Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of environmental Actinobacteria in buildings by means of chemotaxonomy, 16S rRNA sequencing, and MALDI-TOF MS

ABSTRACT Actinobacteria are abundant in soil and other environmental ecosystems and are also an important part of the human microbiota. Hence, they can also be detected in indoor environments and on building materials, where actinobacterial proliferation on damp materials can indicate moisture damage. The aim of this study was to evaluate the matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) for the identification of 28 environmental strains of Actinobacteria isolated from building materials and indoor and outdoor air samples, mainly collected in the context of moisture damage investigations in buildings in Finland. The 16S rRNA gene sequencing and chemotaxonomic analyses were performed, and results were compared with the MALDI-TOF MS Biotyper identification. Using 16S rRNA gene sequencing, all isolates were identified on the species or genus level and were representatives of Streptomyces, Nocardia, and Pseudonocardia genera. Based on MALDI-TOF MS analysis, initially, 11 isolates were identified as Streptomyces spp. and 1 as Nocardia carnea with a high identification score. After an upgrade in the MALDI-TOF MS in-house database and re-evaluation of mass spectra, 13 additional isolates were identified as Nocardia, Pseudonocardia, and Streptomyces. MALDI-TOF MS has the potential in environmental strain identification; however, the standard database needs to be considerably enriched by environmental Actinobacteria representatives. IMPORTANCE The manuscript addresses the challenges in identifying environmental bacteria using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) Biotyper-based protein profiling. The matter of the studies—actinobacterial strains—has been isolated mostly from building materials that originated from a confirmed moisture-damaged situation. Polyphasic taxonomy, 16S RNA gene sequencing, and MALDI-TOF mass spectrometry were applied for identification purposes. In this experimental paper, a few important facts are highlighted. First, Actinobacteria are abundant in the natural as well as built environment, and their identification on the species and genus levels is difficult and time-consuming. Second, MALDI-TOF MS is an effective tool for identifying bacterial environmental strains, and in parallel, continuous enrichment of the proteomics mass spectral databases is necessary for proper identification. Third, the chemical approach aids in the taxonomical inquiry of Actinobacteria environmental strains.
Automated size‐specific dose estimates framework in thoracic CT using convolutional neural network based on U‐Net model

Abstract Purpose This study aimed to develop an automated method that uses a convolutional neural network (CNN) for calculating size‐specific dose estimates (SSDEs) based on the corrected effective diameter (Deff corr) in thoracic computed tomography (CT). Methods Transaxial images obtained from 108 adult patients who underwent non‐contrast thoracic CT scans were analyzed. To calculate the Deff corr according to Mihailidis et al., the average relative electron densities for lung, bone, and other tissues were used to correct the lateral and anterior–posterior dimensions. The CNN architecture based on the U‐Net algorithm was used for automated segmentation of three classes of tissues and the background region to calculate dimensions and Deff corr values. Then, 108 thoracic CT images and generated segmentation masks were used for network training. The water‐equivalent diameter (Dw) was determined according to the American Association of Physicists in Medicine Task Group 220. Linear regression and Bland–Altman analysis were performed to determine the correlations between SSDEDeff corr(automated), SSDEDeff corr(manual), and SSDEDw. Results High agreement was obtained between the manual and automated methods for calculating the Deff corr SSDE. The mean values for the SSDEDeff corr(manual), SSDEDw, and SSDEDeff corr(automated) were 14.3 ± 2.1 mGy, 14.6 ± 2.2 mGy, and 14.5 ± 2.4 mGy, respectively. The U‐Net model was successfully trained and used to accurately predict SSDEs, with results comparable to manual‐labeling results. Conclusion The proposed automated framework using a CNN offers a reliable and efficient solution for determining the Deff corr SSDE in thoracic CT.
5-Hydroxymethylcytosine Profiling of Cell-Free DNA Identifies Bivalent Genes That Are Prognostic of Survival in High-Risk Neuroblastoma.

PURPOSE Neuroblastoma is the most common extracranial solid tumor in childhood. We previously showed that circulating cell-free DNA (cfDNA) and tumor biopsy derived 5-hydroxymethylcytosime (5-hmC) profiles identified patients with neuroblastoma who experienced subsequent relapse. Here, we hypothesized that 5-hmC modifications selectively enriched in cfDNA compared with tumor biopsy samples would identify epigenetic changes associated with aggressive tumor behavior and identify novel biomarkers of outcome in patients with high-risk neuroblastoma. METHODS 5-hmC profiles from cfDNA (n = 64) and tumor biopsies (n = 48) were compared. Two neuroblastoma cell lines underwent chromatin immunoprecipitation followed by sequencing (ChIP-Seq) for H3K27me3, H3K4me3, and H3K27ac; kethoxal-associated single-stranded DNA sequencing; hmC-Seal for 5-hmC; and RNA-sequencing (RNA-Seq). Genes enriched for both H3K27me3 and H3K4me3 in the included cell lines were defined as bivalent. Using bivalent genes defined in vitro, a bivalent signature was established in three publicly available cohorts of patients with neuroblastoma through gene set variation analysis. Differences between tumors with high or low bivalent signatures were assessed by the Kaplan-Meier method and Cox proportional hazards models. RESULTS In cfDNA compared with tumor biopsy derived 5-hmC profiles, we found increased 5-hmC deposition on Polycomb Repressive Complex 2 target genes, a finding previously described in the context of bivalent genes. We identified 313 genes that bore bivalent chromatin marks, were enriched for mediators of neuronal differentiation, and were transcriptionally repressed across a panel of heterogeneous neuroblastoma cell lines. In three distinct clinical cohorts, low bivalent signature was significantly and independently associated with worse clinical outcome in patients with high-risk neuroblastoma. CONCLUSION Low expression of bivalent genes is a biomarker of worse outcome in patients with high-risk neuroblastoma.
Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework

Abstract The advent of perturbation-based massively parallel reporter assays (MPRAs) technique has facilitated the delineation of the roles of non-coding regulatory elements in orchestrating gene expression. However, computational efforts remain scant to evaluate and establish guidelines for sequence design strategies for perturbation MPRAs. In this study, we propose a framework for evaluating and comparing various perturbation strategies for MPRA experiments. Within this framework, we benchmark three different perturbation approaches from the perspectives of alteration in motif-based profiles, consistency of MPRA outputs, and robustness of models that predict the activities of putative regulatory motifs. While our analyses show very similar results across multiple benchmarking metrics, the predictive modeling for the approach involving random nucleotide shuffling shows significant robustness compared with the other two approaches. Thus, we recommend designing sequences by randomly shuffling the nucleotides of the perturbed site in perturbation-MPRA, followed by a coherence check to prevent the introduction of other variations of the target motifs. In summary, our evaluation framework and the benchmarking findings create a resource of computational pipelines and highlight the potential of perturbation-MPRA in predicting non-coding regulatory activities.
Feasibility and Clinical Utility of Reporting Hereditary Cancer Predisposition Pathogenic Variants Identified in Research Germline Sequencing: A Prospective Interventional Study

PURPOSE Patients with cancer frequently undergo research-grade germline sequencing but clinically actionable results are not routinely disclosed. The objective of this study is to evaluate the feasibility of reporting clinically relevant secondary findings (SF) identified in germline research sequencing using the institutional molecular tumor board (MTB) and the treating oncology physician. METHODS This prospective, interventional cohort study enrolled Total Cancer Care participants with any cancer diagnosis at a single institution. Patients underwent research-grade germline whole-exome sequencing, with bioinformatic analysis in a Clinical Laboratory Improvement Amendments–certified laboratory to verify pathogenic/likely pathogenic germline variants (PGVs) in any American College of Medical Genomics and Genetics SF v2.0 genes. After a protocol modification in consenting patients, the MTB reported PGVs to treating oncology physicians with recommendations for referral to a licensed genetic counselor and clinical confirmatory testing. RESULTS Of the 781 enrolled participants, 32 (4.1%) harbored cancer predisposition PGVs, 24 (3.1%) were heterozygous carriers of an autosomal recessive cancer predisposition syndrome, and 14 (1.8%) had other hereditary disease PGVs. Guideline-directed testing would have missed 37.5% (12/32) of the inherited cancer predisposition PGVs, which included BRCA1, BRCA2, MSH6, SDHAF2, SDHB, and TP53 variants. Three hundred fifteen participants consented to reporting results; results for all living patients were reported to the clinical team with half referred to a licensed genetic counselor. There was concordance between all research variants identified in patients (n = 9) who underwent clinical confirmatory sequencing. CONCLUSION MTB reporting of research-grade germline sequencing to the clinical oncology team is feasible. Over a third of PGVs identified using a universal testing strategy would have been missed by guideline-based approach, suggesting a role for expanding germline testing.
Widespread dissolved inorganic carbon-modifying toolkits in genomes of autotrophic Bacteria and Archaea and how they are likely to bridge supply from the environment to demand by autotrophic pathways

ABSTRACT Using dissolved inorganic carbon (DIC) as a major carbon source, as autotrophs do, is complicated by the bedeviling nature of this substance. Autotrophs using the Calvin-Benson-Bassham cycle (CBB) are known to make use of a toolkit comprised of DIC transporters and carbonic anhydrase enzymes (CA) to facilitate DIC fixation. This minireview provides a brief overview of the current understanding of how toolkit function facilitates DIC fixation in Cyanobacteria and some Proteobacteria using the CBB and continues with a survey of the DIC toolkit gene presence in organisms using different versions of the CBB and other autotrophic pathways (reductive citric acid cycle, Wood-Ljungdahl pathway, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate cycle, and dicarboxylate-hydroxybutyrate cycle). The potential function of toolkit gene products in these organisms is discussed in terms of CO2 and HCO3− supply from the environment and demand by the autotrophic pathway. The presence of DIC toolkit genes in autotrophic organisms beyond those using the CBB suggests the relevance of DIC metabolism to these organisms and provides a basis for better engineering of these organisms for industrial and agricultural purposes.
Long-term suboptimal dietary trace element supply does not affect trace element homeostasis in murine cerebellum

Abstract The ageing process is associated with alterations of systemic trace element (TE) homeostasis increasing the risk, e.g. neurodegenerative diseases. Here, the impact of long-term modulation of dietary intake of copper, iron, selenium, and zinc was investigated in murine cerebellum. Four- and 40-wk-old mice of both sexes were supplied with different amounts of those TEs for 26 wk. In an adequate supply group, TE concentrations were in accordance with recommendations for laboratory mice while suboptimally supplied animals received only limited amounts of copper, iron, selenium, and zinc. An additional age-adjusted group was fed selenium and zinc in amounts exceeding recommendations. Cerebellar TE concentrations were measured by inductively coupled plasma–tandem mass spectrometry. Furthermore, the expression of genes involved in TE transport, DNA damage response, and DNA repair as well as selected markers of genomic stability [8-oxoguanine, incision efficiency toward 8-oxoguanine, 5-hydroxyuracil, and apurinic/apyrimidinic sites and global DNA (hydroxy)methylation] were analysed. Ageing resulted in a mild increase of iron and copper concentrations in the cerebellum, which was most pronounced in the suboptimally supplied groups. Thus, TE changes in the cerebellum were predominantly driven by age and less by nutritional intervention. Interestingly, deviation from adequate TE supply resulted in higher manganese concentrations of female mice even though the manganese supply itself was not modulated. Parameters of genomic stability were neither affected by age, sex, nor diet. Overall, this study revealed that suboptimal dietary TE supply does not substantially affect TE homeostasis in the murine cerebellum.
Developing a spatial decision support system for sustainable built environments in Abu Dhabi

The research aims at developing a set of sustainability indicators for the challenging Abu Dhabi built environment and examine the possible use of GIS. The research has illustrated the real potential of the sustainability indicators for managing built environment sustainability performance and provides a clear perspective on how the proposed indicators can be used to develop a DSS to assess and improve Abu Dhabi’s sustainability.
ACCURATE CALCULATION OF THE POWER TRANSFER AND EFFICIENCY IN RESONATOR ARRAYS FOR INDUCTIVE POWER TRANSFER

This paper studies the power transfer characteristics of a resonator array for inductive power transfer by means of the accurate analytical solution of its circuit model. Through the mathematical inversion of a tridiagonal matrix, it is possible to obtain closed-form expressions for the current in each resonator and consequently expressions for the power transfer and efficiency of the system. The method can be applied to a resonator array powering a load at the end of the array or a receiver facing the array at any position. With the expressions obtained, it is possible not only to achieve a better understanding of the power transfer characteristics in resonator arrays but also to obtain the conditions for maximum power transfer or maximum efficiency, for several conditions and parameters of the system. A prototype of a stranded-wire resonator array powered by a resonant inverter, capable of delivering power to a load from 65 W to 90 W with efficiency values between 63% and 88%, was built in order not only to validate the expressions obtained but also to show their practical applicability and demonstrate that these arrays can be used for higher power transfer applications.
Biofield Therapies: Guidelines for Reporting Clinical Trials

A set of guidelines has been developed to help improve reporting of clinical trials of biofield therapies. The need for enhanced transparency when reporting trials of this family of integrative health practices, eg, External Qigong, Healing Touch, Reiki and Therapeutic Touch, has been advocated in systematic reviews of these studies. The guidelines, called Biofield Therapies: Reporting Evidence Guidelines (BiFi REGs), supplement CONsolidated Standards of Reporting Trials (CONSORT) 2010 by including details of the intervention protocols relevant to biofield therapy trials. BiFi REGs evolved through a draft document created by a core group, two rounds of a Delphi process with an international group of subject matter experts and two panels, meeting via Zoom, which included editors of complementary and integrative medicine journals. BiFi REGs comprises a 15-item Intervention checklist. Modifications of two other CONSORT topic areas are also proposed to enhance their relevance to trials of biofield therapies. Included for each item are an explanation, and exemplars of reporting from peer-reviewed published reports of biofield therapy trials. When used in conjunction with all other items from CONSORT 2010, we anticipate that BiFi REGs will expedite the peer review process for biofield therapy trials, facilitate attempts at trial replication and help to inform decision-making in the clinical practice of biofield therapies.
Remotely sensed sedimentology of Plymouth Sound

As part of the Plymouth Sound research project, remotely sensed data are used to evaluate the present day estuarine hydrography of the Sound. Re-examination of 1983 Thermal Linescan images shows a series of small tidal water bodies in the Hamoaze and Drake Channel area. In July 1989 an Airborne Thematic Mapper was flown over Plymouth Sound and concurrent in situ surface samples were taken to analyse the suspended sediment, % organics, temperature and salinity. Secchi disc depths were measured to compare with spectral response. A direct correlation is found between surface currents and tidal bodies, and the present day sea-bed deposits.
Understanding communication between patients and healthcare professionals regarding comprehensive biomarker testing in precision oncology: A scoping review

Abstract Background Precision oncology, using comprehensive biomarker testing (cBT) to inform individual cancer diagnosis, prognosis and treatment, includes increasingly complex technology and clinical data sets. People impacted by cancer (patients and caregivers) and healthcare professionals (HCPs) face distinct challenges in navigating the cBT and personalized treatment landscape. This review summarizes evidence regarding cBT‐related communication between people impacted by cancer and HCPs and identifies important avenues for future research in precision oncology. Methods A scoping review was conducted using records published in PubMed during January 2017–August 2022, focusing on the breadth of topics on patient‐HCP communication and knowledge resources used by HCPs as guidance in cBT‐related communication. Data were extracted from records meeting inclusion criteria, and findings were summarized according to main topics. Results The search identified 287 unique records and data were extracted from 42 records, including nine from expert input. Most records originated from the United States included patients with different types of cancer, and oncologists were the main HCPs. Patients' motivation for undergoing cBT and receiving results was generally high in different settings. However, patients' understanding of cBT‐related concepts was limited, and their knowledge and information preferences changed based on cBT implications and significance to family members. HCPs were valued by patients as a trusted source of information. Limited evidence was available on HCPs' information‐seeking behavior and factors influencing cBT‐related knowledge and confidence, often self‐reported as insufficient. Conclusions Patient education by knowledgeable and confident HCPs, information management and a caring patient‐HCP relationship communicating continuity of care regardless of cBT results are crucial to empower patients and shared decision‐making in precision oncology. More data on the process and structure of cBT‐related communication, distinction between and characterization of different timepoints of patient‐HCP interactions are needed.
Perceptions of integrated rehabilitation service delivery in a metropolitan district

Background There is a recognised need for rehabilitation services at primary health care (PHC) level. In addition, there are clear policies (international and national) and guidelines for use by healthcare planners in South Africa to implement rehabilitation services. Although rehabilitation services are provided on the primary platform, its operationalisation has not been in an integrated manner. Clarity on the level of integration within existing PHC rehabilitation service delivery is required for its inclusion in a reengineered PHC. Aim The study explored the extent to which rehabilitation services are integrated into PHC service delivery based on the expressed reality of rehabilitation professionals. Setting The Johannesburg Metropolitan District of Gauteng, South Africa. Methods In-depth interviews with 12 PHC rehabilitation professionals were completed to elicit their experiences with PHC rehabilitation services. Results The theme the current state of rehabilitation services – ‘this is the reality; you need to do what you need to do’ along with its two subcategories, was generated from this study. The theme describes the expressed reality of suboptimal, underdeveloped and poorly integrated rehabilitation services within the Johannesburg Metropolitan District. Rehabilitation service providers have adapted service delivery by including isolated components of rehabilitation integration models, but this has not yielded an integrated service. Conclusion Rehabilitation services although recognised as a crucial service in PHC must be critically analysed and adapted to develop integrated service delivery models. There should be a shift from selected coping mechanisms to targeted, integrated services. Contribution The study describes PHC rehabilitation services and explores best practice models for integrated service planning and delivery.
Detection of Perfectly-conducting Targets with Airborne Electromagnetic Systems

Detection of Perfectly-Conducting Targets with Airborne Electromagnetic Systems Adam Smiarowski Doctor of Philosophy Graduate Department of Physics University of Toronto 2012 A significant problem with exploring for electrically conductive mineral deposits with airborne electromagnetic (AEM) methods is that many of the most valuable sulphide deposits are too conductive to be detected with conventional systems. High-grade sulphide deposits with electrical conductivities on the order of 100,000 S/m can appear as “perfect conductors” to most EM systems because the decay of secondary fields (the “time constant” of the deposit) generated in the target by the system transmitter takes much longer than the short measuring time of EM systems. Their EM response is essentially undetectable with off-time measurements. One solution is to make measurements during the transmitter on-time when the secondary field of the target produced by magnetic flux exclusion is large. The difficulty is that the secondary field must be measured in the presence of a primary field which is orders of magnitude larger. The goal of this thesis is to advance the methodology of making AEM measurements during transmitter on-time by analysing experimental data from three different AEM systems. The first system analysed is a very large separation, two helicopter system where geometry is measured using GPS sensors. In order to calculate the primary field at the receiver with sufficient accuracy, the very large (nominally 400 m) separation requires geometry to be known to better than 1 m. Using the measured geometry to estimate and remove the primary field, I show that a very conductive target can be detected at depths of 200m using the total secondary field. I then used fluxgate magnetometers to correct for receiver rotation which allowed the component of the secondary field to be determined. The second system I examined was a large separation fixed-wing AEM system. Using a towed receiver bird with a smaller (≈ 135m) separation, the geometry must be known much more accurately. In the absence of direct measurement of this geometry, I used a least-squares prediction approach using measurements of aircraft manoeuvres which