bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative assessment of seismic design provisions for buildings with torsional irregularities
Authors: DeBock D Jared , Valley Michael , Hohener Conrad (Sandy)
Published: December 2020

ASCE/SEI 7 design requirements for seismic-induced torsion in buildings are evaluated to determine their effectiveness for resisting seismic-induced collapse of torsionally irregular buildings. The ASCE/SEI 7-16 provisions are found to be generally conservative for most torsionally irregular building configurations—exceptions are some buildings that rely heavily on lines of lateral resistance orthogonal to the design earthquake force to resist torsional moments, and also some torsionally flexible buildings designed using modal response spectrum analysis. Modifications to provide better consistency in collapse resistance over a large range of building configurations and degrees of torsional irregularity are recommended. The study also demonstrates that buildings classified as extremely torsionally irregular may not need to be prohibited from Seismic Design Categories E and F, as long as the lateral system is proportioned properly.
MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data
Authors: Leung Chi-Ming , Li Dinghua , Xin Yan , Law Wai-Chun , Zhang Yifan , Ting Hing-Fung , Luo Ruibang , Lam Tak-Wah
Published: December 2020

Background

Next-generation sequencing (NGS) enables unbiased detection of pathogens by mapping the sequencing reads of a patient sample to the known reference sequence of bacteria and viruses. However, for a new pathogen without a reference sequence of a close relative, or with a high load of mutations compared to its predecessors, read mapping fails due to a low similarity between the pathogen and reference sequence, which in turn leads to insensitive and inaccurate pathogen detection outcomes.

Results

We developed MegaPath, which runs fast and provides high sensitivity in detecting new pathogens. In MegaPath, we have implemented and tested a combination of polishing techniques to remove non-informative human reads and spurious alignments. MegaPath applies a global optimization to the read alignments and reassigns the reads incorrectly aligned to multiple species to a unique species. The reassignment not only significantly increased the number of reads aligned to distant pathogens, but also significantly reduced incorrect alignments. MegaPath implements an enhanced maximum-exact-match prefix seeding strategy and a SIMD-accelerated Smith-Waterman algorithm to run fast.

Conclusions

In our benchmarks, MegaPath demonstrated superior sensitivity by detecting eight times more reads from a low-similarity pathogen than other tools. Meanwhile, MegaPath ran much faster than the other state-of-the-art alignment-based pathogen detection tools (and compariable with the less sensitivity profile-based pathogen detection tools). The running time of MegaPath is about 20 min on a typical 1 Gb dataset.
Retraction Note: The specific MYB binding sites bound by TaMYB in the GAPCp2/3 promoters are involved in the drought stress response in wheat
Authors: Zhang Lin , Song Zhiqiang , Li Fangfang , Li Xixi , Ji Haikun , Yang Shushen
Published: December 2020

This article has been retracted. Please see the retraction notice for more detail: https://doi.org/10.1186/s12870-020-02782-w.
Comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats
Authors: Palacios-Gimenez Octavio M. , Koelman Julia , Palmada-Flores Marc , Bradford Tessa M. , Jones Karl K. , Cooper Steven J. B. , Kawakami Takeshi , Suh Alexander
Published: December 2020

Background

Repetitive DNA sequences, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), collectively called the “repeatome”, are found in high proportion in organisms across the Tree of Life. Grasshoppers have large genomes, averaging 9 Gb, that contain a high proportion of repetitive DNA, which has hampered progress in assembling reference genomes. Here we combined linked-read genomics with transcriptomics to assemble, characterize, and compare the structure of repetitive DNA sequences in four chromosomal races of the morabine grasshopperVandiemenella viaticaspecies complex and determine their contribution to genome evolution.

Results

We obtained linked-read genome assemblies of 2.73–3.27 Gb from estimated genome sizes of 4.26–5.07 Gb DNA per haploid genome of the four chromosomal races ofV. viatica. These constitute the third largest insect genomes assembled so far. Combining complementary annotation tools and manual curation, we found a large diversity of TEs and satDNAs, constituting 66 to 75% per genome assembly. A comparison of sequence divergence within the TE classes revealed massive accumulation of recent TEs in all four races (314–463 Mb per assembly), indicating that their large genome sizes are likely due to similar rates of TE accumulation. Transcriptome sequencing showed more biased TE expression in reproductive tissues than somatic tissues, implying permissive transcription in gametogenesis. Out of 129 satDNA families, 102 satDNA families were shared among the four chromosomal races, which likely represent a diversity of satDNA families in the ancestor of theV. viaticachromosomal races. Notably, 50 of these shared satDNA families underwent differential proliferation since the recent diversification of theV. viaticaspecies complex.

Conclusion

This in-depth annotation of the repeatome in morabine grasshoppers provided new insights into the genome evolution of Orthoptera. Our TEs analysis revealed a massive recent accumulation of TEs equivalent to the size of entireDrosophilagenomes, which likely explains the large genome sizes in grasshoppers. Despite an overall high similarity of the TE and satDNA diversity between races, the patterns of TE expression and satDNA proliferation suggest rapid evolution of grasshopper genomes on recent timescales.
Efficacy of hyperthermic isolated limb perfusion in the treatment of locally recurrent high-grade soft tissue sarcoma of the extremities
Authors: Farzaliyev Farhad , Touma Alexander , Taeger Georg , Steinau Hans-Ulrich , Hardes Jendrik , Streitbürger Arne , Podleska Lars Erik
Published: December 2020

Background

This novel study compared the use of tumor necrosis factor (TNF)-alpha and melphalan-based isolated limb perfusion (TM-ILP) to the standard treatment of locally recurrent soft tissue extremity sarcoma. The aim was to assess whether TM-ILP positively influences the recurrence-free survival of locally recurrent high-grade soft tissue sarcoma (STS) of the extremities.

Methods

We retrospectively analyzed our clinical database for patients with STS. Variables were analyzed using chi-square test or Mann-Whitney rank-sum test. Furthermore, Kaplan-Meier survival plots were calculated and a proportional hazard regression model was developed.

Results

Out of 448 patients with extraabdominal STS treated between August 2012 and December 2015, 52 cases involving 47 patients had locally recurrent STS. Twenty-eight of these patients were treated with TM-ILP prior to surgical resection (TM-ILP-group), and 24 were treated with standard therapy (without TM-ILP). The 3-year recurrence-free survival for the TM-ILP-group was estimated at 75% (95% confidence interval (CI), 71.5–78.5). Local recurrence-free survival in the standard group was significantly lower (LRFS: 43.4%, 95% CI 38.7–48.1, p = 0.026). Multivariable analysis revealed resection with negative margins, lower number of previous recurrences, and TM-ILP as positive predictors for recurrence-free survival.

Conclusions

TM-ILP and consecutive resection of residual tumor with negative resection margins significantly improves local recurrence-free survival for patients with a first local recurrence of high-grade STS in the extremities.
Convergence of scaffold-guided bone regeneration and RIA bone grafting for the treatment of a critical-sized bone defect of the femoral shaft
Authors: Kobbe Philipp , Laubach Markus , Hutmacher Dietmar W. , Alabdulrahman Hatem , Sellei Richard M. , Hildebrand Frank
Published: December 2020

Background

Critical-sized bone defects, mainly from trauma, infection or tumor resection are a challenging condition, often resulting in prolonged, complicated course of treatment. Autografts are considered as the gold standard to replace lost bone. However, limited amount of bone graft volume and donor-site morbidity have established the need for the development of alternative methods such as scaffold-based tissue engineering (TE). The emerging market of additive manufacturing (3D-printing) has markedly influenced the manufacturing of scaffolds out of a variety of biodegradable materials. Particularly medical-grade polycaprolactone and tricalcium phosphate (mPCL–TCP) scaffolds show appropriate biocompatibility and osteoconduction with good biomechanical strength in large preclinical animal models. This case report aims to show first evidence of the feasibility, safety, and efficacy of mPCL–TCP scaffolds applied in a patient with a long bone segmental defect.

Case presentation

The presented case comprises a 29-year-old patient who has suffered a left-sided II° open femoral shaft fracture. After initial external fixation and subsequent conversion to reamed antegrade femoral nailing, the patient presented with an infection in the area of the formerly open fracture. Multiple revision surgeries followed to eradicate microbial colonization and attempt to achieve bone healing. However, 18 months after the index event, still insufficient diaphyseal bone formation was observed with circumferential bony defect measuring 6 cm at the medial and 11 cm at the lateral aspect of the femur. Therefore, the patient received a patient-specific mPCL–TCP scaffold, fitting the exact anatomical defect and the inserted nail, combined with autologous bone graft (ABG) harvested with the Reamer–Irrigator–Aspirator system (RIA—Synthes®) as well as bone morphogenetic protein-2 (BMP-2). Radiographic follow-up 12 months after implantation of the TE scaffold shows advanced bony fusion and bone formation inside and outside the fully interconnected scaffold architecture.

Conclusion

This case report shows a promising translation of scaffold-based TE from bench to bedside. Preliminary evidence indicates that the use of medical-grade scaffolds is safe and has the potential to improve bone healing. Further, its synergistic effects when combined with ABG and BMP-2 show the potential of mPCL–TCP scaffolds to support new bone formation in segmental long bone defects.
Correction to: Biological determinants of physical activity across the life course: a “Determinants of Diet and Physical Activity” (DEDIPAC) umbrella systematic literature review
Authors: Aleksovska Katina , Puggina Anna , Giraldi Luca , Buck Christoph , Burns Con , Cardon Greet , Carlin Angela , Chantal Simon , Ciarapica Donatella , Colotto Marco , Condello Giancarlo , Coppinger Tara , Cortis Cristina , D’Haese Sara , De Craemer Marieke , Di Blasio Andrea , Hansen Sylvia , Iacoviello Licia , Issartel Johann , Izzicupo Pascal , Jaeschke Lina , Kanning Martina , Kennedy Aileen , Ling Fiona , Luzak Agnes , Napolitano Giorgio , Nazare Julie-Anne , Perchoux Camille , Pischon Tobias , Polito Angela , Sannella Alessandra , Schulz Holger , Sohun Rhoda , Steinbrecher Astrid , Schlicht Wolfgang , Ricciardi Walter , MacDonncha Ciaran , Capranica Laura , Boccia Stefania
Published: December 2020

An amendment to this paper has been published and can be accessed via the original article.
Immigration in the populist crucible: comparing Brexit and Trump
Authors: Joppke Christian
Published: December 2020

The successful Brexit referendum and the election of Trump in 2016 mark the breakthrough of populism in the West. Opposition to immigration has been central to both events. However, it has been central in different ways. This paper maps these differences and the implications of both populisms for a liberal immigration policy. Driven by hostility to free mobility within the EU, the ironic consequence of Brexit will be an immigration policy that is less discriminatory than previously, in the sense that favoritism for other Europeans is now ruled out. By contrast, Trump’s immigration policy is openly and brazenly discriminatory. In particular, its Muslim Ban breaches the “anti-populist norm” (Freeman 1995) and thus the essence of a liberal immigration policy.
Atypical presentation and management of an epithelioid hemangioma: a case report and review of the literature
Authors: Wiggins Claire J. , Dibbs Rami P. , Bartlett Erica L. , Ashton Daniel J. , Maricevich Renata S.
Published: December 2020

Background

Epithelioid hemangioma is a rare, benign vascular lesion classically presenting with painless nodules in the head and neck region. Hemangioma lesions are typically small, located within the dermis and subcutaneous tissue, and rarely exceed 10 cm in size. Complete surgical excision, with negative margins, is the recommended treatment as local recurrence is common. We describe an unusual presentation of epithelioid hemangioma that, to our knowledge, has not been previously described in the literature, epithelioid.

Case presentation

We report an atypical case of a large epithelioid hemangioma lesion with deep intramuscular involvement in a 16-year-old male. Ultrasound and MRI showed a hypervascular mass on the patient’s left upper back, and biopsy confirmed the diagnosis. Treatment consisted of preoperative embolization followed by excision and local tissue rearrangement.

Conclusions

Epithelioid hemangiomas are considered uncommon in the pediatric population. Moreover, it is challenging to diagnose these lesions due to their similarities to other vascular anomalies. We aim to increase awareness of this condition and obtain more precision in diagnosis, thus standardizing the approach for those treating individuals with vascular anomalies.
Long-term development of post-traumatic stress symptoms and associated risk factors in military service members deployed to Afghanistan: Results from the PRISMO 10-year follow-up
Authors: van der Wal Sija J. , Vermetten Eric , Elbert Geuze
Published: December 2020

Background

Symptoms of post-traumatic stress disorder (PTSD) can manifest several years after trauma exposure, and may impact everyday life even longer. Military deployment can put soldiers at increased risk for developing PTSD symptoms. Longitudinal evaluations of PTSD symptoms in deployed military personnel are essential for mapping the long-term psychological burden of recent operations on our service members, and may improve current practice in veterans’ mental health care.

Methods

The current study examined PTSD symptoms and associated risk factors in a cohort of Dutch Afghanistan veterans 10 years after homecoming. Participants (N = 963) were assessed seven times from predeployment up to 10 years after deployment. Growth mixture modeling was used to identify distinct trajectories of PTSD symptom development.

Results

The probable PTSD prevalence at 10 years after deployment was 8%. Previously identified risk factors like younger age, lower rank, more deployment stressors, and less social support were still relevant 10 years after deployment. Four trajectories of PTSD symptom development were identified: resilient (85%), improved (6%), severely elevated-recovering (2%), and delayed onset (7%). Only the delayed onset group reported increasing symptom levels between 5 and 10 years postdeployment, even though 77% reported seeking help.

Conclusions

This study provides insights into the long-term burden of deployment on the psychological health of military service members. It identifies a group of veterans with further increasing PTSD symptoms that does not seem to improve from currently available mental health support, and underlines the urgent need for developing and implementing alternative treatment opportunities for this group.
Duality principle of the zero-point length of spacetime and Generalized Uncertainty Principle
Authors: Mondal Vikramaditya
Published: December 2020

A strong theoretical motivation persists, in quantum gravity, to consider the existence of a fundamental lower bound on the physically measurable length, namely the Planck length

. The Planck length can be considered as a zero-point length of spacetime. For a relativistic particle with action

, the invariance of its path integral amplitude under the duality transformation

encodes the information of such “zero-point length” of spacetime (Padmanabhan T., Phys. Rev. Lett., 78 (1997) 1854). We show that, when we take the non-relativistic limit, this duality principle deforms the canonical commutation relation similarly to a certain variation of the Generalized Uncertainty Principle (GUP). We interpret this as an equivalence between the principle of path integral duality and GUP.
Exact hyperuniformity exponents and entropy cusps in models of active-absorbing transition
Authors: Dandekar Rahul
Published: December 2020

Recent studies of nonequilibrium phase transitions have shown that in many systems which have transitions involving an arrested phase, the arrested states show suppressed density fluctuations and a cusp in the configurational entropy at the transition point. We study quasistatic driving in the 1D fixed-energy Abelian Sandpile Model, and in Conserved Lattice Gases with range n in 1D, and exactly determine the measure over the absorbing states for both cases, along with the behaviour of density fluctuations and the configurational entropy of absorbing states. We show that both models exhibit hyperuniformity near the transition, and also that the configurational entropy shows a cusp at the transition point in the Conserved Lattice Gases.
Metagrating in ancient Luoyang Bridge
Authors: Chen Shiming , Zhou Yangyang , Wang Zhenyu , Chen Huanyang
Published: December 2020

The ancient Chinese bridge, Luoyang Bridge, has been revealed to obey similar laws to diminish waves like an optical model, metagrating. Numerical simulations have been performed to verify this finding.
PROSPECTS FOR USING LOW-FREQUENCY ACOUSTIC VIBRATIONS IN MEDICINE
Authors: Zinkin V.
Published: December 2020

Noise, infrasound, ultrasound, and vibration are harmful production factors. They are widely used in medicine for diagnosis and treatment. Low-frequency acoustic vibrations stimulate mechanoreceptors, improve microcirculation and metabolism at the organ, tissue and cellular levels, which allows us to consider them as a promising treatment method
DEVELOPMENT OF EXPRESS DIAGNOSTICS OF COLD ENDURANCE AND PROPENSION TO BRONCHOPULUM DISEASES ON THE BASIS OF REGISTRATION OF BRAIN MICROVIBRATIONS
Authors: Shabanov Gennadiy , Rybchenko Aleksandr
Published: December 2020

The paper explored the possibility of using the complex for registration and spectral analysis of microvibrations of the brain for mass examinations, professional selection of contingents working in difficult climatic conditions of the North and the Far East. Spectral characteristics of factors leading to increased expression of TRPM8 cold receptors were studied in the rhythms of brain activity using a menthol functional test. The results of the work can be used to identify people at risk of developing bronchopulmonary pathology.
Psychometric properties of the Persian Version of Youth anxiety measure for DSM-5 (YAM-5) in nonclinical sample
Authors: soltani esmail , Bazrafshan Amir , Moghimi Ebrahim , Hedayati Arvin , Sheikholeslami Sajedeh
Published: December 2020

Aim of the study

The purpose of this study was to investigate the psychometric properties Youth anxiety measure for DSM-5(YAM-5) in nonclinical sample

Subject or material and methods

This was a descriptive cross-sectional study. The statistical population of this study included all elementary and middle school students in Shiraz during 2017-18, among which 400 persons were selected with random cluster sampling and who participated in the research by completing the children's and adolescent's anxiety scales and child behavior checklist. A total of 30 students were selected for re-test reliability that was performed four weeks later. In order to examine the agreement between the child-parent form, 50 parents of students were randomly selected from this population. Data were analyzed using SPSS22 and Amos 18 software.

Results

The results showed that the five-factor structure of YAM-I and YAM-II is acceptable with data. The correlation coefficient of YAM-I with internalization and externalization problems was equal to 0.50 and 0.17 respectively; and that of YAM-II was 0.36 and 0.15, respectively. The YAM-I agreement for a parent was 0.67; and agreement of YAM-II child with parent was 0.89. Cronbach’s Alpha of YAM-I and YAM-II was 0.84 and 0.78 respectively. The reliability of YAM-I retest was 0.98 and for the subscales it was between 0.90 and 0.95. The reliability of YAM-II retest was 0.96 and for the sub-scales it was between 0.94 and 0.96.

Discussion

The Youth anxiety measure for DSM-5 has good psychometric properties in nonclinical sample

Conclusions

The YAM is a valid and reliable questionnaire to be utilized in research and therapeutic interventions.
The Technique of Development of Readiness of the Future Teachers to Designing of Individual Methodical System
Authors:   State Institution Luhansk Taras Shevchenko National University, Koteneva Iryna , Vovk Serhii ,   State Institution Luhansk Taras Shevchenko National University
Published: December 2020

Article is devoted to a problem of vocational training of the future teachers. The theoretical substantiation of methodical culture of the future teacher is given, as integrative set of its professional and personal values, qualities and methodical competence which allows to carry out creatively the future methodical activity on the basis of a reflexion, the got experience and self-development taking into account standard requirements of the state. The characterised process of methodical preparation of the future teacher has allowed to offer structure of methodical preparation. It is defined that the individual methodical system displays pedagogical ideals, values, an internal position and experience of professional work of the future teacher, its personal qualities and system of mutual relations. In a theory context curriculum (from English curriculum), it is proved a technique of development of readiness of the future teachers to designing of individual methodical system, stages and steps which are characterised. The structure of an investigated phenomenon - readiness of the future teacher for designing of individual methodical system which is presented by four components (motivational -modeling, cognitive- designing, constructive-technological and reflexive-estimated) is defined. The training maintenance has found reflexion in «The program of formation of methodical culture of the future teachers» which is constructed by a modular principle. The conclusion is drawn - the technique of development of readiness of the future teachers to designing of individual methodical system includes a complex of methods which cover all development of the considered readiness: from ordering of knowledge available for the future teacher about methodical system before control of its efficiency. It promotes development of each structural component of investigated readiness of the future teachers to designing of individual methodical system: motivational-modeling, cognitive-designing, constructive-technological and reflexive-estimated. The offered technique is designed on use in vocational training of the future teachers in higher education establishments.
Prospects for the Development of Distance Education Technologies in Ukraine
Authors:   State Institution Luhansk Taras Shevchenko National University, Teteriev Vladyslav
Published: December 2020

The article outlines prospects for the development of distance education technologies in Ukraine, analysis of the characteristics of the model of distance learning in the education system. The necessity of training specialists in the field of distance education is emphasized. The importance of development of information resources and educational and methodological developments in support of new technologies of distance learning in higher education institutions of Ukraine is noted. Based on the analysis of technological advances that contribute to the improvement of the results of the use of remote technologies in the HEA, the most promising of them are identified: adaptive learning technologies, mobile learning, virtual, augmented and hybrid realities, next-generation learning management systems, artificial intelligence and natural user interfaces. As a result of the analysis of scientific works, the following prospects for the development of distance learning in Ukraine were highlighted: updating of software and hardware base for the introduction of new technologies in higher education; organization of cooperation between developers of distance learning software products, distance education methodologists and teachers of HEA to develop strategies for the use of new information technologies in distance learning; staffing of distance learning, training of specialists in the field of distance education; development and distribution of platforms with an intuitive not complex software interface for creating distance courses; creation or adaptation of information technologies and electronic educational and methodological developments to support new technologies of distance learning in the Defense Law of Ukraine.
Formation of Multiculturalism of Future Teachers of Foreign Languages in the Context of Multicultural Education
Authors:   State Institution Luhansk Taras Shevchenko National University, Shkarlet Valeriia
Published: December 2020

The article explains the key concept "multicultural education of future teachers of foreign languages". The essence and content of the notions "multiculturalism", "multicultural education" are clarified; the connection between them is established. The influence of these concepts on the process of professional training of future teachers of foreign languages is also revealed. The concept of culture is defined, namely the origin and history of ancient, medieval and modern times of the use of this concept. The relevance of teaching humanitarian disciplines in higher education institutions, especially a foreign language, is highlighted, which expands the language knowledge of students and gives them the opportunity to become full members of a multicultural environment. Also, synonymous terms for the concept of "polyculture" and the main goals of polycultural education are presented. So, we can state that the multiculturalism of the personality of future teachers of a foreign language consists in striving during intercultural communication with representatives of other languages; to understand a specific foreign language system of language and concepts of culture, their system of value-semantic guidelines, to integrate new experience into one's own system of language and concepts of culture, and also to analyze the system of one's own culture through cognition of a new culture, which leads to the formation of multicultural value guidelines.
Organization of Speech Therapy Practice in the System of Training Competitive Specialists in the Field of Special Education
Authors:   State Institution Luhansk Taras Shevchenko National University, Grigoreva Inna , Makarenko Iryna ,   State Institution Luhansk Taras Shevchenko National University, Makhukova Tetiana ,   State Institution Luhansk Taras Shevchenko National University
Published: December 2020

The article deals with the problem of the content of the training speech therapists at the higher educational establishment at the present stage of democratic change in society. Areas of improvement of training, content, organization and methods of it's implementation for students specializing in "Logopedics" have been determined. The current state of the growth in the number of children with impaired psychophysical development according to the Ministry of Health of Ukraine is analyzed. The state program “The concept of teacher education” is considered, which indicates the main goal of the Ukrainian education system. A pedagogical experiment, due to the transition to the European technology of training, during which much attention is paid to the independent work of students and the active passage of practical training, is disclosed. Organization of speech therapy practice on credit-modular technology is an integral element of the educational process and is included in the calendar-thematic and curriculum of the curriculum as mandatory for all students. During independent practical activity, the student's mental activity develops both at the level of knowledge gained, and attracting them to solving problems, problems, situations. It is the credit-modular system of training specialists in a higher educational institution that takes into account the organization of one of the forms of educational activity, namely production practice, based on the principles of consistency, and ensures its passage over 5 years. Vocational training of students is represented by three links of speech therapy practice: 1 – Speech therapy practice in preschool institutions in groups for children with severe speech impairments; 2 – Speech therapist practice in educational institutions in groups for schoolchildren with impaired speech and writing; 3 – Speech therapy practice in healthcare facilities. The vocational training of speech therapists is determined by the modern requirements of the region, as the central link in correctional and pedagogical activity and helps in solving the problems of competitiveness of young speech therapists in the employment market.
Fiber-compatible photonic feed-forward with 99% fidelity
Authors: Luiz Zanin Guilherme , Jacquet Maxime J , Spagnolo Michele , Schiansky Peter , Calafell Irati Alonso , Rozema Lee A , Walther Philip
Published: December 2020

Both photonic quantum computation and the establishment of a quantum internet require fiber-based measurement and feed-forward in order to be compatible with existing infrastructure. Here we present a fiber-compatible scheme for measurement and feed-forward, whose performance is benchmarked by carrying out remote preparation of single-photon polarization states at telecom-wavelengths. The result of a projective measurement on one photon deterministically controls the path a second photon takes with ultrafast optical switches. By placing well-calibrated bulk passive polarization optics in the paths, we achieve a measurement and feed-forward fidelity of (99.0 ± 1)%, after correcting for other experimental errors. Our methods are useful for photonic quantum experiments including computing, communication, and teleportation.
Modular microring laser cavity sensor
Authors: Chang Lantian , de Goede Michiel , Dijkstra Meindert , van Emmerik Carlijn I. , García-Blanco Sonia M.
Published: December 2020

We propose and experimentally demonstrate a modular microring laser (MML) cavity for sensing applications. The proposed MML permits much more design freedom compared with a traditional simple ring cavity by decoupling the performance parameters into several regions in the cavity. Thus, the different biosensor performance parameters can be optimized semi-independently limiting the need for trade-offs on the design of the biosensing device. The first generation MML has been fabricated and tested. A fiber-to-fiber slope efficiency of up to 1.2%, a temperature coefficient of 1.35 GHz/K and a 3σ limit of detection (LOD) of 3.1 × 10−7 RIU without averaging and 6.0 × 10−8 RIU with a 60 s averaging, has been measured for the MML sensor, which is a record-low LOD in on-chip ring cavity optical sensors. Further optimization is possible, capitalizing on the key advantage of the MML concept, namely the potential for designing the laser cavity to achieve the desired optimization goals.
Preliminary measurement scales for sparkle and graininess
Authors: Ferrero A. , Perales E. , Basic N. , Pastuschek M. , Porrovecchio G. , Schirmacher A. , Velázquez J. L. , Campos J. , Martínez-Verdú F. M. , Šmid M. , Linduska P. , Dauser T. , Blattner P.
Published: December 2020

Large effect pigments, widely used in various fields of industrial applications, produce characteristic visual textures known as sparkle and graininess, which need to be quantified by objective or subjective methods. The development of preliminary measurement scales for sparkle and graininess, whose recommendation is now under discussion in the International Commission on Illumination (CIE), is described in this article. These scales are absolute, linear and traceable to standards of optical radiation metrology. The main purpose of this article is to justify the convenience of adopting these preliminary measurements scales, showing clear evidence that they correlate well with subjective evaluations. Before standardization, these scales need to be validated with more experimental data, including different specimens and experimental systems from other research groups.
Dynamic phase manipulation of vertical-cavity surface-emitting lasers via on-chip integration of microfluidic channels
Authors: Zhao Zhuangzhuang , Xie Yiyang , Pan Guanzhong , Ni Peinan , Wang Qiuhua , Dong Yibo , Hu Liangchen , Sun Jie , Chen Hongda , Xu Chen , Genevet Patrice
Published: December 2020

Vertical-cavity surface-emitting lasers (VCSELs) play a key role in the development of the next generation of optoelectronic technologies, thanks to their unique characteristics, such as low-power consumption, circular beam profile, high modulation speed, and large-scale two-dimensional array. Dynamic phase manipulation of VCSELs within a compact system is highly desired for a large variety of applications. In this work, we incorporate the emerging microfluidic technologies into the conventional VCSELs through a monolithic integration approach, enabling dynamic phase control of lasing emissions with low power consumption and low thermal generation. As a proof of concept, a beam steering device is experimentally demonstrated by integrating microfluidic channel on a coherently coupled VCSELs array. Experimental results show that the deflection angles of the laser beam from the chip can be tuned from 0° to 2.41° under the injection of liquids with different refractive index into the microchannel. This work opens an entirely new solution to implement a compact laser system with real-time wavefront controllability. It holds great potentials in various applications, including optical fiber communications, laser printing, optical sensing, directional displays, ultra-compact light detection and ranging (LiDAR).
Optical memories and switching dynamics of counterpropagating light states in microresonators
Authors: Del Bino Leonardo , Moroney Niall , Del’Haye Pascal
Published: December 2020

The Kerr nonlinearity can be a key enabler for many digital photonic circuits as it allows access to bistable states needed for all-optical memories and switches. A common technique is to use the Kerr shift to control the resonance frequency of a resonator and use it as a bistable, optically-tunable filter. However, this approach works only in a narrow power and frequency range or requires the use of an auxiliary laser. An alternative approach is to use the asymmetric bistability between counterpropagating light states resulting from the interplay between self- and cross-phase modulation, which allows light to enter a ring resonator in just one direction. Logical high and low states can be represented and stored as the direction of circulation of light, and controlled by modulating the input power. Here we study the switching speed, operating laser frequency and power range, and contrast ratio of such a device. We reach a bitrate of 2 Mbps in our proof-of-principle device over an optical frequency range of 1 GHz and an operating power range covering more than one order of magnitude. We also calculate that integrated photonic circuits could exhibit bitrates of the order of Gbps, paving the way for the realization of robust and simple all-optical memories, switches, routers and logic gates that can operate at a single laser frequency with no additional electrical power.
Chromo-modal dispersion for optical communication and time-stretch spectroscopy
Authors: Liao Ruolin , Hon Nick K. , Buckley Brandon W. , Diebold Eric D. , Jalali Bahram
Published: December 2020

Dispersion management is critical in many optical applications, whether to reduce impairments in fiber optic communication or chirp pulse amplification, or to create time stretch instruments for single-shot continuous recording of fast phenomena. The most common solutions for achieving large dispersion with low loss include dispersion compensation fiber, fiber Bragg grating, and diffraction grating pairs. Such dispersive elements have finite operational bandwidth, limited total dispersion, or insufficient power handling. In this Letter, we demonstrate a new, to the best of our knowledge, implementation of the chromo-modal dispersion device based on a silicon waveguide slab that addresses these limitations. The device provides extremely large dispersion with a widely tunable spectrum. We also propose a new time-stretch spectrometer where the absorption cell simultaneously provides spectrum-to-time mapping for fast single-shot spectroscopy.
The SARS-CoV-2 Spike protein has a broad tropism for mammalian ACE2 proteins
Authors: Conceicao Carina , Thakur Nazia , Human Stacey , Kelly James T. , Logan Leanne , Bialy Dagmara , Bhat Sushant , Stevenson-Leggett Phoebe , Zagrajek Adrian K. , Hollinghurst Philippa , Varga Michal , Tsirigoti Christina , Tully Matthew , Chiu Chris , Moffat Katy , Silesian Adrian Paul , Hammond John A. , Maier Helena J. , Bickerton Erica , Shelton Holly , Dietrich Isabelle , Graham Stephen C. , Bailey Dalan
Published: December 2020

SARS Coronavirus 2 (SARS-CoV-2) emerged in late 2019, leading to the Coronavirus Disease 2019 (COVID-19) pandemic that continues to cause significant global mortality in human populations. Given its sequence similarity to SARS-CoV, as well as related coronaviruses circulating in bats, SARS-CoV-2 is thought to have originated in Chiroptera species in China. However, whether the virus spread directly to humans or through an intermediate host is currently unclear, as is the potential for this virus to infect companion animals, livestock, and wildlife that could act as viral reservoirs. Using a combination of surrogate entry assays and live virus, we demonstrate that, in addition to human angiotensin-converting enzyme 2 (ACE2), the Spike glycoprotein of SARS-CoV-2 has a broad host tropism for mammalian ACE2 receptors, despite divergence in the amino acids at the Spike receptor binding site on these proteins. Of the 22 different hosts we investigated, ACE2 proteins from dog, cat, and cattle were the most permissive to SARS-CoV-2, while bat and bird ACE2 proteins were the least efficiently used receptors. The absence of a significant tropism for any of the 3 genetically distinct bat ACE2 proteins we examined indicates that SARS-CoV-2 receptor usage likely shifted during zoonotic transmission from bats into people, possibly in an intermediate reservoir. Comparison of SARS-CoV-2 receptor usage to the related coronaviruses SARS-CoV and RaTG13 identified distinct tropisms, with the 2 human viruses being more closely aligned. Finally, using bioinformatics, structural data, and targeted mutagenesis, we identified amino acid residues within the Spike–ACE2 interface, which may have played a pivotal role in the emergence of SARS-CoV-2 in humans. The apparently broad tropism of SARS-CoV-2 at the point of viral entry confirms the potential risk of infection to a wide range of companion animals, livestock, and wildlife.
Simple models including energy and spike constraints reproduce complex activity patterns and metabolic disruptions
Authors: Fardet Tanguy , Levina Anna
Published: December 2020

In this work, we introduce new phenomenological neuronal models (eLIF and mAdExp) that account for energy supply and demand in the cell as well as the inactivation of spike generation how these interact with subthreshold and spiking dynamics. Including these constraints, the new models reproduce a broad range of biologically-relevant behaviors that are identified to be crucial in many neurological disorders, but were not captured by commonly used phenomenological models. Because of their low dimensionality eLIF and mAdExp open the possibility of future large-scale simulations for more realistic studies of brain circuits involved in neuronal disorders. The new models enable both more accurate modeling and the possibility to study energy-associated disorders over the whole time-course of disease progression instead of only comparing the initially healthy status with the final diseased state. These models, therefore, provide new theoretical and computational methods to assess the opportunities of early diagnostics and the potential of energy-centered approaches to improve therapies.
An investig-ation into the epidemiology of chikungunya virus across neglected regions of Indonesia
Authors: Stubbs Samuel C. B. , Johar Edison , Yudhaputri Frilasita A. , Yohan Benediktus , Santoso Marsha S. , Hayati Rahma F. , Denis Dionisius , Blacklaws Barbara A. , Powers Ann M. , Sasmono R. Tedjo , Myint Khin Saw Aye , Frost Simon D. W.
Published: December 2020

Background

Chikungunya virus (CHIKV) is an important emerging and re-emerging public health problem worldwide. In Indonesia, where the virus is endemic, epidemiological information from outside of the main islands of Java and Bali is limited.

Methodology/Principal Findings

Four hundred and seventy nine acutely febrile patients presenting between September 2017–2019 were recruited from three city hospitals situated in Ambon, Maluku; Banjarmasin, Kalimantan; and Batam, Batam Island as part of a multi-site observational study. CHIKV RNA was detected in a single serum sample while a separate sample was IgM positive. IgG seroprevalence was also low across all three sites, ranging from 1.4–3.2%. The single RT-PCR positive sample from this study and 24 archived samples collected during other recent outbreaks throughout Indonesia were subjected to complete coding region sequencing to assess the genetic diversity of Indonesian strains. Phylogenetic analysis revealed all to be of a single clade, which was distinct from CHIKV strains recently reported from neighbouring regions including the Philippines and the Pacific Islands.

Conclusions/Significance

Chikungunya virus strains from recent outbreaks across Indonesia all belong to a single clade. However, low-level seroprevalence and molecular detection of CHIKV across the three study sites appears to contrast with the generally high seroprevalences that have been reported for non-outbreak settings in Java and Bali, and may account for the relative lack of CHIKV epidemiological data from other regions of Indonesia.
Gene expression profiles of esophageal squamous cell cancers in Hodgkin lymphoma survivors versus sporadic cases
Authors: Ykema Berbel L. M. , Hoefnagel Sanne J. M. , Rigter Lisanne S. , Kodach Liudmila L. , Meijer Gerrit A. , van Leeuwen Flora E. , Khan Hina N. , Snaebjornsson Petur , Aleman Berthe M. P. , Broeks Annegien , Meijer Sybren L. , Wang Kenneth K. , Carvalho Beatriz , Krishnadath Kausilia K. , van Leerdam Monique E. ,   on behalf of GIOCA-OES
Published: December 2020

Hodgkin lymphoma (HL) survivors are at increased risk of developing second primary esophageal squamous cell cancer (ESCC). We aimed to gain insight in the driving events of ESCC in HL survivors (hESCC) by using RNA sequencing and NanoString profiling. Objectives were to investigate differences in RNA signaling between hESCC and sporadic ESCC (sESCC), and to look for early malignant changes in non-neoplastic esophageal tissue of HL survivors (hNN-tissue). We analyzed material of 26 hESCC cases, identified via the Dutch pathology registry (PALGA) and 17 sESCC cases from one academic institute and RNA sequencing data of 44 sESCC cases from TCGA. Gene expression profiles for the NanoString panel PanCancer IO 360 were obtained from 16/26 hESCC and four hNN-tissue, while non-neoplastic squamous tissue of four sporadic cases (sNN-tissue) served as reference profile. Hierarchical clustering, differential expression and pathway analyses were performed. Overall, the molecular profiles of hESCC and sESCC were similar. There was increased immune, HMGB1 and ILK signaling compared to sNN-tissue. The profiles of hNN-tissue were distinct from sNN-tissue, indicating early field effects in the esophagus of HL survivors. The BRCA1 pathway was upregulated in hESCC tissue, compared to hNN tissue. Analysis of expression profiles reveals overlap between hESCC and sESCC, and differences between hESCC and its surrounding hNN-tissue. Further research is required to validate our results and to investigate whether the changes observed in hNN-tissue are already detectable before development of hESCC. In the future, our findings could be used to improve hESCC patient management.
Study of the thermal regime of a reservoir on the Qinghai-Tibetan Plateau, China
Authors: Yang Yanjing , Deng Yun , Tuo Youcai , Li Jia , He Tianfu , Chen Min
Published: December 2020

The Qinghai-Tibetan Plateau region has unique meteorological characteristics, with low air temperature, low air pressure, low humidity, little precipitation, and strong diurnal variation. A two-dimensional hydrodynamic CE-QUAL-W2 model was configured for the Pangduo Reservoir to better understand the thermal structure and diurnal variation inside the reservoir under the local climate and hydrological conditions on the Qinghai-Tibetan Plateau. Observation data were used to verify the model, and the results showed that the average error of the 6 profile measured monthly from August to December 2016 was 0.1°C, and the root-mean-square error (RMSE) was 0.173°C. The water temperature from August 2016 to September 2017 was simulated by inputting measured data as model inputs. The results revealed that the reservoir of the Qinghai-Tibetan Plateau was a typical dimictic reservoir and the water mixed vertically at the end of March and the end of October. During the heating period, thermal stratification occurred, with strong diurnal variation in the epilimnion. The mean variance of the diurnal water temperature was 0.10 within a 5 m water depth but 0.04 in the whole water column. The mixing mode of inflow changed from undercurrent, horizontal-invaded flow and surface layer flow in one day. In winter, the diurnal variation was weak due to the thermal protection of the ice cover, while the mean variance of diurnal water temperature was 0.00 within both 5 m and the whole water column. Compared to reservoirs in areas with low altitude but the same latitude, significant differences occurred between the temperature structure of the low-altitude reservoir and the Pangduo Reservoir (P<0.01). The Pangduo Reservoir presented a shorter stratification period and weaker stratification stability, and the annual average SI value was 26.4 kg/m2, which was only 7.5% that of the low-altitude reservoir. The seasonal changes in the net heat flux received by the surface layers determined the seasonal cycle of stratification and mixing in reservoirs. This study provided a scientific understanding of the thermal changes in stratified reservoirs under the special geographical and meteorological conditions on the Qinghai-Tibetan Plateau. Moreover, this model can serve as a reference for adaptive management of similar dimictic reservoirs in cold and high-altitude areas.