bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome
Authors: Ettwiller Laurence , Buswell John , Yigit Erbay , Schildkraut Ira 
Published: December 2015

AbstractWe have developed Cappable-seq that specifically captures primary RNA transcripts by enzymatically modifying the 5’ triphosphorylated end of RNA with a selectable tag. We first applied Cappable-seq toE. coli, achieving up to 50 fold enrichment of primary transcripts and identifying an unprecedented 16539 transcription start sites (TSS) genome-wide at single base resolution. We also applied Cappable-seq to a mouse cecum sample and for the first time identified TSS in a microbiome. Furthermore, Cappable-seq universally depletes ribosomal RNA and reduces the complexity of the transcriptome to a single quantifiable tag per TSS enabling digital profiling of gene expression in any microbiome.
Meta3C analysis of a mouse gut microbiome
Authors: Marbouty Martial , Baudry Lyam , Cournac Axel , Koszul Romain 
Published: December 2015

AbstractMicrobial populations as well as they biochemical activities are important components of environmental ecosystems, including the human microbiome. Deciphering the genomic content of these complex mixes of species is an important challenge but is essential to fully understand the regulation of their ecological balance. Here we apply meta3C, an experimental and computational approach that exploits the physical contacts between chromosomes to characterize large genomic regions of bacterial species mixed together, on a truly complex ecosystem: the mouse gut microbiota. Meta3C, which was initially described and applied onto controlled mixes of microorganisms, allowed thede novoassembly and scaffolding of numerous bacteria present into this natural mix. Importantly, the scaffolds analyzed exhibit the structural properties expected from typical bacterial chromosomes. Meta3C therefore paves the way to the in-depth analysis of genomic structuration of complex populations.
SMEs and social capital: exploring the Brazilian context
Authors: Clarke Ruth , Chandra Ramdas , Machado Marcilio 
Published: December 2015

Purpose
– This study aims to explore the extent to which social capital plays a role in firm development, internationalization and growth, in the context of an emerging market, Brazil. The study aims to provide a new context and perspective on the role social capital plays in fostering growth and internationalization among small and medium enterprises (SMEs) in an emerging market.

Design/methodology/approach
– This is an exploratory study. First, empirical data are drawn from a commodity industry, the Brazilian Stone industry, which is a competitive, well-established sector in the country. Using a previously validated questionnaire from the World Bank, the extent of social capital possessed and used by the firms in this industry is correlated to their growth and performance. Based on the exploratory results, a set of research propositions are developed that point the way to questions that are important and interesting to further understand the role of social capital in this context.

Findings
– The results point to fairly low levels of social capital among Brazilian SMEs in this sector and relatively low levels of awareness of the potential opportunities to exploit social capital to further development and internationalization.

Research limitations/implications
– Social capital matters for firm growth and performance, but the extent of development of social capital in this context is fairly low. The limitations include the sample size and the homogeneity of the sample, which restricts generalizability.

Practical implications
– Building and exploiting social capital is a void that currently exists in the commodity sector in Brazil. Developing this can lead to more positive firm performance and growth, especially as the institutional context in Brazil continues to develop.

Originality/value
– The paper offers a unique context, as well as a new perspective on the role of firm social capital, by using an emerging market and a commodity industry that has been rarely studied in the literature.
Spatial health and life sciences business ecosystem: a case study of San Diego
Authors: Majava Jukka , Leviäkangas Pekka , Kinnunen Tuomo , Kess Pekka , Foit Del 
Published: December 2015

Purpose– Increasing competition in global markets requires many countries to seek new growth sectors. In addition, the nature of competition is changing. This paper applies the business ecosystem concept and studies San Diego as a spatial health and life sciences ecosystem. The purpose of this paper is to identify issues that should be considered in design of innovation policies and regional industry development.Design/methodology/approach– The research approach is built on a literature review of business ecosystems and spatial innovation. The empirical study is based on semi-structured interviews, observations, and information gathering and verification during field research.Findings– The results include a description of the ecosystem structure and dynamics. This paper demonstrates the bottom-up nature of San Diego’s health and life sciences ecosystem without a dominant lead actor, and presents prerequisites for fostering spatial ecosystems.Research limitations/implications– A single case may not be able to offer a generalized picture of this topic. However, the study raises several considerations for researchers and decision-makers involved in innovation policy design. Future work should extend the study and involve other spatial and substance contexts to compare findings and to pursue a more generic picture of innovation ecosystems and networks.Originality/value– This paper demonstrates that applying the concept of business ecosystems to the spatial context provides new insights in terms of dynamic mechanisms and factors contributing to economic growth in a particular location. Understanding how to facilitate the creation of successful spatial ecosystems is in the focal point of innovation policies.
An introduced parasitic fly may lead to local extinction of Darwin's finch populations
Authors: Koop Jennifer A. H. , Kim Peter S. , Knutie Sarah A. , Adler Fred , Clayton Dale H. 
Published: December 2015

Summary

Introduced pathogens and other parasites are often implicated in host population‐level declines and extinctions. However, such claims are rarely supported by rigorous real‐time data. Indeed, the threat of introduced parasites often goes unnoticed until after host populations have declined severely. The recent introduction of the parasitic nest fly, Philornis downsi, to the Galápagos Islands provides an opportunity to monitor the current impact of an invasive parasite on endemic land bird populations, including Darwin's finches.

In this paper, we present a population viability model to explore the potential long‐term effect of P. downsi on Darwin's finch populations. The goal of our study was to determine whether P. downsi has the potential to drive host populations to extinction and whether management efforts are likely to be effective.

Our model is based on data from five years of experimental field work documenting the effect of P. downsi on the reproductive success of medium ground finch Geospiza fortis populations on Santa Cruz Island. Under two of the three scenarios tested, the model predicted medium ground finches are at risk of extinction within the next century.

However, sensitivity analyses reveal that even a modest reduction in the prevalence of the parasite could improve the stability of finch populations. We discuss the practicality of several management options aimed at achieving this goal.

Synthesis and applications. Our study demonstrates the predicted high risk of local extinction of an abundant host species, the medium ground finch G. fortis due to an introduced parasite, P. downsi. However, our study further suggests that careful management practices aimed at reducing parasite prevalence have the potential to significantly lower the risk of host species extinction.
Quantifying relative fish abundance with eDNA: a promising tool for fisheries management
Authors: Lacoursière‐Roussel Anaïs , Côté Guillaume , Leclerc Véronique , Bernatchez Louis 
Published: December 2015

Summary

Assessment and monitoring of exploited fish populations are challenged by costs, logistics and negative impacts on target populations. These factors therefore limit large‐scale effective management strategies.

Evidence is growing that the quantity of eDNA may be related not only to species presence/absence, but also to species abundance. In this study, the concentrations of environmental DNA (eDNA) from a highly prized sport fish species, Lake Trout Salvelinus namaycush (Walbaum 1792), were estimated in water samples from 12 natural lakes and compared to abundance and biomass data obtained from standardized gillnet catches as performed routinely for fisheries management purposes. To reduce environmental variability among lakes, all lakes were sampled in spring, between ice melt and water stratification.

The eDNA concentration did not vary significantly with water temperature, dissolved oxygen, pH and turbidity, but was significantly positively correlated with relative fish abundance estimated as catch per unit effort (CPUE), whereas the relationship with biomass per unit effort (BPUE) was less pronounced.

The value of eDNA to inform about local aquatic species distribution was further supported by the similarity between the spatial heterogeneity of eDNA distribution and spatial variation in CPUE measured by the gillnet method.

Synthesis and applications. Large‐scale empirical evidence of the relationship between the eDNA concentration and species abundance allows for the assessment of the potential to integrate eDNA within fisheries management plans. As such, the eDNA quantitative method represents a promising population abundance assessment tool that could significantly reduce the costs associated with sampling and increase the power of detection, the spatial coverage and the frequency of sampling, without any negative impacts on fish populations.
International Reserves Holdings in the CEMAC Area: Adequacy and Motives
Authors: Cyrille Samba Michel 
Published: December 2015

AbstractThe main objective of this paper is to investigate CEMAC's demand for international reserves, with an emphasis on the role of the monetary disequilibrium. Prior to this task, we assess CEMAC's position in terms of reserve adequacy. Using some relevant measures of reserve adequacy, we find that CEMAC countries have sufficient international reserves to meet the minimum adequacy requirements. To better analyze CEMAC's international reserves demand, we extend the usual buffer stock model to account for overall economic growth and imports. Moreover, an importance is given to the devaluation of the CFA franc, the peg of this currency to the euro, and the effect of the recent Global Financial Crisis. Using quarterly data from 1985:1 to 2009:4, we show that the long‐run reserve demand in the CEMAC area can be described as a function of uncertainty and economic growth. It also appears that a disequilibrium in the money market significantly affects reserve demand in the CEMAC area. Moreover, both the devaluation of the CFA franc and the peg of this currency to the euro positively affect the demand for international reserves in the short run. Finally, there is evidence of an inertia in the reserve management of the central bank.
Effect of niacin on triglyceride‐rich lipoprotein apolipoprotein B‐48 kinetics in statin‐treated patients with type 2 diabetes
Authors: Pang J. , Chan D. C. , Hamilton S. J. , Tenneti V. S. , Watts G. F. , Barrett P. H. R. 
Published: December 2015

AimTo investigate the effects of extended‐release (ER) niacin on apolipoprotein B‐48 (apoB‐48) kinetics in statin‐treated patients with type 2 diabetes (T2DM).MethodsA total of 12 men with T2DM were randomized to rosuvastatin or rosuvastatin plus ER niacin for 12 weeks and then crossed to the alternate therapy. Postprandial metabolic studies were performed at the end of each treatment period. D3‐leucine tracer was administered as subjects consumed a high‐fat liquid meal. ApoB‐48 kinetics were determined using stable isotope tracer kinetics with fractional catabolic rates (FCRs) and secretion rates derived using a non‐steady‐state compartmental model. Area‐under‐the‐curve (AUC) and incremental AUC (iAUC) for plasma triglyceride and apoB‐48 were also calculated over the 10‐h period after ingestion of the fat meal.ResultsIn statin‐treated patients with T2DM, apoB‐48 concentration was lower with ER niacin (8.24 ± 1.98 vs 5.48 ± 1.14 mg/l, p = 0.03) compared with statin alone. Postprandial triglyceride and apoB‐48 AUC were also significantly lower on ER niacin treatment (‐15 and ‐26%, respectively; p < 0.05), without any change to triglyceride and apoB‐48 iAUC. ApoB‐48 secretion rate in the basal state (3.21 ± 0.34 vs 2.50 ± 0.31 mg/kg/day; p = 0.04) and number of apoB‐48‐containing particles secreted in response to the fat load (1.35 ± 0.19 vs 0.84 ± 0.12 mg/kg; p = 0.02) were lower on ER niacin. ApoB‐48 FCR was not altered with ER niacin (8.78 ± 1.04 vs 9.17 ± 1.26 pools/day; p = 0.79).ConclusionsER niacin reduces apoB‐48 concentration by lowering fasting and postprandial apoB‐48 secretion rate. This effect may be beneficial for lowering atherogenic postprandial lipoproteins and may provide cardiovascular disease risk benefit in patients with T2DM.
Lymphoblastic lymphoma: an updated review on biology, diagnosis, and treatment
Authors: Bassan Renato , Maino Elena , Cortelazzo Sergio 
Published: December 2015

AbstractLymphoblastic lymphoma is a rare aggressive neoplasm of T‐/B‐precursors resembling acute lymphoblastic leukemia, with no or limited bone marrow involvement (<25%), that develops more frequently in children and young adults and is typically characterized by a grossly enlarged mediastinum, and whose diagnostic hallmark is the expression of a T‐/B‐precursor cell immunophenotype, the T‐cell subset accounting for 90% of all cases. The adoption of pediatric‐derived, intensive lymphoblastic leukemia‐like protocols led to significantly improved results, with survival rates of about 70% and 90% in adults and children, respectively. Adequate central nervous system prophylaxis and mediastinal irradiation contributed to the therapeutic success; however, the role of radiation therapy is debated due to toxicity concerns and the excellent results obtained with radiation‐free programs especially in pediatric patients. With these modern schedules, localized radiotherapy and/or hematopoietic stem cell transplants could be generally omitted, and considered only for high‐risk patients identified through postinduction computed tomography/positron‐emission tomography scans, minimal residual disease analysis, and new genetics and genomics. New clinical studies will have to confirm the value of these assays for risk‐oriented therapy, while further therapeutic progress is expected from the introduction of new drugs and targeting agents.
Unrelated bone marrow transplantation or immediate umbilical cord blood transplantation for patients with acute myeloid leukemia in first complete remission
Authors: Yanada Masamitsu , Kanda Junya , Ohtake Shigeki , Fukuda Takahiro , Sakamaki Hisashi , Miyamura Koichi , Miyawaki Shuichi , Uchida Naoyuki , Maeda Tomoya , Nagamura‐Inoue Tokiko , Asou Norio , Morishima Yasuo , Atsuta Yoshiko , Miyazaki Yasushi , Kimura Fumihiko , Kobayashi Yukio , Takami Akiyoshi , Naoe Tomoki , Kanda Yoshinobu 
Published: December 2015

AbstractBackgroundWhile unrelated bone marrow transplantation (UBMT) has been widely used as alternative donor transplantation, the use of umbilical cord blood transplantation (UCBT) is increasing recently.MethodsWe conducted a decision analysis to address which transplantation procedure should be prioritized for younger patients with acute myeloid leukemia (AML) harboring high‐ or intermediate‐risk cytogenetics in first complete remission (CR1), when they lack a matched related donor but have immediate access to a suitable umbilical cord blood unit. Main sources for our analysis comprised the data from three phase III trials for a chemotherapy cohort (n = 907) and the registry data for a transplantation cohort (n = 752).ResultsThe baseline analysis showed that when the 8/8 match was considered for UBMT, the expected 5‐year survival rate was higher for UBMT than for UCBT (58.1% vs. 51.8%). This ranking did not change even when the 7/8 match was considered for UBMT. Sensitivity analysis showed consistent superiority of UBMT over UCBT when the time elapsed between CR1 and UBMT was varied within a plausible range of 3–9 months.ConclusionsThese results suggest that 8/8 or 7/8 UBMT is a better transplantation option than UCBT even after allowing time required for donor coordination.
Tailoring the Thermal Expansion of Glass‐Ceramics by Controlled Twofold Crystallization of Li2Si2O5 and CsAlSi5O12
Authors: Rampf Markus , Fisch Martin , Dittmer Marc , Ritzberger Christian , Schweiger Marcel , Höland Wolfram 
Published: December 2015

The mechanical and optical properties of Li2Si2O5 glass‐ceramics can be precisely controlled via the crystal morphology and content. However, the materials' coefficient of thermal expansion (CTE) depends on the fraction as well as the CTE of Li2Si2O5 and the residual glass phase, and therefore covers a rather narrow range between 10.2 and 11.3 *10−6 K−1 (100–400°C). This study presents a way to tailor the CTE of lithium disilicate‐based glass‐ceramics by controlled twofold precipitation of Li2Si2O5 and CsAlSi5O12 as a minor crystal phase with high CTE from homogenous Cs2O comprising bulk base glasses. The Cs2O content in the base glass significantly influences the nucleation and crystallization process of Li2Si2O5 as well as the microstructure of the glass‐ceramic materials. While the precipitation of Li2SiO3 and Li2Si2O5 starts at temperatures ≤700°C, CsAlSi5O12 forms in parallel to the enhanced formation of Li2Si2O5 as a result of Li2SiO3 dissolution at crystallization temperatures >850°C. Glass‐ceramics with a CTE ranging from 11 to 13.1*10−6 K−1 (25–500°C) and a mean biaxial strength ≥370 MPa were produced. The preliminary study of this glass system proofs the potential of twofold crystallization to control the CTE of lithium disilicate glass‐ceramics.
Tonsillectomy and the risk of inflammatory bowel disease: A systematic review and meta‐analysis
Authors: Sun Weili , Han Xiao , Wu Siyuan , Yang Chuanhua 
Published: December 2015

AbstractBackground and Aim:Tonsillectomy remains a controversial environmental factor in the etiology of inflammatory bowel disease (IBD). This meta‐analysis aims to elucidate a more defined role of tonsillectomy in the development of IBD.Methods:Four databases, including PubMed, EMBASE, the Cochrane Library, and Web of Science, were searched for studies exploring the association between tonsillectomy and the risk of IBD. The pooled estimates of odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using a random effects model. Heterogeneity was assessed using chi‐squared and I2 statistical analysis. A funnel plot was performed to assess publication bias.Results:A total of 23 observational studies involving 19 569 patients were included in our meta‐analysis. Of these, 17 studies investigated the association between tonsillectomy and Crohn's disease (CD), and 22 studies explored its relationship with ulcerative colitis (UC). Overall, a positive relationship between tonsillectomy and development of CD (OR 1.37, 95% CI: 1.16−1.62) was observed, while there was no association between tonsillectomy and UC (OR 0.94, 95% CI: 0.84−1.05). When ORs were adjusted for smoking, the pooled OR for CD increased to 1.66 (95% CI: 1.03−2.68) and, for UC, changed to 1.03 (95% CI: 0.74−1.44).Conclusions:This meta‐analysis demonstrates that tonsillectomy is associated with an increased risk of developing CD. We found no evidence to suggest that tonsillectomy exerts a protective effect on the development of UC, as is the case with appendectomy. Further prospective studies are required to confirm the validity of these observations.
The protective effect of melatonin on smoke‐induced vascular injury in rats and humans: a randomized controlled trial
Authors: Wang Zhanqi , Ni Leng , Wang Jing , Lu Chengran , Ren Meng , Han Wei , Liu Changwei 
Published: December 2015

AbstractSmoking is one of the most harmful lifestyles in the world. Very few studies have investigated the effects of melatonin in smoke‐induced vascular injury. This study was designed to investigate whether melatonin could protect rats and humans from smoke‐induced vascular injury. 32 male rats and a double‐blind randomized controlled trial (RCT) containing 63 participants formed the subjects of this study. In rats, 10 mg/kg of melatonin was intraperitoneally injected. Blood samples and abdominal artery were harvested two weeks later. Melatonin decreased the expression of platelet endothelial cell adhesion molecule‐1 (CD31), intercellular adhesion molecule‐1 (ICAM‐1), vascular cell adhesion molecule‐1 (VCAM‐1) and endothelin‐1 (ET‐1) compared with the smoke exposed group (P < 0.05), whereas endothelial nitric oxide synthase (eNOS), nuclear erythroid 2‐related factor 2 (Nrf2), NAD(P)H quinone oxidoreductase 1 (NQO‐1), catalytic glutamate cysteine ligase (GCLC) and heme oxygenase‐1 (HO‐1) recovered markedly (P < 0.05). In humans, 3 mg/day of melatonin was taken orally by the participants. Blood samples were drawn at baseline and after two weeks of treatment. Compared with the oral placebo group, melatonin decreased the concentration of fibrinogen (Fbg) (P = 0.04) and free fatty acids (FFA) (P = 0.04) in smokers, along with the decreased expression of ICAM‐1, VCAM‐1 and ET‐1 (P = 0.004, P = 0.001, P < 0.0001, respectively). In contrast, Nrf2 and HO‐1 expression were markedly increased (P = 0.0001, P = 0.0049, respectively) after smokers took melatonin orally. In summary, our present data suggest that melatonin could ameliorate smoke‐induced vascular injury.
Atrial Fibrillation as a Prognostic Indicator in Medium to Large‐Sized Dogs with Myxomatous Mitral Valvular Degeneration and Congestive Heart Failure
Authors: Jung S.W. , Sun W. , Griffiths L.G. , Kittleson M.D. 
Published: December 2015

BackgroundThe prevalence and prognostic importance of atrial fibrillation (AF) on survival in nonsmall breed dogs with myxomatous mitral valvular disease (MMVD) and congestive heart failure (CHF) remain unknown.AimTo identify the prevalence ofAFin nonsmall breed dogs withCHFbecause ofMMVDand to characterize the impact ofAFon survival outcome.AnimalSixty‐four client‐owned dogs (>15 kg) withMMVDandCHF.MethodsRetrospective review of medical records for dogs weighing >15 kg withMMVDtreated forCHF.ResultsThirty‐three dogs presented withAFor developedAFduring follow‐up examinations, and 31 dogs were free ofAFuntil cardiac‐related death. For dogs withAF, median survival time (MST) was 142 days (range: 9–478) while dogs withoutAFlived 234 days (range: 13–879 days).AFincreased risk of cardiac‐related death (HR= 2.544; 95%CI= 1.41–4.59;P= .0019) when compared to dogs withoutAF.MSTwas significantly prolonged for dogs withAFwhose rates were adequately controlled (<160 bpm; 171 days; n = 13) when compared to dogs that failed to respond to negative chronotropic agents (61 days; n = 20;P= .032). The administration of combination treatment (diltiazem and digoxin) significantly decreased medianHRto 144 bpm (range: 84–218 bpm) in dogs withAFand significantly prolongedMST(diltiazem+digoxin: 130 days versus diltiazem: 35 days,P= .0241) when compared to diltiazem alone.Conclusions and Clinical ImportanceInadequately controlledAFis associated with a higher rate of mortality. Optimization of therapeutic strategies for the rate control ofAFremains determined.