bluuebunny/crossref_metadata_2025_split huggingface dataset:
MIXed plastics biodegradation and UPcycling using microbial communities: EU Horizon 2020 project MIX-UP started January 2020
Authors: Ballerstedt Hendrik , Tiso Till , Wierckx Nick , Wei Ren , Averous Luc , Bornscheuer Uwe , O’Connor Kevin , Floehr Tilman , Jupke Andreas , Klankermayer Jürgen , Liu Luo , de Lorenzo Victor , Narancic Tanja , Nogales Juan , Perrin Rémi , Pollet Eric , Prieto Auxiliadora , Casey William , Haarmann Thomas , Sarbu Alexandru , Schwaneberg Ulrich , Xin Fengxue , Dong Weiliang , Xing Jiamin , Chen Guo-Qiang , Tan Tianwei , Jiang Min , Blank Lars M. 
Published: August 2021

AbstractThis article introduces the EU Horizon 2020 research project MIX-UP, "Mixed plastics biodegradation and upcycling using microbial communities". The project focuses on changing the traditional linear value chain of plastics to a sustainable, biodegradable based one. Plastic mixtures contain five of the top six fossil-based recalcitrant plastics [polyethylene (PE), polyurethane (PUR), polypropylene (PP), polyethylene terephthalate (PET), polystyrene (PS)], along with upcoming bioplastics polyhydroxyalkanoate (PHA) and polylactate (PLA) will be used as feedstock for microbial transformations. Consecutive controlled enzymatic and microbial degradation of mechanically pre-treated plastics wastes combined with subsequent microbial conversion to polymers and value-added chemicals by mixed cultures. Known plastic-degrading enzymes will be optimised by integrated protein engineering to achieve high specific binding capacities, stability, and catalytic efficacy towards a broad spectrum of plastic polymers under high salt and temperature conditions. Another focus lies in the search and isolation of novel enzymes active on recalcitrant polymers. MIX-UP will formulate enzyme cocktails tailored to specific waste streams and strives to enhance enzyme production significantly. In vivo and in vitro application of these cocktails enable stable, self-sustaining microbiomes to convert the released plastic monomers selectively into value-added products, key building blocks, and biomass. Any remaining material recalcitrant to the enzymatic activities will be recirculated into the process by physicochemical treatment. The Chinese–European MIX-UP consortium is multidisciplinary and industry-participating to address the market need for novel sustainable routes to valorise plastic waste streams. The project's new workflow realises a circular (bio)plastic economy and adds value to present poorly recycled plastic wastes where mechanical and chemical plastic recycling show limits.
AttentionDDI: Siamese attention-based deep learning method for drug–drug interaction predictions
Authors: Schwarz Kyriakos , Allam Ahmed , Perez Gonzalez Nicolas Andres , Krauthammer Michael 
Published: August 2021

Abstract
Background
Drug–drug interactions (DDIs) refer to processes triggered by the administration of two or more drugs leading to side effects beyond those observed when drugs are administered by themselves. Due to the massive number of possible drug pairs, it is nearly impossible to experimentally test all combinations and discover previously unobserved side effects. Therefore, machine learning based methods are being used to address this issue.

Methods
We propose a Siamese self-attention multi-modal neural network for DDI prediction that integrates multiple drug similarity measures that have been derived from a comparison of drug characteristics including drug targets, pathways and gene expression profiles.

Results
Our proposed DDI prediction model provides multiple advantages: (1) It is trained end-to-end, overcoming limitations of models composed of multiple separate steps, (2) it offers model explainability via an Attention mechanism for identifying salient input features and (3) it achieves similar or better prediction performance (AUPR scores ranging from 0.77 to 0.92) compared to state-of-the-art DDI models when tested on various benchmark datasets. Novel DDI predictions are further validated using independent data resources.

Conclusions
We find that a Siamese multi-modal neural network is able to accurately predict DDIs and that an Attention mechanism, typically used in the Natural Language Processing domain, can be beneficially applied to aid in DDI model explainability.
Skin microbiota dynamics following B. subtilis formulation challenge: an in vivo study in mice
Authors: Moskovicz Veronica , Ben-El Rina , Horev Guy , Mizrahi Boaz 
Published: August 2021

Abstract
Background
Modulating the microbiota is a leading-edge strategy for the restoration and maintenance of a healthy, balanced environment. The use of health-promoting bacteria has demonstrated some potential benefits as an alternative for skin microbiota intervention. Here, we investigate the manipulation of mice skin microbiota using B. subtilis incorporated into a supportive Pluronic F-127 hydrogel formulation. The formula plays an important role in delivering the bacteria to the desired action site.

Results
The B. subtilis challenge induced a shift in the composition and abundance of the skin microbiota. Containment of B. subtilis in the Pluronic F-127 hydrogel accelerated bacterial modulation compared with free B. subtilis. The abundance of both Staphylococcus and Corynebacterium spp. was altered as a result of the live bacterial intervention: the abundance of Corynebacterium increased while that of Staphylococcus decreased. Four days after last application of the B. subtilis formulation, B. subtilis counts returned to its initial level.

Conclusions
B. subtilis intervention can induce a shift in the skin microbiota, influencing the abundance of commensal, beneficial, and pathogenic bacteria. Containment of B. subtilis in Pluronic hydrogel accelerates the microbial alteration, probably by facilitating bacterial attachment and supporting continuous growth. Our results reveal the ability of B. subtilis in Pluronic to modulate the skin microbiota composition, suggesting that the formulation holds therapeutic potential for skin disease treatment.
GWAS provides biological insights into mechanisms of the parasitic plant (Striga) resistance in sorghum
Authors: Kavuluko Jacinta , Kibe Magdaline , Sugut Irine , Kibet Willy , Masanga Joel , Mutinda Sylvia , Wamalwa Mark , Magomere Titus , Odeny Damaris , Runo Steven 
Published: August 2021

Abstract
Background
Sorghum yields in sub-Saharan Africa (SSA) are greatly reduced by parasitic plants of the genus Striga (witchweed). Vast global sorghum genetic diversity collections, as well as the availability of modern sequencing technologies, can be potentially harnessed to effectively manage the parasite.

Results
We used laboratory assays – rhizotrons to screen a global sorghum diversity panel to identify new sources of resistance to Striga; determine mechanisms of resistance, and elucidate genetic loci underlying the resistance using genome-wide association studies (GWAS). New Striga resistant sorghum determined by the number, size and biomass of parasite attachments were identified. Resistance was by; i) mechanical barriers that blocked parasite entry, ii) elicitation of a hypersensitive reaction that interfered with parasite development, and iii) the inability of the parasite to develop vascular connections with hosts. Resistance genes underpinning the resistance corresponded with the resistance mechanisms and included pleiotropic drug resistance proteins that transport resistance molecules; xylanase inhibitors involved in cell wall fortification and hormonal regulators of resistance response, Ethylene Response Factors.

Conclusions
Our findings are of fundamental importance to developing durable and broad-spectrum resistance against Striga and have far-reaching applications in many SSA countries where Striga threatens the livelihoods of millions of smallholder farmers that rely on sorghum as a food staple.
A homologous gene of OsREL2/ASP1, ASP-LSL regulates pleiotropic phenotype including long sterile lemma in rice
Authors: Wu Tingkai , Ali Asif , Wang Jinhao , Song Jiahe , Fang Yongqiong , Zhou Tingting , Luo Yi , Zhang Hongyu , Chen Xiaoqiong , Liao Yongxiang , Liu Yutong , Xu Peizhou , Wu Xianjun 
Published: August 2021

Abstract
Background
Panicle is a harvesting organ of rice, and its morphology and development are closely associated with grain yield. The current study was carried on a mutant screened through an EMS (ethyl-methane sulphonate) mutagenized population of a Japonica cultivar Kitaake (WT).

Results
A mutant, named as asp-lsl (aberrant spikelet-long sterile lemma), showed a significant decrease in plant height, number of tillers, thousand-grains weight, seed setting rate, spikelet length, kernel length and effective number of grains per panicle as compared to WT. Asp-lsl showed a pleiotropic phenotype coupled with the obvious presence of a long sterile lemma. Cross-sections of lemma showed an increase in the cell volume rather than the number of cells. Genetic segregation analysis revealed its phenotypic trait is controlled by a single recessive nuclear gene. Primary and fine mapping indicated that candidate gene controlling the phenotype of asp-lsl was located in an interval of 212 kb on the short arm of chromosome 8 between RM22445 and RM22453. Further sequencing and indels markers analysis revealed LOC_Os08g06480 harbors a single base substitution (G→A), resulting in a change of 521st amino acid(Gly→Glu. The homology comparison and phylogenetic tree analysis revealed mutation was occurred in a highly conserved domain and had a high degree of similarity in Arabidopsis, corn, and sorghum. The CRISPR/Cas9 mutant line of ASP-LSL produced a similar phenotype as that of asp-lsl. Subcellular localization of ASP-LSL revealed that its protein is localized in the nucleus. Relative expression analysis revealed ASP-LSL was preferentially expressed in panicle, stem, and leaves. The endogenous contents of GA, CTK, and IAA were found significantly decreased in asp-lsl as compared to WT.

Conclusions
Current study presents the novel phenotype of asp-lsl and also validate the previously reported function of OsREL2 (ROMOSA ENHANCER LOCI2), / ASP1(ABERRANT SPIKELET AND PANICLE 1).
Comparative transcriptomic analyses of glucosinolate metabolic genes during the formation of Chinese kale seeds
Authors: Zhao Yijiao , Chen Zeyuan , Chen Jiaxuan , Chen Bingxing , Tang Weiling , Chen Xiaodong , Lai Zhongxiong , Guo Rongfang 
Published: August 2021

Abstract
Background
To understand the mechanism of glucosinolates (GSs) accumulation in the specific organs, combined analysis of physiological change and transcriptome sequencing were applied in the current study. Taking Chinese kale as material, seeds and silique walls were divided into different stages based on the development of the embryo in seeds and then subjected to GS analysis and transcriptome sequencing.

Results
The main GS in seeds of Chinese kale were glucoiberin and gluconapin and their content changed with the development of the seed. During the transition of the embryo from torpedo- to the early cotyledonary-embryo stage, the accumulation of GS in the seed was accompanied by the salient decline of GS in the corresponding silique wall. Thus, the seed and corresponding silique wall at these two stages were subjected to transcriptomic sequencing analysis. 135 genes related to GS metabolism were identified, of which 24 genes were transcription factors, 81 genes were related to biosynthetic pathway, 25 genes encoded catabolic enzymes, and 5 genes matched with transporters. The expression of GS biosynthetic genes was detected both in seeds and silique walls. The high expression of FMOGS-OX and AOP2, which is related to the production of gluconapin by side modification, was noted in seeds at both stages. Interestingly, the expression of GS biosynthetic genes was higher in the silique wall compared with that in the seed albeit lower content of GS existed in the silique wall than in the seed. Combined with the higher expression of transporter genes GTRs in silique walls than in seeds, it was proposed that the transportation of GS from the silique wall to the seed is an important source for seed GS accumulation. In addition, genes related to GS degradation expressed abundantly in the seed at the early cotyledonary-embryo stage indicating its potential role in balancing seed GS content.

Conclusions
Two stages including the torpedo-embryo and the early cotyledonary-embryo stage were identified as crucial in GS accumulation during seed development. Moreover, we confirmed the transportation of GS from the silique wall to the seed and proposed possible sidechain modification of GS biosynthesis may exist during seed formation.
Protective responses of tolerant and sensitive wheat seedlings to systemic and local zearalenone application – Electron paramagnetic resonance studies
Authors: Apolonia Sieprawska , Maria Łabanowska , Magdalena Kurdziel , Maria Filek , Magdalena Skórka , Anna Barbasz 
Published: August 2021

Abstract
Background
Mycotoxins are among the environmental stressors whose oxidative action is currently widely studied. The aim of this paper was to investigate the response of seedling leaves to zearalenone (ZEA) applied to the leaves (directly) and to the grains (indirectly) in tolerant and sensitive wheat cultivars.

Results
Biochemical analyses of antioxidant activity were performed for chloroplasts and showed a similar decrease in this activity irrespective of plant sensitivity and the way of ZEA application. On the other hand, higher amounts of superoxide radical (microscopic observations) were generated in the leaves of plants grown from the grains incubated in ZEA solution and in the sensitive cultivar. Electron paramagnetic resonance (EPR) studies showed that upon ZEA treatment greater numbers of Mn - aqua complexes were formed in the leaves of the tolerant wheat cultivar than in those of the sensitive one, whereas the degradation of Fe-protein complexes occurred independently of the cultivar sensitivity.

Conclusion
The changes in the quantity of stable, organic radicals formed by stabilizing reactive oxygen species on biochemical macromolecules, indicated greater potential for their generation in leaf tissues subjected to foliar ZEA treatment. This suggested an important role of these radical species in protective mechanisms mainly against direct toxin action. The way the defense mechanisms were activated depended on the method of the toxin application.
Abnormalities in lysine degradation are involved in early cardiomyocyte hypertrophy development in pressure-overloaded rats
Authors: Liu Jialing , Hu Junhao , Tan Lanlan , Zhou Qi , Wu Xiaojing 
Published: August 2021

Abstract
Background
Cardiomyocyte metabolism changes before cardiac remodeling, but its role in early cardiac hypertrophy detection remains unclear. This study investigated early changes in plasma metabolomics in a pressure-overload cardiac hypertrophy model induced by transverse aortic constriction (TAC).

Methods
The TAC model was constructed by partly ligating the aortic arch. Twelve Sprague–Dawley rats were randomly divided into the TAC group (n = 6) and sham group (n = 6). Three weeks after surgery, cardiac echocardiography was performed to assess cardiac remodeling and function. Hematoxylin/eosin (HE), Masson, and wheat germ agglutinin (WGA) stains were used to observe pathological changes. Plasma metabolites were detected by UPLC-QTOFMS and Q-TOFMS. Specific metabolites were screened by orthogonal partial least squares discriminant analysis (OPLS-DA). Metabolic pathways were characterized by Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and the predictive value of the screened metabolites was analyzed by receiver operating characteristic (ROC) curve analysis.

Results
Three weeks after surgery, the TAC and sham groups had similar left heart function and interventricular septum and diastolic left ventricular posterior wall thicknesses. However, on pathological examination, the cross-sectional area of cardiomyocytes and myocardial fibrosis severity were significantly elevated in TAC rats. OPLS-DA showed different metabolic patterns between the TAC and sham groups. Based on the criteria VIP > 1 and P < 0.05, 13 metabolites were screened out. KEGG analysis identified disrupted lysine degradation through the related metabolites 5-aminopentanoic acid, N6-acetyl-l-lysine, and l-lysine, with areas under the ROC curve (AUCs) of 0.917, 0.889, and 0.806, respectively, for predicting compensated cardiomyocyte hypertrophy.

Conclusion
Disruption of lysine degradation might be involved in early cardiac hypertrophy development, and related metabolites might be potential predictive and interventional targets for subclinical cardiomyocyte hypertrophy.
Association of stent diameter and target vessel revascularization in patients undergoing percutaneous coronary intervention: a secondary retrospective analysis based on a Chinese cohort study
Authors: Xu Tiancheng , Feng Beili , Zheng Zaixing , Li Licheng , Zeng Weifang , Wang Dongjuan , Zhang Lin , Li Hengdong 
Published: August 2021

AbstractBackgroundIn the treatment of coronary heart disease, target vessel revascularization (TVR) has attracted increasing attention as an efficient means of percutaneous coronary intervention (PCI). The purpose of this study was to explore the association between stent diameter and TVR in patients undergoing PCI.MethodsThis was a secondary retrospective analysis involving patients with PCI with at least one stent implanted. Information was obtained from the Dryad Digital Repository. Multivariable logistic regression models, interaction analyses, subgroup analyses and piecewise linear regression models were used to evaluate the association between stent diameter and TVR.ResultsA total of 2522 patients were eventually enrolled in this study, of which 122 (4.8%) had undergone TVR. Significant positive associations were observed between stent diameter and TVR (continuous: odds ratio [OR] 0.485, 95% confidence interval [CI] 0.305–0.773, P = 0.002; categorical variable: T2 vs. T1, OR 0.541, 95% CI 0.348–0.843; T3 vs. T1, OR 0.520, 95% CI 0.334–0.809; P for trend = 0.005). The association remained stable in the fully adjusted model (continuous: OR 0.526, 95% CI 0.306–0.902, P = 0.020; categorical variable: T2 vs. T1, OR 0.510, 95% CI 0.310–0.839; T3 vs. T1, OR 0.585, 95% CI 0.352–0.973; P for trend = 0.042). Among the subgroups of differing clinical presentations, stent diameter was a powerful protective factor for TVR, especially in the delayed PCI group (P for interaction = 0.002). The association was highly consistent across all the other subgroups studied (all P for interaction > 0.05). In the piecewise linear regression model, the need for TVR decreased with an increase in stent diameter when this ranged between 2.5 and 2.9 mm (OR 0.01, 95% CI: 0.01–0.13, P < 0.001).ConclusionsA large stent diameter is a powerful protective factor for TVR in PCI patients, especially in the delayed PCI group. This “bigger-is-better” protective effect is remarkable in stents with diameter 2.5–2.9 mm.
Use of research electronic data capture (REDCap) in a COVID-19 randomized controlled trial: a practical example
Authors: Kianersi Sina , Luetke Maya , Ludema Christina , Valenzuela Alexander , Rosenberg Molly 
Published: August 2021

AbstractBackgroundRandomized controlled trials (RCT) are considered the ideal design for evaluating the efficacy of interventions. However, conducting a successful RCT has technological and logistical challenges. Defects in randomization processes (e.g., allocation sequence concealment) and flawed masking could bias an RCT’s findings. Moreover, investigators need to address other logistics common to all study designs, such as study invitations, eligibility screening, consenting procedure, and data confidentiality protocols. Research Electronic Data Capture (REDCap) is a secure, browser-based web application widely used by researchers for survey data collection. REDCap offers unique features that can be used to conduct rigorous RCTs.MethodsIn September and November 2020, we conducted a parallel group RCT among Indiana University Bloomington (IUB) undergraduate students to understand if receiving the results of a SARS-CoV-2 antibody test changed the students’ self-reported protective behavior against coronavirus disease 2019 (COVID-19). In the current report, we discuss how we used REDCap to conduct the different components of this RCT. We further share our REDCap project XML file and instructional videos that investigators can use when designing and conducting their RCTs.ResultsWe reported on the different features that REDCap offers to complete various parts of a large RCT, including sending study invitations and recruitment, eligibility screening, consenting procedures, lab visit appointment and reminders, data collection and confidentiality, randomization, blinding of treatment arm assignment, returning test results, and follow-up surveys.ConclusionsREDCap offers powerful tools for longitudinal data collection and conduct of rigorous and successful RCTs. Investigators can make use of this electronic data capturing system to successfully complete their RCTs.Trial registrationThe RCT was prospectively (before completing data collection) registered at ClinicalTrials.gov; registration number:NCT04620798, date of registration: November 9, 2020.
“I must, and I can live with that”: a thematic analysis of patients’ perspectives on polypharmacy and a digital decision support system for GPs
Authors: Brünn Robin , Müller Beate S. , Flaig Benno , Kellermann-Mühlhoff Petra , Karbach Ute , Söling Sara , Muth Christiane , van den Akker Marjan ,   AdAM Study consortium, Düvel Lara , Beckmann Till , Hammerschmidt Reinhard , Jachmich Julia , Leicher Eva , Brandt Benjamin , Richard Johanna , Meyer Frank , Flume Mathias , Müller Thomas , Gerlach Ferdinand M. , González-González Ana Isabel , Dinh Truc Sophia , Chapidi Kiran , Ihle Peter , Meyer Ingo , Timmesfeld Nina , Trampisch Hans Joachim , Klaaßen-Mielke Renate , Basten Jale , Greiner Wolfgang , Surmann Bastian , Pfaff Holger , Köberlein-Neu Juliane , Piotrowski Alexandra , Beifuß Karolina , Meyer Sarah , Grandt Daniel , Grandt Simone 
Published: August 2021

Abstract
Background
To investigate patients’ perspectives on polypharmacy and the use of a digital decision support system to assist general practitioners (GPs) in performing medication reviews.

Methods
Qualitative interviews with patients or informal caregivers recruited from participants in a cluster-randomized controlled clinical trial (cRCT). The interviews were transcribed verbatim and analyzed using thematic analysis.

Results
We conducted 13 interviews and identified the following seven themes: the patients successfully integrated medication use in their everyday lives, used medication plans, had both good and bad personal experiences with their drugs, regarded their healthcare providers as the main source of medication-related information, discussed medication changes with their GPs, had trusting relationships with them, and viewed the use of digital decision support tools for medication reviews positively. No unwanted adverse effects were reported.

Conclusions
Despite drug-related problems, patients appeared to cope well with their medications. They also trusted their GPs, despite acknowledging polypharmacy to be a complex field for them. The use of a digital support system was appreciated and linked to the hope that reasons for selecting specific medication regimens would become more comprehensible. Further research with a more diverse sampling might add more patient perspectives.

Trial registration
ClinicalTrials.gov, NCT03430336. Registered on February 6, 2018.