bluuebunny/crossref_metadata_2025_split huggingface dataset:
NMR studies reveal that protein dynamics critically mediate aggregation of the well-folded and very solubleE. coliS1 ribosomal protein
Authors: Lu Yimei , Lim Liangzhong , Song Jianxing 
Published: August 2017

AbstractUnlike mammalian aging associated with many hallmarks,E. coliaging is only significantly characterized by protein aggregation, thus offering an excellent model for addressing the relationship between protein aggregation and aging. Here we characterized conformations, unfolding and dynamics of ribosomal protein S1 and its D3/D5 domains using NMR, CD and fluorescence spectroscopy. S1 is a 557-residue modular protein containing six S1 motifs. Paradoxically, while S1 is well-folded and very solublein vitro, it was found in various lists of aggregatedE. coliproteins. Our results decipher: 1) S1 has dynamic inter-domain interactions. Strikingly, S1 and its D3/D5 domains have significantly exposed hydrophobic patches characterized by irreversible unfolding. 2) Although D5 has significantly restricted backbone motion on ps-ns time scale, it has global μs-ms conformational dynamics and particularly high “global breathing” motions. 3) D5 assumes the conserved β-barrel fold but contains large hydrophobic patches at least dynamically accessible. Taken together, our study reveals that S1 could be prone to aggregation due to significant dynamics at two levels: inter-domain interactions and individual domains, which may even render buried hydrophobic patches/cores accessible for driving aggregation. This mechanism is most likely to operate in many proteins ofE. coliand other organisms including human.
Oncogenic G12D mutation alters local conformations and dynamics of K-Ras
Authors: Vatansever Sezen , Erman Burak , Gümüş Zeynep H. 
Published: August 2017

AbstractK-Ras is the most frequently mutated oncoprotein in human cancers, and G12D is its most prevalent mutation. To understand how G12D mutation impacts K-Ras function, we need to understand how it alters the regulation of its dynamics. Here, we present local changes in K-Ras structure, conformation and dynamics upon G12D mutation, from long-timescale Molecular Dynamics simulations of active (GTP-bound) and inactive (GDP-bound) forms of wild-type and mutant K-Ras, with an integrated investigation of atomistic-level changes, local conformational shifts and correlated residue motions. Our results reveal that the local changes in K-Ras are specific to bound nucleotide (GTP or GDP), and we provide a structural basis for this. Specifically, we show that G12D mutation causes a shift in the population of local conformational states of K-Ras, especially in Switch-II (SII) and α3-helix regions, in favor of a conformation that is associated with a catalytically impaired state through structural changes; it also causes SII motions to anti-correlate with other regions. This detailed picture of G12D mutation effects on the local dynamic characteristics of both active and inactive protein helps enhance our understanding of local K-Ras dynamics, and can inform studies on the development of direct inhibitors towards the treatment of K-RasG12D-driven cancers.
Chiron: Translating nanopore raw signal directly into nucleotide sequence using deep learning
Authors: Teng Haotian , Cao Minh Duc , Hall Michael B. , Duarte Tania , Wang Sheng , Coin Lachlan J.M. 
Published: August 2017

ABSTRACTSequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology which offers faster and cheaper sequencing than other approaches. However, accurately deciphering the DNA sequence from the noisy and complex electrical signal is challenging. Here, we report Chiron, the first deep learning model to achieve end-to-end basecalling: directly translating the raw signal to DNA sequence without the error-prone segmentation step. Trained with only a small set of 4000 reads, we show that our model provides state-of-the-art basecalling accuracy even on previously unseen species. Chiron achieves basecalling speeds of over 2000 bases per second using desktop computer graphics processing units.
Meta-analysis and Commentary: Preemptive Correction of Arteriovenous Access Stenosis
Authors: Raimann Jochen G. , Waldron Levi , Koh Elsie , Miller Gregg A. , Sor Murat H. , Gray Richard J. , Kotanko Peter 
Published: August 2017

AbstractBackgroundA recent meta-analysis by Ravani and colleagues (Ravani, P., et al., Am J Kidney Dis, 2016. 67(3): p. 446-60.) studied the effect of pre-emptive correction of arterio-venous dialysis vascular access versus deferred care, based on data from 11 trials. The authors reported a non-significant protective treatment effect of pre-emptive correction on access loss, while showing a significant protective effect on thrombosis rates conferred by pre-emptive correction. We revisit this analysis, including data extraction and effects of a heterogenous study population.MethodsWe repeated data extraction from all referenced publications in the meta-analysis by Ravani et al. and corrected event counts where applicable. We repeated the meta-analyses with access loss as the outcome for studies that recruited patients with arterio-venous fistulae (AVF) and grafts (AVG), respectively, using a random effects model with relative risk (RR) and risk difference (RD) of access loss as the outcomes of interest. We repeated data extraction from all referenced publications, and corrected event counts where applicable.ResultsOur conclusions differ from the original findings in two ways. First, after some amendment of the event counts extracted from Mayer et al. (Vascular and Endovascular Surgery 1993), we find a significant overall positive effect of pre-emptive correction on arterio-venous access loss in the overall study population [RR 0.80 (95% CI 0.64 to 0.99), RD −0.07 (95% CI −0.12 to −0.02); Figure 1]. Secondly, we highlight the impact of heterogeneous study populations on the meta-analysis. Whereas the data do not conclusively show a benefit of pre-emptive correction for arteriovenous grafts (AVG; RR = 0.87, 95% CI: 0.69 – 1.11), they show a strong protective effect for arteriovenous fistulae (AVF; RR = 0.5, 95% CI: 0.29 to 0.86).Figure 1:Meta-analysis of access loss, overall and by access type using risk ratio (RR) as the measure of association.Discussion and ConclusionThese findings corroborate clinical arguments such as superior long-term patency of AVF and the nature of AVG failure that often involve infectious causes. The available data indicate mild or no benefit of pre-emptive correction for AVG, but strongly support tight monitoring of dialysis accesses and preemptive intervention and correction upon the slightest suspicion of access stenosis for AVF.
A risk stratification model for lung cancer based on gene coexpression network
Authors: Choi Hongyoon , Na Kwon Joong 
Published: August 2017

AbstractRisk stratification model for lung cancer with gene expression profile is of great interest. Instead of the previously reported models based on individual prognostic genes, we aimed to develop a novel system-level risk stratification model for lung adenocarcinoma based on gene coexpression network. Using multiple microarray datasets obtained from lung adenocarcinoma, gene coexpression network analysis was performed to identify survival-related network modules. Representative genes of these network modules were selected and then, risk stratification model was constructed exploiting deep learning algorithm. The model was validated in two independent test cohorts. Survival analysis using univariate and multivariate Cox regression was performed using the output of the model to evaluate whether the model could predict patients’ overall survival independent of clinicopathological variables. Five network modules were significantly associated with patients’ survival. Considering prognostic significance and representativeness, genes of the two survival-related modules were selected for input data of the risk stratification model. The output of the model was significantly associated with patients’ overall survival in the two independent test sets as well as training set (p < 0.00001, p < 0.0001 and p = 0.02 for training set, test set 1 and 2, respectively). In multivariate analyses, the model was associated with patients’ prognosis independent of other clinical and pathological features. Our study presents a new perspective on incorporating gene coexpression networks into the gene expression signature, and the clinical application of deep learning in genomic data science for prognosis prediction.
A Mathematical model to predict Trichodesmiunspp. bloom during a sewage burst
Authors: Rosales Guido Santos 
Published: August 2017

AbstractA modified version of the Monod equation is proposed to understand the bloom emergence ofTrichodesmiun spp. in presence of sewage outburst. The mathematical model predicts that the bacterial population does not affect the bloom growth. Also, the quotient between the bacteria during the sewage outburst and before is proposed to be equal to the quotient between the influx of limiting resources during burst and the influx before the burst.
Financial constraints and optimal working capital – evidence from an emerging market
Authors: Chauhan Gaurav S. , Banerjee Pradip 
Published: August 2017

Purpose
The purpose of this paper is to investigate the existence of an optimal or target level of working capital for the Indian manufacturing firms, and whether firms intensely follow the target or not.

Design/methodology/approach
The paper uses cash conversion cycle as a measure of net working capital and employs partial-adjustment dynamic panel models to test its target-following behavior.

Findings
The empirical results show that there is no evidence of systematic target-following behavior of working capital for the Indian manufacturing firms. The results hold true even after dividing the sample into four groups depending on the sign and magnitude of deviation. The results further show that lack of target-following tendency is not quite influenced by varying firm-specific characteristics and, therefore, seems to be a systematic feature across firms in India.

Research limitations/implications
Scarcity of such working capital management studies across emerging economies, facing several financial constraints, limits the comparison of findings. Future studies should be conducted to confirm the results.

Practical implications
The findings imply that even though an optimal working capital might exist, emerging market firms may not be able to actively pursue it on account of several financial constraints and managerial considerations.

Originality/value
The study contributes to the scant existing literature on the target-following behavior of working capital management in the Indian manufacturing firms, representing a typical emerging market facing several financial constraints.
Rhetorical strategies in Indian commercial microfinance
Authors: Sarma Sushanta Kumar 
Published: August 2017

Purpose
This paper examines the rhetorical strategies of two Indian microfinance organizations as they transformed from non-profit to commercial format. They shifted forms at a time (year 2010), when commercialization had been criticized severely. The purpose of this paper is to understand “How does a microfinance organization justify its action of transformation to retain legitimacy?”

Design/methodology/approach
The paper adopts a qualitative case study method to understand the phenomena. Interview, archival documents, and field observations are the major source of data for the study. Data analysis is carried out through coding method.

Findings
Drawing from Suddaby and Greenwood’s (2005) work on rhetorical strategies, the paper suggests that these organizations have used two types of rhetorical strategies – cosmological and teleological. These strategies operate in a performative role and link deviant practices with routines. It focuses on institutional maintenance rather than change.

Research limitations/implications
The paper acknowledges two important limitations. First, the rhetorical focus may be influenced by the history of organization. So depending on organization selected, the focus may vary. Second, the paper is constricted by the low-documentation practices prevailing in many civil society organizations.

Originality/value
The paper contributes to the literature on hybrid organization by unpacking the process of sense making in a hybrid form. The paper also reinforces the argument that language operates in a performative role. The paper provides a new context (India) to understand the process of rhetorical strategies.
Physical activity promotion in care homes
Authors: Turpie Lindsay , Whitelaw Sandy , Topping Christopher 
Published: August 2017

Purpose
The purpose of this paper is to report on the implementation of a physical activity (PA) scheme – Let’s Motivate (LM) – within private care homes (CHs) in Dumfries and Galloway (D&G), Scotland; aiming to provide an insight into the different factors which might contribute to its success and further sustainability.

Design/methodology/approach
A qualitative study is described in which one-to-one semi-structured interviews were carried out with eight key staff involved in implementing the project within two purposively sampled CHs; in order to explore their views and experiences of implementation.

Findings
The paper provides an insight into the different factors which stand to both promote and impede the successful implementation of LM, within the two CHs involved.

Originality/value
This paper explores a new and innovative PA initiative in CHs in D&G, Scotland. Studies exploring the factors which can both promote and impede implementation are important as they can help to usefully inform the implementation and sustainability of initiatives.
Disseminated cutaneous Mycobacterium kansasii infection presenting with Rosai–Dorfman disease‐like histological features in a patient carrying anti‐interferon‐γ autoantibodies
Authors: King Yih‐An , Hu Chung‐Hong , Lee Yuarn‐Jang , Lin Chiou‐Feng , Liu Donald , Wang Kuo‐Hsien 
Published: August 2017

AbstractTypical cutaneous non‐tuberculous mycobacteria (NTM) infections show a histopathology pattern of granulomas with admixed Langhans giant cells, and abscesses may be observed in acute lesions. Herein, we describe a patient carrying a high titer of autoantibodies to interferon (IFN)‐γ with disseminated Mycobacterium kansasii infection presenting with emperipolesis and Rosai–Dorfman disease (RDD)‐like histopathological features characterized by remarkable, large, pale‐staining “RD cells”, which were CD68 and S100 positive and CD1a negative. The patient was misdiagnosed with RDD initially, but exhibited a poor response to all interventions. A re‐biopsy revealed Langhans‐type multinucleated giant cells; multiple definite acid‐fast bacilli were also found. M. kansasii was isolated from cultured tissues. Anti‐NTM treatment was initiated. After treatment, all lesions resolved almost completely within the following month. High‐titer anti‐IFN‐γ autoantibodies were detected during follow up, leading to the diagnosis of adult‐onset immunodeficiency syndrome. In conclusion, patients carrying high‐titer autoantibodies to IFN‐γ who also have a disseminated cutaneous M. kansasii infection may present with RDD‐like histopathological features, which may be a pitfall in the diagnosis of disseminated cutaneous NTM infections.
Simulated moult reduces flight performance but overlap with breeding does not affect breeding success in a long‐distance migrant
Authors: Tomotani Barbara M. , Muijres Florian T. , Koelman Julia , Casagrande Stefania , Visser Marcel E. 
Published: August 2017

Abstract

Long‐distance migrants are time‐constrained as they need to incorporate many annual cycle stages within a year. Migratory passerines moult in the short interval between breeding and migration. To widen this interval, moult may start while still breeding, but this results in flying with moulting wings when food provisioning.
We experimentally simulated wing gaps in breeding male pied flycatchers by plucking two primary feathers from both wings. We quantified the nest visitations of both parents, proportion of high‐quality food brought to the nestlings and adults and nestlings condition. Differences in oxidative damage caused by a possible reduction in flight efficiency were measured in amounts of ROMs and OXY in the blood. We also measured how flight performance was affected with recordings of the male`s escape flight using high‐speed cameras. Finally, we collected data on adult survival, clutch size and laying date in the following year.
“Plucked” males travelled a 5% shorter distance per wingbeat, showing that our treatment reduced flight performance. In line with this, “plucked” males visited their nests less often. Females of “plucked” males, however, visited the nest more often than controls, and fully compensated their partner's reduced visitation rate. As a result, there were no differences between treatments in food quality brought to the nest, adult or chick mass or number of successfully fledged chicks. Males did not differ in their oxidative damage or local survival to the following year. In contrast, females paired with plucked males tended to return less often to breed in the next year in comparison to controls, but this difference was not significant. For the birds that did return, there were no effects on breeding.
Our results reveal that wing gaps in male pied flycatchers reduce their flight performance, but when it occurs during breeding they prioritise their future reproduction by reducing parental care. As a result, there is no apparent detriment to their condition during breeding. Because non‐moulting females are able to compensate their partner's reduced care, there is also no immediate cost to the offspring, but females may pay the cost suffering from a reduced survival.

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Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate‐reducing benthic microbial populations
Authors: Saad Sainab , Bhatnagar Srijak , Tegetmeyer Halina E. , Geelhoed Jeanine S. , Strous Marc , Ruff S. Emil 
Published: August 2017

SummaryFor the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate‐reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investigated the community response. Chemical measurements, provisional genomes and transcriptomic profiles revealed trophic networks of microbial populations. Sulfate reducers coexisted with facultative nitrate reducers or aerobes enabling the community to adjust to nitrate or oxygen pulses. Exposure to oxygen and nitrate impacted the community structure, but did not suppress fermentation or sulfate reduction as community functions, highlighting their stability under dynamic conditions. The most abundant sulfate reducer in all cultures, related to Desulfotignum balticum, appeared to have coupled both acetate‐ and hydrogen oxidation to sulfate reduction. We describe a novel representative of the widespread uncultured candidate phylum Fermentibacteria (formerly candidate division Hyd24‐12). For this strictly anaerobic, obligate fermentative bacterium, we propose the name ‘USabulitectum silens’ and identify it as a partner of sulfate reducers in marine sediments. Overall, we provide insights into the function of fermentative, as well as sulfate‐reducing microbial communities and their adaptation to a dynamic environment.
House price to income ratio and fundamentals: Evidence on long‐horizon forecastability
Authors: Chen Nan‐Kuang , Cheng Han‐Liang 
Published: August 2017

AbstractThis paper studies the relationship between the house price‐to‐income ratio (PIR) and economic fundamentals, and investigates the long‐horizon forecastability of the PIR. We first construct a small DSGE model to derive a dynamic expression of PIR, linking PIR to macroeconomic fundamentals and the stance of monetary policy. Based on the theoretically derived PIR, variance decomposition suggests that interest rate and real income growth appear to be the main sources for the deviations of PIR. Using the difference between actual PIR and the estimated fundamental PIR as the predictor, we find that both in‐sample and out‐of‐sample forecastability of the PIR over the future dynamics of PIR are significant.
Effects of capital flow on the equity and housing markets in Hong Kong
Authors: Cheung Yin‐Wong , Chow Kenneth K. , Yiu Matthew S. 
Published: August 2017

AbstractThe revival of strong capital flows to emerging economies following the global financial crisis in 2008–2009 has rekindled the debate on effects of excessive capital inflows. We study the effects of official and illicit capital flows on Hong Kong, which is a small and open economy with minimal restrictions on cross‐border fund movements. It is found that the official and illicit capital flow measures display a low level of comovement and exhibit differential effects on Hong Kong's equity and residential housing markets. The results highlight the complexity of managing capital flows, and the relevance of sector‐specific capital management policies.
Listeria monocytogenes survival during production and storage of water buffalo Mozzarella cheese
Authors: Murru Nicoletta , Peruzy Maria Francesca , De Carlo Esterina , Mercogliano Raffaelina , Aponte Maria , Morena Carmelo , Serluca Giovanna , Fraulo Pasquale 
Published: August 2017

The ability of Listeria monocytogenes to survive during the manufacture of water buffalo Mozzarella and to grow during its shelf life was evaluated. A wild‐type and a reference strain were used to contaminate raw milk. The viable count of the reference strain ATCC 9525 dropped after the stretching process, and in the cheese, it fell to below 100 cfu/g. When the wild‐type strain was used, however, stretching did not appear to have any effect on the pathogen. The artificially contaminated cheeses were stored, for eleven days, at 4, 20 and 30 °C. Pathogen populations increased at 20 (≈2.60 log cfu/g) and 30 °C (≈1.95 log cfu/g).