bluuebunny/crossref_metadata_2025 huggingface dataset:
How Much Cleaning is Needed When Processing Otoliths from Fish Larvae for Microchemical Analysis?
Authors: Gover Theodore R. , Nims Megan K. , Van Tassell Jason J. , Collingsworth Paris D. , Olesik John W. , Ludsin Stuart A. , Marschall Elizabeth A.
Published: May 2014

Otolith microchemistry is a widely used tool in fish ecology and fisheries management. Cleaning‐protocol assessments are lacking, however, especially for larval fish otoliths, which are more fragile and difficult to manipulate than larger otoliths. Herein, we assess the value of cleaning larval fish otoliths with sonication, a commonly used technique that is time consuming and risks loss or breakage of small otoliths, as well as with a lesser‐known technique using a low‐power laser cleaning pulse (LPLCP). We measured trace elements in larval Walleye Sander vitreus reared in different water strontium concentrations. Strontium and Ba did not differ among any cleaning treatments, indicating that neither sonication nor a LPLCP is necessary. Likewise, Mn did not differ between sonicated and nonsonicated treatments; however, Mn was lower when a LPLCP was used. We suggest omitting the sonication step when preparing otoliths for trace element analysis of Sr, Ba, Mn, and other trace elements found in high abundances. The addition of a LPLCP is useful, although more research in this arena is warranted. Our findings should greatly reduce otolith processing time and the risk of losing and breaking larval otoliths during the cleaning process.
Fish and Benthic Macroinvertebrate Densities in Small Streams with and without American Eels
Authors: Stranko Scott A. , Ashton Matthew J. , Hilderbrand Robert H. , Weglein Sara L. , Kazyak David C. , Kilian Jay V.
Published: May 2014

The American Eel Anguilla rostrata has been excluded from many streams along the Atlantic slope of the USA because of movement barriers such as large dams. Loss of this formerly common top predator has the potential to influence many aspects of headwater streams. We used existing survey data for a landscape‐scale comparison of fish, benthic macroinvertebrate, and crayfish densities at 95 sites where American Eel access was excluded by dams and 74 sites containing eels. Benthic fish densities were significantly lower at eel‐containing sites, whereas benthic macroinvertebrate densities were significantly higher. Densities of nonbenthic fish, non‐eel top predators, and crayfish were not different between eel occurrence categories. While these initial results are correlative, we believe that American Eel may be capable of influencing lower trophic levels, and their presence may produce noticeable changes to headwater stream ecosystems.
Influence of Natural and Anthropogenic Disturbances on Spawning Sockeye Salmon Distributions in the Cedar River, Washington
Authors: Timm Raymond K. , Wissmar Robert C.
Published: May 2014

Human management of river ecosystems dampens natural disturbance regimes that drive critical habitat‐forming processes. However, the quantification of processes can be difficult and is typically accomplished through surrogate analyses. In 2001, a channel‐damming landslide in the Cedar River, Washington, changed habitat conditions and spawning distributions of Sockeye Salmon Oncorhynchus nerka. We evaluated annual changes in a number of key indicators of river processes during the pre‐ and post‐disturbance periods. We used an exhaustive chi‐square automatic interaction detection (CHAID) model to evaluate the effect of changes in habitat complexity, discharge characteristics, and parental generation spawning distributions on 54years (1952–2006) of weekly spawning fish surveys. Before the landslide, the spatial and temporal patterns of Sockeye Salmon distributions were heavily influenced by the spawning locations of their parents. Densities of spawning fish were highest in the uppermost river reaches. After the landslide, habitat complexity and fish densities increased in the lower, landslide‐affected river reaches. The CHAID model analyses indicated that fluvial habitat complexity, river discharge characteristics, and the density of fish in respective parental generations were significant factors explaining the spawning distributions by reach. Our analyses of the salmon population response to annual changes in habitat complexity affirm that our metrics were useful surrogates for measuring the habitat‐forming processes restored when the landslide reconnected the river channel with its floodplain. Furthermore, this study provides an “order of magnitude” insight into the amount of restoration that will elicit a population‐scale response in salmon.
Contingents of Southern Flounder from Subtropical Estuaries Revealed by Otolith Chemistry
Authors: Nims Megan K. , Walther Benjamin D.
Published: May 2014

The identification of contingents within populations that exhibit distinct migratory behaviors and patterns of habitat use can lead to the understanding of the fitness consequences of individual variability in a population and an increased understanding of population dynamics. This study examines the variation in migratory behavior and habitat use patterns in Southern Flounder Paralichthys lethostigma in the northwestern Gulf of Mexico, whose populations have declined rapidly over the last 25–30years. The putative life history for this species includes short postsettlement movements into low‐salinity habitats, followed by estuarine and marine residency for the remainder of life. However, using otolith Ba:Ca in wild‐captured fish, two primary contingents were observed: (1) 54% of fish showed marine–estuarine residency for their entire lifetimes, and (2) 46% showed residence in oligohaline habitats for some portion of their lifetimes. For the second group, oligohaline residence varied widely with life history profiles, having between < 5% up to > 95% of values above the oligohaline threshold. Relationships between the proportion of life spent in oligohaline waters and proxies of growth performance were not significant, indicating no apparent difference in the relative advantage of specific residency patterns. Residence in oligohaline habitats thus appears to be facultative for this population, which may be a local adaptation to interannual drought cycles and variable freshwater inputs in the region.
Age and Growth of the Bull Shark in the Western North Atlantic Ocean
Authors: Natanson Lisa J. , Adams Douglas H. , Winton Megan V. , Maurer Jasmine R.
Published: May 2014

Age and growth estimates for the Bull Shark Carcharhinus leucas were derived from 121 vertebral centra collected from Bull Sharks (59.1–223.5cm FL) between 1966 and 2010 in the western North Atlantic Ocean. Size at birth was confirmed with an additional 20 embryos (44.2–54.4cm FL). The maximum age based on vertebral band pair counts was 25 (184cm FL) and 27 (196cm FL) years for males and females, respectively. The logistic and Gompertz growth models fitted the size‐at‐age data best for males and females, respectively. Based on previously published estimates of length at maturity, males mature at 15–17years (176–185cm FL) and females at 15years (189cm FL). Bull Sharks in the western North Atlantic Ocean and the Gulf of Mexico have similar growth rates and reach similar sizes at age.
Tim Burton at 50: the hero's mid-life crisis
Authors: Bassil-Morozow Helena Victor
Published: May 2014

It is difficult to predict the development of Tim Burton's career now that his original protagonist, the eccentric creative mourning the loss of his father, is dead – or rather, now that the child element of the protagonist is gone. To find a way out of his ideological crisis, Burton has been trying different directions, including a female protagonist and reviving an old character that belongs to the times when Burton's heroes were still ‘children’ as well as ‘monsters’.
CX3CL1 (fractalkine) and its receptor CX3CR1 regulate atopic dermatitis by controlling effector T cell retention in inflamed skin
Authors: Staumont-Sallé Delphine , Fleury Sébastien , Lazzari Anne , Molendi-Coste Olivier , Hornez Nicolas , Lavogiez Céline , Kanda Akira , Wartelle Julien , Fries Anissa , Pennino Davide , Mionnet Cyrille , Prawitt Janne , Bouchaert Emmanuel , Delaporte Emmanuel , Glaichenhaus Nicolas , Staels Bart , Julia Valérie , Dombrowicz David
Published: May 2014

Atopic dermatitis (AD) is a chronic allergic dermatosis characterized by epidermal thickening and dermal inflammatory infiltrates with a dominant Th2 profile during the acute phase, whereas a Th1 profile is characteristic of the chronic stage. Among chemokines and chemokine receptors associated with inflammation, increased levels of CX3CL1 (fractalkine) and its unique receptor, CX3CR1, have been observed in human AD. We have thus investigated their role and mechanism of action in experimental models of AD and psoriasis. AD pathology and immune responses, but not psoriasis, were profoundly decreased in CX3CR1-deficient mice and upon blocking CX3CL1–CX3CR1 interactions in wild-type mice. CX3CR1 deficiency affected neither antigen presentation nor T cell proliferation in vivo upon skin sensitization, but CX3CR1 expression by both Th2 and Th1 cells was required to induce AD. Surprisingly, unlike in allergic asthma, where CX3CL1 and CX3CR1 regulate the pathology by controlling effector CD4+ T cell survival within inflamed tissues, adoptive transfer experiments established CX3CR1 as a key regulator of CD4+ T cell retention in inflamed skin, indicating a new function for this chemokine receptor. Therefore, although CX3CR1 and CX3CL1 act through distinct mechanisms in different pathologies, our results further indicate their interest as promising therapeutic targets in allergic diseases.
A novel Aβ-fibrinogen interaction inhibitor rescues altered thrombosis and cognitive decline in Alzheimer’s disease mice
Authors: Ahn Hyung Jin , Glickman J. Fraser , Poon Ka Lai , Zamolodchikov Daria , Jno-Charles Odella C. , Norris Erin H. , Strickland Sidney
Published: May 2014

Many Alzheimer’s disease (AD) patients suffer from cerebrovascular abnormalities such as altered cerebral blood flow and cerebral microinfarcts. Recently, fibrinogen has been identified as a strong cerebrovascular risk factor in AD, as it specifically binds to β-amyloid (Aβ), thereby altering fibrin clot structure and delaying clot degradation. To determine if the Aβ–fibrinogen interaction could be targeted as a potential new treatment for AD, we designed a high-throughput screen and identified RU-505 as an effective inhibitor of the Aβ–fibrinogen interaction. RU-505 restored Aβ-induced altered fibrin clot formation and degradation in vitro and inhibited vessel occlusion in AD transgenic mice. Furthermore, long-term treatment of RU-505 significantly reduced vascular amyloid deposition and microgliosis in the cortex and improved cognitive impairment in mouse models of AD. Our studies suggest that inhibitors targeting the Aβ–fibrinogen interaction show promise as therapy for treating AD.
Every laboratory with a fluorescence microscope should consider counting molecules
Authors: Coffman Valerie C. , Wu Jian-Qiu
Published: May 2014

Protein numbers in cells determine rates of biological processes, influence the architecture of cellular structures, reveal the stoichiometries of protein complexes, guide in vitro biochemical reconstitutions, and provide parameter values for mathematical modeling. The purpose of this essay is to increase awareness of methods for counting protein molecules using fluorescence microscopy and encourage more cell biologists to report these numbers. We address the state of the field in terms of utility and accuracy of the numbers reported and point readers to references for details of specific techniques and applications.
Textual Engagement with the Other in Cyrano de Bergerac's
L'Autre Monde
Authors: Delehanty Ann T. , Blakeney Tyler
Published: May 2014

This article argues that Cyrano de Bergerac's two novels, known collectively as
L'Autre Monde
, offer both a critique of efforts to categorize the Other in late seventeenth-century travel narratives, and a model for privileging an ethical, rather than definitional, approach to it. The first section, through an analysis of the scene where the narrator is mistakenly thought to be the female of an animal in the queen's zoo, shows how Cyrano lambasts this gesture of categorizing the Other in one's own terms. The second section analyses two scenes where Cyrano presents a different version of the biblical tree of life in order to show how he privileges multiplicity and openness of meaning. Cyrano's project employs both form and content to shift from an authoritative and narrative mode to a mode of what we call ‘reading the Other’. We define this term with regard to Cyrano to mean that one encounters the world as an attentive reader of fiction would: attuned to multiplicity, seeking an accretion of meaning via stories rather than via a one-to-one correspondence between word and thing, a willingness to be passive rather than authoritative when encountering something new, and valuing ethical relationships between beings.
‘En vue de plus tard ou de jamais’: Poetic Community in Stéphane Mallarmé's
Tombeaux
Authors: Pekron Rebecca
Published: May 2014

In 1891 Stéphane Mallarmé described his view of the widening rift between poets and modern society: ‘Pour moi, le cas d'un poëte, en cette société qui ne lui permet pas de vivre, c'est le cas d'un homme qui s'isole pour sculpter son propre tombeau.’ This article reads Mallarmé's three
tombeaux
— ‘Le Tombeau d'Edgar Poe’, ‘Le Tombeau de Charles Baudelaire’, and ‘Tombeau’ (for Verlaine) — as responses to this perceived rupture and isolation. These poems establish a community of poets around the departed, distinct from the society in which Mallarmé felt the poet no longer had a place. Mallarmé's
tombeaux
can thus be understood in connection with his involvement in the construction of other poetic communities, such as his role in founding La Société internationale des poètes, as well as with the modest
tombeau
revival of the latter half of the nineteenth century. Understanding this historical moment as an interregnum, the poet developed a concept of poetic fraternity that, he hoped, could serve as a model for sociability more broadly in the future. This article emphasizes the commonalities that link the
tombeaux
to one another and to Mallarmé's notion of community, using close readings to analyse the unique visions of poetic community each poem presents.
Regulation of intestinal health and disease by innate lymphoid cells
Authors: Sonnenberg Gregory F.
Published: May 2014

Innate lymphoid cells (ILCs) are a recently appreciated immune cell population that is constitutively found in the healthy mammalian gastrointestinal (GI) tract and associated lymphoid tissues. Translational studies have revealed that alterations in ILC populations are associated with GI disease in patients, such as inflammatory bowel disease, HIV infection and colon cancer, suggesting a potential role for ILCs in either maintaining intestinal health or promoting intestinal disease. Mouse models identified that ILCs have context-dependent protective and pathologic functions either during the steady state, or following infection, inflammation or tissue damage. This review will discuss the associations of altered intestinal ILCs with human GI diseases, and the functional consequences of targeting ILCs in mouse models. Collectively, our current understanding of ILCs suggests that the development of novel therapeutic strategies to modulate ILC responses will be of significant clinical value to prevent or treat human GI diseases.
Identification of a Hidden Resistance Gene in Tetraploid Wheat Using Laboratory Strains of Pyricularia oryzae Produced by Backcrossing
Authors: Cumagun Christian Joseph R. , Anh Vu Lan , Vy Trinh Thi Phuong , Inoue Yoshihiro , Asano Hokuto , Hyon Gang-Su , Chuma Izumi , Tosa Yukio
Published: May 2014

In the process (BC3F1 generation) of backcrossing an Avena isolate of Pyricularia oryzae with a Triticum isolate, color mutants with white mycelia were obtained. These white mutants lacked virulence on all (31/31) hexaploid and most (28/32) tetraploid wheat lines tested. In a BC4F1 population, white and black cultures segregated in a 1:1 ratio, suggesting that the mutant phenotype is controlled by a single gene. Furthermore, the mycelial color was perfectly linked with avirulence in the BC4F1 population; white cultures were all avirulent on common wheat (Triticum aestivum) ‘Norin 4’ (N4) whereas black cultures were all virulent. White cultures in the BC3F1 and BC4F1 generations were also avirulent on tetraploid wheat (T. dicoccoides) accession ‘KU109’ (Tat4), which was susceptible to all cultures derived from the parental wild isolates through the BC2F1 generation. A cross between Tat4 and a susceptible tetraploid (T. paleocolchicum) accession ‘KU196’ (Tat14) produced resistant and susceptible F2 seedlings in a 3:1 ratio against the white cultures. In the F3 generation homozygous resistant/segregating/homozygous susceptible lines segregated in a 1:2:1 ratio. These results suggest that the resistance of Tat4 to the white cultures is controlled by a single major gene. This gene, tentatively designated as RmgTd(t), is considered to be a hidden resistance gene because it was not detected with the Br58, F1, BC1F1, or BC2F1 cultures. Cytological analysis revealed that the moderate resistance controlled by RmgTd(t) was associated with a hypersensitive reaction of mesophyll cells.
Cardioprotective Trafficking of Caveolin to Mitochondria Is Gi-protein Dependent
Authors: Wang Jiawan , Schilling Jan M. , Niesman Ingrid R. , Headrick John P. , Finley J. Cameron , Kwan Evan , Patel Piyush M. , Head Brian P. , Roth David M. , Yue Yun , Patel Hemal H.
Published: May 2014

Background:

Caveolae are a nexus for protective signaling. Trafficking of caveolin to mitochondria is essential for adaptation to cellular stress though the trafficking mechanisms remain unknown. The authors hypothesized that G protein–coupled receptor/inhibitory G protein (Gi) activation leads to caveolin trafficking to mitochondria.

Methods:

Mice were exposed to isoflurane or oxygen vehicle (30 min, ±36 h pertussis toxin pretreatment, an irreversible Gi inhibitor). Caveolin trafficking, cardioprotective “survival kinase” signaling, mitochondrial function, and ultrastructure were assessed.

Results:

Isoflurane increased cardiac caveolae (n = 8 per group; data presented as mean ± SD for Ctrl versus isoflurane; [caveolin-1: 1.78 ± 0.12 vs. 3.53 ± 0.77; P < 0.05]; [caveolin-3: 1.68 ± 0.29 vs. 2.67 ± 0.46; P < 0.05]) and mitochondrial caveolin levels (n = 16 per group; [caveolin-1: 0.87 ± 0.18 vs. 1.89 ± .19; P < 0.05]; [caveolin-3: 1.10 ± 0.29 vs. 2.26 ± 0.28; P < 0.05]), and caveolin-enriched mitochondria exhibited improved respiratory function (n = 4 per group; [state 3/complex I: 10.67 ± 1.54 vs. 37.6 ± 7.34; P < 0.05]; [state 3/complex II: 37.19 ± 4.61 vs. 71.48 ± 15.28; P < 0.05]). Isoflurane increased phosphorylation of survival kinases (n = 8 per group; [protein kinase B: 0.63 ± 0.20 vs. 1.47 ± 0.18; P < 0.05]; [glycogen synthase kinase 3β: 1.23 ± 0.20 vs. 2.35 ± 0.20; P < 0.05]). The beneficial effects were blocked by pertussis toxin.

Conclusions:

Gi proteins are involved in trafficking caveolin to mitochondria to enhance stress resistance. Agents that target Gi activation and caveolin trafficking may be viable cardioprotective agents.
Lung Ultrasound Predicts Well Extravascular Lung Water but Is of Limited Usefulness in the Prediction of Wedge Pressure
Authors: Volpicelli Giovanni , Skurzak Stefano , Boero Enrico , Carpinteri Giuseppe , Tengattini Marco , Stefanone Valerio , Luberto Luca , Anile Antonio , Cerutti Elisabetta , Radeschi Giulio , Frascisco Mauro F.
Published: May 2014

Background:

Pulmonary congestion is indicated at lung ultrasound by detection of B-lines, but correlation of these ultrasound signs with pulmonary artery occlusion pressure (PAOP) and extravascular lung water (EVLW) still remains to be further explored. The aim of the study was to assess whether B-lines, and eventually a combination with left ventricular ejection fraction (LVEF) assessment, are useful to differentiate low/high PAOP and EVLW in critically ill patients.

Methods:

The authors enrolled 73 patients requiring invasive monitoring from the intensive care unit of four university-affiliated hospitals. Forty-one patients underwent PAOP measurement by pulmonary artery catheterization and 32 patients had EVLW measured by transpulmonary thermodilution method. Lung and cardiac ultrasound examinations focused to the evaluation of B-lines and gross estimation of LVEF were performed. The absence of diffuse B-lines (A-pattern) versus the pattern showing prevalent B-lines (B-pattern) and the combination with normal or impaired LVEF were correlated with cutoff levels of PAOP and EVLW.

Results:

PAOP of 18 mmHg or less was predicted by the A-pattern with 85.7% sensitivity (95% CI, 70.5 to 94.1%) and 40.0% specificity (CI, 25.4 to 56.4%), whereas EVLW 10 ml/kg or less with 81.0% sensitivity (CI, 62.6 to 91.9%) and 90.9% specificity (CI, 74.2 to 97.7%). The combination of A-pattern with normal LVEF increased sensitivity to 100% (CI, 84.5 to 100%) and specificity to 72.7% (CI, 52.0 to 87.2%) for the prediction of PAOP 18 mmHg or less.

Conclusions:

B-lines allow good prediction of pulmonary congestion indicated by EVLW, whereas are of limited usefulness for the prediction of hemodynamic congestion indicated by PAOP. Combining B-lines with estimation of LVEF at transthoracic ultrasound may improve the prediction of PAOP.
After 2015: infectious diseases in a new era of health and development
Authors: Dye Christopher
Published: May 2014

Running over timescales that span decades or centuries, the epidemiological transition provides the central narrative of global health. In this transition, a reduction in mortality is followed by a reduction in fertility, creating larger, older populations in which the main causes of illness and death are no longer acute infections of children but chronic diseases of adults. Since the year 2000, the Millennium Development Goals (MDGs) have provided a framework for accelerating the decline of infectious diseases, backed by a massive injection of foreign investment to low-income countries. Despite the successes of the MDGs era, the inhabitants of low-income countries still suffer an enormous burden of disease owing to diarrhoea, pneumonia, HIV/AIDS, tuberculosis, malaria and other pathogens. Adding to the predictable burden of endemic disease, the threat of pandemics is ever-present and global. With a view to the future, this review spotlights five aspects of the fight against infection beyond 2015, when the MDGs will be replaced by a new set of goals for poverty reduction and sustainable development. These aspects are: exploiting the biological links between infectious and non-infectious diseases; controlling infections among the new urban majority; enhancing the response to international health threats; expanding childhood immunization programmes to prevent acute and chronic diseases in adults; and working towards universal health coverage. By scanning the wider horizon now, infectious disease specialists have the chance to shape the post-2015 era of health and development.
Human genetics of tuberculosis: a long and winding road
Authors: Abel Laurent , El-Baghdadi Jamila , Bousfiha Ahmed Aziz , Casanova Jean-Laurent , Schurr Erwin
Published: May 2014

Only a small fraction of individuals exposed to
Mycobacterium tuberculosis
develop clinical tuberculosis (TB). Over the past century, epidemiological studies have shown that human genetic factors contribute significantly to this interindividual variability, and molecular progress has been made over the past decade for at least two of the three key TB-related phenotypes: (i) a major locus controlling resistance to infection with
M. tuberculosis
has been identified, and (ii) proof of principle that severe TB of childhood can result from single-gene inborn errors of interferon-γ immunity has been provided; genetic association studies with pulmonary TB in adulthood have met with more limited success. Future genetic studies of these three phenotypes could consider subgroups of subjects defined on the basis of individual (e.g. age at TB onset) or environmental (e.g. pathogen strain) factors. Progress may also be facilitated by further methodological advances in human genetics. Identification of the human genetic variants controlling the various stages and forms of TB is critical for understanding TB pathogenesis. These findings should have major implications for TB control, in the definition of improved prevention strategies, the optimization of vaccines and clinical trials and the development of novel treatments aiming to restore deficient immune responses.
The role of vector control in stopping the transmission of malaria: threats and opportunities
Authors: Hemingway Janet
Published: May 2014

Malaria control, and that of other insect borne diseases such as dengue, is heavily dependent on our ability to control the mosquito populations that transmit these diseases. The major push over the last decade to reduce the global burden of malaria has been driven by the distribution of pyrethroid insecticide-treated bednets and an increase in coverage of indoor residual spraying (IRS). This has reduced malaria deaths by a third. Progress towards the goal of reducing this further is threatened by lack of funding and the selection of drug and insecticide resistance. When malaria control was initially scaled up, there was little pyrethroid resistance in the major vectors, today there is no country in Africa where the vectors remain fully susceptible to pyrethroids. The first pyrethroid resistance mechanisms to be selected produced low-level resistance which had little or no operational significance. More recently, metabolically based resistance has been selected, primarily in West Africa, which in some mosquito populations produces more than 1000-fold resistance. As this spreads the effectiveness of pyrethroid-based bednets and IRS will be compromised. New public health insecticides are not readily available. The pipeline of agrochemical insecticides that can be re-purposed for public health dried up 30 years ago when the target product profile for agricultural insecticides shifted from broad spectrum, stable, contact-acting insecticides to narrow spectrum stomach poisons that could be delivered through the plant. A public–private partnership, the Innovative Vector Control Consortium, was established in 2005 to stimulate the development of new public health pesticides. Nine potential new classes of chemistry are in the pipeline, with the intention of developing three into new insecticides. While this has been successfully achieved, it will still take 6–9 years for new insecticides to reach the market. Careful management of the resistance situation in the interim will be needed if current gains in malaria control are not to be reversed.
Plasma LL-37 correlates with vitamin D and is reduced in human immunodeficiency virus-1 infected individuals not receiving antiretroviral therapy
Authors: Honda Jennifer R. , Connick Elizabeth , MaWhinney Samantha , Chan Edward D. , Flores Sonia C.
Published: May 2014

Low levels of the vitamin D-regulated antimicrobial peptide cathelicidin (LL-37) may negatively impact the immune status of human immunodeficiency virus-1 (HIV-1) infected individuals (HIV+). We compared plasma LL-37 levels in healthy controls (HIV−) and HIV+ individuals on or off antiretroviral therapies (ARTs) (ART+ and ART−, respectively), and evaluated the relationship between vitamin D and LL-37 levels. In this cross-sectional study, levels of LL-37, 25-hydroxycholecalciferol [25(OH)D3] and 1,25-dihydroxycholecalciferol [1,25(OH)2D3] were measured from an initial cohort of 18 healthy controls and 10 HIV+/ART− individuals. Because this cohort lacked HIV+/ART+ subjects, LL-37 was also quantified from a second cohort of 10 HIV+/ART− and 13 HIV+/ART+ individuals. LL-37 levels were significantly lower in the HIV+/ART− group compared to the healthy controls (P = 0.01). A direct relationship was observed between LL-37 and both 25(OH)D3 and 1,25(OH)2D3. The level of 25(OH)D3 was predictive of higher LL-37 (P = 0.04) and for any given level of 25(OH)D3, HIV+/ART− subjects averaged 20 % lower LL-37 compared to the healthy controls (P = 0.045). For any given level of 1,25(OH)2D3, HIV+/ART− subjects averaged 25 % lower LL-37 compared to the healthy controls (P = 0.018), although 1,25(OH)2D3 was not predictive of higher LL-37 (P = 0.28). Finally, LL-37 levels were significantly lower in the HIV+/ART− group compared to the HIV+/ART+ group from the second cohort (P = 0.045). Untreated HIV infection may contribute to lower LL-37 levels, independent of vitamin D levels. ART treatment may potentially mitigate this decrease in LL-37 levels.
bíogo: a simple high-performance bioinformatics toolkit for the Go language
Authors: Kortschak R. Daniel , Adelson David L.
Published: May 2014

bíogo is a framework designed to ease development and maintenance of computationally intensive bioinformatics applications. The library is written in the Go programming language, a garbage-collected, strictly typed compiled language with built in support for concurrent processing, and performance comparable to C and Java. It provides a variety of data types and utility functions to facilitate manipulation and analysis of large scale genomic and other biological data. bíogo uses a concise and expressive syntax, lowering the barriers to entry for researchers needing to process large data sets with custom analyses while retaining computational safety and ease of code review. We believe bíogo provides an excellent environment for training and research in computational biology because of its combination of strict typing, simple and expressive syntax, and high performance.
The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin
Authors: Thyagarajan Bargavi , Bloom Jesse D.
Published: May 2014

Influenza is notable for its evolutionary capacity to escape immunity targeting the viral hemagglutinin. We used deep mutational scanning to examine the extent to which a high inherent mutational tolerance contributes to this antigenic evolvability. We created mutant viruses that incorporate most of the≈104amino-acid mutations to hemagglutinin from A/WSN/1933 (H1N1) influenza. After passaging these viruses in tissue culture to select for functional variants, we used deep sequencing to quantify mutation frequencies before and after selection. These data enable us to infer the preference for each amino acid at each site in hemagglutinin. These inferences are consistent with existing knowledge about the protein’s structure and function, and can be used to create a model that describes hemagglutinin’s evolution far better than existing phylogenetic models. We show that hemagglutinin has a high inherent tolerance for mutations at antigenic sites, suggesting that this is one factor contributing to influenza’s antigenic evolution.
Independent Theta Phase Coding Accounts for CA1 Population Sequences and Enables Flexible Remapping
Authors: Chadwick Angus , van Rossum Mark C. W. , Nolan Matthew F.
Published: May 2014

Populations of hippocampal place cells encode an animal’s past, current and future location through sequences of action potentials generated within each cycle of the network theta rhythm. These sequential representations have been suggested to result from temporally coordinated synaptic interactions within and between cell assemblies. In contrast, we show that a model based on rate and phase coding in independent neurons is sufficient to explain the organization of CA1 population activity during theta states. We show that CA1 population activity can be described as an evolving traveling wave that exhibits phase coding, rate coding, spike sequences and that generates an emergent population theta rhythm. We identify measures of global remapping and intracellular theta dynamics as critical for distinguishing mechanisms for pacemaking and coordination of sequential population activity. Our analysis suggests that independent coding enables flexible generation of sequential population activity within the duration of a single theta cycle.
CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes
Authors: Aach John , Mali Prashant , Church George M.
Published: May 2014

CRISPR/Cas9 systems enable many molecular activities to be efficiently directedin vivoto user-specifiable DNA sequences of interest, including generation of dsDNA cuts and nicks, transcriptional activation and repression, and fluorescence. CRISPR targeting relies on base pairing of short RNA transcripts with their target DNA sequences that must also be adjacent to fixed DNA motifs. However, rules for Cas9 targeting specificity are incompletely known. With increasing numbers of Cas9 systems being developed and deployed in more and more organisms, there is now strong need for a flexible and rational method for finding Cas9 sites with low off-targeting potential. We address this through the CasFinder system, which we demonstrate by generating human and mouse exome-wide catalogs of specific sites for three varieties of Cas9 –S. pyogenes,S. thermophilus(ST1), andN. meningitidis– that each target 56-74% of all exons. We also generate reduced sets of up to 3 targets per gene for use in high-throughput Cas9-based gene knockout screens that target 75-80% of all genes.
diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals
Authors: Tataru Paula , Nirody Jasmine A. , Song Yun S.
Published: May 2014

Summary:We present a tool, diCal-IBD, for detecting identity-by-descent (IBD) tracts between pairs of genomic sequences. Our method builds on a recent demographic inference method based on the coalescent with recombination, and is able to incorporate demographic information as a prior. Simulation study shows that diCal-IBD has significantly higher recall and precision than that of existing IBD detection methods, while retaining reasonable accuracy for IBD tracts as small as 0.1 cM.

Availability:http://sourceforge.net/p/dical-ibd

Contact:yss@eecs.berkeley.edu
Promises in psychological contract drive commitment for clinicians
Authors: Ellershaw Julia , Steane Peter , McWilliams John , Dufour Yvon
Published: May 2014

Purpose

– Job satisfaction, mental health and organisational commitment are important for clinician retention. Psychological contracts, organisational justice and negative affectivity (NA) have been linked with these outcomes but there is limited research examining these concepts in combination, particularly for clinicians. The aim of this paper is to examine the relationships between psychological contract breach, organisational justice and NA, on the outcomes of organisational commitment, psychological distress and job satisfaction, in a medical context.

Design/methodology/approach

– Surveys were distributed to Australian hospital clinicians through their internal mail and 81 completed surveys were returned (response rate=24 per cent).

Findings

– Multiple regression analyses revealed that organisational commitment was related to NA, psychological contract obligation and the interaction between psychological contract breach and distributive justice. Psychological distress was related to NA and procedural justice. Job satisfaction was related to the interaction between psychological contract breach and informational justice, however, the overall model for job satisfaction was not significant.

Practical implications

– By implementing innovative social exchange processes, healthcare organisations can ensure distributive justice is maintained in the culture in event of contract breach, and by so doing build safety mechanisms into sustaining commitment from clinicians.

Originality/value

– This paper contributes to the literature on clinical governance in managing the psychological contract to sustain commitment from clinical staff. The findings provide new insights into the factors effecting employee outcomes for clinicians.
Perceptions of nurses on the impact of accreditation on quality of care
Authors: Yildiz Ahmet , Kaya Sidika
Published: May 2014

Purpose

– This article aims to investigate perceptions of Turkish nurses on the impact of accreditation on quality of care and the effect of accreditation on quality results.

Design/methodology/approach

– This study was performed as a cross-sectional, questionnaire-based survey on 258 nurses who started working in the hospital before it was accredited and continued to work during and after accrediation and who therefore knew both the hospital's pre-accrediation and post-accreditation periods. In this study, descriptive statistical analyses (means and standard deviations) were carried out to explore the views of the participants on “quality results,” “benefits of accreditation” and “participation of employees.” “Quality results” was considered to be the dependent variable, while “benefits of accreditation” and “participation of employees” were accepted as the independent variables. The relationship between the dependent variable and the independent variables was tested using Pearson correlation and multiple regression analysis. External patient satisfaction data collected by the quality department of the hospital before and after accreditation were also investigated.

Findings

– It was found that nurses had generally high scores for the items concerning the benefits of accreditation. There was a statistically significant positive correlation between the dependent variable (quality results) and the independent variables (benefits of accreditation and participation of employees). Regression analysis indicated that R2=0.461 and the extent to which the independent variables explained the dependent variable was 46.1 per cent, which is a high rate. Patient satisfaction scores increased after accreditation.

Practical implications

– Our study suggest that providing support for nurses, especially nurses with administrative responsibilities and incorporating employees into the process are important for exercising quality standards.

Originality/value

– Hospital accreditation has a positive impact on quality results especially on quality of care provided to patients and patient satisfaction. Study findings could guide policy makers and hospital managers in Turkey and in other countries who are preparing or implementing accreditation.
Improving trainee psychiatrist's handover: standard setting and audit
Authors: Gupta Arun , Bevan Ruth , Vasudev Akshya
Published: May 2014

Purpose

– The 2006 Post Graduate Medical Education Trust Board (PMETB) trainees' survey indicated inadequacies in handover procedures amongst medical and psychiatry trainees nationwide; and in 2007 a local psychiatry trainees' survey found inadequate handover procedures. The purpose of this paper is to show how to improve handover practice through standard setting and sequential audit.

Design/methodology/approach

– A Trust wide Standard Operating Procedure (SOP) for handover was developed. Trainees were audited on perception of handover experiences (2008, 2009 and 2010).

Findings

– The audit revealed that the SOP was not consistently followed. Handing over “active problems” (AP) was perceived to occur frequently in 2008 (93.75 per cent), improved in 2009 (100 per cent for AP, 98 per cent for “problems which may arise”, (PA)); however deteriorated in 2010 (93 per cent for AP, 69 per cent for PA). Trainee satisfaction rates with handover improved each year (57 per cent in 2008, 75 per cent in 2009, 87 per cent in 2010, X2=3.7, df=2, p=0.16).

Practical implications

– SOP development, subsequent audits and sharing of results improved handover practice. This has implications for training and patient safety. This project demonstrates a method of improving handover practices in a large mental health trust.

Originality/value

– The work conducted is of interest to those working in psychiatry, not only from an education and training perspective, but also for clinical practice, in the UK as well as internationally.
Orthopaedic triage: cost effectiveness, diagnostic/surgical and management rates
Authors: Burn Damon , Beeson Elaine
Published: May 2014

Purpose

– The purpose of this paper is to investigate cost effectiveness, diagnostic rates, surgical percentage and appropriateness for orthopaedic referrals and number of patients able to be seen in orthopaedic triage from GP orthopaedic referrals.

Design/methodology/approach

– The study involved triaging paper referrals for orthopaedic outpatients to an interface service, orthotics or continue normal route. Data were collected on outcome of the interface appointment and outcomes for those patients referred to orthopaedics from the appointment.

Findings

– The study demonstrated a 27.3 per cent cost saving from the normal orthopaedic route with 86.1 per cent of patients able to be managed by an extended scope physiotherapist (ESP) without requiring orthopaedic assessment. Appropriateness of onward orthopaedic referrals was 80.5 per cent with surgery conversion rate of 75 per cent.

Originality/value

– Although triage and ESP positions have been studied before, this is the first known study to look at cost effectiveness across the patient pathway despite this being a large reason for the creation of these positions. Further larger studies are required to build upon this base in terms of demonstrating the cost effectiveness of the value of these positions.
Engaging and disengaging doctoral experiences in the behavioural sciences
Authors: Vekkaila Jenna , Pyhältö Kirsi , Lonka Kirsti
Published: May 2014

Purpose

– The aim of this paper is to explore doctoral students' engaging and disengaging experiences among a group of students whose doctoral processes had been prolonged for more than seven years.

Design/methodology/approach

– The participants were 16 doctoral students in the behavioural sciences. The data were collected with interviews employing a visualisation of their doctoral journeys, and were content analysed qualitatively.

Findings

– The results suggested that the students described their engagement in doctoral work in terms of dedication, vigour and occasionally absorption. In turn, disengagement was described in terms of insufficiency, cynicism and sometimes exhaustion. Interestingly, the source of engagement was typically a sense of belonging in the scholarly community, whereas the students often reported a lack of autonomy and a lack of belonging as sources for disengagement.

Research limitations/implications

– Further longitudinal studies are needed to explore the development of engagement in doctoral work among students from different contexts.

Practical implications

– In terms of developing more engaging learning environments, the findings imply that by enhancing students' sense of belonging to their scholarly community and their experiences of autonomy within it their engagement in doctoral work, and further, development as researchers can be fostered.

Originality/value

– This study extends the understanding of what may engage or disengage students from their doctoral studies and the essential relationship between the sense of autonomy and that of belonging in doctoral student engagement, in particular in the context of prolonged doctoral studies in the behavioural sciences.
The problems of resistance to scuffing of heavily loaded lubricated friction joints with WC/C-coated parts
Authors: Michalczewski Remigiusz , Piekoszewski Witold , Tuszynski Waldemar , Szczerek Marian
Published: May 2014

Purpose

– The purpose of this paper was to explore the mechanisms of scuffing propagation of heavily loaded lubricated friction pair elements coated with low-friction WC/C coating for various material combinations.

Design/methodology/approach

– The investigations were performed for low-friction coatings WC/C (a-C:H:W) deposited by the reactive sputtering physical vapour deposition (PVD) process. Experiments were carried out using a four-ball tester with continuously increasing loads. Tests were conducted for the following four material combinations: steel/steel tribosystem (all balls uncoated); steel/coating tribosystem (one upper ball uncoated/three lower balls WC/C-coated); coating/steel tribosystem (one upper ball WC/C-coated/three lower balls uncoated); and coating/coating tribosystem (all balls WC/C-coated).

Findings

– The better scuffing resistance is achieved by coating only one element (coating/steel tribosystem) than all elements (coating/coating tribosystem). The description of scuffing propagation for all investigated tribosystems was done. The high scuffing resistance of the coating/steel tribosystem resulted from reducing the adhesion between rubbing surfaces due to low chemical affinity (similarities) between the steel and the coating material and the presence of solid lubricant in the friction zone.

Practical implications

– In all cases, when a coating is applied, an increase in scuffing resistance is observed. However, it is better to coat only one element than all. Furthermore, the scuffing resistance for the coating/steel tribosystem is significantly higher than for the steel/coating tribosystem.

Originality/value

– The main value of this paper is description of scuffing propagation and revealing the new aspects in application of low-friction WC/C coating for heavily loaded lubricated friction pair elements. The overlapping ratio has been defined as an important factor influencing the scuffing resistance of the coated tribosystems.
A three-dimensional fusion prediction model for fractal rough surfaces in the sliding contact process
Authors: Lu Yan , Liu Zuomin
Published: May 2014

Purpose

– The purpose of this manuscript is to analyze the fusion micro-zone generated by typical rough surfaces and investigate the factors of thermal effects on the tribological performance of surface asperities and its results verified by the experiment.

Design/methodology/approach

– A three-dimensional fractal rough surfaces sliding contact model has been developed, which takes into account temperature rise and distribution. The finite-element method, Green's function method, thermal conduct theory and contact mechanics are used as the solution methods.

Findings

– The results yield insights into the effects of the sliding velocity, thermal properties of the material, normal load and surface roughness on the temperature rise of the sliding contact surface. It allows the specification of working conductions' properties to reduce fusion.

Originality/value

– The model is developed and described by using the features of the contact between one flat surface and one rough surface with varied topographies. It can be easily applied for solving the sliding contact problems with different working conditions and specified for designing the surface accuracy in the severe working condition.
Squeeze film characteristics of conical bearings operating with non-Newtonian lubricants – Rabinowitsch fluid model
Authors: Hsu Cheng-Hsing , Lin Jaw-Ren , Mou Lian-Jong , Kuo Chia-Chuan
Published: May 2014

Purpose

– The purpose of this paper is to present a theoretical study of non-Newtonian effects in conical squeeze-film plates that is based on the Rabinowitsch fluid model.

Design/methodology/approach

– A non-linear, modified Reynolds equation accounting for the non-Newtonian properties following the cubic stress law equation is derived. Through a small perturbation method, first-order closed-form solutions are obtained.

Findings

– It is found that the non-Newtonian properties of dilatant fluids increase the load capacity and lengthen the response time as compared to the case using a Newtonian lubricant; however, the non-Newtonian behaviors of pseudoplastic lubricants result in reverse influences.

Originality/value

– Numerical tables for squeeze-film loads of conical plates are also provided for engineering applications.