bluuebunny/crossref_metadata_2025 huggingface dataset:
Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome
Authors: Wolf Yuri I. , Silas Sukrit , Wang Yongjie , Wu Shuang , Bocek Michael , Kazlauskas Darius , Krupovic Mart , Fire Andrew , Dolja Valerian V. , Koonin Eugene V.
Published: July 2020

RNA viruses in aquatic environments remain poorly studied. Here, we analysed the RNA virome from approximately 10 l water from Yangshan Deep-Water Harbour near the Yangtze River estuary in China and identified more than 4,500 distinct RNA viruses, doubling the previously known set of viruses. Phylogenomic analysis identified several major lineages, roughly, at the taxonomic ranks of class, order and family. The 719-member-strong Yangshan virus assemblage is the sister clade to the expansive class Alsuviricetes and consists of viruses with simple genomes that typically encode only RNA-dependent RNA polymerase (RdRP), capping enzyme and capsid protein. Several clades within the Yangshan assemblage independently evolved domain permutation in the RdRP. Another previously unknown clade shares ancestry with Potyviridae, the largest known plant virus family. The ‘Aquatic picorna-like viruses/Marnaviridae’ clade was greatly expanded, with more than 800 added viruses. Several RdRP-linked protein domains not previously detected in any RNA viruses were identified, such as the small ubiquitin-like modifier (SUMO) domain, phospholipase A2 and PrsW-family protease domain. Multiple viruses utilize alternative genetic codes implying protist (especially ciliate) hosts. The results reveal a vast RNA virome that includes many previously unknown groups. However, phylogenetic analysis of the RdRPs supports the previously established five-branch structure of the RNA virus evolutionary tree, with no additional phyla.
A novel model concept for modelling the leaching of natural toxins: results for the case of ptaquiloside
Authors: García-Jorgensen D. B. , Hansen H. C. B. , Abrahamsen P. , Diamantopoulos E.
Published: July 2020

Illustration of the processes considered in the model affecting toxin fate at the pedon-scale ( = ptaquiloside).
Sub-monolayer Au9cluster formationviapulsed nozzle cluster deposition
Authors: Daughtry Jesse , Andersson Gunther G. , Metha Gregory F. , Tesana Siriluck , Nakayama Tomonobu
Published: July 2020

Submonolayer coverages of chemically synthesised triphenylphosphine-protected Au9clusters on mica and TiO2substrates were achieved through the development of a Pulsed Nozzle Cluster Deposition (PNCD) technique under high vacuum conditions.
Hollow N-doped carbon nanofibers provide superior potassium-storage performance
Authors: Pei Ya Ru , Zhao Ming , Zhou Hong Yu , Yang Chun Cheng , Jiang Qing
Published: July 2020

As an anode in potassium-ion batteries, the hollow N-doped carbon nanofibers fabricated from polyaniline exhibit ultra-high rate capability and ultra-long cycling life.
Assembly of chiral 3d–4f wheel-like cluster complexes with achiral ligands: single-molecule magnetic behavior and magnetocaloric effect
Authors: Liu Cai-Ming , Zhang De-Qing , Hao Xiang , Zhu Dao-Ben
Published: July 2020

With the help of perchlorate ions, chiral M3Ln3 wheel-like cluster complexes were constructed from achiral ligands, and showed single-molecule magnetic behavior and magnetocaloric effect.
Photochromism and photocatalysis of organic–inorganic hybrid iodoargentates modulated by argentophilic interactions
Authors: Hao Pengfei , Xu Yi , Li Xia , Shen Junju , Fu Yunlong
Published: July 2020

A series of organic–inorganic hybrid iodoargentates exhibit photochromic and photocatalytic properties, which could be effectively modulated by argentophilic interactions.
Cavity-based applications of metallo-supramolecular coordination cages (MSCCs)
Authors: Yadav Sarita , Kannan Palanisamy , Qiu Guanyinsheng
Published: July 2020

This review describes cavity-based applications of cage-like SCCs such as molecular recognition and separation, stabilization of reactive species by encapsulation, as drug delivery systems and as molecular flasks.
Synthesis and application of α-carbonyl nitrile oxides
Authors: Guo Xuanhua , Xu Guangqiang , Zhou Li , Yan Huating , Hao Xin-Qi , Wang Qinggang
Published: July 2020

A strategy has been developed to synthesize α-carbonylfuran and isoxazole using tert-butyl nitrite (TBN) as a nitrogen source.
Onion-derived activated carbons with enhanced surface area for improved hydrogen storage and electrochemical energy application
Authors: Musyoka Nicholas M. , Mutuma Bridget K. , Manyala Ncholu
Published: July 2020

Graphene-like activated carbons (ACs), with excellent properties for enhanced hydrogen storage and supercapacitor applications, were prepared from waste onion peels.
The role of Ce addition in catalytic activity enhancement of TiO2-supported Ni for CO2 methanation reaction
Authors: Makdee Ammarika , Chanapattharapol Kingkaew Chayakul , Kidkhunthod Pinit , Poo-arporn Yingyot , Ohno Teruhisa
Published: July 2020

Small amount of Ce addition promote CO2 and H2 adsorption which facilitate the surface reaction and enhancing the catalytic activity.
Two-stage one-pot synthesis of N-(dibutylaminomethyl)methacrylamide by Mannich reaction under mild conditions with high yield
Authors: Kazantsev Oleg A. , Arifullin Ildar R. , Savinova Maria V. , Sivokhin Alexey P. , Bol'shakova Yevgeniya A. , Shchegravina Ekaterina S.
Published: July 2020

N-(Dibutylaminomethyl)methacrylamide can be easily obtained via a two-stage one-pot Mannich reaction under mild conditions. By-products are practically absent and the monomer can be easily isolated from the reaction mixture with a 96% yield.
Gradient-aligned Au/graphene meshes with confined heat at multiple levels for solar evaporation and anti-gravity catalytic conversion
Authors: Meng Xiangyu , Yang Jianhui , Ramakrishna Seeram , Sun Yueming , Dai Yunqian
Published: July 2020

Plasmonic-antenna-integrated and gradient-aligned Au/graphene meshes are demonstrated with concentrated heat, towards an efficient evaporation (97.1%) and anti-gravity catalytic conversion.
Flexible freestanding all-MXene hybrid films with enhanced capacitive performance for powering a flex sensor
Authors: Li Zhemin , Dall'Agnese Yohan , Guo Jin , Huang Haifu , Liang Xianqing , Xu Shuaikai
Published: July 2020

Different few-layer MXene nanosheets are combined to fabricate freestanding all-MXene hybrid films with high gravimetric capacitance and excellent rate performance.
Candle flame-treatment as an effective strategy to enhance the photoelectrochemical properties of Ti-doped hematite thin films
Authors: Saeidi Marjan , Yourdkhani Amin , Seyed Ebrahimi Seyed Ali , Poursalehi Reza
Published: July 2020

Flame-treatment as a simple, low cost, and highly reliable strategy was applied to effectively enhance the photoelectrochemical (PEC) properties of liquid phase deposited Ti-doped hematite thin films.
Gas and dust from metal-rich AGB stars
Authors: Ventura P. , Dell’Agli F. , Lugaro M. , Romano D. , Tailo M. , Yagüe A.
Published: July 2020

Context. Stars evolving through the asymptotic giant branch (AGB) phase provide significant feedback to their host system, which is both gas enriched in nuclear-burning products, and dust formed in their winds, which they eject into the interstellar medium. Therefore, AGB stars are an essential ingredient for the chemical evolution of the Milky Way and other galaxies.

Aims. We study AGB models with super-solar metallicities to complete our vast database, so far extending from metal-poor to solar-chemical compositions. We provide chemical yields for masses in the range 1−8 M⊙ and metallicities Z = 0.03 and Z = 0.04. We also study dust production in this metallicity domain.

Methods. We calculated the evolutionary sequences from the pre-main sequence through the whole AGB phase. We followed the variation of the surface chemical composition to calculate the chemical yields of the various species and model dust formation in the winds to determine the dust production rate and the total dust mass produced by each star during the AGB phase.

Results. The physical and chemical evolution of the star is sensitive to the initial mass: M >  3 M⊙ stars experience hot bottom burning, whereas the surface chemistry of the lower mass counterparts is altered only by third dredge-up. The carbon-star phase is reached by 2.5−3.5 M⊙ stars of metallicity Z = 0.03, whereas all the Z = 0.04 stars (except the 2.5 M⊙) remain O-rich for the whole AGB phase. Most of the dust produced by metal-rich AGBs is in the form of silicate particles. The total mass of dust produced increases with the mass of the star, reaching ∼0.012 M⊙ for 8 M⊙ stars.
Piezoelectric β-polymorph formation of new textiles by surface modification with coating process based on interfacial interaction on the conformational variation of poly (vinylidene fluoride) (PVDF) chains
Authors: Chakhchaoui Nabil , Farhan Rida , Boutaldat Meriem , Rouway Marwane , Eddiai Adil , Meddad Mounir , Hajjaji Abdelowahed , Cherkaoui Omar , Boughaleb Yahia , Van Langenhove L.
Published: July 2020

Novel textiles have received a lot of attention from researchers in the last decade due to some of their unique features. The introduction of intelligent materials into textile structures offers an opportunity to develop multifunctional textiles, such as sensing, reacting, conducting electricity and performing energy conversion operations. In this research work nanocomposite-based highly piezoelectric and electroactive β-phase new textile has been developed using the pad-dry-cure method. The deposition of poly (vinylidene fluoride) (PVDF) − carbon nanofillers (CNF) − tetraethyl orthosilicate (TEOS), Si(OCH2CH3)4 was acquired on a treated textile substrate using coating technique followed by evaporation to transform the passive (non-functional) textile into a dynamic textile with an enhanced piezoelectric β-phase. The aim of the study is the investigation of the impact the coating of textile via piezoelectric nanocomposites based PVDF-CNF (by optimizing piezoelectric crystalline phase). The chemical composition of CT/PVDF-CNC-TEOS textile was detected by qualitative elemental analysis (SEM/EDX). The added of 0.5% of CNF during the process provides material textiles with a piezoelectric β-phase of up to 50% has been measured by FTIR experiments. These results indicated that CNF has high efficiency in transforming the phase α introduced in the unloaded PVDF, to the β-phase in the case of nanocomposites. Consequently, this fabricated new textile exhibits glorious piezoelectric β-phase even with relatively low coating content of PVDF-CNF-TEOS. The study demonstrates that the pad-dry-cure method can potentially be used for the development of piezoelectric nanocomposite-coated wearable new textiles for sensors and energy harvesting applications. We believe that our study may inspire the research area for future advanced applications.
Therapie und Prävention von Problemnarben
Authors: Zumhasch Rainer
Published: July 2020

Keloide, hypertrophe und schmerzhafte Narben können physische und psychische Problematiken mit sich bringen. Die Therapie mit Silikon und Kompression hat sich in der Prophylaxe dieser Komplikationen bewährt. Sie sind neben Desensibilisierung und Narbenmassage häufig durchgeführte Behandlungsmaßnahmen. Erfahren Sie, wie sich verschiedene Problemnarben voneinander unterscheiden und worauf Sie bei der Anwendung der einzelnen Behandlungsmaßnahmen achten sollten.
Clary Sage Essential Oil and Its Effect on Human Mood and Pulse Rate: An in vivo Pilot Study
Authors: Mitic Milena , Zrnić Adrijana , Wanner Jürgen , Stappen Iris
Published: July 2020

Clary sage (Salvia sclarea) is a xerophytic biennial plant typical for the Mediterranean region. It is cultivated for its essential oil, which is widely used in the flavor and fragrance industry as well as in aromatherapy for its relaxing and immunomodulatory effect. In this pilot investigation, clary sage essential oil was analyzed by GC-MS as well as GC-FID and examined regarding its effects on pulse, blood pressure and mood in healthy human female and male subjects. Analysis of the used CSEO identified linalylacetat (61.3%) and linalool (22.1%) as main compounds. Sclareol was found at 0.3%. In the first experiment with 30 participants (with 15 female), CSEO, diluted in peanut oil, was administered to the left forearm, leading to an increase in pulse rate in women (peanut oil served as control). In men, pulse rate deceased over time (p = 0.013). In the second experiment (32 participants; 16 females) the oil was inhaled for 30 min (pure water as control). The
observed decrease of pulse rate was significantly stronger in women than in men (p = 0.026). To evaluate the influence of the mode of application, a comparison of both experiments was performed showing a significant difference between sexes for the parameter of pulse rate (p = 0.034). Overall, the effects elicited by CSEO may depend on application method (inhaled/dermal) and sex (male/female).
Quality of Life in Children with Migraine: A Case–Control Study
Authors: Sadeghian Saeid , Momen Aliakbar , Jelodar Gholamreza , Nasiri Shahram , Khalafinia Azin , Azizimalamiri Reza
Published: July 2020

In this article, we conducted a case–control study to determine the effects of migraine on quality of life (QOL) in children. Participants, aged between 6 and 18 years, were assigned to migraine (n = 70) and control (n = 70) groups. We used a translated version of Pediatric Quality of Life Inventory 4.0 questionnaire. From the children's perspective, the overall QOL scores in all domains were lower in children with migraine. Children in the migraine group had significant lower scores in the social, emotional, and physical functioning (p-value < 0.05) than control group. Interestingly, a significant difference in the educational performance was not seen (p-value = 0.101). Relative to the parents' responses and children, the overall scores in all domains were lower in children with migraine. Statistically significant lower scores were found only in emotional and physical domains (p-value < 0.05). The results of this study indicated that migraine imposes a substantial negative impact on the different aspects of QOL in children.
The Association between Needle Size and Waste Product and Its Effect on Cost-Effectiveness of Botulinum Toxin Injections?
Authors: Golan Shani , Pena John , Moore Jeffrey , Tandalam Sangeetha , Lelli Gary
Published: July 2020

Clostridium botulinum toxin (BT) must be administered intramuscularly with a syringe, but dead space in the syringe–needle complex may cause product waste and result in cost implications for the patient and provider. Syringe dead space is the volume of residual fluid that remains within the syringe after the plunger is fully depressed during medication injection. We calculated the average volume of remaining product in a syringe–needle complex and cost loss implication of this volume of BT. This is a single-center, analytical study using saline and four different sized needles for analytics of waste product and cost-effectiveness. Syringes of 1 mL with attached 18, 21, 30, and 32-gauge (G) needles, respectively, were compared. The syringe–needle complex was weighed before drawing 0.05 mL of saline. The fluid was then discarded with the appropriate syringe and then weighed again. This procedure was repeated for the four needle types and the average difference in weight of the syringe–needle complex before and after saline waste was measured. The volume was converted to units of BT used in clinical practice and the cost of waste product evaluated. The mean difference in needle–syringe complex weight before and after intervention was 0.068, 0.056, 0.04, and 0.026 g for the 18, 21, 30, and 32G needles, respectively. We found a statistically significant difference comparing the 18G with the 30 and 32G (0.02 and 0.0007, respectively) and comparing the 21G with the 30 and 32G (0.0042 and 0.00002, respectively). When we extrapolated the data to BT units (4U/0.1 mL), we found that theoretically 2.72, 2.24, 1.6, and 1.04 units of BT are left in the syringe–needle complex for the 18, 21, 30, and 32G syringes, respectively. At a cost of $6.01/U of onabotulinum toxin A, we then calculated a provider loss of a gross average (mean) revenue of $96 and 62.4 per 10 syringes used with 30 and 32G needles. Needle size used for drawing up and administering BT has an effect on the amount of waste product and subsequently on cost-effectiveness.
Biallelic Mutation of SETX and Additional Likely “In Cis” SETX Sequence Change in Ataxia with Oculomotor Apraxia Type 2
Authors: Perry Michael D. , Evans Martin J. , Byrd Philip J. , Taylor Malcolm R.
Published: July 2020

Ataxia with oculomotor apraxia type 2 (AOA2) is a slowly progressive, autosomal recessive disease characterized by the triad of ataxia, oculomotor apraxia, and sensorimotor neuropathy. The genetic basis of AOA2 is biallelic mutation of the SETX gene, resulting in reduced or absent senataxin, a DNA/RNA repair protein essential for genomic stability.

In this case report, we described a case of AOA2 with two clear pathogenic SETX mutations, one of which is novel. We then discussed two further likely “in cis” SETX sequence changes (previously reported in the literature as pathogenic), and presented the case that they are likely benign polymorphisms.
Methylenetetrahydrofolate Reductase (MTHFR) C677T and A1298C Polymorphisms in Georgian Females with Hypothyroidism
Authors: Kvaratskhelia Tamar , Abzianidze Elene , Asatiani Ketevan , Kvintradze Merab , Surmava Sandro , Kvaratskhelia Eka
Published: July 2020

The aim of this study was to investigate the frequency of methylenetetrahydrofolate reductase (MTHFR) gene polymorphisms in Georgian females with hypothyroidism. Thirty-four patients and 29 healthy individuals were recruited in this study. Polymerase chain reaction-restriction fragment length polymorphism analyses were used for genotyping of MTHFR polymorphisms. The results of this study suggest that the MTHFR C677T variant was significantly associated with hypothyroidism. In addition, in individuals with T allele risk of hypothyroidism significantly increased. Combination of CT/AA genotypes was more prevalent in the hypothyroid patients than in the control group. Thus, C677T polymorphism could be a possible genetic factor contributing to the pathophysiology of hypothyroidism, possibly through hyperhomocysteinemia.
Comparison of Simultaneous Capillary Blood Gases and End-Tidal Carbon Dioxide in Mechanically Ventilated Pediatric Patients with Acute Respiratory Failure
Authors: Konca Capan , Tekin Mehmet , Uckardes Fatih , Benli Samet , Kucuk Ahmet
Published: July 2020

In the follow-up of ventilation, invasive blood gas analysis and noninvasive monitoring of end-tidal carbon dioxide (ETCO2) are used. We aimed to investigate the relationship between capillary partial pressure of carbon dioxide (PcCO2) levels and ETCO2 and also to investigate ETCO2's predictive feature of PcCO2 levels. This study included 28 female and 30 male pediatric patients; 28 patients were type-1 respiratory failure (RF), 16 patients were acute respiratory distress syndrome, and 14 patients were type-2 RF. Our results showed a significant correlation between ETCO2 and PcCO2. Although the strength of the correlation was weak throughout the measurements, the strength of this correlation increased significantly in type-2 RF.
Exploring the Role of Pediatric Neurology in Determinations of Futility, Identifying Vulnerability, and Participating in Shared Decision Making through Case-Based Analysis
Authors: Quezada Julio , Lantos John D.
Published: July 2020

It is not uncommon for pediatric neurologists to encounter ethical dilemmas in clinical practice. These dilemmas not only require an exploration of the basic bioethical principles, but also considering that neurological disease can have impact on a person's self-identity. Patients with neurological disease are particularly vulnerable and at risk of having long-term sequelae of their nervous system and their individual selves. These important considerations can then raise the question of futility of treatment in a setting of uncertainty of outcome. In these complex situations, a pediatric neurologist plays an important role in shared decision making with both families and multidisciplinary teams. In this paper, we explore case-based scenarios that serve to demonstrate the unique character of ethics in neurology and the role of pediatric neurologists in finding solutions that are in a patient's best interest, have a minimal chance of harm, respect a patient's autonomy, and are just and promote justice.
Boron cracks the case on damage-resistant glass
Authors: Bandari Anashe
Published: July 2020

Because glass cracking is very challenging to study experimentally, the mechanism by which boron improves a glass system’s resistance to cracks has been confounding researchers. Simulations help uncover the mystery.
Conformational state switching and pathways of chromosome dynamics in cell cycle
Authors: Chu Xiakun , Wang Jin
Published: July 2020

The cell cycle is a process and function of a cell with different phases essential for cell growth, proliferation, and replication. It depends on the structure and dynamics of the underlying DNA molecule, which underpins the genome function. A microscopic structural-level understanding of how a genome or its functional module chromosome performs the cell cycle in terms of large-scale conformational transformation between different phases, such as the interphase and the mitotic phase, is still challenging. Here, we develop a non-equilibrium, excitation-relaxation energy landscape-switching model to quantify the underlying chromosome conformational transitions through (de-)condensation for a complete microscopic understanding of the cell cycle. We show that the chromosome conformational transition mechanism from the interphase to the mitotic phase follows a two-stage scenario, in good agreement with the experiments. In contrast, the mitotic exit pathways show the existence of an over-expanded chromosome that recapitulates the chromosome in the experimentally identified intermediate state at the telophase. We find the conformational pathways are heterogeneous and irreversible as a result of the non-equilibrium dynamics of the cell cycle from both structural and kinetic perspectives. We suggest that the irreversibility is mainly due to the distinct participation of the ATP-dependent structural maintenance of chromosomal protein complexes during the cell cycle. Our findings provide crucial insights into the microscopic molecular structural and dynamical physical mechanism for the cell cycle beyond the previous more macroscopic descriptions. Our non-equilibrium landscape framework is general and applicable to study diverse non-equilibrium physical and biological processes such as active matter, differentiation/development, and cancer.
Interfacing topological insulators and ferrimagnets: Bi2Te3 and Fe3O4 heterostructures grown by molecular beam epitaxy
Authors: Pereira V. M. , Wu C. N. , Knight C.-A. , Choa A. , Tjeng L. H. , Altendorf S. G.
Published: July 2020

Relying on the magnetism induced by the proximity effect in heterostructures of topological insulators and magnetic insulators is one of the promising routes to achieve the quantum anomalous Hall effect. Here, we investigate heterostructures of Bi2Te3 and Fe3O4. By growing two different types of heterostructures by molecular beam epitaxy, Fe3O4 on Bi2Te3 and Bi2Te3 on Fe3O4, we explore differences in chemical stability, crystalline quality, electronic structure, and transport properties. We find the heterostructure Bi2Te3 on Fe3O4 to be a more viable approach, with transport signatures in agreement with a gap opening in the topological surface states.
Manipulation of cellular behaviour on surface-modified polyvinylidene difluoride using wet chemistry
Authors: Gabriel Matthias , Bollensdorff Christian , Raynaud Christophe Michel
Published: July 2020

The surface modification of polyvinylidene difluoride (PVDF) for various biomedical uses is notoriously hampered by the chemical inertness of the polymer. A wet chemical approach aiming at covalently grafting biomolecules was demonstrated by means of an elimination reaction of fluorine from the polymer backbone followed by subsequent modification steps. Exemplified as a possible biological application, the coupling of the peptide REDV rendered the material adhesive for endothelial cells while adhesion of thrombocytes was dramatically reduced.
Physicist leads arXiv as first executive director
Authors: Allen Michael
Published: July 2020

The arXiv preprint server has appointed its first executive director to run the repository’s operations. Eleonora Presani, who has a background in particle physics, says that one of her first tasks will be to make the preprint server more user friendly.
Former Royal Society president Robert May dies aged 84
Authors: Banks Michael
Published: July 2020

The Australian physicist Robert May, who served as president of the Royal Society and as chief scientific adviser to the UK government, died on 28 April aged 84.
US urged to develop domestic fusion power plant
Authors: Kruesi Liz
Published: July 2020

The US should construct its own fusion power plant as well as remain a partner in the ITER fusion experiment currently being built in France.
Review criticizes ISS management
Authors: Gwynne Peter
Published: July 2020

An independent review of the management of the International Space Station National Laboratory (ISSNL) has sharply criticized NASA and the non-profit Center for the Advancement of Science in Space (CASIS) that oversees the lab.
Phone apps could tackle sexual harassment in science, says report
Authors: Blaustein Richard
Published: July 2020

More needs to be done to make the perpetrators of sexual harassment in science accountable. That is according to a report by the American Geophysical Union (AGU)
Hubble’s Helix history
Authors: Soderblom David
Published: July 2020

In response to Keith Cooper’s blog series celebrating the 30th anniversary of the Hubble Space Telescope, in which he chose and explored its 10 best images.
The potential of far-UV for the next pandemic
Authors: Cartwright Jon
Published: July 2020

According to the physicist Charlie Ironside, our ability to deal with future deadly pandemics could be better – if we look to the far-ultraviolet. Jon Cartwright reports on a call to arms for the LED industry
Explorer versus salesman
Authors: Randall Ian
Published: July 2020

I need to start this review by saying that I loved the premise of this collection of essays by the physicist-turned-computer scientist Stephen Wolfram. The cover blurb of Adventures of a Computational Explorer teases "science consulting for a Hollywood movie, solving problems of AI ethics, hunting for the source of an unusual polyhedron, communicating with extraterrestrials" and even "finding the fundamental theory of physics and exploring the digits of pi".
Imaginative intersection
Authors: Brazil Rachel
Published: July 2020

The seemingly unconnected worlds of quantum physics and art have been linked from early in the 20th century. Part exhibition catalogue, part discourse on this relationship, Entangle: Physics and the Artistic Imagination, makes the case that imagination is critical for both practices, and both can learn from each other. The beautifully illustrated book is edited by Ariane Koek, the founder of the Arts at CERN programme and curator of the 2019 exhibition held at Bildsmuseet in Sweden.
Safe training: the linac simulator
Authors: Freeman Tami
Published: July 2020

Marco Carlone, founder of Linax Technologies, talks to Tami Freeman about his motivation for creating an online learning tool that teaches medical physicists how to use and understand linear accelerators
From the lab to the courtroom
Authors: Perkowitz Sidney
Published: July 2020

Not many physicists carry a gun to defend themselves against attackers provoked by their research, but that’s exactly what Wilmer Souder once felt the need to do.
Efficiency boost for quantum computer
Authors: Wogan Tim
Published: July 2020

Researchers in the US have created a new energy-based benchmark for “quantum advantage” and have used it to show that quantum computers use several orders of magnitude less energy than the world’s most powerful supercomputer when doing a specific task
How to transform graph states using single-qubit operations: computational complexity and algorithms
Authors: Dahlberg Axel , Helsen Jonas , Wehner Stephanie
Published: July 2020

Graph states are ubiquitous in quantum information with diverse applications ranging from quantum network protocols to measurement based quantum computing. Here we consider the question whether one graph (source) state can be transformed into another graph (target) state, using a specific set of quantum operations (LC + LPM + CC): single-qubit Clifford operations (LC), single-qubit Pauli measurements (LPM) and classical communication (CC) between sites holding the individual qubits. This question is of interest for effective routing or state preparation decisions in a quantum network or distributed quantum processor and also in the design of quantum repeater schemes and quantum error-correction codes. We first show that deciding whether a graph state |G⟩ can be transformed into another graph state |G′⟩ using LC + LPM + CC is

N
P

-complete, which was previously not known. We also show that the problem remains NP-complete even if |G′⟩ is restricted to be the GHZ-state. However, we also provide efficient algorithms for two situations of practical interest. Our results make use of the insight that deciding whether a graph state |G⟩ can be transformed to another graph state |G′⟩ is equivalent to a known decision problem in graph theory, namely the problem of deciding whether a graph G′ is a vertex-minor of a graph G. The computational complexity of the vertex-minor problem was prior to this paper an open question in graph theory. We prove that the vertex-minor problem is

N
P

-complete by relating it to a new decision problem on 4-regular graphs which we call the semi-ordered Eulerian tour problem.
Nitrogen-induced shift of photoluminescence from green to blue emission for xylose-derived carbon dots
Authors: Wang Shanshan , Yang Dong-Sheng , Yang Fuqian
Published: July 2020

The discovery of carbon dots opens a new avenue to the applications of nanomaterials in biosensing and bioimaging. In this work, we develop simple methods to prepare carbon nanoparticles from xylose and to tune the photoluminescence (PL) characteristics of the xylose-derived carbon nanoparticles via the combination of three different processes: hydrothermal carbonization (HTC), annealing at 850 °C and laser ablation (LA) in a NH4OH solution. The HTC-synthesized carbon dots (CDs) exhibit green emission under the 365 nm UV excitation, the annealing of the HTC-synthesized CDs leads to complete loss of the PL characteristics, and the LA processing of the annealed carbon nanoparticles recovers the PL characteristics with blue shift in comparison to the HTC-synthesized CDs under the same UV excitation. the PL characteristics of the HTC-CDs and the LA-CDs are dependent on the π-π* transition of C-containing surface-functional groups and π-π* and n-π* transitions of N-containing surface-functional groups, respectively, which are responsible for the difference in the PL characteristics between the HTC-synthesized CDs and the LA-processed CDs. The approaches demonstrated in this work provide a viable method to introduce and tune surface-functional groups on the surface of carbon nanoparticles.
Genome-wide discovery of pre-miRNAs: comparison of recent approaches based on machine learning
Authors: Bugnon Leandro A , Yones Cristian , Milone Diego H , Stegmayer Georgina
Published: July 2020

Motivation

The genome-wide discovery of microRNAs (miRNAs) involves identifying sequences having the highest chance of being a novel miRNA precursor (pre-miRNA), within all the possible sequences in a complete genome. The known pre-miRNAs are usually just a few in comparison to the millions of candidates that have to be analyzed. This is of particular interest in non-model species and recently sequenced genomes, where the challenge is to find potential pre-miRNAs only from the sequenced genome. The task is unfeasible without the help of computational methods, such as deep learning. However, it is still very difficult to find an accurate predictor, with a low false positive rate in this genome-wide context. Although there are many available tools, these have not been tested in realistic conditions, with sequences from whole genomes and the high class imbalance inherent to such data.

Results

In this work, we review six recent methods for tackling this problem with machine learning. We compare the models in five genome-wide datasets: Arabidopsis thaliana, Caenorhabditis elegans, Anopheles gambiae, Drosophila melanogaster, Homo sapiens. The models have been designed for the pre-miRNAs prediction task, where there is a class of interest that is significantly underrepresented (the known pre-miRNAs) with respect to a very large number of unlabeled samples. It was found that for the smaller genomes and smaller imbalances, all methods perform in a similar way. However, for larger datasets such as the H. sapiens genome, it was found that deep learning approaches using raw information from the sequences reached the best scores, achieving low numbers of false positives.

Availability

The source code to reproduce these results is in: http://sourceforge.net/projects/sourcesinc/files/gwmirna Additionally, the datasets are freely available in: https://sourceforge.net/projects/sourcesinc/files/mirdata
AEMDA: inferring miRNA–disease associations based on deep autoencoder
Authors: Ji Cunmei , Gao Zhen , Ma Xu , Wu Qingwen , Ni Jiancheng , Zheng Chunhou
Published: July 2020

Motivation

MicroRNAs (miRNAs) are a class of non-coding RNAs that play critical roles in various biological processes. Many studies have shown that miRNAs are closely related to the occurrence, development and diagnosis of human diseases. Traditional biological experiments are costly and time consuming. As a result, effective computational models have become increasingly popular for predicting associations between miRNAs and diseases, which could effectively boost human disease diagnosis and prevention.

Results

We propose a novel computational framework, called AEMDA, to identify associations between miRNAs and diseases. AEMDA applies a learning-based method to extract dense and high-dimensional representations of diseases and miRNAs from integrated disease semantic similarity, miRNA functional similarity and heterogeneous related interaction data. In addition, AEMDA adopts a deep autoencoder that does not need negative samples to retrieve the underlying associations between miRNAs and diseases. Furthermore, the reconstruction error is used as a measurement to predict disease-associated miRNAs. Our experimental results indicate that AEMDA can effectively predict disease-related miRNAs and outperforms state-of-the-art methods.

Availability and implementation

The source code and data are available at https://github.com/CunmeiJi/AEMDA.

Supplementary information

Supplementary data are available at Bioinformatics online.
Scalable machine learning-assisted model exploration and inference using Sciope
Authors: Singh Prashant , Wrede Fredrik , Hellander Andreas
Published: July 2020

Discrete stochastic models of gene regulatory networks are fundamental tools for in silico study of stochastic gene regulatory networks. Likelihood-free inference and model exploration are critical applications to study a system using such models. However, the massive computational cost of complex, high-dimensional and stochastic modelling currently limits systematic investigation to relatively simple systems. Recently, machine-learning-assisted methods have shown great promise to handle larger, more complex models. To support both ease-of-use of this new class of methods, as well as their further development, we have developed the scalable inference, optimization and parameter exploration (Sciope) toolbox. Sciope is designed to support new algorithms for machine-learning-assisted model exploration and likelihood-free inference. Moreover, it is built ground up to easily leverage distributed and heterogeneous computational resources for convenient parallelism across platforms from workstations to clouds.

Availability and implementation

The Sciope Python3 toolbox is freely available on https://github.com/Sciope/Sciope, and has been tested on Linux, Windows and macOS platforms.

Supplementary information

Supplementary information is available at Bioinformatics online.
Percutaneous closure of iatrogenic anterior mitral leaflet perforation: a case report
Authors: Naeim Hesham Abdo , Amoudi Osama , Mahmood Abeer , Abuelatta Reda
Published: July 2020

Background

Severe mitral regurgitation (MR) through the body of the anterior mitral leaflet (AML) is rare. The cause either iatrogenic during open-heart surgery or due to infective endocarditis. We present a case where a successful percutaneous closure of the AML perforation was an alternative to surgery.

Case summary

A 60-year-old male presented with shortness of breath (SOB) class III of 12 months duration. He underwent coronary artery bypass surgery with four grafts plus mitral valve (MV) repair 20 months ago. Transthoracic echocardiogram (TTE) and transoesophageal echocardiogram (TOE) revealed severe MR through the body of AML at A3. The percutaneous closure plan was to cross the AML perforation from the left ventricular side. The venacontracta of the perforation was 6 mm, an amplatzer septal occluder device 6 mm considered appropriate for closure of this hole. A snare catheter snared the wire and exteriorized creating arteriovenous loop. Amplatzer septal occluder 6 mm loaded to the delivery system till larger disc (left-sided) opened safely and freely below the MV apparatus. Once the left ventricular side disc opposed the ventricular surface of AML, the waist and left atrial disc gently released. The patient discharged in the next day. After 6 months, the patient had no more SOB, he returned to his daily activity. Follow-up TTE showed no MR, the closure device was stable in place.

Discussion

We added a successful case of transcatheter AML perforation to the literature. The role of TOE is crucial in diagnosis and procedure guidance.
Empire and information: the French Ministry of the Navy and Madagascar (1767–1819)
Authors: Tricoire Damien
Published: July 2020

This article discusses the question of how the history of administrative knowledge about distant world regions should be written. It analyses which intelligence was processed about Madagascar in the eighteenth century, and links the analysis of knowledge production about a specific world region with the colonial policy toward this region. A study of the texts written about Madagascar gives us insight into the ways the Ministry of the Navy ‘learned’ about the Indian Ocean colonies it took over from the Compagnie des Indes after the Seven Years War. This essay departs from the recent critique to the ‘colonial machine’ thesis, according to which the Ministry of the Navy could hardly take into consideration the great amount of information produced by officials in overseas. It contends that the commis of the Ministry did indeed read the letters from colonial officials, summarised their content for the minister, and proposed policies based on these information. However, while the propositions and claims of overseas officials clearly counted, this does not necessarily mean that the information received from overseas enabled the Minister of the Navy and their commis to design policies adapted to the reality on the spot. The case of writings about Madagascar shows why colonial policies might be built on wrong assumptions even when intelligence from overseas was taken into consideration. The article enhances particularly six factors that impacted information production: the degree of centralisation of the empire, the number of informers, patronage relationships, aristocratic sociabilities, the use of memoranda, and the Enlightenment.
Applying the proportionality principle to COVID-19 antibody testing
Authors: Gunnarsdóttir H D , Sinha M S , Gerke S , Minssen T
Published: July 2020

As the COVID-19 pandemic continues to ravage the globe, many nations have started to relax stringent restrictions in an effort to restart the economy. While Member States of the European Union have approached reopening without the use of antibody testing for COVID-19, such testing may be central to a long-term, sustainable strategy for international travel, employment, and the allocation and monitoring of vaccines. As the use of antibody testing to dictate the enjoyment of individual freedom remains highly controversial, we describe its use in the context of three case studies (return to the workplace, travel and vaccination), applying the substantive legal balancing entailed in the proportionality principle. Differential treatment of individuals based on COVID-19 antibody test results can be justified through the proportionality principle, which offers a sound dividing line between a reasonable and legitimate response and an unjust and discriminatory response.
Recurrent Spontaneous Pneumothorax in a 47-Year-Old Woman
Authors: Guenther Timothy M , Gustafson Joshua D , Pribyl Shea M , Wozniak Curtis J
Published: July 2020

Pneumothorax is a condition where air exists in the chest cavity, outside the lung. The causes of pneumothorax are numerous and determining the etiology can aid in treatment and prevent recurrence. We describe a 47-year-old female patient with past medical history of endometriosis who presented to the emergency room with recurrent right sided pneumothorax, its onset correlating with onset of menses. She underwent video assisted thorascopic surgery for a suspected catamenial pneumothorax whereby nodular “chocolate” appearing areas were noted on the middle lobe and multiple similar appearing lesions and fenestrations were noted on the diaphragm. A biologic mesh was affixed to the diaphragm after which mechanical and chemical pleurodesis were performed. She tolerated the procedure well and has been symptom free since. Herein, we review the pathophysiology, diagnosis, and treatment strategies for catamenial pneumothorax in the hopes of increasing awareness and understanding of this rare cause of spontaneous pneumothorax.
The effects of high-oleic peanuts as an alternative feed ingredient on broiler performance, ileal digestibility, apparent metabolizable energy, and histology of the intestine1
Authors: Toomer Ondulla T , Sanders Elliot , Vu Thien C , Malheiros Ramon D , Redhead Adam K , Livingston Matthew L , Livingston Kim A , Carvalho Luiz Victor , Ferket Peter R
Published: July 2020

Locally grown feed ingredients of high energy and protein content, such as peanuts, maybe economically feasible alternatives to corn and soybean meal in broiler diets. Even though normal-oleic peanuts have been demonstrated to be a viable feed ingredient for poultry, few studies to date have examined the use of high-oleic peanuts (HO PN) as an alternative feed ingredient for broiler chickens. Thus, we aimed to determine the effect of feeding HO PN on broiler performance, nutrient digestibility, and intestinal morphology. Three isocaloric, isonitrogenous experimental diets were formulated with 1) dietary inclusion of ~10% coarse-ground whole HO PN; 2) a corn-soybean meal control diet with 5.5% added poultry fat; and 3) a control diet supplemented with 5.5% oleic fatty acid oil. Three-hundred Ross 708 broilers were randomly placed in 10 replicate pens per treatment with 10 chicks per pen and raised until 42 d. Body weights (BW) and feed intake were determined weekly, and feed conversion ratio (FCR) was calculated. Jejunum samples were collected at 42 d for histomorphometric analysis. Analysis of variance was performed on all variables using a general linear mixed model in JMP Pro14. Broilers in the HO PN group had lower (P < 0.05) BW and higher FCR than other treatment groups at weeks 2 and 6. There were no significant differences in the jejunum villi surface area between the treatment groups. However, broilers fed the HO PN diet had greater (P = 0.019) apparent metabolizable energy relative to the other treatment groups, suggesting improved nutrient uptake of dietary fats and/or carbohydrates in the HO PN treatment group. However, additional studies are warranted to further define the nutritional value of HO PN as an alternative poultry feed ingredient.
Dependence of Radiation-induced Signals on Geometry of Tooth Enamel Using a 1.15 GHz Electron Paramagnetic Resonance Spectrometer: Improvement of Dosimetric Accuracy
Authors: Park Jong In , Choi Kwon , Koo Chang Uk , Oh Jeonghun , Hirata Hiroshi , Swartz Harold M. , Ye Sung-Joon
Published: July 2020

We aim to improve the accuracy of electron paramagnetic resonance (EPR)-based in vivo tooth dosimetry using the relationship between tooth geometry and radiation-induced signals (RIS). A homebuilt EPR spectrometer at L-band frequency of 1.15 GHz originally designed for non-invasive and in vivo measurements of intact teeth was used to measure the RIS of extracted human teeth. Twenty human central incisors were scanned by microCT and irradiated by 220 kVp x-rays. The RISs of the samples were measured by the EPR spectrometer as well as simulated by using the finite element analysis of the electromagnetic field. A linear relationship between simulated RISs and tooth geometric dimensions, such as enamel area, enamel volume, and labial enamel volume, was confirmed. The dose sensitivity was quantified as a slope of the calibration curve (i.e., RIS vs. dose) for each tooth sample. The linear regression of these dose sensitivities was established for each of three tooth geometric dimensions. Based on these findings, a method for the geometry correction was developed by use of expected dose sensitivity of a certain tooth for one of the tooth geometric dimensions. Using upper incisors, the mean absolute deviation (MAD) without correction was 1.48 Gy from an estimated dose of 10 Gy; however, the MAD corrected by enamel area, volume, and labial volume was reduced to 1.04 Gy, 0.77 Gy, and 0.83 Gy, respectively. In general, the method corrected by enamel volume showed the best accuracy in this study. This homebuilt EPR spectrometer for the purpose of non-invasive and in vivo tooth dosimetry was successfully tested for achieving measurements in situ. We demonstrated that the developed correction method could reduce dosimetric uncertainties resulting from the variations in tooth geometric dimensions.
Design and Implementation of Matryoshka-type Neutron Spectrometer
Authors: Lv Ning , Lv Jinxu , Sun Mingyan , Lv Wenhui , Xiao Qizhan
Published: July 2020

Aiming at portability and mobility, the design and implementation of a portable neutron spectrometer, namely the Matryoshka-type Neutron Spectrometer, was completed while considering the idea of a Bonner Sphere Spectrometer. The Matryoshka-type Neutron Spectrometer used a spherical 3He proportional counter as a thermal neutron detector. A number of cylindrical acrylic cups with diameters from 4 cm to 40 cm were made as containers for water as a moderator. The Monte Carlo method was adopted in order to obtain the energy response matrix of the Matryoshka-type Neutron Spectrometer. During the measurement, each acrylic cup contained water as a moderator, and the 3He proportional counter was set to the geometric center to perform neutron counting. With the energy response matrix obtained above, the neutron spectrum was resolved by a classical inversion algorithm. After the measurement, water was drained and the acrylic cups were placed one inside the other, like a Matryoshka doll. The design of a Matryoshka-type Neutron Spectrometer has reduced the mass and volume of the Bonner Sphere Spectrometer and was not difficult to carry around. Comparison tests acquiring background and Am-Be source neutron spectra between the Matryoshka-type Neutron Spectrometer and Bonner Sphere Spectrometer proved the effectiveness of the Matryoshka-type Neutron Spectrometer.