bluuebunny/crossref_metadata_2025_split huggingface dataset:
Olfactory perception of chemically diverse molecules
Authors: Keller Andreas , Vosshall Leslie B. 
Published: April 2016

ABSTRACTBackground: Understanding the relationship between a stimulus and how it is perceived reveals fundamental principles about the mechanisms of sensory perception. While this stimulus-percept problem is mostly understood for color vision and tone perception, it is not currently possible to predict how a given molecule smells. While there has been some progress in predicting the pleasantness and intensity of an odor, perceptual data for a larger number of diverse molecules are needed to improve current predictions. Towards this goal, we tested the olfactory perception of 480 structurally and perceptually diverse molecules at two concentrations using a panel of 55 healthy human subjects.Results: For each stimulus, we collected data on perceived intensity, pleasantness, and familiarity. In addition, subjects were asked to apply 20 semantic odor quality descriptors to these stimuli, and were offered the option to describe the smell in their own words. Using this dataset, we replicated several previous correlations between molecular features of the stimulus and olfactory perception. The number of sulfur atoms in a molecule was highly correlated with the descriptors “garlic” “fish” “decayed,” and large and structurally complex molecules were perceived to be more pleasant. We discovered a number of strong correlations in intensity perception between molecules, which suggests a shared mechanism for perceiving these molecules. We show that familiarity had a strong effect on the ability of subjects to describe a smell. Many subjects used commercial products to describe familiar odors, highlighting the role of prior experience in biasing verbal report of perceived smells. Nonspecific descriptors like “chemical” were applied frequently to unfamiliar smells, and unfamiliar odors were generally rated as neither pleasant nor unpleasant.Conclusions: We present a very large psychophysical dataset and use this to correlate molecular features of a stimulus to olfactory percept. Our work reveals robust correlations between molecular features and perceptual qualities, and highlights the dominant role of familiarity and experience in assigning verbal descriptors to smells.
New insights in host-associated microbial diversity with broad and accurate taxonomic resolution
Authors: Agler Matthew T. , Mari Alfredo , Dombrowski Nina , Haquard Stéphane , Kemen Eric M. 
Published: April 2016

SummaryDeep microbiome profiling has sparked a revolution in biology, recontextualizing mechanisms such as macroorganismal adaptation and evolution. Amplicon sequencing has been critical for characterization of highly diverse microbiomes, but several challenges still hinder their investigation: (1) Poor coverage of the full diversity, (2) Read depth losses and (3) Erroneous diversity inflation/distortion.We developed a modular approach to quickly profile at least 8 interchangeable loci in a single sequencing run, including a simple and cost-effective way to block amplification of non-targets (like host DNA). We further correct observed distortion in amplified diversity by phylogenetically grouping erroneous OTUs, creating a phylogeny-based unit we call OPUs.Our approach achieves full, accurate characterization of a mixed-kingdom mock community of bacteria, fungi and oomycetes at high depth even in non-target contaminated systems. The OPU concept enables much more accurate estimations of alpha and beta diversity trends than OTUs and overcomes disagreements between studies caused by methodology. Leveraging the approach in theArabidopsis thalianaphyllosphere, we generated to our knowledge the most complete microbiome survey to date.Microbiomes are extremely diverse, extending well beyond bacteria and fungi. Our method makes new questions in a variety of fields tractable with accurate, systems-based overviews of microbial community structures.
Direct binding to RPA-coated ssDNA allows recruitment of the ATR activator TopBP1 to sites of DNA damage
Authors: Acevedo Julyana , Yan Shan , Michael Matthew 
Published: April 2016

ABSTRACTA critical event for the ability of cells to tolerate DNA damage and replication stress is activation of the ATR kinase. ATR activation is dependent on the BRCT repeat-containing protein TopBP1. Previous work has shown that recruitment of TopBP1 to sites of DNA damage and stalled replication forks is necessary for downstream events in ATR activation, however the mechanism for this recruitment was not known. Here, we use protein binding assays and functional studies inXenopusegg extracts to show that TopBP1 makes a direct interaction, via its BRCT2 domain, with RPA-coated ssDNA. We identify a point mutant that abrogates this interaction, and show that this mutant fails to accumulate at sites of DNA damage, and that the mutant cannot activate ATR. These data thus supply a mechanism for how the critical ATR activator, TopBP1, senses DNA damage and stalled replication forks to initiate assembly of checkpoint signaling complexes.
Scalable Production of Human Erythrocytes from Induced Pluripotent Stem Cells
Authors: Wang Ying , Gao Yongxing , He Chaoxia , Ye Zhaohui , Gerecht Sharon , Cheng Linzhao 
Published: April 2016

ABSTRACTIn vitro production of erythrocytes in physiologic numbers from human induced pluripotent stem cells (hiPSCs) holds great promise for improved transfusion medicine and novel cell therapies. We report here, for the first time, a strategy for scalable and xeno-free differentiation of hematopoietic stem/progenitor cells from hiPSCs and subsequent erythrocytes specification, by using stepwise cell culture conditions and by integrating spinner flasks and rocker. This system supported robust and reproducible definitive hematopoietic differentiation of multiple hiPSC lines. We demonstrated an ultra-high yield of up to 4×109CD235a+erythrocytes at >98% purity when using a 1-litre spinner flask for suspension culture. Erythrocytes generated from our system can reach a mature stage with red blood cell (RBC) characteristics of enucleation, β-globin protein expression and oxygen-binding ability. The entire process is xeno-free and clinically compliant, allowing future mass production of hiPSC-derived RBCs for transfusion medicine purposes.
PODOCYTURIA mRNAs: EARLIER AND SUPERIOR PREDICTORS OF CARDIOVASCULAR OUTCOMES
Authors: Eid Assaad A. , Habib Robert H. , Abdel Fattah Ahmed , Al Jalbout Nour , Badr Kamal F. 
Published: April 2016

AbstractIncreased filtration of albumin, a result of injury to glomerular endothelial and epithelial cells (podocytes), leads to increased albumin excretion rate (AER) which defines “moderate albuminuria”, a predictor of cardiovascular events (CVD). Since filtered albumin is modified by renal proximal tubule albumin retrieval, we hypothesized that urinary podocyte shedding (podocyturia), as a biomarker of ongoing glomerular microvascular injury, may be a more relevant and earlier predictor of CVD than moderate albuminuria.Type II diabetic subjects (mean age: 46/60 men/women) with normal AER [<2.26 mg/mmole (20 μg/mg) creatinine] and free of overt cardiovascular disease (CVD) were studied. AER and podocyte-specific proteins (podocin and nephrin) mRNAs were measured at baseline (Visit 1), 3-4 years later (Visit 2) and at 7 years (Visit 3). Development of CVD (acute coronary syndrome, stroke, and/or peripheral vascular disease) was collected as outcome. Seven-year Kaplan-Meier time-to-event (log rank) data were compared among baseline biomarker tercile groups (low, intermediate, high).All three biomarkers increased significantly between visits. Visit 1AER terciles exhibited similar time to CVD (p=0.127), in contrast with step-wise and substantial increases in CVD events predicted by Visit 1 podocin and nephrin terciles. Considered as continuous factors, the covariate-adjusted hazard ratios (95% confidence intervals) [HR] were highest for podocin mRNA [HR=15.9 (6.1-41.8); p<0.001], intermediate for nephrin mRNA [HR=7.61 (3.75-15.5); p<0•001] and lowest for AER [HR=1.17 (1.01-1.36); p=0•041].Compared to moderate albuminuria, podocyturia predicts more accurately and at a significantly earlier time point the presence of silent systemic vascular injury ultimately manifesting as overt cardiovascular events.
Genetic and chemical differentiation ofCampylobacter coliandCampylobacter jejunilipooligosaccharide pathways
Authors: Culebro Alejandra , Revez Joana , Pascoe Ben , Friedmann Yasmin , Hitchings Matthew D , Stupak Jacek , Sheppard Samuel K , Li Jianjun , Rossi Mirko 
Published: April 2016

ABSTRACTDespite the importance of lipooligosaccharides (LOS) in the pathogenicity of campylobacteriosis, little is known about the genetic and phenotypic diversity of LOS inC. coli. In this study, we investigated the distribution of LOS locus classes among a large collection of unrelatedC. coliisolates sampled from several different host species. Furthermore, we pairedC. coligenomic information and LOS chemical composition for the first time to identify mechanisms consistent with the generation of LOS phenotypic heterogeneity. After classifying three new LOS locus classes, only 85% of the 144 isolates tested were assigned to a class, suggesting higher genetic diversity than previously thought. This genetic diversity is at the basis of a completely unexplored LOS structure heterogeneity. Mass spectrometry analysis of the LOS of nine isolates, representing four different LOS classes, identified two features distinguishingC. coliLOS fromC. jejuni’s. GlcN-GlcN disaccharides were present in the lipid A backbone in contrast to the GlcN3N-GlcN backbone observed inC. jejuni. Moreover, despite that many of the genes putatively involved in Qui3pNAcyl were absence in the genomes of various isolates, this rare sugar was found in the outer core of allC. coli. Therefore, regardless the high genetic diversity of LOS biosynthes is locus inC. coli, we identified species-specific phenotypic features ofC. coliLOS which might explain differences betweenC. jejuniandC. coliin terms of population dynamics and host adaptation.Depositories (where applicable)The whole genome sequences ofC. coliare publicly available on the RAST server (http://rast.nmpdr.org) with guest account (login and password ‘guest’) under IDs: 195.91, 195.96-195.119, 195.124-195.126, 195.128-195.130, 195.133, 195.134, 6666666.94320
Measuring healthcare productivity – from unit to system level
Authors: Kämäräinen Vesa Johannes , Peltokorpi Antti , Torkki Paulus , Tallbacka Kaj 
Published: April 2016

Purpose
Healthcare productivity is a growing issue in most Western countries where healthcare expenditure is rapidly increasing. Therefore, accurate productivity metrics are essential to avoid sub-optimization within a healthcare system. In this article, we focus on healthcare production system productivity measurement.

Design/methodology/approach
Traditionally, healthcare productivity has been studied and measured independently at the unit, organization, and system level. Suggesting that productivity measurement should be done in different levels, while simultaneously linking productivity measurement to incentives, this study presents the challenges of productivity measurement at the different levels. The study introduces different methods to measure productivity in healthcare. In addition, it provides background information on the methods used to measure productivity and the parameters used in these methods. A pilot investigation of productivity measurement is used to illustrate the challenges of measurement, to test the developed measures, and to prove the practical information for managers.

Findings
The study introduces different approaches and methods to measure productivity in healthcare.

Research limitations/implications

Practical implications
A pilot investigation of productivity measurement is used to illustrate the challenges of measurement, to test the developed measures, and to prove the practical benefits for managers.

Originality/value
We focus on the measurement of the whole healthcare production system and try to avoid sub-optimization. Additionally considering an individual patient approach, productivity measurement is examined at the unit level, the organizational level, and the system level.
Healthcare managers’ construction of the manager role in relation to the medical profession
Authors: von Knorring Mia , Alexanderson Kristina , Eliasson Miriam A 
Published: April 2016

Purpose
– The purpose of this paper is to explore how healthcare managers construct the manager role in relation to the medical profession in their organisations.

Design/methodology/approach
– In total, 18 of Sweden’s 20 healthcare chief executive officers (CEOs) and 20 clinical department managers (CDMs) were interviewed about their views on management of physicians. Interviews were performed in the context of one aspect of healthcare management; i.e., management of physicians’ sickness certification practice. A discourse analysis approach was used for data analysis.

Findings
– Few managers used a management-based discourse to construct the manager role. Instead, a profession-based discourse dominated and managers frequently used the attributes “physician” or “non-physician” to categorise themselves or other managers in their managerial roles. Some managers, both CEOs and CDMs, shifted between the management- and profession-based discourses, resulting in a kind of “yes, but […]” approach to management in the organisations. The dominating profession-based discourse served to reproduce the power and status of physicians within the organisation, thereby rendering the manager role weaker than the medical profession for both physician and non-physician managers.

Research limitations/implications
– Further studies are needed to explore the impact of gender, managerial level, and basic profession on how managers construct the manager role in relation to physicians.

Practical implications
– The results suggest that there is a need to address the organisational conditions for managers’ role taking in healthcare organisations.

Originality/value
– Despite the general strengthening of the manager position in healthcare through political reforms during the last decades, this study shows that a profession-based discourse clearly dominated in how the managers constructed the manager role in relation to the medical profession on the workplace level in their organisations.
Accounting, identity, autopoiesis + sustainability
Authors: Khan Tehmina , Gray Rob 
Published: April 2016

Purpose
This paper is prompted by an analysis of accounting and accounting education by Lawrence et al. (2013) in this journal. In that paper, the authors use the theory of autopoiesis to articulate and explore, what they argue is, an inappropriate conservatism in accounting. This aims to develop the insights offered by Lawrence et al., to advance the understanding of autopoiesis and to use the insights from the theory of autopoiesis to try and confront (what we see as) the resistance shown in business and accounting to the possibilities of a more substantive sustainability agenda.

Design/methodology/approach
The essay takes its departure point as the paper by Lawrence et al. and uses the theory of autopoiesis as a metaphorical lens through which to re-examine accounting, business and educational practice with respect to sustainability.

Findings
This paper depart somewhat from Lawrence et al.’s arguments and inferences but broadly supports their contentions that accounting and accounting education are autopoietic. Some advances are offered to the theory and some issues for future research are briefly speculated upon. The analysis succeeds in highlighting that the accounting, business and educational systems may well be protecting their “cores” but are doing so by ignoring crucial and life-threatening information. In autopoietic terms, the sub-systems are behaving as closed systems that are causing self-harm and are being psychopathic. It is speculate that accounting educators may be, themselves, acting as autopoietic persons.

Research limitations/implications
The essay, in identifying some of the empirical weaknesses inherent in the theory of autopoiesis in a social science context, suggests that the persuasiveness or otherwise of the theory will probably lie in the extent to which a reader finds the heuristic plausible and not in any easily testable propositions. The implications, if this limitation is accepted, are, broadly, that accounting and accounting education are acting psychopathically in the face of (arguably) life-threatening data.

Practical Implications
There are extensive implications for research and policy but only those for education are explored here.

Social Implications
If the analysis is persuasive, the implication for engagement with the exigencies of sustainability is profound and disturbing.

Originality/value
The paper has two primary purposes: to challenge and develop debate around Lawrence et al.’s arguments and to use autopoiesis as one explanation for the inertia around sustainability, business and accounting. The paper extends the theory of autopoiesis as articulated in accounting to embrace both the issue of nesting systems and the autopoietic person. The combination of these contributions is combined with Lawrence et al., in offering a substantive challenge to accounting educators: albeit a substantively different one than those authors offered. It is these matters of difference that ultimately challenge the authors’ roles as educators, researchers and accountants.
Role of tumour necrosis factor‐a in the regulation of T‐type calcium channel current in HL‐1 cells
Authors: Rao Fang , Xue Yu‐mei , Wei Wei , Yang Hui , Liu Fang‐zhou , Chen Shao‐xian , Kuang Su‐juan , Zhu Jie‐ning , Wu Shu‐lin , Deng Chun‐yu 
Published: April 2016

SummaryIncreasing evidence indicates that inflammation contributes to the initiation and perpetuation of atrial fibrillation (AF). Although tumour necrosis factor (TNF)‐α levels are increased in patients with AF, the role of TNF‐α in the pathogenesis of AF remains unclear. Besides L‐type Ca2+ currents (ICa,L), T‐type Ca2+ currents (ICa,T) also plays an important role in the pathogenesis of AF. This study was designed to use the whole‐cell voltage‐clamp technique and biochemical assays to explore if TNF‐α is involved in the pathogenesis of AF through regulating ICa,T in atrial myocytes. It was found that compared with sinus rhythm (SR) controls, T‐type calcium channel (TCC) subunit mRNA levels were decreased, while TNF‐α expression levels were increased, in human atrial tissue from patients with AF. In murine atrial myocyte HL‐1 cells, after culturing for 24 h, 12.5, 25 and 50 ng/mL TNF‐α significantly reduced the protein expression levels of the TCC α1G subunit in a concentration‐dependent manner. The peak current was reduced by the application of 12.5 or 25 ng/mL TNF‐α in a concentration‐dependent manner (from −15.08 ± 1.11 pA/pF in controls to −11.89 ± 0.83 pA/pF and −8.54 ± 1.55 pA/pF in 12.5 or 25 ng/mL TNF‐α group respectively). TNF‐α application also inhibited voltage‐dependent inactivation of ICa,T, shifted the inactivation curve to the left. These results suggest that TNF‐α is involved in the pathogenesis of AF, probably via decreasing ICa,T current density in atrium‐derived myocytes through impaired channel function and down‐regulation of channel protein expression. This pathway thus represents a potential pathogenic mechanism in AF.
C‐di‐GMP regulates the expression of lapA and bcs operons via FleQ in Pseudomonas putida KT2440
Authors: Xiao Yujie , Nie Hailing , Liu Huizhong , Luo Xuesong , Chen Wenli , Huang Qiaoyun 
Published: April 2016

SummaryCyclic diguanylate (c‐di‐GMP) positively modulates the production of biofilm matrix components from the transcriptional to the post‐translational level in a variety of bacterial species. However, mechanisms by which it regulates these opponents in Pseudomonas putida KT2440 remain unclear. Here we show that c‐di‐GMP regulates the adhesin LapA, LapF and exopolysaccharides Bcs, Pea at transcriptional level. Transcriptional regulator FleQ is required for the modulation of lapA and bcs expression by c‐di‐GMP, but seems not to be necessary for that of lapF and pea. We also found that fleQ mutant of P. putida was defective in biofilm formation and had smooth colony morphology. Transcription assay indicates that FleQ acts as an activator of lapA, but a repressor of bcs. In vitro experiments show that FleQ binds to lapA and bcs promoter DNA. The binding to lapA promoter was slightly promoted by c‐di‐GMP, while binding to bcs promoter was inhibited by c‐di‐GMP. Our results show that c‐di‐GMP regulates the expression of lapA and bcs operons via FleQ in P. putida.
Postoperative Mycoplasma hominis infection after robot‐assisted laparoscopic radical prostatectomy: A case report
Authors: Yokoyama Hitoshi , Domen Takahisa , Hiragata Shiro , Ogawa Teruyuki , Matsumoto Takehisa , Ishizuka Osamu 
Published: April 2016

AbstractA 59‐year‐old man developed a high fever, elevated white blood cell count, elevated C‐reactive protein level, and perineal pain 5 days after robot‐assisted laparoscopic radical prostatectomy. Treatment with cefmetazole was ineffective. A urine specimen was submitted for culture on postoperative day 7, and Mycoplasma hominis (M. hominis) was detected 1 week later. Cefmetazole was therefore switched to quinolone. The clinical symptoms and laboratory data immediately showed marked improvement. M. hominis has been shown to inhabit the genitourinary tract. Although it is considered to induce urethritis, its pathogenicity in healthy male subjects has not been investigated. M. hominis is difficult to detect and is resistant to β‐lactams because it lacks a cell wall. Urine culture sometimes results in false‐negative results. In cases where empirical therapy for postoperative infection is ineffective, surgeons should recognize the possibility of M. hominis involvement and consider changing the antibiotic used.
Indications for the laparoscopic approach to acute small bowel obstruction: A retrospective review of 50 cases, a literature review, and a single hospital's preliminary experience
Authors: Cantarella Francesco , Evoli Luca Pio , Renzi Claudio , Cavazzoni Emanuel , Contine Alessandro , Cesari Maurizio , Donini Annibale 
Published: April 2016

AbstractSmall bowel obstruction (SBO) is mainly caused by postoperative adhesions, but a broad spectrum of diseases may cause this pathogenetic condition. Laparoscopic treatment represents an efficient approach to SBO. The aim of this paper was to review a single center's experience with a minimally invasive approach to multiple pathologic scenarios causing SBO. From January 2010 to December 2012, 50 consecutive patients underwent laparoscopic surgery for mechanical SBO. In 90% of patients, the surgical procedure was totally laparoscopic, while 10% required conversion to midline laparotomy. In‐hospital morbidity was 15% among totally laparoscopic patients and 40% among those who underwent conversion to midline laparotomy. Thirty‐day mortality was zero. One patient died 4 months postoperatively from neoplastic disease progression; the remaining patients were free from occlusive symptoms at follow‐up. The minimally invasive technique applies to a broad spectrum of cases. A larger cohort of patients seems necessary to reproduce our results and confirm the effectiveness of a laparoscopic approach to SBO.