bluuebunny/crossref_metadata_2025 huggingface dataset:
geneRFinder: gene finding in distinct metagenomic data complexities
Authors: Silva Raíssa , Padovani Kleber , Góes Fabiana , Alves Ronnie
Published: February 2021

Background

Microbes perform a fundamental economic, social, and environmental role in our society. Metagenomics makes it possible to investigate microbes in their natural environments (the complex communities) and their interactions. The way they act is usually estimated by looking at the functions they play in those environments and their responsibility is measured by their genes. The advances of next-generation sequencing technology have facilitated metagenomics research however it also creates a heavy computational burden. Large and complex biological datasets are available as never before. There are many gene predictors available that can aid the gene annotation process though they lack handling appropriately metagenomic data complexities. There is no standard metagenomic benchmark data for gene prediction. Thus, gene predictors may inflate their results by obfuscating low false discovery rates.

Results

We introduce geneRFinder, an ML-based gene predictor able to outperform state-of-the-art gene prediction tools across this benchmark by using only one pre-trained Random Forest model. Average prediction rates of geneRFinder differed in percentage terms by 54% and 64%, respectively, against Prodigal and FragGeneScan while handling high complexity metagenomes. The specificity rate of geneRFinder had the largest distance against FragGeneScan, 79 percentage points, and 66 more than Prodigal. According to McNemar’s test, all percentual differences between predictors performances are statistically significant for all datasets with a 99% confidence interval.

Conclusions

We provide geneRFinder, an approach for gene prediction in distinct metagenomic complexities, available at gitlab.com/r.lorenna/generfinder and https://osf.io/w2yd6/, and also we provide a novel, comprehensive benchmark data for gene prediction—which is based on The Critical Assessment of Metagenome Interpretation (CAMI) challenge, and contains labeled data from gene regions—available at https://sourceforge.net/p/generfinder-benchmark.
Transcriptome analysis of the transdifferentiation of canine BMSCs into insulin producing cells
Authors: Wang Jinglu , Dai Pengxiu , Zou Tong , Lv Yangou , Zhao Wen , Zhang Xinke , Zhang Yihua
Published: February 2021

Background

Bone marrow mesenchymal stem cells are a potential resource for the clinical therapy of certain diseases. Canine, as a companion animal, living in the same space with human, is an ideal new model for human diseases research. Because of the high prevalence of diabetes, alternative transplantation islets resource (i.e. insulin producing cells) for diabetes treatment will be in urgent need, which makes our research on the transdifferentiation of Bone marrow mesenchymal stem cells into insulin producing cells become more important.

Result

In this study, we completed the transdifferentiation process and achieved the transcriptome profiling of five samples with two biological duplicates, namely, “BMSCs”, “islets”, “stage 1”, “stage 2” and “stage 3”, and the latter three samples were achieved on the second, fifth and eighth day of induction. A total of 11,530 differentially expressed transcripts were revealed in the profiling data. The enrichment analysis of differentially expressed genes revealed several signaling pathways that are essential for regulating proliferation and transdifferentiation, including focal adhesion, ECM-receptor interaction, tight junction, protein digestion and absorption, and the Rap1 signaling pathway. Meanwhile, the obtained protein–protein interaction network and functional identification indicating involvement of three genes, SSTR2, RPS6KA6, and VIP could act as a foundation for further research.

Conclusion

In conclusion, to the best of our knowledge, this is the first survey of the transdifferentiation of canine BMSCs into insulin-producing cells according with the timeline using next-generation sequencing technology. The three key genes we pick out may regulate decisive genes during the development of transdifferentiation of insulin producing cells.
Long-term stability of the urogenital microbiota of asymptomatic European women
Authors: Ksiezarek Magdalena , Ugarcina-Perovic Svetlana , Rocha Joana , Grosso Filipa , Peixe Luísa
Published: February 2021

Background

To date, information on healthy female urinary microbiota is available mostly at genus level and at one time point. However, profound species-level characterization of healthy urinary microbiome and its stability over time are essential for further correct interpretation of its role in healthy urogenital tract. In this study, we investigated female urogenital microbiome (FUM) at two timepoints (within 2.5-year interval) in young asymptomatic European women. We used culturomics with accurate isolates’ identification (MALDI-TOF MS and gene markers sequencing) to understand species stability within healthy FUM.

Results

Extended culturomics of voided midstream urine sample pairs revealed a mean Shannon diversity index of 1.25 and mean of 19 species/sample (range 5–39 species; total of 115 species; 1830 isolates). High overall species variability between individuals was captured by beta diversity and a variety of community structure types, with the largest cluster characterized by Lactobacillus crispatus, often in combination with Gardnerella vaginalis or Gardnerella genomospecies 3. Significant FUM composition differences, related to Finegoldia magna and Streptococcus anginosus, according to smoking status were found.

A high species variability within individuals (Shannon index SD > 0.5 in 7 out of 10 sample pairs) with a mean of 29% of shared species (range 9.1–41.7%) was observed. Moreover, 4 out of 10 sample pairs clustered in the same community structure type. The stable FUM sample pairs presented high abundance of Lactobacillus crispatus, Streptococcus agalactiae or Lactobacillus paragasseri and Bifidobacterium spp.. Moreover, Gardnerella vaginalis, Gardnerella genomospecies 3 or Gardnerella swidsinskii were often maintained within individuals in high abundance.

Conclusions

Shift in species composition at two distant timepoints was frequently observed among urogenital microbiome of European asymptomatic women. This suggests possible interchange of particular species in healthy FUM and the existence of multiple health-associated FUM compositions in certain individuals.

Additionally, we provided additional evidence on resilience of particular bacterial communities and identified certain species more prone to persist in urogenital tract.

This study revealed important details on the FUM composition complexity relevant for studies aiming to understand microbiota role in the urogenital tract health and for identification of eubiotic and dysbiotic FUM.
Marker-trait association analysis for drought tolerance in smooth bromegrass
Authors: Saeidnia F. , Majidi M. M. , Mirlohi A.
Published: February 2021

Background

Little information is available on the application of marker-trait association (MTA) analysis for traits related to drought tolerance in smooth bromegrass. The objectives of this study were to identify marker loci associated with important agronomic traits and drought tolerance indices as well as fining stable associations in a diverse panel of polycross derived genotypes of smooth bromegrass. Phenotypic evaluations were performed at two irrigation regimes (normal and deficit irrigation) during 2 years; and association analysis was done with 626 SRAP markers.

Results

The results of population structure analysis identified three main subpopulations possessing significant genetic differences. Under normal irrigation, 68 and 57 marker-trait associations were identified using general linear model (GLM) and mixed linear mode1 (MLM), respectively. While under deficit irrigation, 61 and 54 markers were associated with the genes controlling the studied traits, based on these two models, respectively. Some of the markers were associated with more than one trait. It was revealed that markers Me1/Em5–11, Me1/Em3–15, and Me5/Em4–7 were consistently linked with drought-tolerance indices.

Conclusion

Following marker validation, the MTAs reported in this panel could be useful tools to initiate marker-assisted selection (MAS) and targeted trait introgression of smooth bromegrass under normal and deficit irrigation regimes, and possibly fine mapping and cloning of the underlying genes and QTLs.
The effect of high-dose intramuscular epinephrine on the recovery of spontaneous circulation in an asphyxia‐induced cardiac arrest rat model
Authors: Lim Daesung , Lee Soo Hoon , Kim Dong Hoon , Kang Changwoo , Jeong Jin Hee , Lee Sang Bong
Published: February 2021

Background

Obtaining vascular access can be challenging during resuscitation following cardiac arrest, and it is particularly difficult and time-consuming in paediatric patients. We aimed to compare the efficacy of high-dose intramuscular (IM) versus intravascular (IV) epinephrine administration with regard to the return of spontaneous circulation (ROSC) in an asphyxia-induced cardiac arrest rat model.

Methods

Forty-five male Sprague-Dawley rats were used for these experiments. Cardiac arrest was induced by asphyxia, and defined as a decline in mean arterial pressure (MAP) to 20 mmHg. After asphyxia-induced cardiac arrest, the rats were randomly allocated into one of 3 groups (control saline group, IV epinephrine group, and IM epinephrine group). After 540 s of cardiac arrest, cardiopulmonary resuscitation was performed, and IV saline (0.01 cc/kg), IV (0.01 mg/kg, 1:100,000) epinephrine or IM (0.05 mg/kg, 1:100,000) epinephrine was administered. ROSC was defined as the achievement of an MAP above 40 mmHg for more than 1 minute. Rates of ROSC, haemodynamics, and arterial blood gas analysis were serially observed.

Results

The ROSC rate (61.5%) of the IM epinephrine group was less than that in the IV epinephrine group (100%) but was higher than that of the control saline group (15.4%) (log-rank test). There were no differences in MAP between the two groups, but HR in the IM epinephrine group (beta coefficient = 1.02) decreased to a lesser extent than that in the IV epinephrine group with time.

Conclusions

IM epinephrine induced better ROSC rates compared to the control saline group in asphyxia-induced cardiac arrest, but not compared to IV epinephrine. The IM route of epinephrine administration may be a promising option in an asphyxia-induced cardiac arrest.
A qualitative inquiry of access to and quality of primary healthcare in seven communities in East and West Africa (SevenCEWA): perspectives of stakeholders, healthcare providers and users
Authors: Ameh Soter , Akeem Bolarinwa Oladimeji , Ochimana Caleb , Oluwasanu Abayomi Olabayo , Mohamed Shukri F. , Okello Samson , Muhihi Alfa , Danaei Goodarz
Published: February 2021

Background

Universal health coverage is one of the Sustainable Development Goal targets known to improve population health and reduce financial burden. There is little qualitative data on access to and quality of primary healthcare in East and West Africa. The aim of this study was to describe the viewpoints of healthcare users, healthcare providers and other stakeholders on health-seeking behaviour, access to and quality of healthcare in seven communities in East and West Africa.

Methods

A qualitative study was conducted in four communities in Nigeria and one community each in Kenya, Uganda and Tanzania in 2018. Purposive sampling was used to recruit: 155 respondents (mostly healthcare users) for 24 focus group discussions, 25 healthcare users, healthcare providers and stakeholders for in-depth interviews and 11 healthcare providers and stakeholders for key informant interviews. The conceptual framework in this study combined elements of the Health Belief Model, Health Care Utilisation Model, four ‘As’ of access to care, and pathway model to better understand the a priori themes on access to and quality of primary healthcare as well as health-seeking behaviours of the study respondents. A content analysis of the data was done using MAXQDA 2018 qualitative software to identify these a priori themes and emerging themes.

Results

Access to primary healthcare in the seven communities was limited, especially use of health insurance. Quality of care was perceived to be unacceptable in public facilities whereas cost of care was unaffordable in private facilities. Health providers and users as well as stakeholders highlighted shortage of equipment, frequent drug stock-outs and long waiting times as major issues, but had varying opinions on satisfaction with care. Use of herbal medicines and other traditional treatments delayed or deterred seeking modern healthcare in the Nigerian sites.

Conclusions

There was a substantial gap in primary healthcare coverage and quality in the selected communities in rural and urban East and West Africa. Alternative models of healthcare delivery that address social and health inequities, through affordable health insurance, can be used to fill this gap and facilitate achieving universal health coverage.
Endoscopic transmural drainage is associated with improved outcomes in disconnected pancreatic duct syndrome: a systematic review and meta-analysis
Authors: Chong Eric , Ratnayake Chathura Bathiya , Saikia Samantha , Nayar Manu , Oppong Kofi , French Jeremy J. , Windsor John A. , Pandanaboyana Sanjay
Published: February 2021

Background

Disconnected pancreatic duct syndrome (DPDS) is a complication of acute necrotizing pancreatitis in the neck and body of the pancreas often manifesting as persistent pancreatic fluid collection (PFC) or external pancreatic fistula (EPF). This systematic review and pairwise meta-analysis aimed to review the definitions, clinical presentation, intervention, and outcomes for DPDS.

Methods

The PubMed, EMBASE, MEDLINE, and SCOPUS databases were systematically searched until February 2020 using the PRISMA framework. A meta-analysis was performed to assess the success rates of endoscopic and surgical interventions for the treatment of DPDS. Success of DPDS treatment was defined as long-term resolution of symptoms without recurrence of PFC, EPF, or pancreatic ascites.

Results

Thirty studies were included in the quantitative analysis comprising 1355 patients. Acute pancreatitis was the most common etiology (95.3%, 936/982), followed by chronic pancreatitis (3.1%, 30/982). DPDS commonly presented with PFC (83.2%, 948/1140) and EPF (13.4%, 153/1140). There was significant heterogeneity in the definition of DPDS in the literature. Weighted success rate of endoscopic transmural drainage (90.6%, 95%-CI 81.0–95.6%) was significantly higher than transpapillary drainage (58.5%, 95%-CI 36.7–77.4). Pairwise meta-analysis showed comparable success rates between endoscopic and surgical intervention, which were 82% (weighted 95%-CI 68.6–90.5) and 87.4% (95%-CI 81.2–91.8), respectively (P = 0.389).

Conclusions

Endoscopic transmural drainage was superior to transpapillary drainage for the management of DPDS. Endoscopic and surgical interventions had comparable success rates. The significant variability in the definitions and treatment strategies for DPDS warrant standardisation for further research.
Diagnostic accuracy assessment of molecular prediction model for the risk of NAFLD based on MRI-PDFF diagnosed Chinese Han population
Authors: Zhang Qing , Zhu Yueli , Yu Wanjiang , Xu Zhipeng , Zhao Zhenzhen , Liu Shousheng , Xin Yongning , Lv Kuirong
Published: February 2021

Background

Several molecular prediction models based on the clinical parameters had been constructed to predict and diagnosis the risk of NAFLD, but the accuracy of these molecular prediction models remains need to be verified based on the most accurate NAFLD diagnostic method. The aim of this study was to verify the accuracy of three molecular prediction models Fatty liver index (FLI), NAFLD liver fat score system (NAFLD LFS), and Liver fat (%) in the prediction and diagnosis of NAFLD in MRI-PDFF diagnosed Chinese Han population.

Patients and methods

MRI-PDFF was used to diagnose the hepatic steatosis of all the subjects. Information such as name, age, lifestyle, and major medical histories were collected and the clinical parameters were measured by the standard clinical laboratory techniques. The cut-off values of each model for the risk of NAFLD were calculated based on the MRI-PDFF results. All data were analyzed using the statistical analysis software SPSS 23.0.

Results

A total of 169 subjects were recruited with the matched sex and age. The ROC curves of FLI, NAFLD LFS, and Liver fat (%) models were plotted based on the results of MRI-PDFF. We founded that the accuracy of FLI, NAFLD LFS, and Liver fat (%) models for the prediction and diagnosis of NAFLD were comparative available in Chinese Han population as well as the validity of them in other ethnics and regions.

Conclusions

The molecular prediction models FLI, NAFLD LFS, and Liver fat (%) were comparative available for the prediction and diagnosis of NAFLD in Chinese Han population. MRI-PDFF could be used as the golden standard to develop the new molecular prediction models for the prediction and diagnosis of NAFLD.
A practical laboratory index to predict institutionalization and mortality – an 18-year population-based follow-up study
Authors: Heikkilä Elisa , Salminen Marika , Viljanen Anna , Katajamäki Taina , Koivula Marja-Kaisa , Pulkki Kari , Isoaho Raimo , Kivelä Sirkka-Liisa , Viitanen Matti , Löppönen Minna , Vahlberg Tero , Viikari Laura , Irjala Kerttu
Published: February 2021

Background

Previously, several indexes based on a large number of clinical and laboratory tests to predict mortality and frailty have been produced. However, there is still a need for an easily applicable screening tool for every-day clinical practice.

Methods

A prospective study with 10- and 18-year follow-ups. Fourteen common laboratory tests were combined to an index. Cox regression model was used to analyse the association of the laboratory index with institutionalization and mortality.

Results

The mean age of the participants (n = 1153) was 73.6 (SD 6.8, range 64.0–100.0) years. Altogether, 151 (14.8%) and 305 (29.9%) subjects were institutionalized and 422 (36.6%) and 806 (69.9%) subjects deceased during the 10- and 18-year follow-ups, respectively. Higher LI (laboratory index) scores predicted increased mortality. Mortality rates increased as LI scores increased both in unadjusted and in age- and gender-adjusted models during both follow-ups. The LI did not significantly predict institutionalization either during the 10- or 18-year follow-ups.

Conclusions

A practical index based on routine laboratory tests can be used to predict mortality among older people. An LI could be automatically counted from routine laboratory results and thus an easily applicable screening instrument in clinical settings.
Individualized predictions of early isolated distal deep vein thrombosis in patients with acute ischemic stroke: a retrospective study
Authors: Cheng Hao-Ran , Huang Gui-Qian , Wu Zi-Qian , Wu Yue-Min , Lin Gang-Qiang , Song Jia-Ying , Liu Yun-Tao , Luan Xiao-Qian , Yuan Zheng-Zhong , Zhu Wen-Zong , He Jin-Cai , Wang Zhen
Published: February 2021

Background

Although isolated distal deep vein thrombosis (IDDVT) is a clinical complication for acute ischemic stroke (AIS) patients, very few clinicians value it and few methods can predict early IDDVT. This study aimed to establish and validate an individualized predictive nomogram for the risk of early IDDVT in AIS patients.

Methods

This study enrolled 647 consecutive AIS patients who were randomly divided into a training cohort (n = 431) and a validation cohort (n = 216). Based on logistic analyses in training cohort, a nomogram was constructed to predict early IDDVT. The nomogram was then validated using area under the receiver operating characteristic curve (AUROC) and calibration plots.

Results

The multivariate logistic regression analysis revealed that age, gender, lower limb paralysis, current pneumonia, atrial fibrillation and malignant tumor were independent risk factors of early IDDVT; these variables were integrated to construct the nomogram. Calibration plots revealed acceptable agreement between the predicted and actual IDDVT probabilities in both the training and validation cohorts. The nomogram had AUROC values of 0.767 (95% CI: 0.742–0.806) and 0.820 (95% CI: 0.762–0.869) in the training and validation cohorts, respectively. Additionally, in the validation cohort, the AUROC of the nomogram was higher than those of the other scores for predicting IDDVT.

Conclusions

The present nomogram provides clinicians with a novel and easy-to-use tool for the prediction of the individualized risk of IDDVT in the early stages of AIS, which would be helpful to initiate imaging examination and interventions timely.
The fluid management and hemodynamic characteristics of PiCCO employed on young children with severe hand, foot, and mouth disease—a retrospective study
Authors: Wang Fengyun , Qiang Xinhua , Jiang Suhua , Shao Jingsong , Fang Bin , Zhou Lixin
Published: February 2021

Background

Hand, foot, and mouth disease (HFMD) is an acute infectious disease caused by human enterovirus 71 (EV71), coxsackievirus, or echovirus, which is particularly common in preschool children. Severe HFMD is prone to cause pulmonary edema before progressing to respiratory and circulatory failure; thus hemodynamic monitoring and fluid management are important to the treatment process.

Methods

We did a review of young patients who had been successfully treated in our department for severe HFMD, which had been caused by EV71. A total of 20 patients met the inclusion criteria. Eight cases were monitored by the pulse indicator continuous cardiac output (PiCCO) technique, and fluid management was administered according to its parameters. With regard to the treatment with PiCCO monitoring, patients were divided into two groups: the PiCCO group (8 patients) and the control group (12 patients). The groups were then compared comprehensively to evaluate whether PiCCO monitoring could improve patients’ clinical outcomes.

Results

After analysis, the findings informed that although PiCCO failed to shorten the length of ICU stay, reduce the days of vasoactive drug usage, or lower the number of cases which required mechanical ventilation, PiCCO did reduce the incidence of fluid overload (p = 0.085) and shorten the days of mechanical ventilation (p = 0.028). After effective treatment, PiCCO monitoring indicated that the cardiac index (CI) increased gradually(p < 0.0001), in contrast to their pulse (P, p < 0.0001), the extra vascular lung water index (EVLWI, p < 0.0001), the global end diastolic volume index (GEDVI, p = 0.0043), and the systemic vascular resistance index (SVRI, p < 0.0001), all of which decreased gradually.

Conclusion

Our study discovered that PiCCO hemodynamic monitoring in young children with severe HFMD has some potential benefits, such as reducing fluid overload and the duration of mechanical ventilation. However, whether it can ameliorate the severity of the disease, reduce mortality, or prevent multiple organ dysfunction remain to be further investigated.
A novel fluorescent cardiac imaging system for preclinical intraoperative angiography
Authors: Mashalchi Sara , Pahlavan Sara , Hejazi Marjaneh
Published: February 2021

Background

Intraoperative coronary angiography can tremendously reduce early coronary bypass graft failures. Fluorescent cardiac imaging provides an advanced method for intraoperative observation and real-time quantitation of blood flow with high resolution.

Methods

We devised a system comprised of an LED light source, special filters, lenses and a detector for preclinical coronary artery angiography. The optical setup was implemented by using two achromatic doublet lenses, two positive meniscus lenses, a band-pass filter, a pinhole and a CCD sensor. The setup was optimized by Zemax software. Optical design was further challenged to obtain more parallel light beams, less diffusion and higher resolutions to levels as small as arterioles. Ex vivo rat hearts were prepared and coronary arteries were retrogradely perfused by indocyanine green (ICG). Video angiography was employed to assess blood flow and plot time-dependent fluorescence intensity curve (TIC). Quantitation of blood flow was performed by calculating either the gradient of TIC or area under curve. The correlation between blood flow and each calculated parameters was assessed and used to evaluate the quality of flow.

Results

High-resolution images of flow in coronary arteries were obtained as precise as 62 µm vessel diameter, by our custom-made ICG angiography system. The gradient of TIC was 3.4–6.3 s−1, while the area under curve indicated 712–1282 s values which ultimately gained correlation coefficients of 0.9938 and 0.9951 with relative blood flow, respectively.

Conclusion

The present ICG angiography system may facilitate evaluation of blood flow in animal studies of myocardial infarction and coronary artery grafts intraoperatively.
Low plasma magnesium concentration and future abdominal aortic calcifications in moderate chronic kidney disease
Authors: ter Braake Anique D. , Govers Larissa P. , Peeters Mieke J. , van Zuilen Arjan D. , Wetzels Jack F. M. , Blankenstijn Peter J. , Hoenderop Joost G. J. , de Baaij Jeroen H. F. , van den Brand Jan A. J. G. ,   For the MASTERPLAN study group
Published: February 2021

Background

Higher plasma magnesium concentrations are associated with reduced cardiovascular disease risk in chronic kidney disease (CKD) patients. The importance of plasma magnesium concentration for vascular calcification in earlier stages of CKD remains underexplored. This study investigated whether plasma magnesium is a determinant for the presence and severity of vascular calcification in moderate CKD.

Methods

Retrospective analysis was performed using abdominal aortic calcification (AAC) scores in 280 patients with stage 3 and 4 CKD enrolled in the MASTERPLAN trial. Lateral abdominal X-ray was used to evaluate AAC. Plasma magnesium concentration were measured over time. A zero-inflated Poisson model determined the association between plasma magnesium concentration and AAC.

Results

79 out of 280 patients did not have AAC, and in patients with AAC the median calcification score was 3.5 (interquartile range: 0.0–8.6). The mean plasma magnesium concentration was 0.76 ± 0.10 mmol/L at baseline. A 0.1 mmol/L higher plasma magnesium concentration was associated with lower AAC of 0.07 point (95% CI -0.28 – 0.14). A 0.1 mmol/L higher plasma magnesium lowered the odds of detecting any AAC by 30% (OR = 0.63; 95% CI 0.29–1.37). After 1 year and 4 years (at time of X-ray) of follow-up this association was attenuated (OR = 0.93; 95% CI 0.61–1.43 and 0.93; 95% CI 0.60–1.45, respectively). None of these associations reached statistical significance.

Conclusions

Plasma magnesium concentration at baseline is not associated with the risk for future AAC. Interventions increasing magnesium to avoid vascular calcification may have greatest potential in early CKD stages prior to onset of vascular calcification.
Clinically accessible neuroimaging predictors of post-stroke neurocognitive disorder: a prospective observational study
Authors: Schellhorn Till , Aamodt Eva Birgitte , Lydersen Stian , Aam Stina , Wyller Torgeir Bruun , Saltvedt Ingvild , Beyer Mona Kristiansen
Published: February 2021

Background

Neurocognitive disorder (NCD) is common in stroke survivors. We aimed to identify clinically accessible imaging markers of stroke and chronic pathology that are associated with early post-stroke NCD.

Methods

We included 231 stroke survivors from the “Norwegian Cognitive Impairment after Stroke (Nor-COAST)” study who underwent a standardized cognitive assessment 3 months after the stroke. Any NCD (mild cognitive impairment and dementia) and major NCD (dementia) were diagnosed according to “Diagnostic and Statistical Manual of Mental Disorders (DSM-5)” criteria. Clinically accessible imaging findings were analyzed on study-specific brain MRIs in the early phase after stroke. Stroke lesion volumes were semi automatically quantified and strategic stroke locations were determined by an atlas based coregistration. White matter hyperintensities (WMH) and medial temporal lobe atrophy (MTA) were visually scored. Logistic regression was used to identify neuroimaging findings associated with major NCD and any NCD.

Results

Mean age was 71.8 years (SD 11.1), 101 (43.7%) were females, mean time from stroke to imaging was 8 (SD 16) days. At 3 months 63 (27.3%) had mild NCD and 65 (28.1%) had major NCD. Any NCD was significantly associated with WMH pathology (odds ratio (OR) = 2.73 [1.56 to 4.77],p = 0.001), MTA pathology (OR = 1.95 [1.12 to 3.41],p = 0.019), and left hemispheric stroke (OR = 1.8 [1.05 to 3.09],p = 0.032). Major NCD was significantly associated with WMH pathology (OR = 2.54 [1.33 to 4.84],p = 0.005) and stroke lesion volume (OR (per ml) =1.04 [1.01 to 1.06],p = 0.001).

Conclusion

WMH pathology, MTA pathology and left hemispheric stroke were associated with the development of any NCD. Stroke lesion volume and WMH pathology were associated with the development of major NCD 3 months after stroke. These imaging findings may be used in the routine clinical setting to identify patients at risk for early post-stroke NCD.

Trial registration

ClinicalTrials.gov,NCT02650531, Registered 8 January 2016 – Retrospectively registered.
Survival analysis of elderly patients over 65 years old with stage II/III gastric cancer treated with adjuvant chemotherapy after laparoscopic D2 gastrectomy: a retrospective cohort study
Authors: Liang Yanrui , Zhao Liying , Chen Hao , Lin Tian , Chen Tao , Zhao Mingli , Hu Yanfeng , Yu Jiang , Liu Hao , Li Guoxin
Published: February 2021

Background

The benefits of adjuvant chemotherapy for elderly patients with gastric cancer (GC) remain unknown because elderly patients are underrepresented in most clinical trials. This study aimed to evaluate the effectiveness and complications of adjuvant chemotherapy in patients > 65 years of age after laparoscopic D2 gastrectomy.

Methods

This was a single-center retrospective cohort study of elderly patients (> 65 years) with stage II/III GC who underwent curative laparoscopic D2 gastrectomy with R0 resection between 2004 and 2018. The adjuvant chemotherapy regimens included monotherapy (oral capecitabine) and doublet chemotherapy (oral capecitabine plus intravenous oxaliplatin [XELOX] or intravenous oxaliplatin, leucovorin, and 5-fluorouracil [FOLFOX]). The data were retrieved from a prospectively registered database maintained at the Department of General Surgery in Nanfang Hospital, China. The patients were divided as surgery alone and surgery plus adjuvant chemotherapy (chemo group). The overall survival (OS), disease-free survival (DFS), chemotherapy duration, and toxicity were examined.

Results

There were 270 patients included: 169 and 101 in the surgery and chemo groups, respectively. There were 10 (10/101) and six (6/101) patients with grade 3+ non-hematological and hematological adverse events. The 1−/3−/5-year OS rates of the surgery group were 72.9%/51.8%/48.3%, compared with 90.1%/66.4%/48.6% for the chemo group (log-rank test: P = 0.018). For stage III patients, the 1−/3−/5-year OS rates of the surgery group were 83.7%/40.7%/28.7%, compared with 89.9%/61.2%/43.6% for the chemo group (log-rank test: P = 0.015). Adjuvant chemotherapy was significantly associated with higher OS (HR = 0.568, 95%CI: 0.357–0.903, P = 0.017) and DFS (HR = 0.511, 95%CI: 0.322–0.811, P = 0.004) in stage III patients.

Conclusions

This study suggested that adjuvant chemotherapy significantly improves OS and DFS compared with surgery alone in elderly patients with stage III GC after D2 laparoscopic gastrectomy, with a tolerable adverse event profile.
Haem relieves hyperoxia-mediated inhibition of HMEC-1 cell proliferation, migration and angiogenesis by inhibiting BACH1 expression
Authors: Jian Lan , Mei Yang , Xing Chen , Rongdi Yuan
Published: February 2021

Background

Hyperoxia-mediated inhibition of vascular endothelial growth factor (VEGF) in the retina is the main cause of impeded angiogenesis during phase I retinopathy of prematurity (ROP). Human retinal angiogenesis involves the proliferation, migration and vessel-forming ability of microvascular endothelial cells. Previous studies have confirmed that BTB and CNC homology l (BACH1) can inhibit VEGF and angiogenesis, while haem can specifically degrade BACH1. However, the effect of haem on endothelial cells and ROP remains unknown.

Methods

In this report, we established a model of the relative hyperoxia of phase I ROP by subjecting human microvascular endothelial cells (HMEC-1) to 40% hyperoxia. Haem was added, and its effects on the growth and viability of HMEC-1 cells were evaluated. Cell counting kit 8 (CCK8) and 5-ethynyl-2′-deox-yuridine (EdU) assays were used to detect proliferation, whereas a wound healing assay and Matrigel cultures were used to detect the migration and vessel-forming ability, respectively. Western blot (WB) and immunofluorescence (IF) assays were used to detect the relative protein levels of BACH1 and VEGF.

Results

HMEC-1 cells could absorb extracellular haem under normoxic or hyperoxic conditions. The proliferation, migration and angiogenesis abilities of HMEC-1 cells were inhibited under hyperoxia. Moderate levels of haem can promote endothelial cell proliferation, while 20 μM haem could inhibit BACH1 expression, promote VEGF expression, and relieve the inhibition of proliferation, migration and angiogenesis in HMEC-1 cells induced by hyperoxia.

Conclusions

Haem (20 μM) can relieve hyperoxia-induced inhibition of VEGF activity in HMEC-1 cells by inhibiting BACH1 and may be a potential medicine for overcoming stunted retinal angiogenesis induced by relative hyperoxia in phase I ROP.
A rare case of unilateral Cogan’s anterior internuclear ophthalmoplegia, upgaze palsy and ataxia caused by dorsal tegmentum lesion at pontomesencephalic junction
Authors: Wai Yong Zheng , Ng Qi Xiong , Lim Tsu Hong , Lim Lik Thai
Published: February 2021

Background

Cogan’s anterior internuclear ophthalmoplegia (INO) is characterized by INO with inability to converge and commonly thought to be due to rostral midbrain lesion. A lesion outside midbrain that causes unilateral Cogan’s anterior INO combined with upgaze palsy and ataxia are rarely described.

Case presentation

A 67-year old male presented with left Cogan’s anterior internuclear ophthalmoplegia (INO), left appendicular ataxia and bilateral upgaze palsy. A Magnetic Resonance Imaging (MRI) and Magnetic Resonance Angiography (MRA) brain showed a left dorsal tegmental infarct at the level of pontomesencephalic junction.

Conclusions

This case highlights the clinical importance of Cogan’s anterior INO in combination with upgaze palsy and ataxia, and report possible site of lesion in patients with such constellation. Clinicians should consider looking for cerebellar signs in cases of Cogan’s anterior INO, apart from just considering localizing the lesion at the midbrain.
Combined pars plana glaucoma drainage device placement and vitrectomy using a vitrectomy sclerotomy site for tube placement: a case series
Authors: Chang Enchi Kristina , Gupta Sanchay , Chachanidze Marika , Miller John B. , Chang Ta Chen , Solá-Del Valle David A.
Published: February 2021

Purpose

The purpose of this study is to report the safety and efficacy of pars plana glaucoma drainage devices with pars plana vitrectomy using one of the vitrectomy sclerotomy sites for tube placement in patients with refractory glaucoma.

Methods

Retrospective case series of 28 eyes of 28 patients who underwent combined pars plana glaucoma drainage device and pars plana vitrectomy between November 2016 and September 2019 at Massachusetts Eye and Ear. Main outcome measures were intraocular pressure (IOP), glaucoma medication burden, best corrected visual acuity, and complications. Statistical tests were performed with R and included Kaplan-Meier analyses, Wilcoxon paired signed-rank tests, and Fisher tests.

Results

Mean IOP decreased from 22.8 mmHg to 11.8 mmHg at 1.5 years (p = 0.002), and mean medication burden decreased from 4.3 to 2.1 at 1.5 years (p = 0.004). Both IOP and medication burden were significantly lower at all follow-up time points. The probability of achieving 5 < IOP ≤ 18 mmHg with at least 20% IOP reduction from preoperative levels was 86.4% at 1 year and 59.8% at 1.5 years. At their last visit, three eyes (10.7%) achieved complete success with IOP reduction as above without medications, and 14 eyes (50.0%) achieved qualified success with medications. Hypotony was observed in 1 eye (3.6%) prior to 3 months postoperatively and 0 eyes after 3 months. Visual acuity was unchanged or improved in 23 eyes (82.1%) at their last follow-up. Two patients had a visual acuity decrease of > 2 lines. Two eyes required subsequent pars plana vitrectomies for tube obstruction, and one eye had transient hypotony.

Conclusions

The results of pars plana glaucoma drainage device and pars plana vitrectomy using one of the vitrectomy sclerotomy sites for tube placement are promising, resulting in significant IOP and medication-burden reductions through postoperative year 1.5 without additional risk of postoperative complications. Inserting glaucoma drainage devices into an existing vitrectomy sclerotomy site may potentially save surgical time by obviating the need to create another sclerotomy for tube placement and suture one of the vitrectomy ports.
Electrocardiographic pattern of apparently healthy African adolescent athletes in Nigeria
Authors: Sokunbi Ogochukwu J. , Okoromah Christy A. N. , Ekure Ekanem N. , Olawale Olajide A. , Eke Wuraola S.
Published: February 2021

Background

Strategies to prevent sudden cardiac death (SCD) among young athletes have become topical worldwide and unrecognized cardiac pathology has been identified as a leading cause. Black ethnicity has been reported as an independent predictor of abnormal electrocardiography (ECG) findings among athletes and the frequency and significance of training-related ECG findings versus findings suggestive of an underlying pathology in the young African athletes is crucial.

Methods

This cross sectional study aimed to determine the prevalence and distribution of ECG patterns in young athletes and controls. A total of 360 participants (180 athletes and 180 controls) were recruited from six secondary schools in Lagos, Nigeria between November 2014 and July 2015. Evaluation included interviewer-administered questionnaires for relevant history, physical examination and resting 12 - lead ECG for each participant.

Results

Abnormal ECG patterns were found in 48.3% of athletes and 35.6% of controls. Training-related ECG findings occurred in 33.3% of athletes and 18.3% of controls. Athletes and controls had 7.7% prevalence of training un-related ECG patterns respectively. Left ventricular hypertrophy was the most common ECG finding among the athletes and male athletes had a higher prevalence of ECG abnormalities compared to females.

Conclusion

Adolescent athletes in Nigeria have a high prevalence of training-related ECG patterns and athletes and non-athletes alike have similar proportions of ECG findings suggestive of underlying structural heart disease. Cardiovascular evaluation including ECG should be performed for young athletes prior to competition at any level and should also be considered as part of pre-school entry assessment for all children.
Association of osteoporosis and varus inclination of the tibial plateau in postmenopausal women with advanced osteoarthritis of the knee
Authors: Wang Shun-Ping , Wu Po-Kuan , Lee Cheng-Hung , Shih Cheng-Min , Chiu Yung-Cheng , Hsu Cheng-En
Published: February 2021

Background

Although varus inclination of the tibial plateau has increasingly been recognized as a major risk factor in the progression of Osteoarthritis of the knee (OA knee), little attention has been placed on the development of the varus inclination of the tibial plateau. Osteoporosis is a disease characterized by low bone mass and may increase the risk of a stress fracture in the proximal tibia. To date, risk factors for varus inclination of the tibial plateau are rarely reported. In this study, we investigated Bone Mineral Density (BMD) as a risk factor of varus inclination of the tibial plateau in postmenopausal women with advanced OA knee.

Methods

A total of 90 postmenopausal women with varus OA knee who had received a total knee arthroplasty in our department between January 2016 and December 2019 were reviewed. Certain factors may correlate to inclination of the tibial plateau (Medial Tibial Plateau Angle, MTPA), including age, operation side, Kellgren-Lawrence grade of OA knee, BMD, Body Mass Index (BMI), Lateral Distal Femur Angle (LDFA), lower extremity alignment (Hip-Knee-Ankle angle, HKAA), and history of both spinal compression fracture and hip fracture were collected and analyzed.

Results

Osteoporosis, lower extremity varus malalignment and age were significantly associated with varus inclination of the tibial plateau (MTPA) (P = 0.15, 0.013 and 0.033 respectively). For patients with a lower extremity varus malalignment (HKAA < 175°), osteoporosis (T-score ≤ -2.5) was significantly associated with inclination of the tibial plateau. For patients with a normal lower extremity alignment (HKAA ≥ 175°), no significant association was found between osteoporosis (T-score ≤ -2.5) and varus inclination of the tibial plateau.

Conclusions

Osteoporosis, lower extremity varus malalignment and age are major risk factors for inclination of the tibial plateau in postmenopausal women with OA knee. More attention needs to be given to the progression of varus OA knee in postmenopausal women who simultaneously has osteoporosis and lower extremity varus malalignment.
Comprehensive analysis of tumour mutational burden and its clinical significance in prostate cancer
Authors: Wang Lijuan , Pan Shucheng , Zhu Binbin , Yu Zhenliang , Wang Wei
Published: February 2021

Background

The tumorigenesis of prostate cancer involves genetic mutations. Tumour mutational burden (TMB) is an emerging biomarker for predicting the efficacy of immunotherapy.

Results

Single-nucleotide polymorphisms were the most common variant type, and C>T transversion was the most commonly presented type of single-nucleotide variant. The high-TMB group had lower overall survival (OS) than the low-TMB group. TMB was associated with age, T stage and N stage. Functional enrichment analysis of differentially expressed genes (DEGs) showed that they are involved in pathways related to the terms spindle, chromosomal region, nuclear division, chromosome segregation, cell cycle, oocyte meiosis and other terms associated with DNA mutation and cell proliferation. Six hub genes, PLK1, KIF2C, MELK, EXO1, CEP55 and CDK1, were identified. All the genes were associated with disease-free survival, and CEP55 and CDK1 were associated with OS.

Conclusions

The present study provides a comprehensive analysis of the significance of TMB and DEGs and infiltrating immune cells related to TMB, which provides helpful information for exploring the significance of TMB in prostate cancer.
Biomechanical properties of the bone during implant placement
Authors: Nagy Ádám László , Tóth Zsolt , Tarjányi Tamás , Práger Nándor Tamás , Baráth Zoltán Lajos
Published: February 2021

Background

In this research the biomechanical properties of a bone model was examined. Porcine ribs are used as experimental model. The objective of this research was to investigate and compare the biomechanical properties of the bone model before and after implant placement.

Methods

The bone samples were divided in three groups, Group 1 where ALL-ON-FOUR protocol was used during pre-drilling and placing the implants, Group 2 where ALL-ON-FOUR protocol was used during pre-drilling, and implants were not placed, and Group 3 consisting of intact bones served as a control group. Static and dynamic loading was applied for examining the model samples. Kruskal–Wallis statistical test and as a post-hoc test Mann–Whitney U test was performed to analyze experimental results.

Results

According to the results of the static loading, there was no significant difference between the implanted and original ribs, however, the toughness values of the bones decreased largely on account of predrilling the bones. The analysis of dynamic fatigue measurements by Kruskal–Wallis test showed significant differences between the intact and predrilled bones.

Conclusion

The pre-drilled bone was much weaker in both static and dynamic tests than the natural or implanted specimens. According to the results of the dynamic tests and after a certain loading cycle the implanted samples behaved the same way as the control samples, which suggests that implantation have stabilized the skeletal bone structure.
Three-dimensional analysis of the root canal preparation with Reciproc Blue®, WaveOne Gold® and XP EndoShaper®: a new method in vivo
Authors: Caviedes-Bucheli Javier , Rios-Osorio Nestor , Usme Diana , Jimenez Cristian , Pinzon Adriana , Rincón Jorge , Azuero-Holguin María M. , Zubizarreta-Macho Alvaro , Gomez-Sosa Jose F. , Munoz Hugo R.
Published: February 2021

Background

The purpose of this study was to evaluate the changes in canal volume after root canal preparation in vivo with 3 different single-file techniques (Reciproc-Blue®, WaveOne-Gold® and XP-EndoShaper®), with a new method using CBCT and 3D reconstruction.

Methods

In this prospective study, thirty human lower premolars from healthy patients were used, in which extraction was indicated for orthodontic reasons. All the teeth used were caries- and restoration-free with complete root development, without signs of periodontal disease or traumatic occlusion, and with only one straight canal (up to 25º curvature). Teeth were randomly divided into three different groups: Reciproc-Blue, WaveOne-Gold and XP-EndoShaper. CBCT scans before root canal preparation were used to create a 3D reconstruction with RHINOCEROS 5.0 software to assess the initial canal volume, and then compared with 3D reconstructions after canal preparation to measure the increase in canal volume. Student’s t test for paired data were used to determine statistically significant differences between the before and after canal volumes. Anova test was used to determine statistically significant differences in the percentage of canal volume increase between the groups and Tukey's post-hoc test were used to paired comparison.

Results

Reciproc-Blue showed the higher increase in canal volume, followed by WaveOne-Gold and XP-EndoShaper (p = 0.003). XP-EndoShaper did not show a statistically significant increase in canal volume after root canal preparation (p = 0.06).

Conclusion

With this model, Reciproc-Blue showed higher increase in root canal volume, followed by WaveOne-Gold, while XP-EndoShaper did not significantly increase root canal volume during preparation.