bluuebunny/crossref_metadata_2025 huggingface dataset:
Methylenetetrahydrofolate Dehydrogenase 1 Polymorphisms Modify the Associations of Plasma Glycine and Serine With Risk of Acute Myocardial Infarction in Patients With Stable Angina Pectoris in WENBIT (Western Norway B Vitamin Intervention Trial)
Authors: Ding Yunpeng , Pedersen Eva R. , Svingen Gard F.T. , Helgeland Øyvind , Gregory Jesse F. , Løland Kjetil H. , Meyer Klaus , Tell Grethe S. , Ueland Per M. , Nygård Ottar K.
Published: November 2016

Background—

Serine and glycine interconversion and methylenetetrahydrofolate dehydrogenase 1 (MTHFD1)–mediated 1-carbon transfer are the major sources of methyl groups for 1-carbon metabolism. Recently, plasma glycine and a common polymorphism in MTHFD1 have been associated with risk of acute myocardial infarction (AMI). It is, therefore, of interest to explore if these 2 pathways interact in relation to AMI.

Methods and Results—

A total of 2571 participants in the WENBIT (Western Norway B Vitamin Intervention Trial) undergoing coronary angiography for stable angina pectoris were studied. Associations of plasma serine and glycine concentrations with risk of AMI across 2 common and functional MTHFD1 polymorphisms (
rs2236225
and
rs1076991
) were explored in Cox regression models. During a median follow-up of 4.7 years, 212 patients (8.2%) experienced an AMI. In age- and sex-adjusted analyses, plasma glycine (
P
<0.01), but not serine (
P
=0.52), showed an overall association with AMI. However, interactions of MTHFD1
rs2236225
polymorphism with both plasma serine and glycine were observed (
P
interaction
=0.03 for both). Low plasma serine and glycine were associated with an increased risk of AMI among patients carrying the
rs2236225
minor A allele. Similarly, low plasma glycine showed stronger risk relationship with AMI in the
rs1076991
CC genotype carriers but weaker associations in patients carrying the minor T allele (
P
interaction
=0.02).

Conclusions—

Our results showed that 2 common and functional polymorphisms in the
MTHFD1
gene modulate the risk associations of plasma serine and glycine with AMI. These findings emphasize the possible role of the MTHFD1 in regulating serine and glycine metabolism in relation to atherosclerotic complications.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique Identifier: NCT00354081.
Incident Type 2 Myocardial Infarction in a Cohort of Patients Undergoing Coronary or Peripheral Arterial Angiography
Authors: Gaggin Hanna K. , Liu Yuyin , Lyass Asya , van Kimmenade Roland R. J. , Motiwala Shweta R. , Kelly Noreen P. , Mallick Aditi , Gandhi Parul U. , Ibrahim Nasrien E. , Simon Mandy L. , Bhardwaj Anju , Belcher Arianna M. , Harisiades Jamie E. , Massaro Joseph M. , D’Agostino Ralph B. , Januzzi James L.
Published: November 2016

Background:

Despite growing recognition of type 2 myocardial infarction (T2MI; related to supply/demand mismatch), little is known about its risk factors or its association with outcome.

Methods:

A single-center cohort of patients undergoing coronary or peripheral angiography with or without intervention was prospectively enrolled and followed for incident type 1 and T2MI, and major adverse cardiovascular events (MACE, a composite of all-cause death, nonfatal myocardial infarction [MI], heart failure, stroke, transient ischemic attack, peripheral arterial complication, and cardiac arrhythmia), as well. T2MI was adjudicated using criteria from the Third Universal Definition of MI. Baseline characteristics, blood samples, and angiography information were obtained. Major end points subsequent to first MI were assessed using landmark analyses to compare the rates of first events only where everyone with a prior history of any MACE before MI were censored and adjusted for follow-up times. Cox proportional hazard models were used for time-to-event analyses with age and sex forced into all models and additional covariates evaluated by using the stepwise option for the selection.

Results:

One thousand two hundred fifty-one patients were enrolled and followed for a median of 3.4 years. Of these patients, 152 (12.2%) had T2MI during follow-up; T2MI was frequently recurrent. Multivariable predictors of T2MI were older age, lower systolic blood pressure, history of coronary artery disease, heart failure, chronic obstructive pulmonary disease, diabetes mellitus, nitrate use, and elevated concentrations of glucose, N-terminal pro-B type natriuretic peptide, and cystatin C. Patients with T2MI had higher rates of subsequent adverse events than those without T2MI (per 100 person-years: MACE, 53.7 versus 21.1,
P
<0.001; all-cause death, 23.3 versus 3.3,
P
<0.001; cardiovascular death, 17.5 versus 2.6,
P
<0.001; heart failure events, 22.4 versus 7.4,
P
<0.001); these rates are similar to those seen in patients with type 1 MI. Incident diagnosis of T2MI strongly predicted risk for subsequent MACE (adjusted hazard ratio, 1.90; 95% confidence interval, 1.46–2.48;
P
<0.001), all-cause death (adjusted hazard ratio, 2.96; 95% confidence interval, 2.01–4.36;
P
<0.001), and cardiovascular death (adjusted hazard ratio, 2.16; 95% confidence interval, 1.36–3.43;
P
=0.001).

Conclusions:

T2MI is common and associated with poor prognosis. Studies evaluating treatment strategies for management of T2MI are needed.

Clinical Trial Registration:

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT00842868.
Negation and Modality
Authors: Hedin Eva
Published: November 2016

This paper deals with the question of negation and mood in Modern Greek verb complementation where there is a choice between an indicative and a subjunctive complement, in particular those with the verb pistévo (πιστεύω) ‘think, believe’, but also nomízo (νομίζω) ‘think, believe’, kséro (ξέρω) ‘know’, thimáme (θυμάμαι) ‘remember’, vlépo (βλέπω) ‘see’, akúo (ακούω) ‘hear’, and vrísko (βρίσκω) ‘find’. It presents the result of an empirical study of pistévo, based on an investigation undertaken in the Hellenic National Corpus (HNC) of sentential complements following pistévo. The factor of negation in the matrix is investigated along with two other factors, hypothesized to be of interest, namely first person singular of the present tense in the matrix and second person (singular and plural) in the complement. As was expected, neither any of the three factors individually or any combination of the three can be considered decisive for the choice of mood. What seems to be certain, however, is that the combination of all three constitutes a context that favours the subjunctive and in one case actually seems to exclude an indicative complement, namely when the illocutionary force of the utterance is that of a question, more or less rhetorically eliciting feedback. It thus does not seem to be the presence of the negation, nor any other syntactic factor, that actually triggers the subjunctive with this verb in some contexts, but a particular speech situation (where the three investigated factors are typically present). That is, the prerequisite is not syntactic, but pragmatic.
Au sujet d’un mot prétendûment introuvable dans les dictionnaires
Authors: Rāġib Yūsuf
Published: November 2016

The existence of the word ǧaytar which nominates small-sized persons has been formally refuted by Werner Diem simply because he did not find it in any dictionary. Yet this term is attested in some medieval Arabic lexicography works.

L’existence du mot ǧaytar qui désigne les personnes de petite taille a été formellement réfutée par Werner Diem simplement parce qu’il ne l’a trouvé dans aucun dictionnaire. Le terme est pourtant bien attesté dans des ouvrages de lexicographie arabes médiévaux.

This article is in French.
Typhoon Nina and the August 1975 Flood over Central China
Authors: Yang Long , Liu Maofeng , Smith James A. , Tian Fuqiang
Published: November 2016

The August 1975 flood in central China was one of the most destructive floods in history. Catastrophic flooding was the product of extreme rainfall from Typhoon Nina over a 3-day period from 5 to 7 August 1975. Despite the prominence of the August 1975 flood, relatively little is known about the evolution of rainfall responsible for the flood. Details of extreme rainfall and flooding for the August 1975 event in central China are examined based on empirical analyses of rainfall and streamflow measurements and based on downscaling simulations using the Weather Research and Forecasting (WRF) Model, driven by Twentieth Century Reanalysis (20CR) fields. Key hydrometeorological features of the flood event are placed in a climatological context through hydroclimatological analyses of 20CR fields. Results point to the complex evolution of rainfall over the 3-day period with distinctive periods of storm structure controlling rainfall distribution in the flood region. Blocking plays a central role in controlling anomalous storm motion of Typhoon Nina and extreme duration of heavy rainfall. Interaction of Typhoon Nina with a second tropical depression played a central role in creating a zone of anomalously large water vapor transport, a central feature of heavy rainfall during the critical storm period on 7 August. Analyses based on the quasigeostrophic omega equation identified the predominant role of warm air advection for synoptic-scale vertical motion. Back-trajectory analyses using a Lagrangian parcel tracking algorithm are used to assess and quantify water vapor transport for the flood. The analytical framework developed in this study is designed to improve hydrometeorological approaches for flood-control design.
Case Studies of a MODIS-Based Potential Evapotranspiration Input to the Sacramento Soil Moisture Accounting Model
Authors: Bowman Angela L. , Franz Kristie J. , Hogue Terri S.
Published: November 2016

A satellite-based potential evapotranspiration (PET) estimate derived from Moderate Resolution Imaging Spectroradiometer (MODIS) observations was tested for input to the spatially lumped and gridded Sacramento Soil Moisture Accounting (SAC-SMA) model. The 15 forecast points within the National Weather Service (NWS) North Central River Forecast Center (NCRFC) forecasting region were the basis for this analysis. Through a series of case studies, the MODIS-derived PET estimate (M-PET) was evaluated for input to the SAC-SMA model by comparing streamflow simulations with those from traditional SAC-SMA evapotranspiration (ET) demand. Two prior studies have evaluated the M-PET data 1) to compute new long-term average ET demand values and 2) to input a time series (i.e., daily time-varying PET) to the NWS Hydrology Laboratory–Research Distributed Hydrologic Model (HL-RDHM), a spatially distributed version of the SAC-SMA model. This current paper presents results from a third test in which the M-PET time series is input to the lumped SAC-SMA model. In all cases, evaluation is between the M-PET data and the long-term average values used by the NWS. Similar to prior studies, results of the current analysis are mixed with improved model evaluation statistics for 4 of 15 basins tested. Of the three cases, using the time-varying M-PET as input to the distributed SAC-SMA model led to the most promising results, with model simulations that are at least as good as those when using the SAC-SMA ET demand. Analyses of the model-simulated ET suggest that the time-varying M-PET input may produce a more physically realistic representation of ET processes in both the lumped and distributed versions of the SAC-SMA model.
The internal relationships of the dimensions of democracy: The relevance of trade-offs for measuring the quality of democracy
Authors: Lauth Hans-Joachim
Published: November 2016

Definitions of democracy almost always refer to dimensions. An important question arises about the internal relationships between them. This article presents arguments in favor of the ideas of mutual reinforcement as well as of intrinsic tensions or trade-offs. A well-known example of these kinds of trade-offs is the complex relationship between liberty and equality. Surprisingly, trade-offs are not reported when measuring democracy. The article identifies the basic methodological problem and develops a new strategy for evaluating the indicators which makes trade-offs visible in the empirical research. The proposal combines two measurement strategies, arguing that in addition to established measurements of democracy, a further measurement to assess trade-offs should be employed.
Risking value theory in the political economy of finance and nature
Authors: Christophers Brett
Published: November 2016

Responding to calls for geographers to re-engage value theory in examining the political economy of nature, this article questions the capacity of such theory to grasp nature’s growing representation, valuation and exchange through financial instruments ranging from catastrophe bonds to carbon credits and from green bonds to index insurance. Drawing on and extending recent debates in political economy, it submits that understanding the contemporary nexus of climate change and financial innovation requires incorporating risk into value theory – it requires, that is, ‘risking’ value theory. Parsing the literature on climate finance, the article demonstrates how such risking might be achieved.
Health and Rural Context Among Victims of Partner Abuse: Does Justice Matter?
Authors: Walker Robert , Logan T. K.
Published: November 2016

Research typically compartmentalizes health and justice as separate areas of study. However, the current health literature on inequality suggests the two concepts are overlapping. For victims of partner violence, procedural justice (defined in this article as access to protective orders and enforcement of protective orders) potentially provides a step toward improved health and well-being by improving safety. There has been limited research examining these factors in rural compared with urban areas. This study examines the impact of procedural justice on health and well-being through interviews with rural and urban women 6 months prior to, and 6 months after, obtaining a protective order. Consistent with other literature, rural women who were victims of partner violence reported worse health, higher stress, and higher Stress-Related Consequences Scale scores compared with urban women. Women’s reported health consequences were related to the interaction of perceived ineffectiveness of the protective orders and their rural/urban environment. Thus, the perceived effectiveness of procedural justice may play an important role in alleviating victims’ safety, health, and well-being, all of which are components of contemporary views of justice.
Do debts lead to disability pension? Evidence from a 15-year follow-up of 54,000 Finnish men and women
Authors: Blomgren Jenni , Maunula Nico , Hiilamo Heikki
Published: November 2016

While over-indebtedness has emerged as a new social risk among Europeans as a consequence of economic recessions, its associations with health and disability are poorly understood. This study utilises longitudinal, register-based data to assess the associations of over-indebtedness with disability retirement. Severely over-indebted people were identified from the Finnish credit information register. For each over-indebted person, one matched control was retrieved from the population register (total N: 54,494). Register data on socio-demographics, health-related factors and pensions were used to analyse the incidence of disability pensions due to different diagnoses among over-indebted people and their controls during the period 1995–2009 using Cox regression analysis. The analyses showed that over-indebtedness was strongly associated with the risk of disability retirement in all diagnostic groups. The associations were stronger among women than among men. The adverse effects of over-indebtedness on health and disability should be acknowledged. In addition to standard socio-demographic indicators, debtor status may add to our knowledge of the predictors of poor health. Policymakers should adopt measures to prevent over-indebtedness and to overcome its harmful effects.
Psychometric properties of the Chinese version of the Affective Style Questionnaire and its role as a moderator of the relationship between stress and negative affect
Authors: Wang Jianping , Xu Wei , Fu Zhongfang , Yu Wei , He Li , Sun Ling , He Jiao , Hofmann Stefan G.
Published: November 2016

The Affective Style Questionnaire is a self-report instrument for assessing affective style. Study 1 investigated the psychometric properties of the Chinese Affective Style Questionnaire in a sample of 459 Chinese participants. The confirmatory factor analysis supported a three-factor structure. Study 1 indicated that the Chinese Affective Style Questionnaire can be used as a simple, reliable, and valid scale for measuring individual differences in affective style. Study 2 examined the moderating role of different affective styles in the relationship between stress and negative affect. Concealing and tolerating moderated the relationship between stress and anxiety, and adjusting moderated the relationship between stress and depression.
Experimental study on seismic performance of reinforced concrete column retrofitted by asymmetric increased single lateral section
Authors: Liu Chunyang , Ma Hua , Chen Lei , Li Zhenbao , Yang Dabin
Published: November 2016

In this article, a new retrofit method that the frame column is strengthened by asymmetric increased single lateral concrete section is proposed. The new added section could be ordinary reinforced concrete, bonded prestressed concrete, or unbonded prestressed concrete. The new added section could be connected with the column through anchor rebars, or prefabricated first, then be connected to the column through high strength bolts. The low cyclic reversed load experiment has been launched on understanding the seismic performance of one unretrofit specimen and six retrofitted specimens. The experiment has considered four main factors that is loading direction, material adopted on the new added section, different orders of unification of the retrofit column, and the process of prestress applying. Based on the experiment study, the characteristics including the failure mode, hysteresis loops behavior, bearing capacity, ductility, stiffness degradation, and energy dissipation ability are demonstrated. The bearing capacity calculation method of the retrofit column under compression–bending action is established. The calculation results and the experiment results show good agreement. Some suggestions for seismic design of the retrofit column are proposed. The experimental results show that the retrofitted column has good seismic performance and good retrofit effects. The research results could be references to the practical engineering design works.
Biomechanical Indices for Rupture Risk Estimation in Abdominal Aortic Aneurysms
Authors: Leemans Eva L. , Willems Tineke P. , van der Laan Maarten J. , Slump Cornelis H. , Zeebregts Clark J.
Published: November 2016

Purpose: To review the use of biomechanical indices for the estimation of abdominal aortic aneurysm (AAA) rupture risk, emphasizing their potential use in a clinical setting. Methods: A search of the PubMed, Embase, Scopus, and Compendex databases was made up to June 2015 to identify articles involving biomechanical analysis of AAA rupture risk. Outcome variables [aneurysm diameter, peak wall stress (PWS), peak wall shear stress (PWSS), wall strain, peak wall rupture index (PWRI), and wall stiffness] were compared for asymptomatic intact AAAs vs symptomatic or ruptured AAAs. For quantitative analysis of the pooled data, a random effects model was used to calculate the standard mean differences (SMDs) with the 95% confidence interval (CI) for the biomechanical indices. Results: The initial database searches yielded 1894 independent articles of which 19 were included in the analysis. The PWS was significantly higher in the symptomatic/ruptured group, with a SMD of 1.11 (95% CI 0.93 to 1.26, p<0.001). Likewise, the PWRI was significantly higher in the ruptured or symptomatic group, with a SMD of 1.15 (95% CI 0.30 to 2.01, p=0.008). After adjustment for the aneurysm diameter, the PWS remained higher in the ruptured or symptomatic group, with a SMD of 0.85 (95% CI 0.46 to 1.23, p<0.001). Less is known of the wall shear stress and wall strain indices, as too few studies were available for analysis. Conclusion: Biomechanical indices are a promising tool in the assessment of AAA rupture risk as they incorporate several factors, including geometry, tissue properties, and patient-specific risk factors. However, clinical implementation of biomechanical AAA assessment remains a challenge owing to a lack of standardization.
What do we need to consider when planning, implementing and researching the use of alternatives to face-to-face consultations in primary healthcare?
Authors: Atherton Helen , Ziebland Sue
Published: November 2016

Objectives

Communications technologies are variably utilised in healthcare. Policymakers globally have espoused the potential benefits of alternatives to face-to-face consultations, but research is in its infancy. The aim of this essay is to provide thinking tools for policymakers, practitioners and researchers who are involved in planning, implementing and evaluating alternative forms of consultation in primary care.

Methods

We draw on preparations for a focussed ethnographic study being conducted in eight general practice settings in the UK, knowledge of the literature, qualitative social science and Cochrane reviews. In this essay we consider different types of patients, and also reflect on how the work, practice and professional identities of different members of staff in primary care might be affected.

Results

Elements of practice are inevitably lost when consultations are no longer face-to-face, and we know little about the impact on core aspects of the primary care relationship. Resistance to change is normal and concerns about the introduction of alternative methods of consultation are often expressed using proxy reasons; for example, concerns about patient safety. Any planning or research in the field of new technologies should be attuned to the potential for unintended consequences.

Conclusions

Implementation of alternatives to the face-to-face consultation is more likely to succeed if approached as co-designed initiatives that start with the least controversial and most promising changes for the practice. Researchers and evaluators should explore actual experiences of the different consultation types amongst patients and the primary care team rather than hypothetical perspectives.
How I treat FLT3-mutated AML
Authors: Pratz Keith W. , Levis Mark
Published: November 2016

FLT3-mutated acute myeloid leukemia (AML), despite not being recognized as a distinct entity in the World Health Organization (WHO) classification system, is readily recognized as a particular challenge by clinical specialists who treat acute leukemia. This is especially true with regards to the patients harboring the most common type of FLT3 mutation, the internal tandem duplication (FLT3-ITD) mutation. Here we present 4 patient cases from our institution and discuss how our management reflects what we have learned about this subtype of the disease. We also reflect on how we anticipate the management might change in the near future, with the emergence of clinically useful tyrosine kinase inhibitors.
A statistical model for the analysis of beta values in DNA methylation studies
Authors: Weinhold Leonie , Wahl Simone , Pechlivanis Sonali , Hoffmann Per , Schmid Matthias
Published: November 2016

Background

The analysis of DNA methylation is a key component in the development of personalized treatment approaches. A common way to measure DNA methylation is the calculation of beta values, which are bounded variables of the form M/(M+U) that are generated by Illumina’s 450k BeadChip array. The statistical analysis of beta values is considered to be challenging, as traditional methods for the analysis of bounded variables, such as M-value regression and beta regression, are based on regularity assumptions that are often too strong to adequately describe the distribution of beta values.

Results

We develop a statistical model for the analysis of beta values that is derived from a bivariate gamma distribution for the signal intensities M and U. By allowing for possible correlations between M and U, the proposed model explicitly takes into account the data-generating process underlying the calculation of beta values. Using simulated data and a real sample of DNA methylation data from the Heinz Nixdorf Recall cohort study, we demonstrate that the proposed model fits our data significantly better than beta regression and M-value regression.

Conclusion

The proposed model contributes to an improved identification of associations between beta values and covariates such as clinical variables and lifestyle factors in epigenome-wide association studies. It is as easy to apply to a sample of beta values as beta regression and M-value regression.
Intramolecular interactions that control voltage sensitivity in the jShak1 potassium channel from Polyorchis penicillatus
Authors: Sharmin Nazlee , Gallin Warren J.
Published: November 2016

Voltage-gated potassium ion (Kv) channel proteins respond to changes in membrane potential by changing the probability of K+ flux through an ion-selective pore. Kv channels from different paralogous and orthologous families have widely varying V50 values. The voltage-sensing transmembrane helices (S4) of different channels contain 4-7 basic residues that are responsible for transducing changes in transmembrane potential into the energy required to shift the equilibrium between the open- and closed-channel conformations. These residues also form electrostatic interaction networks with acidic residues in the S2 and S3 helices that stabilize the open and the closed states to different extents. The length and composition of the extracellular loop connecting the S3 and S4 helices (S3-S4 loop) also shape the voltage response. We describe mutagenesis experiments on the jellyfish (Polyorchis penicillatus) Kv1 family jShak1 channel to evaluate how variants of the S3-S4 loop affect the voltage sensitivity of this channel. In combination with changes in the length and composition of the S3-S4 linker we mutated a residue on the S2 helix (N227) that in most Kv1 family channels is glutamate (E226 in mouse Kv1.2, E283 in D. melanogaster Shaker). Some individual loop replacement mutants cause major changes in voltage sensitivity, depending on a combination of length and composition. Pairwise combinations of the loop mutations and the S2 mutations interact to yield quantitatively distinct, non-additive changes in voltage sensitivity. We conclude that the S3-S4 loop interacts energetically with the residue at position N227 during the transitions between open and closed states of the channel.
Effects of prolonged anoxia on electrical activity of the heart in Crucian carp (Carassius carassius)
Authors: Tikkanen Elisa , Haverinen Jaakko , Egginton Stuart , Hassinen Minna , Vornanen Matti
Published: November 2016

The effects of sustained anoxia on cardiac electrical excitability were examined in the anoxia-tolerant Crucian carp (Carassius carassius). The electrocardiogram (ECG) and expression of excitation-contraction coupling genes were studied in fish acclimatised to normoxia in summer (+18°C) or winter (+2°C), and in winter fish after 1, 3 and 6 weeks of anoxia. Anoxia induced a sustained bradycardia from a heart rate of 10.3±0.77 to 4.1±0.29 bpm (P<0.05) after 5 weeks, and heart rate slowly recovered to control levels when oxygen was restored. Heart rate variability greatly increased under anoxia, and completely recovered under re-oxygenation. The RT interval increased from 2.8±0.34 s in normoxia to 5.8±0.44 s under anoxia (P<0.05), which reflects a doubling of the ventricular action potential (AP) duration. Acclimatisation to winter induced extensive changes in gene expression relative to summer-acclimatised fish, including depression in those coding for the sarcoplasmic reticulum calcium pump (Serca2-q2) and ATP-sensitive K+ channels (Kir6.2) (P<0.05). Genes of delayed rectifier K+ (kcnh6) and Ca2+ channels (cacna1c) were up-regulated in winter fish (P<0.05). In contrast, the additional challenge of anoxia caused only minor changes in gene expression, e.g. depressed expression of Kir2.2b K+ channel gene (kcnj12b), whereas expression of Ca2+ (cacna1a, -c and –g) and Na+ channel genes (scn4a and scn5a) were not affected. These data suggest that low temperature pre-conditions the Crucian carp heart for winter anoxia, whereas sustained anoxic bradycardia and prolongation of AP duration are directly induced by oxygen shortage without major changes in gene expression.
Influence of two bulge loops on the stability of RNA duplexes
Authors: Crowther Claire V. , Jones Laura E. , Morelli Jessica N. , Mastrogiacomo Eric M. , Porterfield Claire , Kent Jessica L. , Serra Martin J.
Published: November 2016

Fifty-three RNA duplexes containing two single nucleotide bulge loops were optically melted in 1 M NaCl in order to determine the thermodynamic parameters ΔH°, ΔS°, ΔG°37, and TM for each duplex. Because of the large number of possible combinations and lack of sequence effects observed previously, we limited our initial investigation to adenosine bulges, the most common naturally occurring bulge. For example, the following duplexes were investigated: 5′GGCAXYAGGC/3′CCG YX CCG, 5′GGCAXY GCC/3′CCG YXACGG, and 5′GGC XYAGCC/3′CCGAYX CGG. The identity of XY (where XY are Watson–Crick base pairs) and the total number of base pairs in the terminal and central stems were varied. As observed for duplexes with a single bulge loop, the effect of the two bulge loops on duplex stability is primarily influenced by non-nearest neighbor interactions. In particular, the stability of the stems influences the destabilization of the duplex by the inserted bulge loops. The model proposed to predict the influence of multiple bulge loops on duplex stability suggests that the destabilization of each bulge is related to the stability of the adjacent stems. A database of RNA secondary structures was examined to determine the naturally occurring abundance of duplexes containing multiple bulge loops. Of the 2000 examples found in the database, over 65% of the two bulge loops occur within 3 base pairs of each other. A database of RNA three-dimensional structures was examined to determine the structure of duplexes containing two single nucleotide bulge loops. The structures of the bulge loops are described.
Identification of urinary exosomal noncoding RNAs as novel biomarkers in chronic kidney disease
Authors: Khurana Rimpi , Ranches Glory , Schafferer Simon , Lukasser Melanie , Rudnicki Michael , Mayer Gert , Hüttenhofer Alexander
Published: November 2016

In chronic kidney disease (CKD), the decline in the glomerular filtration rate is associated with increased morbidity and mortality and thus poses a major challenge for healthcare systems. While the contribution of tissue-derived miRNAs and mRNAs to CKD progression has been extensively studied, little is known about the role of urinary exosomes and their association with CKD. Exosomes are small, membrane-derived endocytic vesicles that contribute to cell-to-cell communication and are present in various body fluids, such as blood or urine. Next-generation sequencing approaches have revealed that exosomes are enriched in noncoding RNAs and thus exhibit great potential for sensitive nucleic acid biomarkers in various human diseases. Therefore, in this study we aimed to identify urinary exosomal ncRNAs as novel biomarkers for diagnosis of CKD. Since up to now most approaches have focused on the class of miRNAs, we extended our analysis to several other noncoding RNA classes, such as tRNAs, tRNA fragments (tRFs), mitochondrial tRNAs, or lincRNAs. For their computational identification from RNA-seq data, we developed a novel computational pipeline, designated as ncRNASeqScan. By these analyses, in CKD patients we identified 30 differentially expressed ncRNAs, derived from urinary exosomes, as suitable biomarkers for early diagnosis. Thereby, miRNA-181a appeared as the most robust and stable potential biomarker, being significantly decreased by about 200-fold in exosomes of CKD patients compared to healthy controls. Using a cell culture system for CKD indicated that urinary exosomes might indeed originate from renal proximal tubular epithelial cells.
Bringing your tools to CyVerse Discovery Environment using Docker
Authors: Devisetty Upendra Kumar , Kennedy Kathleen , Sarando Paul , Merchant Nirav , Lyons Eric
Published: November 2016

Docker has become a very popular container-based virtualization platform for software distribution that has revolutionized the way in which scientific software and software dependencies (software stacks) can be packaged, distributed, and deployed. Docker makes the complex and time-consuming installation procedures needed for scientific software a one-time process. Because it enables platform-independent installation, versioning of software environments, and easy redeployment and reproducibility, Docker is an ideal candidate for the deployment of identical software stacks on different compute environments such as XSEDE and Amazon AWS. Cyverse's Discovery Environment also uses Docker for integrating its powerful, community-recommended software tools into CyVerse's production environment for public use. This paper will help users bring their tools into CyVerse DE which will not only allows users to integrate their tools with relative ease compared to the earlier method of tool deployment in DE but also help users to share their apps with collaborators and also release them for public use.
Comparative analysis of economic efficiency of Polish and German listed companies
Authors: Sajnóg Artur
Published: November 2016

The main subject of theoretical-empirical study presented in this paper is economic efficiency of companies listed on the Polish and German capital market. The discussed research problem was investigated in the form of a comparative analysis and realized in two parts. The discussion presented in the first part depicts mainly theoretical reflections on the essence and assessment measures of companies’ economic efficiency. The second part presents the results of a comparative empirical research on economic efficiency of the companies listed on the Warsaw Stock Exchange and included in the WIG30 index as well as the companies listed on the Frankfurt Stock Exchange, which belong to the DAX index. The research period comprises years between 2004-2013. A comparative analysis of economic efficiency of the companies was conducted using a traditional ratio analysis and the nonparametric DEA method. The results of the empirical research confirm that German companies achieved significantly higher values of basic economic categories in the analysed decade, financial results in particular; however, their generated profits did not reflect in higher values of profitability ratios. Polish companies performed much better as they also showed higher efficiency from  the DEA’s point of view.
Net profit distribution policy in companies using state-owned enterprises against payment
Authors: Matuszewska-Pierzynka Agnieszka
Published: November 2016

The main objective of this paper is to present the results of empirical studies on net profit distribution in companies using state–owned enterprises against payment. The main research hypothesis states that the majority of companies using state–owned enterprises against payment waive their right to the dividend and transfer a major part of retained earnings to supplementary capital. The empirical investigation of the main hypothesis has been conducted among 21 companies based in Mazowieckie Province, which concluded privatisation agreements with the State Treasury in years 2000–2005. The analysis of net profit distribution in companies using state–owned enterprises against payment is based on data collected and processed by the author of the article from the National Court Register, for the period from the privatisation date of the surveyed enterprises to 2010, using measures of descriptive statistics. The paper consists of the following parts: the introduction, the essence of giving state–owned enterprise for use against payment, the characteristics of companies qualified to the research sample, net profit distribution policy in companies using state–owned enterprises against payment. Finally, it is concluded that over the first three years of operation every second company using a state–owned enterprise against payment did not pay a dividend transferring all of retained earnings to supplementary capital.
Pro-investment local policies in the area of real estate economics – similarities and differences in the strategies used by communes
Authors: Małkowska Agnieszka , Głuszak Michał
Published: November 2016

In the article we discuss the importance of the real estate related instruments used by local government to attract investment and stimulate local economic development. The article discusses economic literature related to public economics at the local government level, with the special emphasis put on the link between urban and real estate economics and development.  In the empirical part of the paper, we analyze the results of the survey conducted at the local government level in Poland (Malopolska). There are two major research objectives: (1) to identify the scope of the real estate economic instruments used by the communes as part of their development policies’ strategies; (2) to examine the coexistence of certain types of instruments as part of the commune development strategies. To find relevant answers, both multidimensional scaling and cluster analysis are applied. Additionally, we discuss whether there are evidence of mimicking behavior in local development policies.
Accomplishment of the European Union lifelong learning objectives in Poland
Authors: Kryk Barbara
Published: November 2016

One of the preconditions for the economic success of a country is education, which today should assume the form of lifelong and life-time learning-LLL). This condition is so important that it was first reflected in the the Lisbon Strategy goals and, subsequently, in the Europe 2020 strategy and its flagship initiatives. It is known that each EU Member State is obliged to achieve the common goals. Hence, this work undertakes to assess the degree to which the EU LLL goals have been accomplished in Poland. This work presents: the essence of LLL, the educational goals set out in the two abovementioned strategies, and the EU recommendations for Poland in this field. Selected indicators were used to determine the level of educational achievements in the country. The following research methodologies were applied for the purpose of this paper: desk research, indicator-based research and deductive research.
Small and medium enterprises and the support policy of local government
Authors: Adamowicz Mieczysław , Machla Aldona
Published: November 2016

The subject of this research are small and medium enterprises (SME) in the Polish economy, the support of this sector by local government and the functioning of small and medium enterprises in the local system of the town and commune of Pułtusk. The aim of this study is to present the condition and the role of SME in the local systems in light of the selected features of this sector in the country and evaluation of support for SME given by local government of the town and the commune. The case study research methods applied were literature research, documentation review and survey-based research using questionnaire. The survey was conducted in spring, 2014, on a random sample. The research resulted in learning the profile of a local entrepreneurs and the action characteristics of SME in the examined unit. The diagnosis of the sector’s situation was made, the stimulating and limiting factors of its prosperity were identified. The SME support system of local government and the entrepreneurs’ expectations towards commune government in the field of development of local enterprises were evaluated. The results and conclusions confirm the need for development of local government activity in formulating and implementation of the development of local enterprises policy.
Innovation in contemporary economies
Authors: Pohulak-Żołędowska Elżbieta
Published: November 2016

The hereby article discusses the issues related to the existing or required support given by the State to enterprises in order to provide them conditions to innovate. Neoclassical economy puts an emphasis to the price mechanism as a decision making effective tool, but enterprises meet many barriers in creating and introducing innovation, like high cost, high risk or lack of demand for innovation. These phenomena tend to inhibit innovation of enterprises. This means that market is not an efficient mechanism for innovation activity of enterprises, and its imperfections provoke the State’s intervention. The goal of the article is to shape the objectives of State’s impact on decisions of innovative enterprises. Research method is the critical literature review and public data on State’s support on business R&D analysis. The research results show State’s support for both – incremental and radical innovation, which proves that innovative activity of enterprises is far from being a spontaneous, market-based process.
Contemporary organization and a perspective on integration and development
Authors: Piekarczyk Anna
Published: November 2016

The modern organization is becoming more complex and dynamic. Handling such an organization often requires new solutions in order to quickly counter complexity in economy, politics and private life sectors. The cure to this situation may be understanding the complex connections between elements in the system. Thereupon, in the article the modern organization is presented with the use of a network using know-why type thinking as also a model of an effective system taken from nature, which refers to two determinants – integration and development. The aim of the article is an attempt to answer the question what conditions have to be fulfilled, for the organization to give a feeling of integration and development with a detailed focus on the balance between the two factors.
A light in dark places: School staff can provide crucial support
Authors: Seager-Smith Lauren
Published: November 2016

As Anti-Bullying Week approaches, the amazing impact that professionals working in and with schools can have on students is being shown in the Power for Good Awards. Lauren Seager-Smith explains
Supporting the survivors of domestic physical abuse
Authors: Thornton Stephanie
Published: November 2016

Stephanie Thornton looks at the incidence of physical abuse on children and young people, its impact and what can be done to help support victims.
Children missing in education: New rule for schools
Authors: Pickworth Frances
Published: November 2016

As part of a drive to protect children missing education from harm, the government has introduced new requirements on sharing information. Frances Pickworth explains
The EBacc effect – teachers' anger at narrowing curriculum
Authors: Henshaw Pete
Published: November 2016

Teachers reveal how pupils are being forced away from creative disciplines and made to take EBacc subjects they ‘dislike the least’
Examinations
Authors: Chima Jugjit
Published: November 2016

What are the examination policies that schools must have in place in order to satisfy both JCQ and Ofqual requirements? Jugjit Chima explains
ANÁLISE DE CONTEÚDO, ANÁLISE DO DISCURSO E ANÁLISE DE CONVERSAÇÃO: ESTUDO PRELIMINAR SOBRE DIFERENÇAS CONCEITUAIS E TEÓRICO-METODOLÓGICAS
Authors: Gonçalves Anderson Tiago Peixoto
Published: November 2016

Este ensaio teórico tem como objetivo refletir sobre três modelos de interpretação de textos utilizados na pesquisa qualitativa, muitas vezes, confundidos em seus conceitos e suas metodologias: Análise de Conteúdo, Análise do Discurso e Análise de Conversação. Após a apresentação dos seus conceitos, propõe-se discutir, preliminarmente, acerca das diferenças teórico-metodológicas perceptíveis entre eles. Foi realizada uma pesquisa bibliográfica para subsidiar a discussão conceitual e teórico-metodológica. Verificou-se que os modelos revelam diferenças relacionadas ao tipo de estratégia utilizada no tratamento dos textos, ao tipo de abordagem e à postura teórica em que se enquadram.
Biomarkers and Genetics in Peripheral Artery Disease
Authors: Hazarika Surovi , Annex Brian H
Published: November 2016

BACKGROUND

Peripheral artery disease (PAD) is highly prevalent and there is considerable diversity in the initial clinical manifestation and disease progression among individuals. Currently, there is no ideal biomarker to screen for PAD, to risk stratify patients with PAD, or to monitor therapeutic response to revascularization procedures. Advances in human genetics have markedly enhanced the ability to develop novel diagnostic and therapeutic approaches across a host of human diseases, but such developments in the field of PAD are lagging.

CONTENT

In this article, we will discuss the epidemiology, traditional risk factors for, and clinical presentations of PAD. We will discuss the possible role of genetic factors and gene–environment interactions in the development and/or progression of PAD. We will further explore future avenues through which genetic advances can be used to better our understanding of the pathophysiology of PAD and potentially find newer therapeutic targets. We will discuss the potential role of biomarkers in identifying patients at risk for PAD and for risk stratifying patients with PAD, and novel approaches to identification of reliable biomarkers in PAD.

The exponential growth of genetic tools and newer technologies provides opportunities to investigate and identify newer pathways in the development and progression of PAD, and thereby in the identification of newer biomarkers and therapies.
Reviews
Authors: Simpson Hyacinth , Scafe Suzanne
Published: November 2016

WRITING JAMAICA, ONCE AGAIN OLIVE SENIOR’S THE PAIN TREE (2015) Toronto: Cormorant Books, 194 pp., ISBN: 9781770864344, p/bk, $22.95

COMMUNITIES IN CONTEMPORARY ANGLOPHONE CARIBBEAN SHORT STORIES, LUCY EVANS (2014) Liverpool: Liverpool University Press, 240 pp., ISBN: 9781781381182, h/bk, £75
‘Old Age Has No Remedy’: Selected narratives on the aged and ageing in Barbara Jenkins’ Sic Transit Wagon and Other Stories
Authors: Skeete Geraldine Elizabeth
Published: November 2016

A particular voice in Caribbean women’s short-fiction writing stands out, not only because of the talent and skill displayed by the author and by the numerous awards bestowed upon her, but also because Barbara Jenkins is a septuagenarian who in 2013 published her debut collection Sic Transit Wagon and Other Stories. Her age makes her distinctive among her younger peers who are contributing to a literary renaissance in Trinidad and Tobago. This article explores Jenkins’ positioning as a successful older writer as well as two of her short narratives on marriage, family and health as they relate to older characters. Theories on intelligence, creativity and achievement regarding age and ageing, and the socio-political situation related to the aged in Trinidad and Tobago, are discussed to contextualize Jenkins’ success and the foci of the narratives. This article examines particular discourse strategies used in the two selected stories, as well as themes of marital infidelity, and the impact of age-related disease on spousal and filial relationships.