bluuebunny/crossref_metadata_2025 huggingface dataset:
If You Eat It or Secrete It, They Will Grow: the Expanding List of Nutrients Utilized by Human Gut Bacteria
Authors: Glowacki Robert W. P. , Martens Eric C.
Published: November 2020

In order to persist, successful bacterial inhabitants of the human gut need to adapt to changing nutrient conditions, which are influenced by host diet and a variety of other factors. For members of the
Bacteroidetes
and several other phyla, this has resulted in the diversification of a variety of enzyme-based systems that equip them to sense and utilize carbohydrate-based nutrients from host, diet, and bacterial origins.
Agrobacterium tumefaciens Deploys a Versatile Antibacterial Strategy To Increase Its Competitiveness
Authors: Yu Manda , Wang Yi-Chieh , Huang Ching-Jou , Ma Lay-Sun , Lai Erh-Min
Published: November 2020

The T6SS encodes multiple effectors with diverse functions, but little is known about the biological significance of harboring such a repertoire of effectors. We reported that the T6SS antibacterial activity of the plant pathogen
Agrobacterium tumefaciens
can be enhanced under carbon starvation or when recipient cell wall peptidoglycan is disturbed.
Transposon Insertion Sequencing in a Clinical Isolate of Legionella pneumophila Identifies Essential Genes and Determinants of Natural Transformation
Authors: Hardy Léo , Juan Pierre-Alexandre , Coupat-Goutaland Bénédicte , Charpentier Xavier
Published: November 2020

Legionella pneumophila
is the etiologic agent of a severe form of nosocomial and community-acquired pneumonia in humans. The environmental life traits of
L. pneumophila
are essential to its ability to accidentally infect humans.
cDNA-Derived RNA Phage Assembly Reveals Critical Residues in the Maturation Protein of the Pseudomonas aeruginosa Leviphage PP7
Authors: Kim Eun Sook , Lee Jae-Yeol , Park Chanseop , Ahn Se-Jeong , Bae Hee-Won , Cho You-Hee
Published: November 2020

The biological significance of RNA phages has been largely ignored, ironically, because few studies have focused on RNA phages. As an initial attempt to properly represent RNA phages in the phageome, we previously created, by using reverse-transcribed cDNA, a reverse genetic system for the small RNA phage PP7, which infects the opportunistic human pathogen
Pseudomonas aeruginosa
.
N-Linked Glycosylation Plays an Important Role in Budding of Neuraminidase Protein and Virulence of Influenza Viruses
Authors: Bao Danqi , Xue Ruixue , Zhang Min , Lu Chenyang , Ma Tianxin , Ren Chaochao , Zhang Ting , Yang Jianmei , Teng Qiaoyang , Li Xuesong , Li Zejun , Liu Qinfang
Published: November 2020

NA is a highly glycosylated protein. Nevertheless, how the NLG affects the function of NA protein remains largely unclear.
Characterization of Localization and Export Signals of Bovine Torovirus Nucleocapsid Protein Responsible for Extensive Nuclear and Nucleolar Accumulation and Their Importance for Virus Growth
Authors: Ujike Makoto , Kawachi Yukako , Matsunaga Yui , Etho Yuka , Asanuma Hideki , Kamitani Wataru , Taguchi Fumihiro
Published: November 2020

ToVs are diarrhea-causing pathogens detected in many species, including humans. BToV has spread worldwide, leading to economic loss, and there is currently no treatment or vaccine available.
The Putative APSES Transcription Factor RgdA Governs Growth, Development, Toxigenesis, and Virulence in Aspergillus fumigatus
Authors: Jun Sang-Cheol , Choi Yong-Ho , Lee Min-Woo , Yu Jae-Hyuk , Shin Kwang-Soo
Published: November 2020

Immunocompromised patients are susceptible to infections with the opportunistic human-pathogenic fungus
Aspergillus fumigatus
. This fungus causes systemic infections such as invasive aspergillosis (IA), which is one of the most life-threatening fungal diseases. To control this serious disease, it is critical to identify new antifungal drug targets. In fungi, the transcriptional regulatory proteins of the APSES family play crucial roles in controlling various biological processes, including mating, asexual sporulation and dimorphic growth, and virulence traits. This study found that a putative APSES transcription factor, RgdA, regulates normal growth, asexual development, conidium germination, spore wall architecture and hydrophobicity, toxin production, and virulence in
A. fumigatus
. Better understanding the molecular mechanisms of RgdA in human-pathogenic fungi may reveal a novel antifungal target for future drug development.
Improving rates of appropriate skeletal survey use in a district general paediatric emergency department
Authors: Jacob Hannah , Hewitson Rebecca , Waterfield Lucy , Turkoglu Leyla , Laud Rose , Hann Gayle
Published: November 2020

Improving rates of appropriate skeletal survey use in a district general paediatric emergency department.
Changes in heart rate from 5 s to 5 min after birth in vaginally delivered term newborns with delayed cord clamping
Authors: Bjorland Peder Aleksander , Ersdal Hege Langli , Eilevstjønn Joar , Øymar Knut , Davis Peter G , Rettedal Siren Irene
Published: November 2020

Objective

To determine heart rate centiles during the first 5 min after birth in healthy term newborns delivered vaginally with delayed cord clamping.

Design

Single-centre prospective observational study.

Setting

Stavanger University Hospital, Norway, March–August 2019.

Patients

Term newborns delivered vaginally were eligible for inclusion. Newborns delivered by vacuum or forceps or who received any medical intervention were excluded.

Interventions

A novel dry electrode electrocardiography monitor (NeoBeat) was applied to the newborn’s chest immediately after birth. The newborns were placed on their mother’s chest or abdomen, dried and stimulated, and cord clamping was delayed for at least 1 min.

Main outcome measures

Heart rate was recorded at 1 s intervals, and the 3rd, 10th, 25th, 50th, 75th, 90th and 97th centiles were calculated from 5 s to 5 min after birth.

Results

898 newborns with a mean (SD) birth weight 3594 (478) g and gestational age 40 (1) weeks were included. The heart rate increased rapidly from median (IQR) 122 (98–146) to 168 (146–185) beats per minute (bpm) during the first 30 s after birth, peaking at 175 (157–189) bpm at 61 s after birth, and thereafter slowly decreasing. The third centile reached 100 bpm at 34 s, suggesting that heart rates <100 bpm during the first minutes after birth are uncommon in healthy newborns after delayed cord clamping.

Conclusion

This report presents normal heart rate centiles from 5 s to 5 min after birth in healthy term newborns delivered vaginally with delayed cord clamping.
Scotopic microperimetric sensitivity and inner choroid flow deficits as predictors of progression to nascent geographic atrophy
Authors: Corradetti Giulia , Tiosano Liran , Nassisi Marco , Alagorie Ahmed Roshdy , Corvi Federico , Nittala Muneeswar Gupta , Sadda SriniVas
Published: November 2020

Background/Aims

To assess the role of microperimetric retinal sensitivity (MPRS) and inner choroid flow deficits (IC FD) in predicting the development of incomplete retinal pigment epithelial and outer retinal atrophy (iRORA) in intermediate AMD (i-AMD).

Methods

Thirty eyes with i-AMD evaluated at the Doheny-UCLA Eye Centres were enrolled in this prospective IRB-approved study. Subjects underwent several diagnostic tests: (a) 6×6 mm swept-source optical coherence tomography angiography (SS-OCTA) with the IC slab used to quantify the FDs, (b) 20°×20° spectral-domain optical coherence tomography (SD-OCT) to monitor progression to iRORA and (c) scotopic MPRS within an area of 18° centred on the fovea. All subjects were followed-up for 24 months. The baseline IC FD and MPRS were correlated with the development of iRORA. At 24-month follow-up, the stage of AMD was re-assessed and the eyes were divided into two sub-groups based on the development of iRORA.

Results

Twenty-eight eyes completed the 2-year follow-up. At baseline, the mean MPRS was 13.40±4.66 dB and the mean IC FD was 27.55±8.67%. The morpho-functional regression showed a significant correlation between baseline MPRS and IC FD and the development of iRORA within 24 months (R
2
=0.744, p<0.05). A Kaplan–Meier survival curve was fit to determine the cumulative incidence of iRORA over the 24 months.

Conclusions

A lower MPRS and greater IC FD at baseline were predictors of progression to iRORA in eyes with i-AMD. These parameters may be useful biomarkers for risk stratification and prognostication.
Teprotumumab reduces extraocular muscle and orbital fat volume in thyroid eye disease
Authors: Jain Amy Patel , Gellada Norman , Ugradar Shoaib , Kumar Ada , Kahaly George , Douglas Raymond
Published: November 2020

Purpose

Thyroid eye disease (TED) is a progressive, debilitating and potentially vision-threatening autoimmune disease. Teprotumumab, a novel human monoclonal antibody, has been shown to reverse the clinical manifestations of TED. Patients receiving teprotumumab have been shown in two multicenter, randomized placebo-controlled trials to have decreased proptosis, diplopia and inflammation after 24 weeks of treatment. This study aims to analyse volumetric and inflammatory changes on orbital imaging prior to and after teprotumumab treatment from one of these trials.

Design

Retrospective review.

Subjects

Six patients enrolled in the phase III teprotumumab clinical trial (OPTIC, NCT03298867) with active TED who received 24 weeks of teprotumumab and had pre- and post-treatment orbital imaging (CT or MRI). Additionally, 12 non-TED patients (24 orbits) were analysed as a comparative control group.

Methods

3D volumetric calculations of the extraocular muscles (EOMs), orbital fat, and bony orbit were measured using previously validated image processing software. 3D volumetric results and changes in EOM inflammation were compared with clinical measurements of TED.

Results

Total EOM volume within each orbit was markedly reduced post-teprotumumab in all patients (n=six patients, 12/12 orbits, p<0.02). There was no statistical difference in post-treatment EOM volume when compared to non-TED controls. Total orbital fat volume was also reduced in 11 of 12 studied orbits (n=six patients, p=0.04). Overall EOM inflammation based on MRI signal intensity ratio was reduced in 8/8 orbits (n=four patients, p<0.01).

Conclusion

Orbital imaging demonstrated decreased EOM volumes and orbital fat tissue volumes after teprotumumab treatment.
Social media and vaccine hesitancy
Authors: Wilson Steven Lloyd , Wiysonge Charles
Published: November 2020

Background

Understanding the threat posed by anti-vaccination efforts on social media is critically important with the forth coming need for world wide COVID-19 vaccination programs. We globally evaluate the effect of social media and online foreign disinformation campaigns on vaccination rates and attitudes towards vaccine safety.

Methods

We use a large-n cross-country regression framework to evaluate the effect of social media on vaccine hesitancy globally. To do so, we operationalize social media usage in two dimensions: the use of it by the public to organize action (using Digital Society Project indicators), and the level of negatively oriented discourse about vaccines on social media (using a data set of all geocoded tweets in the world from 2018-2019). In addition, we measure the level of foreign-sourced coordinated disinformation operations on social media ineach country (using Digital Society Project indicators). The outcome of vaccine hesitancy is measured in two ways. First, we use polls of what proportion of the public per country feels vaccines are unsafe (using Wellcome Global Monitor indicators for 137 countries). Second, we use annual data of actual vaccination rates from the WHO for 166 countries.

Results

We found the use of social media to organise offline action to be highly predictive of the belief that vaccinations are unsafe, with such beliefs mounting as more organisation occurs on social media. In addition, the prevalence of foreign disinformation is highly statistically and substantively significant in predicting a drop in mean vaccination coverage over time. A 1-point shift upwards in the 5-point disinformation scale is associated with a 2-percentage point drop in mean vaccination coverage year over year. We also found support for the connection of foreign disinformation with negative social media activity about vaccination. The substantive effect of foreign disinformation is to increase the number of negative vaccine tweets by 15% for the median country.

Conclusion

There is a significant relationship between organisation on social media and public doubts of vaccine safety. In addition, there is a substantial relationship between foreign disinformation campaigns and declining vaccination coverage.
Simulation study to demonstrate biases created by diagnostic criteria of mental illnesses: major depressive episodes, dysthymia, and manic episodes
Authors: Chao Yi-Sheng , Lin Kuan-Fu , Wu Chao-Jung , Wu Hsing-Chien , Hsu Hui-Ting , Tsao Lien-Cheng , Cheng Yen-Po , Lai Yi-Chun , Chen Wei-Chih
Published: November 2020

Objectives

Composite diagnostic criteria alone are likely to create and introduce biases into diagnoses that subsequently have poor relationships with input symptoms. This study aims to understand the relationships between the diagnoses and the input symptoms, as well as the magnitudes of biases created by diagnostic criteria and introduced into the diagnoses of mental illnesses with large disease burdens (major depressive episodes, dysthymic disorder, and manic episodes).

Settings

General psychiatric care.

Participants

Without real-world data available to the public, 100 000 subjects were simulated and the input symptoms were assigned based on the assumed prevalence rates (0.05, 0.1, 0.3, 0.5 and 0.7) and correlations between symptoms (0, 0.1, 0.4, 0.7 and 0.9). The input symptoms were extracted from the diagnostic criteria. The diagnostic criteria were transformed into mathematical equations to demonstrate the sources of biases and convert the input symptoms into diagnoses.

Primary and secondary outcomes

The relationships between the input symptoms and diagnoses were interpreted using forward stepwise linear regressions. Biases due to data censoring or categorisation introduced into the intermediate variables, and the three diagnoses were measured.

Results

The prevalence rates of the diagnoses were lower than those of the input symptoms and proportional to the assumed prevalence rates and the correlations between the input symptoms. Certain input or bias variables consistently explained the diagnoses better than the others. Except for 0 correlations and 0.7 prevalence rates of the input symptoms for the diagnosis of dysthymic disorder, the input symptoms could not fully explain the diagnoses.

Conclusions

There are biases created due to composite diagnostic criteria and introduced into the diagnoses. The design of the diagnostic criteria determines the prevalence of the diagnoses and the relationships between the input symptoms, the diagnoses, and the biases. The importance of the input symptoms has been distorted largely by the diagnostic criteria.
Trends in the diagnosis of diseases of despair in the United States, 2009–2018: a retrospective cohort study
Authors: Brignone Emily , George Daniel R , Sinoway Lawrence , Katz Curren , Sauder Charity , Murray Andrea , Gladden Robert , Kraschnewski Jennifer L
Published: November 2020

Background and objective

Increasing mortality and decreasing life expectancy in the USA are largely attributable to accidental overdose, alcohol-related disease and suicide. These ‘deaths of despair’ often follow years of morbidity, yet little is known about trends in the clinical recognition of ‘diseases of despair’. The objective of this study is to characterise rates of clinically documented diseases of despair over the last decade and identify sociodemographic risk factors.

Design

Retrospective study using a healthcare claims database with 10 years of follow-up.

Setting

Participants resided nationwide but were concentrated in US states disproportionately affected by deaths of despair, including Pennsylvania, West Virginia and Delaware.

Participants

Cohort included 12 144 252 participants, with no restriction by age or gender.

Outcome measures

Diseases of despair were defined as diagnoses related to alcohol misuse, substance misuse and suicide ideation/behaviours. A lookback period was used to identify incident diagnoses. Annual and all-time incidence/prevalence estimates were computed, along with risk for current diagnosis and patterns of comorbidity.

Results

515 830 participants received a disease of despair diagnosis (58.5% male, median 36 years). From 2009 to 2018, the prevalence of alcohol-related, substance-related and suicide-related diagnoses respectively increased by 37%, 94%, and 170%. Ages 55–74 had the largest increase in alcohol/substance-related diagnoses (59% and 172%). Ages <18 had the largest increase in suicide-related diagnoses (287%). Overall, odds for current-year diagnosis were higher among men (adjusted OR (AOR) 1.49, 95% CI 1.47 to 1.51), and among those with Affordable Care Act or Medicare coverage relative to commercial coverage (AOR 1.30, 1.24 to 1.37; AOR 1.51, 1.46 to 1.55).

Conclusions

Increasing clinical rates of disease of despair diagnoses largely mirror broader societal trends in mortality. While the opioid crisis remains a top public health priority, parallel rises in alcohol-related diagnoses and suicidality must be concurrently addressed. Findings suggest opportunities for healthcare systems and providers to deploy targeted prevention to mitigate the progression of morbidities towards mortality.
Association between birth interval and wasting in children under 5 years of age in Ethiopia: a systematic review and meta-analysis protocol
Authors: Kassaw Mesfin Wudu , Abebe Ayele Mamo , Abate Biruk Beletew , Kassie Ayelign Mengesha , Açık Murat
Published: November 2020

Introduction

According to the UNICEF, WHO and World Bank joint estimation, 1 in every 13 children suffered from wasting globally. The highest burden of undernutrition recorded in Asia and Africa. Wasting remains a considerable public health problem in Ethiopia despite the introduction of exhaustive nutritional programmes. As reported in the literature, the prevalence of wasting in Ethiopia has remained high over the last four decades. In Ethiopia, more than one-third of child deaths are associated with malnutrition. The current nutritional interventions implemented in Ethiopia need to be evidence based. For this purpose, systematic review is preferable as it can present a more reliable and precise estimate than individual studies. The aim of this review is to assess the pooled prevalence of wasting and its association with birth interval in Ethiopia.

Methodology

Studies published after 20 January 2012 will be retrieved from databases, mainly PubMed/Medline, Scopus, Embase, CINAHL and HINARI. The articles retrieved from databases will be selected after reading the title, abstract and full text. Three reviewers will independently assess the quality of each study using both the Joanna Briggs Institute and Ottawa Scale critical appraisal checklists. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses checklist will be used to maintain scientific strength. Funnel plots, Egger’s test and Begg’s test will be used to deal with publication bias, and I2, forest plots and Cochrane’s Q square statistics will be used for heterogeneity. Potential causes of heterogeneity will be explored through sensitivity and subgroup analyses. Because heterogeneity among studies is inevitable, given the wide geographical area and variety of study designs, the Der-Simonian and Laird random-effects model will be used. The presence of a statistical association between birth interval and wasting will be declared if the p value is <0.05 with the 95% CI.

Ethics and dissemination

Ethical issues will not be applicable to this review and meta-analysis. This review and meta-analysis will report the pooled prevalence of wasting and its association with birth interval in Ethiopia. Effort will be made to publish the findings in a peer-reviewed journal such as the Ethiopian Journal of Health and Development, and the findings will be presented at national conferences. A hard copy will also be sent to Woldia University and Debre Berhan University.
Prediction of type 2 diabetes mellitus using fasting plasma glucose and HbA1c levels among individuals with impaired fasting plasma glucose: a cross-sectional study in Thailand
Authors: Sitasuwan Tullaya , Lertwattanarak Raweewan
Published: November 2020

Objectives

About 11%–30% of individuals with impaired fasting plasma glucose (IFG) have type 2 diabetes mellitus (T2DM), diagnosed by the 75 g oral glucose tolerance test (75 g OGTT). This study investigated (1) the prevalence and cut-off levels for fasting plasma glucose (FPG) and glycated haemoglobin A1c (HbA1c) in IFG individuals that most effectively predict the presence of T2DM diagnosed by a 75 g OGTT; (2) the predictors associated with T2DM; and (3) the pathophysiological characteristics of patients with IFG.

Materials and methods

A single-centre, cross-sectional study was conducted in a primary care setting. A standard 75 g OGTT was performed on 123 subjects with IFG. Their beta-cell function and insulin resistance were calculated through plasma glucose and insulin levels monitored during the 75 g OGTT.

Results

In the IFG subjects, the prevalence of T2DM using the 2-hour postload plasma glucose (2hPG) criterion was 28.5%. Pre-diabetes and normal glucose metabolism were found in 48.7% and 22.8%, respectively, by 75 g OGTT. An HbA1c level ≥6.0% or FPG ≥5.9 mmol/L were the optimal cut-off thresholds for the prediction of the presence of T2DM. HbA1c had a sensitivity of 76.7% and specificity of 55.7% (95% CI 57.7% to 90.1% and 95% CI 43.3% to 67.6%, respectively), while FPG had a sensitivity of 85.7% and specificity of 23.9% (95% CI 69.7% to 95.2% and 95% CI 15.4% to 34.1%, respectively). The presence of metabolic syndrome, a higher HbA1c and higher FPG levels were associated with the risk of T2DM in the Thai IFG population.

Conclusions

Almost one-third of the people with IFG had T2DM diagnosed by the 2hPG criterion. HbA1c was more effective than FPG in predicting the presence of T2DM in the IFG subjects. IFG individuals with HbA1c≥6.0% or FPG≥5.9 mmol/L should be advised to undergo a 75 g OGTT to detect T2DM earlier than otherwise.
Multicentre longitudinal study of fluid and neuroimaging BIOmarkers of AXonal injury after traumatic brain injury: the BIO-AX-TBI study protocol
Authors: Graham Neil Samuel Nyholm , Zimmerman Karl A , Bertolini Guido , Magnoni Sandra , Oddo Mauro , Zetterberg Henrik , Moro Federico , Novelli Deborah , Heslegrave Amanda , Chieregato Arturo , Fainardi Enrico , Fleming Joanne M , Garbero Elena , Abed-Maillard Samia , Gradisek Primoz , Bernini Adriano , Sharp David J
Published: November 2020

Introduction and aims

Traumatic brain injury (TBI) often results in persistent disability, due particularly to cognitive impairments. Outcomes remain difficult to predict but appear to relate to axonal injury. Several new approaches involving fluid and neuroimaging biomarkers show promise to sensitively quantify axonal injury. By assessing these longitudinally in a large cohort, we aim both to improve our understanding of the pathophysiology of TBI, and provide better tools to predict clinical outcome.

Methods and analysis

BIOmarkers of AXonal injury after TBI is a prospective longitudinal study of fluid and neuroimaging biomarkers of axonal injury after moderate-to-severe TBI, currently being conducted across multiple European centres. We will provide a detailed characterisation of axonal injury after TBI, using fluid (such as plasma/microdialysate neurofilament light) and neuroimaging biomarkers (including diffusion tensor MRI), which will then be related to detailed clinical, cognitive and functional outcome measures. We aim to recruit at least 250 patients, including 40 with cerebral microdialysis performed, with serial assessments performed twice in the first 10 days after injury, subacutely at 10 days to 6 weeks, at 6 and 12 months after injury.

Ethics and dissemination

The relevant ethical approvals have been granted by the following ethics committees: in London, by the Camberwell St Giles Research Ethics Committee; in Policlinico (Milan), by the Comitato Etico Milano Area 2; in Niguarda (Milan), by the Comitato Etico Milano Area 3; in Careggi (Florence), by the Comitato Etico Regionale per la Sperimentazione Clinica della Regione Toscana, Sezione area vasta centro; in Trento, by the Trento Comitato Etico per le Sperimentazioni Cliniche, Azienda Provinciale per i Servizi Sanitari della Provincia autonoma di Trento; in Lausanne, by the Commission cantonale d’éthique de la recherche sur l’être humain; in Ljubljana, by the National Medical Ethics Committee at the Ministry of Health of the Republic of Slovenia. The study findings will be disseminated to patients, healthcare professionals, academics and policy-makers including through presentation at conferences and peer-reviewed publications. Data will be shared with approved researchers to provide further insights for patient benefit.

Trial registration number

NCT03534154.
Cardiovascular genetics: the role of genetic testing in diagnosis and management of patients with hypertrophic cardiomyopathy
Authors: Ahluwalia Monica , Ho Carolyn Y
Published: November 2020

Genetic testing in hypertrophic cardiomyopathy (HCM) is a valuable tool to manage patients and their families. Genetic testing can help inform diagnosis and differentiate HCM from other disorders that also result in increased left ventricular wall thickness, thereby directly impacting treatment. Moreover, genetic testing can definitively identify at-risk relatives and focus family management. Pathogenic variants in sarcomere and sarcomere-related genes have been implicated in causing HCM, and targeted gene panel testing is recommended for patients once a clinical diagnosis has been established. If a pathogenic or likely pathogenic variant is identified in a patient with HCM, predictive genetic testing is recommended for their at-risk relatives to determine who is at risk and to guide longitudinal screening and risk stratification. However, there are important challenges and considerations to implementing genetic testing in clinical practice. Genetic testing results can have psychological and other implications for patients and their families, emphasising the importance of genetic counselling before and after genetic testing. Determining the clinical relevance of genetic testing results is also complex and requires expertise in understanding of human genetic variation and clinical manifestations of the disease. In this review, we discuss the genetics of HCM and how to integrate genetic testing in clinical practice.
Caffeine, exercise physiology, and time-trial performance: no effect ofADORA2AorCYP1A2genotypes
Authors: Glaister Mark , Chopra Kiran , Pereira De Sena Ana Luís , Sternbach Cassie , Morina Liridon , Mavrommatis Yiannis
Published: November 2020

The aim of this study was to investigate the influence of ADORA2A and CYP1A2 genotypes on the physiological and ergogenic effects of caffeine. Sixty-six male cyclists were screened for ADORA2A and CYP1A2 genotypes; with 40 taking part subsequently in a randomised, double-blind, placebo-controlled study. Trial 1 was used to establish the oxygen uptake−power output relationship and maximal oxygen uptake. In trials 2 and 3, participants ingested 5 mg·kg−1of caffeine or placebo 1 h before completing a submaximal incremental cycling test, followed by a time-trial (∼30 min). Relative to placebo, caffeine led to a significant reduction in time to complete the time-trial (caffeine: 29.7 ± 1.8 min; placebo: 30.8 ± 2.3 min); but there was no effect of genotype. During submaximal exercise, caffeine reduced mean heart rate by 2.9 ± 3.7 beats·min−1, with effects dissipating as exercise intensity increased. Caffeine also significantly reduced perceived exertion by 0.5 ± 0.8, and increased blood lactate by 0.29 ± 0.42 mmol·L−1, respiratory exchange ratio by 0.013 ± 0.032, and minute ventilation by 3.1 ± 6.8 L·min−1. Nonetheless, there were no supplement × genotype interactions. In conclusion, caffeine influences physiological responses to submaximal exercise and improves time-trial performance irrespective of ADORA2A or CYP1A2 genotypes.

Novelty: Caffeine affects physiological responses at rest and during submaximal exercise independent of ADORA2A or CYP1A2 genotypes. Variability in the effect of caffeine on time-trial performance is not explained by ADORA2A or CYP1A2 genotypes.
Amplified LncRNA PVT1 promotes lung cancer proliferation and metastasis by facilitating VEGFC expression
Authors: Pan Yanming , Liu Lantao , Cheng Yongxia , Yu Jianbo , Feng Yukuan
Published: November 2020

Although the abundance of long non-coding RNA (lncRNA) plasmacytoma variant translocation 1 (PVT1) in lung cancer has been well researched, the underlying mechanisms behind its effects were unknown. Here we investigated the molecular events regulating PVT1 in lung cancer. The pro-proliferative property of PVT1 was examined using a xenograft tumor model. Transwell chambers were used to analyze the impact of PVT1 expression on cell invasiveness and migration. In vivo metastasis was examined by tail-vein-injection in mice. Direct binding of miR-128 to PVT1 was investigated using a probe pulldown assay. The relative expression levels of miR-128 and PVT1 were quantified by real-time polymerase chain reaction and Western blotting. We show here that when PVT1 is amplified, there is a poor survival prognosis for patients with lung cancer. Elevated levels of PVT1 promoted lung cancer cell proliferation and metastasis, both in vitro and in vivo. Mechanistically, we found that PVT1 competes endogenously with miR-128 in the regulation of vascular endothelial growth factor C (VEGFC) expression, which is significantly associated with an unfavorable prognosis in lung cancer. We identified that copy number amplification significantly contributes to the high level of PVT1 transcripts in lung cancer, which promotes cell proliferation and metastatic behavior via modulating VEGFC expression by endogenous competition with miR-128.
DNA barcodes and new primers for nature’s pest controllers: the social wasps
Authors: Onah Ikechukwu Eugene , Sumner Seirian
Published: November 2020

Globally, biodiversity is declining because of anthropogenic pressures, and this could lead to extinction of some species before they are discovered. The loss of insect taxa is of prime concern, given recent reports of significant declines in the populations of many taxa across the globe. Efforts to document biodiversity have met with several challenges, amongst which are the difficulties in using morphological features to discriminate species, especially in insects. DNA barcoding is a rapid and reliable method for species identification and discovery but choosing appropriate primers to amplify the barcode region without co-amplifying contaminants remains a key challenge. We developed and tested a set of primers for PCR amplification of the DNA barcode region of the COI gene in polistine wasps. We tested their efficacy in 36 species of vespid wasps, and the solitary wasp Zethus miniatus Saussure. Samples were obtained from Africa, Americas, Asia, and Europe. The polistine-specific primers successfully amplified the barcode region for all polistines tested, without amplifying any Wolbachia present; they also worked with many species from the other Vespidae wasp subfamilies. The new primers are valuable for the discovery and accurate documentation of polistine wasps in the four continents.
Optical tweezers in single-molecule experiments
Authors: Zaltron Annamaria , Merano Michele , Mistura Giampaolo , Sada Cinzia , Seno Flavio
Published: November 2020

In the last decades, optical tweezers have progressively emerged as a unique tool to investigate the biophysical world, allowing to manipulate and control forces and movements of one molecule at a time with unprecedented resolution. In this review, we present the use of optical tweezers to perform single-molecule force spectroscopy investigations from an experimental perspective. After a comparison with other single-molecule force spectroscopy techniques, we illustrate at an introductory level the physical principles underlying optical trapping and the main experimental configurations employed nowadays in single-molecule experiments. We conclude with a brief summary of some remarkable results achieved with this approach in different biological systems, with the aim to highlight the great variety of experimental possibilities offered by optical tweezers to scientists interested in this research field.
An integrated biostratigraphic, seismic reservoir characterization and numerical stratigraphic forward modelling approach to imaging drowned carbonate platforms: a case study from eastern Indonesia
Authors: Gold David P. , Baillard Francois , Rathore Rajat , Zhang Zhengmin , Arbi Safrin
Published: November 2020

The New Guinea Limestone Group was deposited across much of New Guinea, including the Indonesian provinces of West Papua and Papua, as part of a widespread shallow-water carbonate platform during the Paleogene and Neogene. This platform was drowned beneath deeper-water strata from the Middle to Late Miocene. Review of biostratigraphic and seismic data from the Aru Basin, offshore New Guinea, reveals a drowning succession
c.
600 m thick deposited during a drowning event that lasted around 4 Ma. The objective of this study was to create a well-to-seismic tie from a single well in the study area using biostratigraphic, seismic and log data. The well-to-seismic tie was built to constrain a new velocity model to better image the drowned carbonate platform and understand the reservoir potential of the drowning succession in the zone of interest using two complimentary techniques: seismic reservoir characterization and numerical stratigraphic forward modelling. The well-to-seismic tie was achieved by matching significant biostratigraphic events, such as unconformities, with seismic horizons using stratigraphy-to-seismic. Modern stratigraphic and seismic reservoir characterization techniques, including stratigraphy-to-seismic, numerical forward modelling, velocity model building, rock physics and seismic inversion, were applied to predict rock properties such as lithology and porosity within the drowning succession.
NNBench-X
Authors: Xie Xinfeng , Hu Xing , Gu Peng , Li Shuangchen , Ji Yu , Xie Yuan
Published: November 2020

The tremendous impact of deep learning algorithms over a wide range of application domains has encouraged a surge of neural network (NN) accelerator research. Facilitating the NN accelerator design calls for guidance from an evolving benchmark suite that incorporates emerging NN models. Nevertheless, existing NN benchmarks are not suitable for guiding NN accelerator designs. These benchmarks are either selected for general-purpose processors without considering unique characteristics of NN accelerators or lack quantitative analysis to guarantee their completeness during the benchmark construction, update, and customization.

In light of the shortcomings of prior benchmarks, we propose a novel benchmarking methodology for NN accelerators with a quantitative analysis of application performance features and a comprehensive awareness of software-hardware co-design. Specifically, we decouple the benchmarking process into three stages: First, we characterize the NN workloads with quantitative metrics and select the representative applications for the benchmark suite to ensure diversity and completeness. Second, we refine the selected applications according to the customized model compression techniques provided by specific software-hardware co-design. Finally, we evaluate a variety of accelerator designs on the generated benchmark suite. To demonstrate the effectiveness of our benchmarking methodology, we conduct a case study of composing an NN benchmark from the TensorFlow Model Zoo and compress these selected models with various model compression techniques. Finally, we evaluate compressed models on various architectures, including GPU, Neurocube, DianNao, and Cambricon-X.
A Black-box Monitoring Approach to Measure Microservices Runtime Performance
Authors: Brondolin Rolando , Santambrogio Marco D.
Published: November 2020

Microservices changed cloud computing by moving the applications’ complexity from one monolithic executable to thousands of network interactions between small components. Given the increasing deployment sizes, the architectural exploitation challenges, and the impact on data-centers’ power consumption, we need to efficiently track this complexity. Within this article, we propose a black-box monitoring approach to track microservices at scale, focusing on architectural metrics, power consumption, application performance, and network performance. The proposed approach is transparent w.r.t. the monitored applications, generates less overhead w.r.t. black-box approaches available in the state-of-the-art, and provides fine-grain accurate metrics.
A RISC-V Simulator and Benchmark Suite for Designing and Evaluating Vector Architectures
Authors: Ramírez Cristóbal , Hernández César Alejandro , Palomar Oscar , Unsal Osman , Ramírez Marco Antonio , Cristal Adrián
Published: November 2020

Vector architectures lack tools for research. Consider the gem5 simulator, which is possibly the leading platform for computer-system architecture research. Unfortunately, gem5 does not have an available distribution that includes a flexible and customizable vector architecture model. In consequence, researchers have to develop their own simulation platform to test their ideas, which consume much research time. However, once the base simulator platform is developed, another question is the following: Which applications should be tested to perform the experiments? The lack of Vectorized Benchmark Suites is another limitation. To face these problems, this work presents a set of tools for designing and evaluating vector architectures. First, the gem5 simulator was extended to support the execution of RISC-V Vector instructions by adding a parameterizable Vector Architecture model for designers to evaluate different approaches according to the target they pursue. Second, a novel Vectorized Benchmark Suite is presented: a collection composed of seven data-parallel applications from different domains that can be classified according to the modules that are stressed in the vector architecture. Finally, a study of the Vectorized Benchmark Suite executing on the gem5-based Vector Architecture model is highlighted. This suite is the first in its category that covers the different possible usage scenarios that may occur within different vector architecture designs such as embedded systems, mainly focused on short vectors, or High-Performance-Computing (HPC), usually designed for large vectors.
MemSZ
Authors: Eldstål-Ahrens Albin , Sourdis Ioannis
Published: November 2020

This article describes Memory Squeeze (MemSZ), a new approach for lossy general-purpose memory compression. MemSZ introduces a low latency, parallel design of the Squeeze (SZ) algorithm offering aggressive compression ratios, up to 16:1 in our implementation. Our compressor is placed between the memory controller and the cache hierarchy of a processor to reduce the memory traffic of applications that tolerate approximations in parts of their data. Thereby, the available off-chip bandwidth is utilized more efficiently improving system performance and energy efficiency. Two alternative multi-core variants of the MemSZ system are described. The first variant has a shared last-level cache (LLC) on the processor-die, which is modified to store both compressed and uncompressed data. The second has a 3D-stacked DRAM cache with larger cache lines that match the granularity of the compressed memory blocks and stores only uncompressed data. For applications that tolerate aggressive approximation in large fractions of their data, MemSZ reduces baseline memory traffic by up to 81%, execution time by up to 62%, and energy costs by up to 25% introducing up to 1.8% error to the application output. Compared to the current state-of-the-art lossy memory compression design, MemSZ improves the execution time, energy, and memory traffic by up to 15%, 9%, and 64%, respectively.
Design and Evaluation of an Ultra Low-power Human-quality Speech Recognition System
Authors: Pinto Dennis , Arnau Jose-María , González Antonio
Published: November 2020

Automatic Speech Recognition (ASR) has experienced a dramatic evolution since pioneer development of Bell Lab’s single-digit recognizer more than 50 years ago. Current ASR systems have taken advantage of the tremendous improvements in AI during the past decade by incorporating Deep Neural Networks into the system and pushing their accuracy to levels comparable to that of humans. This article describes and characterizes a representative ASR system with state-of-the-art accuracy and proposes a hardware platform capable of decoding speech in real-time with a power dissipation close to 1 Watt. The software is based on the so-called hybrid approach with a vocabulary of 200K words and RNN-based language model re-scoring, whereas the hardware consists of a commercially available low-power processor along with two accelerators used for the most compute-intensive tasks. The article shows that high performance can be obtained with very low power, enabling the deployment of these systems in extremely power-constrained environments such as mobile and IoT devices.
Mechanisms for Robotic Grasping and Manipulation
Authors: Babin Vincent , Gosselin Clément
Published: November 2020

This article reviews the literature on the design of robotic mechanical grippers, with a focus on the mechanical aspects, which are believed to be the main bottleneck for effective designs. Our discussion includes gripper architectures and means of actuation, anthropomorphism and grasp planning, and robotic manipulation, emphasizing the complementary concepts of intrinsic and extrinsic dexterity. We also consider interactions of robotic grippers with the environment and with the objects to be grasped and argue that the proper handling of such interactions is key to the development of grasping and manipulation tools and scenarios. Finally, we briefly present examples of recent designs to support the discussion.
Drastic Improvement in Capacity-Retention and Polarization of Vanadium Redox Flow Battery with Hydrophilic Co3O4 Nanostructure Modified Activated Graphite Felt Electrodes
Authors: Mahanta Vivekananda , M. Raja , Khan Harun , R. Kothandaraman
Published: November 2020

Metal oxides supported on carbon materials are reported as catalysts for the positive and negative electrodes of vanadium redox flow battery (VRFB). In this study, thermally activated graphite felt (TGF) is decorated with Co3O4 nanostructure by a low-temperature hydrothermal method. The functional groups on the TGF are believed to nucleate the Co3O4 particles establishing a covalent bridging between them. The bridge improves the electron tunnelling across the electrolyte/electrolyte interface, reducing the overpotential of vanadium redox reactions. The covalent bridge, coupled with the enhanced surface area of the nanostructured-Co3O4 coated TGF (TGF/Co-100–12), are responsible for improved VO2
+/VO2+ and V3+/V2+ redox kinetics in VRFB. A 25 cm2 VRFB employing TGF/Co-100–12 electrodes, compared to TGF, enhances the specific capacity from ∼ 38 Ah l−1 to ∼ 45 Ah l−1 and energy efficiency (EE) from 81 to 87.6% at 100 mA cm−2 and its capacity retention (after 50 cycles) is ∼ 100% higher than that of TGF based VRFB. Besides, a two-cell stack is demonstrated with an EE of 84% and 89% of initial capacity even after 50 cycles, and 3% loss in EE vis-à-vis single cell is mainly due to the additional contact resistance arising out of coupling the cells.
Efficacy and Safety of Acupuncture at Tianshu (ST25) for Functional Constipation: Evidence from 10 Randomized Controlled Trials
Authors: Li Pengfan , Luo Yue , Wang Qi , Shu Shi , Chen Kanjun , Yu Donghai , Fan Chunxiang
Published: November 2020

Objective. To evaluate the evidence for the efficacy and safety of acupuncture at Tianshu (ST25) for functional constipation (FC). Methods. We systematically searched seven databases to identify randomized controlled trials of acupuncture at ST25 alone or in combination with conventional therapy in the treatment of FC. Risk ratios (RRs) and mean differences (MDs) were calculated using RevMan 5.3 with 95% confidence interval (CI). Results. The study included ten trials with 1568 participants. Meta‐analysis showed that the Cleveland Constipation Score (CCS) for deep needling was significantly lower than that for lactulose (deep needling with low‐frequency dilatational wave: MD −0.58, 95% CI −0.94 to −0.22; deep needling with sparse wave: MD −3.67, 95% CI −6.40 to −0.94; deep needling with high‐frequency dilatational wave: MD −3.42, 95% CI −5.03 to −1.81). Furthermore, CCS for shallow needling with high‐frequency dilatational wave was lower than that for lactulose (MD −1.77, 95% CI −3.40 to −0.14). In addition, when deep needling was combined with high‐frequency dilatational wave, the weekly frequency of spontaneous defecation (FSD) was significantly higher than that for lactulose (MD 1.57, 95% CI 0.93 to 2.21). Colonic Transit Time (CTT) scores were significantly higher when deep needling was combined with sparse wave (MD −14.36, 95% CI −18.31 to −10.41) or high‐frequency dilatational wave (MD −11.53, 95% CI −19.25 to −3.81). The time of first defecation after treatment (TFD) of the shallow needling therapy was significantly longer than that of the lactulose (MD 13.67, 95% CI 5.66 to 21.67). The CCS 6 months after treatment (CCS6m) for deep needling was significantly lower than that for lactulose (MD −4.90, 95% CI −5.97 to −3.84). Moreover, the FSD 6 months after treatment (FSD6m) for shallow needling was significantly higher than that for lactulose (MD 0.49, 95% CI 0.02 to 0.97). The adverse event (AE) rate for lactulose was significantly higher than that achieved with the needling treatments, and this held true for both deep needling therapy (RR 0.41, 95% CI 0.23 to 0.72) and shallow needling therapy (RR 0.33, 95% CI 0.15 to 0.77). Conclusions. The meta‐analysis demonstrates that acupuncture at ST25 appears to be more effective than lactulose in the treatment of functional constipation. This was found to be especially true for deep needling with high‐frequency dilatational wave, which had a greater impact on improving CCS, FSD, CTT, and CCS6m. Additionally, acupuncture at ST25 was shown to be safer than conventional treatment, with the rate of AE being significantly lower for both deep needling and shallow needling. The trial is registered with https://www.crd.york.ac.uk/prospero/(CRD42019141017)).