bluuebunny/crossref_metadata_2025 huggingface dataset:
The twoKronik Tionghuaof Semarang and Cirebon: A note on provenance and reliability
Authors: Wain Alexander
Published: May 2017

This article is the first comprehensive evaluation of the provenance and reliability of the two enigmaticKronik Tionghuatexts of Semarang and Cirebon (the ‘Malay Annals of Semarang and Cerbon’). Initially published by M.O. Parlindungan in 1964, historians have increasingly begun to use these documents when reconstructing Java's early Islamic history. This article is a long overdue attempt to positively identify the Dutch colonial official (Cornelis Poortman) whom Parlindungan claims to have received the texts from. Although the article establishes that Parlindungan almost certainly knew this individual, discrepancies between his version of Poortman's career and official Dutch records raise questions about whether Poortman could have found the twoKronik Tionghua, at least in the manner described. The article then ends with a close textual analysis of bothKronik Tionghuawhich demonstrates the possibility that both texts were written by a modern, Dutch-educated author. The article therefore concludes that both texts are probable fabrications, albeit ones based on authentic texts.
Mediating the local: Representing Javanese cultures on local television in Indonesia
Authors: Bogaerts Els
Published: May 2017

The end of the New Order regime and the passing of new legislation in Indonesia offered the mushrooming local broadcasting industry ample opportunities. This article examines how the changing circumstances have enabled television stations to foreground local identities within a national frame of reference. It focuses on developments in local television in the Special Region of Yogyakarta, Central Java, between 1998 and 2009. Using various localising strategies, the stations provide a more diversified local content than was the case during the Soeharto period. The analysis is based on local resources and supported by inside information, generously provided by media workers and artists.
Colonial sugar production in the Spanish Philippines: Calamba and Negros compared
Authors: Aguilar Filomeno V.
Published: May 2017

This article presents two modes of export-oriented sugar hacienda production in the late-nineteenth-century Spanish Philippines. The Hacienda de Calamba epitomised a large-scale estate under a religious corporation; it was an enclave economy reliant on local capital and technology. In contrast, Negros showcased a range of haciendas of varying sizes in a frontier setting involving different ethnicities and supported by capital and technology mediated directly by foreign merchant houses. In both locations sugar planters opposed the colonial state, but whereas leaseholders in Calamba, led by Rizal's family, became intentionally political in their resistance, in Negros planters engaged in a persistent and calibrated evasion of the state.
Not Isolated, Actively Isolationist: Towards a subaltern history of the Nilgiri hills before British imperialism*
Authors: KELLY GWENDOLYN I. O.
Published: May 2017

The Nilgiri hill communities have for a long time been the focus of anthropological inquiry, though they have rarely been the focus of historical inquiry that delves more deeply into the past than the colonial period. And, while the fields of history and anthropology have moved beyond tropes of primitive and timeless, our studies of those formerly so-called ‘timeless primitives’ have remained stuck in time. I argue, therefore, for an interdisciplinary modified Subaltern Studies approach, integrating data from anthropology, archaeology, linguistics, and genetics, to develop alongue duréesocial history of the Nilgiri hills. For the Nilgiri communities, as with other tribal communities, narratives about their past have tended to emphasize their isolation until the modern period. In this article, drawing together data from several disciplines, I argue that the communities of the Nilgiris, especially the Toda, so frequently held up as examples of cultural isolation, were not truly isolated, neither from neighbouring tribal communities, nor from the states and empires of the plains below. I argue that the maintenance of distinctive religious, subsistence, and linguistic practices, despite contact with a wider world, is evidence of an active process of isolationist group formation/maintenance and resistance to other ways of being.
Naturalism and the Idea of Nature
Authors: Baker Lynne Rudder
Published: May 2017

There are many versions of naturalism. In contemporary Anglophone philosophy, the dominant versions are forms of scientific naturalism. After discussing three forms of scientific naturalism – eliminative, reductive, and nonreductive naturalism – I turn to the idea of nature that scientific naturalism presupposes, and I argue that the presupposed idea of nature is inadequate: It does not include everything in nature. I shall argue that all forms of naturalism – even so-called liberal naturalism, a nonscientific version – suffer from presupposed and unargued-for closure principles that limit the scope of reality. Finally, I'll briefly discuss my own view that I call ‘near-naturalism’.
Risk of transition to schizophrenia following first admission with substance-induced psychotic disorder: a population-based longitudinal cohort study
Authors: Alderson H. L. , Semple D. M. , Blayney C. , Queirazza F. , Chekuri V. , Lawrie S. M.
Published: May 2017

Background

The potential for drugs of abuse to induce acute psychotic symptoms is well recognised. However, the likelihood of transition from initial substance-induced psychotic disorder (SIPD) to chronic psychosis is much less well understood. This study investigated the rate of SIPD transition to schizophrenia (F20), the time to conversion and other possible related factors.

Methods

Using data from the Scottish Morbidity Record, we examined all patients (n = 3486) since their first admission to psychiatric hospital with a diagnosis of SIPD [International Classification of Diseases, Tenth Revision (ICD-10) codes F10–F19, with third digit five] from January 1997 to July 2012. Patients were followed until first episode of schizophrenia (ICD-10 code F20, with any third digit) or July 2012. Any change in diagnosis was noted in the follow-up period, which ranged from 1 day to 15.5 years across the groups.

Results

The 15.5-year cumulative hazard rate was 17.3% (s.e. = 0.007) for a diagnosis of schizophrenia. Cannabis, stimulant, opiate and multiple drug-induced psychotic disorder were all associated with similar hazard rates. The mean time to transition to a diagnosis of schizophrenia was around 13 years, although over 50% did so within 2 years and over 80% of cases presented within 5 years of SIPD diagnosis. Risk factors included male gender, younger age and longer first admission.

Conclusions

SIPD episodes requiring hospital admission for more than 2 weeks are more likely to be associated with later diagnosis of schizophrenia. Follow-up periods of more than 2 years are needed to detect the majority of those individuals who will ultimately develop schizophrenia.
The specific effect of systematic exposure in irritable bowel syndrome: complier average causal effect analysis using growth mixture modeling
Authors: Hesser H. , Hedman E. , Lindfors P. , Andersson E. , Ljótsson B.
Published: May 2017

Background

We reanalyzed data from a previously published randomized component study that aimed to test the incremental effect of systematic exposure in an internet-delivered cognitive behavioral treatment (ICBT) for irritable bowel syndrome (IBS).

Methods

Three hundred and nine individuals with IBS were randomly assigned to either the full treatment protocol (experimental condition) or the same treatment protocol without systematic exposure (control). Participants were assessed weekly for IBS symptoms over the active treatment phase. We used a complier average causal effect (CACE) analysis, in the growth mixture modeling framework, to (1) examine the specific effect of exposure among those who received the intervention (i.e. compliers), and (2) explore the associations of pre-treatment patient characteristics with compliance status and outcome changes.

Results

Fifty-five per cent of those assigned to the experimental condition were classified as compliers. The CACE analysis that took into account compliance status demonstrated that the magnitude of the incremental effect of systematic exposure on IBS symptoms was larger than the effect observed in an intention-to-treat analysis that ignored compliance status (d = 0.81 v. d = 0.44). Patients with university education showed more improvement during the exposure phase of the treatment. Pre-treatment patient characteristics did not predict compliance status.

Conclusions

The effect of systematic exposure on IBS symptoms is of substantial magnitude among those individuals who actually receive the intervention (CACE). Studying the subsample of individuals who discontinue treatment prematurely and tailoring interventions to improve compliance may increase overall improvement rates in ICBT for IBS.
Patterns of white matter microstructure in individuals at ultra-high-risk for psychosis: associations to level of functioning and clinical symptoms
Authors: Krakauer K. , Ebdrup B. H. , Glenthøj B. Y. , Raghava J. M. , Nordholm D. , Randers L. , Rostrup E. , Nordentoft M.
Published: May 2017

Background

Individuals at ultra-high-risk (UHR) for psychosis present with emerging symptoms and decline in functioning. Previous univariate analyses have indicated widespread white matter (WM) aberrations in multiple brain regions in UHR individuals and patients with schizophrenia. Using multivariate statistics, we investigated whole brain WM microstructure and associations between WM, clinical symptoms, and level of functioning in UHR individuals.

Methods

Forty-five UHR individuals and 45 matched healthy controls (HCs) underwent magnetic resonance diffusion tensor imaging (DTI) at 3 Tesla. UHR individuals were assessed with the Comprehensive Assessment of At-Risk Mental States, Scale for the Assessment of Negative Symptoms, and Social and Occupational Functioning Assessment Scale. Partial least-squares correlation analysis (PLSC) was used as statistical method.

Results

PLSC group comparisons revealed one significant latent variable (LV) accounting for 52% of the cross-block covariance. This LV indicated a pattern of lower fractional anisotropy (FA), axial diffusivity (AD), and mode of anisotropy (MO) concomitant with higher radial diffusivity (RD) in widespread brain regions in UHR individuals compared with HCs. Within UHR individuals, PLSC revealed five significant LVs associated with symptoms and level of functioning. The first LV accounted for 31% of the cross-block covariance and indicated a pattern where higher symptom score and lower level of functioning correlated to lower FA, AD, MO, and higher RD.

Conclusions

UHR individuals demonstrate complex brain patterns of WM abnormalities. Despite the subtle psychopathology of UHR individuals, aberrations in WM appear associated with positive and negative symptoms as well as level of functioning.
Robust adaptive control of door opening by a mobile rescue manipulator based on unknown-force-related constraints estimation
Authors: Ding Liang , Xia Kerui , Gao Haibo , Liu Guangjun , Deng Zongquan
Published: May 2017

This study focuses on a door-opening mobile manipulator operating in four phases (reaching the door, grasping the door handle, turning the door handle, and pulling the door). We use force/torque feedback-based control, achieving compliance of the mobile base when it comes into contact with the handle. A method is proposed for estimating the unknown force-related constraints from manipulator joint position measurements. A robust adaptive control strategy is developed for tracking the planned trajectory to open the door. Finally, a mobile manipulator opens a real door with a locked latch and unknown force-related constraints, demonstrating the validity of the proposed approach.
Utilization Criteria for Prehospital Ultrasound in a Canadian Critical Care Helicopter Emergency Medical Service: Determining Who Might Benefit
Authors: O’Dochartaigh Domhnall , Douma Matthew , Alexiu Chris , Ryan Shell , MacKenzie Mark
Published: May 2017

Introduction

Prehospital ultrasound (PHUS) assessments by physicians and non-physicians are performed on medical and trauma patients with increasing frequency. Prehospital ultrasound has been shown to be of benefit by supporting interventions.

Problem

Which patients may benefit from PHUS has not been clearly identified.

Methods

A multi-variable logistic regression analysis was performed on a previously created retrospective dataset of five years of physician- and non-physician-performed ultrasound scans in a Canadian critical care Helicopter Emergency Medical Service (HEMS). For separate medical and trauma patient groups, the a-priori outcome assessed was patient characteristics associated with the outcome variable of “PHUS-supported intervention.”

Results

Both models were assessed (Likelihood Ratio, Score, and Wald) as a good fit. For medical patients, the characteristics of heart rate (HR) and shock index (SI) were found to be most significant for an intervention being supported by PHUS. An extremely low HR was found to be the most significant (OR=15.86 [95% confidence interval (CI), 1.46-171.73]; P=.02). The higher the SI, the more likely that an intervention was supported by PHUS (SI 0.9 to<1.3: OR=9.15 [95% CI, 1.36-61.69]; P=.02; and SI 1.3+: OR=8.37 [95% CI, 0.69-101.66]; P=.09). For trauma patients, the characteristics of Prehospital Index (PHI) and SI were found to be most significant for PHUS support. The greatest effect was PHI, where increasing ORs were seen with increasing PHI (PHI 14-19: OR=13.36 [95% CI, 1.92-92.81]; P=.008; and PHI 20-24: OR=53.10 [95% CI, 4.83-583.86]; P=.001). Shock index was found to be similar, though, with lower impact and significance (SI 0.9 to<1.3: OR=9.11 [95% CI, 1.31-63.32]; P=.025; and SI 1.3+: OR=35.75 [95% CI, 2.51-509.81]; P=.008).

Conclusions:

In a critical care HEMS, markers of higher patient acuity in both medical and trauma patients were associated with occurrences when an intervention was supported by PHUS. Prospective study with in-hospital follow-up is required to confirm these hypothesis-generating results.

O’DochartaighD, DoumaM, AlexiuC, RyanS, MacKenzieM. Utilization criteria for prehospital ultrasound in a Canadian critical care Helicopter Emergency Medical Service: determining who might benefit. Prehosp Disaster Med. 2017;32(5):536–540.
Advanced Identification and Quantification of In-Bearing Minerals by Scanning Electron Microscope-Based Image Analysis
Authors: Bachmann Kai , Frenzel Max , Krause Joachim , Gutzmer Jens
Published: May 2017

The identification and accurate characterization of discrete grains of rare minerals in sulfide base-metal ores is usually a cumbersome procedure due to the small grain sizes (typically <10 μm) and complex mineral assemblages in the material. In this article, a new strategy for finding and identifying indium minerals, and quantifying their composition and abundance is presented, making use of mineral liberation analysis (MLA) and electron probe microanalysis (EPMA). The method was successfully applied to polymetallic massive sulfide ores from the Neves-Corvo deposit in Portugal. The presence of roquesite and sakuraiite could be systematically detected, their concentration quantified by MLA measurements, and their identity later confirmed by EPMA analyses. Based on these results, an almost complete indium deportment could be obtained for the studied samples. This validates the approach taken, combining automated mineralogy data with electron microprobe analysis. A similar approach could be used to find minerals of other common minor and trace elements in complex base-metal sulfide ores, for example Se, Ge, Sb, or Ag, thus permitting the targeted development of resource technologies suitable for by-product recovery.
Family members' experiences of integrated palliative advanced home and heart failure care: A qualitative study of the PREFER intervention
Authors: Alvariza Anette , Årestedt Kristofer , Boman Kurt , Brännström Margareta
Published: May 2017

Objective:

Chronic heart failure is a disease with high morbidity and symptom burden for patients, and it also places great demands on family members. Patients with heart failure should have access to palliative care for the purpose of improving quality of life for both patients and their families. In the PREFER randomized controlled intervention, patients with New York Heart Association classes III–IV heart failure received person-centered care with a multidisciplinary approach involving collaboration between specialists in palliative and heart failure care. The aim of the present study was to describe family members' experiences of the intervention, which integrated palliative advanced home and heart failure care.

Method:

This study had a qualitative descriptive design based on family member interviews. Altogether, 14 family members participated in semistructured interviews for evaluation after intervention completion. The data were analyzed by means of content analysis.

Results:

Family members expressed gratitude and happiness after witnessing the patient feeling better due to symptom relief and empowerment. They also felt relieved and less worried, as they were reassured that the patient was being cared for properly and that their own responsibility for care was shared with healthcare professionals. However, some family members also felt as though they were living in the shadow of severe illness, without receiving any support for themselves.

Significance of results:

Several benefits were found for family members from the PREFER intervention, and our results indicate the significance of integrated palliative advanced home and heart failure care. However, in order to improve this intervention, psychosocial professionals should be included on the intervention team and should contribute by paying closer attention and providing targeted support for family members.
Enhancing multifunctional benefits of living mulch in organic vegetable cropping systems
Authors: Canali S. , Diacono M. , Montemurro F. , Delate K.
Published: May 2017

Over the last several decades, agriculture in industrialized countries experienced a significant intensification as a result of the diffusion of mechanization, the widespread use of genetically improved genotypes, and the large-scale use of off-farm inputs, mainly in the form of fossil fuel energy and synthetic fertilizers and pesticides. Under the pressure of the growing agro-industrial sector, which has been oriented to promote models based on large volumes and long-distance supply chains, intensification was accompanied by progressive specialization of farms and cropping systems (Ratnadass et al., 2012). Indeed, the reduction of diversity at the field, farm, and territory level, a result of a low number of crops, the shortening of crop rotations, and a decrease in the number of cultivated genotypes, is becoming evident in many agro-environments in developed countries.
Romantic Relationship Quality in the Digital Age: A Study with Young Adults
Authors: Sánchez Virginia , Muñoz-Fernández Noelia , Ortega-Ruiz Rosario
Published: May 2017

Recent studies suggest that the online and offline behaviors young people display in romantic relationships are closely related. However, the differential effects of the dimensions of couple quality in the online context have not yet been explored in depth. The aim of this study was to explore online couple quality in young-adult relationships, and its association with romantic relationship satisfaction, also looking at effects of gender, age, and length of the relationship. 431 university students currently in a romantic relationship (68.2% females; mean age = 21.57) participated in this study. They completed different self-report measures to tap the online quality of their romantic relationships (online intimacy, control, jealousy, intrusiveness, cyberdating practices, and communication strategies) and level of satisfaction with those relationships. Results showed that participants more often reported online intimacy (Mmen = 2.49; Mwomen = 2.38) than the negative scales of online quality (mean ranged from .43 to 1.50), and all the online quality scales decreased with age (correlations ranged from –.12 to –.30) and relationship length (correlations ranged from –.02 to –.20). Linear regression analyses indicated that online intimacy (b = .32, p = .001) and intrusiveness (b = .11, p = .035) were positively related to relationship satisfaction, while cyberdating practices (b = –.20, p = .001) and communication strategies (b = –.34, p = .001) were negatively correlated with relationship satisfaction. Moreover, gender and relationship length moderated some of these associations. Results indicate that while online quality and relationship satisfaction are related, the impact of different online quality dimensions on relationship satisfaction differs depending on a participant’s sex, age, and relationship length.
Comprehensive population-wide analysis of Lynch syndrome in Iceland reveals founder mutations in MSH6 and PMS2
Authors: Haraldsdottir Sigurdis , Rafnar Thorunn , Frankel Wendy L. , Einarsdottir Sylvia , Sigurdsson Asgeir , Hampel Heather , Snaebjornsson Petur , Masson Gisli , Weng Daniel , Arngrimsson Reynir , Kehr Birte , Yilmaz Ahmet , Haraldsson Stefan , Sulem Patrick , Stefansson Tryggvi , Shields Peter G. , Sigurdsson Fridbjorn , Bekaii-Saab Tanios , Moller Pall H. , Steinarsdottir Margret , Alexiusdottir Kristin , Hitchins Megan , Pritchard Colin C. , de la Chapelle Albert , Jonasson Jon G. , Goldberg Richard M. , Stefansson Kari
Published: May 2017

Lynch syndrome, caused by germline mutations in the mismatch repair genes, is associated with increased cancer risk. Here using a large whole-genome sequencing data bank, cancer registry and colorectal tumour bank we determine the prevalence of Lynch syndrome, associated cancer risks and pathogenicity of several variants in the Icelandic population. We use colorectal cancer samples from 1,182 patients diagnosed between 2000–2009. One-hundred and thirty-two (11.2%) tumours are mismatch repair deficient per immunohistochemistry. Twenty-one (1.8%) have Lynch syndrome while 106 (9.0%) have somatic hypermethylation or mutations in the mismatch repair genes. The population prevalence of Lynch syndrome is 0.442%. We discover a translocation disruptingMLH1and three mutations inMSH6andPMS2that increase endometrial, colorectal, brain and ovarian cancer risk. We find thirteen mismatch repair variants of uncertain significance that are not associated with cancer risk. We find that founder mutations inMSH6andPMS2prevail in Iceland unlike most other populations.
Temporal and tissue-specific requirements for T-lymphocyte IL-6 signalling in obesity-associated inflammation and insulin resistance
Authors: Xu Elaine , Pereira Mafalda M. A. , Karakasilioti Ismene , Theurich Sebastian , Al-Maarri Mona , Rappl Gunter , Waisman Ari , Wunderlich F. Thomas , Brüning Jens C.
Published: May 2017

Low-grade inflammation links obesity to insulin resistance through the activation of tissue-infiltrating immune cells. Interleukin-6 (IL-6) is a crucial regulator of T cells and is increased in obesity. Here we report that classical IL-6 signalling in T cells promotes inflammation and insulin resistance during the first 8 weeks on a high-fat diet (HFD), but becomes dispensable at later stages (after 16 weeks). Mice with T cell-specific deficiency of IL-6 receptor-α (IL-6RαT-KO) exposed to a HFD display improved glucose tolerance, insulin sensitivity and inflammation in liver and EWAT after 8 weeks. However, after 16 weeks, insulin resistance in IL-6RαT-KO epididymal white adipose tissue (EWAT) is comparable to that of controls, whereas the inflammatory profile is significantly worse. This coincided with a shift from classical T cell IL-6 signalling at 8 weeks, to enhanced IL-6 trans-signalling at 16 weeks. Collectively, our studies reveal that IL-6 action in T cells through classical IL-6 signalling promotes inflammation and insulin resistance early during obesity development, which can be compensated for by enhanced IL-6 trans-signalling at later stages.
The comparative immunology of wild and laboratory mice, Mus musculus domesticus
Authors: Abolins Stephen , King Elizabeth C. , Lazarou Luke , Weldon Laura , Hughes Louise , Drescher Paul , Raynes John G. , Hafalla Julius C. R. , Viney Mark E. , Riley Eleanor M.
Published: May 2017

The laboratory mouse is the workhorse of immunology, used as a model of mammalian immune function, but how well immune responses of laboratory mice reflect those of free-living animals is unknown. Here we comprehensively characterize serological, cellular and functional immune parameters of wild mice and compare them with laboratory mice, finding that wild mouse cellular immune systems are, comparatively, in a highly activated (primed) state. Associations between immune parameters and infection suggest that high level pathogen exposure drives this activation. Moreover, wild mice have a population of highly activated myeloid cells not present in laboratory mice. By contrast,in vitrocytokine responses to pathogen-associated ligands are generally lower in cells from wild mice, probably reflecting the importance of maintaining immune homeostasis in the face of intense antigenic challenge in the wild. These data provide a comprehensive basis for validating (or not) laboratory mice as a useful and relevant immunological model system.
A domain in human EXOG converts apoptotic endonuclease to DNA-repair exonuclease
Authors: Szymanski Michal R. , Yu Wangsheng , Gmyrek Aleksandra M. , White Mark A. , Molineux Ian J. , Lee J. Ching , Yin Y. Whitney
Published: May 2017

Human EXOG (hEXOG) is a 5′-exonuclease that is crucial for mitochondrial DNA repair; the enzyme belongs to a nonspecific nuclease family that includes the apoptotic endonuclease EndoG. Here we report biochemical and structural studies of hEXOG, including structures in its apo form and in a complex with DNA at 1.81 and 1.85 Å resolution, respectively. A Wing domain, absent in other ββα-Me members, suppresses endonuclease activity, but confers on hEXOG a strong 5′-dsDNA exonuclease activity that precisely excises a dinucleotide using an intrinsic ‘tape-measure’. The symmetrical apo hEXOG homodimer becomes asymmetrical upon binding to DNA, providing a structural basis for how substrate DNA bound to one active site allosterically regulates the activity of the other. These properties of hEXOG suggest a pathway for mitochondrial BER that provides an optimal substrate for subsequent gap-filling synthesis by DNA polymerase γ.
Pointwise error estimates in localization microscopy
Authors: Lindén Martin , Ćurić Vladimir , Amselem Elias , Elf Johan
Published: May 2017

Pointwise localization of individual fluorophores is a critical step in super-resolution localization microscopy and single particle tracking. Although the methods are limited by the localization errors of individual fluorophores, the pointwise localization precision has so far been estimated using theoretical best case approximations that disregard, for example, motion blur, defocus effects and variations in fluorescence intensity. Here, we show that pointwise localization precision can be accurately estimated directly from imaging data using the Bayesian posterior density constrained by simple microscope properties. We further demonstrate that the estimated localization precision can be used to improve downstream quantitative analysis, such as estimation of diffusion constants and detection of changes in molecular motion patterns. Finally, the quality of actual point localizations in live cell super-resolution microscopy can be improved beyond the information theoretic lower bound for localization errors in individual images, by modelling the movement of fluorophores and accounting for their pointwise localization uncertainty.
Arabidopsis proteins with a transposon-related domain act in gene silencing
Authors: Ikeda Yoko , Pélissier Thierry , Bourguet Pierre , Becker Claude , Pouch-Pélissier Marie-Noëlle , Pogorelcnik Romain , Weingartner Magdalena , Weigel Detlef , Deragon Jean-Marc , Mathieu Olivier
Published: May 2017

Transposable elements (TEs) are prevalent in most eukaryotes, and host genomes have devised silencing strategies to rein in TE activity. One of these, transcriptional silencing, is generally associated with DNA methylation and short interfering RNAs. Here we show that the Arabidopsis genes MAIL1 and MAIN define an alternative silencing pathway independent of DNA methylation and short interfering RNAs. Mutants for MAIL1 or MAIN exhibit release of silencing and appear to show impaired condensation of pericentromeric heterochromatin. Phylogenetic analysis suggests not only that MAIL1 and MAIN encode a retrotransposon-related plant mobile domain, but also that host plant mobile domains were captured by DNA transposons during plant evolution. Our results reveal a role for Arabidopsis proteins with a transposon-related domain in gene silencing.
A sequential EMT-MET mechanism drives the differentiation of human embryonic stem cells towards hepatocytes
Authors: Li Qiuhong , Hutchins Andrew P. , Chen Yong , Li Shengbiao , Shan Yongli , Liao Baojian , Zheng Dejin , Shi Xi , Li Yinxiong , Chan Wai-Yee , Pan Guangjin , Wei Shicheng , Shu Xiaodong , Pei Duanqing
Published: May 2017

Reprogramming has been shown to involve EMT–MET; however, its role in cell differentiation is unclear. We report here that in vitro differentiation of hESCs to hepatic lineage undergoes a sequential EMT–MET with an obligatory intermediate mesenchymal phase. Gene expression analysis reveals that Activin A-induced formation of definitive endoderm (DE) accompanies a synchronous EMT mediated by autocrine TGFβ signalling followed by a MET process. Pharmacological inhibition of TGFβ signalling blocks the EMT as well as DE formation. We then identify SNAI1 as the key EMT transcriptional factor required for the specification of DE. Genetic ablation of SNAI1 in hESCs does not affect the maintenance of pluripotency or neural differentiation, but completely disrupts the formation of DE. These results reveal a critical mesenchymal phase during the acquisition of DE, highlighting a role for sequential EMT–METs in both differentiation and reprogramming.
Organ-specific transcriptome profiling of metabolic and pigment biosynthesis pathways in the floral ornamental progenitor species Anthurium amnicola Dressler
Authors: Suzuki Jon Y. , Amore Teresita D. , Calla Bernarda , Palmer Nathan A. , Scully Erin D. , Sattler Scott E. , Sarath Gautam , Lichty Joanne S. , Myers Roxana Y. , Keith Lisa M. , Matsumoto Tracie K. , Geib Scott M.
Published: May 2017

Anthurium amnicola Dressler possesses a number of desirable and novel ornamental traits such as a purple-colored upright spathe, profuse flowering, and floral scent, some of which have been introgressed into modern Anthurium cultivars. As a first step in identifying genes associated with these traits, the transcriptome from root, leaf, spathe, and spadix from an accession of A. amnicola was assembled, resulting in 28,019 putative transcripts representing 19,458 unigenes. Genes involved in pigmentation, including those for the metabolism of chlorophyll and the biosynthesis of carotenoids, phenylpropanoids, and flavonoids were identified. The expression levels of one MYB transcription factor was highly correlated with naringenin 3-dioxygenase (F3H) and dihydroflavonol-4-reductase (DFR) in leaves, whereas a bHLH transcription factor was highly correlated with flavonoid 3′-monooxygenase (F3′H) and a DFR in spathes, suggesting that these two transcription factors might regulate flavonoid and anthocyanin synthesis in A. amnicola. Gene sequence and expression data from four major organs of A. amnicola provide novel basal information for understanding the genetic bases of ornamental traits and the determinants and evolution of form and function in the Araceae.
A series of rat segmental forelimb ectopic implantation models
Authors: Zhou Xianyu , Luo Xusong , Gao Bowen , Liu Fei , Gu Chuan , Yu Qingxiong , Li Qingfeng , Zhu Hainan
Published: May 2017

Temporary ectopic implantation has been performed in clinical practice to salvage devascularized amputated tissues for delayed replantation purpose. In this study, we established a series of segmental forelimb ectopic implantation models in rats, including forelimb, forearm, forepaw, digit, and double forelimbs, to mimic the clinical context. Time of amputated limbs harvesting in donors and ectopic implantation process in recipients were recorded. Survival time and mortalities of recipients were also recorded. Sixty days after ectopic implantation, a full-field laser perfusion imager (FLPI) was used to detect the blood flow of amputated limbs and micro-CT imaging was used to examine bone morphological changes. Histological sections of amputated limbs were stained with hematoxylin and eosin to evaluate pathological changes. Implanted amputated limbs in all models achieved long term survival and there were no obvious morphological and histological changes were found according to results of micro-CT and histology study. Thus, a series of rat segmental forelimb temporary ectopic implantation models have been well established. To our knowledge, this is the first rodent animal model related to forelimb temporary ectopic implantation. These models might facilitate further research related to salvage, reconstruction and better aesthetic and functional outcome of upper extremity/digit in temporary ectopic implantation scenario.
Fabrication and application of indium-tin-oxide nanowire networks by polystyrene-assisted growth
Authors: Li Qiang , Yun Feng , Li Yufeng , Ding Wen , Zhang Ye
Published: May 2017

The fabrication and application of polystyrene (PS)-assisted ITO nanowire (NW) networks are reported. The ITO-NW networks are fabricated by means of electron-beam deposition via PS. This method has the advantages of low-temperature (~300 °C), low-cost, facile and efficient operation. The growth mechanism of PS-assisted ITO NWs was analyzed in detail, and the morphology of which could be regulated by the size of PS. X-ray diffraction and high-resolution transmission electron microscope show that the ITO NWs are close to an integral cubic lattice. The transmittance of ITO-NW networks layer is above 90% after 400 nm and the sheet resistance is ~200 Ω/□. When they applied on vertical blue and green LEDs, the light output power all has been improved ~30%. And, the resistive switching behaviors of ITO-NWs were measured and analyzed in Ag/ITO-NW networks/Al capacitor. The application of ITO-NW networks on special morphological devices was discussed. The PS-assisted ITO-NW networks show a strong researching and application value.
Influence of depression on genetic predisposition to type 2 diabetes in a multiethnic longitudinal study
Authors: Garasia Sophiya , Samaan Zainab , Gerstein Hertzel C. , Engert James C. , Mohan Viswanathan , Diaz Rafael , Anand Sonia S. , Meyre David
Published: May 2017

We assessed the association between depression status and prevalent and incident type 2 diabetes (T2D) as well as the interaction between depression and a genetic risk score (GS) based on 20 T2D single-nucleotide polymorphisms (SNPs) in a multi-ethnic longitudinal study. We studied 17,375 participants at risk for dysglycemia. All participants had genotypic and phenotypic data collected at baseline and 9,930 participants were followed-up for a median of 3.3 years. Normal glucose tolerance (NGT), impaired fasting glucose (IFG)/impaired glucose tolerance (IGT) and T2D statuses were determined using an oral glucose tolerance test and the 2003 American Diabetes Association criteria. Depression was diagnosed at baseline using Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM IV). Multivariate logistic regression models were adjusted for age, sex, ethnicity and body-mass index and an interaction term GS X depression was added to the model. After appropriate Bonferroni correction, no significant association between depression and T2D-related traits (IFG/IGT, T2D and dysglycemia), and no significant interaction between the GS and depression status was observed at baseline or follow-up. Our longitudinal data do not support an association between depression and abnormal glycemic status. Moreover, depression does not modify the effect of T2D predisposing gene variants.
Oxidative stress biomarkers are associated with visible clinical signs of a disease in frigatebird nestlings
Authors: Sebastiano Manrico , Eens Marcel , Abd Elgawad Hamada , Thoisy Benoît de , Lacoste Vincent , Pineau Kévin , Asard Han , Chastel Olivier , Costantini David
Published: May 2017

Infectious diseases are one of the most common threats for both domestic and wild animals, but little is known about the effects on the physiological condition and survival of wild animals. Here, we have tested for the first time in a wild vertebrate facing a viral disease possibly due to herpesvirus (i) whether nestlings with either low levels of oxidative damage or high levels of antioxidant protection are less susceptible to develop visible clinical signs, (ii) whether the disease is associated with the nestlings’ oxidative status, (iii) whether the association between the disease and oxidative status is similar between males and females (iv), and whether cloacal and tracheal swabs might be used to detect herpesvirus. To address our questions, we took advantage of a population of Magnificent frigatebirds (Fregata magnificens) whose nestlings have experienced high mortality rates in recent times. Our work shows that (i) blood lipid oxidative damage is associated with observable clinical signs and survival probabilities of nestling frigatebirds, and (ii) that high glutathione levels in red blood cells are associated with the emergence of visible clinical signs of the disease. Our work provides evidence that differences in the oxidative status of nestlings might underlie individual health and survival.
An ovine hepatorenal fibrocystic model of a Meckel-like syndrome associated with dysmorphic primary cilia and TMEM67 mutations
Authors: Stayner C. , Poole C. A. , McGlashan S. R. , Pilanthananond M. , Brauning R. , Markie D. , Lett B. , Slobbe L. , Chae A. , Johnstone A. C. , Jensen C. G. , McEwan J. C. , Dittmer K. , Parker K. , Wiles A. , Blackburne W. , Leichter A. , Leask M. , Pinnapureddy A. , Jennings M. , Horsfield J. A. , Walker R. J. , Eccles M. R.
Published: May 2017

Meckel syndrome (MKS) is an inherited autosomal recessive hepatorenal fibrocystic syndrome, caused by mutations in TMEM67, characterized by occipital encephalocoele, renal cysts, hepatic fibrosis, and polydactyly. Here we describe an ovine model of MKS, with kidney and liver abnormalities, without polydactyly or occipital encephalocoele. Homozygous missense p.(Ile681Asn; Ile687Ser) mutations identified in ovine TMEM67 were pathogenic in zebrafish phenotype rescue assays. Meckelin protein was expressed in affected and unaffected kidney epithelial cells by immunoblotting, and in primary cilia of lamb kidney cyst epithelial cells by immunofluorescence. In contrast to primary cilia of relatively consistent length and morphology in unaffected kidney cells, those of affected cyst-lining cells displayed a range of short and extremely long cilia, as well as abnormal morphologies, such as bulbous regions along the axoneme. Putative cilia fragments were also consistently located within the cyst luminal contents. The abnormal ciliary phenotype was further confirmed in cultured interstitial fibroblasts from affected kidneys. These primary cilia dysmorphologies and length control defects were significantly greater in affected cells compared to unaffected controls. In conclusion, we describe abnormalities involving primary cilia length and morphology in the first reported example of a large animal model of MKS, in which we have identified TMEM67 mutations.
Auditory Target and Novelty Processing in Patients with Unilateral Hippocampal Sclerosis: A Current-Source Density Study
Authors: Vilà-Balló Adrià , François Clément , Cucurell David , Miró Júlia , Falip Mercè , Juncadella Montserrat , Rodríguez-Fornells Antoni
Published: May 2017

The capacity to respond to novel events is crucial for adapting to the constantly changing environment. Here, we recorded 29-channel Event Related Brain Potentials (ERPs) during an active auditory novelty oddball paradigm and used for the first time Current Source Density-transformed Event Related Brain Potentials and associated time-frequency spectra to study target and novelty processing in a group of epileptic patients with unilateral damage of the hippocampus (N = 18) and in healthy matched control participants (N = 18). Importantly, we used Voxel-Based Morphometry to ensure that our group of patients had a focal unilateral damage restricted to the hippocampus and especially its medial part. We found a clear deficit for target processing at the behavioral level. In addition, compared to controls, our group of patients presented (i) a reduction of theta event-related synchronization (ERS) for targets and (ii) a reduction and delayed P3a source accompanied by reduced theta and low-beta ERS and alpha event-related synchronization (ERD) for novel stimuli. These results suggest that the integrity of the hippocampus might be crucial for the functioning of the complex cortico-subcortical network involved in the detection of novel and target stimuli.
Novel Chemically-modified DNAzyme targeting Integrin alpha-4 RNA transcript as a potential molecule to reduce inflammation in multiple sclerosis
Authors: Chakravarthy Madhuri , Aung-Htut May T. , Le Bao T. , Veedu Rakesh N.
Published: May 2017

Integrin alpha-4 (ITGA4) is a validated therapeutic target for multiple sclerosis (MS) and Natalizumab, an antibody targeting ITGA4 is currently approved for treating MS. However, there are severe side effects related to this therapy. In this study, we report the development of a novel DNAzyme that can efficiently cleave the ITGA4 transcript. We designed a range of DNAzyme candidates across various exons of ITGA4. RNV143, a 30mer arm-loop-arm type DNAzyme efficiently cleaved 84% of the ITGA4 mRNA in human primary fibroblasts. RNV143 was then systematically modified by increasing the arm lengths on both sides of the DNAzymes by one, two and three nucleotides each, and incorporating chemical modifications such as inverted-dT, phosphorothioate backbone and LNA-nucleotides. Increasing the arm length of DNAzyme RNV143 did not improve the efficiency however, an inverted-dT modification provided the most resistance to 3′ → 5′ exonuclease compared to other modifications tested. Our results show that RNV143A could be a potential therapeutic nucleic acid drug molecule towards the treatment for MS.
A robust in vitro model for trans-lymphatic endothelial migration
Authors: Xiong Yanbao , Brinkman C. Colin , Famulski Konrad S , Mongodin Emmanuel F. , Lord Colin J. , Hippen Keli L. , Blazar Bruce R. , Bromberg Jonathan S.
Published: May 2017

Trans-endothelial migration (TEM) is essential for leukocyte circulation. While much is known about trans-blood endothelial migration, far less is known about trans-lymphatic endothelial migration. We established anin vitrosystem to evaluate lymphatic TEM for various cell types across primary mouse and human lymphatic endothelial cells (LEC), and validated the model for the murine LEC cell line SVEC4-10. T cells exhibited enhanced unidirectional migration from the basal (abluminal) to the apical (luminal) surface across LEC, whereas for blood endothelial cells (BEC) they migrated similarly in both directions. This preferential, vectorial migration was chemotactic toward many different chemoattractants and dose-dependent. Stromal protein fibers, interstitial type fluid flow, distribution of chemokines in the stromal layer, and inflammatory cytokines influenced LEC phenotype and leukocyte TEM. Activated and memory CD4 T cells, macrophages, and dendritic cell (DC) showed chemoattractantΔdriven vectorial migration, while CD8 T cell migration across LEC was not. The system was further validated for studying cancer cell transmigration across lymphatic endothelium. This model for lymphatic TEM for various migrating and endothelial cell types possesses the capacity to be high-throughput, highly reproducible and integrate the complexities of lymphatic biology, stromal variability, chemoattractant distribution, and fluid flow.
Entropy of radiation: the unseen side of light
Authors: Delgado-Bonal Alfonso
Published: May 2017

Despite the fact that 2015 was the international year of light, no mention was made of the fact that radiation contains entropy as well as energy, with different spectral distributions. Whereas the energy function has been vastly studied, the radiation entropy distribution has not been analysed at the same speed. The Mode of the energy distribution is well known –Wien’s law– and Planck’s law has been analytically integrated recently, but no similar advances have been made for the entropy. This paper focuses on the characterization of the entropy of radiation distribution from an statistical perspective, obtaining a Wien’s like law for the Mode and integrating the entropy for the Median and the Mean in polylogarithms, and calculating the Variance, Skewness and Kurtosis of the function. Once these features are known, the increasing importance of radiation entropy analysis is evidenced in three different interdisciplinary applications: defining and determining the second law Photosynthetically Active Radiation (PAR) region efficiency, measuring the entropy production in the Earth’s atmosphere, and showing how human vision evolution was driven by the entropy content in radiation.
The invasive Neisseria meningitidis MenC CC103 from Brazil is characterized by an accessory gene repertoire
Authors: Marin Michel Abanto , Fonseca Erica , Encinas Fernando , Freitas Fernanda , Camargo Dhian Almeida , Coimbra Roney Santos , de Filippis Ivano , Vicente Ana Carolina
Published: May 2017

Neisseria meningitidis infections are a major issue for global health. The invasive MenC ST-103 clonal complex (CC103) has been the most prevalent in meningococcal outbreaks in Brazil, occurring also in several countries worldwide. Here we have analysed the population structure and accessory genome of MenC CC103 strains from a global perspective. An in-depth phylogenomic analysis revealed a lineage of N. meningitidis causing meningitis in Brazil and the United Kingdom. This lineage was also characterized as harbouring a particular accessory genome composed of CRISPR/Cas and restriction modification systems. This lineage was also characterized by a genomic island resembling an integrative and conjugative element. This island carried genes potentially associated with virulence and fitness. We propose this accessory gene repertoire could be contributing to the spatial-temporal persistence of the invasive MenC CC103 lineage.