bluuebunny/crossref_metadata_2025_split huggingface dataset:
Keratins 8 and 18 are type II acute‐phase responsive genes overexpressed in human liver disease
Authors: Guldiken Nurdan , Usachov Valentyn , Levada Kateryna , Trautwein Christian , Ziol Marianne , Nahon Pierre , Strnad Pavel 
Published: June 2014

AbstractBackground & AimsKeratins (Ks) 7, 8, 18 and 19 constitute important markers and modifiers of liver disease. In mice, K8 and K18 are stress inducible and a dysregulated K8 > K18 stoichiometry predisposes to formation of Mallory–Denk bodies (MDBs), i.e. aggregates characteristic of chronic liver disorders such as alcoholic liver disease (ALD). In our study, we analyse the expression and the regulation of keratins in context of human liver disease.MethodsK7, K8, K18 and K19 mRNA levels were determined in liver biopsies from patients with ALD, non‐alcoholic steatohepatitis (NASH), chronic hepatitis B (HBV), hepatitis C (HCV) and from control subjects. HepG2 and Hep3B cells were treated with IL‐1β, IL‐6 and TNF‐α. Mice were injected with turpentine, an established IL‐6 inducer.ResultsK7, K8 and K18 were 1.5‐ to 3‐fold upregulated in livers of ALD and HCV patients with a more active disease, but not in HBV/NASH subjects, while K19 was significantly elevated in all analysed disorders. K8 and K18 expression displayed a strong correlation (r = 0.89), but dysregulated levels with the K8 > K18 state were seen in ALD. All keratins were overexpressed in subjects with moderate vs. minimal inflammation, while K7, K8 and K18 were upregulated in patients with advanced liver fibrosis. In HepG2/Hep3B cells, IL‐6 treatment but not IL‐1β or TNF‐α significantly increased K8 and K18 expression and elevated K18 levels were seen after turpentine injection.ConclusionsKeratins represent type II acute‐phase responsive genes overexpressed in specific human liver disorders. A K8 > K18 state occurs in ALD and predisposes to MDB formation.
The Intergenerational Propagation of Wealth Inequality
Authors: Isaac Alan G. 
Published: June 2014

AbstractThis paper highlights the crucial role of demographic assumptions in models of the intergenerational transmission of wealth inequality. Specifically, we show that Alan Blinder's surprising predictions that bequest and mating practices can sustain but cannot cause wealth inequality are extremely fragile. We show that these predictions depend on a common and apparently minor demographic assumption: fixed sex ratios in family composition. We implement the Blinder model as an agent‐based simulation and show that without this demographic assumption such familial institutions are causative for wealth inequality, even in the long run.
Evaluation of BSP expression and apoptosis in the periodontal ligament during orthodontic relapse: a preliminary study
Authors: McManus A. , Utreja A. , Chen J. , Kalajzic Z. , Yang W. , Nanda R. , Wadhwa S. , Uribe F. 
Published: June 2014

Structured AbstractObjectiveTo examine the expression of bone sialoprotein (BSP) and apoptosis in an in vivo orthodontic relapse model.Materials and MethodsMale mice (10–12 weeks old), either transgenic [green fluorescent protein (GFP) driven by the BSP promoter] or wild type, were used in this study. To achieve orthodontic tooth movement (OTM), maxillary right first molars were moved mesially using closed‐coil springs. Animals were divided into an OTM group (14 days continuous orthodontic force – 11 animals) or Relapse group (10 days of force application followed by 4 days of relapse – 8 animals). The control group was comprised of the contralateral maxillary molars. The periodontal ligament (PDL) was analyzed in areas of compression and tension for transgenic expression, osteoclast localization, and the presence of apoptotic cells.ResultsThere was a significant decrease in GFP‐labeled cells on the compression and tension sides of the PDL in the OTM group compared with control. In the relapse group, GFP‐labeled cells were significantly decreased only on the old compression side. Osteoclasts were localized on the compression side of the OTM group, whereas in the Relapse group, they were present on both sides. PDL apoptosis significantly increased on the compression side in OTM and Relapse groups.ConclusionBoth OTM and Relapse groups exhibited a decreased number of GFP‐labeled cells in areas of compression and tension. There was significant PDL apoptosis in regions under compressive forces following OTM and to a lesser extent following relapse.
Control of NF‐kB activity in human melanoma by bromodomain and extra‐terminal protein inhibitor I‐BET151
Authors: Gallagher Stuart J. , Mijatov Branka , Gunatilake Dilini , Gowrishankar Kavitha , Tiffen Jessamy , James Wilmott , Jin Lei , Pupo Gulietta , Cullinane Carleen , McArthur Grant A. , Tummino Peter J. , Rizos Helen , Hersey Peter 
Published: June 2014

SummaryThe transcription factor NF‐kappaB (NF‐kB) is a key regulator of cytokine and chemokine production in melanoma and is responsible for symptoms such as anorexia, fatigue, and weight loss. In addition, NF‐kB is believed to contribute to progression of the disease by upregulation of cell cycle and anti‐apoptotic genes and to contribute to resistance against targeted therapies and immunotherapy. In this study, we have examined the ability of the bromodomain and extra‐terminal (BET) protein inhibitor I‐BET151 to inhibit NF‐kB in melanoma cells. We show that I‐BET151 is a potent, selective inhibitor of a number of NF‐kB target genes involved in induction of inflammation and cell cycle regulation and downregulates production of cytokines such as IL‐6 and IL‐8. SiRNA studies indicate that BRD2 is the main BET protein involved in regulation of NF‐kB and that I‐BET151 caused transcriptional downregulation of the NF‐kB subunit p105/p50. These results suggest that BET inhibitors may have an important role in treatment of melanoma where activation of NF‐kB may have a key pathogenic role.
geneGIS: Geoanalytical Tools and Arc Marine Customization for Individual‐Based Genetic Records
Authors: Dick Dorothy M. , Walbridge Shaun , Wright Dawn J. , Calambokidis John , Falcone Erin A. , Steel Debbie , Follett Tomas , Holmberg Jason , Baker C. Scott 
Published: June 2014

AbstractTo improve understanding of population structure, ecosystem relationships and predictive models of human impact in cetaceans and other marine megafauna, we developed geneGIS, a suite of GIS tools and a customized Arc Marine data model to facilitate visual exploration and spatial analyses of individual‐based records from DNA profiles and photo‐identification records. We used the open source programming language Python 2.7 and ArcGIS 10.1 software to create a user‐friendly, menu‐driven toolbar linked to a Python Toolbox containing customized geoprocessing scripts. For ease of sharing and installation, we compiled the geneGIS program into an ArcGIS Python Add‐In, freely available for download from the website http://genegis.org. We used the Lord‐Castillo et al. (2009) Arc Marine data model customization as the starting point for our work and retained nine key base Arc Marine classes. We demonstrate the utility of geneGIS using an integrated database of more than 18,000 records of humpback whales (Megaptera novaeangliae) in the North Pacific collected during the Structure of Populations, Levels of Abundance and Status of Humpback Whales in the North Pacific (SPLASH) program. These records represent more than 8,000 naturally marked individuals and 2,700 associated DNA profiles, including 10 biparentally inherited microsatellite loci, maternally inherited mitochondrial DNA, and genetic sex.
A Combined Biophysical and EconomicGISFramework to Assess Sugarcane Cropping Potential inBrazil
Authors: Hissa Letícia de Barros Viana , Filho Britaldo Silveira Soares 
Published: June 2014

AbstractRecently, the increasing demand for biofuels triggered a new phase for the sugar‐alcohol sector. InBrazil, as well as in other tropical countries, this process raised worries regarding the possible direct and indirect effects of the crop's expansion on the conversion of native vegetation coverings. Therefore, the modeling of spatial‐economic surfaces, representing the potential rent variation in its spatial component, for economic activities, may be a useful tool in the decision‐making process. Hence, here we propose and present the results of a combined framework composed of two modules using the modeling platformDinamicaEGO. The first module simulates sugarcane's growth, calculating the daily response of the crop to environmental conditions during the stages of the plant's development. The second module estimates rents for sugarcane cultivation inBrazil, identifying areas where this activity would bring higher economic return, looking at simulated productivity, production costs and selling prices in a way that is spatially explicit forBrazil. Two different scenarios for production costs were tested, and results ranged from negative values to maxima of R$/ha 929 and R$/ha 1176 for standard and efficient costs of production, respectively. The model successfully indicated non‐profitable and profitable areas, and regions where high expected economic return overlaps endangered ecosystems.
Understanding User Interaction Patterns within Online Systems for Public‐Participation Transportation Planning
Authors: Swobodzinski Martin , Jankowski Piotr 
Published: June 2014

AbstractMany research projects in public‐participation geographic information systems focused on the development of software prototypes that were conceptualized to complement traditional forms of public participation. Given the challenges introduced by the heterogeneity of their user base, system design, and decision making process, empirical evaluations of such systems based on actual use have been scarce. This article reports on a rigorous empirical assessment of human‐computer interaction of users of a web‐based system for participatory transportation planning. We devised three groups of participants with below‐average, average, and above‐average interaction duration through hierarchical cluster analysis. Subsequently, the characteristics of the clusters were subjected to logistic regression analysis to determine the significance and strength of statistical associations between duration of interaction and a host of individual‐level variables. Our results indicate a statistically significant reduction of the odds‐ratio for participants with above‐average duration of interaction in the case of no prior experience with online transportation discussions. No significant associations were found between overall duration of interaction and sociodemographic background, cognitive decision‐making style, and travel behavior. We advocate for the development of adaptable participatory systems which accommodate flexibility in terms of both the user interface and pathways of the decision making process.
Detecting Non‐personal and Spam Users on Geo‐tagged Twitter Network
Authors: Guo Diansheng , Chen Chao 
Published: June 2014

AbstractWith the rapid growth and popularity of mobile devices and location‐aware technologies, online social networks such as Twitter have become an important data source for scientists to conduct geo‐social network research. Non‐personal accounts, spam users and junk tweets, however, pose severe problems to the extraction of meaningful information and the validation of any research findings on tweets or twitter users. Therefore, the detection of such users is a critical and fundamental step for twitter‐related geographic research. In this study, we develop a methodological framework to: (1) extract user characteristics based on geographic, graph‐based and content‐based features of tweets; (2) construct a training dataset by manually inspecting and labeling a large sample of twitter users; and (3) derive reliable rules and knowledge for detecting non‐personal users with supervised classification methods. The extracted geographic characteristics of a user include maximum speed, mean speed, the number of different counties that the user has been to, and others. Content‐based characteristics for a user include the number of tweets per month, the percentage of tweets with URLs or Hashtags, and the percentage of tweets with emotions, detected with sentiment analysis. The extracted rules are theoretically interesting and practically useful. Specifically, the results show that geographic features, such as the average speed and frequency of county changes, can serve as important indicators of non‐personal users. For non‐spatial characteristics, the percentage of tweets with a high human factor index, the percentage of tweets with URLs, and the percentage of tweets with mentioned/replied users are the top three features in detecting non‐personal users.
Exploring Mobility Indoors: an Application of Sensor‐based and GIS Systems
Authors: Petrenko Anastasia , Sizo Anton , Qian Winchel , Knowles A. Dylan , Tavassolian Amin , Stanley Kevin , Bell Scott 
Published: June 2014

AbstractThe popularization of tracking devices, such as GPS, accelerometers and smartphones, have made it possible to detect, record, and analyze new patterns of human movement and behavior. However, employing GPS alone for indoor localization is not always possible due to the system's inability to determine location inside buildings or in places of signal occlusion. In this context, the application of local wireless networks for determining position is a promising alternative solution, although they still suffer from a number of limitations due to energy and IT‐resources. Our research outlines the potential for employing indoor wireless network positioning and sensor‐based systems to improve the collection of tracking data indoors. By applying various methods of GIScience we developed a methodology that can be applicable for diverse human indoor mobility analysis. To show the advantage of the proposed method, we present the result of an experiment that included mobility analysis of 37 participants. We tracked their movements on a university campus over the course of 41 days and demonstrated that their movement behavior can be successfully studied with our proposed method.
Mpl Traffics to the Cell Surface Through Conventional and Unconventional Routes
Authors: Cleyrat Cédric , Darehshouri Anza , Steinkamp Mara P. , Vilaine Mathias , Boassa Daniela , Ellisman Mark H. , Hermouet Sylvie , Wilson Bridget S. 
Published: June 2014

AbstractMyeloproliferative neoplasms (MPNs) are often characterized by JAK2 or calreticulin (CALR) mutations, indicating aberrant trafficking in pathogenesis. This study focuses on Mpl trafficking and Jak2 association using two model systems: human erythroleukemia cells (HEL; JAK2V617F) and K562 myeloid leukemia cells (JAK2WT). Consistent with a putative chaperone role for Jak2, Mpl and Jak2 associate on both intracellular and plasma membranes (shown by proximity ligation assay) and siRNA‐mediated knockdown of Jak2 led to Mpl trapping in the endoplasmic reticulum (ER). Even in Jak2 sufficient cells, Mpl accumulates in punctate structures that partially colocalize with ER‐tracker, the ER exit site marker (ERES) Sec31a, the autophagy marker LC3 and LAMP1. Mpl was fused to miniSOG, a genetically encoded tag for correlated light and electron microscopy. Results suggest that a fraction of Mpl is taken up into autophagic structures from the ER and routed to autolyososomes. Surface biotinylation shows that both immature and mature Mpl reach the cell surface; in K562 cells Mpl is also released in exosomes. Both forms rapidly internalize upon ligand addition, while recovery is primarily attributed to immature Mpl. Mpl appears to reach the plasma membrane via both conventional ER‐Golgi and autolysosome secretory pathways, as well as recycling.
Complete Genome Sequence of Bacillus cereus
Sensu Lato
Bacteriophage Bcp1
Authors: Schuch Raymond , Pelzek Adam J. , Fazzini Monica M. , Nelson Daniel C. , Fischetti Vincent A. 
Published: June 2014

ABSTRACT

Bacillus cereus
sensu lato
organisms are an ecologically diverse group that includes etiologic agents of food poisoning, periodontal disease, and anthrax. The recently identified Bcp1 bacteriophage infects
B. cereus
sensu lato
and is being developed as a therapeutic decontamination agent and diagnostic countermeasure. We announce the complete genome sequence of Bcp1.
Draft Genome Sequence of a Rare Smut Relative,
Tilletiaria anomala
UBC 951
Authors: Toome Merje , Kuo Alan , Henrissat Bernard , Lipzen Anna , Tritt Andrew , Yoshinaga Yuko , Zane Matthew , Barry Kerrie , Grigoriev Igor V. , Spatafora Joseph W. , Aime M. Catherine 
Published: June 2014

ABSTRACT

The draft genome sequence of the smut fungus
Tilletiaria anomala
UBC 951 (Basidiomycota, Ustilaginomycotina) is presented. The sequenced genome size is 18.7 Mb, consisting of 289 scaffolds and a total of 6,810 predicted genes. This is the first genome sequence published for a fungus in the order Georgefisheriales (Exobasidiomycetes).
Draft Genome Sequence of Stenotrophomonas maltophilia Strain M30, Isolated from a Chronic Pressure Ulcer in an Elderly Patient
Authors: Huedo Pol , Conchillo-Solé Óscar , Yero Daniel , Martínez-Servat Sònia , Daura Xavier , Gibert Isidre 
Published: June 2014

ABSTRACT

Stenotrophomonas maltophilia
is an emerging opportunistic pathogen with an increasing prevalence of multidrug-resistant strains. Here, we report the draft genome sequence of
S. maltophilia
strain M30, isolated from a pressure ulcer in an elderly patient.
Genome Sequences of Strain ATCC 29281 and Pin and Northern Red Oak Isolates of Lonsdalea quercina subsp.
quercina
Authors: Ibarra Caballero Jorge , Zerillo Marcelo M. , Snelling Jacob , Cranshaw Whitney , Boucher Christina , Tisserat Ned 
Published: June 2014

ABSTRACT

Two bacteria identified as
Lonsdalea quercina
subsp.
quercina
were isolated from oak trees showing symptoms of drippy blight. Here, we present their draft genome assemblies, as well as that of the type strain of this species. To our knowledge, these are the first published genome sequences of this subspecies of
Lonsdalea quercina
.
Mathematics that has intrigued me
Authors: Olver F. W. J. 
Published: June 2014

I trace the main steps of the first fifty-five years of my career as an applied mathematician, pausing from time to time to describe problems that arose in asymptotics and numerical analysis and had far-reaching effects on this career. Lecture delivered at Asymptotics and Applied Analysis, Conference in Honor of Frank W. J. Olver's 75th Birthday, January 10–14, 2000, San Diego State University, San Diego, California. Editors' Note: Frank W. J. Olver died on April 23, 2013. The following text was typed by his son, Peter J. Olver, from handwritten notes found among his papers. At times the writing is unpolished, including incomplete sentences, but the editors have decided to leave it essentially the way it was written. However, for clarity, some abbreviations have been written out in full. A couple of handwritten words could not be deciphered, and a guess for what was intended is enclosed in brackets: […]. Endnotes have been made into footnotes within the body of the article. References were mostly not included in the handwritten text, but rather listed in order at the end. Citations to references have been included at the appropriate point in the text.
Did
Dactylioceras
eat fish?
Authors: Paul Christopher R. C. 
Published: June 2014

Summary

Ammonites that preserve evidence of their soft anatomy or gut contents are exceedingly rare. An example of the Toarcian ammonite,
Dactylioceras
, with tightly packed fish scales in the supposed position of the stomach, plus further scales and three articulated fish vertebrae in the approximate position of the crop, is described. The body-chamber is largely filled with fine sedimentary rock, but shows several thin areas now lined with diagenetic calcite where the sediment was unable to penetrate. These are interpreted as the positions of ammonite soft tissue because they line parts of the body-chamber, which is consistent with the idea that the stomach and crop remained intact long enough for their contents to be preserved in place. Inquilinism is thought unlikely as an explanation because the fish remains are largely disarticulated and packed together in the rear of the body-chamber, but the fish debris could represent food of an animal that sheltered within the dead ammonite shell. Equally, passive fill of the body-chamber with sediment containing fish scales seems unlikely due to the local concentration at the rear of the body-chamber. Possibly this
Dactylioceras
ate fish either as a predator or scavenger.
Make Your Own Cigarettes: Toxicant Exposure, Smoking Topography, and Subjective Effects
Authors: Koszowski Bartosz , Rosenberry Zachary R. , Viray Lauren C. , Potts Jennifer L. , Pickworth Wallace B. 
Published: June 2014

AbstractBackground: Despite considerable use of make your own (MYO) cigarettes worldwide and increasing use in the United States, relatively little is known about how these cigarettes are smoked and the resultant toxicant exposure.Methods: In a laboratory study, we compared two types of MYO cigarettes—roll your own (RYO) and personal machine made (PMM)—with factory-made (FM) cigarettes in three groups of smokers who exclusively used RYO (n = 34), PMM (n = 23), or FM (n = 20). Within each group, cigarettes were smoked in three conditions: (i) after confirmed overnight tobacco abstinence; (ii) in an intense smoking paradigm; and (iii) without restrictions. All cigarettes were smoked ad lib through a smoking topography unit.Results: Plasma nicotine significantly increased after cigarettes in all conditions except PMM in the intense smoking paradigm. Puff volume, puff duration, total puff volume, and puff velocity did not differ between cigarette types but the puffs per cigarette and time to smoke were significantly smaller for RYO compared with PMM and FM. Regardless of the cigarette, participants consumed the first three puffs more vigorously than the last three puffs.Conclusions: Despite the belief of many of their consumers, smoking MYO cigarettes is not a safe alternative to FM cigarettes. Like FM, MYO cigarettes expose their users to harmful constituents of tobacco smoke. Despite differences in size and design their puffing profiles are remarkably similar.Impact: These data are relevant to health and regulatory considerations on the MYO cigarettes. Cancer Epidemiol Biomarkers Prev; 23(9); 1793–803. ©2014 AACR.