bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling allele-specific gene expression by single-cell RNA sequencing
Authors: Jiang Yuchao , Zhang Nancy R , Li Mingyao 
Published: February 2017

AbstractAllele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing (scRNA-seq) allows the comparison of expression distribution between the two alleles of a diploid organism and thus the characterization of allele-specific bursting. We propose SCALE to analyze genome-wide allele-specific bursting, with adjustment of technical variability. SCALE detects genes exhibiting allelic differences in bursting parameters, and genes whose alleles burst non-independently. We apply SCALE to mouse blastocyst and human fibroblast cells and find that, globally,ciscontrol in gene expression overwhelmingly manifests as differences in burst frequency.
MinE recruits, stabilizes, releases, and inhibits MinD interactions with membrane to drive oscillation
Authors: Vecchiarelli Anthony G. , Li Min , Mizuuchi Michiyo , Ivanov Vassili , Mizuuchi Kiyoshi 
Published: February 2017

SUMMARYThe MinD and MinE proteins ofEscherichia coliself-organize into a standing-wave oscillator on the membrane to help align division at mid-cell. When unleashed from cellular confines, we find that MinD and MinE form a wide spectrum of patterns on artificial bilayers - static amoebas, traveling waves, traveling mushrooms, and bursts with standing-wave dynamics. We recently focused our cell-free studies on bursts because their dynamics closely resemble those foundin vivo. The data unveiled a patterning mechanism largely governed by MinE regulation of MinD interaction with membrane. We proposed that the MinD to MinE ratio on the membrane acts as a toggle switch between MinE-stimulated recruitment or release of MinD from the membrane. Here we provide data that further refines and extends our model that explains the remarkable spectrum of patterns supported by these two ‘simple’ proteins.
Relational uncertainty in service dyads
Authors: Kreye Melanie E. 
Published: February 2017

PurposeRelational uncertainty determines how relationships develop because it enables the building of trust and commitment. However, relational uncertainty has not been explored in an inter-organisational setting. The purpose of this paper is to investigate how organisations experience relational uncertainty in service dyads and how they resolve it through suitable organisational responses to increase the level of service quality.Design/methodology/approachThe author applies the overall logic of organisational information-processing theory and presents empirical insights from two industrial case studies collected via semi-structured interviews and secondary data.FindingsThe findings suggest that relational uncertainty is caused by the partner’s unresolved organisational uncertainty, i.e. their lacking capabilities to deliver or receive (parts of) the service. Furthermore, the author found that resolving the relational uncertainty increased the functional quality while resolving the partner’s organisational uncertainty increased the technical quality of the delivered service.Originality/valueThe author makes two contributions: first,the author introduces relational uncertainty to the OM literature as the inability to predict and explain the actions of a partnering organisation due to a lack of knowledge about their abilities and intentions; and second, the author presents suitable organisational responses to relational uncertainty and their effect on service quality.
High‐resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils
Authors: Narrowe Adrienne B. , Angle Jordan C. , Daly Rebecca A. , Stefanik Kay C. , Wrighton Kelly C. , Miller Christopher S. 
Published: February 2017

SummaryDespite being key contributors to biogeochemical processes, archaea are frequently outnumbered by bacteria, and consequently are underrepresented in combined molecular surveys. Here, we demonstrate an approach to concurrently survey the archaea alongside the bacteria with high‐resolution 16S rRNA gene sequencing, linking these community data to geochemical parameters. We applied this integrated analysis to hydric soils sampled across a model methane‐emitting freshwater wetland. Geochemical profiles, archaeal communities, and bacterial communities were independently correlated with soil depth and water cover. Centimeters of soil depth and corresponding geochemical shifts consistently affected microbial community structure more than hundreds of meters of lateral distance. Methanogens with diverse metabolisms were detected across the wetland, but displayed surprising OTU‐level partitioning by depth. Candidatus Methanoperedens spp. archaea thought to perform anaerobic oxidation of methane linked to iron reduction were abundant. Domain‐specific sequencing also revealed unexpectedly diverse non‐methane‐cycling archaeal members. OTUs within the underexplored Woesearchaeota and Bathyarchaeota were prevalent across the wetland, with subgroups and individual OTUs exhibiting distinct occupancy and abundance distributions aligned with environmental gradients. This study adds to our understanding of ecological range for key archaeal taxa in a model freshwater wetland, and links these taxa and individual OTUs to hypotheses about processes governing biogeochemical cycling.
Cold adaptation of the Antarctic haloarchaea Halohasta litchfieldiae and Halorubrum lacusprofundi
Authors: Williams Timothy J. , Liao Yan , Ye Jun , Kuchel Rhiannon P. , Poljak Anne , Raftery Mark J. , Cavicchioli Ricardo 
Published: February 2017

SummaryHalohasta litchfieldiae represents ∼ 44% and Halorubrum lacusprofundi ∼ 10% of the hypersaline, perennially cold (≥ −20°C) Deep Lake community in Antarctica. We used proteomics and microscopy to define physiological responses of these haloarchaea to growth at high (30°C) and low (10 and 4°C) temperatures. The proteomic data indicate that both species responded to low temperature by modifying their cell envelope including protein N‐glycosylation, maintaining osmotic balance and translation initiation, and modifying RNA turnover and tRNA modification. Distinctions between the two species included DNA protection and repair strategies (e.g. roles of UspA and Rad50), and metabolism of glycerol and pyruvate. For Hrr. lacusprofundi, low temperature led to the formation of polyhydroxyalkanoate‐like granules, with granule formation occurring by an unknown mechanism. Hrr. lacusprofundi also formed biofilms and synthesized high levels of Hsp20 chaperones. Hht. litchfieldiae was characterized by an active CRISPR system, and elevated levels of the core gene expression machinery, which contrasted markedly to the decreased levels of Hrr. lacusprofundi. These findings greatly expand the understanding of cellular mechanisms of cold adaptation in psychrophilic archaea, and provide insight into how Hht. litchfieldiae gains dominance in Deep Lake.
Examining Facilitative Configurations of Entrepreneurially Oriented Growth: An Information Processing Perspective
Authors: Kearney Claudine , Soleimanof Sohrab , Wales William J. 
Published: February 2017

AbstractThis study examines how the relationship between entrepreneurial orientation and firm growth is shaped by learning orientation in technologically sophisticated environments. We draw upon an information processing perspective that emphasizes alignment between information processing demands and support mechanisms. Using data from 116 small to medium‐sized enterprises in the Netherlands, we observe that the ability of entrepreneurial orientation to drive firm growth greatly depends on the joint consideration of technological sophistication and learning orientation. Our findings contribute to a better understanding of how configurations of strategic orientations and environmental considerations work in concert to influence the efficacy of organizational entrepreneurial efforts dramatically.
An evaluation of the effectiveness of a computer‐assisted reading intervention
Authors: Messer David , Nash Gilly 
Published: February 2017

BackgroundA cost‐effective method to address reading delays is to use computer‐assisted learning, but these techniques are not always effective.MethodsWe evaluated a commercially available computer system that uses visual mnemonics, in a randomised controlled trial with 78 English‐speaking children (mean age 7 years) who their schools identified as needing reading support. School‐based individual tutorials usually took place 2–3 times/week. Only the experimental group received the intervention in the first 10 months; thereafter, both the experimental and control groups received the intervention for 6 months.ResultsAfter 10 months, the experimental group had significantly higher standardised scores than the waiting list control group of decoding, phonological awareness, naming speed, phonological short‐term memory and executive loaded working memory.ConclusionsThe computer‐assisted intervention was effective, and this suggests that this medium can be used for reading interventions with English‐speaking children.What is already known about this topic

There are comparatively few randomised controlled trial evaluations of computer‐based reading interventions.
Meta‐analyses report small positive effect sizes for such interventions with English‐speaking children.
The use of visual mnemonics to improve reading has rarely been investigated.
What this paper adds

The findings suggest that computer‐based interventions for English‐speaking, struggling readers can be effective.
The effects extended beyond the targeted abilities, and a longer intervention was more effective than a shorter one.
Apart from spelling, the mean reading and reading related standardised scores for children at the end of the intervention were above or just below 100.
Implications for theory, policy or practice

Computer‐based interventions can be used to support English‐speaking, struggling readers, and their effects can go beyond targeted abilities.
The use of visual mnemonics and the development of the intervention programme over a number of years could have contributed to this success.
The role of visual mnemonics as a help for struggling readers deserves further investigation.
Serous tubal intraepithelial carcinomas associated with high‐grade serous ovarian carcinomas: a systematic review
Authors: Chen F , Gaitskell K , Garcia MJ , Albukhari A , Tsaltas J , Ahmed AA 
Published: February 2017

BackgroundSerous tubal intraepithelial carcinomas (STICs) have been documented in high‐grade serous ovarian carcinomas (HGSOCs). However, the rate of association between STICs and HGSOCs and, therefore, the fraction of HGSOCs that are likely to have originated from the fallopian tube (FT), has remained unclear.ObjectiveTo appraise the literature describing the association between STICs and established HGSOCs.Search strategyOvid MEDLINE and EMBASE were searched.Selection criteriaStudies were included if they evaluated the frequency of STICs in HGSOCs, and were published in an English peer‐reviewed journal.Data collection and analysisAppropriate studies were evaluated for their compliance with the ‘Strengthening and Reporting of Observational Studies in Epidemiology (STROBE)’ criteria.Main resultsTen articles met the study selection criteria. The reported coexistence between STICs and HGSOCs ranged from 11% to 61% (mean: 31%, 95% CI: 17–46%). STICs were rarely found in other gynaecological cancers. Small sample size, lack of objective criteria to identify STICs and the retrospective nature of the studies contributed to the variability in reporting the rate of the association.ConclusionsSTICs were identified commonly in the FTs of women with HGSOC. Finding the true rate of association between STICs and HGSOCs will require further investigations. While there is evidence that a fraction of HGSOCs arise from the FTs, an accurate estimate of that fraction remains to be determined. The lack of an accurate estimate of the association makes it difficult to evaluate the potential magnitude of reduction of HGSOCs following prophylactic salpingectomy.Tweetable abstractA systematic review of the incidence of STICs in HGSOCs identifies significant methodological inconsistencies.
Identifying Primary Care Pathways from Quality of Care to Outcomes and Satisfaction Using Structural Equation Modeling
Authors: Ricci‐Cabello Ignacio , Stevens Sarah , Dalton Andrew R. H. , Griffiths Robert I. , Campbell John L. , Valderas Jose M. 
Published: February 2017

ObjectiveTo study the relationships between the different domains of quality of primary health care for the evaluation of health system performance and for informing policy decision making.Data SourcesA total of 137 quality indicators collected from 7,607 English practices between 2011 and 2012.Study DesignCross‐sectional study at the practice level. Indicators were allocated to subdomains of processes of care (“quality assurance,” “education and training,” “medicine management,” “access,” “clinical management,” and “patient‐centered care”), health outcomes (“intermediate outcomes” and “patient‐reported health status”), and patient satisfaction. The relationships between the subdomains were hypothesized in a conceptual model and subsequently tested using structural equation modeling.Principal FindingsThe model supported two independent paths. In the first path, “access” was associated with “patient‐centered care” (β = 0.63), which in turn was strongly associated with “patient satisfaction” (β = 0.88). In the second path, “education and training” was associated with “clinical management” (β = 0.32), which in turn was associated with “intermediate outcomes” (β = 0.69). “Patient‐reported health status” was weakly associated with “patient‐centered care” (β = −0.05) and “patient satisfaction” (β = 0.09), and not associated with “clinical management” or “intermediate outcomes.”ConclusionsThis is the first empirical model to simultaneously provide evidence on the independence of intermediate health care outcomes, patient satisfaction, and health status. The explanatory paths via technical quality clinical management and patient centeredness offer specific opportunities for the development of quality improvement initiatives.
Home Health Care: Nurse–Physician Communication, Patient Severity, and Hospital Readmission
Authors: Pesko Michael F. , Gerber Linda M. , Peng Timothy R. , Press Matthew J. 
Published: February 2017

ObjectiveTo evaluate whether communication failures between home health care nurses and physicians during an episode of home care after hospital discharge are associated with hospital readmission, stratified by patients at high and low risk of readmission.Data Source/Study SettingWe linked Visiting Nurse Services of New York electronic medical records for patients with congestive heart failure in 2008 and 2009 to hospitalization claims data for Medicare fee‐for‐service beneficiaries.Study DesignLinear regression models and a propensity score matching approach were used to assess the relationship between communication failure and 30‐day readmission, separately for patients with high‐risk and low‐risk readmission probabilities.Data Collection/Extraction MethodsNatural language processing was applied to free‐text data in electronic medical records to identify failures in communication between home health nurses and physicians.Principal FindingsCommunication failure was associated with a statistically significant 9.7 percentage point increase in the probability of a patient readmission (32.6 percent of the mean) among high‐risk patients.ConclusionsPoor communication between home health nurses and physicians is associated with an increased risk of hospital readmission among high‐risk patients. Efforts to reduce readmissions among this population should consider focusing attention on this factor.
CEO Inside Debt Incentives and Corporate Tax Sheltering
Authors: CHI SABRINA , HUANG SHAWN X. , SANCHEZ JUAN MANUEL 
Published: February 2017

ABSTRACTThis paper examines the relation between CEO inside debt holdings (pension benefits and deferred compensation) and corporate tax sheltering. Because inside debt holdings are generally unsecured and unfunded liabilities of the firm, CEOs are exposed to risk similar to that faced by outside creditors. As such, theory (Jensen and Meckling [1976]) suggests that inside debt holdings negatively impact CEO risk‐appetite. To the extent that corporate tax shelters are likely to result in high cash flow volatility in the future, we expect that inside debt holdings will curb CEOs from engaging in tax shelter transactions. Consistent with the prediction, we document a negative association between CEO inside debt holdings and tax sheltering. Additional analyses suggest that the effect of inside debt on tax sheltering is more (less) pronounced in the presence of high default risk and liquidity threats (cash‐out options in pension packages). Overall, our results highlight the importance of investigating the implication of CEO debt‐like compensation for corporate tax policies.
Potato aphid Macrosiphum euphorbiae performance is determined by aphid genotype and not mycorrhizal fungi or water availability
Authors: Karley Alison Jane , Emslie‐Smith Matthew , Bennett Alison Elizabeth 
Published: February 2017

AbstractIntra‐ and interspecific variation in plant and insect traits can alter the strength and direction of insect–plant interactions, with outcomes modified by soil biotic and abiotic conditions. We used the potato aphid (Macrosiphum euphorbiae Thomas) feeding on cultivated Solanum tuberosum and wild Solanum berthaulti to study the impact of water availability and plant mutualistic arbuscular mycorrhizal (AM) fungi on aphid performance and susceptibility to a parasitoid wasp (Aphidius ervi Haliday). Plants were grown under glass with live or sterile AM fungal spores and supplied with sufficient or reduced water supply. Plants were infested with 1 of 3 genotypes of M. euphorbiae or maintained as aphid‐free controls; aphid abundance was scored after 1 week, after which aphid susceptibility to A. ervi was assayed ex planta. Solanum tuberosum accumulated c. 20% more dry mass than S. berthaultii, and root mass of S. berthaultii was smallest under reduced water supply in the presence of AM fungi. Aphid abundance was lowest on S. berthaultii and highest for genotype “2” aphids; genotype “1” aphid density was particularly reduced on S. berthaultii. Aphid genotype “1” exhibited low susceptibility to parasitism and was attacked less frequently than the other two more susceptible aphid genotypes. Neither AM fungi nor water availability affected insect performance. Our study suggests a fitness trade‐off in M. euphorbiae between parasitism resistance and aphid performance on poor quality Solanum hosts that warrants further exploration, and indicates the importance of accounting for genotype identity in determining the outcome of multitrophic interactions.
Ultrastructure of compatible and incompatible interactions in phloem sieve elements during the stylet penetration by cotton aphids in melon
Authors: Garzo Elisa , Fernández‐Pascual Mercedes , Morcillo Cesar , Fereres Alberto , Gómez‐Guillamón M. Luisa , Tjallingii W. Fred 
Published: February 2017

AbstractResistance of the melon line TGR‐1551 to the aphid Aphis gossypii is based on preventing aphids from ingesting phloem sap. In electrical penetration graphs (EPGs), this resistance has been characterized with A. gossypii showing unusually long phloem salivation periods (waveform E1) mostly followed by pathway activities (waveform C) or if followed by phloem ingestion (waveform E2), ingestion was not sustained for more than 10 min. Stylectomy with aphids on susceptible and resistant plants was performed during EPG recording while the stylet tips were phloem inserted. This was followed by dissection of the penetrated leaf section, plant tissue fixation, resin embedding, and ultrathin sectioning for transmission electron microscopic observation in order to study the resistance mechanism in the TGR. The most obvious aspect appeared to be the coagulation of phloem proteins inside the stylet canals and the punctured sieve elements. Stylets of 5 aphids per genotype were amputated during sieve element (SE) salivation (E1) and SE ingestion (E2). Cross‐sections of stylet bundles in susceptible melon plants showed that the contents of the stylet canals were totally clear and also, no coagulated phloem proteins occurred in their punctured sieve elements. In contrast, electron‐dense coagulations were found in both locations in the resistant plants. Due to calcium binding, aphid saliva has been hypothesized to play an essential role in preventing/suppressing such coagulations that cause occlusion of sieves plate and in the food canal of the aphid's stylets. Doubts about this role of E1 salivation are discussed on the basis of our results.
Shut the fridge door! HRM alignment, job redesign and energy performance
Authors: Christina Sian , Dainty Andrew , Daniels Kevin , Tregaskis Olga , Waterson Patrick 
Published: February 2017

AbstractAnchored within the strategic HRM and alignment literature, and drawing on efficiency and legitimacy perspectives of organisational behaviour, we investigated a HRM intervention targeted at energy reduction goals in a large multinational retailer. The HRM intervention was focused on embedding the environmental and economic performance goals of the firm within the workplace through redesigning the job so that energy tasks were aligned with training and performance management systems, as well as organisational performance goals. Using a randomised control trial design, we tracked changes in energy behaviours and energy consumption in 769 retail stores (685 in the intervention condition, 84 in the control condition). The findings provide evidence that changing the alignment of HRM practices can influence both worker behaviour and organisational outcomes, including environmental outcomes. This work contributes to debates concerning the impact of HRM alignment on both the work and organisational performance context.