bluuebunny/crossref_metadata_2025 huggingface dataset:
Cognate interaction with iNKT cells expands IL-10–producing B regulatory cells
Authors: Vomhof-DeKrey Emilie E. , Yates Jennifer , Hägglöf Thomas , Lanthier Paula , Amiel Eyal , Veerapen Natacha , Besra Gurdyal S. , Karlsson Mikael C. I. , Leadbetter Elizabeth A.
Published: September 2015

Significance

Invariant natural killer T (iNKT) cells can facilitate B-cell responses by enhancing helper signals from protein-specific T cells or independently induce a B-cell developmental program; however, key differences in humoral memory after iNKT-cell help remain unclear. We determined that, unlike protein-specific T-cell help, cognate iNKT-cell help expands a large number of IL-10–producing B10 regulatory cells. These findings have broad implications for the types of B cells that may be generated when synthetic iNKT glycolipid ligands are used as vaccine adjuvants and also, outline a direct means to elicit B regulatory cells, which are increasingly being pursued as immunotherapeutic targets for protection against autoimmune disease.
Direct measurement of the 3-dimensional DNA lesion distribution induced by energetic charged particles in a mouse model tissue
Authors: Mirsch Johanna , Tommasino Francesco , Frohns Antonia , Conrad Sandro , Durante Marco , Scholz Michael , Friedrich Thomas , Löbrich Markus
Published: September 2015

Significance

Charged particles are applied in cancer radiotherapy because they are more efficient than X-rays or γ-rays in tumor cell killing. This efficiency results from the high dose deposition along the path of the particles. However, charged particles damage tissue inhomogeneously, such that many cells not directly hit by the particles receive a low dose and can survive with mutations. Because mutations can lead to secondary malignancies, this effect limits the applicability of charged particles in cancer radiotherapy. We provide the first direct measurement of the 3D DNA lesion distribution induced by energetic charged particles in a mouse model tissue. Our detailed analysis of the dose distribution will serve to benchmark biophysical models currently used for irradiation planning in cancer radiotherapy.
Type II integral membrane protein, TM of J paramyxovirus promotes cell-to-cell fusion
Authors: Li Zhuo , Hung Cher , Paterson Reay G. , Michel Frank , Fuentes Sandra , Place Ryan , Lin Yuan , Hogan Robert J. , Lamb Robert A. , He Biao
Published: September 2015

Significance

J paramyxovirus represents a group of unclassified paramyxoviruses that encode an integral membrane protein, transmembrane (TM), that is not found in other classified paramyxoviruses. In this work we have found that TM expression is involved in cell-to-cell fusion when coexpressed with the viral fusion protein F or coexpressed with F and the receptor-binding protein G. This work may define a separate class of viral proteins that promote cell-to-cell fusion.
Searching molecular structure databases with tandem mass spectra using CSI:FingerID
Authors: Dührkop Kai , Shen Huibin , Meusel Marvin , Rousu Juho , Böcker Sebastian
Published: September 2015

Significance

Untargeted metabolomics experiments usually rely on tandem MS (MS/MS) to identify the thousands of compounds in a biological sample. Today, the vast majority of metabolites remain unknown. Recently, several computational approaches were presented for searching molecular structure databases using MS/MS data. Here, we present CSI:FingerID, which combines fragmentation tree computation and machine learning. An in-depth evaluation on two large-scale datasets shows that our method can find 150% more correct identifications than the second-best search method. In comparison with the two runner-up methods, CSI:FingerID reaches 5.4-fold more unique identifications. We also present evaluations indicating that the performance of our method will further improve when more training data become available. CSI:FingerID is publicly available at
www.csi-fingerid.org
.
Gender contributes to personal research funding success in The Netherlands
Authors: van der Lee Romy , Ellemers Naomi
Published: September 2015

Significance

Women remain underrepresented in academia as they continue to face a leadership gap, salary gap, and funding gap. Closing the funding gap is of particular importance, because this may directly retain women in academia and foster the closing of other gaps. In this study, we examined the grant funding rates of a national full population of early career scientists. Our results reveal gender bias favoring male applicants over female applicants in the prioritization of their “quality of researcher” (but not “quality of proposal”) evaluations and success rates, as well as in the language use in instructional and evaluation materials. This work illuminates how and when the funding gap and the subsequent underrepresentation of women in academia are perpetuated.
Assessing sequence plasticity of a virus-like nanoparticle by evolution toward a versatile scaffold for vaccines and drug delivery
Authors: Lu Yuan , Chan Wei , Ko Benjamin Y. , VanLang Christopher C. , Swartz James R.
Published: September 2015

Significance

Particle instability, antigen fusion limitations, and intrinsic immunogenicity greatly limit the development of virus-like particles (VLPs). To address these problems, the Hepatitis B core protein (HBc) VLP was extensively modified to improve its functional properties by introducing an artificial disulfide network, removing the surface charge, and transplanting a new surface spike region. This study systematically explores the plasticity of viral capsids and, thereby, expands our knowledge regarding the relevant structure function relationships. Notably, we uncovered the influence of the HBc spike and its negative charges on capsid assembly and immunogenicity. Our observations on the unexpected importance of the HBc spike tip charged state suggest unexplored mechanisms for antiviral therapeutics that block capsid assembly.
Nascent chain-monitored remodeling of the Sec machinery for salinity adaptation of marine bacteria
Authors: Ishii Eiji , Chiba Shinobu , Hashimoto Narimasa , Kojima Seiji , Homma Michio , Ito Koreaki , Akiyama Yoshinori , Mori Hiroyuki
Published: September 2015

Significance

Bacteria living in seawater must cope with low-sodium environments that they may encounter. Here we show an unexpected finding that remodeling of the Sec protein export machinery plays a pivotal role in this adaptation.
Vibrio alginolyticus
possesses alternative SecDF1 and SecDF2 homologs that use the transmembrane gradient of Na
+
and that of H
+
, respectively, to enhance protein export by cooperating with the SecYEG translocon. The synthesis of SecDF2 is induced in low-Na
+
environments, and this induction is essential for the bacterium to survive low salinity. Remarkably, the
Vibrio
species use a nascent polypeptide, VemP, to monitor the functional state of the Sec pathway and to up-regulate translation of SecDF2 when activity of the SecDF1-containing Sec machinery declines.
Comprehensive assessment of cancer missense mutation clustering in protein structures
Authors: Kamburov Atanas , Lawrence Michael S. , Polak Paz , Leshchiner Ignaty , Lage Kasper , Golub Todd R. , Lander Eric S. , Getz Gad
Published: September 2015

Significance

Tumor sequencing efforts have enabled the identification of cancer genes based on an excess of mutations in the gene or clustering of mutations along the (one-dimensional) DNA sequence of the gene. Here, we show that this approach can be extended to identify cancer genes based on clustering of mutations relative to the 3D structure of the protein product. By analyzing the PanCancer compendium of somatic mutations in nearly 5,000 tumors, we identified known cancer genes and previously unidentified candidates based on clustering of missense mutations in protein structures or at interfaces with binding partners. In addition, we found that 3D clustering is present in both oncoproteins and tumor suppressors—contrary to the view that such clustering is a hallmark of oncoproteins.
SCN5A
variant that blocks fibroblast growth factor homologous factor regulation causes human arrhythmia
Authors: Musa Hassan , Kline Crystal F. , Sturm Amy C. , Murphy Nathaniel , Adelman Sara , Wang Chaojian , Yan Haidun , Johnson Benjamin L. , Csepe Thomas A. , Kilic Ahmet , Higgins Robert S. D. , Janssen Paul M. L. , Fedorov Vadim V. , Weiss Raul , Salazar Christina , Hund Thomas J. , Pitt Geoffrey S. , Mohler Peter J.
Published: September 2015

Significance

Cardiovascular disease remains the leading cause of mortality in the United States, and cardiac arrhythmia underlies the majority of these deaths. Here, we report a new mechanism for congenital human cardiac arrhythmia due to defects in the regulation of the primary cardiac Na
v
channel, Na
v
1.5 (
SCN5A
), by a family of signaling molecules termed fibroblast growth factor homologous factors (FHFs). Individuals harboring
SCN5A
variants that affect Na
v
1.5/FHF interactions display atrial and ventricular phenotypes, syncope, and sudden cardiac death. The human variant results in aberrant Na
v
1.5 inactivation, causing prolonged action potential duration and afterdepolarizations in murine myocytes, thereby providing a rationale for the human arrhythmia.
Simulating the function of sodium/proton antiporters
Authors: Alhadeff Raphael , Warshel Arieh
Published: September 2015

Significance

Understanding the molecular nature of the function of transporters is of significant interest in view of their biological importance. However, the actual structure–function relationship of transporters is far from being clear. To advance this understanding, we simulated the activity of the Na
+
/H
+
antiporter NhaA by a Monte Carlo approach, based on the calculated coarse-grained electrostatic landscape of the system. The simulations reproduce the observed trend and provide a powerful insight into the origin of the transporting function and the molecular basis of its control. We also show that a large conformational alternation is essential for the transporter function. The approach used should be useful for general studies of other transporters.
Increased brain uptake of targeted nanoparticles by adding an acid-cleavable linkage between transferrin and the nanoparticle core
Authors: Clark Andrew J. , Davis Mark E.
Published: September 2015

Significance

Treatment for many neurological diseases is hindered by the inability of therapeutic agents to cross the blood–brain barrier (BBB). Here, we show a method for increasing the ability of high-avidity, transferrin (Tf)-containing nanoparticles to enter the brain through transcytosis. Tf was attached to nanoparticles through an acid-cleavable linkage that facilities release of nanoparticles from Tf that are bound to Tf receptors (TfR) during transcytosis, promoting entry of the nanoparticles into the brain. This method is an improvement over previous high-affinity, TfR-targeted therapeutics that were restricted by BBB endothelium and mostly excluded from entering the brain. Increased brain accumulation of nanoparticles via this methodology should allow for greater delivery of encapsulated therapeutic agents at lower systemic doses.
Historicity in metapragmatics – a study on ‘discernment’ in Italian metadiscourse
Authors: Kádár Dániel Z. , Paternoster Annick
Published: September 2015

The present paper contributes to meta pragmatics, by examining the question of how historicity influences the validity of certain modern meta terms that are accepted as ‘neutral’ and ‘scientific’ in pragmatics. We argue that it is fundamental to explore the history and development of such meta terms, and also to study their historically situated meanings, in order to increase the self-reflexivity and rigour of analyses. We analyse the notion of ‘discernment’ as a case study, and we will show that the way in which the Italian equivalent of this term (discernere) – which supposedly influenced historical English understandings of ‘discernment’ as well – is used in historical Italian meta discourses contradicts the modern application of this meta term.
Conducting a task while reconstructing its meaning
Authors: Nissi Riikka , Lehtinen Esa
Published: September 2015

This article investigates the way an institutional task of a meeting is oriented to by different meeting participants and developed in and through local interaction. Our data come from a city organization, where a large organizational change is planned and prepared through a series of face-to-face encounters and accompanying written texts. Using the notion of recontextualization and by connecting it to the conversation analytical method and to the notion of intersubjectivity, the study examines how the institutional task that is verbalized in written form prior to the meeting is conceptualized by meeting participants in their turns of talk. By doing so, the study will particularly shed light on the question of how different recontextualizations are motivated by their sequential position in interaction. Based on this, it also investigates how the meeting participants construct their professional identities through the conceptualizations made. In a wider sense, the article shows how spoken interaction and written texts interweave and form a reciprocal relationship in organizational life. Thus, it contributes to a deeper understanding about the multifaceted connections between the interactional management of meetings and wider organizational practices and processes that these encounters have been set up to advance.
“Russian celebrations” and American debates about Russia in 1813
Authors: Kurilla Ivan
Published: September 2015

In the article, the author uses a sociocultural approach to analyze debates in the US press that accompanied “Russian celebrations” in 1813. During the War of 1812, the Federalist opposition to President Madison's administration organized several celebrations of Russia's victories over Napoleon, who was a de facto ally of the USA in its war against England. As a result, harsh debates arose about the relative merits of the Russian nation. Madison's supporters described Russia in extremely critical terms, while the critics of the administration mostly spoke positively of the distant country. For both sides, the Russian victories were just a pretext for formulating their own political views, but by using an image of “the Other,” they elaborated and affirmed two major characterizations of Russia: in one view, it was a barbaric and uncivilized country; in the other, a guarantor of liberty and a rapidly developing and freedom-loving nation. The main difference was summarized in a pamphlet publication of correspondence between Robert Harper and Robert Walsh. The article affirms that the level of civilization in Russia was not just used as an argument in domestic polemics, but was determined according to the demands of that polemic.
Assessing the Magnitude of Effect of Hydroelectric Production on Lake Sturgeon Abundance in Ontario
Authors: Haxton Tim , Friday Mike , Cano Tim , Hendry Charles
Published: September 2015

The presence of hydroelectric power generating facilities has been identified as the primary factor affecting the variation in relative abundance of Lake Sturgeon Acipenser fulvescens in rivers across Ontario. Qualitatively, these facilities are known to have impacts on the aquatic environment, and they can be inferred to have effects on Lake Sturgeon; however, few studies quantifying these effects are available. Our objectives were to (1) determine and compare the magnitude of effect (d) of hydroelectric facility operating regimes on Lake Sturgeon abundance; (2) compare Lake Sturgeon biological responses among river systems with different operating regimes in order to understand the potential limiting factors within these systems; and (3) assess the effectiveness of mitigation efforts where they have been employed. A standardized index netting program targeting juveniles and adults was conducted over two field seasons at 23 river sites across Ontario. The magnitude of effect on abundance (as indicated by d) was lowest in run-of-the-river systems and was considered large in peaking systems and winter reservoir systems. Relative abundance was significantly greater in unregulated rivers than in regulated rivers. Juvenile abundance was significantly greater in run-of-the-river systems than in peaking systems and winter reservoirs and was significantly greater in peaking systems than in winter reservoirs. Adult abundance did not significantly differ among operating regimes. Growth was faster and condition was significantly greater in unregulated systems than in regulated systems. Recruitment of Lake Sturgeon was highly variable in both regulated and unregulated systems, whereas recruitment failure was more evident in regulated systems, particularly in peaking systems.

Received April 5, 2015; accepted July 2, 2015
Characterization of a novel thiosulfate dehydrogenase from a marine acidophilic sulfur-oxidizing bacterium, Acidithiobacillus thiooxidans strain SH
Authors: Sharmin Sultana , Yoshino Eriko , Kanao Tadayoshi , Kamimura Kazuo
Published: September 2015

A marine acidophilic sulfur-oxidizing bacterium, Acidithiobacillus thiooxidans strain SH, was isolated to develop a bioleaching process for NaCl-containing sulfide minerals. Because the sulfur moiety of sulfide minerals is metabolized to sulfate via thiosulfate as an intermediate, we purified and characterized the thiosulfate dehydrogenase (TSD) from strain SH. The enzyme had an apparent molecular mass of 44 kDa and was purified 71-fold from the solubilized membrane fraction. Tetrathionate was the product of the TSD-oxidized thiosulfate and ferricyanide or ubiquinone was the electron acceptor. Maximum enzyme activity was observed at pH 4.0, 40 °C, and 200 mM NaCl. To our knowledge, this is the first report of NaCl-stimulated TSD activity. TSD was structurally different from the previously reported thiosulfate-oxidizing enzymes. In addition, TSD activity was strongly inhibited by 2-heptyl-4-hydroxy-quinoline N-oxide, suggesting that the TSD is a novel thiosulfate:quinone reductase.
Vertical Distribution of Age-0 Walleye Pollock during Late Summer: Environment or Ontogeny?
Authors: Parker-Stetter Sandra L. , Horne John K. , Urmy Samuel S. , Heintz Ron A. , Eisner Lisa B. , Farley Edward V.
Published: September 2015

Variability in the late-summer vertical distribution of age-0 Walleye Pollock Gadus chalcogrammus in the southeastern Bering Sea has been attributed to a range of physical and biological factors. Using acoustic data (38 and 120 kHz) collected during the 2010 Bering Aleutian Salmon International Survey (BASIS) and dedicated high-resolution surveys (HR1 and HR2), we evaluated whether late-summer distributions could be explained by water column properties (environment) or whether sampling was likely occurring during the ontogenetic shift of age-0 Walleye Pollock from near-surface habitat to demersal habitat (ontogeny). Neither water column attributes (temperature, relative temperature, salinity, dissolved oxygen, and density gradient) nor the acoustic density of zooplankton prey strongly predicted the acoustic estimates of age-0 Walleye Pollock vertical presence or density. At 6 of 10 paired BASIS–HR1 stations, age-0 Walleye Pollock shifted deeper in the water column between BASIS sampling and the HR1 sampling conducted 8–34 d later. There were no consistent differences in FL (P > 0.05 for 2 of 4 station pairs) or energy density (P > 0.05 for 3 station pairs) between age-0 Walleye Pollock caught in near-surface trawls and those caught in midwater trawls. Our data suggest that the observation of both near-surface and midwater age-0 Walleye Pollock during late summer is likely due to an ontogenetic habitat shift; however, the causative factor was not clear given the limited sample sizes and explanatory variables. The timing of the ontogenetic shift, which appears to have begun before August 18, 2010, can ultimately affect survey strategies, and knowledge of this timing can provide additional insight into factors affecting the overwinter survival of age-0 Walleye Pollock.

Received December 5, 2014; accepted May 10, 2015
Integrins activate trimeric G proteins via the nonreceptor protein GIV/Girdin
Authors: Leyme Anthony , Marivin Arthur , Perez-Gutierrez Lorena , Nguyen Lien T. , Garcia-Marcos Mikel
Published: September 2015

Signal transduction via integrins and G protein–coupled receptors is critical to control cell behavior. These two receptor classes have been traditionally believed to trigger distinct and independent signaling cascades in response to extracellular cues. Here, we report a novel mechanism of integrin signaling that requires activation of the trimeric G protein Gαi by the nonreceptor guanine nucleotide exchange factor (GEF) GIV (also known as Girdin), a metastasis-associated protein. We demonstrate that GIV enhances integrin-dependent cell responses upon extracellular matrix stimulation and makes tumor cells more invasive. These responses include remodeling of the actin cytoskeleton and PI3K-dependent signaling, resulting in enhanced haptotaxis and invasion. We show that both GIV and its substrate Gαi3 are recruited to active integrin complexes and that tumor cells engineered to express GEF-deficient GIV fail to transduce integrin signals into proinvasive responses via a Gβγ-PI3K axis. Our discoveries delineate a novel mechanism by which integrin signaling is rewired during metastasis to result in increased tumor invasiveness.
Spectral Theory for Noncommuting Operators
Authors: Johnson Gerald W. , Lapidus Michel L. , Nielsen Lance
Published: September 2015

This chapter, on spectral theory for noncommuting operators, seeks to extend the operational calculus beyond the setting of the analytic functions in the disentangling algebra. When the Banach space is replaced with a Hilbert space, and the operators under consideration are bounded and self-adjoint, it is shown that the domain of the operational calculus (i.e. the domain of the disentangling map) is much richer than the disentangling algebra. The approach taken in this chapter relies in part on a stability result from Chapter 7, as well as on techniques from probability theory and the theory of distributions (in particular, the Paley–Wiener–Schwartz theorem). Also considered in this chapter is a simple class of “Trotter product formulas” that are suitable for Feynman’s operational calculus in the general Banach space setting.
Microbiology of nests and eggs
Authors: West A. , Cassey P. , Thomas C. M.
Published: September 2015

Microbes on the surface of the eggshell are associated with increased infection rates of the inner egg and reduced hatchability. The species of microbes and their relative abundance are highly variable between the nests and eggs of different birds. Various strategies are employed by the incubating bird and the egg itself, to reduce the chances of microbial infection, including using nest materials with particular anti-microbial properties. The avian egg is largely an inhospitable environment for microbial growth, incorporating a variety of anti-microbial chemicals with a broad range of targets and modes of activity, from direct lysis of bacterial cells to sequestration of molecules essential for their metabolism. This chapter discusses these strategies and the influence of other factors on infection rates such as nest humidity, uropygial secretions, male quality, egg laying sequence and incubation delay, and how these affect microbes in the nest, on the shell, and inside the egg.
Influence of incubation temperature on offspring phenotype and fitness in birds
Authors: Hepp G.R. , DuRant S.E. , Hopkins W.A.
Published: September 2015

Incubation is an important reproductive cost in birds. Because optimal development of avian embryos occurs within a narrow range of incubation temperatures, incubating birds are challenged to balance the demands of self-maintenance with the thermal requirements of developing embryos. the chapter's review shows that low incubation temperatures slow the development of avian embryos leading to longer incubation periods and reduced neonate quality. Embryos incubated at low temperatures generally use more energy which reduces the body mass and nutrient reserves of newly hatched chicks. Furthermore, this carries over to later life stages of young birds and negatively affects their subsequent growth, immunocompetence, metabolic rate, thermoregulatory ability, and locomotor performance. Evidence suggests that changes to the phenotypic quality of birds induced by low incubation temperatures reduce their survival, recruitment to the breeding population, and subsequent reproductive success. The chapter proposes additional research to test the strength, generality, and consequences of temperature-induced phenotypes in birds.
Abel-Poisson and Fejér Means of Fourier Series
Authors: Taheri Ali
Published: September 2015

This chapter presents a thorough discussion of Fourier analysis on the circle and various summability methods, including Cesaro-Fejer and Abel-Poisson. The chapter also introduces the Banach algebra L1 and discussing some related concepts.
Convolution Semigroups; The Poisson and Heat Kernels on Rn
Authors: Taheri Ali
Published: September 2015

This chapter discusses convolutions on ℝn in detail. The Banach algebra L1 and approximations to identity are introduced and studied. Various applications including Young’s convolution inequality, boundedness of Riesz potentials and Loomis-Whitney inequality are discussed. A detailed discussion of the Cauchy initial value problem for the wave equation on ℝn is also covered at the end.
Second Order Equations in Divergence Form: Measurable Coefficients
Authors: Taheri Ali
Published: September 2015

Optimal Holder regularity results on solutions to second order equations in divergence form with measurable coefficients are presented. Caccioppolli inequality on level sets and De Girogis method along with Moser iteration are discussed. Harnack inequality and local boundedness of solutions are also studied at the end.
The Unwaved Flag
Authors: Lee Lois
Published: September 2015

This chapter focuses on material and symbolic non-religious representations, calling particular attention to the banal forms that surround people in contemporary England, as, perhaps, elsewhere. These incarnations of the non-religious often seem unremarkable and yet they establish and reproduce non-religious norms as well as secularist ones. This taken-for-grantedness is perhaps especially powerful when it comes to material non-religion, not only because people in Western cultural contexts are more attuned to intellectual aspects of non-religion over other dimensions, but also because people often take the material world for granted in general. Recognizing the diversity of material forms of non-religion therefore opens up new ways of understanding these cultures beyond the intellectual and, in considering the mundaneness of these forms, shows how what is ostensibly secular may have non-religious currents running beneath.
Disaffiliation and Misaffiliation
Authors: Lee Lois
Published: September 2015

This chapter is a case study of self-classification, looking at representations of the self as ‘atheist’, ‘non-religious’, and ‘secular’, and the work that these representations do. It points to ways in which people in so-called secular societies are required to conceive of themselves in non-religious terms, that is, in relation to the religious people and cultures also present in these societies. It problematizes the idea of ‘secularity’ as a way to capture these empirical realities, demonstrating how the idea of the insubstantial secular is instead inscribed in self-understandings and social relations through the use of negative or inverted identities—‘atheist’, ‘not religious’, and ‘indifferent to religion’. Despite taking these forms, though, apparently negative identities express much richer and discrete commitments and therefore compete with more explicitly positive identities such as ‘humanism’.
A subpopulation that may correspond to granulocytic myeloid-derived suppressor cells reflects the clinical stage and progression of cutaneous melanoma
Authors: Stanojevic Ivan , Miller Karolina , Kandolf-Sekulovic Lidija , Mijuskovic Zeljko , Zolotarevski Lidija , Jovic Milena , Gacevic Milomir , Djukic Mirjana , Arsenijevic Nebojsa , Vojvodic Danilo
Published: September 2015

Seventy-eight melanoma patients and 10 healthy individuals were examined. Follow-up examinations of all melanoma patients were performed regularly every three months. Myeloid-derived suppressor cells (MDSC) were defined as lineage negative (CD3 − , CD19 − , CD56 − ), HLA-DR −/low , CD11b + and CD33 + . Classification of granulocytic (GrMDSC) and monocytic (MoMDSC) subsets was based on the CD15 and CD14 expression, respectively. Unlike the MoMDSC, that were present in 60% of healthy controls and 15% of melanoma patients, the GrMDSC were present in all examined participants, and the melanoma patients were found to have statistically higher frequencies compared with healthy controls. Accordingly, we kept focused on GrMDSC frequencies in relation to the melanoma stages and course of the disease. The GrMDSC values are highest in stage IV melanoma patients, with statistical significance compared with stages IA, IB, IIA and IIB. Patients with progression had statistically higher GrMDSC counts comparing with those with stable disease ( P = 0.0079). Patients who had progression-free interval (PFI) < 12 months showed significantly higher GrMDSC values compared with those with PFI > 12 months ( P = 0.0333). GrMDSC showed significant negative correlation with PFI intervals ( P = 0.0095). The GrMDSC subset was predominant in all our patients. We confirmed that GrMDSC do accumulate early in the peripheral blood of melanoma patients and their frequencies correlate narrowly with the clinical stage and the spread of the disease. The increase in GrMDSC frequencies correlates well with a progressive disease and could be considered a potential predictive biomarker of high-risk melanoma cases that are more likely to have a shorter PFI.
Incidence of Carpal Coalition in the Pediatric Population
Authors: Pruszczynski Blazej , Saller Jeremy , Rogers Kenneth J. , Holmes Laurens , Ty Jennifer M.
Published: September 2015

Background:

Carpal coalitions (CCs) result from the failure of segmentation of the carpal anlage in early development. In the adult population, CC is usually described as an asymptomatic radiographic finding. Data on CC in the pediatric population are limited. This study examines the prevalence of CC in the pediatric population and characterizes the presentation and associated musculoskeletal conditions.

Methods:

We used a cross-sectional design to assess data collected from all patients seen in our institution and associated facilities from August 2004 through February 2013. In total, 20,929 patients had an upper extremity x-ray taken that included the wrist. A natural language software recognition program for key words identified 104 patients with CC. Period prevalence and demographic and radiographic data were estimated using frequency and percentages.

Results:

The period prevalence of CC in this population was 5:1000. The initial age at the radiologic CC presentation varies between types. The most common CC (luno-triquetral, 69.2%) had a mean age at presentation of 12 y 11 mo. The second most frequent CC (capito-hamate, 17.2%) had a mean age at presentation of 8 y 2 mo. CCs were more prevalent among African American children; however, capito-hamate coalitions (the second most common coalition) were more often observed in whites. CC was symptomatic in 2 patients. Thirty-nine patients had associated conditions such as skeletal dysplasia and limb deformity, and most of these patients were diagnosed with capito-hamate coalitions.

Conclusions:

The period prevalence of CC in this pediatric population is 5:1000. Similar prevalence has been reported in other studies. Although the prevalence of CC is comparable by sex, it is most common among African American children. The most common CC is luno-triquetral followed by capito-hamate. Capito-hamate coalitions were more common among patients with associated conditions and were diagnosed at a younger age relative to other subtypes in our group.

Level of Evidence:

Level IV—prognostic case series.
Childhood Obesity Increases the Risk of Failure in the Treatment of Distal Forearm Fractures
Authors: Auer Ronald T. , Mazzone Paul , Robinson Luke , Nyland John , Chan Gilbert
Published: September 2015

Background:

Childhood obesity is a national problem that has gained significant attention in both the medical literature and the national media. Obesity in the adult population has been associated with increased failure of conservative treatments. Our hypothesis is that childhood obesity is associated with a loss of reduction after closed treatment of distal radius fractures.

Methods:

A total of 157 patients with consecutive distal radius fractures who underwent closed reduction in the emergency department or the operating room were included from the office records of the sole pediatric orthopaedic subspecialist group in a metropolitan area from January 2011 to June 2012. All cases were initially treated with fiberglass casting with or without closed reduction. All patients completed the casting treatment and demonstrated radiographic union. Patients’ age, weight, height, number of office visits, subsequent surgeries, and fracture angulation were recorded and analyzed.

Results:

Sixty-six (42%) children were overweight (BMI>85th percentile) and 46 (29%) children met the criteria for obesity (BMI>95th percentile). Fourteen normal-sized children (12%) and 13 obese children (28%) required a reduction in the operating room after initial treatment, which was significant (P=0.02). Obese children needed significantly more visits requiring radiographs (P=0.004). Obese children were significantly less likely to have an initial perfect reduction in the emergency room (P=0.005).

Conclusions:

The results of closed reduction and casting for displaced distal radius fractures are typically excellent with few complications or risks. The present study supports the hypothesis that obesity results in a higher rate of malreduction and subsequent manipulations with closed reduction and casting. Close follow-up and early consideration for additional treatment in this patient population may help reduce the need for further manipulations.

Level of Evidence:

Level III.
The quest for wisdom: lessons from 17 tsunamis, 2004–2014
Authors: Okal Emile A.
Published: September 2015

Since the catastrophic Sumatra–Andaman tsunami took place in 2004, 16 other tsunamis have resulted in significant damage and 14 in casualties. We review the fundamental changes that have affected our command of tsunami issues as scientists, engineers and decision-makers, in the quest for improved wisdom in this respect. While several scientific paradigms have had to be altered or abandoned, new algorithms, e.g. the W seismic phase and real-time processing of fast-arriving seismic P waves, give us more powerful tools to estimate in real time the tsunamigenic character of an earthquake. We assign to each event a ‘wisdom index’ based on the warning issued (or not) during the event, and on the response of the population. While this approach is admittedly subjective, it clearly shows several robust trends: (i) we have made significant progress in our command of far-field warning, with only three casualties in the past 10 years; (ii) self-evacuation by educated populations in the near field is a key element of successful tsunami mitigation; (iii) there remains a significant cacophony between the scientific community and decision-makers in industry and government as documented during the 2010 Maule and 2011 Tohoku events; and (iv) the so-called ‘tsunami earthquakes’ generating larger tsunamis than expected from the size of their seismic source persist as a fundamental challenge, despite scientific progress towards characterizing these events in real time.
Response to the 2011 Great East Japan Earthquake and Tsunami disaster
Authors: Koshimura Shunichi , Shuto Nobuo
Published: September 2015

We revisited the lessons of the 2011 Great East Japan Earthquake Tsunami disaster specifically on the response and impact, and discussed the paradigm shift of Japan's tsunami disaster management policies and the perspectives for reconstruction. Revisiting the modern histories of Tohoku tsunami disasters and pre-2011 tsunami countermeasures, we clarified how Japan's coastal communities have prepared for tsunamis. The discussion mainly focuses on structural measures such as seawalls and breakwaters and non-structural measures of hazard map and evacuation. The responses to the 2011 event are discussed specifically on the tsunami warning system and efforts to identify the tsunami impacts. The nation-wide post-tsunami survey results shed light on the mechanisms of structural destruction, tsunami loads and structural vulnerability to inform structural rehabilitation measures and land-use planning. Remarkable paradigm shifts in designing coastal protection and disaster mitigation measures were introduced, leading with a new concept of potential tsunami levels: Prevention (Level 1) and Mitigation (Level 2) levels according to the level of ‘protection’. The seawall is designed with reference to Level 1 tsunami scenario, while comprehensive disaster management measures should refer to Level 2 tsunami for protection of human lives and reducing potential losses and damage. Throughout the case study in Sendai city, the proposed reconstruction plan was evaluated from the tsunami engineering point of view to discuss how the post 2011 paradigm was implemented in coastal communities for future disaster mitigation. The analysis revealed that Sendai city's multiple protection measures for Level 2 tsunami will contribute to a substantial reduction of the tsunami inundation zone and potential losses, combined with an effective tsunami evacuation plan.
Geological and historical evidence of irregular recurrent earthquakes in Japan
Authors: Satake Kenji
Published: September 2015

Great (M∼8) earthquakes repeatedly occur along the subduction zones around Japan and cause fault slip of a few to several metres releasing strains accumulated from decades to centuries of plate motions. Assuming a simple ‘characteristic earthquake’ model that similar earthquakes repeat at regular intervals, probabilities of future earthquake occurrence have been calculated by a government committee. However, recent studies on past earthquakes including geological traces from giant (M∼9) earthquakes indicate a variety of size and recurrence interval of interplate earthquakes. Along the Kuril Trench off Hokkaido, limited historical records indicate that average recurrence interval of great earthquakes is approximately 100 years, but the tsunami deposits show that giant earthquakes occurred at a much longer interval of approximately 400 years. Along the Japan Trench off northern Honshu, recurrence of giant earthquakes similar to the 2011 Tohoku earthquake with an interval of approximately 600 years is inferred from historical records and tsunami deposits. Along the Sagami Trough near Tokyo, two types of Kanto earthquakes with recurrence interval of a few hundred years and a few thousand years had been recognized, but studies show that the recent three Kanto earthquakes had different source extents. Along the Nankai Trough off western Japan, recurrence of great earthquakes with an interval of approximately 100 years has been identified from historical literature, but tsunami deposits indicate that the sizes of the recurrent earthquakes are variable. Such variability makes it difficult to apply a simple ‘characteristic earthquake’ model for the long-term forecast, and several attempts such as use of geological data for the evaluation of future earthquake probabilities or the estimation of maximum earthquake size in each subduction zone are being conducted by government committees.
On the characteristics of landslide tsunamis
Authors: Løvholt F. , Pedersen G. , Harbitz C. B. , Glimsdal S. , Kim J.
Published: September 2015

This review presents modelling techniques and processes that govern landslide tsunami generation, with emphasis on tsunamis induced by fully submerged landslides. The analysis focuses on a set of representative examples in simplified geometries demonstrating the main kinematic landslide parameters influencing initial tsunami amplitudes and wavelengths. Scaling relations from laboratory experiments for subaerial landslide tsunamis are also briefly reviewed. It is found that the landslide acceleration determines the initial tsunami elevation for translational landslides, while the landslide velocity is more important for impulsive events such as rapid slumps and subaerial landslides. Retrogressive effects stretch the tsunami, and in certain cases produce enlarged amplitudes due to positive interference. In an example involving a deformable landslide, it is found that the landslide deformation has only a weak influence on tsunamigenesis. However, more research is needed to determine how landslide flow processes that involve strong deformation and long run-out determine tsunami generation.
Source mechanisms of volcanic tsunamis
Authors: Paris Raphaël
Published: September 2015

Volcanic tsunamis are generated by a variety of mechanisms, including volcano-tectonic earthquakes, slope instabilities, pyroclastic flows, underwater explosions, shock waves and caldera collapse. In this review, we focus on the lessons that can be learnt from past events and address the influence of parameters such as volume flux of mass flows, explosion energy or duration of caldera collapse on tsunami generation. The diversity of waves in terms of amplitude, period, form, dispersion, etc. poses difficulties for integration and harmonization of sources to be used for numerical models and probabilistic tsunami hazard maps. In many cases, monitoring and warning of volcanic tsunamis remain challenging (further technical and scientific developments being necessary) and must be coupled with policies of population preparedness.
Spiribacter curvatus sp. nov., a moderately halophilic bacterium isolated from a saltern
Authors: León María José , Rodríguez-Olmos Ángel , Sánchez-Porro Cristina , López-Pérez Mario , Rodríguez-Valera Francisco , Soliveri Juan , Ventosa Antonio , Copa-Patiño José Luis
Published: September 2015

A novel pink-pigmented bacterial strain, UAH-SP71T, was isolated from a saltern located in Santa Pola, Alicante (Spain) and the complete genome sequence was analysed and compared with that of Spiribacter salinus M19-40T, suggesting that the two strains constituted two separate species, with a 77.3 % ANI value. In this paper, strain UAH-SP71T was investigated in a taxonomic study using a polyphasic approach. Strain UAH-SP71T was a Gram-stain-negative, strictly aerobic, non-motile curved rod that grew in media containing 5–20 % (w/v) NaCl (optimum 10 % NaCl), at 5–40 °C (optimum 37 °C) and at pH 5–10 (optimum pH 8). Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed that strain UAH-SP71T is a member of the genus Spiribacter, showing a sequence similarity of 96.5 % with Spiribacter salinus M19-40T. Other related species are also members of the family Ectothiorhodospiraceae, including Arhodomonas recens RS91T (95.5 % 16S rRNA gene sequence similarity), Arhodomonas aquaeolei ATCC 49307T (95.4 %) and Alkalilimnicola ehrlichii MLHE-1T (94.9 %). DNA–DNA hybridization between strain UAH-SP71T and Spiribacter salinus M19-40T was 39 %. The major cellular fatty acids of strain UAH-SP71T were C18 : 1ω6c and/or C18 : 1ω7c, C16 : 0, C16 : 1ω6c and/or C16 : 1ω7c, C10 : 0 3-OH and C12 : 0, a pattern similar to that of Spiribacter salinus M19-40T. Phylogenetic, phenotypic and genotypic differences between strain UAH-SP71T and Spiribacter salinus M19-40T indicate that strain UAH-SP71T represents a novel species of the genus Spiribacter, for which the name Spiribacter curvatus sp. nov. is proposed. The type strain is UAH-SP71T ( = CECT 8396T = DSM 28542T).
Cryptosporangium cibodasense sp. nov., isolated from leaf litter in Indonesia
Authors: Nurkanto Arif , Lisdiyanti Puspita , Hamada Moriyuki , Ratnakomala Shanti , Shibata Chiyo , Tamura Tomohiko
Published: September 2015

A novel actinomycete strain, designated LIPI11-2-Ac046T, was isolated from a leaf litter sample obtained from Cibodas Botanical Garden, West Java, Indonesia, using the rehydration and centrifugation method. The taxonomic status of this organism was established using a polyphasic approach. Comparative 16S rRNA gene sequence analysis revealed that strain LIPI11-2-Ac046T had the closest sequence similarities with members of the genus Cryptosporangium (97.99–98.90 %). The strain grew well on ISP 4 and ISP 5 media and formed sporangia. Spores of this strain were motile. The strain grew in the presence of 0–2 % (w/v) NaCl and the temperature range of 15–28 °C. The cell-wall hydrolysate contained meso-diaminopimelic acid as the diagnostic diamino acid and the whole-cell hydrolysate contained mannose, glucose, galactose, ribose and xylose, together with one unidentified O-methyl-pentose. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8), and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were C18 : 1ω9c, iso-C16 : 0, C16 : 0 and C17 : 1ω9c. These phenotypic characteristics corresponded to those of the genus Cryptosporangium. Meanwhile, the results of DNA–DNA hybridization as well as physiological and biochemical analyses distinguished strain LIPI11-2-Ac046T from known members of the genus Cryptosporangium. On the basis of these data, it is proposed that strain LIPI11-2-Ac046T represents a novel species of the genus Cryptosporangium, with the name Cryptosporangium cibodasense sp. nov. The type strain is LIPI11-2-Ac046T ( = InaCC A457T = NBRC 110976T).
Recombination-mediated remodelling of host–pathogen interactions during Staphylococcus aureus niche adaptation
Authors: Spoor Laura E. , Richardson Emily , Richards Amy C. , Wilson Gillian J. , Mendonca Chriselle , Gupta Ravi Kr. , McAdam Paul R. , Nutbeam-Tuffs Stephen , Black Nikki S. , O'Gara James P. , Lee Chia Y. , Corander Jukka , Ross Fitzgerald J.
Published: September 2015

Large-scale recombination events have led to the emergence of epidemic clones of several major bacterial pathogens. However, the functional impact of the recombination on clonal success is not understood. Here, we identified a novel widespread hybrid clone (ST71) of livestock-associated Staphylococcus aureus that evolved from an ancestor belonging to the major bovine lineage CC97, through multiple large-scale recombination events with other S. aureus lineages occupying the same ruminant niche. The recombination events, affecting a 329 kb region of the chromosome spanning the origin of replication, resulted in allele replacement and loss or gain of an array of genes influencing host–pathogen interactions. Of note, molecular functional analyses revealed that the ST71 hybrid clone has acquired multiple novel pathogenic traits associated with acquired and innate immune evasion and bovine extracellular matrix adherence. These findings provide a paradigm for the impact of large-scale recombination events on the rapid evolution of bacterial pathogens within defined ecological niches.