bluuebunny/crossref_metadata_2025_split huggingface dataset:
DeepciRGO: functional prediction of circular RNAs through hierarchical deep neural networks using heterogeneous network features
Authors: Deng Lei , Lin Wei , Wang Jiacheng , Zhang Jingpu 
Published: November 2020

Abstract
Background
Circular RNAs (circRNAs) are special noncoding RNA molecules with closed loop structures. Compared with the traditional linear RNA, circRNA is more stable and not easily degraded. Many studies have shown that circRNAs are involved in the regulation of various diseases and cancers. Determining the functions of circRNAs in mammalian cells is of great significance for revealing their mechanism of action in physiological and pathological processes, diagnosis and treatment of diseases. However, determining the functions of circRNAs on a large scale is a challenging task because of the high experimental costs.

Results
In this paper, we present a hierarchical deep learning model, DeepciRGO, which can effectively predict gene ontology functions of circRNAs. We build a heterogeneous network containing circRNA co-expressions, protein–protein interactions and protein–circRNA interactions. The topology features of proteins and circRNAs are calculated using a novel representation learning approach HIN2Vec across the heterogeneous network. Then, a deep multi-label hierarchical classification model is trained with the topology features to predict the biological process function in the gene ontology for each circRNA. In particular, we manually curated a benchmark dataset containing 185 GO annotations for 62 circRNAs, namely, circRNA2GO-62. The DeepciRGO achieves promising performance on the circRNA2GO-62 dataset with a maximum F-measure of 0.412, a recall score of 0.400, and an accuracy of 0.425, which are significantly better than other state-of-the-art RNA function prediction methods. In addition, we demonstrate the considerable potential of integrating multiple interactions and association networks.

Conclusions
DeepciRGO will be a useful tool for accurately annotating circRNAs. The experimental results show that integrating multi-source data can help to improve the predictive performance of DeepciRGO. Moreover, The model also can combine RNA structure and sequence information to further optimize predictive performance.
Period prevalence and identification challenges of viral haemorrhagic fever suspect cases in a tertiary referral hospital in Guinea: a cross-sectional, retrospective study of triage and emergency room patient profiles
Authors: Raab Manuel , Pfadenhauer Lisa M. , Nguyen Vinh-Kim , Doumbouya Dansira , Hoelscher Michael , Froeschl Guenter 
Published: November 2020

Abstract
Background
A functioning Viral Haemorrhagic Fever (VHF) surveillance system in countries at risk for outbreaks can reduce early transmission in case of an outbreak. Surveillance performance depends on the application of suspect case definitions in daily clinical practice. Recommended suspect case criteria during outbreaks are designed for high sensitivity and include general symptoms, pyrexia, haemorrhage, epidemiological link and unexplained death in patients. Non-outbreak criteria are narrower, relying on the persistence of fever and the presence of haemorrhagic signs.

Methods
This study ascertains VHF suspect case prevalence based on outbreak and non-outbreak criteria in a Guinean regional hospital for a period of three months. The study further describes clinical trajectories of patients who meet non-outbreak VHF suspect case criteria in order to discuss challenges in their identification. We used cross-sectional data collection at triage and emergency room to record demographic and clinical data of all admitted patients during the study period. For the follow-up study with description of diagnostic trajectories of VHF suspect cases, we used retrospective chart review.

Results
The most common symptoms of all patients upon admission were fever, tiredness/weakness and abdominal pain. 686 patients met EVD outbreak criteria, ten adult patients and two paediatric patients met study-specific non-outbreak VHF suspect case criteria. None of the suspect cases was treated as VHF suspect case and none tested positive for malaria upon admission. Their most frequent discharge diagnosis was unspecific gastrointestinal infection. The most common diagnostic measures were haemoglobin level and glycaemia for both adults and for children; of the requested examinations for hospitalized suspect cases, 36% were not executed or obtained. Half of those patients self-discharged against medical advice.

Conclusions
Our study shows that the number of VHF suspect cases may vary greatly depending on which suspect case criteria are applied. Identification of VHF suspect cases seems challenging in clinical practice. We suggest that this may be due to the low use of laboratory diagnostics to support certain diagnoses and the non-application of VHF suspect case definitions in clinical practice. Future VHF suspect case management should aim to tackle such challenges in comparable hospital settings.
Prognostic role of follicular fluid tumor necrosis factor alpha in the risk of early ovarian hyperstimulation syndrome
Authors: Alhilali Miaad Jabbar , Parham Abbas , Attaranzadeh Armin , Amirian Malihe , Azizzadeh Mohammad 
Published: November 2020

Abstract
Background
Ovarian hyperstimulation syndrome (OHSS) is an iatrogenic condition characterized by capillary hyperpermeability which can be predicted by preovulatory ovarian responses such as number of follicles. A variety of cytokines are thought to be involved in pathophysiology of this syndrome.

Methods
A prospective cohort study invloving sixty intracytoplasmic sperm injection (ICSI) patients. On the day of hCG injection, we explored the threshold of larger follicles ≥11 mm diameter with a count of ≥18 follicles for the high-risk moderate-to-severe OHSS and 13–18 follicles for the low-risk moderate-to-severe OHSS. Whereas larger follicles count of less than 13 were classified as normoresponders. Pooled follicular fluid (FF) samples of each patient were collected on the day of oocyte retrieval. Magnetic multiplex immunoassay was explored to measure the concentrations of some intrafollicular cytokines including: GM-CSF, INF-γ, TNF-α, IL-10, CXCL8/IL-8, IL-6, IL-5, IL-4, IL-2, and IL-1β. All sixty patients underwent controlled ovarian hyperstimulation (COH) with either GnRH agonist or antagonist protocols.

Results
Intrafollicular TNF-α concentration was significantly different (p < 0.05) in the high-risk moderate-to-severe OHSS patients compared to low-risk moderate-to-severe OHSS patients and normoresponders. TNF-α in FF had a negative correlation with the chance of high-risk moderate-to-severe OHSS. The differences in the risk of OHSS between patients who received GnRH agonist or antagonist were not significant (p > 0.05).

Conclusions
In accordance to the negative correlation of TNF-α and high risk of early OHSS, we did not expect TNF-α to play a role in increasing vascular permeability in ovarian tissues. In addition, the risk of early moderate-to-severe OHSS was not affected by different GnRH superovulation protocols.
Prevalence of symptoms, ever having received a diagnosis and treatment of depression and anxiety, and associations with health service use amongst the general population in two Russian cities
Authors: Cook Sarah , Kudryavtsev Alexander V. , Bobrova Natalia , Saburova Lyudmila , Denisova Diana , Malyutina Sofia , Lewis Glyn , Leon David A. 
Published: November 2020

AbstractBackgroundLittle is known about the burden of common mental disorders in Russia despite high levels of suicide and alcohol-related mortality. Here we investigated levels of symptoms, self-reports of ever having received a diagnosis and treatment of anxiety and depression in two Russian cities.MethodsThe study population was men and women aged 35–69 years old participating in cross-sectional population-based studies in the cities of Arkhangelsk and Novosibirsk (2015–18). Participants completed an interview which included the PHQ-9 and GAD-7 scales, questions on whether participants had ever received a diagnosis of depression or anxiety, and health service use in the past year. Participants also reported current medication use and medications were coded in line with the WHO anatomical therapeutic classification (ATC). Depression was defined as PHQ-9 ≥ 10 and Anxiety as GAD-7 ≥ 10.ResultsAge-standardised prevalence of PHQ-9 ≥ 10 was 10.7% in women and 5.4% in men (GAD-7 ≥ 10 6.2% in women; 3.0% in men). Among those with PHQ-9 ≥ 10 17% reported ever having been diagnosed with depression (equivalent finding for anxiety 29%). Only 1.5% of those with PHQ-9 ≥ 10 reported using anti-depressants and 0.6% of those with GAD-7 ≥ 10 reported using anxiolytics. No men with PHQ-9 ≥ 10 and/or GAD-7 ≥ 10 reported use of anti-depressants or anxiolytics. Use of health services increased with increasing severity of both depression and anxiety.ConclusionThere was a large gap between symptoms and reporting of past diagnosis and treatment of common mental disorders in two Russian cities. Interventions aimed at improving mental health literacy and reducing stigma could be of benefit in closing this substantial treatment gap.
Cross-segment spinal plasma cell granuloma:a case report
Authors: Lin Renqin , Wang Shenglin , Lin Jianhua , Zhang Zhenzhen , Chen Xuanwei 
Published: November 2020

AbstractBackgroundPlasma cell granuloma (PCG) is a rare non-neoplastic entity, with the precise etiology remaining unclear. Vertebra-affected spinal PCG has not been reported yet. This report presented a case with cross-segment spinal PCG in thoracolumbar region.Case presentationA 32-year-old male patient presented to the authors’ hospital since his health check-up results showed osteolytic lesions in the thoracolumbar spine. He felt asymptomatic throughout the course. Radiological examination revealed destructive changes at T12 and L1 vertebrae. Whereas laboratory examination excluded malignant tumor. The results of routine incisional biopsy remained inconclusive, thereby necessitating complete excision of the lesions. Finally, the infiltration of plasma cells observed by pathological examination of the surgical specimen confirmed the diagnosis of PCG.ConclusionsTo the authors’ knowledge, this was the first case of cross-segment spinal PCG with osteolytic property. The possibility of PCG should be considered for the diagnosis and differential diagnosis of an osteolytic lesion in the spine. Since the etiology of PCG is unknown, the disorder was confirmed based on excluded diagnosis. Surgical resection is recommended both for the definite diagnosis and treatment of spinal PCG.
Esophagogastric polyurethane bezoar complicated by stomach wall microperforation and acute peritonitis: case report
Authors: Ziaja Krzysztof , Chudek Jerzy , Chlubek Aleksander , Sznapka Mariola , Toborek Tomasz , Ziaja Damian 
Published: November 2020

Abstract

Background
Bezoars are collections of indigestible material in the gastrointestinal tract, mostly described in children. Polyurethane “plastobezoars” consisting of composites used in the construction industry are rarely described bezoars formed in the esophagus and stomach, causing gastrointestinal obstruction, usually necessitating gastrectomy.
We describe an unusual presentation of polyurethane bezoar with a volcanic rock consistency, that caused gastrointestinal obstruction and perforation of the stomach wall.

Case presentation
A 39-year-old man, a construction worker, was referred with signs and symptoms of high gastrointestinal obstruction and abdominal pain. Esophagoscopy revealed a foreign body in the esophagus, 20 cm from the incisor line, causing its obstruction. The attempt to collect the material with forceps failed as the material was too hard. Spiral computed tomography visualized a wide, gas-filled esophagus and a large stomach. The patient with symptoms of acute peritonitis was operated. There were several microperforations of the stomach wall, caused by sharp bezoar fragments that filled the upper one-third of the stomach and lower part of the esophagus. After a longitudinal stomach incision, the bezoar was bluntly dissected from the wall and removed, and the stomach microperforations were closed by wall duplication. After the operation, the patient confessed to drinking, of his own free will, a two-component building foam used to seal pipes. The patient started normal feeding on the 4th day and was discharge home.

Conclusions
Polyurethane bezoars may cause stomach wall perforation and acute peritonitis. Computed tomography has limited usefulness in patients with polyurethane bezoars due to their low specific weight.
Impact of malnutrition on systemic immune and metabolic profiles in type 2 diabetes
Authors: Rajamanickam Anuradha , Munisankar Saravanan , Dolla Chandra Kumar , Thiruvengadam Kannan , Babu Subash 
Published: November 2020

Abstract

Background
While obesity and overweight status are firmly established risk factors for Type 2 diabetes mellitus (T2DM), a substantial proportion of diabetic individuals, especially in Africa and Asia, are often underweight or normal weight. However, very little is known about the immunological and metabolic profiles of these individuals.

Methods
This study aimed to assess the relationship between malnutrition and Type 2 diabetes mellitus (T2DM). We examined a variety of analytes associated with the immunological and metabolic profiles of T2DM individuals with low (< 18.5 kg/m2) or normal (18.5–24.9 kg/m2) body mass index (BMI). To this end, we measured plasma levels of HbA1c, glucose, insulin, glucagon, adipocytokines and Type 1, Type 2, Type 17, pro-inflammatory and regulatory cytokines in T2DM individuals with low BMI (LBMI) or normal BMI (NBMI) with small sample size n = 44 in each group.

Results
LBMI individuals exhibited significantly higher levels of HbA1c, random blood glucose, insulin and glucagon compared to NBMI individuals. Similarly, LBMI individuals exhibited significantly higher levels of adiponectin and adipsin and significantly lower levels of leptin in comparison to NBMI individuals. LBMI individuals also exhibited significantly lower levels of the Type 1, Type 2, Type 17, pro-inflammatory and regulatory cytokines in comparison to NBMI individuals. Finally, while the metabolic parameters exhibited a significant negative correlation with BMI, the immunological parameters exhibited a significant positive correlation with BMI.

Conclusions
Malnutrition is associated with a significant modulation of glycemic, hormonal and cytokine parameters in T2DM. Hence, the biochemical and immunological profiles of T2DM is significantly influenced by BMI.
The 2020 blast in the Port of Beirut: can the Lebanese health system “build back better”?
Authors: Landry Michel D. , Alameddine Mohamad , Jesus Tiago S. , Sassine Saydeh , Koueik Elie , Raman Sudha R. 
Published: November 2020

AbstractThe August 2020 explosion in Lebanon resulted in casualties, injuries, and a great number of internally displaced persons. The blast occurred during an economically and politically complex time in the country. Given multiple and competing post-explosion reconstruction priorities, in ths editorial we briefly examine the requirements for a build back better scenario.
Presence of antibodies against tick-borne encephalitis virus in sheep in Tunisia, North Africa
Authors: Khamassi Khbou Médiha , Romdhane Rihab , Foughali Asma Amina , Sassi Limam , Suin Vanessa , Rekik Mourad , Benzarti M’hammed 
Published: November 2020

AbstractBackgroundTick-borne encephalitis virus (TBEv) is a flavivirus that circulates in a complex cycle involving small mammals as amplifying hosts and ticks as vectors and reservoirs. The current study aimed to investigate the presence of TBEv in Tunisian sheep. A sample of 263 adult sheep were selected from 6 localities whereIxodes ricinusis well established. Sera were screened using ELISA for TBEv IgG detection, then the doubtful and positive sera were tested by the seroneutralisation test (SNT) and screened for West Nile Virus (WNv) IgG for cross-reaction assessment.ResultsThe ELISA for TBEv IgG detected one positive serum and 17 borderlines. The SNT showed one positive serum among the 18 tested, giving an overall antibody prevalence of 0.38% (95% CI = 0.07–2.12%). All but one serum tested negative to WNv ELISA. None of the sheep farmers reported neurological signs among sheep or humans in their households.ConclusionsThe results may indicate the circulation of TBEv for the first time in Tunisia and in North Africa. Further studies based on either virus isolation or RNA detection, are needed to confirm the presence of TBEv in North Africa.
Conversion of poplar biomass into high-energy density tricyclic sesquiterpene jet fuel blendstocks
Authors: Geiselman Gina M. , Kirby James , Landera Alexander , Otoupal Peter , Papa Gabriella , Barcelos Carolina , Sundstrom Eric R. , Das Lalitendu , Magurudeniya Harsha D. , Wehrs Maren , Rodriguez Alberto , Simmons Blake A. , Magnuson Jon K. , Mukhopadhyay Aindrila , Lee Taek Soon , George Anthe , Gladden John M. 
Published: November 2020

Abstract
Background
In an effort to ensure future energy security, reduce greenhouse gas emissions and create domestic jobs, the US has invested in technologies to develop sustainable biofuels and bioproducts from renewable carbon sources such as lignocellulosic biomass. Bio-derived jet fuel is of particular interest as aviation is less amenable to electrification compared to other modes of transportation and synthetic biology provides the ability to tailor fuel properties to enhance performance. Specific energy and energy density are important properties in determining the attractiveness of potential bio-derived jet fuels. For example, increased energy content can give the industry options such as longer range, higher load or reduced takeoff weight. Energy-dense sesquiterpenes have been identified as potential next-generation jet fuels that can be renewably produced from lignocellulosic biomass.

Results
We developed a biomass deconstruction and conversion process that enabled the production of two tricyclic sesquiterpenes, epi-isozizaene and prespatane, from the woody biomass poplar using the versatile basidiomycete Rhodosporidium toruloides. We demonstrated terpene production at both bench and bioreactor scales, with prespatane titers reaching 1173.6 mg/L when grown in poplar hydrolysate in a 2 L bioreactor. Additionally, we examined the theoretical fuel properties of prespatane and epi-isozizaene in their hydrogenated states as blending options for jet fuel, and compared them to aviation fuel, Jet A.

Conclusion
Our findings indicate that prespatane and epi-isozizaene in their hydrogenated states would be attractive blending options in Jet A or other lower density renewable jet fuels as they would improve viscosity and increase their energy density. Saturated epi-isozizaene and saturated prespatane have energy densities that are 16.6 and 18.8% higher than Jet A, respectively. These results highlight the potential of R. toruloides as a production host for the sustainable and scalable production of bio-derived jet fuel blends, and this is the first report of prespatane as an alternative jet fuel.
Analysis of initial laboratory diagnosis of malaria and its accuracy compared with re-testing from 2013 to 2018 in Yunnan Province, China
Authors: Dong Ying , Deng Yan , Xu Yanchun , Chen Mengni , Wei Chun , Zhang Canglin , Mao Xianghua , Xue Jingbo 
Published: November 2020

Abstract
Background
According to China’s Malaria Eradication Action Plan, malaria cases diagnosed and reported by health authorities at the county level must be further re-confirmed by provincial laboratories. The Yunnan Province Malaria Diagnostic Reference Laboratory (YPMDRL) began the synchronous implementation of microscopic examinations and nested polymerase chain reaction (nested-PCR) testing to re-test the malaria cases initially diagnosed by county-level laboratories and to evaluate the consistency of Plasmodium species identified between by YPMDRL and by the county-level laboratories from 2013 to 2018 in Yunnan Province.

Methods
Data on malaria initial diagnosis completed by county-level laboratories in Yunnan Province were collected weekly from the “China Disease Prevention and Control Information System” from 2013 to 2018. The YPMDRL performed Plasmodium microscopic examination and 18S rRNA gene nested-PCR testing on every malaria case managed by the China Disease Prevention and Control Information System. The re-testing detection results were fed back to the initial diagnosis and reporting unit for revision of malaria case types.

Results
A total of 2,869 malaria cases were diagnosed and reported by county-level laboratories in Yunnan Province from 2013 to 2018. The re-testing rate was 95.6% (2,742/2,869), and the re-testing rate increased from 2013 to 2018. Among the re-tested 2,742 cases, 96.7% (2651/2742), 2.2% (59/2742), and 1.1% (32/2742) were doubly examined by microscopy and by nested-PCR, only by microscopy, and only by nested-PCR, respectively. The total Plasmodium species accuracy rate at county-level laboratories was 92.6% (2,543/2,742) reference to the diagnosis by YPMDRL. Among the inconsistent 199 cases, they were identified as including 103 negative cases, 45 falciparum malaria cases, 30 vivax malaria cases, 11 ovale malaria cases, and 10 malariae malaria cases by YPMDRL. From 2013 to 2018, the revised and registered malaria cases by the China Disease Prevention and Control Information System in Yunnan Province was 2,747 cases, including 2,305 vivax malaria cases, 421 falciparum malaria cases, 11 ovale malaria cases, and 10 malariae malaria cases.

Conclusions
The double re-testing strategy by microscopy and by gene testing increases the accuracy of diagnoses malaria in Yunnan Province, and gene testing can reliably differentiate Plasmodium species. The re-testing results provided by YPMDRL are the authoritative basis for revising malaria kind in Yunnan Province.
Income-related inequalities in unmet dental care needs in Spain: traces left by the Great Recession
Authors: Urbanos-Garrido Rosa M. 
Published: November 2020

Abstract
Background
Dental health is an important component of general health. Socioeconomic inequalities in unmet dental care needs have been identified in the literature, but some knowledge gaps persist. This paper tries to identify the determinants of income-related inequality in unmet need for dental care and the reasons for its recent evolution in Spain, and it inquires about the traces left by the Great Recession.

Methods
Data from the EU-SILC forming a decade (2007–2017) were used. Income-related inequalities for three years were measured by calculating corrected concentration indices (CCI), which were further decomposed in order to compute the contribution of different factors to inequality. An Oaxaca-type decomposition approach was also used to analyze the origin of changes over time. Men and women were analyzed separately.

Results
Pro-rich inequality in unmet dental care needs significantly increased over time (CCI 2007: − 0.0272 and − 0.0334 for males and females, respectively; CCI 2017: − 0.0704 and − 0.0776; p < 0.001). Inequality showed a clear “pro-cycle” pattern, growing during the Great Recession and starting to decrease just after the economic recovery began. Gender differences only were significant for 2009 (p = 0.004) and 2014 (p = 0.063). Income was the main determinant of inequality and of its variation along time -particularly for women-, followed by far by unemployment –particularly for men-; the contributions of both were mainly due to changes in elasticites.

Conclusions
The Great Recession left its trace in form of a higher inequality in the access to dental care. Also, unmet need for dental care, as well as its inequality, became more sensitive to the ability to pay and to unemployment along recent years. To broaden public coverage of dental care for vulnerable groups, such as low-income/unemployed people with high oral health needs, would help to prevent further growth of inequality.