bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving protein domain classification for third-generation sequencing reads using deep learning
Authors: Du Nan , Shang Jiayu , Sun Yanni
Published: April 2021

Background

With the development of third-generation sequencing (TGS) technologies, people are able to obtain DNA sequences with lengths from 10s to 100s of kb. These long reads allow protein domain annotation without assembly, thus can produce important insights into the biological functions of the underlying data. However, the high error rate in TGS data raises a new challenge to established domain analysis pipelines. The state-of-the-art methods are not optimized for noisy reads and have shown unsatisfactory accuracy of domain classification in TGS data. New computational methods are still needed to improve the performance of domain prediction in long noisy reads.

Results

In this work, we introduce ProDOMA, a deep learning model that conducts domain classification for TGS reads. It uses deep neural networks with 3-frame translation encoding to learn conserved features from partially correct translations. In addition, we formulate our problem as an open-set problem and thus our model can reject reads not containing the targeted domains. In the experiments on simulated long reads of protein coding sequences and real TGS reads from the human genome, our model outperforms HMMER and DeepFam on protein domain classification.

Conclusions

In summary, ProDOMA is a useful end-to-end protein domain analysis tool for long noisy reads without relying on error correction.
Development and validation of genome-wide InDel markers with high levels of polymorphism in bitter gourd (Momordica charantia)
Authors: Cui Junjie , Peng Jiazhu , Cheng Jiaowen , Hu Kailin
Published: April 2021

Background

The preferred choice for molecular marker development is identifying existing variation in populations through DNA sequencing. With the genome resources currently available for bitter gourd (Momordica charantia), it is now possible to detect genome-wide insertion-deletion (InDel) polymorphisms among bitter gourd populations, which guides the efficient development of InDel markers.

Results

Here, using bioinformatics technology, we detected 389,487 InDels from 61 Chinese bitter gourd accessions with an average density of approximately 1298 InDels/Mb. Then we developed a total of 2502 unique InDel primer pairs with a polymorphism information content (PIC) ≥0.6 distributed across the whole genome. Amplification of InDels in two bitter gourd lines ‘47–2–1-1-3’ and ‘04–17,’ indicated that the InDel markers were reliable and accurate. To highlight their utilization, the InDel markers were employed to construct a genetic map using 113 ‘47–2–1-1-3’ × ‘04–17’ F2 individuals. This InDel genetic map of bitter gourd consisted of 164 new InDel markers distributed on 15 linkage groups with a coverage of approximately half of the genome.

Conclusions

This is the first report on the development of genome-wide InDel markers for bitter gourd. The validation of the amplification and genetic map construction suggests that these unique InDel markers may enhance the efficiency of genetic studies and marker-assisted selection for bitter gourd.
Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics
Authors: Karp Peter D. , Midford Peter E. , Caspi Ron , Khodursky Arkady
Published: April 2021

Background

Enrichment or over-representation analysis is a common method used in bioinformatics studies of transcriptomics, metabolomics, and microbiome datasets. The key idea behind enrichment analysis is: given a set of significantly expressed genes (or metabolites), use that set to infer a smaller set of perturbed biological pathways or processes, in which those genes (or metabolites) play a role. Enrichment computations rely on collections of defined biological pathways and/or processes, which are usually drawn from pathway databases. Although practitioners of enrichment analysis take great care to employ statistical corrections (e.g., for multiple testing), they appear unaware that enrichment results are quite sensitive to the pathway definitions that the calculation uses.

Results

We show that alternative pathway definitions can alter enrichmentp-values by up to nine orders of magnitude, whereas statistical corrections typically alter enrichmentp-values by only two orders of magnitude. We present multiple examples where the smaller pathway definitions used in the EcoCyc database produces stronger enrichmentp-values than the much larger pathway definitions used in the KEGG database; we demonstrate that to attain a given enrichmentp-value, KEGG-based enrichment analyses require 1.3–2.0 times as many significantly expressed genes as does EcoCyc-based enrichment analyses. The large pathways in KEGG are problematic for another reason: they blur together multiple (as many as 21) biological processes. When such a KEGG pathway receives a high enrichmentp-value, which of its component processes is perturbed is unclear, and thus the biological conclusions drawn from enrichment of large pathways are also in question.

Conclusions

The choice of pathway database used in enrichment analyses can have a much stronger effect on the enrichment results than the statistical corrections used in these analyses.
Transcriptomic, proteomic and ultrastructural studies on salinity-tolerant Aedes aegypti in the context of rising sea levels and arboviral disease epidemiology
Authors: Ramasamy Ranjan , Thiruchenthooran Vaikunthavasan , Jayadas Tibutius T. P. , Eswaramohan Thampoe , Santhirasegaram Sharanga , Sivabalakrishnan Kokila , Naguleswaran Arunasalam , Uzest Marilyne , Cayrol Bastien , Voisin Sebastien N. , Bulet Philippe , Surendran Sinnathamby N.
Published: April 2021

Background

Aedes aegyptimosquito, the principal global vector of arboviral diseases, lays eggs and undergoes larval and pupal development to become adult mosquitoes in fresh water (FW). It has recently been observed to develop in coastal brackish water (BW) habitats of up to 50% sea water, and such salinity tolerance shown to be an inheritable trait. Genomics of salinity tolerance inAe. aegyptihas not been previously studied, but it is of fundamental biological interest and important for controlling arboviral diseases in the context of rising sea levels increasing coastal ground water salinity.

Results

BW- and FW-Ae. aegyptiwere compared by RNA-seq analysis on the gut, anal papillae and rest of the carcass in fourth instar larvae (L4), proteomics of cuticles shed when L4 metamorphose into pupae, and transmission electron microscopy of cuticles in L4 and adults. Genes for specific cuticle proteins, signalling proteins, moulting hormone-related proteins, membrane transporters, enzymes involved in cuticle metabolism, and cytochrome P450 showed different mRNA levels in BW and FW L4 tissues. The salinity-tolerantAe. aegyptiwere also characterized by altered L4 cuticle proteomics and changes in cuticle ultrastructure of L4 and adults.

Conclusions

The findings provide new information on molecular and ultrastructural changes associated with salinity adaptation in FW mosquitoes. Changes in cuticles of larvae and adults of salinity-tolerantAe. aegyptiare expected to reduce the efficacy of insecticides used for controlling arboviral diseases. Expansion of coastal BW habitats and their neglect for control measures facilitates the spread of salinity-tolerantAe. aegyptiand genes for salinity tolerance. The transmission of arboviral diseases can therefore be amplified in multiple ways by salinity-tolerantAe. aegyptiand requires appropriate mitigating measures. The findings inAe. aegypti have attendant implications for the development of salinity tolerance in other fresh water mosquito vectors and the diseases they transmit.
Impact of comorbidity assessment methods to predict non-cancer mortality risk in cancer patients: a retrospective observational study using the National Health Insurance Service claims-based data in Korea
Authors: Lee Sanghee , Chang Yoon Jung , Cho Hyunsoon
Published: April 2021

Background

Cancer patients’ prognoses are complicated by comorbidities. Prognostic prediction models with inappropriate comorbidity adjustments yield biased survival estimates. However, an appropriate claims-based comorbidity risk assessment method remains unclear. This study aimed to compare methods used to capture comorbidities from claims data and predict non-cancer mortality risks among cancer patients.

Methods

Data were obtained from the National Health Insurance Service-National Sample Cohort database in Korea; 2979 cancer patients diagnosed in 2006 were considered. Claims-based Charlson Comorbidity Index was evaluated according to the various assessment methods: different periods in washout window, lookback, and claim types. The prevalence of comorbidities and associated non-cancer mortality risks were compared. The Cox proportional hazards models considering left-truncation were used to estimate the non-cancer mortality risks.

Results

The prevalence of peptic ulcer, the most common comorbidity, ranged from 1.5 to 31.0%, and the proportion of patients with ≥1 comorbidity ranged from 4.5 to 58.4%, depending on the assessment methods. Outpatient claims captured 96.9% of patients with chronic obstructive pulmonary disease; however, they captured only 65.2% of patients with myocardial infarction. The different assessment methods affected non-cancer mortality risks; for example, the hazard ratios for patients with moderate comorbidity (CCI 3–4) varied from 1.0 (95% CI: 0.6–1.6) to 5.0 (95% CI: 2.7–9.3). Inpatient claims resulted in relatively higher estimates reflective of disease severity.

Conclusions

The prevalence of comorbidities and associated non-cancer mortality risks varied considerably by the assessment methods. Researchers should understand the complexity of comorbidity assessments in claims-based risk assessment and select an optimal approach.
Is mass screening for coeliac disease a wise use of resources? A health economic evaluation
Authors: Norström Fredrik , Myléus Anna , Nordyke Katrina , Carlsson Annelie , Högberg Lotta , Sandström Olof , Stenhammar Lars , Ivarsson Anneli , Lindholm Lars
Published: April 2021

Background

Living with undiagnosed symptomatic coeliac disease is connected with deteriorated health, and persons with coeliac disease often wait a long time for their diagnosis. A mass screening would lower the delay, but its cost-effectiveness is still unclear. Our aim was to determine the cost-effectiveness of a coeliac disease mass screening at 12 years of age, taking a life course perspective on future benefits and drawbacks.

Methods

The cost-effectiveness was derived as cost per quality-adjusted life-year (QALY) using a Markov model. As a basis for our assumptions, we mainly used information from the Exploring the Iceberg of Celiacs in Sweden (ETICS) study, a school-based screening conducted in 2005/2006 and 2009/2010, where 13,279 12-year-old children participated and 240 were diagnosed with coeliac disease, and a study involving members of the Swedish Coeliac Association with 1031 adult participants.

Results

The cost for coeliac disease screening was 40,105 Euro per gained QALY. Sensitivity analyses support screening based on high compliance to a gluten-free diet, rapid progression from symptom-free coeliac disease to coeliac disease with symptoms, long delay from celiac disease with symptoms to diagnosis, and a low QALY score for undiagnosed coeliac disease cases.

Conclusions

A coeliac disease mass screening is cost-effective based on the commonly used threshold of 50,000 Euro per gained QALY. However, this is based on many assumptions, especially regarding the natural history of coeliac disease and the effects on long-term health for individuals with coeliac disease still eating gluten.
Distinct clinical phenotypes for Crohn’s disease derived from patient surveys
Authors:   the 23andMe Research Team, Liu Tianyun , Han Lichy , Tilley Mera , Afzelius Lovisa , Maciejewski Mateusz , Jelinsky Scott , Tian Chao , McIntyre Matthew , Bing Nan , Hung Kenneth , Altman Russ B.
Published: April 2021

Background

Defining clinical phenotypes provides opportunities for new diagnostics and may provide insights into early intervention and disease prevention. There is increasing evidence that patient-derived health data may contain information that complements traditional methods of clinical phenotyping. The utility of these data for defining meaningful phenotypic groups is of great interest because social media and online resources make it possible to query large cohorts of patients with health conditions.

Methods

We evaluated the degree to which patient-reported categorical data is useful for discovering subclinical phenotypes and evaluated its utility for discovering new measures of disease severity, treatment response and genetic architecture. Specifically, we examined the responses of 1961 patients with inflammatory bowel disease to questionnaires in search of sub-phenotypes. We applied machine learning methods to identify novel subtypes of Crohn’s disease and studied their associations with drug responses.

Results

Using the patients’ self-reported information, we identified two subpopulations of Crohn’s disease; these subpopulations differ in disease severity, associations with smoking, and genetic transmission patterns. We also identified distinct features of drug response for the two Crohn’s disease subtypes. These subtypes show a trend towards differential genotype signatures.

Conclusion

Our findings suggest that patient-defined data can have unplanned utility for defining disease subtypes and may be useful for guiding treatment approaches.
HIV voluntary counseling and testing uptake and associated factors among Ethiopian youths: evidence from the 2016 EDHS using multilevel modeling
Authors: Nigatu Mamo , Kabeta Teshome , Taye Abonesh , Belina Merga
Published: April 2021

Background

Existing evidence showed that Human Immunodeficiency Virus counselling and testing uptake among Ethiopian youths is low, and factors contributing to it are not well studied. Therefore, this study aims to assess the status of uptake and identify its determinants using the 2016 Ethiopia Demographic and Health Survey data.

Method

Data of 10,903 Ethiopian youths were extracted from the 2016 Ethiopian Demographic and Health Survey. The association between the response variable and the predictors was modeled by multilevel binary logistic regression, whereas adjusted odds ratio and confidence intervals were used to measure associations and their statistical significance. The variation in the uptake of counselling and testing of HIV across regions of Ethiopia was quantified by intra-class correlation.

Result

The current study revealed that, overall, 34.9% (95% CI: 33.5, 36.2%) Ethiopian youths were ever tested for human immunodeficiency virus. Results show that about 9% of the variation in the probability of being tested for the disease was due to the regional variations. Moreover, having moderate and comprehensive HIV knowledge, being rich, having risky sexual behaviour, having a better educational level, having professional work, being married, owning of mobile, and having access to media were positively associated with human immunodeficiency virus voluntary counselling and testing uptake. On the other hand, being male, following protestant religion, following Muslim religion, and following other religions than orthodox religion were negatively associated with the uptake of human immunodeficiency virus counselling and testing.

Conclusion

Voluntary human immunodeficiency virus counselling and testing uptake among Ethiopian youths is very low and varies across the regions which might hamper the ambitious plan of Ethiopia to end the disease as a public health threat by 2030. Emphasis should be given to promoting the youths’ HIV-related knowledge through community-based education, encouraging and empowering the youths to participate in professional works by giving due focus to poor youths, and promoting mass media utilization to better achieve the plan.
High precision localization of pulmonary nodules on chest CT utilizing axial slice number labels
Authors: Chillakuru Yeshwant Reddy , Kranen Kyle , Doppalapudi Vishnu , Xiong Zhangyuan , Fu Letian , Heydari Aarash , Sheth Aditya , Seo Youngho , Vu Thienkhai , Sohn Jae Ho
Published: April 2021

Background

Reidentification of prior nodules for temporal comparison is an important but time-consuming step in lung cancer screening. We develop and evaluate an automated nodule detector that utilizes the axial-slice number of nodules found in radiology reports to generate high precision nodule predictions.

Methods

888 CTs from Lung Nodule Analysis were used to train a 2-dimensional (2D) object detection neural network. A pipeline of 2D object detection, 3D unsupervised clustering, false positive reduction, and axial-slice numbers were used to generate nodule candidates. 47 CTs from the National Lung Cancer Screening Trial (NLST) were used for model evaluation.

Results

Our nodule detector achieved a precision of 0.962 at a recall of 0.573 on the NLST test set for any nodule. When adjusting for unintended nodule predictions, we achieved a precision of 0.931 at a recall 0.561, which corresponds to 0.06 false positives per CT. Error analysis revealed better detection of nodules with soft tissue attenuation compared to ground glass and undeterminable attenuation. Nodule margins, size, location, and patient demographics did not differ between correct and incorrect predictions.

Conclusions

Utilization of axial-slice numbers from radiology reports allowed for development of a lung nodule detector with a low false positive rate compared to prior feature-engineering and machine learning approaches. This high precision nodule detector can reduce time spent on reidentification of prior nodules during lung cancer screening and can rapidly develop new institutional datasets to explore novel applications of computer vision in lung cancer imaging.
Uterine pseudoaneurysm on the basis of deep infiltrating endometriosis during pregnancy-a case report
Authors: Zwimpfer Tibor Andrea , Monod Cécile , Redling Katharina , Willi Heike , Takes Martin , Fellmann-Fischer Bernhard , Manegold-Brauer Gwendolin , Hösli Irene
Published: April 2021

Background

Pseudoaneurysm of the uterine artery (UPA) is a rare cause of potentially life-threatening hemorrhage during pregnancy and puerperium. It is an uncommon condition that mainly occurs after traumatic injury to a vessel following pelvic surgical intervention, but also has been reported based on underlying endometriosis. There is an increased risk of developing UPA during pregnancy. Diagnosis includes clinical symptoms, with severe abdominal pain and is confirmed by sonographic or magnetic resonance imaging (MRI). Due to its potential risk of rupture, with a subsequent hypovolemic maternal shock and high fetal mortality, an interdisciplinary treatment should be considered expeditiously.

Case presentation

We present the case of a 34-year old pregnant symptomatic patient, where a large UPA was detected at 26 weeks, based on deep infiltrating endometriosis (DIE). The UPA was successfully treated by selective arterial embolization. After embolization, the pain decreased but the woman still required intravenous analgesics during follow-up. At 37 weeks she developed a sepsis from the intravenous catheter which led to a cesarean section and delivery of a healthy boy. She was discharged 10 days postpartum.

Conclusions

UPA should be considered in pregnant women with severe abdominal and pelvic pain, once other obstetrical factors have been excluded. DIE might be the underlying diagnosis. It is a rare but potentially life-threatening condition for mother and fetus.
Clinical characteristics and survival outcomes of malignant struma ovarii confined to the ovary
Authors: Li Sijian , Yang Tengyu , Xiang Yang , Li Xiaoyan , Zhang Limeng , Deng Shan
Published: April 2021

Background

Malignant struma ovarii (MSO) is a unique type of ovarian malignancy that data on the survival outcome is limited and management strategy remains controversial due to its extreme rarity.

Methods

To investigate the clinical characteristics and treatment options in patients with MSO confined to the ovary, while also evaluating the recurrent-free survival (RFS) and overall survival (OS) rate in this population, a retrospective study was conducted. One hundred twenty-five cases of MSO confined to the ovary were enrolled and their clinical characteristics, treatment strategies, and results of follow-up were analyzed. OS and RFS were assessed by Kaplan-Meier analyses and Cox regression models.

Results

The most common pathological subtype in this cohort was papillary carcinoma (44.8%). Other reported subtypes, in order of prevalence, were follicular variant of papillary carcinoma, follicular carcinoma, and mixed follicular-papillary carcinoma. Surgical treatment options varied in this cohort that 8.0% of the patients received ovarian cystectomy, 33.6% underwent unilateral salpingo-oophorectomy (USO), 5.6% received bilateral salpingo-oophorectomy (BSO), 21.6% received total abdominal hysterectomy with BSO (TAH/BSO), and 17.6% were treated with debulking surgery; 20.0% of them received radioiodine therapy (RAI). Twenty-seven patients experienced recurrence with a median RFS of 14.0 years (95% confidence interval [CI], 9.5–18.5). The 5-year and 10-year recurrent rate were 27.1, 35.2%, respectively. Eight patients died during follow-up, with five attributed to MSO; the 5-year, 10-year, and 20-year OS rate was 95.3, 88.7 and 88.7%, respectively. However, the univariate and multivariate Cox regression showed no potential risk factor for RFS and OS.

Conclusion

Patients with MSO confined to the ovary had an excellent survival outcome, despite varied treatment strategies, and the recurrent rate was relatively high. We recommend USO as the preferred surgical option in this population since more aggressive surgery does not improve outcomes and the benefits of RAI are uncertain.
A prospective interventional study evaluating seizure activity during a radiotherapy course for high-grade gliomas (SURF-ROGG)
Authors: Rades Dirk , Witteler Jaspar , Olbrich Denise , Trillenberg Peter , Schild Steven E. , Tvilsted Soeren , Kjaer Troels W.
Published: April 2021

Background

Gliomas are often associated with symptoms including seizures. Most patients with high-grade gliomas are treated with radiotherapy or radio-chemotherapy. Since irradiation causes inflammation, it may initially aggravate symptoms. Studies focusing on seizure activity during radiotherapy for gliomas are not available. Such knowledge may improve patient monitoring and anti-epileptic treatment. This study evaluates seizure activity during radiotherapy for high-grade gliomas.

Methods

The primary objective this prospective interventional study is the evaluation of seizure activity during a course of radiotherapy for high-grade gliomas. Progression of seizure activity is defined as increased frequency of seizures by > 50%, increased severity of seizures, or initiation/increase by ≥25% of anti-epileptic medication. Seizure frequency up to 6 weeks following radiotherapy and electroencephalography activity typical for epilepsy will also be evaluated. Patients keep a seizure diary during and up to 6 weeks following radiotherapy. Every day, they will document number (and type) of seizures and anti-epileptic medication. Once a week, the findings of the diary are checked and discussed with a neurologist to initiate or adjust anti-epileptic medication, if necessary. Patients complete a questionnaire regarding their satisfaction with the seizure diary. If the dissatisfaction rate is > 40%, the seizure diary will be considered not suitable for the investigated indication. Thirty-five patients (32 patients plus drop-outs) should be enrolled. With this sample size, a one-sample binomial test with a one-sided significance level of 2.5% has a power of 80% to yield statistical significance, if the rate of patients with progression of seizure activity is 30% (rate under the alternative hypothesis), assuming a ‘natural’ background progression-rate of 10% without radiotherapy (null hypothesis).

Discussion

If an increase in seizure activity during a course of radiotherapy for high-grade glioma occurs, the findings of this study may pave the way for a larger prospective trial and will likely lead to closer patient monitoring and better anti-epileptic treatment.

Trial registration

clinicaltrials.gov (NCT04552756); registered on 16th of September, 2020.
Targeted next generation sequencing and family survey enable correct genetic diagnosis in CRX associated macular dystrophy – a case report
Authors: Al-Khuzaei Saoud , Hudspith Karl A. Z. , Broadgate Suzanne , Shanks Morag E. , Clouston Penny , Németh Andrea H. , Halford Stephanie , Downes Susan M.
Published: April 2021

Background

We present 3 members of a family with macular dystrophy, originally diagnosed as Stargardt disease, with a significantly variable age at onset, caused by a heterozygous mutation in CRX.

Case presentation

A 43-year-old female with bull’s eye maculopathy, whose sister was diagnosed with Stargardt disease previously at another centre, was found to have a single ABCA4 variant. Further examination of the family revealed that the asymptomatic father was also affected, indicating a dominant pattern of inheritance. In addition, the ABCA4 variant was not identified in the sister originally diagnosed with Stargardt disease. Next generation sequencing identified a heterozygous c.121C > T, p.R41W missense mutation in CRX in all 3 affected members.

Conclusions

We describe a common phenotype, but with variable age at onset, with autosomal dominant inheritance and reduced penetrance in a family found to have a pathogenic sequence variant in CRX. This illustrates the importance of panel based molecular genetic testing accompanied by family studies to establish a definitive diagnosis.
Restarting cataract surgery during the COVID-19 pandemic; a prospective study analysing 30 day outcomes after elective cataract surgery in the United Kingdom
Authors: Carr Francis , Agarwal Paras , Narula Harmehak , Keragala Tiran S. , Awwad Samer Elshikh Hassan , Roble Ahmed , Gangwani Vinod
Published: April 2021

Background

Cataract is a significant cause of preventable blindness in the United Kingdom and worldwide. Prior to the COVID-19 pandemic, cataract surgery was the most commonly performed operation by the National Health Service in the United Kingdom. The aim of this study is to evaluate the safety of elective cataract surgery performed in the United Kingdom in a COVID-19 free hospital during the COVID-19 pandemic.

Methods

Single centre prospective observational cohort study of consecutive patients undergoing elective cataract surgery in the United Kingdom over a 3 month period from May to August 2020. Electronic medical records were reviewed and patients were contacted at 30 days post-operatively. Data collection included symptoms suggestive of COVID-19 infection, hospital admission, mortality, intra-operative and post-operative surgical complications.

Results

A total of 649 elective cataract surgeries were performed. Two patients (0.3%) developed worsening dyspnoea during the 30 day post-operative period, but tested negative for COVID-19 infection. Three patients (0.5%) were hospitalised, unrelated to COVID-19 infection, of which one patient (0.2%) passed. Four patients (0.6%) suffered posterior capsular rupture. 601 (93.2%) had no post-operative complications.

Conclusion

This study demonstrates a safe model for the resumption of elective cataract surgery during the COVID-19 pandemic, providing strict infection control measures are in place.
Correction to: Assessment of violence risk in 440 psychiatric patients in China: examining the feasibility and acceptability of a novel and scalable approach (FoVOx)
Authors:   FoVOx group, Zhong Shaoling , Yu Rongqin , Cornish Robert , Wang Xiaoping , Fazel Seena
Published: April 2021

An amendment to this paper has been published and can be accessed via the original article.
Adolescents who are overweight or obese - the relevance of a social network to engaging in physical activity: a qualitative study
Authors: Skogen Ingeborg B. , Høydal Kjetil L.
Published: April 2021

Background

Increased level of physical activity (PA) is one of the approaches offered by school health services in Norway for the prevention and treatment of children and adolescents with overweight and obesity. Research has found that young people with overweight and obesity tend to participate in less physical activity than youth of healthier weight. They also tend to perceive several barriers to PA at the environmental, interpersonal, and individual levels. This paper explores how adolescents’, who receive follow-up of weight management in primary health care, experience barriers to and facilitators for engaging in physical activity within their social networks.

Methods

This is a qualitative study with an explorative design inspired by phenomenological ideas based on analysis of semi-structured interviews with 10 adolescents aged 13–18. Interviews were conducted with young people with overweight or obesity in weight-related follow-up in primary health care settings in various regions in Norway.

Results

The results describe the barriers to and facilitators of PA in the adolescents’ social networks. The study reveals a strong emphasis on the importance of a social network for engaging in PA. According to these adolescents’ experiences of PA in their social networks, organizing PA groups that consist of similarly young people with overweight can contribute to an increased level of PA and help modify their negative perceptions of such activity.

Conclusions

This study finds that young people with overweight and obesity place a strong emphasis on a social network where they feel equal to others if they are to engage in PA. The study suggests that School Health Nurses should establish a social network of adolescents in the same situation, in the form of organized activity groups for young people with overweight or obesity, rather than advice on increased participation in ordinary organized sports or individual exercising. This can facilitate an increase in the PA level among this group of young people.
Biomechanical effect of different plate-to-disc distance on surgical and adjacent segment in anterior cervical discectomy and fusion - a finite element analysis
Authors: Guo Xing , Zhou Jiaming , Tian Yueyang , Kang Liang , Xue Yuan
Published: April 2021

Background

The plate-to-disc distance (PDD) is an important factor affecting the degeneration of adjacent segments after anterior cervical discectomy and fusion (ACDF). However, the most suitable PDD is controversial. This study examined the adjacent intervertebral disc stress, bone graft stress, titanium plate stress and screw stress to evaluate the biomechanical effect of different PDD on surgical segment and adjacent segment following C5/C6 ACDF.

Methods

We constructed 10 preoperative finite element models of intact C4–C7 segments and validated them in the present study. We simulated ACDF surgery based on the 10 intact models in software. We designed three different distance of plate-to-disc titanium plates: long PDD (10 mm), medium PDD (5 mm) and short PDD (0 mm). The changes in C4/C5 and C6/C7 intervertebral disc stress, bone graft stress, titanium plate stress and screw stress were analyzed.

Results

The von Mises stress of C4/C5 and C6/C7 intervertebral discs had no significant differences (P > 0.05) in three different PDD groups. Titanium plate stress increased as the PDD decreased. The bone graft stress and screws stress decreased as the PDD decreased. The maximum stress of each part occurred was mostly in the conditions of rotation and lateral bending.

Conclusions

The PDD has no effect on adjacent intervertebral disc stress, but it is an important factor that affecting the bone graft stress, titanium plate stress and screws stress after ACDF. Shorter PDD plate can provide better stability to reduce stress on screws and bone graft, which may be helpful to prevent cage subsidence, pseudarthrosis and instrument failure. This can serve as a reference for clinical choice of plate.
Entropic measures of complexity in a new medical coding system
Authors: Niyirora Jerome
Published: April 2021

Background

Transitioning from an old medical coding system to a new one can be challenging, especially when the two coding systems are significantly different. The US experienced such a transition in 2015.

Objective

This research aims to introduce entropic measures to help users prepare for the migration to a new medical coding system by identifying and focusing preparation initiatives on clinical concepts with more likelihood of adoption challenges.

Methods

Two entropic measures of coding complexity are introduced. The first measure is a function of the variation in the alphabets of new codes. The second measure is based on the possible number of valid representations of an old code.

Results

A demonstration of how to implement the proposed techniques is carried out using the 2015 mappings between ICD-9-CM and ICD-10-CM/PCS. The significance of the resulting entropic measures is discussed in the context of clinical concepts that were likely to pose challenges regarding documentation, coding errors, and longitudinal data comparisons.

Conclusion

The proposed entropic techniques are suitable to assess the complexity between any two medical coding systems where mappings or crosswalks exist. The more the entropy, the more likelihood of adoption challenges. Users can utilize the suggested techniques as a guide to prioritize training efforts to improve documentation and increase the chances of accurate coding, code validity, and longitudinal data comparisons.
Targeting necroptosis as therapeutic potential in chronic myocardial infarction
Authors: Piamsiri Chanon , Maneechote Chayodom , Siri-Angkul Natthaphat , Chattipakorn Siriporn C. , Chattipakorn Nipon
Published: April 2021

Cardiovascular diseases (CVDs) are considered the predominant cause of morbidity and mortality globally. Of these, myocardial infarction (MI) is the most common cause of CVD mortality. MI is a life-threatening condition which occurs when coronary perfusion is interrupted leading to cardiomyocyte death. Subsequent to MI, consequences include adverse cardiac remodeling and cardiac dysfunction mainly contribute to the development of heart failure (HF). It has been shown that loss of functional cardiomyocytes in MI-induced HF are associated with several cell death pathways, in particular necroptosis. Although the entire mechanism underlying necroptosis in MI progression is still not widely recognized, some recent studies have reported beneficial effects of necroptosis inhibitors on cell viability and cardiac function in chronic MI models. Therefore, extensive investigation into the necroptosis signaling pathway is indicated for further study. This article comprehensively reviews the context of the underlying mechanisms of necroptosis in chronic MI-induced HF in in vitro, in vivo and clinical studies. These findings could inform ways of developing novel therapeutic strategies to improve the clinical outcomes in MI patients from this point forward.
Study on the mechanism of production of γ-PGA and nattokinase in Bacillus subtilis natto based on RNA-seq analysis
Authors: Li Min , Zhang Zilong , Li Shenwei , Tian Zhengan , Ma Xia
Published: April 2021

Poly-γ-glutamic acid (γ-PGA) and nattokinase (NK) are the main substances produced by Bacillus subtilis natto in solid-state fermentation and have wide application prospects. We found that our strains had higher activity of nattokinase when soybeans were used as substrate to increase the yield of γ-PGA. Commercial production of γ-PGA and nattokinase requires an understanding of the mechanism of co-production. Here, we obtained the maximum γ-PGA yield (358.5 g/kg, w/w) and highest activity of NK during fermentation and analyzed the transcriptome of Bacillus subtilis natto during co-production of γ-PGA and NK. By comparing changes in expression of genes encoding key enzymes and the metabolic pathways associated with the products in genetic engineering, the mechanism of co-production of γ-PGA and nattokinase can be summarized based on RNA-seq analysis. This study firstly provides new insights into the mechanism of co-production of γ-PGA and nattokinase by Bacillus subtilis natto and reveals potential molecular targets to promote the co-production of γ-PGA and nattokinase.
On-demand pH-sensitive surface charge-switchable polymeric micelles for targeting Pseudomonas aeruginosa biofilms development
Authors: Chen Xiangjun , Guo Rong , Wang Changrong , Li Keke , Jiang Xinyu , He Huayu , Hong Wei
Published: April 2021

Bacterial biofilm is the complicated clinical issues, which usually results in bacterial resistance and reduce the therapeutic efficacy of antibiotics. Although micelles have been drawn attention in treatment of the biofilms, the micelles effectively permeate and retain in biofilms still facing a big challenge. In this study, we fabricated on-demand pH-sensitive surface charge-switchable azithromycin (AZM)-encapsulated micelles (denoted as AZM-SCSMs), aiming to act as therapeutic agent for treating Pseudomonas aeruginosa (P. aeruginosa) biofilms. The AZM-SCSMs was composed of poly(l-lactide)-polyetherimide-hyd-methoxy polyethylene glycol (PLA-PEI-hyd-mPEG). It was noteworthy that the pH-sensitive acylhydrazone bond could be cleaved in acidic biofilm microenvironment, releasing the secondary AZM-loaded cationic micelles based on PLA-PEI (AZM-SCMs) without destroying the micellar integrity, which could tailor drug-bacterium interaction using micelles through electrostatic attraction. The results proved that positively charged AZM-SCMs could facilitate the enhanced penetration and retention inside biofilms, improved binding affinity with bacterial membrane, and added drug internalization, thus characterized as potential anti-biofilm agent. The excellent in vivo therapeutic performance of AZM-SCSMs was confirmed by the targeting delivery to the infected tissue and reduced bacterial burden in the abscess-bearing mice model. This study not only developed a novel method for construction non-depolymerized pH-sensitive SCSMs, but also provided an effective means for the treatment of biofilm-related infections.
Postnatal growth of preterm infants during the first two years of life: catch-up growth accompanied by risk of overweight
Authors: Han Junyan , Jiang Yuan , Huang Jun , Zhang Yue , Zhang Ying , Zhang Yi , Chen Xiaotian , Li Yun , Yan Weili
Published: April 2021

Background

Early postanal growth of preterm infants has many effects on early and late health. However, evidence on growth pattern in Chinese preterm infant population during early life is insufficient. This study aims to describe the growth trajectory, catch-up growth, and risk of overweight of preterm infants during the first 2 years of life in a Chinese community population.

Methods

All preterm infants (n = 10,624) received routine childcare in one primary maternal and child healthcare network in 8 years were included. Body weight and length/height at corrected age (CA) 40 weeks, CA 3 months, 6 months, 9 months, 12 months, 18 months, and 24 months were extracted and converted to z-scores based on the World Health Organization (WHO) standards. According to the intrauterine growth status, infants were divided into small for gestational age (SGA), appropriate for gestational age (AGA), and large for gestational age (LGA) infants. Changes of z-score were used to describe the growth velocity. Generalized estimating equation (GEE) model was used to analyze growth trajectory trends over time.

Results

Body weight and length/height were overall above the WHO standards during the first 2 years of life. Z-score increased significantly by 0.08 (95% CI: 0.06–0.10) in weight and 0.07 (95% CI: 0.04–0.09) in length/height from CA 40 weeks to 3 months and then levelled off until CA 24 months after adjustment. Almost 90% of AGA and LGA infants achieved growth targets (≥25th percentile of WHO standards), and over 85% of SGA infants achieved catch-up growth (≥10th percentile of WHO standards) before CA 24 months. However, the risk of overweight appeared during this period, with the proportion of infants with the risk of overweight being at the peak at CA 3 months (25.6% of all preterm infants and 39.4% of LGA infants). Growth trajectories of SGA showed increasing trends, but those of LGA showed decreasing trends during the first 2 years.

Conclusions

Body weight and length/height of preterm infants are above the WHO standards in the Chinese community population during the first 2 years of life. Catch-up growth is accompanied by risk of overweight as early as CA 3 months.

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Paraventricular Calcitonin Receptor–Expressing Neurons Modulate Energy Homeostasis in Male Mice
Authors: Gonzalez Ian E , Ramirez-Matias Julliana , Lu Chunxia , Pan Warren , Zhu Allen , Myers Martin G , Olson David P
Published: April 2021

The paraventricular nucleus of the hypothalamus (PVH) is a heterogeneous collection of neurons that play important roles in modulating feeding and energy expenditure. Abnormal development or ablation of the PVH results in hyperphagic obesity and defects in energy expenditure whereas selective activation of defined PVH neuronal populations can suppress feeding and may promote energy expenditure. Here, we characterize the contribution of calcitonin receptor–expressing PVH neurons (CalcRPVH) to energy balance control. We used Cre-dependent viral tools delivered stereotaxically to the PVH of CalcR2Acre mice to activate, silence, and trace CalcRPVH neurons and determine their contribution to body weight regulation. Immunohistochemistry of fluorescently-labeled CalcRPVH neurons demonstrates that CalcRPVH neurons are largely distinct from several PVH neuronal populations involved in energy homeostasis; these neurons project to regions of the hindbrain that are implicated in energy balance control, including the nucleus of the solitary tract and the parabrachial nucleus. Acute activation of CalcRPVH neurons suppresses feeding without appreciably augmenting energy expenditure, whereas their silencing leads to obesity that may be due in part due to loss of PVH melanocortin-4 receptor signaling. These data show that CalcRPVH neurons are an essential component of energy balance neurocircuitry and their function is important for body weight maintenance. A thorough understanding of the mechanisms by which CalcRPVH neurons modulate energy balance might identify novel therapeutic targets for the treatment and prevention of obesity.
Αστικά πολιτικά κόμματα στην Ελλάδα, 1944-1949
Authors: Μπαλτά Μαρία - Έλλη
Published: April 2021

Η παρούσα διατριβή φιλοδοξεί να θέσει ερωτήματα και να δώσει απαντήσεις στο ιστορικό υλικό που σχετίζεται με τη δράση και την οργάνωση των αστικών πολιτικών κομμάτων, από την Απελευθέρωση μέχρι και τη λήξη του εμφυλίου. Στο επίκεντρό της βρίσκεται όχι η μελέτη των γεγονότων του εμφυλίου, αλλά η πορεία των αστικών κομμάτων, ο ρόλος των πολιτικών προσώπων στις εξελίξεις, η διερεύνηση της ταυτότητας, της στρατηγικής και των τακτικών του κάθε κόμματος, πλην του Κ.Κ.Ε. Στοχεύει στην ανάδειξη των ποικίλλων διαφοροποιήσεων στην πολιτική που ασκήθηκε, όχι μόνο μεταξύ των δυο κυρίαρχων κομμάτων της εποχής (Κόμμα Φιλελευθέρων και Λαϊκό Κόμμα) αλλά και εντός του ίδιου κομματικού σχηματισμού.
Εξορυκτικές κοινότητες στην Κύπρο κατά τη βρετανική αποικιακή περίοδο
Authors: Σιούλας Μιχαήλ
Published: April 2021

Η διατριβή εξετάζει τις εξορυκτικές κοινότητες που αναπτύχθηκαν στην Κύπρο, κατά τη Βρετανική αποικιακή περίοδο (1878-1960), από ξένες εταιρείες, των ΗΠΑ, του Ηνωμένου Βασιλείου, της Ελλάδας και άλλων χωρών, για την εκμετάλλευση κοιτασμάτων χαλκούχου σιδηροπυρίτη, αμιάντου, χρωμίτη, χρυσού και αργύρου. Χρησιμοποιώντας μεθόδους της βιομηχανικής αρχαιολογίας και της κριτικής ιστοριογραφίας, δηλαδή έρευνα πεδίου, αρχειακή και βιβλιογραφική έρευνα, αναλύει τις γενικές στρατηγικές, που καθόρισαν την οργάνωση των εξορυκτικών κοινοτήτων, την πολεοδομική οργάνωση των επιμέρους χωρικών ενοτήτων που τις συγκρότησαν, τις εργατικές κατοικίες και άλλες χρήσεις που υποστήριξαν τη λειτουργία τους στην κλίμακα του κτηρίου. Οι εξορυκτικές κοινότητες εξετάζονται σε συνάρτηση με τον κυπριακό χώρο, με συσχετισμούς χωρικών δεδομένων και φαινομένων εντός και εκτός ορυχείων. Παράλληλα, διερευνώνται οι ρόλοι των παικτών που επηρέαζαν την ανάπτυξή τους και ευρύτερα η επιρροή που ασκούσαν οι μεταβαλλόμενες πολιτικές, κοινωνικές και οικονομικές συνθήκες της εποχής. Επιπλέον, τα ορυχεία συσχετίζονται με άλλα βιομηχανικά σύνολα της νήσου και εξετάζεται ο ρόλος τους στο φαινόμενο της αστικοποίησης και σε έκτακτες καταστάσεις και κρίσεις, για να αναδειχθεί η μεταβαλλόμενη δυναμική τους στο επίπεδο της αποικίας. Για την ανάλυση των εξορυκτικών κοινοτήτων της νήσου και την αποκάλυψη ευρύτερων μηχανισμών που προκάλεσαν φαινόμενα που ήταν άμεσα συναρτόμενα με την ανάπτυξη και τους μετασχηματισμούς τους, συσχετίζονται με αντίστοιχες βιομηχανικές κοινότητες των δυτικών ανεπτυγμένων χωρών και των αποικιών. Η διατριβή μέσα από την συστηματική ανάγνωση και ανάλυση των εξορυκτικών κοινοτήτων αποκαλύπτει τις χωρικές συστρωματώσεις τους, ρίχνοντας φως στην πλήρη σύνθεση και πολυπλοκότητα των παραγόντων που συνέβαλαν στην ανάπτυξη και τους μετασχηματισμούς τους. Αναλύοντας κριτικά το χωρικό αποτύπωμα της πιο σημαντικής οικονομικής δραστηριότητας της αποικιοκρατίας στην Κύπρο, συνεισφέρει στην κατανόηση των μεταβολών του κυπριακού χώρου τη δεδομένη περίοδο, οι οποίες δεν έχουν επαρκώς ερευνηθεί, καθώς η σχετική βιβλιογραφία είναι εστιασμένη κυρίως στα αστικά κέντρα και στα θεσμικά κτήρια της Βρετανικής αποικιακής περιόδου. Συνεισφέρει κατά αυτό τον τρόπο ευρύτερα στην επιστημονική γνώση γύρω από τις χωρικές και κοινωνικές επιδράσεις της εκμετάλλευσης φυσικών πόρων στη Μέση Ανατολή κατά το πρώτο μισό του 20ου αιώνα και στην επιστημονική γνώση σχετικά με το φαινόμενο της ίδρυσης κοινοτήτων από βιομήχανους στις αποικίες.
Ein Spaziergang durch 2100 Jahre Geschichte
Authors: Bargetzi Dagmar , Hagendorn Andrea , Lassau Guido
Published: April 2021

Der Münsterhügel ist mit seiner über 3000 Jahre langen Besiedlungsgeschichte das historische Herzstück Basels. Seine strategisch und verkehrsgeografisch hervorragende Lage am Rheinknie bot den Bewohnern Schutz und liess das Hügelplateau bereits im 1. Jahrhundert v. Chr. zu einem Ort der Repräsentation von Macht und Wohlstand werden.

Auf dem Münsterhügel ist Jahrtausende alte Geschichte in ihrer Vielfalt erlebbar. Die Archäologischen Informationsstellen auf dem Münsterhügel lassen sich im Rahmen eines archäologischen Spazierganges besuchen. Sie werden in diesem Beitrag ausführlich vorgestellt.
Von Fischen und Fischern
Authors: Häberle Simone
Published: April 2021

Der Rhein und seine Nebenflüsse boten Lebensraum für eine Vielzahl an Fischarten, die für die ansässige Bevölkerung in vergangenen Zeiten eine wichtige Nahrungsressource darstellten. Davon zeugt die hohe Anzahl an archäologischen Fischresten, welche im Laufe der langjährigen Ausgrabungstätigkeit der Archäologischen Bodenforschung Basel-Stadt in mittelalterlichen und neuzeitlichen Befunden entdeckt wurden. Widmet man sich dieser auf den ersten Blick etwas unscheinbaren Fundgattung, lässt sich viel Interessantes über den Rhein, die Rheinfischerei und die vom Fluss und dem Fischereigewerbe geprägte Stadt und deren Bewohnerinnen und Bewohner in Erfahrung bringen.