bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation of the Design for Mass Adaptation Method – A Case for Higher Medical Treatment Quality
Authors: Üreten Selin , Spallek Johanna , Üreten Ece , Krause Dieter
Published: September 2020

This contribution demonstrates the application of the new Design Method Validation System ( DMVS) for the validation of engineering design methods in product development. The application example is a case from the medical branch. The product design method Design for Mass Adaptation ( DfMAd) with individualization and modification steps as triggers is compared to an adapted design method with product individualization but without modification triggers. This experimental study was conducted in accordance with the DMVS procedure. Measured outcomes refer to the usefulness, applicability and acceptance of the design method DfMAd. Two groups of student participants were compared to each other through research tools based on quantitative and qualitative data collection and analysis. Findings show that the considered DfMAd phase successfully leads to the desired benefit for the consideration of variant-oriented alternatives, thus confirming the test hypothesis. In the example of a product, a crutch, a high treatment quality can be achieved by specific adaptability of the product. In addition, it is shown that DMVS is suitable for the development of experiments and that the data collection means are differently suited for the validation of the three criteria.
Preliminary Interview Study on the Opioid Prescription Decision Making Process
Authors: Wang Xiaomei , Roth Emilie M. , Kim Tracy , Arora Jessica , Franklin Ella S. , Hettinger Aaron Z. , Bisantz Ann M.
Published: September 2020

To date, studies have found scattered and inconsistent use of existing opioid prescription support tools, such as Prescription Drug Monitoring Systems (PDMPs) and guidelines, and little research has been done to identify barriers for adopting them and better ways to support clinician decision making. This pilot study aims to better understand the flow, resources used, and challenges faced when prescribing opioid medications. The study will help shape research questions for a larger study geared towards informing future decision aid designs and considerations for clinicians in the emergency department (ED). Semi-structured interviews were conducted with a total of six emergency medicine physicians and nurses using an abbreviated variant of the Critical Decision Method. Discussions were focused around how participants made their decisions and what was difficult about them, in addition to whether current aids and tools are helpful. Common themes were identified from free-text notes in the following categories: cognitive and communication challenges, challenges with existing tools and databases, and decision-making strategies. Nurse responses were most commonly related to gaps in communication between physicians and patients and ensuring patient satisfaction. Physicians most commonly reported challenges with existing tools. While existing resources were said to be very helpful, several improvements were suggested by each group. By understanding these types of challenges and dynamics between physicians and nurses in the ED, we can better identify ways to improve the design of opioid prescription decision-making aids in the future.
Designing a Cardiovascular Health App for Citizens Returning from Incarceration: Where You Start May Not Be Where You End Up
Authors: Zachary Wayne W. , Wilkin Theresa , Puglisi Lisa , Butler Marc , Ferdousi Ishita , Smart Jerry , Pethkar Prathmesh , Surkan Pamela J
Published: September 2020

A mobile health (mHealth) smartphone app can help persons returning from incarceration better manage cardiovascular disease (CVD) and CVD risk factors during their re-entry period. A successful intervention to educate and increase self-efficacy in this population around cardiovascular health has potential to produce broad population health benefits. A participatory design (PD) approach was used to define the features and functionality of such an intervention in the form of a smart phone app. The PD process forced the research team to view CV health in the broader context of other challenges that RCs face day to day. It also led to a broadening of the process to include other stakeholders that work closely with RCs, and to explore how these challenges affect the re-entry process. Ultimately, PD led to an app design that emphasized a common problem-solving approach that can be applied to a broad range of problems. An interactive prototype of the app’s interface was assessed by a sample of RCs, users, with consensus that the problem-areas were appropriate and that the app was easy to use and to navigate. A quantitative assessment with the System Usability Survey instrument, yielded an average score of 81.5, placing it in the 90th percentile.
The Patient in Patient Safety: Unique Perspectives of Researchers Who are also Patients
Authors: Papautsky Elizabeth Lerner , Holden Richard J. , Valdez Rupa S. , Ernst Katie , Kushniruk Andre
Published: September 2020

In a panel format, four systems researchers who are also patients described their experiences navigating their care continuum in relation to human factors topics. Getting inside the heads of researcher-patients is an opportunity to elicit unique perspectives on healthcare, which may not be captured through research alone. Researcher-patients may navigate and observe their care continuum with a lens attuned to identifying research questions, as well as gaps and opportunities for interventions that support patients in health-related work, clinicians in decision making, and a culture shift towards effective patient-clinician teaming in service of improved safety and quality. We provide detailed recommendations, as well as a concise take-away tool intended for healthcare organizations.
Scheduling Delayed Treatment and Surgeries Post-Pandemic: A Stakeholder Analysis
Authors: Patterson Emily S. , Papautsky Elizabeth Lerner , Krok-Schoen Jessica L. , Lee Clara , Park Ko Un , White Julia R. , Moffatt-Bruce Susan , Chirumamilla Varshita , Lustberg Maryam
Published: September 2020

Many are interested in how to safely ramp up elective surgeries after national, state, and voluntary shutdowns of operating rooms to minimize the spread of COVID-19 infections to patients and providers. We conducted an analysis of diverse perspectives from stakeholders regarding how to trade off risks and benefits to patients, healthcare providers, and the local community. Our findings indicate that there are a large number of different categories of stakeholders impacted by the post-pandemic decisions to reschedule delayed treatments and surgeries. For a delayed surgery, the primary stakeholders are the surgeon with expertise about the clinical benefits of undergoing an operation and the patient’s willingness to tolerate uncertainty and the increased risk of infection. For decisions about how much capacity in the operating rooms and in the inpatient setting after the surgery, the primary considerations are minimizing staff infections, preventing patients from getting COVID-19 during operations and during post-surgical recovery at the hospital, conserving critical resources such as PPE, and meeting the needs of hospital staff for quality of life, such as child care needs and avoiding infecting members of their household. The timing and selection of elective surgery cases has an impact on the ability of hospitals to steward finances, which in turns affects decisions about maintaining employment of staff when operating rooms and inpatient rooms are not being used.
A Human Factors Perspective to Characterize Treatment and Surgery During the COVID-19 Pandemic
Authors: Papautsky Elizabeth Lerner , Lustberg Maryam , Krok-Schoen Jessica L. , Lee Clara , Park Ko Un , Attai Deanna J. , Patterson Emily S.
Published: September 2020

At the outset of the COVID-19 pandemic, many cancer surgeries were delayed due to the unique challenges around allocating and conserving resources to treat patients with COVID-19 and reduce risk of infection for clinicians and communities. Thus there is an urgent need to develop support solutions to ensure that more time-sensitive surgeries can be prioritized, planned, and scheduled in an appropriate, safe, and patient-centered manner during pandemic recovery, across pandemic waves, and for future public health crises. Using SEIPS 2.0 as a framework, we provide an analysis of this problem space to characterize the known factors and processes. We also highlight the importance of the patient perspective.
The Convergence of Emotionally Supportive Learning Environments and College and Career Ready Mathematical Engagement in Upper Elementary Classrooms
Authors: Berlin Rebekah , Cohen Julie
Published: September 2020

Research focused on emotionally supportive teaching has typically run in parallel to the study of rigorous, standards-aligned mathematics teaching. However, recent work theorizes that positive and warm classroom environments may be necessary to help students meet the ambitious goals outlined in newer mathematics standards. We analyze the relationship between facets of classroom environments and the prevalence of standards-aligned mathematics instruction across more than 400 mathematics lessons in Washington, D.C., classrooms. We find no evidence of consistent standards-aligned mathematical engagement absent an engaging, emotionally supportive learning environment. These findings suggest that efforts to help teachers make the instructional shifts outlined in college and career ready standards might also need to support the provision of productive, warm, and nurturing learning environments.
Younger and Older Adults’ Mood and Expectations Regarding Aging During COVID-19
Authors: Whatley Mary C. , Siegel Alexander L. M. , Schwartz Shawn T. , Silaj Katie M. , Castel Alan D.
Published: September 2020

The 2019 novel coronavirus disease (COVID-19) has broadly impacted our daily lives. Here, we used a longitudinal approach to investigate older adults’ mood and expectations regarding aging before and during the global pandemic (Study 1). We also examined age differences in mood, expectations regarding aging, COVID-19 attitudes, and loneliness using a cross-sectional approach (Study 2). In Study 1, older adults completed a mood and expectations regarding aging survey up to 2 years prior to the pandemic and again in April, 2020 (during the pandemic). Participants also completed surveys regarding COVID-19 attitudes and loneliness. In Study 2, a United States sample of younger and older adults completed these surveys during the pandemic. Older adults’ mood and expectations regarding aging remained fairly constant, and younger adults showed lower mood and expectations regarding aging than did older adults, despite older adults showing greater concern about COVID-19. Overall, we find that some older adults seem to be resilient with respect to their mood and expectations regarding aging. These findings reveal important preliminary implications for how older adults may be impacted as a result of lifestyle changes necessary for well-being and the well-being of society.
Why Do People Undergo THR and What Do They Expect to Gain—A Comparison of the Views of Patients and Health Care Professionals
Authors: Bahadori Shayan , Collard Sarah , Williams Jonathan Mark , Swain Ian
Published: September 2020

Little concerted effort has been made to understand why individuals undergo total hip replacement (THR) surgery and their rehabilitation goals. Similarly, insight of views and perspective of health care professionals’ (HCPs) regarding surgery and what objective measures help them with decision-making is lacking. This patient and public involvement report aimed to explore both patients’ and HCPs’ perspectives of THR surgery. Twenty patients, 10 pre-THR, 10 post-THR, 9 physiotherapists, and 6 surgeons took part. Results suggest a consensus among patients and HCPs on pain reduction being the main reason for undergoing THR. The inability to carry out simple daily activities such as dog walking and sleep deprivation had a significant effect on patients’ mental and physical well-being. This article is the first to explore the views of THR patients and HCPs on reasons behind THR surgery amalgamated into a single report. As walking is important, wearable activity monitors are suggested as a possible motivator to enhance patient compliance to self-care rehabilitation and increase quality of life. A future research project on the use of such wearable activity monitors in enhancing mobility post-THR is therefore planned.
COVID-19 Pandemic Accelerates Need to Improve Online Patient Engagement Practices to Enhance Patient Experience
Authors: Meyer Melanie A
Published: September 2020

The COVID-19 pandemic has led to rapid change in health care, accelerating the use of digital health services, including telehealth. Moreover, growth in value-based care has compelled consumers to become more engaged in care processes. It has also provided opportunities to enhance patient experiences by increasing patients’ access to online health information and services. This study assessed online patient engagement practices for 6 common patient touchpoints by reviewing the websites of the top 32 hospitals, including the top 10 children’s hospitals. The great majority of these hospitals provided some information related to these patient touchpoints. However, the scope and extent of task automation varied significantly and many options were not convenient. Based on this study, it is clear that patient experience can be enhanced by improving online patient engagement, particularly during the current global pandemic.
Morphea after Borrelia-induced facial nerve palsy
Authors: Xie Catherine B , Cowper Shawn , Odell Ian D
Published: September 2020

Morphea, also known as localized scleroderma, is characterized by inflammation and fibrosis of the skin. The exact pathogenesis of morphea is unknown, but generally includes genetic predisposition to autoimmunity combined with an environmental insult. Previous cases have been associated with active Borrelia infection; however, Borrelia infection as a direct cause of morphea was not generalizable to most patients. Within endemic areas, Borrelia burgdorferi is the most common cause of facial nerve paralysis, another autoimmune phenomenon. We report a case of facial morphea in a young man with family history of autoimmune disease who developed morphea in the same location as two previous episodes of Borrelia-induced facial nerve palsy. This case is remarkable because it suggests Borrelia burgdorferi induced loss of local immune tolerance to host antigens, first with facial nerve palsy and followed years later by development of morphea.
Developing More Value Flexibility for Organisation Development in India: Lessons Learnt from Different Value Orientations Across the World
Authors: Shevat Allon
Published: September 2020

Organisation development is riddled with values from the Occident; these Western values fly in the face of driving, developing trust and facilitating change in global organisations. Organisation development, via its Western values thus can vitiate to be seen as the handmaiden of cultural force-feeding, albeit perhaps not with malicious intent. This article explores episodes where the occidental and the relatively non-occidental, including the oriental context, make painful and ineffective interface. It raises the possibilities that organisation development can be and must be retooled. This article provides both vignettes and pertinent insight-bearing inferences from a qualitative lens, which will enable the reader and practitioner to hone awareness of the value-laden skill sets required to support effectiveness of global organisations. The intercultural outlay has special reference to India and the phenomena therein are stretched between several national cultures from real-life episodes, where consultation presented challenges to the author.
Stress–strain relationship model of glulam bamboo under axial loading
Authors: Wei Yang , Zhou Mengqian , Zhao Kunpeng , Zhao Kang , Li Guofen
Published: September 2020

Glulam bamboo has been preliminarily explored for use as a structural building material, and its stress–strain model under axial loading has a fundamental role in the analysis of bamboo components. To study the tension and compression behaviour of glulam bamboo, the bamboo scrimber and laminated bamboo as two kinds of typical glulam bamboo materials were tested under axial loading. Their mechanical behaviour and failure modes were investigated. The results showed that the bamboo scrimber and laminated bamboo have similar failure modes. For tensile failure, bamboo fibres were ruptured with sawtooth failure surfaces shown as brittle failure; for compression failure, the two modes of compression are buckling and compression shear failure. The stress–strain relationship curves of the bamboo scrimber and laminated bamboo are also similar. The tensile stress–strain curves showed a linear relationship, and the compressive stress–strain curves can be divided into three stages: elastic, elastoplastic and post-yield. Based on the test results, the stress–strain model was proposed for glulam bamboo, in which a linear equation was used to describe the tensile stress–strain relationship and the Richard–Abbott model was employed to model the compressive stress–strain relationship. A comparison with the experimental results shows that the predicted results are in good agreement with the experimental curves.
Comparison of traditional vs low-damage structural and non-structural building systems through a cost/performance-based evaluation
Authors: Bianchi Simona , Ciurlanti Jonathan , Pampanin Stefano
Published: September 2020

Innovative damage-mitigation technologies have been recently developed to improve the seismic performance of structural and non-structural elements. The combination of these solutions can lead to a high-performance and cost-efficient building system, capable of sustaining earthquakes with limited damage and reduced socio-economic losses. This article investigates the convenience of implementing damage-control solutions through a cost/performance-based evaluation of multi-story-reinforced concrete buildings, comprising alternative combinations of traditional vs low-damage technologies for both structural skeletons (frames, walls) and non-structural elements (heavy/light facades, heavy/light partitions, suspended ceilings). The significant benefits of the innovative systems are investigated through loss assessment studies, implemented using a practical approach based on numerical pushover analyses and the capacity spectrum method. The parametric analyses confirm that the integrated low-damage structural/non-structural system can lead to significant savings, in these specific cases, in the range of 150–300 €/m2 during the 50-year building-life and downtime reductions at ultimate limit state in the order of 2–7 months.
Re-Creating Organizational Routines to Transition Through the Project Life Cycle: A Case Study of the Reconstruction of London’s Bank Underground Station
Authors: Addyman Simon , Pryke Stephen , Davies Andrew
Published: September 2020

This article provides new insights into the project life cycle by proposing an alternative image to the predefined time boundary between life cycle stages. It makes a theoretical contribution by identifying how project organizations re-create patterns of action—organizational routines—as they transition through life cycle stages. It presents the findings of an autoethnographic empirical study and, through the lens of routine dynamics, contributes to the project management literature by identifying a five-stage process model of transitioning and the generative mechanisms involved in re-creating patterns of action.
γ-Glutamyl carboxylase mutations differentially affect the biological function of vitamin K–dependent proteins
Authors: Hao Zhenyu , Jin Da-Yun , Chen Xuejie , Schurgers Leon J. , Stafford Darrel W. , Tie Jian-Ke
Published: September 2020

γ-Glutamyl carboxylase (GGCX) is an integral membrane protein that catalyzes posttranslational carboxylation of a number of vitamin K–dependent (VKD) proteins involved in a wide variety of physiologic processes, including blood coagulation, vascular calcification, and bone metabolism. Naturally occurring GGCX mutations are associated with multiple distinct clinical phenotypes. However, the genotype–phenotype correlation of GGCX remains elusive. Here, we systematically examined the effect of all naturally occurring GGCX mutations on the carboxylation of 3 structure–function distinct VKD proteins in a cellular environment. GGCX mutations were transiently introduced into GGCX-deficient human embryonic kidney 293 cells stably expressing chimeric coagulation factor, matrix Gla protein (MGP), or osteocalcin as VKD reporter proteins, and then the carboxylation efficiency of these reporter proteins was evaluated. Our results show that GGCX mutations differentially affect the carboxylation of these reporter proteins and the efficiency of using vitamin K as a cofactor. Carboxylation of these reporter proteins by a C-terminal truncation mutation (R704X) implies that GGCX’s C terminus plays a critical role in the binding of osteocalcin but not in the binding of coagulation factors and MGP. This has been confirmed by probing the protein–protein interaction between GGCX and its protein substrates in live cells using bimolecular fluorescence complementation and chemical cross-linking assays. Additionally, using a minigene splicing assay, we demonstrated that several GGCX missense mutations affect GGCX’s pre–messenger RNA splicing rather than altering the corresponding amino acid residues. Results from this study interpreted the correlation of GGCX’s genotype and its clinical phenotypes and clarified why vitamin K administration rectified bleeding disorders but not nonbleeding disorders.
Region-specific brain area reductions and increased cholecystokinin positive neurons in diabetic OLETF rats: implication for anxiety-like behavior
Authors: Ochi Ryosuke , Fujita Naoto , Goto Natsuki , Nguyen Son Tien , Le Duc Trung , Matsushita Kojiro , Ono Taketoshi , Nishijo Hisao , Urakawa Susumu
Published: September 2020

Metabolic disorders can induce psychiatric comorbidities. Both brain and neuronal composition imbalances reportedly induce an anxiety-like phenotype. We hypothesized that alterations of localized brain areas and cholecystokinin (CCK) and parvalbumin (PV) expression could induce anxiety-like behavior in type 2 diabetic Otsuka Long-Evans Tokushima fatty (OLETF) rats. Twenty-week-old OLETF and non-diabetic Long-Evans Tokushima Otsuka (LETO) rats were used. The areas of corticolimbic regions were smaller in OLETF rats. The densities of CCK positive neurons in the lateral and basolateral amygdala, hippocampal cornu ammonis area 2, and prelimbic cortex were higher in OLETF rats. The densities of PV positive neurons were comparable between OLETF and LETO rats. Locomotion in the center zone in the open field test was lower in OLETF rats. These results suggest that imbalances of specific brain region areas and neuronal compositions in emotion-related areas increase the prevalence of anxiety-like behaviors in OLETF rats.
Variable-order reference-free variant discovery with the Burrows-Wheeler Transform
Authors: Prezza Nicola , Pisanti Nadia , Sciortino Marinella , Rosone Giovanna
Published: September 2020

Background

In [Prezza et al., AMB 2019], a new reference-free and alignment-free framework for the detection of SNPs was suggested and tested. The framework, based on the Burrows-Wheeler Transform (BWT), significantly improves sensitivity and precision of previous de Bruijn graphs based tools by overcoming several of their limitations, namely: (i) the need to establish a fixed value, usually small, for the order k, (ii) the loss of important information such as k-mer coverage and adjacency of k-mers within the same read, and (iii) bad performance in repeated regions longer than k bases. The preliminary tool, however, was able to identify only SNPs and it was too slow and memory consuming due to the use of additional heavy data structures (namely, the Suffix and LCP arrays), besides the BWT.

Results

In this paper, we introduce a new algorithm and the corresponding tool ebwt2InDel that (i) extend the framework of [Prezza et al., AMB 2019] to detect also INDELs, and (ii) implements recent algorithmic findings that allow to perform the whole analysis using just the BWT, thus reducing the working space by one order of magnitude and allowing the analysis of full genomes. Finally, we describe a simple strategy for effectively parallelizing our tool for SNP detection only. On a 24-cores machine, the parallel version of our tool is one order of magnitude faster than the sequential one. The tool ebwt2InDel is available at github.com/nicolaprezza/ebwt2InDel.

Conclusions

Results on a synthetic dataset covered at 30x (Human chromosome 1) show that our tool is indeed able to find up to 83% of the SNPs and 72% of the existing INDELs. These percentages considerably improve the 71% of SNPs and 51% of INDELs found by the state-of-the art tool based on de Bruijn graphs. We furthermore report results on larger (real) Human whole-genome sequencing experiments. Also in these cases, our tool exhibits a much higher sensitivity than the state-of-the art tool.
Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito
Authors: Savojardo Castrense , Martelli Pier Luigi , Tartari Giacomo , Casadio Rita
Published: September 2020

Background

The prediction of protein subcellular localization is a key step of the big effort towards protein functional annotation. Many computational methods exist to identify high-level protein subcellular compartments such as nucleus, cytoplasm or organelles. However, many organelles, like mitochondria, have their own internal compartmentalization. Knowing the precise location of a protein inside mitochondria is crucial for its accurate functional characterization. We recently developed DeepMito, a new method based on a 1-Dimensional Convolutional Neural Network (1D-CNN) architecture outperforming other similar approaches available in literature.

Results

Here, we explore the adoption of DeepMito for the large-scale annotation of four sub-mitochondrial localizations on mitochondrial proteomes of five different species, including human, mouse, fly, yeast and Arabidopsis thaliana. A significant fraction of the proteins from these organisms lacked experimental information about sub-mitochondrial localization. We adopted DeepMito to fill the gap, providing complete characterization of protein localization at sub-mitochondrial level for each protein of the five proteomes. Moreover, we identified novel mitochondrial proteins fishing on the set of proteins lacking any subcellular localization annotation using available state-of-the-art subcellular localization predictors. We finally performed additional functional characterization of proteins predicted by DeepMito as localized into the four different sub-mitochondrial compartments using both available experimental and predicted GO terms. All data generated in this study were collected into a database called DeepMitoDB (available at http://busca.biocomp.unibo.it/deepmitodb), providing complete functional characterization of 4307 mitochondrial proteins from the five species.

Conclusions

DeepMitoDB offers a comprehensive view of mitochondrial proteins, including experimental and predicted fine-grain sub-cellular localization and annotated and predicted functional annotations. The database complements other similar resources providing characterization of new proteins. Furthermore, it is also unique in including localization information at the sub-mitochondrial level. For this reason, we believe that DeepMitoDB can be a valuable resource for mitochondrial research.
An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs
Authors: Bertolazzi Giorgio , Benos Panayiotis V. , Tumminello Michele , Coronnello Claudia
Published: September 2020

MicroRNA are small non-coding RNAs that post-transcriptionally regulate the expression levels of messenger RNAs. MicroRNA regulation activity depends on the recognition of binding sites located on mRNA molecules. ComiR is a web tool realized to predict the targets of a set of microRNAs, starting from their expression profile. ComiR was trained with the information regarding binding sites in the 3’utr region, by using a reliable dataset containing the targets of endogenously expressed microRNA in D. melanogaster S2 cells. This dataset was obtained by comparing the results from two different experimental approaches, i.e., inhibition, and immunoprecipitation of the AGO1 protein--a component of the microRNA induced silencing complex.

In this work, we tested whether including coding region binding sites in ComiR algorithm improves the performance of the tool in predicting microRNA targets. We focused the analysis on the D. melanogaster species and updated the ComiR underlying database with the currently available releases of mRNA and microRNA sequences. As a result, we find that ComiR algorithm trained with the information related to the coding regions is more efficient in predicting the microRNA targets, with respect to the algorithm trained with 3’utr information. On the other hand, we show that 3’utr based predictions can be seen as complementary to the coding region based predictions, which suggests that both predictions, from 3’utr and coding regions, should be considered in comprehensive analysis.

Furthermore, we observed that the lists of targets obtained by analyzing data from one experimental approach only, that is, inhibition or immunoprecipitation of AGO1, are not reliable enough to test the performance of our microRNA target prediction algorithm. Further analysis will be conducted to investigate the effectiveness of the tool with data from other species, provided that validated datasets, as obtained from the comparison of RISC proteins inhibition and immunoprecipitation experiments, will be available for the same samples. Finally, we propose to upgrade the existing ComiR web-tool by including the coding region based trained model, available together with the 3’utr based one.
miRTissue ce: extending miRTissue web service with the analysis of ceRNA-ceRNA interactions
Authors: Fiannaca Antonino , Paglia Laura La , Rosa Massimo La , Rizzo Riccardo , Urso Alfonso
Published: September 2020

Background

Non-coding RNAs include different classes of molecules with regulatory functions. The most studied are microRNAs (miRNAs) that act directly inhibiting mRNA expression or protein translation through the interaction with a miRNAs-response element. Other RNA molecules participate in the complex network of gene regulation. They behave as competitive endogenous RNA (ceRNA), acting as natural miRNA sponges to inhibit miRNA functions and modulate the expression of RNA messenger (mRNA). It became evident that understanding the ceRNA–miRNA–mRNA crosstalk would increase the functional information across the transcriptome, contributing to identify new potential biomarkers for translational medicine.

Results

We present miRTissue ce, an improvement of our original miRTissue web service. By introducing a novel computational pipeline, miRTissue ce provides an easy way to search for ceRNA interactions in several cancer tissue types. Moreover it extends the functionalities of previous miRTissue release about miRNA-target interaction in order to provide a complete insight about miRNA mediated regulation processes. miRTissue ce is freely available at http://tblab.pa.icar.cnr.it/mirtissue.html.

Conclusions

The study of ceRNA networks and its dynamics in cancer tissue could be applied in many fields of translational biology, as the investigation of new cancer biomarker, both diagnostic and prognostic, and also in the investigation of new therapeutic strategies of intervention. In this scenario, miRTissue ce can offer a powerful instrument for the analysis and characterization of ceRNA-ceRNA interactions in different tissue types, representing a fundamental step in order to understand more complex regulation mechanisms.
Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species
Authors: Nielsen Erica S. , Henriques Romina , Beger Maria , Toonen Robert J. , von der Heyden Sophie
Published: September 2020

Background

As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species’ potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis).

Results

Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, onlyS. granularisshowed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation inC. punctatusandP. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts forS. granularisandP. angulosus, but not forC. punctatus.

Conclusion

The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.
Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes
Authors: Duarte-Delgado Diana , Dadshani Said , Schoof Heiko , Oyiga Benedict C. , Schneider Michael , Mathew Boby , Léon Jens , Ballvora Agim
Published: September 2020

Background

Bread wheat is one of the most important crops for the human diet, but the increasing soil salinization is causing yield reductions worldwide. Improving salt stress tolerance in wheat requires the elucidation of the mechanistic basis of plant response to this abiotic stress factor. Although several studies have been performed to analyze wheat adaptation to salt stress, there are still some gaps to fully understand the molecular mechanisms from initial signal perception to the onset of responsive tolerance pathways. The main objective of this study is to exploit the dynamic salt stress transcriptome in underlying QTL regions to uncover candidate genes controlling salt stress tolerance in bread wheat. The massive analysis of 3′-ends sequencing protocol was used to analyze leave samples at osmotic and ionic phases. Afterward, stress-responsive genes overlapping QTL for salt stress-related traits in two mapping populations were identified.

Results

Among the over-represented salt-responsive gene categories, the early up-regulation of calcium-binding and cell wall synthesis genes found in the tolerant genotype are presumably strategies to cope with the salt-related osmotic stress. On the other hand, the down-regulation of photosynthesis-related and calcium-binding genes, and the increased oxidative stress response in the susceptible genotype are linked with the greater photosynthesis inhibition at the osmotic phase. The specific up-regulation of some ABC transporters and Na+/Ca2+exchangers in the tolerant genotype at the ionic stage indicates their involvement in mechanisms of sodium exclusion and homeostasis. Moreover, genes related to protein synthesis and breakdown were identified at both stress phases. Based on the linkage disequilibrium blocks, salt-responsive genes within QTL intervals were identified as potential components operating in pathways leading to salt stress tolerance. Furthermore, this study conferred evidence of novel regions with transcription in bread wheat.

Conclusion

The dynamic transcriptome analysis allowed the comparison of osmotic and ionic phases of the salt stress response and gave insights into key molecular mechanisms involved in the salt stress adaptation of contrasting bread wheat genotypes. The leveraging of the highly contiguous chromosome-level reference genome sequence assembly facilitated the QTL dissection by targeting novel candidate genes for salt tolerance.
Comparative analysis of maca (Lepidium meyenii) proteome profiles reveals insights into response mechanisms of herbal plants to high-temperature stress
Authors: Wang Zhan Qi , Zhao Qi Ming , Zhong Xueting , Xiao Li , Ma Li Xuan , Wu Chou Fei , Zhang Zhongshan , Zhang Li Qin , Tian Yang , Fan Wei
Published: September 2020

Background

High-temperature stress (HTS) is one of the main environmental stresses that limit plant growth and crop production in agricultural systems. Maca (Lepidium meyenii) is an important high-altitude herbaceous plant adapted to a wide range of environmental stimuli such as cold, strong wind and UV-B exposure. However, it is an extremely HTS-sensitive plant species. Thus far, there is limited information about gene/protein regulation and signaling pathways related to the heat stress responses in maca. In this study, proteome profiles of maca seedlings exposed to HTS for 12 h were investigated using a tandem mass tag (TMT)-based proteomic approach.

Results

In total, 6966 proteins were identified, of which 300 showed significant alterations in expression following HTS. Bioinformatics analyses indicated that protein processing in endoplasmic reticulum was the most significantly up-regulated metabolic pathway following HTS. Quantitative RT-PCR (qRT-PCR) analysis showed that the expression levels of 19 genes encoding proteins mapped to this pathway were significantly up-regulated under HTS. These results show that protein processing in the endoplasmic reticulum may play a crucial role in the responses of maca to HTS.

Conclusions

Our proteomic data can be a good resource for functional proteomics of maca and our results may provide useful insights into the molecular response mechanisms underlying herbal plants to HTS.
A nationwide survey of intraoperative management for one-lung ventilation in Taiwan: time to accountable for diversity in protective lung ventilation
Authors: Kuo Chuan-Yi , Liu Ying-Tung , Chen Tzu-Shan , Lam Chen-Fuh , Wu Ming-Cheng
Published: September 2020

Background

There is a major paradigm shift for intraoperative mechanical ventilator support by the introduction of lung protective ventilation strategies to reduce postoperative pulmonary complications and improve overall clinical outcomes in non-thoracic surgeries. However, there is currently a lack of standardized practice guideline for lung protection during thoracic surgeries that require one-lung ventilation (OLV). This study aimed to collect the expert opinions of the thoracic anesthesiologists in perioperative care for OLV surgery in Taiwan.

Methods

This prospective cross-sectional study was undertaken in 16 tertiary hospitals in Taiwan from January to February 2019. A structured survey form was distributed across the participating hospitals and the thoracic anesthesiologists were invited to complete the form voluntarily. The survey form consisted of three parts, including the basic information of the institutional anesthesia care standards, ventilatory settings for a proposed patient receiving OLV surgery and expert opinions on OLV.

Results

A total of 71 thoracic anesthesiologists responded to the survey. Double-lumen tubes are the most commonly used (93.8%) airway devices for OLV. The most commonly recommended ventilator setting during OLV is a tidal volume of 6–7 ml/kg PBW (67.6%) and a PEEP level of 4–6 cmH2O (73.5%). Dual controlled ventilator modes are used by 44.1% of the anesthesiologists. During OLV, high oxygen fraction (FiO2 > 0.8) is more commonly supplemented to achieve an oxygen saturation higher than 94%. The consensus of anesthesiologists on the indices for lung protection in thoracic surgery is considerably low. Large majority of the anesthesiologists (91.5%) highly recommend that an international clinical practice guideline on the protective lung ventilation strategy for thoracic anesthesia should be established.

Conclusions

This study found that the thoracic anesthesiologists in Taiwan share certain common practices in ventilator support during OLV. However, they are concerned about the lack of fundamental clinical evidences to support the beneficial outcomes of the current lung protective strategies applicable to OLV. Large-scale trials are needed to form an evidence-based clinical practice guideline for thoracic anesthesia.
Investigation of the underlying genes and mechanism of familial hypercholesterolemia through bioinformatics analysis
Authors: Wang Dinghui , Liu Bin , Xiong Tianhua , Yu Wenlong , She Qiang
Published: September 2020

Background

Familial hypercholesterolemia (FH) is one of the commonest inherited metabolic disorders. Abnormally high level of low-density lipoprotein cholesterol (LDL-C) in blood leads to premature atherosclerosis onset and a high risk of cardiovascular disease (CVD). However, the specific mechanisms of the progression process are still unclear. Our study aimed to investigate the potential differently expressed genes (DEGs) and mechanism of FH using various bioinformatic tools.

Methods

GSE13985 and GSE6054 were downloaded from the Gene Expression Omnibus (GEO) database for bioinformatic analysis in this study. First, limma package of R was used to identify DEGs between blood samples of patients with FH and those from healthy individuals. Then, the functional annotation of DEGs was carried out by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and Gene Ontology (GO) analysis. Based on Search Tool for the Retrieval of Interacting Genes (STRING) tool, we constructed the Protein-Protein Interactions (PPIs) network among DEGs and mined the core genes as well.

Results

A total of 102 communal DEGs (49 up-regulated and 53 down-regulated) are identified in FH samples compared with control samples. The functional changes of DEGs are mainly associated with the focal adhere and glucagon signaling pathway. Ten genes (ITGAL, TLN1, POLR2A, CD69, GZMA, VASP, HNRNPUL1, SF1, SRRM2, ITGAV) were identified as core genes. Bioinformatic analysis showed that the core genes are mainly enriched in numerous processes related to cell adhesion, integrin-mediated signaling pathway and cell-matrix adhesion. In the transcription factor (TF) target regulating network, 219 nodes were detected, including 214 DEGs and 5 TFs (SP1, EGR3, CREB, SEF1, HOX13). In conclusion, the DEGs and hub genes identified in this study may help us understand the potential etiology of the occurrence and development of AS.

Conclusion

Up-regulated ITGAL, TLN1, POLR2A, VASP, HNRNPUL1, SF1, SRRM2, and down-regulated CD69, GZMA and ITGAV performed important promotional effects for the formation of atherosclerotic plaques those suffering from FH. Moreover, SP1, EGR3, CREB, SEF1 and HOX13 were the potential transcription factors for DEGs and could serve as underlying targets for AS rupture prevention. These findings provide a theoretical basis for us to understand the potential etiology of the occurrence and development of AS in FH patients and we may be able to find potential diagnostic and therapeutic targets.
Modeling socio-demographic and clinical factors influencing psychiatric inpatient service use: a comparison of models for zero-Inflated and overdispersed count data
Authors: Sharker Sharmin , Balbuena Lloyd , Marcoux Gene , Feng Cindy Xin
Published: September 2020

Background

Psychiatric disorders may occur as a single episode or be persistent and relapsing, sometimes leading to suicidal behaviours. The exact causes of psychiatric disorders are hard to determine but easy access to health care services can help to reduce their severity. The aim of this study was to investigate the factors associated with repeated hospitalizations among the patients with psychiatric illness, which may help the policy makers to target the high-risk groups in a more focused manner.

Methods

A large linked administrative database consisting of 200,537 patients with psychiatric diagnosis in the years of 2008-2012 was used in this analysis. Various counts regression models including zero-inflated and hurdle models were considered for analyzing the hospitalization rate among patients with psychiatric disorders within three months follow-up since their index visit dates. The covariates for this study consisted of socio-demographic and clinical characteristics of the patients.

Results

The results show that the odds of hospitalization are significantly higher among registered Indians, male patients and younger patients. Hospitalization rate depends on the patients’ disease types. Having previously visited a general physician served a protective role for psychiatric hospitalization during the study period. Patients who had seen an outpatient psychiatrist were more likely to have a higher number of psychiatric hospitalizations. This may indicate that psychiatrists tend to see patients with more severe illnesses, who require hospital-based care for managing their illness.

Conclusions

Providing easier access to registered Indian people and youth may reduce the need for hospital-based care. Patients with mental health conditions may benefit from greater and more timely access to primary care.