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The human genome expresses vast numbers of long noncoding RNAs (lncRNA) that fulfil diverse roles in gene regulation, cell biology, development, and human disease. These roles are often mediated by sequence motifs and secondary structures bound by proteins and can regulate epigenetic, transcriptional, and translational pathways. These functional domains can be further optimised and engineered into RNA devices that are widely used in synthetic biology. We propose that natural lncRNA structures can be explored and exploited for the rational design and assembly of synthetic RNA therapies. This potential has been enabled by advances in the stability, immunogenicity, manufacture, and delivery of other RNA-based therapies, from which we can anticipate the pharmacological properties of lncRNA therapies that have not yet otherwise entered clinical trials. Advances in long noncoding RNA (lncRNA) biology have identified sequence motifs and secondary structures that bind DNA, RNA, or protein targets. An understanding of these structures and their function is needed for the rational and programmable design of lncRNA therapies. LncRNAs contribute to diverse disease aetiologies and may be targeted using small molecules and antisense oligonucleotides. Advances in RNA chemistry, including sequence optimisation and nucleotide modifications, have improved the stability and reduced the immunogenicity of RNA therapies. Formulation of RNA therapies with delivery vehicles, such as lipid nanoparticles, improves stability and enables delivery to target cells and tissues at sufficient dosage. Cellular reprogramming using synthetic mRNAs has demonstrated the ability to modulate gene expression and affect cellular phenotype. Studies have demonstrated the effectiveness of synthetic lncRNA therapies in treating animal disease models. [ABSTRACT FROM AUTHOR]

Access to efficient laboratory services is critical to patient care. Turnaround Time (TAT) is one of the most important measures when judging the efficiency of any laboratory and care system. Few studies on TAT exist for inpatient care settings within low- and middle-income countries (LMICs). Methods: We evaluated therapeutic TAT for a tertiary hospital in Western Kenya, using a time-motion study focusing specifically on common hematology and biochemistry orders. The aim was to determine significant bottlenecks in diagnostic testing processes at the institution. Results: A total of 356 (155 hematology and 201 biochemistry) laboratory tests were fully tracked from the time of ordering to availability of results to care providers. The total therapeutic TAT for all tests was 21.5 ± 0.249 hours (95% CI). The therapeutic TAT for hematology was 20.3 ± 0.331 hours (95% CI) while that for biochemistry tests was 22.2 ± 0.346 hours (95% CI). Printing, sorting and dispatch of the printed results emerged as the most significant bottlenecks, accounting for up to 8 hours of delay (Hematology—8.3 ± 1.29 hours (95% CI), Biochemistry—8.5 ± 1.18 hours (95% CI)). Time of test orders affected TAT, with orders made early in the morning and those in the afternoon experiencing the most delays in TAT. Conclusion: Significant inefficiencies exist at multiple steps in the turnaround times for routine laboratory tests at a large referral hospital within an LMIC setting. Multiple opportunities exist to improve TAT and streamline processes around diagnostic testing in this and other similar settings. [ABSTRACT FROM AUTHOR]

The effects of magnetic layer thickness on the noise characteristics of advanced metal particle tape have been observed using a dc demagnetization process generated with a uniform in-plane magnetizer. The three-dimensional (3D) surface maps of spectral noise power plotted as a function of remanent magnetization state showed a change in behavior as the recording layer became thinner. The thickest magnetic coating of 310 nm showed "trough-like" characteristics associated with conventional thick particulate media. The thinnest sample with a 165 nm magnetic coating showed a "peak-like" response that is observed in continuous thin-film media, with a graduated trend from one to the other for the two intermediate samples. A simulation of these results has been made with an 8000 spherical particle micromagnetic model of the media remanent states and a simulated magnetoresistive read head. Noise maps produced from the simulation compared well with experiment. Spatial isolation of the noise contributions was achieved by dividing the modeled magnetic layer into sublayers. This revealed that particles at the surface were the source of the "peak-like" response, and their contributions became more dominant as the magnetic coating got thinner. Further model investigations showed an association of the different sublayer characteristics with a change in the mean magnetostatic interaction field. The interaction field of particles at the surface had characteristics similar to those of 2D granular thin films and hence generated "thin film-like" noise. A further effect was associated with the spacing between the head and various regions of particles. As this was increased, not only was the amplitude of the noise reduced, but the increased region of integration meant that longer range correlations were incorporated into the observed characteristics, resulting in noise maps more like those of conventional thick particulate media. [ABSTRACT FROM AUTHOR]

A series of advanced metal particle tapes with identical particles but different magnetic coating thicknesses from 300 to 150 nm have been taken through a dc-demagnetization remanent process from positive to negative saturation. Magnetization was achieved with an electromagnetic device, which produced uniform magnetization in the longitudinal direction of the tape. Spectral noise power maps have been generated for the tapes following these demagnetization processes. The thickest tape showed characteristics similar to those of conventional thick tapes, such as video, with demagnetized noise lower than the saturation noise, whereas the thinnest was characteristic of a thin film with demagnetized noise greater than that at saturation. A representation of the experimental measurement process, based on a Landau-Lifshitz-Gilbert model of the medium and a simulation of the "reading" process, generated many of the experimental features. The changes in the noise maps with magnetic coating thickness were attributed to the increased contributions from the free surfaces of the tape as the magnetic coating thickness was reduced. [ABSTRACT FROM AUTHOR]

A method of identifying in-plane anisotropy axes in soft magnetic materials has been developed using an in-field-only measurement technique. The method is based on an extended bi-axial vibrating sample magnetometer (VSM) technique that simulates the torque on a sample; giving rise to equivalent torque curves that are comparable with those determined directly using a torque magnetometer. Testing of the new methodology was carried out on magnetically soft and multi-axial nickel ferrite textured films deposited with various crystal orientations. The results compare well with the accepted bi-axial VSM technique, identifying the same in-plane anisotropy directions and relative easy and hard axes from the in-field measurement alone. This means that these characteristics could be determined using a standard VSM measuring magnetization in the field direction as long as it is fitted with a rotating sample stage. [ABSTRACT FROM AUTHOR]

We compared quantitative RT-PCR (qRT-PCR), RNA-seq and capture sequencing (CaptureSeq) in terms of their ability to assemble and quantify long noncoding RNAs and novel coding exons across 20 human tissues. CaptureSeq was superior for the detection and quantification of genes with low expression, showed little technical variation and accurately measured differential expression. This approach expands and refines previous annotations and simultaneously generates an expression atlas. [ABSTRACT FROM AUTHOR]

The precise splicing of genes confers an enormous transcriptional complexity to the human genome. The majority of gene splicing occurs cotranscriptionally, permitting epigenetic modifications to affect splicing outcomes. Here we show that select exonic regions are demarcated within the three-dimensional structure of the human genome. We identify a subset of exons that exhibit DNase I hypersensitivity and are accompanied by 'phantom' signals in chromatin immunoprecipitation and sequencing (ChIP-seq) that result from cross-linking with proximal promoter- or enhancer-bound factors. The capture of structural features by ChIP-seq is confirmed by chromatin interaction analysis that resolves local intragenic loops that fold exons close to cognate promoters while excluding intervening intronic sequences. These interactions of exons with promoters and enhancers are enriched for alternative splicing events, an effect reflected in cell type-specific periexonic DNase I hypersensitivity patterns. Collectively, our results connect local genome topography, chromatin structure and cis-regulatory landscapes with the generation of human transcriptional complexity by cotranscriptional splicing. [ABSTRACT FROM AUTHOR]

The response of a scanning column magnetometer (SCM) used to measure concentration profiles of columns of magnetic dispersions has been investigated experimentally and theoretically. From the observed linearity of the total SCM output signal as a function of magnetic particle concentration, a consistent theoretical description is developed that assumes a small sensing coil field and no on-going particle agglomeration. Further theoretical development resulted in a detection coil response function that compared well with the measured response of a delta function approximation in the form of a thin ferrite disk and means that the SCM response function and spatial resolution may be determined from the coil design alone. [ABSTRACT FROM AUTHOR]

Background: Actinobacteria form a major bacterial phylum that includes numerous human pathogens. Actinobacteria are primary contributors to carbon cycling and also represent a primary source of industrial high value products such as antibiotics and biopesticides. Consistent with other members of the actinobacterial phylum, Saccharopolyspora erythraea undergo a transitional switch. This switch is characterized by numerous metabolic and morphological changes. Results: We performed RNA sequencing to analyze the transcriptional changes that occur during growth of Saccharopolyspora erythraea in batch culture. By sequencing RNA across the fermentation time course, at a mean coverage of 4000X, we found the vast majority of genes to be prominently expressed, showing that we attained close to saturating sequencing coverage of the transcriptome. During the metabolic switch, global changes in gene expression influence the metabolic machinery of Saccharopolyspora erythraea, resetting an entirely novel gene expression program. After the switch, global changes include the broad repression of half the genes regulated by complex transcriptional mechanisms. Paralogous transposon clusters, delineate these transcriptional programs. The new transcriptional program is orchestrated by a bottleneck event during which mRNA levels are severely restricted by targeted mRNA degradation. Conclusions: Our results, which attained close to saturating sequencing coverage of the transcriptome, revealed unanticipated transcriptional complexity with almost one third of transcriptional content originating from un-annotated sequences. We showed that the metabolic switch is a sophisticated mechanism of transcriptional regulation capable of resetting and re-synchronizing gene expression programs at extraordinary speed and scale. [ABSTRACT FROM AUTHOR]

Genomes of complex organisms encode an abundance and diversity of long noncoding RNAs (lncRNAs) that are expressed throughout the cell and fulfill a wide variety of regulatory roles at almost every stage of gene expression. These roles, which encompass sensory, guiding, scaffolding and allosteric capacities, derive from folded modular domains in lncRNAs. In this diverse functional repertoire, we focus on the well-characterized ability for lncRNAs to function as epigenetic modulators. Many lncRNAs bind to chromatin-modifying proteins and recruit their catalytic activity to specific sites in the genome, thereby modulating chromatin states and impacting gene expression. Considering this regulatory potential in combination with the abundance of lncRNAs suggests that lncRNAs may be part of a broad epigenetic regulatory network. [ABSTRACT FROM AUTHOR]

Transcriptomic analyses have revealed an unexpected complexity to the human transcriptome, whose breadth and depth exceeds current RNA sequencing capability. Using tiling arrays to target and sequence select portions of the transcriptome, we identify and characterize unannotated transcripts whose rare or transient expression is below the detection limits of conventional sequencing approaches. We use the unprecedented depth of coverage afforded by this technique to reach the deepest limits of the human transcriptome, exposing widespread, regulated and remarkably complex noncoding transcription in intergenic regions, as well as unannotated exons and splicing patterns in even intensively studied protein-coding loci such as p53 and HOX. The data also show that intermittent sequenced reads observed in conventional RNA sequencing data sets, previously dismissed as noise, are in fact indicative of unassembled rare transcripts. Collectively, these results reveal the range, depth and complexity of a human transcriptome that is far from fully characterized. [ABSTRACT FROM AUTHOR]

Summary: The human mitochondrial genome comprises a distinct genetic system transcribed as precursor polycistronic transcripts that are subsequently cleaved to generate individual mRNAs, tRNAs, and rRNAs. Here, we provide a comprehensive analysis of the human mitochondrial transcriptome across multiple cell lines and tissues. Using directional deep sequencing and parallel analysis of RNA ends, we demonstrate wide variation in mitochondrial transcript abundance and precisely resolve transcript processing and maturation events. We identify previously undescribed transcripts, including small RNAs, and observe the enrichment of several nuclear RNAs in mitochondria. Using high-throughput in vivo DNaseI footprinting, we establish the global profile of DNA-binding protein occupancy across the mitochondrial genome at single-nucleotide resolution, revealing regulatory features at mitochondrial transcription initiation sites and functional insights into disease-associated variants. This integrated analysis of the mitochondrial transcriptome reveals unexpected complexity in the regulation, expression, and processing of mitochondrial RNA and provides a resource for future studies of mitochondrial function (accessed at http://mitochondria.matticklab.com). [ABSTRACT FROM AUTHOR]

Background: Long non-protein-coding RNAs (ncRNAs) are emerging as important regulators of cellular differentiation and are widely expressed in the brain. Results: Here we show that many long ncRNAs exhibit dynamic expression patterns during neuronal and oligodendrocyte (OL) lineage specification, neuronal-glial fate transitions, and progressive stages of OL lineage elaboration including myelination. Consideration of the genomic context of these dynamically regulated ncRNAs showed they were part of complex transcriptional loci that encompass key neural developmental protein-coding genes, with which they exhibit concordant expression profiles as indicated by both microarray and in situ hybridization analyses. These included ncRNAs associated with differentiation-specific nuclear subdomains such as Gomafu and Neat1, and ncRNAs associated with developmental enhancers and genes encoding important transcription factors and homeotic proteins. We also observed changes in ncRNA expression profiles in response to treatment with trichostatin A, a histone deacetylase inhibitor that prevents the progression of OL progenitors into post-mitotic OLs by altering lineage-specific gene expression programs. Conclusion: This is the first report of long ncRNA expression in neuronal and glial cell differentiation and of the modulation of ncRNA expression by modification of chromatin architecture. These observations explicitly link ncRNA dynamics to neural stem cell fate decisions, specification and epigenetic reprogramming and may have important implications for understanding and treating neuropsychiatric diseases. [ABSTRACT FROM AUTHOR]

In mammals and other eukaryotes most of the genome is transcribed in a developmentally regulated manner to produce large numbers of long non-coding RNAs (ncRNAs). Here we review the rapidly advancing field of long ncRNAs, describing their conservation, their organization in the genome and their roles in gene regulation. We also consider the medical implications, and the emerging recognition that any transcript, regardless of coding potential, can have an intrinsic function as an RNA. [ABSTRACT FROM AUTHOR]

Current research exploring the molecular basis of memory focuses mainly on proteins despite recent genomic studies reporting the abundant transcription of non-protein-coding RNA (ncRNA). Although ncRNAs are involved in a diverse range of biological processes, they are particularly prevalent within the nervous system, where they contribute towards the complexity and function of the mammalian brain. In this review, we apply recent advances in ncRNA biology to predict a critical role for ncRNAs in the molecular mechanisms underlying memory formation and maintenance. We describe the role of ncRNAs in regulating the translation, stability, and editing of mRNA populations in response to synaptic activity during memory formation and the role of ncRNAs in the epigenetic and transcriptional programs that underlie long-term memory storage. We also consider ncRNAs acting as an additional avenue of communication between neurons by their intercellular trafficking. Taken together, the emerging evidence suggests a central role for ncRNAs in memory formation and provokes novel research directions in this field. [ABSTRACT FROM AUTHOR]

A major proportion of the mammalian transcriptome comprises long RNAs that have little or no protein-coding capacity (ncRNAs). Only a handful of such transcripts have been examined in detail, and it is unknown whether this class of transcript is generally functional or merely artifact. Using in situ hybridization data from the Allen Brain Atlas. we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Examination of their genomic context revealed that the ncRNAs were expressed from diverse places including intergenic, intronic, and imprinted loci and that many overlap with, or are transcribed antisense to, protein- coding genes of neurological importance. Comparisons between the expression profiles of ncRNAs and their associated protein-coding genes revealed complex relationships that, in combination with the specific expression profiles exhibited at both regional and subcellular levels, are inconsistent with the notion that they are transcriptional noise or artifacts of chromatin remodeling. Our results show that the majority of ncRNAs are expressed in the brain and provide strong evidence that the majority of processed transcripts with no protein-coding capacity function intrinsically as RNAs. [ABSTRACT FROM AUTHOR]

Background: Hypertension is a major risk factor for cardiovascular disease (CVD), yet treatment and control rates for hypertension are very low in low- and middle-income countries (LMICs). Lack of effective referral networks between different levels of the health system is one factor that threatens the ability to achieve adequate blood pressure control and prevent CVD-related morbidity. Health information technology and peer support are two strategies that have improved care coordination and clinical outcomes for other disease entities in other settings; however, their effectiveness and cost-effectiveness in strengthening referral networks to improve blood pressure control and reduce CVD risk in low-resource settings are unknown.Methods/design: We will use the PRECEDE-PROCEED framework to conduct transdisciplinary implementation research, focused on strengthening referral networks for hypertension in western Kenya. We will conduct a baseline needs and contextual assessment using a mixed-methods approach, in order to inform a participatory, community-based design process to fully develop a contextually and culturally appropriate intervention model that combines health information technology and peer support. Subsequently, we will conduct a two-arm cluster randomized trial comparing 1) usual care for referrals vs 2) referral networks strengthened with our intervention. The primary outcome will be one-year change in systolic blood pressure. The key secondary clinical outcome will be CVD risk reduction, and the key secondary implementation outcomes will include referral process metrics such as referral appropriateness and completion rates. We will conduct a mediation analysis to evaluate the influence of changes in referral network characteristics on intervention outcomes, a moderation analysis to evaluate the influence of baseline referral network characteristics on the effectiveness of the intervention, as well as a process evaluation using the Saunders framework. Finally, we will analyze the incremental cost-effectiveness of the intervention relative to usual care, in terms of costs per unit decrease in systolic blood pressure, per percentage change in CVD risk score, and per disability-adjusted life year saved.Discussion: This study will provide evidence for the implementation of innovative strategies for strengthening referral networks to improve hypertension control in LMICs. If effective, it has the potential to be a scalable model for health systems strengthening in other low-resource settings worldwide.Trial Registration: Clinicaltrials.gov, NCT03543787 . Registered on 29 June 2018. [ABSTRACT FROM AUTHOR]

Provides information on a study which measured hindered settling in magnetic dispersions using a scanning column magnetometry technique. Methods; Results; Discussion.

High levels of burnout among healthcare providers (HCPs) have been a widely documented phenomenon, which have been exacerbated during the COVID-19 pandemic. In the United States, qualitative studies that are inclusive of HCPs in diverse professional roles have been limited. Therefore, we utilized a qualitative–quantitative design to examine professional quality of life in terms of compassion fatigue, burnout, and secondary traumatic stress among hospital-based HCPs, including social workers, hospitalists, residents, and palliative care team members during COVID-19. HCPs (n = 26) participated in virtual semi-structured focus groups or individual interviews and online surveys (n = 30) including the Professional Quality of Life (ProQOL) Scale. While ProQOL scores indicated low levels of compassion fatigue, burnout, and secondary traumatic stress, thematic analysis of our qualitative data included rich descriptions of compassion fatigue, burnout, and secondary traumatic stress. Safety concerns and value misalignment characterized structural stressors perceived to contribute to HCP compassion fatigue, burnout, and secondary traumatic stress. The discrepancy between our qualitative and quantitative findings may be indication that modifications to current screenings are warranted. These findings also suggest a need to identify and implement structural and policy changes that increase HCPs' physical and emotional safety and promote better alignment of institutional interests with HCP values. [ABSTRACT FROM AUTHOR]

In this opinion paper, we argue that global health crises are also information crises. Using as an example the coronavirus disease 2019 (COVID‐19) epidemic, we (a) examine challenges associated with what we term "global information crises"; (b) recommend changes needed for the field of information science to play a leading role in such crises; and (c) propose actionable items for short‐ and long‐term research, education, and practice in information science. [ABSTRACT FROM AUTHOR]

Background: The Academic Model Providing Access to Healthcare (AMPATH) has been a model academic partnership in global health for nearly three decades, leveraging the power of a public-sector academic medical center and the tripartite academic mission - service, education, and research - to the challenges of delivering health care in a low-income setting. Drawing our mandate from the health needs of the population, we have scaled up service delivery for HIV care, and over the last decade, expanded our focus on non-communicable chronic diseases, health system strengthening, and population health more broadly. Success of such a transformative endeavor requires new partnerships, as well as a unification of vision and alignment of strategy among all partners involved. Leveraging the Power of Partnerships and Spreading the Vision for Population Health. We describe how AMPATH built on its collective experience as an academic partnership to support the public-sector health care system, with a major focus on scaling up HIV care in western Kenya, to a system poised to take responsibility for the health of an entire population. We highlight global trends and local contextual factors that led to the genesis of this new vision, and then describe the key tenets of AMPATH's population health care delivery model: comprehensive, integrated, community-centered, and financially sustainable with a path to universal health coverage. Finally, we share how AMPATH partnered with strategic planning and change management experts from the private sector to use a novel approach called a 'Learning Map®' to collaboratively develop and share a vision of population health, and achieve strategic alignment with key stakeholders at all levels of the public-sector health system in western Kenya.Conclusion: We describe how AMPATH has leveraged the power of partnerships to move beyond the traditional disease-specific silos in global health to a model focused on health systems strengthening and population health. Furthermore, we highlight a novel, collaborative tool to communicate our vision and achieve strategic alignment among stakeholders at all levels of the health system. We hope this paper can serve as a roadmap for other global health partners to develop and share transformative visions for improving population health globally. [ABSTRACT FROM AUTHOR]

Background: Hypertension is the leading cause of death and disability. Clinical care for patients with hypertension in Kenya leverages referral networks to provide basic and specialized healthcare services. However, referrals are characterized by non-adherence and delays in completion. An integrated health information technology (HIT) and peer-based support strategy to improve adherence to referrals and blood pressure control was proposed. A formative assessment gathered perspectives on barriers to referral completion and garnered thoughts on the proposed intervention. Methods: We conducted a qualitative study in Kitale, Webuye, Kocholya, Turbo, Mosoriot and Burnt Forest areas of Western Kenya. We utilized the PRECEDE-PROCEED framework to understand the behavioral, environmental and ecological factors that would influence uptake and success of our intervention. We conducted four mabaraza (customary heterogenous community assemblies), eighteen key informant interviews, and twelve focus group discussions among clinicians, patients and community members. The data obtained was audio recorded alongside field note taking. Audio recordings were transcribed and translated for onward coding and thematic analysis using NVivo 12. Results: Specific supply-side and demand-side barriers influenced completion of referral for hypertension. Key demand-side barriers included lack of money for care and inadequate referral knowledge. On the supply-side, long distance to health facilities, low availability of services, unaffordable services, and poor referral management were reported. All participants felt that the proposed strategies could improve delivery of care and expressed much enthusiasm for them. Participants appreciated benefits of the peer component, saying it would motivate positive patient behavior, and provide health education, psychosocial support, and assistance in navigating care. The HIT component was seen as reducing paper work, easing communication between providers, and facilitating tracking of patient information. Participants also shared concerns that could influence implementation of the two strategies including consent, confidentiality, and reduction in patient-provider interaction. Conclusions: Appreciation of local realities and patients' experiences is critical to development and implementation of sustainable strategies to improve effectiveness of hypertension referral networks. Incorporating concerns from patients, health care workers, and local leaders facilitates adaptation of interventions to respond to real needs. This approach is ethical and also allows research teams to harness benefits of participatory community-involved research. Trial registration: Clinicaltrials.gov, NCT03543787, Registered June 1, 2018. https://clinicaltrials.gov/ct2/show/NCT03543787 [ABSTRACT FROM AUTHOR]

Background: Hepatitis C virus (HCV) is the leading indication for liver transplantation and liver-related mortality. The development of direct-acting antivirals (DAA) and a simplified treatment algorithm with a > 97% cure rate should make global elimination of HCV an achievable goal. Yet, vulnerable populations with high rates of HCV still have limited access to treatment. By designing locally contextualized site-specific HCV treatment workflows, we aim to cure HCV in vulnerable, high-risk populations, including people experiencing homelessness (PEH) and people who inject drugs (PWID), in Austin, TX, USA. Methods: Our implementation science study will utilize a qualitative and design thinking approach to characterize patient and systemic barriers and facilitators to HCV treatment in vulnerable, high-risk populations seeking care across seven diverse primary care clinics serving PEHs and PWIDs. Qualitative interviews guided by the Practical, Robust Implementation and Sustainability Model (PRISM) framework will identify barriers and facilitators by leveraging knowledge and experience from both clinic staff and patients. Data synthesized using thematic analysis and design thinking will feed into workshops with clinic stakeholders for idea generation to design site-specific HCV treatment workflows. Providers will be trained on the use of a simplified HCV treatment algorithm with DAAs and clinic staff on the new site-specific HCV treatment workflows. These workflows will be implemented by the seven diverse primary care clinics serving vulnerable, high-risk populations. Implementation and clinical outcomes will be measured using data collected through interviews with staff as well as through medical chart review. Discussion: Our study provides a model of how to contextualize and implement site-specific HCV treatment workflows targeting vulnerable, high-risk populations in other geographic locations. This model can be adopted for future implementation research programs aiming to develop and implement site-specific treatment workflows for vulnerable, high-risk populations and in primary care clinical settings for other disease states beyond just HCV. Trial registration: Registered on ClinicalTrials.gov on July, 14, 2022. Identifier: NCT05460130. [ABSTRACT FROM AUTHOR]

An expansive functionality and complexity has been ascribed to the majority of the human genome that was unanticipated at the outset of the draft sequence and assembly a decade ago. We are now faced with the challenge of integrating and interpreting this complexity in order to achieve a coherent view of genome biology. We argue that the linear representation of the genome exacerbates this complexity and an understanding of its three-dimensional structure is central to interpreting the regulatory and transcriptional architecture of the genome. Chromatin conformation capture techniques and high-resolution microscopy have afforded an emergent global view of genome structure within the nucleus. Chromosomes fold into complex, territorialized three-dimensional domains in concert with specialized subnuclear bodies that harbor concentrations of transcription and splicing machinery. The signature of these folds is retained within the layered regulatory landscapes annotated by chromatin immunoprecipitation, and we propose that genome contacts are reflected in the organization and expression of interweaved networks of overlapping coding and noncoding transcripts. This pervasive impact of genome structure favors a preeminent role for the nucleoskeleton and RNA in regulating gene expression by organizing these folds and contacts. Accordingly, we propose that the local and global three-dimensional structure of the genome provides a consistent, integrated, and intuitive framework for interpreting and understanding the regulatory and transcriptional complexity of the human genome. [ABSTRACT FROM AUTHOR]

The combination of pervasive transcription and prolific alternative splicing produces a mammalian transcriptome of great breadth and diversity. The majority of transcribed genomic bases are intronic, antisense, or intergenic to protein-coding genes, yielding a plethora of short and long non-protein-coding regulatory RNAs. Long noncoding RNAs (lncRNAs) share most aspects of their biogenesis, processing, and regulation with mRNAs. However, lncRNAs are typically expressed in more restricted patterns, frequently from enhancers, and exhibit almost universal alternative splicing. These features are consistent with their role as modular epigenetic regulators. We describe here the key studies and technological advances that have shaped our understanding of the dimensions, dynamics, and biological relevance of the mammalian noncoding transcriptome. [ABSTRACT FROM AUTHOR]

The complexity of the eukaryotic transcriptome is generated by the interplay of transcription initiation, termination, alternative splicing, and other forms of post-transcriptional modification. It was recently shown that RNA transcripts may also undergo cleavage and secondary 5' capping. Here, we show that post-transcriptional cleavage of RNA contributes to the diversification of the transcriptome by generating a range of small RNAs and long coding and noncoding RNAs. Using genome-wide histone modification and RNA polymerase II occupancy data, we confirm that the vast majority of intraexonic CAGE tags are derived from post-transcriptional processing. By comparing exonic CAGE tags to tissue-matched PARE data, we show that the cleavage and subsequent secondary capping is regulated in a developmental-stage- and tissue-specific manner. Furthermore, we find evidence of prevalent RNA cleavage in numerous transcriptomic data sets, including SAGE, cDNA, small RNA libraries, and deep-sequenced size-fractionated pools of RNA. These cleavage products include mRNA variants that retain the potential to be translated into shortened functional protein isoforms. We conclude that post-transcriptional RNA cleavage is a key mechanism that expands the functional repertoire and scope for regulatory control of the eukaryotic transcriptome. [ABSTRACT FROM AUTHOR]

Background: Health system approaches to improve hypertension control require an effective referral network. A national referral strategy exists in Kenya; however, a number of barriers to referral completion persist. This paper is a baseline assessment of a hypertension referral network for a cluster-randomized trial to improve hypertension control and reduce cardiovascular disease risk. Methods: We used sociometric network analysis to understand the relationships between providers within a network of nine geographic clusters in western Kenya, including primary, secondary, and tertiary care facilities. We conducted a survey which asked providers to nominate individuals and facilities to which they refer patients with controlled and uncontrolled hypertension. Degree centrality measures were used to identify providers in prominent positions, while mixed-effect regression models were used to determine provider characteristics related to the likelihood of receiving referrals. We calculated core-periphery correlation scores (CP) for each cluster (ideal CP score = 1.0). Results: We surveyed 152 providers (physicians, nurses, medical officers, and clinical officers), range 10–36 per cluster. Median number of hypertensive patients seen per month was 40 (range 1–600). While 97% of providers reported referring patients up to a more specialized health facility, only 55% reported referring down to lower level facilities. Individuals were more likely to receive a referral if they had higher level of training, worked at a higher level facility, were male, or had more job experience. CP scores for provider networks range from 0.335 to 0.693, while the CP scores for the facility networks range from 0.707 to 0.949. Conclusions: This analysis highlights several points of weakness in this referral network including cluster variability, poor provider linkages, and the lack of down referrals. Facility networks were stronger than provider networks. These shortcomings represent opportunities to focus interventions to improve referral networks for hypertension. Trial registration: Trial Registered on ClinicalTrials.gov NCT03543787, June 1, 2018. [ABSTRACT FROM AUTHOR]

Three-dimensional distributions of demagnetization factors Nd within assemblies of magnetic nanoparticles have been investigated along the axes of cuboid containing vessels. From the results of a numerical polar-based model, a significant skew toward high values in the number distribution is observed and often overlooked by the assumed uniformity of the conventional analytical approach. To enable comparison with experiment, new transverse susceptibility techniques have been developed, which are also applicable to superparamagnetic assemblies that do not have the magnetization features normally required using conventional methods. Applying the two techniques to a system of ∼13 nm magnetite (Fe3O4) particles resulted in the difference between the in-plane and out-of-plane Nd factors of (0.21 ± 0.03) and (0.201 ± 0.009), respectively, which shows closest agreement with the simulation value for the mode of (0.19 ± 0.02). The median and mean results of the model move further away from the experimental result, yielding values of (0.17 ± 0.02) and (0.16 ± 0.02), respectively, which is consistent with the skewed distributions observed here. In all cases, the sum of the Nd factors from each orthogonal axis was equal to 1, giving further confidence in the model. The new methods allow measurements on the superparamagnetic systems often found at this scale, and the agreement with the model means that the spatial distribution of Nd factors may now be taken into account in studies on any nanoscale material that considers the whole structure as a distribution of magnetic elements. [ABSTRACT FROM AUTHOR]

Here we study the effect of an additional interfacial spin-transfer torque, as well as the well-established spin–orbit torque and bulk spin-transfer torque, on skyrmion collections—group of skyrmions dense enough that they are not isolated from one another—in ultrathin heavy metal/ferromagnetic multilayers, by comparing modelling with experimental results. Using a skyrmion collection with a range of skyrmion diameters and landscape disorder, we study the dependence of the skyrmion Hall angle on diameter and velocity, as well as the velocity as a function of diameter. We show that inclusion of the interfacial spin-transfer torque results in reduced skyrmion Hall angles, with values close to experimental results. We also show that for skyrmion collections the velocity is approximately independent of diameter, in marked contrast to the motion of isolated skyrmions, as the group of skyrmions move together at an average group velocity. Moreover, the calculated skyrmion velocities are comparable to those obtained in experiments when the interfacial spin-transfer torque is included. Our results thus show the significance of the interfacial spin-transfer torque in ultrathin magnetic multilayers, which helps to explain the low skyrmion Hall angles and velocities observed in experiment. We conclude that the interfacial spin-transfer torque should be considered in numerical modelling for reproduction of experimental results. [ABSTRACT FROM AUTHOR]

Here we study the effect of an additional interfacial spin-transfer torque, as well as the well-established spin–orbit torque and bulk spin-transfer torque, on skyrmion collections—group of skyrmions dense enough that they are not isolated from one another—in ultrathin heavy metal/ferromagnetic multilayers, by comparing modelling with experimental results. Using a skyrmion collection with a range of skyrmion diameters and landscape disorder, we study the dependence of the skyrmion Hall angle on diameter and velocity, as well as the velocity as a function of diameter. We show that inclusion of the interfacial spin-transfer torque results in reduced skyrmion Hall angles, with values close to experimental results. We also show that for skyrmion collections the velocity is approximately independent of diameter, in marked contrast to the motion of isolated skyrmions, as the group of skyrmions move together at an average group velocity. Moreover, the calculated skyrmion velocities are comparable to those obtained in experiments when the interfacial spin-transfer torque is included. Our results thus show the significance of the interfacial spin-transfer torque in ultrathin magnetic multilayers, which helps to explain the low skyrmion Hall angles and velocities observed in experiment. We conclude that the interfacial spin-transfer torque should be considered in numerical modelling for reproduction of experimental results. [ABSTRACT FROM AUTHOR]

Summary The idea that stem cell therapies work only via cell replacement is challenged by the observation of consistent intercellular molecule exchange between the graft and the host. Here we defined a mechanism of cellular signaling by which neural stem/precursor cells (NPCs) communicate with the microenvironment via extracellular vesicles (EVs), and we elucidated its molecular signature and function. We observed cytokine-regulated pathways that sort proteins and mRNAs into EVs. We described induction of interferon gamma (IFN-γ) pathway in NPCs exposed to proinflammatory cytokines that is mirrored in EVs. We showed that IFN-γ bound to EVs through Ifngr1 activates Stat1 in target cells. Finally, we demonstrated that endogenous Stat1 and Ifngr1 in target cells are indispensable to sustain the activation of Stat1 signaling by EV-associated IFN-γ/Ifngr1 complexes. Our study identifies a mechanism of cellular signaling regulated by EV-associated IFN-γ/Ifngr1 complexes, which grafted stem cells may use to communicate with the host immune system. [ABSTRACT FROM AUTHOR]

Background: Health system approaches to improve hypertension control require an effective referral network. A national referral strategy exists in Kenya; however, a number of barriers to referral completion persist. This paper is a baseline assessment of a hypertension referral network for a cluster-randomized trial to improve hypertension control and reduce cardiovascular disease risk.Methods: We used sociometric network analysis to understand the relationships between providers within a network of nine geographic clusters in western Kenya, including primary, secondary, and tertiary care facilities. We conducted a survey which asked providers to nominate individuals and facilities to which they refer patients with controlled and uncontrolled hypertension. Degree centrality measures were used to identify providers in prominent positions, while mixed-effect regression models were used to determine provider characteristics related to the likelihood of receiving referrals. We calculated core-periphery correlation scores (CP) for each cluster (ideal CP score = 1.0).Results: We surveyed 152 providers (physicians, nurses, medical officers, and clinical officers), range 10-36 per cluster. Median number of hypertensive patients seen per month was 40 (range 1-600). While 97% of providers reported referring patients up to a more specialized health facility, only 55% reported referring down to lower level facilities. Individuals were more likely to receive a referral if they had higher level of training, worked at a higher level facility, were male, or had more job experience. CP scores for provider networks range from 0.335 to 0.693, while the CP scores for the facility networks range from 0.707 to 0.949.Conclusions: This analysis highlights several points of weakness in this referral network including cluster variability, poor provider linkages, and the lack of down referrals. Facility networks were stronger than provider networks. These shortcomings represent opportunities to focus interventions to improve referral networks for hypertension.Trial Registration: Trial Registered on ClinicalTrials.gov NCT03543787 , June 1, 2018. [ABSTRACT FROM AUTHOR]

Background Accurate bacterial genome annotations provide a framework to understanding cellular functions, behavior and pathogenicity and are essential for metabolic engineering. Annotations based only on in silico predictions are inaccurate, particularly for large, high G + C content genomes due to the lack of similarities in gene length and gene organization to model organisms. Results Here we describe a 2D systems biology driven re-annotation of the Saccharopolyspora erythraea genome using proteogenomics, a genome-scale metabolic reconstruction, RNAsequencing and small-RNA-sequencing. We observed transcription of more than 300 intergenic regions, detected 59 peptides in intergenic regions, confirmed 164 open reading frames previously annotated as hypothetical proteins and reassigned function to open reading frames using the genome-scale metabolic reconstruction. Finally, we present a novel way of mapping ribosomal binding sites across the genome by sequencing small RNAs. Conclusions The work presented here describes a novel framework for annotation of the Saccharopolyspora erythraea genome. Based on experimental observations, the 2D annotation framework greatly reduces errors that are commonly made when annotating largehigh G + C content genomes using computational prediction algorithms. [ABSTRACT FROM AUTHOR]

• Parallel atomistic spin-lattice Monte-Carlo algorithm, classical and constrained. • Applicable efficiently to fcc, bcc, hcp, and simple cubic lattices on the GPU. • Domain decomposition allows any number of neighbors to be considered. • Over 200 times faster than commonly used serial Monte-Carlo. • Validated by extensive numerical testing of magnetic parameter temperature scaling. Monte Carlo algorithms are frequently used in atomistic simulations, including for computation of magnetic parameter temperature dependences in multiscale simulations. Even though parallelization strategies for Monte Carlo simulations of lattice spin models are known, its application to computation of magnetic parameter temperature dependences is lacking in the literature. Here we show how, not only the unconstrained algorithm, but also the constrained atomistic Monte Carlo algorithm, can be parallelized for any spin–lattice crystal structure. Compared to the serial algorithms, the parallel Monte Carlo algorithms are typically over 200 times faster, allowing computations in systems with over 10 million atomistic spins on a single graphical processing unit with relative ease. Implementation and testing of the algorithms was carried out in large-scale systems, where finite-size effects are reduced, by accurately computing temperature dependences of magnetization, uniaxial and cubic anisotropies, exchange stiffness, and susceptibilities. In particular for the exchange stiffness the Bloch domain wall method was used with a large cross-sectional area, which allows accurate computation of the domain wall width up to the Curie temperature. The exchange stiffness for a simple cubic lattice closely follows an mk scaling at low temperatures, with k < 2 dependent on the anisotropy strength. However, close to the Curie temperature the scaling exponent tends to k = 2. Furthermore, the implemented algorithms are applied to the computation of magnetization temperature dependence in granular thin films with over 15 million spins, as a function of average grain size and film thickness. We show the average Curie temperature in such systems may be obtained from a weighted Bloch series fit, which is useful for analysis of experimental results in granular thin films. [ABSTRACT FROM AUTHOR]

The assumption that RNA can be readily classified into either protein-coding or non-protein- coding categories has pervaded biology for close to 50 years. Until recently, discrimination between these two categories was relatively straightforward: most transcripts were clearly identifiable as protein-coding messenger RNAs (mRNAs), and readily distinguished from the small number of well-characterized non-protein-coding RNAs (ncRNAs), such as transfer, ribosomal, and spliceosomal RNAs. Recent genome-wide studies have revealed the existence of thousands of noncoding transcripts, whose function and significance are unclear. The discovery of this hidden transcriptome and the implicit challenge it presents to our understanding of the expression and regulation of genetic information has made the need to distinguish between mRNAs and ncRNAs both more pressing and more complicated. In this Review, we consider the diverse strategies employed to discriminate between protein-coding and noncoding transcripts and the fundamental difficulties that are inherent in what may superficially appear to be a simple problem. Misannotations can also run in both directions: some ncRNAs may actually encode peptides, and some of those currently thought to do so may not. Moreover, recent studies have shown that some RNAs can function both as mRNAs and intrinsically as functional ncRNAs, which may be a relatively widespread phenomenon. We conclude that it is difficult to annotate an RNA unequivocally as proteincoding or noncoding, with overlapping protein-coding and noncoding transcripts further confounding this distinction. In addition, the finding that some transcripts can function both intrinsically at the RNA level and to encode proteins suggests a false dichotomy between mRNAs and ncRNAs. Therefore, the functionality of any transcript at the RNA level should not be discounted. [ABSTRACT FROM AUTHOR]

Background: Human-centered design (HCD) is an increasingly recognized approach for engaging stakeholders and developing contextually appropriate health interventions. As a component of the ongoing STRENGTHS study (Strengthening Referral Networks for Management of Hypertension Across the Health System), we report on the process and outcomes of utilizing HCD to develop the implementation strategy prior to a cluster-randomized controlled trial.Methods: We organized a design team of 15 local stakeholders to participate in an HCD process to develop implementation strategies. We tested prototypes for acceptability, appropriateness, and feasibility through focus group discussions (FGDs) with various community stakeholder groups and a pilot study among patients with hypertension. FGD transcripts underwent content analysis, and pilot study data were analyzed for referral completion and reported barriers to referral. Based on this community feedback, the design team iteratively updated the implementation strategy. During each round of updates, the design team reflected on their experience through FGDs and a Likert-scale survey.Results: The design team developed an implementation strategy consisting of a combined peer navigator and a health information technology (HIT) package. Overall, community participants felt that the strategy was acceptable, appropriate, and feasible. During the pilot study, 93% of referrals were completed. FGD participants felt that the implementation strategy facilitated referral completion through active peer engagement; enhanced communication between clinicians, patients, and health administrators; and integrated referral data into clinical records. Challenges included referral barriers that were not directly addressed by the strategy (e.g. transportation costs) and implementation of the HIT package across multiple health record systems. The design team reflected that all members contributed significantly to the design process, but emphasized the need for more transparency in how input from study investigators was incorporated into design team discussions.Conclusions: The adaptive process of co-creation, prototyping, community feedback, and iterative redesign aligned our implementation strategy with community stakeholder priorities. We propose a new framework of human-centered implementation research that promotes collaboration between community stakeholders, study investigators, and the design team to develop, implement, and evaluate HCD products for implementation research. Our experience provides a feasible and replicable approach for implementation research in other settings.Trial Registration: Clinicaltrials.gov, NCT02501746 , registration date: July 17, 2015. [ABSTRACT FROM AUTHOR]

We have developed a low-cost molecularly imprinted polymer (MIP)-based fluorometric assay to directly quantify myoglobin in a biological sample. The assay uses a previously unreported method for the development of microwave-assisted rapid synthesis of aldehyde functionalized magnetic nanoparticles, in just 20 min. The aldehyde functionalized nanoparticles have an average size of 7.5 nm ± 1.8 and saturation magnetizations of 31.8 emu g−1 with near-closed magnetization loops, confirming their superparamagnetic properties. We have subsequently shown that protein tethering was possible to the aldehyde particles, with 0.25 ± 0.013 mg of myoglobin adsorbed to 20 mg of the nanomaterial. Myoglobin-specific fluorescently tagged MIP (F-MIP) particles were synthesized and used within the assay to capture myoglobin from a test sample. Excess F-MIP was removed from the sample using protein functionalized magnetic nanoparticles (Mb-SPION), with the remaining sample analyzed using fluorescence spectroscopy. The obtained calibration plot of myoglobin showed a linear correlation ranging from 60 pg ml−1 to 6 mg ml−1 with the limit of detection of 60 pg ml−1. This method was successfully used to detect myoglobin in spiked fetal calf serum, with a recovery rate of more than 93%. [ABSTRACT FROM AUTHOR]

The credo of the generalist physician has always been the promotion of health for all, in every aspect: not just multiple vulnerable organ systems, but multiple social, cultural, and political factors that contribute to poor health and exacerbate health inequity. In recent years, the field of global health has also adopted this same mission: working across both national and clinical specialty borders to improve health for all and end health disparities worldwide. Yet within the Society for General Internal Medicine, and among American generalists, engagement in global health, both within and outside the USA, remains uncommon. We see this gap as an opportunity, because in fact generalists in America already have the skills and experience that global health badly needs. SGIM could promote generalists to global health’s vanguard, with three core steps. First, we generalists must continue to integrate health for the vulnerable into our domestic work, generating care models applicable in low-resource settings around the globe. Conversely, we must also engage with and implement international ideas and solutions for universal access to primary care for vulnerable patients in the USA. And lastly, we must build platforms to connect ourselves with colleagues worldwide to exchange these learnings. [ABSTRACT FROM AUTHOR]

DNA synthesis in vitro has enabled the rapid production of reference standards. These are used as controls, and allow measurement and improvement of the accuracy and quality of diagnostic tests. Current reference standards typically represent target genetic material, and act only as positive controls to assess test sensitivity. However, negative controls are also required to evaluate test specificity. Using a pair of chimeric A/B RNA standards, this allowed incorporation of positive and negative controls into diagnostic testing for the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The chimeric standards constituted target regions for RT-PCR primer/probe sets that are joined in tandem across two separate synthetic molecules. Accordingly, a target region that is present in standard A provides a positive control, whilst being absent in standard B, thereby providing a negative control. This design enables cross-validation of positive and negative controls between the paired standards in the same reaction, with identical conditions. This enables control and test failures to be distinguished, increasing confidence in the accuracy of results. The chimeric A/B standards were assessed using the US Centres for Disease Control real-time RT-PCR protocol, and showed results congruent with other commercial controls in detecting SARS-CoV-2 in patient samples. This chimeric reference standard design approach offers extensive flexibility, allowing representation of diverse genetic features and distantly related sequences, even from different organisms. [ABSTRACT FROM AUTHOR]

Reference 1 Desai A, O'Neal L, Reinis K. Development, implementation, and feasibility of site-specific hepatitis C virus treatment workflows for treating vulnerable, high-risk populations: protocol of the Erase Hep C study - a prospective single-arm intervention trial. Correction: Development, implementation, and feasibility of site-specific hepatitis C virus treatment workflows for treating vulnerable, high-risk populations: protocol of the Erase Hep C study - a prospective single-arm intervention trial B Correction: Pilot Feasibility Stud 9, 78 (2023) b B https://doi.org/10.1186/s40814-023-01311-4 b Following publication of the original article [[1]], the authors identified an error in Table 2. [Extracted from the article]

Superparamagnetic iron oxide nanoparticles (SPIONs) and core-shell type nanoparticles, consisting of SPIONs coated with mesoporous silica and/or lipid, were synthesised and tested for their potential theranostic applications in drug delivery, magnetic hyperthermia and as a contrast agent. Transmission Electron Microscopy (TEM) confirmed the size of bare and coated SPIONs was in the range of 5–20 nm and 100–200 nm respectively. The superparamagnetic nature of all the prepared nanomaterials as indicated by Vibrating Sample Magnetometry (VSM) and their heating properties under an AC field confirm their potential for hyperthermia applications. Scanning Column Magnetometry (SCM) data showed that extrusion of bare-SPION (b-SPION) dispersions through a 100 nm polycarbonate membrane significantly improved the dispersion stability of the sample. No sedimentation was apparent after 18 h compared to a pre-extrusion estimate of 43% settled at the bottom of the tube over the same time. Lipid coating also enhanced dispersion stability. Transversal relaxation time (T2) measurements for the nanoparticles, using a bench-top relaxometer, displayed a significantly lower value of 46 ms, with a narrow relaxation time distribution, for lipid silica coated SPIONs (Lip-SiSPIONs) as compared to that of 1316 ms for the b-SPIONs. Entrapment efficiency of the anticancer drug, Doxorubicin (DOX) for Lip-SPIONs was observed to be 35% which increased to 58% for Lip-SiSPIONs. Moreover, initial in-vitro cytotoxicity studies against human breast adenocarcinoma, MCF-7 cells showed that % cell viability increased from 57% for bSPIONs to 82% for Lip-SPIONs and to 87% for Lip-SiSPIONs. This suggests that silica and lipid coatings improve the biocompatibility of bSPIONs significantly and enhance the suitability of these particles as drug carriers. Hence, the magnetic nanomaterials prepared in this work have potential theranostic properties as a drug carrier for hyperthermia cancer therapy and also offer enhancement of contrast agent efficacy and a route to a significant increase in dispersion stability. [ABSTRACT FROM AUTHOR]

Novel hierarchically ordered porous magnetic nanocomposites with interconnecting macroporous windows and meso-microporous walls containing well dispersed magnetic nanoparticles have been fabricated and used as a support to immobilise lipase for the efficient hydrolysis of ester. [ABSTRACT FROM AUTHOR]

The past few years have revealed that the genomes of all studied eukaryotes are almost entirely transcribed, generating an enormous number of non-protein-coding RNAs (ncRNAs). In parallel, it is increasingly evident that many of these RNAs have regulatory functions. Here, we highlight recent advances that illustrate the diversity of ncRNA control of genome dynamics, cell biology, and developmental programming. [ABSTRACT FROM AUTHOR]