bluuebunny/crossref_metadata_2025_split huggingface dataset:
First report on Vitamin B9 production including quantitative analysis of its vitamers in the yeast Scheffersomyces stipitis
Authors: Mastella Luca , Senatore Vittorio G. , Guzzetti Lorenzo , Coppolino Martina , Campone Luca , Labra Massimo , Beltrani Tiziana , Branduardi Paola 
Published: September 2022

Abstract
Background
The demand for naturally derived products is continuously growing. Nutraceuticals such as pre- and post-biotics, antioxidants and vitamins are prominent examples in this scenario, but many of them are mainly produced by chemical synthesis. The global folate market is expected to register a CAGR of 5.3% from 2019 to 2024 and reach USD 1.02 billion by the end of 2024. Vitamin B9, commonly known as folate, is an essential micronutrient for humans. Acting as a cofactor in one-carbon transfer reactions, it is involved in many biochemical pathways, among which the synthesis of nucleotides and amino acids. In addition to plants, many microorganisms can naturally produce it, and this can pave the way for establishing production processes. In this work, we explored the use of Scheffersomyces stipitis for the production of natural vitamin B9 by microbial fermentation as a sustainable alternative to chemical synthesis.

Results
Glucose and xylose are the main sugars released during the pretreatment and hydrolysis processes of several residual lignocellulosic biomasses (such as corn stover, wheat straw or bagasse). We optimized the growth conditions in minimal medium formulated with these sugars and investigated the key role of oxygenation and nitrogen source on folate production. Vitamin B9 production was first assessed in shake flasks and then in bioreactor, obtaining a folate production up to 3.7 ± 0.07 mg/L, which to date is the highest found in literature when considering wild type microorganisms. Moreover, the production of folate was almost entirely shifted toward reduced vitamers, which are those metabolically active for humans.

Conclusions
For the first time, the non-Saccharomyces yeast S. stipitis was used to produce folate. The results confirm its potential as a microbial cell factory for folate production, which can be also improved both by genetic engineering strategies and by fine-tuning the fermentation conditions and nutrient requirements.
Large-scale and small-scale population genetic structure of the medically important gastropod species Bulinus truncatus (Gastropoda, Heterobranchia)
Authors: Maes Tim , De Corte Zoë , Vangestel Carl , Virgilio Massimiliano , Smitz Nathalie , Djuikwo-Teukeng Félicité F. , Papadaki Maria Ioanna , Huyse Tine 
Published: September 2022

AbstractBackgroundGastropod snails remain strongly understudied, despite their important role in transmitting parasitic diseases. Knowledge of their distribution and population dynamics increases our understanding of the processes driving disease transmission. We report the first study to use high-throughput sequencing (HTS) to elucidate the population genetic structure of the hermaphroditic snailBulinus truncatus(Gastropoda, Heterobranchia) on a regional (17–150 km) and inter-regional (1000–5400 km) scale. This snail species acts as an intermediate host ofSchistosoma haematobiumandSchistosoma bovis, which cause human and animal schistosomiasis respectively.MethodsBulinus truncatussnails were collected in Senegal, Cameroon, Egypt and France and identified through DNA barcoding. A single-end genotyping-by-sequencing (GBS) library, comprising 87 snail specimens from the respective countries, was built and sequenced on an Illumina HiSeq 2000 platform. Reads were mapped againstS. bovisandS. haematobiumreference genomes to identify schistosome infections, and single nucleotide polymorphisms (SNPs) were scored using the Stacks pipeline. These SNPs were used to estimate genetic diversity, assess population structure and construct phylogenetic trees ofB. truncatus.ResultsA total of 10,750 SNPs were scored and used in downstream analyses. The phylogenetic analysis identified five clades, each consisting of snails from a single country but with two distinct clades within Senegal. Genetic diversity was low in all populations, reflecting high selfing rates, but varied between locations due to habitat variability. Significant genetic differentiation and isolation by distance patterns were observed at both spatial scales, indicating that gene flow is not strong enough to counteract the effects of population bottlenecks, high selfing rates and genetic drift. Remarkably, the population genetic differentiation on a regional scale (i.e. within Senegal) was as large as that between populations on an inter-regional scale. The blind GBS technique was able to pick up parasite DNA in snail tissue, demonstrating the potential of HTS techniques to further elucidate the role of snail species in parasite transmission.ConclusionsHTS techniques offer a valuable toolbox to further investigate the population genetic patterns of intermediate schistosome host snails and the role of snail species in parasite transmission.Graphical Abstract
Relationship between cognitive function in individuals with diabetic foot ulcer and mortality
Authors: Sela Yael , Grinberg Keren , Cukierman-Yaffe Tali , Natovich Rachel 
Published: September 2022

Abstract
Background
Diabetic foot ulcer (DFU) is a common diabetes mellitus (DM) complication. Individuals with DM and a DFU achieved significantly lower scores in cognitive tests than those without a DFU. We investigated whether baseline cognitive function in individuals with a DFU is a determinant of mortality.

Methods
A prospective study using data collected during a case–control study conducted in 2010–2012 whereby 90 participants with a DFU (mean age at baseline 58.28 ± 6.95 years, 75.6% male) took the paper and pencil and the NeuroTrax battery of cognitive tests. Depression was assessed, and the DFU status was evaluated. In 2020, information pertaining to participants’ vital status (dead/alive) was collected and the relationship between baseline cognitive status and vital status was assessed.

Results
During a median follow-up of 6.8 years (range 0.2–9.5), 39 participants died (43.3%). Individuals alive vs. those who had died during follow-up had a higher global cognitive score at baseline (92.16 ± 10.95 vs. 87.18 ± 12.24, p = 0.045), but increased risk was not found. Individuals who were alive vs. those who had died during follow-up had statistically significantly higher baseline executive function, reaction time and digit symbol substitution test results. However, after adjustment for glycosylated hemoglobin (HbA1c), microvascular and macrovascular complications, no relationship between cognitive tests and mortality remained significant.

Conclusions
The higher mortality rate among people with type 2 DM and a DFU was not significant after adjustment for HbA1c, micro- and macrovascular complications. There may be common pathophysiological pathways to both DM complications and cognitive impairment, which may contribute to increased mortality. Further studies are warranted.
Distribution, cytotoxicity, and antioxidant activity of fungal endophytes isolated from Tsuga chinensis (Franch.) Pritz. in Ha Giang province, Vietnam
Authors: Vu Thi Hanh Nguyen , Pham Ngoc Son , Le Phuong Chi , Pham Quynh Anh , Quach Ngoc Tung , Nguyen Van The , Do Thi Thao , Chu Hoang Ha , Phi Quyet Tien 
Published: September 2022

Abstract
Purpose
An endangered Tsuga chinensis (Franch.) Pritz. is widely used as a natural medicinal herb in many countries, but little has been reported on its culturable endophytic fungi capable of producing secondary metabolites applied in modern medicine and pharmacy. The present study aimed to evaluate the distribution of fungal endophytes and their cytotoxic and antioxidant properties.

Methods
This study used the surface sterilization method to isolate endophytic fungi which were then identified using morphological characteristics and ITS sequence analysis. The antimicrobial and cytotoxic potentials of fungal ethyl acetate extracts were evaluated by the minimum inhibitory concentration (MIC) and sulforhodamine B (SRB) assays, respectively. Paclitaxel-producing fungi were primarily screened using PCR-based molecular markers. Additionally, biochemical assays were used to reveal the antioxidant potencies of selected strains.

Results
A total of sixteen endophytic fungi that belonged to 7 known and 1 unknown genera were isolated from T. chinensis. The greatest number of endophytes was found in leaves (50%), followed by stems (31.3%) and roots (18.7%). Out of 16 fungal strains, 33.3% of fungal extracts showed significant antimicrobial activities against at least 4 pathogens with inhibition zones ranging from 11.0 ± 0.4 to 25.8 ± 0.6 mm. The most prominent cytotoxicity against A549 and MCF7 cell lines (IC50 value < 92.4 μg/mL) was observed in Penicillium sp. SDF4, Penicillium sp. SDF5, Aspergillus sp. SDF8, and Aspergillus sp. SDF17. Out of three key genes (dbat, bapt, ts) involved in paclitaxel biosynthesis, strains SDF4, SDF8, and SDF17 gave one or two positive hits, holding the potential for producing the billion-dollar anticancer drug paclitaxel. Furthermore, four bioactive strains also displayed remarkable and wide-range antioxidant activity against DPPH, hydroxyl radical, and superoxide anion, which was in relation to the high content of flavonoids and polyphenols detected.

Conclusion
The present study exploited for the first time fungal endophytes from T. chinensis as a promising source for the discovery of new bioactive compounds or leads for the new drug candidates.
Brachiopod and mollusc biomineralisation is a conserved process that was lost in the phoronid–bryozoan stem lineage
Authors: Wernström Joel Vikberg , Gąsiorowski Ludwik , Hejnol Andreas 
Published: September 2022

AbstractBackgroundBrachiopods and molluscs are lophotrochozoans with hard external shells which are often believed to have evolved convergently. While palaeontological data indicate that both groups are descended from biomineralising Cambrian ancestors, the closest relatives of brachiopods, phoronids and bryozoans, are mineralised to a much lower extent and are comparatively poorly represented in the Palaeozoic fossil record. Although brachiopod and mollusc shells are structurally analogous, genomic and proteomic evidence indicates that their formation involves a complement of conserved, orthologous genes. Here, we study a set of genes comprised of 3 homeodomain transcription factors, one signalling molecule and 6 structural proteins which are implicated in mollusc and brachiopod shell formation, search for their orthologs in transcriptomes or genomes of brachiopods, phoronids and bryozoans, and present expression patterns of 8 of the genes in postmetamorphic juveniles of the rhynchonelliform brachiopodT. transversa.ResultsTranscriptome and genome searches for the 10 target genes in the brachiopodsTerebratalia transversa,Lingula anatina,Novocrania anomala, the bryozoansBugula neritinaandMembranipora membranacea, and the phoronidsPhoronis australisandPhoronopsis harmeriresulted in the recovery of orthologs of the majority of the genes in all taxa. While the full complement of genes was present in all brachiopods with a single exception inL. anatina, a bloc of four genes could consistently not be retrieved from bryozoans and phoronids. The genesengrailed,distal-less,ferritin,perlucin,sp1andsp2were shown to be expressed in the biomineralising mantle margin ofT. transversajuveniles.ConclusionsThe gene expression patterns we recovered indicate that while mineralised shells in brachiopods and molluscs are structurally analogous, their formation builds on a homologous process that involves a conserved complement of orthologous genes. Losses of some of the genes related to biomineralisation in bryozoans and phoronids indicate that loss of the capacity to form mineralised structures occurred already in the phoronid–bryozoan stem group and supports the idea that mineralised skeletons evolved secondarily in some of the bryozoan subclades.
What makes a reaction network “chemical”?
Authors: Müller Stefan , Flamm Christoph , Stadler Peter F. 
Published: September 2022

Abstract
Background
Reaction networks (RNs) comprise a set X of species and a set $$\mathscr {R}$$
R
of reactions $$Y\rightarrow Y'$$

Y
→

Y
′

, each converting a multiset of educts $$Y\subseteq X$$

Y
⊆
X

into a multiset $$Y'\subseteq X$$

Y
′

⊆
X

of products. RNs are equivalent to directed hypergraphs. However, not all RNs necessarily admit a chemical interpretation. Instead, they might contradict fundamental principles of physics such as the conservation of energy and mass or the reversibility of chemical reactions. The consequences of these necessary conditions for the stoichiometric matrix $$\mathbf {S}\in \mathbb {R}^{X\times \mathscr {R}}$$

S
∈

R

X
×
R

have been discussed extensively in the chemical literature. Here, we provide sufficient conditions for $$\mathbf {S}$$
S
that guarantee the interpretation of RNs in terms of balanced sum formulas and structural formulas, respectively.

Results
Chemically plausible RNs allow neither a perpetuum mobile, i.e., a “futile cycle” of reactions with non-vanishing energy production, nor the creation or annihilation of mass. Such RNs are said to be thermodynamically sound and conservative. For finite RNs, both conditions can be expressed equivalently as properties of the stoichiometric matrix $$\mathbf {S}$$
S
. The first condition is vacuous for reversible networks, but it excludes irreversible futile cycles and—in a stricter sense—futile cycles that even contain an irreversible reaction. The second condition is equivalent to the existence of a strictly positive reaction invariant. It is also sufficient for the existence of a realization in terms of sum formulas, obeying conservation of “atoms”. In particular, these realizations can be chosen such that any two species have distinct sum formulas, unless $$\mathbf {S}$$
S
implies that they are “obligatory isomers”. In terms of structural formulas, every compound is a labeled multigraph, in essence a Lewis formula, and reactions comprise only a rearrangement of bonds such that the total bond order is preserved. In particular, for every conservative RN, there exists a Lewis realization, in which any two compounds are realized by pairwisely distinct multigraphs. Finally, we show that, in general, there are infinitely many realizations for a given conservative RN.

Conclusions
“Chemical” RNs are directed hypergraphs with a stoichiometric matrix $$\mathbf {S}$$
S
whose left kernel contains a strictly positive vector and whose right kernel does not contain a futile cycle involving an irreversible reaction. This simple characterization also provides a concise specification of random models for chemical RNs that additionally constrain $$\mathbf {S}$$
S
by rank, sparsity, or distribution of the non-zero entries. Furthermore, it suggests several interesting avenues for future research, in particular, concerning alternative representations of reaction networks and infinite chemical universes.
Roughage biodegradation by natural co-cultures of rumen fungi and methanogens from Qinghai yaks
Authors: Wei Yaqin , Yang Hui , Wang Zhiye , Zhao Jiang , Qi Hongshan , Wang Chuan , Zhang Jingrong , Yang Tao 
Published: September 2022

AbstractAnaerobic fungus–methanogen co-cultures from rumen liquids and faeces can degrade lignocellulose efficiently. In this study, 31 fungus–methanogen co-cultures were first obtained from the rumen of yaks grazing in Qinghai Province, China, using the Hungate roll-tube technique. The fungi were identified according to morphological characteristics and internal transcribed spacer (ITS) sequences. The methanogens associated with each fungus were identified by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rRNA gene sequencing. They were five co-culture types: Neocallimastix frontalis + Methanobrevibacter ruminantium, Neocallimastix frontalis + Methanobrevibacter gottschalkii, Orpinomyces joyonii + Methanobrevibacter ruminantium, Caecomyces communis + Methanobrevibacter ruminantium, and Caecomyces communis + Methanobrevibacter millerae. Among the 31 co-cultures, during the 5-day incubation, the N. frontalis + M. gottschalkii co-culture YakQH5 degraded 59.0%–68.1% of the dry matter (DM) and 49.5%–59.7% of the neutral detergent fiber (NDF) of wheat straw, corn stalk, rice straw, oat straw and sorghum straw to produce CH4 (3.0–4.6 mmol/g DM) and acetate (7.3–8.6 mmol/g DM) as end-products. Ferulic acid (FA) released at 4.8 mg/g DM on corn stalk and p-coumaric acid (PCA) released at 11.7 mg/g DM on sorghum straw showed the highest values, with the following peak values of enzyme activities: xylanase at 12,910 mU/mL on wheat straw, ferulic acid esterase (FAE) at 10.5 mU/mL on corn stalk, and p-coumaric acid esterase (CAE) at 20.5 mU/mL on sorghum straw. The N. frontalis + M. gottschalkii co-culture YakQH5 from Qinghai yaks represents a new efficient combination for lignocellulose biodegradation, performing better than previously reported fungus–methanogen co-cultures from the digestive tract of ruminants.
Molecular identification of nontuberculous mycobacteria using the rpoB, argH and cya genes analysis
Authors: Khosravi Azar Dokht , Hashemzadeh Mohammad , Rokhfirooz Parisa 
Published: September 2022

AbstractNontuberculous mycobacterial (NTM) infections are growing worldwide especially in immunocompromised individuals. Since treatment of NTM infections is species-specific, the precise identification of NTM to species level is critical for an optimal treatment. This study was aimed to identify different NTM species by sequencing the rpoB gene and evaluating the effectiveness of argH and cya gene markers. In total 64 clinical isolates suspected to NTM were collected. The identification of the isolates was done by standard conventional methods and PCR-based rpoB gene and sequence analysis. PCR sequencing of argH and cya genes was performed to evaluate the efficacy of these genes in identifying and differentiating different species and subspecies of NTM. Among 64 isolates tested, 51 (79.68%) were detected by conventional tests as NTM. The results of rpoB sequence analysis revealed that the 56 clinical isolates were identified in 10 species of NTM and 8 remaining isolates which showed ambiguous results by rpoB sequencing, application of argH and cya sequencing could detect these isolates. Furthermore, by using cya gene sequencing, M. abscessus subspecies were properly differentiated. Although the rpoB sequencing as a standard method, is beneficial for detecting various species of NTM, however, based on our findings, argH and cya gene markers have a superb ability to discriminate closely related species. Further investigations are required to verify our outcomes.
Dynamic resource provisioning and secured file sharing using virtualization in cloud azure
Authors: Perumal Kumaresan , Mohan Senthilkumar , Frnda Jaroslav , Divakarachari Parameshachari Bidare 
Published: September 2022

AbstractVirtual machines (VMs) are preferred by the majority of organizations due to their high performance. VMs allow for reduced overhead with multiple systems running from the same console at the same time. A physical server is a bare-metal system whose hardware is controlled by the host operating system. A physical server runs on a single instance of OS and application. A virtual server or virtual machine encapsulates the underlying hardware and networking resources. With the existing physical server, it is difficult to migrate the tasks from one platform to another platform or to a datacentre. Centralized security is difficult to setup. But with Hypervisor the virtual machine can be deployed, for instance, with automation. Virtualization cost increases as well as a decrease in hardware and infrastructure space costs. We propose an efficient Azure cloud framework for the utilization of physical server resources at remote VM servers. The proposed framework is implemented in two phases first by integrating physical servers into virtual ones by creating virtual machines, and then by integrating virtual servers into cloud service providers in a cost-effective manner. We create a virtual network in the Azure datacenter using the local host physical server to set up the various virtual machines. Two virtual machine instances, VM1 and VM2, are created using Microsoft Hyper-V with the server Windows 2016 R. The desktop application is deployed and VM performance is monitored using the PowerShell script. Tableau is used to evaluate the physical server functionality of the worksheet for the deployed application.The proposed Physical to Virtual to Cloud model (P2V2C) model is being tested, and the performance result shows that P2V2C migration is more successful in dynamic provisioning than direct migration to cloud platform infrastructure. The research work was carried out in a secure way through the migration process from P2V2C.
A stochastic approach to feasibility analysis of boiler replacement in educational buildings in Extremadura (Spain)
Authors: Garrido-Píriz Pablo , Sánchez-Barroso Gonzalo , García-Sanz-Calcedo Justo 
Published: September 2022

Abstract
Background
Energy efficiency in buildings must be increased in order to reduce both energy intensity and greenhouse gas emissions. This study proposed the replacement of existing diesel boilers with biomass boilers, using four fuels (bulk pellets, wood chip, olive kernel and milled nutshell) to meet the energy demands of educational buildings in the region of Extremadura (Spain). High uncertainty surrounds biomass price prediction affecting the accuracy of economic feasibility analyses; thus, stochastic processes are suitable to support an improvement in the accuracy of predictions. The objective of the study is to demonstrate the feasibility of replacing diesel boilers with biomass boilers in order to revalorize agroforestry residues.

Results
A stochastic simulation of the feasibility of replacing oil-fired boilers with biomass-fired boilers was carried out in this research. Up to 20 million possible scenarios of 10 years of fuel price evolution were simulated by Monte Carlo method based on empirical price trends data. Regression models were built to relate Net Present Values with discount rates, whose statistical dependency was significant. Predictions on financial indicators showed biomass fuels as the most profitable investment, rather than fuel oil. Specifically, in this study, milled nutshell was found the most profitable fuel in the simulation runs, with Net Present Value = 27,151.09 € (standard deviation = 7939.88 €) and Internal Rate of Return = 16.9% (standard deviation = 3.4%).

Conclusions
Continuing to use oil-fired boilers costs more than the purchase and operation of new biomass-fired boilers, since the latter produce a higher cumulative cash flow than the initial investment within the next years. The payback period lies within the range of 4 to 6 years depending on the type of biomass fuel. Getting on the path to sustainability in education buildings can reduce up to 94.4% GHG emissions. This research contributes to promoting the use of low-emission fuels to meet the energy demand of educational buildings. Its results will have a positive effect in the region of Extremadura (Spain), as it boosts the appreciation of agro-industrial waste and economically strengthens the sector.