bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural analysis of 3’UTRs in insect flaviviruses reveals novel determinants of sfRNA biogenesis and provides new insights into flavivirus evolution
Authors: Slonchak Andrii , Parry Rhys , Pullinger Brody , Sng Julian D. J. , Wang Xiaohui , Buck Teresa F. , Torres Francisco J. , Harrison Jessica J. , Colmant Agathe M. G. , Hobson-Peters Jody , Hall Roy A. , Tuplin Andrew , Khromykh Alexander A. 
Published: March 2022

AbstractSubgenomic flaviviral RNAs (sfRNAs) are virus-derived noncoding RNAs produced by pathogenic mosquito-borne flaviviruses (MBF) to counteract the host antiviral response. To date, the ability of non-pathogenic flaviviruses to produce and utilise sfRNAs remains largely unexplored, and it is unclear what role XRN1 resistance plays in flavivirus evolution and host adaptation. Herein the production of sfRNAs by several insect-specific flaviviruses (ISFs) that replicate exclusively in mosquitoes is shown, and the secondary structures of their complete 3’UTRs are determined. The xrRNAs responsible for the biogenesis of ISF sfRNAs are also identified, and the role of these sfRNAs in virus replication is demonstrated. We demonstrate that 3’UTRs of all classical ISFs, except Anopheles spp-asscoaited viruses, and of the dual-host associated ISF Binjari virus contain duplicated xrRNAs. We also reveal novel structural elements in the 3’UTRs of dual host-associated and Anopheles-associated classical ISFs. Structure-based phylogenetic analysis demonstrates that xrRNAs identified in Anopheles spp-associated ISF are likely ancestral to xrRNAs of ISFs and MBFs. In addition, our data provide evidence that duplicated xrRNAs are selected in the evolution of flaviviruses to provide functional redundancy, which preserves the production of sfRNAs if one of the structures is disabled by mutations or misfolding.
Multiscale modeling of ultrafast melting phenomena
Authors: Calogero Gaetano , Raciti Domenica , Acosta-Alba Pablo , Cristiano Fuccio , Deretzis Ioannis , Fisicaro Giuseppe , Huet Karim , Kerdilès Sébastien , Sciuto Alberto , La Magna Antonino 
Published: March 2022

AbstractUltraviolet Nanosecond Laser Annealing (LA) is a powerful tool for both fundamental investigations of ultrafast, nonequilibrium phase-change phenomena and technological applications (e.g., the processing of 3D sequentially integrated nano-electronic devices) where strongly confined heating and melting is desirable. Optimizing the LA process along with the experimental design is challenging, especially when involving complex 3D-nanostructured systems with various shapes and phases. To this purpose, it is essential to model critical nanoscale physical LA-induced phenomena, such as shape changes or formation and evolution of point and extended defects. To date, LA simulators are based on continuum models, which cannot fully capture the microscopic kinetics of a solid–liquid interface. In this work a fully atomistic LA simulation methodology is presented, based on the parallel coupling of a continuum, finite elements, μm-scale electromagnetic-thermal solver with a super-lattice Kinetic Monte Carlo atomistic model for melting. Benchmarks against phase-field models and experimental data validate the approach. LA of a Si(001) surface is studied varying laser fluence and pulse shape, assuming both homogeneous and inhomogeneous nucleation, revealing how liquid Si nuclei generate, deform and coalesce during irradiation. The proposed methodology is applicable to any system where the atom kinetics is determined by a strongly space- and time-dependent field, such as temperature or strain.
A chiral one-dimensional atom using a quantum dot in an open microcavity
Authors: Antoniadis Nadia O. , Tomm Natasha , Jakubczyk Tomasz , Schott Rüdiger , Valentin Sascha R. , Wieck Andreas D. , Ludwig Arne , Warburton Richard J. , Javadi Alisa 
Published: March 2022

AbstractIn a chiral one-dimensional atom, a photon propagating in one direction interacts with the atom; a photon propagating in the other direction does not. Chiral quantum optics has applications in creating nanoscopic single-photon routers, circulators, phase-shifters, and two-photon gates. Here, we implement chiral quantum optics using a low-noise quantum dot in an open microcavity. We demonstrate the non-reciprocal absorption of single photons, a single-photon diode. The non-reciprocity, the ratio of the transmission in the forward-direction to the transmission in the reverse direction, is as high as 10.7 dB. This is achieved by tuning the photon-emitter coupling in situ to the optimal operating condition (β = 0.5). Proof that the non-reciprocity arises from a single quantum emitter lies in the photon statistics—ultralow-power laser light propagating in the diode’s reverse direction results in a highly bunched output (g(2)(0) = 101), showing that the single-photon component is largely removed.
Cortical thinning over two years after first-episode psychosis depends on age of onset
Authors: Pina-Camacho Laura , Martinez Kenia , Diaz-Caneja Covadonga M. , Mezquida Gisela , Cuesta Manuel J. , Moreno Carmen , Amoretti Silvia , González-Pinto Ana , Arango Celso , Vieta Eduard , Castro-Fornieles Josefina , Lobo Antonio , Fraguas David , Bernardo Miguel , Janssen Joost , Parellada Mara ,   PEPs Group, Madero Santiago , Gómez-Ramiro Marta , Rodriguez-Toscano Elisa , Santonja Javier , Zorrilla Iñaki , González-Ortega Itxaso , Fayed Nicolás , Santabárbara Javier , Berge Daniel , Toll Alba , Nacher Juan , Martí Gracián García , Sague-Vilavella Maria , Sanchez-Moreno Jose , de la Serna Elena , Baeza Immaculada , Saiz-Masvidal Cristina , Contreras Fernando , González-Blanco Leticia , Bobes-Bascarán Teresa , Dompablo Mónica , Rodriguez-Jimenez Roberto , Usall Judith , Butjosa Anna , Pomarol-Clotet Edith , Sarró Salvador 
Published: March 2022

AbstractFirst-episode psychosis (FEP) patients show structural brain abnormalities at the first episode. Whether the cortical changes that follow a FEP are progressive and whether age at onset modulates these changes remains unclear. This is a multicenter MRI study in a deeply phenotyped sample of 74 FEP patients with a wide age range at onset (15–35 years) and 64 neurotypical healthy controls (HC). All participants underwent two MRI scans with a 2-year follow-up interval. We computed the longitudinal percentage of change (PC) for cortical thickness (CT), surface area (CSA) and volume (CV) for frontal, temporal, parietal and occipital lobes. We used general linear models to assess group differences in PC as a function of age at FEP. We conducted post-hoc analyses for metrics where PC differed as a function of age at onset. We found a significant age-by-diagnosis interaction effect for PC of temporal lobe CT (d = 0.54; p = 002). In a post-hoc-analysis, adolescent-onset (≤19 y) FEP showed more severe longitudinal cortical thinning in the temporal lobe than adolescent HC. We did not find this difference in adult-onset FEP compared to adult HC. Our study suggests that, in individuals with psychosis, CT changes that follow the FEP are dependent on the age at first episode, with those with an earlier onset showing more pronounced cortical thinning in the temporal lobe.
High prevalence of intrathecal IgA synthesis in multiple sclerosis patients
Authors: Muñoz Úrsula , Sebal Cristina , Escudero Esther , García Sánchez Maria Isabel , Urcelay Elena , Jayo Asier , Arroyo Rafael , García-Martínez Maria A. , Álvarez-Lafuente Roberto , Sádaba María C. 
Published: March 2022

AbstractThe detection of intrathecal IgA synthesis (IAS) in multiple sclerosis (MS) could be underestimated. To assess it, we develop a highly sensitive assay based on isoelectric focusing (IEF). 151 MS patients and 53 controls with different neurological diseases were recruited. IgA concentration was analyzed using a newly developed in house ELISA. IgA oligoclonal bands to detect IAS were determined by IEF. Most individuals showed an IgA concentration within normal range in serum samples (90.69%) but 31.37% of individuals had a IgA concentration below the normal range in the cerebrospinal fluid (CSF). No significant differences were observed between MS and control groups, neither in CSF nor in serum. The new IEF was more sensitive than those previously described (0.01 mg/dl of IgA), and clearly identified patients with and without IAS, that was not related with IgA concentration. Using IEF, MS patients showed higher percentage of IAS-IEF (43.00%) than the control group (16.98) (p = 0.001). The incidence was especially higher in patients with clinically isolated syndrome (66.00%). The new IFE demonstrated a higher percentage of IAS in MS patients than assumed in the past. The presence of IAS-IEF in MS is higher than in other neurological diseases.
Weather fluctuation can override the effects of integrated nutrient management on fungal disease incidence in the rice fields in Taiwan
Authors: Chiu Ming-Chih , Chen Chi-Ling , Chen Chun-Wei , Lin Hsing-Juh 
Published: March 2022

AbstractBoth weather fluctuation and farming system influence the epidemiology of crop diseases. However, short-term experiments are difficult to mechanistically extrapolate into long-term ecological responses. Using a mechanistic model with Bayesian inference, long-term data spanning 10 years were used to construct relationships among weather fluctuation (temperature, relative humidity, wind, and rainfall), farming system (conventional and low-external-input farming), and crop disease in experimental rice fields in Taiwan. Conventional and low-external-input farming had similar influences on the disease incidence of rice blast. Temperature had a positive influence on the disease incidence only under high relative humidity. Rainfall positively affected the disease incidence until an optimum level of rainfall. Low-external-input farming, with a lower application of fertilizers and other sustainable nutrient management, achieved similar effects on the disease incidence to those achieved by conventional farming. This suggests that weather fluctuation may override the effect of the farming systems on fungal disease incidence in rice fields.
Epigenome-wide association study and epigenetic age acceleration associated with cigarette smoking among Costa Rican adults
Authors: Cardenas Andres , Ecker Simone , Fadadu Raj P. , Huen Karen , Orozco Allan , McEwen Lisa M. , Engelbrecht Hannah-Ruth , Gladish Nicole , Kobor Michael S. , Rosero-Bixby Luis , Dow William H. , Rehkopf David H. 
Published: March 2022

AbstractSmoking-associated DNA methylation (DNAm) signatures are reproducible among studies of mostly European descent, with mixed evidence if smoking accelerates epigenetic aging and its relationship to longevity. We evaluated smoking-associated DNAm signatures in the Costa Rican Study on Longevity and Healthy Aging (CRELES), including participants from the high longevity region of Nicoya. We measured genome-wide DNAm in leukocytes, tested Epigenetic Age Acceleration (EAA) from five clocks and estimates of telomere length (DNAmTL), and examined effect modification by the high longevity region. 489 participants had a mean (SD) age of 79.4 (10.8) years, and 18% were from Nicoya. Overall, 7.6% reported currently smoking, 35% were former smokers, and 57.4% never smoked. 46 CpGs and five regions (e.g. AHRR, SCARNA6/SNORD39, SNORA20, and F2RL3) were differentially methylated for current smokers. Former smokers had increased Horvath’s EAA (1.69-years; 95% CI 0.72, 2.67), Hannum’s EAA (0.77-years; 95% CI 0.01, 1.52), GrimAge (2.34-years; 95% CI1.66, 3.02), extrinsic EAA (1.27-years; 95% CI 0.34, 2.21), intrinsic EAA (1.03-years; 95% CI 0.12, 1.94) and shorter DNAmTL (− 0.04-kb; 95% CI − 0.08, − 0.01) relative to non-smokers. There was no evidence of effect modification among residents of Nicoya. Our findings recapitulate previously reported and novel smoking-associated DNAm changes in a Latino cohort.
Simultaneous strength and ductility enhancements of high thermal conductive Ag7.5Cu alloy by selective laser melting
Authors: Xiong Wei , Hao Liang , Peijs Ton , Yan Chunze , Cheng Kaka , Gong Ping , Cui Qian , Tang Danna , Al Islam Shamoon , Li Yan 
Published: March 2022

AbstractHigh electrical and thermal conductive metals (HETCM) play a key role in smart electronics, green energy, modern communications and healthcare, however, typical HETCM (e.g., Ag, Au, Cu) usually have relatively low mechanical strength, hindering further applications. Selective laser melting (SLM) is a potentially transformative manufacturing technology that is expected to address the issue. Ag is the metal with the highest thermal conductivity, which induces microscale grain refinement, but also leads to high internal stresses by SLM. Here, we select Ag7.5Cu alloy as an example to demonstrate that multi-scale (micro/meso/macro) synergies can take advantage of high thermal conductivity and internal stresses to effectively strengthen Ag alloy. The mimicry of metal-hardened structures (e.g., large-angle boundary) is extended to the mesoscale by controlling the laser energy density and laser scanning strategy to manipulate the macroscale internal stress intensity and mesoscale internal stress direction, respectively, to form mesoscale large-angle "grains", resulting in multiple mutual perpendicular shear bands during fracture. The presented approach achieved a significant enhancement of yield strength (+ 145%) and ductility (+ 28%) without post-treatment. The results not only break the strength-ductility trade-off of conventional SLM alloys, but also demonstrate a multi-scale synergistic enhancement strategy that exploits high thermal conductivity and internal stresses.
A spectrum of preferential flow alters solute mobility in soils
Authors: Radolinski Jesse , Le Hanh , Hilaire Sheldon S. , Xia Kang , Scott Durelle , Stewart Ryan D. 
Published: March 2022

AbstractPreferential flow reduces water residence times and allows rapid transport of pollutants such as organic contaminants. Thus, preferential flow is considered to reduce the influence of soil matrix-solute interactions during solute transport. While this claim may be true when rainfall directly follows solute application, forcing rapid chemical and physical disequilibrium, it has been perpetuated as a general feature of solute transport—regardless of the magnitude preferential flow. A small number of studies have alternatively shown that preferential transport of strongly sorbing solutes is reduced when solutes have time to diffuse and equilibrate within the soil matrix. Here we expand this inference by allowing solute sorption equilibrium to occur and exploring how physiochemical properties affect solute transport across a vast range of preferential flow. We applied deuterium-labeled rainfall to field plots containing manure spiked with eight common antibiotics with a range of affinity for the soil after 7 days of equilibration with the soil matrix and quantified preferential flow and solute transport using 48 soil pore water samplers spread along a hillslope. Based on > 700 measurements, our data showed that solute transport to lysimeters was similar—regardless of antibiotic affinity for soil—when preferential flow represented less than 15% of the total water flow. When preferential flow exceeded 15%, however, concentrations were higher for compounds with relatively low affinity for soil. We provide evidence that (1) bypassing water flow can select for compounds that are more easily released from the soil matrix, and (2) this phenomenon becomes more evident as the magnitude of preferential flow increases. We argue that considering the natural spectrum preferential flow as an explanatory variable to gauge the influence of soil matrix-solute interactions may improve parsimonious transport models.
The impact of psychopathology on academic performance in school-age children and adolescents
Authors: Pagerols Mireia , Prat Raquel , Rivas Cristina , Español-Martín Gemma , Puigbó Júlia , Pagespetit Èlia , Haro Josep Maria , Ramos-Quiroga Josep Antoni , Casas Miquel , Bosch Rosa 
Published: March 2022

AbstractPsychiatric symptoms have consistently been associated with negative educational outcomes. However, possible confounding variables, such as comorbid mental and environmental conditions, have not been well addressed. This study examined whether mental health problems were significantly linked to academic performance in a Spanish school-based sample, after adjustment for co-occurring psychiatric symptoms and multiple contextual factors. Parents completed a questionnaire regarding child’s sociodemographic characteristics (i.e., gender, age, type of school, socioeconomic status, ethnicity), stressful events (i.e., adoption, parental divorce/separation, grade retention) and lifestyle (i.e., diet, sleep, screen time), along with the Child Behavior Checklist (CBCL). Academic performance was obtained from school records. The sample comprised 7036 students aged 5–17 with full data on the CBCL. Mixed-effects ordinal logistic regression analyses were conducted to investigate the association between psychopathology and academic achievement, controlling for potential confounders. When examined separately, higher scores on the CBCL scales were related to lower grades, regardless of sociodemographic factors. However, after controlling for the presence of other psychiatric symptoms, we found that students who reported more anxious/depressed and thought problems were less likely to perform poorly, while those with increased levels of attention problems and delinquent behavior had higher risk for academic underachievement. These associations remained mainly the same once stressful events and lifestyle were taken into account. This investigation demonstrates that anxious/depressed symptoms, thought problems, attention problems, and delinquent behavior are independently associated with academic performance, which emphasize the need for preventive and treatment interventions targeted at students’ mental health to improve their psychological well-being and functioning at school.
Prediction of residual astigmatism in cataract surgery at different diameter zones using optical biometry measurement
Authors: Chang Yin-Hsi , Pu Christy , Lin Ken-Kuo , Lee Jiahn-Shing , Hou Chiun-Ho 
Published: March 2022

AbstractThe studies for astigmatism prediction error at different diameters using optical biometry are scant. We investigated patients who underwent cataract surgery with monofocal, nontoric intraocular lens (IOL) from 2017 through 2019 in a medical center. Patients with prior refractive surgeries, corneal opacity, or surgical complications were excluded. Corneal astigmatism (CA) was measured using AL-Scan at 2.4- and 3.3-mm diameter zones and calculated using the Barrett toric calculator preoperatively and postoperatively. The mean absolute error and centroid prediction error for the two zones were computed using double-angle plots. In total, 101 eyes of 76 patients were analyzed. Mean patient age was 68.7 ± 9.3 years and mean preoperative CA power was 0.7 ± 0.5 D. The overall centroid prediction error a 3.3 mm (0.09 ± 0.58 D@25) was significantly lower than that at 2.4 mm (0.09 ± 0.68 D@87) on the X-axis (P = 0.003). The 3.3-mm measurement also had a lower centroid prediction error than the 2.4-mm did for eyes with against-the-rule (ATR) and oblique astigmatism (P = 0.024; 0.002 on X-axis, respectively). The 3.3-mm measurement provided a more accurate CA estimation than the 2.4-mm did, particularly for ATR astigmatism. Diameter zone and astigmatism type should be considered crucial to precise astigmatism calculation.
Inverted internal limiting membrane flap technique for retinal detachment due to macular holes in high myopia with axial length ≥ 30 mm
Authors: Xu Changzhong , Feng Chao , Han Mengyao , He Junwen , Zhang Rui , Yan Tao , Li Xiangyun , Liu Yong , Li Yanzi , Wu Jianhua 
Published: March 2022

AbstractTo compare the efficacy of internal limiting membrane (ILM) flap covering to that of ILM flap insertion for the treatment of macular hole retinal detachment (MHRD) in highly myopic eyes with axial length (AL) ≥ 30 mm. We retrospectively analysed the medical records of 48 MHRD patients with high myopia (AL ≥ 30 mm). According to different surgical methods, the patients were divided into a covering group (23 eyes) and an insertion group (25 eyes). The rate of retinal reattachment and MH closure were compared between the two groups, and the related factors affecting the initial anatomical results were analysed. After primary vitrectomy and single silicone oil removal, there were 18 eyes (78.3%) in the covering group, and 20 eyes (80.0%) in the insertion group had retinal reattachment (P = 1.000). Moreover, 16 eyes (69.6%) in the covering group and 17 eyes (68.0%) in the insertion group had their MHs sealed (P = 0.907). The best-corrected visual acuity (BCVA) at 12 months and the improvement in BCVA postoperatively in the two groups were not statistically significant (P = 0.543, 0.955). Logistic regression analysis showed that elongated AL (OR = 1.844, 95% CI 1.037–3.280, P = 0.037) and higher choroidal atrophy (OR = 2.986, 95% CI 1.011–8.821, P = 0.048) were risk factors affecting initial anatomical success. For extremely high-myopia MHRD with AL ≥ 30 mm, ILM flap covering and insertion can both effectively seal the MH and promote retinal reattachment, but the visual function improvement may still be limited. The longer the AL and the higher the choroidal atrophy, the greater is the risk of initial anatomical failure.
Femtosecond laser-assisted cataract surgery after corneal refractive surgery
Authors: Ahn Hyunmin , Jun Ikhyun , Seo Kyoung Yul , Kim Eung Kweon , Kim Tae-im 
Published: March 2022

AbstractCataract is the leading cause of blindness worldwide, and advanced cataract techniques such as femtosecond laser-assisted cataract surgery (FLACS) have been commercially available. Corneal refractive surgery (CRS) is one of the most popular surgeries for the correction of refractive errors. CRS changes the cornea not only anatomically but also pathophysiologically. However, there has been no clinical research analyzing the refractive and safety outcomes of FLACS after CRS. The aim of this retrospective chart review and comparative study is to evaluate the effect and safety of FLACS after CRS comparing with conventional PCS. Participants with a previous CRS history who underwent FLACS or conventional PCS were included in this study. The visual outcomes and the refractive outcomes including refractive, corneal, and ocular residual astigmatism were compared. The safety outcomes were then studied intraoperatively and postoperatively. A total of 102 patients with age-related cataract were enrolled. At 3 months postoperatively, UCVA, BCVA, and predictive error were not significantly different between the FLACS and conventional PCS groups. Reduction of refractive astigmatism was higher in FLACS. Postoperative ORA was significant lower in FLACS. Reduction of ORA was higher in FLACS. The intraoperative and postoperative complications were also not significantly different between the two groups. FLACS could effectively change refractive astigmatism and ORA; without more complications than conventional PCS. FLACS’ competitive edge in postoperative ORA may provide better visual quality than conventional PCS in patients with a previous history of CRS.