bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phase separation and scaling in correlation structures of financial markets
Authors: Chakraborti Anirban , Hrishidev  , Sharma Kiran , Pharasi Hirdesh K 
Published: October 2020

Abstract
Financial markets, being spectacular examples of complex systems, display rich correlation structures among price returns of different assets. The correlation structures change drastically, akin to critical phenomena in physics, as do the influential stocks (leaders) and sectors (communities), during market events like crashes. It is crucial to detect their signatures for timely intervention or prevention. Here we use eigenvalue decomposition and eigen-entropy, computed from eigenvector centralities of different stocks in the cross-correlation matrix, to extract information about the disorder in the market. We construct a ‘phase space’, where different market events (bubbles, crashes, etc) undergo phase separation and display order–disorder movements. An entropy functional exhibits scaling behavior. We propose a generic indicator that facilitates the continuous monitoring of the internal structure of the market—important for managing risk and stress-testing the financial system. Our methodology would help in understanding and foreseeing tipping points or fluctuation patterns in complex systems.
Root morphophysiology changes during the habitat transition from soil to canopy of the aroid vine Rhodospatha oblongata
Authors: Liz Filartiga Arinawa , Mantuano Dulce , Vieira Ricardo Cardoso , De Toni Karen Lucia Gama , Vasques Gustavo M , Mantovani André 
Published: October 2020

Abstract

Background and Aims
The aroid vine Rhodospatha oblongata is characterized by a habitat change from terrestrial to canopy, relying on aerial roots at maturity to obtain water and nutrients from the forest soil. We hypothesize that morphophysiological acclimation occurs in roots as they grow under atmospheric conditions. These changes would guarantee the whole-plant survival of aroid vines in the new and potentially stressful habitat of the canopy.

Methods
Terrestrial and aerial roots were compared on a morphophysiological basis. Root anatomy, water balance, water absorption capacity via fluorescent tracer, and photochemical activity via chlorophyll fluorescence were measured.

Key Results
While thin fasciculate roots occur on terrestrial crawling individuals, two clearly distinct aerial roots (anchor and feeder) are produced on canopy individuals, which both adhere to the host trunk. The colour of both aerial roots changes during development from red and brownish to striped and green at maturity. Colour changes are induced by the replacement of epidermis, exodermis and outer cortex by an inner layer of lignified cork on the root region exposed to the atmosphere. In the root region that is in contact with the host, covering substitutions do not occur and both exodermis and lignified cork, along with several epidermal hairs, appear. Water retention capacity was higher in green roots than in other root types. Rehydration capacity via water absorption by hairs of aerial roots was confirmed by fluorescence. Chlorophyll fluorescence data indicated low levels of photosynthetic capacity in aerial roots.

Conclusions
Plants should evolve strategies to survive stress situations. The transition from soil to canopy imposes abiotic changes and potentially stressful situations on R. oblongata. We conclude that the morphophysiological changes observed represent an important strategy that permits the maintenance of aroid roots and the survival of R. oblongata in the canopy.
Exploring subclass-specific therapeutic agents for hepatocellular carcinoma by informatics-guided drug screen
Authors: Yang Chen , Chen Junfei , Li Yan , Huang Xiaowen , Liu Zhicheng , Wang Jun , Jiang Hua , Qin Wenxin , Lv Yuanyuan , Wang Hui , Wang Cun 
Published: October 2020

Abstract
Almost all currently approved systemic therapies for hepatocellular carcinoma (HCC) failed to achieve satisfactory therapeutic effect. Exploring tailored treatment strategies for different individuals provides an approach with the potential to maximize clinical benefit. Previously, multiple studies have reported that hepatoma cell lines belonging to different molecular subtypes respond differently to the same treatment. However, these studies only focused on a small number of typical chemotherapy or targeted drugs across limited cell lines due to time and cost constraints. To compensate for the deficiency of previous experimental researches as well as link molecular classification with therapeutic response, we conducted a comprehensive in silico screening, comprising nearly 2000 compounds, to identify compounds with subclass-specific efficacy. Here, we first identified two transcriptome-based HCC subclasses (AS1 and AS2) and then made comparison of drug response between two subclasses. As a result, we not only found that some agents previously considered to have low efficacy in HCC treatment might have promising therapeutic effects for certain subclass, but also identified novel therapeutic compounds that were not routinely used as anti-tumor drugs in clinic. Discovery of agents with subclass-specific efficacy has potential in changing the status quo of population-based therapies in HCC and providing new insights into precision oncology.
A Siamese neural network model for the prioritization of metabolic disorders by integrating real and simulated data
Authors: Messa Gian Marco , Napolitano Francesco , Elsea Sarah H. , di Bernardo Diego , Gao Xin 
Published: October 2020

Abstract

Motivation
Untargeted metabolomic approaches hold a great promise as a diagnostic tool for inborn errors of metabolisms (IEMs) in the near future. However, the complexity of the involved data makes its application difficult and time consuming. Computational approaches, such as metabolic network simulations and machine learning, could significantly help to exploit metabolomic data to aid the diagnostic process. While the former suffers from limited predictive accuracy, the latter is normally able to generalize only to IEMs for which sufficient data are available. Here, we propose a hybrid approach that exploits the best of both worlds by building a mapping between simulated and real metabolic data through a novel method based on Siamese neural networks (SNN).

Results
The proposed SNN model is able to perform disease prioritization for the metabolic profiles of IEM patients even for diseases that it was not trained to identify. To the best of our knowledge, this has not been attempted before. The developed model is able to significantly outperform a baseline model that relies on metabolic simulations only. The prioritization performances demonstrate the feasibility of the method, suggesting that the integration of metabolic models and data could significantly aid the IEM diagnosis process in the near future.

Availability and implementation
Metabolic datasets used in this study are publicly available from the cited sources. The original data produced in this study, including the trained models and the simulated metabolic profiles, are also publicly available (Messa et al., 2020).
HD-eXplosion: visualization of hydrogen–deuterium exchange data as chiclet and volcano plots with statistical filtering
Authors: Zhang Naifu , Yu Xiaohe , Zhang Xinchao , D’Arcy Sheena 
Published: October 2020

Abstract

Summary
Hydrogen–Deuterium eXchange coupled to mass spectrometry is a powerful tool for the analysis of protein dynamics and interactions. Bottom-up experiments looking at deuterium uptake differences between various conditions are the most common. These produce multi-dimensional data that can be challenging to depict in a single visual format. Each user must also set significance thresholds to define meaningful differences and make these apparent in data presentation. To assist in this process, we have created HD-eXplosion, an open-source, web-based application for the generation of chiclet and volcano plots with statistical filters. HD-eXplosion fills a void in available software packages and produces customizable plots that are publication quality.

Availability and implementation
The HD-eXplosion application is available at http://hd-explosion.utdallas.edu. The source code can be found at https://github.com/HD-Explosion.
An escape-to-radiate model for explaining the high plant diversity and endemism in campos rupestres
Authors: Rapini Alessandro , Bitencourt Cássia , Luebert Federico , Cardoso Domingos 
Published: October 2020

AbstractWith extraordinary levels of plant diversity and endemism, the Brazilian campos rupestres across the Espinhaço Range have a species/area ratio 40 times higher than the lowland Amazon. Although diversification drivers in campos rupestres remain a matter of debate, the Pleistocene refugium hypothesis (PRH) is often adopted as the most plausible explanation for their high diversity. The PRH has two main postulates: highland interglacial refugia and a species pump mechanism catalysed by climatic changes. We critically assessed studies on campos rupestres diversification at different evolutionary levels and conclude that most of them are affected by sampling biases, unrealistic assumptions or inaccurate results that do not support the PRH. By modelling the palaeo-range of campos rupestres based on the distribution of 1123 species of vascular plants endemic to the Espinhaço Range and using climate and edaphic variables, we projected a virtually constant suitable area for campos rupestres across the last glacial cycle. We challenge the great importance placed on Pleistocene climatic oscillations in campos rupestres plant diversification and offer an alternative explanation named escape-to-radiate model, which emphasizes niche shifts. Under this biogeographic model of diversification, the long-term fragmentation of campos rupestres combined with recurrent extinctions after genetic drift and sporadic events of adaptive radiation may provide an explanation for the current diversity and endemism in the Espinhaço Range. We conclude that long-term diversification dynamics in campos rupestres are mainly driven by selection, while most endemic diversity is ephemeral, extremely fragile and mainly driven by drift.
Can morphological and behavioral traits predict the foraging and feeding dynamics of social arachnids?
Authors: Moura Renan F , Tizo-Pedroso Everton , Del-Claro Kleber 
Published: October 2020

Abstract
Complex social insect species exhibit task specialization mediated by morphological and behavioral traits. However, evidence of such traits is scarce for other social arthropods. We investigated whether the social pseudoscorpion Paratemnoides nidificator exhibits morphologically and behaviorally specialized individuals in prey capture. We measured body and chela sizes of adult pseudoscorpions and analyzed predation processes. Larger individuals spent more time moving through the colony and foraging than smaller pseudoscorpions. Individuals that captured prey had increased body and absolute chelae sizes. Although larger individuals had relatively small chelae size, they showed a higher probability of prey capture. Larger individuals manipulated prey often, although they fed less than smaller pseudoscorpions. Individuals that initiated captures fed more frequently and for more time than the others. Natural selection might be favoring individuals specialized in foraging and colony protection, allowing smaller and less efficient adults to avoid contact with dangerous prey. To our knowledge, there is incipient information regarding specialized individuals in arachnids, and our results might indicate the emergence of a morphologically specialized group in this species.
Abundance and Diversity of Dung Beetles (Coleoptera: Scarabaeoidea) as Affected by Grazing Management in the Nebraska Sandhills Ecosystem
Authors: Wagner Patrick M , Abagandura Gandura Omar , Mamo Martha , Weissling Thomas , Wingeyer Ana , Bradshaw Jeffrey D 
Published: October 2020

Abstract
Dung beetles (Coleoptera: Scarabaeoidea) serve a significant role in regulating ecosystem services on rangelands. However, the influence of grazing management on dung beetle communities remains largely unknown. The purpose of this study was to investigate dung beetle abundance and diversity throughout the grazing season in the Nebraska Sandhills Ecoregion. Grazing treatments included: continuous grazing (CONT), low-stocking rotational grazing (LSR), high-stocking rotational grazing (HSR), and no grazing (NG). The abundance and diversity of dung beetles were measured in the 2014 and 2015 grazing seasons using dung-baited pitfall traps. Dung beetle abundance for each grazing treatment was characterized through four indices: peak abundance, species richness, Simpson’s diversity index, and Simpson’s evenness. A total of 4,192 dung beetles were collected through both years of trapping in this study. Peak abundance and species richness were greater in grazed treatments when compared to NG in both years. Peak abundance in the HSR was 200% (2014) and 120% (2015) higher than in the LSR. Species richness in the HSR was 70% (2014) and 61% (2015) higher than in the LSR, and 89% (2014) and 133% (2015) higher than in CONT. Simpson’s diversity index was lower in the NG and CONT treatments when compared to the LSR or HSR treatments for both years. We conclude that rotational grazing, regardless of stocking density, promoted dung beetle abundance and diversity within the Nebraska Sandhills Ecoregion.
Efficacy and safety of icosapent ethyl in hypertriglyceridaemia: a recap
Authors: Parhofer Klaus G , Chapman M John , Nordestgaard Børge G 
Published: October 2020

Abstract
Although low-density lipoprotein cholesterol lowering is effective in atherosclerotic cardiovascular disease (ASCVD) prevention, considerable ‘lipid-associated’ residual risk remains, particularly in patients with mild-to-moderate hypertriglyceridaemia (2–10 mmol/L; 176–880 mg/dL). Triglyceride (TG)-rich lipoproteins carry both TGs and cholesterol (remnant-cholesterol). At TG levels &gt;5 mmol/L (440 mg/dL) vs. &lt;1 mmol/L (88 mg/dL) or remnant-cholesterol &gt;2.3 mmol/L (89 mg/dL) vs. &lt;0.5 mmol/L (19 mg/dL), risk is ∼1.5-fold elevated for aortic stenosis, 2-fold for all-cause mortality, 3-fold for ischaemic stroke, 5-fold for myocardial infarction (MI), and 10-fold for acute pancreatitis. Furthermore, Mendelian randomization studies indicate that elevated TG-rich lipoproteins are causally related to increased risk of ASCVD and even all-cause mortality. While genetic and epidemiological data strongly indicate that TG-rich lipoproteins are causally linked to ASCVD, intervention data are ambiguous. Fibrates, niacin and low-dose omega-3 fatty acids have all been used in outcome trials, but have failed to demonstrate clear benefit in combination with statins. Whether the lack of additional benefit relates to methodological issues or true failure is indeterminate. Importantly, a recent intervention trial evaluating a high dose of eicosapentaenoic-acid showed clear benefit. Thus, REDUCE-IT evaluated the effect of icosapent ethyl (4 g/day) on cardiovascular outcomes in 8179 high-risk patients with moderate TG elevation on statin therapy. Over a median duration of 4.9 years, the relative risk for the primary endpoint (composite of cardiovascular death, non-fatal MI, non-fatal stroke, coronary revascularization, or unstable angina) was reduced by 25% (absolute risk 17.2% vs. 22.0%; P &lt; 0.0001; number needed to treat 21). High-dose icosapent ethyl intervention therefore confers substantial cardiovascular benefit in high-risk patients with moderate hypertriglyceridaemia on statin therapy.
Mineral oil: safety and use as placebo in REDUCE-IT and other clinical studies
Authors: Olshansky Brian , Chung Mina K , Budoff Matthew J , Philip Sephy , Jiao Lixia , Doyle, Jr. Ralph T , Copland Christina , Giaquinto Alex , Juliano Rebecca A , Bhatt Deepak L 
Published: October 2020

Abstract
Mineral oil is often used as a clinical trial placebo. Pharmaceutical-grade mineral oil consists of a mixture of saturated hydrocarbons, with a purity and chemical structure that differs substantially from food-grade or technical-/industrial-grade mineral oils. Interest in mineral oil was piqued by suggestions that a portion of the substantially positive results of the Reduction of Cardiovascular Events with Icosapent Ethyl–Intervention Trial (REDUCE-IT) might be attributable to the theoretical negative effects of mineral oil rather than being due to the clinical benefits of icosapent ethyl. The objective of this review was to explore possible mineral oil safety and efficacy effects and contextualize these findings in light of the REDUCE-IT conclusions. A literature search identified studies employing mineral oil placebos. Eighty studies were identified and relevant data extracted. Adverse events associated with mineral oil were generally gastrointestinal and consistent with use as a lubricant laxative. Changes in triglycerides, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, high-sensitivity C-reactive protein, and other biomarkers were inconsistent and generally not statistically significant, or clinically meaningful with mineral oil, as were changes in blood pressure. There was no consistent evidence that mineral oil in the amounts used in the REDUCE-IT or Effect of Vascepa on Progression of Coronary Atherosclerosis in Patients With Elevated Triglycerides on Statin Therapy (EVAPORATE) trials affects absorption of essential nutrients or drugs, including statins. These results were then considered alongside publicly available data from REDUCE-IT. Based on available evidence, mineral oil does not appear to impact medication absorption or efficacy, or related clinical outcomes, and, therefore, does not meaningfully affect study conclusions when used as a placebo at the quantities used in clinical trials.
Sinus rhythm voltage fingerprinting in patients with mitral valve disease using a high-density epicardial mapping approach
Authors: van Schie Mathijs S , Starreveld Roeliene , Bogers Ad J J C , de Groot Natasja M S 
Published: October 2020

Abstract

Aims
Unipolar voltage (UV) mapping is increasingly used for guiding ablative therapy of atrial fibrillation (AF) as unipolar electrograms (U-EGMs) are independent of electrode orientation and atrial wavefront direction. This study was aimed at constructing individual, high-resolution sinus rhythm (SR) UV fingerprints to identify low-voltage areas and study the effect of AF episodes in patients with mitral valve disease (MVD).

Methods and results
Intra-operative epicardial mapping (interelectrode distance 2 mm) of the right and left atrium, Bachmann’s bundle (BB), and pulmonary vein area was performed in 67 patients (27 male, 67 ± 11 years) with or without a history of paroxysmal AF (PAF). In all patients, there were considerable regional variations in voltages. UVs at BB were lower in patients with PAF compared with those without [no AF: 4.94 (3.56–5.98) mV, PAF: 3.30 (2.25–4.57) mV, P = 0.006]. A larger number of low-voltage potentials were recorded at BB in the PAF group [no AF: 2.13 (0.52–7.68) %, PAF: 12.86 (3.18–23.59) %, P = 0.001]. In addition, areas with low-voltage potentials were present in all patients, yet we did not find any predilection sites for low-voltage potentials to occur.

Conclusion
Even in SR, advanced atrial remodelling in MVD patients shows marked inter-individual and regional variation. Low UVs are even present during SR in patients without a history of AF indicating that low UVs should carefully be used as target sites for ablative therapy.
Accurate Estimation of Commercial Volume in Tropical Forests
Authors: de Lima Robson Borges , Rutishauser Ervan , da Silva José Antônio Aleixo , Guedes Marcelino Carneiro , Herault Bruno , de Oliveira Cinthia Pereira , da Silva Aparício Perseu , Sotta Eleneide Doff , da Silva Diego Armando Silva , Ferreira Rinaldo Luiz Caraciolo 
Published: October 2020

Abstract
Accurate estimates of commercial volume in tropical forests are key for the implementation of sustainable forest management plans. Because of the lack of local or generic volumetric equations, most forest managers and forestry services are still using traditional expansion factors (i.e., multiplication of the diameter by a given value) to estimate the volume of commercial tree species in the Amazon. Volumetric models were developed through a unique data set of 1,264 fallen trees fully measured in 150 sample plots located across a broad range of forests in Amapá, Brazil. Forest-specific volumetric models were developed and compared with a generic (i.e., across all forests) model and with published equations developed elsewhere in the Amazon. The generic equation performed well in all forest types and allowed precise predictions. The most efficient sampling design to develop volumetric models consists of measuring approximately 50 trees across four different size classes representing the whole population. The form factors (FF) developed locally generated substantial bias but performed better than the traditional FF (0.7). Overall, our results suggest that it is possible to develop accurate generic models to estimate commercial timber volume, and this study can serve as a guideline for forest managers or scientists interested in calibrating volumetric models in a cost-efficient way.
In vitro screening of probiotic properties of Lactobacillus plantarum isolated from fermented milk product
Authors: Nath Soumitra , Sikidar Jibalok , Roy Monisha , Deb Bibhas 
Published: October 2020

Abstract

Objectives
The screening of traditional fermented products is essential for the assessment of safety, security, and further development of functional foods for the well-being of human health. The aim of the present study was to isolate and identify bacteria from fermented raw milk samples that exhibit health benefits upon consumption.

Methods
In order to confirm the isolates as probiotics, several in vitro assays were conducted to assess the probiotic properties of isolated bacteria. The initial screening includes tolerance to acid, bile, pancreatin, and NaCl. The cell surface properties demonstrate their interaction with mucosal epithelium, which includes hydrophobicity and auto-aggregation assay. Safety assessment was done by performing haemolytic test and antibiotic susceptibility test. The antagonistic activity of probiotic strain was further evaluated against some pathogenic bacteria.

Results
Lactobacillus plantarum (L. plantarum) isolated from fermented raw milk was preliminarily identified by biochemical tests and further confirmed using 16S rRNA identification. The isolate designated as L. plantarum strain GCC_19M1 demonstrated significant tolerance to low pH, 0.3% bile, 0.5% pancreatin, and 5% NaCl. In the presence of simulated gastric juice (at pH 3), the isolate exhibited a survival rate of 93.48–96.97%. Furthermore, the development of ecological niches in the human gut and their successful accumulation have been revealed by auto-aggregation and hydrophobicity properties. Absence of haemolytic activity ensures the non-virulent nature of the strain. Lactobacillus plantarum strain GCC_19M1 showed susceptibility towards gentamicin, tetracycline, kanamycin, meropenem, and ceftriaxone and exhibited an antagonistic effect on pathogenic bacteria.

Conclusion
The obtained results conveyed that L. plantarum strain GCC_19M1 has strong probiotic potential, and its presence in the fermented raw milk products may serve as a potent functional probiotic food.