bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of Agaricus Bisporus Establishment and Fungicidal Treatments on Casing Soil Metataxonomy During Mushroom Cultivation
Authors: Tello Maria Luisa , Lavega Rebeca , Pérez Margarita , Pérez Antonio J. , Thon Michael , Pérez Ernesto 
Published: November 2021

Abstract
The cultivation of edible mushroom is an emerging sector with a potential yet to be discovered. Unlike plants, it is a less developed agriculture where many studies are lacking to optimize the cultivation. Mushrooms are a source of resources still to be revealed, which have applications not only in food, but in many other sectors such as health, industry and biotechnology. Mushroom cultivation consists of the development of selective substrates through composting where the mushroom grows via solid fermentation process. In case of Agaricus bisporus, the compost fully colonized by mycelium hardly produces mushrooms and it is necessary to apply a casing layer with certain physical, chemical and biological characteristics to shift from the vegetative mycelium to the reproductive one, where the native microbiota plays crucial roles. Currently, the industry faces a challenge to substitute the actual peat based casing materials due to the limited natural resources and the impact on the peatlands where peat is extracted.In this work we have employed high-throughput techniques by next generation sequencing to screen the microbial structure of casing soil employed in mushroom cultivation while sequencing V3-V4 of the 16S rRNA gene for bacteria and the ITS2 region of rRNA for fungi in an Illumina MiSeq. In addition, the microbiome dynamics and evolution (bacterial and fungal communities) in peat based casing along the process of incubation of Agaricus bisporus have been studied, while comparing the effect of fungicidal treatment (Chlorothalonil and Metrafenone). Statistically significant changes in populations of bacteria and fungi were observed. Microbial composition differed significantly based on incubation day, changing radically from the original communities to a specific microbial composition adapted to enhance the A. bisporus mycelium growth. Chlorothalonil treatment seems to delay casing colonization by A. bisporus. Proteobacteria and Bacteroidota appeared as the most dominant bacterial phyla. We observed a great change in the structure of the bacteria populations between day 0 and the following days. Fungi populations changed more gradually, A. bisporus displacing the rest of the species as the cultivation cycle progresses. A better understanding of the microbial communities in the casing will hopefully allow us to increase the biological efficiency during production as well as possibly help us to have a clearer view of the microbial community-pathogen relationships as they are directly related to disease development.
Tumor Microenvironment-Aware, Single-Transcriptome Prediction of Microsatellite Instability in Colorectal Cancer
Authors: Seo Mi-Kyoung , Kang Hyundeok , Kim Sangwoo 
Published: November 2021

Abstract
Background: Detecting microsatellite instability (MSI) in colorectal cancers (CRCs) is essential since it is therapeutic strategy determinant feature, including immunotherapy and chemotherapy. Yet, no attempt has been made to exploit transcriptomic profile and tumor microenvironment (TME) of it to unveil MSI status in CRC. Methods: Hence, we developed a novel TME-aware, single-transcriptome predictor of MSI for CRC, called MAP (Microsatellite instability Absolute single sample Predictor). MAP was developed utilizing recursive feature elimination-random forest with 466 CRC samples from The Cancer Genome Atlas, and its performance was validated in independent cohorts, including 1118 samples. Results: MAP showed robustness and predictive power in predicting MSI status in CRC. Additional advantages for MAP were demonstrated through comparative analysis with existing MSI classifier and other cancer types. Conclusions: Our novel approach will provide access to untouched vast amounts of publicly available transcriptomic data and widen the door for MSI CRC research and be useful for gaining insights to help with translational medicine.
Biased TCR gene usage in citrullinated Tenascin C specific T-cells in rheumatoid arthritis
Authors: Sharma Ravi , Boddul Sanjay V. , Yoosuf Niyaz , Turcinov Sara , Dubnovitsky Anatoly , Kozhukh Genadiy , Wermeling Fredrik , Kwok William W. , Klareskog Lars , Malmström Vivianne 
Published: November 2021

Abstract
Objectives
To search for common features in the autoreactive T cell receptor (TCR)-repertoire in patients with rheumatoid arthritis (RA), focusing on the newly identified candidate antigen citrullinated Tenascin C (cit-TNC).
Methods
Mononuclear cells from peripheral blood or synovial fluid of eight RA-patients positive for the RA-associated HLA-DRB1*04:01 allele were in-vitro cultured with recently identified citrullinated peptides from Tenascin C. Antigen-specific T cells were isolated using peptide-HLA tetramer staining and subsequently single-cell sequenced for paired alpha/beta TCR analyses by bioinformatic tools. TCRs were re-expressed for further studies of antigen-specificity and T cell responses.
Results
Autoreactive T cell lines could be grown out from both peripheral blood and synovial fluid. We demonstrate the feasibility of retrieving true autoreactive TCR sequences by validating antigen-specificity in T cell lines with re-expressed TCRs. One of the Tenascin C peptides, cit-TNC22, gave the most robust T cell responses including biased TCR gene usage patterns. The shared TCR-beta chain signature among the citTNC22-specific TCRs was evident in blood and synovial fluid of different patients.
Conclusion
The identification of common elements in the autoreactive TCR repertoire gives promise to the possibility of both immune monitoring of the autoimmune components in RA and of future antigen- or TCR-targeted specific intervention in subsets of patients.
Acute pancreatitis in pregnancy: A 10-year, multi-center, retrospective study in Beijing
Authors: Zhang Tingting , Wang Guoxing , Cao Zheng , Huang Wenyang , Xiao Hongli , Wei Hongtao , Lu Junli , Liu Ruixia , Yin Chenghong 
Published: November 2021

Abstract
Objective

Acute pancreatitis in pregnancy (APIP) is a rare and serious complication during pregnancy. It has acute onset and is difficult to diagnose and treat. The aim of the present study was to describe the etiology, clinical manifestations, and maternofetal outcomes of APIP.
Methods

We retrospectively reviewed 32 pregnant women who were treated at three tertiary care hospitals in Beijing, China. The correlation between the causes of APIP, severity, laboratory indices, and outcomes was analyzed.
Results

The most common causes of APIP were hypertriglyceridemia (56.2%,18/32) and gallstones (28.1%, 9/32). Hypertriglyceridemia-induced APIP was associated with a higher rate of severe acute pancreatitis (P = 0.025). Serum level of triglycerides showed a positive correlation with the severity of APIP (P = 0.039). The most frequent presentation of APIP was abdominal pain (93.7%, 30/32). There were no maternal or fetal deaths in our study. Neonatal asphyxia was correlated with the severity of APIP (P = 0.039).
Conclusion

High level of triglycerides may serve as a useful marker of the severity of APIP. The severity of APIP was associated with higher risk of neonate asphyxia. Appropriate timing of termination of pregnancy is a key imperative for APIP patients.
Soot Distribution and Thermal Regeneration of Marine Diesel Particulate Filter
Authors: Wang Xiangli , Ni Peiyong 
Published: November 2021

Abstract
Particles from marine diesel engine exhaust gas have caused serious air pollution and human health. Diesel particulate filter (DPF) can effectively reduce particle emissions from marine diesel engines. The distribution and regeneration of soot in DPF are two important issues. In this paper, a mathematical model of a marine DPF was built up and the particle trap process and the regeneration dynamics were simulated. The results show that the cake soot mass concentrations during trap process increase linearly with the increase of the exhaust gas flows while the depth soot mass concentrations firstly increase linearly and then keep constant. Soot is mainly concentrated in the front and rear portion of the filter and less soot is in the middle. The soot distribution in the cake and depth layer shows the unevenness during the trap and regeneration process. The initial soot loadings have great effects on pressure drops and soot mass concentrations before regeneration, but little effect after regeneration. The exhaust gas temperature heated to 850 K can achieve 94% efficiency for the DPF regeneration. There is no obvious difference in pressure drops and soot mass concentrations between fast heating and slow heating. The heating duration of exhaust gas has an important impact on DPF regeneration.
Synergistic PAHs biodegradation by a mixed bacterial community: Based on a multisubstrate enrichment approach
Authors: Li Kang , Liu Yanzehua , Li Yangda , Li Dan , Liu Na , Wang Liping 
Published: November 2021

Abstract
Polycyclic aromatic hydrocarbons (PAHs) are highly hard-biodegradable compounds. Therefore, in this work, a multisubstrate enrichment approach was proposed to develop a bacterial community named MBF from activated sludge of coking wastewater plant capable of degrading mixed-PAHs consisting of phenanthrene and pyrene (50 mg/L of each) by 98.8% and 73.3% within 5 days, respectively. The bacterial community could maintain its degradation ability to mixed PAHs relatively under temperatures (20°C–35°C), pH values (5.0–9.0), and salinities (0–10 g/L NaCl). Additionally, the bacterial community MBF degraded 58.9%, 79.9%, and 80.7% of mixed PAHs in the presence of catechol, salicylic acid, and phthalic acid, respectively within 5 days. High-throughput sequencing of 16S rRNA gene amplicon analysis showed that the bacterial community MBF was dominated by Pseudomonas in most treatments, and Burkholderia was predominant under both acidic condition and high salt concentrations. Furthermore, the composition of microbial communities of the bacterial community was significantly different with/without addition of pathway intermediate metabolites after biodegradation of mixed PAHs, revealing the metabolic burden may be distributed between members of this bacterial community. Those results demonstrate that the biodegradation ability of MBF could be maintained with the bacterial community structure altering when facing environmental variations or changes in composition of target contaminants.
Contact Tracing During The COVID-19 Pandemic In District Health Directorate Example in Istanbul, Turkey
Authors: ARMAN İkbal Hümay , Arman Yusuf , ÖREN Meryem Merve 
Published: November 2021

Abstract
Background: After March 2020, with the first case of novel coronavirus, Turkish health care system switched to state of emergency to manage the COVID-19 pandemic. In order to control the pandemic, a scientific committee was established, guidelines were prepared, and filiation/contact tracing studies were started. Field investigation and isolation teams were established, and District Health Directorates (DHD) became frontline primary care organizations to manage contact tracing in Turkey. Case presentation: In this report, pandemic management and contact tracing were evaluated in example of Kartal DHD from Istanbul, Turkey. The report contains the details about the planning process, Kartal DHD Pandemic Management priorities, aim and planning of this policy, coordination and cooperation with other institutes to overcome this extraordinary state. Also, evaluation of the contact tracing and telemedicine usage in the pandemic management is examined as well with future implications. Conclusions: From the SWOT analysis to planning process, this report attempts to describe how this state of emergency was managed and how effective the contact tracing management process was. With its detailed key points of the pandemic management and future perspectives, it has been written in terms of preparation for the future pandemics.
Genetically predicted levels of the human plasma proteome and risk of stroke: a Mendelian Randomization study
Authors: Chen Lingyan , Peters James , Prins Bram , Persyn Elodie , Traylor Matthew , Surendran Praveen , Karthikeyan Savita , Yonova-Doing Ekaterina , Angelantonio Emanuele Di , Roberts David , Watkins Nick , Ouwehand Willem , Danesh John , Lewis Cathryn , Bronson Paola , Markus Hugh , Burgess Stephen , Butterworth Adam , Howson Joanna 
Published: November 2021

Abstract
Proteins are the effector molecules of biology and are the target of most drugs. To identify proteins and related pathways that may play a causal role in stroke pathogenesis, we used Mendelian randomisation (MR). We tested potential causal effects of 308 plasma proteins (measured in 4,994 blood donors from the INTERVAL study) on stroke outcomes (derived from the MEGASTROKE GWAS) in a two-sample MR framework and assessed whether these associations could be mediated by cardiovascular risk factors. We extended the analysis to identify whether pharmacological targeting of these proteins might have potential adverse side-effects or beneficial effects for other conditions through Phenome-wide MR (Phe-MR) in UK Biobank. MR showed an association between stroke and genetically predicted plasma levels of TFPI, IL6RA, MMP12, CD40, TMPRSS5 and CD6 (P≤1.62⋅10−4). We identified six risk factors (atrial fibrillation, body mass index, smoking, blood pressure, white matter hyperintensities and type 2 diabetes) that were associated with stroke (P≤0.0071) using MR. The association of TFPI, IL6RA and TMPRSS5 with stroke could be mediated by these risk factors, such as body mass index, white matter hyperintensity and atrial fibrillation. Thirty-six additional proteins were potentially causal for one or more of these risk factors. The Phe-MR suggested that targeting TFPI could have potential beneficial effects on other disorders of arteries and hyperlipidaemia in addition to stroke. Our results highlight novel causal pathways and potential therapeutic targets for stroke.
Prime Minister Narendra Modi visit to Sri Lanka and its impacts on Indo-Sri Lankan relations
Authors: Jeeva S. , Sivakumar D. 
Published: November 2021

In Globe, no nation is not an isolate it depends upon one another to fulfill their needs as a result of these multilateral relations build-up. Such a strong relationship we need to maintain means we need strong leadership. Such strong leaders are there before and after independence also. The several party leaders and their alliances are formed and implemented the policies for the development of India at the Internal level as well as external level. The National Democratic Alliance (NDA) government was formed under two prominent leaders known as Atal Bihari Vajpayee and Narendra Modi. After Vajpayee, the NDA Government under the leadership of Narendra Modi realized the importance of foreign policy and maintaining a good relationship. Sri Lanka is also one of the closest neighboring countries; Prime Minister Narendra Modi from 2014 to 2019 he officially visited Sri Lanka three times within these three visits he used to make several new initiatives in many fields.
Conjugation of Silver Nanoparticles With De Novo–Engineered Cationic Antimicrobial Peptides: Exploratory Proposal
Authors: Hu Alvin 
Published: November 2021

Background
Cationic antimicrobial peptides have broad antimicrobial activity and provide a novel way of targeting multidrug-resistant bacteria in the era of increasing antimicrobial resistance. Current developments show positive prospects for antimicrobial peptides and silver nanoparticles (AgNPs) individually.

Objective
The primary objective is to propose another method for enhancing antimicrobial activity by conjugating AgNPs with cationic antimicrobial peptides, with a subsequent preliminary assessment of the minimum inhibitory concentration of multidrug-resistant bacteria. The secondary objective is to evaluate the safety of the conjugated compound and assess its viability for in vivo use.

Methods
The proposal involves 3 stages. First, WLBU2C, a modified version of the antimicrobial peptide WLBU2 with an added cysteine group, needs to be synthesized using a standard Fmoc procedure. It can then be stably conjugated with AgNPs ideally through photochemical means. Second, the WLBU2C-AgNP conjugate should be tested for antimicrobial activity according to the Clinical & Laboratory Standards Institute manual on standard minimum inhibitory concentration testing. Third, the cytotoxicity of the conjugate should be tested using cell lysis assays if the above stages are completed.

Results
I-TASSER (iterative threading assembly refinement) simulation revealed that the modified peptide WLBU2C has a secondary structure similar to that of the original WLBU2 peptide. No other results have been obtained at this time.

Conclusions
The addition of AgNPs to already developed de novo–engineered antimicrobial peptides provides an opportunity for the development of potent antimicrobials. Future prospects include emergency last-line therapy and treatment for current difficult-to-eradicate bacterial colonization, such as in cystic fibrosis, implantable medical devices, cancer, and immunotherapy. As I do not anticipate funding at this time, I hope this proposal provides inspiration to other researchers.

International Registered Report Identifier (IRRID)
PRR1-10.2196/28307
Methods for Human-Centered eHealth Development: Narrative Scoping Review
Authors: Kip Hanneke , Keizer Julia , da Silva Marcia C , Beerlage-de Jong Nienke , Köhle Nadine , Kelders Saskia M 
Published: November 2021

Background
Thorough holistic development of eHealth can contribute to a good fit among the technology, its users, and the context. However, despite the availability of frameworks, not much is known about specific research activities for different aims, phases, and settings. This results in researchers having to reinvent the wheel. Consequently, there is a need to synthesize existing knowledge on research activities for participatory eHealth development processes.

Objective
The 3 main goals of this review are to create an overview of the development strategies used in studies based on the CeHRes (Center for eHealth Research) Roadmap, create an overview of the goals for which these methods can be used, and provide insight into the lessons learned about these methods.

Methods
We included eHealth development studies that were based on the phases and/or principles of the CeHRes Roadmap. This framework was selected because of its focus on participatory, iterative eHealth design in context and to limit the scope of this review. Data were extracted about the type of strategy used, rationale for using the strategy, research questions, and reported information on lessons learned. The most frequently mentioned lessons learned were summarized using a narrative, inductive approach.

Results
In the included 160 papers, a distinction was made between overarching development methods (n=10) and products (n=7). Methods are used to gather new data, whereas products can be used to synthesize previously collected data and support the collection of new data. The identified methods were focus groups, interviews, questionnaires, usability tests, literature studies, desk research, log data analyses, card sorting, Delphi studies, and experience sampling. The identified products were prototypes, requirements, stakeholder maps, values, behavior change strategies, personas, and business models. Examples of how these methods and products were applied in the development process and information about lessons learned were provided.

Conclusions
This study shows that there is a plethora of methods and products that can be used at different points in the development process and in different settings. To do justice to the complexity of eHealth development, it seems that multiple strategies should be combined. In addition, we found no evidence for an optimal single step-by-step approach to develop eHealth. Rather, researchers need to select the most suitable research methods for their research objectives, the context in which data are collected, and the characteristics of the participants. This study serves as a first step toward creating a toolkit to support researchers in applying the CeHRes Roadmap to practice. In this way, they can shape the most suitable and efficient eHealth development process.
Characterization and evaluation of mountain sweet thorn (Flacourtia montana J. Grah) collections
Authors: Tripathi P C , Ganeshan S , Radhika V , Shetti D L 
Published: November 2021

Mountain sweet thorn (Flacourtia montana J. Grah) is an indigenous underutilized fruit of the Western Ghats and other regions of peninsular India. It is a close relative of Governor’s plum. It is a bushy shrub or small tree with spiny trunks and branches which may grow up to 2.5 m in height. The fruits are bright dark red 1-2 cm in diameter, sweet edible, and have the potential for processing into jams and jellies. The presence of thorn is one of the major hurdles for the commercialization of this crop. Thus, seeds of the thorny plants of the Mountain sweet thorn were collected from different locations, and seedlings were planted to identify the suitable line. The plant height ranged from 425 cm (accession 0208) to 710 cm (accession​ ​0202). The plant girth ranged from 34.5 cm to 82 cm. The growth data revealed that all​ ​the accessions are vigorous, fast-growing, and have various levels of thorniness. All the​ ​accessions were found to be spreading type. Significant variability was recorded for leaf​ ​characteristics among the accessions studied. Three major clusters were observed in​ ​cluster analysis for morphological and fruiting characters consisting of 1, 8, and 9 accessions,​ ​respectively. The number of fruits ranged from 0 to 4008. The highest yield (9.46 kg/plant)​ ​was obtained in accession - 0106 followed by accession- 0201 (7.83 kg). The average​ ​fruit weight ranged from 1.51 g to 3.94 g. The highest fruit weight (3.94g) was also recorded​ ​in 0106 followed by 2.84 (0102). The total soluble solids ranged from 10 0 Brix to 15.1 0​ ​Brix. Overall, accession 0201 was found better than others with respect to yield, regular​ ​bearing, and less thorniness.
Optimization of methodology for the extraction of polyphenolic compounds with antioxidant potential and α-glucosidase inhibitory activity from Jamun (Syzygium cumini L.) seeds
Authors: Arivalagan M , Priyanka D R , Rekha A 
Published: November 2021

Jamun (Syzygium cumini L.) seed is one of the rich sources of polyphenolic compounds​ ​with antioxidant potential and α-glucosidase inhibitory activity. A study was conducted to​ ​optimize the methodology for the extraction of polyphenolic compounds (total phenolic​ ​and flavonoid contents) with antioxidant potential and α-glucosidase inhibitory activity​ ​from Jamun seed powder. The study showed that the nature of solvent and extraction​ ​conditions had a significant effect on total phenolic content (TPC), total flavonoid content​ ​(TFC), antioxidant potential, and α-glucosidase inhibitory activity. The TPC varied between​ ​6.0 (mg/g Jamun seed powder) for the acetone extract to 119.2 (mg/g) for 80% aqueous​ ​acetone extract and TFC varied between 1.06 mg/g for the acetone to 10.81 mg/g for the​ ​80% aqueous methanol. From the study, it was apparent that an aqueous form of acetone​ ​(acetone: water 80:20, v/v) is a better solvent system for extraction of polyphenolic​ ​compounds with high antioxidant potential and α-glucosidase inhibitory activity.​ ​Ultrasonication for 60 min increased the efficiency of phenolic extraction.