bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comprehensive genomic catalog from global cold seeps
Authors: Han Yingchun , Zhang Chuwen , Zhao Zhuoming , Peng Yongyi , Liao Jing , Jiang Qiuyun , Liu Qing , Shao Zongze , Dong Xiyang 
Published: September 2023

AbstractCold seeps harbor abundant and diverse microbes with tremendous potential for biological applications and that have a significant influence on biogeochemical cycles. Although recent metagenomic studies have expanded our understanding of the community and function of seep microorganisms, knowledge of the diversity and genetic repertoire of global seep microbes is lacking. Here, we collected a compilation of 165 metagenomic datasets from 16 cold seep sites across the globe to construct a comprehensive gene and genome catalog. The non-redundant gene catalog comprised 147 million genes, and 36% of them could not be assigned to a function with the currently available databases. A total of 3,164 species-level representative metagenome-assembled genomes (MAGs) were obtained, most of which (94%) belonged to novel species. Of them, 81 ANME species were identified that cover all subclades except ANME-2d, and 23 syntrophic SRB species spanned the Seep-SRB1a, Seep-SRB1g, and Seep-SRB2 clades. The non-redundant gene and MAG catalog is a valuable resource that will aid in deepening our understanding of the functions of cold seep microbiomes.
Postharvest starch and sugars adjustment in potato tubers of wide-ranging dormancy genotypes subjected to various sprout forcing techniques
Authors: Haider Muhammad Wasim , Nafees Muhammad , Iqbal Rashid , Asad Habat Ullah , Azeem Farrukh , Ali Baber , Shaheen Ghazala , Iqbal Javed , Vyas Shweta , Arslan Muhammad , Rahman Muhammad Habib Ur , Elshikh Mohamed S. , Ali M. Ajmal 
Published: September 2023

AbstractThe development of an efficient, safe, and environment-friendly technique to terminate tuber dormancy in potatoes (Solanum tuberosum L.) is of great concern due to the immense scope of multiple cropping all over the globe. The breakage of tuber dormancy has been associated with numerous physiological changes, including a decline in the level of starch and an increase in the levels of sugars during storage of freshly harvested seed potatoes, although their consistency across genotypes and various dormancy-breaking techniques have not yet been fully elucidated. The purpose of the present research is to assess the efficacy of four different dormancy-breaking techniques, such as soaking in 90, 60, or 30 mg L−1 solutions of benzyl amino purine (BAP) and 30, 20, or 10 mg L−1 gibberellic acid (GA3) alone and in the combination of optimized concentrations; cold pre-treatment at 6, 4, or 2 °C; electric shock at 80, 60, 40, or 20 Vs; and irradiation at 3.5, 3, 2.5, 2, 1.5, or 1 kGy on the tuber dormancy period and sprout length of six genotypes. Furthermore, the changes that occurred in tuber weight and endogenous starch, sucrose, fructose, and glucose contents in experimental genotypes following the application of these techniques were also examined. Overall, the most effective technique to terminate tuber dormancy and hasten spout growth was the combined application of BAP and GA3, which reduced the length of dormancy by 9.6 days compared to the untreated control, following 6.7 days of electric current, 4.4 days of cold pre-treatment, and finally irradiation (3.3 days). The 60 mg L−1 solution of BAP greatly reduced the dormancy period in all genotypes but did not affect the sprout length at all. The genotypes showed a weak negative correlation (r =  − 0.4) (P < 0.05) of endogenous starch contents with dormancy breakage and weight loss or a moderate (r =  − 0.5) correlation with sprout length, but a strong positive correlation (r = 0.8) of tuber glucose, fructose, and sucrose contents with dormancy breakage and weight loss. During 3 weeks of storage, sprouting commencement and significant weight loss occurred as tuber dormancy advanced towards breakage due to a reduction in starch and an increase in the sucrose, fructose, and glucose contents of the tubers. These findings could be advantageous for postponing or accelerating seed potato storage as well as investigating related physiological research in the future.
Structural dynamics influences the antibacterial activity of a cell-penetrating peptide (KFF)3K
Authors: Macyszyn Julia , Chyży Piotr , Burmistrz Michał , Lobka Małgorzata , Miszkiewicz Joanna , Wojciechowska Monika , Trylska Joanna 
Published: September 2023

AbstractGiven the widespread demand for novel antibacterial agents, we modified a cell-penetrating peptide (KFF)3K to transform it into an antibacterial peptide. Namely, we inserted a hydrocarbon staple into the (KFF)3K sequence to induce and stabilize its membrane-active secondary structure. The staples were introduced at two positions, (KFF)3K[5–9] and (KFF)3K[2–6], to retain the initial amphipathic character of the unstapled peptide. The stapled analogues are protease resistant contrary to (KFF)3K; 90% of the stapled (KFF)3K[5–9] peptide remained undigested after incubation in chymotrypsin solution. The stapled peptides showed antibacterial activity (with minimal inhibitory concentrations in the range of 2–16 µM) against various Gram-positive and Gram-negative strains, contrary to unmodified (KFF)3K, which had no antibacterial effect against any strain at concentrations up to 32 µM. Also, both stapled peptides adopted an α-helical structure in the buffer and micellar environment, contrary to a mostly undefined structure of the unstapled (KFF)3K in the buffer. We found that the antibacterial activity of (KFF)3K analogues is related to their disruptive effect on cell membranes and we showed that by stapling this cell-penetrating peptide, we can induce its antibacterial character.
Quantifying root colonization by a symbiotic fungus using automated image segmentation and machine learning approaches
Authors: Sciascia Ivan , Crosino Andrea , Genre Andrea 
Published: September 2023

AbstractArbuscular mycorrhizas (AM) are one of the most widespread symbiosis on earth. This plant-fungus interaction involves around 72% of plant species, including most crops. AM symbiosis improves plant nutrition and tolerance to biotic and abiotic stresses. The fungus, in turn, receives carbon compounds derived from the plant photosynthetic process, such as sugars and lipids. Most studies investigating AM and their applications in agriculture requires a precise quantification of the intensity of plant colonization. At present, the majority of researchers in the field base AM quantification analyses on manual visual methods, prone to operator errors and limited reproducibility. Here we propose a novel semi-automated approach to quantify AM fungal root colonization based on digital image analysis comparing three methods: (i) manual quantification (ii) image thresholding, (iii) machine learning. We recognize machine learning as a very promising tool for accelerating, simplifying and standardizing critical steps in analysing AM quantification, answering to an urgent need by the scientific community studying this symbiosis.
Effects of rainfall amount and frequencies on soil net nitrogen mineralization in Gahai wet meadow in the Qinghai-Tibetan Plateau
Authors: Xu Guorong , Li Guang , Wu Jiangqi , Ma Weiwei , Wang Haiyan , Yuan Jianyu , Li Xiaodan 
Published: September 2023

AbstractGlobal climate change has led to a significant increase in the frequency of extreme rainfall events in the Qinghai-Tibetan Plateau (QTP), thus potentially increasing the annual rainfall amounts and, consequently, affecting the net soil nitrogen (N) mineralization process. However, few studies on the responses of the soil net N mineralization rates to the increases in rainfall amounts and frequencies in alpine wet meadows have been carried out. Therefore, the present study aims to assess the effects of rainfall frequency and amount changes on the N fixation capacity of wet meadow soils by varying the rainfall frequency and amount in the Gahai wet meadow in the northeastern margin of the QTP during the plant-growing season in 2019. The treatment scenarios consisted of ambient rain (CK) and supplementary irrigation at a rate of 25 mm, with different irrigation frequencies, namely weekly (DF1), biweekly (DF2), every three weeks (DF3), and every four weeks (DF4). According to the obtained results, the increased rainfall frequency and amount decreased the soil mineral N stock and increased the aboveground vegetation biomass (AB) amounts and soil water contents in the wet meadows of the QTP. Ammonium (NH4+-N) and nitrate N (NO3–-N) contributed similarly to the mineral N contents. However, the ammonification process played a major role in the soil mineralization process. The effects of increasing rainfall amount and frequency on N mineralization showed seasonal variations. The N mineralization rate showed a single-peaked curve with increasing soil temperature during the rapid vegetation growth phase, reaching the highest value in August. In addition, the N mineralization rates showed significant positive correlations with soil temperatures and NH4+-N contents and a significant negative correlation with AB (P < 0.05). The results of this study demonstrated the key role of low extreme rainfall event frequencies in increasing the net soil N mineralization rates in the vegetation growing season, which is detrimental to soil N accumulation, thereby affecting the effectiveness of soil N contents.
Leveraging the COVID-19 pandemic as a natural experiment to assess changes in antibiotic use and antibiotic-resistant E. coli carriage in semi-rural Ecuador
Authors: Amato Heather K. , Loayza Fernanda , Salinas Liseth , Paredes Diana , García Daniela , Sarzosa Soledad , Saraiva-Garcia Carlos , Johnson Timothy J. , Pickering Amy J. , Riley Lee W. , Trueba Gabriel , Graham Jay P. 
Published: September 2023

AbstractThe coronavirus 2019 (COVID-19) pandemic has had significant impacts on health systems, population dynamics, public health awareness, and antibiotic stewardship, which could affect antibiotic resistant bacteria (ARB) emergence and transmission. In this study, we aimed to compare knowledge, attitudes, and practices (KAP) of antibiotic use and ARB carriage in Ecuadorian communities before versus after the COVID-19 pandemic began. We leveraged data collected for a repeated measures observational study of third-generation cephalosporin-resistant E. coli (3GCR-EC) carriage among children in semi-rural communities in Quito, Ecuador between July 2018 and September 2021. We included 241 households that participated in surveys and child stool sample collection in 2019, before the pandemic, and in 2021, after the pandemic began. We estimated adjusted Prevalence Ratios (aPR) and 95% Confidence Intervals (CI) using logistic and Poisson regression models. Child antibiotic use in the last 3 months declined from 17% pre-pandemic to 5% in 2021 (aPR: 0.30; 95% CI 0.15, 0.61) and 3GCR-EC carriage among children declined from 40 to 23% (aPR: 0.48; 95% CI 0.32, 0.73). Multi-drug resistance declined from 86 to 70% (aPR: 0.32; 95% CI 0.13; 0.79), the average number of antibiotic resistance genes (ARGs) per 3GCR-EC isolate declined from 9.9 to 7.8 (aPR of 0.79; 95% CI 0.65, 0.96), and the diversity of ARGs was lower in 2021. In the context of Ecuador, where COVID-19 prevention and control measures were strictly enforced after its major cities experienced some of the world’s the highest mortality rates from SARS-CoV-2 infections, antibiotic use and ARB carriage declined in semi-rural communities of Quito from 2019 to 2021.
Topographic and climatic controls of peatland distribution on the Tibetan Plateau
Authors: Sun Jingjing , Gallego-Sala Angela , Yu Zicheng 
Published: September 2023

AbstractThe Tibetan Plateau (TP) hosts a variety of mountain peatlands that are sensitive to the amplified warming in this region. However, we still lack a basic understanding of environmental and climatic factors controlling peatland distribution in the region. Here we use a bioclimatic envelope model (PeatStash) and environmental analysis that utilise three peatland datasets—(a) the well-studied Zoige peatland complex, (b) a literature-based dataset of TP peatlands sites, and (c) an existing global peatland map (PEATMAP)—to investigate major drivers of peatland distribution in the TP. The Zoige peatland complex is defined by gentle slopes (< 2°), mean annual temperature at 0–2 °C, and soil moisture index > 1.7, much narrower thresholds than those stemming from PEATMAP. Using these narrower thresholds to predict future changes, we found that the Zoige peatland complex will shrink greatly under full-range future warming scenarios (both SSP1–2.6 and SSP5–8.5). Modelling peatland distribution in the entire TP remains challenging because accurate environmental and climate data at high resolution and a reliable peatland distribution map are still lacking. Improved peatland mapping supported by ground-truthing is necessary to understand drivers of peatland distribution, assess carbon storage and other ecosystem services, and predict the TP’s peatlands fate under climate change.
First identification of an evolving Middle Stone Age ochre culture at Porc-Epic Cave, Ethiopia
Authors: Rosso Daniela Eugenia , Regert Martine , d’Errico Francesco 
Published: September 2023

AbstractThe use of mineral pigments, in particular iron-rich rocks, holds significant importance in understanding the emergence and evolution of human cultures. However, sites that have yielded a number of pieces large enough to precisely identify how the use of this material changed through time are rare. In this study, we examine one of the largest known Middle Stone Age (MSA) ochre collections, from Porc-Epic Cave, Ethiopia, consisting of more than 40 kg of ochre (n = 4213 pieces), 21 ochre processing tools and two ochre-stained artefacts. By combining the analysis of the elemental and mineralogical composition of the archaeological material with that of natural ochre collected in the surroundings of the site, and correlating this information with shifts in ochre modification techniques over time, we unveil how MSA inhabitants of Porc-Epic Cave exploited mineral resources. We show that they could predict the properties of different ochre types accessible in their environment, and gradually adapted their technology to cope with changes in raw material availability. Furthermore, the analysis of ochre residues on a painted pebble, likely used to produce red dots on a surface, identifies an ochre type that was specifically employed for symbolic purposes.
Influence of child and adult faces with face masks on emotion perception and facial mimicry
Authors: Kastendieck Till , Dippel Nele , Asbrand Julia , Hess Ursula 
Published: September 2023

AbstractEmotional mimicry, the imitation of others’ emotion expressions, is related to increased interpersonal closeness and better interaction quality. Yet, little research has focused on the effect of face masks on emotional mimicry and none on (masked) child faces. To address this gap, we conducted an online experiment (N = 235, German sample, adult perceivers). Masks reduced emotion recognition accuracy for all expressions, except in the case of anger in masked child faces, where perceived anger was even increased. Perceived interpersonal closeness was reduced for masked happy and sad faces. For both child and adult expressers, masks reduced facial mimicry of happy expressions, with no mask effects for sadness and anger expression. A stronger mask effect on facial happiness mimicry of child faces was mediated by the degree of emotion recognition accuracy. Smiles shown by masked children were not recognized well, likely due to the absence of wrinkles around the eyes in child faces. Independent of masks, sadness shown by children was mimicked even more strongly than when shown by adults. These results provide evidence for facial mimicry of child expressions by adult perceivers and show that the effects of face masks on emotion communication may vary when children wear them.
Cross-reactive MHC class I T cell epitopes may dictate heterologous immune responses between respiratory viruses and food allergens
Authors: Balz Kathrin , Kaushik Abhinav , Cemic Franz , Sampath Vanitha , Heger Vanessa , Renz Harald , Nadeau Kari , Skevaki Chrysanthi 
Published: September 2023

AbstractRespiratory virus infections play a major role in asthma, while there is a close correlation between asthma and food allergy. We hypothesized that T cell-mediated heterologous immunity may induce asthma symptoms among sensitized individuals and used two independent in silico pipelines for the identification of cross-reactive virus- and food allergen- derived T cell epitopes, considering individual peptide sequence similarity, MHC binding affinity and immunogenicity. We assessed the proteomes of human rhinovirus (RV1b), respiratory syncytial virus (RSVA2) and influenza-strains contained in the seasonal quadrivalent influenza vaccine 2019/2020 (QIV 2019/2020), as well as SARS-CoV-2 for human HLA alleles, in addition to more than 200 most common food allergen protein sequences. All resulting allergen-derived peptide candidates were subjected to an elaborate scoring system considering multiple criteria, including clinical relevance. In both bioinformatics approaches, we found that shortlisted peptide pairs that are potentially binding to MHC class II molecules scored up to 10 × lower compared to MHC class I candidate epitopes. For MHC class I food allergen epitopes, several potentially cross-reactive peptides from shrimp, kiwi, apple, soybean and chicken were identified. The shortlisted set of peptide pairs may be implicated in heterologous immune responses and translated to peptide immunization strategies with immunomodulatory properties.
Aspacochioside C from Asparagus cochinchinensis attenuates eumelanin synthesis via inhibition of TRP2 expression
Authors: Yunmam Silvia , Lee Hae Ran , Hong Seong Min , Kim Ji-Young , Kang Tong Ho , Lee Ai Young , Jang Dae Sik , Kim Sun Yeou 
Published: September 2023

AbstractAspacochioside C (ACC) is a steroidal saponin isolated from Asparagus cochinchinensis. Steroidal saponins, such as pseudoprotodioscin and dioscin, are known to inhibit melanogenesis, but the role of ACC in melanogenesis remains unknown. Due to the toxic effect of the commonly used skin whitening agents like arbutin, kojic acid and α-lipoic acid alternative plant products are recentlybeen studied for their anti-hypergmentation effect. This study explores the role of ACC in melanogenesis in both in vivo and in vitro models. Here, we for the first time demonstrate that ACC attenuated α-MSH- and UVB-induced eumelanin production by inhibiting tyrosinase-related protein (TRP)-2 protein expression in both murine B16F10 and human melanoma MNT1 cells. However, ACC had no significant effect on pheomelanin concentration. ACC also decreased the pigmentation density in zebrafish embryos, which indicates that ACC targets TRP2 and inhibits eumelanin synthesis. Our results demonstrate that ACC inhibits TRP2, thereby attenuating eumelanin synthesis both in in vitro and in vivo zebrafish model. Therefore, ACC can potentially be used as an anti-melanogenic agent for both aesthetic and pharmaceutical purposes.
A permutation-based approach using a rank-based statistic to identify sex differences in epigenetics
Authors: Sommer Alice J. , Okonkwo Jude , Monteiro Jonathan , Bind Marie-Abèle C. 
Published: September 2023

AbstractEpigenetic sex differences and their resulting implications for human health have been studied for about a decade. The objective of this paper is to use permutation-based inference and a new ranked-based test statistic to identify sex-based epigenetic differences in the human DNA methylome. In particular, we examine whether we could identify separations between the female and male distributions of DNA methylation across hundred of thousands CpG sites in two independent cohorts, the Swedish Adoption Twin study and the Lamarck study. Based on Fisherian p-values, we set a threshold for methylation differences “worth further scrutiny”. At this threshold, we were able to confirm previously-found CpG sites that stratify with respect to sex. These CpG sites with sex differences in DNA methylation should be further investigated for their possible contribution to various physiological and pathological functions in the human body. We followed-up our statistical analyses with a literature review in order to inform the proposed disease implications for the loci we uncovered.
Numerical correlation between non-visual metrics and brightness metrics—implications for the evaluation of indoor white lighting systems in the photopic range
Authors: Khanh Tran Quoc , Vinh Trinh Quang , Bodrogi Peter 
Published: September 2023

AbstractFrom the beginning of the $$21\textrm{st}$$

21
st

century until today, the demand for lighting systems includes not only visual parameters (brightness, contrast perception, color quality), but also non-visual parameters. It is necessary to define the new non-visual parameters for the realization of the new concept of Human Centric Lighting (HCL) or Integrative Lighting. As a contribution to this approach, many international research groups have tried to quantify the non-visual parameters such as Circadian Stimulus by Rea et. al. in USA ($$CS_{2018}$$

C

S
2018

, $$CS_{2021}$$

C

S
2021

), Melanopic Equivalent Daylight ($$D_{65}$$

D
65

) illuminance, mEDI of the CIE S 026/E:2018 or the latest formula by Giménez et al., for the nocturnal melatonin suppression. Therefore, it is necessary to analyze the correlation between these non-visual metrics and brightness metrics such as the equivalent luminance of Fotios et al., or the latest brightness model of TU Darmstadt so that scientists, lighting engineers and lighting system users can correctly apply them in their work. In this context, this paper attempts to investigate and analyze these correlations between the three metric groups based on the database of 884 light sources of different light source technologies and daylight spectra. The obtained results show that the latest Circadian Stimulus model of Rea et. al. $$CS_{2021}$$

C

S
2021

with the improvement of Circadian Light $$CL_{A,2021}$$

C

L

A
,
2021

($$CL_{A\,2.0}$$

C

L

A

2.0

) has solved the disadvantage of $$CS_{2018}$$

C

S
2018

, especially for the interrupted point between warm and cold white (about $$3710\,K$$

3710

K

) or the junction between negative and positive signal of the opponent channel ($$B -(L+M)$$

B
-
(
L
+
M
)

). Moreover, these three metrics of the three research groups contain a high correlation coefficient, so that one metric can be transformed by linear functions to the other two parameters.