scholarly journals Evaluating the impact of sampling strategies and bioinformatics on ethanol-based DNA metabarcoding

2021 ◽  
Vol 4 ◽  
Author(s):  
Filipa MS Martins ◽  
Nuno A Fonseca ◽  
Bastian Egeter ◽  
Joana Pinto ◽  
Tiago Assunção ◽  
...  
Keyword(s):  
Treatment Strategies ◽  
Pcr Amplification ◽  
Potential Method ◽  
Sample Volume ◽  
Community Diversity ◽  
Lower Amount ◽  
Recent Developments ◽  
Tree Models ◽  
Pre Treatment ◽  
The Impact

Recent developments on ethanol-based DNA (etDNA) metabarcoding have shown that it is possible to extract meaningful information about macroinvertebrate community diversity and composition from the ethanol used to preserve bulk samples. The major advantages of this molecular approach are the reduced processing time and costs, and the possibility to keep specimens intact for other experiments. Yet, organisms with highly sclerotised exoskeleton or that are rare in the sample have been found to release a lower amount of DNA into solution and tend to be consistently missed by etDNA metabarcoding, thereby compromising the viability of the method. Few studies have shown that the first steps of the metabarcoding workflow are crucial for the good performance of etDNA-based assays, such as the decision on storage time before sampling and the ethanol phase to be analysed, the inclusion of pre-treatment strategies (i.e., freezing), and the choice of the DNA extraction protocol. In this study, we aimed to evaluate the combined effect of various technical choices on the performance of etDNA metabarcoding, considering factors such as sample volume, ethanol phase of sorted and unsorted samples, pre-capture treatments (evaporation vs filtration) and bioinformatic pipelines. Through the application of decision-tree models, our preliminary data revealed that the increase of volume (by itself) is enough to improve PCR amplification yields and proportion of families matching the morphological identifications, with great impact on the detection of hard-bodied and cased taxa. Also, no major differences among phases with or without a sorting step nor among bioinformatic pipelines were detected, particularly at higher volumes. Our results suggest that the higher performance (with lower observed variation) in taxonomic detection at higher volumes is likely a consequence of a higher availability of longer fragments of DNA in solution. This study highlights the importance of understanding the impact of technical choices to improve the efficiency of a DNA-based method, and reinstates etDNA metabarcoding as a potential method in the context of biomonitoring.

scholarly journals Monitoring the heart during cancer therapy

2019 ◽  
Vol 21 (Supplement_M) ◽  
pp. M44-M49 ◽  
Author(s):  
Mohsen Habibian ◽  
Alexander R Lyon
Keyword(s):  
Myocardial Injury ◽  
Treatment Strategies ◽  
Cancer Therapies ◽  
Monitoring Strategies ◽  
Increased Risk ◽  
Oncology Care ◽  
Pre Treatment ◽  
The Impact ◽  
Protective Treatment ◽  
Clinical Strategy

Abstract A growing number of effective cancer therapies is associated with cardiovascular (CV) toxicities including myocardial injury or dysfunction, leading to reduced ventricular function, and increased risk of heart failure. As the timing of administration of cancer treatment is known, the potential for risk stratification pre-treatment, and appropriate surveillance and monitoring during treatment, and intervention with cardio-protective treatment strategies in patients exhibiting early evidence of CV toxicity is an appealing clinical strategy. The field of cardio-oncology has developed, and the application of monitoring strategies using CV biomarkers and CV imaging has been to focus of many studies and is now implemented in dedicated cardio-oncology services supporting oncology centres. In this article, we review the background and rationale for monitoring, the different options and their strengths, weaknesses and where they are helpful in specific cardiotoxic cancer therapies, and the impact in cardio-oncology care.

scholarly journals Ultrasonic effect on pH, electric conductivity, and tissue surface of button mushrooms, Brussels sprouts and cauliflower.

2008 ◽  
Vol 25 (No. 2) ◽  
pp. 90-99 ◽  
Author(s):  
A.R Jambrak ◽  
T.J. Mason ◽  
L. Paniwnyk ◽  
V. Lelas
Keyword(s):  
Electric Conductivity ◽  
Potential Method ◽  
Surrounding Water ◽  
Ultrasonic Probe ◽  
Brussels Sprouts ◽  
Tissue Surface ◽  
Before And After ◽  
Button Mushrooms ◽  
Pre Treatment ◽  
The Impact

The aim of this work was to use ultrasound pre-treatment as a potential method prior to the subsequent processing in the food industry, for button mushrooms, Brussels sprouts, and cauliflower in order to observe the impact of ultrasound on the vegetable surrounding media properties in the processing conditions. The samples treated with 20 kHz probe and 40 kHz bath for 3 and 10 min were compared with blanched (80°C/3 min) and untreated samples. The effect was followed of ultrasound and blanching treatments on pH, electrical conductivity, and temperature changes. The effect of ultrasound on the sample tissue surface was also studied. The pH decreased after the ultrasound treatment with the probe, the largest change having been observed after using a 20 kHz probe for 10 min in all samples as compared with the blanching treatment, whereas it increased in mushroom and cauliflower and decreased in Brussels sprouts. Electric conductivity of the surrounding water before and after the ultrasound and blanching treatments of vegetables increased with all the treatments suggesting the loss of electrolyte. The highest increase was observed with the blanching treatment in all samples, followed by the treatments using an ultrasonic bath (10 min > 3 min) and an ultrasonic probe (3 min > 10 min). The temperature increase in the surrounding water during the ultrasonic treatments was by 1°C using the bath, and by 25&des;C using the probe. Staining of cauliflower and button mushroom tissues surfaces carried out for the damage determination showed that cavitation damage (blue spots) was present after the ultrasonical treatment with 20 kHz probe for 3 min, followed by 20 kHz probe for 10 min, while very little cavitational damage occurred after sonication with 40 kHz bath for 3 and 10 min. In Brussels sprouts, the results showed cavitation after sonication with 20 kHz probe for 3 min, followed by 20 kHz probe for 10 min, but no cavitation was present after sonication with 40 kHz bath.

Radiotherapy for Brain Tumors: Current Practice and Future Directions

2020 ◽  
Vol 16 (3) ◽  
pp. 182-195
Author(s):  
Sarah Baker ◽  
Natalie Logie ◽  
Kim Paulson ◽  
Adele Duimering ◽  
Albert Murtha
Keyword(s):  
Brain Tumors ◽  
Treatment Strategies ◽  
Brain Parenchyma ◽  
Benign Tumors ◽  
Tumor Control ◽  
Normal Brain ◽  
Neurocognitive Deficits ◽  
Close Proximity ◽  
Recent Developments ◽  
High Level

Radiotherapy is an important component of the treatment for primary and metastatic brain tumors. Due to the close proximity of critical structures and normal brain parenchyma, Central Nervous System (CNS) radiotherapy is associated with adverse effects such as neurocognitive deficits, which must be weighed against the benefit of improved tumor control. Advanced radiotherapy technology may help to mitigate toxicity risks, although there is a paucity of high-level evidence to support its use. Recent advances have been made in the treatment for gliomas, meningiomas, benign tumors, and metastases, although outcomes remain poor for many high grade tumors. This review highlights recent developments in CNS radiotherapy, discusses common treatment toxicities, critically reviews advanced radiotherapy technologies, and highlights promising treatment strategies to improve clinical outcomes in the future.

The Impact of Translational Research in Breast Cancer Care: Can we Improve the Therapeutic Scenario?

2018 ◽  
Vol 18 (6) ◽  
pp. 832-836
Author(s):  
Giuseppe Buono ◽  
Francesco Schettini ◽  
Francesco Perri ◽  
Grazia Arpino ◽  
Roberto Bianco ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Translational Research ◽  
Cell Biology ◽  
Cancer Biology ◽  
Hormone Receptors ◽  
Treatment Strategies ◽  
Growth Factor Receptor ◽  
Molecular Heterogeneity ◽  
Therapeutic Implications ◽  
The Impact

Traditionally, breast cancer (BC) is divided into different subtypes defined by immunohistochemistry (IHC) according to the expression of hormone receptors and overexpression/amplification of human epidermal growth factor receptor 2 (HER2), with crucial therapeutic implications. In the last few years, the definition of different BC molecular subgroups within the IHC-defined subtypes and the identification of the important role that molecular heterogeneity can play in tumor progression and treatment resistance have inspired the search for personalized therapeutic approaches. In this scenario, translational research represents a key strategy to apply knowledge from cancer biology to the clinical setting, through the study of all the tumors “omics”, including genomics, transcriptomics, proteomics, epigenomics, and metabolomics. Importantly, the introduction of new high-throughput technologies, such as next generation sequencing (NGS) for the study of cancer genome and transcriptome, greatly amplifies the potential and the applications of translational research in the oncology field. Moreover, the introduction of new experimental approaches, such as liquid biopsy, as well as new-concept clinical trials, such as biomarker-driven adaptive studies, may represent a turning point for BC translational research. </P><P> It is likely that translational research will have in the near future a significant impact on BC care, especially by giving us the possibility to dissect the complexity of tumor cell biology and develop new personalized treatment strategies.

Theory and Method and the Stakes of a Fragmented Discipline: Or, What Economics Taught Me About the Study of Religion

2020 ◽  
Author(s):  
Thomas A Lewis
Keyword(s):  
Religious Studies ◽  
The Public ◽  
Global Pandemic ◽  
Recent Developments ◽  
The Common ◽  
The Impact ◽  
Academic Study

Abstract As a discipline, the academic study of religion is strikingly fragmented, with little engagement or shared criteria of excellence across subfields. Although important recent developments have expanded the traditions and peoples studied as well as the methods used, the current extent of fragmentation limits the impact of this diversification and pluralization. At a moment when the global pandemic is catalyzing profound pressures on our universities and disciplines, this fragmentation makes it difficult to articulate to the public, to non-religious studies colleagues, and to students why the study of religion matters. We therefore too often fall back on platitudes. I argue for a revitalized methods and theories conversation that connects us even as it bears our arguments and disagreements about what we do and how. Courses in methods and theories in the study of religion represent the most viable basis we have for bringing the academic study of religion into the common conversation or argument that constitutes a discipline without sacrificing our pluralism.

scholarly journals Pre-treatment clinical and gene expression patterns predict developmental change in early intervention in autism

2021 ◽  
Author(s):  
Michael V. Lombardo ◽  
Elena Maria Busuoli ◽  
Laura Schreibman ◽  
Aubyn C. Stahmer ◽  
Tiziano Pramparo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Treatment Outcome ◽  
Early Intervention ◽  
Developmental Change ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Time In Treatment ◽  
Pre Treatment ◽  
Blood Leukocyte ◽  
The Impact

AbstractEarly detection and intervention are believed to be key to facilitating better outcomes in children with autism, yet the impact of age at treatment start on the outcome is poorly understood. While clinical traits such as language ability have been shown to predict treatment outcome, whether or not and how information at the genomic level can predict treatment outcome is unknown. Leveraging a cohort of toddlers with autism who all received the same standardized intervention at a very young age and provided a blood sample, here we find that very early treatment engagement (i.e., <24 months) leads to greater gains while controlling for time in treatment. Pre-treatment clinical behavioral measures predict 21% of the variance in the rate of skill growth during early intervention. Pre-treatment blood leukocyte gene expression patterns also predict the rate of skill growth, accounting for 13% of the variance in treatment slopes. Results indicated that 295 genes can be prioritized as driving this effect. These treatment-relevant genes highly interact at the protein level, are enriched for differentially histone acetylated genes in autism postmortem cortical tissue, and are normatively highly expressed in a variety of subcortical and cortical areas important for social communication and language development. This work suggests that pre-treatment biological and clinical behavioral characteristics are important for predicting developmental change in the context of early intervention and that individualized pre-treatment biology related to histone acetylation may be key.

scholarly journals Time-to-Treatment in Oral Cancer: Causes and Implications for Survival

Cancers ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1321
Author(s):  
Constanza Saka-Herrán ◽  
Enric Jané-Salas ◽  
Antoni Mari-Roig ◽  
Albert Estrugo-Devesa ◽  
José López-López
Keyword(s):  
Oral Cancer ◽  
Previous Treatment ◽  
Diagnostic Procedures ◽  
Original Data ◽  
Primary Treatment ◽  
Medical Attention ◽  
Time Interval ◽  
Pre Treatment ◽  
The Impact ◽  
Lack Of Knowledge

The purpose of this review was to identify and describe the causes that influence the time-intervals in the pathway of diagnosis and treatment of oral cancer and to assess its impact on prognosis and survival. The review was structured according to the recommendations of the Aarhus statement, considering original data from individual studies and systematic reviews that reported outcomes related to the patient, diagnostic and pre-treatment intervals. The patient interval is the major contributor to the total time-interval. Unawareness of signs and/or symptoms, denial and lack of knowledge about oral cancer are the major contributors to the process of seeking medical attention. The diagnostic interval is influenced by tumor factors, delays in referral due to higher number of consultations and previous treatment with different medicines or dental procedures and by professional factors such as experience and lack of knowledge related to the disease and diagnostic procedures. Patients with advanced stage disease, primary treatment with radiotherapy, treatment at an academic facility and transitions in care are associated with prolonged pre-treatment intervals. An emerging body of evidence supports the impact of prolonged pre-treatment and treatment intervals with poorer survival from oral cancer.

scholarly journals Boosting Immunity against Multiple Myeloma

Cancers ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1221
Author(s):  
Raquel Lopes ◽  
Bruna Velosa Ferreira ◽  
Joana Caetano ◽  
Filipa Barahona ◽  
Emilie Arnault Carneiro ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Residual Disease ◽  
Proteasome Inhibitors ◽  
Treatment Strategies ◽  
Complete Response ◽  
Drug Conjugates ◽  
Incurable Disease ◽  
Car T ◽  
Patient’S Outcome ◽  
The Impact

Despite the improvement of patient’s outcome obtained by the current use of immunomodulatory drugs, proteasome inhibitors or anti-CD38 monoclonal antibodies, multiple myeloma (MM) remains an incurable disease. More recently, the testing in clinical trials of novel drugs such as anti-BCMA CAR-T cells, antibody–drug conjugates or bispecific antibodies broadened the possibility of improving patients’ survival. However, thus far, these treatment strategies have not been able to steadily eliminate all malignant cells, and the aim has been to induce a long-term complete response with minimal residual disease (MRD)-negative status. In this sense, approaches that target not only myeloma cells but also the surrounding microenvironment are promising strategies to achieve a sustained MRD negativity with prolonged survival. This review provides an overview of current and future strategies used for immunomodulation of MM focusing on the impact on bone marrow (BM) immunome.

Swine manure biogas production improvement using pre-treatment strategies: lab-scale studies and full-scale application

2021 ◽  
pp. 100716
Author(s):  
Deisi Cristina Tápparo ◽  
Daniela Cândido ◽  
Ricardo Luis Radis Steinmetz ◽  
Christian Etzkorn ◽  
André Cestonaro do Amaral ◽  
...  
Keyword(s):  
Biogas Production ◽  
Swine Manure ◽  
Treatment Strategies ◽  
Full Scale ◽  
Production Improvement ◽  
Pre Treatment

scholarly journals Comparison of Selected Immune and Hematological Parameters and Their Impact on Survival in Patients with HPV-Related and HPV-Unrelated Oropharyngeal Cancer

Cancers ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 3256
Author(s):  
Adam Brewczyński ◽  
Beata Jabłońska ◽  
Agnieszka Maria Mazurek ◽  
Jolanta Mrochem-Kwarciak ◽  
Sławomir Mrowiec ◽  
...  
Keyword(s):  
Prognostic Factors ◽  
Oropharyngeal Cancer ◽  
Hematological Parameters ◽  
White Blood Cells ◽  
Post Treatment ◽  
Neutrophil Lymphocyte Ratio ◽  
Lymphocyte Ratio ◽  
Hpv Status ◽  
Pre Treatment ◽  
The Impact

Several immune and hematological parameters are associated with survival in patients with oropharyngeal cancer (OPC). The aim of the study was to analyze selected immune and hematological parameters of patients with HPV-related (HPV+) and HPV-unrelated (HPV-) OPC, before and after radiotherapy/chemoradiotherapy (RT/CRT) and to assess the impact of these parameters on survival. One hundred twenty seven patients with HPV+ and HPV− OPC, treated with RT alone or concurrent chemoradiotherapy (CRT), were included. Patients were divided according to HPV status. Confirmation of HPV etiology was obtained from FFPE (Formalin-Fixed, Paraffin-Embedded) tissue samples and/or extracellular circulating HPV DNA was determined. The pre-treatment and post-treatment laboratory blood parameters were compared in both groups. The neutrophil/lymphocyte ratio (NLR), platelet/lymphocyte ratio (PLR), monocyte/lymphocyte ratio (MLR), and systemic immune inflammation (SII) index were calculated. The impact of these parameters on overall (OS) and disease-free (DFS) survival was analyzed. In HPV+ patients, a high pre-treatment white blood cells (WBC) count (>8.33 /mm3), NLR (>2.13), SII (>448.60) significantly correlated with reduced OS, whereas high NLR (>2.29), SII (>462.58) significantly correlated with reduced DFS. A higher pre-treatment NLR and SII were significant poor prognostic factors for both OS and DFS in the HPV+ group. These associations were not apparent in HPV− patients. There are different pre-treatment and post-treatment immune and hematological prognostic factors for OS and DFS in HPV+ and HPV− patients. The immune ratios could be considered valuable biomarkers for risk stratification and differentiation for HPV− and HPV+ OPC patients.

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