bluuebunny/crossref_metadata_2025_split huggingface dataset:
Helicobacter pylori‐downregulated tumor necrosis factor receptor‐associated protein 1 mediates apoptosis of human gastric epithelial cells
Authors: Teng Yongsheng , Liu Xin , Han Bin , Ma Qiang , Liu Yugang , Kong Hui , Lv Yipin , Mao Fangyuan , Cheng Ping , Hao Chuanjie , Yang Shiming , Zhang Jinyu , Peng Liusheng , Zou Quanming , Zhuang Yuan 
Published: February 2019

AbstractHeat shock proteins (HSPs) are crucial proteins in maintaining the homeostasis of human gastric epithelial cells. Tumor necrosis factor receptor‐associated protein 1 (TRAP1), a member of the HSP90 family, has been shown to be involved in various crucial physiological processes, particularly against apoptosis. However, the regulation and function of TRAP1 in Helicobacter pylori infection is still unknown. Here, we found that TRAP1 expression was downregulated on human gastric epithelial cells during
H. pylori infection by real‐time polymerase chain reaction (PCR) and western blot analysis. Through virulence factors mutant
H. pylori strains infection and inhibitors screening, we found that
H. pylori vacuolating cytotoxin A (
vacA), but not cytotoxin‐associated gene A (
cagA) protein, induced human gastric epithelial cells to downregulate TRAP1 via P38MAPK pathway by real‐time PCR and western blot analysis. Furthermore, downregulation of TRAP1 with lentivirus carrying TRAP1 short hairpin RNA constructs impairs mitochondrial function, and increases apoptosis of gastric epithelial cells. The results indicate that
H. pylori vacA downregulated TRAP1 is involved in the regulation of gastric epithelial cell apoptosis.
NUCKS1 is a novel regulator of milk synthesis in and proliferation of mammary epithelial cells via the mTOR signaling pathway
Authors: Yuan Xiaohan , Zhang Minghui , Ao Jinxia , Zhen Zhen , Gao Xuejun , Li Meng 
Published: February 2019

AbstractNuclear ubiquitous casein and cyclin‐dependent kinase substrate 1 (NUCKS1) is a highly phosphorylated nuclear protein ubiquitously expressed in vertebrates. NUCKS1 has been reported to be a key chromatin modifier and transcriptional regulator of a number of signaling pathways, but the physiological role and detailed mechanism are still limited. In this study, we assessed the role of NUCKS1 on milk synthesis in and proliferation of mammary epithelial cells from a dairy cow. NUCKS1 was located in the nucleus of mammary epithelial cells, and the expression of NUCKS1 was stimulated by amino acids (Met and Leu) and hormones (estrogen and prolactin). Gene function study approaches detected that NUCKS1 positively regulated milk protein, milk fat, and lactose synthesis, and also increased the cell number, cell viability, and cell cycle progression. NUCKS1 mediated the stimulation of amino acids and hormones on the messenger RNA expression of the mechanistic target of rapamycin (mTOR), SREBP‐1c, and Cyclin D1. The expression of NUCKS1 is dramatically higher in mouse mammary tissue of lactating period, compared with that in puberty and dry period. Taken together, these results reveal that NUCKS1 is a new mediator of milk synthesis in and proliferation of mammary epithelial cells via regulating the mTOR signaling pathway.
Beyond medical actionability: Public perceptions of important actions in response to hypothetical genetic testing results
Authors: Seiffert David J. , McCarthy Veach Patricia , LeRoy Bonnie , Guan Weihua , Zierhut Heather 
Published: February 2019

AbstractRationales for returning results from whole genome sequencing (WGS) and genetic testing have historically focused on medical utility. Understanding the wide array of actions individuals might take following genetic testing results could have important implications for clinical care. We aimed to survey the public regarding their perceptions of the importance of a wide variety of different actions one might take upon receiving hypothetical results from a WGS test where the results indicate a high risk of developing a genetic condition. We assessed whether demographic characteristics, type of condition, and perceived severity of the condition differentially affected importance ratings of actions they would take. In a survey administered at the 2015 Minnesota State Fair, 909 participants imagined that they had a blood test that looked at their genes and indicated that they were at high risk of developing one of three randomized conditions (Alzheimer's disease, macular degeneration, or colon cancer). Participants rated the importance of 35 actions. Principal component analysis, used to categorize actions, yielded eight categories: (1) medical management and communication; (2) partner support; (3) support and life fulfillment; (4) diet and exercise; (5) distal planning; (6) religion/spiritual support; (7) reproductive actions; and (8) proximal planning. Participants rated a wide range of actions as important, with medical management and communication, and partner support receiving the highest mean ratings. Linear regression yielded significant associations between importance ratings and demographics variables (age and gender), genetic condition, and perceived severity of the condition for different action categories. Genetic counselors and other healthcare professionals should consider a variety of possible patient actions beyond medical actionability when discussing genetic testing results.
Employing positive psychology to improve radiation therapy workplace culture
Authors: Hunter Darren , Wright Caroline , Pearson Sue 
Published: February 2019

AbstractThe Australian radiotherapy profession is challenged by job dissatisfaction, stress, burnout and unfavourable attrition. This paper will use psychological models to discuss the confluence of job demands, resources and personal characteristics that contribute to these challenges. Factors contributing to burnout and attrition amongst Australian Radiation Therapists will be explored, and a number of leadership strategies will be introduced to improve workplace culture. These strategies – aligned with positive psychology – seek to address staff engagement, emotional needs, and job stressors.
Efficacy of Spawning Alligator Gars in Recreational-Grade Swimming Pools
Authors: Porta Michael J , Snow Richard A , Graves Kerry G 
Published: February 2019

Abstract
Alligator Gar Atractosteus spatula numbers have declined throughout much of the species’ historic range due to anthropogenic effects (habitat alteration or loss, commercial fishing, and recreational fishing). As a result, many conservation agencies now rely on hatchery production of Alligator Gars to aid in recovery and reintroduction efforts. Because of difficulty in harvesting juvenile Alligator Gars from hatchery ponds, we evaluated the use of recreational-grade swimming pools (4.6 m in diameter × 1.2 m deep) for spawning Alligator Gars, as this may result in increased production and more efficient harvest of juveniles. In May 2018, two recreational-grade swimming pools were used to successfully spawn Alligator Gars, producing a total of approximately 159,000 fingerlings. Recreational-grade swimming pools provided an efficient, low-cost environment for the spawning of Alligator Gars. Alligator Gar fingerlings can be harvested from these pools with near 100% efficiency. Furthermore, this method reduced the need to use multiple males per female during spawning because they are confined to a small spawning environment. The use of recreational-grade swimming pools for the culture of Alligator Gars resulted in refinement and increased efficiency in spawning this species, thereby offering a technique that should enhance Alligator Gar restoration efforts by increasing hatchery production capabilities.
Nursery and Grow-Out Strategy Optimization in Bay Scallop Argopecten irradians Aquaculture
Authors: Tobi Harrison , Ward Daniel 
Published: February 2019

Abstract
The northeastern United States once had a robust and profitable wild bay scallop Argopecten irradians commercial fishery that generated revenue for fishermen and quality seafood for regional consumption. Since the 1980s, bay scallop landings have been declining due to overfishing, habitat loss, and coastal water quality degradation. There is potential for bay scallop aquaculture to fill the void left by the decline of the wild fishery. However, further investigation into optimizing growth and survival in the nursery, grow-out, and overwintering phases is needed. Growth and survival as related to stocking density were investigated during the nursery phase using a floating downweller system. Over the 6-week nursery period, survival, growth, and food availability were documented in relation to flow rates and initial stocking densities. Initial bay scallop stocking density largely predicted mean bay scallop growth rates (mm/d) over the 6-week observation period but had little impact on survival. At the end of the observation period, bay scallops were moved out of the nursery system to three different grow-out locations on Cape Cod. At each location, bay scallops were stocked into three surface gear types (floating bags of two different mesh sizes [6 or 9 mm] or hanging trays) and bottom cages to investigate grow-out phase strategies. In exposed, high-energy environments, the surface gear was susceptible to damage, and bay scallop growth rates and survival were impacted. In low-energy environments, growth rates and survival were similar between surface and bottom gear. In both low- and high-energy environments, bay scallop growth rates (mm/d) declined significantly once temperatures dropped below 15°C. Observed growth rates and survival in the configurations examined in this study indicate that bay scallop farming on New England shellfish farms is viable.
Improving MHC‐I Ligand Identifications from LC‐MS/MS Data by Incorporating Allelic Peptide Motifs
Authors: Konda Prathyusha , Murphy J. Patrick , Gujar Shashi 
Published: February 2019

AbstractMHC class I (MHC‐I)‐bound ligands play a pivotal role in CD8 T cell immunity and are hence of major interest in understanding and designing immunotherapies. One of the most commonly utilized approaches for detecting MHC ligands is LC‐MS/MS. Unfortunately, the effectiveness of current algorithms to identify MHC ligands from LC‐MS/MS data is limited because the search algorithms used were originally developed for proteomics approaches detecting tryptic peptides. Consequently, the analysis often results in inflated false discovery rate (FDR) statistics and an overall decrease in the number of peptides that pass FDR filters. Andreatta et al. describe a new scoring tool (MS‐rescue) for peptides from MHC‐I immunopeptidome datasets. MS‐rescue incorporates the existence of MHC‐I peptide motifs to rescore peptides from ligandome data. The tool is demonstrated here using peptides assigned from LC‐MS/MS data with PEAKs software but can be deployed on data from any search algorithm. This new approach increased the number of peptides identified by up to 20–30% and promises to aid the discovery of novel MHC‐I ligands with immunotherapeutic potential.
Opening the dialogue: Research networks between high‐ and low‐income countries further understanding of global agro‐climatic challenges
Authors: Smith Stephanie , Bandyopadhyay Tirthankar 
Published: February 2019

Societal Impact Statement
In the modern world it has become increasingly urgent to balance human food security needs with environmental needs. These needs are not necessarily mutually exclusive, and can be synergistic. The Cambridge‐India Network for Translational Research in Nitrogen (CINTRIN) seeks to reduce nitrogen fertilizer overapplication (and the resulting environmental pollution) in Indian agriculture: a situation with various scientific and sociopolitical drivers, which equally have various sociopolitical and scientific solutions. By listening to the needs of local farmers and applying the knowledge and resources of global plant science research, achieving higher crop yields with less nitrogen is an achievable prospect for India.
Application of molecular dynamics simulation to improve the theoretical prediction for collisional cross section of aromatic compounds with long alkyl chains in crude oils
Authors: Lim Dongwan , Park Yunjae , Chang Rakwoo , Ahmed Arif , Kim Sunghwan 
Published: February 2019

RationaleMolecular dynamics (MD) simulations with finite temperature were performed to improve the theoretical prediction of collisional cross section (CCS) values, especially for aromatic compounds containing long alkyl chains.MethodsIn this study, the CCS values of 11 aromatic compounds with long alkyl chains were calculated by MD simulations while considering internal energy at 300, 500, and 700 K, and the results were compared with experimentally determined values.ResultsThe CCS values calculated at higher energies showed better agreement with the experimental values. Polycyclic aromatic hydrocarbons (PAHs) such as pentacene and benz[b]anthracene were also investigated, and better agreement between the theoretical and experimental results was observed when higher temperature (or higher internal energy) was considered.ConclusionsThe data presented in this study show that the internal degrees of freedom of ions must be considered to accurately predict the CCS values of aromatic compounds with a flexible structure measured by ion mobility mass spectrometry.
Spontaneous aspiration of a long tree twig as foreign body
Authors: Hashimoto Kosuke , Kaira Kyoichi , Kobayashi Kunihiko , Murayama Yoshitake , Kagamu Hiroshi 
Published: February 2019

Key messageSpontaneous aspiration of a long tree twig as foreign body is an extremely rare condition. The presence of a permanent tracheal stoma in a laryngectomized patient should be considered as a predisposing factor for foreign body aspiration.
Assessing analytical methods for detecting spatiotemporal interactions between species from camera trapping data
Authors: Niedballa Jürgen , Wilting Andreas , Sollmann Rahel , Hofer Heribert , Courtiol Alexandre 
Published: February 2019

AbstractAssessing spatiotemporal interactions between species is of fundamental interest to behavioural and community ecology. Observer‐independent methods such as camera trapping facilitate the study of interactions, but analyses are hampered by the lack of comparative assessment of available approaches. We present a flexible and expandable framework to simulate and explore spatiotemporal interactions between species from camera trapping data with well‐defined properties, and compare methods to detect such interactions in a two‐species system with two types of (spatio)temporal interactions: spatiotemporal avoidance (of a site by a species after the presence of another species) and temporal segregation (shifts in daily activity patterns between species), across a range of daily activity patterns and interaction strengths. For spatiotemporal avoidance, we analysed time intervals between species records using linear models, the Mann–Whitney U‐test, a permutation test and a test based on randomly generated records. For temporal segregation, we applied a permutation test. Statistical power (the ability to detect an existing effect) for detecting spatiotemporal avoidance between species was strongly affected by interaction strength, highest for linear models and reliable above 50 records per species. Reliably detecting strong temporal segregation required fewer records (10–20 records) but depended heavily on the underlying activity pattern. All tests were valid (uniform distribution of P‐values under the null hypothesis) even at low sample sizes above a minimum of 10 records per species. Linear models were the most suitable approach to analyse spatiotemporal avoidance and can easily correct for other sources of variation in interactions. The framework presented here can help to improve survey design in camera trapping and be extended to more complex settings (e.g. with imperfect detection). In addition, it allows researchers to validate the methods used for inference of spatiotemporal interactions from camera trapping data in their specific circumstances.
An innovative use of orthophotos – possibilities to assess plant productivity from colour infrared aerial orthophotos
Authors: Erlandsson Rasmus , Stoessel Marianne , Skånes Helle , Wennbom Marika , Angerbjörn Anders 
Published: February 2019

AbstractStudies of ecological processes should focus on a relevant spatial scale, as crude spatial resolution will fail to detect small scale variation which is of potentially critical importance. Remote sensing methods based on multispectral satellite images are used to assess primary productivity and aerial photos to map vegetation structure. Both methods are based on the principle that photosynthetically active vegetation has a characteristic spectral signature. Yet they are applied differently due to technical differences. Satellite images are suitable for calculations of vegetation indices, for example Normalized Difference Vegetation Index (NDVI). Colour infrared aerial photography was developed for visual interpretation and never regarded for calculation of indices since the spectrum recorded and post processing differ from satellite images. With digital cameras and improved techniques for generating colour infrared orthophotos, the implications of these differences are uncertain and should be explored. We tested if plant productivity can be assessed using colour infrared aerial orthophotos (0.5 m resolution) by applying the standard NDVI equation. With 112 vegetation samples as ground truth, we evaluated an index that we denote rel‐NDVIortho in two areas of the Fennoscandian mountain tundra. We compared the results with conventional SPOT5 satellite‐based NDVI (10 m resolution). rel‐NDVIortho was related to plant productivity (Northern area: P = <0.001, R2 = 0.73; Southern area: P = <0.001, R2 = 0.39), performed similar to SPOT5 satellite NDVI (Northern area: P = <0.001, R2 = 0.76; Southern area: P = <0.001, R2 = 0.40) and the two methods were highly correlated (cor = 0.95 and cor = 0.84). Despite different plant composition, the results were consistent between areas. Our results suggest that vegetation indices based on colour infrared aerial orthophotos can be a valuable tool in the remote sensing toolbox, offering a high‐spatial resolution proxy for plant productivity with less signal degradation due to atmospheric interference and clouds, compared to satellite images. Further research should aim to investigate if the method is applicable to other ecosystems.
Effect of mixing on reductive dechlorination of persistent organic pollutants by Fe/Pd nanoparticles
Authors: Moujahid Abdellatif , Bang John J. , Yan Fei 
Published: February 2019

AbstractHerein, we report the comparison of two different mixing methods for reductive dechlorination of gamma‐hexachlorocyclohexane (γ‐HCH), aldrin, and p, p’‐dichlorodiphenyl‐trichloroethane (p, p’‐DDT), using iron/palladium (Fe/Pd) bimetallic nanoparticles. A noticeable enhancement of the reaction rate was found when the reductive dechlorination reaction was carried out in an ultrasound bath as compared with a platform shaker. These enhancements could be attributed to (a) the continuous cleaning and chemical activation of the surfaces of nanoscale Fe/Pd bimetallic nanoparticles by the combined chemical and physical effects of acoustic cavitation; and (b) the accelerated mass transport rates of target POPs to the surfaces of the Fe/Pd nanoparticles. Finally, the degradation intermediates and final products were determined by gas chromatography/mass spectrometry (GC/MS) analysis and the plausible degradation pathways for γ‐HCH, aldrin, and p, p’‐DDT by Fe/Pd bimetallic nanoparticles were proposed.Practitioner points

Exposure to POPs is a resilient global environmental and health issue.

Fe/Pd bimetallic nanoparticles demonstrated > 90 % removal of POPs in the first 30 minutes of the reaction via ultrasonic mixing.

GC‐MS analyses provided verification of POPs degradation intermediates and final products.
Humanizing and conducive to learning: an adolescent students’ perspective on the central attributes of positive relationships with teachers
Authors: García-Moya Irene , Brooks Fiona , Moreno Carmen 
Published: February 2019

AbstractThe aim of this qualitative study was to identify central attributes of positive relationships with teachers from the adolescent students’ perspectives that could help delineate the meaning of student–teacher connectedness while exploring to what extent its main attributes were similar or different in England and Spain. As part of the EU-funded project “Well-being among European youth: The contribution of student-teacher relationships in the secondary-school population”, we conducted focus groups in England and Spain with 42 students aged 11 to 18 years. Using a bottom-up approach for thematic analysis, we identified two main attributes that were linked to positive relationships with teachers as seen by our participating students from England and Spain:humanizing relationships, in which the students are acknowledged and respected as individuals and feel understood and supported by their teachers; andrelationships conducive to learning, encompassing aspects such as a perception of a genuine commitment with their learning on the part of the teachers, a positive classroom management, and teachers motivating students. This study contributes to the conceptualization of student–teacher connectedness and provides useful insights for teachers and educational professionals. In addition, the study findings pointed to the importance of power and authority dynamics in student–teacher relationships that foster or undermine connectedness, and they revealed some cross-cultural differences in the role of emotions in the class, two important aspects which deserve further attention in future research.
COMT-Val158Met polymorphism modulates antipsychotic effects on auditory verbal hallucinations and temporal lobe gray matter volumes in healthy individuals—symptom relief accompanied by worrisome volume reductions
Authors: Zhuo Chuanjun , Cheng Langlang , Li Gongying , Xu Yong , Jing Rixing , Li Shen , Zhang Li , Lin Xiaodong , Zhou Chunhua 
Published: February 2019

Abstract
Investigation of auditory verbal hallucinations (AVHs) in schizophrenics is complicated by psychiatric symptoms. Investigating healthy individuals with AVHs (H-AVHs) can obviate such confounding factors. The objective of this study was to explore the effects of antipsychotic treatment on AVHs and gray matter volumes (GMVs) in H-AVH subjects and whether such are effects are influenced by COMT-Val158Met genotype. Magnetic resonance imaging (MRI) and genotyping studies were completed for 42 H-AVH subjects and 42 well-matched healthy controls (HCs). COMT-Met/Met homozygotes (158th codon) were identified as COMT-Met genotype; COMT-Met/Val heterozygotes and COMT-Val/Val homozygotes were identified as COMT-Val genotype. Data were compared across groups (H-AVH vs. HC, and between genotypes) with two-sample t-tests. The H-AVH COMT-Met group showed a stronger response to antipsychotic treatment than the H-AVH COMT-Val group (p < 0.001). Both H-AVH genotype groups exhibited temporal lobe GMV reductions after treatment, and relative to their respective genotype-matched HC groups. Antipsychotic treatment effects in H-AVH subjects were influenced by COMT-Val158Met genotype and associated with widespread GMV reductions. These findings provide clues for further exploration of treatment targets for AVHs. Treatment associated GMV reductions, however, raise concerns about use of antipsychotics in H-AVH subjects.