bluuebunny/crossref_metadata_2025 huggingface dataset:
The Impact of Migration and Innovations on the Life Cycles and Size Distribution of Cities
Authors: Broitman Dani , Benenson Itzhak , Czamanski Daniel
Published: March 2020

We present a comprehensive agent-based model of a closed system of cities. The model includes two types of agents—employees and firms. Firms compete for workers and make decisions concerning what to produce and whether to adopt innovations. Individual employees make migration decisions. Some migrants become intrapreneurs when their employers adopt production process innovations that they propose. Some migrants become entrepreneurs when the product innovations that they propose are implemented by their employers in new subsidiary firms. These firms tend to be technological leaders. The decisions of individuals and of firms generate innovation–migration dynamics that generate a variety of city sizes. A city that is home to firms that are currently relatively attractive to migrating innovators experience moderate or fast growth. Because of particular decision patterns by individuals and firms, this growth may decline and stop, and the city may stagnate and loose workers as its relative attractiveness decreases. Cities that remain unattractive for long periods can stop growing and shrink. We model explicitly the extent to which cities attract immigrants and innovators and demonstrate that the size distribution of cities is defined by the ability of its resident firms to adopt the innovations and to let the product innovators establish technologically advanced enterprises. These decisions result in high market value of the most productive firms, of the entire industrial system the city where the firm is located, and of the entire urban system.
Spectrum of Posttransplant Lymphoproliferations in NSG Mice and Their Association With EBV Infection After Engraftment of Pediatric Solid Tumors
Authors: Tillman Heather , Vogel Peter , Rogers Tiffani , Akers Walter , Rehg Jerold E.
Published: March 2020

Pediatric patients receiving solid organ transplants may develop lymphoproliferative diseases, including graft-versus-host disease (GvHD) and posttransplant lymphoproliferative diseases (PTLDs). We characterized lesions in 11 clinically ill NOD.Cg- Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice that received pediatric-patient-derived solid tumors (PDXs) and developed immunodeficiency-associated lymphoproliferations comparable to GvHD and PTLDs over a period of 46 to 283 days after implantation. Lymphoproliferations were diffusely positive for human-specific biomarkers, including NUMA1, CD45, and CD43, but lacked immunoreactivity for murine CD45. Human immune cells were CD3-positive, with subsets having immunoreactivity for CD4 and CD8 as well as PAX5, CD79a, and IRF4, resulting from populations of human T and B cells present within the xenotransplants. Tissues and organs infiltrated included mucocutaneous zones (oral cavity and perigenital and perianal regions), haired skin, tongue, esophagus, forestomach, thyroid, salivary glands, lungs, liver, kidneys, spleen, lymph nodes, bone marrow, and brain. In 4 of 5 mice with PTLD, Epstein-Barr virus (EBV)-encoded small RNAs (EBERs) were detected by in situ hybridization in PAX5+ human B cells associated with the PDX ( n = 1/4) or with engrafted human immune cells at other anatomic locations ( n = 4/11). One of the 4 mice had an EBV-associated human large B-cell lymphoma. NSG mice receiving xenotransplants can develop combinations of GvHD, EBV-driven PTLD, and B-cell lymphoma similar to those occurring in human pediatric patients. Therefore, pediatric xenotransplants should undergo histopathologic and immunohistochemical assessment upon collection to ensure that the specimen is not a lymphoma and does not contain lymphoma cells because these neoplasms can morphologically mimic small round blue cell pediatric solid tumors.
Methods for Source Characterization of Organic Air Pollutants
Authors: Th. Bloemen H. J. , Kliest J. J. G.
Published: March 2020

Organic compounds are becoming increasingly more of interest as air pollutants, indoor as well as outdoor. Sources emitting such compounds are numerous and of various origin. For toxicological and epidemiological examination and for deciding on remedial actions information is required on the occurrences of compounds as well as on the emitting sources. For this purpose a number of investigations have been carried out with only limited success. To increase the quality of the description of air pollution related to complaints of dwellers and to exposure evaluation analytical and mathematical methods have tested in our laboratory.

Analytical methods for the determination of different groups of organic compounds and mathematical methods for defining minimum sampling strategies and for the characterization of sources are discussed and illustrated with applications dealt with in the passed years.

It is concluded that the application of a combination of these methods offers a manner to better describe and understand air pollution with organic compounds.
Sources of Mutagenic Activity in Urban Fine Particles
Authors: Stevens Robert K. , Lewis C. W. , Dzubay T. G. , Cupitt L. T. , Lewtas Joellen
Published: March 2020

Samples were collected during the winter of 1984—1985 in the cities of Albuquerque, NM and Raleigh NC as part of a US Environmental Protection Agency study to evaluate methods to determine the emission sources contributing to the mutagenic properties of extractable organic matter (EOM) present in fine particles. Data derived from the analysis of the composition of these fine particles served as input to a multi-linear regression (MLR) model used to calculate the relative contribution of wood burning and motor vehicle sources to mutagenic activity observed in the extractable organic matter. At both sites the mutagenic potency of EOM was found to be greater (3—5 times) for mobile sources when compared to wood smoke extractable organics. Carbon-14 measurements which give a direct determination of the amount of EOM that originated from wood burning were in close agreement with the source apportionment results derived from the MLR model.
Presence of Viable Mould Propagules in the Indoor Air of Houses
Authors: Verhoeff A. P. , Van Wijnen J. H. , Fischer P. , Brunekreef B. , Boleij J. S. M. , Van Reenen E. S. , Samson R. A.
Published: March 2020

The aim of the first port of this study was to select the optimal technique for the enumeration and identification of viable mould propagules in the indoor air of houses. A comparison was made between the results obtained with six commercially available air sampling devices in combination with four culture media. The optimal technique was defined as the technique with the best precision and the highest yield. The coefficients of variation were high (generally > 20%) for all combinations. Statistical analysis showed that the Slit sampler and the N6-Andersen sampler in combination with DG18 and MEA gave the best precision and the highest yield in terms of CFU/m3 and number of species isolated. In the second part of this study the presence of viable mould propagules in the indoor air of 46 houses in relation to the dampness of these houses was investigated, using the N6-Andersen sampler in combination with DG18. To assess the variability in time, the measurements were repeated after five weeks. Overall, between the two periods no difference was found between the average number of CFU/m3 in the investigated homes. However, the variation between homes was much smaller than the variation within homes. The mean number of CFU/m3 was somewhat higher in “damp” houses than in “dry” houses. However, this difference was not significant. Furthermore, there were no demonstrable differences in the presence of specific mould species in “damp” and “dry” houses.
Health Assessment of Hazardous Air Pollutants the Netherlands
Authors: Vermeire Theo , Van Der Heijden Kees
Published: March 2020

In The Netherlands, risk assessment of air pollutants goes back to 1980. From 1985 onwards the risk assessment of chemicals has crystallized in a systematic multi-media approach taking into account air, water, soil, and food. Criteria Documents support the formulation of environmental quality standards. Until now, 23 documents were prepared. Some toxicological aspects of the risk assessment for man in these documents are discussed with emphasis on carcinogenicity. As examples the main aspects of the risk assessments of benzene and trichloroethylene are described. A list of proposed health based standards for air pollutants is added.
Prevalence of Symptoms of Anxiety, Depression, and Post-traumatic Stress Disorder in Parents and Children Following Pediatric Stroke
Authors: Lehman Laura L. , Maletsky Kristin , Beaute Jeanette , Rakesh Kshitiz , Kapur Kush , Rivkin Michael J. , Mrakotsky Christine
Published: March 2020

Post-traumatic stress disorder (PTSD), anxiety, and depression are seen in parents and children following critical illness. Whether this exists in parents and children following pediatric stroke has not been thoroughly studied. We examined emotional outcomes in 54 mothers, 27 fathers, and 17 children with stroke. Parents of children 0-18 years and children 7-18 years who were within 2 years of stroke occurrence were asked to complete questionnaires to determine their emotional outcomes. Of participating mothers, 28% reported PTSD, 26% depression, and 4% anxiety; in fathers, 15% reported PTSD, 24% depression, and none reported anxiety. Further, children reported significant emotional difficulty, with 24% having depression, 14% anxiety, and 6% PTSD by self-report ratings. Maternal PTSD, anxiety and depression, and paternal anxiety were all negatively associated with the child’s functional outcome. Clinically significant anxiety (based on clinical thresholds) was not found in fathers; however, continuous scores were still analyzed for association between subclinical anxiety and functional outcome, which revealed a statistically significant association between more reported symptoms and higher Recovery and Recurrence Questionnaire scores. Prevalence of PTSD and depression are greater in parents compared to the general population in this preliminary study.
Moving with the media: An exploration of how migrant communities in New Zealand use social media
Authors: Ihejirika Kingsley T. , Krtalic Maja
Published: March 2020

This paper explores why and how migrants use social media in different phases of the migration process, how they manage personal information on social media during migration, and whether they use libraries’ social media in any of the migration phases. An anonymous questionnaire was used to collect opinions and investigate the activities of migrant communities in New Zealand in the three above mentioned areas. The paper presents the results of a descriptive statistical analysis performed on the data. These results were categorized and presented under the following themes: demographic data, use of social media during migration, personal information management practices on social media, use of library social media during migration, issues arising from the use of social media during migration and positive impact of social media during migration.

The main findings of our research showed that in the transitioning phase migrants use social media mostly for making the decision to move. In the settling phase, social media help them to cushion the anxieties associated with a move and also help them to make an informed decision in the new country. In the settled phase, participants used social media to stay connected with family and friends in the home country. Language barriers can restrict the use of social media during the moving process. Personal information on social media is not recognized as important and is not managed in any particular way. Libraries are present in the life of migrants but more as physical spaces and services than through their social media presence. Findings from this study can be of interest to libraries and other information providers developing services for migrants in physical and digital environments.
The prevalence of depressive symptoms and related risk factors among diabetic patients with retinopathy attending the Jordan University Hospital
Authors: Abu Ameerh Mohammed Ali , Hamad Ghada Ismail
Published: March 2020

Objectives:

To investigate the prevalence of depressive symptoms among diabetic patients suffering from retinopathy, and to identify crucial risk factors that affect patients’ quality of life and whether social support mediates the relationship between retinopathy and depression.

Methods:

The sample comprises 155 participants with diabetic retinopathy recruited from the Jordan University Hospital during the year 2017. Arabic versions of all study tools were employed as follows: the Beck Depression Inventory; the short form of the health survey; the Berlin social support scale; ophthalmic examinations; patients’ records; and a demographic questionnaire.

Analyses:

Descriptive statistics, the Pearson correlation, linear regression using SPSS, and mediation analysis using the Sobel test were applied. In addition, the odds ratio analysis and qualitative analyses for the open-ended questions were included.

Results:

In general, 13 (8.9%) of our patients did not manifest any symptoms of depression while 42 (27.1%) had a mild mood disturbance, 26 (16.8%) were on the borderline of clinical depression, 47 (30.3%) had moderate depression, 22 (14.2%) with severe depression, and 5 (3.2%) had extreme depression. The results indicate a nonsignificant positive correlation between social support and health-related quality of life and a nonsignificant positive relationship between retinopathy severity and depression. Meanwhile, our results revealed a significant negative relationship between depression and social support and a nonsignificant negative relationship between retinopathy severity and social support.

Conclusion:

Our findings suggest that diabetic patients with retinopathy have a higher risk of developing depression. Hence, psychological interventions are highly needed to meet the mental health needs of these patients.
Target language use of Dutch EFL student teachers: Three longitudinal case studies
Authors: Tammenga-Helmantel Marjon , Mossing Holsteijn Liza , Bloemert Jasmijn
Published: March 2020

This longitudinal research presents case studies of three English as a foreign language (EFL) student teachers showing their development regarding target language (TL) use, taking into account both the amount of TL use and the classroom situations the TL is used in. Additionally, the factors that influence their TL use are discussed. The data consist of four questionnaires, three classroom observations, and a written reflection on TL use. Results show that – similar to experienced teachers – these student teachers used the TL more in senior than in junior classes and mainly in linguistically predictable situations. On the other hand, the amount of their TL use was high, especially in senior classes, compared to earlier studies in the Dutch context. The student teachers displayed different developmental patterns concerning TL use during teacher education: two of them increased their use of English, mainly in junior classes; TL use of the other student remained stable. Teacher education appeared to mediate TL use one year after graduation for two students. TL use had changed after finishing teacher education but no coherent developments could be discerned.
What was lost, missing, sought and hoped for: Qualitatively exploring medical crowdfunding campaign narratives for Lyme disease
Authors: Vassell Anika , Crooks Valorie A , Snyder Jeremy
Published: March 2020

Lyme disease remains a contested illness in Canada, thereby making the diagnostic and treatment journeys difficult for some people. One outcome of this is that increasing numbers of people are turning to medical crowdfunding to support access to alternative therapies, non-local health care providers and assist with managing the costs of everyday life. In this analysis, we qualitatively explore the narratives shared in Canadians’ crowdfunding campaigns to support Lyme disease treatment or diagnosis to identify whether or not any common elements shared in these narratives exist, and if so, what they are. We identified 238 campaigns for inclusion from three prominent crowdfunding platforms. Thematic analysis of the campaign narratives shows four consistent themes shared in these campaigns: what is lost (e.g. bodily ability), what is missing (e.g. local care options), what is sought (e.g. funds to cover treatment abroad) and what is hoped for (e.g. return to wellbeing). These themes demonstrate the highly personal and emotional nature of medical crowdfunding, particularly in the context of a contested illness that may lead some to question the legitimacy of one’s financial need. This analysis contributes valuable new insights to the nascent scholarship on medical crowdfunding, and particularly to our understanding of how people communicate about their health and bodily needs on this public platform. It also identifies important directions for future research, including the potential for crowdfunding narratives to be used for advocacy.
The Advantage of Scoring Just Before the Half-Time Break—Pure Myth? Quasi-Experimental Evidence From European Football
Authors: Meier Philippe , Flepp Raphael , Ruedisser Maximilian , Franck Egon
Published: March 2020

We examine whether the moment just before the half-time break is a particularly good time to score a goal. Using detailed data from the top five European football leagues between the 2013-2014 and 2017-2018 seasons, we exploit the quasi-random occurrence of goals scored just before and just after the half-time break. In the former situation, the game is exogenously interrupted by a break immediately after the goal, whereas in the latter situation, the game continues without interruption. We show that in the case of a goal being scored just before halftime, the scoring team benefits more from the half-time break than the conceding team.
Motivational Interviewing to Increase Physical Activity Behavior in Cancer Patients: A Pilot Randomized Controlled Trials
Authors: Lion Alexis , Backes Anne , Duhem Caroline , Ries Fernand , Delagardelle Charles , Urhausen Axel , Vögele Claus , Theisen Daniel , Malisoux Laurent
Published: March 2020

Objective: This pilot randomized controlled trial (RCT) aimed at evaluating the feasibility and potential efficacy of a motivational interviewing (MI) intervention to increase physical activity (PA) behavior in cancer patients. Methods: Participants were randomly assigned to an experimental group with standard care plus 12 MI sessions within 12 weeks or a control group with standard care only. The number of recruited participants and the modality of recruitment were recorded to describe the reach of the study. The acceptability of the study was estimated using the attrition rate during the intervention phase. The potential efficacy of the intervention was evaluated by analyzing the PA behavior. Results: Twenty-five participants were recruited within the 16-month recruitment period (1.6 participants per month). Five participants (38.5%) from the experimental group (n = 13) and one participant (8.3%) from the control group (n = 12) dropped out of the study before the end of the intervention phase. No group by time interaction effect for PA behavior was observed at the end of the intervention. Conclusion: Due to the low recruitment rate and compliance, no conclusion can be drawn regarding the efficacy of MI to increase PA behavior in cancer patients. Moreover, the current literature cannot provide any evidence on the effectiveness of MI to increase PA in cancer survivors. Future RCTs should consider that the percentage of uninterested patients to join the study may be as high as 60%. Overrecruitment (30% to 40%) is also recommended to accommodate the elevated attrition rate.
Time-of-arrival–based localization algorithm in mixed line-of-sight/non-line-of-sight environments
Authors: Wang Peixin , Li Youming , Chang Shengming , Jin Xiaoping , Wang Xiaoli
Published: March 2020

A novel time-of-arrival–based localization algorithm in mixed line-of-sight/non-line-of-sight environments is proposed. First, an optimization problem of target localization in the known distribution of line-of-sight and non-line-of-sight is established, and mixed semi-definite and second-order cone programming techniques are used to transform the original problem into a convex optimization problem which can be solved efficiently. Second, a worst-case robust least squares criterion is used to form an optimization problem of target localization in unknown distribution of line-of-sight and non-line-of-sight, where all links are treated as non-line-of-sight links. This problem is also solved using the similar techniques used in the known distribution of line-of-sight and non-line-of-sight case. Finally, computer simulation results show that the proposed algorithms have better performance in both the known distribution and the unknown distribution of line-of-sight and non-line-of-sight environments.
STBS-Stega: Coverless text steganography based on state transition-binary sequence
Authors: Wu Ning , Yang Zhongliang , Yang Yi , Li Lian , Shang Poli , Ma Weibo , Liu Zhenru
Published: March 2020

Information-hiding technology has recently developed into an area of significant interest in the field of information security. As one of the primary carriers in steganography, it is difficult to hide information in texts because there is insufficient information redundancy. Traditional text steganography methods are generally not robust or secure. Based on the Markov chain model, a new text steganography approach is proposed that focuses on transition probability, one of the most important concepts of the Markov chain model. We created a state transition-binary sequence diagrams based on the aforementioned concepts and used them to guide the generation of new texts with embedded secret information. Compared to other related works, the proposed method exploits the use of the transition probability in the process of steganographic text generation. The associated developed algorithm also encrypts the serial number of the state transition-binary sequence diagram needed by the receiver to extract the information, which further enhances the security of the steganography information. Experiments were designed to evaluate the proposed model. The results revealed that the model had higher concealment and hidden capacity compared to previous methods.
Making Sense of Complex Narration in Perfect Blue
Authors: Loriguillo-López Antonio , Palao-Errando José Antonio , Marzal-Felici Javier
Published: March 2020

Although identified as a feature of the film by both critics and researchers, the narrative complexity of Perfect Blue (Satoshi Kon, Madhouse, 1997) has been ambiguously defined. In this article, the authors examine the complex narration in Kon’s first feature film, equivocal and obscure in its more confusing points, through a narratological analysis of the film’s most ambiguous scenes. Using cognitive film theory as introduced by David Bordwell and Edward Branigan, they link its approach in terms of the modulation of information flow throughout the film – high knowledgeability, high self-consciousness and (occasionally) low communicativeness – with the conventions of the slasher genre. Their analysis of the more perplexing scenes in Perfect Blue is reinforced by monitoring the veiled changes of focalization between the film’s three focalizers: Mima, Uchida (aka Me-Mania) and Rumi. In order to do this, they explore how the narration – in the tradition of contemporary puzzle films – makes use of judgements, preconceptions and cognitive illusions in the spectators’ activity to conceal Rumi’s involvement in the persecution of Mima and the murders committed. In the conclusion, they associate the film’s complex narration with its critical commentary on the representation of Japanese pop idols (and former idols) and the state of audiovisual entertainment in Japan.
The Technological Smoke Break: An Assessment of Technology Addiction in the Workplace
Authors: Madlock Paul E. , Hessling Ciera N.
Published: March 2020

The purpose of the current study was to extend prior research by examining the impact of policies that allowed or not-allowed employees access to their smartphones while at work on employee job satisfaction and organizational commitment. This study also examined the relationship between technology addiction, impulsivity, and entitlement. Participants ( N = 266; 123 male and 143 female) were full-time working adults. Findings indicated significant differences in job satisfaction and organizational commitment between employees who worked for organizations that allowed versus not-allowed employees access to their smartphones during the workday. Strong relationships between technology addiction, impulsivity, and entitlement where also found.
Housewives and maids: The labor of household recycling in urban India
Authors: Luthra Aman
Published: March 2020

Sorting waste at-source (or household recycling) helps optimize the efficiency of waste management systems and safeguard the health of waste handlers. Recently, segregation of waste has become an urgent policy imperative that has been written into national waste management policies in India. While urban Indian households have had a long-standing tradition of segregating and selling high-value recyclables to actors in the informal sector, in contemporary policy discourse, women are constructed as recalcitrant urban subjects who need to be disciplined in accordance with the new mandates of waste segregation. This paper locates these processes of subject formation within the changing political economy of waste. Waste sorting is a labor-intensive process, and certain waste management technologies require presorted materials. In addition, presorted recyclables also offer up a source of revenue for waste management service providers. Beyond seeing the need for source segregation simply in abstract environmental and public health interests, this paper argues for contextualizing this imperative within the ongoing processes of privatization and mechanization of waste management systems. These processes dispossess informal waste collectors from their means of subsistence while relying on the unpaid labor of certain women, thus reproducing gender, class, and caste relations.
Fast parallelized sampling of Bayesian regression models for whole-genome prediction
Authors: Zhao Tianjing , Fernando Rohan , Garrick Dorian , Cheng Hao
Published: March 2020

Background

Bayesian regression models are widely used in genomic prediction, where the effects of all markers are estimated simultaneously by combining the information from the phenotypic data with priors for the marker effects and other parameters such as variance components or membership probabilities. Inferences from most Bayesian regression models are based on Markov chain Monte Carlo methods, where statistics are computed from a Markov chain constructed to have a stationary distribution that is equal to the posterior distribution of the unknown parameters. In practice, chains of tens of thousands steps are typically used in whole-genome Bayesian analyses, which is computationally intensive.

Methods

In this paper, we propose a fast parallelized algorithm for Bayesian regression models called independent intensive Bayesian regression models (BayesXII, “X” stands for Bayesian alphabet methods and “II” stands for “parallel”) and show how the sampling of each marker effect can be made independent of samples for other marker effects within each step of the chain. This is done by augmenting the marker covariate matrix by addingp(the number of markers) new rows such that columns of the augmented marker covariate matrix are orthogonal. Ideally, the computations at each step of the MCMC chain can be accelerated byktimes, wherekis the number of computer processors, up toptimes, wherepis the number of markers.

Results

We demonstrate the BayesXII algorithm using the prior for BayesC$$\pi $$π, a Bayesian variable selection regression method, which is applied to simulated data with 50,000 individuals and a medium-density marker panel ($$\sim $$∼ 50,000 markers). To reach about the same accuracy as the conventional samplers for BayesC$$\pi $$πrequired less than 30 min using the BayesXII algorithm on 24 nodes (computer used as a server) with 24 cores on each node. In this case, the BayesXII algorithm required one tenth of the computation time of conventional samplers for BayesC$$\pi $$π. Addressing the heavy computational burden associated with Bayesian methods by parallel computing will lead to greater use of these methods.
Hellinger distance-based stable sparse feature selection for high-dimensional class-imbalanced data
Authors: Fu Guang-Hui , Wu Yuan-Jiao , Zong Min-Jie , Pan Jianxin
Published: March 2020

Background

Feature selection in class-imbalance learning has gained increasing attention in recent years due to the massive growth of high-dimensional class-imbalanced data across many scientific fields. In addition to reducing model complexity and discovering key biomarkers, feature selection is also an effective method of combating overlapping which may arise in such data and become a crucial aspect for determining classification performance. However, ordinary feature selection techniques for classification can not be simply used for addressing class-imbalanced data without any adjustment. Thus, more efficient feature selection technique must be developed for complicated class-imbalanced data, especially in the context of high-dimensionality.

Results

We proposed an algorithm called sssHD to achieve stable sparse feature selection applied it to complicated class-imbalanced data. sssHD is based on the Hellinger distance (HD) coupled with sparse regularization techniques. We stated that Hellinger distance is not only class-insensitive but also translation-invariant. Simulation result indicates that HD-based selection algorithm is effective in recognizing key features and control false discoveries for class-imbalance learning. Five gene expression datasets are also employed to test the performance of the sssHD algorithm, and a comparison with several existing selection procedures is performed. The result shows that sssHD is highly competitive in terms of five assessment metrics. In addition, sssHD presents limited differences between performing and not performing re-balance preprocessing.

Conclusions

sssHD is a practical feature selection method for high-dimensional class-imbalanced data, which is simple and can be an alternative for performing feature selection in class-imbalanced data. sssHD can be easily extended by connecting it with different re-balance preprocessing, different sparse regularization structures as well as different classifiers. As such, the algorithm is extremely general and has a wide range of applicability.
QuaDMutNetEx: a method for detecting cancer driver genes with low mutation frequency
Authors: Bokhari Yahya , Alhareeri Areej , Arodz Tomasz
Published: March 2020

Background

Cancer is caused by genetic mutations, but not all somatic mutations in human DNA drive the emergence or growth of cancers. While many frequently-mutated cancer driver genes have already been identified and are being utilized for diagnostic, prognostic, or therapeutic purposes, identifying driver genes that harbor mutations occurring with low frequency in human cancers is an ongoing endeavor. Typically, mutations that do not confer growth advantage to tumors – passenger mutations – dominate the mutation landscape of tumor cell genome, making identification of low-frequency driver mutations a challenge. The leading approach for discovering new putative driver genes involves analyzing patterns of mutations in large cohorts of patients and using statistical methods to discriminate driver from passenger mutations.

Results

We propose a novel cancer driver gene detection method, QuaDMutNetEx. QuaDMutNetEx discovers cancer drivers with low mutation frequency by giving preference to genes encoding proteins that are connected in human protein-protein interaction networks, and that at the same time show low deviation from the mutual exclusivity pattern that characterizes driver mutations occurring in the same pathway or functional gene group across a cohort of cancer samples.

Conclusions

Evaluation of QuaDMutNetEx on four different tumor sample datasets show that the proposed method finds biologically-connected sets of low-frequency driver genes, including many genes that are not found if the network connectivity information is not considered. Improved quality and interpretability of the discovered putative driver gene sets compared to existing methods shows that QuaDMutNetEx is a valuable new tool for detecting driver genes. QuaDMutNetEx is available for download from https://github.com/bokhariy/QuaDMutNetExunder the GNU GPLv3 license.
Transcriptomic profiling of Solanum peruvianum LA3858 revealed a Mi-3-mediated hypersensitive response to Meloidogyne incognita
Authors: Du Chong , Jiang Jingbin , Zhang He , Zhao Tingting , Yang Huanhuan , Zhang Dongye , Zhao Zhentong , Xu Xiangyang , Li Jingfu
Published: March 2020

Background

The Mi-1 gene was the first identified and cloned gene that provides resistance to root-knot nematodes (RKNs) in cultivated tomato. However, owing to its temperature sensitivity, this gene does not meet the need for breeding disease-resistant plants that grow under high temperature. In this study, Mi-3 was isolated from the wild species PI 126443 (LA3858) and was shown to display heat-stable resistance to RKNs. However, the mechanism that regulates this resistance remains unknown.

Results

In this study, 4760, 1024 and 137 differentially expressed genes (DEGs) were enriched on the basis of pairwise comparisons (34 °C vs. 25 °C) at 0 (before inoculation), 3 and 6 days post-inoculation (dpi), respectively. A total of 7035 DEGs were identified from line LA3858 in the respective groups under the different soil temperature treatments. At 3 dpi, most DEGs were enriched in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to plant biotic responses, such as “plant-pathogen interaction” and “plant hormone signal transduction”. Significantly enriched DEGs were found to encode key proteins such as R proteins and heat-shock proteins (HSPs). Moreover, other DEGs were found to participate in Ca2+ signal transduction; the production of ROS; DEGs encoding transcription factors (TFs) from the bHLH, TGA, ERF, heat-shock transcription factor (HSF) and WRKY families were highly expressed, which contribute to be involved into the formation of phytohormones, such as salicylic acid (SA), jasmonic acid (JA) and ethylene (ET), the expression of most was upregulated at 3 dpi at the 25 °C soil temperature compared with the 34 °C soil temperature.

Conclusion

Taken together, the results of our study revealed reliable candidate genes from wild materials LA3858, that are related to Mi-3-mediate resistance to Meloidogyne incognita. A large number of vital pathways and DEGs were expressed specifically in accession LA3858 grown at 34 °C and 25 °C soil temperatures at 3 dpi. Upon infection by RKNs, pattern-recognition receptors (PRRs) specifically recognized conserved pathogen-associated molecular patterns (PAMPs) as a result of pathogen-triggered immunity (PTI), and the downstream defensive signal transduction pathway was likely activated through Ca2+ signal channels. The expression of various TFs was induced to synthesize phytohormones and activate R proteins related to resistance, resulting in the development of effector-triggered immunity (ETI). Last, a hypersensitive response in the roots occurred, which was probably induced by the accumulation of ROS.
Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats
Authors: Ji Zhibin , Chao Tianle , Liu Zhaohua , Hou Lei , Wang Jin , Wang Aili , Zhou Jie , Xuan Rong , Wang Guizhi , Wang Jianmin
Published: March 2020

Background

The mammary gland is a unique organ for milk synthesis, secretion and storage, and it undergoes cyclical processes of development, differentiation, lactation and degeneration. At different developmental periods, the biological processes governing mammary gland physiology and internal environmental homeostasis depend on a complex network of genes and regulatory factors. Emerging evidence indicates that lncRNAs have arbitrarily critical functions in regulating gene expression in many organisms; however, the systematic characteristics, expression, and regulatory roles of lncRNAs in the mammary gland tissues of dairy goats have not been determined.

Result

In the present study, we profiled long noncoding RNA (lncRNA) expression in the mammary gland tissues of Laoshan dairy goats (Capra hircus) from different lactation periods at the whole-genome level, to identify, characterize and explore the regulatory functions of lncRNAs. A total of 37,249 transcripts were obtained, of which 2381 lncRNAs and 37,249 mRNAs were identified, 22,488 transcripts, including 800 noncoding transcripts and 21,688 coding transcripts, differed significantly (p ≤ 0.01) among the different lactation stages. The results of lncRNA-RNA interaction analysis showed that six known lncRNAs belonging to four families were identified as the precursors of 67 known microRNAs; 1478 and 573 mRNAs were predicted as hypothetical cis-regulation elements and antisense mRNAs, respectively. GO annotation and KEGG analysis indicated that the coexpressed mRNAs were largely enriched in biological processes related to such activities as metabolism, immune activation, and stress,., and most genes were involved in pathways related to such phenomena as inflammation, cancer, signal transduction, and metabolism.

Conclusions

Our results clearly indicated that lncRNAs involved in responses to stimuli, multiorganism processes, development, reproductive processes and growth, are closely related to mammary gland development and lactation.
Characterization of the Gh4CL gene family reveals a role of Gh4CL7 in drought tolerance
Authors: Sun Shi-Chao , Xiong Xian-Peng , Zhang Xiao-Li , Feng Hong-Jie , Zhu Qian-Hao , Sun Jie , Li Yan-Jun
Published: March 2020

Background

The function of 4-coumarate-CoA ligases (4CL) under abiotic stresses has been studied in plants, however, limited is known about the 4CL genes in cotton (G. hirsutum L.) and their roles in response to drought stress.

Results

We performed genome-wide identification of the 4CL genes in G. hirsutum and investigated the expression profiles of the identified genes in various cotton tissues and in response to stress conditions with an aim to identify 4CL gene(s) associated with drought tolerance. We identified 34 putative 4CL genes in G. hirsutum that were clustered into three classes. Genes of the same class usually share a similar gene structure and motif composition. Many cis-elements related to stress and phytohormone responses were found in the promoters of the Gh4CL genes. Of the 34 Gh4CL genes, 26 were induced by at least one abiotic stress and 10 (including Gh4CL7) were up-regulated under the polyethylene glycol (PEG) simulated drought stress conditions. Virus-induced gene silencing (VIGS) in cotton and overexpression (OE) in Arabidopsis thaliana were applied to investigate the biological function of Gh4CL7 in drought tolerance. The Gh4CL7-silencing cotton plants showed more sensitive to drought stress, probably due to decreased relative water content (RWC), chlorophyll content and antioxidative enzyme activity, increased stomatal aperture, and the contents of malondialdehyde (MDA) and hydrogen peroxide (H2O2). Arabidopsis lines overexpressing Gh4CL7, however, were more tolerant to drought treatment, which was associated with improved antioxidative enzyme activity, reduced accumulation of MDA and H2O2 and up-regulated stress-related genes under the drought stress conditions. In addition, compared to their respective controls, the Gh4CL7-silencing cotton plants and the Gh4CL7-overexpressing Arabidopsis lines had a ~ 20% reduction and a ~ 10% increase in lignin content, respectively. The expression levels of genes related to lignin biosynthesis, including PAL, CCoAOMT, COMT, CCR and CAD, were lower in Gh4CL7-silencing plants than in controls. Taken together, these results demonstrated that Gh4CL7 could positively respond to drought stress and therefore might be a candidate gene for improvement of drought tolerance in cotton.

Conclusion

We characterized the 4CL gene family in upland cotton and revealed a role of Gh4CL7 in lignin biosynthesis and drought tolerance.
An evaluation of inverse probability weighting using the propensity score for baseline covariate adjustment in smaller population randomised controlled trials with a continuous outcome
Authors: Raad Hanaya , Cornelius Victoria , Chan Susan , Williamson Elizabeth , Cro Suzie
Published: March 2020

Background

It is important to estimate the treatment effect of interest accurately and precisely within the analysis of randomised controlled trials. One way to increase precision in the estimate and thus improve the power for randomised trials with continuous outcomes is through adjustment for pre-specified prognostic baseline covariates. Typically covariate adjustment is conducted using regression analysis, however recently, Inverse Probability of Treatment Weighting (IPTW) using the propensity score has been proposed as an alternative method. For a continuous outcome it has been shown that the IPTW estimator has the same large sample statistical properties as that obtained via analysis of covariance. However the performance of IPTW has not been explored for smaller population trials (< 100 participants), where precise estimation of the treatment effect has potential for greater impact than in larger samples.

Methods

In this paper we explore the performance of the baseline adjusted treatment effect estimated using IPTW in smaller population trial settings. To do so we present a simulation study including a number of different trial scenarios with sample sizes ranging from 40 to 200 and adjustment for up to 6 covariates. We also re-analyse a paediatric eczema trial that includes 60 children.

Results

In the simulation study the performance of the IPTW variance estimator was sub-optimal with smaller sample sizes. The coverage of 95% CI’s was marginally below 95% for sample sizes < 150 and ≥ 100. For sample sizes < 100 the coverage of 95% CI’s was always significantly below 95% for all covariate settings. The minimum coverage obtained with IPTW was 89% with n = 40. In comparison, regression adjustment always resulted in 95% coverage. The analysis of the eczema trial confirmed discrepancies between the IPTW and regression estimators in a real life small population setting.

Conclusions

The IPTW variance estimator does not perform so well with small samples. Thus we caution against the use of IPTW in small sample settings when the sample size is less than 150 and particularly when sample size < 100.
Length of stay after childbirth in India: a comparative study of public and private health institutions
Authors: Kumar Pradeep , Dhillon Preeti
Published: March 2020

Background

This paper discusses length of stay (LOS) following childbirth as an indicator of quality of postnatal care in health institutions. This research aims to describe LOS according to both vaginal and cesarean deliveries in public and private health care institutions in India, and to identify any association of LOS with postnatal care and post-delivery complications.

Methods

We use recently released nationally-representative data from the National Family Health Survey-4 (2015–16) and apply the Cox proportional hazard model to determine the factors associated with LOS at the health facility after childbirth during a five-year period preceding the survey.

Results

Overall, the average LOS after childbirth is 3.4 days; 2.1 days for vaginal deliveries and 8.6 days for cesarean section (CS) deliveries. Strikingly, half of the women are discharged within 48 h. Women who give birth in private hospitals have a more prolonged stay than those who give birth in public health facilities. For vaginal birth in public hospitals, one-fourth of the women are discharged with insufficient LOS as against only 19.2% women in private hospitals. LOS is significantly related to the cost of delivery only in the case of private facilities. Uneducated women belonging to lower wealth quintile households and those living in rural areas stay for a shorter duration for vaginal deliveries but for a longer duration in case of cesarean deliveries. Women who get four or more antenatal check-ups (ANC) done have a longer stay, while those who receive benefits under theJanani Suraksha Yojna(JSY) have a shorter stay. Another key finding is that women who are discharged on the same day report lower levels of postnatal care and a higher proportion of post-delivery complications.

Conclusion

The study concludes that early discharge has a negative association with maternal health outcomes, which has important program implications. Therefore, it is essential to maintain an adequate LOS at a facility after childbirth. We recommend that government programs should strengthen the JSY scheme not only to improve delivery care, but also to provide effective postnatal care by promoting sufficient LOS at facilities.
Knowledge, and use of labour pain relief methods and associated factors among obstetric caregivers at public health centers of East Gojjam zone, Amhara region, Ethiopia: a facility based cross- sectional study
Authors: Bishaw Keralem Anteneh , Sendo Endalew Gemechu , Abebe Workinesh Sinshaw
Published: March 2020

Background

The study was conducted in public health centers of East Gojjam Zone, Amhara region, Ethiopia.The purpose of this study was to assess knowledge, and use of labour pain relief methods and associated factors among obstetric caregivers in the study setting.

Methods

A facility-based cross-sectional study design was conducted from March 1–30, 2018. The study was conducted among three hundred and nine sampled obstetric caregivers. Structured questionnaire was used to collect the data. The data were entered into Epi-data version 4.2 Software for cleaning and exported to SPSS version 23.0 for data analysis. Multivariate logistic regression was carried out for variables with ap-value < 0.25 in bivariate logistic regression to determine significant relationships between the dependent and independent variables. Statistical significance was determined at 95% confidence interval (CI) andp-value below 0.05.

Result

The overall use of labour pain relief methods reported was 34.4%, (30.4% non-pharmacological and 8.4 pharmacological, respectively). More than half of the study participants (54.2%) had adequate knowledge about labour pain relief methods. In multivariate analysis, being a midwifery profession [AOR =2.814, 95% CI = (1.574–5.031)], having positive attitude [AOR = 4.370, 95% CI = (2.523–7.567)], and professionals with a medium level of education [AOR = 3.450, 95% CI = (1.993–5.971)] were factors significantly associated with knowledge of obstetric caregivers about labour pain relief methods. In multivariate analysis, knowledge of obstetric caregivers [AOR = 3.821, 95% CI = (2.091–6.980)], positive attitude of obstetric caregivers [AOR = 2.455, 95% CI = ((1.358–4.436))] and experience of obstetric caregivers [AOR = 2.56, 95% CI = (1.350–4.845) were factors significantly associated with the use of labour pain relief methods.

Conclusion

In this study, the overall use of labour pain relief methods by obstetric caregivers was low. Systemic opioid (Pethdine) was reportedly one of the most known pharmacological pain relief methods in this study. Providers’ knowledge, attitude and work experience had shown statistical significance with the use of labour pain relief methods. Task-oriented in- service training is required to fortify obstetric caregivers’ knowledge and attitude towards the use of labour pain relief methods.