bluuebunny/crossref_metadata_2025 huggingface dataset:
Chaos, Bedbugs, and Delayed Starts: Stories of Student Retention During Extreme Organizational Upheaval
Authors: Olson Joann S. , Strickland Karyna
Published: October 2020

Recent world events and the ever-changing nature of higher education mean that colleges and universities exist in a state of near-constant flux. This qualitative study explored the experiences of seven college seniors who persisted to graduation after beginning their college careers when their university was admitting lower-division students for the first time in the institution’s history—a significant organizational shift. Themes identified in the data highlight students’ choice to attend a college making major structural changes, what it was like to be the “first freshmen” when the institution was not fully prepared for their arrival, and the factors that led to their decision to persist at the institution. Using a theoretical framework of mattering, the findings suggest that helping students feel that they matter to the institution and reminding students that their adjustment may not be immediate are important strategies for those seeking to promote student retention.
A Novel Scoring System for Small Artery Disease and Medial Arterial Calcification Is Strongly Associated With Major Adverse Limb Events in Patients With Chronic Limb-Threatening Ischemia
Authors: Ferraresi Roberto , Ucci Alessandro , Pizzuto Alessandra , Losurdo Fabrizio , Caminiti Maurizio , Minnella Daniela , Casini Andrea , Clerici Giacomo , Montero-Baker Miguel , Mills Joseph
Published: October 2020

Purpose:

To evaluate the roles of small artery disease (SAD) and medial arterial calcification (MAC) in patients with chronic limb-threatening ischemia (CLTI) and to identify any correlation between these factors and peripheral artery disease (PAD) or outcomes after treatment.

Materials and Methods:

A retrospective review was conducted of 259 limbs with tissue loss among 223 CLTI patients (mean age 72.2±11.4 years; 194 men) having an angiographic foot vessel study, foot radiography, and at least 6 months of follow-up after intervention. SAD and MAC were quantified using a 3-level score (0=absent, 1=moderate, 2=severe) based on angiography for SAD and foot radiographs for MAC. The MAC score was validated and compared with the SAD score, evaluating their associations with PAD distribution and clinical outcomes.

Results:

Based on the MAC score, the 259 limbs were classified as 55 group 0 (21.2%), 89 group 1 (34.4%), and 115 group 2 (44.4%). The SAD score stratified the 259 limbs as 67 group 0 (25.9%), 76 group 1 (29.3%), and 116 group 2 (44.8%). Interobserver reproducibility of the MAC score was high (correlation coefficient 0.96). Sensitivity and specificity of the MAC score in detecting SAD was 100% and 98.1%, respectively, in SAD groups 0 and 2 vs 99.1% and 92.7%, respectively, for SAD group 1. PAD was more proximal in MAC and SAD groups 0 and more distal in groups 1 and 2. Both MAC and SAD scores were able to predict clinical endpoints. Multivariable analysis demonstrated that the MAC score represents an independent risk factor for adverse limb events.

Conclusion:

SAD and MAC must be considered expressions of the same obstructing disease, able to adversely impact the fate of CLTI patients. SAD and MAC scores are powerful prognostic indicators of major adverse limb events in CLTI patients.
Construction and Validation of Nomograms for Predicting the Prognosis of Juvenile Osteosarcoma: A Real-World Analysis in the SEER Database
Authors: Jiang Yao , Wang Tianyu , Wei Zizheng
Published: October 2020

Background:

Osteosarcoma is one of the most common malignant bone tumors, with a high incidence in adolescence. The objective of this study was to construct prognostic nomograms for predicting the prognosis of juvenile osteosarcoma.

Methods:

Patients with osteosarcoma diagnosed between 2004 and 2015 were identified in the Surveillance, Epidemiology, and End Results (SEER) database. The essential clinical predictors were identified with univariate and multivariate Cox analysis. Nomograms were constructed to predict the 3- and 5-year cancer- specific survival (CSS) and overall survival (OS). Concordance index (C-index) and calibration plots were performed to validate the predictive performance of nomograms.

Results:

We enrolled 736 adolescents with osteosarcoma from the SEER database, with 516 samples grouped into a training cohort and 220 samples grouped into a validation cohort. In multivariate analysis of the training cohort, predictors including tumor size, surgery treatment and AJCC stage were found to be associated with OS and CSS, while age was only associated with CSS. Construction of nomograms based on these predictors was performed to evaluate the prognosis of adolescents with osteosarcoma. The C-index and calibration curves also showed the satisfactory performance of these nomograms for prognosis prediction.

Conclusion:

The developed nomograms are useful tools for precisely predicting the prognosis of adolescents with osteosarcoma, which could enable patients to be more accurately managed in clinical practice.
Clinical outcomes from profundoplasty performed as a sole procedure for revascularization in critically ischaemic limbs
Authors: Elsharkawi Mohamed , Elkassaby Mohammed , McVeigh Niall , Dowdall Joseph , Barry Mary , Sheehan Stephen
Published: October 2020

Objectives

The aim of this study is to investigate the durability and clinical efficacy of profundoplasty as a sole procedure in patients presenting with critical limb ischaemia associated with profunda femoral artery disease and superficial femoral artery occlusion.

Methods

Retrospective analysis of outcomes from all patients who underwent surgical profundoplasty in a single tertiary referral centre was performed. Patients who presented with either rest pain or tissue loss and had combined profunda femoral artery disease and superficial femoral artery occlusion were included in the study. Outcomes were compared between the rest pain and the tissue loss groups.

Results

Between 2009 and 2019, 51 procedures were performed in 49 patients; 27 (53%) procedures were performed for rest pain and 24 (47%) for tissue loss. Technical success was 100% in both groups. Procedure success was significantly better in the rest pain group owing to lower procedure-related complications ( p = 0.037). Incidence of major adverse cardiovascular events was higher in the tissue loss group with five reported cases compared to only one in the rest pain group ( p = .05); 85.2% of patients with rest pain experienced clinical improvement compared to only 33.3% in the tissue loss group ( p < .001). Higher rates of re-intervention were recorded in the tissue loss group, but this was not statistically significant. Amputation-free survival at 3, 6 and 12 months was 96%, 96% and 92% in the rest pain group, respectively, compared to 77%, 67% and 54% in the tissue loss group ( p = .004). At one-year, freedom from major adverse limb events was lower in patients with tissue loss at 43% compared to 81% in patients with rest pain ( p = .009).

Conclusions

Profundoplasty performed as a sole procedure for revascularisation of the critically ischaemic limb is a viable straightforward option. However, our results suggest that it may be more effective in the treatment of rest pain rather than in the setting of tissue loss when a combined superficial femoral artery angioplasty or distal bypass may be required.
Gout management and outcomes during the COVID-19 pandemic: a cross-sectional internet survey
Authors: Singh Jasvinder A. , Edwards N. Lawrence
Published: October 2020

Aim:

We aimed to assess the gout management during the COVID-19 pandemic.

Methods:

We assessed medication use, healthcare utilization, gout-specific health-related quality of life (HRQoL) on the Gout Impact Scale (GIS), psychological distress using the patient health questionnaire-4 (PHQ-4), and resilience in people with self-reported physician-diagnosed gout during the COVID-19 pandemic in a cross-sectional Internet survey.

Results:

Among the 122 survey respondents with physician-diagnosed gout, 82% were prescribed urate-lowering therapy (ULT) and 66% were taking ULT daily; mean age was 54.2 years [standard deviation (SD), 13.8], 65% were male, and 79% were White. More regular use of gout medication was reported during the COVID-19 pandemic: allopurinol, 44%; colchicine, 37%; non-steroidal anti-inflammatory drugs, 36%. Gout flares were common: 63% had ⩾1 gout flare monthly; 11% went to emergency room/urgent care; and 2% were hospitalized with gout flares. Between 41% and 56% of respondents reported more difficulty with gout management and related functional status related to COVID-19; 17–37% had difficulty with healthcare access for gout. HRQOL deficits were evident for gout concern overall, 79.4 (SD, 25); unmet gout treatment need, 64.5 (SD, 27.1); and gout concern during flare, 67.3 (SD, 27.1); but less so for gout medication side effects, 48.9 (SD, 27.4). Psychological distress was moderate in 19% and severe in 15% (mild, 22%; normal, 45%). Resilience score on Connor–Davidson Resilience Scale (CD-RISC2) was 5.6 (SD, 1.8; range 0–8). Compared with no/mild psychological distress, moderate–severe psychological distress during the COVID-19 pandemic was significantly associated with more difficulty getting gout medication filled ( p = 0.02), flares treated ( p = 0.005), and receiving gout education ( p = 0.001).

Conclusion:

Healthcare gaps, psychological distress, and HRQoL deficits were commonly reported by people with gout during the COVID-19 pandemic. Interventions to address these challenges for people with gout during the COVID-19 pandemic are needed.
Optimal antithrombotic therapy after transcatheter aortic valve replacement in patients with atrial fibrillation
Authors: Zeng Qingchun , Cheng Zhendong , Xia Yi , Cheng Rui , Ou Ailian , Li Xinrui , Xu Xingbo , Huang Yuli , Xu Dingli
Published: October 2020

Atrial fibrillation (AF) is prevalent in patients with aortic stenosis (AS) undergoing transcatheter aortic valve replacement (TAVR). Depending on the timing of AF detection, it is usually categorized as pre-existing AF or new-onset AF. Antiplatelet therapy, rather than a vitamin K antagonist, may be considered as the primary treatment for patients without an indication for oral anticoagulants who undergo TAVR. However, the optimal postprocedural antithrombotic regimen for patients with AF undergoing TAVR remains unknown. In this review, we briefly introduce the management strategies of antithrombotic therapy and list the evidence from related studies to elucidate the optimal antithrombotic management for patients with AF undergoing TAVR.
Advancing the social identity theory of leadership: A meta-analytic review of leader group prototypicality
Authors: Steffens Niklas K. , Munt Katie A. , van Knippenberg Daan , Platow Michael J. , Haslam S. Alexander
Published: October 2020

This research advances a social identity approach to leadership through a meta-analysis examining four novel hypotheses that clarify the nature and impact of leader group prototypicality (the extent to which a leader is perceived to embody shared social identity). A random-effects meta-analysis ( k = 128, N = 32,834) reveals a moderate-to-large effect of prototypicality that holds across evaluative and behavioral outcomes. The effect is stronger (a) when prototypicality is conceptualized as the ideal-type rather than the average group member, (b) for stronger prototypes (indexed by group longevity), and (c) for group members in formal rather than nonformal leadership roles. The effect is not contingent on group prototypicality entailing differentiation from other (out)groups. Additionally, results provide meta-analytic evidence of widely examined key factors: follower group identification (which enhances the relationship) and leader group-serving behavior (which attenuates the relationship). Building on these findings, we outline the implications for the next wave of theoretical and empirical work.
Physiotherapy after tibial plateau fracture fixation: A systematic review of the literature
Authors: Iliopoulos Efthymios , Galanis Nikiforos
Published: October 2020

Background:

Tibial plateau fractures are frequent injuries that orthopaedic surgeons face. It has been reported that they have a significant negative impact on the patients’ lives, decreasing their quality of live, keeping them of work for long periods of time and reducing their activity levels.

Aim:

Interestingly, there is not enough focus in the literature about the post-operative rehabilitation of these patients. The aim of the present review is to investigate this field of the literature and try to give answers in four main questions: the range of motion exercises post-surgery, the immobilisation, the weight-bearing status and the ongoing rehabilitation.

Materials and Methods:

A literature search was conducted using the PubMed and the Google Scholar search engines. A total of 39 articles met the criteria to be included in the study.

Results:

The literature about this subject is scarce and controversial. Early range of motion exercises should be encouraged as soon as possible after the procedure. The immobilisation after plate fixation does not seem to be correlated with any benefits to the patients. The weight-bearing status of the patients was the most controversial in the literature with the early weight-bearing gaining ground at the most recent studies. Tibia plateau fractures can have significant impact on the patients’ lives, so ongoing rehabilitation with focus on quadriceps strengthening and proprioception exercises is recommended.

Conclusion:

The present literature review illuminates the controversy that exists in the literature about the physiotherapy following tibia plateau fracture fixation. Early range of motion exercises and early weight bearing should be encouraged. Immobilisation does not seem to provide any benefit. Ongoing rehabilitation should be considered with the view of better clinical outcomes.
What happens to our amputees? The Darling Downs experience
Authors: Vasudeva Varun , Parr Adam , Loch Alan , Wall Chris
Published: October 2020

Background:

Major lower limb amputation is occasionally required in the management of end-stage pathology where other treatment options have failed. The primary aim of this study was to determine the 30-day and 1-year mortality rates of patients undergoing nontraumatic major lower limb amputation. Secondary aims were to investigate risk factors for poor outcomes, incidence of previous minor amputation, and the rate of subsequent major amputation.

Methods:

All nontraumatic, major lower limb amputations performed at Toowoomba Hospital during an 18-year period were retrospectively reviewed. Mortality data were obtained from the Queensland Registry of Births, Deaths and Marriages. Kaplan–Meier analysis was performed to determine survival after amputation.

Results:

A total of 147 patients were included in the study, with 104 undergoing below knee and 43 undergoing above knee amputations. Ten patients identified as having an Aboriginal and Torres Strait Islander background. For all patients, the 30-day mortality was 4.1% and 1-year mortality was 21.1%. For Indigenous patients, 30-day mortality was 10%. Previous minor amputation had occurred in 40 patients. Twenty-nine patients underwent further minor surgery after their initial major amputation, with thirteen requiring subsequent major amputation. Factors that increased mortality risk were the presence of peripheral vascular disease, an American Society of Anesthesiologists score of four and age greater than 65 years.

Conclusion:

The morbidity and mortality following major lower limb amputation is significant. The findings of this study highlight the importance of preventative measures to minimize the incidence of lower limb amputations in the future.
Advancements in Legal Education in India: Challenges and Opportunities for Interdisciplinary Research
Authors: Rajashree K. , Singai Chetan , Shimray Shimreichon Awungshi
Published: October 2020

Social, economic and political changes have brought new challenges and divergent views to twenty-first-century legal education. Law is an expression of the social idea, and more creative solutions evolve from interdisciplinary collaborations. The resolution by legal luminaries to elevate legal research to a high standing, on par with other disciplines, is yet to find a foothold even after the introduction of reforms to legal education in the past two decades. This article makes an attempt to explore the emerging interdisciplinary trends, with the innumerable challenges that require exploration, identification, analysis and quality enhancement while conducting legal research in order to strike a fine balance between teaching and research, as they supplement each other.

Law is a mechanism for ushering in social change, and the fact that it can never be studied in isolation demands the convergence and divergence of multiple disciplines. Yet, the traditional conceptualization of legal research is largely confined to the judicial process and the exclusion of social process. Keeping in mind the benefits of interdisciplinary association of law with other areas/disciplines and of research being a continuum, the article emphasizes law’s collaboration with other disciplines. The article accentuates the role of law schools to undertake and encourage interdisciplinary legal scholarship to diversify the learning experiences of students in conjunction with other disciplines. Learning through such experiences enables students to find solutions beyond the strict academic discipline of law and at the same time offers ample opportunities for them to explore a wide array of possibilities that interface with legal profession but transcend courtroom practice. A comparative analysis of two educational institutions imparting legal education, taken as cases in point, is performed for the present study.
A Progressive Case of Eosinophilic Myocarditis Due to Eosinophilic Granulomatosis With Polyangiitis in a Caucasian Male
Authors: Civelli Valerie F. , Narang Vishal K. , Sharma Rupam , Sharma Ritika , Kim Jessica , Bhandohal Janpreet , Moosavi Leila , Cobos Everardo
Published: October 2020

Vasculitis is an inflammatory process involving blood vessels of various sizes, including the small vessels in the kidneys to the large vessels, such as the aorta. This inflammatory condition is usually autoimmune in nature and is associated with involvement of many locations, such as the sinuses, lungs, kidneys, and even the heart. Specifically, eosinophilic granulomatosis with polyangiitis (EGPA) is a systemic vasculitis that may initially hide as asthma, allergic rhinitis, and/or sinusitis. However, it is known to become a lethal disease once progressed to include cardiovascular manifestations. It is important to remember EGPA as a differential for any patient with a history of asthma, allergic rhinitis, and/or sinusitis who also presents with cardiovascular complaints and eosinophilia. Treatment recommendations focus on immunosuppression in such cases. In this article, we discuss the case of a 62-year-old male, with a known history of asthma, who presented to the emergency department with concern for his chest pain and right-sided weakness. He was later diagnosed with EGPA with eosinophilic myocarditis. Diagnosis and treatment are described.
Ion microprobe dating of fissure monazite in the Western Alps: insights from the Argentera Massif and the Piemontais and Briançonnais Zones
Authors: Ricchi Emmanuelle , Gnos Edwin , Rubatto Daniela , Whitehouse Martin John , Pettke Thomas
Published: October 2020

Ion probe 208Pb/232Th fissure monazite ages from the Argentera External Massif and from the high-pressure units of the Western Alps provide new insights on its Cenozoic tectonic evolution. Hydrothermal monazite crystallizes during cooling/exhumation in Alpine fissures, an environment where monazite is highly susceptible to fluid-mediated dissolution-(re)crystallization. Monazite growth domains visualized by BSE imaging all show a negative Eu anomaly, positive correlation of Sr and Ca and increasing cheralite component (Ca + Th replacing 2REE) with decreasing xenotime (Y) component. The huttonite component (Th + Si replacing REE and P) is very low. Growth domains record crystallization following chemical disequilibrium in a fissure environment, and growing evidence indicates that they register tectonic activity. Fissure monazite ages obtained in this study corroborate previous ages, recording crystallization at ~ 36 Ma, ~ 32–30 Ma, and ~ 25–23 Ma in the high-pressure regions of the Western Alps, interpreted to be respectively related to top-NNW, top-WNW and top-SW thrusting in association with strike-slip faulting. During this latter transpressive phase, younger fissure monazite crystallization is recorded between ~ 20.6 and 14 Ma in the Argentera Massif, interpreted to have occurred in association with dextral strike-slip faulting related to anticlockwise rotation of the Corsica-Sardinia Block. This strike-slip activity is predating orogen-parallel dextral strike-slip movements along and through the internal part of all other External Crystalline Massifs (ECM), starting only at ~ 12 Ma. Our combined compositional and age data for hydrothermal monazite track crystallization related to tectonic activity during unroofing of the Western Alps for over more than 20 million years, offering chronologic insights into how different tectonic blocks were exhumed. The data show that fissures in the high-pressure units formed during greenschist to amphibolite facies retrograde deformation, and later in association with strike-slip faulting.
Printable, Highly Sensitive Flexible Temperature Sensors for Human Body Temperature Monitoring: A Review
Authors: Su Yi , Ma Chunsheng , Chen Jing , Wu Huiping , Luo Weixiang , Peng Yueming , Luo Zebang , Li Lin , Tan Yongsong , Omisore Olatunji Mumini , Zhu Zhengfang , Wang Lei , Li Hui
Published: October 2020

In recent years, the development and research of flexible sensors have gradually deepened, and the performance of wearable, flexible devices for monitoring body temperature has also improved. For the human body, body temperature changes reflect much information about human health, and abnormal body temperature changes usually indicate poor health. Although body temperature is independent of the environment, the body surface temperature is easily affected by the surrounding environment, bringing challenges to body temperature monitoring equipment. To achieve real-time and sensitive detection of various parts temperature of the human body, researchers have developed many different types of high-sensitivity flexible temperature sensors, perfecting the function of electronic skin, and also proposed many practical applications. This article reviews the current research status of highly sensitive patterned flexible temperature sensors used to monitor body temperature changes. First, commonly used substrates and active materials for flexible temperature sensors have been summarized. Second, patterned fabricating methods and processes of flexible temperature sensors are introduced. Then, flexible temperature sensing performance are comprehensively discussed, including temperature measurement range, sensitivity, response time, temperature resolution. Finally, the application of flexible temperature sensors based on highly delicate patterning are demonstrated, and the future challenges of flexible temperature sensors have prospected.
Expression and functions of N-type Cav2.2 and T-type Cav3.1 channels in rat vasopressin neurons under normotonic conditions
Authors: Sato-Numata Kaori , Numata Tomohiro , Ueta Yoichi , Okada Yasunobu
Published: October 2020

Arginine vasopressin (AVP) neurons play essential roles in sensing the change in systemic osmolarity and regulating AVP release from their neuronal terminals to maintain the plasma osmolarity. AVP exocytosis depends on the Ca2+ entry via voltage-gated Ca2+ channels (VGCCs) in AVP neurons. In this study, suppression by siRNA-mediated knockdown and pharmacological sensitivity of VGCC currents evidenced molecular and functional expression of N-type Cav2.2 and T-type Cav3.1 in AVP neurons under normotonic conditions. Also, both the Cav2.2 and Cav3.1 currents were found to be sensitive to flufenamic acid (FFA). TTX-insensitive spontaneous action potentials were suppressed by FFA and T-type VGCC blocker Ni2+. However, Cav2.2-selective ω-conotoxin GVIA failed to suppress the firing activity. Taken together, it is concluded that Cav2.2 and Cav3.1 are molecularly and functionally expressed and both are sensitive to FFA in unstimulated rat AVP neurons. Also, it is suggested that Cav3.1 is primarily involved in their action potential generation.
EMU: reconfigurable graphical user interfaces for Micro-Manager
Authors: Deschamps Joran , Ries Jonas
Published: October 2020

Background

Advanced light microscopy methods are key to many biological studies. Their ease of use depends, besides experimental aspects, on intuitive graphical user interfaces (GUI). The open-source software Micro-Manager offers a universal GUI for microscope control but requires implementing plugins to further tailor it to specific systems. However, GUIs are often tailored to a single system. Since even similar devices can have different Micro-Manager device properties, such as power percentage versus absolute power, directly transferring a GUI to another instrument usually requires changing the source-code.

Results

We developed Easier Micro-Manager User interface (EMU), a Micro-Manager plugin, to simplify building flexible and reconfigurable GUIs. EMU can be seamlessly used with the Java Swing library to create device-independent GUIs for Micro-Manager. Such GUIs are easily transferred to another microscope thanks to an intuitive configuration menu that includes mapping of the device properties to the GUI functionalities and customization of the graphical elements. We also provide resources such as user and programming guides, a tutorial and code examples.

Conclusions

Micro-Manager users now have a powerful tool to improve the user experience on their instruments. EMU GUIs can be easily configured for new microscopes and shared with other research groups. In the future, newly developed GUIs will be added to EMU to benefit the whole community.
Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients
Authors: Lou Shaoke , Li Tianxiao , Spakowicz Daniel , Yan Xiting , Chupp Geoffrey Lowell , Gerstein Mark
Published: October 2020

Background

The pathogenesis of asthma is a complex process involving multiple genes and pathways. Identifying biomarkers from asthma datasets, especially those that include heterogeneous subpopulations, is challenging. Potentially, autoencoders provide ideal frameworks for such tasks as they can embed complex, noisy high-dimensional gene expression data into a low-dimensional latent space in an unsupervised fashion, enabling us to extract distinguishing features from expression data.

Results

Here, we developed a framework combining a denoising autoencoder and a supervised learning classifier to identify gene signatures related to asthma severity. Using the trained autoencoder with 50 hidden units, we found that hierarchical clustering on the low-dimensional embedding corresponds well with previously defined and clinically relevant clusters of patients. Moreover, each hidden unit has contributions from each of the genes, and pathway analysis of these contributions shows that the hidden units are significantly enriched in known asthma-related pathways. We then used genes that contribute most to the hidden units to develop a secondary random-forest classifier for directly predicting asthma severity. The feature importance metric from this classifier identified a signature based on 50 key genes, which are associated with severity. Furthermore, we can use these key genes to successfully estimate FEV1/FVC ratios across patients, via support-vector-machine regression.

Conclusion

We found that the denoising autoencoder framework can extract meaningful patterns corresponding to functional gene groups and patient clusters from the gene expression of asthma patients.
In silico benchmarking of metagenomic tools for coding sequence detection reveals the limits of sensitivity and precision
Authors: Golob Jonathan Louis , Minot Samuel Schwartz
Published: October 2020

Background

High-throughput sequencing can establish the functional capacity of a microbial community by cataloging the protein-coding sequences (CDS) present in the metagenome of the community. The relative performance of different computational methods for identifying CDS from whole-genome shotgun sequencing is not fully established.

Results

Here we present an automated benchmarking workflow, using synthetic shotgun sequencing reads for which we know the true CDS content of the underlying communities, to determine the relative performance (sensitivity, positive predictive value or PPV, and computational efficiency) of different metagenome analysis tools for extracting the CDS content of a microbial community. Assembly-based methods are limited by coverage depth, with poor sensitivity for CDS at < 5X depth of sequencing, but have excellent PPV. Mapping-based techniques are more sensitive at low coverage depths, but can struggle with PPV. We additionally describe an expectation maximization based iterative algorithmic approach which we show to successfully improve the PPV of a mapping based technique while retaining improved sensitivity and computational efficiency.

Conclusion

Our benchmarking approach reveals the trade-offs of assembly versus alignment-based approaches and the relative performance of specific implementations when one wishes to extract the protein coding capacity of microbial communities.
An R package for an integrated evaluation of statistical approaches to cancer incidence projection
Authors: Knoll Maximilian , Furkel Jennifer , Debus Jürgen , Abdollahi Amir , Karch André , Stock Christian
Published: October 2020

Background

Projection of future cancer incidence is an important task in cancer epidemiology. The results are of interest also for biomedical research and public health policy. Age-Period-Cohort (APC) models, usually based on long-term cancer registry data (> 20 yrs), are established for such projections. In many countries (including Germany), however, nationwide long-term data are not yet available. General guidance on statistical approaches for projections using rather short-term data is challenging and software to enable researchers to easily compare approaches is lacking.

Methods

To enable a comparative analysis of the performance of statistical approaches to cancer incidence projection, we developed an R package (incAnalysis), supporting in particular Bayesian models fitted by Integrated Nested Laplace Approximations (INLA). Its use is demonstrated by an extensive empirical evaluation of operating characteristics (bias, coverage and precision) of potentially applicable models differing by complexity. Observed long-term data from three cancer registries (SEER-9, NORDCAN, Saarland) was used for benchmarking.

Results

Overall, coverage was high (mostly > 90%) for Bayesian APC models (BAPC), whereas less complex models showed differences in coverage dependent on projection-period. Intercept-only models yielded values below 20% for coverage. Bias increased and precision decreased for longer projection periods (> 15 years) for all except intercept-only models. Precision was lowest for complex models such as BAPC models, generalized additive models with multivariate smoothers and generalized linear models with age x period interaction effects.

Conclusion

The incAnalysis R package allows a straightforward comparison of cancer incidence rate projection approaches. Further detailed and targeted investigations into model performance in addition to the presented empirical results are recommended to derive guidance on appropriate statistical projection methods in a given setting.
Genotype-phenotype correlation of HbH disease in northern Iraq
Authors: Shamoon Rawand P. , Yassin Ahmed K. , Polus Ranan K. , Ali Mohamad D.
Published: October 2020

Background

HbH disease results from dysfunction of three, less commonly two, α-globin genes through various combinations of deletion and non-deletion mutations. Characterization of the mutations and the underlying genotypes is fundamental for proper screening and prevention of thalassaemia in any region. The aim of this study was to explore the genetic arrangements of HbH disease and to correlate the genotypes with the clinical phenotypes.

Methods

A total of 44 HbH disease patients were enrolled in this study. They were clinically and haematologically assessed. The patients were tested for 21 common α-globin gene mutations using multiplex PCR and reverse hybridization. According to the genotype, the patients were categorized into two separate sub-groups, deletion and non-deletion types HbH disease.

Results

Within the studied HbH disease patients, eight different α-globin gene mutations were detected in nine different genetic arrangements. The --MEDand -α3.7deletions were the two most frequently encountered mutations (37.5 and 35.2% respectively). Patients with deletion genotypes constituted 70.4%. The most common detected genotype was --MED/−α3.7(59.1%), followed by αpoly-A1α/αpoly-A1α (13.6%). For the first time, coinheritance of two relatively mild mutations (−α3.7/ααAdana) was unpredictably detected in a 1.5 year-old child with Hb of 7.1 g/dL.

Conclusion

The HbH disease patients’ clinical characteristics were variable with no ample difference between the deletion and non-deletion types. These results can be of benefit for the screening and management of thalassaemia in this region.
A novel Vi-diphtheria toxoid typhoid conjugate vaccine is safe and can induce immunogenicity in healthy Indonesian children 2–11 years: a phase II preliminary report
Authors: Medise Bernie Endyarni , Soedjatmiko Soedjatmiko , Gunardi Hartono , Sekartini Rini , Satari Hindra Irawan , Hadinegoro Sri Rezeki , Wirahmadi Angga , Puspita Mita , Sari Rini Mulia , Yang Jae Seung , Sil Arijit , Sahastrabuddhe Sushant , Bachtiar Novilia Sjafri
Published: October 2020

Background

Typhoid fever caused by Salmonella enteric serovar Typhi (S. Typhi) is a common cause of morbidity in the world. In 2017, 14.3 million cases of Typhoid and paratyphoid fever occurred globally. School age children between 3 to 19 years old are the most affected. Poor sanitation and multi drug resistance have increased the need for vaccines to reduce the global burden of disease. Based on previous trials, typhoid conjugate vaccines have longer- lasting protection, higher efficacy, require fewer doses and are suitable from infancy that allows them to be incorporated into the routine immunization program. Our previous phase I trial proved that a novel Vi-DT typhoid conjugate vaccine is safe and immunogenic in subjects 2–5 and 18–40 years. Our phase II trial consisted of subjects 6 months to 40 years. Our previously published paper on subjects 6 to < 24 months proved that this vaccine is safe and immunogenic for this age group. Therefore, with this paper we aimed to evaluate the safety and immunogenicity in children 2–11 years.

Methods

A randomized, observer-blind, superiority design of Vi-DT Typhoid conjugate vaccine compared to Vi-polysaccharide vaccine (Vi-PS) phase II study was conducted from October 2018 to December 2018 where 200 subjects aged 2–11 years were recruited. A blood sample prior to vaccination was taken, followed by administration of a single dose of either test vaccine (Vi-DT) or control vaccine (Vi-PS) and then a second blood sample was collected 28 days post vaccination. Adverse reactions were assessed and antibody increment was evaluated at 28 days post vaccination through collected serum sample.

Results

Pain was the most common local reaction. Fever and muscle pain were the most common systemic reactions. Both Vi-DT and Vi-PS groups had roughly the same number of adverse reactions. At 28 days post vaccination, 100% of subjects in the Vi-DT group and 93% of subjects in the Vi-PS group produced antibody increment ≥4 times. The Vi-DT group produced a higher GMT as compared to Vi-PS.

Conclusion

Vi-DT vaccine is safe and immunogenic in children 2–11 years old.

Trial registration

Trial registration number: NCT03460405.
Geospatial patterns of comorbidity prevalence among people with osteoarthritis in Alberta Canada
Authors: Liu Xiaoxiao , Shahid Rizwan , Patel Alka B. , McDonald Terrence , Bertazzon Stefania , Waters Nigel , Seidel Judy E. , Marshall Deborah A.
Published: October 2020

Background

Knowledge of geospatial pattern in comorbidities prevalence is critical to an understanding of the local health needs among people with osteoarthritis (OA). It provides valuable information for targeting optimal OA treatment and management at the local level. However, there is, at present, limited evidence about the geospatial pattern of comorbidity prevalence in Alberta, Canada.

Methods

Five administrative health datasets were linked to identify OA cases and comorbidities using validated case definitions. We explored the geospatial pattern in comorbidity prevalence at two standard geographic areas levels defined by the Alberta Health Services: descriptive analysis at rural-urban continuum level; spatial analysis (global Moran’s I, hot spot analysis, cluster and outlier analysis) at the local geographic area (LGA) level. We compared area-level indicators in comorbidities hotspots to those in the rest of Alberta (non-hotspots).

Results

Among 359,638 OA cases in 2013, approximately 60% of people resided in Metro and Urban areas, compared to 2% in Rural Remote areas. All comorbidity groups exhibited statistically significant spatial autocorrelation (hypertension: Moran’s I index 0.24, z score 4.61). Comorbidity hotspots, except depression, were located primarily in Rural and Rural Remote areas. Depression was more prevalent in Metro (Edmonton-Abbottsfield: 194 cases per 1000 population, 95%CI 192–195) and Urban LGAs (Lethbridge-North: 169, 95%CI 168–171) compared to Rural areas (Fox Creek: 65, 95%CI 63–68). Comorbidities hotspots included a higher percentage of First Nations or Inuit people. People with OA living in hotspots had lower socioeconomic status and less access to care compared to non-hotspots.

Conclusions

The findings highlight notable rural-urban disparities in comorbidities prevalence among people with OA in Alberta, Canada. Our study provides valuable evidence for policy and decision makers to design programs that ensure patients with OA receive optimal health management tailored to their local needs and a reduction in current OA health disparities.
LncRNA SNHG14 regulates the DDP-resistance of non-small cell lung cancer cell through miR-133a/HOXB13 pathway
Authors: Xu Li , Xu Yan , Yang Min , Li Jia , Xu Fang , Chen Bo-Lin
Published: October 2020

Background

Recently, long non-coding RNAs (lncRNAs) have been reported to be involved in regulating chemo-resistance of NSCLC, however, the role of lncRNA SNHG14 in the DDP-resistance of NSCLC remains unexplored.

Methods

Relative expression of SNHG14, HOXB13 and miR-133a in DDP-resistant A549 (A549/DDP) cell and its parental cell A549 were measured using qRT-PCR. Cell proliferation viability of indicated A549/DDP cell was estimated via CCK-8 and colony formation experiments. Cell cycle and apoptosis were analyzed through flow cytometry. Expression of apoptosis-related protein and HOXB13 were detected via western blot. The interaction among SNHG14, HOXB13 and miR-133a was predicted by bioinformatics and validated by dual-luciferase reporter assay.

Results

LncRNA SNHG14 and HOXB13 were upregulated while miR-133a was downregulated in A549/DDP cell line compared to A549 cell line. SNHG14 knockdown or miR-133a overexpression was demonstrated to increase the DDP-sensitivity of A549/DDP cells. SNHG14 was revealed to compete with HOXB13 for miR-133a binding in A549/DDP cells. Inhibition of miR-133a in A549 cells could reverse the promotive effects of SNHG14 knockdown on DDP-sensitivity, as well as the inhibitory effects on HOXB13 expression. HOXB13 overexpression was revealed to abolish the enhanced effects of miR-133a on the sensitivity of A549/DDP cell to DDP.

Conclusion

Our findings demonstrated that SNHG14 was involved in the development of DDP-resistance of A549/DDP cells through miR-133a/HOXB13 axis, which may present a path to novel therapeutic stratagems for DDP resistance of NSCLC.
Impact of pulmonary rehabilitation on patients’ health care needs and asthma control: a quasi-experimental study
Authors: Salandi Julia , Icks Andrea , Gholami Jalal , Hummel Stefan , Schultz Konrad , Apfelbacher Christian , Sheikh Aziz , Loerbroks Adrian
Published: October 2020

Background

Pulmonary rehabilitation offers potential benefits to people with asthma. It is however unknown if rehabilitation favourably affects patients’ health care needs. We therefore examined if rehabilitation reduced needs and, in addition, if it improved asthma control.

Methods

One hundred fifty patients with asthma were surveyed in three rehabilitation clinics at admission and at discharge. Additionally, we surveyed 78 participants with asthma twice 4 weeks apart. The latter sample (i.e. the control group) was recruited through other pathways than rehabilitation clinics. The Patient Needs in Asthma Treatment (NEAT) questionnaire and the Asthma Control Test (ACT) were completed at baseline and follow-up. Differences between baseline and follow-up and between rehabilitation and control group were examined by t-tests and chi-squared-tests. Univariate ANCOVAS were used to examine if NEAT and ACT follow-up scores differed significantly between groups. Within the rehabilitation group, linear regressions were used to examine if self-reported utilization of more interventions that addressed needs were associated with NEAT scores at follow-up.

Results

At baseline, there were no differences between the rehabilitation and the control group regarding needs and asthma control. At follow-up, the rehabilitation group showed reduced needs (t(149) = 10.33, p <  0.01) and increased asthma control (t(130) = -6.67, p <  0.01), whereas members of the control group exhibited no changes. Univariate ANCOVAS showed that unmet follow-up needs (F(1, 212) = 36.46, p <  0.001) and follow-up asthma control (F(1, 195) = 6.97, p = 0.009) differed significantly between groups. In the rehabilitation group, self-reported utilization of more interventions was associated with reduced needs (β = 0.21; p = 0.03).

Conclusions

This study provides preliminary evidence suggestion that pulmonary rehabilitation in adults with asthma may reduce asthma-related needs and confirms previous findings that rehabilitation may improve asthma control.
Benchmarking the research track record and level of appointment of Australian medical laboratory science academics
Authors: Donkin Rebecca , Broome Kieran , Swanepoel Libby
Published: October 2020

Background

Benchmarking across and within universities is a common tool to evaluate performance of a program and maintain accreditation requirements. While teaching remains a primary responsibility of many academics, academic research performance is a major contributor towards career advancement and standards in the medical laboratory science profession. While anecdotal evidence suggests academics are active contributors to the evidence base of the profession, there is a high variability in research output in relation to institution and level of appointment. The aim of the study was to benchmark the research track record of Australian medical laboratory science academics and provide insight into how research productivity informs the level of appointment of academics across their career pathway.

Methods

A bibliographic analysis of Australian medical laboratory science faculty websites and corresponding Scopus citation database profiles was conducted. A description of current research track record and relationships with holding a doctorate, academic appointment level, research and teaching interests, and institutional characteristics were explored. Quantitative data and frequencies were analysed using IBM SPSS version 26 to benchmark research track records by academic appointment level.

Results

There were 124 academics identified from 13 universities who had a teaching and research position in an undergraduate medical laboratory science program in Australia. Academics at the level of lecturer or higher typically held a doctorate (89%). Holding a doctorate strongly influenced the number of publications. The top 20% of researchers authored around half of the overall publications. The majority of academics did not have alignment of their major research and teaching areas however, alignment had no influence on number of publications. There was, however, an inconsistent relationship between metropolitan or regional university location and the number of publications.

Conclusion

Data from this study provides academics with benchmarks for the research track record required at each level of appointment. When drawing conclusions on academic progression, promotion and tenure through research track record it would be mindful to assess each on a case by case basis. Institution (metropolitan versus regional) and research interest appears to influence publication number, h-index and citation scores.
Effective attention-based network for syndrome differentiation of AIDS
Authors: Pang Huaxin , Wei Shikui , Zhao Yufeng , He Liyun , Wang Jian , Liu Baoyan , Zhao Yao
Published: October 2020

Background

Syndrome differentiation aims at dividing patients into several types according to their clinical symptoms and signs, which is essential for traditional Chinese medicine (TCM). Several previous works were devoted to employing the classical algorithms to classify the syndrome and achieved delightful results. However, the presence of ambiguous symptoms substantially disturbed the performance of syndrome differentiation, This disturbance is always due to the diversity and complexity of the patients’ symptoms.

Methods

To alleviate this issue, we proposed an algorithm based on the multilayer perceptron model with an attention mechanism (ATT-MLP). In particular, we first introduced an attention mechanism to assign different weights for different symptoms among the symptomatic features. In this manner, the symptoms of major significance were highlighted and ambiguous symptoms were restrained. Subsequently, those weighted features were further fed into an MLP to predict the syndrome type of AIDS.

Results

Experimental results for a real-world AIDS dataset show that our framework achieves significant and consistent improvements compared to other methods. Besides, our model can also capture the key symptoms corresponding to each type of syndrome.

Conclusion

In conclusion, our proposed method can learn these intrinsic correlations between symptoms and types of syndromes. Our model is able to learn the core cluster of symptoms for each type of syndrome from limited data, while assisting medical doctors to diagnose patients efficiently.