bluuebunny/crossref_metadata_2025 huggingface dataset:
Simple triple-state polymer actuators with controllable folding characteristics
Authors: Chen Shuyang , Li Jing , Fang Lichen , Zhu Zeyu , Kang Sung Hoon
Published: March 2017

Driven by the interests in self-folding, there have been studies developing artificial self-folding structures at different length scales based on various polymer actuators that can realize dual-state actuation. However, their unidirectional nature limits the applicability of the actuators for a wide range of multi-state self-folding behaviors. In addition, complex fabrication and programming procedures hinder broad applications of existing polymer actuators. Moreover, few of the existing polymer actuators are able to show the self-folding behaviors with the precise control of curvature and force. To address these issues, we report an easy-to-fabricate triple-state actuator with controllable folding behaviors based on bilayer polymer composites with different glass transition temperatures. Initially, the fabricated actuator is in the flat state, and it can sequentially self-fold to angled folding states of opposite directions as it is heated up. Based on an analytical model and measured partial recovery behaviors of polymers, we can accurately control the folding characteristics (curvature and force) for the rational design. To demonstrate an application of our triple-state actuator, we have developed a self-folding transformer robot which self-folds from a two-dimensional sheet into a three-dimensional boat-like configuration and transforms from the boat shape to a car shape with the increase in the temperature applied to the actuator. Our findings offer a simple approach to generate multiple configurations from a single system by harnessing behaviors of polymers with the rational design.
Annual patterns of xylem embolism in high-yield apple cultivars
Authors: Beikircher Barbara , Mayr Stefan
Published: March 2017

Temperate angiosperm species show pronounced annual patterns in xylem embolism. In this study, we investigated whether high-yield cultivars of Malus domestica Borkh. growing under optimised soil water conditions follow similar patterns to wild-type plants, and evaluated crucial factors for the formation of winter embolism and the subsequent restoration of the hydraulic system in spring. In five different cultivars growing at three different sites, various hydraulic and microclimatic parameters were monitored over three successive years. In all cultivars on all sites and in all years, the percentage loss of hydraulic conductivity (PLC) increased in autumn with freeze–thaw events and accumulated over winter. Maximum values were reached in late winter and differed significantly among cultivars. In spring, the hydraulic system was restored and PLC remained negligible during summer. Embolism formation in autumn was significantly correlated with the occurrence of freeze–thaw events, whereas further conductivity losses over winter were related to winter desiccation and influenced by climatic and cultivar-specific parameters. Restoration of the hydraulic system in spring was strongly linked to a decrease in the starch content of wood and buds, and soil temperature. Despite high soil water availability, hydraulic recovery took several weeks and was not completed before bud break. Spring is thus a critical phase for temperate angiosperms, especially for high-yield cultivars with risky hydraulic strategies.
BCL6 promotes glioma and serves as a therapeutic target
Authors: Xu Liang , Chen Ye , Dutra-Clarke Marina , Mayakonda Anand , Hazawa Masaharu , Savinoff Steve E. , Doan Ngan , Said Jonathan W. , Yong William H. , Watkins Ashley , Yang Henry , Ding Ling-Wen , Jiang Yan-Yi , Tyner Jeffrey W. , Ching Jianhong , Kovalik Jean-Paul , Madan Vikas , Chan Shing-Leng , Müschen Markus , Breunig Joshua J. , Lin De-Chen , Koeffler H. Phillip
Published: March 2017

Significance

Glioblastoma (GBM) is the most lethal brain malignancy lacking effective treatment. In this study, we demonstrate that BCL6 is a prognostic marker and a targetable GBM-promoting factor. Silencing of BCL6 inhibits the malignant phenotype of GBM cells and triggers cellular senescence. We also identify AXL as an important BCL6 transcriptional target, the expression of which is also regulated positively by NCoR, a BCL6 cofactor. Either silencing of BCL6 or targeted disruption of the BCL6/NCoR complex diminishes AXL expression and inhibits GBM growth. This study elucidates a crucial BCL6-mediated signaling pathway in GBM biology. More importantly, our results highlight the promise and merit of targeting BCL6 for treating this deadly disease.
Protectin D1
n-3 DPA
and resolvin D5
n-3 DPA
are effectors of intestinal protection
Authors: Gobbetti Thomas , Dalli Jesmond , Colas Romain A. , Federici Canova Donata , Aursnes Marius , Bonnet Delphine , Alric Laurent , Vergnolle Nathalie , Deraison Celine , Hansen Trond V. , Serhan Charles N. , Perretti Mauro
Published: March 2017

The resolution of inflammation is an active process orchestrated by specialized proresolving lipid mediators (SPM) that limit the host response within the affected tissue; failure of effective resolution may lead to tissue injury. Because persistence of inflammatory signals is a main feature of chronic inflammatory conditions, including inflammatory bowel diseases (IBDs), herein we investigate expression and functions of SPM in intestinal inflammation. Targeted liquid chromatography-tandem mass spectrometry-based metabololipidomics was used to identify SPMs from n-3 polyunsaturated fatty acids in human IBD colon biopsies, quantifying a significant up-regulation of the resolvin and protectin pathway compared with normal gut tissue. Systemic treatment with protectin (PD)1
n-3 DPA
or resolvin (Rv)D5
n-3 DPA
protected against colitis and intestinal ischemia/reperfusion-induced inflammation in mice. Inhibition of 15-lipoxygenase activity reduced PD1
n-3 DPA
and augmented intestinal inflammation in experimental colitis. Intravital microscopy of mouse mesenteric venules demonstrated that PD1
n-3 DPA
and RvD5
n-3 DPA
decreased the extent of leukocyte adhesion and emigration following ischemia-reperfusion. These data were translated by assessing human neutrophil–endothelial interactions under flow: PD1
n-3 DPA
and RvD5
n-3 DPA
reduced cell adhesion onto TNF-α–activated human endothelial monolayers. In conclusion, we propose that innovative therapies based on n-3 DPA-derived mediators could be developed to enable antiinflammatory and tissue protective effects in inflammatory pathologies of the gut.
Identification of targets of tumor suppressor microRNA-34a using a reporter library system
Authors: Ito Yoshiaki , Inoue Atsushi , Seers Timothy , Hato Yukari , Igarashi Arisa , Toyama Tatsuya , Taganov Konstantin D. , Boldin Mark P. , Asahara Hiroshi
Published: March 2017

Significance

Identification of miRNA targets is necessary for understanding their functions; however, current approaches to screening for specific targets are inadequate. For example, most miRNA target-prediction tools only match the 3′-UTR sequence with the miRNA sequence. We created a screening system for miRNA targets using a reporter library of 4,891 full-length cDNAs inserted into the 3′ UTR of a luciferase gene. Using this system, we identified targets of tumor suppressor miR-34a. Among the identified targets,
GFRA3
, which is crucial for growth of breast cancer cells and affects the survival of patients with breast cancer, was directly regulated by miR-34a via the coding region. Our study shows the advantage of this full-length reporter library system in identifying functional targets of miRNAs.
Extended responding
Authors: Lee Seung-Hee
Published: March 2017

This chapter proposes an understanding that second pair parts in an adjacency pair can be built with sequences. Using data from
audio-recordings of telephone calls by customers to an airline service, this chapter shows that responses to airline reservation requests
can be composed of several components that grant and fulfill requests and involve several courses of action of processing those
components. The action of responding is implemented piece by piece over a set of sequences that are collaboratively constructed by the
parties, which I term extended responding. The collaborative nature of extended responding is exhibited in the negotiation between the
parties in terms of ‘who’ directs the development of responding sequences.
Towards a life of poverty and uncertainty? The livelihood strategies of Gécamines workers after retrenchment in the DRC
Authors: Rubbers Benjamin
Published: March 2017

In 2003, with the support of the World Bank, the Congolese state-owned enterprise Gécamines implemented a voluntary departure programme for 10,000 employees with more than 25 years of service. These employees were asked to regard their severance pay as a capital to be invested in new activities. Based on ethnographic research, this article explores how ex-Gécamines workers made a living in the phase of their ‘reintegration’. In doing so, it develops a sociological approach to popular economic practices that attempts to move beyond the phenomenology of uncertainty recently advocated by several Africanist scholars.
Adsorption and diffusion of mono, di, and trivalent ions on two-dimensional TiS2
Authors: Samad Abdus , Shafique Aamir , Shin Young-Han
Published: March 2017

A comparative study of the monovalent (Li, Na, and K) and multivalent (Be, Mg, Ca, and Al) metal ion adsorption and diffusion on an electronically semi-metallic two-dimensional nanosheet of 1T structured TiS2 is presented here to contribute to the search for abundant, cheap, and nontoxic ingredients for efficient rechargeable metal ion batteries. The total formation energy of the metal ion adsorption and the Bader charge analysis show that the divalent Mg and Ca ions can have a charge storage density double that of the monovalent Li, Na, and K ions, while the Be and Al ions form metallic clusters even at a low adsorption density because of their high bulk energies. The adsorption of Mg ions shows the lowest averaged open circuit voltage (0.13 V). The activation energy barriers for the diffusion of metal ions on the surface of the monolayer successively decrease from Li to K and Be to Ca. Mg and Ca, being divalent, are capable of storing a higher power density than Li while K and Na have a higher rate capability than the Li ions. Therefore, rechargeable Li ion batteries can be totally or partially replaceable by Mg ion batteries, where high power density and high cell voltage are required, while the abundant, cheap, and fast Na ions can be used for green grid applications.
Fabrication of fluorescent composite hydrogel using in situ synthesis of upconversion nanoparticles
Authors: Dong Yuqing , Lin Min , Jin Guorui , Il Park Yong , Qiu Mushu , Zhao Ying , Yang Hui , Li Ang , Jian Lu Tian
Published: March 2017

Fluorescent composite hydrogels have found widespread applications, especially in spatial and temporal monitoring of in vivo hydrogel behaviors via the emitting optical signal. However, most existing fluorescent composite hydrogels suffer from limited capability of deep tissue imaging and complicated fabrication routes. We herein report a facile method for fabricating fluorescent composite hydrogels based on the in situ synthesis of NaYF4:Yb, Er upconversion nanoparticles (UCNPs). This approach employs polyacrylamide (PAAm) hydrogels as a template, where the interconnected pores within the hydrogel act as nanoreactors to confine the growth of nanocrystals. We then obtained a fluorescent composite hydrogel exhibiting upconversion fluorescence and enhanced mechanical properties. The fluorescence spectra show that the fluorescence intensity decreases with decreasing size of the UCNPs. We investigated the relationship between the optical properties of the fluorescent composite hydrogel and the incorporated UCNPs based on the morphology, size, and distribution of the UCNPs by using scanning electron microscopy and transmission electron microscopy. In addition, we demonstrated the applicability of the synthesized hydrogel for deep tissue imaging through an in vitro tissue penetration experiment. Compressive and dynamic rheological testing reveal enhanced mechanical properties with increasing UCNP concentration. The fabricated upconversion fluorescent composite hydrogel may pave the way for monitoring the in vivo behavior of biomimetic materials via deep tissue imaging.
Cavernous Malformation Associated With Arterialized Developmental Venous Anomaly: A Case Report
Authors: Nakase Kenta , Motoyama Yasushi , Nakai Tokiko , Takeshima Yasuhiro , Nakagawa Ichiro , Park Young-Su , Ohbayashi Chiho , Nakase Hiroyuki
Published: March 2017

BACKGROUND AND IMPORTANCE: Formation of cavernous malformations (CMs) has been recognized to be associated with developmental venous anomaly (DVA) by many authors. Hemodynamic stress due to venous outflow restriction could be hypothesized as a cause. On the other hand, a rare subgroup of DVA with an arterial component has been reported as likely to hemorrhage or be symptomatic. Cases of arterialized DVAs reported previously have not been associated with the presence of CM.

CLINICAL PRESENTATION: We present herein a case report of arterialized DVA in the brainstem with repeated cerebellar hemorrhage. The 49-year-old patient was treated with surgical evacuation of hematoma. A surgical specimen from the hematoma cavity demonstrated CMs on histological examination.

CONCLUSION: To the best of our knowledge, this represents the first report of CM associated with an arterialized DVA. In addition to venous congestion due to outflow obstruction, bleeding from the arterial component of the DVA might be considered as a cause of CM formation.
Scientific Explanation
Authors: Pitt Joseph , Mischler Steven
Published: March 2017

The modern search for an adequate general theory of explanation is an outgrowth of the logical positivist’s agenda: to lay the groundwork for a general unified theory of science. Carl Hempel and Paul Oppenheim’s “Studies in the Logic of Explanation” (Hempel and Oppenheim 1948, cited under the Deductive-Nomological Model of Explanation) was the first major attempt to put forth an account that met the positivist’s criteria. It initiated a lively debate that has continued up to the present. But as the attention of the philosophers of science became increasingly focused on the individual sciences, it quickly became clear that one general theory of explanation would not do since the particulars of the various sciences called for different accounts of what constituted an adequate explanation in physics and biology as well as chemistry, etc. This article attempts to capture the flavor of the debates and the nature of the shifting targets over the years. It does not profess to be complete, being largely restricted to work published in English, but it is a start. While the modern debates surrounding explanation can be said to begin with Hempel and Oppenheim, the history of philosophical accounts of explanation can be traced at least to Aristotle, whose metaphysics set the logical framework for explanations until Galileo urged that appeals to metaphysical categories be replaced by mathematics and measurement. For the most part, Galileo was not interested in appealing to causes or occult forces. The account of how things behaved was to be expressed in the language of mathematics. Descartes tried to capitalize on that insight with his resurrection of medieval discussions of causation relying on Aristotle’s framework framed in a mathematical physics, only to be countered by Newton, who introduced non-Aristotelian causal explanation grounded in mathematical physics. Finally John Stuart Mill begins the long march to contemporary accounts of causal explanation in both the physical and the social sciences, again relying on certain key assumptions about human nature. So the history of explanation is long and intertwined with a variety of metaphysical frameworks. The Positivists of the 20th century unsuccessfully eschewed metaphysics and sought to create an account of causal explanation that somehow aimed to stick strictly to the dictates of science, only to be thwarted by the metaphysical assumptions in the sciences themselves.
Proportionality in International Law
Authors: Gardam Judith
Published: March 2017

In the most general terms proportionality requires a balance to be drawn between frequently conflicting values. Consequently, its application depends on a subjective value judgment and that very indeterminacy sometimes sits uneasily within law. Proportionality, nevertheless, is a pervasive and familiar concept within both the civil and criminal national legal systems of states. The norm first found expression in international law in the doctrine of the just war, the Christian version of which formed the basis of the secular just war writings of early commentators on the developing discipline of international law, such as Grotius and de Vattel. Nowadays the principle is reflected either explicitly or implicitly in several diverse areas of international law. It appears explicitly as either a treaty norm—as, for example, in the regulation of targeting decisions in International Humanitarian Law (IHL)—or as a customary norm in the case of self-defense and Countermeasures. In other situations, proportionality operates as a judicial mechanism of review implicit in the need to balance competing interests such as in European Union Law (EU Law), International Human Rights Law (IHRL), and the dispute settlement regime of the World Trade Organization (WTO). Proportionality is also a component of Maritime Law and Delimitation, the Law of Treaties, and International Criminal Law (ICL). The norm even has considerable support as constituting that elusive concept, a general principle of international law. The significance and scope of its role varies widely depending on the area of international law in question and determines to a considerable extent the amount of literature available on the topic. Despite its increasing importance in international law, exactly what proportionality requires of a particular decision maker in any given area of international law remains unsettled and is the subject of widespread judicial and scholarly debate. There is no one meaning of proportionality that is common in all contexts in which it operates or any consensus as to its application across the board. In order to provide some structure to the debate scholars have identified two major analytical approaches to the application of proportionality that they see reflected in state practice and jurisprudence: the so-called “quantitative” approach where the response is tailored or equivalent to the action against which it is to be measured, and the so called “qualitative” approach where other factors are to be taken into account. It is not suggested in the literature that all practice fits neatly into one or other category, but they are useful for the purposes of analysis and much of the material that follows incorporates these concepts.
Histomorphometric Comparison of Bone Regeneration in Critical-Sized Bone Defects Using Demineralized Bone Matrix, Platelet-Rich Fibrin, and Hyaluronic Acid as Bone Substitutes
Authors: Sindel Alper , Dereci Ömür , Toru Havva Serap , Tozoğlu Sinan
Published: March 2017

Aim:

To compare bone regeneration in the critical-sized bone defects grafted with demineralized bone matrix, platelet-rich fibrin, and hyaluronic acid in rats.

Materials and Methods:

Forty Wistar Albino rats allocated into 4 experimental groups: platelet-rich fibrin (PRF) group, noncross-linked hyaluronic acid gel (HA) group, demineralized bone matrix in putty form (DBM) group, and control group. A critical-sized defect of 8 mm was formed involving the sagittal suture for each rat under anesthetic induction. All animals were sacrificed at 21st day after surgery and histomorphometric parameters of total horizontal length (THL) and total vertical length (TVL) of newly produced bone and longest bone trabecula (LBT) were measured in the histologic slides. The difference between experimental groups for these parameters was analyzed.

Results:

There was statistically significant difference in THL and LBT but not in TVL. Total horizontal length was significantly increased in DBM group compared with control and HA groups (P < 0.05). There was also statistically significant increase in THL in PRF group compared with control group (P < 0.05). Longest bone trabecula significantly increased in DBM group compared with HA group (P < 0.05). There was also statistically significant increase in HA group compared with control group (P < 0.05) and LBT significantly increased in PRF group compared with HA group (P < 0.05).

Conclusion:

The sole usage of HA does not effectively increase bone regeneration when compared with DBM and PRF. The DBM and PRF do not have superiority to each other in the bone regeneration while they are superior to HA.
COULD PLANTS BE SENTIENT?
Authors: Calvo Paco , Sahi Vaidurya , Trewavas Anthony
Published: March 2017

Feelings in humans are mental states representing groups of physiological functions that usually have defined behavioural objectives or purpose. Feelings are thought to be coordinated in the brain stem of animals and are evolutionarily ancient. One function of the brain is to prioritise between competing mental states, and thus groups of physiological functions and in turn behaviour. Anger, fear or pain call for immediate action whereas hunger, or thirst, signify longer term needs and a requirement for search. Plants use groups of coordinated physiological activities to deal with defined environmental situations but currently have no known mental state to prioritise any order of response. Plants do have a nervous system based on phloem which is highly cross linked. Its potential for forming a mental state is unknown but it could be used to distinguish between different and even contradictory signals and thus determine a priority of response. The vascular nervous system stretches throughout the whole plant providing the potential for assessment in all parts and commensurate with its self-organising, phenotypically plastic behaviour.
Genetic Variation in Adaptability and Pleiotropy in Budding Yeast
Authors: Jerison Elizabeth R. , Kryazhimskiy Sergey , Mitchell James , Bloom Joshua S. , Kruglyak Leonid , Desai Michael M.
Published: March 2017

Evolution can favor organisms that are more adaptable, provided that genetic variation in adaptability exists. Here, we quantify this variation among 230 offspring of a cross between diverged yeast strains. We measure the adaptability of each offspring genotype, defined as its average rate of adaptation in a specific environmental condition, and analyze the heritability, predictability, and genetic basis of this trait. We find that initial genotype strongly affects adaptability and can alter the genetic basis of future evolution. Initial genotype also affects the pleiotropic consequences of adaptation for fitness in a different environment. This genetic variation in adaptability and pleiotropy is largely determined by initial fitness, according to a rule of declining adaptability with increasing initial fitness, but several individual QTLs also have a significant idiosyncratic role. Our results demonstrate that both adaptability and pleiotropy are complex traits, with extensive heritable differences arising from naturally occurring variation.
Methomyl Injury to Carbon Exchange Rates and Related Processes in Cotton
Authors: Salem C.E. , Cothren J.T. , Benedict C.R.
Published: March 2017

Some insecticides have the potential to cause varying levels of phytotoxicity. This study examined 1) the time courses of photosynthetic injury in cotton (Gossypium hirsutisms L.) leaves treated with methomyl [S-methyl-N-[(methyl carbamoyl)oxy]-thioacetimidate] and 2) the relationships between carbon exchange rate (CER), stomatal conductance, the chlorophyll fluorescence parameter FX/FP, and ribulose-1,5-bisphosphate carboxylase/ oxygenase (rubisco) activity. Plots were sprayed with either 0 or 0.84 kg methomyl·ha-1 when cotton was in mid-reproductive growth. Starting on the day of spraying, CER, stomatal conductance, FX/FP, and rubisco activity were measured daily for five consecutive days [4, 28, 52, 76 and 100 hours after spraying (HAS)]. In methomyl-treated leaves, CER decreased within hours after spraying, reached their lowest point at 28 HAS in experiment I and 76 HAS in experiment II, then recovered near-control levels by 100 HAS. At their lowest points, CER of methomyl-treated leaves decreased from 20 to 50% compared to controls. Stomatal conductance, FX/FP, and rubisco activity followed similar patterns to CER. Stomatal conductance was more closely related to CER than were FX/FP and rubisco activity. Chlorophyll fluorescence recovered more quickly than did CER. Rubisco activity did not decrease till after CER. From the parameters measured in this study, stomatal conductance appeared to be the major factor influencing methomyl-induced changes in CER, although all three parameters may be involved in the process of CER change.

Abbreviations

CER

carbon exchange rate

rubisco

ribulose-1,5-bisphosphate carboxylase/ oxygenase

DAT

days after treatment

HAS

hours after spraying
Methylation guide RNA evolution in archaea: structure, function, and genomic organization of 110 C/D box sRNA families across sixPyrobaculumspecies
Authors: Lui Lauren M , Uzilov Andrew V. , Bernick David L. , Corredor Andrea , Lowe Todd M. , Dennis Patrick P.
Published: March 2017

Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2′-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genusPyrobaculum, particularly rich in C/D box sRNA genes. Using high-throughput small RNA sequencing, specialized computational searches, and comparative genomics, we analyzed 526PyrobaculumC/D box sRNAs, organizing them into 110 families based on synteny and conservation of guide sequences which determine methylation targets. We examined gene duplications and rearrangements, including one family that has expanded in a pattern similar to retrotransposed repetitive elements in eukaryotes. New training data and inclusion of kink-turn secondary structural features enabled creation of an improved search model. Our analyses provide the most comprehensive, dynamic view of C/D box sRNA evolutionary history within a genus, in terms of modification function, feature plasticity, and gene mobility.
Canvas SPW: callingde novocopy number variants in pedigrees
Authors: Ivakhno Sergii , Roller Eric , Colombo Camilla , Tedder Philip , Cox Anthony J.
Published: March 2017

Motivation

Whole genome sequencing is becoming a diagnostics of choice for the identification of rare inherited andde novocopy number variants in families with various pediatric and late-onset genetic diseases. However, joint variant calling in pedigrees is hampered by the complexity of consensus breakpoint alignment across samples within an arbitrary pedigree structure.

Results

We have developed a new tool, Canvas SPW, for the identification of inherited andde novocopy number variants from pedigree sequencing data. Canvas SPW supports a number of family structures and provides a wide range of scoring and filtering options to automate and streamline identification ofde novovariants.

Availability

Canvas SPW is available for download fromhttps://github.com/Illumina/canvas.

Contact

sivakhno@illumina.com

Supplementary information

Supplementary data are available atBioinformaticsonline.
patternize:AnRpackage for quantifying color pattern variation
Authors: Van Belleghem Steven M. , Papa Riccardo , Ortiz-Zuazaga Humberto , Hendrickx Frederik , Jiggins Chris D. , Owen McMillan W. , Counterman Brian A.
Published: March 2017

The use of image data to quantify, study and compare variation in the colors and patterns of organisms requires the alignment of images to establish homology, followed by color-based segmentation of images. Here we describe anRpackage for image alignment and segmentation that has applications to quantify color patterns in a wide range of organisms.

patternizeis anRpackage that quantifies variation in color patterns obtained from image data.patternizefirst defines homology between pattern positions across specimens either through manually placed homologous landmarks or automated image registration. Pattern identification is performed by categorizing the distribution of colors using an RGB threshold,k-means clustering or watershed transformation.

We demonstrate thatpatternizecan be used for quantification of the color patterns in a variety of organisms by analyzing image data for butterflies, guppies, spiders and salamanders. Image data can be compared between sets of specimens, visualized as heatmaps and analyzed using principal component analysis (PCA).

patternizehas potential applications for fine scale quantification of color pattern phenotypes in population comparisons, genetic association studies and investigating the basis of color pattern variation across a wide range of organisms.
A systematic atlas of chaperome deregulation topologies across the human cancer landscape
Authors: Esfahani Ali Hadizadeh , Sverchkova Angelina , Saez-Rodriguez Julio , Schuppert Andreas A , Brehme Marc
Published: March 2017

Proteome balance is safeguarded by the proteostasis network (PN), an intricately regulated network of conserved processes that evolved to maintain native function of the diverse ensemble of protein species, ensuring cellular and organismal health. Proteostasis imbalances and collapse are implicated in a spectrum of human diseases, from neurodegeneration to cancer. The characteristics of PN disease alterations however have not been assessed in a systematic way. Zooming in on the chaperome as a central PN component we turned to a curated functional ontology of the human chaperome that we connect in a high-confidence physical protein-protein interaction network. Challenged by the lack of a systems-level understanding of proteostasis alterations in the heterogeneous spectrum of human cancers, we assessed gene expression across more than 10,000 patient biopsies covering 22 solid cancers. We derived a novel customized Meta-PCA dimension reduction approach yielding M-scores as quantitative indicators of disease expression changes to condense the complexity of cancer transcriptomics datasets into quantitative functional network topographies. We confirm upregulation of the HSP90 family and also highlight HSP60s, Prefoldins, HSP100s, ER- and mitochondria-specific chaperones as pan-cancer enriched. Our analysis also reveals a surprisingly consistent strong downregulation of small heat shock proteins (sHSPs) and we stratify two cancer groups based on the preferential upregulation of ATP-dependent chaperones. Strikingly, our analysis highlight similarities between stem cell and cancer proteostasis, and diametrically opposed chaperome deregulation between cancers and neurodegenerative diseases. We developed a web-based Proteostasis Profiler tool (Pro2) enabling intuitive analysis and visual exploration of proteostasis disease alterations using gene expression data. Our study showcases a comprehensive profiling of chaperome shifts in human cancers and sets the stage for a systematic global analysis of PN alterations across the human diseasome towards novel hypotheses for therapeutic network re-adjustment in proteostasis disorders.
EMT and MET: necessary or permissive for metastasis?
Authors: Jolly Mohit Kumar , Ware Kathryn E , Gilja Shivee , Somarelli Jason A , Levine Herbert
Published: March 2017

Epithelial-to-mesenchymal transition (EMT) and its reverse mesenchymal-to-epithelial transition (MET) have been often suggested to play crucial roles in metastatic dissemination of carcinomas. Recent studies have revealed that neither of these processes is binary. Instead, carcinoma cells often exhibit a spectrum of epithelial/mesenchymal phenotype(s). While epithelial-mesenchymal plasticity has been observed pre-clinically and clinically, whether any of these phenotypic transitions are indispensable for metastatic outgrowth remains an unanswered question. Here, we focus on epithelial-mesenchymal plasticity in metastatic dissemination and propose alternative mechanisms for successful dissemination and metastases beyond the traditional EMT-MET view. We highlight multiple hypotheses that can help reconcile conflicting observations, and outline the next set of key questions that can offer valuable insights into mechanisms of metastasis in multiple tumor models.
An ancient FMRFamide-related peptide-receptor pair induces defense behavior in a brachiopod larva
Authors: Thiel Daniel , Bauknecht Philipp , Jékely Gáspár , Hejnol Andreas
Published: March 2017

Animals show different behaviors that can consist of various spatially or temporally separated sub-reactions. Even less complex organisms, like ciliated larvae that display important behaviors (e.g. metamorphosis, defense, feeding), need to coordinate coherent sub-reactions with their simple nervous system. These behaviors can be triggered by neuropeptides, which are short signaling peptides. Despite the high diversity of neuropeptides in animals, and although their immunoreactivity is widely used in morphological studies of animal nervous systems (e.g. FMRFamide), their function and role in trochozoan larval behavior has so far only been tested in a few cases. When mechanically disturbed, the planktonic larvae of the brachiopodTerebratalia transversaprotrude their stiff and pointy chaetae in a defensive manner and sink down slowly: a startle reaction that is known from different chaetous trochozoan larvae. We found that both of these reactions can be induced simultaneously by the FMRFamide-related neuropeptide FLRFamide. We deorphanized theTerebrataliaFLRFamide receptor and found its expression spatially separated in the apical lobe at the prototroch of the larvae and in the trunk musculature, which correlates with the tissues that are responsible to perform the two sub-reactions. A behavioral assay showed a decreasing efficiency of modified peptides in triggering this behavior, which correlates with the decreasing efficiency of activating the FLRFamide receptor in transfected CHO-K1 cells. Immunohistochemistry andin situhybridization show FLRFamidergic neurons in the apical lobe as well as next to the trunk musculature. Our results show that the single neuropeptide FLRFamide can specifically induce the two coherent sub-reactions of theT. transversastartle behavior.
Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction
Authors: Mueller Britta , Mieczkowski Jakub , Kundu Sharmistha , Wang Peggy , Sadreyev Ruslan , Tolstorukov Michael Y. , Kingston Robert E.
Published: March 2017

Activation of transcription requires alteration of chromatin by complexes that increase the accessibility of nucleosomal DNA. Removing nucleosomes from regulatory sequences has been proposed to play a significant role in activation. We tested whether changes in nucleosome occupancy occurred on the set of genes that is activated by the unfolded protein response (UPR). We observed no decrease in occupancy on most promoters, gene bodies, and enhancers. Instead, there was an increase in the accessibility of nucleosomes, as measured by micrococcal nuclease (MNase) digestion and ATAC-seq (assay for transposase-accessible chromatin [ATAC] using sequencing), that did not result from removal of the nucleosome. Thus, changes in nucleosome accessibility predominate over changes in nucleosome occupancy during rapid transcriptional induction during the UPR.
Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice
Authors: Saul Michael C. , Seward Christopher H. , Troy Joseph M. , Zhang Huimin , Sloofman Laura G. , Lu Xiaochen , Weisner Patricia A. , Caetano-Anolles Derek , Sun Hao , Zhao Sihai Dave , Chandrasekaran Sriram , Sinha Saurabh , Stubbs Lisa
Published: March 2017

Agonistic encounters are powerful effectors of future behavior, and the ability to learn from this type of social challenge is an essential adaptive trait. We recently identified a conserved transcriptional program defining the response to social challenge across animal species, highly enriched in transcription factor (TF), energy metabolism, and developmental signaling genes. To understand the trajectory of this program and to uncover the most important regulatory influences controlling this response, we integrated gene expression data with the chromatin landscape in the hypothalamus, frontal cortex, and amygdala of socially challenged mice over time. The expression data revealed a complex spatiotemporal patterning of events starting with neural signaling molecules in the frontal cortex and ending in the modulation of developmental factors in the amygdala and hypothalamus, underpinned by a systems-wide shift in expression of energy metabolism-related genes. The transcriptional signals were correlated with significant shifts in chromatin accessibility and a network of challenge-associated TFs. Among these, the conserved metabolic and developmental regulator ESRRA was highlighted for an especially early and important regulatory role. Cell-type deconvolution analysis attributed the differential metabolic and developmental signals in this social context primarily to oligodendrocytes and neurons, respectively, and we show that ESRRA is expressed in both cell types. Localizing ESRRA binding sites in cortical chromatin, we show that this nuclear receptor binds both differentially expressed energy-related and neurodevelopmental TF genes. These data link metabolic and neurodevelopmental signaling to social challenge, and identify key regulatory drivers of this process with unprecedented tissue and temporal resolution.
Temperature-induced first-order displacive phase transition of isonicotinamide-4-methoxybenzoic acid co-crystal
Authors: Chia Tze Shyang , Quah Ching Kheng
Published: March 2017

Isonicotinamide–4-methoxybenzoic acid co-crystal (1), C6H6N2O·C8H8O3, is formed through slow evaporation from methanol solution and it undergoes a first-order isosymmetry (monoclinicI2/a↔ monoclinicI2/a) structural phase transition atTc= 142.5 (5) K, which has been confirmed by an abrupt jump of crystallographic interaxial angle β from variable-temperature single-crystal XRD and small heat hysteresis (6.25 K) in differential scanning calorimetry measurement. The three-dimensional X-ray crystal structures of (1) at the low-temperature phase (LTP) (100, 140 and 142 K) and the high-temperature phase (HTP) (143, 150, 200, 250 and 300 K) were solved and refined as a simple non-disordered model with finalR[F2> 2σ(F2)] ≃ 0.05. The asymmetric unit of (1) consists of crystallographically independent 4-methoxybenzoic acid (A) and isonicotinamide (B) molecules in both enantiotropic phases. MoleculeAadopts a `near-hydroxyl' conformation in which the hydroxyl and methoxy groups are positioned on the same side. Both `near-hydroxyl' and `near-carbonyl' molecular conformations possess minimum conformational energies with an energy difference of < 0.15 kJ mol−1from a potential energy surface scan. In the crystal, molecules are joined into linearABBAarrays by intermolecular N—H...O and O—H...N hydrogen bonds which were preserved in both phases. However, theseABBAarrays are displaced from planarity upon LTP-to-HTP transition and the changes in inter-array interactions are observed in two-dimensional fingerprint plots of their Hirshfeld surfaces. ThePIXELenergies of each molecular pair in both phases were calculated to investigate the difference in intermolecular interaction energies before and after the displacement ofABBAarrays from planarity, which directly leads to the single-crystal-to-single-crystal phase transition of (1).
IT usage for enhancing trade show performance: evidence from the aviation services
Authors: Singh Jaywant , Shukla Paurav , Kalafatis Stavros P.
Published: March 2017

Purpose

While trade shows remain an important customer relationship management (CRM) tool, recent advancements in information technology (IT) have raised concerns about the future of trade shows. This study aims to examine the antecedents and consequences of IT integration into trade shows.

Design/methodology/approach

The study uses a questionnaire-based survey with senior and middle managers in the aviation services, resulting in 135 valid responses from industry professionals. The data were analyzed using partial least squares structural equation modelling.

Findings

The findings demonstrate differential but significant impact of perceptions toward website design and firm motivations toward the integration IT in the three stages of trade shows marketing. The results also show significant impact of IT usage on the perceptions toward the accomplishment of trade show objectives. Further, the results vary according to the levels of experience of the professionals.

Research limitations/implications

This study did not account for the differences in perceptions toward IT implementation across personnel from different departments, such as IT, finance and operations management. In addition, it did not examine situational factors and individual characteristics as additional antecedents of IT usage in trade shows, including pricing, return on investment, convenience and the social media.

Practical implications

Exhibitors are advised to integrate IT in supporting pre-trade show activities to approach potential customers. Exhibitors should integrate electronic interactions and personal communications during the show to reduce the amount of unanswered customer queries, focusing on timeliness and accuracy of information content, ease of navigation and graphic attractiveness of corporate websites, as effective CRM tools.

Originality/value

This paper offers novel insights into hitherto unknown aspects of trade show performance. The results have managerial implications for adopting IT as a CRM tool for effective trade show management.
Exploring Big Five personality traits and gender as predictors of entrepreneurs’ cognitive adaptability
Authors: Bajwa Sami Ullah , Shahzad Khuram , Aslam Haris
Published: March 2017

Purpose

The purpose of this study was to explore the predictive role of personality and gender in cognitive adaptability of entrepreneurs. By using the theories of personality development, social learning, situated cognition and meta-cognition, a logical relationship between personality traits, gender difference and entrepreneurs’ cognitive adaptability was established.

Design/methodology/approach

Quantitative strategy and cross-sectional survey method was then deployed to empirically investigate the purposed relationships between variables of interest. Randomly selected 443 working entrepreneurs responded to the survey.

Findings

Factor analyzed structural equation modeling estimated cognitive adaptability as a second-order factor, with extroversion and neuroticism having a significant impact on cognitive adaptability. Multi-group moderation revealed a significant difference among females and males against the same two personality traits.

Originality/value

This study in its nature is the first attempt to link Big Five personality traits with cognitive adaptability of entrepreneurs.
Categorizing product attributes efficiently in QFD-Kano: a case analysis in telecommunication
Authors: Suef Mokh , Suparno Suparno , Singgih Moses Laksono
Published: March 2017

Purpose

The purpose of this paper is to propose a methodology to use complaints, claims and company innovation as an internal data source of customer needs for product development using the quality function deployment (QFD)-Kano approach instead of an ordinary customer survey.

Design/methodology/approach

This paper confirms that the customer complaints and claims and company innovations from the internal data source are equivalent to the Kano model’s product attributes. Data were selected from the company’s documents. To investigate the data category, a Kano questionnaire was designed and tested with 100 random respondents. Based on their answers, categories for the quality characteristics were determined and compared with the initial data categories. A second survey using professional customer respondents was conducted to increase the results’ reliability.

Findings

The approach was shown to be effective in employing complaints, claims and innovations as an alternative source of customer needs in the QFD-Kano approach.

Research limitations/implications

It is assumed that companies document their customer complaints and claims, as well as their strategic innovation plans. The complaint and claim data need to be extracted to reveal their quality characteristics. For future research, data extraction using text or data mining may be useful to bridge this gap.

Practical implications

The product development team may ascertain customer needs as duly classified. This voice of the customer is more accurate and requires less time.

Originality/value

The paper may be of value to researchers and practitioners involved in product design and development, since it offers a new source of customer need data obtained internally as an alternative to customer surveys.
TQM implementation in a least developed country: an exploratory study of Yemen
Authors: Aamer Ammar Mohamed , Al-Awlaqi Mohmmed A. , Alkibsi Sharaf M.
Published: March 2017

Purpose

The purpose of this paper is to assess the TQM readiness level of Yemeni Organizations. In addition, this study compares the level of readiness between the various Yemeni organizations.

Design/methodology/approach

Based on the TQM literature, related and relevant information had been gathered to develop an assessment tool used in this research. The main content of the assessment focused on statements related to the most common TQM principles. Data were collected by an assessment team and analyzed using quantitative methods to answer the related research questions.

Findings

The analysis results showed some of the TQM principles were being practiced by Yemeni organizations, to some extent, and with variant levels. The most widely practiced principle was customer focus, and the lowest principle practiced was continuous improvement. Also, the data showed the level of TQM readiness in Yemeni organizations was 58.93 percent. This level of TQM readiness indicates there is a potential for successful adoption of quality management standards and models in Yemeni organizations.

Research limitations/implications

This study extends previous limited research in TQM readiness level measurement. It also adds to the body of TQM knowledge within the context of Yemen. In addition, this study contributes to the understanding of TQM implementation in an least developed countries (LDC) environment, where LDC organizational culture has its particularities on implementing TQM.

Originality/value

This paper contributes to a better understanding of TQM in an LDC country, which is Yemen. The paper points out which of the TQM principles are important to potential adoption of quality management standards and models. This study could further expand research, regarding the TQM in Yemen.