bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneous bioremediation of cationic copper ions and anionic methyl orange azo dye by brown marine alga Fucus vesiculosus
Authors: El-Naggar Noura El-Ahmady , Hamouda Ragaa A. , Saddiq Amna A. , Alkinani Monagi H. 
Published: February 2021

AbstractTextile wastewater contains large quantities of azo dyes mixed with various contaminants especially heavy metal ions. The discharge of effluents containing methyl orange (MO) dye and Cu2+ ions into water is harmful because they have severe toxic effects to humans and the aquatic ecosystem. The dried algal biomass was used as a sustainable, cost-effective and eco-friendly for the treatment of the textile wastewater. Box–Behnken design (BBD) was used to identify the most significant factors for achieving maximum biosorption of Cu2+ and MO from aqueous solutions using marine alga Fucus vesiculosus biomass. The experimental results indicated that 3 g/L of F. vesiculosus biomass was capable of removing 92.76% of copper and 50.27% of MO simultaneously from aqueous solution using MO (60 mg/L), copper (200 mg/L) at pH 7 within 60 min with agitation at 200 rpm. The dry biomass was also investigated using SEM, EDS, and FTIR before and after MO and copper biosorption. FTIR, EDS and SEM analyses revealed obvious changes in the characteristics of the algal biomass as a result of the biosorption process. The dry biomass of F. vesiculosus can eliminate MO and copper ions from aquatic effluents in a feasible and efficient method.
Bile acids and oxo-metabolites as markers of human faecal input in the ancient Pompeii ruins
Authors: Porru Emanuele , Giorgi Enrico , Turroni Silvia , Helg Riccardo , Silani Michele , Candela Marco , Fiori Jessica , Roda Aldo 
Published: February 2021

AbstractSmall organic molecules, lipids, proteins, and DNA fragments can remain stable over centuries. Powerful and sensitive chemical analysis can therefore be used to characterize ancient remains for classical archaeological studies. This bio-ecological dimension of archaeology can contribute knowledge about several aspects of ancient life, including social organization, daily habits, nutrition, and food storage. Faecal remains (i.e. coprolites) are particularly interesting in this regard, with scientists seeking to identify new faecal markers. Here, we report the analysis of faecal samples from modern-day humans and faecal samples from a discharge pit on the site of the ruins of ancient Pompeii. We propose that bile acids and their gut microbiota oxo-metabolites are the most specific steroid markers for detecting faecal inputs. This is due to their extreme chemical stability and their exclusive occurrence in vertebrate faeces, compared to other ubiquitous sterols and steroids.
Millisecond photonic sintering of iron oxide doped alumina ceramic coatings
Authors: Gilshtein Evgeniia , Pfeiffer Stefan , Rossell Marta D. , Sastre Jordi , Gorjan Lovro , Erni Rolf , Tiwari Ayodhya N. , Graule Thomas , Romanyuk Yaroslav E. 
Published: February 2021

AbstractThe sintering of alumina (Al2O3) traditionally occurs at high temperatures (up to ca. 1700 °C) and in significantly long times (up to several hours), which are required for the consolidation of the material by diffusion processes. Here we investigate the photonic sintering of alumina particles using millisecond flash lamp irradiation with extreme heating rates up to 108 K/min. The limitation of the low visible light absorption of alumina is resolved by adding colored α-Fe2O3 nanoparticles, which initiated the grain growth during sintering. After the millisecond-long light pulses from a xenon flash lamp, a bimodal mixture of α-Al2O3 precursor particles was sintered and iron segregation at the grain boundaries was observed. The proposed photonic sintering approach based on doping with colored centers may be extended to other refractory ceramics with low absorption in the visible light range once appropriate high-absorbing dopants are identified.
A YoeB toxin cleaves both RNA and DNA
Authors: McGillick Julia , Ames Jessica R. , Murphy Tamiko , Bourne Christina R. 
Published: February 2021

AbstractType II toxin-antitoxin systems contain a toxin protein, which mediates diverse interactions within the bacterial cell when it is not bound by its cognate antitoxin protein. These toxins provide a rich source of evolutionarily-conserved tertiary folds that mediate diverse catalytic reactions. These properties make toxins of interest in biotechnology applications, and studies of the catalytic mechanisms continue to provide surprises. In the current work, our studies on a YoeB family toxin from Agrobacterium tumefaciens have revealed a conserved ribosome-independent non-specific nuclease activity. We have quantified the RNA and DNA cleavage activity, revealing they have essentially equivalent dose-dependence while differing in requirements for divalent cations and pH sensitivity. The DNA cleavage activity is as a nickase for any topology of double-stranded DNA, as well as cleaving single-stranded DNA. AtYoeB is able to bind to double-stranded DNA with mid-micromolar affinity. Comparison of the ribosome-dependent and -independent reactions demonstrates an approximate tenfold efficiency imparted by the ribosome. This demonstrates YoeB toxins can act as non-specific nucleases, cleaving both RNA and DNA, in the absence of being bound within the ribosome.
The neurorepellent, Slit2, prevents macrophage lipid loading by inhibiting CD36-dependent binding and internalization of oxidized low-density lipoprotein
Authors: Yusuf Bushra , Mukovozov Ilya , Patel Sajedabanu , Huang Yi-Wei , Liu Guang Ying , Reddy Emily C. , Skrtic Marko , Glogauer Michael , Robinson Lisa A. 
Published: February 2021

AbstractAtherosclerosis is characterized by retention of modified lipoproteins, especially oxidized low density lipoprotein (oxLDL) within the sub-endothelial space of affected blood vessels. Recruited monocyte-derived and tissue-resident macrophages subsequently ingest oxLDL by binding and internalizing oxLDL via scavenger receptors, particularly CD36. The secreted neurorepellent, Slit2, acting through its transmembrane receptor, Roundabout-1 (Robo-1), was previously shown to inhibit recruitment of monocytes into nascent atherosclerotic lesions. The effects of Slit2 on oxLDL uptake by macrophages have not been explored. We report here that Slit2 inhibits uptake of oxLDL by human and murine macrophages, and the resulting formation of foam cells, in a Rac1-dependent and CD36-dependent manner. Exposure of macrophages to Slit2 prevented binding of oxLDL to the surface of cells. Using super-resolution microscopy, we observed that exposure of macrophages to Slit2 induced profound cytoskeletal remodeling with formation of a thick ring of cortical actin within which clusters of CD36 could not aggregate, thereby attenuating binding of oxLDL to the surface of cells. By inhibiting recruitment of monocytes into early atherosclerotic lesions, and the subsequent binding and internalization of oxLDL by macrophages, Slit2 could represent a potent new tool to combat individual steps that collectively result in progression of atherosclerosis.
Sites responsible for infectivity and antigenicity on nervous necrosis virus (NNV) appear to be distinct
Authors: Gye Hyun Jung , Nishizawa Toyohiko 
Published: February 2021

AbstractNervous necrosis virus (NNV) is a pathogenic fish-virus belonging to the genus Betanodavirus (Nodaviridae). Surface protrusions on NNV particles play a crucial role in both antigenicity and infectivity. We exposed purified NNV particles to different physicochemical conditions to investigate the effects on antigenicity and infectivity, in order to reveal information regarding the conformational stability and spatial relationships of NNV neutralizing-antibody binding sites and cell receptor binding sites. Treatment with PBS at 37 °C, drastically reduced NNV antigenicity by 66–79% on day one, whereas its infectivity declined gradually from 107.6 to 105.8 TCID50/ml over 10 days. When NNV was treated with carbonate/bicarbonate buffers at different pHs, both antigenicity and infectivity of NNV declined due to higher pH. However, the rate of decline with respect to antigenicity was more moderate than for infectivity. NNV antigenicity declined 75–84% after treatment with 2.0 M urea, however, there was no reduction observed in infectivity. The antibodies used in antigenicity experiments have high NNV-neutralizing titers and recognize conformational epitopes on surface protrusions. The maintenance of NNV infectivity means that receptor binding sites are functionally preserved. Therefore, it seems highly likely that NNV neutralizing-antibody binding sites and receptor binding sites are independently located on surface protrusions.
Dynamics of detailed components of metabolic syndrome associated with the risk of cardiovascular disease and death
Authors: Lin Ting-Yu , Chien Kuo-Liong , Chiu Yueh-Hsia , Chuang Pi-Chun , Yen Ming-Fang , Chen Hsiu-Hsi 
Published: February 2021

AbstractFew studies quantify a cascade of dynamic transitions on the detailed components of metabolic syndrome (MetS) and subsequent progressions to cardiovascular disease (CVD) and its death. A total of 47,495 subjects repeatedly attending a community-based integrated screening program in Taiwan were recruited. The refined MetS-related classification (RMRC) in relation to five criteria of MetS was defined as free of metabolic disorder (FMD, none of any criteria), mild metabolic disorder (MMD, 1–2 criteria) and MetS. A multistate Markov model was used for modelling such a multistate process. The estimated progression rate from FMD to MMD was 44.82% (95% CI 42.95–46.70%) whereas the regression rate was estimated as 29.11% (95% CI 27.77–30.45%). The progression rate from MMD to MetS was estimated as 6.15% (95% CI 5.89–6.42%). The estimated annual incidence rates of CVD increased with the severity of RMRC, being 1.62% (95% CI 1.46–1.79%) for FMD, 4.74% (95% CI 4.52–4.96%) for MMD, to 20.22% (95% CI 19.52–20.92%) for MetS. The estimated hazard rate of CVD death was 6.1 (95% CI 4.6–7.7) per thousand. Elucidating the dynamics of MetS-related transition and quantifying the incidence and prognosis of CVD provide a new insight into the design and the evaluation of intervention programs for CVD.
Using antisense oligonucleotides for the physiological modulation of the alternative splicing of NF1 exon 23a during PC12 neuronal differentiation
Authors: Biayna Josep , Mazuelas Helena , Gel Bernat , Terribas Ernest , Dumbovic Gabrijela , Rosas Inma , Fernández-Rodriguez Juana , Blanco Ignacio , Castellanos Elisabeth , Carrió Meritxell , Lazaro Conxi , Serra Eduard 
Published: February 2021

AbstractNeurofibromatosis Type 1 (NF1) is a genetic condition affecting approximately 1:3500 persons worldwide. The NF1 gene codes for neurofibromin protein, a GTPase activating protein (GAP) and a negative regulator of RAS. The NF1 gene undergoes alternative splicing of exon 23a (E23a) that codes for 21 amino acids placed at the center of the GAP related domain (GRD). E23a-containing type II neurofibromin exhibits a weaker Ras-GAP activity compared to E23a-less type I isoform. Exon E23a has been related with the cognitive impairment present in NF1 individuals. We designed antisense Phosphorodiamidate Morpholino Oligomers (PMOs) to modulate E23a alternative splicing at physiological conditions of gene expression and tested their impact during PC12 cell line neuronal differentiation. Results show that any dynamic modification of the natural ratio between type I and type II isoforms disturbed neuronal differentiation, altering the proper formation of neurites and deregulating both the MAPK/ERK and cAMP/PKA signaling pathways. Our results suggest an opposite regulation of these pathways by neurofibromin and the possible existence of a feedback loop sensing neurofibromin-related signaling. The present work illustrates the utility of PMOs to study alternative splicing that could be applied to other alternatively spliced genes in vitro and in vivo.
Comparative analysis of the transcriptomes of two rice subspecies during domestication
Authors: Pang Hongbo , Chen Qiang , Li Yueying , Wang Ze , Wu Longkun , Yang Qingwen , Zheng Xiaoming 
Published: February 2021

AbstractTwo subspecies of rice, Oryza sativa ssp. indica and O. sativa ssp. japonica, with reproductive isolation and differences in morphology and phenotypic differences, were established during the process of rice domestication. To understand how domestication has changed the transcriptomes of the two rice subspecies and given rise to the phenotypic differences, we obtained approximately 700 Gb RNA-Seq data from 26 indica and 25 japonica accessions, and identified 97,005 transcribed fragments and 4579 novel transcriptionally active regions. The two rice subspecies had significantly different gene expression profiles, we identified 1,357 (3.3% in all genes) differentially expressed genes (DEGs) between indica and japonica rice. Combining existing gene function studies, it is found that some of these differential genes are related to the differentiation of the two subspecies, such as grain shape and cold tolerance, etc. Functional annotation of these DEGs indicates that they are involved in cell wall biosynthesis and reproductive processes. Furthermore, compared with the non-DEGs, the DEGs from both subspecies had more 5′flanking regions with low polymorphism to divergence ratios, indicating a stronger positive selection pressure on the regulation of the DEGs. This study improves our understanding of the rice genome by comparatively analyzing the transcriptomes of indica and japonica rice and identifies DEGs those may be responsible for the reproductive isolation and phenotypic differences between the two rice subspecies.
Conservation machine learning: a case study of random forests
Authors: Sipper Moshe , Moore Jason H. 
Published: February 2021

AbstractConservation machine learning conserves models across runs, users, and experiments—and puts them to good use. We have previously shown the merit of this idea through a small-scale preliminary experiment, involving a single dataset source, 10 datasets, and a single so-called cultivation method—used to produce the final ensemble. In this paper, focusing on classification tasks, we perform extensive experimentation with conservation random forests, involving 5 cultivation methods (including a novel one introduced herein—lexigarden), 6 dataset sources, and 31 datasets. We show that significant improvement can be attained by making use of models we are already in possession of anyway, and envisage the possibility of repositories ofmodels(not merely datasets, solutions, or code), which could be made available to everyone, thus having conservation live up to its name, furthering the cause of data and computational science.
Helical growth during the phototropic response, avoidance response, and in stiff mutants of Phycomyces blakesleeanus
Authors: Ortega Joseph K. E. , Mohan Revathi P. , Munoz Cindy M. , Sridhar Shankar Lalitha , Vernerey Franck J. 
Published: February 2021

AbstractThe sporangiophores of Phycomyces blakesleeanus have been used as a model system to study sensory transduction, helical growth, and to establish global biophysical equations for expansive growth of walled cells. More recently, local statistical biophysical models of the cell wall are being constructed to better understand the molecular underpinnings of helical growth and its behavior during the many growth responses of the sporangiophores to sensory stimuli. Previous experimental and theoretical findings guide the development of these local models. Future development requires an investigation of explicit and implicit assumptions made in the prior research. Here, experiments are conducted to test three assumptions made in prior research, that (a) elongation rate, (b) rotation rate, and (c) helical growth steepness, R, of the sporangiophore remain constant during the phototropic response (bending toward unilateral light) and the avoidance response (bending away from solid barriers). The experimental results reveal that all three assumptions are incorrect for the phototropic response and probably incorrect for the avoidance response but the results are less conclusive. Generally, the experimental results indicate that the elongation and rotation rates increase during these responses, as does R, indicating that the helical growth steepness become flatter. The implications of these findings on prior research, the “fibril reorientation and slippage” hypothesis, global biophysical equations, and local statistical biophysical models are discussed.
Molecular characterization of a soybean FT homologue, GmFT7
Authors: Zhang Senhao , Singh Mohan B. , Bhalla Prem L. 
Published: February 2021

AbstractSoybean (Glycine max) is a vital oilseed legume crop that provides protein and oil for humans and feedstock for animals. Flowering is a prerequisite for seed production. Floral transition, from vegetative to reproductive stage, in a plant, is regulated by environmental (light, temperature) and endogenous factors. In Arabidopsis, Flowering Locus T (FT) protein is shown to be a mobile signal that moves from leaf to shoot apical meristem to induce flowering. However, FTs role in soybean is not fully resolved due to the presence of multiple (ten) homologs in the genome. Two of the ten FT homologs (GmFT2a and GmFT5a) have a role in the floral transition while GmFT1a and GmFT4 suppress soybean flowering. Recent deep sequencing data revealed that six FT homologs are expressed in shoot apical meristem and leaves during floral transition. One FT homolog, GmFT7 showed strong expression during soybean floral transition. Though bioinformatic analyses revealed that GmFT7 had high similarity with GmFT2a, ectopic GmFT7 expression in Arabidopsis could not promote flowering or rescue the late-flowering phenotype of Arabidopsis ft-10 mutant.
Pembrolizumab in vaginal and vulvar squamous cell carcinoma: a case series from a phase II basket trial
Authors: How Jeffrey A. , Jazaeri Amir A. , Soliman Pamela T. , Fleming Nicole D. , Gong Jing , Piha-Paul Sarina A. , Janku Filip , Stephen Bettzy , Naing Aung 
Published: February 2021

AbstractVaginal and vulvar squamous cell carcinoma (SCC) are rare tumors that can be challenging to treat in the recurrent or metastatic setting. We present a case series of patients with vaginal or vulvar SCC who were treated with single-agent pembrolizumab as part of a phase II basket clinical trial to evaluate efficacy and safety. Two cases of recurrent and metastatic vaginal SCC, with multiple prior lines of systemic chemotherapy and radiation, received pembrolizumab. One patient had significant reduction (81%) in target tumor lesions prior to treatment discontinuation at cycle 10 following confirmed progression of disease with new metastatic lesions (stable disease by irRECIST criteria). In contrast, the other patient with vaginal SCC discontinued treatment after cycle 3 due to disease progression. Both patients had PD-L1 positive vaginal tumors and tolerated treatment well. One case of recurrent vulvar SCC with multiple surgical resections and prior progression on systemic carboplatin had a 30% reduction in her target tumor lesions following pembrolizumab treatment with a PD-L1 positive tumor. Treatment was discontinued for grade 3 mucositis after cycle 5. Pembrolizumab may provide some clinical benefit to some patients with vaginal or vulvar SCC and is overall safe to utilize in this population. Future studies are needed to evaluate the efficacy of pembrolizumab in these rare tumor types and to identify predictive biomarkers of response.
Detection of involved margins in breast specimens with X-ray phase-contrast computed tomography
Authors: Massimi Lorenzo , Suaris Tamara , Hagen Charlotte K. , Endrizzi Marco , Munro Peter R. T. , Havariyoun Glafkos , Hawker P. M. Sam , Smit Bennie , Astolfo Alberto , Larkin Oliver J. , Waltham Richard M. , Shah Zoheb , Duffy Stephen W. , Nelan Rachel L. , Peel Anthony , Jones J. Louise , Haig Ian G. , Bate David , Olivo Alessandro 
Published: February 2021

AbstractMargins of wide local excisions in breast conserving surgery are tested through histology, which can delay results by days and lead to second operations. Detection of margin involvement intraoperatively would allow the removal of additional tissue during the same intervention. X-ray phase contrast imaging (XPCI) provides soft tissue sensitivity superior to conventional X-rays: we propose its use to detect margin involvement intraoperatively. We have developed a system that can perform phase-based computed tomography (CT) scans in minutes, used it to image 101 specimens approximately half of which contained neoplastic lesions, and compared results against those of a commercial system. Histological analysis was carried out on all specimens and used as the gold standard. XPCI-CT showed higher sensitivity (83%, 95% CI 69–92%) than conventional specimen imaging (32%, 95% CI 20–49%) for detection of lesions at margin, and comparable specificity (83%, 95% CI 70–92% vs 86%, 95% CI 73–93%). Within the limits of this study, in particular that specimens obtained from surplus tissue typically contain small lesions which makes detection more difficult for both methods, we believe it likely that the observed increase in sensitivity will lead to a comparable reduction in the number of re-operations.
Smartphone apps for depression and anxiety: a systematic review and meta-analysis of techniques to increase engagement
Authors: Wu Ashley , Scult Matthew A. , Barnes Emily D. , Betancourt Jessica A. , Falk Avital , Gunning Faith M. 
Published: February 2021

AbstractMeta-analyses have shown that digital mental health apps can be efficacious in reducing symptoms of depression and anxiety. However, real-world usage of apps is typically not sustained over time, and no studies systematically examine which features increase sustained engagement with apps or the relationship between engagement features and clinical efficacy. We conducted a systematic search of the literature to identify empirical studies that (1) investigate standalone apps for depression and/or anxiety in symptomatic participants and (2) report at least one measure of engagement. Features intended to increase engagement were categorized using the persuasive system design (PSD) framework and principles of behavioral economics. Twenty-five studies with 4159 participants were included in the analysis. PSD features were commonly used, whereas behavioral economics techniques were not. Smartphone apps were efficacious in treating symptoms of anxiety and depression in randomized controlled trials, with overall small-to-medium effects (g = 0.2888, SE = 0.0999, z(15) = 2.89, p = 0.0119, Q(df = 14) = 41.93, p < 0.0001, I2 = 66.6%), and apps that employed a greater number of engagement features as compared to the control condition had larger effect sizes (β = 0.0450, SE = 0.0164, t(15) = 2.7344, p = 0.0161). We observed an unexpected negative association between PSD features and engagement, as measured by completion rate (β = −0.0293, SE = 0.0121, t(17) = 02.4142, p = 0.0281). Overall, PSD features show promise for augmenting app efficacy, though engagement, as reflected in study completion, may not be the primary factor driving this association. The results suggest that expanding the use of PSD features in mental health apps may increase clinical benefits and that other techniques, such as those informed by behavioral economics, are employed infrequently.