bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electron population properties with different energies in a helicon plasma source
Authors: ZHANG Zun , ZHANG Zhe , TANG Haibin , OUYANG Jiting 
Published: August 2020

Abstract
The characteristics of electrons play a dominant role in determining the ionization and acceleration processes of plasmas. Compared with electrostatic diagnostics, the optical method is independent of the radio frequency (RF) noise, magnetic field, and electric field. In this paper, an optical emission spectroscope was used to determine the plasma emission spectra, electron excitation energy population distributions (EEEPDs), growth rates of low-energy and high-energy electrons, and their intensity jumps with input powers. The 56 emission lines with the highest signal-to-noise ratio and their corresponding electron excitation energy were used for the translation of the spectrum into EEEPD. One discrete EEEPD has two clear different regions, namely the low-energy electron excitation region (neutral lines with threshold energy of 13–15 eV) and the high-energy electron excitation region (ionic lines with threshold energy ≥19 eV). The EEEPD variations with different diameters of discharge tubes (20 mm, 40 mm, and 60 mm) and different input RF powers (200–1800 W) were investigated. By normalized intensity comparison of the ionic and neutral lines, the growth rate of the ionic population was higher than the neutral one, especially when the tube diameter was less than 40 mm and the input power was higher than 1000 W. Moreover, we found that the intensities of low-energy electrons and high-energy electrons jump at different input powers from inductively coupled (H) mode to helicon (W) mode; therefore, the determination of W mode needs to be carefully considered.
Follow-up of a Wuqinxi exercise at home programme to reduce pain and improve function for knee osteoarthritis in older people: a randomised controlled trial
Authors: Xiao Chun Mei , LI Jing Jing , Kang Yong , Zhuang Yong Chang 
Published: August 2020

Abstract

Background
Exercise therapy is a key intervention in the management of knee osteoarthritis (KOA) and recommended in international guidelines on KOA management. An effective home-exercise programme for frail older adults with KOA was successful in achieving high adherence. This randomised controlled trial was to compare the adherence to the exercise and lasting effects of follow-up 3 months.

Methods
Sixty-eight participants in the original Wuqinxi (WQX) exercise study were community dwelling older adults (age = 70.95 ± 9.85 years) with KOA were categorised into 34 controls group, 34 WQX group adherers. The Western Ontario and Mc Master Universities Osteoarthritis Index questionnaire score (WOMAC) pain and Berg Balance Scale, Timed Up and Go Test, 6-min Walk Test, 30-s chair stand test, isokinetic muscle strength testing of knee flexion and extension measured at pre-test and post-test of the intervention period and follow-up for two groups.

Results
The WQX group maintained or improved in all nine measures from post-test to follow-up, whereas the control group significantly declined in WOMAC pain, Knee extensor strength and Knee flexor strength.

Conclusion
The WQX programme was an effective home-exercise programme that achieves high adherence in older adults with KOA who lived in these communities.
Transcriptome analysis in osmo-primed tomato seeds with enhanced longevity by heat shock treatment
Authors: Barbosa Batista Thiago , Javier Fernandez Geysson , Alexandre da Silva Tiago , Maia Júlio , Amaral da Silva Edvaldo Aparecido 
Published: August 2020

Abstract
Seed priming is widely used in commercial seeds and its main function is to accelerate and synchronize seed germination. Undesirably, primed seeds show reduced longevity and treatments like heat shock have been shown to improve longevity in primed seeds. Nonetheless, the effect of heat shock treatment on primed seeds at the mRNA level is not known. Thus, the aim of this work was to investigate the effect of heat shock treatment on the longevity of primed tomato (Solanum lycopersicum) seeds at the physiological and transcriptome levels. Tomato seeds were primed and dried (control). Alternatively, primed seeds were subjected to heat shock treatment (38 °C/32 % relative humidity) before drying. Germination, vigor and longevity were evaluated. Transcriptome analysis was performed by RNA sequencing (RNA-seq) from biological samples collected immediately after priming and another samples collected from primed seeds followed by the heat shock treatments. The gene expression was validated by quantitative real time PCR (RT-qPCR). We showed that applying heat shock treatment after priming increased germination speed, enhanced seed longevity and preserved the vigor during storage of primed tomato seeds. Through transcriptome analysis, 368 differentially expressed genes were identified, from which 298 genes were up-regulated and 70 were down-regulated. We showed the increase of mRNA levels of HEAT SHOCK FACTOR-like and HEAT SHOCK PROTEIN-like chaperone genes, suggesting the involvement of the proteins coded by these transcripts in the enhancement of longevity in primed tomato seeds. The heat shock treatment after priming enhances and preserves the vigor of tomato primed seeds during storage. In addition, improves seed longevity through the increase in the expression of transcripts related to protection by response to stress.
Fine Wrinkle Treatment and Hydration on the Facial Dermis Using HydroToxin Mixture of MicroBotox and MicroHyaluronic Acid
Authors: Kim Jong Seo 
Published: August 2020

Abstract

Background
Hyaluronic acid (HA) is a key contributor to skin moisture (hydration), and MicroBotox demonstrates improvements for fine wrinkles of the face.

Objectives
The author sought to evaluate the safety and efficacy of intradermal injection of hydrotoxin (combined mixture of MicroHA and MicroBotox) for the treatment of skin roughness and dryness on facial dermis.

Methods
Fifty women who had thin, dry skin with fine wrinkles throughout the whole face, especially in the crow’s feet and forehead areas, were enrolled in the study. Two cc stabilized-HA filler and 1 cc (40 U) of botulinumtoxinA were mixed in the novel combined hydrotoxin mixture. Intended to hydrate the dermis and treat fine wrinkles of the face, the mixture was injected into the real dermal layer of the face. The volume of HA per site was 0.002 cc and toxin was 0.04 U. Skin roughness and stratum corneum hydration were measured at 1, 2, 3, and 6 months.

Results
One month post-treatment, skin roughness was reduced to 50.19% in topographic computer analysis utilizing 10× dermascope photos. Stratum corneum hydration on crow’s feet improved to 81.34% at 1 month and 56.12% at 2 months from pre-treatment baseline (P &lt; 0.0001). Global Aesthetic improvement scale of Skin hydration and fine wrinkle improved.

Conclusions
The combination injection method of MicroHA and MicroBotox is not associated with side effects and showed significant synergic effect in improvement of skin roughness and moisturizing. Neuramix-hydrotoxin injection method is an easy and reproducible procedure to make constant injection depth and amount.

Level of Evidence: 4
Deep learning meets metabolomics: a methodological perspective
Authors: Sen Partho , Lamichhane Santosh , Mathema Vivek B , McGlinchey Aidan , Dickens Alex M , Khoomrung Sakda , Orešič Matej 
Published: August 2020

AbstractDeep learning (DL), an emerging area of investigation in the fields of machine learning and artificial intelligence, has markedly advanced over the past years. DL techniques are being applied to assist medical professionals and researchers in improving clinical diagnosis, disease prediction and drug discovery. It is expected that DL will help to provide actionable knowledge from a variety of ‘big data’, including metabolomics data. In this review, we discuss the applicability of DL to metabolomics, while presenting and discussing several examples from recent research. We emphasize the use of DL in tackling bottlenecks in metabolomics data acquisition, processing, metabolite identification, as well as in metabolic phenotyping and biomarker discovery. Finally, we discuss how DL is used in genome-scale metabolic modelling and in interpretation of metabolomics data. The DL-based approaches discussed here may assist computational biologists with the integration, prediction and drawing of statistical inference about biological outcomes, based on metabolomics data.
Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses
Authors: Ciccolella Simone , Ricketts Camir , Soto Gomez Mauricio , Patterson Murray , Silverbush Dana , Bonizzoni Paola , Hajirasouliha Iman , Della Vedova Gianluca 
Published: August 2020

Abstract

Motivation
In recent years, the well-known Infinite Sites Assumption has been a fundamental feature of computational methods devised for reconstructing tumor phylogenies and inferring cancer progressions. However, recent studies leveraging single-cell sequencing (SCS) techniques have shown evidence of the widespread recurrence and, especially, loss of mutations in several tumor samples. While there exist established computational methods that infer phylogenies with mutation losses, there remain some advancements to be made.

Results
We present Simulated Annealing Single-Cell inference (SASC): a new and robust approach based on simulated annealing for the inference of cancer progression from SCS datasets. In particular, we introduce an extension of the model of evolution where mutations are only accumulated, by allowing also a limited amount of mutation loss in the evolutionary history of the tumor: the Dollo-k model. We demonstrate that SASC achieves high levels of accuracy when tested on both simulated and real datasets and in comparison with some other available methods.

Availability and implementation
The SASC tool is open source and available at https://github.com/sciccolella/sasc.

Supplementary information
Supplementary data are available at Bioinformatics online.
Highly Sensitive Quantification of Plasma Severe Acute Respiratory Syndrome Coronavirus 2 RNA Sheds Light on its Potential Clinical Value
Authors: Veyer David , Kernéis Solen , Poulet Geoffroy , Wack Maxime , Robillard Nicolas , Taly Valérie , L’Honneur Anne-Sophie , Rozenberg Flore , Laurent-Puig Pierre , Bélec Laurent , Hadjadj Jérôme , Terrier Benjamin , Péré Hélène 
Published: August 2020

Abstract

Background
Coronavirus disease 2019 (COVID-19) is a global public health problem that has already caused more than 662 000 deaths worldwide. Although the clinical manifestations of COVID-19 are dominated by respiratory symptoms, some patients present other severe damage such as cardiovascular, renal and liver injury, and/or multiple organ failure, suggesting a spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in blood. Recent ultrasensitive polymerase chain reaction (PCR) technology now allows absolute quantification of nucleic acids in plasma. We intend to use the droplet-based digital PCR technology to obtain sensitive detection and precise quantification of plasma SARS-CoV-2 viral load (SARS-CoV-2 RNAemia) in hospitalized COVID-19 patients.

Methods
Fifty-eight consecutive COVID-19 patients with pneumonia 8 to 12 days after onset of symptoms and 12 healthy controls were analyzed. Disease severity was categorized as mild to moderate in 17 patients, severe in 16, and critical in 26. Plasma SARS-CoV-2 RNAemia was quantified by droplet digital Crystal Digital PCR next-generation technology (Stilla Technologies, Villejuif, France).

Results
Overall, SARS-CoV-2 RNAemia was detected in 43 (74.1%) patients. Prevalence of positive SARS-CoV-2 RNAemia correlated with disease severity, ranging from 53% in mild-to-moderate patients to 88% in critically ill patients (P = .036). Levels of SARS-CoV-2 RNAemia were associated with severity (P = .035). Among 9 patients who experienced clinical deterioration during follow-up, 8 had positive SARS-CoV-2 RNAemia at baseline, whereas only 1 critical patient with undetectable SARS-CoV-2 RNAemia at the time of analysis died at day 27.

Conclusion
SARS-CoV-2 RNAemia measured by droplet-based digital PCR constitutes a promising prognosis biomarker in COVID-19 patients.
YQFC: a web tool to compare quantitative biological features between two yeast gene lists
Authors: Wu Wei-Sheng , Wang Lai-Ji , Yen Han-Chen , Tseng Yan-Yuan 
Published: August 2020

AbstractNowadays high-throughput omics technologies are routinely used in biological research. From the omics data, researchers can easily get two gene lists (e.g. stress-induced genes vs. stress-repressed genes) related to their biological question. The next step would be to apply enrichment analysis tools to identify distinct functional/regulatory features between these two gene lists for further investigation. Although various enrichment analysis tools are already available, two challenges remain to be addressed. First, most existing tools are designed to analyze only one gene list, so they cannot directly compare two gene lists. Second, almost all existing tools focus on identifying the enriched qualitative features (e.g. gene ontology [GO] terms, pathways, domains, etc.). Many quantitative features (e.g. number of mRNA isoforms of a gene, mRNA half-life, protein half-life, transcriptional plasticity, translational efficiency, etc.) are available in the yeast, but no existing tools provide analyses on these quantitative features. To address these two challenges, here we present Yeast Quantitative Features Comparator (YQFC) that can directly compare various quantitative features between two yeast gene lists. In YQFC, we comprehensively collected and processed 85 quantitative features from the yeast literature and yeast databases. For each quantitative feature, YQFC provides three statistical tests (t-test, U test and KS test) to test whether this quantitative feature is statistically different between the two input yeast gene lists. The distinct quantitative features identified by YQFC may help researchers to study the underlying molecular mechanisms that differentiate the two input yeast gene lists. We believe that YQFC is a useful tool to expedite the biological research that uses high-throughput omics technologies.Database URLhttp://cosbi2.ee.ncku.edu.tw/YQFC/
A randomized controlled trial comparing controlled reoxygenation and standard cardiopulmonary bypass in paediatric cardiac surgery
Authors: Caputo Massimo , Scott Lauren J , Deave Toity , Dabner Lucy , Parry Andrew , Angelini Gianni D , Sheehan Karen , Stoica Serban , Ellis Lucy , Harris Rosie , Rogers Chris A 
Published: August 2020

Abstract

OBJECTIVES
Controlled reoxygenation on starting cardiopulmonary bypass (CPB) rather than hyperoxic CPB may confer clinical advantages during surgery for congenital cyanotic heart disease.

METHODS
A single-centre, randomized controlled trial was carried out to compare the effectiveness of controlled reoxygenation (normoxia) versus hyperoxic CPB in children with congenital cyanotic heart disease undergoing open-heart surgery (Oxic-2). The co-primary clinical outcomes were duration of inotropic support, intubation time and postoperative intensive care unit (ICU) and hospital stay. Analysis of the primary outcomes included data from a previous trial (Oxic-1) conducted to the same protocol.

RESULTS
Ninety participants were recruited to Oxic-2 and 79 were recruited to the previous Oxic-1 trial. There were no significant differences between the groups for any of the co-primary outcomes: inotrope duration geometric mean ratio (normoxia/hyperoxic) 0.97, 95% confidence interval (CI) (0.69–1.37), P-value = 0.87; intubation time hazard ratio (HR) 1.03, 95% CI (0.74–1.42), P-value = 0.87; postoperative ICU stay HR 1.14 95% CI (0.77–1.67), P-value = 0.52, hospital stay HR 0.90, 95% CI (0.65–1.25), P-value = 0.53. Lower oxygen levels were successfully achieved during the operative period in the normoxic group. Serum creatinine levels were lower in the normoxic group at day 2, but not on days 1, 3–5. Childhood developmental outcomes were similar. In the year following surgery, 85 serious adverse events were reported (51 normoxic group and 34 hyperoxic group).

CONCLUSIONS
Controlled reoxygenation (normoxic) CPB is safe but with no evidence of a clinical advantage over hyperoxic CPB.

Clinical trial registration number
Current Controlled Trials—ISRCTN81773762.
Review of the direct and indirect effects of warming and drought on scale insect pests of forest systems
Authors: Frank Steven D 
Published: August 2020

AbstractHigher temperatures and drought are key aspects of global change with the potential to alter the distribution and severity of many arthropod pests in forest systems. Scale insects (Hemiptera: Coccoidea) infest many tree species and are among the most important pests of trees in urban and rural forests, plantations and other forest systems. Infestations of native or exotic scale insects can kill or sicken trees with economic and ecosystem-wide consequences. Warming can have direct effects on the life history, fitness and population dynamics of many scale insect species by increasing development rate, survival or fecundity. These direct benefits can increase the geographic distribution of scale insects and their consequences for tree health. Warming and drought can affect scale insects indirectly by altering the quality of their host trees. Additive or interactive effects of warming and drought can change tree quality in such a way that it increases scale insect fitness and population growth. However, the effects are species- and context-dependent with some scale insect species negatively affected by drought-induced changes in tree quality. Warming and drought are often coincident in urban forests and predicted to co-occur in many parts of the world under climate change scenarios. The individual and interactive effects of these factors require further research to inform predictions and management of scale insect pests. Warming also indirectly affects scale insects by altering interactions with natural enemies. This includes changes in natural enemy phenology, community composition and abundance. In addition, warming can alter scale insect phenology or voltinism causing asynchrony with natural enemies or population growth too rapid for natural enemies to suppress. Direct and indirect effects of warming and drought on scale insects can increase the potential for some exotic species to become established and for some native species to become invasive. Unfortunately, much research on scale insects is confined to a few particularly important native or exotic pests which limits our ability to predict the effects of warming on many current or potential pests. More research is required to understand how warming and drought affect scale insects, scale insect management and the forest systems they inhabit.
Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy
Authors: Aadland Kelsey , Kolaczkowski Bryan 
Published: August 2020

AbstractAncestral sequence reconstruction (ASR) uses an alignment of extant protein sequences, a phylogeny describing the history of the protein family and a model of the molecular-evolutionary process to infer the sequences of ancient proteins, allowing researchers to directly investigate the impact of sequence evolution on protein structure and function. Like all statistical inferences, ASR can be sensitive to violations of its underlying assumptions. Previous studies have shown that, whereas phylogenetic uncertainty has only a very weak impact on ASR accuracy, uncertainty in the protein sequence alignment can more strongly affect inferred ancestral sequences. Here, we show that errors in sequence alignment can produce errors in ASR across a range of realistic and simplified evolutionary scenarios. Importantly, sequence reconstruction errors can lead to errors in estimates of structural and functional properties of ancestral proteins, potentially undermining the reliability of analyses relying on ASR. We introduce an alignment-integrated ASR approach that combines information from many different sequence alignments. We show that integrating alignment uncertainty improves ASR accuracy and the accuracy of downstream structural and functional inferences, often performing as well as highly accurate structure-guided alignment. Given the growing evidence that sequence alignment errors can impact the reliability of ASR studies, we recommend that future studies incorporate approaches to mitigate the impact of alignment uncertainty. Probabilistic modeling of insertion and deletion events has the potential to radically improve ASR accuracy when the model reflects the true underlying evolutionary history, but further studies are required to thoroughly evaluate the reliability of these approaches under realistic conditions.
Genetic Mutations That Drive Evolutionary Rescue to Lethal Temperature in Escherichia coli
Authors: Batarseh Tiffany N , Hug Shaun M , Batarseh Sarah N , Gaut Brandon S 
Published: August 2020

Abstract
Evolutionary rescue occurs when adaptation restores population growth against a lethal stressor. Here, we studied evolutionary rescue by conducting experiments with Escherichia coli at the lethal temperature of 43.0 °C, to determine the adaptive mutations that drive rescue and to investigate their effects on fitness and gene expression. From hundreds of populations, we observed that ∼9% were rescued by genetic adaptations. We sequenced 26 populations and identified 29 distinct mutations. Of these populations, 21 had a mutation in the hslVU or rpoBC operon, suggesting that mutations in either operon could drive rescue. We isolated seven strains of E. coli carrying a putative rescue mutation in either the hslVU or rpoBC operon to investigate the mutations’ effects. The single rescue mutations increased E. coli’s relative fitness by an average of 24% at 42.2 °C, but they decreased fitness by 3% at 37.0 °C, illustrating that antagonistic pleiotropy likely affected the establishment of rescue in our system. Gene expression analysis revealed only 40 genes were upregulated across all seven mutations, and these were enriched for functions in translational and flagellar production. As with previous experiments with high temperature adaptation, the rescue mutations tended to restore gene expression toward the unstressed state, but they also caused a higher proportion of novel gene expression patterns. Overall, we find that rescue is infrequent, that it is facilitated by a limited number of mutational targets, and that rescue mutations may have qualitatively different effects than mutations that arise from evolution to nonlethal stressors.