bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasmodium vivaxMalaria viewed through the lens of an eradicated European strain
Authors: Dorp Lucy van , Gelabert Pere , Rieux Adrien , Manuel Marc de , de-Dios Toni , Gopalakrishnan Shyam , Carøe Christian , Sandoval-Velasco Marcela , Fregel Rosa , Olalde Iñigo , Escosa Raül , Aranda Carles , Huijben Silvie , Mueller Ivo , Marquès-Bonet Tomàs , Balloux François , Gilbert M. Thomas P , Lalueza-Fox Carles 
Published: August 2019

AbstractThe protozoanPlasmodium vivaxis responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack of genomic information on the extinct European lineage has prevented a clear understanding of historical population structuring and past migrations ofP. vivax. We used medical microscope slides prepared in 1944 from malaria-affected patients from the Ebro Delta in Spain, one of the last footholds of malaria in Europe, to generate a genome of a EuropeanP. vivaxstrain. Population genetics and phylogenetic analyses placed this strain basal to a cluster including samples from the Americas. This genome allowed us to calibrate a genomic mutation rate forP. vivax, and to estimate the mean age of the last common ancestor between European and American strains to the 15th century. This date points to an introduction of the parasite during the European colonisation of the Americas. In addition, we found that some known variants for resistance to anti-malarial drugs, including Chloroquine and Sulfadoxine, were already present in this European strain, predating their use. Our results shed light on the evolution of an important human pathogen and illustrate the value of antique medical collections as a resource for retrieving genomic information on pathogens from the past.
Convolutional Neural Network Analysis of Social Novelty Preference using DeepLabCut
Authors: Worley Nicholas B. , Djerdjaj Anthony , Christianson John P. 
Published: August 2019

AbstractThe description and quantification of social behavior in laboratory rodents is central to basic and translational research. Conventional ethological approaches to social behavior are fraught with challenges including bias, significant human effort and temporal accuracy. Here we show proof of principle that machine learning can be applied to laboratory tests of social decision making. Rats underwent social novelty preference tests which were scored both by hand and again by a convolutional neural network generated in the DeepLabCut computer vision package of Mathis and colleagues. The CNN generated temporally (30Hz) and locally (<5pixels) accurate identification of rat nose, eye and ear positions which were then used to compute social interaction and topography heat maps. In sum, hand- and computer-scoring were strongly correlated, and each identified significant preferences to interact with novel conspecifics which sets the stage for applying DeepLabCut analysis to other types of social interaction in the future.
RASInternal Tandem Duplication Disrupts GAP-binding to Activate Oncogenic Signaling
Authors: Nelson Andrew C. , Turbyville Thomas , Dharmaiah Srisathiyanarayanan , Rigby Megan , Yang Rendong , Columbus John , Stephens Robert , Sciacca Drew , Onsongo Getiria , Sarver Anne , Subramanian Subbaya , Nissley Dwight V. , Simanshu Dhirendra K. , Lou Emil 
Published: August 2019

AbstractMolecular testing of oncogenicRASmutations in colorectal cancer (CRC) have led to increased identification of mutations in patients with CRC.NRAS-mutated CRC has not been well characterized because it is less common (<6%) thanKRASmutations. Here, we report a novel 10 amino acid internal tandem duplication (ITD) inNRAS, which disrupts the switch II domain, in a patient with widely disseminated CRC. Hotspot next generation sequencing of a brain metastasis identified theNRASITD and aTP53missense mutation (p.P275F). Whole exome sequencing of the primary tumor and two metastatic lesions (lung and brain) confirmed that theNRASITD andTP53mutation were conserved between the primary tumor and both metastatic tumors, and identified an additional pathogenic mutation inCSMD1(a tumor suppressor gene). Structural biology and biochemical analyses demonstrated that theNRASITD prevented binding to GAP protein, leading to sustained RAS activation, increased interaction with RAF, and downstream MAPK activation. Additionally, we provide the first crystal structure of theRASITD. In conclusion, these studies indicate that theNRASITD was the probable primary driver mutation of this aggressive CRC. Identical or biologically similar ITDs inNRASandKRASmay be rare drivers of CRC and other aggressive malignancies.
The McdAB Carboxysome Positioning System is Widespread Among β-cyanobacteria
Authors: MacCready Joshua S. , Basalla Joseph L. , Vecchiarelli Anthony G. 
Published: August 2019

SummaryCarboxysomes are protein-based organelles that are essential for allowing cyanobacteria to fix CO2. Previously we identified a two-component system, McdAB, responsible for equidistantly positioning carboxysomes in the model cyanobacterium Synechococcus elongatus PCC 7942. McdA, a ParA-type ATPase, non-specifically binds the nucleoid in the presence of ATP. McdB, a novel factor that directly binds carboxysomes, displaces McdA from the nucleoid. Removal of McdA from the nucleoid in the vicinity of carboxysomes by McdB causes a global break in McdA symmetry, and carboxysome motion occurs via a Brownian-ratchet based mechanism towards the highest concentration of McdA. Despite the importance for cyanobacteria to properly position their carboxysomes, whether the McdAB system is widespread among cyanobacteria remains an open question. Here, we used neighborhood analysis to show that the McdAB system is widespread among β-cyanobacteria and often clusters near carboxysome-related components. Moreover, we show that two distinct McdAB systems exist in β-cyanobacteria, with Type 2 systems being the most abundant (>98% of β-cyanobacteria) and Type 1 systems, like that of S. elongatus, possibly being acquired more recently. Surprisingly, our analysis suggests that the McdAB system is completely absent in α-cyanobacteria. Lastly, all McdB proteins we identified share the sequence signatures of a protein capable of undergoing Liquid-Liquid Phase Separation (LLPS). Indeed, we find that S. elongatus McdB undergoes LLPS in vitro, the first example of a ParA-type ATPase partner protein exhibiting this behavior. This is an intriguing finding given the recent demonstration of LLPS activity by β-carboxysome core components. Our results have broader implications for understanding carboxysome biogenesis and positioning across all β-cyanobacteria.In BriefWe found that the McdAB carboxysome positioning system is widespread among β-cyanobacteria, absent in α-cyanobacteria, exists in two distinct forms, and that S. elongatus McdB undergoes liquid-liquid phase separation.
Query Combinators: Domain Specific Query Languages for Medical Research
Authors: Evans Clark C. , Simonov Kyrylo 
Published: August 2019

AbstractA new way to conceptualize computations, Query Combinators, can be used to create a data processing environment shared among the entire medical research team. For a given research context, a domain specific query language can be created that represents data sources, analysis methods, and integrative domain knowlege. Research questions can then have an intuitive, high-level form that can be reasoned about and discussed.
Chromosomal Mcm2-7 distribution is the primary driver of the genome replication program in species from yeast to humans
Authors: Foss Eric J. , Sripathy Smitha , Gatbonton-Schwager Tonibelle , Kwak Hyunchang , Thiesen Adam H. , Lao Uyen , Bedalov Antonio 
Published: August 2019

AbstractThe spatio-temporal program of genome replication across eukaryotes is thought to be driven both by the uneven loading of pre-replication complexes (pre-RCs) across the genome at the onset of S-phase, and by differences in the timing of activation of these complexes during S-phase. To determine the degree to which distribution of pre-RC loading alone could account for chromosomal replication patterns, we mapped the binding sites of the Mcm2-7 helicase complex (MCM) in budding yeast, fission yeast, mouse and humans. We observed identical MCM double-hexamer footprints across the species, but notable differences in their distribution: In budding yeast, complexes were present in sharp peaks comprised largely of single double-hexamers; in fission yeast, corresponding peaks typically contained 4 to 8 double-hexamers, were more disperse, and showed a striking correlation with AT content. In mouse and humans, complexes were even more disperse, with a preference for regions of high GC content. Nonetheless, most fluctuations in replication timing in all four organisms could be accounted for by differences in chromosomal MCM distribution. This analysis also identified genomic regions whose replication timing was clearly not attributable to MCM density. The most notable was the inactive X-chromosome, which replicates late in S phase despite the fact that both MCM abundance and chromosomal distribution were comparable to those on the early replicating active X-chromosome. We conclude that, although certain genomic regions, most notably the inactive X-chromosome, are subject to post-licensing regulation, most differences in replication timing along the chromosome reflect uneven chromosomal distribution of stochastically firing pre-replication complexes.
mTOR dependent transformed human cells have a distinct set of essential genes from bcr-abl transformed cells
Authors: Benjamin Don , Colombi Marco , Moroni Christoph , Hall Michael N. 
Published: August 2019

AbstractConstitutively active intracellular signaling drives and sustains cancer growth. The mTOR kinase integrates multiple inputs sensing nutrient, energy and growth factor levels to promote protein synthesis and anabolic metabolism, and is hyperactivated in a broad range of cancers. The bcr-abl kinase is a fusion protein generated by chromosomal translocation and gives rise to chronic myeloid leukemia and a small sub-set of leukemias. Using an in vitro transformed murine cell model, we performed shRNA knockdown of 25 genes previously shown to be essential for mTOR dependent oncogenic growth and survival. None of the genes were essential in the bcr-abl transformed line. Interrogation of this gene set in human cancer cell lines revealed that many of these genes were essential in cells dependent on mTOR signaling (defined by sensitivity to pharmacological mTOR inhibition). However, none of the genes were essential in bcr-abl transformed K562 cells that are insensitive to mTOR inhibition. Thus there is a clear divide between cells transformed via bcr-abl directed oncogenesis and other modes of transformation where mTOR, due to its central role in regulating cell growth and metabolism, is recruited as part of an oncogenic program. These validated hits represent a set of genes essential for executing critical functions downstream of mTOR and may be novel therapeutic targets for cancer.
Differences of food intakes with gender, the year in college and body mass index among university students in Beijing, China
Authors: Cheng Li , Liu Zuchen 
Published: August 2019

Purpose
The transition from high school to university poses many challenges for university students including dietary behaviors’ change and subsequent obesity risk. More tailored interventions and promotions to establish a healthier eating habit are needed to reduce obesity risks. The purpose of this paper is to investigate food intake differences on obesity risk among university students in China through exploring the differences of food intakes with gender, the year in college and body mass index (BMI).

Design/methodology/approach
Cross-sectional study was carried in five universities which were randomly selected in all the universities located in different geographical areas of Beijing, China. The sample consisted of 631 university students whom aged from 18 to 25 years. t-tests and one-way ANOVA tests were used to find differences of food intakes with gender, the year in college and BMI.

Findings
Having more consumption of food with high protein, high fat and high sugar, but less consumption of fruits and vegetables, may give university students a greater chance to be obese, and food intakes were significantly varied in different genders among Chinese university students.

Originality/value
There is a lack of evidence for investigating the differences of food intakes with gender on obesity among young adults in China. Findings of this study indicated that the food intakes of male students might make them more prone to obesity than female students, and suggested more tailored interventions, food marketing strategies and promotions on controlling students’ food intakes for a healthier life are needed.
The economic value of using CAW-type models to forecast covariance matrix
Authors: Zhao Shuran , Li Jinchen , Jiang Yaping , Ren Peimin 
Published: August 2019

PurposeThe purpose of this paper is twofold: to improve the traditional conditional autoregressive Wishart (CAW) and heterogeneous autoregressive (HAR)-CAW model to account for heterogeneous leverage effect and to adjust the high-frequency volatility. The other is to confirm whether CAW-type models that have statistical advantages have economic advantages.Design/methodology/approachBased on the high-frequency data, this study proposed a new model to describe the volatility process according to the heterogeneous market hypothesis. Thus, the authors acquire needed and credible high-frequency data.FindingsBy designing two mean-variance frameworks and considering several economic performance measures, the authors find that compared with five other models based on daily data, CAW-type models, especially LHAR-CAW and HAR-CAW, indeed generate the substantial economic values, and matrix adjustment method significantly improves the three CAW-type performances.Research limitations/implicationsThe findings in this study suggest that from the aspect of economics, LHAR-CAW model can more accurately built the dynamic process of return rates and covariance matrix, respectively, and the matrix adjustment can reduce bias of realized volatility as covariance matrix estimator of return rates, and greatly improves the performance of unadjusted CAW-type models.Practical implicationsCompared with traditional low-frequency models, investors should allocate assets according to the LHAR-CAW model so as to get more economic values.Originality/valueThis study proposes LHAR-CAW model with the matrix adjustment, to account for heterogeneous leverage effect and empirically show their economic advantage. The new model and the new bias adjustment approach are pioneering and promote the evolution of financial econometrics based on high-frequency data.
General equity vs DVR share of Tata Motors: investors’ dilemma
Authors: Rajhans Rajni Kant 
Published: August 2019

Subject area
Finance.

Study level/applicability
Graduate/Under Graduate Progammes

Case overview/synopsis
The case presents the valuation gap between general equity and DVRs shares of TML. The case presents DVRs as an alternate asset class for investment for retail investors and shows its various characteristics taking the case of TML. The case presents global evidences of the valuation gaps and hence helps in making informed decisions. The case makes the reader perplex with a varied global evidence and then presents other data (increasing interest by institutional investors in DVRs of TML) which may help to take final decision “BUY or NOT”.

Expected learning outcomes
The readers will be able to recall “how do finance managers use a diverse type of equity for providing new sources of finance?” The readers will be able to describe the characteristics of differential voting right (DVR) shares. The participants will be able to present various reasons for the price difference between DVR shares and general equity shares. The readers will be in a position to analyze the price pattern of Tata Motors Limited (TML’s) DVR together with global experience. The participants will be able to justify the trade-off between extra dividend and loss of voting rights in the case of DVR shares.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS 1: Accounting and Finance.
A Big Data and FMEA-based construction quality risk evaluation model considering project schedule for Shanghai apartment projects
Authors: Ma Guofeng , Wu Ming 
Published: August 2019

Purpose
The purpose of this paper is to mine information on the construction process of previous projects to develop a construction plan that meets both quality requirements and schedule constraints.

Design/methodology/approach
This paper uses a failure mode and effect analysis to evaluate the construction quality of 311 apartments in Shanghai. The authors also evaluate construction-scheduling control using the earned value management technique and implement an artificial neural network to correlate the results. The authors then develop a quality risk and schedule correlation model based on Big Data. The model can predict the relationship between the planned schedule and the project quality risk using multiple variables such as the number of layers, the schedule performance index and budget costs.

Findings
The methodology offers an innovative approach for assessment on the relationship between quality risk and project schedule. The authors have also built a multiple regression analysis model for comparative purposes with the model. The results show that the proposed model can better describe the relationship. The model can provide a quantitative quality risk value that changes with the planned schedule, as well as help project managers to understand the relationship between quality risk and project scheduling more accurately.

Research limitations/implications
The research approach only focuses on quality risk under the impact of scheduling. Future efforts might focus on developing a model that connects failure models with project schedules and costs in order to improve the effort of quality management.

Practical implications
The model based on Big Data in this paper is developed using real projects and reflects the relationship between project quality risk and scheduling in real environments. The created application provides support for project managers to develop and adjust quality plans and schedules, thereby reducing deviations in quality and scheduling objectives.

Originality/value
The authors make full use of historical project data from the perspective of both quality and schedule management, and provide a novel method to intelligently and objectively analyze the relationship between quality risk and scheduling.
Condition monitoring of structures using limited noisy data modal slope and curvature of mode shapes
Authors: Ali Jafar , Bandyopadhyay Debasish 
Published: August 2019

Purpose
Condition monitoring (CM) has become significantly important, particularly in the context of ensuring safety, reliability and future usefulness of civil infrastructural systems. Most of the age old structures require immediate attention. Nondestructive tests and/or load tests along with routine maintenance inspections are common practice. However, most of the NDT techniques are location-dependent and are conducted in a piecewise manner. The paper aims to discuss these issues.

Design/methodology/approach
Numerical methods incorporating inverse techniques are a global approach to identify structural parameters using dynamic responses. However, measurement at all degrees of freedom does not seem to be feasible, due to practical constraints. Parameter identification of structures based on limited dynamic responses like modal slope and curvature mode shapes at the element level in a finite element platform is proposed in the present paper. The structural property for each element is derived adopting a two-phase analysis process, consisting modal extraction and structural parameter identification. It is important to study the accuracy of the predicted parameters with the number of measured modes. The structural property is identified using measured responses at those selected MDOF.

Findings
The proposed method is demonstrated in detail with a numerical example. The method seems to be an attractive proposition as the results obtained are very accurate even with noise-contaminated data.

Research limitations/implications
However, for practical problems, the experimental validation is significantly important prior to its application in real-life problems.

Practical implications
The developed model seems to be feasible for practical applications after experimental validation, as it is able to identify the structural parameters from limited noisy dynamic responses in frequency domains measured for few modes.

Social implications
Structural CM is the need of the hour, particularly for infrastructural systems including buildings and bridges, etc. System identification with a global dynamic response at few measurement locations may address the issue of health assessment of structures, which will have great social implications with respect to safety.

Originality/value
The proposed numerical model is originally developed by the authors with judicial modifications and combination of earlier research contributions to achieve greater accuracy. Limited measurement and the effect of random noise with numerical example are considered for the successful validation.
Weaving together media, technologies and people
Authors: Dodson Samuel , Roll Ido , Harandi Negar M. , Fels Sidney , Yoon Dongwook 
Published: August 2019

PurposeStudents in flipped classrooms are challenged to orchestrate an increasingly heterogeneous collection of learning objects, including audiovisual materials as well as traditional learning objects, such as textbooks and syllabi. This study aims to examine students' information practices interacting with and synthesizing across learning objects, technologies and people in flipped classrooms.Design/methodology/approachThis grounded theory study explores the information practices of 12 undergraduate engineering students as they learned in two flipped classrooms. An artifact walkthrough was used to elicit descriptions of how students conceptualize and work around interoperability problems between the diverse and distributed learning objects by weaving them together into information tapestries.FindingsStudents maintained a notebook as an information tapestry, weaving fragmented information snippets from the available learning objects, including, but not limited to, instructional videos and textbooks. Students also connected with peers on Facebook, a back-channel that allowed them to sidestep the academic honesty policy of the course discussion forum, when collaborating on homework assignments.Originality/valueThe importance of the interoperability of tools with elements of students' information space and the significance of designing for existing information practices are two outcomes of the grounded theory approach. Design implications for educational technology including the weaving of mixed media and the establishment of spaces for student-to-student interaction are also discussed.