboutness. Darnton’s contribution in this volume presents a fairly similar view, while Scott’s takes repetition at a text level. Replacement puts new words in familiar slots. Conjunction, on the other hand, deals with the signalling of connectedness and can be achieved basically by claiming a Matching relation or a Logical sequence relation. A further pattern enabling linkage is Theme choice, which serves to glue the text together by claiming a relatedness of topic focus. That is, by preserving consistency in what is chosen to start each clause, the television advertiser manages to maintain a continuity of the relevant aspect of “what we’re on about”: namely promoting batteries or deodorants.
Note that parallelism of frames and slots, and conjunction and Theme in this view operate at a fairly local, narrow level in connecting two or more consecutive chunks. That is, they are likely on average to be connecting points of detail rather than major changes of gist. As the Thompsons point out, however, there are also larger-scale operators, such as those in the Problem-Solution discourse pattern, which serve to connect and relate and mark off larger chunks where a major change of emphasis and content may be introduced. Examples of larger chunk linkage operators would be “Meanwhile, back at the ranch” in a novel, or “And finally” in the television news, or “But first” in television announcements of upcoming programmes.
It is particularly interesting that evidence is found that sound linkages may well operate to hold together larger rather than smaller text chunks. The patterns of text are thus complex: some linkages may cluster around detail, and others may relate these to larger text divisions.
African weeks
Authors: McCall Daniel F. 
Published: August 2014

Hal Fleming and I were colleagues and friends in the Anthropology Department and the African Studies Center at Boston University for years and remained close after retirement. We had even co-taught a course one year trying to establish a diachronic anthropology. The four fields of American Anthropology are the basis for whatever diachronic dimension is attainable in the study of non-literate peoples. Hal is better steeped in Linguistics and Genetics than I, so I will not try to match him there, but this story of a culture-complex that runs through many millennia is one I know he enjoys. He had heard it before, but it has never been previously published.
The planetary week as a culture-complex is traced from its origins in Babylonia, through the cultures of the Mediterranean Basin, and eventually to its development in the Akan cultures of the Guinea Coast of West Africa.
The problem of pan-African roots
Authors: Blench Roger M. 
Published: August 2014

A problem of establishing macrophylic relations in Africa is the existence of common lexical items that are shared between the phyla in ways which do not suggest can they be used as evidence for a genetic connection. This suggests that proposals for large-scale language classification in Africa may be flawed by a failure to consider the transphylic distribution of many roots. The paper gives some examples of such lexical items and canvasses possible explanations;
a. they are ancient loanwords
b. they are convergent because of common phonaesthemes
c. African language phyla really are all related
d. they are retained from an early stage of world language diversification
Some roots seem to have a wider distribution in Eurasia, which suggests that (d) may be relevant in some cases.
Towards multiactivity as a social and interactional phenomenon
Authors: Haddington Pentti , Keisanen Tiina , Mondada Lorenza , Nevile Maurice 
Published: August 2014

Multiactivity – the different ways in which two or more activities can be intertwined and made co-relevant in social interaction – is an inseparable element of everyday life. At the same time it is a little understood form of human conduct. This introductory chapter builds on the basis that multiactivity is a social, verbal and embodied phenomenon, manifest in people’s participation and conduct in interaction, and can be studied empirically by relying on the close analysis of video-recorded data of naturally occurring situations. The chapter connects to previous research on multitasking and outlines how an interactional and social view of the phenomenon can add to our knowledge of how participants engage in, manage and accomplish multiple activities. The chapter outlines new interactional practices and new concepts to describe them.
Multimodal participation in simultaneous joint projects
Authors: Deppermann Arnulf 
Published: August 2014

This paper analyses paramedic emergency interaction as multi-modal multi-activity. Based on a corpus of video-recordings of emergency drills performed by professional paramedics during advanced training, the focus is on paramedics’ participation in multiple joint projects which become simultaneously relevant. Simultaneity and fast succession of multi-activity does not only characterise work on the team level, but also the work profile of the individual paramedic. Participants have to coordinate their own participation in more than one joint project intra-personally. In the data studied, three patterns of allocating multi-modal resources stood out as routine ways of coordinating participation in two simultaneous projects intra-personally:
1.	Talk and hearing vs. manual action monitored by gaze,
2.	Talk and hearing vs. gazing (and pointing),
3.	Manual action vs. gaze (and talk and hearing).
Enhancing immunomodulation on innate immunity by shape transition among RNA triangle, square and pentagon nanovehicles
Authors: Khisamutdinov Emil F. , Li Hui , Jasinski Daniel L. , Chen Jiao , Fu Jian , Guo Peixuan 
Published: August 2014

Abstract
Modulation of immune response is important in cancer immunotherapy, vaccine adjuvant development and inflammatory or immune disease therapy. Here we report the development of new immunomodulators via control of shape transition among RNA triangle, square and pentagon. Changing one RNA strand in polygons automatically induced the stretching of the interior angle from 60° to 90° or 108°, resulting in self-assembly of elegant RNA triangles, squares and pentagons. When immunological adjuvants were incorporated, their immunomodulation effect for cytokine TNF-α and IL-6 induction was greatly enhanced in vitro and in animals up to 100-fold, while RNA polygon controls induced unnoticeable effect. The RNA nanoparticles were delivered to macrophages specifically. The degree of immunostimulation greatly depended on the size, shape and number of the payload per nanoparticles. Stronger immune response was observed when the number of adjuvants per polygon was increased, demonstrating the advantage of shape transition from triangle to pentagon.
Human fetal globin gene expression is regulated by LYAR
Authors: Ju Junyi , Wang Ying , Liu Ronghua , Zhang Yichong , Xu Zhen , Wang Yadong , Wu Yupeng , Liu Ming , Cerruti Loretta , Zou Fengwei , Ma Chi , Fang Ming , Tan Renxiang , Jane Stephen M. , Zhao Quan 
Published: August 2014

AbstractHuman globin gene expression during development is modulated by transcription factors in a stage-dependent manner. However, the mechanisms controlling the process are still largely unknown. In this study, we found that a nuclear protein, LYAR (human homologue of mouse Ly-1 antibody reactive clone) directly interacted with the methyltransferase PRMT5 which triggers the histone H4 Arg3 symmetric dimethylation (H4R3me2s) mark. We found that PRMT5 binding on the proximal γ-promoter was LYAR-dependent. The LYAR DNA-binding motif (GGTTAT) was identified by performing CASTing (cyclic amplification and selection of targets) experiments. Results of EMSA and ChIP assays confirmed that LYAR bound to a DNA region corresponding to the 5′-untranslated region of the γ-globin gene. We also found that LYAR repressed human fetal globin gene expression in both K562 cells and primary human adult erythroid progenitor cells. Thus, these data indicate that LYAR acts as a novel transcription factor that binds the γ-globin gene, and is essential for silencing the γ-globin gene.
The Psychological and Physiological Effects of Acute Occupational Stress in New Anesthesiology Residents
Authors: Eisenach John H. , Sprung Juraj , Clark Matthew M. , Shanafelt Tait D. , Johnson Bruce D. , Kruse Timothy N. , Chantigian Daniel P. , Carter Jason R. , Long Timothy R. 
Published: August 2014

Abstract

Background:
Occupational stress in resident physicians has profound implications for wellness, professionalism, and patient care. This observational pilot trial measured psychological and physiological stress biomarkers before, during, and after the start of anesthesia residency.

Methods:
Eighteen physician interns scheduled to begin anesthesia residency were recruited for evaluation at three time points: baseline (collected remotely before residency in June 2013); first-month visit 1 (July); and follow-up visit 2 (residency months 3 to 5, September–November). Validated scales were used to measure stress, anxiety, resilience, and wellness at all three time points. During visits 1 and 2, the authors measured resting heart-rate variability, responses to laboratory mental stress (hemodynamic, catecholamine, cortisol, and interleukin-6), and chronic stress indices (C-reactive protein, 24-h ambulatory heart rate and blood pressure, 24-h urinary cortisol and catecholamines, overnight heart-rate variability).

Results:
Thirteen interns agreed to participate (72% enrollment). There were seven men and six women, aged 27 to 33 yr. The mean ± SD of all study variables are reported.

Conclusion:
The novelty of this report is the prospective design in a defined cohort of residents newly exposed to the similar occupational stress of the operating environment. Because of the paucity of literature specific to the measures and stress conditions in this investigation, no data were available to generate a priori definition of primary outcomes and a data analytic plan. These findings will allow power analysis for future design of trials examining occupational stress and stress-reducing interventions. Given the importance of physician burnout in our country, the impact of chronic stress on resident wellness requires further study.
Etiology of Adult-onset Stress Fracture in the Lumbar Spine
Authors: Tezuka Fumitake , Sairyo Koichi , Sakai Toshinori , Dezawa Akira 
Published: August 2014

Study Design:
This study was a case series.

Objective:
The purpose of this paper was to present a case series of fresh stress fractures (spondylolysis) in the lumbar spines of adult athletes.

Summary of Background Data:
Lumbar spondylolysis is a stress fracture of the pars interarticularis, which is generally considered a disease of children or adolescence. There is only 1 case series written in English reporting on adult-onset fresh spondylolysis.

Methods:
Eleven patients aged 20–27 years are included in this case series. A retrospective analysis was made of events that may cause stress fracture such as traumatic episodes or sports activities, spinal level, radiologic findings, stage of spondylolysis, treatment, and prognosis.

Results:
Among the 11 patients, two had bilateral early-stage spondylolysis, 7 had unilateral early-stage spondylolysis and 2 had unilateral progressive-stage spondylolysis. Three occurred subsequent to a preexisting terminal-stage spondylolysis in the contralateral side, 1 occurred subsequent to a terminal-stage spondylolysis at the adjacent spinal level, and 1 occurred subsequent to a terminal-stage spondylolysis at a distant level. Thirteen pedicles adjacent to the pars interarticularis in the 11 patients showed bone marrow edema-like signal on magnetic resonance imaging. Six spondylolyses were found at L5, 2 each at L3 and L4, and 1 spondylolysis at L2. The 11 patients were divided into 4 groups according to suspected pathogenic mechanism: preexistent spondylolysis in the contralateral side, alteration of the athletic event, apparent traumatic episode, and others. Conservative treatment was prescribed for return to sports in all cases. Although 1 patient retired because of persistent low back pain, the remaining 10 patients returned to competition.

Conclusions:
Although lumbar spondylolysis is generally recognized to occur in childhood or adolescence, fresh lumbar spondylolysis should be included in the differential diagnosis of adult low back pain when patients are high-level athletes. Conservative treatment should be attempted for adult patients.
Partially coherent X-ray wavefront propagation simulations including grazing-incidence focusing optics
Authors: Canestrari Niccolo , Chubar Oleg , Reininger Ruben 
Published: August 2014

X-ray beamlines in modern synchrotron radiation sources make extensive use of grazing-incidence reflective optics, in particular Kirkpatrick–Baez elliptical mirror systems. These systems can focus the incoming X-rays down to nanometer-scale spot sizes while maintaining relatively large acceptance apertures and high flux in the focused radiation spots. In low-emittance storage rings and in free-electron lasers such systems are used with partially or even nearly fully coherent X-ray beams and often target diffraction-limited resolution. Therefore, their accurate simulation and modeling has to be performed within the framework of wave optics. Here the implementation and benchmarking of a wave-optics method for the simulation of grazing-incidence mirrors based on the local stationary-phase approximation or, in other words, the local propagation of the radiation electric field along geometrical rays, is described. The proposed method is CPU-efficient and fully compatible with the numerical methods of Fourier optics. It has been implemented in theSynchrotron Radiation Workshop(SRW) computer code and extensively tested against the geometrical ray-tracing codeSHADOW. The test simulations have been performed for cases without and with diffraction at mirror apertures, including cases where the grazing-incidence mirrors can be hardly approximated by ideal lenses. Good agreement between theSRWandSHADOWsimulation results is observed in the cases without diffraction. The differences between the simulation results obtained by the two codes in diffraction-dominated cases for illumination with fully or partially coherent radiation are analyzed and interpreted. The application of the new method for the simulation of wavefront propagation through a high-resolution X-ray microspectroscopy beamline at the National Synchrotron Light Source II (Brookhaven National Laboratory, USA) is demonstrated.