bluuebunny/crossref_metadata_2025_split huggingface dataset:
CPSF6 links alternative polyadenylation to metabolism adaption in hepatocellular carcinoma progression
Authors: Tan Sheng , Zhang Ming , Shi Xinglong , Ding Keshuo , Zhao Qiang , Guo Qianying , Wang Hao , Wu Zhengsheng , Kang Yani , Zhu Tao , Sun Jielin , Zhao Xiaodong 
Published: March 2021

AbstractBackgroundAlternative polyadenylation (APA) is an important mechanism of gene expression regulation through generation of RNA isoforms with distinct 3′ termini. Increasing evidence has revealed that APA is actively involved in development and disease, including hepatocellular carcinoma (HCC). However, how APA functions in tumor formation and progression remains elusive. In this study, we investigated the role of cleavage factor I (CFIm) subunit CPSF6 in human hepatocellular carcinoma (HCC).MethodsExpression levels of CPSF6 in clinical tissues and cell lines were determined by qRT-PCR and western blot. Functional assays, including the cell number, MTT, colony formation and transwell, were used to determine the oncogenic role of CPSF6 in HCC. Animal experiments were used to determine the role of CPSF6 in HCC tumorigenicity in vivo. Deep sequencing-based 3 T-seq was used to profile the transcriptome-wide APA sites in both HCC cells and CPSF6 knockdown HCC cells. The function of CPSF6-affected targetNQO1with distinct 3′UTRs was characterized by metabolism assays.ResultsWe observed CPSF6 was upregulated in HCC and the high expression of CPSF6 was associated with poor prognosis in patients. Overexpression of CPSF6 promoted proliferation, migration and invasion of HCC cells in vitro and in vivo. Transcriptome-wide APA profiling analysis indicated that high expression of CPSF6 promoted the favorable usage of the proximal poly(A) site in the 3′UTR ofNQO1. We demonstrated CPSF6-induced tumorigenic activities were mediated by theNQO1isoform with short 3′UTR. Furthermore, we found that CPSF6 induced metabolic alterations in liver cells through NQO1.ConclusionCPSF6 plays a critical role in HCC progression by upregulating NQO1 expression through APA. These findings provide evidence to demonstrate that APA ofNQO1contributes to HCC progression and may have implications for developing new therapeutic strategy against this disease.
Stem vacuole-targetted sucrose isomerase enhances sugar content in sorghum
Authors: Liu Guoquan , Zhang Yan , Gong Hao , Li Shan , Pan Yunrong , Davis Christopher , Jing Hai-Chun , Wu Luguang , Godwin Ian D. 
Published: March 2021

Abstract
Background
Sugar content is critically important in determining sugar crop productivity. However, improvement in sugar content has been stagnant among sugar crops for decades. Sorghum, especially sweet sorghum with high biomass, shown great potential for biofuel, has lower sugar content than sugarcane. To enhance sugar content, the sucrose isomerase (SI) gene, driven by stem-specific promoters (A2 or LSG) with a vacuole-targetted signal peptide, was transformed into the sorghum inbred line (T×430).

Results
The study demonstrated that transgenic lines of grain sorghum, containing 50–60% isomaltulose, accumulated up to eightfold (1000 mM) more total sugar than the control T×430 did (118 mM) in stalks of T0 generation. Subsequently, the elite engineered lines (A5, and LSG9) were crossed with sweet sorghum (Rio, and R9188). Total sugar contents (over 750 mM), were notably higher in F1, and F2 progenies than the control Rio (480 mM). The sugar contents of the engineered lines (over 750 mM), including T0, T1, F1, and F2, are surprisingly higher than that of the field-grown sugarcane (normal range 600–700 mmol/L). Additionally, analysis of physiological characterization demonstrated that the superior progenies had notably higher rates of photosynthesis, sucrose transportation, and sink strength than the controls.

Conclusions
The genetic engineering approach has dramatically enhanced total sugar content in grain sorghum (T0, and T1) and hybrid sorghum (F1, and F2), demonstrating that sorghum can accumulate as high or higher sugar content than sugarcane. This research illustrates that the SI gene has enormous potential on improvement of sugar content in sorghum, particularly in hybirds and sweet sorghum. The substantial increase on sugar content would lead to significant financial benefits for industrial utilization. This study could have a substantial impact on renewable bioenergy. More importantly, our results demonstrated that the phenotype of high sugar content is inheritable and shed light on improvement for other sugar crops.
Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis
Authors: Plichta Damian R. , Somani Juhi , Pichaud Matthieu , Wallace Zachary S. , Fernandes Ana D. , Perugino Cory A. , Lähdesmäki Harri , Stone John H. , Vlamakis Hera , Chung Daniel C. , Khanna Dinesh , Pillai Shiv , Xavier Ramnik J. 
Published: March 2021

Abstract
Background
Immunoglobulin G4-related disease (IgG4-RD) and systemic sclerosis (SSc) are rare autoimmune diseases characterized by the presence of CD4+ cytotoxic T cells in the blood as well as inflammation and fibrosis in various organs, but they have no established etiologies. Similar to other autoimmune diseases, the gut microbiome might encode disease-triggering or disease-sustaining factors.

Methods
The gut microbiomes from IgG4-RD and SSc patients as well as healthy individuals with no recent antibiotic treatment were studied by metagenomic sequencing of stool DNA. De novo assembly-based taxonomic and functional characterization, followed by association and accessory gene set enrichment analysis, were applied to describe microbiome changes associated with both diseases.

Results
Microbiomes of IgG4-RD and SSc patients distinctly separated from those of healthy controls: numerous opportunistic pathogenic Clostridium and typically oral Streptococcus species were significantly overabundant, while Alistipes, Bacteroides, and butyrate-producing species were depleted in the two diseases compared to healthy controls. Accessory gene content analysis in these species revealed an enrichment of Th17-activating Eggerthella lenta strains in IgG4-RD and SSc and a preferential colonization of a homocysteine-producing strain of Clostridium bolteae in SSc. Overabundance of the classical mevalonate pathway, hydroxyproline dehydratase, and fibronectin-binding protein in disease microbiomes reflects potential functional differences in host immune recognition and extracellular matrix utilization associated with fibrosis. Strikingly, the majority of species that were differentially abundant in IgG4-RD and SSc compared to controls showed the same directionality in both diseases. Compared with multiple sclerosis and rheumatoid arthritis, the gut microbiomes of IgG4-RD and SSc showed similar signatures; in contrast, the most differentially abundant taxa were not the facultative anaerobes consistently identified in inflammatory bowel diseases, suggesting the microbial signatures of IgG4-RD and SSc do not result from mucosal inflammation and decreased anaerobism.

Conclusions
These results provide an initial characterization of gut microbiome ecology in fibrosis-prone IgG4-RD and SSc and reveal microbial functions that offer insights into the pathophysiology of these rare diseases.
Are seminal vesicles a potential pitfall during pelvic exploration using point-of-care ultrasound (POCUS)?
Authors: Fasseaux Antoine , Pès Philippe , Steenebruggen Françoise , Dupriez Florence 
Published: March 2021

Abstract
Background
Trauma is a major cause of death among the working population. Many countries have now adopted a structured approach to trauma management in which ultrasound is used as a primary evaluation tool. While its use has direct therapeutic benefits, many artifacts and pitfalls are inherent to the technique. Knowledge of the most frequently encountered pitfalls in practice could thus help reduce the risk of error and lead to more accurate trauma assessments.

Objective
This study evaluates a potential pitfall caused by seminal vesicles during focused assessment with sonography for trauma examinations of the male pelvis performed by an emergency physician with experience in point-of-care ultrasound.

Methods
We took five static and five dynamic (3-s loops) transverse ultrasound images of the pelvis in five healthy males. The images and videos were then incorporated into an online survey and emailed through the World Interactive Network Focused On Critical UltraSound (WINFOCUS) in France and the Ultrasound and Emergency Medicine (UEM) Organization in Belgium. A questionnaire asked anonymous participants to assess the presence of free fluid in the static and dynamic images and to share information about their training and experience in point-of-care ultrasound. To validate the static and dynamic images, the survey was sent to three external radiologists for independent verification.

Results
A total of 191 individuals responded fully or partially to the survey, 114 of whom completed it. Among the 114 participants who completed the survey, the misinterpretation rate was 0.55 (95CI 0.51–0.60) for all static and dynamic ultrasound transverse pelvic views. The misinterpretation rate was 0.61 (95CI 0.55–0.66) and 0.50 (95CI 0.45–0.55) for static and dynamic ultrasound transverse pelvic views, respectively. The three external radiologists answered the questionnaire correctly without misinterpreting the survey ultrasound views.

Conclusions
Seminal vesicles are a potential pitfall when interpreting transverse ultrasound images of the male pelvis in the context of point-of-care ultrasound.
The association of group IIB intron with integrons in hypersaline environments
Authors: Sonbol Sarah , Siam Rania 
Published: March 2021

Abstract
Background
Group II introns are mobile genetic elements used as efficient gene targeting tools. They function as both ribozymes and retroelements. Group IIC introns are the only class reported so far to be associated with integrons. In order to identify group II introns linked with integrons and CALINS (cluster of attC sites lacking a neighboring integron integrase) within halophiles, we mined for integrons in 28 assembled metagenomes from hypersaline environments and publically available 104 halophilic genomes using Integron Finder followed by blast search for group II intron reverse transcriptases (RT)s.

Results
We report the presence of different group II introns associated with integrons and integron-related sequences denoted by UHB.F1, UHB.I2, H.ha.F1 and H.ha.F2. The first two were identified within putative integrons in the metagenome of Tanatar-5 hypersaline soda lake, belonging to IIC and IIB intron classes, respectively at which the first was a truncated intron. Other truncated introns H.ha.F1 and H.ha.F2 were also detected in a CALIN within the extreme halophile Halorhodospira halochloris, both belonging to group IIB introns. The intron-encoded proteins (IEP) s identified within group IIB introns belonged to different classes: CL1 class in UHB.I2 and bacterial class E in H.ha.Fa1 and H.ha.F2. A newly identified insertion sequence (ISHahl1) of IS200/605 superfamily was also identified adjacent to H. halochloris CALIN. Finally, an abundance of toxin-antitoxin (TA) systems was observed within the identified integrons.

Conclusion
So far, this is the first investigation of group II introns within integrons in halophilic genomes and metagenomes from hypersaline environments. We report the presence of group IIB introns associated with integrons or CALINs. This study provides the basis for understanding the role of group IIB introns in the evolution of halophiles and their potential biotechnological role.
Predicting the incidence of brucellosis in Western Iran using Markov switching model
Authors: Mohammadian-Khoshnoud Maryam , Sadeghifar Majid , Cheraghi Zahra , Hosseinkhani Zahra 
Published: March 2021

Abstract
Objective
Brucellosis is a zoonosis almost chronic disease. Brucellosis bacteria can remain in the environment for a long time. Thus, climate irregularities could pave the way for the survival of the bacterium brucellosis. Brucellosis is more common in men 25 to 29 years of age, in the western provinces, and in the spring months. The aim of this study is to investigate the effect of climatic factors as well as predicting the incidence of brucellosis in Qazvin province using the Markov switching model (MSM). This study is a secondary study of data collected from 2010 to 2019 in Qazvin province. The data include brucellosis cases and climatic parameters. Two state MSM with time lags of 0, 1 and 2 was fitted to the data. The Bayesian information criterion (BIC) was used to evaluate the models.

Results
According to the BIC, the two-state MSM with a 1-month lag is a suitable model. The month, the average-wind-speed, the minimum-temperature have a positive effect on the number of brucellosis, the age and rainfall have a negative effect. The results show that the probability of an outbreak for the third month of 2019 is 0.30%.
Fe(2)OG: an integrated HMM profile-based web server to predict and analyze putative non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenase function in protein sequences
Authors: Kundu Siddhartha 
Published: March 2021

Abstract
Objective
Non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenases (i2OGdd), are a taxonomically and functionally diverse group of enzymes. The active site comprises ferrous iron in a hexa-coordinated distorted octahedron with the apoenzyme, 2-oxoglutarate and a displaceable water molecule. Current information on novel i2OGdd members is sparse and relies on computationally-derived annotation schema. The dissimilar amino acid composition and variable active site geometry thereof, results in differing reaction chemistries amongst i2OGdd members. An additional need of researchers is a curated list of sequences with putative i2OGdd function which can be probed further for empirical data.

Results
This work reports the implementation of $$Fe\left(2\right)OG$$

F
e

2

O
G

, a web server with dual functionality and an extension of previous work on i2OGdd enzymes $$\left(Fe\left(2\right)OG\equiv \{H2OGpred,DB2OG\}\right)$$

F
e

2

O
G
≡

{
H
2
O
G
p
r
e
d
,
D
B
2
O
G
}

. $$Fe\left(2\right)OG$$

F
e

2

O
G

, in this form is completely revised, updated (URL, scripts, repository) and will strengthen the knowledge base of investigators on i2OGdd biochemistry and function. $$Fe\left(2\right)OG$$

F
e

2

O
G

, utilizes the superior predictive propensity of HMM-profiles of laboratory validated i2OGdd members to predict probable active site geometries in user-defined protein sequences. $$Fe\left(2\right)OG$$

F
e

2

O
G

, also provides researchers with a pre-compiled list of analyzed and searchable i2OGdd-like sequences, many of which may be clinically relevant. $$Fe(2)OG$$

F
e
(
2
)
O
G

, is freely available (http://204.152.217.16/Fe2OG.html) and supersedes all previous versions, i.e., H2OGpred, DB2OG.
Effects of compound probiotics and aflatoxin-degradation enzyme on alleviating aflatoxin-induced cytotoxicity in chicken embryo primary intestinal epithelium, liver and kidney cells
Authors: Guo Hong-Wei , Chang Juan , Wang Ping , Yin Qing-Qiang , Liu Chao-Qi , Xu Xiao-Xiang , Dang Xiao-Wei , Hu Xiao-Fei , Wang Quan-Liang 
Published: March 2021

AbstractAflatoxin B1 (AFB1) is one of the most dangerous mycotoxins for humans and animals. This study aimed to investigate the effects of compound probiotics (CP), CP supernatant (CPS), AFB1-degradation enzyme (ADE) on chicken embryo primary intestinal epithelium, liver and kidney cell viabilities, and to determine the functions of CP + ADE (CPADE) or CPS + ADE (CPSADE) for alleviating cytotoxicity induced by AFB1. The results showed that AFB1 decreased cell viabilities in dose-dependent and time-dependent manners. The optimal AFB1 concentrations and reactive time for establishing cell damage models were 200 µg/L AFB1 and 12 h for intestinal epithelium cells, 40 µg/L and 12 h for liver and kidney cells. Cell viabilities reached 231.58% (p < 0.05) for intestinal epithelium cells with CP addition, 105.29% and 115.84% (p < 0.05) for kidney and liver cells with CPS additions. The further results showed that intestinal epithelium, liver and kidney cell viabilities were significantly decreased to 87.12%, 88.7% and 84.19% (p < 0.05) when the cells were exposed to AFB1; however, they were increased to 93.49% by CPADE addition, 102.33% and 94.71% by CPSADE additions (p < 0.05). The relative mRNA abundances of IL-6, IL-8, TNF-α, iNOS, NF-κB, NOD1 (except liver cell) and TLR2 in three kinds of primary cells were significantly down-regulated by CPADE or CPSADE addition, compared with single AFB1 group (p < 0.05), indicating that CPADE or CPSADE addition could alleviate cell cytotoxicity and inflammation induced by AFB1 exposure through suppressing the activations of NF-κB, iNOS, NOD1 and TLR2 pathways.
On oscillation of higher-order advanced trinomial differential equations
Authors: Luo Demou 
Published: March 2021

AbstractWe study the oscillatory property of the higher-order trinomial differential equation with advanced effects$$ x^{(n)}(t)+p(t)x'(t)+q(t)x \bigl(\sigma (t) \bigr)=0,\quad \sigma (t) \geq t. $$x(n)(t)+p(t)x′(t)+q(t)x(σ(t))=0,σ(t)≥t.Suppose that all solutions of the corresponding ($n-1$n−1)th-order two-term differential equation$$ y^{(n-1)}(t)+p(t)y(t)=0 $$y(n−1)(t)+p(t)y(t)=0are non-oscillatory. In order to supplement the research in the theory of oscillation proposed by (Džurina et al. in Electron. J. Differ. Equ. 2015:70, 2015), two types of clearly confirmable criteria for oscillatory behavior of the investigated equation are obtained. Some examples are offered to describe our main results.
The effect of external factors on industry performance: the case of Lalibela City micro and small enterprises, Ethiopia
Authors: Ebabu Engidaw Abriham 
Published: March 2021

AbstractThe purpose of this study was to examine the effect of external factors on industry performance: in micro and small-scale enterprises. To achieve its objectives, the study employed a descriptive and explanatory research design and used quantitative research approach. The target population of the study was 395 MSEs owners working in manufacturing, trade, and service sectors. It used stratified and simple random sampling techniques and the required data have been collected from a sample size of 199 MSEs through standardized 5-point Likert-scale questionnaire. The study used both primary and secondary sources of data. For data analysis purpose, it employed descriptive and inferential statistical data analysis methods like correlation and multiple linear regression analysis. The finding of the study discovered the agreement of respondents to the positively significant relationship between external factors and industry performance in the study area. Specifically, marketing factors, financial factors, infrastructure, work premises factors, trade fair factors, and political-legal factors all have a positive effect on enterprises’ performance in the study area. In addition, the study result shows that financial factors, marketing factors, infrastructure, work premises factors, and trade fair factors have a positive significant effect on industry performance but political-legal factors do not significantly affect the dependent variable industry performance. From the predicting variables, infrastructure has more effect on industry performance than the rest of variables in the study area. The study recommends that the government/micro and small enterprises development offices should maintain different supportive trainings, decrease infrastructural problems, facilitate credit services, and create attractive environment to entice or create productive MSEs. In addition, the MSEs owners should design adoptive plans and programs with the external as well as internal environment to increase their performance.
Cascading rupture of patches of high seismic energy release controls the growth process of episodic tremor and slip events
Authors: Nakamoto Keita , Hiramatsu Yoshihiro , Uchide Takahiko , Imanishi Kazutoshi 
Published: March 2021

AbstractSlip phenomena on plate interfaces reflect the heterogeneous physical properties of the slip plane and, thus, exhibit a wide variety of slip velocities and rupture propagation behaviors. Recent findings on slow earthquakes reveal similarities and differences between slow and regular earthquakes. Episodic tremor and slip (ETS) events, a type of slow earthquake widely observed in subduction zones, likewise show diverse activity. We investigated the growth of 17 ETS events beneath the Kii Peninsula in the Nankai subduction zone, Japan. Analyses of waveform data recorded by a seismic array enabled us to locate tremor hypocenters and estimate the migration patterns and spatial distribution of the energy release of tremor events. Here, we describe three major features in the growth of ETS events. First, independent of their start point and migration pattern, ETS events exhibit patches of high seismic energy release on the up-dip part of the ETS zone, suggesting that the location of these patches is controlled by inherent physical or frictional properties of the plate interface. Second, ETS events usually start outside the high-energy patches, and their final extent depends on whether the patches participate in the rupture. Third, we recognize no size dependence in the initiation phase of ETS events of different sizes with comparable start points. These features demonstrate that the cascading rupture of high-energy patches governs the growth of ETS events, just as the cascading rupture of asperities governs the growth of regular earthquakes.
The surviving sepsis campaign: fluid resuscitation and vasopressor therapy research priorities in adult patients
Authors:   for the Research Committee of the Surviving Sepsis Campaign, Lat Ishaq , Coopersmith Craig M. , De Backer Daniel , Coopersmith Craig M. 
Published: March 2021

Abstract
Objective
To expand upon the priorities of fluid resuscitation and vasopressor therapy research priorities identified by a group of experts assigned by the Society of Critical Care Medicine and the European Society of Intensive Care Medicine.

Data Sources
Original paper and literature search.

Study Selection
Several members of the original task force with expertise specific to the area of fluid resuscitation and vasopressor therapy.

Data Extraction
None.

Data Synthesis
None.

Conclusion
In the second of a series of manuscripts subsequent to the original paper, members with expertise in the subjects expound upon the three identified priorities related to fluid resuscitation and vasopressor therapies. This analysis summarizes what is known and what were identified as ongoing and future research.