bluuebunny/crossref_metadata_2025 huggingface dataset:
OncoTree: A Cancer Classification System for Precision Oncology
Authors: Kundra Ritika , Zhang Hongxin , Sheridan Robert , Sirintrapun Sahussapont Joseph , Wang Avery , Ochoa Angelica , Wilson Manda , Gross Benjamin , Sun Yichao , Madupuri Ramyasree , Satravada Baby A. , Reales Dalicia , Vakiani Efsevia , Al-Ahmadie Hikmat A. , Dogan Ahmet , Arcila Maria , Zehir Ahmet , Maron Steven , Berger Michael F. , Viaplana Cristina , Janeway Katherine , Ducar Matthew , Sholl Lynette , Dogan Snjezana , Bedard Philippe , Surrey Lea F. , Sanchez Iker Huerga , Syed Aijaz , Rema Anoop Balakrishnan , Chakravarty Debyani , Suehnholz Sarah , Nissan Moriah , Iyer Gopakumar V. , Murali Rajmohan , Bouvier Nancy , Soslow Robert A. , Hyman David , Younes Anas , Intlekofer Andrew , Harding James J. , Carvajal Richard D. , Sabbatini Paul J. , Abou-Alfa Ghassan K. , Morris Luc , Janjigian Yelena Y. , Gallagher Meighan M. , Soumerai Tara A. , Mellinghoff Ingo K. , Hakimi Abraham A. , Fury Matthew , Huse Jason T. , Bagrodia Aditya , Hameed Meera , Thomas Stacy , Gardos Stuart , Cerami Ethan , Mazor Tali , Kumari Priti , Raman Pichai , Shivdasani Priyanka , MacFarland Suzanne , Newman Scott , Waanders Angela , Gao Jianjiong , Solit David , Schultz Nikolaus
Published: February 2021

PURPOSE

Cancer classification is foundational for patient care and oncology research. Systems such as International Classification of Diseases for Oncology (ICD-O), Systematized Nomenclature of Medicine Clinical Terms (SNOMED-CT), and National Cancer Institute Thesaurus (NCIt) provide large sets of cancer classification terminologies but they lack a dynamic modernized cancer classification platform that addresses the fast-evolving needs in clinical reporting of genomic sequencing results and associated oncology research.

METHODS

To meet these needs, we have developed OncoTree, an open-source cancer classification system. It is maintained by a cross-institutional committee of oncologists, pathologists, scientists, and engineers, accessible via an open-source Web user interface and an application programming interface.

RESULTS

OncoTree currently includes 868 tumor types across 32 organ sites. OncoTree has been adopted as the tumor classification system for American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE), a large genomic and clinical data-sharing consortium, and for clinical molecular testing efforts at Memorial Sloan Kettering Cancer Center and Dana-Farber Cancer Institute. It is also used by precision oncology tools such as OncoKB and cBioPortal for Cancer Genomics.

CONCLUSION

OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research.
Elinzanetant (NT-814), a Neurokinin 1,3 Receptor Antagonist, Reduces Estradiol and Progesterone in Healthy Women
Authors: Pawsey Steve , Mills Edouard Gregory , Ballantyne Elizabeth , Donaldson Kirsteen , Kerr Mary , Trower Mike , Dhillo Waljit Singh
Published: February 2021

Context

The ideal therapy for endometriosis (EM) and uterine fibroids (UFs) would suppress estrogenic drive to the endometrium and myometrium, while minimizing vasomotor symptoms and bone loss associated with current treatments. An integrated neurokinin-kisspeptin system involving substance P and neurokinin B acting at the neurokinin (NK) receptors 1 and 3, respectively, modulates reproductive hormone secretion and represents a therapeutic target.

Objective

This work aimed to assess the effects of the novel NK1,3 antagonist elinzanetant on reproductive hormone levels in healthy women.

Methods

A randomized, single-blinded, placebo-controlled study was conducted in 33 women who attended for 2 consecutive menstrual cycles. In each cycle blood samples were taken on days 3 or 4, 9 or 10, 15 or 16, and 21 or 22 to measure serum reproductive hormones. In cycle 2, women were randomly assigned to receive once-daily oral elinzanetant 40, 80, 120 mg, or placebo (N = 8 or 9 per group).

Results

Elinzanetant dose-dependently lowered serum luteinizing hormone, estradiol (120 mg median change across cycle: –141.4 pmol/L, P = .038), and luteal-phase progesterone (120 mg change from baseline on day 21 or 22: –19.400 nmol/L, P = .046). Elinzanetant 120 mg prolonged the cycle length by median of 7.0 days (P = .023). Elinzanetant reduced the proportion of women with a luteal-phase serum progesterone concentration greater than 30 nmol/L (a concentration consistent with ovulation) in a dose-related manner in cycle 2 (P = .002). Treatment did not produce vasomotor symptoms.

Conclusion

NK1,3 receptor antagonism with elinzanetant dose-dependently suppressed the reproductive axis in healthy women, with the 120-mg dose lowering estradiol to potentially ideal levels for UFs and EM. As such, elinzanetant may represent a novel therapy to manipulate reproductive hormone levels in women with hormone-driven disorders.
Predicting the effects of climate change on incubation in reptiles: methodological advances and new directions
Authors: Carter A. L. , Janzen Fredric J.
Published: February 2021

The unprecedented advancement of global climate change is affecting thermal conditions across spatial and temporal scales. Reptiles with temperature-dependent sex determination (TSD) are uniquely vulnerable to even fine-scale variation in incubation conditions and are a model system for investigating the impacts of shifting temperatures on key physiological and life-history traits. The ways in which current and predicted future climatic conditions translate from macro- to ultra-fine scale temperature traces in subterranean nests is insufficiently understood. Reliably predicting the ways in which fine-scale, daily and seasonally fluctuating nest temperatures influence embryonic development and offspring phenotypes is a goal that remains constrained by many of the same logistical challenges that have persisted throughout more than four decades of research on TSD. However, recent advances in microclimate and developmental modeling should allow us to move farther away from relatively coarse metrics with limited predictive capacity and towards a fully mechanistic model of TSD that can predict incubation conditions and phenotypic outcomes for a variety of reptile species across space and time and for any climate scenario.
How dryland mammals will respond to climate change: the effects of body size, heat load and a lack of food and water
Authors: Fuller Andrea , Mitchell Duncan , Maloney Shane K. , Hetem Robyn S. , Fonsêca Vinicius F. C. , Meyer Leith C. R. , van de Ven Tanja M. F. N. , Snelling Edward P.
Published: February 2021

Mammals in drylands are facing not only increasing heat loads but also reduced water and food availability as a result of climate change. Insufficient water results in suppression of evaporative cooling and therefore increases in body core temperature on hot days, while lack of food reduces the capacity to maintain body core temperature on cold nights. Both food and water shortage will narrow the prescriptive zone, the ambient temperature range over which body core temperature is held relatively constant, which will lead to increased risk of physiological malfunction and death. Behavioural modifications, such as shifting activity between night and day or seeking thermally buffered microclimates, may allow individuals to remain within the prescriptive zone, but can incur costs, such as reduced foraging or increased competition or predation, with consequences for fitness. Body size will play a major role in predicting response patterns, but identifying all the factors that will contribute to how well dryland mammals facing water and food shortage will cope with increasing heat loads requires a better understanding of the sensitivities and responses of mammals exposed to the direct and indirect effects of climate change.
Towards more integration of physiology, dispersal and land-use change to understand the responses of species to climate change
Authors: Hof Christian
Published: February 2021

The accelerating biodiversity crisis, for which climate change has become an important driver, urges the scientific community for answers to the question of whether and how species are capable of responding successfully to rapidly changing climatic conditions. For a better understanding and more realistic predictions of species' and biodiversity responses, the consideration of extrinsic (i.e. environment-related) and intrinsic (i.e. organism-related) factors is important, among which four appear to be particularly crucial: climate change and land-use change, as extrinsic factors, as well as physiology and dispersal capacity, as intrinsic factors. Here, I argue that these four factors should be considered in an integrative way, but that the scientific community has not yet been very successful in doing so. A quantitative literature review revealed a generally low level of integration within global change biology, with a pronounced gap especially between the field of physiology and other (sub)disciplines. After a discussion of potential reasons for this unfortunate lack of integration, some of which may relate to key deficits e.g. in the reward and incentive systems of academia, I suggest a few ideas that might help to overcome some of the barriers between separated research communities. Furthermore, I list several examples for promising research along the integration frontier, after which I outline some research questions that could become relevant if one is to push the boundary of integration among disciplines, of data and methods, and across scales even further – for a better understanding and more reliable predictions of species and biodiversity in a world of global change.
The role of mechanistic physiology in investigating impacts of global warming on fishes
Authors: Lefevre Sjannie , Wang Tobias , McKenzie David J.
Published: February 2021

Warming of aquatic environments as a result of climate change is already having measurable impacts on fishes, manifested as changes in phenology, range shifts and reductions in body size. Understanding the physiological mechanisms underlying these seemingly universal patterns is crucial if we are to reliably predict the fate of fish populations with future warming. This includes an understanding of mechanisms for acute thermal tolerance, as extreme heatwaves may be a major driver of observed effects. The hypothesis of gill oxygen limitation (GOL) is claimed to explain asymptotic fish growth, and why some fish species are decreasing in size with warming; but its underlying assumptions conflict with established knowledge and direct mechanistic evidence is lacking. The hypothesis of oxygen- and capacity-limited thermal tolerance (OCLTT) has stimulated a wave of research into the role of oxygen supply capacity and thermal performance curves for aerobic scope, but results vary greatly between species, indicating that it is unlikely to be a universal mechanism. As thermal performance curves remain important for incorporating physiological tolerance into models, we discuss potentially fruitful alternatives to aerobic scope, notably specific dynamic action and growth rate. We consider the limitations of estimating acute thermal tolerance by a single rapid measure whose mechanism of action is not known. We emphasise the continued importance of experimental physiology, particularly in advancing our understanding of underlying mechanisms, but also the challenge of making this knowledge relevant to the more complex reality.
Avenues of reef-building coral acclimatization in response to rapid environmental change
Authors: Putnam Hollie M.
Published: February 2021

The swiftly changing climate presents a challenge to organismal fitness by creating a mismatch between the current environment and phenotypes adapted to historic conditions. Acclimatory mechanisms may be especially crucial for sessile benthic marine taxa, such as reef-building corals, where climate change factors including ocean acidification and increasing temperature elicit strong negative physiological responses such as bleaching, disease and mortality. Here, within the context of multiple stressors threatening marine organisms, I describe the wealth of metaorganism response mechanisms to rapid ocean change and the ontogenetic shifts in organism interactions with the environment that can generate plasticity. I then highlight the need to consider the interactions of rapid and evolutionary responses in an adaptive (epi)genetic continuum. Building on the definitions of these mechanisms and continuum, I also present how the interplay of the microbiome, epigenetics and parental effects creates additional avenues for rapid acclimatization. To consider under what conditions epigenetic inheritance has a more substantial role, I propose investigation into the offset of timing of gametogenesis leading to different environmental integration times between eggs and sperm and the consequences of this for gamete epigenetic compatibility. Collectively, non-genetic, yet heritable phenotypic plasticity will have significant ecological and evolutionary implications for sessile marine organism persistence under rapid climate change. As such, reef-building corals present ideal and time-sensitive models for further development of our understanding of adaptive feedback loops in a multi-player (epi)genetic continuum.
Microbiology of Chronic Suppurative Otitis Media: An update from a Tertiary Care Hospital in Bangladesh
Authors: Khatun Mst. Romena , Alam Kh. Md. Faisal , Naznin Mahmuda , Salam Md. Abdus
Published: February 2021

Objectives: Chronic suppurative otitis media is a major cause of acquired hearing impairment, especially in children of developing countries. The study sought to explore the bacteriological profile and their antimicrobial susceptibility among patients of chronic suppurative otitis media from a tertiary care hospital in Bangladesh.

Methods: A cross sectional microbiological study was conducted at the Department of Microbiology, Rajshahi Medical College, Bangladesh from January to December 2019. Aural swabs were collected aseptically from clinically suspected patients irrespective of age and gender attending the ear, nose and throat outpatient department of Rajshahi Medical College Hospital. Aerobic bacterial culture was done and isolates were identified through standard bacteriological identification scheme. Antimicrobial susceptibility testing of isolates was done by modified Kirby-Bauer disk diffusion method following Clinical and Laboratory Standards Institute guidelines.

Results: Of 96 swabs, culture yielded a total of 73 bacterial isolates from 68(70.8%) culture-positive plates including 63 (65.6%) unimicrobial and 5 (5.2%) polymicrobial (mixed growth of a pair of bacteria) growths. Frequency distribution revealed, 40(55%) gram-negative and 33(45%) gram-positive bacteria with Staphylococcus aureus was the leading isolate (37%) followed by Pseudomonas aeruginosa (31.5%), Escherichia coli (13.7%), coagulase-negative Staphylococcus (8.2%), Klebsiella pneumoniae (5.5%) and Proteus spp. (4.1%). Gram-positive bacteria were found to be highly susceptible (100%) to Linezolid and Vancomycin followed by Imipenem (83 to 96.3%), while moderate to high resistance (44 to 67%) was observed against Ciprofloxacin, Ceftriaxone, Ceftazidime, Amoxicillin/Clavulanate and Clindamycin. For gram-negative bacteria, susceptibility ranged from 67 to 100% to Imipenem, 67 to 96% to Piperacillin/Tazobactam and 67 to 83% to Gentamicin, while moderate to high resistance (50 to 75%) was observed against Ciprofloxacin, Ceftriaxone, Ceftazidime and Amoxicillin/Clavulanate.

Conclusion: Moderate to high level of multidrug-resistance especially to 3rd generation cephalosporins, Ciprofloxacin and Amoxicillin/Clavulanate is an alarming situation. It warns reinforcement of judicious antibiotic prescription and introduction of antibiotic stewardship program in the tertiary care hospitals.

doi: https://doi.org/10.12669/pjms.37.3.3942

How to cite this:Khatun MR, Alam KMF, Naznin M, Salam MA. Microbiology of Chronic Suppurative Otitis Media: An update from a Tertiary Care Hospital in Bangladesh. Pak J Med Sci. 2021;37(3):821-826. doi: https://doi.org/10.12669/pjms.37.3.3942

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
2021 Update on obstetrics
Authors: Pauli Jaimey M , Maines Jaimie L.
Published: February 2021

Essential updated guidance on FGR workup and timing of delivery; term and preterm PROM management strategies based on gestational age; and approaches to VTE prophylaxis, including for patients with COVID-19 infection
UMA ABORDAGEM PARA A REPRESENTAÇÃO DAS INCERTEZAS DA FONTE DE GERAÇÃO EÓLICA NO MODELO NEWAVE
Authors: Maceira Maria Elvira P. , Melo Albert C. G. , Pessanha José F. M. , Cruz Cristiane B. , Almeida Victor A. , Justino Thatiana C.
Published: February 2021

Propõe-se uma abordagem para modelar a incerteza da produção eólica mensal no problema de despacho de operação, aderente ao algoritmo de solução utilizado (PDDE) no modelo NEWAVE. A abordagem compreende: (i) agrupamento estatístico dos regimes de ventos; (ii) avaliação de funções de transferência mensais entre ventos e produção eólica; (iii) geração de séries sintéticas de ventos correlacionadas às afluências aos reservatórios das hidroelétricas; e (iv) representação das produções eólicas mensais no algoritmo PDDE do NEWAVE. Resultados iniciais com configurações reais do sistema interligado brasileiro apontam para a sua efetividade.
A anterioridade ontológica da individuação: quarto estudo
Authors: Kreibich Susiane , Leite Thiago Soares
Published: February 2021

O artigo propõe um paralelo entre os pensamentos do psicanalista Sigmund Freud e da filósofa Edith Stein, e de ambos com a teoria da individuação formulada pelo franciscano medieval João Duns Scotus. Primeiramente, trata-se dos pensamentos de Freud e de Stein, apresentando quatro pontos de possíveis convergências teóricas. Em seguida, essas teorias contemporâneas são confrontadas com o pensamento scotista, cujo princípio de individuação considera que o indivíduo é constituído ontologicamente por algo positivo inerente à substância singular. Para Duns Scotus, ainda que os acidentes acompanhem a substância, estes não podem ser a causa de sua individuação, uma vez que lhe são posteriores. Dito de outro modo, não é possível que aquilo que torna algo indivíduo lhe seja ontologicamente posterior. Por fim, expõe-se que, das perspectivas steiniana e scotista, o ser humano é possuidor de uma estrutura ontológica na qual a individuação é pressuposta como anterior ao desenvolvimento de qualquer identidade, o que pode ser considerado um pressuposto implícito na teoria freudiana da subjetividade. Isso implica afirmar que a constituição do ser humano, em termos steinianos e scotistas, tem como base um substrato ontológico denominado indivíduo, a partir do qual podem ser desenvolvidas as identidades do modo como são concebidas da perspectiva freudiana, isto é: a subjetividade é resultado do desenvolvimento do indivíduo, tal qual os processos identitários o são na perspectiva de Woodward. Portanto, a subjetividade pode ser considerada uma expressão da singularidade.
Fenomenologia da técnica e corpo próprio: os desafios da pandemia e a necessidade de uma técnica ética
Authors: Carneiro de Oliveira Isabela Carolina
Published: February 2021

A fenomenologia da técnica é pensada neste artigo, a partir do modo como experienciamos a técnica e os objetos técnicos através do corpo próprio [Leib] nas nossas vivências intencionais, uma vez que somos sujeitos fenomenológicos rodeados por objetos técnicos e virtuais na pandemia. Neste contexto, que assente em uma perspectiva husserliana, enfatizamos a necessidade de uma vida ética e comunitária que auxilie a humanidade em sua conduta nos desafios dos tempos atuais.
Characterization of banana bunchy top virus on Sumatra (Indonesia) wild banana
Authors: Ruth Feti Rahayuniati  , Hartono Sedyo , Somowiyarjo Susamto , Subandiyah Siti , THOMAS JOHN E.
Published: February 2021

Abstract. Rahayuniati RF, Hartono S, Somowiyarjo S, Subandiyah S, Thomas JE. 2021. Characterization of banana bunchy top virus on Sumatra (Indonesia) wild banana. Biodiversitas 22: 1243-1249. Banana bunchy top virus (BBTV) has been a major constrain on banana production worldwide. This virus infection is mostly found in banana cultivation.  The study aimed to characterize the BBTV on Sumatra wild bananas. The survey to collect seeds and typical symptomatic samples had been done in 2017 and 2019 in West Sumatra, South Sumatra, and Bengkulu. The transmission test of the virus was conducted by using the viruliferous vector on four wild banana species, while the identity of BBTV confirmed by nucleotide sequences analysis using primer pairs of DNA R and DNA S. Musa acuminata subsp. sumatrana (AA) have been found naturally infected by BBTV. The transmission confirmed on M. acuminata subsp. longipetiolata, M. acuminata subsp. malacensis, M. acuminata subsp. halabanensis and Musa sp. with typical bunchy top symptoms. The incidence on test plants were 40%, 80% 20%, 20% and 20%, respectively. The virus infection on Sumatra wild bananas prolonged the incubation periods in comparison to cv Mas. BBTV of M. acuminata subsp. sumatrana is similar to the BBTV MK940788 and MN073184 from Sumatra. This is the first report of BBTV on Sumatra wild banana. The result can be used as a reference to study the resistance of the banana against BBTV.
Involvement of purple acid phosphatase gene into nitrogen uptake of oil palm (Elaeis guineensis)
Authors: MARYANTO SIGIT DWI , TANJUNG ZULFIKAR ACHMAD , ROBERDI ROBERDI , SUDANIA WIDYARTINI MADE , PUJIANTO PUJIANTO , HAIRINSYAH HAIRINSYAH , UTOMO CONDRO , LIWANG TONY
Published: February 2021

Abstract. Maryanto SD, Tanjung ZA, Roberdi, Sudania WM, Pujianto, Hairinsyah, Utomo C, Liwang T. 2021. Involvement of purple acid phosphatase gene into nitrogen uptake of oil palm (Elaeis guineensis). Biodiversitas 22: 1385-1390. Nitrogen is the most important nutrient element in terms of plant growth. Plant purple acid phosphatases (PAPs) are known to participate in the phosphate (Pi) acquisition and utilization. Moreover, PAP gene plays an important role in nitrogen fixation. A single nucleotide polymorphism (SNP) was previously detected in the exon 7 of EgPAP3, based on SNP mining analysis of oil palm (Elaeis guineensis Jacq.). genome database. This study was aimed to obtain a Cleaved Amplified Polymorphic Sequences (CAPS) marker based on SNP within EgPAP associated with efficient nitrogen uptake oil palm progenies. Primer pairs were designed and used for PCR amplification of 3 oil palm progenies that showed low N-content, 3 progenies with moderate N-content, and 3 progenies with high N-content. The amplicon was purified prior to single-pass DNA sequencing analysis. Based on Pearson’s chi-square and odds ratio statistical analysis, the SNP has strong positive correlation with the phenotype. The SNP is located at chromosome 13 with a distance of 17.7771 cM from start codon. The sequencing analysis revealed that three progenies with high N-content samples had GG allele motif, while moderate N-content progenies had GA allele and low N-content progenies had AA allele motifs respectively. In addition, a restriction site of NIaIV was found to be adjacent to the SNP location, thus the PCR products of all samples were digested with NIaIV restriction enzyme. NIaIV was able to distinguish between high, medium and low efficient DNA samples. Whole high N-content progenies with GG allele motifs were undigested indicating a single band size of 670 bp identical to the untreated PCR product (control). Moderate N-content progenies produced a 670 bp, 550 bp, and 120 bp bands because of digested by NIaIV. Low N-content progenies also resulted in double bands of 550 bp and 120 bp due to digested by NIaIV. Furthermore, NIaIV restriction enzyme was applied to digest other 54 oil palms DNA samples with unknown genotypes. Whole GG samples were consistently shown to have single band, GA and AA samples were also consistent in producing two bands with different lengths. Based on this result, CAPS marker based on SNP in EgPAP3 was successfully developed to screen between high and low efficient N-uptake of oil palm progenies.
Laser-frequency-comb calibration for the Extremely Large Telescope: an OPO-based infrared astrocomb covering the H and J bands
Authors: Cheng Yuk Shan , Xiao Dong , McCracken Richard A. , Reid Derryck T.
Published: February 2021

The Extremely Large Telescope (ELT) will address an unprecedented optical wavelength range from 370 to 2400 nm, and its high-resolution spectrograph (HIRES) will require a laser frequency comb calibrator of comparable coverage. An architecture based around a Ti:sapphire master comb in principle enables wavelengths across this range to be obtained by a combination of second- and third-order nonlinear effects. In this scheme, near-infrared wavelength coverage can be addressed by downconversion of the comb to 1600 nm using an optical parametric oscillator (OPO), followed by broadband supercontinuum generation in highly nonlinear fiber. Here we present an example of this approach in the form of a 10 GHz astrocomb comprising a Fabry–Perot-filtered supercontinuum derived from a degenerate OPO and spanning 1.15–1.80 µm. We characterize the astrocomb using Fourier-transform spectroscopy, enabling the mode orders within the filtered comb to be identified.
Controlling plasmon propagation and enhancement via reducing agent in wet chemistry synthesized silver nanowires
Authors: Ćwik Michał , Sulowska Karolina , Buczyńska Dorota , Roźniecka Ewa , Domagalska Martyna , Maćkowski Sebastian , Niedziółka-Jönsson Joanna
Published: February 2021

Silver nanowires with varying diameters and submillimeter lengths were obtained by changing a reducing agent used during hydrothermal synthesis. The control over the nanowire diameter turns out to play a critical role in determining their plasmonic properties, including fluorescence enhancement and surface plasmon polariton propagation. Advanced fluorescence imaging of hybrid nanostructures assembled of silver nanowires and photoactive proteins indicates longer propagation lengths for nanowires featuring larger diameters. At the same time, with increasing diameter of the nanowires, we measure a substantial reduction of fluorescence enhancement. The results point at possible ways to control the influence of plasmon excitations in silver nanowires by tuning their morphology.
Large-scale, high-contrast glare suppression with low-transmittance eigenchannels of aperture-target transmission matrices
Authors: Zhang Hengkang , Zhang Bin , Liu Kaige , Fu Xing , Liu Qiang
Published: February 2021

Glare suppression with wavefront shaping is a significant technique in terms of actively controlling the speckle light field. A novel glare suppression method based on transmission matrix (TM) measurement is demonstrated in this Letter. An aperture-target TM model is proposed, and its low-transmittance eigenchannel is utilized to minimize the speckle intensity inside a given target area. We verified the availability of this method by experimentally realizing high-contrast glare suppression in areas of various sizes and shapes. For a large-scale area containing 100 speckle grains, the average intensity was suppressed to 6.3% of the background intensity. We believe our method provides an ideal method for glare suppression, and it holds interesting prospects for areas such as speckle optical tweezers and imaging under scattering conditions.
Effect on nanoscale damage precursors of fused silica with wet etching in KOH solutions
Authors: Zhong Yaoyu , Dai Yifan , Tian Ye , Shi Feng
Published: February 2021

We investigate the nanoscale damage precursors that will cause laser damage initiation on fused silica surface during KOH-based wet etching. Some nanoscale damage precursors, like impurity contamination and chemical structure defects on different etched surface with a KOH solution, are explored through a variety of testing methods at nanoscale spatial resolution. The etched surface roughness and photothermal absorption level are also studied. The results show that KOH-based etching can keep a good surface roughness, reduce impurity contamination significantly, and thus decrease surface photothermal absorption level. However, it can mitigate little chemical structure defect and has a risk of secondary pollution induced by residual deposition such as K2SiO3. The work can be a reference on using KOH-based wet etching technology to mitigate nanoscale damage precursors of fused silica ultraviolet optics.
Detecting SARS-CoV-2 variants with SNP genotyping
Authors: Harper Helen , Burridge Amanda , Winfield Mark , Finn Adam , Davidson Andrew , Matthews David , Hutchings Stephanie , Vipond Barry , Jain Nisha ,   The COVID-19 Genomics UK (COG-UK) Consortium, Edwards Keith , Barker Gary
Published: February 2021

Tracking genetic variations from positive SARS-CoV-2 samples yields crucial information about the number of variants circulating in an outbreak and the possible lines of transmission but sequencing every positive SARS-CoV-2 sample would be prohibitively costly for population-scale test and trace operations. Genotyping is a rapid, high-throughput and low-cost alternative for screening positive SARS-CoV-2 samples in many settings. We have designed a SNP identification pipeline to identify genetic variation using sequenced SARS-CoV-2 samples. Our pipeline identifies a minimal marker panel that can define distinct genotypes. To evaluate the system, we developed a genotyping panel to detect variants-identified from SARS-CoV-2 sequences surveyed between March and May 2020 and tested this on 50 stored qRT-PCR positive SARS-CoV-2 clinical samples that had been collected across the South West of the UK in April 2020. The 50 samples split into 15 distinct genotypes and there was a 61.9% probability that any two randomly chosen samples from our set of 50 would have a distinct genotype. In a high throughput laboratory, qRT-PCR positive samples pooled into 384-well plates could be screened with a marker panel at a cost of < £1.50 per sample. Our results demonstrate the usefulness of a SNP genotyping panel to provide a rapid, cost-effective, and reliable way to monitor SARS-CoV-2 variants circulating in an outbreak. Our analysis pipeline is publicly available and will allow for marker panels to be updated periodically as viral genotypes arise or disappear from circulation.
How does COVID-19 affect electoral participation? evidence from the French municipal elections
Authors: Noury Abdul , François Abel , Gergaud Olivier , Garel Alexandre
Published: February 2021

This article investigates the effects of the COVID-19 outbreak on electoral participation. We study the French municipal elections that took place at the very beginning of the ongoing pandemic and held in over 9,000 municipalities on March 15, 2020. In addition to the simple note that turnout rates decreased to a historically low level, we establish a robust relationship between the depressed turnout rate and the disease. Using various estimation strategies and employing a large number of potential confounding factors, we find that the participation rate decreases with city proximity to COVID-19 clusters. Furthermore, the proximity has conditioned impacts according to the proportion of elderly –who are the most threatened– within the city. Cities with higher population density, where the risk of infection is higher, and cities where only one list ran at the election, which dramatically reduces competitiveness, experienced differentiated effects of distance.
A new perspective and assessment measure for common dissociative experiences: ‘Felt Sense of Anomaly’
Authors: Černis Emma , Beierl Esther , Molodynski Andrew , Ehlers Anke , Freeman Daniel
Published: February 2021

Background

Dissociative experiences occur across a range of mental health disorders. However, the term ‘dissociation’ has long been argued to lack conceptual clarity and may describe several distinct phenomena. We therefore aimed to conceptualise and empirically establish a discrete subset of dissociative experiences and develop a corresponding assessment measure.

Methods

First, a systematic review of existing measures was carried out to identify themes across dissociative experiences. A theme of ‘Felt Sense of Anomaly’ (FSA) emerged. Second, assessment items were generated based on this construct and a measure developed using exploratory (EFA) and confirmatory (CFA) factor analyses of 8861 responses to an online self-report survey. Finally, the resulting measure was validated via CFA with data from 1031 patients with psychosis.

Results

‘Felt sense of anomaly’ (FSA) was identified as common to many dissociative experiences, affecting several domains (e.g. body) and taking different forms (‘types’; e.g. unfamiliarity). Items for a novel measure were therefore systematically generated using a conceptual framework whereby each item represented a type-by-domain interaction (e.g. ‘my body feels unfamiliar’). Factor analysis of online responses found that FSA-dissociation manifested in seven ways: anomalous experiences of the self, body, and emotion, and altered senses of familiarity, connection, agency, and reality (Χ2(553) = 4989.435, p<0.001, CFI = 0.929, TLI = 0.924, RMSEA = 0.052, SRMR = 0.047). Additionally, a single-factor ‘global FSA’ scale was produced (Χ2(9) = 312.350, p<0.001, CFI = 0.970, TLI = 0.950, RMSEA = 0.107, SRMR = 0.021). Model fit was adequate in the clinical (psychosis) group (Χ2(553) = 1623.641, p<0.001, CFI = 0.927, TLI = 0.921, RMSEA = 0.043, SRMR = 0.043). The scale had good convergent validity with a widely used dissociation scale (DES-II) (non-clinical: r = 0.802), excellent internal reliability (non-clinical: Cronbach’s alpha = 0.98; clinical: Cronbach’s alpha = 0.97), and excellent test-retest reliability (non-clinical: ICC = 0.92). Further, in non-clinical respondents scoring highly on a PTSD measure, CFA confirmed adequate model fit (Χ2(553) = 4758.673, CFI = 0.913, TLI = 0.906, RMSEA = 0.052, SRMR = 0.054).

Conclusions

The Černis Felt Sense of Anomaly (ČEFSA) scale is a novel measure of a subset of dissociative experiences that share a core feature of FSA. It is psychometrically robust in both non-clinical and psychosis groups.
Comparative analysis of ACE2 protein expression in rodent, non-human primate, and human respiratory tract at baseline and after injury: A conundrum for COVID-19 pathogenesis
Authors: Soni Sourabh , Jiang Yujie , Tesfaigzi Yohannes , Hornick Jason L. , Çataltepe Sule
Published: February 2021

Angiotensin converting enzyme 2 (ACE2) is the putative functional receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Current literature on the abundance and distribution of ACE2 protein in the human respiratory tract is controversial. We examined the effect of age and lung injury on ACE2 protein expression in rodent and non-human primate (NHP) models. We also examined ACE2 expression in human tissues with and without coronavirus disease 19 (COVID-19). ACE2 expression was detected at very low levels in preterm, but was absent in full-term and adult NHP lung homogenates. This pattern of ACE2 expression contrasted with that of transmembrane protease serine type 2 (TMPRSS2), which was significantly increased in full-term newborn and adult NHP lungs compared to preterm NHP lungs. ACE2 expression was not detected in NHP lungs with cigarette smoke-induced airway disease or bronchopulmonary dysplasia. Murine lungs lacked basal ACE2 immunoreactivity, but responded to hyperoxia, bacterial infection, and allergen exposure with new ACE2 expression in bronchial epithelial cells. In human specimens, robust ACE2 immunoreactivity was detected in ciliated epithelial cells in paranasal sinus specimens, while ACE2 expression was detected only in rare type 2 alveolar epithelial cells in control lungs. In autopsy specimens from patients with COVID-19 pneumonia, ACE2 was detected in rare ciliated epithelial and endothelial cells in the trachea, but not in the lung. There was robust expression of ACE2 expression in F344/N rat nasal mucosa and lung specimens, which authentically recapitulated the ACE2 expression pattern in human paranasal sinus specimens. Thus, ACE2 protein expression demonstrates a significant gradient between upper and lower respiratory tract in humans and is scarce in the lung. This pattern of ACE2 expression supports the notion of sinonasal epithelium being the main entry site for SARS-CoV-2 but raises further questions on the pathogenesis and cellular targets of SARS-CoV-2 in COVID-19 pneumonia.
Comparisons of adipogenesis- and lipid metabolism-related gene expression levels in muscle, adipose tissue and liver from Wagyu-cross and Holstein steers
Authors: Liu Li , Cao Peili , Zhang Lupei , Qi Meiyu , Wang Liang , Li Zhongqiu , Shao Guang , Ding Liyan , Zhao Xiuhua , Zhao Xiaochuan , Xu Shanshan , Zhang Haifeng , Chai Jinbao , Yue Mengmeng , Wang Genlin , Liu Di , Sun Fang
Published: February 2021

The intramuscular fat (IMF) content and fatty acid composition are important meat quality traits that are mostly affected by the cattle breed. Muscle, adipose tissue and liver are important organs involved in the development of intramuscular adipose tissue. Thus, we hypothesized that there were marked differences in the adipogenesis and lipid metabolism of these tissues between Wagyu-cross and Holstein steers during the finishing phases. To test this hypothesis, we analyzed the expression levels of adipogenesis- and lipid metabolism-related genes in longissimus muscle (LM), subcutaneous fat (SCF) and liver from Wagyu-cross and Holstein steers at 26 months of age. The IMF content and fatty acid profile of LM were determined. Wagyu-cross steers had a higher IMF content and MUFA percentages in the LM than Holstein steers (P<0.05). The relative expression ofFGF2,COL1A1,SREBP1c,SCD1,GRP78andLEPwas greater in the LM of Wagyu-cross steers than in Holstein steers (P<0.05). In contrast, Holstein steer SCF had higher (P<0.05) mRNA expression levels ofFABP4andADIPOQthan Wagyu-cross steers. In the liver, the expression ofSREBP1candGRP78in Wagyu-cross steers was significantly higher than that in Holstein steers (P<0.05). The results demonstrate that both intramuscular adipogenesis and fibrogenesis are enhanced in Wagyu-cross steers compared with Holstein steers during the finishing phase and that IMF deposition is positively correlated with the maturity of SCF and hepatic lipid accumulation in Wagyu-cross steers.
Ethics training for theatre artists: A manifesto
Authors: Vandevender Bryan M.
Published: February 2021

Professional theatre practice in the United States rests on a foundation of patriarchal, heteronormative, capitalist white supremacy. Of the many factors reifying theatre’s ties to racial and gender inequity, the theatre curriculum deployed by most American colleges and universities is perhaps one of the most consequential as it both upholds and replicates the profession’s oppressive structures by privileging training in craft over a more humanistic engagement with the discipline. If theatre curriculum actively challenged the profession’s oppressive foundations, and thereby produced artists who are prepared and committed to working for justice, then future generations might be able to change the profession from within the profession. I propose integrating ethics training into theatre curriculum as one way to initiate this process. This manifesto advocates for an ethics-driven theatre education and suggests that training in ethics will prompt students to consider the material consequences of their artistic choices and justify their decision-making using ethical theory. Ethical reasoning requires practice and the classroom is an ideal place for students to rehearse their use of ethics. Working through an ethical dilemma with classmates gives students the opportunity not only to see ethics as a social project, but also to devise anti-racist, feminist and queer-affirming approaches to artmaking. Training the next generation of theatre artists in ethics could lead to profound changes in the way we create and consume theatrical art in the future.
Territorializar el capital desterritorializando lo rural. Consecuencias territoriales asociados a los cambios en el uso del suelo del Valle Antinaco Los Colorados, La Rioja, Argentina
Authors: Montilla Pablo , Torres Laura
Published: February 2021

En la mirada de Haesbaert (2004) no hay manera de definir al individuo, al grupo, a la comunidad, a la sociedad, por fuera del contexto geográfico-territorial que los contiene. Los sujetos producen sus propios territorios, de manera tal que su modificación abre un camino incierto en el que confluyen, se articulan y retroalimentan los procesos de despojo, enajenación del lugar y destrucción de las territorialidades que dan sostén a la vida. Los relatos de algunos productores agropecuarios de Vichigasta, La Rioja, Argentina, exponen, con claridad meridiana, cómo estas dinámicas afectan su reproducción social. Expresan una profunda impotencia frente a la imposibilidad de frenar el avance de las actividades empresariales con una lógica distinta a la del campesinado, no pudiendo haber logrado hasta el momento resultados en sus luchas acordes con sus expectativas. La creación de una reserva natural comienza a avizorarse como una posibilidad de resguardo y barrera al avance expansivo del capital. Una manera renovada, aunque no libre de contradicciones de valorar el patrimonio natural como dador de servicios y bienes ecológicos e incluso emerge como un espacio donde aportar a la gestión del territorio por y para la comunidad vichigasteña. El presente trabajo avanza con el análisis de las tendencias de crecimiento agrícola en los últimos 30 años en la zona y describen las tensiones generadas como consecuencia de ello. Luego, analiza los procesos de desterritorialización en curso y recupera las miradas de los productores agropecuarios a propósito de las tendencias territoriales en curso.
Caligrafías diversas para interpretar el territorio. Lecturas en clave de paisaje en la ruralidad del piedemonte-Mendoza
Authors: Marchionni Franco , Sella Alejandra Adriana , Torres Laura María del Rosario , Pastor Gabriela Claudia
Published: February 2021

Las lógicas urbanas y las preexistencias ambientales y antrópicas escriben caligrafías diversas que, como marcas, pueden ser leídas en el territorio en clave de paisaje. Desde esa perspectiva, este trabajo busca comprender la sucesiva reconfiguración del frente urbano-rural que deviene de la fricción de diversos proyectos territoriales y las múltiples formas en que se inscriben en el ambiente y uso de la tierra. La metodología empleada está basada en la revisión y análisis documental en articulación con los testimonios orales recogidos en el trabajo de campo. Se reconocen cuatro cortes espacio-temporales derivados de proyectos de territorialización diversos. Finalmente, se revisan pautas que podrían devolver al territorio su propio equilibrio.
Rosyjskie wyrażenie не судьба i jego polskie odpowiedniki
Authors: Hordy Mirosława
Published: February 2021

The subject of the article is a comparative analysis of the Russian expression не судьба кому-л. and its Polish equivalents. In the ethno-cultural aspect, it describes one of the Russian key ideas – the concept of SUD’BA. The special status of the discussed unit is evidenced by: the synthetic form and the inability to express its content in the same simple way in another language, the non-assertive type of meaning and informality. The analysis of lexicographic and corpus sources shows that the closest synonyms of the Russian predicate are Polish sentence phrases, coś nie było sądzone komuś and taki los that shows semantic and pragmatic differences. The devaluation of the importance of the Russian unit observed in recent uses consists in changing the attitude of regret towards unfavourable events into a sense of relief and its relation to “light” and ordinary events. This meaning corresponds to Polish – taka już czyjaś uroda.
Współpraca naukowa PRL z drugą Jugosławią
Authors: Małczak Leszek
Published: February 2021

Scientific connections between Polish People’s Republic and The Second Yugoslavia were a very important element of the bilateral relations between both countries. The mechanisms and rules of the scientific cooperation were similar to the rules and mechanisms of the cultural cooperation and faced the same constraints and possibilities. Types of institutions existing in the field of culture had their correspondences in the field of science and education. Developing of the scientific cooperation was not a strategic aim for both countries in the interwar period as well as during the Communism due to the situation on the international political scene. In the era of globalization, in the context of international scientific cooperation, interslavic relations has become the weakest in the last two centuries. Nowadays, even more than before, the scientific cooperation between all Slavic countries depends on individuals and their involvement.
A RELEVÂNCIA DO PORTAL BASE, À LUZ DOS PRINCÍPIOS FUNDAMENTAIS DA CONTRATAÇÃO PÚBLICA E DO PROCEDIMENTO DE FORMAÇÃO DOS CONTRATOS PÚBLICOS EM PORTUGAL
Authors: Anjos Azevedo Patrícia , Rua Carneiro Davide
Published: February 2021

Resumo

Na formação e execução dos contratos públicos devem ser respeitados os princípios da legalidade, prossecução do interesse público, imparcialidade, proporcionalidade, boa-fé, tutela da confiança, sustentabilidade e responsabilidade, concorrência, publicidade e transparência, igualdade de tratamento e não-discriminação. O procedimento de formação de contratos constitui a sucessão ordenada de atos que concorrem para a formação, a conclusão e a produção de uma plena eficácia jurídica de um contrato público. O legislador define os momentos que constituem a tramitação do procedimento, numa lógica de transparência, garantindo a imparcialidade e a igualdade de tratamento e de acesso ao procedimento e a adequação procedimental.

O objetivo principal do portal Base é divulgar informação sobre os contratos públicos celebrados em Portugal sujeitos ao regime do Código dos Contratos Públicos. Para dar cumprimento a este objetivo, o portal constitui-se como uma ferramenta tecnológica que centraliza, num espaço virtual, informações referentes à formação e execução dos contratos públicos.

Palavras-Chave: Portal Base; princípios; contratação pública; procedimento; contratos públicos
Optimal H2O2 concentration in advanced oxidation over titanium dioxide photocatalyst
Authors: Danyliuk Nazarii , Mironyuk Ivan , Tatarchuk Tetiana , Shyichuk Alexander
Published: February 2021

The oxidative degradation of Rhodamine B dye under ultraviolet irradiation was studied. The degradation rate was measured with using of smartphone camera. Photocatalytic degradation of the Rhodamine B dye over the P25-TiO2 catalyst has been found to accelerate substantially in the presence of hydrogen peroxide. The relationship between the photocatalytic degradation rate and H2O2 concentration has been studied. The optimal concentration of H2O2 has been found to in the range of 10-25 mM. The proposed mixture of P25 photocatalyst and H2O2 oxidizer can be used to remove organic pollutions from industrial waste water.
Descolonizar el saber, descolonizar el ser: Una perspectiva (negra) sobre la resistencia desde Brasil / Entrevista a Iyá Sandrali de Campos Bueno
Authors: FONTOURA RODRIGUES Iliriana
Published: February 2021

Entrevista a Iyá Sandrali de Campos Bueno