bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergence of dynamic vortex glasses in disordered polar active fluids
Authors: Chardac Amélie , Shankar Suraj , Marchetti M. Cristina , Bartolo Denis 
Published: March 2021

SignificanceActive systems, from bacteria to human crowds, often move through disordered environments, but the impact of quenched disorder on self-organized collective flow remains largely unexplored. We combine microfluidic experiments involving a colloidal active fluid and hydrodynamic theory to study a flocking fluid navigating a disordered substrate. While weak disorder hardly disrupts the robust collective motion, above a critical disorder strength the system organizes in a remarkable state of correlated flows through a frozen network of defects—a dynamical vortex glass, akin to vortex glasses in dirty superconductors. Strong disorder and activity conspire to generate a gauge field that proliferates pinned vortices, a general mechanism that may apply to a broad class of synthetic and biological active fluids.
Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q
Authors: Shi Ke , Moeller Nicholas H. , Banerjee Surajit , McCann Jennifer L. , Carpenter Michael A. , Yin Lulu , Moorthy Ramkumar , Orellana Kayo , Harki Daniel A. , Harris Reuben S. , Aihara Hideki 
Published: March 2021

Significance
Deamination of cytosine and adenine bases in DNA is one of the most common sources of genetic mutation in biology and a major driver of virus and tumor evolution. Recent studies have identified a novel class of DNA-repair enzyme from archaea and bacteria, designated endonuclease Q (EndoQ), which has unique activity to initiate the repair of both these deaminated lesions. Our X-ray crystallographic and biochemical analyses presented here reveal how EndoQ achieves high selectivity toward these chemically divergent substrates without cleaving undamaged DNA. We also demonstrate that EndoQ, as the only known nuclease that cleaves DNA at deoxyuridine nucleotide, is useful for studying DNA deamination and repair in mammalian systems.
The mechanics and dynamics of cancer cells sensing noisy 3D contact guidance
Authors: Kim Jihan , Cao Yuansheng , Eddy Christopher , Deng Youyuan , Levine Herbert , Rappel Wouter-Jan , Sun Bo 
Published: March 2021

Significance
The spatial organization of ECM fibers biases the polarization and migration of cancer cells, a phenomenon known as contact guidance which is directly linked to the clinical outcome of cancers. In physiological conditions, ECM fibers do not align perfectly in parallel. Therefore, we study the morphological and migrational response of breast cancer cells to ECM fibers aligned to various degrees. We identify the cell’s aspect ratio as an integrated biomarker that determines its sensitivity to contact guidance cues. We also find that the level of ECM alignment modulates transitions between cells of differing morphology. Taken together, we show that cells integrate complex mechanical cues to determine their morphodynamics, thereby controlling polarization and migration in 3D ECM.
An in vivo method for diversifying the functions of therapeutic antibodies
Authors: Tian Ming , Cheng Hwei-Ling , Kimble Michael T. , McGovern Kelly , Waddicor Peyton , Chen Yiwei , Cantor Elizabeth , Qiu Mengting , Tuchel Marie-Elen , Dao Mai , Alt Frederick W. 
Published: March 2021

SignificanceThe immune system can produce enormous varieties of antibodies to counter infections. In this study, we devised a method to harness the power of the immune system to produce therapeutic antibodies. We used this method to generate antibodies against human PD1, a negative regulator of T cell activity. Available anti-PD1 therapeutic antibodies inhibit the function of PD1, thereby boosting T cell activity against tumor cells. We diversified one such anti-PD1 antibody and obtained multiple anti-PD1 antibodies, some of which can stimulate, rather than inhibit, PD1 function in vitro. Such PD1-stimulatory antibodies could potentially be used to suppress pathogenic T cell activities in autoimmune diseases. This method could be used to diversify the functions of other therapeutic antibodies.
Word alignment in a parallel corpus of Old English prose
Authors: Martín Arista Javier 
Published: March 2021

Abstract
This chapter proposes a model of syntactic annotation for the Parallel Corpus of Old English Prose, an aligned corpus of Old English and Present Day English texts. The research focuses on areas of syntactic divergence between the aligned texts. Syntactic divergence is described in terms of four types of alignment asymmetry (markedness, constituency, order, and configuration) and is represented by means of two components: a structural description and a dependency tree. The main conclusion is that these two components constitute a historical micro-grammar that identifies stability and change with respect to specific categories and constructions.
Semantic textual similarity based on deep learning
Authors: Ranasinghe Tharindu , Mitkov Ruslan , Orăsan Constantin , Quintana Rocío Caro 
Published: March 2021

Abstract
This study proposes an original methodology to underpin the operation of new generation Translation Memory (TM) systems where the translations to be retrieved from the TM database are matched not on the basis of Levenshtein (edit) distance but by employing innovative Natural Language Processing (NLP) and Deep Learning (DL) techniques. Three DL sentence encoders were experimented with to retrieve TM matches in English-Spanish sentence pairs from the DGT TM dataset. Each sentence encoder was compared with Okapi which uses edit distance to retrieve the best match.1 The automatic evaluation shows the benefit of the DL technology for TM matching and holds promise for the implementation of the TM tool itself, which is our next project.
Generic analysis of mobile application reviews in English and Spanish
Authors: Mora López Natalia 
Published: March 2021

Abstract
In this paper, the Systemic Functional Linguistics (SFL) approach to genre is applied to English and Spanish mobile application reviews from Google Play Store. These reviews are shown to be divisible into two optional stages, namely Evaluation and Description, the first part being more subjective and based on the author’s opinion and the second one more objective and focused on describing issues. The frequency of use of the Attitude axis from Appraisal Theory provides support for the distinction of those stages. The combination of the polarity of the contents of each stage together with the number of stars given to the item reviewed creates six patterns for the reviews. However, no noticeable differences between English and Spanish reviews were observed.
The 2021 Magnonics Roadmap
Authors: Barman Anjan , Gubbiotti Gianluca , Ladak S , Adeyeye A O , Krawczyk M , Gräfe J , Adelmann C , Cotofana S , Naeemi A , Vasyuchka V I , Hillebrands B , Nikitov S A , Yu H , Grundler D , Sadovnikov A V , Grachev A A , Sheshukova S E , Duquesne J-Y , Marangolo M , Csaba G , Porod W , Demidov V E , Urazhdin S , Demokritov S O , Albisetti E , Petti D , Bertacco R , Schultheiss H , Kruglyak V V , Poimanov V D , Sahoo S , Sinha J , Yang H , Münzenberg M , Moriyama T , Mizukami S , Landeros P , Gallardo R A , Carlotti G , Kim J-V , Stamps R L , Camley R E , Rana B , Otani Y , Yu W , Yu T , Bauer G E W , Back C , Uhrig G S , Dobrovolskiy O V , Budinska B , Qin H , van Dijken S , Chumak A V , Khitun A , Nikonov D E , Young I A , Zingsem B W , Winklhofer M 
Published: March 2021

Abstract
Magnonics is a budding research field in nanomagnetism and nanoscience that addresses the use of spin waves (magnons) to transmit, store, and process information. The rapid advancements of this field during last one decade in terms of upsurge in research papers, review articles, citations, proposals of devices as well as introduction of new sub-topics prompted us to present the first roadmap on magnonics. This is a collection of 22 sections written by leading experts in this field who review and discuss the current status besides presenting their vision of future perspectives. Today, the principal challenges in applied magnonics are the excitation of sub-100 nm wavelength magnons, their manipulation on the nanoscale and the creation of sub-micrometre devices using low-Gilbert damping magnetic materials and its interconnections to standard electronics. To this end, magnonics offers lower energy consumption, easier integrability and compatibility with CMOS structure, reprogrammability, shorter wavelength, smaller device features, anisotropic properties, negative group velocity, non-reciprocity and efficient tunability by various external stimuli to name a few. Hence, despite being a young research field, magnonics has come a long way since its early inception. This roadmap asserts a milestone for future emerging research directions in magnonics, and hopefully, it will inspire a series of exciting new articles on the same topic in the coming years.
Using Tracker to find the minimum angle of deviation and the refractive index of a prism
Authors: Ürek Handan , Özdemir Erdoğan , Coramik Mustafa 
Published: March 2021

Abstract
The target of this study is to determine the minimum angle of deviation of a prism which is one of the optical experiments. Thus, the aim is to state the refractive index of a prism. In this context, the Tracker program, which might also be utilized in terms of distance education purposes, was preferred. The videos of the experiments were recorded with the help of a smartphone. The study showed that the refractive indexes of the prisms which were made of glass and acrylic with different apex angles could be determined with a high level of accuracy as a result of the analysis of videos which were recorded with two different methods. It is believed that the study provides insights for both the conduction of laboratory courses via distance education and for performing experiments for students who do not have access to proper laboratory equipment.
Analogies between momentum current, electric current and entropy current
Authors: Wu Guobin , Wu Amy Yimin 
Published: March 2021

Abstract
This paper starts with an introduction to the concept of momentum current. It is followed by a discussion of its strength and density with the aid of several analogies made between momentum current and electric current. Based on the novel concepts of thermal charge and its quantity (entropy), the analogies are extended to entropy current. The broadened analogies cover the driving force and resistance of each current, the effects that the strength or density of each current has on their conductors, and the relationships between the above three currents and energy current, etc, which involve practical problems such as industrial safety, human thermal sensation, process control parameters as well as energy carriers and energy transport.
Potential Therapeutic Targets for Olfactory Dysfunction in Ciliopathies Beyond Single-Gene Replacement
Authors: Xie Chao , Martens Jeffrey R 
Published: March 2021

Abstract
Olfactory dysfunction is a common disorder in the general population. There are multiple causes, one of which being ciliopathies, an emerging class of human hereditary genetic disorders characterized by multiple symptoms due to defects in ciliary biogenesis, maintenance, and/or function. Mutations/deletions in a wide spectrum of ciliary genes have been identified to cause ciliopathies. Currently, besides symptomatic therapy, there is no available therapeutic treatment option for olfactory dysfunction caused by ciliopathies. Multiple studies have demonstrated that targeted gene replacement can restore the morphology and function of olfactory cilia in olfactory sensory neurons and further re-establish the odor-guided behaviors in animals. Therefore, targeted gene replacement could be potentially used to treat olfactory dysfunction in ciliopathies. However, due to the potential limitations of single-gene therapy for polygenic mutation-induced diseases, alternative therapeutic targets for broader curative measures need to be developed for olfactory dysfunction, and also for other symptoms in ciliopathies. Here we review the current understanding of ciliogenesis and maintenance of olfactory cilia. Furthermore, we emphasize signaling mechanisms that may be involved in the regulation of olfactory ciliary length and highlight potential alternative therapeutic targets for the treatment of ciliopathy-induced dysfunction in the olfactory system and even in other ciliated organ systems.
Smoking and nasopharyngeal cancer: individual data meta-analysis of six prospective studies on 334 935 men
Authors: Lin Jia Huang , Wen Chi Pang , Jiang Chao Qiang , Yuan Jian-Min , Chen Chien Jen , Ho Sai Yin , Gao Wayne , Zhang Weisen , Wang Renwei , Chien Yin-Chu , Xu Lin , Wu Xifeng , Jin Ya Li , Koh Woon-Puay , Hsu Wan-Lun , Zhu Feng , Wen Christopher , Zhu Tong , Lee June Han , Mai Zhi-Ming , Lung Maria Li , Lam Tai-Hing 
Published: March 2021

Abstract

Background
The role of smoking in nasopharyngeal carcinoma (NPC) remains uncertain, especially in endemic regions. We conducted an individual participant data (IPD) meta-analysis of prospective cohort studies to investigate the associations between smoking exposure and risk of NPC.

Methods
We obtained individual participant data of 334 935 male participants from six eligible population-based cohorts in NPC-endemic regions, including two each in Guangzhou and Taiwan, and one each in Hong Kong and Singapore. We used one- and two-stage approaches IPD meta-analysis and Cox proportional hazard models to calculate hazard ratios (HRs) and 95% confidence intervals (CIs) of NPC for smoking exposure adjusting for age and drinking status.

Results
During 2 961 315 person-years of follow-up, 399 NPC evens were ascertained. Risks of NPC were higher in ever versus never smokers (HRone-stage = 1.32, 95% CI = 1.07-1.63, P = 0.0088; HRtwo-stage = 1.27, 1.01-1.60, 0.04). These positive associations appeared to be stronger in ever smokers who consumed 16+ cigarettes/day (HRone-stage = 1.67, 95% CI = 1.29-2.16, P = 0.0001), and in those who started smoking at age younger than 16 (2.16, 1.33-3.50, 0.0103), with dose-response relationships (P-values for trend = 0.0028 and 0.0103, respectively). Quitting (versus daily smoking) showed a small reduced risk (stopped for 5+ years: HRone-stage = 0.91, 95% CI = 0.60-1.39, P = 0.66; for former smokers: HRtwo-stage = 0.84, 0.61-1.14, 0.26).

Conclusions
This first IPD meta-analysis from six prospective cohorts in endemic regions has provided robust observational evidence that smoking increased NPC risk in men. NPC should be added to the 12–16 cancer sites known to be tobacco-related cancers. Strong tobacco control policies, preventing young individuals from smoking, would reduce NPC risk in endemic regions.
Shedding of Culturable Virus, Seroconversion, and 6-Month Follow-up Antibody Responses in the First 14 Confirmed Cases of Coronavirus Disease 2019 in the United States
Authors: Killerby Marie E , Ata Ur Rasheed Mohammed , Tamin Azaibi , Harcourt Jennifer L , Abedi Glen R , Lu Xiaoyan , Kujawski Stephanie , Shah Melisa M , Kirking Hannah L , Gold Jeremy A W , Salvatore Phillip P , Coughlin Melissa M , Whitaker Brett , Tate Jacqueline E , Watson John T , Lindstrom Stephen , Hall Aron J , Fry Alicia M , Gerber Susan I , Midgley Claire M , Thornburg Natalie J 
Published: March 2021

Abstract
We aimed to characterize presence of culturable virus in clinical specimens during acute illness, and antibody kinetics up to 6 months after symptom onset, among 14 early patients with coronavirus disease 2019 in the United States. We isolated viable severe acute respiratory syndrome coronavirus 2 from real-time reverse-transcription polymerase chain reaction–positive respiratory specimens collected during days 0–8 after onset, but not after. All 13 patients with 2 or more serum specimens developed anti-spike antibodies; 12 developed detectable neutralizing antibodies. We did not isolate virus after detection of neutralizing antibodies. Eight participants provided serum at 6 months after onset; all retained detectable anti-spike immunoglobulin G, and half had detectable neutralizing antibodies. Two participants reported not feeling fully recovered at 6 months.
Prevalence and Prognosis of Lynch Syndrome and Sporadic Mismatch Repair Deficiency in Endometrial Cancer
Authors: Post Cathalijne C B , Stelloo Ellen , Smit Vincent T H B M , Ruano Dina , Tops Carli M , Vermij Lisa , Rutten Tessa A , Jürgenliemk-Schulz Ina M , Lutgens Ludy C H W , Jobsen Jan J , Nout Remi A , Crosbie Emma J , Powell Melanie E , Mileshkin Linda , Leary Alexandra , Bessette Paul , Putter Hein , de Boer Stephanie M , Horeweg Nanda , Nielsen Maartje , Wezel Tom van , Bosse Tjalling , Creutzberg Carien L 
Published: March 2021

Abstract

Background
Standard screening of endometrial cancer (EC) for Lynch syndrome (LS) is gaining traction; however, the prognostic impact of an underlying hereditary etiology is unknown. We established the prevalence, prognosis, and subsequent primary cancer incidence of patients with LS-associated EC in relation to sporadic mismatch repair deficient (MMRd)-EC in the large combined Post Operative Radiation Therapy in Endometrial Carcinoma-1, -2, and -3 trial cohort.

Methods
After MMR-immunohistochemistry, MLH1-promoter methylation testing, and next-generation sequencing, tumors were classified into 3 groups according to the molecular cause of their MMRd-EC. Kaplan-Meier method, log-rank test, and Cox model were used for survival analysis. Competing risk analysis was used to estimate the subsequent cancer probability. All statistical tests were 2-sided.

Results
Among the 1336 ECs, 410 (30.7%) were MMRd. A total of 380 (92.7%) were fully triaged: 275 (72.4%) were MLH1-hypermethylated MMRd-ECs; 36 (9.5%) LS MMRd-ECs, and 69 (18.2%) MMRd-ECs due to other causes. Limiting screening of EC patients to 60 years or younger or to 70 years or younger would have resulted in missing 18 (50.0%) and 6 (16.7%) LS diagnoses, respectively. Five-year recurrence-free survival was 91.7% (95% confidence interval [CI] = 83.1% to 100%; hazard ratio = 0.45, 95% CI = 0.16 to 1.24, P = .12) for LS, 95.5% (95% CI = 90.7% to 100%; hazard ratio = 0.17, 95% CI = 0.05 to 0.55, P = .003) for “other” vs 78.6% (95% CI = 73.8% to 83.7%) for MLH1-hypermethylated MMRd-EC. The probability of subsequent LS-associated cancer at 10 years was 11.6% (95% CI = 0.0% to 24.7%), 1.5% (95% CI = 0.0% to 4.3%), and 7.0% (95% CI = 3.0% to 10.9%) within the LS, “other,” and MLH1-hypermethylated MMRd-EC groups, respectively.

Conclusions
The LS prevalence in the Post Operative Radiation Therapy in Endometrial Carcinoma trial population was 2.8% and among MMRd-ECs was 9.5%. Patients with LS-associated ECs showed a trend towards better recurrence-free survival and higher risk for second cancers compared with patients with MLH1-hypermethylated MMRd-EC.
COVID-19-associated invasive pulmonary aspergillosis in a tertiary care center in Mexico City
Authors: Vélez Pintado Mariana , Camiro-Zúñiga Antonio , Aguilar Soto Mercedes , Cuenca Dalia , Mercado Moisés , Crabtree-Ramirez Brenda ,   the ARMII study gruop
Published: March 2021

Abstract

Invasive pulmonary aspergillosis (IPA) is a severe infection caused by aspergillus sp. that usually develops in patients with severe immunosuppression. IPA has been recently described in critically ill COVID-19 patients (termed as COVID-associated pulmonary aspergillosis, or CAPA) that are otherwise immunocompetent. In order to describe the characteristics of patients with CAPA, we conducted a retrospective cohort study in a tertiary care center in Mexico City. We included all patients with confirmed COVID-19 admitted to the intensive care unit that had serum or bronchoalveolar lavage galactomannan measurements. We used the criteria proposed by Koehler et al. to establish the diagnosis of CAPA. Main outcomes were the need for invasive mechanical ventilation (IMV) and in-hospital mortality. Out of a total of 83 hospitalized patients with COVID-19 in the ICU, 16 (19.3%) met the criteria for CAPA. All patients diagnosed with CAPA required IMV whereas only 84% of the patients in the non-IPA group needed this intervention (P = 0.09). In the IPA group, 31% (n = 5) of the patients died, compared to 13% (n = 9) in the non-CAPA group (P = 0.08). We conclude that CAPA is a frequent co-infection in critically ill COVID-19 patients and is associated with a high mortality rate. The timely diagnosis and treatment of IPA in these patients is likely to improve their outcome.

Lay Summary
We studied the characteristics of patients with COVID-19-associated invasive pulmonary aspergillosis (CAPA). Patients with CAPA tended to need invasive mechanical ventilation more frequently and to have a higher mortality rate. Adequate resources for its management can improve their outcome
Barred spiral galaxies in modified gravity theories
Authors: Roshan Mahmood , Banik Indranil , Ghafourian Neda , Thies Ingo , Famaey Benoit , Asencio Elena , Kroupa Pavel 
Published: March 2021

ABSTRACT
When bars form within galaxy formation simulations in the standard cosmological context, dynamical friction with dark matter (DM) causes them to rotate rather slowly. However, almost all observed galactic bars are fast in terms of the ratio between corotation radius and bar length. Here, we explicitly display an 8σ tension between the observed distribution of this ratio and that in the EAGLE simulation at redshift 0. We also compare the evolution of Newtonian galactic discs embedded in DM haloes to their evolution in three extended gravity theories: Milgromian Dynamics (MOND), a model of non-local gravity, and a scalar–tensor–vector gravity theory (MOG). Although our models start with the same initial baryonic distribution and rotation curve, the long-term evolution is different. The bar instability happens more violently in MOND compared to the other models. There are some common features between the extended gravity models, in particular the negligible role played by dynamical friction − which plays a key role in the DM model. Partly for this reason, all extended gravity models predict weaker bars and faster bar pattern speeds compared to the DM case. Although the absence of strong bars in our idealized, isolated extended gravity simulations is in tension with observations, they reproduce the strong observational preference for ‘fast’ bar pattern speeds, which we could not do with DM. We confirm previous findings that apparently ‘ultrafast’ bars can be due to bar-spiral arm alignment leading to an overestimated bar length, especially in extended gravity scenarios where the bar is already fast.
Exploring the tilted accretion disc of AQ Men with TESS
Authors: Iłkiewicz Krystian , Scaringi Simone , Court James M C , Maccarone Thomas J , Altamirano Diego , Bradshaw Corey W , Degenaar Nathalie , Fratta Matteo , Littlefield Colin , Shahbaz Tariq , Wijnands Rudy 
Published: March 2021

ABSTRACT
AQ Men is a nova-like variable that is presumed to have a tilted, precessing accretion disc. Grazing eclipses in this system have been speculated to be useful in exploring the geometry of its accretion disc. In this work, we analysed Transiting Exoplanet Survey Satellite (TESS) observations of AQ Men, which provide the best light curve of this object thus far. We show that the depths of the eclipses are changing with the orientation of the accretion disc, which means that they can serve as a direct test of the tilted accretion disc models. The precession period of the accretion disc is increasing during the TESS observations. However, it is still shorter than the period determined in the previous studies. The amplitude of the variability related to the precession of the accretion disc varies, and so does the shape of this variability. Moreover, we have detected a positive superhump that was previously unseen in AQ Men. Interestingly, the positive superhump has a strongly non-sinusoidal shape, which is not expected for a nova-like variable.