bluuebunny/crossref_metadata_2025 huggingface dataset:
Rhabdomyosarcoma of the Breast in Adolescent and Young Adult (AYA) Women
Authors: Audino Anthony N. , Setty Bhuvana A. , Yeager Nicholas D.
Published: November 2016

Soft tissue sarcoma constitutes 8% of all tumors in adolescent and young adults (AYA), with rhabdomyosarcoma (RMS) accounting for 5.2% to 6.5% of the soft tissue sarcoma total within this group. AYAs have a higher propensity for metastasis and inferior outcomes. Metastases to the breast have been reported in ∼3% to 6% of RMS cases. A review of our hospital’s tumor registry identified cases of RMS diagnosed between January 1, 2004 and December 31, 2013. A total of 46 patients with RMS were identified, having a mean age of 12.5 years (range, 1 to 49 y). There were 26 males (57%) and 20 females (43%). Eighteen patients (39%) were AYAs, including 10 women. Four patients (8.7%) were identified with breast involvement, all of whom were AYA females. Treatment modalities included chemotherapy, surgical resection, and radiation. One patient is a long-term survivor. Although RMS is uncommon in AYAs, breast involvement occurs almost exclusively in AYA women and is associated with alveolar histology, metastatic disease, and poor outcomes. In total, 4/10 of all AYA females had breast involvement. Routine examination or imaging of the breasts in AYAs with RMS is not currently standard practice at diagnosis or follow-up, but this analysis suggests it should be considered in female AYA patients.
DUX4 Immunohistochemistry Is a Highly Sensitive and Specific Marker for CIC-DUX4 Fusion-positive Round Cell Tumor
Authors: Siegele Bradford , Roberts Jon , Black Jennifer O. , Rudzinski Erin , Vargas Sara O. , Galambos Csaba
Published: November 2016

The histologic differential diagnosis of pediatric and adult round cell tumors is vast and includes the recently recognized entity CIC-DUX4 fusion-positive round cell tumor. The diagnosis of CIC-DUX4 tumor can be suggested by light microscopic and immunohistochemical features, but currently, definitive diagnosis requires ancillary genetic testing such as conventional karyotyping, fluorescence in situ hybridization, or molecular methods. We sought to determine whether DUX4 expression would serve as a fusion-specific immunohistochemical marker distinguishing CIC-DUX4 tumor from potential histologic mimics. A cohort of CIC-DUX4 fusion-positive round cell tumors harboring t(4;19)(q35;q13) and t(10;19)(q26;q13) translocations was designed, with additional inclusion of a case with a translocation confirmed to involve the CIC gene without delineation of the partner. Round cell tumors with potentially overlapping histologic features were also collected. Staining with a monoclonal antibody raised against the C-terminus of the DUX4 protein was applied to all cases. DUX4 immunohistochemistry exhibited diffuse, crisp, strong nuclear staining in all CIC-DUX4 fusion-positive round cell tumors (5/5, 100% sensitivity), and exhibited negative staining in nuclei of all of the other tested round cell tumors, including 20 Ewing sarcomas, 1 Ewing-like sarcoma, 11 alveolar rhabdomyosarcomas, 9 embryonal rhabdomyosarcomas, 12 synovial sarcomas, 7 desmoplastic small round cell tumors, 3 malignant rhabdoid tumors, 9 neuroblastomas, and 4 clear cell sarcomas (0/76, 100% specificity). Thus, in our experience, DUX4 immunostaining distinguishes CIC-DUX4 tumors from other round cell mimics. We recommend its use when CIC-DUX4 fusion-positive round cell tumor enters the histologic differential diagnosis.
Support Vector Machines Model of Computed Tomography for Assessing Lymph Node Metastasis in Esophageal Cancer with Neoadjuvant Chemotherapy
Authors: Wang Zhi-Long , Zhou Zhi-Guo , Chen Ying , Li Xiao-Ting , Sun Ying-Shi
Published: November 2016

Objective

The aim of this study was to diagnose lymph node metastasis of esophageal cancer by support vector machines model based on computed tomography.

Materials and Methods

A total of 131 esophageal cancer patients with preoperative chemotherapy and radical surgery were included. Various indicators (tumor thickness, tumor length, tumor CT value, total number of lymph nodes, and long axis and short axis sizes of largest lymph node) on CT images before and after neoadjuvant chemotherapy were recorded. A support vector machines model based on these CT indicators was built to predict lymph node metastasis.

Results

Support vector machines model diagnosed lymph node metastasis better than preoperative short axis size of largest lymph node on CT. The area under the receiver operating characteristic curves were 0.887 and 0.705, respectively.

Conclusions

The support vector machine model of CT images can help diagnose lymph node metastasis in esophageal cancer with preoperative chemotherapy.
Changes in composition and abundance of functional groups of arctic fungi in response to long-term summer warming
Authors: Geml József , Semenova Tatiana A. , Morgado Luis N. , Welker Jeffrey M.
Published: November 2016

We characterized fungal communities in dry and moist tundra and investigated the effect of long-term experimental summer warming on three aspects of functional groups of arctic fungi: richness, community composition and species abundance. Warming had profound effects on community composition, abundance, and, to a lesser extent, on richness of fungal functional groups. In addition, our data show that even within functional groups, the direction and extent of response to warming tend to be species-specific and we recommend that studies on fungal communities and their roles in nutrient cycling take into account species-level responses.
Bacteria facilitate prey retention by the pitcher plant
Darlingtonia californica
Authors: Armitage David W.
Published: November 2016

Bacteria are hypothesized to provide a variety of beneficial functions to plants. Many carnivorous pitcher plants, for example, rely on bacteria for digestion of captured prey. This bacterial community may also be responsible for the low surface tensions commonly observed in pitcher plant digestive fluids, which might facilitate prey capture. I tested this hypothesis by comparing the physical properties of natural pitcher fluid from the pitcher plant
Darlingtonia californica
and cultured ‘artificial’ pitcher fluids and tested these fluids' prey retention capabilities. I found that cultures of pitcher leaves' bacterial communities had similar physical properties to raw pitcher fluids. These properties facilitated the retention of insects by both fluids and hint at a previously undescribed class of plant–microbe interaction.
Where in the air? Aerial habitat use of nocturnally migrating birds
Authors: Horton Kyle G. , Van Doren Benjamin M. , Stepanian Phillip M. , Farnsworth Andrew , Kelly Jeffrey F.
Published: November 2016

The lower atmosphere (i.e. aerosphere) is critical habitat for migrant birds. This habitat is vast and little is known about the spatio-temporal patterns of distribution and abundance of migrants in it. Increased human encroachment into the aerosphere makes understanding where and when migratory birds use this airspace a key to reducing human–wildlife conflicts. We use weather surveillance radar to describe large-scale height distributions of nocturnally migrating birds and interpret these distributions as aggregate habitat selection behaviours of individual birds. As such, we detail wind cues that influence selection of flight heights. Using six radars in the eastern USA during the spring (2013–2015) and autumn (2013 and 2014), we found migrants tended to adjust their heights according to favourable wind profit. We found that migrants' flight altitudes correlated most closely with the altitude of maximum wind profit; however, absolute differences in flight heights and height of maximum wind profit were large. Migrants tended to fly slightly higher at inland sites compared with coastal sites during spring, but not during autumn. Migration activity was greater at coastal sites during autumn, but not during spring. This characterization of bird migration represents a critical advance in our understanding of migrant distributions in flight and a new window into habitat selection behaviours.
The effects of tradition on problem solving by two wild populations of bearded capuchin monkeys in a probing task
Authors: Cardoso Raphael Moura , Ottoni Eduardo B.
Published: November 2016

The effects of culture on individual cognition have become a core issue among cultural primatologists. Field studies with wild populations provide evidence on the role of social cues in the ontogeny of tool use in non-human primates, and on the transmission of such behaviours over generations through socially biased learning. Recent experimental studies have shown that cultural knowledge may influence problem solving in wild populations of chimpanzees. Here, we present the results from a field experiment comparing the performance of bearded capuchin monkeys (
Sapajus libidinosus
) from two wild savannah populations with distinct toolkits in a probing task. Only the population that already exhibited the customary use of probing tools succeeded in solving the new problem, suggesting that their cultural repertoire shaped their approach to the new task. Moreover, only this population, which uses stone tools in a broader range of contexts, tried to use them to solve the problem. Social interactions can affect the formation of learning sets and they affect the performance of the monkeys in problem solving. We suggest that behavioural traditions affect the ways non-human primates solve novel foraging problems using tools.
Improved homeothermy and hypothermia in African lions during gestation
Authors: Trethowan Paul D. , Hart Tom , Loveridge Andrew J. , Haw Anna , Fuller Andrea , Macdonald David W.
Published: November 2016

Mammals use endogenously produced heat to maintain a high and relatively constant core body temperature (
T
b
). How they regulate their
T
b
during reproduction might inform us as to what thermal conditions are necessary for optimal development of offspring. However, few studies have measured
T
b
in free-ranging animals for sufficient periods of time to encounter reproductive events. We measured
T
b
continuously in six free-ranging adult female African lions (
Panthera leo
) for approximately 1 year. Lions reduced the 24 h amplitude of
T
b
by about 25% during gestation and decreased mean 24 h
T
b
by 1.3 ± 0.1°C over the course of the gestation, reducing incidences of hyperthermia (
T
b
> 39.5°C). The observation of improved homeothermy during reproduction may support the parental care model (PCM) for the evolution of endothermy, which postulates that endothermy arose in birds and mammals as a consequence of more general selection for parental care. According to the PCM, endothermy arose because it enabled parents to better control incubation temperature, leading to rapid growth and development of offspring and thus to fitness benefits for the parents. Whether the precision of
T
b
regulation in pregnant lions, and consequently their reproductive success, will be influenced by changing environmental conditions, particularly hotter and drier periods associated with climate change, remains to be determined.
Human selenoprotein P and S variant mRNAs with different numbers of SECIS elements and inferences from mutant mice of the roles of multiple SECIS elements
Authors: Wu Sen , Mariotti Marco , Santesmasses Didac , Hill Kristina E. , Baclaocos Janinah , Aparicio-Prat Estel , Li Shuping , Mackrill John , Wu Yuanyuan , Howard Michael T. , Capecchi Mario , Guigó Roderic , Burk Raymond F. , Atkins John F.
Published: November 2016

Dynamic redefinition of the 10 UGAs in human and mouse selenoprotein P (Sepp1) mRNAs to specify selenocysteine instead of termination involves two 3′ UTR structural elements (SECIS) and is regulated by selenium availability. In addition to the previously known human Sepp1 mRNA poly(A) addition site just 3′ of SECIS 2, two further sites were identified with one resulting in 10–25% of the mRNA lacking SECIS 2. To address function, mutant mice were generated with either SECIS 1 or SECIS 2 deleted or with the first UGA substituted with a serine codon. They were fed on either high or selenium-deficient diets. The mutants had very different effects on the proportions of shorter and longer product Sepp1 protein isoforms isolated from plasma, and on viability. Spatially and functionally distinctive effects of the two SECIS elements on UGA decoding were inferred. We also bioinformatically identify two selenoprotein S mRNAs with different 5′ sequences predicted to yield products with different N-termini. These results provide insights into SECIS function and mRNA processing in selenoprotein isoform diversity.
The functional readthrough extension of malate dehydrogenase reveals a modification of the genetic code
Authors: Hofhuis Julia , Schueren Fabian , Nötzel Christopher , Lingner Thomas , Gärtner Jutta , Jahn Olaf , Thoms Sven
Published: November 2016

Translational readthrough gives rise to C-terminally extended proteins, thereby providing the cell with new protein isoforms. These may have different properties from the parental proteins if the extensions contain functional domains. While for most genes amino acid incorporation at the stop codon is far lower than 0.1%, about 4% of malate dehydrogenase (MDH1) is physiologically extended by translational readthrough and the actual ratio of MDH1x (e
x
tended protein) to ‘normal' MDH1 is dependent on the cell type. In human cells, arginine and tryptophan are co-encoded by the MDH1x UGA stop codon. Readthrough is controlled by the 7-nucleotide high-readthrough stop codon context without contribution of the subsequent 50 nucleotides encoding the extension. All vertebrate MDH1x is directed to peroxisomes via a hidden peroxisomal targeting signal (PTS) in the readthrough extension, which is more highly conserved than the extension of lactate dehydrogenase B. The hidden PTS of non-mammalian MDH1x evolved to be more efficient than the PTS of mammalian MDH1x. These results provide insight into the genetic and functional co-evolution of these dually localized dehydrogenases.
Peripheral self-reactivity regulates antigen-specific CD8 T-cell responses and cell division under physiological conditions
Authors: Swee Lee Kim , Tan Zhen Wei , Sanecka Anna , Yoshida Nagisa , Patel Harshil , Grotenbreg Gijsbert , Frickel Eva-Maria , Ploegh Hidde L.
Published: November 2016

T-cell identity is established by the expression of a clonotypic T-cell receptor (TCR), generated by somatic rearrangement of TCRα and β genes. The properties of the TCR determine both the degree of self-reactivity and the repertoire of antigens that can be recognized. For CD8 T cells, the relationship between TCR identity—hence reactivity to self—and effector function(s) remains to be fully understood and has rarely been explored outside of the H-2bhaplotype. We measured the affinity of three structurally distinct CD8 T-cell-derived TCRs that recognize the identical H-2 Ld-restricted epitope, derived from the Rop7 protein ofToxoplasma gondii. We used CD8 T cells obtained from mice generated by somatic cell nuclear transfer as the closest approximation of primary T cells with physiological TCR rearrangements and TCR expression levels. First, we demonstrate the common occurrence of secondary rearrangements in endogenously rearranged loci. Furthermore, we characterized and compared the response of Rop7-specific CD8 T-cell clones uponToxoplasma gondiiinfection as well as effector function and TCR signalling upon antigenic stimulationin vitro. Antigen-independent TCR cross-linkingin vitrouncovered profound intrinsic differences in the effector functions between T-cell clones. Finally, by assessing the degree of self-reactivity and comparing the transcriptomes of naive Rop7 CD8 T cells, we show that lower self-reactivity correlates with lower effector capacity, whereas higher self-reactivity is associated with enhanced effector function as well as cell cycle entry under physiological conditions. Altogether, our data show that potential effector functions and basal proliferation of CD8 T cells are set by self-reactivity thresholds.
A tilt after-effect for images of buildings: evidence of selectivity for the orientation of everyday scenes
Authors: Hussain Ismail Ahamed Miflah , Solomon Joshua A. , Hansard Miles , Mareschal Isabelle
Published: November 2016

The tilt after-effect (TAE) is thought to be a manifestation of gain control in mechanisms selective for spatial orientation in visual stimuli. It has been demonstrated with luminance-defined stripes, contrast-defined stripes, orientation-defined stripes and even with natural images. Of course, all images can be decomposed into a sum of stripes, so it should not be surprising to find a TAE when adapting and test images contain stripes that differ by 15° or so. We show this latter condition is not necessary for the TAE with natural images: adaptation to slightly tilted and vertically filtered houses produced a ‘repulsive’ bias in the perceived orientation of horizontally filtered houses. These results suggest gain control in mechanisms selective for spatial orientation in natural images.
Formal groups and
Z
-entropies
Authors: Tempesta Piergiulio
Published: November 2016

We shall prove that the celebrated Rényi entropy is the first example of a new family of infinitely many multi-parametric entropies. We shall call them the
Z-entropies
. Each of them, under suitable hypotheses, generalizes the celebrated entropies of Boltzmann and Rényi. A crucial aspect is that every
Z
-entropy is
composable
(Tempesta 2016
Ann. Phys.
365
, 180–197. (
doi:10.1016/j.aop.2015.08.013
)). This property means that the entropy of a system which is composed of two or more independent systems depends, in all the associated probability space, on the choice of the two systems only. Further properties are also required to describe the composition process in terms of a group law. The composability axiom, introduced as a generalization of the fourth Shannon–Khinchin axiom (postulating additivity), is a highly non-trivial requirement. Indeed, in the trace-form class, the Boltzmann entropy and Tsallis entropy are the only known composable cases. However, in the non-trace form class, the
Z
-entropies arise as new entropic functions possessing the mathematical properties necessary for information-theoretical applications, in both classical and quantum contexts. From a mathematical point of view, composability is intimately related to formal group theory of algebraic topology. The underlying group-theoretical structure determines crucially the statistical properties of the corresponding entropies.
Vive la résistance: genome-wide selection against introduced alleles in invasive hybrid zones
Authors: Kovach Ryan P. , Hand Brian K. , Hohenlohe Paul A. , Cosart Ted F. , Boyer Matthew C. , Neville Helen H. , Muhlfeld Clint C. , Amish Stephen J. , Carim Kellie , Narum Shawn R. , Lowe Winsor H. , Allendorf Fred W. , Luikart Gordon
Published: November 2016

Evolutionary and ecological consequences of hybridization between native and invasive species are notoriously complicated because patterns of selection acting on non-native alleles can vary throughout the genome and across environments. Rapid advances in genomics now make it feasible to assess locus-specific and genome-wide patterns of natural selection acting on invasive introgression within and among natural populations occupying diverse environments. We quantified genome-wide patterns of admixture across multiple independent hybrid zones of native westslope cutthroat trout and invasive rainbow trout, the world's most widely introduced fish, by genotyping 339 individuals from 21 populations using 9380 species-diagnostic loci. A significantly greater proportion of the genome appeared to be under selection favouring native cutthroat trout (rather than rainbow trout), and this pattern was pervasive across the genome (detected on most chromosomes). Furthermore, selection against invasive alleles was consistent across populations and environments, even in those where rainbow trout were predicted to have a selective advantage (warm environments). These data corroborate field studies showing that hybrids between these species have lower fitness than the native taxa, and show that these fitness differences are due to selection favouring many native genes distributed widely throughout the genome.
Female monkeys use both the carrot and the stick to promote male participation in intergroup fights
Authors: Arseneau-Robar T. Jean Marie , Taucher Anouk Lisa , Müller Eliane , van Schaik Carel , Bshary Redouan , Willems Erik P.
Published: November 2016

Group-level cooperation often poses a social dilemma in which joint action may be difficult to achieve. Theoretical models and experimental work on humans show that social incentives, such as punishment of defectors and rewarding of cooperators, can promote cooperation in groups of unrelated individuals. Here, we demonstrate that these processes can operate in a non-human animal species, and be used to effectively promote the production of a public good. We took advantage of the fact that intergroup fights in vervet monkeys (Chlorocebus aethiops pygerythrus) are characterized by episodes of intergroup aggression with pauses in-between. During pauses, females selectively groomed males that had participated in the previous aggressive episode, but aggressed male group members that had not. In subsequent (i.e. future) episodes, males who had received either aggression or grooming participated above their personal base-line level. Therefore, female–male aggression and grooming both appear to function as social incentives that effectively promote male participation in intergroup fights. Importantly, females stood to gain much from recruiting males as the probability of winning intergroup fights was dependent on the number of active participants, relative to the number of fighters in the opposing group. Furthermore, females appear to maximize the benefits gained from recruiting males as they primarily used social incentives where and when high-quality food resources, which are the resources primarily limiting to female fitness, were at stake.
Inbreeding parents should invest more resources in fewer offspring
Authors: Duthie A. Bradley , Lee Aline M. , Reid Jane M.
Published: November 2016

Inbreeding increases parent–offspring relatedness and commonly reduces offspring viability, shaping selection on reproductive interactions involving relatives and associated parental investment (PI). Nevertheless, theories predicting selection for inbreeding versus inbreeding avoidance and selection for optimal PI have only been considered separately, precluding prediction of optimal PI and associated reproductive strategy given inbreeding. We unify inbreeding and PI theory, demonstrating that optimal PI increases when a female's inbreeding decreases the viability of her offspring. Inbreeding females should therefore produce fewer offspring due to the fundamental trade-off between offspring number and PI. Accordingly, selection for inbreeding versus inbreeding avoidance changes when females can adjust PI with the degree that they inbreed. By contrast, optimal PI does not depend on whether a focal female is herself inbred. However, inbreeding causes optimal PI to increase given strict monogamy and associated biparental investment compared with female-only investment. Our model implies that understanding evolutionary dynamics of inbreeding strategy, inbreeding depression, and PI requires joint consideration of the expression of each in relation to the other. Overall, we demonstrate that existing PI and inbreeding theories represent special cases of a more general theory, implying that intrinsic links between inbreeding and PI affect evolution of behaviour and intrafamilial conflict.
Sexually satiated male uses gustatory-to-neuropeptide integrative circuits to reduce time investment for mating
Authors: Jae Kim Woo , Gee Lee Seung , Auge Anne-Christine , Yeh Jan Lily , Nung Jan Yuh
Published: November 2016

Males rely on a ‘time investment strategy’ to maximize reproductive success. Here we report a novel behavioral plasticity whereby male fruit flies exhibit a shortened mating duration when sexually satiated, which we named ‘Shorter-Mating-Duration (SMD)’. SMD requires the sexually dimorphic Gr5a-positive neurons for detecting female body pheromones. The memory circuitry within the ellipsoid body (EB) and mushroom body (MB) brain regions is crucial for SMD, which depends on the circadian clock genesClockandcycle, but nottimelessorperiod. SMD also relies on signaling via the neuropeptide sNPF, but not PDF or NPF. Sexual experience modifies the neuronal activity of a subset of sNPF-positive neurons involved in neuropeptide signaling, which modulates SMD. Thus, our study delineates the molecular and cellular basis for SMD – a plastic social behavior that serves as a model system to study how the brain switches the internal states between sexual drive and satiety.
Detecting hierarchical 3-D genome domain reconfiguration with network modularity
Authors: Norton Heidi K. , Huang Harvey , Emerson Daniel J. , Kim Jesi , Gu Shi , Bassett Danielle S. , Phillips-Cremins Jennifer E.
Published: November 2016

Mammalian genomes are folded in a hierarchy of topologically associating domains (TADs), subTADs and looping interactions. The nested nature of chromatin domains has rendered it challenging to identify a sensitive and specific metric for detecting subTADs and quantifying their dynamic reconfiguration across cellular states. Here, we apply graph theoretic principles to quantify hierarchical folding patterns in high-resolution chromatin topology maps. We discover that TADs can be accurately detected using a Louvain-like locally greedy algorithm to maximize network modularity. By varying a resolution parameter in the modularity quality function, we accurately partition the mouse genome across length scales into a hierarchical nested structure of network communities exhibiting a wide range of sizes. To distinguish high probability subTADs from the full detected set, we developed and applied a new ‘hierarchical spatial variance minimization’ method. Moreover, we identified a large number of dynamically altered communities between pluripotent embryonic stem cells and multipotent neural progenitor cells. Cell type specific boundaries correlate with trends in dynamic occupancy of the architectural protein CTCF, thereby validating their biological relevance. Together, these data demonstrate the utility of metrics from network science in quantifying a nested hierarchy of dynamic 3D chromatin communities across length scales. Our findings are significant toward unraveling the link between higher-order genome folding and gene expression during healthy development and the deregulation of molecular pathways linked to disease.
Predator phylogenetic diversity decreases predation rate via antagonistic interactions
Authors: MacDonald A. Andrew M. , Romero Gustavo Q. , Srivastava Diane S.
Published: November 2016

Background:

Predator assemblages can differ substantially in their top-down effects on community composition and ecosystem function, but few studies have sought to explain this variation in terms of the phylogenetic distance between predators. The effect of a local predator assemblage will depend on three things – which predators tend to co-occur, how similar their prey preferences are, and how they interact with each other and the whole community. Phylogenetic distance between predators may correlate with each of these processes, either because related predators are more likely to share the same traits, and therefore have similar habitat and prey preferences, or because predators are more likely to compete, and therefore diverge in habitat and prey preferences. Therefore, the phylogenetic structure of predator assemblages could provide a unifying framework for predicting how predators will impact their prey - and therefore any ecosystem functions mediated by their prey.

Methods:

We examined the effects of predators on macroinvertebrate food webs found in bromeliads, combining field observations, laboratory feeding trials and a manipulative experiment. We determined whether the phylogenetic distance between predators could explain: the co-observed occurrence of predator species among bromeliads, overlap in prey preferences under no-choice conditions, and effects of predator composition on prey survival, prey composition and ecosystem processes.

Results:

We found that phylogenetic distance does not predict either the co-occurrence of predator species nor the overlap in their prey preferences. However, our manipulative experiment showed that prey mortality decreased as the phylogenetic distance between predator species increased, reflecting antagonistic interactions among more distant predators. These effects of phylogenetic distance on prey mortality did not translate into effects on ecosystem function, as measured by rates of detrital decomposition and nitrogen cycling.

Discussion:

We conclude that the effects of predator phylogenetic diversity on the bromeliad food web are primarily determined by antagonistic predator-predator interac-tions, rather than habitat distribution or diet overlap. This study illustrates the potential of a phylogenetic community approach to understanding food webs dynamics.
A new coactivator complex required for retinoic acid-dependent regulation of embryonic symmetry
Authors: Vilhais-Neto Goncalo C. , Fournier Marjorie , Plassat Jean-Luc , Sardiu Mihaela E. , Saraf Anita , Garnier Jean-Marie , Maruhashi Mitsuji , Florens Laurence , Washburn Michael P. , Pourquié Olivier
Published: November 2016

Bilateral symmetry is a striking feature of the vertebrate body plan organization. Vertebral precursors, called somites, provide one of the best illustrations of embryonic symmetry. Maintenance of somitogenesis symmetry requires Retinoic acid (RA) and its coactivator Rere/Atrophin2. Here, using a proteomic approach we identify a protein complex, containingWdr5,Hdac1,Hdac2 and Rere(named WHHERE), which regulates RA signalling and controls embryonic symmetry. We demonstrate that Wdr5, Hdac1 and Hdac2 are required for RA signallingin vitroandin vivo. Mouse mutants forWdr5andHdac1exhibit asymmetrical somite formation characteristic of RA-deficiency. We also identify the Rere-binding histone methyltransferase Ehmt2/G9a, as a RA coactivator controlling somite symmetry. Upon RA treatment, WHHERE and Ehmt2 become enriched at RA target genes to promote RNA Polymerase II recruitment. Our work identifies a novel protein complex linking key epigenetic regulators acting in the molecular control of embryonic bilateral symmetry.
Profiling immunoglobulin repertoires across multiple human tissues by RNA Sequencing
Authors: Mangul Serghei , Mandric Igor , Yang Harry Taegyun , Strauli Nicolas , Montoya Dennis , Rotman Jeremy , Der Wey Will Van , Ronas Jiem R. , Statz Benjamin , Yao Douglas , Zelikovsky Alex , Spreafico Roberto , Shifman Sagiv , Zaitlen Noah , Rossetti Maura , Mark Ansel K. , Eskin Eleazar
Published: November 2016

Assay-based approaches provide a detailed view of the adaptive immune system by profiling immunoglobulin (Ig) receptor repertoires. However, these methods carry a high cost and lack the scale of standard RNA sequencing (RNA-Seq). Here we report the development of ImReP, a novel computational method for rapid and accurate profiling of the immunoglobulin repertoire from regular RNA-Seq data. ImReP can also accurately assemble the complementary determining regions 3 (CDR3s), the most variable regions of Ig receptors. We applied our novel method to 8,555 samples across 53 tissues from 544 individuals in the Genotype-Tissue Expression (GTEx v6) project. ImReP is able to efficiently extract Ig-derived reads from RNA-Seq data. Using ImReP, we have created a systematic atlas of 3.6 million Ig sequences across a broad range of tissue types, most of which have not been studied for Ig receptor repertoires. We also compared the GTEx tissues to track the flow of Ig clonotypes across immune-related tissues, including secondary lymphoid organs and organs encompassing mucosal, exocrine, and endocrine sites, and we examined the compositional similarities of clonal populations between these tissues. The Atlas of Immunoglobulin Repertoires (The AIR), is freely available athttps://github.com/smangul1/TheAIR/wiki, is one of the largest collection of CDR3 sequences and tissue types. We anticipate this recourse will enhance future immunology studies and advance the development of therapies for human diseases. ImReP is freely available athttps://github.com/mandricigor/imrep/wiki
Undercover: gene control by metabolites and metabolic enzymes
Authors: van der Knaap Jan A. , Verrijzer C. Peter
Published: November 2016

To make the appropriate developmental decisions or maintain homeostasis, cells and organisms must coordinate the expression of their genome and metabolic state. However, the molecular mechanisms that relay environmental cues such as nutrient availability to the appropriate gene expression response remain poorly understood. There is a growing awareness that central components of intermediary metabolism are cofactors or cosubstrates of chromatin-modifying enzymes. As such, their concentrations constitute a potential regulatory interface between the metabolic and chromatin states. In addition, there is increasing evidence for a direct involvement of classic metabolic enzymes in gene expression control. These dual-function proteins may provide a direct link between metabolic programing and the control of gene expression. Here, we discuss our current understanding of the molecular mechanisms connecting metabolism to gene expression and their implications for development and disease.
Solvent dependence of the solid-state structures of salicylaldiminate magnesium amide complexes
Authors: Rood Jeffrey A. , Landis Ashley M. , Forster Daniel R. , Goldkamp Timothy , Oliver Allen G.
Published: November 2016

There are challenges in using magnesium coordination complexes as reagents owing to their tendency to adopt varying aggregation states in solution and thus impacting the reactivity of the complexes. Many magnesium complexes are prone to ligand redistributionviaSchlenk equilibrium due to the ionic character within the metal–ligand interactions. The role of the supporting ligand is often crucial for providing stability to the heteroleptic complex. Strategies to minimize ligand redistribution in alkaline earth metal complexes could include using a supporting ligand with tunable sterics and electronics to influence the degree of association to the metal atom. Magnesium bis(hexamethyldisilazide) was reacted with salicylaldimines [1L=N-(2,6-diisopropylphenyl)salicylaldimine and2L= 3,5-di-tert-butyl-N-(2,6-diisopropylphenyl)salicylaldimine] in either nondonor (toluene) or donor solvents [tetrahydrofuran (THF) or pyridine]. The structures of the magnesium complexes were studied in the solid stateviaX-ray diffraction. In the nondonor solvent,i.e.toluene, the heteroleptic complex bis{μ-2-[(2,6-diisopropylphenyl)iminomethyl]phenolato}-κ3N,O:O;κ3O:N,O-bis[(hexamethyldisilazido-κN)magnesium(II)], [Mg2(C19H22NO)2(C6H18NSi2)2] or [1LMgN(SiMe3)2]2, (1), was favored, while in the donor solvent,i.e.pyridine (pyr), the formation of the homoleptic complex {2,4-di-tert-butyl-6-[(2,6-diisopropylphenyl)iminomethyl]phenolato-κ2N,O}bis(pyridine-κN)magnesium(II) toluene monosolvate, [Mg(C27H38NO)2(C5H5N)2]·C5H5N or [{2L2Mg2(pyr)2}·pyr], (2), predominated. Heteroleptic complex (1) was crystallized from toluene, while homoleptic complexes (2) and the previously reported [1L2Mg·THF] [Quinqueet al.(2011).Eur. J. Inorg. Chem.pp. 3321–3326] were crystallized from pyridine and THF, respectively. These studies support solvent-dependent ligand redistribution in solution.In-situ1H NMR experiments were carried out to further probe the solution behavior of these systems.
Traces of equality policy and diversity management in Finnish work organizations
Authors: Ylöstalo Hanna
Published: November 2016

Purpose

The purpose of this paper is to discuss how equality and diversity are experienced in everyday work within Finnish work organizations and how equality policy and diversity management participate in maintaining the inequality regimes of the organizations.

Design/methodology/approach

The empirical findings are based on 31 interviews, which were collected in two private sector work organizations. Inequality regimes, the interlocked practices, and processes that result in continuing inequalities in all work organizations, are used as an analytic tool.

Findings

There is an individualizing tendency of equality in Finnish work organizations, which is also the premise of diversity management. Accordingly, the organizations cannot address structural and historical discrimination based on gender, race, and class. Also, when diversity is intrinsic to the corporate image, the members of the organization downplay and legitimize inequalities in their organization.

Originality/value

The paper analyzes inequality regimes in a context that should be ideal for equality and diversity: Finland, where gender equality policies are relatively progressive, and organizations that strive for equality and diversity. This gives new insight on why inequalities are difficult to change.
Connectivity, cost-efficiency, community and collaboration
Authors: Kyrö Riikka , Peltokorpi Antti , Artto Karlos
Published: November 2016

Purpose

This paper aims to increase understanding on how co-locating in a multi-firm campus setting could be of value to healthcare organizations.

Design/methodology/approach

The paper presents a qualitative case study of two health campuses in Finland. The data comprises interviews with different organizations operating on the campuses, complemented by onsite observations, and analysis of archival data.

Findings

Based on the empirical analysis, the value of co-locating as perceived by the organizations operating on campus is grouped into four categories: connectivity, cost-efficiency, community and collaboration (or the “four Cs”).

Research limitations/implications

The study does not aim at statistical genaralizability but rather seeks to draw analytical generalizations based on identified empirical regularities. The developed value framework, the four Cs, contributes to current scholarly knowledge on location strategies.

Practical implications

Furthermore, the managerial implications of the four Cs entail a new twofold role for property management: the traditional facilitator role, which is suitable for delivering the two tangible values of connectivity and cost-efficiency, and the modern era integrator, a community builder that is able to deliver community and collaboration.

Originality/value

Previous literature on healthcare facilities has focused on the technical performance of the buildings, while previous literature on the collaborative value of co-location has studied mainly single-firm corporate campuses. This study uniquely explores the potential value of health campuses, where different private, public and third sector organizations co-locate.
Performance measurement tool (PMT) to control maintenance-associated infections
Authors: Njuangang Stanley , Lasanthi Liyanage Champika , Akintoye Akintola
Published: November 2016

Purpose

Healthcare maintenance (HM) services have an important role in the control of hospital-acquired infections (HAIs). Notwithstanding, many HM managers still do not measure the performance of HM services in infection control (IC). This research, therefore, aims to establish the level of importance of critical success factors (CSFs) and performance measures in HM IC. A performance measurement tool (PMT) was also developed to improve the performance of the HM unit in IC.

Design/methodology/approach

The CSFs and performance measures identified in the literature were categorised into the four perspectives of balanced scorecard and analysed through Delphi. The Delphi participants were presented with 67 performance measures and asked to rate their level of importance in HM in IC. In total, they identified 53 important performance measures to control maintenance-associated HAIs. The results obtained from the Delphi study were used to categorise the performance measures into four means zones. The mean zones were assigned weights (1-4), and the level of importance of the CSFs was established through weighted average. Liaison and communication, IC practices and maintenance resource availability emerged as the most important CSFs in HM in IC. Conversely, customer satisfaction emerged as the least important. Information gathered about the CSFs and performance measures was used to develop a PMT in HM in IC.

Findings

The following CSFs, liaison and communication, IC practices and maintenance resource availability, emerged as the most important in HM in IC. Conversely, customer satisfaction emerged as the least important. Information gathered about the CSFs and performance measures was used to develop a PMT in HM in IC.

Originality/value

Through the application of the PMT, performance in IC can be estimated at different levels in the HM unit. The PMT allows managers to focus on the most crucial CSFs and performance measures that drive performance in HM in IC. The PMT could also be used for benchmarking purposes.
Thermal analysis of natural convection and radiation in a fully wet porous fin
Authors: Darvishi M.T. , Gorla Rama Subba Reddy , Khani F. , Gireesha B.J.
Published: November 2016

Purpose

The purpose of this paper is to take the thermal analysis of natural convection and radiation heat transfer in fully wet porous fins. The wet porous fins taken for the analysis are straight fins in nature and wet. Their profile being straight helps heat transfer process of fins faster. The analysis is performed using the Darcy’s model to generate the heat equation to analyze the variation of convection and radiation parameters. The porous nature of the fins allows the flow to penetrate through the porous material of the fins leading to solid-fluid interface. The obtained non-dimensional ordinary differential equation involving three highly nonlinear terms are solved numerically by using spectral collocation method after which they are reduced into algebraic equations using Chebyshev polynomials. The study is analyzed using the mathematical analysis on heat equation and generating graphs for finding the parameters important to the heat transfer in the straight fins.

Design/methodology/approach

This study is performed using Darcy’s model to formulate heat transfer equation. To study the thermal performance, the authors considered a finite length fin with insulated tip. The effects of the wet fin parameter m2, porosity parameter Sh, radiation parameter G and temperature ratio CT on the dimensionless temperature distribution and heat transfer rate are discussed.

Findings

The results show that the base heat flow increases when the permeability of the medium is high and/or when the buoyancy effect induced in the fluid is strong.

Research limitations/implications

The analysis is made for the Darcy’s model. Non-Darcy effects will be investigated in a future work.

Practical implications

The approach is useful in enhancing heat transfer rates.

Originality/value

The results of the study will be interest to the researchers of the field of heat exchanger designers.
Unsteady viscous MHD flow over a permeable curved stretching/shrinking sheet
Authors: Pop Ioan , Mohamed Isa Siti Suzilliana Putri , Arifin Norihan M. , Nazar Roslinda , Bachok Norfifah , Ali Fadzilah M.
Published: November 2016

Purpose

The purpose of this paper is to theoretically study the problem of the unsteady boundary layer flow past a permeable curved stretching/shrinking surface in the presence of a uniform magnetic field. The governing nonlinear partial differential equations are converted into ordinary differential equations by similarity transformation, which are then solved numerically.

Design/methodology/approach

The transformed system of ordinary differential equations was solved using a fourth-order Runge-Kutta integration scheme. Results for the reduced skin friction coefficient and velocity profiles are presented through graphs and tables for several sets of values of the governing parameters. The effects of these parameters on the flow characteristics are thoroughly examined.

Findings

Results show that for the both cases of stretching and shrinking surfaces, multiple solutions exist for a certain range of the curvature, mass suction, unsteadiness, stretching/shrinking parameters and magnetic field parameter.

Originality/value

The paper describes how multiple (dual) solutions for the flow reversals are obtained. It is shown that the solutions exist up to a critical value of the shrinking parameter, beyond which the boundary layer separates from the surface and the solution based upon the boundary layer approximations is not possible.
Women’s entrepreneurship in Iran
Authors: Modarresi Meisam , Arasti Zahra , Talebi Kambiz , Farasatkhah Maghsoud
Published: November 2016

Purpose

The purpose of this paper is to identify the growth motivations of women owning and managing home-based businesses (HBBs) in Iran.

Design/methodology/approach

The qualitative approach was used by 20 in-depth interviews with Iranian female HBBs owners/mangers.

Findings

The business growth motivations of women owning and managing HBBs were categorized in intrinsic and extrinsic motivations. Results show that women owning and managing HBBs are motivated to growth their businesses by intrinsic motivations including need for achievement, need for independence, proving competency and socio-cultural concerns. Also, they are motivated by some extrinsic motivations including financial issues, fame, positive feedback from others and the problems of working at home.

Research limitations/implications

Given the importance of entrepreneurial growth, the findings provide additional insight into growth motivations of women entrepreneurs.

Practical implications

The results of this study can help policymakers to develop purposeful growth policies for women’s HBBs that are commensurate with the motivations.

Social implications

Also, women owning and managing HBBs themselves could better concentrate on enhancing business growth by deepening their understanding of their business growth motivations.

Originality/value

The paper contributes to the scarce knowledge about women-owned HBBs in Iran, a rapidly growing, developing country, which can provide better insights from a less explored context. Moreover, as there is only a limited understanding of HBB growth, especially in relation to women business owners, the study results can prove helpful for researchers in the domain of female entrepreneurs. Also, this paper contributes to theory on the motivation for entrepreneurship and to research on growth motivation.