bluuebunny/crossref_metadata_2025_split huggingface dataset:
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)
Authors: Orengo Christine , Velankar Sameer , Wodak Shoshana , Zoete Vincent , Bonvin Alexandre M.J.J. , Elofsson Arne , Feenstra K. Anton , Gerloff Dietland L. , Hamelryck Thomas , Hancock John M. , Helmer-Citterich Manuela , Hospital Adam , Orozco Modesto , Perrakis Anastassis , Rarey Matthias , Soares Claudio , Sussman Joel L. , Thornton Janet M. , Tuffery Pierre , Tusnady Gabor , Wierenga Rikkert , Salminen Tiina , Schneider Bohdan 
Published: April 2020

Structural bioinformatics provides the scientific methods and tools to analyse, archive, validate, and present the biomolecular structure data generated by the structural biology community. It also provides an important link with the genomics community, as structural bioinformaticians also use the extensive sequence data to predict protein structures and their functional sites. A very broad and active community of structural bioinformaticians exists across Europe, and 3D-Bioinfo will establish formal platforms to address their needs and better integrate their activities and initiatives. Our mission will be to strengthen the ties with the structural biology research communities in Europe covering life sciences, as well as chemistry and physics and to bridge the gap between these researchers in order to fully realize the potential of structural bioinformatics. Our Community will also undertake dedicated educational, training and outreach efforts to facilitate this, bringing new insights and thus facilitating the development of much needed innovative applications e.g. for human health, drug and protein design. Our combined efforts will be of critical importance to keep the European research efforts competitive in this respect. Here we highlight the major European contributions to the field of structural bioinformatics, the most pressing challenges remaining and how Europe-wide interactions, enabled by ELIXIR and its platforms, will help in addressing these challenges and in coordinating structural bioinformatics resources across Europe. In particular, we present recent activities and future plans to consolidate an ELIXIR 3D-Bioinfo Community in structural bioinformatics and propose means to develop better links across the community. These include building new consortia, organising workshops to establish data standards and seeking community agreement on benchmark data sets and strategies. We also highlight existing and planned collaborations with other ELIXIR Communities and other European infrastructures, such as the structural biology community supported by Instruct-ERIC, with whom we have synergies and overlapping common interests.
A white city turned pink: Tel Aviv as Israel's homonormative LGBTQ flagship
Authors: Stallone Sabrina 
Published: April 2020

Abstract
In recent years, the reputation of the so-called 'White City' Tel Aviv as one of the global gay capitals has been disseminated and upheld by mainstream media. This article builds upon existing analyses of Israel's supposed liberalness towards non-normative lifestyles and its strong links to the phenomenon of pinkwashing. The term has come to signify the glossing over of Israeli settler colonial occupation that specifically directs attention to Israel's progressive LGBTQ rights by juxtaposition with a narrative of queer oppression among Palestinian communities. Looking at a range of media representations, such as documentary Oriented and the mediatized phenomena of Tel Aviv Pride and LGBTQ-friendly Birthright Trips, I explore how these narratives ultimately contribute towards shaping Tel Aviv as an exclusionary urban space, inaccessible to those subjects who do not comply or fit with a securitized and corporatized new normal. By using a critical approach to the city's founding discourse, and the more recent Israeli state's ethno-nationalist investments towards branding Tel Aviv as a queer city, I argue that non-(homo)normative members of the LGBTQ community, and especially Palestinians, are silenced and pushed further away from what is constructed as the queer subject in the 'White City' space.
Dynamic construction of pan-genome subgraphs
Authors: Dede Kadir , Ohlebusch Enno 
Published: April 2020

AbstractMarcus et al. (Bioinformatics 2014) proposed to use a compressed de Bruijn graph as a description of a pan-genome, comprising the genomes of many individuals/strains of the same or closely related species. Subsequent work improved the construction of the compressed de Bruijn graph in terms of run-time and memory consumption. According to the Computational Pan-Genomics Consortium (Briefings in Bioinformatics 2016), a pan-genome data structure should support the following functionality: “All information within a data structure should be easily accessible for human eyes by visualization support on different scales.” However, a pan-genome graph can have thousands to millions of nodes and such an amount of information is certainly not easily accessible for human eyes. Thus, the possibility to construct pangenome subgraphs on demand would be quite valuable. In this article, we use the space-efficient representation of the compressed de Bruijn graph devised by Beller and Ohle-busch (Algorithms for Molecular Biology 2016) to construct pan-genome subgraphs on the fly. The user can specify a region in one of the genomes and the software tool will build a subgraph that contains the path corresponding to that region and all paths that are in the neighborhood of that path. The size of the neighborhood can be controlled by the user.
Recent advances on hybrid integration of 2D materials on integrated optics platforms
Authors: Ma Qijie , Ren Guanghui , Mitchell Arnan , Ou Jian Zhen 
Published: April 2020

Abstract
The burgeoning research into two-dimensional (2D) materials opens a door to novel photonic and optoelectronic devices utilizing their fascinating electronic and photonic properties in thin-layered architectures. The hybrid integration of 2D materials onto integrated optics platforms thus becomes a potential solution to tackle the bottlenecks of traditional optoelectronic devices. In this paper, we present the recent advances of hybrid integration of a wide range of 2D materials on integrated optics platforms for developing high-performance photodetectors, modulators, lasers, and nonlinear optics. Such hybrid integration enables fully functional on-chip devices to be readily accessible researchers and technology developers, becoming a potential candidate for next-generation photonics and optoelectronics industries.
Recent advances in graphene and black phosphorus nonlinear plasmonics
Authors: Zhou Renlong , Ullah Kaleem , Yang Sa , Lin Qiawu , Tang Liangpo , Liu Dan , Li Shuang , Zhao Yongming , Wang Fengqiu 
Published: April 2020

Abstract
Over the past decade, the plasmonics of graphene and black phosphorus (BP) were widely recognized as promising media for establishing linear and nonlinear light-matter interactions. Compared to the conventional metals, they support significant light-matter interaction of high efficiency and show undispersed optical properties. Furthermore, in contrast to the conventional metals, the plasmonic properties of graphene and BP structure can be tuned by electrical and chemical doping. In this review, a deep attention was paid toward the second- and third-order nonlinear plasmonic modes of graphene and BP. We present a theoretical framework for calculating the lifetime for surface plasmons modes of graphene and BP assisted by the coupled mode theory. The effect of the Fermi energy on the second-order and third-order nonlinear response is studied in detail. We survey the recent advances in nonlinear optics and the applications of graphene and BP-based tunable plasmonic devices such as light modulation devices, switches, biosensors, and other nonlinear photonic devices. Finally, we highlight a few representative current applications of graphene and BP to photonic and optoelectronic devices.
2D molybdenum carbide (Mo2C)/fluorine mica (FM) saturable absorber for passively mode-locked erbium-doped all-fiber laser
Authors: Liu Sicong , Wang Yonggang , Lv Ruidong , Wang Jiang , Wang Huizhong , Wang Yun , Duan Lina 
Published: April 2020

Abstract
As a new member of saturable absorber (SA), molybdenum carbide (Mo2C) has some excellent optical properties. Herein, we report a new type of Mo2C/fluorine mica (FM) SA device. Uniform and compact Mo2C films were deposited on the FM by magnetron sputtering method. In order to increase the laser damage threshold, an additional protective layer of silicon oxide was deposited on the Mo2C. The FM is a single-layer structure of 20 μm, and its high elasticity makes it not easy to fracture. The transmission rate of FM is as high as 90% at near infrared wavelength. FM has better heat dissipation and softening temperature than organic composite materials, so it can withstand higher laser power without being damaged. In this work, Mo2C/FM SA was cut into small pieces and inserted into erbium-doped fiber laser to achieve mode-locked operation. The pulse duration and average output power of the laser pulses were 313 fs and 64.74 mW, respectively. In addition, a 12th-order sub-picosecond harmonic mode-locking was generated. The maximum repetition rate was 321.6 MHz and the shortest pulse duration was 338 fs. The experimental results show that Mo2C/FM SA is a broadband nonlinear optical mode-locker with excellent performance.
Fine structures of valley-polarized excitonic states in monolayer transitional metal dichalcogenides
Authors: Li Zhipeng , Wang Tianmeng , Miao Shengnan , Lian Zhen , Shi Su-Fei 
Published: April 2020

Abstract
Monolayer transitional metal dichalcogenides (TMDCs), a new class of atomically thin semiconductor, respond to optical excitation strongly with robust excitons, which stem from the reduced screening in two dimensions. These excitons also possess a new quantum degree of freedom known as valley spin, which has inspired the field of valleytronics. The strongly enhanced Coulomb interaction allows the exciton to bind with other particles to form new excitonic states. However, despite the discovery of trions, most of the excitonic states in monolayer TMDCs remain elusive until recently, when new light was shed into the fascinating excitonic fine structures with drastically improved sample quality through boron nitride encapsulation. Here, we review the latest research progress on fine structures of excitonic states in monolayer TMDCs, with a focus on tungsten-based TMDCs and related alloy. Many of the new excitonic complexes inherit the valley degree of freedom, and the valley-polarized dark excitonic states are of particular interest because of their long lifetime and possible long valley coherence time. The capability of resolving the excitonic fine structures also enables the investigation of exciton–phonon interactions. The knowledge of the interlayer between excitons and other particles not only advances our understanding of many-body effects in the monolayer TMDCs but also provides guidance on future applications based on TMDCs.
Nonlinear optical microscopies (NOMs) and plasmon-enhanced NOMs for biology and 2D materials
Authors: Ma Jialin , Sun Mengtao 
Published: April 2020

Abstract
In this review, we focus on the summary of nonlinear optical microscopies (NOMs), which are stimulated Raman scattering (SRS), coherent anti-Stokes Raman scattering (CARS), second harmonic generation (SHG), and two-photon excited fluorescence (TPEF). The introduction is divided into two parts: the principle of SRS, CARS, TPEF, and SHG and their application to biology and two-dimensional materials. We also introduce the connections and differences between them. We also discuss the principle of plasmon-enhanced NOM and its application in the above two aspects. This paper not only summarizes the research progress in the frontier but also deepens the readers’ understanding of the physical principles of these NOMs.
Progressive Changes in Sleep and Its Relations to Amyloid-β Distribution and Learning in SingleAppKnock-In Mice
Authors: Maezono Sakura Eri B. , Kanuka Mika , Tatsuzawa Chika , Morita Miho , Kawano Taizo , Kashiwagi Mitsuaki , Nondhalee Pimpimon , Sakaguchi Masanori , Saito Takashi , Saido Takaomi C. , Hayashi Yu 
Published: April 2020

AbstractAlzheimer’s disease (AD) patients often suffer from sleep disturbances. Alterations in sleep, especially rapid eye movement sleep (REMS), can precede the onset of dementia. To accurately characterize the sleep impairments accompanying AD and their underlying mechanisms using animal models, it is crucial to use models in which brain areas are affected in a manner similar to that observed in the actual patients. Here, we focused onAppNL-G-Fmice, in which expression levels and patterns of mutated amyloid precursor protein (APP) follow the endogenous patterns. We characterized the sleep architecture of maleAppNL-G-Fhomozygous and heterozygous mice at two ages (six and 12 months). At six months, homozygous mice exhibited reduced REMS, which was further reduced at 12 months together with a slight reduction in non-REMS (NREMS). By contrast, heterozygous mice exhibited an overall normal sleep architecture. Homozygous mice also exhibited decreased electroencephalogram γ to δ power ratio during REMS from six months, resembling the electroencephalogram slowing phenomenon observed in preclinical or early stages of AD. In addition, homozygous mice showed learning and memory impairments in the trace fear conditioning (FC) at both ages, and task performance strongly correlated with REMS amount at 12 months. Finally, histologic analyses revealed that amyloid-β accumulation in the pontine tegmental area and ventral medulla followed a course similar to that of the REMS reduction. These findings support the notion that changes in REMS are an early marker of AD and provide a starting point to address the mechanism of sleep deficits in AD and the effects on cognition.
Um comparativo entre a utilização de redes neurais perceptron e redes neurais profundas na identificação de radionuclídeos em espectrometria gama
Authors: Gomes Lamas Otero André , Potiens Junior Ademar , Takehiro Marumo Júlio 
Published: April 2020

Apresentamos os resultados da comparação entre uma Rede Neural Profunda e uma Rede Neural Perceptron na classificação de espectros gama obtidos utilizando um detector de germânio hiper-puro. Utilizando dados de diversas fontes seladas (Am-241, Ba-133, Cd-109, Co-57, Co-60, Cs-137, Eu-152, Mn-54, Na-24, and Pb-210) foram gerados uma lista extensa de espectros para treino e validação contendo, respectivamente, 500 e 160 espectros, onde foram mesclados até três radionuclídeos em um único espectro. Depois de 250 épocas de treino foram validadas a acurácia de cada um dos modelos utilizando o conjunto de validação. O modelo de rede neural profunda obteve uma acurácia de classificação de 96,25% enquanto a rede neural perceptron obteve uma acurácia de 80,62%. Os resultados mostram um desempenho robusto e consistentemente melhor das redes neurais profundas, frente as redes neurais perceptron.
Prenatal cigarette smoke exposure slightly alters neurobehavioral development in neonatal rats: Implications for developmental origins of health and disease (DoHAD)
Authors: Mammel B. , Kvárik T. , Szabó Zs. , Gyarmati J. , Ertl T. , Farkas J. , Helyes Zs. , Atlasz T. , Reglődi D. , Kiss P. 
Published: April 2020

AbstractNumerous studies indicate that smoking during pregnancy exerts harmful effects on fetal brain development. The aim of this study was to determine the influence of maternal smoking during pregnancy on the early physical and neurobehavioral development of newborn rats. Wistar rats were subjected to whole-body smoke exposure for 2 × 40 min daily from the day of mating until day of delivery. For this treatment, a manual closed-chamber smoking system and 4 research cigarettes per occasion were used. After delivery the offspring were tested daily for somatic growth, maturation of facial characteristics and neurobehavioral development until three weeks of age. Motor coordination tests were performed at 3 and 4 weeks of age. We found that prenatal cigarette smoke exposure did not alter weight gain or motor coordination. Critical physical reflexes indicative of neurobehavioral development (eyelid reflex, ear unfolding) appeared significantly later in pups prenatally exposed to smoke as compared to the control group. Prenatal smoke exposure also resulted in a delayed appearance of reflexes indicating neural maturity, including hind limb grasping and forelimb placing reflexes. In conclusion, clinically relevant prenatal exposure to cigarette smoke results in slightly altered neurobehavioral development in rat pups. These findings suggest that chronic exposure of pregnant mothers to cigarette smoke (including passive smoking) results in persisting alterations in the developing brain, which may have long-lasting consequences supporting the concept of developmental origins of health and disease (DoHAD).
A T-acute lymphoblastic leukemia in children with CD 117 expression: a case report
Authors: Endrawati Komang Juwita , Mahartini Ni Nyoman , Herawati Sianny 
Published: April 2020

Background: Leukemia is a group of clonal disorders originating from single cells with genetic changes in the bone marrow or peripheral lymphoid tissue.Â Acute T-cell lymphoblastic leukemia is estimated to be 12-15% of ALL cases.Â Immunotyping examination is essential in establishing the diagnosis of T-ALL, CD 1a, CD 2, CD 3 (membranous and cytoplasm), CD 4, CD 5, CD 7, and CD 8 as T- cell antigen markers. CD 33, CD 117, CD 34 and CD 56Â are a myeloid-related antigen.Â The occurrence of co-expression of T cell markers with markers myeloid isÂ infrequent. This study aimed toÂ report cases of T-Â Acute Lymphoblastic LeukemiaÂ (ALL)Â in children with CD 117 expression.Case description:Â A-13 years boy had a fever and bruising on the skin one year ago.Â Physical examination found a blood pressures 150/70 mmHg , axillary temperature 37.8Â Â°Â C, right and left enlargement of the glands of the neck and inguinal, enlarged liver and petechiae in both lower extremities.Â Complete blood tests showed leukocytosis, anemia, and thrombocytopenia.Â Edge blood smear suggests the presence ofÂ cigarÂ cells, target cells and lymphoblasts > 50%.Â Bone marrowÂ aspiration smearÂ revealed lymphoblastÂ >30% and concludes an ALL (L2). Immunophenotyping examination found CD 3, CD 5, CD 117 positively supported T-ALL with co-expression of CD 117. During treatment, the patient experienced seizures due to spontaneous intracerebral bleeding that caused the patient to die.Conclusion:Â The case of a 13-year-old boy suffering from T-ALL (L2) with co-expression of CD 117 had a poor prognosis.
Increasing the quality of life of post-shackling patients through multilevel Health promotion of shackling prevention
Authors: Widodo Arif , Prabandari Yayi Suryo , Sudiyanto Aris , Rahmat Ibrahim 
Published: April 2020

Introduction:Â Shackling still poses a significant obstacle to rehabilitate patient with mental disorder and often resorted by family or community. Shackling could have a negative impact toward patientâ€™s mental health and often resorted due to lack of information. Therefore, this study aimed to evaluate the effect of multilevel health promotion to shackling prevention (MHPSP) toward the behavioral component of family/caregivers, neighbors, cadres, and health workers (stakeholders) and also evaluating its effect toward patientâ€™s quality of life. Method:Â This study uses a quasi exeperimental method with pre-test and post-test model with repetead measures design. The research subjects were 32 post-shackling patients lived in Sukoharjo Regency and 31 from Klaten Regency as well as. MHPSP was given to 32 caregivers and stakeholders who come from Sukoharjo Regency as a treatment group and psychoeducation only to 31 caregivers of control group from Klaten Regency. Quality of life measurments were carried out before treatment and four months after giving MHPSP.Result : The result showed that MHPSP significantly enhance the behavioral component of the family/caregivers as well as neighbors, cadres and health workers (p<0.05). Furthermore, patient quality of life was significantly improved in the treatment group (MHPSP) compared to the control. Conclusion: It can be concluded that MHPSP could significantly enhance the behavioral aspects of the families, neighbors, and health workers toward post-shackled PMD patients and significantly improved their quality of life. Therefore, MHPSP is needed to be implemented not only to the patient but also to the people that directly interact with them.
The characteristics of neurocognitive function in farmers exposed to chronic pesticides at Banjar Tengah Kelod, Kerambitan, Tabanan, Bali, Indonesia
Authors: Samatra Dewa Putu Gde Purwa , Putri Ni Luh Putu Dirasandhi Semedi 
Published: April 2020

Purpose: This study aims to evaluate the characteristics of neurocognitive function in farmers exposed to chronic pesticides.Material and Methods: This study uses a descriptive cross-sectional design with total sampling methods. The study was conducted from 1st January 2019 until 31st January 2019 located in Banjar Tengah Kelod, Kerambitan sub-district, Tabanan district, Bali, Indonesia.Results: A total of 60 samples, consisted of 36 samples (60%) were women and 24 samples (40%) were men were obtained. The median age of the study sample was 55 year-old. Most of the samples who experienced neurocognitive impairment used organophosphate pesticides (60%), followed by organochlorine (20%), carbamate (13.3%), and pyrethroid (6.7%). Organophosphate users experienced neurocognitive impairment in both memory domain (mean score of 1.5 what scoring was used?) and visuospatial executive functions (mean score of 1, what scoring system?). The mean memory function score in the organochlorine user group was the highest compared to other groups of pesticide users while the average score of visuospatial function was 1. The samples of the study using carbamate pesticides had the same average score in both domains of neurocognitive function. The mean score of memory function in pyrethroid user was 2.5 and the average score of executive visuospatial function was 1.Conclusion: Chronic exposure to the four types of pesticides provided a picture of neurocognitive function impairment, including memory, visuospatial and executive functions.Â This result did not show clinical significance. The addition of sample size and analytic method studies should be considered for further research.