bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimizing the diagnosis and assessment of chronic thromboembolic pulmonary hypertension with advancing imaging modalities
Authors: Kligerman Seth , Hsiao Albert
Published: March 2021

Imaging is key to nearly all aspects of chronic thromboembolic pulmonary hypertension including management for screening, assessing eligibility for pulmonary endarterectomy, and post‐operative follow‐up. While ventilation/perfusion scintigraphy, the gold standard technique for chronic thromboembolic pulmonary hypertension screening, can have excellent sensitivity, it can be confounded by other etiologies of pulmonary malperfusion, and does not provide structural information to guide operability assessment. Conventional computed tomography pulmonary angiography has high specificity, though findings of chronic thromboembolic pulmonary hypertension can be visually subtle and unrecognized. In addition, computed tomography pulmonary angiography can provide morphologic information to aid in pre‐operative workup and assessment of other structural abnormalities. Advances in computed tomography imaging techniques, including dual‐energy computed tomography and spectral‐detector computed tomography, allow for improved sensitivity and specificity in detecting chronic thromboembolic pulmonary hypertension, comparable to that of ventilation/perfusion scans. Furthermore, these advanced computed tomography techniques, compared with conventional computed tomography, provide additional physiologic data from perfused blood volume maps and improved resolution to better visualize distal chronic thromboembolic pulmonary hypertension, an important consideration for balloon pulmonary angioplasty for inoperable patients. Electrocardiogram‐synchronized techniques in electrocardiogram‐gated computed tomography can also show further information regarding right ventricular function and structure. While the standard of care in the workup of chronic thromboembolic pulmonary hypertension includes a ventilation/perfusion scan, computed tomography pulmonary angiography, direct catheter angiography, echocardiogram, and coronary angiogram, in the future an electrocardiogram‐gated dual‐energy computed tomography angiography scan may enable a “one‐stop” imaging study to guide diagnosis, operability assessment, and treatment decisions with less radiation exposure and cost than traditional chronic thromboembolic pulmonary hypertension imaging modalities.
Advances in balloon pulmonary angioplasty for chronic thromboembolic pulmonary hypertension
Authors: Mahmud Ehtisham , Patel Mitul , Ang Lawrence , Poch David
Published: March 2021

Balloon pulmonary angioplasty (BPA) is an emerging treatment option for patients with chronic thromboembolic pulmonary hypertension (CTEPH) who have inoperable, segmental/subsegmental disease, or residual disease after pulmonary endarterectomy. In the past decade, advances in the techniques for BPA have led to better clinical outcomes with improvements in hemodynamics, pulmonary perfusion, exercise tolerance, functional capacity, and quality of life. We present the experience with BPA at our university, the largest CTEPH center in the world, followed by reviewing the published data regarding the efficacy and safety of BPA in patients with CTEPH. There is increasing evidence to support that the initial hemodynamic improvement is sustained for ≥3 years after the procedure. Although infrequent, complications observed with BPA are associated with pulmonary vascular injury or rarely reperfusion pulmonary edema. As the technique for percutaneous pulmonary artery revascularization has improved, the procedural risk and complications have continued to decrease. This promising technique continues to develop, and future research is required to demonstrate the long‐term benefits of BPA, standardize the technique, and define a uniform institutional infrastructure for providing BPA as a part of the treatment of CTEPH.
Surgical treatment of a distal oesophageal stricture by mucosal radial incision and dilation in a kitten with secondary megaoesophagus
Authors: Kurtz Maxime , Paulin Mathieu V , Fournet Alexandre , Decambron Adeline , Fabrès Virginie , Freiche Valérie
Published: March 2021

Case summary

A 7-month-old intact female Maine Coon cat was presented with a 2-month history of regurgitations. Contrast radiographic and endoscopic examinations revealed a diffuse megaoesophagus secondary to a severe lower oesophageal stricture. An epiphrenic diverticulum was noted. Endoscopic balloon dilation was unsuccessful. Gastrotomy was thus performed in order to incise the oesophageal wall radially along the stricture site, and then to dilate the stricture. A diameter of 20 mm was reached. With the aim of preventing stricture recurrence, submucosal injections of triamcinolone acetonide were performed. An 18 Fr oesophagogastric feeding tube was placed and a left gastropexy was performed in order to exert some traction on the gastroesophageal junction, with the aim of reducing the oesophageal diverticulum. Twelve months postoperatively, clinical signs had completely resolved and follow-up radiographs revealed marked improvement of the oesophageal dilatation.

Relevance and novel information

Lower oesophageal strictures should be considered when evaluating regurgitations or megaoesophagus in a kitten. Surgical mucosal radial incision is a therapeutic option in cases of lower oesophageal stricture refractory to balloon dilation, and can lead to a marked improvement of clinical signs and of the oesophagus diameter leading to clinical success.
Health and Demographic Surveillance System: A Potential Tool for Solving Challenges Associated with Epidemic Surveillance and Social Protection Scheme for COVID-19 Pandemic Response in Nigeria
Authors: Alabi Olatunji , Omoleke Semeeh A. , Abdulwahab Ahmad
Published: March 2021

Nigeria recorded her first case of COVID 19 in Lagos State on 27th February 2019, and the number of confirmed cases of COVID 19 has risen to 59 287, with 1113 deaths as of 4th October 2020. The commentary highlighted the importance of a health and demographic surveillance system (HDSS) and its potential in addressing surveillance gap, and the inadequacy of existing sociodemographic database used for palliative administration. The authors examined the HDSS in the context of the COVID-19 pandemic response and learning from the Nahuche model. The Nahuche HDSS model has the potential of identifying poor households as it collects standard data on the socio-economic status of each of the households within the demographic surveillance area (DSA). Standard questionnaire in assessing the household socio-economic status adapted from standard surveys, such as Nigeria Health and Demographic Survey and Malaria Indicator Survey, was administered on the household heads of each household every 2 years to monitor socio-economic advancement of the households. Data on variables such as household possessions, including animals and livestock, were collected and analyzed using factor analysis to group the households into different wealth indices. HDSS provides an opportunity to ameliorate the challenges associated with halting the spread of the virus in the areas of surveillance and administration of palliatives in Nigeria, where there is a paucity of reliable demographic and household-level socio-economic data. This paper calls for the setting up of a functioning HDSS in each region of Nigeria to address the dearth of reliable data for planning health and socio-economic interventions.
Preoperative Cognitive Impairment as a Perioperative Risk Factor in Patients Undergoing Total Knee Arthroplasty
Authors: Krishnan Sindhu , Brovman Ethan Y. , Urman Richard D.
Published: March 2021

Background:

The study assessed whether pre-existing cognitive impairment (CI) prior to elective total knee arthroplasty (TKA) is associated with worse postoperative outcomes such as delirium, in-hospital medical complications, 30-day mortality, hospital length of stay and non-home discharge.

Methods:

A retrospective database analysis from the NSQIP Geriatric Surgery Pilot Project was used. There was an initial cohort of 6350 patients undergoing elective TKA, 104 patients with CI were propensity score matched to 104 patients without CI.

Results:

Analysis demonstrated a significantly increased incidence of post-operative delirium (POD) in the cohort with pre-op CI (p = < .001), a worsened functional status (p = < .001) and increased nonhome discharge postoperatively compared to the group without CI (p = 0.029). Other post-operative outcomes included 30-day mortality of 0% in both groups, and low rate of complications such as infection (2.88% vs 0.96%), pneumonia (1.92% vs 0%), failure to wean (0.96% vs 0%), and reintubation (0.96% vs 0%). Some other differences between the CI group and non-CI group, although not statistically significant, included increased rate of transfusion (10.58% vs 6.73%), and sepsis (1.92% vs 0%). The length of stay was increased in the non-CI group (4.28% vs 2.32%, p = 0.122).

Conclusion:

CI in patients undergoing TKA is associated with an increased risk of POD, worsened postoperative functional status, and discharge to non-home facility.
The Development of a Mobile Application for Older Adults for Rehabilitation Instructions After Hip Fracture Surgery
Authors: Ko YoungJi , Hwang Jong-Moon , Baek Seung-Hoon
Published: March 2021

Introduction:

Older patients with hip fractures require a long time to rehabilitate and recover after surgery. Although effective discharge instructions for long-term recovery are important, the discharge instructions of most acute-care hospitals are often presented as a brochure, which is difficult for older adults to follow. The purpose of this study was to develop rehabilitation instructions in the form of a mobile application for the physical recovery of older adults after hip fracture surgery.

Materials and Methods:

A mobile application for rehabilitation instructions after hip fracture surgery was developed in ADDIE order of analysis, design, development, implementation, and evaluation. The contents of the mobile application composed of rehabilitative exercises, activities of daily living, pain and nutrition management, fall prevention, and hospital visits. Nine experts evaluated the application and SPSS version 23.0 program was used for data analysis.

Results:

In the mobile application evaluation by the experts, the average score of the contents was 2.22 out of 3 points. The average score of understanding was the highest at 2.42, while accuracy was the lowest at 2.00 in the contents. The average score of the interface design was 2.32 out of 3 points. The average score of consistency was the highest at 2.42, while design suitability was the lowest at 2.25 in the interface design. The experts perceived the mobile application as simple and easy to understand while also suggesting some improvements.

Conclusion:

The average scores were highest for understanding of contents and consistency of the interface design and lowest for accuracy of contents and design suitability of the interface design. The mobile application was easy to understand and had consistency in design.
MALL in Collaborative Learning as a Vocabulary-Enhancing Tool for EFL Learners: A Study Across Two Universities in Saudi Arabia
Authors: Al-Ahdal Arif Ahmed Mohammed Hassan , Alharbi Mohammed Abdullah
Published: March 2021

Vocabulary, as important as it is, is largely relegated to the domain of memorization in the English as a foreign language (EFL) situations in the Kingdom of Saudi Arabia (KSA). Assessment and achievement tests have proven time and again that this strategy is not doing any good for the learners’ proficiency. This study was conceived to suggest means of improving critical knowledge application. In pilot studies with intermediate EFL learners at Majmaah University and Qassim University, preliminary findings after using mobile-assisted language learning (MALL) as a tool of collaborative learning indicated improved vocabulary retention. The study employed a mixed-method approach by comparing pre- and posttest results across genders and obtaining direct teacher–learner feedback using questionnaires, with 80 participants from two Universities over a period of 3 months. The questions were centered around seeking their opinion on collaborative learning and using smart devices as study tools on the campuses. Results showed that, the experimental group’s use of mobile devices for collaboration helped them for better retention of vocabulary, postintervention, and group performance was improved drastically with more learners scoring closer to the mean value, while the control group showed no remarkable difference in performance.
A Systematic Scoping Review on Portfolios of Medical Educators
Authors: Hong Daniel Zhihao , Lim Annabelle Jia Sing , Tan Rei , Ong Yun Ting , Pisupati Anushka , Chong Eleanor Jia Xin , Quek Chrystie Wan Ning , Lim Jia Yin , Ting Jacquelin Jia Qi , Chiam Min , Chin Annelissa Mien Chew , Lee Alexia Sze Inn , Wijaya Limin , Cook Sandy , Krishna Lalit Kumar Radha
Published: March 2021

Background:

Heralded as a teaching, assessment and reflective tool, and increasingly as a longitudinal and holistic perspective of the educator’s development, medical educator’s portfolios (MEP)s are increasingly employed to evaluate progress, assess for promotions and career switches, used as a reflective tool and as a means of curating educational activities. However, despite its blossoming role, there is significant dissonance in the content and structure of MEPs. As such, a systematic scoping review (SSR) is proposed to identify what is known of MEPs and its contents.

Methods:

Krishna’s Systematic Evidenced Based Approach (SEBA) was adopted to structure this SSR in SEBA of MEPs. SEBA’s constructivist approach and relativist lens allow data from a variety of sources to be considered to paint a holistic picture of available information on MEPs.

Results:

From the 12 360 abstracts reviewed, 768 full text articles were evaluated, and 79 articles were included. Concurrent thematic and content analysis revealed similar themes and categories including: (1) Definition and Functions of MEPs, (2) Implementing and Assessing MEPs, (3) Strengths and limitations of MEPs and (4) electronic MEPs.

Discussion:

This SSR in SEBA proffers a novel 5-staged evidence-based approach to constructing MEPs which allows for consistent application and assessment of MEPs. This 5-stage approach pivots on assessing and verifying the achievement of developmental milestones or ‘micro-competencies’ that facilitate micro-credentialling and effective evaluation of a medical educator’s development and entrust-ability. This allows MEPs to be used as a reflective and collaborative tool and a basis for career planning.
Collective resources for individual recovery: The moderating role of social climate on the relationship between job stressors and work-related rumination – A multilevel approach
Authors: Pauli Roman , Lang Jessica
Published: March 2021

In this study, we link cognitive processes of recovery to the social context in which employees experience job stressors. The aim was to examine how the social context in which employees experience work stressors is associated with individuals’ work-related thoughts in nonwork time and thus may prolong work-related mental efforts beyond working hours. We used aggregated individual ratings on social relations with colleagues and supervisors as a primer for social climate within workgroups, calculated the rate of permanent employment contracts per workgroup as a proxy for the stability of social relations within workgroups and used organizational affiliations to specify job settings in terms of routine versus creative tasks. Drawing on cross-sectional data from a psychosocial risk assessment and occupational health promotion survey of N = 1836 employees in 118 workgroups with different occupations at a German university, we tested multilevel random-coefficient models for affective rumination and problem-solving pondering. Results indicated a negative association of collegial climate with affective rumination but no association with problem-solving pondering. Supervisory climate was unrelated to both types of ruminative thinking. The stability of social relations within workgroups was negatively associated with affective rumination as well as with problem-solving pondering, whereas the job setting was only associated with problem-solving pondering. A cross-level interaction indicated a positive moderation effect of collegial climate on the relationship between job stressors and affective rumination. The findings indicate that a positive collegial climate can buffer the negative impact of low to average levels of job stressors on work-related thoughts and lead to the conclusion that the social context in which job stressors are experienced may alter individuals’ ability to mentally unwind from work.
Improving assessment of urban racial segregation by partitioning a region into racial enclaves
Authors: Dmowska Anna , Stepinski Tomasz F
Published: March 2021

Frequently, a single-value metric is needed to rank urban regions with respect to the level of multiracial segregation or to compare a segregation level of a single urban region at two different times. Assessment of segregation depends not only on a metric used but also on a choice of region’s partitioning. The standard practice is to partition the region into single-scale subregions. In the United States, census tracts are the subregions of choice. Census aggregation units including tracts are delineated without a direct regard to racial homogeneity and are in fact heterogeneous. Consequently, using tracts as subdivisions leads to the underestimation of the segregation level of the entire region. Here we propose to partition a region into racial enclaves—units having boundaries that align with transitions between different racial compositions. By reflecting true demographic structure, such units minimize their internal racial inhomogeneity resulting in improved assessment of segregation. Enclaves are defined as aggregates of adjacent census blocks (smallest and the most racially homogeneous census units) of similar composition. In a typical US urban region, effective population size of enclaves is an order of magnitude larger than the size of a census tract and yet the segregation calculated based on enclaves is larger than segregation based on census tracts. The proposed methodology is described and applied to a set of 61 largest cities in the US in their metropolitan statistical areas as well as their urban areas boundaries using 1990 and 2010 block-level data. The method is compared to the standard methodology using correlations between cities’ segregation rankings.
Creating a quantitative, ecosystem-service-based index of nature in the highly urbanized and arid Los Angeles County
Authors: Freitag Amy , Burkart Heidi , Fleming Chloe S , Regan Seann D
Published: March 2021

Before evaluating the abundance and quality of nature in a city, one must define the concept of nature according to resident experience and climatological conditions. For Los Angeles (L.A.) County, home to a sociologically diverse and highly developed city in a Mediterranean climate that experienced drought conditions for the last decade, this represents a formidable theoretical and empirical challenge. In support of an Integrated Vulnerability Assessment, we developed an index of natural resources with the aid of local partnerships. This effort required local expert participation and resulted in the creation of a large database of available regional data. This index was created to investigate the spatial footprint of natural resources in relation to predicted high risk natural hazard areas. This paper demonstrates analytical applications of this index, which consists of six component indicators: greenness, biodiversity, habitat fragmentation, significant ecological areas, tree canopy cover, and wetland cover. Data for each component were compiled into a geodatabase, scaled, aggregated to Census block group areas, and combined to create the natural resources index (the Index). The Index can then be compared with natural hazard spatial data to determine relative vulnerability to these hazards, interactions with other types of vulnerabilities, and where adaptive capacity may be lacking. Results highlight areas of opportunity for multifaceted risk mitigation and adaptation efforts.
Impact of Religion on Traditional Health Care Practices Among the Lepchas of Upper and Lower Lingthem of Upper Dzongu, Sikkim, India
Authors: Thapa Manisha , Tarafdar Pinak
Published: March 2021

In all cultures and regions, the concept of health varies, based on the type of environment and prevalent sociocultural traditions. The present study is conducted among the Lepchas of the village of Lingthem divided into two sectors—Upper and Lower Lingthem, Upper Dzongu, North Sikkim. This population comprising Buddhist Lepchas residing away from the mainstream through poor infrastructural facilities still maintain ethnomedical health care practices without influence of major Indian healing systems. Living in the area of Dzongu exclusively inhabited by Lepchas revival of ancient cultural practices is evident among Lepchas of Lingthem. The structure of religious beliefs prevalent among the Lepchas, including traditional animistic as well as Buddhist practices, greatly influence forms of treatment sought for specific ailments. Even today, the use and maintenance of traditional health care with syncretized Buddhist religious belief among residents of Lingthem act as a vital source for understanding the influence of religion on traditional health care practices. Despite the presence of a few modern health care agencies, the traditional treatment of Bongthing (Lepcha shaman) and Buddhist monks remain widely popular as primary means of health care.
Optimizing the Virtual Otolaryngology Residency Information Sessions: A Survey of Applicants
Authors: Grauer Jordan , Hakimi Amir Aaron , Malekzadeh Sonya
Published: March 2021

The 2020‐2021 otolaryngology residency application cycle has been immensely distorted by travel restrictions mandated in response to coronavirus disease 2019, limiting opportunities for applicants to meet and rotate with programs of interest. The purpose of this study was to evaluate otolaryngology applicants’ preferences toward the content and format of virtual residency information sessions. An anonymous online survey was developed to gauge applicants’ virtual exposure to otolaryngology programs and investigate their preferences during virtual sessions. Almost all respondents attended at least 1 virtual information session (89%). Respondents felt that the most important aspects of these sessions were meeting residents, learning about operative volume, and meeting faculty. The majority (85%) preferred these sessions last no longer than 2 hours. Participants preferred virtual sessions to include breakout sessions with participant video/microphone on. These findings have implications for future virtual resident recruitment strategies.
Foregrounding the community: Geo-historical entanglements of community energy, environmental justice, and place in Taihsi Village, Taiwan
Authors: Lai Huei-Ling
Published: March 2021

Studies on community energy have generated many useful insights concerning its potentials and challenges in facilitating energy transitions. However, this line of inquiry tends to overlook the crucial significance of site-specific contexts, concerns, and needs beyond the energy system and often generalizes these under a “civil society” umbrella. To study community energy on its own terms, this paper proposes a more grounded approach based on the relational place-making framework. It draws upon the case of the Taihsi Green Energy and Health Community Initiative in Taiwan to investigate how the emergence, development, and framing of this initiative are entangled with geo-historically produced concerns about the village’s socio-economic marginalization and suffering from petrochemical pollution. The findings suggest that community energy in this context was a proactive continuation of place-based activism for environmental justice; its value to this damaged community lied in its potential to create self-reliant socio-material relations alternative to those relied on the patronage of petrochemical interests. However, this justice-oriented aspiration tended to be discounted in national-level energy transitions agenda, revealing a tension between citizen-oriented and community-based energy projects. The paper argues that a relational place-based analysis is crucial in recognizing the grounded meanings and values of a community energy initiative, which can address the decontextualizing tendency in many community energy studies to better help policymakers and advocates enhance energy justice in disadvantaged communities.
Risk perception on the labour ward: A mixed methods study
Authors: McCarthy Claire , Meaney Sarah , Rochford Marie , O’Donoghue Keelin
Published: March 2021

Healthcare providers commonly experience risky situations in the provision of maternity care, and there has been increased focus on the lived experience in recent years. We aimed to assess opinions on, understanding of and behaviours of risk on the LW by conducting a mixed methods study.

Staff working in a LW setting completed a descriptive questionnaire-based study, followed by qualitative structured interviews. Statistical analysis was performed with SPSS on quantitative data and thematic analysis performed on qualitative data.

Nearly two thirds of staff (64%; 73/114) completed the questionnaire, with 56.2% (n = 47) experiencing risk on a daily basis. Experiencing risk evoked feelings of apprehension (68.4%; n = 50) and worry (60.2%; n = 44) which was echoed in the qualitative work. Structured clinical assessment was utilised in risky situations, and staff described “ going on autopilot” to manage these situations. A large number of respondents reflected on their provision of care following an adverse event (87.7%; n = 64). Debriefing was mentioned as an important practice following such events by all respondents.

This study describes the negative terminology prevailing in emergency obstetric care. These experiences can have a profound impact on staff. Risk reduction strategies and the provision of increased staff support and training are crucial to improve staff wellbeing in stressful scenarios.
Idiopathic pulmonary fibrosis cluster analysis highlights diagnostic delay and cardiovascular comorbidity association with outcome
Authors: Bordas-Martínez Jaume , Gavaldà Ricard , Shull Jessica G. , Vicens-Zygmunt Vanesa , Planas-Cerezales Lurdes , Bermudo-Peloche Guadalupe , Santos Salud , Salord Neus , Monasterio Carmen , Molina-Molina Maria , Suarez-Cuartin Guillermo
Published: March 2021

Introduction

Idiopathic pulmonary fibrosis (IPF) prognosis is heterogeneous despite antifibrotic treatment. Cluster analysis has proven to be a useful tool in identifying interstitial lung disease phenotypes, which has yet to be performed in IPF. The aim of this study is to identify phenotypes of IPF with different prognoses and requirements.

Methods

Observational retrospective study including 136 IPF patients receiving antifibrotic treatment between 2012 and 2018. Six patients were excluded due to follow-up in other centres. Cluster analysis of 30 variables was performed using approximate singular value-based tensor decomposition method and comparative statistical analysis.

Results

The cluster analysis identified three different groups of patients according to disease behaviour and clinical features, including mortality, lung transplant and progression-free survival time after 3-year follow-up. Cluster 1 (n=60) was significantly associated (p=0.02) with higher mortality. Diagnostic delay was the most relevant characteristic of this cluster, as 48% of patients had ≥2 years from first respiratory symptoms to antifibrotic treatment initiation. Cluster 2 (n=22) had the longest progression-free survival time and was correlated to subclinical patients evaluated in the context of incidental findings or familial screening. Cluster 3 (n=48) showed the highest percentage of disease progression without cluster 1 mortality, with metabolic syndrome and cardiovascular comorbidities as the main characteristics.

Conclusion

This cluster analysis of IPF patients suggests that diagnostic and treatment delay are the most significant factors associated with mortality, while IPF progression was more related to metabolic syndrome and cardiovascular comorbidities.
In silico comparative study of SARS-CoV-2 proteins and antigenic proteins in BCG, OPV, MMR and other vaccines: evidence of a possible putative protective effect
Authors: Haddad-Boubaker Sondes , Othman Houcemeddine , Touati Rabeb , Ayouni Kaouther , Lakhal Marwa , Ben Mustapha Imen , Ghedira Kais , Kharrat Maher , Triki Henda
Published: March 2021

Background

Coronavirus Disease 2019 (COVID-19) is a viral pandemic disease that may induce severe pneumonia in humans. In this paper, we investigated the putative implication of 12 vaccines, including BCG, OPV and MMR in the protection against COVID-19. Sequences of the main antigenic proteins in the investigated vaccines and SARS-CoV-2 proteins were compared to identify similar patterns. The immunogenic effect of identified segments was, then, assessed using a combination of structural and antigenicity prediction tools.

Results

A total of 14 highly similar segments were identified in the investigated vaccines. Structural and antigenicity prediction analysis showed that, among the identified patterns, three segments in Hepatitis B, Tetanus, and Measles proteins presented antigenic properties that can induce putative protective effect against COVID-19.

Conclusions

Our results suggest a possible protective effect of HBV, Tetanus and Measles vaccines against COVID-19, which may explain the variation of the disease severity among regions.
A new algorithm to train hidden Markov models for biological sequences with partial labels
Authors: Li Jiefu , Lee Jung-Youn , Liao Li
Published: March 2021

Background

Hidden Markov models (HMM) are a powerful tool for analyzing biological sequences in a wide variety of applications, from profiling functional protein families to identifying functional domains. The standard method used for HMM training is either by maximum likelihood using counting when sequences are labelled or by expectation maximization, such as the Baum–Welch algorithm, when sequences are unlabelled. However, increasingly there are situations where sequences are just partially labelled. In this paper, we designed a new training method based on the Baum–Welch algorithm to train HMMs for situations in which only partial labeling is available for certain biological problems.

Results

Compared with a similar method previously reported that is designed for the purpose of active learning in text mining, our method achieves significant improvements in model training, as demonstrated by higher accuracy when the trained models are tested for decoding with both synthetic data and real data.

Conclusions

A novel training method is developed to improve the training of hidden Markov models by utilizing partial labelled data. The method will impact on detecting de novo motifs and signals in biological sequence data. In particular, the method will be deployed in active learning mode to the ongoing research in detecting plasmodesmata targeting signals and assess the performance with validations from wet-lab experiments.
Development of genic KASP SNP markers from RNA-Seq data for map-based cloning and marker-assisted selection in maize
Authors: Chen Zhengjie , Tang Dengguo , Ni Jixing , Li Peng , Wang Le , Zhou Jinhong , Li Chenyang , Lan Hai , Li Lujiang , Liu Jian
Published: March 2021

Background

Maize is one of the most important field crops in the world. Most of the key agronomic traits, including yield traits and plant architecture traits, are quantitative. Fine mapping of genes/ quantitative trait loci (QTL) influencing a key trait is essential for marker-assisted selection (MAS) in maize breeding. However, the SNP markers with high density and high polymorphism are lacking, especially kompetitive allele specific PCR (KASP) SNP markers that can be used for automatic genotyping. To date, a large volume of sequencing data has been produced by the next generation sequencing technology, which provides a good pool of SNP loci for development of SNP markers. In this study, we carried out a multi-step screening method to identify kompetitive allele specific PCR (KASP) SNP markers based on the RNA-Seq data sets of 368 maize inbred lines.

Results

A total of 2,948,985 SNPs were identified in the high-throughput RNA-Seq data sets with the average density of 1.4 SNP/kb. Of these, 71,311 KASP SNP markers (the average density of 34 KASP SNP/Mb) were developed based on the strict criteria: unique genomic region, bi-allelic, polymorphism information content (PIC) value ≥0.4, and conserved primer sequences, and were mapped on 16,161 genes. These 16,161 genes were annotated to 52 gene ontology (GO) terms, including most of primary and secondary metabolic pathways. Subsequently, the 50 KASP SNP markers with the PIC values ranging from 0.14 to 0.5 in 368 RNA-Seq data sets and with polymorphism between the maize inbred lines 1212 and B73 in in silico analysis were selected to experimentally validate the accuracy and polymorphism of SNPs, resulted in 46 SNPs (92.00%) showed polymorphism between the maize inbred lines 1212 and B73. Moreover, these 46 polymorphic SNPs were utilized to genotype the other 20 maize inbred lines, with all 46 SNPs showing polymorphism in the 20 maize inbred lines, and the PIC value of each SNP was 0.11 to 0.50 with an average of 0.35. The results suggested that the KASP SNP markers developed in this study were accurate and polymorphic.

Conclusions

These high-density polymorphic KASP SNP markers will be a valuable resource for map-based cloning of QTL/genes and marker-assisted selection in maize. Furthermore, the method used to develop SNP markers in maize can also be applied in other species.
Viral etiology and epidemiology of pediatric patients hospitalized for acute respiratory tract infections in Macao: a retrospective study from 2014 to 2017
Authors: Lei Cheng , Yang Lisong , Lou Cheong Tat , Yang Fan , SiTou Kin Ian , Hu Hao , Io King , Cheok Kun Tat , Pan Baoquan , Ung Carolina Oi Lam
Published: March 2021

Background

Acute respiratory infections (ARIs) are among the leading causes of hospitalization in children. Understanding the local dominant viral etiologies is important to inform infection control practices and clinical management. This study aimed to investigate the viral etiology and epidemiology of respiratory infections among pediatric inpatients in Macao.

Methods

A retrospective study using electronic health records between 2014 and 2017 at Kiang Wu Hospital was performed. Nasopharyngeal swab specimens were obtained from hospitalized children aged 13 years or younger with respiratory tract diseases. xMAP multiplex assays were employed to detect respiratory agents including 10 respiratory viruses. Data were analyzed to describe the frequency and seasonality.

Results

Of the 4880 children enrolled in the study, 3767 (77.1%) were positive for at least one of the 13 viral pathogens tested, of which 2707 (55.5%) being male and 2635 (70.0%) under 2 years old. Among the positive results, there were 3091 (82.0%) single infections and 676 (18.0%) multiple infections. The predominant viruses included human rhinovirus/enterovirus (HRV/EV 27.4%), adenovirus (ADV, 15.8%), respiratory syncytial virus B (RSVB, 7.8%) and respiratory syncytial virus A (RSVA, 7.8%). The detection of viral infection was the most prevalent in autumn (960/1176, 81.6%), followed by spring (1095/1406, 77.9%), winter (768/992, 77.4%), and summer (944/1306, 72.3%), with HRV/EV and ADV being most commonly detected throughout the 4 years of study period. The detection rate of viral infection was highest among ARI patients presented with croup (123/141, 87.2%), followed by lower respiratory tract infection (1924/2356, 81.7%) and upper respiratory tract infection (1720/2383, 72.2%). FluA, FluB and ADV were positive factors for upper respiratory tract infections. On the other hand, infection with RSVA, RSVB, PIV3, PIV4, HMPV, and EV/RHV were positively associated with lower respiratory tract infections; and PIV1, PIV2, and PIV3 were positively associated with croup.

Conclusions

This is the first study in Macao to determine the viral etiology and epidemiology of pediatric patients hospitalized for ARIs. The study findings can contribute to the awareness of pathogen, appropriate preventative measure, accurate diagnosis, and proper clinical management of respiratory viral infections among children in Macao.
Optimal empiric treatment for KPC-2-producing Klebsiella pneumoniae infections in critically ill patients with normal or decreased renal function using Monte Carlo simulation
Authors: Wang Guoan , Yu Wei , Cui Yushan , Shi Qingyi , Huang Chen , Xiao Yonghong
Published: March 2021

Background

Limited clinical studies describe the pharmacodynamics of fosfomycin (FOS), tigecycline (TGC) and colistin methanesulfonate (CMS) in combination against KPC-producing Klebsiella pneumoniae (KPC-Kp). Population pharmacokinetic models were used in our study. Monte Carlo simulation was conducted to calculate probability of target attainment (PTA) and cumulative fraction of response (CFR) of each agent alone and in combination against KPC-Kp in patients with normal or decreased renal function.

Results

The simulated regimen of FOS 6 g q8h reached ≥90% PTA against a MIC of 64 mg/L in patients with normal renal function. For patients with renal impairment, FOS 4 g q8h could provide sufficient antimicrobial coverage against a MIC of 128 mg/L. And increasing the daily dose could result to the cut-off value to 256 mg/L in decreased renal function. For TGC, conventional dosing regimens failed to reach 90% PTA against a MIC of 2 mg/L. Higher loading and daily doses (TGC 200/400 mg loading doses followed by 100 mg q12h/200 mg q24h) were needed. For CMS, none achieved 90% PTA against a MIC of 2 mg/L in normal renal function. Against KPC-Kp, the regimens of 200/400 mg loading dose followed by 100 q12h /200 mg q24h achieved > 80% CFRs regardless of renal function, followed by CMS 9 million IU loading dose followed by 4.5/3 million IU q12h in combination with FOS 8 g q8h (CFR 75–91%).

Conclusions

The use of a loading dose and high daily dose of TGC and CMS in combination with FOS can provide sufficient antimicrobial coverage against critically ill patients infected with KPC-Kp.
Health outcomes of smoking during pregnancy and the postpartum period: an umbrella review
Authors: Avşar Tuba Saygın , McLeod Hugh , Jackson Louise
Published: March 2021

Background

Smoking during pregnancy (SDP) and the postpartum period has serious health outcomes for the mother and infant. Although some systematic reviews have shown the impact of maternal SDP on particular conditions, a systematic review examining the overall health outcomes has not been published. Hence, this paper aimed to conduct an umbrella review on this issue.

Methods

A systematic review of systematic reviews (umbrella review) was conducted according to a protocol submitted to PROSPERO (CRD42018086350). CINAHL, EMBASE, MEDLINE, PsycINFO, Web of Science, CRD Database and HMIC databases were searched to include all studies published in English by 31 December 2017, except those focusing exclusively on low-income countries. Two researchers conducted the study selection and quality assessment independently.

Results

The review included 64 studies analysing the relationship between maternal SDP and 46 health conditions. The highest increase in risks was found for sudden infant death syndrome, asthma, stillbirth, low birth weight and obesity amongst infants. The impact of SDP was associated with the number of cigarettes consumed. According to the causal link analysis, five mother-related and ten infant-related conditions had a causal link with SDP. In addition, some studies reported protective impacts of SDP on pre-eclampsia, hyperemesis gravidarum and skin defects on infants. The review identified important gaps in the literature regarding the dose-response association, exposure window, postnatal smoking.

Conclusions

The review shows that maternal SDP is not only associated with short-term health conditions (e.g. preterm birth, oral clefts) but also some which can have life-long detrimental impacts (e.g. obesity, intellectual impairment).

Implications

This umbrella review provides a comprehensive analysis of the overall health impacts of SDP. The study findings indicate that while estimating health and cost outcomes of SDP, long-term health impacts should be considered as well as short-term effects since studies not including the long-term outcomes would underestimate the magnitude of the issue. Also, interventions for pregnant women who smoke should consider the impact of reducing smoking due to health benefits on mothers and infants, and not solely cessation.
Drug-drug interactions in subjects enrolled in SWOG trials of oral chemotherapy
Authors: Marcath Lauren A. , Finley Colin M. , Wong Siu Fun , Hertz Daniel L.
Published: March 2021

Background

Patients with cancer are at increased risk of drug-drug interactions (DDI), which can increase treatment toxicity or decrease efficacy. It is especially important to thoroughly screen DDI in oncology clinical trial subjects to ensure trial subject safety and data accuracy. This study determined the prevalence of potential DDI involving oral anti-cancer trial agents in subjects enrolled in two SWOG clinical trials.

Methods

Completed SWOG clinical trials of commercially available agents with possible DDI that had complete concomitant medication information available at enrollment were included. Screening for DDI was conducted through three methods: protocol-guided screening, Lexicomp® screening, and pharmacist determination of clinical relevance. Descriptive statistics were calculated.

Results

SWOG trials S0711 (dasatinib, n = 83) and S0528 (everolimus/lapatinib, n = 84) were included. Subjects received an average of 6.6 medications (standard deviation = 4.9, range 0–29) at enrollment. Based on the clinical trial protocols, at enrollment 18.6% (31/167) of subjects had a DDI and 12.0% (20/167) had a DDI that violated a protocol exclusion criterion. According to Lexicomp®, 28.7% of subjects (48/167) had a DDI classified as moderate or worse, whereas pharmacist review indicated that 7.2% of subjects (12/167) had a clinically relevant interaction. The majority of clinically relevant DDI identified were due to the coadministration of acid suppression therapies with dasatinib (83.3%, 10/12).

Conclusions

The high DDI prevalence in subjects enrolled on SWOG clinical trials, including a high prevalence that violate trial exclusion criteria, support the need for improved processes for DDI screening to ensure trial subject safety and trial data accuracy.
Examining the mediating role of resources in the temporal relationship between proactive burnout prevention and burnout
Authors: Otto Madelon C. B. , Van Ruysseveldt Joris , Hoefsmit Nicole , Van Dam Karen
Published: March 2021

Background

Employees who engage in proactive burnout prevention can prevent burnout by changing aspects of the work, home, and personal domain. However, these proactive behaviors may be impeded by high initial levels of burnout. Based on the conservation of resources theory and the dual-pathway proactivity model, resources were expected to play a vital role in the relationship between proactive burnout prevention and burnout through two distinct processes: a resource-generation process in which proactive burnout prevention negatively affects burnout through an increase in resources, and a resource-depletion process in which proactive burnout prevention is hindered because high initial levels of burnout negatively affected resources.

Methods

A two-wave longitudinal panel design was used in which 617 employees, mainly employed in government agencies, healthcare and education, were asked to complete an online survey twice with an interval of 1 month.

Results

Results of structural equation modelling showed clear evidence for the resource-generation process in the work, home, and personal domain, and only limited evidence for the resource-depletion process. Solely in the personal domain a small negative indirect effect of burnout on proactive burnout prevention through personal resources was found.

Conclusions

The findings of this study confirm that employees can proactively prevent burnout by investing in resources, yet proactive actions should be taken before increased burnout-complaints impede employees to do so. This study contributes to scientific knowledge on proactive behaviors and burnout prevention by investigating the mechanism underlying the temporal relationship between proactive burnout prevention and burnout. An important practical implication of this study is that it highlights that more attention should be given to employees’ self-initiated actions to prevent burnout, as proactive burnout prevention can effectively reduce levels of burnout.
A novel integrated global coronal aligner helps prevent post-operative standing coronal imbalance in adult spinal deformity patients fused to pelvis: technical notes and preliminary results
Authors: Zhang Jiandang , Chi Pengfei , Cheng Junyao , Wang Zheng
Published: March 2021

Background

Chieving postoperative coronal balance in adult spinal deformity correction surgeries can be challenging. Even with T square rod technique, there were still some cases with good intraoperative coronal alignment but unsatisfactory post-operative standing coronal imbalance. Thus, the novel techniques to obtain global coronal balance are still in great needs. The purpose of this study was to describe a novel integrated global coronal aligner (IGCA) and evaluate its efficacy on avoidance of post-operative coronal imbalance in adult spinal deformity patients fused to pelvis.

Methods

A detailed description of IGCA technique was presented. 52 ASD patients fused to pelvis were divided into two groups (IGCA group, n = 27; and non-IGCA group, n = 25) according to whether intraoperative IGCA was used or not. Preoperative demographics and postoperative outcomes were compared.

Results

There were no significant differences regarding coronal balance difference (CBD) and imbalance/balance ratio between IGCA and non-IGCA groups preoperatively. After surgery, CBD in IGCA group was significantly improved from 24.7 ± 20.3 mm preoperatively to 12.6 ± 6.4 mm postoperatively (t = 3.185 p = 0.004), and imbalance/balance ratio decreased significantly from 55.6% (15/27) preoperatively to 11.1% (3/27) postoperatively (χ2 = 12.000, p = 0.001), while CBD and imbalance/balance ratio in non-IGCA group were not significantly improved. Compared to non-IGCA group, the amount of correction in CBD was significantly larger in IGCA group (t = 3.274, P = 0.002), and imbalance/balance ratio in IGCA group was significantly lowered (χ2 = 8.606 p = 0.003). Further logistic regression analysis revealed IGCA technique was associated with increased odds ratio for postoperative coronal balance (odds ratio: 7.385; 95% confidence interval 1.760–30.980; P = 0.006).

Conclusions

The novel intraoperative IGCA technique could help improve CBD and reduce imbalance/balance ratio. It could help prevent post-operative coronal imbalance in adult spinal deformity patients fused to pelvis.

Level of evidence

3