bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combined use of feature engineering and machine-learning to predict essential genes in Drosophila melanogaster
Authors: Campos Tulio L , Korhonen Pasi K , Hofmann Andreas , Gasser Robin B , Young Neil D 
Published: July 2020

AbstractCharacterizing genes that are critical for the survival of an organism (i.e. essential) is important to gain a deep understanding of the fundamental cellular and molecular mechanisms that sustain life. Functional genomic investigations of the vinegar fly, Drosophila melanogaster, have unravelled the functions of numerous genes of this model species, but results from phenomic experiments can sometimes be ambiguous. Moreover, the features underlying gene essentiality are poorly understood, posing challenges for computational prediction. Here, we harnessed comprehensive genomic-phenomic datasets publicly available for D. melanogaster and a machine-learning-based workflow to predict essential genes of this fly. We discovered strong predictors of such genes, paving the way for computational predictions of essentiality in less-studied arthropod pests and vectors of infectious diseases.
Untangling biological factors influencing trajectory inference from single cell data
Authors: Charrout Mohammed , Reinders Marcel J T , Mahfouz Ahmed 
Published: July 2020

Abstract
Advances in single-cell RNA sequencing over the past decade has shifted the discussion of cell identity toward the transcriptional state of the cell. While the incredible resolution provided by single-cell RNA sequencing has led to great advances in unraveling tissue heterogeneity and inferring cell differentiation dynamics, it raises the question of which sources of variation are important for determining cellular identity. Here we show that confounding biological sources of variation, most notably the cell cycle, can distort the inference of differentiation trajectories. We show that by factorizing single cell data into distinct sources of variation, we can select a relevant set of factors that constitute the core regulators for trajectory inference, while filtering out confounding sources of variation (e.g. cell cycle) which can perturb the inferred trajectory. Script are available publicly on https://github.com/mochar/cell_variation.
Proposed methodology for measuring the effectiveness of policies designed to further research
Authors: Bautista-Puig Núria , Moreno Lorente Luis , Sanz-Casado Elías 
Published: July 2020

Abstract
The effects of economic incentives on research have been widely debated in the literature. Some authors deem them to have no or even an adverse impact, particularly, if they are perceived as irrelevant to or an attempt to control researcher activity, whilst others believe they enhance research productivity by inducing new habits such as international collaboration or publication in high-impact journals. In 2007, the Carlos III University of Madrid introduced bonuses associated with research merits to reward research and educational excellence. The policy aims to enhance the quantity and quality of the institution’s scholarly publications. This study analyses whether and to what extent the new policy has had a potential effect on scientific output, impact, and visibility. Scientific activity indicators between 1991 and 2018 were analysed and a state-space model was used to establish possible scenarios (pre- and post-bonus periods) and 3 year predictions. Further to the findings, despite weak growth in researcher staff size, the number of papers rose during the period slightly more than in the pre-bonus simulation. The number of first-quartile papers also rose substantially, attesting to higher impact and visibility of the university’s research. Greater internationalization was also observed. The incentives were found to be highly suggestive of a change in university researchers’ publication habits.
MACHINE LEARNING ALGORITHMS FOR IDENTIFICATION OF ABNORMAL GLOW CURVES AND ASSOCIATED ABNORMALITY IN CaSO4:DY-BASED PERSONNEL MONITORING DOSIMETERS
Authors: Pathan Munir S , Pradhan S M , Selvam T Palani 
Published: July 2020

AbstractIn the present study, machine learning (ML) methods for the identification of abnormal glow curves (GC) of CaSO4:Dy-based thermoluminescence dosimeters in individual monitoring are presented. The classifier algorithms, random forest (RF), artificial neural network (ANN) and support vector machine (SVM) are employed for identifying not only the abnormal glow curve but also the type of abnormality. For the first time, the simplest and computationally efficient algorithm based on RF is presented for GC classifications. About 4000 GCs are used for the training and validation of ML algorithms. The performance of all algorithms is compared by using various parameters. Results show a fairly good accuracy of 99.05% for the classification of GCs by RF algorithm. Whereas 96.7% and 96.1% accuracy is achieved using ANN and SVM, respectively. The RF-based classifier is recommended for GC classification as well as in assisting the fault determination of the TLD reader system.
CAESIUM RETENTION CHARACTERISTICS OF KNIFC–PAN RESIN FROM RIVER WATER
Authors: Hegedűs Miklós , Tazoe Hirofumi , Yang Guosheng , Tamakuma Yuki , Hosoda Masahiro , Akata Naofumi , Tokonami Shinji 
Published: July 2020

Abstract
The caesium retention characteristics of a potassium-nickel hexacyanoferrate resin in a polyacrylnitrile (KNiFC–PAN) matrix were tested in fresh water over the range of 2.5–400 mL min−1. The experimental setup used 2 mL resin and 4-L aliquots of freshwater samples. The results showed nearly 100% retention at speeds below 10 mL min−1, above 80% up to 100 mL min−1, and approached 50% at 400 mL min−1. Using 100 mL min−1 flow rate and KNiFC–PAN resin in a well-type HPGe detector, the minimum detectable concentration was reduced to 3 mBq kg−1 for 4-L aliquots of water samples from the previous 15 mBq kg−1 achieved by Powdex ion-exchange resin and a planar type HPGe detector.
The decline in the wage share: falling bargaining power of labour or technological progress? Industry-level evidence from the OECD
Authors: Guschanski Alexander , Onaran Özlem 
Published: July 2020

Abstract
We investigate whether the downward trend in the wage share is driven by technological change or a decline in labour’s bargaining power. We present an econometric analysis using industry-level data for 14 Organisation for Economic Co-operation and Development (OECD) countries for the 1970–2014 period and test whether the determinants of the wage share differ between manufacturing and service industries, between workers of different skill groups and across countries with different bargaining regimes. Our findings suggest that the wage share declined due to a fall in labour’s bargaining power driven by offshoring to developing countries and changes in labour market institutions such as union density, social government expenditure and minimum wages. In contrast, the effect of technological change is not robust. While we find evidence for a negative effect on medium-skilled workers, our results cast doubt on the hypothesis of skill-biased technological change.
Apnea Testing Using Continuous Positive Airway Pressure When Determining Death by Neurologic Criteria in Children: Retrospective Analysis of Potential Adverse Events*
Authors: Puccetti Deirdre F. , Morrison Wynne , Francoeur Conall , Mai Mark , Kirschen Matthew P. 
Published: July 2020

Objectives:
To determine the prevalence of adverse events during apnea testing for determination of death by neurologic criteria using continuous positive airway pressure in children.

Design:
Single-center retrospective descriptive study.

Setting:
Academic children’s hospital.

Patients:
Children evaluated for death by neurologic criteria in the PICU from 2013 to 2018.

Interventions:
None.

Measurements and Main Results:
For each patient evaluated for death by neurologic criteria, we abstracted the number of apnea tests performed, vital signs and arterial blood gases during apnea testing, and outcome from the medical record. Adverse events were defined as oxygen-hemoglobin desaturation (arterial oxygen saturation < 85%), hypotension, or other significant event (e.g. arrhythmia, cardiac arrest) based on documentation in the medical record. We determined which adverse events resulted in early termination of the apnea test. We used oxygenation index, ventilator variables, and presence of vasopressors to determine preapnea test cardiopulmonary dysfunction. Seventy-two patients (age 7 yr [2.7–13.2 yr]; 48% male) underwent 121 apnea tests. Nine patients (12%) had 13 potential apnea tests deferred due to concern for cardiopulmonary instability as determined by the attending physician. Patients who underwent apnea testing had an oxygenation index of 3.5 (2.5–4.8) and were receiving vasopressors at the time of 108 apnea tests (89%). Hypotension was reported during seven apnea tests (6%) and resulted in the early termination of one apnea test (<1%). No other adverse events were reported. One hundred and twenty apnea tests (99%) were consistent with death by neurologic criteria.

Conclusions:
Apnea testing following a protocol that uses continuous positive airway pressure for apneic oxygenation has a low rate of adverse events in children meeting prerequisite criteria and determined by a pediatric intensivist to be physiologically appropriate for testing.
Association Between Elevated RBC Distribution Width and Multiple Organ Dysfunction in Pediatric Critical Illness
Authors: Matehuala Sonia , Pasala Sanjiv , Goudie Anthony , Fiser Richard , Weiss Scott , Irby Katherine , Crary Shelley , Wang Angela , Sanders Ronald 
Published: July 2020

Objectives:
RBC distribution width, a part of the complete blood count, has been shown in several published studies to be a strong biomarker of adverse outcomes. We sought to determine the association between admission RBC distribution width value and clinical outcomes including multiple organ dysfunction, mechanical ventilation days, PICU length of stay, and hospital length of stay in children admitted to the PICU.

Design:
Single center, retrospective study.

Setting:
A tertiary pediatric hospital in the United States.

Patients:
All subjects admitted to the PICU from 2016 to 2017. Exclusions: Greater than 21 years old, pregnancy, and history of packed RBC transfusion within 120 days prior to admission.

Interventions:
None.

Measurements and Main Results:
One-thousand five-hundred one subjects were screened and 856 were included in data analysis. RBC distribution width value was categorized into four separate groups: group I (RBC distribution width < 13.4%), group II (13.4–14.3%), group III (14.4–15.7%), and group IV (RBC distribution width > 15.7%). Increased RBC distribution width at admission was associated with multiple organ dysfunction syndrome in the first 7 days (group I = 11.8% vs group IV = 30.1%; p < 0.0001) (odds ratio, 3.22; 95% CI, 1.95–5.30; p < 0.0001). Increased RBC distribution width was associated with increased median mechanical ventilation duration (group IV = 7 d vs group I = 5 d; p = 0.001), median hospital length of stay (group IV = 13 d vs group I = 5 d; p < 0.0001), and median PICU length of stay (group IV = 4 d vs group I = 3 d; p = 0.01). Mortality was not statistically associated with admission RBC distribution width (p = 0.12).

Conclusions:
PICU admission RBC distribution width values greater than 15.7% obtained upon admission to the PICU in patients who have not received a RBC transfusion are associated with multiple organ dysfunction syndrome in the first 7 days of admission, increased duration of mechanical ventilation, and increased hospital length of stay.
Age-Specific Risk Scores Do Not Improve HIV-1 Prediction Among Women in South Africa
Authors: Peebles Kathryn , Palanee-Phillips Thesla , Balkus Jennifer E. , Beesham Ivana , Makkan Heeran , Deese Jennifer , Smit Jennifer , Heffron Renee , Morrison Charles S. , Philip Neena M. , Malahleha Mookho , Kasaro Margaret , Naidoo Yuthika , Nielson Tanya , Reddy Krishnaveni , Kotze Philip , Ahmed Khatija , Rees Helen , Baeten Jared M. , Barnabas Ruanne V. ,   for the Evidence for Contraceptive Options and HIV Outcomes (ECHO) Trial Consortium
Published: July 2020

Background:
HIV-1 risk scoring tools could help target provision of prevention modalities such as pre-exposure prophylaxis. Recent research suggests that risk scores for women aged 18–45 may not predict risk well among young women aged 18–24. We evaluated the predictive performance of age-specific risk scores compared with the existing non–age-specific VOICE risk score, developed for women aged 18–45.

Methods:
We conducted a secondary analysis of the Evidence for Contraceptive Options and HIV Outcomes Trial to develop and internally validate HIV-1 risk scores for women aged 18–24 and 25–35 in South Africa. Candidate predictors included baseline demographic, clinical, behavioral, and contextual characteristics readily available in clinical settings. The VOICE risk score was applied to women aged 18–35. We evaluated predictive performance of each risk score by area under the receiver operating characteristic curve (AUC).

Results:
Predictive performance of all risk scores was moderate, with AUC (95% confidence interval) of 0.64 (0.60 to 0.67) among women aged 18–24, 0.68 (0.62 to 0.73) among those aged 25–35, and 0.61 (0.58 to 0.65) for the VOICE risk score applied to women aged 18–35; The AUC was similar in internal validation. Among women aged 18–24, HIV-1 incidence was high even at low risk scores, at 3.9 per 100 person-years (95% confidence interval: 3.2 to 4.7).

Conclusions:
All risk scores were moderately predictive of HIV-1 acquisition, and age-specific risk scores performed only marginally better than the VOICE non–age-specific risk score. Approaches for targeted pre-exposure prophylaxis provision to women in South Africa may require more extensive data than are currently available to improve prediction.
Analogue gravity on a superconducting chip
Authors: Blencowe Miles P. , Wang Hui 
Published: July 2020

We describe how analogues of a Hawking evaporating black hole as well as the Unruh effect for an oscillatory, accelerating photodetector in vacuum may be realized using superconducting, microwave circuits that are fashioned out of Josephson tunnel junction and film bulk acoustic resonator elements.
This article is part of a discussion meeting issue ‘The next generation of analogue gravity experiments’.
Polariton fluids for analogue gravity physics
Authors: Jacquet M. J. , Boulier T. , Claude F. , Maître A. , Cancellieri E. , Adrados C. , Amo A. , Pigeon S. , Glorieux Q. , Bramati A. , Giacobino E. 
Published: July 2020

Analogue gravity enables the study of fields on curved space–times in the laboratory. There are numerous experimental platforms in which amplification at the event horizon or the ergoregion has been observed. Here, we demonstrate how optically generating a defect in a polariton microcavity enables the creation of one- and two-dimensional, transsonic fluid flows. We show that this highly tuneable method permits the creation of horizons. Furthermore, we present a rotating geometry akin to the water-wave bathtub vortex. These experiments usher in the possibility of observing stimulated as well as spontaneous amplification by the Hawking, Penrose and Zeld’ovich effects in fluids of light.
This article is part of a discussion meeting issue ‘The next generation of analogue gravity experiments’.
Estimate of the superradiance spectrum in dispersive media
Authors: Torres Theo 
Published: July 2020

In 2016, the Nottingham group detected the rotational superradiance effect. While this experiment demonstrated the robustness of the superradiance process, it still lacks a complete theoretical description due to the many effects at stage in the experiment. In this paper, we shine new light on this experiment by deriving an estimate of the reflection coefficient in the dispersive regime by means of a Wentzel–Kramers–Brillouin analysis. This estimate is used to evaluate the reflection coefficient spectrum of counter-rotating modes in the Nottingham experiment. Our finding suggests that the vortex flow in the superradiance experiment was not purely absorbing, contrary to the event horizon of a rotating black hole. While this result increases the gap between this experimental vortex flow and a rotating black hole, it is argued that it is in fact this gap that is the source of novel ideas.
This article is part of a discussion meeting issue ‘The next generation of analogue gravity experiments’.
Clinical and functional connectivity outcomes of 5-Hz repeated transcranial magnetic stimulation as an add-on treatment in cocaine use disorder: a double-blind randomized controlled trial
Authors: Garza-Villarreal Eduardo A. , Alcala-Lozano Ruth , Fernandez-Lozano Sofia , Morelos-Santana Erik , Dávalos Alan , Villicaña Viviana , Alcauter Sarael , Castellanos F. Xavier , Gonzalez-Olvera Jorge J. 
Published: July 2020

AbstractBACKGROUNDCocaine use disorder (CUD) is a global condition lacking effective treatment. Repeated magnetic transcranial stimulation (rTMS) may reduce craving and frequency of cocaine use, but little is known about its efficacy and neural effects.METHODSUsing a double-blind placebo-controlled randomized clinical trial (RCT) [NCT02986438], we sought to elucidate short- and long-term clinical benefits of 5-Hz rTMS as an add-on to standard treatment in CUD patients and discern underlying functional connectivity effects using magnetic resonance imaging. Forty-four randomly assigned CUD patients completed the 2-week double-blind acute phase [Sham (n=20, 2f/18m) and Active (n=24, 4f/20m)], in which they received 2 daily sessions of rTMS (5,000 pulses) on the left dorsolateral prefrontal cortex. Subsequently, n=20 CUD patients continued to open-label maintenance (2 weekly sessions for up to 6 months). Measures were acquired at baseline, 2 weeks, 3 months and 6 months.RESULTSOverall, 5-Hz rTMS plus standard treatment for 2 weeks significantly reduced craving and impulsivity in the Active group; decreased impulsivity correlated with improvements in functional connectivity in executive control and default mode networks. Clinical and functional connectivity effects were maintained for 3 months but they dissipated by 6 months. We did not observe reduction of positive cocaine urine tests, however, self-reported frequency and grams consumed for 6 months were reduced.CONCLUSIONSWith this RCT we show that 5-Hz rTMS has potential promise as an adjunctive treatment for CUD and merits further research.
Bibliometric analysis of COVID-19 literature
Authors: Al-Zaman Md. Sayeed 
Published: July 2020

AbstractThis study analyzesN=16384 COVID-19-related literature published between December 2019 to June 2020. The data were extracted from the Web of Science database using four keywords: “COVID-19”, “Coronavirus”, “2019-nCoV”, and “SARS-CoV-2”. The analysis found that almost all but a tiny number of the papers are published in 2020 (95.16%). Of the 15 types of publications,article(40.015%) is on the top of the list. All publications are in 19 different languages where English (95.313%) is the dominant one. A total of 159 countries produce COVID-19-related researches, and the USA (25.433%) is in the leading position. According to the findings, Wang Y (n=94) is the top author, and the British Medical Journal (BMJ) (n=488) is the top source. Also, the University of London (n=488) is the leading organization with the highest number of papers, and medicine-related papers (n=2259) are the highest in numbers. Apart from these novel findings, this study is perhaps the largest COVID-19-related bibliometric analysis to date.
Rheumatoid arthritis synovial fluid neutrophils drive inflammation through production of chemokines, reactive oxygen species and neutrophil extracellular traps
Authors: Wright Helen L , Lyon Max , Chapman Elinor A , Moots Robert J , Edwards Steven W 
Published: July 2020

ABSTRACTRheumatoid arthritis (RA) is a chronic inflammatory disorder affecting synovial joints. Neutrophils are believed to play an important role in both the initiation and progression of RA, and large numbers of activated neutrophils are found within both synovial fluid (SF) and synovial tissue from RA joints. In this study we analysed paired blood and SF neutrophils from patients with severe, active RA (DAS28> 5.1, n=3) using RNA-seq. 772 genes were significantly different between blood and SF neutrophils. IPA analysis predicted that SF neutrophils had increased expression of chemokines and ROS production, delayed apoptosis, and activation of signalling cascades regulating the production of NETs. This activated phenotype was confirmed experimentally by incubating healthy control neutrophils in cell-free RA SF, which was able to delay apoptosis and induce ROS production in both unprimed and TNFαprimed neutrophils (p< 0.05). RA SF significantly increased neutrophil migration through 3mM transwell chambers (p< 0.05) and also increased production of NETs by healthy control neutrophils, including exposure of myeloperoxidase (MPO) and citrullinated histone-H3-positive DNA NETs. IPA analysis predicted NET production was mediated by signalling networks including AKT, RAF1, SRC and NF-κB. Our results expand the understanding of the molecular changes that take place in the neutrophil transcriptome during migration into inflamed joints in RA, and the altered phenotype in RA SF neutrophils. Specifically, RA SF neutrophils lose their migratory properties, residing within the joint to generate signals that promote joint damage, as well as inflammation via recruitment and activation of both innate and adaptive immune cells. We propose that this activated SF neutrophil phenotype contributes to the chronic inflammation and progressive damage to cartilage and bone observed in patients with RA.
Distinct signatures of calcium activity in brain pericytes
Authors: Glück Chaim , Ferrari Kim David , Keller Annika , Saab Aiman S. , Stobart Jillian L. , Weber Bruno 
Published: July 2020

AbstractEven though pericytes have been implicated in various neurological disorders, little is known about their function and signaling pathways in the healthy brain. Here, we characterized cortical pericyte calcium dynamics using two-photon imaging ofPdgfrβ-CreERT2;GCaMP6s mice under anesthesiain vivoand in brain slicesex vivo. We found distinct differences between pericyte subtypesin vivo: Ensheathing pericytes exhibited smooth muscle cell-like calcium dynamics, while calcium signals in capillary pericytes were irregular, higher in frequency and occurred in cellular microdomains. In contrast to ensheathing pericytes, capillary pericytes retained their spontaneous calcium signals during prolonged anesthesia and in the absence of blood flowex vivo. Chemogenetic activation of neuronsin vivoand acute increase of extracellular potassium in brain slices strongly decreased calcium activity in capillary pericytes. We propose that neuronal activity-induced elevations in extracellular potassium suppress calcium activity in capillary pericytes, likely mediated by Kir2.2 and KATPchannel activation.