bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular characterization of Chlamydomonas reinhardtii telomeres and telomerase mutants
Authors: Eberhard Stephan , Valuchova Sona , Ravat Julie , Jolivet Pascale , Bujaldon Sandrine , Lemaire Stéphane D. , Wollman Francis-André , Teixeira Maria Teresa , Riha Karel , Xu Zhou 
Published: January 2019

ABSTRACTTelomeres are repeated sequences found at the end of the linear chromosomes of most eukaryotes and are required for chromosome integrity. They shorten with each cell division because of the end-replication problem. Expression of the reverse transcriptase telomerase allows for extension of telomeric repeats to counteract telomere shortening. Although Chlamydomonas reinhardtii, a photosynthetic unicellular green alga, is widely used as a model organism in photosynthesis and flagella research, and for biotechnological applications, the biology of its telomeres has not been investigated in depth. Here, we show that the C. reinhardtii (TTTTAGGG)n telomeric repeats are mostly non-degenerate and that the telomeres form a protective structure, ending with a 3′ overhang. While telomere size and length distributions are stable under various standard growth conditions, they vary substantially between 12 genetically close reference strains. Finally, we identify CrTERT, the gene encoding the catalytic subunit of telomerase and show that mutants of this gene display an “ever shortening telomere” phenotype and eventually enter replicative senescence, demonstrating that telomerase is required for long-term maintenance of telomeres in C. reinhardtii.
Is the 2014 E-Rate reform a game changer? An empirical analysis of Pennsylvania data
Authors: Grzeslo Jenna , Bai Yang , Min Bumgi , Jayakar Krishna 
Published: January 2019

Purpose
This study aims to analyze the impact of the 2014 E-Rate reforms on the pattern of distribution of funds of the program.

Design/methodology/approach
Using Pennsylvania data, the paper investigates whether a school district that successfully applied for funding received increased support post-reforms, and what socio-economic characteristics of school districts were associated with successful applications. Furthermore, it asks whether the reforms reduced the barriers that disadvantaged school districts face in obtaining support.

Findings
The finding suggests that, even after controlling for changes in the school districts’ eligibility and application skills, the amount of funding committed to the school districts was still significantly higher after the reform.

Originality/value
The analysis shows that, immediately after the reform, the non-urban school districts were committed more funding than urban school districts were; they also received more funds than they would have without the reforms. This indicates that the 2014 reform might have benefited disadvantaged applicants, especially rural school districts.
Outcomes of open government
Authors: Schmidthuber Lisa , Stütz Simone , Hilgers Dennis 
Published: January 2019

Purpose
Governments all over the world have implemented citizensourcing initiatives to integrate citizens into decision-making processes. A more participative decision-making process is associated with an open government and assumed to benefit public service quality and interactive value creation. The purpose of this paper is to highlight the outcomes of open government initiatives and ask to what extent open government participation is related to perceived outcomes of open government.

Design/methodology/approach
Data conducted from a survey among users of a citizensourcing platform and platform data are used to perform non-parametric analyses and examine the relationship between platform participation and perceived outcomes of open government.

Findings
The findings of this paper suggest that active platform usage positively relates to several outcomes perceived by citizens, such as improved information flow, increased trust in and satisfaction with local government. In contrast, repetitive participation does not significantly relate to users’ outcome evaluation.

Practical implications
This study suggests public managers to provide possibilities for citizen participation and interaction with government such as citizensourcing initiatives. In particular, it recommends promoting participants’ platform activity, as proactive platform participation has positive effects on perceived outcomes of open government.

Originality/value
Previous literature discussed what it needs to realize a transparent and participatory government. First empirical studies deal with government institutions’ reasons to promote exchange with citizens, and investigate citizens’ motivation to participate in citizensourcing activities, but have disregarded the consequences of open government so far. This study thus provides first insights into the outcomes of open government, as perceived by the users.
Intra‐clade metabolomic profiling of MAR4 Streptomyces from the Macaronesia Atlantic region reveals a source of anti‐biofilm metabolites
Authors: Bauermeister Anelize , Pereira Florbela , Grilo Inês R. , Godinho Camila C. , Paulino Marisa , Almeida Vanessa , Gobbo‐Neto Leonardo , Prieto‐Davó Alejandra , Sobral Rita G. , Lopes Norberto P. , Gaudêncio Susana P. 
Published: January 2019

SummaryThe search for new and effective strategies to reduce bacterial biofilm formation is of utmost importance as bacterial resistance to antibiotics continues to emerge. The use of anti‐biofilm agents that can disrupt recalcitrant bacterial communities can be an advantageous alternative to antimicrobials, as their use does not lead to the development of resistance mechanisms. Six MAR4 Streptomyces strains isolated from the Madeira Archipelago, at the unexplored Macaronesia Atlantic ecoregion, were used to study the chemical diversity of produced hybrid isoprenoids. These marine actinomycetes were investigated by analysing their crude extracts using LC–MS/MS and their metabolomic profiles were compared using multivariate statistical analysis (principal component analysis), showing a separation trend closely related to their phylogeny. Molecular networking unveiled the presence of a class of metabolites not previously described from MAR4 strains and new chemical derivatives belonging to the napyradiomycin and marinone classes. Furthermore, these MAR4 strains produce metabolites that inhibit biofilm formation of Staphylococcus aureus and Marinobacter hydrocarbonoclasticus. The anti‐biofilm activity of napyradiomycin SF2415B3 (1) against S. aureus was confirmed.
Real time monitoring of Aeromonas salmonicida evolution in response to successive antibiotic therapies in a commercial fish farm
Authors: Du Xiaochen , Bayliss Sion C. , Feil Edward J. , Liu Ying , Wang Chao , Zhang Gang , Zhou Dongsheng , Wei Dawei , Tang Na , Leclercq Sébastien O. , Feng Jie 
Published: January 2019

SummaryOur ability to predict evolutionary trajectories of pathogens in response to antibiotic pressure is one of the promising leverage to fight against the present antibiotic resistance worldwide crisis. Yet, few studies tackled this question in situ at the outbreak level, due to the difficulty to link a given pathogenic clone evolution with its precise antibiotic exposure over time. In this study, we monitored the real‐time evolution of an Aeromonas salmonicida clone in response to successive antibiotic and vaccine therapies in a commercial fish farm. The clone was responsible for a four‐year outbreak of furunculosis within a Recirculating Aquaculture System Salmo salar farm in China, and we reconstructed the precise tempo of mobile genetic elements (MGEs) acquisition events during this period. The resistance profile provided by the acquired MGEs closely mirrored the antibiotics used to treat the outbreak, and we evidenced that two subclonal groups developed similar resistances although unrelated MGE acquisitions. Finally, we also demonstrated the efficiency of vaccination in outbreak management and its positive effect on antibiotic resistance prevalence. Our study provides unprecedented knowledge critical to understand evolutionary trajectories of resistant pathogens outside the laboratory.
Minority species influences microbiota formation: the role of Bifidobacterium with extracellular glycosidases in bifidus flora formation in breastfed infant guts
Authors: Gotoh Aina , Ojima Miriam Nozomi , Katayama Takane 
Published: January 2019

SummaryThe human body houses a variety of microbial ecosystems, such as the microbiotas on the skin, in the oral cavity and in the digestive tract. The gut microbiota is one such ecosystem that contains trillions of bacteria, and it is well established that it can significantly influence host health and diseases. With the advancement in bioinformatics tools, numerous comparative studies based on 16S ribosomal RNA (rRNA) gene sequences, metabolomics, pathological and epidemical analyses have revealed the correlative relationship between the abundance of certain taxa and disease states or amount of certain causative bioactive compounds. However, the 16S rRNA‐based taxonomic analyses using next‐generation sequencing (NGS) technology essentially detect only the majority species. Although the entire gut microbiome consists of 1013 microbial cells, NGS read counts are given in multiples of 106, making it difficult to determine the diversity of the entire microbiota. Some recent studies have reported instances where certain minority species play a critical role in creating locally stable conditions for other species by stabilizing the fundamental microbiota, despite their low abundance. These minority species act as ‘keystone species’, which is a species whose effect on the community is disproportionately large compared to its relative abundance. One of the attributes of keystone species within the gut microbiota is its extensive enzymatic capacity for substrates that are rare or difficult to degrade for other species, such as dietary fibres or host‐derived complex glycans, like human milk oligosaccharides (HMOs). In this paper, we propose that more emphasis should be placed on minority taxa and their possible role as keystone species in gut microbiota studies by referring to our recent studies on HMO‐mediated microbiota formation in the infant gut.
A roadmap for high‐throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture
Authors: White Lauren C. , Fontsere Claudia , Lizano Esther , Hughes David A. , Angedakin Samuel , Arandjelovic Mimi , Granjon Anne‐Céline , Hans Jörg B. , Lester Jack D. , Rabanus‐Wallace M. Timothy , Rowney Carolyn , Städele Veronika , Marques‐Bonet Tomas , Langergraber Kevin E. , Vigilant Linda 
Published: January 2019

AbstractLarge‐scale genomic studies of wild animal populations are often limited by access to high‐quality DNA. Although noninvasive samples, such as faeces, can be readily collected, DNA from the sample producers is usually present in low quantities, fragmented, and contaminated by microorganism and dietary DNAs. Hybridization capture can help to overcome these impediments by increasing the proportion of subject DNA prior to high‐throughput sequencing. Here we evaluate a key design variable for hybridization capture, the number of rounds of capture, by testing whether one or two rounds are most appropriate, given varying sample quality (as measured by the ratios of subject to total DNA). We used a set of 1,780 quality‐assessed wild chimpanzee (Pan troglodytes schweinfurthii) faecal samples and chose 110 samples of varying quality for exome capture and sequencing. We used multiple regression to assess the effects of the ratio of subject to total DNA (sample quality), rounds of capture and sequencing effort on the number of unique exome reads sequenced. We not only show that one round of capture is preferable when the proportion of subject DNA in a sample is above ~2%–3%, but also explore various types of bias introduced by capture, and develop a model that predicts the sequencing effort necessary for a desired data yield from samples of a given quality. Thus, our results provide a useful guide and pave a methodological way forward for researchers wishing to plan similar hybridization capture studies.
Inclusion of Sex and Gender in Emergency Medicine Research—A 2018 Update
Authors: Safdar Basmah , Ona Ayala Kimberly E. , Ali Syed Shayan , Seifer Benjamin J. , Hong Michelle , Greenberg Marna Rayl , Choo Esther K. , McGregor Alyson J. 
Published: January 2019

AbstractObjectivesThe objectives were to 1) evaluate the inclusion of sex and gender in publications by emergency medicine (EM) researchers following the 2014 federal mandate and an Academic Emergency Medicine consensus conference on sex‐ and gender‐based research and 2) assess trends compared with 2011 status report that showed 29% studies used sex and gender in the study design and 2% reported it as a primary outcome.MethodsUsing MEDLINE, the term “emergency” was used to identify all English‐language studies of adult humans published between 2014 and 2017 as EM affiliated (i.e., the first, second, or last author belonged to an EM section, division, center, or institution functioning as emergency department). Four trained abstractors reviewed the data using a standardized data abstraction form.ResultsThe search revealed 6,442 articles using the selected “emergency” terms, and 2,628 original studies coded as EM‐affiliated publications were reviewed, 2,340 met inclusion criteria, and 2,336 were analyzed. This compared to 750 articles reviewed in 2011 using similar search strategy. The adjusted inter‐rater reliability for data abstraction was 97% (95% confidence interval [CI] = 95.4%–98.6%]. The leading study areas contributing the most articles were cardiovascular (17.5%), administration/crowding (15.8%), infectious diseases (9.2%), trauma/injury (9.2%), emergency medical services (6.1%), and pulmonary (6.1%). Eighty‐six percent (n = 1,921) reported the sex/gender composition of the sample and 0.4% (n = 8) reported transgender identity. Thirty‐four percent used sex/gender in the study design, with 27% (n = 609) reporting it as a control variable, 24% (n = 543) as an independent variable, and 2% using sex/gender as primary outcome. Studies funded by federal sources were significantly more likely to include sex/gender in the study design than other sources of funding (odds ratio = 1.77; 95% CI = 1.4–2.2).ConclusionsCompared to 2011, we noted an increase in the number of EM scholarship and use of sex and gender in study design, yet the proportion evaluating it as a primary outcome remained unchanged.
A EAACI drug allergy interest group survey on how European allergy specialists deal with β‐lactam allergy
Authors: Torres Maria Jose , Celik Gulfem Elif , Whitaker Paul , Atanaskovic‐Markovic Marina , Barbaud Annick , Bircher Andreas , Blanca Miguel , Brockow Knut , Caubet Jean‐Christoph , Cernadas Josefina Rodrigues , Chiriac Anca , Demoly Pascal , Garvey Lene Heise , Merk Hans F. , Mosbech Holger , Nakonechna Alla , Romano Antonino 
Published: January 2019

AbstractAn accurate diagnosis of β‐lactam (BL) allergy can reduce patient morbidity and mortality. Our aim was to investigate the availability of BL reagents, their use and test procedures in different parts of Europe, as well as any differences in the diagnostic workups for evaluating subjects with BL hypersensitivity. A survey was emailed to all members of the EAACI Drug Allergy Interest Group (DAIG) between February and April 2016, and the questionnaire was meant to study the management of suspected BL hypersensitivity. The questionnaire was emailed to 82 DAIG centres and answered by 57. Amoxicillin alone or combined to clavulanic acid were the most commonly involved BL except in the Danish centre, where penicillin V was the most frequently suspected BL. All centres performed an allergy workup in subjects with histories of hypersensitivity to BL: 53 centres (93%) followed DAIG guidelines, two national guidelines and two local guidelines. However, there were deviations from DAIG recommendations concerning allergy tests, especially drug provocation tests. A significant heterogeneity exists in current practice not only among countries, but also among centres within the same country. This suggests the need to re‐evaluate, update and standardize protocols on the management of patients with suspected BL allergy.
Radiation exposure and longitudinal changes in peripheral monocytes over 50 years: the Adult Health Study of atomic‐bomb survivors
Authors: Yoshida Kengo , French Benjamin , Yoshida Noriaki , Hida Ayumi , Ohishi Waka , Kusunoki Yoichiro 
Published: January 2019

SummaryEnhanced inflammatory responses have been suggested decades after radiation exposure in atomic‐bomb survivors, but cellular and molecular alterations related to prolonged inflammation remain unclear. This study, utilizing longitudinal haematological data over 50 years for 14 000 persons, investigated whether radiation exposure promoted the relative increase in peripheral myeloid cells, known as an aging‐associated indicator of low‐grade inflammation. Statistical modelling was performed with a linear mixed‐effects model for leucocyte subsets, together with a proportional hazards regression model for all‐cause mortality. We found that age trends in lymphocyte, neutrophil and monocyte percentages or counts differed before versus after age 60 years. Radiation dose was associated with monocyte percentages and counts, but not with the lymphoid‐myeloid cell ratio. Radiation effects on monocytes were stronger after versus before age 60 years. Increases in monocyte percentages and counts were associated with higher risk of all‐cause mortality. Studies of chromosomal aberrations have shown a clonal expansion of haematopoietic stem cells among atomic‐bomb survivors. Therefore, radiation exposure might accelerate aging‐associated clonal haematopoiesis, which could result in a long‐lasting elevation of circulating monocytes.
Computational insights into the different catalytic activities of CYP3A4 and CYP3A5 toward schisantherin E
Authors: Xue Yuhan , Li Junhao , Wu Zengrui , Liu Guixia , Tang Yun , Li Weihua 
Published: January 2019

AbstractThe cytochromes CYP3A4 and CYP3A5 share 84% sequence identity, but they exhibit different catalytic activities toward some substrates. Schisantherin E (SE) was recently identified as a selective substrate of CYP3A5, which exhibited catalytic efficiency that was more than 23 times higher than CYP3A4. At present, however, the structural determinants responsible for the different catalytic activities of the two enzymes toward SE have not been fully understood. In this study, a combination of molecular docking, molecular dynamic simulations, and binding free energy calculation was performed on the CYP3A4/CYP3A5‐SE systems to investigate the issue. The results demonstrate that Ser119 in CYP3A4 and Glu374 in CYP3A5 formed direct hydrogen bonding with SE, respectively. Additionally, one water molecule located between the B‐C loop and the I helix mediated different hydrogen‐bonding networks between CYP3A4/3A5 and SE. The residue differences (Phe/Leu108 and Leu/Phe210) triggered the distinct conformational changes of the Phe‐cluster residues, especially Phe213 and Phe215, which formed stronger hydrophobic interactions with SE in CYP3A5. The calculated binding free energies were consistent with the experimental results.
Bisubstrate inhibitors to target histone acetyltransferase 1
Authors: Ngo Liza , Brown Tyler , Zheng Yujun G. 
Published: January 2019

AbstractDeveloping selective enzyme inhibitors allows for the expansion of molecular toolboxes to investigate functions and activities of target enzymes. The histone acetyltransferase 1 (HAT1) is among the first histone acetyltransferase (HAT) enzymes that were discovered in the mid‐1990s; however, it remains one of the poorly studied enzymes in comparison with the other HATs. Although HAT1 has been linked to various disease states, no inhibitors have been reported to target HAT1. Here, we designed a set of peptide‐CoA conjugates as bisubstrate inhibitors of HAT1 with submicromolar potency. In particular, the bisubstrate inhibitor H4K12CoA exhibited a low Ki value of 1.1 nM for HAT1. In addition, H4K12CoA was shown to be a competitive inhibitor with respect to both AcCoA and H4 peptide, suggesting a unique kinetic mechanism of HAT1 catalysis. Creating these submicromolar inhibitors offers mechanistic tools to better understand how HAT1 recognizes substrates and cofactors, as well as provides chemical leads to further develop therapeutic agents to target this important enzyme for disease therapy.
The effect of isolated nocturnal oxygen desaturations on serum hs‐CRP and IL‐6 in patients with chronic obstructive pulmonary disease
Authors: Macrea Madalina M. , Owens Robert L. , Martin Thomas , Smith Dan , Oursler Krisann K. , Malhotra Atul 
Published: January 2019

AbstractIntroductionA majority of patients with chronic obstructive pulmonary disease (COPD) die of cardiovascular disease (CVD), yet the mechanisms responsible for this association are not fully understood. It remains unknown if isolated nocturnal oxygen desaturation (iNOD) could be one of the potential pathways by which the ‘inflammatory COPD’ phenotype leads to CVD.ObjectivesWe aimed to evaluate if COPD patients who meet the Medicare guidelines for nocturnal oxygen therapy (iNOT+) had higher serum hs‐CRP and IL‐6 than those who did not meet the guidelines for iNOT (iNOT−).MethodsPatients with moderate to severe COPD (ie FEV1 < 80% and FEV1/FVC < 70), who were not on oxygen, underwent nocturnal oximetry on room air. Serum IL‐6 and hs‐CRP were collected the morning after the nocturnal oximetry testing.ResultsA total of 28 patients were included in the study, 8 of whom had more than 5 minutes and 5% of their sleep time spent at oxygen saturation less than 88% and constituted the iNOT+ group. Only serum hs‐CRP was significantly higher in iNOT+ than iNOT− (P = 0.050). There was no difference in the rate of COPD exacerbations at one and three months, or five‐year survival between the groups (P > 0.3).ConclusionCOPD patients who have more than 5 minutes and 5% of their sleep time spent at oxygen saturation less than 88% have increased hs‐CRP, which is associated with increased risk of future CVD.
Continuity, Discontinuity and Incoherence in the Bretton Woods Order: A Hirschmanian Reading
Authors: Grabel Ilene 
Published: January 2019

ABSTRACTThis article examines the effects of the Asian crisis and especially the global financial crisis on developmental finance (that is, long‐term project finance and counter‐cyclical liquidity support) and the global financial architecture. In this connection three claims are advanced. The first is positive: that the crises occasioned meaningful although ad hoc, uneven discontinuities. The conjunction of discontinuities and continuities is imparting incoherence to the developmental and global financial architecture. The second claim is normative and controversial. Contrary to the common narrative, emergent incoherence is (on balance) productive of development and stability rather than debilitating. Actors in parts of the global South and East enjoy greater opportunities for institutional experimentation today in comparison with the limited space available in the coherent neoliberal era when the Bretton Woods institutions were monolithic. All of the experiments underway are not equally likely to survive, but even failures can provide lessons and networks that contribute to future successes. Emergent redundancy and new networks of institutional cooperation increase financial resilience. The article also explores the risks of incoherence and redundancy. The third claim is that productive incoherence can be understood within a ‘Hirschmanian mindset’ — an understanding of change and development informed by Albert Hirschman's theoretical and epistemic commitments.