bluuebunny/crossref_metadata_2025_split huggingface dataset:
PP2ARts1enforces a proportional relationship between cell size and growth rate
Authors: Leitao Ricardo M. , Pham Annie , Okobi Quincy , Kellogg Douglas R. 
Published: May 2018

AbstractCell size is proportional to growth rate. Thus, cells growing slowly in poor nutrients can be nearly half the size of cells growing rapidly in rich nutrients. The relationship between cell size and growth rate appears to hold across all orders of life, yet the underlying mechanisms are unknown. In budding yeast, most growth occurs during mitosis, and the proportional relationship between cell size and growth rate is therefore enforced primarily by modulating growth in mitosis. When growth is slow, the duration of mitosis is increased to allow more time for growth, yet the amount of growth required to complete mitosis is reduced, leading to birth of small daughter cells. Previous studies found that PP2A associated with the Rts1 regulatory subunit (PP2ARts1) works in a TORC2-dependent feedback loop that sets cell size and growth rate to match nutrient availability. However, it was unknown whether PP2ARts1influences growth in mitosis. Here, we show that PP2ARts1is required for the proportional relationship between cell size and growth rate during mitosis. Moreover, nutrients and PP2ARts1influence the duration of mitosis, and thus the extent of growth in mitosis, via Wee1 and Pds1/securin, two conserved regulators of mitotic progression. Together, the data suggest a model in which the same global signals that set growth rate also set the critical amount of growth required for cell cycle progression, which would provide a simple mechanistic explanation for the proportional relationship between size and growth rate.
Learning list concepts through program induction
Authors: Rule Joshua , Schulz Eric , Piantadosi Steven T. , Tenenbaum Joshua B. 
Published: May 2018

AbstractHumans master complex systems of interrelated concepts like mathematics and natural language. Previous work suggests learning these systems relies on iteratively and directly revising a language-like conceptual representation. We introduce and assess a novel concept learning paradigm called Martha’s Magical Machines that captures complex relationships between concepts. We model human concept learning in this paradigm as a search in the space of term rewriting systems, previously developed as an abstract model of computation. Our model accurately predicts that participants learn some transformations more easily than others and that they learn harder concepts more easily using a bootstrapping curriculum focused on their compositional parts. Our results suggest that term rewriting systems may be a useful model of human conceptual representations.
Highly diverged novel subunit composition of apicomplexan F-type ATP synthase identified fromToxoplasma gondii
Authors: Salunke Rahul , Mourier Tobias , Banerjee Manidipa , Pain Arnab , Shanmugam Dhanasekaran 
Published: May 2018

AbstractThe mitochondrial F-type ATP synthase, a multi-subunit nanomotor, is critical for maintaining cellular ATP levels. InToxoplasma gondiiand other apicomplexan parasites, many subunit components, necessary for proper assembly and functioning of this enzyme, appear to be missing. Here, we report the identification of 20 novel subunits ofT. gondiiF-type ATP synthase from mass spectrometry analysis of partially purified monomeric (~600 kDa) and dimeric (>1 MDa) forms of the enzyme. Despite extreme sequence diversification, key FOsubunits, a, b and d, can be identified from conserved structural features. Orthologs for these proteins are restricted to apicomplexan, chromerid and dinoflagellate species. Interestingly, their absence in ciliates indicates a major diversion, with respect to subunit composition of this enzyme, within the alveolate clade. Discovery of these highly diversified novel components of the apicomplexan F-type ATP synthase complex could facilitate the development of novel anti-parasitic agents. Structural and functional characterization of this unusual enzyme complex will advance our fundamental understanding of energy metabolism in apicomplexan species.
The complex geography of domestication of the African riceOryza glaberrima
Authors: Choi Jae Young , Dorph Katherine , Purugganan Michael D. 
Published: May 2018

AbstractWhile the domestication history of Asian rice has been extensively studied, details of the evolution of African rice remains elusive. The inner Niger delta has been suggested as the center of origin but molecular data for its support are lacking. Here, we present the most comprehensive analysis to date on the evolutionary and domestication history of African rice. By analyzing whole genome re-sequencing data from 282 individuals in domesticated African riceOryza glaberrimaand its progenitorO. barthii, we hypothesize a non-centric domestication origin for African rice. Our analyses show geographically based population structure inO. glaberrima, as well as significant evidence of admixture between genetic groups. Furthermore, we have evidence that the previously hypothesizedO. barthiiprogenitor populations in West Africa have evolutionary signatures similar to domesticated rice and carried causal domestication mutations, suggesting those progenitors may actually represent feral wild-domesticated hybrid rice. Demography modeling suggested the inlandO. glaberrimahad a protracted period of bottlenecking that preceded the coastal population by 800–1,800 years. Phylogeographic analysis of genes involved in the core domestication process suggests that the origins of causal domestication mutations could be traced to wild progenitors in multiple different locations in West and Central Africa. Based on our evidence, we hypothesizeO. glaberrimawas not domesticated from a single centric location but was rather a diffuse process where multiple regions contributed key alleles for different domestication traits.Author SummaryFor many crops it is not clear how they got domesticated from their wild progenitors. Transition from a wild to domesticated state required a series of genetic changes, and studying the evolutionary origin of these domestication-causing mutations are key to understanding the domestication origins of a crop. Moreover, population relationships within a crop holds insight into the evolutionary history of domestication and whether there was gene flow between different genetic groups. In this study, we investigate the domestication history ofOryza glaberrima, a rice species that was domesticated in West Africa independently from the Asian rice speciesO. sativa. Using genome-wide data from a large sample of domesticated and wild African rice samples we did not find evidence that supported the established domestication model forO. glaberrima—a single domestication origin. Rather, our evidence suggests the domestication process for African rice was initiated in multiple regions of West Africa, caused potentially by the local environmental and cultivation preference of people. Admixture between different genetic groups had facilitated the exchange and spread of core domestication mutations. Hence domestication of African rice was a multi-regional process.
CytoBinning: immunological insights from multi-dimensional data
Authors: Shen Yang , Chaigne-Delalande Benjamin , Lee Richard W.J. , Losert Wolfgang 
Published: May 2018

AbstractNew cytometric techniques continue to push the boundaries of multi-parameter quantitative data acquisition at the single-cell level particularly in immunology and medicine. Sophisticated analysis methods for such ever higher dimensional datasets are rapidly emerging, with advanced data representations and dimensional reduction approaches. However, these are not yet standardized and clinical scientists and cell biologists are not yet experienced in their interpretation. More fundamentally their range of statistical validity is not yet fully established. We therefore propose a new method for the automated and unbiased analysis of high-dimensional single cell datasets that is simple and robust, with the goal of reducing this complex information into a familiar 2D scatter plot representation that is of immediate utility to a range of biomedical and clinical settings. Using publicly available flow cytometry and mass cytometry datasets we demonstrate that this method (termed CytoBinning), recapitulates the results of traditional manual cytometric analyses and leads to new and testable hypotheses.
Thymidylate synthase maintains the de-differentiated state of aggressive breast cancers
Authors: Siddiqui Aarif , Gollavilli Paradesi , Schwab Annemarie , Vazakidou Maria Eleni , Ersan Pelin G , Ramakrishnan Mallika , Pluim Dick , Coggins Si′Ana , Saatci Ozge , Annaratone Laura , Schellens Jan HM , Kim Baek , Asangani Irfan Ahmed , Rasheed Suhail Ahmed Kabeer , Marchiò Caterina , Sahin Ozgur , Ceppi Paolo 
Published: May 2018

ABSTRACTCancer cells frequently boost nucleotide metabolism (NM) to support their increased proliferation, but the consequences of elevated NM on tumor de-differentiation are mostly unexplored. Here, we identified a role for thymidylate synthase (TS), a NM enzyme and established drug target, in cancer cell de-differentiation and investigated its clinical significance in breast cancer (BC).In vitro, TS knockdown increased the population of CD24+differentiated cells, and attenuated migration and sphere-formation. RNA-seq profiling indicated a repression of epithelial-to-mesenchymal transition (EMT) signature genes upon TS knockdown, and TS-deficient cells showed an increased ability to invade and metastasizein vivo, consistent with the occurrence of a partial EMT phenotype. Mechanistically, TS enzymatic activity was found essential for the maintenance of the EMT/stem-like state by fueling a DPYD-dependent pyrimidine catabolism. In patient tissues, TS levels were found significantly higher in poorly differentiated and in triple negative BC (TNBC), and strongly correlated with worse prognosis. The present study provides therationaleto study in-depth the role of NM at the crossroads of proliferation and differentiation, and depicts new avenues for the design of novel drug combinations for the treatment of BC.
Tyrosinase mediated humic substances synthesis by Bacillus aryabhattai TFG5
Authors: Muniraj Iniyakumar , Shameer Syed , Ramachandran Priyadarshini , Uhandi Sivakumar 
Published: May 2018

AbstractThe present investigation aims at understanding the mechanism of Humic Substances (HS) formation and enhancement through tyrosinase produced by Bacillus aryabhattai TFG5. A bacterium isolated from termite mound produced tyrosinase (1.34 U.ml−1) and laccase (2.1 U.ml−1) at 48 and 60 h of fermentation respectively. The protein from B. aryabhattai TFG5 was designated as TyrB and it had a predicted molecular weight of 35.23 kDa. Swiss modelling of protein revealed a bi copper protein with its conserved residues required for activity. Interestingly, TyrB efficiently transformed and polymerized standard phenols besides transforming free phenols of Coir pith Wash Water (CWW). In addition, spectroscopic evidences suggest that TyrB enhanced the HS production from coir pith biomass. Furthermore, degradative products and changes in biomass structure by TyrB analysed through FT-IR suggests that TyrB might follow the polyphenol theory of HS synthesis.
Prevalence and factors associated with Skilled Birth Attendants use among post-partum women in Arusha Tanzania
Authors: Shirima Febronia Lawrence , Komba Aurelia Severine , Msuya Sia E , Mahande Michael Johnson 
Published: May 2018

ABSTRACTIntroductionDeath related to pregnancy complications and delivery remains a public health problem in developing countries including Tanzania where majority of women and newborns die each year due to preventable causes. Delivery with a skilled birth attendant (SBA) is an important intervention to avert maternal and newborn mortality. This study aimed to determine factors influencing skilled birth attendant’s use among postpartum women in Arusha city and Arumeru district in Arusha region.MethodsThis was a cross-sectional study which was conducted from April to July 2017. The study utilized secondary data from the parent study which was conducted in Arusha city and Arumeru district in Arusha region. The parent study aimed to assess knowledge of danger signs in obstetric complication, birth preparedness and utilization of skilled birth attendants among post-partum women in urban and rural Arusha region in Tanzania. Data analysis was performed using SPSS version 20. Chi square statistics was used to determine the association between a set of independent variables and utilization of skilled birth attendance in bivariate analysis. Odds ratios with 95% confidence interval for factors influencing skilled birth attendants’ use were estimated in a multivariable logistic regression models. A p-value of less than 0.05 was considered statistically significant.ResultsA total of 1218 post-partum women were studied. Their mean age was 26.2 (SD 5.9) years. Of these, 1020 used skilled birth attendants during delivery; this corresponds to prevalence of 83.7%. Mother’s education level, area of residence, distance from health facility, frequency of antenatal care and parity were significantly associated utilization of skilled birth attendants during delivery.ConclusionThe prevalence of skilled birth attendants’ use among postpartum women is high in the studied population compared to the national level. Strategies to create community awareness on important of skilled birth attendants’ use will increase its uptake and my help to reduce both mother and child mortality.
SWI/SNF remains localized to chromatin in the presence of SCHLAP1
Authors: Raab Jesse R. , Smith Keriayn N. , Spear Camarie C. , Manner Carl J. , Calabrese J. Mauro , Magnuson Terry 
Published: May 2018

AbstractSCHLAP1 is a long-noncoding RNA that is prognostic for progression to metastatic prostate cancer and promotes an invasive phenotype. SCHLAP1 is reported to function by depleting the core SWI/SNF subunit, SMARCB1, from the genome. SWI/SNF is a large, multi-subunit, chromatin remodeling complex that can be combinatorially assembled to yield hundreds to thousands of distinct complexes. Here, we investigated the hypothesis that SCHLAP1 affects only specific forms of SWI/SNF and that the remaining SWI/SNF complexes were important for the increased invasion in SCHLAP1 expressing prostate cells. Using several assays we found that SWI/SNF is not depleted from the genome by SCHLAP1 expression. We find that SCHLAP1 induces changes to chromatin openness but is not sufficient to drive changes in histone modifications. Additionally, we show that SWI/SNF binds many coding and non-coding RNAs. Together these results suggest that SCHLAP1 has roles independent of canonical SWI/SNF and that SWI/SNF broadly interacts with RNA.
Studies of Bending Effects of Microvilli of Leukocyte on Rolling Adhesion
Authors: Wu Tai-Hsien , Qi Dewei 
Published: May 2018

AbstractIt has been widely acknowledged that further understanding about the cell adhesion (e.g., leukocyte rolling adhesion) can help us gain more knowledge about the causes of relevant diseases and design more effective treatments and diagnoses. Although recent simulation studies considered the deformability of the leukocytes, most of them, however, did not consider the bending deformation of microvilli. In this paper, an advanced leukocyte model based on an immersed boundary lattice-Boltzmann lattice-spring model (LLM) and an adhesive dynamics (AD) is presented in details. The flexural stiffness of microvilli is introduced into the model for simulations of leukocyte rolling adhesion. This innovative model is applied to investigate the influences of bending deformation of microvilli on the process of leukocyte rolling adhesion and the underlying mechanism at different shear rates. It is demonstrated that the bending deformation of microvilli can be influenced by the flexural stiffness of microvilli and shear rates, resulting in the different rolling velocity of leukocytes, number of receptor-ligand bonds, and bond forces. The findings clearly indicate that the bending of microvilli plays a crucial role in the dynamics of leukocyte adhesion.
Are publicly funded Czech incubators effective? The comparison of performance of supported and non-supported firms
Authors: Dvouletý Ondřej , Longo Maria Cristina , Blažková Ivana , Lukeš Martin , Andera Michal 
Published: May 2018

Purpose
Even in established economies, empirical studies on the relationship between business incubation and firm performance do not show unequivocally positive results. The purpose of this paper is to contribute to this debate based on the empirical evidence from the under-researched Central and Eastern European region in which no similar study has been conducted before. Due to the shorter experience with the management of business incubators and less developed institutions, business incubators may not be so effective in supporting their tenants in this region.

Design/methodology/approach
The authors utilise firm-level data from incubated Czech enterprises (n=205) founded after 2003 and compare them with those that have not received support from incubators. The authors implement three matching techniques to pair incubated and non-incubated companies. The outcome variables measured sales, price-cost margin, assets turnover, value added, size of total assets and size of personnel costs.

Findings
Compared to the control group, incubated firms reported on average lower values of the above-mentioned indicators. Presented study shows that Czech incubators have not been successful in supporting growth of incubated firms.

Practical implications
The study suggests that there is a clear room for improvements. Incubators should improve in attracting and selecting high potentials and in providing more effective support focussed on tenants’ growth, whereas policymakers should exercise stricter control regarding the money spent and effectiveness of incubators.

Originality/value
The empirical analysis was conducted based on the research gap in the studies related to the impact of business incubation in the under-researched Central and Eastern European region. It also shows that positive results from similar studies done in established economies cannot be taken for granted as they depend on the quality of institutions in a particular country.
Domain-specific readability measures to improve information retrieval in the Persian language
Authors: Arastoopoor Sholeh 
Published: May 2018

Purpose
The degree to which a text is considered readable depends on the capability of the reader. This assumption puts different information retrieval systems at the risk of retrieving unreadable or hard-to-be-read yet relevant documents for their users. This paper aims to examine the potential use of concept-based readability measures along with classic measures for re-ranking search results in information retrieval systems, specifically in the Persian language.

Design/methodology/approach
Flesch–Dayani as a classic readability measure along with document scope (DS) and document cohesion (DC) as domain-specific measures have been applied for scoring the retrieved documents from Google (181 documents) and the RICeST database (215 documents) in the field of computer science and information technology (IT). The re-ranked result has been compared with the ranking of potential users regarding their readability.

Findings
The results show that there is a difference among subcategories of the computer science and IT field according to their readability and understandability. This study also shows that it is possible to develop a hybrid score based on DS and DC measures and, among all four applied scores in re-ranking the documents, the re-ranked list of documents based on the DSDC score shows correlation with re-ranking of the participants in both groups.

Practical implications
The findings of this study would foster a new option in re-ranking search results based on their difficulty for experts and non-experts in different fields.

Originality/value
The findings and the two-mode re-ranking model proposed in this paper along with its primary focus on domain-specific readability in the Persian language would help Web search engines and online databases in further refining the search results in pursuit of retrieving useful texts for users with differing expertise.
How signaling mechanisms reduce “lemons” from online group buying (OGB) markets? A study of China
Authors: Hossain Mohammad Alamgir , Rahman Shams , Chowdhury Tamgid Ahmed , Chan Caroline , Yang Xiaoyan , Su Qingxin 
Published: May 2018

Purpose
A major transformation in retail logistics over the few years is backed by enormous improvements in internet technologies. It is now easy for e-retailers to entertain delivery progression, or consumers can share use-experience with future customers and thereby reducing information asymmetry. The purpose of this paper is to investigate the effect of different signals on consumer behavior in the presence of information asymmetry, in the context of online group buying (OGB) markets in China.

Design/methodology/approach
Based on the lemon market theory (LMT) and signaling theory, the study develops a research model of the OGB consumers’ context in China, which is validated using data from an online survey. A total of 528 responses are used for data analysis applying structural equation modeling technique.

Findings
The findings of the study show that perceived vendor quality (PVQ) and perceived product quality (PPQ) have significantly positive effects on intention to purchase from OGB websites. PVQ is associated with perceived reputation and perceived trustworthiness (PT) of vendor, and the determinants of PPQ are quality assurance information of products, and information about mer-chants. Further, PT has a mediating effect, while asymmetry of information has a moderating effect.

Research limitations/implications
The research model is valid as a generic OGB model that can be investigated in other contexts to understand the generalizability of the findings. Future research is needed to incorporate additional relevant factors (e.g. price, advertising activity/investments) that may help increase the acceptability of the model to a wide range of e-commerce contexts. Two of the control variables (gender and prior internet experience) were found to be significant; this could be further examined in future studies to determine the relative impact on each causal relationship.

Originality/value
Whereas prior studies in the domain of consumer service proposed different signaling mechanisms that were believed to eliminate information asymmetry from a market, the study sheds light on the effectiveness of the signals in the OGB context. This is a unique effort that applies and extends LMT and signaling theory in OGB context by theorizing the associated dimensions and their causal effects.