bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experiments on Pool Formation in Bedrock Canyons
Authors: Cao Zhihao (Eric) , Venditti Jeremy G. , Li Tingan 
Published: May 2022

AbstractRivers cut into rock exhibit a wide range of morphologies that do not occur in alluvial rivers. The reach‐scale morphology of bedrock canyons has not been widely explored. Many rivers bound by rock on both banks exhibit a constriction‐pool‐widening morphology characterized by a lateral channel constriction, a deeply scoured pool that typically forms downstream of the constriction, and a channel widening coincident with the scour pool. Lateral constrictions are thought to cause plunging flows that carve pools which then shallow and widen downstream. A flume experiment was conducted to test this hypothesis. Experiments show that flow deceleration upstream of the constricted canyon promotes alluviation. Flow acceleration through the canyon prevents persistent alluvium from developing before a pool is formed. At the canyon entrance, flow and sediment plunge toward the bed, creating a primary scour pool. The primary scour pool reaches equilibrium morphology for a given constant discharge and sediment supply by cutting a slot, which then gets deep enough to maintain a permanent alluvial cover, protecting the pool from further vertical erosion. Downstream of the primary pool, an alluvial cover intermittently develops that causes flow to plunge, carving secondary pools. Shear stresses are counterintuitively large in alluviated areas and low in places where the bed is clear of sediment. However, near‐bed velocity was strongly correlated with alluviation patterns and erosion rate, suggesting near‐bed velocity may be a more practical way to calculate rock erosion rates in non‐uniform flows.
Characterizing the Importance of Denitrification for N2O Production in Soils Using Natural Abundance and Isotopic Labeling Techniques
Authors: Stuchiner E. R. , von Fischer J. C. 
Published: May 2022

AbstractNitrous oxide (N2O), a potent greenhouse gas that contributes significantly to climate change, is emitted mostly from soils by a suite of microbial metabolic pathways that are nontrivial to identify, and subsequently, to manage. Using either natural abundance or enriched stable isotope methods has aided in identifying microbial sources of N2O, but each approach has limitations. Here, we conducted a novel pairing of natural abundance and enriched assays on two dissimilar soils, hypothesizing this pairing would better constrain microbial sources of N2O. We incubated paired natural abundance and enriched soils from a corn agroecosystem and a subalpine forest in the laboratory at 10%–95% soil saturation for 28 hr. The natural abundance method measured intramolecular site preference (SP) from emitted N2O, whereas the enriched method measured emitted 15N2O from soils amended with 15N‐labeled substrate. The isotopic composition of emitted N2O was measured using a laser‐based N2O isotopic analyzer, yielding two key findings. First, both methods revealed that denitrification was the primary source of N2O in all soils: isotopic enrichment revealed clear reduction to N2O, while SP indicated a likely combination of fungal and bacterial denitrification. Second, we quantified, to our knowledge for the first time, persistent (>55%) β‐position‐specific enrichment in N2O emitted from 15‐amended soils. This counter‐intuitive enrichment pattern could be indicative of codenitrification, an understudied but potentially important contributor to N2O emissions. Our work revealed the ubiquity of denitrification among the soils tested. Future pairings of natural abundance and enriched methods could better characterize diverse denitrification pathways.
Interannual Modulation of Subthermocline Eddy Kinetic Energy East of the Philippines
Authors: Hui Yuchao , Zhang Linlin , Wang Zhenxiao , Wang Fan , Hu Dunxin 
Published: May 2022

AbstractInterannual variation of subthermocline eddy kinetic energy (EKE) east of the Philippines is investigated based on mooring measurements during 2015–2019 and ocean‐state estimates during 1995–2017 from the Oceanic General Circulation Model for the Earth Simulator (OFES). Prominent interannual variation of EKE is detected below the thermocline east of the Philippine coast, which is closely related to the El Niño and Southern Oscillation (ENSO) events and generally lags the Nino3.4 index by 14 months. Further energy diagnostic analysis indicates that the interannual variation of subthermocline EKE is controlled by both baroclinic and barotropic instability of the background flows and dominated by the barotropic instability especially. Barotropic instability in the southern part of the Philippine coast is associated with the subsurface component of the quasi‐permanent anticyclonic Halmahera Eddy (HE), while that in the northern part is closely related to the Mindanao Undercurrent (MUC). Both HE and MUC are modulated by the ENSO events. When El Niño occurs, negative sea surface height anomalies appear near the dateline and propagate westward in the form of the first‐mode baroclinic Rossby wave, exerting delayed impacts upon the western boundary currents east of the Philippine coast and further modulating the interannual variation of subthermocline EKE. Moreover, the barotropic energy conversion rate and its corresponding subthermocline EKE at lower latitudes respond relatively faster to ENSO due to the higher Rossby wave group velocity there.
EPicker is an exemplar-based continual learning approach for knowledge accumulation in cryoEM particle picking
Authors: Zhang Xinyu , Zhao Tianfang , Chen Jiansheng , Shen Yuan , Li Xueming 
Published: May 2022

AbstractDeep learning is a popular method for facilitating particle picking in single-particle cryo-electron microscopy (cryo-EM), which is essential for developing automated processing pipelines. Most existing deep learning algorithms for particle picking rely on supervised learning where the features to be identified must be provided through a training procedure. However, the generalization performance of these algorithms on unseen datasets with different features is often unpredictable. In addition, while they perform well on the latest training datasets, these algorithms often fail to maintain the knowledge of old particles. Here, we report an exemplar-based continual learning approach, which can accumulate knowledge from the new dataset into the model by training an existing model on only a few new samples without catastrophic forgetting of old knowledge, implemented in a program called EPicker. Therefore, the ability of EPicker to identify bio-macromolecules can be expanded by continuously learning new knowledge during routine particle picking applications. Powered by the improved training strategy, EPicker is designed to pick not only protein particles but also general biological objects such as vesicles and fibers.
SPIN enables high throughput species identification of archaeological bone by proteomics
Authors: Rüther Patrick Leopold , Husic Immanuel Mirnes , Bangsgaard Pernille , Gregersen Kristian Murphy , Pantmann Pernille , Carvalho Milena , Godinho Ricardo Miguel , Friedl Lukas , Cascalheira João , Taurozzi Alberto John , Jørkov Marie Louise Schjellerup , Benedetti Michael M. , Haws Jonathan , Bicho Nuno , Welker Frido , Cappellini Enrico , Olsen Jesper Velgaard 
Published: May 2022

AbstractSpecies determination based on genetic evidence is an indispensable tool in archaeology, forensics, ecology, and food authentication. Most available analytical approaches involve compromises with regard to the number of detectable species, high cost due to low throughput, or a labor-intensive manual process. Here, we introduce “Species by Proteome INvestigation” (SPIN), a shotgun proteomics workflow for analyzing archaeological bone capable of querying over 150 mammalian species by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Rapid peptide chromatography and data-independent acquisition (DIA) with throughput of 200 samples per day reduce expensive MS time, whereas streamlined sample preparation and automated data interpretation save labor costs. We confirm the successful classification of known reference bones, including domestic species and great apes, beyond the taxonomic resolution of the conventional peptide mass fingerprinting (PMF)-based Zooarchaeology by Mass Spectrometry (ZooMS) method. In a blinded study of degraded Iron-Age material from Scandinavia, SPIN produces reproducible results between replicates, which are consistent with morphological analysis. Finally, we demonstrate the high throughput capabilities of the method in a high-degradation context by analyzing more than two hundred Middle and Upper Palaeolithic bones from Southern European sites with late Neanderthal occupation. While this initial study is focused on modern and archaeological mammalian bone, SPIN will be open and expandable to other biological tissues and taxa.
Selectively anchoring single atoms on specific sites of supports for improved oxygen evolution
Authors: Zhang Zhirong , Feng Chen , Wang Dongdi , Zhou Shiming , Wang Ruyang , Hu Sunpei , Li Hongliang , Zuo Ming , Kong Yuan , Bao Jun , Zeng Jie 
Published: May 2022

AbstractThe homogeneity of single-atom catalysts is only to the first-order approximation when all isolated metal centers interact identically with the support. Since the realistic support with various topologies or defects offers diverse coordination environments, realizing real homogeneity requires precise control over the anchoring sites. In this work, we selectively anchor Ir single atoms onto the three-fold hollow sites (Ir1/TO–CoOOH) and oxygen vacancies (Ir1/VO–CoOOH) on defective CoOOH surface to investigate how the anchoring sites modulate catalytic performance. The oxygen evolution activities of Ir1/TO–CoOOH and Ir1/VO–CoOOH are improved relative to CoOOH through different mechanisms. For Ir1/TO–CoOOH, the strong electronic interaction between single-atom Ir and the support modifies the electronic structure of the active center for stronger electronic affinity to intermediates. For Ir1/VO–CoOOH, a hydrogen bonding is formed between the coordinated oxygen of single-atom Ir center and the oxygenated intermediates, which stabilizes the intermediates and lowers the energy barrier of the rate-determining step.
Context-specific effects of sequence elements on subcellular localization of linear and circular RNAs
Authors: Ron Maya , Ulitsky Igor 
Published: May 2022

AbstractLong RNAs vary extensively in their post-transcriptional fates, and this variation is attributed in part to short sequence elements. We used massively parallel RNA assays to study how sequences derived from noncoding RNAs influence the subcellular localization and stability of circular and linear RNAs, including spliced and unspliced forms. We find that the effects of sequence elements strongly depend on the host RNA context, with limited overlap between sequences that drive nuclear enrichment of linear and circular RNAs. Binding of specific RNA binding proteins underpins some of these differences—SRSF1 binding leads to nuclear enrichment of circular RNAs; SAFB binding is associated with nuclear enrichment of predominantly unspliced linear RNAs; and IGF2BP1 promotes export of linear spliced RNA molecules. The post-transcriptional fate of long RNAs is thus dictated by combinatorial contributions of specific sequence elements, of splicing, and of the presence of the terminal features unique to linear RNAs.
Spindle motility skews division site determination during asymmetric cell division in Physcomitrella
Authors: Kozgunova Elena , Yoshida Mari W. , Reski Ralf , Goshima Gohta 
Published: May 2022

AbstractAsymmetric cell division (ACD) underlies the development of multicellular organisms. In animal ACD, the cell division site is determined by active spindle-positioning mechanisms. In contrast, it is considered that the division site in plants is determined prior to mitosis by the microtubule-actin belt known as the preprophase band (PPB) and that the localization of the mitotic spindle is typically static and does not govern the division plane. However, in some plant species, ACD occurs in the absence of PPB. Here, we isolate a hypomorphic mutant of the conserved microtubule-associated protein TPX2 in the moss Physcomitrium patens (Physcomitrella) and observe spindle motility during PPB-independent cell division. This defect compromises the position of the division site and produces inverted daughter cell sizes in the first ACD of gametophore (leafy shoot) development. The phenotype is rescued by restoring endogenous TPX2 function and, unexpectedly, by depolymerizing actin filaments. Thus, we identify an active spindle-positioning mechanism that, reminiscent of acentrosomal ACD in animals, involves microtubules and actin filaments, and sets the division site in plants.
Prevalence of molar incisor hypomineralization among school children in Rome, Italy
Authors: Nisii F. , Mazur M. , De Nuccio C. , Martucci C. , Spuntarelli M. , Labozzetta S. , Fratini A. , Sozzi S. , Maruotti A. , Vozza I. , Luzzi V. , Bossu M. , Ottolenghi L. , Polimeni A. 
Published: May 2022

AbstractMolar incisor hypomineralization (MIH) is a highly prevalent condition associated with increased caries experience, dental pain and treatment need. Aim of this study was to determine the prevalence and severity of MIH in a group of 7–8 years old primary school children living in Rome, Italy; and to assess the association with caries experience and possible perinatal risk factors. A survey has been conducted in the city of Rome, between April 2019 and March 2020 with a total of 49 primary schools and 176 2nd grade primary school classes and a total of 3611 children being involved. Of these, a subset of 346 children of 21 primary schools was selected for the epidemiological investigation. The prevalence of MIH was of 18.2%, with girls showing twice the probability of being subject to a mild-severe condition. Molar location was present in 71.4%, while location on both molar plus incisor was present in 28.6% of cases. The mean DMFT was 0.44 ± 0.78, “D” was 0.17 ± 0.58; the mean dmft was 1.7 ± 2.56, “d” was 1.32 ± 2.21. Female gender, caries experience, insufficient oral hygiene were risk factors. The incidence of MIH is increasing in the pediatric population. Knowledge about diagnosis and treatment options should be disseminated among dental professionals.
Laser slice thinning of GaN-on-GaN high electron mobility transistors
Authors: Tanaka Atsushi , Sugiura Ryuji , Kawaguchi Daisuke , Wani Yotaro , Watanabe Hirotaka , Sena Hadi , Ando Yuto , Honda Yoshio , Igasaki Yasunori , Wakejima Akio , Ando Yuji , Amano Hiroshi 
Published: May 2022

AbstractAs a newly developed technique to slice GaN substrates, which are currently very expensive, with less loss, we previously reported a laser slicing technique in this journal. In the previous report, from the perspective of GaN substrate processing, we could only show that the GaN substrate could be sliced by a laser and that the sliced GaN substrate could be reused. In this study, we newly investigated the applicability of this method as a device fabrication process. We demonstrated the thinning of GaN-on-GaN high-electron-mobility transistors (HEMTs) using a laser slicing technique. Even when the HEMTs were thinned by laser slicing to a thickness of 50 μm after completing the fabrication process, no significant fracture was observed in these devices, and no adverse effects of laser-induced damage were observed on electrical characteristics. This means that the laser slicing process can be applied even after device fabrication. It can also be used as a completely new semiconductor process for fabricating thin devices with thicknesses on the order of 10 μm, while significantly reducing the consumption of GaN substrates.
Perception thresholds and qualitative perceptions for electrocutaneous stimulation
Authors: Dölker Eva-Maria , Lau Stephan , Bernhard Maria Anne , Haueisen Jens 
Published: May 2022

AbstractOur long-term goal is the development of a wearable warning system that uses electrocutaneous stimulation. To find appropriate stimulation parameters and electrode configurations, we investigate perception amplitude thresholds and qualitative perceptions of electrocutaneous stimulation for varying pulse widths, electrode sizes, and electrode positions. The upper right arm was stimulated in 81 healthy volunteers with biphasic rectangular current pulses varying between 20 and$$2000\,\upmu \hbox {s}$$2000μs. We determined perception, attention, and intolerance thresholds and the corresponding qualitative perceptions for 8 electrode pairs distributed around the upper arm. For a pulse width of$$150\,\upmu \hbox {s}$$150μs, we find median values of 3.5, 6.9, and 13.8 mA for perception, attention, and intolerance thresholds, respectively. All thresholds decrease with increasing pulse width. Lateral electrode positions have higher intolerance thresholds than medial electrode positions, but perception and attention threshold are not significantly different across electrode positions. Electrode size between$$15 \times 15\,\hbox {mm}^{2}$$15×15mm2and$$40\times 40\,\hbox {mm}^{2}$$40×40mm2has no significant influence on the thresholds. Knocking is the prevailing perception for perception and attention thresholds while mostly muscle twitching, pinching, and stinging are reported at the intolerance threshold. Biphasic stimulation pulse widths between$$150\,\upmu \hbox {s}$$150μsand$$250\,\upmu \hbox {s}$$250μsare suitable for electric warning wearables. Within the given practical limits at the upper arm, electrode size, inter-electrode distance, and electrode position are flexible parameters of electric warning wearables. Our investigations provide the basis for electric warning wearables.
Accurate THz ellipsometry using calibration in time domain
Authors: Mazaheri Zahra , Koral Can , Andreone Antonello 
Published: May 2022

AbstractWe report on the realisation of a customized THz time domain spectroscopic ellipsometer (THz-TDSE) based on fiber-coupled photoconductive antennas, operating in a wide range of incident angles and allowing also standard transmission spectroscopy without any optical realignment. To ensure accurate parameter extraction for a broad range of materials, we developed a fast and effective algorithm-assisted method to calibrate the setup and compensate for the nonideality in the response of the THz system. The procedure allows to minimise errors induced by imperfect response of the antennas and polarizers, imprecise setting of the impinging and receiving angles in the goniometric mechanical arms, and unavoidable mismatches in the THz beam optics. Differently from other calibration methods applied in the literature, our approach compares in time domain the ellipsometric derived electric field s- and p-polarised components at a given angle of incidence with the reconstructed ones, attained by using the complex dielectric function of a known sample. The calibrated response is determined with high precision by setting the system in transmission mode. In order to validate the technique, ellipsometric measurements have been carried out at various angle of incidences on a number of materials both in solid and liquid form, and their data compared with what obtained by conventional THz spectroscopy. Results show that THz-TDSE accompanied with an accurate calibration procedure is an effective technique for material characterization, especially in case of samples with a high absorption rate that are not easily investigated through transmission measurements.
Anxiety increases information-seeking in response to large changes
Authors: Charpentier Caroline J. , Cogliati Dezza Irene , Vellani Valentina , Globig Laura K. , Gädeke Maria , Sharot Tali 
Published: May 2022

AbstractSeeking information when anxious may help reduce the aversive feeling of uncertainty and guide decision-making. If information is negative or confusing, however, this may increase anxiety further. Information gathered under anxiety can thus be beneficial and/or damaging. Here, we examine whether anxiety leads to a general increase in information-seeking, or rather to changes in the type of information and/or situations in which it is sought. In two controlled laboratory studies, we show that both trait anxiety and induced anxiety lead to a selective alteration in information-seeking. In particular, anxiety did not enhance the general tendency to seek information, nor did it alter the valence of the information gathered. Rather, anxiety amplified the tendency to seek information more in response to large changes in the environment. This was true even when the cause of the anxiety was not directly related to the information sought. As anxious individuals have been shown to have problems learning in changing environments, greater information-seeking in such environments may be an adaptive compensatory mechanism.
Spatial analysis of photoplethysmography in cutaneous squamous cell carcinoma
Authors: Rasmussen Simon Mylius , Nielsen Thomas , Hager Henrik , Schousboe Lars Peter 
Published: May 2022

AbstractThe primary treatment of the common malignancy squamous cell carcinoma is surgical removal. In this process, sufficient tissue removal is balanced against unnecessary mutilation. We recently presented a remote photoplethysmography algorithm, which revealed significant differences between processed video recordings of cancer biopsy areas and surrounding tissue. The aim of this study was to investigate whether spatial analyses of photoplethysmography data correlate with post-excision pathological analyses and thus have potential to assist in tumour delineation. Based on high speed video recordings of 11 patients with squamous cell carcinoma, we examined different parameters derived from temporal remote photoplethysmography variations. Signal characteristics values in sites matching histological sections were compared with pathological measures. Values were ranked and statistically tested with a Kendall correlation analysis. A moderate, negative correlation was found between signal oscillations and the width and transversal area of squamous cell carcinoma in the frequencies below 1 Hz and specifically from 0.02 to 0.15 Hz. We have presented a correlation between frequency content and prevalence of cancer based on regular video recordings of squamous cell carcinoma. We believe this is supported by published findings on malignant melanoma. Our findings indicate that photoplethysmography can be used to distinguish SCC from healthy skin.
A cost-efficient and alternative technique of managing fall armyworm Spodoptera frugiperda (J.E. Smith) larvae in maize crop
Authors: Kushwaha Ujjawal Kumar Singh 
Published: May 2022

AbstractAn experiment was conducted to test the efficacy of grease and emamectin benzoate in a randomized complete block design with five replications to reduce fall armyworm,Spodoptera frugiperda(J.E. Smith) larvae load from a maize field in the winter seasons of 2020 and 2021 in Sarlahi, Nepal. Standard agronomic package of practices followed for crop proper growth and development, and plant spacing maintained at 20 × 60 cm2with a plot size of 390 m2. The treatments were applied when the maize crop was at knee height and larvae damaged nearly 5–8% of the total plants. Emamectin benzoate sprayed at 0.4 g/liter of water and grease of about 0.15 g applied to the maize whorl or tip of a drooping leaf that touched the soil. A significant reduction in larval infestation was observed after 7-days of treatment applications. Fall armyworm larvae were found dead in the chemical-sprayed plots, but they were absent in the grease-applied fields. No crop damage was observed among the grease-treated plants, which might be due to restrictions in the movement of larvae on the maize crop. The armyworm larvae might get irritated, feel insecure, and move far away from the test plots searching for food materials. Thus, an eco-friendly material like grease can be used as an agroecological method for managing fall armyworm larvae among small-scale land-holding maize farmers.