bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial Regulation of Polo-like Kinase Activity during C. elegans Meiosis by the Nucleoplasmic HAL-2/HAL-3 Complex
Authors: Roelens Baptiste , Barroso Consuelo , Montoya Alex , Cutillas Pedro , Zhang Weibin , Woglar Alexander , Girard Chloe , Martinez-Perez Enrique , Villeneuve Anne M.
Published: January 2019

Proper partitioning of homologous chromosomes during meiosis relies on the coordinated execution of multiple interconnected events: Homologs must locate, recognize and align with their correct pairing partners. Further, homolog pairing must be coupled to assembly of the synaptonemal complex (SC), a meiosis-specific tripartite structure that maintains stable associations between the axes of aligned homologs and regulates formation of crossovers between their DNA molecules to create linkages that enable their segregation. Here we identify HAL-3 (Homolog Alignment 3) as an important player in coordinating these key events during C. elegans meiosis. HAL-3 and the previously-identified HAL-2 are interacting and interdependent components of a protein complex that localizes to the nucleoplasm of germ cells. hal-3 (or hal-2) mutants exhibit multiple meiotic prophase defects including failure to establish homolog pairing, inappropriate loading of SC subunits onto unpaired chromosome axes, and premature loss of synapsis checkpoint protein PCH-2. Further, loss of hal function results in misregulation of the subcellular localization and activity of polo-like kinases (PLK-1 and PLK-2), which dynamically localize to different defined subnuclear sites during wild-type prophase progression to regulate distinct cellular events. Moreover, loss of PLK-2 activity partially restores tripartite SC structure in a hal mutant background, suggesting that the defect in pairwise SC assembly in hal mutants reflects inappropriate PLK activity. Together our data support a model in which the nucleoplasmic HAL-2/HAL-3 protein complex constrains both localization and activity of meiotic Polo-like kinases, thereby preventing premature interaction with stage-inappropriate targets.
Distinct ROPGEFs successively drive polarization and outgrowth of root hairs
Authors: Denninger Philipp , Reichelt Anna , Schmidt Vanessa A. F. , Mehlhorn Dietmar G. , Asseck Lisa Y. , Stanley Claire E. , Keinath Nana F. , Evers Jan-Felix , Grefen Christopher , Grossmann Guido
Published: January 2019

Root hairs are tubular protrusions of the root epidermis that significantly enlarge the exploitable soil volume in the rhizosphere. Trichoblasts, the cell type responsible for root hair formation, switch from cell elongation to tip growth through polarization of the growth machinery to a pre-defined root hair initiation domain (RHID) at the plasma membrane. The emergence of this polar domain resembles the establishment of cell polarity in other eukaryotic systems [1–3]. Rho-type GTPases of plants (ROPs) are among the first molecular determinants of the RHID [4, 5] and later play a central role in polar growth [6]. Numerous studies have elucidated mechanisms that position the RHID in the cell [7–9] or regulate ROP activity [10–18]. The molecular players that target ROPs to the RHID and initiate outgrowth, however, have not been identified. We dissected the timing of the growth machinery assembly in polarizing hair cells and found that positioning of molecular players and outgrowth are temporally separate processes that are each controlled by specific ROP guanine nucleotide exchange factor (GEFs). A functional analysis of trichoblast-specific GEFs revealed GEF3 to be required for normal ROP polarization and thus efficient root hair emergence, while GEF4 predominantly regulates subsequent tip growth. Ectopic expression of GEF3 induced the formation of spatially confined, ROP-recruiting domains in other cell types, demonstrating the role of GEF3 to serve as a membrane landmark during cell polarization. Our findings suggest that morphogenetic programs in plants employ distinct regulatory modules for the alignment and activation of the cellular growth machinery.
PAN: Personalized Annotation-based Networks for the Prediction of Breast Cancer Relapse
Authors: Nguyen Thin , Lee Samuel C. , Quinn Thomas P. , Truong Buu , Li Xiaomei , Tran Truyen , Venkatesh Svetha , Le Thuc Duy
Published: January 2019

The classification of clinical samples based on gene expression data is an important part of precision medicine. However, it has proved difficult to accurately predict survival outcomes and treatment responses for cancer patients. In this manuscript, we show how transforming gene expression data into a set of personalized (sample-specific) networks can allow us to harness existing graph-based methods to improve classifier performance. Existing approaches to personalized gene networks all have the limitation that they depend on other samples in the data and must get re-computed whenever a new sample is introduced. Here, we propose a novel method, called Personalized Annotation-based Networks (PAN), that avoids this limitation by using curated annotation databases to transform gene expression data into a graph. These databases organize genes into overlapping gene sets, called annotations, that we use to build a network where nodes represent functional terms and edges represent the similarity between them. Unlike competing methods, PANs are calculated for each sample independent of the population, making it a more efficient way to obtain single-sample networks. Using three breast cancer datasets as a case study (METABRIC and a super-set of GEO studies), we show that PAN classifiers not only predict cancer relapse better than gene features alone, but also outperform PPI and population-level graph-based classifiers. This work demonstrates the practical advantages of graph-based classification for high-dimensional genomic data, while offering a new approach to making sample-specific networks.

Supplementary information

The codes and data are available at https://github.com/thinng/PAN.

Contact

Thuc.Le@unisa.edu.au
Multi-Neuromodulator Measurements across Fronto-Striatal Network Areas of the Behaving Macaque using Solid-Phase Microextraction
Authors: Hassani Seyed-Alireza , Lendor Sofia , Boyaci Ezel , Pawliszyn Janusz , Womelsdorf Thilo
Published: January 2019

Different neuromodulators rarely act independent from each other to modify neural processes but are instead co-released, gated, or modulated. To understand this interdependence of neuromodulators and their collective influence on local circuits during different brain states, it is necessary to reliably extract local concentrations of multiple neuromodulators in vivo. Here we describe results using solid phase microextraction (SPME), a method providing sensitive, multi-neuromodulator measurements. SPME is a sampling method that is coupled with mass spectrometry to quantify collected analytes. Reliable measurements of glutamate, dopamine, acetylcholine and choline were made simultaneously within frontal cortex and striatum of two macaque monkeys (Macaca mulatta) during goal-directed behavior. We find glutamate concentrations several orders of magnitude higher than acetylcholine and dopamine in all brain regions. Dopamine was reliably detected in the striatum at tenfold higher concentrations than acetylcholine. Acetylcholine and choline concentrations were detected with high consistency across brain areas, within monkeys and between monkeys. These findings illustrate that SPME microprobes provide a versatile novel tool to characterize multiple neuromodulators across different brain areas in vivo to understand the interdependence and co-variation of neuromodulators during goal directed behavior. Such data will be important to better distinguish between different behavioral states and characterize dysfunctional brain states that may be evident in psychiatric disorders.
Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data
Authors: Kim Hyeon-Jin , Gürkan Yardımcı Galip , Bonora Giancarlo , Ramani Vijay , Liu Jie , Qiu Ruolan , Lee Choli , Hesson Jennifer , Ware Carol B. , Shendure Jay , Duan Zhijun , Stafford Noble William
Published: January 2019

Single-cell Hi-C (scHi-C) interrogates genome-wide chromatin interaction in individual cells, allowing us to gain insights into 3D genome organization. However, the extremely sparse nature of scHi-C data poses a significant barrier to analysis, limiting our ability to tease out hidden biological information. In this work, we approach this problem by applying topic modeling to scHi-C data. Topic modeling is well-suited for discovering latent topics in a collection of discrete data. For our analysis, we generate twelve different single-cell combinatorial indexed Hi-C (sciHi-C) libraries from five human cell lines (GM12878, H1Esc, HFF, IMR90, and HAP1), consisting over 25,000 cells. We demonstrate that topic modeling is able to successfully capture cell type differences from sciHi-C data in the form of “chromatin topics.” We further show enrichment of particular compartment structures associated with locus pairs in these topics.
TRPV4 inhibition prevents increased water diffusion and blood-retina barrier breakdown in the retina of streptozotocin-induced diabetic mice
Authors: Ríos Maricruz Orduña , Imm Ramsés Noguez , Godínez Nicole Marilú Hernández , Cortes Ana María Bautista , Liedtke Wolfgang , Torres Ataúlfo Martínez , Concha Luis , Thébault Stéphanie
Published: January 2019

A better understanding of the molecular and cellular mechanisms involved in retinal hydro-ionic homeostasis imbalance during diabetic macular edema (DME) is needed to gain insights into retinal physio(patho)logy that will help elaborating innovative therapies with lower health care costs. Transient receptor potential cation channel subfamily vanilloid member 4 (TRPV4) plays an intricate role in homeostatic processes that needs to be deciphered in normal and diabetic retina. Based on previous findings showing that TRPV4 antagonists resolve blood-retina barrier (BRB) breakdown in diabetic rats, we evaluated whether TRPV4 channel inhibition prevents and reverts retinal edema in streptozotocin(STZ)-induced diabetic mice. We assessed retinal edema using common metrics, including retinal morphology/thickness (histology) and BRB integrity (albumin-associated tracer), and also by quantifying water mobility through apparent diffusion coefficient (ADC) measures. ADC was measured by diffusion-weighted magnetic resonance imaging (DW-MRI), acquiredex vivoat 4 weeks after STZ injection in diabetes and control groups. DWI images were also used to assess retinal thickness. TRPV4 was genetically ablated or pharmacologically inhibited as follows: left eyes were used as vehicle control and right eyes were intravitreally injected with TRPV4-selective antagonist GSK2193874, 24 h before the end of the 4 weeks of diabetes. Histological data show that retinal thickness was similar in nondiabetic and diabetic wt groups but increased in diabeticTrpv4−/−mice. In contrast, DWI shows retinal thinning in diabetic wt mice that was absent in diabeticTrpv4−/−mice. Disorganized outer nuclear layer was observed in diabetic wt but not in diabeticTrpv4−/−retinas. We further demonstrate increased water diffusion and BRB hyperpermeability in diabetic wt mice, effects that were absent in diabeticTrpv4−/−mice. Retinas of diabetic mice treated with PBS showed increased water diffusion that was not inhibited by GSK2193874. ADC maps in nondiabeticTrpv4−/−mouse retinas showed restricted diffusion. Our data provide evidence that water diffusion is increased in diabetic mouse retinas and that TRPV4 function contributes to retinal hydro-ionic homeostasis and structure under control conditions, and to the development of BRB breakdown and increased water diffusion in the retina under diabetes conditions. A single intravitreous injection of TRPV4 antagonist is however not sufficient to revert these alterations in diabetic mouse retinas.
Engineering-out hazards: digitising the management working safety in confined spaces
Authors: Parn Erika A. , Edwards David , Riaz Zainab , Mehmood Fahad , Lai Joseph
Published: January 2019

Purpose

This paper aims to report upon the further development of a hybrid application programming interface (API) plug-in to building information modelling (BIM) entitled confined spaces safety monitoring system “CoSMoS”. Originally designed to engineer-out environmental hazards associated with working in a building’s confined spaces (during the construction phase of a building’s life-cycle), this second generation version is expanded upon to use archival records to proactively learn from data generated within a sensor network during the building’s operations and maintenance (O&M) phase of asset management (AM).

Design/methodology/approach

An applied research methodological approach adopted used a two-phase process. In phase one, a conceptual model was created to provide a “blueprint map” to integrate BIM, sensor-based networks and data analytics (DA) into one integral system. A literature review provided the basis for the conceptual model’s further development. In phase two, the conceptual model was transposed into the prototype’s development environment as a proof of concept using primary data accrued from a large educational building.

Findings

An amalgamation of BIM, historical sensor data accrued and the application of DA demonstrate that CoSMoS provides an opportunity for the facilities management (FM) team to monitor pertinent environmental conditions and human behaviour within buildings that may impact upon occupant/worker safety. Although working in confined spaces is used to demonstrate the inherent potential of CoSMoS, the system could readily be expanded to analyse sensor-based network’s historical data of other areas of building performance, maintenance and safety.

Originality/value

This novel prototype has automated safety applications for FM during the asset lifecycle and maintenance phase of a building’s O&M phase of AM. Future work is proposed in several key areas, namely, develop instantaneous indicators of current safety performance within a building; and develop lead indicators of future safety performance of buildings.
Psychological contract fulfilment, engagement and nurse professional turnover intention
Authors: Sheehan Cathy , Tham Tse Leng , Holland Peter , Cooper Brian
Published: January 2019

Purpose

The purpose of this paper is to analyse the effect of nurses’ experience of the fulfilment of their psychological contract on their intention to leave the nursing profession and to consider employee engagement as a mediator between the fulfilment of the psychological contract of nurses and their intention to leave their profession.

Design/methodology/approach

The authors used a quantitative, cross-sectional research design. In total, 1,039 Australian nurses completed an anonymous online survey conducted via the Australian Nursing and Midwifery Federation website. Structural equation modelling was used to test the hypotheses.

Findings

The fulfilment of promises related to interesting job content and social atmosphere were negatively associated with intentions to leave the nursing profession, and these relationships were mediated by engagement. The fulfilment of promises related to career development, financial rewards and work–life balance were not associated with intentions to leave the nursing profession.

Research limitations/implications

To ensure professional nurse retention, it is necessary to not just promise nurses interesting jobs and a supportive social atmosphere, but to manage nurse perceptions regarding the fulfilment of these promises.

Originality/value

Although there has been extensive research on nurse intention to leave their current job, the important area of nurse professional turnover has received less attention. The research highlights the importance of fulfilling expectations and promises related to interesting nurse job content that encourages nurse responsibility and autonomy as well as promises of a social atmosphere that includes co-operative relationships and good communication with colleagues.
Peer coaching in a school in Cairo, Egypt
Authors: Sider Steve
Published: January 2019

Purpose

The purpose of this paper is to examine how peer coaching was introduced in one school in Egypt and to identify barriers and opportunities for successful implementation.

Design/methodology/approach

The methodology included semi-structured interviews with eight teachers, participant observation of their classes and meetings, and three focus group meetings with teachers and school administrators.

Findings

Ladyshewsky’s (2017) five key aspects of peer coaching are considered in the findings: establishing peer partners, building trust between the partners, identifying specific areas to target for learning, training on non-evaluative questions and feedback, and supporting each other as new ideas are attempted. Each aspect of these is reviewed in light of the implementation process in the school.

Practical implications

The study provides practical suggestions for teachers and school administrators that include considerations for implementation. Numerous connections are made to research on peer coaching that is relevant to the implementation of peer coaching in schools in Egypt and other countries in the Global South.

Originality/value

The study provides an examination of the implementation of peer coaching in a school in Egypt. Thus, it contributes to the limited literature on peer coaching in the Global South. The discussion and conclusion sections consider further questions and research opportunities for effective practices in peer coaching in international contexts.
Temperature analysis of CFG pile composite foundation in high latitudes and low altitude island permafrost
Authors: Liu Jinliang , Jia Yanmin
Published: January 2019

Purpose

Cement fly ash gravel (CFG) pile composite foundation is an effective and economic foundation treatment approach, which is significant to build foundation, subgrade construction, and so forth. The purpose of this paper is to present a research on the temperature behaviours of high-latitude and low-altitude island permafrost under CFG pile composite foundation treatment.

Design/methodology/approach

In the process of CFG pile construction, the temperature of permafrost and pile body was monitored using the temperature sensors. The influence of subgrade height and atmospheric temperature cycle on permafrost temperature was analysed by finite element simulation.

Findings

In the process of CFG pile construction, the change curve of pile temperature and the temperature of permafrost beside pile following time can be divided into six stages, and the duration of these stages is at least one month. The temperature variation of permafrost while constructing subgrade in FEM has a good agreement with the results of field temperature monitoring. The height of subgrade not only affects the maximum temperature increase of permafrost and the re-frozen time of permafrost after the construction of CFG pile composite foundation, but also affects the temperature variation amplitude of permafrost during atmospheric temperature cycle.

Originality/value

The research will provide a reference for the design on the CFG pile composite foundation used for island permafrost and guarantee the stability of the structure; thus, it has an important significance.
Diversity management at the tertiary level: an attempt to extend existing paradigms
Authors: Gaisch Martina , Preymann Silke , Aichinger Regina
Published: January 2019

Purpose

The purpose of this paper is to adopt a holistic diversity lens with the aim to enhance the understanding of the multifaceted paradigms for diversity management at the tertiary level.

Design/methodology/approach

This contribution takes the inspiration of existing diversity paradigms used in business settings and relates them to higher education. It then articulates them in greater depths in line with the diversity segments of the so-called higher education awareness for diversity wheel and seeks a common denominator that may be shared across disciplines by adding an eclectic and context-specific approach.

Findings

It was identified that the underlying assumptions which constitute the commonly known diversity paradigms are only partially applicable for the tertiary level. It is further suggested that in view of the highly dynamic kaleidoscope of higher education institutions, multiple, at times conflicting rationales for diversity management need to be addressed.

Originality/value

This paper seeks to address the paucity of studies with regard to diversity management at the tertiary level. By drawing on relevant paradigms and relating them to specific diversity segments, this study intends to make a meaningful scholarly contribution to the existing body of knowledge.
Determinants of housing prices from an urban economic point of view: evidence from Hungary
Authors: Czinkan Norbert , Horváth Áron
Published: January 2019

Purpose

The purpose of the paper is to investigate a cross section of Hungarian settlement-level unit housing prices with a special emphasis on measuring the effect of population and its growth, along with accessibility to the centre of an aggregated spatial unit such as a micro-region, county or region, for the period of 2001-2011.

Design/methodology/approach

The analysis uses cross-sectional ordinary least squares techniques with Moulton-corrected standard errors. The estimation is guided by the implications of a simplified monocentric urbanized area framework following the model of DiPasquale and Wheaton (1996), and the econometric model is augmented with population growth rate at the settlement level to bridge the theory explaining rents and data base containing prices instead.

Findings

The location is a key factor in determining housing prices: living 10 min further from the centre results in 11 per cent cheaper housing. When estimating bid-rent curves, results show that it is crucial to control for city size and the income effect. The elasticity of housing price with respect to city size is 0.09 according to our preferred model. Population growth has an asymmetric impact on housing prices: municipalities with positive expected population growth have higher prices today.

Practical implications

Estimating the quantitative relationship between commuting time and housing price is crucial for a cautious infrastructure development. The benefits of improved roads and faster access could be capitalized in appreciating the housing stock. Estimating the slope of the bid-rent curve is one possible ex ante quantification of the benefits of a public development.

Originality/value

One contribution of this research is providing empirical evidence to surprisingly limited applied work in the field of (monocentric) urban models using data from the CEE region. Second, to the best of the authors’ knowledge, this is the first study to investigate Hungarian settlement-level unit prices from an urban economic point of view.
Religiosity scale development
Authors: Mohd Dali Nuradli Ridzwan Shah , Yousafzai Shumaila , Abdul Hamid Hanifah
Published: January 2019

Purpose

The purpose of this paper is to develop an Islamic religiosity measurement which can be applied in many various sectors and fields.

Design/methodology/approach

The religiosity measurement developed by the authors had undergone systematic qualitative and quantitative approaches taking into consideration the expert opinion survey in ensuring the measurement content validity and reliability.

Findings

The study found that Islamic religiosity measurement is multi-dimensional. The dimensions found were beliefs and commitment or practice.

Research limitations/implications

The research limitation of the study is that the research is in its exploratory stages and needs to be replicated and to be tested in different contextual settings.

Originality/value

The instrument was developed through a rigorous systematic database search, qualitative and quantitative scale development stages which can be used as the basis in measuring Islamic religiosity.
Disturbance analysis and performance test of the polarization sensor based on polarizing beam splitter
Authors: Yang Jian , Niu Ben , Du Tao , Liu Xin , Wang Shanpeng , Guo Lei
Published: January 2019

Purpose

Multiple-source disturbances exist in the polarization sensor, which severely affect the sensor accuracy and stability. Hence, the disturbance analysis plays a vital role in improving the sensor orientation performance. This paper aims to present a novel sensor error model, a disturbances quantitative analysis, a calibration and performance test of polarization sensor based on a polarizing beam splitter.

Design/methodology/approach

By combining with the sensor coefficient errors, the Azimuth of Polarization (AoP) error model and the Degree of Polarization (DoP) error model are established, respectively. In addition, the multiple-source disturbances are classified, while the influence on the orientation accuracy is quantitative analyzed. Moreover, the least square optimization algorithm is employed to calibrate the sensor coefficients. Finally, an outdoor test is carried out to test the sensor long-term accuracy.

Findings

The theoretical analysis and numerical simulations illustrate that the sensor accuracy is closely related to the disturbances. To eliminate the influence of the disturbances, the least square optimization algorithm, which can minimize the sum of squares of the residual difference of AoP and DoP, is used to calibrate the sensor coefficients. The outdoor test indicates that the sensor can maintain long-term accuracy and stability.

Originality/value

The main contribution of this paper is to establish a novel sensor error model, where the sensor coefficient errors are introduced. In addition, the disturbances are classified and analyzed to evaluate the orientation accuracy of the sensor.
Assessing the effect of predator control on an endangered goose population subjected to predator‐mediated food web dynamics
Authors: Marolla Filippo , Aarvak Tomas , Øien Ingar J. , Mellard Jarad P. , Henden John‐André , Hamel Sandra , Stien Audun , Tveraa Torkild , Yoccoz Nigel G. , Ims Rolf A.
Published: January 2019

Assessing the effectiveness of conservation actions to halt population declines is challenging when confounded by other factors. We assessed whether culling of red fox, a predator currently increasing in number in the sub‐Arctic, contributed to recent recovery of the critically endangered Fennoscandian population of Lesser White‐fronted GooseAnser erythropus, while controlling for potentially confounding food web dynamics.

Using 19 years of data, 10 before and 9 after the implementation of annual red fox culling, we estimated the effect of this action on annual performance of the goose population. We corrected for the potentially confounding effects of cyclic rodent dynamics and semi‐domestic reindeer carrion abundance, both of which are expected to trigger predator functional and numerical responses, as well as for annual variation in spring phenology.

Goose reproductive success fluctuated in synchrony with the rodent cycle and was negatively related to abundant carrion. When accounting for these aspects of food web dynamics, there was no evidence for an effect of red fox culling on reproductive success. There was, however, a tendency for fox culling to increase adult survival.

Our analysis suggests that goose performance in their breeding area is influenced by fluctuating offspring predation, mediated by mainly natural (rodents) and partly anthropogenic (semi‐domestic reindeer) dynamic components of the food web.

Synthesis and applications. The effect of a decade‐long red fox culling on goose reproductive success and survival is currently uncertain, despite predation driving reproductive success through changes in rodent and reindeer carrion abundance. New management actions may consist of regulation of reindeer herd sizes and/or removal of carcasses to reduce the subsidizing effect of reindeer carrion on mesopredators. Getting robust evidence regarding the impact of red fox culling on population recovery depends on continuing research to disentangle food web dynamics and efficiency of management actions.
Novice occupational therapists: Navigating complex practice contexts in South Africa
Authors: van Stormbroek Kirsty , Buchanan Helen
Published: January 2019

Background/aim

The transition from student to occupational therapy practitioner is challenging. In South Africa, this transition is undertaken in rural and underserved areas, as graduate health professionals are deployed by the government for a year of compulsory Community Service. This study set out to establish the characteristics of these practice settings, the resources available for occupational therapy services, the availability and quality of supervision, and participants’ perceived ability to communicate with their patients and negotiate cultural differences.

Methods

A cross‐sectional survey design was utilised and a questionnaire was sent to all occupational therapists completing Community Service in 2013 (N = 240). Data were analysed using Stata 12 and IBM SPSS Statistics 21.0. Frequencies and percentages were calculated for categorical variables and associations tested with Odds Ratios and the Pearson's Chi square test. Responses to open‐ended questions were post‐coded.

Results

A 44.3% (n = 103) response rate was achieved. Practice settings often provided few resources. Although most participants had supervisors (89.6%), many did not find supervision satisfactory (65.9%). Communication difficulties featured strongly (73.9%), but the majority of participants felt they possessed basic cultural competence.

Conclusion

Participants worked within complex practice settings that were frequently resource‐restricted with less than satisfactory supervision. Practice required cultural competence and an ability to work across language barriers. Undergraduate curricula need to be tailored to equip new graduates to navigate these contextual realities. Furthermore, human resourcing strategies need to be evaluated and effective supervision and support structures need to be developed.
Dormancy and germination strategies of a desert winter annual Echinops gmelini Turcz. in a temperate desert of China
Authors: Wang YanLi , Li XinRong , Liu LiChao , Zhao JieCai , Song Guang , Zhou YuanYuan
Published: January 2019

Echinops gmelini Turcz. is an annual Asteraceae species widely distributed in the desert habitats of northern China. However, little is known about how this species adapts to harsh desert habitats. In this study, E. gmelini germination behaviors were observed in a natural population at the southeastern edge of the Tengger Desert. In addition, the effects of temperature, light, hydration–dehydration (H–D) cycles and different storage conditions on seed germination were tested in the laboratory. E. gmelini behaves as a winter annual, and its seeds germinate during the summer and early autumn in the field. Fresh seeds have non‐deep physiological dormancy (PD). A 15‐day dry storage treatment under laboratory conditions was required to break PD. Non‐dormant seeds can germinate rapidly and at a high rate in light at 30/20°C. Dry storage with seasonal temperature changes had little effect on seed germination and dormancy. However, under natural field conditions, greater and faster germination at a wide range of temperatures was observed after seeds were stored for 1–2 months, which allows seeds to germinate during short periods of moisture availability; seeds were induced into secondary dormancy after storage for 3 months which may prevent germination in autumn. Furthermore, seed germination was reduced and became faster after exposure to four or more H–D cycles. Our results suggest that precipitation is the key factor in determining E. gmelini seed germination time in natural habitats, and they provide information about the strategies that annual plants need to adapt to climatically unpredictable environments in temperate deserts.
On the use of r and r squared in correlation and regression
Authors: Kasuya Eiiti
Published: January 2019

Notations for coefficients in correlation and regression are discussed. r or R, not r squared or R squared, is inappropriate to denote the coefficient of determination because of the risk of the confusion with other coefficients with different meanings.
Real‐time polymerase chain reaction assays for environmental DNA detection of three salmonid fish in Hokkaido, Japan: Application to winter surveys
Authors: Minamoto Toshifumi , Hayami Kana , Sakata Masayuki K. , Imamura Akio
Published: January 2019

Dolly Varden (Salvelinus malma) and Whitespotted Char (Salvelinus leucomaenis) are representative native fish of the family Salmonidae that inhabit the upper reaches of rivers on Hokkaido Island, Japan. They are threatened by the invasive Rainbow Trout (Oncorhynchus mykiss). In this study, environmental DNA (eDNA) real‐time polymerase chain reaction (PCR) assays to detect these three salmonids were developed and used to clarify the distribution pattern of these fish. A specificity test for each assay was conducted using DNA extracted from both target and closely related fish, and the specificity of each assay was confirmed. Then, we carried out eDNA surveys in two mountainous rivers around Mt. Daisetsu in winter, when snow depth was maximized. In the winter surveys, eDNA of all three species were successfully detected from river water samples, including under‐ice water samples. The results of eDNA detection corresponded with the results of an earlier distribution survey performed with Japanese‐style fly‐fishing and lure‐fishing. These results suggested that the eDNA assays developed in this study are applicable for inter‐seasonal surveys for these species.
Acid rain decelerates the decomposition of Cunninghamia lanceolata needle and Cinnamomum camphora leaf litters in a karst region in China
Authors: Tang Li , Lin Yonghui , He Xingbing , Han Guomin
Published: January 2019

Acid rain is generally believed to inhibit litter decomposition, but this inhibition effect often depends on local soil environmental factors such as nutrient and physicochemical property. Karst ecosystem is typically characterized by rich CaCO3, which can potentially react with H+ from acid rain. However, it is unknown whether the effect of acid rain on litter decomposition will be mitigated by this potential reaction. To investigate the effect of acid rain on decomposition, we undertook a field experiment on the decomposition of litters of Cunninghamia lanceolata needle and Cinnamomum camphora leaf during 1 year in a karst region in subtropical China. Contrary to hypothesis, litter decomposition was significantly decelerated by acid rain for the two litter types. For C. lanceolata litter, at the end of incubation, we noted that moderate acid rain resulted in the highest loss in mass (43%), while severe one showed the lowest loss (39%); for C. camphora litter, the mass loss was as follows: ambient treatment (66%) > moderate treatment (56%) > severe treatment (42%). Also microbial activities (including CO2 flux, fungal biomass and microbial degrading enzymes) showed similar variation patterns among acid rain treatments to mass loss. These responses indicated that the deceleration effect of acid rain on litter decomposition did not depend on calcareous soil as well as litter quality. Together, these results suggest that acid rain had a predominant controlling of litter decomposition over soil and litter qualities, and this information may be useful for predicting functional responses of karst ecosystem to environmental factors.
Relationship between soil properties and leaf functional traits in early secondary succession of tropical montane cloud forest
Authors: Hernández‐Vargas Guadalupe , Sánchez‐Velásquez Lázaro R. , López‐Acosta Juan C. , Noa‐Carrazana Juan C. , Perroni Yareni
Published: January 2019

Recognizing soil properties associated with the plant strategy in relation to use and acquisition of resources during early secondary succession (ESS) is an important issue in plant ecology. We analyzed the relationship between 10 leaf functional traits (LFTs) and 17 soil properties including soil nutrients, transformation flows and pH along a plant chronosequence spanning first 40 years of ESS in a tropical mountain cloud forest. To recognize the multivariate variation of soil properties, a principal component analysis (PCA) was performed. The first axis of PCA was mainly associated with soil pH, P, Ca, Mg, K, C:N and N transformation flow, and this first axis was tightly associated with vegetation ages. The community weighted mean of the LFTs was also associated with vegetation ages. In particular, leaf P declined while leaf density, C, C:P and N:P increased with vegetation ages. Our analyses suggest associations between soil properties (the first axis of the PCA) and the LFTs (leaf area, leaf thickness, leaf density, leaf C, leaf C:P and leaf N:P) over the plant chronosequence. A fast acquisition strategy was observed in the younger sites and a resource conservation strategy in the older sites. Our results highlight the possible importance of changes in soil properties along secondary succession on plant functional traits in tropical cloud forest.
Either or? Reconciling Findings on Mental Health and Extremism using a Dimensional Rather than Categorical Paradigm
Authors: Gøtzsche‐Astrup Oluf , Lindekilde Lasse
Published: January 2019

The background for this paper is the debate over what role mental illness plays in radicalization to violent extremism. While one camp points to cases of abnormal functioning of perpetrators, another argues that normal psychological mechanisms are central. Through a review of these perspectives, it becomes clear that mental illness cannot be ruled out as an epi‐phenomenon, but is not a necessary condition either. The paper draws on work in psychiatric nosology on dimensional and categorical conceptions of illness and argues that the perspectives in this literature reflect a categorical approach to normal and abnormal functioning. Under a dimensional perspective, findings converge. The paper concludes by showing how this new dimensional approach to the role of mental illness in radicalization has implications for the design of risk assessment tools and leads to the recommendation for stronger inter‐agency cooperation between mental health professionals, social services, and police and intelligence services.
How Quickly Do Firms Adjust to Optimal Levels of Tax Avoidance?
Authors: Kim Jaewoo , McGuire Sean T. , Savoy Steven , Wilson Ryan , Caskey Judson
Published: January 2019

The trade‐off literature asserts that managers weigh the direct benefits of tax avoidance against the associated nontax costs. This literature implies each firm has a unique optimal level of tax avoidance that balances these costs and benefits. Our study is the first to document how quickly the average firm moves toward its optimal level of tax avoidance. We find that the typical firm converges toward its optimum at a rate that ranges from approximately 69 to 84 percent over a three‐year period, depending upon model specifications. Consistent with asymmetric levels of frictions across the tax avoidance distribution, we find the speed of adjustment is greater for firms below their optimal level of tax avoidance than for firms above. We perform additional cross‐sectional analyses to provide insight into some of the frictions that prevent firms from adjusting completely to their optimal level of tax avoidance. We generally find growth firms exhibit slower adjustment speeds and provide limited evidence that both multinational firms and income‐mobile firms exhibit faster adjustment speeds.
Population closure and the bias‐precision trade‐off in spatial capture–recapture
Authors: Dupont Pierre , Milleret Cyril , Gimenez Olivier , Bischof Richard
Published: January 2019

Spatial capture–recapture (SCR) is an increasingly popular method for estimating ecological parameters. SCR often relies on data collected over relatively long sampling periods. While longer sampling periods can yield larger sample sizes and thus increase the precision of estimates, they also increase the risk of violating the closure assumption, thereby potentially introducing bias. The sampling period characteristics are therefore likely to play an important role in this bias‐precision trade‐off. Yet few studies have studied this trade‐off and none has done so for SCR models.

In this study, we explored the influence of the length and timing of the sampling period on the bias‐precision trade‐off of SCR population size estimators. Using a continuous time‐to‐event approach, we simulated populations with a wide range of life histories and sampling periods before quantifying the bias and precision of population size estimates returned by SCR models.

While longer sampling periods benefit the study of slow‐living species (increased precision and lower bias), they lead to pronounced overestimation of population size for fast‐living species. In addition, we show that both bias and uncertainty increase when the sampling period overlaps the reproductive season of the study species.

Based on our findings, we encourage investigators to carefully consider the life history of their study species when contemplating the length and the timing of the sampling period. We argue that both spatial and non‐spatial capture–recapture studies can safely extend the sampling period to increase precision, as long as it is timed to avoid peak recruitment periods. The simulation framework we propose here can be used to guide decisions regarding the sampling period for a specific situation.
A Nabataean and Roman shrine with civic and military gods at Humayma, Jordan
Authors: Reeves M. Barbara
Published: January 2019

The lifecycle of a Nabataean and Roman community shrine at Humayma, Jordan reflects the evolving values of the town's inhabitants from the first to the third centuryCE. This paper reviews the evidence for the shrine's appearance and significance over this period, as well as the nature of the cult practised there. Beginning its existence as a Nabataean shrine, whose design incorporated the rising sun and the town's primary peak, the building was damaged when the Romans converted Nabataea intoProvincia Arabia. The Roman garrison initially dismantled the shrine to build their fort, but a few decades later the shrine was restored with a centrally placed Nabataean betyl and legionary altar symbolising harmony between the garrison and the town. The garrison's god, Jupiter‐Ammon‐Serapis, and possibly Isis, were now worshipped alongside the town's Nabataean deity. This shrine stressing military‐civilian harmony was later deliberately damaged, most likely during Zenobia's revolt.
Alcohol Abstainer Status and Prazosin Treatment in Association with Changes in Posttraumatic Stress Disorder Symptoms in Veterans with Comorbid Alcohol Use Disorder and Posttraumatic Stress Disorder
Authors: Verplaetse Terril L. , Ralevski Elizabeth , Roberts Walter , Gueorguieva Ralitza , McKee Sherry A. , Petrakis Ismene L.
Published: January 2019

Background

The noradrenergic system has been implicated in alcohol use disorder (AUD) and posttraumatic stress disorder (PTSD), with adrenergic agents reducing drinking in individuals with AUD and improving sleep disturbances in individuals with PTSD. In a recent clinical trial, prazosin, an α1‐adrenergic antagonist, was not superior to placebo in reducing PTSD symptoms, sleep problems, or alcohol consumption in a comorbid population; however, patients in both treatment conditions improved in all symptom domains over the course of treatment. It remains unknown whether alcohol abstinence is related to changes in PTSD symptoms and medication effects in individuals with this comorbidity.

Methods

Veterans with comorbid alcohol dependence and PTSD (n = 96) were randomized to prazosin (16 mg) or placebo in a 12‐week outpatient, double‐blind clinical trial. In this secondary data analysis, we examined main effects of alcohol abstainer status (abstainer vs. nonabstainer), treatment, and their interaction on changes in PTSD symptoms over time using linear mixed models.

Results

There was a main effect of alcohol abstainer status on symptoms of PTSD (p = 0.03), such that nonabstainers had lower total Clinician‐Administered PTSD Scale (CAPS) scores than abstainers. There was a significant treatment by alcohol abstainer status interaction (p = 0.01); specifically, among placebo‐treated individuals, those who did not abstain from alcohol had lower total CAPS scores compared to alcohol abstainers. Within the prazosin‐treated group, abstainers and nonabstainers did not differ on total CAPS scores. Results were similar for the avoidance (p = 0.02), reexperiencing (p = 0.01), and hyperarousal (p = 0.04) subscales, such that placebo‐treated nonabstainers had lower CAPS scores overall.

Conclusions

Overall, prazosin treatment was not significantly related to changes in PTSD symptoms over the course of the 12‐week clinical trial in a comorbid population. Interestingly, placebo‐treated alcohol nonabstainers had a significant reduction in PTSD symptoms. Whether placebo‐treated individuals continued to use alcohol because of ongoing symptoms of PTSD is not known.
Abnormality of Very Long‐Chain Fatty Acids of Erythrocyte Membrane in Alcoholic Patients
Authors: Adachi Junko , Miwa Atsuko , Ueno Yasuhiro , Asano Migiwa , Naito Takeaki , Imamichi Hiroyuki , Tatsuno Yoshitsugu
Published: January 2019

Profiles of very long‐chain fatty acids were studied in the erythrocyte membrane of five alcoholic patients. We identified three fatty acids as cis‐16‐pentacosenoic acid (C25:1), cis‐17‐hexacosenoic acid (C26:1), and hexacosenoic acid (C26:1), and hexacosanoic acid (C26:0) by gas chromatography‐mass spectrometry. The ratios of C26:1/C22:0, C26:0/C22:0, C24:1/C22:0, and C24:0/C22:0 were increased. These findings suggest that active oxygen species or free radicals generated by chronic alcohol consumption in alcohol patients interupt the peroxisomal β‐oxidation of fatty acids, because very long‐chain fatty acids are mainly metabolized by the peroxisomal β‐oxidation system. This is the first study showing accumulation of very long‐chain fatty acids in the erythrocyte membrane of alcoholic patients.