bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome profiling of developing leaf and shoot apices to reveal the molecular mechanism and co-expression genes responsible for the wheat heading date
Authors: Yang Yuxin , Zhang Xueying , Wu Lifen , Zhang Lichao , Liu Guoxiang , Xia Chuan , Liu Xu , Kong Xiuying 
Published: December 2020

Abstract
Background: Wheat is one of the most widely planted crops worldwide. The heading date is important for wheat environmental adaptability; it not only controls flowering time but also determines the yield component in terms of the grain number per spike. Results: In this research, homozygous genotypes with early and late heading dates derived from backcrossed progeny were selected to conduct RNA-seq analysis at the double ridge stage (W2.0) and androgynous primordium differentiation stage (W3.5) of the leaf and apical meristem, respectively. In total, 18,352 differentially expressed genes (DEGs) were identified, many of which are strongly associated with the wheat heading date genes. Gene Ontology (GO) enrichment analysis revealed that carbohydrate metabolism, trehalose metabolic process, photosynthesis, and light reaction are closely related to the flowering time regulation pathway. MapMan metabolic analysis showed that the DEGs mainly functioned in light reaction, hormone signaling, lipid metabolism, secondary metabolism, and nucleotide synthesis. In addition, 1,225 DEGs were annotated to 45 transcription factor gene families, including LFY, SBP, and MADS-box transcription factors that closely related to the flowering time. Weighted gene co-expression network analysis (WGCNA) showed that 16, 336, 446, and 124 DEGs had biological connections with Vrn1-5A, Vrn3-7B, Ppd-1D, and WSOC1, respectively. Furthermore, TraesCS2D02G181400 is a MADS-MIKC transcriptional factor that is co-expressed with Vrn1-5A, which indicates this gene is a potential gene related to the flowering timeConclusions: The RNA-seq analysis enriched the transcriptome data of wheat heading date at the key flower development stages of double ridge (W2.0) and androgynous primordium differentiation (W3.5). Based on the DEGs, the co-expression networks of key flowering time genes in Vrn1-5A, Vrn3-7B, WSOC1, and Ppd-1D were established. Moreover, we discovered a potential candidate flowering time gene TraesCS2D02G181400. Taken together, these results serve as a foundation for further study on the regulatory mechanism of wheat heading date.
Boolean Implication Analysis Unveils Candidate Universal Relationships in Microbiome Data
Authors: Vo Daniella , Singh Shayal Charisma , Safa Sara , Sahoo Debashis 
Published: December 2020

Abstract
Background: Microbiomes consist of bacteria, viruses, and other microorganisms, and are responsible for many different functions in both organisms and the environment. Past analyses of microbiomes focused on using correlation to determine linear relationships between microbes and diseases. Weak correlations due to nonlinearity between microbe pairs may cause researchers to overlook critical components of the data. With the abundance of available microbiome, we need a method that comprehensively studies microbiomes and how they are related to each other.Results: We collected publicly available datasets from human, environment, and animal samples to determine both symmetric and asymmetric Boolean implication relationships between a pair of microbes. We then found relationships that are potentially invariants, meaning they will hold in any microbe community. In other words, if we determine there is a relationship between two microbes, we expect the relationship to hold in almost all contexts. We discovered that around 330,000 pairs of microbes universally exhibit the same relationship in almost all the datasets we studied, thus making them good candidates for invariants. Our results also confirm known biological properties and seem promising in terms of disease diagnosis. Conclusions: Since the relationships are likely universal, we expect them to hold in clinical settings, as well as general populations. If these strong invariants are present in disease settings, it may provide insight into prognostic, predictive, or therapeutic properties of clinically relevant diseases. For example, our results indicate that there is a difference in the microbe distributions between patients who have or do not have IBD, eczema and psoriasis. These new analyses may improve disease diagnosis and drug development in terms of accuracy and efficiency.
Suppression of TCAB1 expression induced cellular senescence by lessening proteasomal degradation of p21 in cancer cells
Authors: Niu Jing , Gao Rui-Qi , Cui Meng-Tian , Zhang Chen-Guang , Li Shen-Tao , Cheng Shan , Ding Wei 
Published: December 2020

Abstract
Background: TCAB1, a.k.a. WRAP53β or WDR79, is an important molecule for the maintenance of Cajal bodies and critically involved in telomere elongation and DNA repair. Upregulation of TCAB1 were discovered in a variety types of cancers. However, the function of TCAB1 in tumor cell senescence remains absent.Methods: The TCAB1 knockdown cell lines were constructed. The expression levels of TCAB1, p21, p16 and p53 were detected by qRT-PCR and western blotting. Staining of senescence-associated β-galactosidase was used to detect senescent cells. The ubiquitination of the p21 was analysed by immunoprecipitatation and in vivo ubiquitination assay. TCGA databases were employed to perform in silico analyses for the mRNA expression of TCAB1, p21, p16 and p53. Results: Here, we discovered that knockdown of TCAB1 induced rapid progression of cellular senescence in A549, H1299 and HeLa cells. In exploiting the mechanism underlining the role of TCAB1 on senescence, we found a significant increase of p21 at the protein levels upon TCAB1 depletion, whereas the p21 mRNA expression was not altered. We verified that TCAB1 knockdown was able to shunt p21 from proteasomal degradation by regulating the ubiquitination of p21. In rescue assays, it was demonstrated that decreasing the expression of p21 or increasing the expression of TCAB1 were able to attenuate the cellular senescence process induced by TCAB1 silencing.Conclusions: This study revealed the importance of TCAB1 for its biological functions in the regulation of cell senescence. Our results will be helpful to understand the mechanisms of senescence in cancer cells, which could provide clues for designing novel strategies for developing effective treatment regimens.
SET1B facilitates activation of the hypoxia response through site-specific histone methylation
Authors: Ortmann Brian , Burrows Natalie , Bailey Peter , Lobb Ian , Peñalver Ana , Wit Niek , Rayner Louise , Seear Rachel , Mole David , Ratcliffe Peter , Maxwell Patrick , Nathan James 
Published: December 2020

Abstract
Hypoxia-inducible transcription factors (HIFs) are fundamental to the cellular adaptation to low oxygen levels but how they interact with chromatin and efficiently activate their target genes is unclear. Using genome-wide mutagenesis in human cancer cells, we define genes required for HIF transcriptional activation, and identify a requirement for the Histone 3 lysine 4 (H3K4) methyltransferase SET1B. Loss of SET1B leads to a selective reduction in HIF transcriptional activity in hypoxia, with SET1B driving expression of genes involved in angiogenesis rather than glycolysis, resulting in impaired tumour establishment in SET1B deficient xenografts. Mechanistically, we show that SET1B is itself oxygen regulated, accumulates on chromatin in hypoxia, and is recruited to HIF target genes through HIF-1α. Accordingly, we show that the hypoxic induction of H3K4me3 at specific HIF targets is both HIF and SET1B dependent, and when impaired, decreases promoter acetylation and gene expression. Together, these findings reveal SET1B as a determinant of site-specific histone methylation and provide insight into how HIF target genes are differentially regulated.
Effects of variety and maturity stage of coconut on physicochemical and sensory characteristics of powdered coconut drink
Authors: Azra Jeallyza Muthia , Setiawan Budi , Nasution Zuraidah , Sulaeman Ahmad 
Published: December 2020

Introduction. Coconut water is rich in nutrients and biologically-active compounds. However, it has a short shelf life that can be prolonged by freeze drying. The purpose of this study was to analyze the physicochemical and sensory characteristics of fresh and powdered coconut drinks.
Study objects and methods. The experiments included eight samples, namely fresh and powdered coconut drinks obtained from coconuts of different varieties (tall and hybrid) and maturity stages (4 and 6 m.o.). The samples were analyzed for nutrient content (ash, protein, fat, total carbohydrate, and fibre), physicochemical properties (titratable acidity, pH, viscosity, total soluble solids, turbidity, water activity, and browning index), and sensory characteristics (color, aroma, taste, texture, and overall acceptance).
Results and discussion. The results obtained showed that there were significant differences among the coconut drinks of different varieties and maturity stages. They differed in nutrient content, pH value, titratable acidity, viscosity, and water activity. Meanwhile, the aroma, taste, and overall acceptance scores of all the samples were not significantly different. The powdered drink from 6 m.o. hybrid coconut was selected as the optimal sample due to its good sensory and physicochemical attributes. These attributes were similar to those of the fresh coconut drink.
Conclusion. The powdered drink from 6 m.o. hybrid coconut obtained by freeze drying could be considered as an alternative healthy drink with good quality characteristics.
Water resources and flooding risk in Kumamoto based on observed hydrologic data analysis
Authors: Higashino Makoto , Stefan Heinz G. 
Published: December 2020

Abstract
Variability and change of precipitation were investigated in Kumamoto on Kyushu Island in southwestern Japan, to assess water resources and flooding risk. Annual precipitation, annual maximum daily precipitation, and annual maximum hourly precipitation have increased over the period from 1891 to 2018 (128 years). Trends are 26.2 mm per decade, 6.07 mm/day per decade, and 2.17 mm/h/decade, respectively. Precipitation in the rainy season (June and July) is on average 37% (ranging from 12 to 59%) of annual precipitation for the 128-year period. Maximum daily precipitation in a year occurred at Kumamoto in the rainy season in 92/128 (72%) of the years of observation from 1891 to 2018, in the typhoon (August to November) season in 23/128 (18%), and in the March to May season in 12/128 (10%). This indicates that the rainy monsoon season poses the largest daily flooding risk. A wavelet analysis revealed that from 1891 to 2018 annual precipitation and daily maximum precipitation fluctuate with 2 and 4 years periods, which may be related to the El Nino-Southern Oscillation (ENSO). It is likely that air temperature rises, ENSO and topographical characteristics contributed to an increase in precipitation in the period. The analysis also showed that typhoons hitting or approaching Kumamoto have significantly affected annual precipitation and annual maximum daily precipitation, while the interval between typhoons affecting Kumamoto has been getting longer since the 1970s.
Quantification of microplastics by count, size and morphology in beverage containers using Nile Red and ImageJ
Authors: Chen Shujuan , Li Yue , Mawhorter Christopher , Legoski Saamon 
Published: December 2020

Abstract
Abundant evidence of microplastics (MP) found in the environment, and its toxicity effect in animals calls for human-related research. However, well-established quantitative controlled studies on the potential route of human exposure to MP are still sparse. MP count, size and morphology in 15 polylactic acid (PLA)-lined plastic cups and 15 PLA-lined paper cups were examined using Nile Red fluorescence tagging, microscopic photography, and morphology assessment and quantification based on ImageJ. In the plastic cups, the count and area of MP fibers were found to be significantly higher compared with blanks (p &lt; 0.05), but not MP particles or total MP. In paper cups, count or area was not significantly different in terms of MP particle, MP fibers or total MP. No interesting trend was observed in the distribution regarding the size of MP particles or fibers. These results indicate that selected paper cups and plastic cups could be considered as safe beverage containers, but further research on the toxicological effects of MPs in different morphologies released from plastic cups on human health is needed.
Biofoam formation and defoamation in global wastewater treatment systems
Authors: Dlangamandla Cynthia , Basitere Moses , Okeleye Benjamin Ifeoluwa , Chidi Boredi Silas , Karabo Obed Ntwampe Seteno 
Published: December 2020

AbstractMunicipal wastewater treatment is largely based on activated sludge (AS) systems due to their ability to reduce biological and chemical oxygen demand (BOD/COD). They are similarly efficient in nitrification and denitrification. However, major drawbacks such as foaming associated with the prevalence of lipids (fats, oil, grease (FOG)) and proteinaceous material arise, which reduces AS efficiency – a focus of this review. Many strategies are employed for foam reduction in AS systems, where proliferation of foam-forming microorganisms can be challenging. To understand foam formation, prevention and deterioration, including destabilisation, a multidisciplinary mitigation approach is required, in which some bioprocess aspects such as foam destabilisation kinetics should be understood and quantified. This review reports on biological foam formation and source in wastewater treatment, defoaming strategies, and biofoam destabilisation kinetics as well as factors affecting foam stability.
Synthesis and Biological Analysis of Anti-addiction Effect and Hepatotoxicity of Tow Baclofen Analogues Complexed with β-Cyclodextrin
Authors: Keniche Assia , EL Ouar Ibtissem , Zeghina Ibtissem , Dib Mohammed El Amine 
Published: December 2020

Aim and Objective :
The excessive consumption of alcohol and the installation of
dependence is, in most cases, facilitated by favorable psychological factors that trigger and
maintain the behavior of consumers. Examples more frequently encountered in individuals having
difficulty with alcohol are, in particular: one or more anxiety disorders, deficits in the capacities to
manage stress and anxiety. The main objective of this work was to study in vivo the anti-addiction
effect and hepatotoxicity of tow baclofen analogues complexed with β-Cyclodextrin (βCD) on an
alcohol-dependent rat model.

Materials and Methods:
The synthesis of two analogues, ABF1 and ABF2, close to baclofen was
reported. The structural determination of the two compounds was confirmed by NMR and IR
analysis. The complexation of analogues with β-Cyclodextrin (βCD) was performed in water at
room temperature (25 °C). The interactions of ABF with β-Cyclodextrin, and the stability constant
(Ka) of the inclusion complex formed between them were investigated by using UV-visible
spectroscopy. The biological effects of baclofen and the two analogues on alcohol dependence
were studied in wistar rats. The anti-addiction effect of the analogues was tested by measuring the
alcohol intake and the variation of the animal behaviour. The toxicity of the compounds was also
analysed on liver injury markers.

Results:
The amino-3-phenylbutanoic acid (ABF1) and 3,4,5-trihydroxy-N-(methyl-2-acetate)
benzamide (ABF2) were synthesized. The complexation of both analogues of baclofen (BF) with
β-cyclodextrin (βCD) (ABF- βCD) was realized and confirmed by the stability constant of the
inclusion complex (Ka) and Job’s method. The evaluation of anti-addiction activity in vivo showed
that ABF1-βCD inhibits the consumption of alcohol at doses equivalent to those of baclofen. Both
baclofen analogues have shown an anxiolytic effect. Regarding the toxicity of the two compounds,
our results showed that ABF1-βCD has less toxic effect than baclofen; it reduces the activity of
ALT and AST enzymes. Histologically, ABF1-βCD has no effect on the liver structure and has a
protective effect against lesions alcohol-induced liver disease.

Conclusion:
Therefore, it can be suggested that ABF1 analogue combined with β-Cyclodextrin can
be used as a treatment for alcohol dependence. Further clinical works are needed to confirm its
effectiveness.
Nanoemulsions: A Better Approach for Antidiabetic Drug Delivery
Authors: Manimaran V. , Sivakumar Ponnurengam Malliappan , Narayanan J. , Parthasarathi Shanmugam , Prabhakar Pranav Kumar 
Published: December 2020

Abstract::
Conventional delivery of antidiabetic drugs faces many problems like poor absorption,
low bioavailability, and drug degradation. Nanoemulsion is a unique drug technology, which is
very suitable for the delivery of antidiabetic drugs. In recent years, the flaws of delivering anti-hypoglycaemic
drugs have been overcome by choosing nanoemulsion drug technology. They are thermodynamically
stable and also provide the therapeutic agent for a longer duration. Generally, nanoemulsions
are made up of either oil-in-water or water-in-oil and the size of the droplets is from
fifty to thousand nanometer. Surfactants are critical substances that are added in the manufacturing
of nanoemulsions. Only the surfactants which are approved for human use can be utilized in the
manufacturing of nanoemulsions. Generally, the preparation of emulsions includes mixing of the
aqueous phase and organic phase and using surfactant with proper agitation. Nanoemulsions are
used for antimicrobial drugs, and they are also used in the prophylaxis of cancer. Reduction in the
droplet size may cause variation in the elastic and optical behaviour of nanoemulsions.
Ginger and Heart Health: From Mechanisms to Therapeutics
Authors: Fakhri Sajad , Patra Jayanta K. , Das Swagat K. , Das Gitishree , Majnooni Mohammad B. , Farzaei Mohammad H. 
Published: December 2020

Background:
As a major cause of morbidity and mortality, cardiovascular diseases (CVDs) are globally
increasing. In spite of recent development in the management of cardiovascular complications, CVDs have remained a
medical challenge. Numerous conventional drugs are used to play cardioprotective roles; however, they are associated
with several side effects. Considering the rich phytochemistry and fewer side effects of herbal medicines, they have
gained particular attention to develop novel herbal drugs with cardioprotective potentials. Amongst natural entities, ginger
is an extensively used and well-known functional food and condiment, possessing plentiful bioactivities, like antiinflammatory, antioxidant, and antimicrobial properties in several disorders management.

Objective:
The current review deliberated phytochemical properties as well as the ginger/ginger constituents' biological
activities and health benefits in several diseases, with particular attention to cardiovascular complications.

Methods:
A comprehensive research was conducted using multiple databases, including Scopus, PubMed, Medline, Web
of Science, national database (Irandoc and SID), and related articles in terms of the health benefits and cardioprotective
effects of ginger/ginger constituents. These data were collected from inception until August 2019.

Results:
In recent years, several herbal medicines were used to develop new drugs with more potency and also minor side
effects. Amongst natural entities, ginger is an extensively used traditional medicine in several diseases. The crude extract,
along with related pungent active constituents, is mostly attributed to heart health. The cardioprotective effects of ginger
are contributed to its cardiotonic, antihypertensive, anti-hyperlipidemia, and anti-platelet effects. The signaling pathways
and molecular mechanisms of ginger regarding its cardioprotective effects are also clarified.

Conclusion:
This study revealed the biological activities, health benefits, and cardioprotective properties of ginger/ginger
constituents along with related mechanisms of action, which gave new insights to show new avenue in the treatment of
CVDs.
Clinical Presentation and Short Term Treatment Response in Catatonia: An Observational Study
Authors: Surjan Kunal , Aggarwal Shivali , Sharma Mohit , Dhiman Vishal , Singh Vijender 
Published: December 2020

Background:
Clinical features and treatment response in catatonia is unpredictable and
needs to be studied further.

Objective:
: The aim of this research is to study clinical presentations of catatonia and its response to
various modalities of treatment.

Methods:
This study recruited 50 patients in the age group of 15-65 years, with a diagnosis of catatonia
as per DSM 5 criteria, selected by a stepwise process of sample selection. Patients with significant
medical or surgical illness warranting immediate intervention were excluded. A detailed
history and clinical information was obtained following informed consent from patient’s caregivers
and other significant relatives. Rating on the severity of symptoms as well as treatment response
was done using the Bush-Francis Catatonia Rating Scale (BFCRS) on 1st, 3rd, 7th, and 14th day of
admission. Modified Electro-Convulsive Therapy (MECT) was administered to patients who had an
inadequate response to intravenous lorazepam.

Results:
It was found that 32 (64%) patients had a psychotic disorder, and 18 (36%) patients had
mood disorders as an underlying diagnosis in catatonic presentation. Mutism was the most common
catatonic sign-on rating with BFCRS, found in 50 (100%) of the patients. Complete resolution of
catatonia was observed in 26 (52%) of patients following the use of intravenous lorazepam, while
24 (48%) required MECT. Patients with a diagnosis of schizophrenia required higher doses of intravenous
lorazepam (p=0.001) and showed a lesser response to intravenous lorazepam compared to
patients with diagnoses of mood disorders and other psychotic disorders.

Conclusion:
Most common diagnosis in patients of catatonia was found to be psychotic disorder.
Retarded signs of catatonia were found to be the commonest presentation. MECT was required to
achieve resolution of catatonic symptoms in around half (48%) of the cases. The patients with diagnoses
of schizophrenia required higher doses and also showed a lesser response to intravenous
lorazepam, hence MECT was required in a higher proportion of such cases.