bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Contribution of Convection to the Stratospheric Water Vapor: The First Budget Using a Global Storm‐Resolving Model
Authors: Dauhut Thibaut , Hohenegger Cathy 
Published: February 2022

AbstractThe deepest convection on Earth injects water in the tropical stratosphere, but its contribution to the global stratospheric water budget remains uncertain. The Global Storm‐Resolving Model ICOsahedral Non‐hydrostatic is used to simulate the moistening of the lower stratosphere for 40 days during boreal summer. The decomposition of the water vapor budget in the tropical lower stratosphere (TLS, 10°S–30°N, and 17–20 km altitude) indicates that the average moistening (+21 Tg) over the simulated 40‐day period is the result of the combined effect of the vertical water vapor transport from the troposphere (+27 Tg), microphysical phase changes and subgrid‐scale transport (+2 Tg), partly compensated by horizontal water vapor export (−8 Tg). The very deep convective systems, explicitly represented thanks to the employed 2.5 km grid spacing of the model, are identified using the very low Outgoing Longwave Radiation of their cold cloud tops. The water vapor budget reveals that the vertical transport, the sublimation and the subgrid‐scale transport at their top contribute together to 11% of the water vapor mass input into the TLS.
Sediment Trap Study Reveals Dominant Contribution of Metazoans and Dinoflagellates to Carbon Export and Dynamic Impacts of Microbes in a Subtropical Marginal Sea
Authors: Lin Senjie , Li Tangcheng , Yuan Huatao , Li Hongfei , Yu Liying , Zhuang Yunyun , Li Ling , Huang Bangqin , Liu Guangxing 
Published: February 2022

AbstractFlux and efficiency of carbon export in the ocean has been widely studied using sediment traps, but due to limitations of traditional methods, differential contribution of different organisms is poorly understood. Here, we used DNA metabarcoding to document taxonomic composition for sediment traps deployed at a continental shelf (C6) and a continental slope (C9) site in the South China Sea. The results indicated that metazoans (mainly copepods) and dinoflagellates were the most dominant contributors overall, while dinoflagellates, diatoms, and haptophytes dominated the photosynthetic assemblage. For prokaryotes, Gammaproteobacteria dominated all samples. Furthermore, comparing the trap flora to overlying plankton revealed that metazoans and Polycystinea from Eukaryota and Gammaproteobacteria and Bacteroidetes from Prokaryota were enriched in the trap at both stations whereas haptophytes and Dinophyceae were consistently attenuated during sinking. In addition, Oceanospirillaceae and Rhodobacteraceae exhibited negative correlations with dinoflagellates, and based on overlying plankton metatranscriptomes, were most transcriptionally active lineages for metabolizing labile and semi‐labile organic carbon, potentially contributing to the Martin's decay of sinking particulate organic carbon. Using DNA and RNA sequencing technologies, this study provides novel insights into the lineage‐specific contribution and dynamic impacts of microbes to carbon export in a subtropical marginal sea.
Global metrics on ocular biometry: representative averages and standard deviations across ten countries from four continents
Authors: Ganesh Durga , Lin Shawn R. 
Published: February 2022

Abstract
Background/Objectives
We provide global averages and standard deviations for ocular biometry—axial length (AL), corneal radius of curvature (CR), anterior chamber depth (ACD), lens thickness (LT), white to white (WTW), and central corneal thickness (CT). We hope a better understanding of normal and abnormal values will help clinicians gain further insight into their surgical outcomes, especially for off-target eyes.

Subjects/Methods
We searched the MEDLINE database using keywords “axial length, corneal power, anterior chamber depth, lens thickness, white to white, and corneal thickness.” We included studies that reported averages and standard deviations on eye biometry for at least 1300 eyes. Global weighted averages and standard deviations were calculated using the Cochrane method.

Results
Fourteen studies were included, originating from Asia (Japan, Singapore, Myanmar, Iran, South Korea, China), Europe (Germany, United Kingdom, Portugal), Australia, and North America (United States). Global ocular biometry metrics were: AL—23.49 mm ± 1.35 mm, CR—7.69 mm ± 0.28 mm, ACD—3.10 mm ± 0.47 mm, WTW—11.80 mm ± 0.42 mm, LT—4.37 mm ± 0.43 mm, and CT—544 μm ± 38 μm. Total eyes per value ranged from 19,538 to 90,814.

Conclusions
We report global ocular biometry averages and standard deviations. No eyes were from studies in Africa or South America, highlighting the need to publish eye biometry data from these continents. We hope that promoting a deeper understanding of biometry values will help clinicians gain insight into surgical outcomes and drive innovations in lens calculations.
Global and transcription-coupled repair of 8-oxoG is initiated by nucleotide excision repair proteins
Authors: Kumar Namrata , Theil Arjan F. , Roginskaya Vera , Ali Yasmin , Calderon Michael , Watkins Simon C. , Barnes Ryan P. , Opresko Patricia L. , Pines Alex , Lans Hannes , Vermeulen Wim , Van Houten Bennett 
Published: February 2022

AbstractUV-DDB, consisting of subunits DDB1 and DDB2, recognizes UV-induced photoproducts during global genome nucleotide excision repair (GG-NER). We recently demonstrated a noncanonical role of UV-DDB in stimulating base excision repair (BER) which raised several questions about the timing of UV-DDB arrival at 8-oxoguanine (8-oxoG), and the dependency of UV-DDB on the recruitment of downstream BER and NER proteins. Using two different approaches to introduce 8-oxoG in cells, we show that DDB2 is recruited to 8-oxoG immediately after damage and colocalizes with 8-oxoG glycosylase (OGG1) at sites of repair. 8-oxoG removal and OGG1 recruitment is significantly reduced in the absence of DDB2. NER proteins, XPA and XPC, also accumulate at 8-oxoG. While XPC recruitment is dependent on DDB2, XPA recruitment is DDB2-independent and transcription-coupled. Finally, DDB2 accumulation at 8-oxoG induces local chromatin unfolding. We propose that DDB2-mediated chromatin decompaction facilitates the recruitment of downstream BER proteins to 8-oxoG lesions.
Protease activities of vaginal Porphyromonas species disrupt coagulation and extracellular matrix in the cervicovaginal niche
Authors: Lithgow Karen V. , Buchholz Vienna C. H. , Ku Emily , Konschuh Shaelen , D’Aubeterre Ana , Sycuro Laura K. 
Published: February 2022

AbstractPorphyromonas asaccharolyticaandPorphyromonas uenonisare common inhabitants of the vaginal microbiome, but their presence has been linked to adverse health outcomes for women, including bacterial vaginosis and preterm birth. However, little is known about the pathogenesis mechanisms of these bacteria. The related oral opportunistic pathogen,Porphyromonas gingivalis, is comparatively well-studied and known to secrete numerous extracellular matrix-targeting proteases. Among these are the gingipain family of cysteine proteases that drive periodontal disease progression and hematogenic transmission to the placenta. In this study, we demonstrate that vaginalPorphyromonasspecies secrete broad-acting proteases capable of freely diffusing within the cervicovaginal niche. These proteases degrade collagens that are enriched within the cervix (type I) and chorioamniotic membranes (type IV), as well as fibrinogen, which inhibits clot formation. Bioinformatic queries confirmed the absence of gingipain orthologs and identified five serine, cysteine, and metalloprotease candidates in each species. Inhibition assays revealed that each species’ proteolytic activity can be partially attributed to a secreted metalloprotease with broad substrate specificity that is distantly related to theP. gingivalisendopeptidase PepO. This characterization of virulence activities in vaginalPorphyromonasspecies highlights their potential to alter the homeostasis of reproductive tissues and harm human pregnancy through clotting disruption, fetal membrane weakening, and premature cervical remodeling.
Universal relation for life-span energy consumption in living organisms: Insights for the origin of aging
Authors: Escala Andrés 
Published: February 2022

AbstractMetabolic energy consumption has long been thought to play a major role in the aging process (Pearl, The rate of living. University of London Press, London, 1928). Across species, a gram of tissue expends approximately the same amount of energy during the lifespan on average (Speakman, J Exp Biol 208:1717–1730, 2005). Energy restriction has also been shown to increase the maximum lifespan (McCay et al. J Nutr 10:63–79, 1935) and to retard age-associated changes (Weindruch and Walford, The retardation of aging and disease by dietary restriction. CC Thomas, Springfield, 1988). However, there are significant exceptions to universal energy consumption during the lifespan, mainly found by interclass comparison (Ramsey et al. Free Rad Biol Med 29:946–968, 2000; Atanasov, Trakia J Sci 10(3):1–14, 2012). Here, we present a universal relation that relates lifespan energy consumption to several physiological variables, such as body mass, temperature and the ratio of heart rate to respiratory rate, which have been shown to be valid for$$\sim 300$$∼300species representing different classes of living organisms, from unicellular organisms to the largest mammals. This relation has an average scattered pattern restricted to factors of 2, with 95% ($$2-\sigma$$2-σ) of the organisms having departures of less than a factor of$$\pi$$πfrom the relation, despite the difference of$$\sim 20$$∼20orders of magnitude in body mass, reducing any possible interclass variation in the relation to only a geometrical factor. This result can be interpreted as supporting evidence for the existence of an approximately constant total number$${\mathrm{N}}_{{\mathrm{r}}} \sim 10^8$$Nr∼108of respiration cycles per lifetime for all organisms studied, effectively predetermining the extension of life through the basic energetics of respiration (quantified by$${\mathrm{t}}_{{\mathrm{life}}} = \mathrm{N}_\mathrm{r}/\mathrm{f}_{{\mathrm{resp}}}$$tlife=Nr/fresp); this is an incentive to conduct future studies on the relation of such a constant number$${\mathrm{N}}_{\mathrm{r}}$$Nrof cycles per lifetime due to the production rates of free radicals and oxidants or alternative mechanisms, which may yield definite constraints on the origin of aging.
Laser fabrication and evaluation of holographic intrinsic physical unclonable functions
Authors: Anastasiou Aggeliki , Zacharaki Evangelia I. , Tsakas Anastasios , Moustakas Konstantinos , Alexandropoulos Dimitris 
Published: February 2022

AbstractOptical Physical Unclonable Functions (PUFs) are well established as the most powerful anticounterfeiting tool. Despite the merits of optical PUFs, widespread use is hindered by existing implementations that are complicated and expensive. On top, the overwhelming majority of optical PUFs refer to extrinsic implementations. Here we overcome these limitations to demonstrate for the first time strong intrinsic optical PUFs with exceptional security characteristics. In doing so, we use Computer-Generated Holograms (CGHs) as optical, intrinsic, and image-based PUFs. The required randomness is offered by the non-deterministic fabrication process achieved with industrial friendly, nanosecond pulsed fiber lasers. Adding to simplicity and low cost, the digital fingerprint is derived by a setup which is designed to be adjustable in a production line. In addition, we propose a novel signature encoding and authentication mechanism that exploits manifold learning techniques to efficiently differentiate data reconstruction-related variation from counterfeit attacks. The proposed method is applied experimentally on silver plates. The robustness of the fabricated intrinsic optical PUFs is evaluated over time. The results have shown exceptional values for robustness and a probability of cloning up to $$10^{-14}$$

10

-
14

, which exceeds the standard acceptance rate in security applications.
Spatiotemporal dynamics in spiking recurrent neural networks using modified-full-FORCE on EEG signals
Authors: Ioannides Georgios , Kourouklides Ioannis , Astolfi Alessandro 
Published: February 2022

AbstractMethods on modelling the human brain as a Complex System have increased remarkably in the literature as researchers seek to understand the underlying foundations behind cognition, behaviour, and perception. Computational methods, especially Graph Theory-based methods, have recently contributed significantly in understanding the wiring connectivity of the brain, modelling it as a set of nodes connected by edges. Therefore, the brain’s spatiotemporal dynamics can be holistically studied by considering a network, which consists of many neurons, represented by nodes. Various models have been proposed for modelling such neurons. A recently proposed method in training such networks, called full-Force, produces networks that perform tasks with fewer neurons and greater noise robustness than previous least-squares approaches (i.e. FORCE method). In this paper, the first direct applicability of a variant of the full-Force method to biologically-motivated Spiking RNNs (SRNNs) is demonstrated. The SRNN is a graph consisting of modules. Each module is modelled as a Small-World Network (SWN), which is a specific type of a biologically-plausible graph. So, the first direct applicability of a variant of the full-Force method to modular SWNs is demonstrated, evaluated through regression and information theoretic metrics. For the first time, the aforementioned method is applied to spiking neuron models and trained on various real-life Electroencephalography (EEG) signals. To the best of the authors’ knowledge, all the contributions of this paper are novel. Results show that trained SRNNs match EEG signals almost perfectly, while network dynamics can mimic the target dynamics. This demonstrates that the holistic setup of the network model and the neuron model which are both more biologically plausible than previous work, can be tuned into real biological signal dynamics.
Analysis of fecal bile acids and metabolites by high resolution mass spectrometry in farm animals and correlation with microbiota
Authors: Porru Emanuele , Scicchitano Daniel , Interino Nicolò , Tavella Teresa , Candela Marco , Roda Aldo , Fiori Jessica 
Published: February 2022

AbstractThere is a growing interest in the named “acidic sterolbiome” and in the genetic potential of the gut microbiome (GM) to modify bile acid (BA) structure. Indeed, the qualitative composition of BAs in feces correlates with the bowel microorganisms and their collective genetic material. GM is responsible for the production of BA metabolites, such as secondary and oxo-BAs. The specific BA profiles, as microbiome-host co-metabolic products, could be useful to investigate the GM-host interaction in animals under physiological conditions, as well as in specific diseases. In this context, we developed and validated an ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry method for the simultaneous analysis of up to 21 oxo-BAs and their 9 metabolic precursors. Chromatographic separation was achieved in 7 min with adequate analytical performance in terms of selectivity, sensitivity (LOQ from 0.05 to 0.1 µg/mL), accuracy (bias% < 5%), precision (CV% < 5%) and matrix effect (ME% < 10%). A fast solvent extraction protocol has been fine-tuned, achieving recoveries > 90%. In parallel, the gut microbiota assessment in farming animals was evaluated by 16S rRNA next-generation sequencing, and the correlation with the BA composition was performed by multivariate analysis, allowing to reconstruct species-specific associations between the BA profile and specific GM components.
Association between recurrent breast cancer and phthalate exposure modified by hormone receptors and body mass index
Authors: Yang Pei-Jing , Hou Ming-Feng , Ou-Yang Fu , Hsieh Tsung-Hua , Lee Yen-Jung , Tsai Eing-Mei , Wang Tsu-Nai 
Published: February 2022

AbstractThe association between phthalate exposure and breast cancer remains controversial. We performed a prospective patient cohort design to explore the interaction between creatinine-corrected urinary phthalate metabolites and hormone receptors as well as body mass index (BMI) on recurrent breast cancer. In this follow-up study, 636 female breast cancer patients and 45 new recurrent cases diagnosed for a total of 1576.68 person-years of follow-up were recruited. Mono-(2-ethyl-5-oxohexyl) phthalate (MEOHP) was negatively associated with breast cancer recurrence, with adjusted hazard ratio (aHR) 3rd vs. 1st quartile of 0.15 (95% CI 0.04–0.51). The MEOHP presented as a non-monotonic dose–response (NMDR) curve, being U-shaped. In the stratification of hormone receptors, MEOHP still exhibited a U-shaped dose–response curve. The third quartile of MEOHP showed significant lowest recurrent risk in the status of ER-positive (aHR 0.18, 95% CI 0.05–0.66), PR-negative (aHR 0.14, 95% CI 0.03–0.63), and HER2-negative (aHR 0.24, 95% CI 0.08–0.76). Whether in BMI < 25 or in BMI ≥ 25, the third quartile of MEOHP was negatively associated with recurrent breast cancer, and there was a negative interaction on an additive scale between MEOHP and BMI (pinteraction = 0.042). The association between MEOHP and recurrent breast cancer was modified by hormone receptors and BMI.
Automated human cell classification in sparse datasets using few-shot learning
Authors: Walsh Reece , Abdelpakey Mohamed H. , Shehata Mohamed S. , Mohamed Mostafa M. 
Published: February 2022

AbstractClassifying and analyzing human cells is a lengthy procedure, often involving a trained professional. In an attempt to expedite this process, an active area of research involves automating cell classification through use of deep learning-based techniques. In practice, a large amount of data is required to accurately train these deep learning models. However, due to the sparse human cell datasets currently available, the performance of these models is typically low. This study investigates the feasibility of using few-shot learning-based techniques to mitigate the data requirements for accurate training. The study is comprised of three parts: First, current state-of-the-art few-shot learning techniques are evaluated on human cell classification. The selected techniques are trained on a non-medical dataset and then tested on two out-of-domain, human cell datasets. The results indicate that, overall, the test accuracy of state-of-the-art techniques decreased by at least 30% when transitioning from a non-medical dataset to a medical dataset. Reptile and EPNet were the top performing techniques tested on the BCCD dataset and HEp-2 dataset respectively. Second, this study evaluates the potential benefits, if any, to varying the backbone architecture and training schemes in current state-of-the-art few-shot learning techniques when used in human cell classification. To this end, the best technique identified in the first part of this study, EPNet, is used for experimentation. In particular, the study used 6 different network backbones, 5 data augmentation methodologies, and 2 model training schemes. Even with these additions, the overall test accuracy of EPNet decreased from 88.66% on non-medical datasets to 44.13% at best on the medical datasets. Third, this study presents future directions for using few-shot learning in human cell classification. In general, few-shot learning in its current state performs poorly on human cell classification. The study proves that attempts to modify existing network architectures are not effective and concludes that future research effort should be focused on improving robustness towards out-of-domain testing using optimization-based or self-supervised few-shot learning techniques.
Design, synthesis and biological activities of echinopsine derivatives containing acylhydrazone moiety
Authors: Cui Peipei , Cai Mingjiang , Meng Yanan , Yang Yan , Song Hongjian , Liu Yuxiu , Wang Qingmin 
Published: February 2022

AbstractBased on the broad-spectrum biological activities of echinopsine and acylhydrazones, a series of echinopsine derivatives containing acylhydrazone moieties have been designed, synthesized and their biological activities were evaluated for the first time. The bioassay results indicated that most of the compounds showed moderate to good antiviral activities against tobacco mosaic virus (TMV), among which echinopsine (I) (inactivation activity, 49.5 ± 4.4%; curative activity, 46.1 ± 1.5%; protection activity, 42.6 ± 2.3%) and its derivatives 1 (inactivation activity, 44.9 ± 4.6%; curative activity, 39.8 ± 2.6%; protection activity, 47.3 ± 4.3%), 3 (inactivation activity, 47.9 ± 0.9%; curative activity, 43.7 ± 3.1%; protection activity, 44.6 ± 3.3%), 7 (inactivation activity, 46.2 ± 1.6%; curative activity, 45.0 ± 3.7%; protection activity, 41.7 ± 0.9%) showed higher anti-TMV activity in vivo at 500 mg/L than commercial ribavirin (inactivation activity, 38.9 ± 1.4%; curative activity, 39.2 ± 1.8%; protection activity, 36.4 ± 3.4%). Some compounds exhibited insecticidal activities against Plutella xylostella, Mythimna separate and Spodoptera frugiperda. Especially, compounds 7 and 27 displayed excellent insecticidal activities against Plutella xylostell (mortality 67 ± 6% and 53 ± 6%) even at 0.1 mg/L. Additionally, most echinopsine derivatives exhibited high fungicidal activities against Physalospora piricola and Sclerotinia sclerotiorum.
Polarisation-sensitive optical coherence tomography measurement of retardance in fibrosis, a non-invasive biomarker in patients with systemic sclerosis
Authors: Marjanovic E. J. , Sharma V. , Smith L. , Pinder C. , Moore T. L. , Manning J. B. , Dinsdale G. , Berks M. , Newton V. L. , Wilkinson S. , Dickinson M. R. , Herrick A. L. , Watson R. E. B. , Murray A. K. 
Published: February 2022

AbstractPolarisation-sensitive optical coherence tomography (PS-OCT) offers a novel, non-invasive method of assessing skin fibrosis in the multisystem disease systemic sclerosis (SSc) by measuring collagen retardance. This study aimed to assess retardance as a biomarker in SSc. Thirty-one patients with SSc and 27 healthy controls (HC) underwent PS-OCT imaging. ‘Skin score’ was assessed by clinical palpation (0–3 scale). A subset of ten patients and ten age/sex-matched HC had a biopsy and longitudinal imaging. Histological assessment included quantification of epidermal thickness, collagen content (to assess fibrosis) and matrix metalloproteinase (MMP) activity (in situ zymography). PS-OCT images were assessed for epidermal thickness (structure) and fibrosis (retardance). Positive correlation was observed between epidermal thickness as measured by histology and structural PS-OCT (r = 0.79; p < 0.001). Retardance was: HC mean 0.21 (SD 0.21) radian/pixel; SSc skin score 0, 0.30 (0.19); skin score 1, 0.11 (0.16); skin score 2, 0.06 (0.12); skin score 3, 0.36 (0.35). Longitudinal retardance decreased at one-week across groups, increasing at one-month for HC/skin score 0–1; HC biopsy site retardance suggests scarring is akin to fibrosis. Relationships identified between retardance with both biopsy and skin score data indicate that retardance warrants further investigation as a suitable biomarker for SSc-related fibrosis.