bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autoregulation of JARID2 through PRC2 interaction with its antisense ncRNA
Authors: Al-Raawi Diaa , Kanhere Aditi 
Published: October 2020

Abstract

Objective
JARID2 is a member of chromatin-modifying Polycomb Repressive Complex-2 or PRC2. It plays a role in recruiting PRC2 to developmental genes and regulating its activity. JARID2 along with PRC2 is indispensable for normal development. However, it remains unclear how JARID2 expression itself is regulated. Recently a number of non-protein-coding RNAs or ncRNAs are shown to regulate transcription. An antisense ncRNA, JARID2-AS1, is expressed from the first intron of JARID2 isoform-1 but its role in regulation of JARID2 expression has not been investigated. The objective of this study was to explore the role of JARID2-AS1 in regulating JARID2 and consequently PRC2.

Results
We found that JARID2-AS1 is localised in the nucleus and shows anti-correlated expression pattern to that of JARID2 isoform-1 mRNA. More interestingly, data mining approach strongly indicates that JARID2-AS1 binds to PRC2. These are important observations that provide insights into transcriptional regulation of JARID2, especially because they indicate that JARID2-AS1 by interacting and probably recruiting PRC2 participates in an auto-regulatory loop that controls levels of JARID2. This holds importance in regulation of developmental and differentiation processes. However, to support this hypothesis, further in-depth studies are needed which can verify JARID2-AS1-PRC2 interactions.
Robust performance of a novel stool DNA test of methylated SDC2 for colorectal cancer detection: a multicenter clinical study
Authors: Wang Jianping , Liu Side , Wang Hui , Zheng Lei , Zhou Changchun , Li Guoxin , Huang Rongkang , Wang Huaiming , Li Chujun , Fan Xinjuan , Fu Xinhui , Wang Xinying , Guo Hongliang , Guan Jie , Sun Yanlai , Song Xilin , Li Zengjun , Mu Dianbin , Sun Jujie , Liu Xianglin , Qi Yan , Niu Feng , Chen Chunhua , Wu Xiaolin , Wang Xianshu , Song Xianrang , Zou Hongzhi 
Published: October 2020

Abstract

Background and Aims
Stool DNA testing is an emerging and attractive option for colorectal cancer (CRC) screening. We previously evaluated the feasibility of a stool DNA (sDNA) test of methylated SDC2 for CRC detection. The aim of this study was to assess its performance in a multicenter clinical trial setting.

Methods
Each participant was required to undergo a sDNA test and a reference colonoscopy. The sDNA test consists of quantitative assessment of methylation status of SDC2 promoter. Results of real-time quantitative methylation-specific PCR were dichotomized as positive and negative, and the main evaluation indexes were sensitivity, specificity, and kappa value. All sDNA tests were performed and analyzed independently of colonoscopy.

Results
Among the 1110 participants from three clinical sites analyzed, 359 and 38 were diagnosed, respectively, with CRC and advanced adenomas by colonoscopy. The sensitivity of the sDNA test was 301/359 (83.8%) for CRC, 16/38 (42.1%) for advanced adenomas, and 134/154 (87.0%) for early stage CRC (stage I–II). Detection rate did not vary significantly according to age, tumor location, differentiation, and TNM stage, except for gender. The follow-up testing of 40 postoperative patients with CRC returned negative results as their tumors had been surgically removed. The specificity of the sDNA test was 699/713 (98.0%), and unrelated cancers and diseases did not seem to interfere with the testing. The kappa value was 0.84, implying an excellent diagnostic consistency between the sDNA test and colonoscopy.

Conclusion
Noninvasive sDNA test using methylated SDC2 as the exclusive biomarker is a clinically viable and accurate CRC detection method.

Chinese Clinical Trial Registry
Chi-CTR-TRC-1900026409, retrospectively registered on October 8, 2019; http://www.chictr.org.cn/edit.aspx?pid=43888&htm=4.
Biodegradation and metabolic pathway of fenvalerate by Citrobacter freundii CD-9
Authors: Tang Jie , Lei Dan , Wu Min , Hu Qiong , Zhang Qing 
Published: October 2020

Abstract
Fenvalerate is a pyrethroid insecticide with rapid action, strong targeting, broad spectrum, and high efficiency. However, continued use of fenvalerate has resulted in its widespread presence as a pollutant in surface streams and soils, causing serious environmental pollution. Pesticide residues in the soil are closely related to food safety, yet little is known regarding the kinetics and metabolic behaviors of fenvalerate. In this study, a fenvalerate-degrading microbial strain, CD-9, isolated from factory sludge, was identified as Citrobacter freundii based on morphological, physio-biochemical, and 16S rRNA sequence analysis. Response surface methodology analysis showed that the optimum conditions for fenvalerate degradation by CD-9 were pH 6.3, substrate concentration 77 mg/L, and inoculum amount 6% (v/v). Under these conditions, approximately 88% of fenvalerate present was degraded within 72 h of culture. Based on high-performance liquid chromatography and gas chromatography-mass spectrometry analysis, ten metabolites were confirmed after the degradation of fenvalerate by strain CD-9. Among them, o-phthalaldehyde is a new metabolite for fenvalerate degradation. Based on the identified metabolites, a possible degradation pathway of fenvalerate by C. freundii CD-9 was proposed. Furthermore, the enzyme localization method was used to study CD-9 bacteria and determine that its degrading enzyme is an intracellular enzyme. The degradation rate of fenvalerate by a crude enzyme solution for over 30 min was 73.87%. These results showed that strain CD-9 may be a suitable organism to eliminate environmental pollution by pyrethroid insecticides and provide a future reference for the preparation of microbial degradation agents and environmental remediation.
Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter
Authors: Santos-Júnior Célio Dias , Sarmento Hugo , de Miranda Fernando Pellon , Henrique-Silva Flávio , Logares Ramiro 
Published: October 2020

AbstractBackgroundThe Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analysing 106 metagenomes from 30 sampling points distributed along the river.ResultsWe constructed theAmazon River basin Microbial non-redundant Gene Catalogue(AMnrGC) that includes ~ 3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant known environments (rivers and rainforest soil). Genes encoding for proteins potentially involved in lignin degradation pathways were correlated to tripartite tricarboxylates transporters and hemicellulose degradation machinery, pointing to a possiblepriming effect. Based on this, we propose a model on how the degradation of recalcitrant TeOM could be modulated by labile compounds in the Amazon River waters. Our results also suggest changes of the microbial community and its genomic potential along the river course.ConclusionsOur work contributes to expand significantly our comprehension of the world’s largest river microbiome and its potential metabolism related to TeOM degradation. Furthermore, the produced gene catalogue (AMnrGC) represents an important resource for future research in tropical rivers.
Expanding magnetic organelle biogenesis in the domain Bacteria
Authors: Lin Wei , Zhang Wensi , Paterson Greig A. , Zhu Qiyun , Zhao Xiang , Knight Rob , Bazylinski Dennis A. , Roberts Andrew P. , Pan Yongxin 
Published: October 2020

AbstractBackgroundThe discovery of membrane-enclosed, metabolically functional organelles inBacteriahas transformed our understanding of the subcellular complexity of prokaryotic cells. Biomineralization of magnetic nanoparticles within magnetosomes by magnetotactic bacteria (MTB) is a fascinating example of prokaryotic organelles. Magnetosomes, as nano-sized magnetic sensors in MTB, facilitate cell navigation along the local geomagnetic field, a behaviour referred to as magnetotaxis or microbial magnetoreception. Recent discovery of novel MTB outside the traditionally recognized taxonomic lineages suggests that MTB diversity across the domainBacteriaare considerably underestimated, which limits understanding of the taxonomic distribution and evolutionary origin of magnetosome organelle biogenesis.ResultsHere, we perform the most comprehensive metagenomic analysis available of MTB communities and reconstruct metagenome-assembled MTB genomes from diverse ecosystems. Discovery of MTB in acidic peatland soils suggests widespread MTB occurrence in waterlogged soils in addition to subaqueous sediments and water bodies. A total of 168 MTB draft genomes have been reconstructed, which represent nearly a 3-fold increase over the number currently available and more than double the known MTB species at the genome level. Phylogenomic analysis reveals that these genomes belong to 13 Bacterial phyla, six of which were previously not known to include MTB. These findings indicate a much wider taxonomic distribution of magnetosome organelle biogenesis across the domainBacteriathan previously thought. Comparative genome analysis reveals a vast diversity of magnetosome gene clusters involved in magnetosomal biogenesis in terms of gene content and synteny residing in distinct taxonomic lineages. Phylogenetic analyses of core magnetosome proteins in this largest available and taxonomically diverse dataset support an unexpectedly early evolutionary origin of magnetosome biomineralization, likely ancestral to the origin of the domainBacteria.ConclusionsThese findings expand the taxonomic and phylogenetic diversity of MTB across the domainBacteriaand shed new light on the origin and evolution of microbial magnetoreception. Potential biogenesis of the magnetosome organelle in the close descendants of the last bacterial common ancestor has important implications for our understanding of the evolutionary history of bacterial cellular complexity and emphasizes the biological significance of the magnetosome organelle.
Post-normal times: re-thinking the futures of the EU-Africa relationship
Authors: Bourgeois Robin , Mattheis Frank , Kotsopoulos John 
Published: October 2020

AbstractThe nature of the relationship between the European Union (EU) and Africa is in permanent evolution. Historically, the EU mostly dominated the relationship while Africa developed adaptive/reactive strategies. With the establishment of new powers as well as efforts to decolonise the thought and practise of North-South interactions, it is crucial to understand what the future of the relationship could be. The purpose of this paper is to draw lessons from the “Broadening the debate on EU-Africa relations” workshop whose aim was to advance perspectives on EU-Africa relations from the point of view of African scholars. The process consisted of identifying major influential factors in the relationship and assessing what role they played in the past and what role they could play in the future. The results indicate a decline of the importance of EU-dominated factors and the emergence of African agency related factors. We interpret these results as a transformation of this relationship, using the concept “post-normal” to highlight indeterminacy, insolvability and irreversibility as the new context. Implications are discussed regarding the type of research that needs to be developed in order to further investigate this transformation, particularly the meaning of a shifting focus from (normal times) EU-Africa relationship to (post-normal times) Africa-EU relationships.
Error estimation and adaptivity for PGD based on complementary solutions applied to a simple 1D problem
Authors: Reis Jonatha , Moitinho de Almeida José Paulo , Díez Pedro , Zlotnik Sergio 
Published: October 2020

AbstractReduced order methods are powerful tools for the design and analysis of sophisticated systems, reducing computational costs and speeding up the development process. Among these reduced order methods, the Proper Generalized Decomposition is a well-established one, commonly used to deal with multi-dimensional problems that often suffer from thecurse of dimensionality. Although the PGD method has been around for some time now, it still lacks mechanisms to assess the quality of the solutions obtained. This paper explores the dual error analysis in the scope of the PGD, using complementary solutions to compute error bounds and drive an adaptivity process, applied to a simple 1D problem. The energy of the error obtained from the dual analysis is used to determine the quality of the PGD approximations. We define a new adaptivity indicator based on the energy of the error and use it to drive parametric h- and p- adaptivity processes. The results are positive, with the indicator accurately capturing the parameter that will lead to lowest errors.
Adding a modified Lemaire procedure to ACLR in knees with severe rotational knee instability does not compromise isokinetic muscle recovery at the time of return-to-play
Authors: Joseph Leopold , Demey Guillaume , Chamu Thomas , Schmidt Axel , Germain Alexandre , van Rooij Floris , Saffarini Mo , Dejour David 
Published: October 2020

AbstractPurposeTo determine whether isokinetic muscle recovery following ACLR using a hamstring tendon (HT) would be equivalent (non-inferior) in knees that had high-grade pivot-shift and adjuvant modified Lemaire procedure versus knees that had minimal pivot-shift and no adjuvant modified Lemaire procedure.MethodsWe evaluated 96 consecutive patients that underwent primary ACLR. Nine were excluded because of contralateral knee injury, and of the remaining 87, ACLR was performed stand-alone in 52 (Reference group), and with a Lemaire procedure in 35 (Lemaire group) who had high-grade pivot-shift, age < 18, or genu recurvatum > 20°. At 6 months, isokinetic tests were performed at 240°/s and 90°/s to calculate strength deficits of hamstrings (H) and quadriceps (Q). At 8 months, patients were evaluated using IKDC, Lysholm, and Tegner scores.ResultsCompared to the Reference group, the Lemaire group were younger (23.0 ± 2.5 vs 34.2 ± 10.5,p = 0.021) with a greater proportion of males (80% vs 56%,p < 0.001). The Lemaire group had no complications, but the Reference group had one graft failure and one cyclops syndrome. Strength deficits at 240°/s and at 90°/s were similar in both groups, but mixed H/Q ratios were lower for the Lemaire group (1.02 ± 0.19 vs 1.14 ± 0.24,p = 0.011). IKDC and Lysholm scores were similar in both groups, but Tegner scores were higher in the Lemaire group (median, 6.5 vs 6.0,p = 0.024).ConclusionsACLR with a modified Lemaire procedure for knees with rotational instability grants equivalent isokinetic muscle recovery as stand-alone ACLR in knees with no rotational instability. For ACL-deficient knees with high-grade pivot-shift, a Lemaire procedure restores rotational stability without compromising isokinetic muscle recovery.Study designLevel III, comparative study.
Intersecting social structures and human actors: Ganfoso refugees’ settling experiences and impact on children’s education
Authors: Akua-Sakyiwah Beatrice 
Published: October 2020

Abstract
The myth that Ghana is stable and peaceful, cause many refugees from across Africa and elsewhere, escaping wars from their countries to flee there. Whilst here, refugees face transitional problems in acculturation and settlement, stemming from a lack of education, as many have not had formal education before coming to Ghana. The problem is worsened by an immigration system and a social structure that delays responding to refugees’ needs. With a lack of viable employment to support parents’ settlement needs, these cumulatively function to affect refugee children’s educational attainment. Using ideas from Giddens’ structuration theory as a conceptual framework, the research seeks to understand how immigration rules and other mediated rules at the Ganfoso Refugee Camp, interlacing refugee parents’ acculturation/settlement experiences, impact children’s educational lives. The article uses narratives from teachers/head-teachers, refugee camp management, and a cross-section of community members to highlight how social structures, policy regulation and implementation, combined with issues of refugees’ agency (personal experiences and responses to situation), impact upon their settlement and affect their children’s education.
Through qualitative interviews with 69 participants, the article highlight discussions on the effect of institutional barriers to refugees’ experiences, and impact on educational access of refugee children in Ghana.
Postoperative tetraplegia due to conversion disorder upon emergence from general anesthesia
Authors: Ito Asuka , Nakamoto Tatsuo , Ohira Sayaka , Kamibayashi Takahiko 
Published: October 2020

Abstract

Background
Acute neurological deficit upon emergence from general anesthesia is a serious emergency. Conversion disorder, previously known as hysteria, is a somatoform disorder that causes neurological deficits without anatomical or physiological explanations. It is particularly rare after general anesthesia.

Case presentation
A 28-year-old healthy Japanese woman presented tetraplegia with normal sensory function upon waking from general anesthesia. She was evaluated for the causes of tetraplegia. There were no abnormal findings, and her symptoms were inconsistent with any anatomical or neurological pathology. Although she could not flex her knee actively, she could maintain the passive flexed position, suggesting that her paralysis was nonorganic. The most likely diagnosis was conversion disorder. After a 12-h observation, the patient fully recovered.

Conclusions
In patients with neurological deficits not correlating with neurological findings after general anesthesia, the presence of somatic disorders, such as conversion disorder, should be considered.
Outcome measures and treatment effectiveness in late onset myasthenia gravis
Authors: Pasqualin Francesca , Guidoni Silvia V. , Ermani Mario , Pegoraro Elena , Bonifati Domenico M. 
Published: October 2020

Abstract

Background
Recently different subtypes of myasthenia gravis (MG) have been described. They differ for clinical features and pathogenesis but the prognosis and response to treatment is less clear. The aim of the study was to evaluate outcome and treatment effectiveness including side effects in late onset MG (LOMG) compared with early onset MG (EOMG).

Methods
We analysed retrospectively 208 MG patients. Clinical features were recorded as well as treatment and side effects. Outcome at the last follow-up was evaluated with MGSTI and MGPIS scales.

Results
The 208 patients included were classified as follow: 36 ocular MG, 40 EOMG, 72 LOMG, 25 thymoma-associated, 14 anti-MuSK and 21 double seronegative. Similar positive outcome was achieved in either early and late onset subgroup. We found pharmacological remission and minimal manifestations at the MGFA-PIS in the 95% and 94,4% of EOMG and LOMG respectively but in LOMG a lower dose of immunosuppressors (MGSTI< 2) was required compared to EOMG (p = 0,048). Severe side effects were present in a small percentage of patients in both group but diabetes was more frequent in LOMG vs EOMG (2,2% vs 5%, p = 0.017).

Conclusions
Despite LOMG has more comorbidities that might interfere with treatment and outcome, therapeutic management does not seem to differ between EOMG and LOMG. A similar positive outcome was seen in both subgroups but LOMG group seems to require lower doses of medication to control symptoms.
Cognitive dysfunction among inpatients and outpatients with schizophrenia: relationship to positive and negative symptoms
Authors: Okasha Tarek Ahmed , Hussein Hanan , Shorub Eman , Nagi Hamed , Moustafa Ahmed A. , El-Serafi Doha 
Published: October 2020

Abstract

Background
Cognitive impairment is an established feature of schizophrenia and is a strong predictor of eventual social and functional outcome. Few studies have investigated cognitive impairment in hospital long-stay patients with schizophrenia. This study evaluates and compares cognitive function among a sample of patients with schizophrenia in both inpatient and outpatient departments in order to determine the relationship between cognitive impairment and clinical variables.
A cross-sectional comparative study based on a semi-structured interview investigating 100 inpatients with schizophrenia recruited from El-Abassia Mental Health Hospital departments compared to 100 patients with schizophrenia selected from the outpatients’ clinic matched with cases. The assessment tools included SCID-I, the Adult Wechsler Intelligence Scale, the computerized version of Wisconsin Card Sorting Test (WCST), Mini-Mental State Examination (MMSE), and Positive and Negative Syndrome Scale (PANSS).

Results
Patients with schizophrenia showed significant deficits on cognitive function with no statistically significant difference between the inpatient and outpatient groups. Executive function was significantly correlated with verbal, non-verbal, and total IQ. Executive function was negatively correlated with the positive and general symptoms of PANSS and not correlated with its negative symptoms. In addition, we did not find any statistically significant relationship between cognitive functions and the duration of illness.

Conclusion
The study provides evidence that institutionalization is not an influential factor on cognitive impairment patients with schizophrenia. However, the psychopathological aspects of the disorder are one of the crucial factors affecting the cognitive function in schizophrenia.
A comparative cross-sectional analysis on prevalence of depression and associated risk factors among medical students and doctors of Karachi, Pakistan
Authors: Qureshi Muhammad Fazal Hussain , Mohammad Danish , Sadiq Sara , Abubaker Zain Jawed , Kumari Ujalla , Devnani Joti , Dawani Nakeeta , Soleja Fahad Khalid , Haroon Ayesha 
Published: October 2020

Abstract

Background
It has been noted that there is high prevalence of depression among medical personnel whether it is a student or an on-duty doctor. However, no study has been done to highlight these two vulnerable groups. Accordingly, the objective of current study is to compare the prevalence of depression among medical students and doctors working in hospitals, and its correlation with demographic variables, associated symptoms and history of any recent trauma. A descriptive cross-sectional study design was selected for this study. PHQ-9 was used as study tool.

Result
Mean age of students was 21 ± 1.83 while the mean age of the doctors included in study was 31 ± 7.8. A multivariate analysis model (MANOVA) was applied where male doctor and students were found to have a significantly high association (p = < 0.001) with depression scores as compared to their counterpart and students. Positive association was observed among sector and symptom of hopelessness, sleep changes and appetite/weight changes. The most common symptom among both groups was sleep changes while the least common symptom among doctors was concentration problem and among students was feeling of helplessness. It was also found that 26% of the students were having suicidal thoughts while only 16% of the doctors were having suicidal intentions.

Conclusion
It is concluded that depression is highly prevalent among medical students when comparing with on-duty doctors, so they should be screened with regular intervals and good counselling sessions to prepare them for a better health care system.