bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduced ceftazidime and ertapenem susceptibility due to production of OXA-2 in Klebsiella pneumoniae ST258
Authors: Iovleva Alina , Mettus Roberta T , McElheny Christi L , Mustapha Mustapha M , Van Tyne Daria , Shields Ryan K , Pasculle A William , Cooper Vaughn S , Doi Yohei 
Published: April 2019

Abstract

Background
OXA-2 is a class D β-lactamase that confers resistance to penicillins, as well as narrow-spectrum cephalosporins. OXA-2 was recently reported to also possess carbapenem-hydrolysing activity. Here, we describe a KPC-2-encoding Klebsiella pneumoniae isolate that demonstrated reduced susceptibility to ceftazidime and ertapenem due to production of OXA-2.

Objectives
To elucidate the role of OXA-2 production in reduced ceftazidime and ertapenem susceptibility in a K. pneumoniae ST258 clinical isolate.

Methods
MICs were determined by the agar dilution method. WGS was conducted to identify and compare resistance genes between isolates. Expression of KPC-2 was quantified by quantitative RT–PCR and immunoblotting. OXA-2 was expressed in Escherichia coli TOP10, as well as in K. pneumoniae ATCC 13883, to define the relative contribution of OXA-2 in β-lactam resistance. Kinetic studies were conducted using purified OXA-2 enzyme.

Results
K. pneumoniae 1761 belonged to ST258 and carried both blaKPC-2 and blaOXA-2. However, expression of blaKPC-2 was substantially reduced due to an IS1294 insertion in the promoter region. K. pneumoniae 1761, K. pneumoniae ATCC 13883 and E. coli TOP10 carrying blaOXA-2-harbouring plasmids showed reduced susceptibility to ertapenem and ceftazidime, but meropenem, imipenem and cefepime were unaffected. blaOXA-2 was carried on a 2910 bp partial class 1 integron containing aacA4-blaOXA-2-qacEΔ1-sul1 on an IncA/C2 plasmid, which was not present in the earlier ST258 isolates possessing blaKPC-2 with intact promoters. Hydrolysis of ertapenem by OXA-2 was confirmed using purified enzyme.

Conclusions
Production of OXA-2 was associated with reduced ceftazidime and ertapenem susceptibility in a K. pneumoniae ST258 isolate.
Activity of imipenem/relebactam against MDR Pseudomonas aeruginosa in Europe: SMART 2015–17
Authors: Lob Sibylle H , Karlowsky James A , Young Katherine , Motyl Mary R , Hawser Stephen , Kothari Nimmi D , Gueny Melinda E , Sahm Daniel F 
Published: April 2019

AbstractObjectivesRelebactam is a diazabicyclooctane non-β-lactam inhibitor of Ambler class A and C β-lactamases that is in clinical development in combination with imipenem/cilastatin. The current study evaluated the in vitro activity of imipenem/relebactam against 5447 isolates of Pseudomonas aeruginosa submitted to the SMART global surveillance programme in 2015–17 by 67 clinical laboratories in 22 European countries.MethodsMICs were determined using the CLSI broth microdilution reference method (Eleventh Edition: M07, 2018). Relebactam was tested at a fixed concentration of 4 mg/L in combination with doubling dilutions of imipenem. MICs were interpreted using EUCAST clinical breakpoints (version 8.1); imipenem breakpoints were applied to imipenem/relebactam.ResultsRates of susceptibility to imipenem and imipenem/relebactam (MIC ≤4 mg/L) were 69.4% and 92.4%, respectively, for all isolates of P. aeruginosa. Over one-third of all isolates (34.9%, 1902/5447) were MDR; lower respiratory tract isolates (38.3%, 1327/3461) were more frequently MDR than were intraabdominal (28.5%, 355/1245) or urinary tract (29.7%, 212/714) isolates. Of all MDR isolates, 78.2% were susceptible to imipenem/relebactam, a rate that was 50–77 percentage points higher than the rate of susceptibility to imipenem or any other β-lactam tested; rates of susceptibility to imipenem/relebactam were similar for MDR isolates from lower respiratory tract (77.8% susceptible), intraabdominal (80.3%) and urinary tract (76.4%) infections. Overall, relebactam restored imipenem susceptibility to 75.2% (1254/1668) of imipenem-non-susceptible isolates of P. aeruginosa and to 69.6% (947/1361) of imipenem-non-susceptible isolates with an MDR phenotype.ConclusionsRelebactam restored in vitro susceptibility to imipenem for most imipenem-non-susceptible and MDR clinical isolates of P. aeruginosa from European patients.
Identification of novel genes that promote persister formation by repressing transcription and cell division in Pseudomonas aeruginosa
Authors: Long Yuqing , Fu Weixin , Li Shouyi , Ren Huan , Li Mei , Liu Chang , Zhang Buyu , Xia Yushan , Fan Zheng , Xu Chang , Liu Jianfeng , Jin Yongxin , Bai Fang , Cheng Zhihui , Liu Xiaoyun , Jin Shouguang , Wu Weihui 
Published: April 2019

AbstractObjectivesBacterial persisters are a small subpopulation of cells that are highly tolerant of antibiotics and contribute to chronic and recalcitrant infections. Global gene expression in Pseudomonas aeruginosa persister cells and genes contributing to persister formation remain largely unknown. The objective of this study was to examine the gene expression profiles of the persister cells and those that regained growth in fresh medium, as well as to identify novel genes related to persister formation.MethodsP. aeruginosa persister cells and those that regrew in fresh medium were collected and subjected to RNA sequencing analysis. Genes up-regulated in the persister cells were overexpressed to evaluate their roles in persister formation. The functions of the persister-contributing genes were assessed with pulse–chase assay, affinity chromatography, fluorescence and electron microscopy, as well as a light-scattering assay.ResultsAn operon containing PA2282–PA2287 was up-regulated in the persister cells and down-regulated in the regrowing cells. PA2285 and PA2287 play key roles in persister formation. PA2285 and PA2287 were found to bind to RpoC and FtsZ, which are involved in transcription and cell division, respectively. Pulse–chase assays demonstrated inhibitory effects of PA2285 and PA2287 on the overall transcription. Meanwhile, light-scattering and microscopy assays demonstrated that PA2285 and PA2287 interfere with cell division by inhibiting FtsZ aggregation. PA2285 and PA2287 are conserved in pseudomonads and their homologous genes in Pseudomonas putida contribute to persister formation.ConclusionsPA2285 and PA2287 are novel bifunctional proteins that contribute to persister formation in P. aeruginosa.
National survey on total-body irradiation prior to reduced-intensity stem cell transplantation in Japan: The Japanese Radiation Oncology Study Group
Authors: Kawaguchi Hiroki , Soejima Toshinori , Ishibashi Naoya , Akiba Takeshi , Hasegawa Masatoshi , Isobe Kouichi , Ito Hitoshi , Imai Michiko , Ejima Yasuo , Hata Masaharu , Sasai Keisuke , Shimoda Emiko , Oguchi Masahiko , Akimoto Tetsuo 
Published: April 2019

AbstractReduced-intensity stem cell transplantation (RIST) minimizes the adverse effects of traditional hematopoietic stem cell transplantation, and low-dose total-body irradiation (TBI) is administered over a short period prior to RIST (TBI–RIST). Different institutes adopt different approaches for the administration of TBI–RIST, and since no study had previously investigated this issue, a survey of the TBI schedules in Japan was conducted. In October 2015, the Japanese Radiation Oncology Study Group initiated a national survey of TBI–RIST procedures conducted between 2010 and 2014. Of 186 institutions performing TBI, 90 (48%) responded to the survey, 78 of which performed TBI–RIST. Of 2488 patients who underwent TBI for malignant disease at these institutions, 1412 (56.8%) patients were treated for leukemia, 477 (19.2%) for malignant lymphoma, 453 (18.2) for myelodysplastic syndrome, 44 (1.8%) for multiple myeloma, and 102 (4.1%) for other malignant diseases. Further, 206 (52.0%) of 396 patients (a high proportion of patients) who underwent TBI for benign disease had aplastic anemia. The TBI–RIST equipment and treatment methods were similar to those used for myeloablative regimens. Routinely shielded organs included the lungs (43.6%), eyes (50.0%) and kidneys (10.2%). The ovaries (14.1%), thyroid (6.4%) and testicles (16.7%) were also frequently shielded, possibly reflecting an emphasis on shielding reproductive organs in children. TBI–RIST was performed more frequently than myeloablative conditioning in patients with benign disease. Genital and thyroid shielding were applied more frequently in patients treated with TBI–RIST than in patients treated with myeloablative conditioning. In conclusion, this study indicates the status of TBI–RIST in Japan and can assist future efforts to standardize TBI–RIST treatment methods and to design a future multicenter collaborative research study.
Mapping of transgenic alleles in soybean using a nanopore-based sequencing strategy
Authors: Li Shengjun , Jia Shangang , Hou Lili , Nguyen Hanh , Sato Shirley , Holding David , Cahoon Edgar , Zhang Chi , Clemente Tom , Yu Bin 
Published: April 2019

Abstract
Transgenic technology was developed to introduce transgenes into various organisms to validate gene function and add genetic variations >40 years ago. However, the identification of the transgene insertion position is still challenging in organisms with complex genomes. Here, we report a nanopore-based method to map the insertion position of a Ds transposable element originating in maize in the soybean genome. In this method, an oligo probe is used to capture the DNA fragments containing the Ds element from pooled DNA samples of transgenic soybean plants. The Ds element-enriched DNAs are then sequenced using the MinION-based platform of Nanopore. This method allowed us to rapidly map the Ds insertion positions in 51 transgenic soybean lines through a single sequencing run. This strategy is high throughput, convenient, reliable, and cost-efficient. The transgenic allele mapping protocol can be easily translated to other eukaryotes with complex genomes.
Systemic signalling through translationally controlled tumour protein controls lateral root formation in Arabidopsis
Authors: Branco Rémi , Masle Josette 
Published: April 2019

AbstractThe plant body plan and primary organs are established during embryogenesis. However, in contrast to animals, plants have the ability to generate new organs throughout their whole life. These give them an extraordinary developmental plasticity to modulate their size and architecture according to environmental constraints and opportunities. How this plasticity is regulated at the whole-organism level is elusive. Here we provide evidence for a role for translationally controlled tumour protein (TCTP) in regulating the iterative formation of lateral roots in Arabidopsis. AtTCTP1 modulates root system architecture through a dual function: as a general constitutive growth promoter enhancing root elongation and as a systemic signalling agent via mobility in the vasculature. AtTCTP1 encodes mRNAs with long-distance mobility between the shoot and roots. Mobile shoot-derived TCTP1 gene products act specifically to enhance the frequency of lateral root initiation and emergence sites along the primary root pericycle, while root elongation is controlled by local constitutive TCTP1 expression and scion size. These findings uncover a novel type for an integrative signal in the control of lateral root initiation and the compromise for roots between branching more profusely or elongating further. They also provide the first evidence in plants of an extracellular function of the vital, highly expressed ubiquitous TCTP1.
MISIM v2.0: a web server for inferring microRNA functional similarity based on microRNA-disease associations
Authors: Li Jianwei , Zhang Shan , Wan Yanping , Zhao Yingshu , Shi Jiangcheng , Zhou Yuan , Cui Qinghua 
Published: April 2019

AbstractMicroRNAs (miRNAs) are one class of important small non-coding RNA molecules and play critical roles in health and disease. Therefore, it is important and necessary to evaluate the functional relationship of miRNAs and then predict novel miRNA-disease associations. For this purpose, here we developed the updated web server MISIM (miRNA similarity) v2.0. Besides a 3-fold increase in data content compared with MISIM v1.0, MISIM v2.0 improved the original MISIM algorithm by implementing both positive and negative miRNA-disease associations. That is, the MISIM v2.0 scores could be positive or negative, whereas MISIM v1.0 only produced positive scores. Moreover, MISIM v2.0 achieved an algorithm for novel miRNA-disease prediction based on MISIM v2.0 scores. Finally, MISIM v2.0 provided network visualization and functional enrichment analysis for functionally paired miRNAs. The MISIM v2.0 web server is freely accessible at http://www.lirmed.com/misim/.
Genome Sequencing Verifies Relapsed Infection of Helicobacter cinaedi
Authors: Sawada Osamu , Gotoh Yasuhiro , Taniguchi Takako , Furukawa Shota , Yoshimura Dai , Sasaki Satomi , Shida Haruki , Kusunoki Yoshihiro , Yamamura Tsuyoshi , Furuya Ken , Itoh Takehiko , Horita Tetsuya , Hayashi Tetsuya , Misawa Naoaki 
Published: April 2019

Abstract

Background
Recurrent infections of Helicobacter cinaedi are often reported, and long-term antimicrobial treatment is empirically recommended to prevent such infections. However, there have been no studies examining whether recurrent infections are relapses of former infections or reinfections with different clones.

Methods
A 69-year-old woman presented with recurrent H cinaedi bacteremia-associated cellulitis after a 51-day interval. We isolated 10 colonies from the blood cultures obtained during each of the 2 episodes and subjected them to whole-genome sequencing (WGS). High-confidence single-nucleotide polymorphisms (SNPs) were identified by an assembly based method. Heterogeneous SNP sites were identified by read mapping. The susceptibility of a representative isolate to 14 antimicrobials was also examined.

Results
Whole-genome sequence analysis revealed only 6 SNP sites among the 20 isolates at the whole-genome level. Based on the 6 SNPs, 5 within-host variants (referred to as genotypes) were identified. All 5 genotypes were detected in the first infection; however, only 2 genotypes were detected in the second infection. Although the H cinaedi clone showed a higher minimum inhibitory concentration to fluoroquinolones and macrolides and responsible mutations were identified, none of the 6 SNPs appeared related to additional resistance.

Conclusions
The second infection analyzed here was a relapse of the first infection. A certain level of within-host genomic heterogeneity of the H cinaedi clone was already present in the first infection. Our results suggest the importance of longer treatment courses to eradicate H cinaedi for preventing the relapse of its infection.
The Origin of Carbonatites from Amba Dongar within the Deccan Large Igneous Province
Authors: Chandra Jyoti , Paul Debajyoti , Stracke Andreas , Chabaux François , Granet Mathieu 
Published: April 2019

Abstract
There are disparate views about the origin of global rift- or plume-related carbonatites. The Amba Dongar carbonatite complex, Gujarat, India, which intruded into the basalts of the Deccan Large Igneous Province (LIP), is a typical example. On the basis of new comprehensive major and trace element and Sr–Nd–Pb isotope data, we propose that low-degree primary carbonated melts from off-center of the Deccan–Réunion mantle plume migrate upwards and metasomatize part of the subcontinental lithospheric mantle (SCLM). Low-degree partial melting (∼2%) of this metasomatized SCLM source generates a parental carbonated silicate magma, which becomes contaminated with the local Archean basement during its ascent. Calcite globules in a nephelinite from Amba Dongar provide evidence that the carbonatites originated by liquid immiscibility from a parental carbonated silicate magma. Liquid immiscibility at crustal depths produces two chemically distinct, but isotopically similar magmas: the carbonatites (20% by volume) and nephelinites (80% by volume). Owing to their low heat capacity, the carbonatite melts solidified as thin carbonate veins at crustal depths. Secondary melting of these carbonate-rich veins during subsequent rifting generated the carbonatites and ferrocarbonatites now exposed at Amba Dongar. Carbonatites, if formed by liquid immiscibility from carbonated silicate magmas, can inherit a wide range of isotopic signatures that result from crustal contamination of their parental carbonated silicate magmas. In rift or plume-related settings, they can, therefore, display a much larger range of isotope signatures than their original asthenosphere or mantle plume source.
Dolbeault cohomology of complex nilmanifolds foliated in toroidal groups
Authors: Fino Anna , Rollenske Sönke , Ruppenthal Jean 
Published: April 2019

Abstract
It is conjectured that the Dolbeault cohomology of a complex nilmanifold $X$ is computed by left-invariant forms. We prove this under the assumption that $X$ is suitably foliated in toroidal groups and deduce that the conjecture holds in real dimension up to six. Our approach generalizes previous methods, where the existence of a holomorphic fibration was a crucial ingredient.
Racial Reconciliation as a Suppressive Frame in Evangelical Multiracial Churches
Authors: Oyakawa Michelle 
Published: April 2019

ABSTRACT
This article analyzes interviews with evangelical multiracial church pastors from the Religious Leadership and Diversity Project (RLDP), drawing on the framing literature from social movements. While a small number of evangelical pastors in the sample utilize a racial justice frame to understand and address racial issues, consistent with prior research, the data indicates that most evangelical multiracial church pastors use a racial reconciliation frame. This frame holds that racial conflict can be eliminated through shared faith, which allows churches to avoid politics and prioritize internal unity. However, findings reveal that the racial reconciliation can function as a suppressive frame that precludes discussions about racial inequality and discourages collective action to promote racial justice. The article discusses the implications of this for social change and cross-racial solidarity.
The Effectiveness of Interventions to Maintain Exercise and Physical Activity in Post-Cardiac Rehabilitation Populations
Authors: Martinello Novella , Saunders Stephanie , Reid Robert 
Published: April 2019

Purpose:
Cardiac rehabilitation is a medically supervised program addressing health behavior changes and promoting self-management among individuals with heart disease. This includes initiation of regular physical activity. However, long-term physical activity after cardiac rehabilitation among this population remains a challenge.

Methods:
This study was a systematic review and meta-analysis according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Randomized controlled trials were identified by searching multiple databases and were selected if they evaluated an intervention with a physical activity or exercise component among individuals who completed cardiac rehabilitation. A descriptive synthesis was performed for all studies and means and standard deviations were used for meta-analysis when possible. Risk of bias, heterogeneity, and publication bias were assessed.

Results:
Twenty-five studies met the inclusion criteria and 19 were included in the meta-analysis. The mean age of participants across studies was 60 yr and 80% were male. Descriptive synthesis of the studies combined with meta-analysis results provided evidence of increased physical activity among intervention groups compared with control groups at follow-up.

Conclusion:
There is evidence to support the effectiveness of interventions aimed at maintaining physical activity and exercise among adults who have completed cardiac rehabilitation.
Referral to Cardiac Rehabilitation and Outcomes for Patients With Takotsubo Cardiomyopathy
Authors: Wu Carolyn M. , McKeon John , Abbott J. Dawn , Jiang Lan , Wu Wen-Chih 
Published: April 2019

Purpose:
The aim of this study was to determine participation rates and outcomes for patients with Takotsubo cardiomyopathy (TC) in a cardiac rehabilitation (CR) program.

Methods:
Patients at 2 academic medical centers with a discharge diagnosis of TC from January 2008 to March 2015 were retrospectively identified. Patients meeting the Mayo Clinic criteria for TC were cross-matched to the CR center affiliated with the hospitals to determine the referral rate and outcomes after completion of the program.

Results:
In total, 380 unique patients were identified who survived the index hospitalization. Eighteen patients (5%) were referred to CR, 15 enrolled, and of those enrolled, 10 patients (67%) completed the program. Patients undergoing percutaneous coronary intervention of a nonculprit vessel at the time of diagnosis was the only predictor for referral to CR (11% vs 1%, P = .01). The 10 patients who completed CR attended 33 ± 6 (range, 20-36) sessions. Weight and body mass index reduction were 2.8 ± 3.5 lb and 0.6 ± 0.7 kg/m2 (P = .04, both), respectively. Post-CR exercise duration was 37 ± 4 min/session, which improved by 13 ± 6 min/session from baseline (P < .01). Two patients entered the phase III maintenance program. One-year cardiac readmission rates were comparable among patients who completed CR and those who were referred but did not attend or complete CR (0% vs 13%, P = .47).

Conclusions:
Referral for the TC population was low; however, enrollment and completion rates were adequate, with percutaneous coronary intervention in nonculprit vessel as the only predictor of CR referral. Limited data showed CR may help with weight reduction and improve exercise duration.
Measuring cardiac output at the bedside
Authors: Huang Stephen J. 
Published: April 2019

Purpose of review
Bedside cardiac output (CO) measurement is an important part of routine hemodynamic monitoring in the differential diagnosis of circulatory shock and fluid management. Different choices of CO measurement devices are available. The purpose of this review is to review the importance of CO [or stroke volume (SV)] measurement and to discuss the various methods (devices) used in determination of CO.

Recent findings
CO measurement devices can be classified into two types: those use simple physical principles with minimal assumptions, and those predicting CO via mathematical modelling with a number of assumptions. Both have pros and cons, with the former being more accurate but with limited continuous monitoring capability whereas the latter less accurate but usually equipped with continuous monitoring functionality. With frequent updates in mathematical models, research data constantly become outdated in this area. Recent data suggest devices based on mathematical modelling have limited accuracies and poor precisions.

Summary
Measurement of CO or SV is important in critically ill patients. Most devices have accuracy and reliability issues. The choice of device should depend on the purpose of measurement. For diagnostic purposes, devices based on simple physical principles, especially thermodilution and transthoracic echocardiography are more reliable due to accuracy.