bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benchmarking simplified template cross sections in W H production
Authors: Brehmer Johann , Dawson Sally , Homiller Samuel , Kling Felix , Plehn Tilman 
Published: November 2019

Abstract
Simplified template cross sections define a framework for the measurement and dissemination of kinematic information in Higgs measurements. We benchmark the currently proposed setup in an analysis of dimension-6 effective field theory operators for W H production. Calculating the Fisher information allows us to quantify the sensitivity of this framework to new physics and study its dependence on phase space. New machine- learning techniques let us compare the simplified template cross section framework to the full, high-dimensional kinematic information. We show that the way in which we truncate the effective theory has a sizable impact on the definition of the optimal simplified template cross sections.
Jackiw-Teitelboim gravity and rotating black holes
Authors: Moitra Upamanyu , Sake Sunil Kumar , Trivedi Sandip P. , Vishal V. 
Published: November 2019

AbstractWe show that the free energy at low temperatures for near-extremal black holes is correctly obtained from the Jackiw-Teitelboim (JT) model of gravity. Our arguments apply to all black holes, including rotating ones, whose metric has a near-horizon AdS2factor and the associated SL (2,ℝ) symmetry. We verify these arguments by explicit calculations for rotating black holes in 4 and 5 dimensions. Our results suggest that the JT model could prove useful in analysing the dynamics of near-extremal Kerr black holes found in nature.
Gene co-regulation and co-expression in the aryl hydrocarbon receptor-mediated transcriptional regulatory network in the mouse liver
Authors: Josyula Navya , Andersen Melvin E. , Kaminski Norbert E. , Dere Edward , Zacharewski Timothy R. , Bhattacharya Sudin 
Published: November 2019

AbstractFour decades after its discovery, the aryl hydrocarbon receptor (AHR), a ligand-inducible transcription factor (TF) activated by the persistent environmental contaminant 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), remains an enigmatic molecule with a controversial endogenous role. Here, we have assembled a global map of the AHR gene regulatory network in female C57BL/6 mice orally gavaged with 30 µg/kg of TCDD from a combination of previously published gene expression and genome-wide TF-binding data sets. Using Kohonen self-organizing maps and subspace clustering, we show that genes co-regulated by common upstream TFs in the AHR network exhibit a pattern of co-expression. Directly bound, indirectly bound, and non-genomic AHR target genes exhibit distinct expression patterns, with the directly bound targets associated with highest median expression. Interestingly, among the directly bound AHR target genes, the expression level increases with the number of AHR-binding sites in the proximal promoter regions. Finally, we show that co-regulated genes in the AHR network activate distinct groups of downstream biological processes. Although the specific findings described here are restricted to hepatic effects under short-term TCDD exposure, this work describes a generalizable approach to the reconstruction and analysis of transcriptional regulatory cascades underlying cellular stress response, revealing network hierarchy and the nature of information flow from the initial signaling events to phenotypic outcomes. Such reconstructed networks can form the basis of a new generation of quantitative adverse outcome pathways.
Trace-element geochemistry of diamond-hosted olivine inclusions from the Akwatia Mine, West African Craton: implications for diamond paragenesis and geothermobarometry
Authors: De Hoog J. C. M. , Stachel T. , Harris J. W. 
Published: November 2019

AbstractTrace-element concentrations in olivine and coexisting garnets included in diamonds from the Akwatia Mine (Ghana, West African Craton) were measured to show that olivine can provide similar information about equilibration temperature, diamond paragenesis and mantle processes as garnet. Trace-element systematics can be used to distinguish harzburgitic olivines from lherzolite ones: if Ca/Al ratios of olivine are below the mantle lherzolite trend (Ca/Al < 2.2), they are derived from a harzburgitic mantle source, and syngenetic garnets are without exception subcalcic G10 garnets. For harzburgitic olivines that cannot be identified this way, Na and Ca contents can be used: olivine inclusions with < 60 µg/g Na and Na/Al < 0.7 are all harzburgitic, whereas those with > 300 µg/g Ca or > 60 µg/g Na are lherzolitic. Conventional geothermobarometry indicates that Akwatia diamonds formed and resided close to a 39 mW/m2 conductive geotherm. A similar value can be derived from Al in olivine geothermometry, with TAl-ol ranging from 1020 to 1325 °C. Ni in garnet temperatures is on average somewhat higher (TNi-grt = 1115–1335 °C) and the correlation between the two thermometers is weak, which may be not only due to the large uncertainties in the calibrations, but also due to disequilibrium between inclusions from the same diamond. Calcium in olivine should not be used as a geothermobarometer for harzburgitic olivines, and often gives unrealistic P–T estimates for lherzolitic olivine as well. Diamond-hosted olivine inclusions indicate growth in an extremely depleted (low Ti, Ca, Na, high Cr#) environment with no residual clinopyroxene. They are distinct from olivines from mantle xenoliths which show higher, more variable Ti contents and lower Cr#. Hence, most olivine inclusions in Akwatia diamonds escaped the refertilisation processes that have affected most mantle xenoliths. Lherzolitic inclusions are probably the result of refertilisation after undergoing high-degree melting first. Trivalent cations appear to behave differently in harzburgitic diamond-hosted olivine inclusions than lherzolitic inclusions and olivine from mantle xenoliths. Some divalent chromium is predicted to be present in most olivine inclusions, which may explain high concentrations up to 0.16 wt% Cr2O3 observed in some diamond inclusions. Strong heterogeneity of Cr, V and Al in several inclusions may also result in apparent high Cr contents, and is probably due to late-stage processes during exhumation. However, in general, diamond-hosted olivine inclusions have lower Cr and V than expected compared to mantle xenoliths. Reduced Na activity in depleted harzburgites limits the uptake of Cr, V and Sc via Na–M3+ exchange. In contrast, Al partitioning in harzburgites is not significantly reduced compared to lherzolites, presumably due to uptake of Al in olivine by Al–Al exchange.
Video-assisted neck surgery (VANS) using a gasless lifting procedure for thyroid and parathyroid diseases: “The VANS method from A to Z”
Authors: Shimizu Kazuo , Shimizu Kazuhide , Okamura Ritsuko , Igarashi Takehito , Nagaoka Ryuta , Sanada Marie , Sugitani Iwao , Fukumori Tatsuya , Yamada Tetsu 
Published: November 2019

Abstract
Purpose
To describe and evaluate our video-assisted neck surgery (VANS) method for thyroid and parathyroid diseases.

Methods
We describe in detail the VANS method for enucleation, lobectomy, total (nearly total) thyroidectomy, and lymph node dissection for malignancy and Graves’ disease. In collaboration with the Japan Society of Endoscopic Surgery (JSES), we evaluated several aspects of this method. The JSES evaluated the method for working-space formation and surgical complications, whereas we examined the learning curve of the surgeons, and the cosmetic satisfaction of the patients and the degree of numbness and pain they experienced. We also asked patients who underwent conventional surgery whether they would have selected VANS had it been available.

Results
The working space for 81.5% of the procedures in Japan was created using the gasless lifting method. The learning curve, considering both blood loss and operating time, decreased after 30 cases. Both factors improved for tumors smaller than 5 cm in diameter. Over 60% of the patients who underwent conventional surgery stated that they would have selected VANS, had it been available. Postoperative pain was worse after conventional surgery than after VANS, but neck numbness after VANS was more frequent than expected.

Conclusions
The VANS method is a feasible, safe, and cost-effective procedure with clear cosmetic advantages over conventional surgery.
Digitization and profitability
Authors: Masuda Yasushi , Whang Seungjin 
Published: November 2019

AbstractConsider a monopolistic vendor who faces a known demand curve. By setting a price that equates marginal revenue with marginal cost, the vendor will maximize his profit. This logic holds true of both physical and digital goods. But since digitization will lower the variable production cost, it will strictly increase the profit to the vendor. Then, can we conclude that digitization always improves the vendor’s profitability? Not necessarily. Now consider what will happen on the next day of the sales. Facing deterministic demand, the physical goods vendor must have prepared the exact quantity of the product to sell, and thus all products are sold out. By contrast, the digital goods vendor will have no stock out, thanks to the nature of the digital good. Therefore, the rational vendor will try to sell more and achieve a higher profit after the sales date. To this end, the vendor will now lower the price to attract additional customers with lower reservation prices. The process will indefinitely continue. Knowing this would happen, customers will wait for the price reduction. Even the customers who would have purchased on the first day would defer the purchase until price gets lower. The digital goods vendor will anticipate this and accordingly lower the price on the first day and later, thereby compromising his profitability. Note that this downward spiral takes place as a result of digitization. Thus, digitization may not necessarily improve the profitability to the vendor. We develop an economic model to formally analyze the impact of digitization on the profitability to the vendor.
The Emotional Facet of Subjective and Neural Indices of Similarity
Authors: Riberto Martina , Pobric Gorana , Talmi Deborah 
Published: November 2019

AbstractEmotional similarity refers to the tendency to group stimuli together because they evoke the same feelings in us. The majority of research on similarity perception that has been conducted to date has focused on non-emotional stimuli. Different models have been proposed to explain how we represent semantic concepts, and judge the similarity among them. They are supported from behavioural and neural evidence, often combined by using Multivariate Pattern Analyses. By contrast, less is known about the cognitive and neural mechanisms underlying the judgement of similarity between real-life emotional experiences. This review summarizes the major findings, debates and limitations in the semantic similarity literature. They will serve as background to the emotional facet of similarity that will be the focus of this review. A multi-modal and overarching approach, which relates different levels of neuroscientific explanation (i.e., computational, algorithmic and implementation), would be the key to further unveil what makes emotional experiences similar to each other.
Sorting living mesenchymal stem cells using a TWIST1 RNA-based probe depends on incubation time and uptake capacity
Authors: Voskamp Chantal , van de Peppel Jeroen , Gasparini Simona , Giannoni Paolo , van Leeuwen Johannes P. T. M. , van Osch Gerjo J. V. M. , Narcisi Roberto 
Published: November 2019

AbstractBone marrow derived mesenchymal stromal cells (BMSCs) are multipotent progenitors of particular interest for cell-based tissue engineering therapies. However, one disadvantage that limit their clinical use is their heterogeneity. In the last decades a great effort was made to select BMSC subpopulations based on cell surface markers, however there is still no general consensus on which markers to use to obtain the best BMSCs for tissue regeneration. Looking for alternatives we decided to focus on a probe-based method to detect intracellular mRNA in living cells, the SmartFlare technology. This technology does not require fixation of the cells and allows us to sort living cells based on gene expression into functionally different populations. However, since the technology is available it is debated whether the probes specifically recognize their target mRNAs. We validated the TWIST1 probe and demonstrated that it specifically recognizes TWIST1 in BMSCs. However, differences in probe concentration, incubation time and cellular uptake can strongly influence signal specificity. In addition we found that TWIST1high expressing cells have an increased expansion rate compared to TWIST1low expressing cells derived
from the same initial population of BMSCs. The SmartFlare probes recognize their target gene, however for each probe and cell type validation of the protocol is necessary.
Cinnamon powder: an in vitro and in vivo evaluation of antifungal and plant growth promoting activity
Authors: Kowalska Jolanta , Tyburski Józef , Krzymińska Joanna , Jakubowska Magdalena 
Published: November 2019

AbstractIn this study, the effects of organic powder ofCinnamomum zeylanicumon the development ofBotrytis cinereaand its influence on tomato plants were evaluated. The cinnamon bark powder and its water suspensions and filtrates were used at 0.5 and 1% rates. After 6 days of the start of an in vitro experiment the mycelium growth was inhibited by both 0.5 and 1% cinnamon water filtrates - to a greater degree in the case of the higher concentration, by 54.4 and 81.4%, respectively. Spraying with cinnamon water filtrates positively influenced the growth of plants both in the greenhouse and the field. Antifungal activity of cinnamon was proved in the greenhouse tests - the disease symptoms of grey mould on infected tomato plants decreased. The fresh weight of non-inoculated tomato plants treated with cinnamon filtrates was significantly higher than control plants (17.17 g compared to 12.83 g) showing a stimulating effect of cinnamon filtrates. In the case of inoculated plants due to treatment, their weight increased from 7.83 to 10.50 g. In the field experiment, tomato plants sprayed six times with cinnamon were better developed than the control plants. The most significant effect was observed for Hamlet variety - the mean number of leaves was higher by 27.3% and the mean number of branches by 19.7% compared to the untreated control plants. Thus it was proved that cinnamon powder has potential to inhibitB. cinereagrowth and also has a stimulating effect for tomato plants.
Recognizing lines of code violating company-specific coding guidelines using machine learning
Authors: Ochodek Miroslaw , Hebig Regina , Meding Wilhelm , Frost Gert , Staron Miroslaw 
Published: November 2019

AbstractSoftware developers in big and medium-size companies are working with millions of lines of code in their codebases. Assuring the quality of this code has shifted from simple defect management to proactive assurance of internal code quality. Although static code analysis and code reviews have been at the forefront of research and practice in this area, code reviews are still an effort-intensive and interpretation-prone activity. The aim of this research is to support code reviews by automatically recognizing company-specific code guidelines violations in large-scale, industrial source code. In our action research project, we constructed a machine-learning-based tool for code analysis where software developers and architects in big and medium-sized companies can use a few examples of source code lines violating code/design guidelines (up to 700 lines of code) to train decision-tree classifiers to find similar violations in their codebases (up to 3 million lines of code). Our action research project consisted of (i) understanding the challenges of two large software development companies, (ii) applying the machine-learning-based tool to detect violations of Sun’s and Google’s coding conventions in the code of three large open source projects implemented in Java, (iii) evaluating the tool on evolving industrial codebase, and (iv) finding the best learning strategies to reduce the cost of training the classifiers. We were able to achieve the average accuracy of over 99% and the average F-score of 0.80 for open source projects when using ca. 40K lines for training the tool. We obtained a similar average F-score of 0.78 for the industrial code but this time using only up to 700 lines of code as a training dataset. Finally, we observed the tool performed visibly better for the rules requiring to understand a single line of code or the context of a few lines (often allowing to reach the F-score of 0.90 or higher). Based on these results, we could observe that this approach can provide modern software development companies with the ability to use examples to teach an algorithm to recognize violations of code/design guidelines and thus increase the number of reviews conducted before the product release. This, in turn, leads to the increased quality of the final software.
Vulnerability and the Consenting Subject: Reimagining Informed Consent in Embryo Donation
Authors: Hewer Rebecca 
Published: November 2019

AbstractInformed consent is medico-legal orthodoxy and the principal means by which research encounters with the body are regulated in the UK. However, biomedical advancements increasingly frustrate the degree to which informed consent can be practiced, whilst introducing ambiguity into its legal significance. What is more, feminist theory fundamentally disrupts the ideologically liberal foundations of informed consent, exposing it as a potentially inadequate mode of bioethical regulation. This paper explores these critiques by reference to a case study—embryo donation to health research, following fertility treatment, as regulated by the HFEA 1990—and contends that informed consent cannot adequately respond to the material realities of this research encounter. Thereafter, by drawing on feminist theories of vulnerability, this paper proffers an alternative bioethical approach, which calls for structural reform in recognition of the fundamentally bilateral constitution of self and society and a renewed appreciation for the affective/dispositional tenor of lived experience.
Myocardial phenotypes and dysfunction in HFpEF and HFrEF assessed by echocardiography and cardiac magnetic resonance
Authors: Berlot Bostjan , Bucciarelli-Ducci Chiara , Palazzuoli Alberto , Marino Paolo 
Published: November 2019

AbstractHeart failure (HF) with either reduced or preserved ejection fraction is an increasingly prevalent condition. Cardiac imaging plays a central role in trying to identify the underlying cause of the underlying systolic and diastolic dysfunction, as the imaging findings have implications for patient’s management and individualised treatment. The imaging modalities used more frequently in patients with heart failure in clinical routine are echocardiography and cardiac magnetic resonance. Both techniques keep some strengths and weakness due to their spatial and temporal resolution. Notably, several features in the diagnostic algorithm of heart failure with preserved systolic function (HFpEF) may be improved by an integrated approach. This review focuses on the role of each modality in characterising cardiac anatomy, systolic and diastolic function as well as myocardial tissue characterisation in the most common phenotypes of dilated and hypertrophied hearts.
Aquatic bryophytes play a key role in sediment-stressed boreal headwater streams
Authors: Turunen Jarno , Muotka Timo , Aroviita Jukka 
Published: November 2019

AbstractForestry-related land use can cause increasing instream sedimentation, burying and eradicating stream bryophytes, with severe ecological consequences. However, there is limited understanding of the relative roles and overall importance of the two frequently co-occurring stressors, increased fine sediments and loss of bryophytes, to stream biodiversity and ecosystem functions. By using random forest modeling and partial dependence functions, we studied the relative importance of stream bryophytes and fine sediments to multiple biological endpoints (leaf-decaying fungi, diatom, bryophyte, and benthic macroinvertebrate communities; leaf decomposition) using field survey data from headwater streams. Stream bryophyte abundance and richness were negatively related to fine sediment cover, highlighting the detrimental effect of sedimentation on bryophytes. However, bryophyte abundance was consistently more important a determinant of variation in community composition than was fine sediment cover. Leaf decomposition was influenced by shredder abundance, water temperature and, to a lesser degree, stream size. Our results suggest that the loss of stream bryophytes due to increasing sedimentation, rather than fine sediments per se, seems to be the key factor affecting multiple biological responses. Enhancing the re-establishment of bryophyte stands could partly compensate for the negative impacts of sedimentation on bryophytes and, consequently, on several other components of boreal stream ecosystems.
Prevalence of obstructive sleep apnea in patients with peripheral arterial diseases
Authors: Szymanski Filip M. , Gorko Dariusz , Platek Anna E. , Ostrowski Tomasz , Celejewski Krzysztof , Chudzinski Witold , Szymanska Anna , Stepkowski Kamil , Rys-Czaporowska Anna , Semczuk-Kaczmarek Karolina , Galazka Zbigniew , Filipiak Krzysztof J. 
Published: November 2019

Abstract
Background
The presence of obstructive sleep apnea (OSA), a novel cardiovascular risk factor, contributes to the development of peripheral arterial diseases (PAD). There is a lack of data showing how often these diseases coexist.

Aims
The aim of the study was to determine the prevalence of OSA in the population of patients with PAD.

Methods
Patients previously qualified for the first revascularization due to PAD were included in the study. All patients underwent an overnight sleep study to detect OSA. Diagnosis of OSA was made when the apnea–hypopnea index (AHI) was ≥5 per hour.

Results
From 141 patients (60% men, age 69.6 ± 9.5 years), OSA was diagnosed in 68 patients (48%). OSA occurred in mild form (5 ≤ AHI < 15/h) in 39 cases (28%), in moderate form (15 ≤ AHI < 30/h) in 21 cases (15%), and in severe form (AHI ≥ 30/h) in 8 cases (6%). Patients without OSA had significantly lower body mass index (BMI; 26.9 ± 5.5 vs. 27.7 ± 5.3 kg/m2, p = 0.01) and lower hip circumference (97.4 ± 11.7 vs. 98.7 ± 7.4, p = 0.04). There were no differences in the distribution of other investigated cardiovascular risk factors and diseases between these groups. There were no significant differences in OSA distribution or its severity between patients with lower extremity artery disease and carotid artery disease.

Conclusions
The prevalence of OSA in patients with PAD is very high, affecting nearly half of the studied population.