bluuebunny/crossref_metadata_2025_split huggingface dataset:
LiPLike: Towards gene regulatory network predictions of high-certainty
Authors: Magnusson Rasmus , Gustafsson Mika 
Published: May 2019

AbstractMotivationReverse engineering of gene regulatory networks has for years struggled with high correlation in expression between regulatory elements. If two regulators have matching expression patterns it is impossible to differentiate between the two, and thus false positive identifications are abundant.ResultsTo allow for gene regulation predictions of high confidence, we propose a novel method, LiPLike, that assumes a regression model and iteratively searches for interactions that cannot be replaced by a linear combination of other predictors. To compare the performance of LiPLike with other available inference methods, we benchmarked LiPLike using three independent datasets from the previous DREAM5 challenge. We found that LiPLike could be used to stratify predictions of other inference tools, and when applied to the predictions of DREAM5 participants we observed the accuracy to on average be improved >140% compared to individual methods. Furthermore, we observed that LiPLike independently predicted networks better than all DREAM5 participants when applied to biological data. When predicting the Escherichia coli network, LiPLike had an accuracy of 0.38 for the top-ranked 100 interactions, whereas the corresponding DREAM5 consensus model yielded an accuracy of 0.11.AvailabilityWe made LiPLike available to the community as a Python toolbox, available at https://gitlab.com/Gustafsson-lab/liplike. We believe that LiPLike will be used for high confidence predictions in studies where individual model interactions are of high importance, and that LiPLike will be used to remove false positive predictions made by other state-of-the-art gene-gene regulation prediction tools.Contactrasmus.magnusson@liu.se, mika.gustafsson@liu.se
Resistance is futile: A CRISPR homing gene drive targeting a haplolethal gene
Authors: Champer Jackson , Yang Emily , Lee Yoo Lim , Liu Jingxian , Clark Andrew G. , Messer Philipp W. 
Published: May 2019

ABSTRACTEngineered gene drives are being explored as a potential strategy for the control of vector-borne diseases due to their ability to rapidly spread genetic modifications through a population. While an effective CRISPR homing gene drive for population suppression has recently been demonstrated in mosquitoes, formation of resistance alleles that prevent Cas9 cleavage remains the major obstacle for drive strategies aiming at population modification, rather than elimination. Here, we present a homing drive in Drosophila melanogaster that reduces resistance allele formation below detectable levels by targeting a haplolethal gene with two gRNAs while also providing a rescue allele. This is because any resistance alleles that form by end-joining repair will typically disrupt the haplolethal target gene, rendering the individuals carrying them nonviable. We demonstrate that our drive is highly efficient, with 91% of the progeny of drive heterozygotes inheriting the drive allele and with no resistance alleles observed in the remainder. In a large cage experiment, the drive allele successfully spread to all individuals. These results show that a haplolethal homing drive can be a highly effective tool for population modification.
Dual midbrain and forebrain origins of thalamic inhibitory interneurons
Authors: Jager Polona , Moore Gerald , Calpin Padraic , Durmishi Xhuljana , Kita Yoshiaki , Salgarella Irene , Wang Yan , Schultz Simon R. , Brickley Stephen , Shimogori Tomomi , Delogu Alessio 
Published: May 2019

AbstractThe proportion and distribution of local inhibitory neurons (interneurons) in the thalamus varies widely across mammals. The ubiquitous presence of interneurons in the thalamus of primates contrasts with the extreme sparsity of interneurons reported in mice and other small-brained mammals. This is reflected in the structure and function of thalamic local circuits, which are more complex in primates compared to rodents. To what extent the broad range of interneuron densities observed in mammalian species reflect the appearance of novel interneuron types or the elaboration of a plesiomorphic ontogenetic program, remains unclear.Here, we identify a larger than expected complexity and distribution of interneurons across the mouse thalamus, where all thalamic interneurons can be traced back to two developmental programs: one specified in the midbrain and the other in the forebrain. Interneurons migrate to functionally distinct thalamocortical nuclei depending on their origin the abundant, midbrain-derived class populates the first and higher order sensory thalamus while the rarer, forebrain-generated class is restricted to some higher order associative regions. We also observe that markers for the midbrain-born class are abundantly expressed throughout the thalamus of the New World monkey marmoset. These data therefore reveal that, despite the broad variability in interneuron density across mammalian species, the blueprint of the ontogenetic organization of thalamic interneurons of larger-brained mammals exists and can be studied in mice.
Pseudo-chromosome length genome assembly of a double haploid ‘Bartlett’ pear (Pyrus communis L.)
Authors: Linsmith Gareth , Rombauts Stephane , Montanari Sara , Deng Cecilia H. , Celton Jean-Marc , Guérif Philippe , Liu Chang , Lohaus Rolf , Zurn Jason D. , Cestaro Alessandro , Bassil Nahla V. , Bakker Linda V. , Schijlen Elio , Gardiner Susan E. , Lespinasse Yves , Durel Charles-Eric , Velasco Riccardo , Neale David B. , Chagné David , Van de Peer Yves , Troggio Michela , Bianco Luca 
Published: May 2019

AbstractWe report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII Long read sequencing (PacBio), Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. A total of 496.9 million bases (Mb) corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 chromosomes of the pear genome. About 50% (247 Mb) of the genome consists of repetitive sequences. Comparison with previous assemblies of Pyrus communis. and Pyrus x bretschneideri confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.
STK11 is required for the normal program of ciliated cell differentiation in airways
Authors: Chu Qiqi , Yao Changfu , Qi Xiangbing , Stripp Barry Raymond , Tang Nan 
Published: May 2019

AbstractThe functional properties of mucosal surfaces are dependent on establishing the correct proportions of specialized epithelial cell types. Multiciliated cells (also known as ciliated cells) are evolutionarily conserved and functionally indispensable epithelial cells, as suggested by the link between ciliated cell dysfunction and chronic human disease. Ciliated cell differentiation is an ordered process that involves initial cell fate determination and multiciliogenesis. STK11, a serine/threonine kinase, has been reported to be down-regulated in human diseases associated with ciliopathies and functions as a tumor suppressor. Here, we show that STK11 is a physiological factor for the normal program of ciliated cell differentiation by phosphorylating MARK3, which directly suppresses ERK1/2 mediated pRB inactivation. Loss ofStk11in airway progenitors impairs the differentiation of ciliated cells in both embryonic and adult airways. Our study establishes that STK11/MARK3/ERK1/2 signaling cascade is a key regulator to integrate ciliated cell fate commitment and the subsequent process of multiciliogenesis.
Aeroelastic stability analysis of hingeless rotor blades in hover using fully intrinsic equations and dynamic wake model
Authors: Amoozgar Mohammadreza , Shahverdi Hossein 
Published: May 2019

PurposeThis paper aims to develop a new approach for aeroelastic analysis of hingeless rotor blades.Design/methodology/approachThe aeroelastic approach developed here is based on the geometrically exact fully intrinsic beam equations and three-dimensional unsteady aerodynamics.FindingsThe developed approach is accurate, fast and very useful in rotorcraft aeroelastic analysis.Originality/valueThis beam formulation has been never combined with three-dimensional aerodynamic model to be used for aeroelastic analysis of blades. In addition, it is possible to handle the composite blades, as well as blades with initial curvatures and twist with this proposed formulation.
A survey on the Internet of Things security
Authors: Yousuf Omerah , Mir Roohie Naaz 
Published: May 2019

Purpose
Internet of Things (IoT) is a challenging and promising system concept and requires new types of architectures and protocols compared to traditional networks. Security is an extremely critical issue for IoT that needs to be addressed efficiently. Heterogeneity being an inherent characteristic of IoT gives rise to many security issues that need to be addressed from the perspective of new architectures such as software defined networking, cryptographic algorithms, federated cloud and edge computing.

Design/methodology/approach
The paper analyzes the IoT security from three perspectives: three-layer security architecture, security issues at each layer and security countermeasures. The paper reviews the current state of the art, protocols and technologies used at each layer of security architecture. The paper focuses on various types of attacks that occur at each layer and provides the various approaches used to countermeasure such type of attacks.

Findings
The data exchanged between the different devices or applications in the IoT environment are quite sensitive; thus, the security aspect plays a key role and needs to be addressed efficiently. This indicates the urgent needs of developing general security policy and standards for IoT products. The efficient security architecture needs to be imposed but not at the cost of efficiency and scalability. The paper provides empirical insights about how the different security threats at each layer can be mitigated.

Originality/value
The paper fulfills the need of having an extensive and elaborated survey in the field of IoT security, along with suggesting the countermeasures to mitigate the threats occurring at each level of IoT protocol stack.
Faculty placement strategies for international higher education institutes
Authors: Swanson Mary K. , Swanson Brian A. 
Published: May 2019

Purpose
This paper aims to focus on enhancing the learning experience for both expatriate academics and students in international higher education institutions (HEIs) through understanding students’ cultural perspectives, analyzing student feedback and evaluating faculty placement strategies. The analysis can be used to aid international educational programs in understanding student values and increasing the quality of instructor–student interaction.

Design/methodology/approach
This research surveyed over 1,300 undergraduate students enrolled in a US and Chinese dual-degree program located in China. A voluntary survey with open and closed questions assessed the cultural values of students, and the cultural values and behavior they believe are important for their instructors to observe in the classroom.

Findings
The results of this case study suggest that students’ perceived importance of Western cultural values demonstrated only one significant change during their time of enrollment in a US degree program. However, the research indicates that the importance of Chinese cultural values decreased from the students’ first year to their fourth year. Some notable propositions include the importance of culturally competent and experienced faculty in the students’ early US courses and data-driven recommendations for placement, training and development of new foreign faculty to increase the likelihood of a satisfactory experience for both the faculty and students in the cross-border classroom.

Originality/value
Ultimately, this research can aid international HEI’s by enabling enhanced student and instructor experiences and superior HR practices in the less observed area of faculty placement. These improved practices can contribute to the quality and sustainability of such international programs. In addition, this research provides perspective on the impact of international education on student cultural values and presents student feedback to increase understanding of student expectations and desires in the international classroom.
How does capital market respond to Certified Emission Reductions (CERs) announcements in India
Authors: Kumar Praveen , Firoz Mohammad 
Published: May 2019

Purpose
The purpose of this paper is to analyze the relationship between Certified Emission Reductions (CERs) information and a firm’s stock prices.

Design/methodology/approach
The present study is based on 193 CERs announcements by Indian firms over a 13-year period 2005–2017. The event study methodology is used to examine the impact of CERs announcements on a firm’s share prices.

Findings
The study suggests that the issuance of CERs did not produce any significant abnormal return. More specifically, the outcomes of event study shows that over a two-day event window from the event day to the day after the event (i.e. days 0 to 1), the mean and median of AARs are −0.25 and −0.34 percent, respectively. The abnormal returns on day 1 are not statistically significant as per the t-test. Moreover, the mean and median of abnormal returns after one day (−1) are negative, indicating that investors react negatively to CERs announcements. However, the mean and median of CAARs over both the two-day (i.e. days −1 to 0 and days 0 to +1) and three-day (i.e. days −1 to +1) event windows are positive, but not statistically significant based on the t-test.

Research limitations/implications
The findings of the study are quite comprehensive, relatively used only market-based criteria of a firm’s financial performance, e.g., share price, at times, inhibits generalizing the results.

Originality/value
To the best of the author’s knowledge, the present study is a first of its kind to investigate the relationship between the CERs information and a firm’s stock prices.
Beyond police culture
Authors: Paesen Heidi , Maesschalck Jeroen , Loyens Kim 
Published: May 2019

Purpose
Combining insights from the traditional literature on police culture with insights from the broader literature on organisational culture and on grid-group cultural theory (Douglas, 1970), the purpose of this paper is to introduce a new 15-dimensional framework of “organisational culture in the police” and test this framework via a survey instrument. This new conceptualisation is broader than the traditional police culture concept and allows for comparisons of the police with other organisations.

Design/methodology/approach
A newly developed instrument to measure the 15-dimensional framework, called the “Leuven Organisational Culture Questionnaire (LOCQ)”, was tested in 64 local police forces in Belgium (n=3,847).

Findings
The hypothesised 15-dimensional model is largely confirmed by confirmatory factor analysis. Assessments of between-unit variation show that the LOCQ is sufficiently sensitive to identify differences between work units in police organisations. The authors also find that traditional police culture characteristics tend to vary slightly less between units than the other characteristics. Also, there is less variation for characteristics related to police work (e.g. law enforcement orientation and citizen orientation) than for characteristics associated with the unit level (e.g. weak supervisory support and internal solidarity) or the organisational level (e.g. rule orientation and results orientation).

Originality/value
This paper expands the traditional “police culture” concept to a more generic and theory-driven conceptualisation of “organisational culture in the police”. The survey instrument offers a standardised way to map and compare culture within police organisations, and to compare it with the culture of other organisations both within and outside law enforcement.
Research on the adaptive mechanism of photosynthetic apparatus under salt stress: New directions to increase crop yield in saline soils
Authors: Huang Luyao , Li Zhuangzhuang , Liu Qian , Pu Gaobin , Zhang Yongqing , Li Jia 
Published: May 2019

AbstractPhotosynthesis is the largest organic synthesis on Earth, salinity limits crop yield and quality worldwide directly or indirectly related to the decrease in photosynthetic efficiency. The mechanism by which photosynthetic apparatus responds to salt stress is extremely complex and varies with plant genotype, developmental stage, the history of the plant cell and duration of stress imposed. Recent studies have partially revealed the mechanisms from different levels: molecular, physiological and biochemical, morphological; but there is currently no unified mechanism to explain the effect of stress on photosynthesis. This study comprehensively reviews the adaptive mechanism of photosynthetic apparatus under salt stress, summarises methods for increasing the resistance and provides a practical way to increase grain yield in saline soils.
A prospective review of perinatal mortality at Hospital Nacional Guido Valadares (HNGV)
Authors: Jayaratnam Skandarupan , Lucia de Fatima Godinho Soares Maria , Bucens Ingrid , Jennings Belinda , Woods Cindy , Shub Alexis 
Published: May 2019

BackgroundTimor‐Leste has one of the highest perinatal mortality rates in the Asia‐Pacific region. Consistent and accurate data collection improves understanding of perinatal outcomes and facilitates the development of interventions to reduce stillbirths and early neonatal deaths.Aims(1) To identify changes in the rates of stillbirth and early neonatal deaths from previous published data. (2) To determine if prospective data collection and the application of the simplified Causes Of Death and Associated Conditions (CODAC) classification allows better identification of perinatal deaths in Timor‐Leste.MethodsA prospective audit of perinatal deaths of women delivering at Hospital Nacional Guido Valadares (HNGV) was undertaken from January to June 2016 inclusive. The hospital birth registry, maternal and neonatal records were reviewed to determine the most likely aetiology and classification of perinatal deaths using the simplified CODAC system.ResultsOne hundred and ten stillbirths and 28 early neonatal deaths were identified. Fifty‐four percent of perinatal deaths occurred antepartum, 26% intrapartum and 20% were early neonatal deaths. Cause of death among stillbirths could not be ascertained in 40% of cases. Intrapartum asphyxia was the commonest identified aetiology of intrapartum and early neonatal deaths.ConclusionThere has been limited improvement in the rate of stillbirths and early neonatal deaths at HNGV. Intrapartum hypoxia and maternal hypertensive conditions were the most common identified aetiologies highlighting areas where targeted interventions may help reduce high perinatal mortality rates. Aetiology of perinatal deaths, particularly antepartum stillbirths was difficult to discern even when well‐tested classification systems are used.
Letter: reassuringly normal response to ACTH in children treated with swallowed topical corticosteroids for eosinophilic oesophagitis – authors’ reply
Authors: Philpott Hamish , Dougherty Michael , Torpy David , Dellon Evan 
Published: May 2019

Linked ContentThis article is linked to Philpott et al and Rodríguez Manchón et al papers. To view these articles, visit https://doi.org/10.1111/apt.14573 and https://doi.org/10.1111/apt.15243.
Impact of a single treatment of injectable doramectin on weight gain post weaning in beef heifers and steers in central Queensland, Australia
Authors: Taylor LF , Hodge A 
Published: May 2019

ObjectivesTo demonstrate the impact of a single drench with a label dose of injectable doramectin subsequent to weaning on the growth and performance of heifers and steers in central Queensland beef herds.MethodsThree studies were undertaken on recently‐weaned Bos indicus‐cross beef calves with ≥ 75% B. indicus content on two farms in central Queensland, just north of the Tropic of Capricorn. Farm 1 was located 50 km north and Farm 2 75 km north‐west of Rockhampton. In each study, half of a group of recently‐weaned beef calves were treated by random allocation with 0.2 mg/kg of injectable doramectin, and the remainder acting as untreated controls. Study 1 (Farm 1) enrolled 250 heifers, while studies 2 and 3 (Farm 2) both enrolled 200 steers and 200 heifers. The farms involved did not historically use macrocyclic lactone‐based drenches on their cattle. There were varying periods of follow‐up, with treated and control cattle pastured as one group throughout the study period. Worm burdens were monitored using standard faecal egg counts and larval differentiation procedures. In all studies, the worm genera present were a mix of Cooperia spp., Haemonchus spp. and Oesophagostomum spp.ResultsIn study 1, conducted on Farm 1 beginning 9 July 2012, doramectin‐treated cattle gained an average of 0.27 kg/day while control cattle gained 0.19 kg/day over a monitoring period of 121 days (P < 0.0001). In study 2, conducted on Farm 2 beginning 28 July 2015, doramectin‐treated cattle gained an average of 0.15 kg/day versus 0.145 kg/day in the control group (P = 0.44) over a 231‐day study period. In study 3, conducted on Farm 2 beginning 4 August 2016, doramectin‐treated steers and heifers gained an average of 0.431 and 0.402 kg/day versus 0.342 and 0.311 kg/day in the control group, respectively, over the first 91 days of the study (P < 0.0001 in both cases). The differences in average daily gain (ADG) in subsequent time periods were not statistically significant for steers or heifers. However, overall differences in ADG from day 0 remained statistically significant out to day 258, when the study ended for the heifers. By day 594, when the study ended for the steers, the difference in ADG was no longer significant.ConclusionTreatment with injectable doramectin soon after weaning resulted in improved weight gain in the 3 months after weaning in two of the three studies.
Is canine heartworm (Dirofilaria immitis) endemic to South Australia?
Authors: Dearsley EJ , O’Handley RM , Caraguel CGB 
Published: May 2019

BackgroundCanine heartworm (Dirofilaria immitis) was reported as endemic to South Australia over 25 years ago, but the current status of canine heartworm infection in South Australia is unknown.MethodsWe surveyed South Australian veterinary practices to collect evidence about canine heartworm cases, prevention, screening and treatment practices.ResultsIn total, 141 veterinary practices operating in South Australia (92.3% response rate) completed a 12‐question telephone survey. Five confirmed cases of heartworm and one suspected false‐positive case were reported from separate practices over the 2016–17 financial year. All confirmed cases had recently relocated to South Australia from interstate. Incidence of canine heartworm was estimated at 0.00% (95% confidence interval (CI): 0.00–0.0006) and prevalence at 0.002% (95%CI: 0.00–0.004) using conservative estimates of the South Australian dog population. Attitudes and protocols regarding heartworm differed significantly between metropolitan and rural veterinary practices. All metropolitan practices recommend systematic medicated prevention against heartworm, while some rural practices (20.7%) recommend prevention only when travelling interstate (P < 0.001).ConclusionAlthough there is a minor source of heartworm from introduction of infected dogs into South Australia, there is no evidence that the infection is transmitted to other dogs within the state. Therefore, it is unlikely that heartworm is currently endemic to South Australia as reported in the past. This new evidence provides a strong case to refine current prevention practices to reflect the current negligible risk of heartworm infection within South Australia.