bluuebunny/crossref_metadata_2025_split huggingface dataset:
Homoploid hybridization signals due to ancestral subdivision: a case study on the D lineage in wheat
Authors: Jiang Yunfeng , Yuan Zhongwei , Hu Haiyan , Ye Xueling , Zheng Zhi , Wei Yuming , Zheng You-Liang , Wang You-Gan , Liu Chunji 
Published: May 2019

AbstractHomoploid hybrid speciation has been reported in a wide range of species since the exploitation of genome sequences in evolutionary studies. However, the interference of ancestral subdivision has not been adequately considered in many such investigations. Using the D lineage in wheat as an example, we showed clearly that ancestral subdivision has led to false detection of homoploid hybridization signals. We develop a novel statistical framework by examining the changes in shared ancestral variations and infer on the likelihood of speciation due to genuine homoploid hybridization or ancestral subdivisions. Applying this to wheat data, we found that homoploid hybridization was not involved in the origin of the D lineage contrary to the now widely held belief. This example indicates that the significance of homoploid hybrid speciation is likely exaggerated. The underlying methodology developed in this study should be valuable for clarifying whether homoploid hybridization has contributed to the speciation of many other species.
Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains
Authors: Ueda Mahoko Takahashi , Kryukov Kirill , Mitsuhashi Satomi , Mitsuhashi Hiroaki , Imanishi Tadashi , Nakagawa So 
Published: May 2019

AbstractEndogenous retroviruses (ERVs) are remnants of ancient retroviral infections of mammalian germline cells. A large proportion of ERVs lose their open reading frames (ORFs), while others retain them and become exapted by the host species. However, it remains unclear what proportion of ERVs possess ORFs (ERV-ORFs), become transcribed, and serve as candidates for co-opted genes. Hence, we investigated characteristics of 176,401 ERV-ORFs containing retroviral-like protein domains (gag, pro, pol, andenv) in 19 mammalian genomes. The fractions of ERVs possessing ORFs were overall small (∼0.15%) although they varied depending on domain types as well as species. The observed divergence of ERV-ORF from their consensus sequences suggested that a large proportion of ERV-ORFs either recently or anciently inserted themselves into mammalian genomes. Alternatively, very few ERVs lacking ORFs were found to exhibit similar divergence patterns. To identify ERV-ORFs transcribed as proteins, we compared ERV-ORFs with various multi-omics data including transcriptome data, trimethylation at histone H3 lysine 36, and transcription initiation sites from 2,834 cell types, and found 408 and 752 ERV-ORFs, accounting for 2-3% of all ERV-ORFs, with high transcriptional potential in humans and mice, respectively. Moreover, many of these ERV-ORFs with transcriptional potential were lineage-specific sequences exhibiting tissue-specific expression. These results suggest a possibility for the expression of uncharacterized functional genes containing ERV-ORFs hidden within mammalian genomes. Together, our analyses suggest that more ERV-ORFs may be co-opted in a host-species specific manner than we currently know, which are likely to have contributed to mammalian evolution and diversification.
Heme minimizes Parkinson’s disease-associated toxicity by inducing a conformational distortion in the oligomers of alpha-Synuclein
Authors: Chakraborty Ritobrita , Dey Sandip , Paul Simanta Sarani , Sil Pallabi , Sengupta Jayati , Chattopadhyay Krishnananda 
Published: May 2019

AbstractAggregation of the intrinsically disordered protein alpha-Synuclein (α-Syn) into insoluble fibrils with a cross-β sheet amyloid structure plays a key role in the neuronal pathology of Parkinson’s disease (PD). The fibrillation pathway of α-Syn encompasses a multitude of transient oligomeric forms differing in size, secondary structure, hydrophobic exposure and toxicity. According to a recent solid state NMR study, the fibrillating unit of α-Syn contains the core residues of the protein arranged into in-register parallel β sheets with a unique Greek key topology. Here, we have shown that the physiologically available small molecule heme (hemin chloride) when added at sub-stoichiometric ratios to either monomeric or aggregated α-Syn, arrests its aggregation in an oligomeric state, which is minimally toxic. Using cryo-EM, we observed that these heme-induced oligomers are ‘mace’-shaped and consist of approximately four monomers. However, the presence of a crucial twist or contortion in their Greek key structural architecture prevents further hierarchical appending into annular oligomers and protofilament formation. We confirm using a His50Gln mutant that the binding of heme onto His50 is crucial in inflicting the structural distortion and is responsible for the stabilization of the non-toxic and off-pathway α-Syn oligomers. We believe that this study provides a novel strategy of developing a therapeutic solution of PD, which has been elusive so far.
Thresholds for post-rebound SHIV control after CCR5 gene-edited autologous hematopoietic cell transplantation
Authors: Cardozo-Ojeda E. Fabian , Duke Elizabeth R. , Peterson Christopher W. , Reeves Daniel B. , Mayer Bryan T. , Kiem Hans-Peter , Schiffer Joshua T. 
Published: May 2019

AbstractAutologous, CCR5 gene-edited hematopoietic stem and progenitor cell (HSPC) transplantation is a promising strategy for achieving HIV remission. However, only a fraction of HSPCs can be editedex vivoto provide protection against infection prior to autologous transplantation. The optimal transplantation conditions for achieving viral control in the absence of suppressive antiretroviral therapy (ART) are still unknown. We analyzed data from SHIV-1157ipd3N4-infected juvenile pig-tailed macaques that underwent autologous HSPC transplantation with and without CCR5 gene editing. We developed a mathematical model that recapitulates reconstitution of T cell subset counts and SHIV plasma viral loads in control and transplanted macaques. The model predicts that viral control can be obtained following ART treatment interruption (ATI) when: 1) levels of transplanted HSPCs are at least 10-fold higher than residual endogenous HSPCs after total body irradiation and 2) the fraction of protected HSPCs in the transplant achieves a threshold (73%-90%) sufficient to overcome transplantation-dependent loss of SHIV immunity. Under these conditions, if ATI is withheld until transplanted gene-modified cells engraft and reconstitute to a steady state, then spontaneous viral control is projected to occur immediately. Our results support strategies that 1) increase stem cell dose, 2) enhance potency of conditioning regimen, 3) elevate fraction of gene modified SHIV-resistant cells, 4) extend periods between HSPC transplantation and ATI with tracking of CD4+CCR5-cell recovery and / or 5) augment anti-SHIV immunity to achieve sustained SHIV remission.One Sentence SummaryAutologous transplantation of ΔCCR5 HSPCs may induce post-ATI SHIV control when the gene-edited cell dose is sufficient to overcome SHIV immunity loss.
Niche complementarity among pollinators increases community-level plant reproductive success
Authors: Magrach Ainhoa , Molina Francisco P. , Bartomeus Ignasi 
Published: May 2019

AbstractOur understanding of how the structure of species interactions shapes natural communities has increased, particularly regarding plant-pollinator interactions. However, research linking pollinator diversity to reproductive success has focused on pairwise plant-pollinator interactions, largely overlooking community-level dynamics. Here, we present one of the first empirical studies linking pollinator visitation to plant reproduction from a community-wide perspective. We use a well-replicated dataset encompassing 16 plant-pollinator networks and data on reproductive success for 19 plant species from Mediterranean shrub ecosystems. We find that statistical models including simple visitation metrics are sufficient to explain the variability observed. However, a mechanistic understanding of how pollinator diversity affects reproductive success requires additional information on network structure. Specifically, we find positive effects of increasing complementarity in the plant species visited by different pollinators on plant reproductive success. Hence, maintaining communities with a diversity of species but also of functions is paramount to preserving plant diversity.
Analysis on the steady state performance of a multi pad externally adjustable fluid film bearing
Authors: Hariharan Girish , Pai Raghuvir 
Published: May 2019

Purpose
This study aims to investigate the performance characteristics of an externally adjustable bearing with multiple pads in steady state conditions. The proposed adjustable bearing geometry can effectively control the hydrodynamic operation in bearing clearances by adjusting the pads in radial and tilt directions. These pad adjustments have a significant role in improving the bearing characteristics such as load capacity, attitude angle, side leakage, friction variable and Sommerfeld number, which will be analysed in this paper.

Design/methodology/approach
The adjustable bearing is designed with circumferentially spaced four bearing pads subjected to similar radial and tilt adjustments. Tilt angles are applied along the leading edges of bearing pads. A modified film thickness equation is used to incorporate the pad adjustments and accurately predict the variation in film profile. Finite difference approximation is adopted to solve the Reynolds equation and discretize the fluid film domain.

Findings
For negative radial and tilt adjustments, higher hydrodynamic pressures are generated in bearing clearances, which increases the bearing load capacity at different eccentricity ratios. From comparative analysis for different pad adjustments, superior bearing performance is observed for bearing pads under negative radial and negative tilt adjustments.

Originality/value
This research presents a detailed theoretical approach to analyse the performance capability of a four pad adjustable bearing geometry, which is not available in literatures. Improved bearing performances with negative pad adjustments can attract bearing designers to implement the proposed adjustability-bearing concept in rotating machineries.
Deformation modeling of remote handling EAMA robot by recurrent neural networks
Authors: Zhang Tao , Song Yuntao , Wu Huapeng , Handroos Heikki , Cheng Yong , Zhang Xuanchen 
Published: May 2019

Purpose
Remote handling (RH) manipulators have been widely studied for maintenance tasks in fusion reactors. Those tasks always require heavy load, high accuracy and large work space for manipulators. Traditionally, the maintenance of fusion devices always depends on manual RH. With the development of calculating ability, the intelligent automatic maintenance makes it possible for a fusion device instead of the previous manual operation. As the flexibility of arm and the deformation of manipulator will cause problems, which are mainly inaccuracy and lower efficiency. This paper aims to study an effective way to promote the arm behavior to solve these problems.

Design/methodology/approach
By making use of the experimental advanced superconducting tokamak articulated maintenance arm as a platform, a series of experiments is designed to measure errors of kinematics and to collect the database of the flexible arm. Through studying the data and the arm structure, recurrent neural network (RNN) method was adopted to estimate the deformation of flexible arm and eventually compensate deformation in robot control to achieve higher accuracy.

Findings
By means of delicate RNN modeling, errors of kinematics have been reduced to a smaller order than the RH mode. This intelligent maintenance method will also reduce complexity of operations in maintenance.

Originality/value
This paper presents the use of an artificial intelligent algorithm to solve a nonlinear deformation problem of the flexible arm. The results demonstrate that it is efficient in dealing with this problem in fusion application. The RNN’s successful application has also shown that intelligent algorithms can be widely applied in fusion maintenance.
Inspiring organizational commitment
Authors: Mousa Mohamed , Puhakka Vesa 
Published: May 2019

Purpose
The purpose of this paper is to focus on physicians in the four public hospitals located in the October province (Egypt) in an attempt to explore the effect of responsible leadership on physicians’ affective, continuance and normative commitment with and without mediating the role of organizational inclusion.

Design/methodology/approach
A total of 360 physicians were contacted and all of them received a set of questionnaires. After two follow-ups, a total of 240 responses were collected with a response rate of 66.67 percent. The authors used the χ2 test to determine the association between responsible leadership and organizational inclusion. Multiple regressions were employed to show how much variation in affective, continuance and normative commitment can be explained by responsible leadership and organizational inclusion.

Findings
The findings highlight a positive association between responsible leadership and organizational inclusion. Moreover, another positive association is also explored between organizational inclusion and affective, continuance and normative commitment. Furthermore, the statistical analysis proved that having an atmosphere of respect, equality and sameness in the workplace fosters the effect of responsible leaders on physicians’ affective, normative and continuance commitment.

Originality/value
This paper contributes by filling a gap in HR management, cultural diversity and organization literature, in which empirical studies on the relationship between responsible leadership, organizational inclusion and organizational commitment have been limited until now.
Rapid Determination of Complete Distribution of Pore and Throat in Tight Oil Sandstone of Triassic Yanchang Formation in Ordos Basin, China
Authors: DU Shuheng , SHI Yongmin 
Published: May 2019

AbstractThis study aimed to investigate the complete distribution of reservoir space in tight oil sandstone combining casting slices, field emission scanning electron microscopy (FE‐SEM), the pore‐throat theory model, high‐resolution image processing, mathematical statistics, and other technical means. Results of reservoir samples from the Xin'anbian area of Ordos Basin showed that the total pore radius curve of the tight oil sandstone reservoir exhibited a multi‐peak distribution, and the peaks appeared to be more focused on the ends of the range. This proved that pores with a radius of 1–50,000 nm provided the most significant storage space for tight oil, indicating that special attention should be paid to this range of the pore size distribution. Meanwhile, the complete throat radius curve of the tight oil sandstone reservoir exhibited a multi‐peak distribution. However, the peak values were distributed throughout the scales. This confirmed that the throat radius in the tight oil sandstone reservoir was not only in the range of hundreds of nanometers but was also widely distributed in the scale approximately equal to the pore size. The new rapid determination method could provide a precise theoretical basis for the comprehensive evaluation, exploration, and development of a tight oil sandstone reservoir.
Hearing loss in ankylosing spondylitis
Authors: Ajmani Sajal , Keshri Amit , Srivastava Rakesh , Aggarwal Amita , Lawrence Able 
Published: May 2019

AbstractAimSeveral studies have described sensorineural deafness in ankylosing spondylitis (AS) patients while conductive hearing loss has been reported to be rare. In our study we have studied the prevalence of hearing loss (HL) among AS patients and its association with non‐steroidal anti‐inflammatory drug (NSAID) intake.MethodsWe studied 100 AS patients and 40 controls. HL was defined as pure‐tone thresholds greater than 20 dB (decibel) in at least two frequencies of the audiogram. Severity of HL was defined as given by World Health Organization. Clinical details and cumulative NSAID doses were noted.ResultsNinety‐six of the 100 patients were male with mean age of 32 ± 12 years and mean duration of illness of 8.2 ± 6 years. Median Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), Bath Ankylosing Spondylitis Functional Index (BASFI), Bath Ankylosing Spondylitis Metrology Index (BASMI) and cumulative NSAID dose were 3.5 ± 2.2, 2.75 ± 2, 3.7 ± 2.6 and 1202 ± 1290, respectively. Of the 48 with HL, 28 patients had bilateral HL. Twenty‐nine patients had pure conductive HL while 16 had mixed HL (components of both sensory and conductive) and 3 had pure sensorineural HL. HL was mild in 38 patients, and moderate to severe in 10 patients. The presence of HL was associated with higher age (P ≤ 0.05). Conductive HL was at low frequency (0.25, 0.5, 1 kHz) in 70% of cases. Sensorineural HL was at high frequency (4, 8 kHz) in 75% of cases. There was no association of HL with disease parameters such as BASMI, BASDI, BASFI or cumulative NSAID dose.ConclusionHL is common in AS. Conductive HL is more common than sensorineural HL. It is usually mild and occurs at low frequencies.
Transient synaptic potentiation in nucleus accumbens shell during refraining from cocaine seeking
Authors: Roberts‐Wolfe Douglas J. , Heinsbroek Jasper A. , Spencer Sade M. , Bobadilla Ana Clara , Smith Alexander C.W. , Gipson Cassandra D. , Kalivas Peter W. 
Published: May 2019

AbstractRepeated exposure to drug‐associated cues without reward (extinction) leads to refraining from drug seeking in rodents. We determined if refraining is associated with transient synaptic plasticity (t‐SP) in nucleus accumbens shell (NAshell), akin to the t‐SP measured in the NAcore during cue‐induced reinstatement of drug seeking. Using whole cell patch electrophysiology, we found that medium spiny neurons (MSNs) in NAshell expressed increased ratio of AMPA to NMDA glutamate receptor currents during refraining, which normalized to baseline levels by the end of the 2‐hour extinction session. Unlike t‐SP observed in NAcore during reinstated drug seeking, neither dendrite spine head enlargement nor activation of matrix metalloproteases (MMP2/9) accompanied the increased AMPA:NMDA in NAshell during refraining. Refraining was also not associated with changes in paired pulse ratio, NMDA receptor current decay time, or AMPA receptor rectification index in NAshell MSNs. Our preliminary data in transgenic mice suggest that t‐SP may increase D2‐MSN inputs relative to D1‐MSN inputs.
The role of agricultural professionals in identifying, mitigating and supporting farming families during times of stress: Findings of a qualitative study
Authors: Stanley‐Clarke Nicky 
Published: May 2019

AbstractObjectiveThe prevalence of suicidality within the farming community, especially during time of stress, is well documented. During 2016, the global milk prices fell, impacting the New Zealand dairy farm profitability and viability, as well as taking a toll on farmer well‐being. This article discusses the role of agricultural professionals as a support mechanism for farming families during times of stress and their ongoing contribution in recognising and mitigating stress on farmers.DesignQualitative, using thematic analysis.SettingNorth Island, New Zealand.ParticipantsDairy farming women, large animal veterinarians, farm consultants and members of rural support organisations.ResultsThematic analysis demonstrated the following aspects: the value of the long‐term relationships between agricultural professionals and their clients; the duty of care agricultural professionals feel towards their clients; and the benefits of the planning and practical problem‐solving services offered by these professionals, especially in times of crisis.ConclusionFarmers prefer to use established relationships with agricultural professionals and focus on problem‐solving in times of stress. Agricultural professionals should therefore be included as part of any integrated approach to addressing farmer stress.
Assessing UNGC pharmaceutical signatories stakeholders using big data
Authors: Zilic Ivana , LaVan Helen , Cook Lori S. 
Published: May 2019

AbstractThis article aims to focus on how signatories versus nonsignatories in the U.S. pharmaceutical sector compare with respect to the internal and external stakeholders and principles of the United Nations Global Compact (UNGC). We seek to answer the question: Do signatories to the UNGC walk the talk better than nonsignatories as determined by a variety of published rankings and data? This research presents an innovative approach to the evaluation of UNGC signatories. It uses several objective and independent data sources to assess a matched group of signatories versus nonsignatories in the U.S. pharmaceutical sector. Signatory organizations in the same sector as determined by SIC codes were matched with nonsignatories on variables such as size and number of employees in U.S. pharmaceutical companies. Then both types of organizations were compared on the following data sources: Coalition for Environmentally Responsible Economies ratings, ratings by external stakeholders, ratings by employees, unionization data, financial measures, and annual reports to shareholders. Using nonparametric testing the research found there are differences between signatories and nonsignatories in the U.S. pharmaceutical sector for some of the external stakeholder measures and no differences were found for the internal stakeholder measures.
Inequality, Growth, Poverty and Lunar Eclipses: Policy and Arithmetic
Authors: Basu Kaushik , Subramanian S. 
Published: May 2019

ABSTRACTAlleviating poverty, mitigating inequality and achieving growth are all acknowledged goals of development, whatever the degree of success with which these goals might have been addressed in various economies of the world. Apart from questions of resolve and genuine commitment, what makes it hard to engage with these goals is that the pursuit of any one of them does not necessarily secure the ends of either or both of the other two. Such engagement requires a measure of conceptual clarity, an identification of normative priorities, and the deployment of carefully crafted policies that accommodate trade‐offs among competing goals. In particular, policies such as the single‐minded pursuit of growth as a panacea for all the difficulties of development appear to be misguided, and based on a faulty application of deductive reasoning to past experience. These issues are addressed here by attending to some elementary arithmetic revolving around the measurement of money‐metric poverty and inequality, and the decomposition of poverty changes into effects attributable to growth and distributional changes.