bluuebunny/crossref_metadata_2025 huggingface dataset:
Speed control of asynchronous motor based on improved deadbeat predictive algorithm
Authors: Wang Tao , Li Jikun , Hou Qiang
Published: February 2020

In this article, the three-phase asynchronous motor is taken as the research object, and the deadbeat predictive control is the control core, and its control performance is studied. Considering the overshoot of flux linkage and speed response in deadbeat predictive control, an improved deadbeat predictive control algorithm based on synergy theory is proposed. Different from deadbeat predictive control, improved deadbeat predictive control can control the flux linkage and speed independently through two adjustment parameters, which are achieved through the manifold of synergy theory. To accurately obtain the feedback flux linkage and load torque in the control, a flux observer and a load torque observer are designed. Based on these, a simulation platform is built, and the control performance of the two control algorithms is compared. The robustness of the two control algorithms is further verified by changing parameters. Finally, the experimental platform of three-phase asynchronous motor is built in this article. The experimental program based on deadbeat predictive control is designed. The no-load experiment and loading experiment are carried out, respectively. The feasibility of the algorithm is verified by experimental data.
“I Want to Leave ASAP”: Black Women Teachers Discuss the Role of Administrative Support and Teacher Turnover
Authors: Stanley Darrius A.
Published: February 2020

This article utilizes a qualitative case study methodology informed by a Black feminist theoretical lens to explore the experiences of Black women teachers, administrative support, and teacher turnover. Five self-identified Black women teachers discuss the impact that school leaders have on their decisions to leave their schools. Three common leadership practices emerged as contributory factors that influence teacher turnover: (a) arresting social justice efforts, (b) insufficient support for discipline, and (c) relationships with administration. This article concludes with a discussion about the requisite school leader philosophical orientations that support the unique needs of Black women teachers.
A Scale to Measure Science Communication Training Effectiveness
Authors: Rodgers Shelly , Wang Ze , Schultz Jack C.
Published: February 2020

The research describes efforts toward developing a valid and reliable scale used to assess science communication training effectiveness (SCTE) undertaken in conjunction with a 4-year project funded by the National Science Foundation. Results suggest that the SCTE scale possesses acceptable psychometric properties, specifically reliability and validity, with regard to responses from graduate students in science, technology, engineering, and math fields. While it cannot be concluded that the SCTE scale is the “be-all-end-all” tool, it may assist investigators in gauging success of science communication training efforts and by identifying aspects of the program that are working or that need improving.
Management of a patient with primary mucinous testicular adenocarcinoma as a rare case with adjuvant and metastatic sequential treatments
Authors: Tanriverdi Ozgur , Tarimer Mehmet Levent , Pak Ceren Deniz , Uylas Selcuk , Alkan Ali , Dere Yelda , Yazici Ayse , Sen Serdar , Sahin Hayrettin
Published: February 2020

Introduction

Mucinous adenocarcinomas of the testicular surface epithelial tumors are very rare and are similar to malignant ovarian-type surface epithelial tumors. Although only 32 cases have been reported to date, there are only five cases of primary testicular mucinous carcinoma with access to literature in English. So there is still limited information about clinical, etiopathogenesis and treatment options.

Case report

In this article, we discuss a 56-year-old male patient diagnosed with testicular mucinous adenocarcinoma due to its rarity in the light of literature review. Management and outcome: We preferred cisplatin-paclitaxel regimen for adjuvant treatment. We then used sequential treatments including oxaliplatin, 5-fluorourasil, etoposide, gemcitabine, and docetaxel to treat metastatic disease. The patient underwent lung metastasectomy for the first relapse. The patient was diagnosed in November 2013 and the response to treatment was evaluated in December 2019 and stable disease was detected. The patient, who has a total survival of 73 months, is still under treatment.

Discussion

Excluding malign transformation and borderline mucinous testicular tumors from mucinous cystadenomas of the testis, the knowledge on carcinogenesis, clinical course, and treatment of primary testicular mucinous adenocarcinomas is very limited.
Fixational microsaccades: A quantitative and objective measure of disability in multiple sclerosis
Authors: Sheehy Christy K , Bensinger Ethan S , Romeo Andrew , Rani Lakshmisahithi , Stepien-Bernabe Natalie , Shi Bingyan , Helft Zachary , Putnam Nicole , Cordano Christian , Gelfand Jeffrey M , Bove Riley , Stevenson Scott B , Green Ari J
Published: February 2020

Background:

Objective tools for prognosis and disease progression monitoring in multiple sclerosis (MS) are lacking. The visuomotor system could be used to track motor dysfunction at the micron scale through the monitoring of fixational microsaccades.

Aims:

The aim of this study was to evaluate whether microsaccades are correlated with standard MS disability metrics and to assess whether these methods play a predictive role in MS disability.

Method:

We used a custom-built retinal eye tracker, the tracking scanning laser ophthalmoscope (TSLO), to record fixation in 111 participants with MS and 100 unaffected controls.

Results:

In MS participants, a greater number of microsaccades showed significant association with higher Expanded Disability Status Scale score (EDSS, p < 0.001), nine-hole peg test (non-dominant: p = 0.006), Symbol Digit Modalities Test (SMDT, p = 0.014), and Functional Systems Scores (FSS) including brainstem ( p = 0.005), cerebellar ( p = 0.011), and pyramidal ( p = 0.009). Both brainstem FSS and patient-reported fatigue showed significant associations with microsaccade number, amplitude, and peak acceleration. Participants with MS showed a statistically different average number ( p = 0.020), peak vertical acceleration ( p = 0.003), and vertical amplitude ( p < 0.001) versus controls. Logistic regression models for MS disability were created using TSLO microsaccade metrics and paraclinical tests with ⩾80% accuracy.

Conclusion:

Microsaccades provide objective measurements of MS disability level and disease worsening.
An integrated risk assessment for maintenance prediction of oil wetted gearbox and bearing in marine and offshore industries using a fuzzy rule base method
Authors: Asuquo Maurice , Wang Jin , Zhang Lihong , Phylip-Jones Geraint
Published: February 2020

This article presents an integrated risk assessment methodology for maintenance prediction of oil wetted gearbox and bearing in marine and offshore machinery with emphasis on ship cranes. Predictive maintenance uses important parameters measured in the equipment to ‘feel’ when breakdown is eminent. This type of maintenance intends to make interventions on machinery before harmful events may occur. This article assesses the risk levels of bearing and gearbox, which are the most sensitive components of the ship crane using fuzzy rule–based judgement for common elements and their sources. This will provide the ship crane operators with a means to predict possible impending failure without having to dismantle the crane. Furthermore, to monitor the rate of wear in gearbox and bearing of a ship crane, the ship crane reliability, and a trend to provide an operational baseline of data that will help the engineers to detect abnormal wear rates as they develop, is established. Within the scope of this research, a risk assessment model is developed for determining the risk levels of a crane’s components and recommending solutions using all the diagnostic capability obtainable for effective condition monitoring of the gearbox and bearing in ship cranes.
Children’s Perspectives on Their Relationships with Friends With and Without Complex Communication Needs
Authors: Biggs Elizabeth E. , Snodgrass Melinda R.
Published: February 2020

Friendships are central to children’s development and well-being, but children with intellectual and developmental disabilities who have complex communication needs are at risk of social isolation. This qualitative study used methods informed by grounded theory to investigate the nature of how elementary-age children without disabilities described the experience of friendship and the dynamics of friendship development with their friends with and without complex communication needs. Sixteen children participated in semi-structured interviews. Each indicated they were friends with one of four children who received special education services under categories of autism and/or intellectual disability and was learning to use aided augmentative and alternative communication (AAC). Interviews were structured to hear each child talk separately about two different friendships: (a) one with any friend they chose and (b) one with the friend with complex communication needs who was learning to use aided AAC. Findings included the development of a model to conceptualize the substance and development of these friendships. Findings also highlighted how children’s experiences of friendship with the friend with complex communication needs intersected with how they experienced, talked about, and made meaning of their friend’s disability. Implications for research and practice discuss potential pathways for promoting friendships in schools.
Double-letter processing in developmental and skilled handwriting production: Evidence from kinematics
Authors: Hess Stefan , Mousikou Petroula , Schroeder Sascha
Published: February 2020

In this study, we investigated the effects of double-letter processing on handwriting production in beginning and skilled writers of German. One hundred and thirty-seven children from Grades 2 and 3 and 31 adult participants were asked to copy words with double consonants (e.g., “Kanne”) and matched words without double consonants (e.g., “Kante”) from a computer screen onto a pen tablet, while their handwriting was recorded with high spatio-temporal resolution. Handwriting productions were analysed in terms of Reading Duration, Writing Onset Duration, and Letter Duration at the letter positions preceding or forming the onset of the corresponding consonant clusters. Our results showed that second graders take less time to initiate writing words with double consonants than words without double consonants, while both second and third graders take less time to read words with double consonants than words without double consonants. Critically, although second and third graders write down a letter faster when it corresponds to the first letter of a double-letter unit than a consonant cluster, it is the other way around for adults. We interpret these findings within extant theories of handwriting production and offer an explanation for the different nature of the effects observed in beginning and skilled writers.
The Influence of a Single Intra-Articular Lidocaine Injection on the Viability of Articular Cartilage in the Knee
Authors: Ravnihar Klemen , Marš Tomaž , Pirkmajer Sergej , Alibegović Armin , Koželj Gordana , Stožer Andraž , Drobnič Matej
Published: February 2020

Objective

To evaluate the in vivo effect of a single intra-articular injection of local anesthetic (LA) lidocaine on the viability of articular cartilage in the intact or osteoarthritic (OA) human knees, and to measure the synovial postinjection concentration of lidocaine in the knee

Design

This study includes 3 interconnected experiments: (A) Synovial LA concentration measurement after a 2% lidocaine injection before knee arthroscopy in 10 patients by liquid chromatography–tandem mass spectrometry (LC-MS/MS). (B) Human osteochondral explants ( N = 27) from intact knees procured at autopsies were incubated for different time intervals (30 minutes, 2 hours, 24 hours) with 2% lidocaine, 0.04% lidocaine (measured), or culture medium (control), and later evaluated for cell viability by LIVE/DEAD staining. (C) Ten out of 19 matched patients scheduled for knee replacement received a single intra-articular injection of 2% lidocaine approximately 30 minutes prior to the procedure; 9 patients served as control. Osteochondral samples with OA changes were harvested during surgery and analyzed for chondrocyte viability by LIVE/DEAD staining.

Results

(A) The synovial LA concentration was significantly lower than the primary concentration injected: average 0.23 mg/mL (0.02%), highest measured 0.37 mg/mL (0.04%). (B) In vitro exposure to a reduced LA concentration had no significant influence on chondrocyte viability in intact cartilage explants (24-hour averages: control, 93%; 0.04% lidocaine, 92%; 2% lidocaine, 79%). (C) Viability of chondrocytes in OA knees was similar between 2% lidocaine injection (85%) and control (80%).

Conclusions

A single intra-articular knee injection of 2% lidocaine did not influence the chondrocyte viability neither in healthy nor in OA cartilage. A fast postinjection reduction of synovial LA concentration (more than 40 times) is the most likely protective mechanism.
Sex hormone exposure and reproductive factors in pulmonary arterial hypertension: a case–control study
Authors: Badlam Jessica B. , Badesch David , Brittain Evan , Cordell Shannon , Ding Tan , Fox Kelly , Hemnes Anna , Loyd James , Pugh Meredith , Robbins Ivan , Yu Chang , Austin Eric D.
Published: February 2020

Pulmonary arterial hypertension (PAH) is a sexually dimorphic disease that for unknown reasons affects women more than men. The role of estrogens, both endogenous and exogenous, and reproductive factors in this female susceptibility is still poorly understood. It has been strongly suggested that sex hormones may influence the development and progression of the disease. We sought to determine whether sex hormone exposures and reproductive factors associate with PAH patients compared to control subjects, using a questionnaire and interview to obtain information regarding these potential risk factors. We conducted a single‐center unmatched case–control study. Six hundred and thirty‐four women and men with PAH, as well as 27 subjects with BMPR2 mutations but no PAH and 132 healthy population controls were enrolled from the Vanderbilt Pulmonary Hypertension Research Cohort and researchmatch.org. Questionnaires and nurse‐led interviews were conducted to obtain information regarding sex hormone exposures and reproductive factors. Additional history was obtained on enrolled patients including disease severity variables and comorbidities. Responses to the questionnaires were analyzed to describe these exposures in this population as well as assess the association between disease severity variables and sex hormone exposures. Reproductive and endogenous factors that determine lifelong estrogen exposure were similar between PAH cases and controls. Patients with associated PAH were significantly more likely to be postmenopausal compared to controls. There were similar rates of “ever‐use” and duration of use of oral contraceptive pills and hormone replacement therapy in patients when compared to controls. Disease severity variables were not significantly affected by any exposure after adjusting for PAH sub‐group. In contrast to our hypothesis, that a greater exposure to exogenous sources of female sex hormones associates with PAH case status, we found similar rates of endogenous and exogenous sex hormone exposure between PAH patients and unmatched controls.
Are scurs in heterozygous polled (Pp) cattle a complex quantitative trait?
Authors: Gehrke Lilian Johanna , Capitan Aurélien , Scheper Carsten , König Sven , Upadhyay Maulik , Heidrich Kristin , Russ Ingolf , Seichter Doris , Tetens Jens , Medugorac Ivica , Thaller Georg
Published: February 2020

Background

Breeding genetically hornless, i.e. polled, cattle provides an animal welfare-friendly and non-invasive alternative to the dehorning of calves. However, the molecular regulation of the development of horns in cattle is still poorly understood. Studying genetic characters such as polledness and scurs, can provide valuable insights into this process. Scurs are hornlike formations that occur occasionally in a wide variety of sizes and forms as an unexpected phenotype when breeding polled cattle.

Methods

We present a unique dataset of 885 Holstein–Friesian cattle with polled parentage. The horn phenotype was carefully examined, and the phenotypic heterogeneity of the trait is described. Using a direct gene test for polledness, the polled genotype of the animals was determined. Subsequently, the existence of a putativescurslocus was investigated using high-density genotype data of a selected subset of 232 animals and two mapping approaches: mixed linear model-based association analyses and combined linkage disequilibrium and linkage analysis.

Results

The results of an exploratory data analysis indicated that the expression of scurs depends on age at phenotyping, sex and polled genotype. Scurs were more prevalent in males than in females. Moreover, homozygous polled animals did not express any pronounced scurs and we found that the Friesianpolledallele suppresses the development of scurs more efficiently than the Celticpolledallele. Combined linkage and linkage disequilibrium mapping revealed four genome-wide significant loci that affect the development of scurs, one on BTA5 and three on BTA12. Moreover, suggestive associations were detected on BTA16, 18 and 23. The mixed linear model-based association analysis supports the results of the combined linkage and linkage disequilibrium analysis. None of the mapping approaches provided convincing evidence for a monogenic inheritance of scurs.

Conclusions

Our results contradict the initial and still broadly accepted model for the inheritance of horns and scurs. We hypothesise an oligogenetic model to explain the development of scurs and polledness.
pCADD: SNV prioritisation in Sus scrofa
Authors: Groß Christian , Derks Martijn , Megens Hendrik-Jan , Bosse Mirte , Groenen Martien A. M. , Reinders Marcel , de Ridder Dick
Published: February 2020

Background

In animal breeding, identification of causative genetic variants is of major importance and high economical value. Usually, the number of candidate variants exceeds the number of variants that can be validated. One way of prioritizing probable candidates is by evaluating their potential to have a deleterious effect, e.g. by predicting their consequence. Due to experimental difficulties to evaluate variants that do not cause an amino-acid substitution, other prioritization methods are needed. For human genomes, the prediction of deleterious genomic variants has taken a step forward with the introduction of the combined annotation dependent depletion (CADD) method. In theory, this approach can be applied to any species. Here, we present pCADD (p for pig), a model to score single nucleotide variants (SNVs) in pig genomes.

Results

To evaluate whether pCADD captures sites with biological meaning, we used transcripts from miRNAs and introns, sequences from genes that are specific for a particular tissue, and the different sites of codons, to test how well pCADD scores differentiate between functional and non-functional elements. Furthermore, we conducted an assessment of examples of non-coding and coding SNVs, which are causal for changes in phenotypes. Our results show that pCADD scores discriminate between functional and non-functional sequences and prioritize functional SNVs, and that pCADD is able to score the different positions in a codon relative to their redundancy. Taken together, these results indicate that based on pCADD scores, regions with biological relevance can be identified and distinguished according to their rate of adaptation.

Conclusions

We present the ability of pCADD to prioritize SNVs in the pig genome with respect to their putative deleteriousness, in accordance to the biological significance of the region in which they are located. We created scores for all possible SNVs, coding and non-coding, for all autosomes and the X chromosome of the pig reference sequence Sscrofa11.1, proposing a toolbox to prioritize variants and evaluate sequences to highlight new sites of interest to explain biological functions that are relevant to animal breeding.
Epistatic regulation of growth in Atlantic salmon revealed: a QTL study performed on the domesticated-wild interface
Authors: Besnier Francois , Solberg Monica F. , Harvey Alison C. , Carvalho Gary R. , Bekkevold Dorte , Taylor Martin I. , Creer Simon , Nielsen Einar E. , Skaala Øystein , Ayllon Fernando , Dahle Geir , Glover Kevin A.
Published: February 2020

Background

Quantitative traits are typically considered to be under additive genetic control. Although there are indications that non-additive factors have the potential to contribute to trait variation, experimental demonstration remains scarce. Here, we investigated the genetic basis of growth in Atlantic salmon by exploiting the high level of genetic diversity and trait expression among domesticated, hybrid and wild populations.

Results

After rearing fish in common-garden experiments under aquaculture conditions, we performed a variance component analysis in four mapping populations totaling ~ 7000 individuals from six wild, two domesticated and three F1 wild/domesticated hybrid strains. Across the four independent datasets, genome-wide significant quantitative trait loci (QTLs) associated with weight and length were detected on a total of 18 chromosomes, reflecting the polygenic nature of growth. Significant QTLs correlated with both length and weight were detected on chromosomes 2, 6 and 9 in multiple datasets. Significantly, epistatic QTLs were detected in all datasets.

Discussion

The observed interactions demonstrated that the phenotypic effect of inheriting an allele deviated between half-sib families. Gene-by-gene interactions were also suggested, where the combined effect of two loci resulted in a genetic effect upon phenotypic variance, while no genetic effect was detected when the two loci were considered separately. To our knowledge, this is the first documentation of epistasis in a quantitative trait in Atlantic salmon. These novel results are of relevance for breeding programs, and for predicting the evolutionary consequences of domestication-introgression in wild populations.
ClpP participates in stress tolerance, biofilm formation, antimicrobial tolerance, and virulence of Enterococcus faecalis
Authors: Zheng Jinxin , Wu Yang , Lin Zhiwei , Wang Guangfu , Jiang Sibo , Sun Xiang , Tu Haopeng , Yu Zhijian , Qu Di
Published: February 2020

Background

ClpP is important for bacterial growth and plays an indispensable role in cellular protein quality control systems by refolding or degrading damaged proteins, but the physiological significance of ClpP in Enterococcus faecalis remains obscure. A clpP deletion mutant (△clpP) was constructed using the E. faecalis OG1RF strain to clarify the effect of ClpP on E. faecalis. The global abundance of proteins was determined by a mass spectrometer with tandem mass tag labeling.

Results

The ΔclpP mutant strain showed impaired growth at 20 °C or 45 °C at 5% NaCl or 2 mM H2O2. The number of surviving ΔclpP mutants decreased after exposure to the high concentration (50× minimal inhibitory concentration) of linezolid or minocycline for 96 h. The ΔclpP mutant strain also demonstrated decreased biofilm formation but increased virulence in a Galleria mellonella model. The mass spectrometry proteomics data indicated that the abundances of 135 proteins changed (111 increased, 24 decreased) in the ΔclpP mutant strain. Among those, the abundances of stress response or virulence relating proteins: FsrA response regulator, gelatinase GelE, regulatory protein Spx (spxA), heat-inducible transcription repressor HrcA, transcriptional regulator CtsR, ATPase/chaperone ClpC, acetyl esterase/lipase, and chaperonin GroEL increased in the ΔclpP mutant strain; however, the abundances of ribosomal protein L4/L1 family protein (rplD), ribosomal protein L7/L12 (rplL2), 50S ribosomal protein L13 (rplM), L18 (rplR), L20 (rplT), 30S ribosomal protein S14 (rpsN2) and S18 (rpsR) all decreased. The abundances of biofilm formation-related adapter protein MecA increased, while the abundances of dihydroorotase (pyrC), orotate phosphoribosyltransferase (pyrE), and orotidine-5′-phosphate decarboxylase (pyrF) all decreased in the ΔclpP mutant strain.

Conclusion

The present study demonstrates that ClpP participates in stress tolerance, biofilm formation, antimicrobial tolerance, and virulence of E. faecalis.
Novel citation-based search method for scientific literature: a validation study
Authors: Janssens A. Cecile J. W. , Gwinn Marta , Brockman J. Elaine , Powell Kimberley , Goodman Michael
Published: February 2020

Background

We recently developed CoCites, a citation-based search method that is designed to be more efficient than traditional keyword-based methods. The method begins with identification of one or more highly relevant publications (query articles) and consists of two searches: the co-citation search, which ranks publications on their co-citation frequency with the query articles, and the citation search, which ranks publications on frequency of all citations that cite or are cited by the query articles.

Methods

We aimed to reproduce the literature searches of published systematic reviews and meta-analyses and assess whether CoCites retrieves all eligible articles while screening fewer titles.

Results

A total of 250 reviews were included. CoCites retrieved a median of 75% of the articles that were included in the original reviews. The percentage of retrieved articles was higher (88%) when the query articles were cited more frequently and when they had more overlap in their citations. Applying CoCites to only the highest-cited article yielded similar results. The co-citation and citation searches combined were more efficient when the review authors had screened more than 500 titles, but not when they had screened less.

Conclusions

CoCites is an efficient and accurate method for finding relevant related articles. The method uses the expert knowledge of authors to rank related articles, does not depend on keyword selection and requires no special expertise to build search queries. The method is transparent and reproducible.
Copeptin is independently associated with vascular calcification in chronic kidney disease stage 5
Authors: Golembiewska Edyta , Qureshi Abdul Rashid , Dai Lu , Lindholm Bengt , Heimbürger Olof , Söderberg Magnus , Brismar Torkel B. , Ripsweden Jonaz , Barany Peter , Johnson Richard J. , Stenvinkel Peter
Published: February 2020

Background

Vascular calcification (VC) is an independent predictor of cardiovascular disease (CVD) present in 30–70% of patients with chronic kidney disease (CKD). Copeptin is a sensitive surrogate marker of arginine vasopressin (AVP), which is involved in many pathophysiologic processes in CKD. The aim of the present study was to explore the association of copeptin with VC in CKD stage 5.

Methods

Copeptin was investigated in conjunction with living donor kidney transplantation in 149 clinically stable CKD stage 5 patients (CKD5), including 53 non-dialyzed (CKD5-ND) and 96 dialysis patients treated by peritoneal dialysis (PD) (n = 43) or hemodialysis (HD) (n = 53). We analyzed the association of copeptin with presence and extent of VC ascertained both histologically in biopsies from the inferior epigastric artery (n = 137) and by coronary artery calcification (CAC) score measured by computed tomography.

Results

Patients with higher copeptin were older, had higher systolic blood pressure, higher prevalence of CVD and their preceding time on chronic dialysis was longer. In Spearman’s rank correlations (Rho), copeptin concentrations were significantly associated with CAC score (Rho = 0.27; p = 0.003) and presence of medial VC (Rho = 0.21; p = 0.016). Multivariate logistic regression analysis showed that 1-SD higher age, male gender, diabetes and 1-SD higher copeptin were significantly associated with the presence of moderate-extensive VC.

Conclusions

High circulating levels of copeptin in CKD5 patients are independently associated with the degree of medial calcification ascertained by histology of arterial biopsies. Thus, plasma copeptin may serve as a marker of the uremic calcification process.
Better efficacy in differentiating WHO grade II from III oligodendrogliomas with machine-learning than radiologist’s reading from conventional T1 contrast-enhanced and fluid attenuated inversion recovery images
Authors: Zhao Sha-Sha , Feng Xiu-Long , Hu Yu-Chuan , Han Yu , Tian Qiang , Sun Ying-Zhi , Zhang Jie , Ge Xiang-Wei , Cheng Si-Chao , Li Xiu-Li , Mao Li , Shen Shu-Ning , Yan Lin-Feng , Cui Guang-Bin , Wang Wen
Published: February 2020

Background

The medical imaging to differentiate World Health Organization (WHO) grade II (ODG2) from III (ODG3) oligodendrogliomas still remains a challenge. We investigated whether combination of machine leaning with radiomics from conventional T1 contrast-enhanced (T1 CE) and fluid attenuated inversion recovery (FLAIR) magnetic resonance imaging (MRI) offered superior efficacy.

Methods

Thirty-six patients with histologically confirmed ODGs underwent T1 CE and 33 of them underwent FLAIR MR examination before any intervention from January 2015 to July 2017 were retrospectively recruited in the current study. The volume of interest (VOI) covering the whole tumor enhancement were manually drawn on the T1 CE and FLAIR slice by slice using ITK-SNAP and a total of 1072 features were extracted from the VOI using 3-D slicer software. Random forest (RF) algorithm was applied to differentiate ODG2 from ODG3 and the efficacy was tested with 5-fold cross validation. The diagnostic efficacy of radiomics-based machine learning and radiologist’s assessment were also compared.

Results

Nineteen ODG2 and 17 ODG3 were included in this study and ODG3 tended to present with prominent necrosis and nodular/ring-like enhancement (P < 0.05). The AUC, ACC, sensitivity, and specificity of radiomics were 0.798, 0.735, 0.672, 0.789 for T1 CE, 0.774, 0.689, 0.700, 0.683 for FLAIR, as well as 0.861, 0.781, 0.778, 0.783 for the combination, respectively. The AUCs of radiologists 1, 2 and 3 were 0.700, 0.687, and 0.714, respectively. The efficacy of machine learning based on radiomics was superior to the radiologists’ assessment.

Conclusions

Machine-learning based on radiomics of T1 CE and FLAIR offered superior efficacy to that of radiologists in differentiating ODG2 from ODG3.
Prevalence and associated factors for rural households food insecurity in selected districts of east Gojjam zone, northern Ethiopia: cross-sectional study
Authors: Ayele Amare Wubishet , Kassa Mulusew , Fentahun Yenesew , Edmealem Hayimro
Published: February 2020

Background

Food insecurity is a pressing social and public health issue that varies in degree and impact on individuals and social groups, requiring immediate attention for policymakers and decision-makers. This study was conducted to identify the prevalence and associated factors of food insecurity of rural households particularly in the Shebel Berenta and Machakel districts of East Gojjam zone.

Methods

A cross-sectional study design was conducted, in the fall of March 2017 among 504 households. Households are selected using a systematic sampling technique through multistage cluster sampling technique (two stage cluster sampling). The data were collected using a structured interviewer-administered questionnaire covering a range of topics including 18 core food security modules (CFSM) question series, socioeconomic, demographic and related variables. Multivariable Partial proportional odds model (PPOM) was employed to identify the factors associated with food insecurity in rural households.

Result

Of a total of 504 households considered in the study, 54 (10.71%) were highly food secure, 75 (14.88%) were marginally food secure, 157 (31.15%) were low food secure, and 218 (43.25%) were severely food insecure. District (Machakel) (AOR = 3.28 95% CI: 1.73, 6.24), household head education status, illiterate (AOR = 113.4, 95% CI:7.02,1832.02), read and write (AOR = 169.29, 95%CI:11.64, 2461.39), and elementary completed (AOR = 119.75,95%CI:8.43,1700.74), agro-ecological zone, Woina Dega (AOR = 0.0021,95% CI: 0.00009,0.0514), Dega (AOR = 0.0323, 95%CI: 0.002, 0.5209), family size (AOR = 1.18, 95%CI: 1.01, 1.36), landholding (AOR = 0.767, 95% CI: 0.605, 0.972), TLU (AOR = 0.151, 95% CI: 0.0716, 0.3189), access to toilet (no) (AOR = 7.63, 95% CI: 1.459, 39.78), practicing irrigation (yes) (AOR = 0.121, 95% CI: 0.037, 0.38), loan (no) (AOR = 2.83, 95% CI:1.36, 5.89), access to energy, government electric (AOR = 0.468, 95% CI: 0.23, 0.94), solar panels (AOR = 0.45, 95% CI: 0.25, 0.79), soil fertility, moderate (AOR = 0.28, 95% CI: 0.12, 0.87), fertile (AOR = 0.15, 95% CI: 0.032, 0.72) were significant associated food insecurity factors in the study area.

Conclusion

In this study, a high prevalence of food insecurity and various associated food insecurity factors have been identified in the study area. Thus, the concerned stockholders should intervene in food insecure households via different irrigation practices and by considering household size, community-based household head education, and landholding in hectare.
A life-threatening complication due to pulmonary haemorrhage following hump-nosed viper bite
Authors: Srirangan Arthihai , Pushpakumara Jagath , Wanigasuriya Kamani
Published: February 2020

Background

Hump-nosed viper bite, the commonest venomous snake bite in Sri Lanka, is associated with significant morbidity. Specific anti-venom is not available for hump-nosed viper envenomation which is usually managed with supportive treatment. Pulmonary haemorrhage is an unusual manifestation of hump-nosed viper bite. Here we present a case of hump-nosed viper envenomation which complicated by pulmonary haemorrhage and was successfully treated with systemic steroids. To the best of our knowledge, it has not been reported in the literature before.

Case presentation

A previously healthy 55-year-old man presented to the local hospital 18 h after a hump-nosed viper bite. He developed bilateral severe pulmonary haemorrhages, evidenced by rapid desaturation which needed intubation and mechanical ventilation, bleeding from the endotracheal tube and bilateral alveolar shadows in a chest x-ray. He had no other bleeding manifestations. Because of the life-threatening situation, he was treated with methylprednisolone pulse therapy. There was a rapid improvement of hypoxia with a resolution of x-ray changes. He was successfully weaned off from the ventilation after 24 h.

Conclusion

This case highlights the importance of suspecting pulmonary haemorrhage in a patient who develops desaturation and alveolar shadow following hump-nosed viper bite even in the absence of other bleeding manifestation. Early and timely treatment with systemic steroid can be lifesaving in such patients.
The Evi5 oncogene promotes laryngeal cancer cells proliferation by stabilizing c-Myc protein
Authors: Mao Cheng-Gang , Zhou Xiao-Chun , Jiang Yi-Dao , Wan Li-Jia , Tao Ze-Zhang , Guo Jun
Published: February 2020

Background

The Ecotropic viral integration site 5 (Evi5) is recognized as a potential oncogene and a cell cycle regulator. Evi5 regulates the abundance of Emi1, an inhibitor of the anaphase-promoting complex/cyclosome, to govern mitotic fidelity. Evi5 has been shown to be dysregulated in several cancer types. However, the expression and biological function of Evi5 in human laryngeal squamous cell carcinoma (LSCC) are still unknown.

Methods

Clustered regularly interspaced short palindromic repeats (CRISPR)-based gene editing was used to generate Evi5 knockout (KO) LSCC cells. The proliferation and cell cycle distribution of LSCC cells was determined. The effect of Evi5 on LSCC tumor growth in vivo was studied in a tumor xenograft model in mice. The interaction between Evi5 and c-Myc was detected by immunoprecipitation (IP) assay. Luciferase assay was used to determine the transcriptional activity of c-Myc.

Results

Here, we show that Evi5 controls LSCC tumorigenesis via the stabilization of c-MYC oncogene. CRISPR-mediated knockout (KO) of Evi5 decreased the proliferation and decreased colony formation ability of LSCC cells. Knockout of Evi5 caused increased G1 phase and decreased S phase cells. In the tumor-bearing nude mice, The transplanted tumors originated from Evi5-KO TU212 cells were significantly decreased when compared with control TU212 cells. At the molecular level, we found that Evi5 interacted with c-MYC and Evi5 antagonized E3 ligase FBXW7-mediated ubiquitination and degradation of c-Myc protein, and promoted c-Myc-dependent transactivation.

Conclusion

Given the critical role of c-Myc in tumorigenesis, our data suggest that Evi5 is a potential therapeutic target in LSCC, and inhibition of Evi5 should be a prospective strategy for LSCC therapy.
Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data
Authors: Qin Qian , Fan Jingyu , Zheng Rongbin , Wan Changxin , Mei Shenglin , Wu Qiu , Sun Hanfei , Brown Myles , Zhang Jing , Meyer Clifford A. , Liu X. Shirley
Published: February 2020

We developed Lisa (http://lisa.cistrome.org/) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input gene sets, Lisa first uses histone mark ChIP-seq and chromatin accessibility profiles to construct a chromatin model related to the regulation of these genes. Using TR ChIP-seq peaks or imputed TR binding sites, Lisa probes the chromatin models using in silico deletion to find the most relevant TRs. Applied to gene sets derived from targeted TF perturbation experiments, Lisa boosted the performance of imputed TR cistromes and outperformed alternative methods in identifying the perturbed TRs.
Purifying selection of long dsRNA is the first line of defense against false activation of innate immunity
Authors: Barak Michal , Porath Hagit T. , Finkelstein Gilad , Knisbacher Binyamin A. , Buchumenski Ilana , Roth Shalom Hillel , Levanon Erez Y. , Eisenberg Eli
Published: February 2020

Background

Mobile elements comprise a large fraction of metazoan genomes. Accumulation of mobile elements is bound to produce multiple putative double-stranded RNA (dsRNA) structures within the transcriptome. These endogenous dsRNA structures resemble viral RNA and may trigger false activation of the innate immune response, leading to severe damage to the host cell. Adenosine to inosine (A-to-I) RNA editing is a common post-transcriptional modification, abundant within repetitive elements of all metazoans. It was recently shown that a key function of A-to-I RNA editing by ADAR1 is to suppress the immunogenic response by endogenous dsRNAs.

Results

Here, we analyze the transcriptomes of dozens of species across the Metazoa and identify a strong genomic selection against endogenous dsRNAs, resulting in their purification from the canonical transcriptome. This purifying selection is especially strong for long and nearly perfect dsRNAs. These are almost absent from mRNAs, but not pre-mRNAs, supporting the notion of selection due to cytoplasmic processes. The few long and nearly perfect structures found in human transcripts are weakly expressed and often heavily edited.

Conclusion

Purifying selection of long dsRNA is an important defense mechanism against false activation of innate immunity. This newly identified principle governs the integration of mobile elements into the genome, a major driving force of genome evolution. Furthermore, we find that most ADAR1 activity is not required to prevent an immune response to endogenous dsRNAs. The critical targets of ADAR1 editing are, likely, to be found mostly in non-canonical transcripts.
Transcriptomics of Gabra4 knockout mice reveals common NMDAR pathways underlying autism, memory, and epilepsy
Authors: Fan Cuixia , Gao Yue , Liang Guanmei , Huang Lang , Wang Jing , Yang Xiaoxue , Shi Yiwu , Dräger Ursula C. , Zhong Mei , Gao Tian-Ming , Yang Xinping
Published: February 2020

Autism spectrum disorder (ASD) is a neuronal developmental disorder with impaired social interaction and communication, often with abnormal intelligence and comorbidity with epilepsy. Disturbances in synaptic transmission, including the GABAergic, glutamatergic, and serotonergic systems, are known to be involved in the pathogenesis of this disorder, yet we do not know if there is a common molecular mechanism. As mutations in the GABAergic receptor subunit gene GABRA4 are reported in patients with ASD, we eliminated the Gabra4 gene in mice and found that the Gabra4 knockout mice showed autistic-like behavior, enhanced spatial memory, and attenuated susceptibility to pentylenetetrazol-induced seizures, a constellation of symptoms resembling human high-functioning autism. To search for potential molecular pathways involved in these phenotypes, we performed a hippocampal transcriptome profiling, constructed a hippocampal interactome network, and revealed an upregulation of the NMDAR system at the center of the converged pathways underlying high-functioning autism-like and anti-epilepsy phenotypes.
Different approaches for transformation of mesenchymal stem cells into hepatocyte-like cells
Authors: Afshari Afsoon , Shamdani Sara , Uzan Georges , Naserian Sina , Azarpira Negar
Published: February 2020

Due to the prominent role of the liver in the body and detoxification, its functionality can be affected in an irreversible manner by diseases. This phenomenon renders the liver to stop working, leading to morbidity and mortality. Therefore, liver transplantation is the only way to tackle this issue.

In order to compensate for the lack of adequate healthy liver tissue for transplantation, therapeutic approaches such as hepatocyte transplantation have been proposed as an alternative. Recognizing the fact that mesenchymal stem cells are adult stem cells with the capacity to differentiate into several cell types, different methods have been invented to produce hepatocyte-like cells from mesenchymal stem cells. They can be divided into three main categories, such as addition of cytokines and growth factors, genetic modifications, and adjustment of microenvironment as well as physical parameters.

In this review, we attempted to introduce diverse efficient methods for differentiating mesenchymal stem cells and their capability for transformation into hepatocyte-like cells.
Infusion-related thrombogenesis by liver-derived mesenchymal stem cells controlled by anticoagulant drugs in 11 patients with liver-based metabolic disorders
Authors: Coppin Louise C. F. , Smets Françoise , Ambroise Jérome , Sokal Etienne E. M. , Stéphenne Xavier
Published: February 2020

Background

Mesenchymal stem cell (MSC) transplantation is a fast-developing therapy in regenerative medicine. However, some concerns have been raised regarding their safety and the infusion-related pro-coagulant activity. The aim of this study is to analyze the induced thrombogenic risk and the safety of adding anticoagulants during intraportal infusions of liver-derived MSCs (HepaStem), in patients with Crigler-Najjar (CN) and urea cycle disorders (UCD).

Methods

Eleven patients (6 CN and 5 UCD patients) were included in this partially randomized phase 1/2 study. Three cell doses of HepaStem were investigated: low (12.5 × 106 cells/kg), intermediate (50 × 106 cells/kg), and high doses (200 × 106 cells/kg). A combination of anticoagulants, heparin (10 I.U./5 × 106cells), and bivalirudin (1.75 mg/kg/h) were added during cell infusions. The infusion-related thrombogenic risk and anticoagulation were evaluated by clinical monitoring, blood sampling (platelet and D-dimer levels, activated clotting time, etc.) and liver Doppler ultrasound. Mixed effects linear regression models were used to assess statistically significant differences.

Results

One patient presented a thrombogenic event such as a partial portal vein thrombus after 6 infusions. Minor adverse effects such as petechiae, epistaxis, and cutaneous hemorrhage at the site of catheter placement were observed in four patients. A significant decrease in platelet and increase in D-dimer levels were observed at the end of the infusion cycle, normalizing spontaneously after 7 days. No significant and clinically relevant increase in portal vein pressure could be observed once the infusion cycle was completed.

Conclusions

The safety- and the infusion-related pro-coagulant activity remains a concern in MSC transplantation. In our study, a combination of heparin and bivalirudin was added to prevent the thrombogenic risk induced by HepaStem infusions in 11 patients. A significant decrease in platelet and increase in D-dimer levels were observed, suggesting the activation of coagulation in these patients; however, this was spontaneously reversible in time. We can conclude that adding this combination of anticoagulants is safe and limits infusion-related thrombogenesis to subclinical signs in most of the patients.

Trial registration

ClinicalTrials.gov identifier: NCT01765283—January 10, 2013
Application of supervised descent method for 2D magnetotelluric data inversion
Authors: Guo Rui , Li Maokun , Yang Fan , Xu Shenheng , Abubakar Aria
Published: February 2020

The supervised descent method (SDM) is applied to 2D magnetotellurics (MT) data inversion. SDM contains offline training and online prediction. The training set is composed of the models generated according to prior knowledge and the data simulated by MT forward modeling. In the training process, a set of descent directions from an initial model to the training models is learned. In the prediction, model reconstruction is achieved by optimizing an online regularized objective function with a restart scheme, where the learned descent directions and the computed data residual are involved. SDM inversion has the advantages of (1) being more efficient than traditional gradient-descent methods because the computation of local derivatives of the objective function is avoided, (2) incorporating prior uncertain knowledge easier than deterministic inversion approach by generating training models flexibly, and (3) having high generalization ability because the physical modeling can guide the online model reconstruction. Furthermore, a way of designing general training set is introduced, which can be used for training when the prior knowledge is weak. The efficiency and accuracy of this method are validated by two numerical examples. The results indicate that the reconstructed models are consistent with prior information, and the simulated responses agree well with the data. This method also shows good potential to improve the accuracy and efficiency in field MT data inversion.