bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of three serological tests for the detection of Coxiella burnetii specific antibodies in European wild rabbits
Authors: Caraguel Charles , Bassett Sarah , González-Barrio David , Elsworth Peter , Chaber Anne-Lise
Published: August 2020

Background

Coxiella burnetii causes Q fever, a zoonotic bacterial disease with a multi-host cycle and reservoirs in wild and domestic animal species. Q fever has a significant impact on the Australian public health and economy but its ecology and contributing reservoir species remain poorly understood. In Europe, rabbits (Oryctolagus cuniculus) were identified as a major reservoir of C. burnetii and it is possible that they play a similar role in Australia. In absence of commercial kit available for rabbit, the Thermo Fisher - PrioCHECK™ Ruminant Q fever Ab Plate Kit was adapted to successfully screen rabbits population in Europe. However, this assay is not accessible in Australia and we assessed the equivalency of two commercially available kits in Australia – IDEXX - CHEKIT Q Fever Antibody ELISA kit and IDVet - ID Screen® Q Fever Indirect Multi-species with the Thermo Fisher kit (reference kit).

Results

A total of 94 rabbit sera were screened by all three ELISA kits using the same confirmed positive and negative controls. While the IDEXX kit failed to agree the other two assays (concordance correlation coefficient, rb < 0.77), IDVet kit showed satisfactory equivalency with Thermo Fisher (rb = 0.927).

Conclusion

IDvet kit provides the best alternative for Thermo Fisher in the detection of C. burnetii specific antibodies in rabbits in Australia. Further trials are required to confirm these preliminary results due to the low seroprevalence of Coxiella burnetii observed in the study sera.
Machine learning based refined differential gene expression analysis of pediatric sepsis
Authors: Abbas Mostafa , EL-Manzalawy Yasser
Published: August 2020

Background

Differential expression (DE) analysis of transcriptomic data enables genome-wide analysis of gene expression changes associated with biological conditions of interest. Such analysis often provides a wide list of genes that are differentially expressed between two or more groups. In general, identified differentially expressed genes (DEGs) can be subject to further downstream analysis for obtaining more biological insights such as determining enriched functional pathways or gene ontologies. Furthermore, DEGs are treated as candidate biomarkers and a small set of DEGs might be identified as biomarkers using either biological knowledge or data-driven approaches.

Methods

In this work, we present a novel approach for identifying biomarkers from a list of DEGs by re-ranking them according to the Minimum Redundancy Maximum Relevance (MRMR) criteria using repeated cross-validation feature selection procedure.

Results

Using gene expression profiles for 199 children with sepsis and septic shock, we identify 108 DEGs and propose a 10-gene signature for reliably predicting pediatric sepsis mortality with an estimated Area Under ROC Curve (AUC) score of 0.89.

Conclusions

Machine learning based refinement of DE analysis is a promising tool for prioritizing DEGs and discovering biomarkers from gene expression profiles. Moreover, our reported 10-gene signature for pediatric sepsis mortality may facilitate the development of reliable diagnosis and prognosis biomarkers for sepsis.
LncRNA TTN-AS1 promotes the progression of oral squamous cell carcinoma via miR-411-3p/NFAT5 axis
Authors: Fu Su-Wei , Zhang Yan , Li Shen , Shi Zhi-Yan , Zhao Juan , He Qing-Li
Published: August 2020

Background

Oral squamous cell carcinoma (OSCC) is a common kind of squamous cell carcinoma of the head and neck, which is a threat to public health. Long noncoding RNAs (lncRNAs) are associated with the development of various diseases, including cancers. LncRNA titin antisense RNA 1 (TTN-AS1) is known as a crucial regulatory factor in several cancers. Nevertheless, the specific functions of TTN-AS1 in OSCC remains obscure.

Methods

The expression of TTN-AS1 in OSCC samples or cells was analyzed through qRT-PCR. Colony formation assay, EdU assay, flow cytometry assay, TUNEL assay and wound healing assay were conducted to estimate the functions of TTN-AS1 in OSCC cells. RIP and luciferase reporter assays were utilized to detect the interaction between TTN-AS1 and miR-411-3p as well as between miR-411-3p and NFAT5.

Results

TTN-AS1 expression was stronger in OSCC cells. Knockdown of TTN-AS1 effectively restrained cell proliferation and migration but had inductive role in apoptosis. Moreover, TTN-AS1 could function as the miR-411-3p sponge in OSCC and miR-411-3p exerted the inhibitory functions on OSCC cell growth. In addition, NFAT5 was proven as the target of miR-411-3p. Rescue assay indicated that overexpressing NFAT5 could reverse the inhibitory function of TTN-AS1 depletion on cell growth.

Conclusion

lncRNA TTN-AS1 contributed to the progression of OSCC via miR-411-3p/NFAT5 axis.
MiR-145-5p suppresses the proliferation, migration and invasion of gastric cancer epithelial cells via the ANGPT2/NOD_LIKE_RECEPTOR axis
Authors: Zhou Kai , Song Binbin , Wei Ming , Fang Jubo , Xu Yufen
Published: August 2020

Objective

This study aimed to investigate the relationship among miR-145-5p, ANGPT2 and the NOD_LIKE_RECEPTOR pathway, thereby revealing the molecular mechanism of these three factors underlying the proliferation, migration and invasion of gastric cancer (GC) epithelial cells.

Methods

qRT-PCR was carried out to detect the expression of miR-145-5p and ANGPT2 mRNA. Western blot was performed to test the protein levels of ANGPT2 as well as NOD1, NOD2 and NF-κB in the NOD_LIKE_RECEPTOR pathway. The targeting relationship between miR-145-5p and ANGPT2 was verified via a dual-luciferase reporter gene assay. The proliferation, migration and invasion of GC cells were detected through MTT and Transwell assays, respectively.

Results

The expression of miR-145-5p was significantly down-regulated in GC cells, while that of ANGPT2 was notably up-regulated. MiR-145-5p directly bound with the 3′-UTR of ANGPT2 mRNA, thereby targeting ANGPT2 after transcription. Overexpression of miR-145-5p inhibited the proliferation, migration and invasion of GC cells by suppressing ANGPT2. Moreover, low expression of ANGPT2 affected the protein levels of NOD1, NOD2 and NF-κB in the NOD_LIKE_RECEPTOR pathway, thus weakening the abilities of cell proliferation, migration and invasion.

Conclusions

MiR-145-5p plays an important role in GC epithelial cells, and it can affect cell proliferation, migration and invasion of GC cells by targeting ANGPT2 and regulating the NOD_LIKE_RECEPTOR pathway. Overall, our study further elucidates the molecular mechanism underlying the malignant progression of GC.
Down-regulation of TRIB3 inhibits the progression of ovarian cancer via MEK/ERK signaling pathway
Authors: Wang Shuang , Wang Caixia , Li Xiao , Hu Yuexin , Gou Rui , Guo Qian , Nie Xin , Liu Juanjuan , Zhu Liancheng , Lin Bei
Published: August 2020

Background

Tribbles pseudokinase 3 (TRIB3) protein is a pseudokinase which plays an important role in cellular stress, metabolism, and tumor progression. However, the expression and function of TRIB3 in ovarian cancer is unknown.

Methods

TRIB3 expression was detected by immunohistochemistry in the ovarian tissue samples. Following down-regulation of TRIB3 by siRNA, multiple aspects of ovarian cancer cells were detected by the MTT assay, flow cytometry, scratch test and Transwell. Additionally, changes in related molecules and the MEK/ERK pathway were detected by western blotting. Finally, many bioinformatic methods, websites and databases, such as gene set enrichment analysis (GSEA), DVAID, Genemania, TISIDB and cBioPortal were used to study the TRIB3.

Results

The expression level of TRIB3 was higher in ovarian epithelial malignant tumors as compared to other groups. Patients with a high expression level of TRIB3 had significantly shorter survival times,which was consistent with the results of analysis of the KM-plot database. Down-regulation ofTRIB3expression significantly inhibited the proliferation, invasion, and migration capabilities of ovarian cancer cells, and induced apoptosis and cell cycle arrest. Following TRIB3 siRNA transfection, expression levels of relative proteins were found to be decreased. Additionally, analysis in DAVID website and GSEA revealed that TRIB3 expression was associated with multiple biological processes. Protein phosphorylation levels of MEK and ERK also decreased following TRIB3-siRNA transfection. The Genemania website was used to analyze the proteins that interact with TRIB3. Analysis ofTRIB3in the TISIDB database and cBioPortal website showed that ovarian cancer patients with high levels of mutation in TRIB3 had poor prognosis, and that the expression of TRIB3 was related to immunomodulation.

Conclusions

The TRIB3 was highly expressed and promoting the malignant behavior of ovarian cancer cells by activating the MEK-ERK signaling pathway. It was also found to be associated with genetic variations and immune modulators.
Preliminary clinical and radiographic outcomes of proximal humeral fractures: comparison of ALPS and PHILOS plating in Asian patients in Taiwan
Authors: Chen Chun-Yen , Chang Hao-Wei , Hsieh Shang-Lin , Chang Chien-Chun , Tsai Chun-Hao , Chen Yi-Wen , Lin Tsung-Li , Hsu Chin-Jung
Published: August 2020

Background

Up to 20% of proximal humeral fractures need to be treated operatively. However, numerus complications were reported by using fixed angled locking plates. The ALPS Proximal Humerus Plating System is a new design implant with novel design features.

The aim of this study was to compare the preliminary clinical outcomes and complications of proximal humeral fractures treated with either ALPS or the proximal humeral internal locking system (PHILOS) in Asian patients in Taiwan.

Methods

Between January 2016 and December 2018, 66 patients with displaced proximal humeral fractures were analyzed retrospectively, of whom 31 underwent ALPS implant treatment and 35 underwent PHILOS implant treatment. Intraoperative blood loss and operation time, postoperative Constant-Murley Shoulder Outcome (Constant-Murley) score, and complications variables were recorded for the comparison. All cases were regularly followed up for at least 1 year.

Results

The mean follow-up period was 400.8 days (range, 367–446 days). Union was achieved in 98.5% of patients (65/66). The ALPS group yielded similar radiologic and clinical outcomes to the PHILOS plating group for treating displaced proximal humeral fractures, including operation time, intraoperative blood loss, the Constant-Murley score, and varus malunion (P > 0.05, respectively). However, the incidence of total postoperative complications in the ALPS group was significantly lower than in the PHILOS group (P < 0.05). There was a trend of a lower complication rate of screws/pegs protrusion, avascular necrosis, subacromial impingement, postoperative infection, and reoperation in the ALPS group, although it was not statistically significant (P > 0.05, respectively).

Conclusion

The ALPS group yielded similar radiologic and clinical outcomes to the PHILOS plating group for displaced proximal humeral fractures, but the ALPS group had a significantly lower total rate of complications. Therefore, ALPS may be a better option for treating proximal humeral fractures. Further larger clinical studies are needed to confirm the findings presented here.

Trial registration

Retrospective study
Angioleiomyoma of the pulmonary artery: a case report and literature review
Authors: Hu Yan , Ren Siying , Tan Sichuang , Chen Chen , Wang Xiang , Liang Qingchun , Yu Fenglei , Liu Wenliang
Published: August 2020

Background

Angioleiomyoma of the pulmonary artery is rare in the literature and few studies have been reported. Here we present a rare case of angioleiomyoma arising from the pulmonary artery in a young patient.

Case presentation

A 27-year-old male patient presented to our clinic due to the incidental finding of a nodule in the right lower lobe of the lung, which was unchanged from the prior year. Preoperative CT scans showed a well-demarcated nodule of soft tissue density penetrated by the basal branch of the right anterior basilar artery (RA8b). Single-port video-assisted RS8 segmentectomy was performed under the guidance of preoperative 3-dimensional reconstruction for histologic confirmation of the tumour. The tumour appeared as a solid tumour of a tube-like structure with vascular endothelium, composed of spindle-shaped smooth muscle cells lacking nuclear atypia and homogenous red-dye substances. The spindle cells were positive for immunostaining for smooth muscle actin (SMA), desmin and Ki-67 and were negative for immunostaining for Dog-1, HMB45, and Melan-A. A pathological diagnosis of primary angioleiomyoma of the pulmonary artery was finally made.

Conclusions

This report is a reminder for thoracic surgeons that angioleiomyoma should be included in the differential diagnosis of lung neoplasms, especially for the mass of soft tissue density penetrated by pulmonary blood vessels shown by CT. Awareness of this rare entity should potentially prevent underdiagnosis and improper surgical treatment.
Respiratory physiology of COVID-19-induced respiratory failure compared to ARDS of other etiologies
Authors: Grieco Domenico Luca , Bongiovanni Filippo , Chen Lu , Menga Luca S. , Cutuli Salvatore Lucio , Pintaudi Gabriele , Carelli Simone , Michi Teresa , Torrini Flava , Lombardi Gianmarco , Anzellotti Gian Marco , De Pascale Gennaro , Urbani Andrea , Bocci Maria Grazia , Tanzarella Eloisa S. , Bello Giuseppe , Dell’Anna Antonio M. , Maggiore Salvatore M. , Brochard Laurent , Antonelli Massimo
Published: August 2020

Background

Whether respiratory physiology of COVID-19-induced respiratory failure is different from acute respiratory distress syndrome (ARDS) of other etiologies is unclear. We conducted a single-center study to describe respiratory mechanics and response to positive end-expiratory pressure (PEEP) in COVID-19 ARDS and to compare COVID-19 patients to matched-control subjects with ARDS from other causes.

Methods

Thirty consecutive COVID-19 patients admitted to an intensive care unit in Rome, Italy, and fulfilling moderate-to-severe ARDS criteria were enrolled within 24 h from endotracheal intubation. Gas exchange, respiratory mechanics, and ventilatory ratio were measured at PEEP of 15 and 5 cmH2O. A single-breath derecruitment maneuver was performed to assess recruitability. After 1:1 matching based on PaO2/FiO2, FiO2, PEEP, and tidal volume, COVID-19 patients were compared to subjects affected by ARDS of other etiologies who underwent the same procedures in a previous study.

Results

Thirty COVID-19 patients were successfully matched with 30 ARDS from other etiologies. At low PEEP, median [25th–75th percentiles] PaO2/FiO2 in the two groups was 119 mmHg [101–142] and 116 mmHg [87–154]. Average compliance (41 ml/cmH2O [32–52] vs. 36 ml/cmH2O [27–42], p = 0.045) and ventilatory ratio (2.1 [1.7–2.3] vs. 1.6 [1.4–2.1], p = 0.032) were slightly higher in COVID-19 patients. Inter-individual variability (ratio of standard deviation to mean) of compliance was 36% in COVID-19 patients and 31% in other ARDS. In COVID-19 patients, PaO2/FiO2 was linearly correlated with respiratory system compliance (r = 0.52 p = 0.003). High PEEP improved PaO2/FiO2 in both cohorts, but more remarkably in COVID-19 patients (p = 0.005). Recruitability was not different between cohorts (p = 0.39) and was highly inter-individually variable (72% in COVID-19 patients and 64% in ARDS from other causes). In COVID-19 patients, recruitability was independent from oxygenation and respiratory mechanics changes due to PEEP.

Conclusions

Early after establishment of mechanical ventilation, COVID-19 patients follow ARDS physiology, with compliance reduction related to the degree of hypoxemia, and inter-individually variable respiratory mechanics and recruitability. Physiological differences between ARDS from COVID-19 and other causes appear small.
sgBE: a structure-guided design of sgRNA architecture specifies base editing window and enables simultaneous conversion of cytosine and adenosine
Authors: Wang Yanhong , Zhou Lifang , Tao Rui , Liu Nan , Long Jie , Qin Fengming , Tang Wenling , Yang Yang , Chen Qiang , Yao Shaohua
Published: August 2020

We present a base editing system, in which base editors are attached to different sites of sgRNA scaffold (sgBE). Each independent sgBE has its own specific editing pattern for a given target site. Among tested sgBEs, sgBE-SL4, in which deaminase is attached to the last stem-loop of sgRNA, yields the highest editing efficiency in the window several nucleotides next to the one edited by BE3. sgBE enables the simultaneous editing of adenine and cytosine. Finally, in order to facilitate in vivo base editing, we extend our sgBE system to an AAV-compatible Cas9, SaCas9 (Staphylococcus aureus), and observe robust base editing.
Systems genetics analysis identifies calcium-signaling defects as novel cause of congenital heart disease
Authors: Izarzugaza Jose M. G. , Ellesøe Sabrina G. , Doganli Canan , Ehlers Natasja Spring , Dalgaard Marlene D. , Audain Enrique , Dombrowsky Gregor , Banasik Karina , Sifrim Alejandro , Wilsdon Anna , Thienpont Bernard , Breckpot Jeroen , Gewillig Marc ,   Competence Network for Congenital Heart Defects, Germany, Abdul-Khaliq Hashim , Kramer Hans-Heiner , Berger Felix , Stiller Brigitte , Bauer Ulrike , Pickardt Thomas , Klaassen Sabine , Brook J. David , Hitz Marc-Phillip , Larsen Lars A. , Brunak Søren
Published: August 2020

Background

Congenital heart disease (CHD) occurs in almost 1% of newborn children and is considered a multifactorial disorder. CHD may segregate in families due to significant contribution of genetic factors in the disease etiology. The aim of the study was to identify pathophysiological mechanisms in families segregating CHD.

Methods

We used whole exome sequencing to identify rare genetic variants in ninety consenting participants from 32 Danish families with recurrent CHD. We applied a systems biology approach to identify developmental mechanisms influenced by accumulation of rare variants. We used an independent cohort of 714 CHD cases and 4922 controls for replication and performed functional investigations using zebrafish as in vivo model.

Results

We identified 1785 genes, in which rare alleles were shared between affected individuals within a family. These genes were enriched for known cardiac developmental genes, and 218 of these genes were mutated in more than one family. Our analysis revealed a functional cluster, enriched for proteins with a known participation in calcium signaling. Replication in an independent cohort confirmed increased mutation burden of calcium-signaling genes in CHD patients. Functional investigation of zebrafish orthologues of ITPR1, PLCB2, and ADCY2 verified a role in cardiac development and suggests a combinatorial effect of inactivation of these genes.

Conclusions

The study identifies abnormal calcium signaling as a novel pathophysiological mechanism in human CHD and confirms the complex genetic architecture underlying CHD.
RETRACTED ARTICLE: Long non-coding RNA LINC00525 regulates the proliferation and epithelial to mesenchymal transition of human glioma cells by sponging miR-338-3p
Authors: Wan Yilv , Liang Feng , Wei Minjun , Liu Ying
Published: August 2020

Long non-coding RNA (LncRNA) LINC00525 has been shown to be upregulated in several human cancers and deduced to possess caner regulatory role. The regulation of molecular mechanics of human glioma by lncRNA-LINC00525 through microRNA sponging in glioma is elusive. The lncRNA-LINC00525 showed significant (P < 0.05) upregulation in glioma cancer cells. The upregulation of lncRNA-LINC00525 was upto 6.6-fold in glioma cells relative to the normal cells. Knockdown of lncRNA-LINC00525 significantly declined the proliferation of the glioma cancer cells. Additionally, the colony formation was inhibited by around 60% in glioma cells. The wound healing and transwell assays revealed significant (P < 0.05) inhibition of migration and invasion potential under lncRNA-LINC00525 knockdown. The western blotting study of biomarkers of epithelial to mesenchymal transition (EMT) revealed that lncRNA-LINC00525 gene silencing reduced the expression of mesenchymal molecular markers but increased the protein levels of epithelial markers. miR-338-3p was predicted to be interacting with lncRNA-LINC00525 in glioma and was shown to mediated the regulatory role of lncRNA-LINC00525. Taken together, the results of present study are supportive of the prognostic applicability of lncRNA-LINC00525 against human glioma together with its therapeutic potential against the said malignancy.
Anthracycline-based and gemcitabine-based chemotherapy in the adjuvant setting for stage I uterine leiomyosarcoma: a retrospective analysis at two reference centers
Authors: Fucà Giovanni , Fabbroni Chiara , Mancari Rosanna , Manglaviti Sara , Bogani Giorgio , Fumagalli Elena , Bertulli Rossella , Morosi Carlo , Collini Paola , Raspagliesi Francesco , Colombo Nicoletta , Casali Paolo G. , Sanfilippo Roberta
Published: August 2020

Background

Radically resected early uterine leiomyosarcoma (eULMS) is still marked by a poor prognosis. Adjuvant strategies investigated up to now have not been corroborated by controlled studies. We retrospectively reviewed the clinical outcome of eULMS patients treated with adjuvant anthracycline-based or gemcitabine-based chemotherapy at two Italian reference centers.

Methods

In this explorative, retrospective, cohort analysis, we included all the consecutive patients with radically resected eULMS treated at two centers between 1997 and 2017.

Results

A total of 109 consecutive patients were included. Sixty-six (60%) received an anthracycline-based regimen, whereas 43 (40%) received a gemcitabine-based regimen. Median disease-free survival (DFS) was 41.3 months with anthracycline-based regimens compared to 20.9 months with gemcitabine-based regimens (HR: 0.49; 95% CI: 0.30–0.80; P = 0.004). In the multivariable model, anthracycline-based regimens were independently associated with a better DFS. No difference in terms of overall survival was observed.

Conclusions

DFS was not the same by using an anthracycline-based or a gemcitabine-based adjuvant chemotherapy for patients with radically resected eULMS. The results of our study are in line with recent prospective controlled evidence in limb and superficial trunk soft tissue sarcomas. The role of anthracycline-based adjuvant chemotherapy should still be viewed as a research issue in eULMS.
Thermal impacts of basaltic lava flows to buried infrastructure: workflow to determine the hazard
Authors: Tsang Sophia W. R. , Lindsay Jan M. , Kennedy Ben , Deligne Natalia I.
Published: August 2020

Lava flows can cause substantial physical damage to elements of the built environment. Often, lava flow impacts are assumed to be binary, i.e. cause complete damage if the lava flow and asset are in contact, or no damage if there is no direct contact. According to this paradigm, buried infrastructure would not be expected to sustain damage if a lava flow traverses the ground above. However, infrastructure managers (“stakeholders”) have expressed concern about potential lava flow damage to such assets. We present a workflow to assess the thermal hazard posed by lava flows to buried infrastructure. This workflow can be applied in a pre-defined scenario. The first step in this workflow is to select an appropriate lava flow model(s) and simulate the lava flow’s dimensions, or to measure an in situ lava flow’s dimensions. Next, stakeholders and the modellers collaborate to identify where the lava flow traverses buried network(s) of interest as well as the thermal operating conditions of these networks. Alternatively, instead of direct collaboration, this step could be done by overlaying the flow’s areal footprint on local infrastructure maps, and finding standard and maximum thermal operating conditions in the literature. After, the temperature of the lava flow at the intersection point(s) is modelled or extracted from the results of the first step. Fourth, the lava flow-substrate heat transfer is calculated. Finally, the heat transfer results are simplified based on the pre-identified thermal operating conditions. We illustrate how this workflow can be applied in an Auckland Volcanic Field (New Zealand) case study. Our case study demonstrates considerable heat is transferred from the hypothetical lava flow into the ground and that maximum operating temperatures for electric cables are exceeded within 1 week of the lava flow front’s arrival at the location of interest. An exceedance of maximum operating temperatures suggests that lava flows could cause thermal damage to buried infrastructure, although mitigation measures may be possible.
Weak and strong singularities problems to Liénard equation
Authors: Xin Yun , Hu Guixin
Published: August 2020

This paper is devoted to an investigation of the existence of a positive periodic solution for the following singular Liénard equation: $$ x''+f\bigl(x(t)\bigr)x'(t)+a(t)x= \frac{b(t)}{x^{\alpha }}+e(t), $$

x
″

+
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(
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(
t
)
)

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(
t
)
+
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)
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(
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)

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α

+
e
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)
,
where the external force $e(t)$
e
(
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)
may change sign, α is a constant and $\alpha >0$
α
>
0
. The novelty of the present article is that for the first time we show that weak and strong singularities enables the achievement of a new existence criterion of positive periodic solution through an application of the Manásevich–Mawhin continuation theorem. Recent results in the literature are generalized and significantly improved, and we give the existence interval of periodic solution of this equation. At last, two examples and numerical solution (phase portraits and time portraits of periodic solutions of the example) are given to show applications of the theorem.
Antimicrobial resistance preparedness in sub-Saharan African countries
Authors: Elton Linzy , Thomason Margaret J. , Tembo John , Velavan Thirumalaisamy P. , Pallerla Srinivas Reddy , Arruda Liã Bárbara , Vairo Francesco , Montaldo Chiara , Ntoumi Francine , Abdel Hamid Muzamil M. , Haider Najmul , Kock Richard , Ippolito Giuseppe , Zumla Alimuddin , McHugh Timothy D. ,   the PANDORA-ID-NET consortium
Published: August 2020

Background

Antimicrobial resistance (AMR) is of growing concern globally and AMR status in sub-Saharan Africa (SSA) is undefined due to a lack of real-time data recording, surveillance and regulation. World Health Organization (WHO) Joint External Evaluation (JEE) reports are voluntary, collaborative processes to assess country capacities and preparedness to prevent, detect and rapidly respond to public health risks, including AMR. The data from SSA JEE reports were analysed to gain an overview of how SSA is working towards AMR preparedness and where strengths and weaknesses lie.

Methods

SSA country JEE AMR preparedness scores were analysed. A cumulative mean of all the SSA country AMR preparedness scores was calculated and compared to the overall mean SSA JEE score. AMR preparedness indicators were analysed, and data were weighted by region.

Findings

The mean SSA AMR preparedness score was 53% less than the overall mean SSA JEE score. East Africa had the highest percentage of countries reporting having AMR National Action Plans in place, as well as human and animal pathogen AMR surveillance programmes. Southern Africa reported the highest percentage of countries with training programmes and antimicrobial stewardship.

Conclusions

The low mean AMR preparedness score compared to overall JEE score, along with the majority of countries lacking implemented National Action Plans, suggests that until now AMR has not been a priority for most SSA countries. By identifying regional and One Health strengths, AMR preparedness can be fortified across SSA with a multisectoral approach.
Effect of sodium silicate on early growth stages of wheat under drought stress
Authors: Lee Sang Gyu , Lee Hyeri , Lee Byung Cheon , Lee Hojoung , Moon Jun Cheol , Choi Changhyun , Chung Namhyun
Published: August 2020

Wheat yield is decreasing due to climate change, and a method to prevent decreasing yield during drought stress is desirable. In this study, wheat cultivars (Koso and Jokyung) were treated with 15% polyethylene glycol-6000 (PEG) and PEG + Si solution (6.5, 8.7, 13.1 and 26.1 mM). The effect of Si treatment on the alleviation of drought stress was measured using the germination test, shoot relative water content (RWC), seedling stage observation, and quantitative real time polymerase chain reaction (qRT-PCR). The results of root/shoot length ratio and shoot length ratio showed that Si treatment induced the alleviation of drought stress in Jokyung cultivar. The result of qRT-PCR showed the alleviation of drought stress in Koso cultivar. In addition, the results with shoot RWC and seedling stage observation showed that the alleviation effects of Si treatment was observed with both Koso and Jokyung cultivar at the high concentration of Si (26.1 mM). All these results suggest that Si treatment at a high concentration could be employed to alleviate drought stress in wheat.
Interpersonal reactivity index adaptation among expectant seroconcordant couples with HIV in Zambézia Province, Mozambique
Authors: Sack Daniel E. , Frisby Michael B. , Diemer Matthew A. , De Schacht Caroline , Graves Erin , Kipp Aaron M. , Emílio Almiro , Matino Ariano , Barreto Ezequiel , Van Rompaey Sara , Wallston Kenneth A. , Audet Carolyn M.
Published: August 2020

Background

The ability to understand another’s emotions and act appropriately, empathy, is an important mediator of relationship function and health intervention fidelity. We adapted the Interpersonal Reactivity Index (IRI) – an empathy scale – among seroconcordant expectant couples with HIV in the Homens para Saúde Mais (HoPS+) trial – a cluster randomized controlled trial assessing couple-based versus individual treatment on viral suppression – in Zambézia Province, Mozambique.

Methods

Using baseline data from 1332 HoPS+ trial participants (666 couples), an exploratory factor analysis assessed culturally relevant questions from the IRI. Because empathy is interdependent among couples, we validated the results of the exploratory factor analysis using a dyadic confirmatory factor analysis (CFA) with dyadic measurement invariance testing. Finally, we assessed the relationship between scores on our final scale and basic demographic characteristics (sex, age, education, and depression) using t-tests.

Results

We found two subscales: 1) a seven-item cognitive empathy subscale (Cronbach’s alpha 0.78) and 2) a six-item affective empathy subscale (Cronbach’s alpha 0.73). The dyadic CFA found acceptable model fit and metric invariance across partners (Comparative Fit Index (CFI) = 0.914, Tucker Lewis Index = 0.904, Root Mean Squared Error of Approximation = 0.056, ΔCFI = 0.011). We observed higher cognitive (p: 0.012) and affective (p: 0.049) empathy among males and higher cognitive (p: 0.031) and affective (p: 0.030) empathy among younger participants. More educated participants had higher affective empathy (p: 0.017) and depressed participants had higher cognitive empathy (p: < 0.001). This two-subscale, 13-item version of the IRI measures cognitive and affective empathy in HoPS+ trial participants and adults while accounting for the interdependent nature of empathy within partner dyads.

Conclusions

This scale will allow us to assess the interplay between empathy and other psychometric constructs (stigma, social support, etc.) in the HoPS+ trial and how each relates to retention in HIV, adherence to treatment, and prevention of maternal to child HIV transmission. Furthermore, this scale can be adapted for other sub-Saharan African populations, which will allow researchers to better assess HIV-related intervention efficacy.

Trial registration

This study is within the context of the HoPS+ trial, registered at ClinicalTrials.gov as number NCT03149237. Registered May 11, 2017.
Comprehensive analysis of diverse low-grade neuroepithelial tumors with FGFR1 alterations reveals a distinct molecular signature of rosette-forming glioneuronal tumor
Authors: Lucas Calixto-Hope G. , Gupta Rohit , Doo Pamela , Lee Julieann C. , Cadwell Cathryn R. , Ramani Biswarathan , Hofmann Jeffrey W. , Sloan Emily A. , Kleinschmidt-DeMasters Bette K. , Lee Han S. , Wood Matthew D. , Grafe Marjorie , Born Donald , Vogel Hannes , Salamat Shahriar , Puccetti Diane , Scharnhorst David , Samuel David , Cooney Tabitha , Cham Elaine , Jin Lee-way , Khatib Ziad , Maher Ossama , Chamyan Gabriel , Brathwaite Carole , Bannykh Serguei , Mueller Sabine , Kline Cassie N. , Banerjee Anu , Reddy Alyssa , Taylor Jennie W. , Clarke Jennifer L. , Oberheim Bush Nancy Ann , Butowski Nicholas , Gupta Nalin , Auguste Kurtis I. , Sun Peter P. , Roland Jarod L. , Raffel Corey , Aghi Manish K. , Theodosopoulos Philip , Chang Edward , Hervey-Jumper Shawn , Phillips Joanna J. , Pekmezci Melike , Bollen Andrew W. , Tihan Tarik , Chang Susan , Berger Mitchel S. , Perry Arie , Solomon David A.
Published: August 2020

TheFGFR1gene encoding fibroblast growth factor receptor 1 has emerged as a frequently altered oncogene in the pathogenesis of multiple low-grade neuroepithelial tumor (LGNET) subtypes including pilocytic astrocytoma, dysembryoplastic neuroepithelial tumor (DNT), rosette-forming glioneuronal tumor (RGNT), and extraventricular neurocytoma (EVN). These activatingFGFR1alterations in LGNET can include tandem duplication of the exons encoding the intracellular tyrosine kinase domain, in-frame gene fusions most often withTACC1as the partner, or hotspot missense mutations within the tyrosine kinase domain (either at p.N546 or p.K656). However, the specificity of these differentFGFR1events for the various LGNET subtypes and accompanying genetic alterations are not well defined. Here we performed comprehensive genomic and epigenomic characterization on a diverse cohort of 30 LGNET withFGFR1alterations. We identified that RGNT harbors a distinct epigenetic signature compared to other LGNET withFGFR1alterations, and is uniquely characterized byFGFR1kinase domain hotspot missense mutations in combination with eitherPIK3CAorPIK3R1mutation, often with accompanyingNF1orPTPN11mutation. In contrast, EVN harbors its own distinct epigenetic signature and is characterized byFGFR1-TACC1fusion as the solitary pathogenic alteration. Additionally, DNT and pilocytic astrocytoma are characterized by either kinase domain tandem duplication or hotspot missense mutations, occasionally with accompanyingNF1orPTPN11mutation, but lacking the accompanyingPIK3CAorPIK3R1mutation that characterizes RGNT. The glial component of LGNET withFGFR1alterations typically has a predominantly oligodendroglial morphology, and many of the pilocytic astrocytomas withFGFR1alterations lack the biphasic pattern, piloid processes, and Rosenthal fibers that characterize pilocytic astrocytomas withBRAFmutation or fusion. Together, this analysis improves the classification and histopathologic stratification of LGNET withFGFR1alterations.
Multi Region-Based Feature Connected Layer (RB-FCL) of deep learning models for bone age assessment
Authors: Wibisono Ari , Mursanto Petrus
Published: August 2020

Prediction of bone age from an x-ray is one of the methods in the medical field to support predicting endocrine gland disease, growth abnormalities, and genetic disorders. A decision support system to predict the bone age from the x-ray image has been implemented. It utilizes traditional machine learning methods and deep learning. We propose the Region-Based Feature Connected Layer (RB-FCL) from the essential segmented region of hand x-ray. We treat the deep learning models as the feature extraction for each region of the hand x-ray bone. The Feature Connected Layers are the output from the trained important region, such as 1-radius-ulna, 2-carpal, 3-metacarpal, 4-phalanges, and 5-ephypisis. DenseNet121, InceptionV3, and InceptionResNetV2 are the deep learning models that we used to train the critical region. From the evaluation results, the Mean Absolute Error (MAE) results produced is 6.97. This result is better compared to standard deep learning models, which are 9.41.
Trends of Mycobacterium tuberculosis and rifampicin resistance in Adigrat General Hospital, Eastern zone of Tigrai, North Ethiopia
Authors: Abay Getachew Kahsu , Abraha Bahlbi Hailay
Published: August 2020

Background

Tuberculosis is an infectious disease usually caused by Mycobacterium tuberculosis bacteria. The global emergence of mono- or multidrug-resistant tuberculosis and extensively drug-resistant forms of tuberculosis pose a considerable challenge to tuberculosis control programs. There has been no reliable and organized data on trends and drug resistance of Mycobacterium tuberculosis in the study area. Therefore, this study aimed to determine the trends of Mycobacterium tuberculosis and rifampicin resistance in the Adigrat General Hospital, eastern Zone of Tigrai, North Ethiopia.

Methods

A hospital-based retrospective cross-sectional study was conducted at Adigrat General Hospital from January 2015 to 2018.Data was collected retrospectively from the GeneXpert™ TB registration book using a data extraction format. Data was entered into Epi-Info 3.1 and subsequently exported and analyzed using SPSS Version 20.The results were summarized using descriptive statistics, tables, and figures. Bivariate and multi-variant regression analysis was employed to measure the association between dependent and independent variables. P values < 0.05 were considered statistically significant.

Result

A total of 5944 Mycobacterium tuberculosis presumptive patients were included in the study. The majority of the study participants were male (58.1%) with participants’ median age of 40.0 (IQR 26–57) years, the majority were 30–44 years. The overall positive cases of Mycobacterium tuberculosis was 24.3% (1446) with a total of 132 (9.1%) found to be resistant to rifampicin. Of the total confirmed positive cases 8.7% (103/1188) and 11.2% (29/258) were rifampicin resistance of presumptive tuberculosis and presumptive drug resistance tuberculosis patients respectively. Age, the reason for diagnosis, site of presumptive tuberculosis, and/or being HIV infected showed significant association with our dependent variable; however, only age and being HIV infected were associated with rifampicin resistance.

Conclusion

In our study, the overall trends of Mycobacterium tuberculosis and rifampicin resistance were found to be high. Rifampicin resistance is more common in patients with HIV and presumptive drug resistance tuberculosis individuals. Therefore, maximizing early detection of drug-resistant and strengthening tuberculosis infection control activities are recommended to reduce the burden of this contagious and potentially deadly disease.
COVID-19 in adult patients with pre-existing chronic cardiac, respiratory and metabolic disease: a critical literature review with clinical recommendations
Authors: Flaherty Gerard Thomas , Hession Paul , Liew Chee Hwui , Lim Bryan Chang Wei , Leong Tan Kok , Lim Victor , Sulaiman Lokman Hakim
Published: August 2020

Background

A high burden of severe disease and death from the coronavirus disease 2019 (COVID-19) has been consistently observed in older patients, especially those with pre-existing medical co-morbidities. The global pandemic lockdown has isolated many patients with chronic illnesses from their routine medical care. This narrative review article analyses the multitude of issues faced by individuals with underlying medical conditions during the COVID-19 pandemic.

Methods

Sources for this publication were identified through searches of PubMed for articles published between 31st December 2019 and 4th June 2020, using combinations of search terms. Guidelines and updates from reputable agencies were also consulted. Only articles published in the English language were included.

Results

The volume of literature on COVID-19 continues to expand, with 17,845 articles indexed on PubMed by 4th June 2020, 130 of which were deemed particularly relevant to the subject matter of this review. Older patients are more likely to progress to severe COVID-19 disease requiring intensive care unit (ICU) admission. Patients with pre-existing cardiovascular disease, especially hypertension and coronary heart disease, are at greatly increased risk of developing severe and fatal COVID-19 disease. A controversial aspect of the management of COVID-19 disease has been the use of angiotensin-converting enzyme inhibitors and angiotensin receptor blockers. Obese COVID-19 patients are more likely to require complex ICU management. Putative mechanisms of increased COVID-19 disease severity in diabetes include hyperglycaemia, altered immune function, sub-optimal glycaemic control during hospitalisation, a pro-thrombotic and pro-inflammatory state. Patients with mental health disorders are particularly vulnerable to social isolation, and this has been compounded by the suspension of non-emergency care in hospitals around the world, making it difficult for patients with chronic mental illness to attend outpatient appointments.

Conclusions

The global pandemic of COVID-19 disease has had a disproportionately negative impact on patients living with chronic medical illness. Future research should be directed at efforts to protect vulnerable patients from possible further waves of COVID-19 and minimising the negative impact of pandemic mitigation strategies on these individuals.
Public knowledge about Alzheimer disease in Mecca Region, Kingdom of Saudi Arabia: a cross-sectional study
Authors: Alhumaidi Faisal Salem , Siddiqui Muhammad Irfanullah , Altowairqi Abdulaziz Fahad , Alshawkani Hattan Hassan , Babkour Bashar Omar , Alaugla Fahad Khalid
Published: August 2020

Background

Raising the general population knowledge of Alzheimer’s disease is crucial for optimizing care and ultimately enhancing the quality of life of people diagnosed and their caregivers.

Aim

To assess knowledge among the general population in Makkah Region about symptoms, diagnosis, causes, course, life impact, care giving, and management of Alzheimer disease.

Material and methods

A descriptive cross-sectional study was conducted during July to August 2018 in three main cities of Makkah Region, i.e., Makkah, Jeddah, and Taif, Saudi Arabia. Two to three mosques and/or malls were selected randomly from a list of all mosques and malls in each city, and then every fifth subject was selected using a systematic random technique, entering the mall or getting out from the mosques. Both genders, aged 18 years or more and able to understand Arabic were included. Valid and reliable Alzheimer’s Disease Knowledge Scale (ADKS) was used to assess knowledge about the diseases, in addition to socio-demographic characteristics of the participants.

Results

The study included 862 adult participants. Their age ranged between 18 and 65 years with a mean ± standard deviation (SD) of 31.2 ± 10.3 years. History of having a relative with Alzheimer’s disease was mentioned by 20.8% of the participants. Overall, the percentage of total Alzheimer’s disease knowledge score ranged between 26.7 and 100% with a mean of 58.5%, median of 60%, mode of 56.7%, and standard deviation of ± 11.5%. There was a significant positive correlation between participant’s age and their knowledge regarding Alzheimer’s disease (Spearman’s correlation coefficient “r” = 0.099, p = 0.004). The highest known subscale of Alzheimer’s disease was assessment (mean percentage was 62.21%), followed by treatment (62.09), care giving (61.83%) and course of the disease (60.99%) whereas the lowest known subscale was symptoms (53.25%). Participants who reported a history of having a relative with Alzheimer’s disease were more knowledgeable regarding symptoms than those who did not had such history (mean ranks were 470.48 and 421.28, respectively), p = 0.014.

Conclusion

Knowledge of the general population in Makkah Region is deficient, particularly regarding symptoms, risk factors and life impacts. Therefore, health education campaigns are required for general public in this regards.
Prevalence of internal carotid artery morphological variations and its association with cerebrovascular ischemic stroke (hospital-based study)
Authors: AboElfetouh Noha , Khedr Eman , Aboloyoun Hesham , Nageeb Mahmoud , Nasreldein Ahmed
Published: August 2020

Background and objectives

Morphological variations (MV) in the course of the internal carotid artery (ICA) are commonly identified. Their prevalence and relationship with ischemic stroke (IS) remain unclear. The present study attempted to estimate the prevalence and pattern of MV of ICA among Egyptian patients and to detect whether these MV associated with increased risk of IS or not.

Methods

Out of the recruited 550 acute ischemic stroke patients, 102 met the inclusion and exclusion criteria and were included in our study. Each patient was subjected to detailed history including risk factors and clinical assessment using the National Institute of Health Stroke Scale, mRS, and extracranial duplex ultrasound (US) assessment.

Results

Eleven patients out of 102 (10.8%) showed MV in their ICA course, 6 of them were women and 5 were men. These MV were unilateral in 90.9% (10/11) of cases and more in the left ICA (72.7%), while one case (9.1%) showed MV of both ICA. The commonest pattern of MV was tortuosity in 7 cases (63.6%) and kinking in 4 cases (36.4%). The history of previous IS and TIA was recorded in 9.1% of patients with MV in ICA for each group, while the history of IS was recorded in 13.2% of patients without MV and TIA in 4.3% patients without MV in ICA. There were no statistically significant differences between both groups.

Conclusion

The prevalence of MV in the present study is 10.8%. MV are more frequent in women and older patients and are not associated with an increased risk of ischemic stroke.