bluuebunny/crossref_metadata_2025 huggingface dataset:
Unfiltered Nanofat Injections Rejuvenate Postburn Scars of Face
Authors: Jan Saadia Nosheen , Bashir Muhammad Mustehsan , Khan Farid Ahmad , Hidayat Zohaib , Ansari Hamid Hussain , Sohail Muhammad , Bajwa Afzaal Bashir , Shami Hussan Birkhez , Hanif Asif , Aziz Faiza , Choudhery Mahmood S.
Published: October 2018

The aim of this study was to compare the quality of postburn facial scars before and after injection of unfiltered nanofat. The study was performed in the Plastic Surgery Department of Mayo Hospital, Lahore, Pakistan, from January 2015 to December 2016. Forty-eight patients with postburn facial scars were included; age range was 4 to 32 years with Fitzpatrick skin types between 3 and 4. Patients with hypertrophic scars, contractures, or keloids were excluded. Scars were assessed by a senior plastic surgeon and the patient on the POSAS (Patient Observer Scar Assessment Scale). Fat was harvested from the abdomen and/or thighs with a 3-mm multiport liposuction cannula (containing several sharp side holes of 1 mm) using Coleman technique. The harvested fat was emulsified and transferred into 1-mL Luer-Lock syringes for injection into the subdermal or intradermal plane. Final follow-up was scheduled at 6 months, and scar was rated by the patient and the same surgeon on the POSAS. Preoperative and postoperative scar scores were compared, andPvalues were calculated. Results indicated that after nanofat grafting, there was a statistically significant improvement in scar quality. The most significant improvements on the observer scale were seen in pigmentation and pliability (P< 0.0001). Thickness and relief were the least improved variables (P= of 0.785 and 0.99, respectively). ImageJ scanning also showed pigmentation change (P= 0.076). A statistically significant improvement was seen in all parameters of the patient section of the POSAS (P< 0.0001). In conclusion, unfiltered nanofat grafting seems to be a promising and effective therapeutic approach in postburn facial scars, showing significant improvement in scar quality. The trial was registered on www.clinicaltrials.gov with following ID NCT03352297.
Learners' Experiences During Rapid Cycle Deliberate Practice Simulations
Authors: Chancey Rebecca J. , Sampayo Esther M. , Lemke Daniel S. , Doughty Cara B.
Published: October 2018

Introduction

Rapid Cycle Deliberate Practice (RCDP) is a team-based simulation method, emphasizing repetitive practice over reflective debriefing, with progressively more challenging rounds, frequent starts and stops, and direct coaching. Although some studies have shown improved performance, no study has evaluated learners' perceptions. We aimed to explore learners' experiences during RCDP.

Methods

This was a qualitative study of participants' perceptions regarding RCDP during their pediatric emergency medicine rotation. Participants completed surveys about RCDP learning. A purposive sample of residents and nurses were interviewed. Two coders analyzed all interview transcripts to identify emerging themes. Constant comparison analysis was performed until thematic saturation was achieved.

Results

Forty-four participants completed surveys. Participants found RCDP interruptions beneficial and felt that they learned most during interruptions. Participants who were able to compare traditional and RCDP simulations felt that RCDP allowed more focused correction of mistakes, acquisition of new skills, and timely practice of team behaviors. Fourteen participants were interviewed. Three themes emerged. (1) The real-time corrections during RCDP allowed for learning and creation of new skills through repetition and practice. (2) The RCDP allowed learners to gain confidence, decrease anxiety, and learn in a safe environment. (3) By introducing new information in smaller chunks, participants maximized learning without cognitive overload.

Conclusions

Rapid Cycle Deliberate Practice is well received by learners. Because of frequent interruptions, learners noted early error correction, a safe learning environment, and skill improvement during RCDP. Learners recognized that the progressive advancement of RCDP helped prevent cognitive overload. Future studies should measure cognitive load and skills retention.
Noether's symmetry and conserved quantity for a time-delayed Hamiltonian system of Herglotz type
Authors: Zhang Yi
Published: October 2018

The variational problem of Herglotz type and Noether's theorem for a time-delayed Hamiltonian system are studied. Firstly, the variational problem of Herglotz type with time delay in phase space is proposed, and the Hamilton canonical equations with time delay based on the Herglotz variational problem are derived. Secondly, by using the relationship between the non-isochronal variation and the isochronal variation, two basic formulae of variation of the Hamilton–Herglotz action with time delay in phase space are derived. Thirdly, the definition and criterion of the Noether symmetry for the time-delayed Hamiltonian system are established and the corresponding Noether's theorem is presented and proved. The theorem we obtained contains Noether's theorem of a time-delayed Hamiltonian system based on the classical variational problem and Noether's theorem of a Hamiltonian system based on the variational problem of Herglotz type as its special cases. At the end of the paper, an example is given to illustrate the application of the results.
Determination of the instantaneous geostrophic flow within the three-dimensional magnetostrophic regime
Authors: Hardy Colin M. , Livermore Philip W. , Niesen Jitse , Luo Jiawen , Li Kuan
Published: October 2018

In his seminal work, Taylor (1963Proc. R. Soc. Lond. A274, 274–283. (doi:10.1098/rspa.1963.0130).) argued that the geophysically relevant limit for dynamo action within the outer core is one of negligibly small inertia and viscosity in the magnetohydrodynamic equations. Within this limit, he showed the existence of a necessary condition, now well known as Taylor's constraint, which requires that the cylindrically averaged Lorentz torque must everywhere vanish; magnetic fields that satisfy this condition are termed Taylor states. Taylor further showed that the requirement of this constraint being continuously satisfied through time prescribes the evolution of the geostrophic flow, the cylindrically averaged azimuthal flow. We show that Taylor's original prescription for the geostrophic flow, as satisfying a given second-order ordinary differential equation, is only valid for a small subset of Taylor states. An incomplete treatment of the boundary conditions renders his equation generally incorrect. Here, by taking proper account of the boundaries, we describe a generalization of Taylor's method that enables correct evaluation of the instantaneous geostrophic flow for any three-dimensional Taylor state. We present the first full-sphere examples of geostrophic flows driven by non-axisymmetric Taylor states. Although in axisymmetry the geostrophic flow admits a mild logarithmic singularity on the rotation axis, in the fully three-dimensional case we show that this is absent and indeed the geostrophic flow appears to be everywhere regular.
Expression of a novel surfactant protein gene is associated with sites of extrapulmonary respiration in a lungless salamander
Authors: Lewis Zachary R. , Dorantes Jorge A. , Hanken James
Published: October 2018

Numerous physiological and morphological adaptations were achieved during the transition to lungless respiration that accompanied evolutionary lung loss in plethodontid salamanders, including those that enable efficient gas exchange across extrapulmonary tissue. However, the molecular basis of these adaptations is unknown. Here, we show that lungless salamanders express in the larval integument and the adult buccopharynx—principal sites of respiratory gas exchange in these species—a novel paralogue of the genesurfactant-associated protein C(SFTPC), which is a critical component of pulmonary surfactant expressed exclusively in the lung in other vertebrates. The paralogous gene appears to be found only in salamanders, but, similar toSFTPC, in lunged salamanders it is expressed only in the lung. This heterotopic gene expression, combined with predictions from structural modelling and respiratory tissue ultrastructure, suggests that lungless salamanders may produce pulmonary surfactant-like secretions outside the lungs and that the novel paralogue ofSFTPCmight facilitate extrapulmonary respiration in the absence of lungs. Heterotopic expression of theSFTPCparalogue may have contributed to the remarkable evolutionary radiation of lungless salamanders, which account for more than two thirds of urodele species alive today.
CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes
Authors: Bayati Masroor , Rabiee Hamid Reza , Mehrbod Mehrdad , Vafaee Fatemeh , Ebrahimi Diako , Forrest Alistair , Alinejad-Rokny Hamid
Published: September 2018

Analyses of large somatic mutation datasets, using advanced computational algorithms, have revealed at least 30 independent mutational signatures in tumor samples. These studies have been instrumental in identification and quantification of responsible endogenous and exogenous molecular processes in cancer. The quantitative approach used to deconvolute mutational signatures is becoming an integral part of cancer research. Therefore, development of a stand-alone tool with a user-friendly graphical interface for analysis of cancer mutational signatures is necessary. In this manuscript, we introduce CANCERSIGN as an open access bioinformatics tool that uses raw mutation data (BED files) as input, and identifies 3-mer and 5-mer mutational signatures. CANCERSIGN enables users to identify signatures within whole genome, whole exome or pooled samples. It can also identify signatures in specific regions of the genome (defined by user). Additionally, this tool enables users to perform clustering on tumor samples based on the raw mutation counts as well as using the proportion of mutational signatures in each sample. Using this tool, we analysed all the whole genome somatic mutation datasets profiled by the International Cancer Genome Consortium (ICGC) and identified a number of novel signatures. By examining signatures found in exonic and non-exonic regions of the genome using WGS and comparing this to signatures found in WES data we observe that WGS can identify additional non-exonic signatures that are enriched in the non-coding regions of the genome while the deeper sequencing of WES may help identify weak signatures that are otherwise missed in shallower WGS data.
Polyfunctional tumor-reactive T cells are effectively expanded from non-small cell lung cancers, and correlate with an immune-engaged T cell profile
Authors: de Groot Rosa , van Loenen Marleen M. , Guislain Aurélie , Nicolet Benoit P. , Freen-van Heeren Julian J. , Verhagen Onno , van den Heuvel Michel M. , de Jong Jeroen , Burger Patrick , van der Schoot C. Ellen , Spaapen Robbert M. , Amsen Derk , Haanen John B. A. G. , Monkhorst Kim , Hartemink Koen J. , Wolkers Monika C.
Published: September 2018

Non-small cell lung cancer (NSCLC) is the second most prevalent type of cancer. With the current treatment regimens, the mortality rate remains high. Therefore, better therapeutic approaches are necessary. NSCLCs generally possess many genetic mutations and are well infiltrated by T cells (TIL), making TIL therapy an attractive option. Here we show that T cells from treatment naive, stage I-IVa NSCLC tumors can effectively be isolated and expanded, with similar efficiency as from normal lung tissue. Importantly, 76% (13/17) of tested TIL products isolates from NSCLC lesions exhibited clear reactivity against primary tumor digests, with 0.5%-30% of T cells producing the inflammatory cytokine Interferon (IFN)-γ. Both CD4+and CD8+T cells displayed tumor reactivity. The cytokine production correlated well with CD137 and CD40L expression. Furthermore, almost half (7/17) of the TIL products contained polyfunctional T cells that produced Tumor Necrosis Factor (TNF)-α and/or IL-2 in addition to IFN-γ, a hallmark of effective immune responses. Tumor-reactivity in the TIL products correlated with high percentages of CD103+CD69+CD8+T cell infiltrates in the tumor lesions, with PD-1hiCD4+T cells, and with FoxP3+CD25+CD4+regulatory T cell infiltrates, suggesting that the composition of T cell infiltrates may predict the level of tumor reactivity. In conclusion, the effective generation of tumor-reactive and polyfunctional TIL products implies that TIL therapy will be a successful treatment regimen for NSCLC patients.
High diversity, turnover, and structural constraints characterize TCR α and β repertoire selection
Authors: Kamga Larisa , Gil Anna , Song Inyoung , Chirravuri Ramakanth , Aslan Nuray , Ghersi Dario , Stern Lawrence J. , Selin Liisa K. , Luzuriaga Katherine
Published: September 2018

Recognition modes of individual T-cell receptors (TCR) are well studied, but how TCR repertoires are selected during acute through persistent human virus infections is less clear. Here, we show that persistent EBV-specific clonotypes account for only 9% of unique clonotypes but are highly expanded in acute infectious mononucleosis, and have distinct antigen-specific public features that drive selection into convalescence. The other 91% of highly diverse unique clonotypes disappear and are replaced in convalescence by equally diverse “de-novo” clonotypes. These broad fluctuating repertoires lend plasticity to antigen recognition and potentially protect against T-cell clonal loss and viral escape.
Estimating yields of prenatal carrier screening and implications for design of expanded carrier screening panels
Authors: Guo Michael H. , Gregg Anthony R.
Published: September 2018

Purpose

Prenatal genetic carrier screening can identify parents at risk of having a child affected by a recessive condition. However, the conditions/genes most appropriate for screening remain a matter of debate. Estimates of carrier rates across genes are needed to guide construction of carrier screening panels.

Methods

We leveraged an exome sequencing database (n=123,136) to estimate carrier rates across 6 major ancestries for 416 genes associated with severe recessive conditions.

Results

36.5% (East Asian) to 65% (Ashkenazi Jewish) of individuals are variant carriers in at least one of the 416 genes. For couples, screening all 416 genes would identify 0.4-2.8% of couples as being at-risk for having a child affected by one of these conditions. Screening just the 47 genes with carrier rate > 1.0% would identify more than 85% of these at-risk couples. An ancestry-specific panel designed to capture genes with carrier rates > 1.0% would include 6 to 30 genes, while a comparable pan-ethnic panel would include 47 genes.

Conclusion

Our work guides the design of carrier screening panels and provides data to assist in counseling prospective parents. Our results highlight a high cumulative carrier rate across genes, underscoring the need for careful selection of genes for screening.
Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen
Authors: Sesterhenn F , Galloux M , Vollers SS , Csepregi L , Yang C , Descamps D , Bonet J , Friedensohn S , Gainza P , Corthésy P , Chen M , Rosset S , Rameix-Welti MA , Eléouët JF , Reddy ST , Graham BS , Riffault S , Correia BE
Published: September 2018

Throughout the last decades, vaccination has been key to prevent and eradicate infectious diseases. However, many pathogens (e.g. respiratory syncytial virus (RSV), influenza, dengue and others) have resisted vaccine development efforts, largely due to the failure to induce potent antibody responses targeting conserved epitopes. Deep profiling of human B-cells often reveals potent neutralizing antibodies that emerge from natural infection, but these specificities are generally subdominant (i.e., are present in low titers). A major challenge for next-generation vaccines is to overcome established immunodominance hierarchies and focus antibody responses on crucial neutralization epitopes. Here, we show that a computationally designed epitope-focused immunogen presenting a single RSV neutralization epitope elicits superior epitope-specific responses compared to the viral fusion protein. In addition, the epitope-focused immunogen efficiently boosts antibodies targeting the Palivizumab epitope, resulting in enhanced neutralization. Overall, we show that epitope-focused immunogens can boost subdominant neutralizing antibody responsesin vivoand reshape established antibody hierarchies.
Assessing connectivity despite high diversity in island populations of a malaria mosquito
Authors: Bergey Christina M. , Lukindu Martin , Wiltshire Rachel M. , Fontaine Michael C. , Kayondo Jonathan K. , Besansky Nora J.
Published: September 2018

Documenting isolation is notoriously difficult for species with vast polymorphic populations. High proportions of shared variation impede estimation of connectivity, even despite leveraging information from many genetic markers. We overcome these impediments by combining classical analysis of neutral variation with assays of the structure of selected variation, demonstrated using populations of the principal African malaria vectorAnopheles gambiae. Accurate estimation of mosquito migration is crucial for efforts to combat malaria. Modeling and cage experiments suggest that mosquito gene drive systems will enable malaria eradication, but establishing safety and efficacy requires identification of isolated populations in which to conduct field-testing. We assess Lake Victoria islands as candidate sites, finding one island 30 kilometers offshore is as differentiated from mainland samples as populations from across the continent. Collectively, our results suggest sufficient contemporary isolation of these islands to warrant consideration as field-testing locations and illustrate shared adaptive variation as a useful proxy for connectivity in highly polymorphic species.
MicroRNA-223 protects neurons from degeneration in Experimental Autoimmune Encephalomyelitis
Authors: Morquette Barbara , Juźwik Camille A. , Drake Sienna S. , Charabati Marc , Zhang Yang , Lécuyer Marc-André , Galloway Dylan , Dumas Aline , de Faria Omar , Bueno Mardja , Rambaldi Isabel , Moore Craig , Bar-Or Amit , Vallières Luc , Prat Alexandre , Fournier Alyson E.
Published: September 2018

Multiple sclerosis (MS) is an autoimmune disease characterized by demyelination and neurodegeneration in the brain, spinal cord and optic nerve. Neuronal degeneration and death underlie progressive forms of MS and cognitive dysfunction. Neuronal damage is triggered by numerous harmful factors in the brain that engage diverse signalling cascades in neurons thus therapeutic approaches to protect neurons will need to focus on agents that can target broad biological processes. To target the broad spectrum of signaling events that mediate neurodegeneration in MS we have focused on non-coding small microRNAs (miRNAs). microRNAs are epigenetic regulators of protein expression, targeting messenger RNAs (mRNAs) and inhibiting their translation. Dysregulation of miRNAs has been described in many neurodegenerative diseases including MS. In this study we identified two miRNAs, miR-223-3p and miR-27a-3p, that were upregulated in neurons in the experimental autoimmune encephalomyelitis (EAE) mouse model of CNS inflammation and in active MS lesions. Overexpression of miR-27a-3p or miR-223-3p protected dissociated cortical neurons from degeneration in response to peripheral blood mononuclear cell conditioned media (PBMC-CM). Introduction of miR-223-3p in vivo in mouse retinal ganglion cells (RGCs) protected RGC axons from degeneration in the EAE model. By in silico analysis we found that mRNAs in the glutamate receptor (GluR) pathway are enriched in miR-27a-3p and miR-223-3p targets. Antagonism of the GluR pathway protected neurons from PBMC-CM-dependent degeneration. Our results suggest that miR-223-3p and miR-27a-3p are upregulated in response to inflammation to mediate a compensatory neuroprotective gene expression program that desensitizes neurons to glutamate by downregulating mRNAs involved in GluR signalling.
Identification andin silicoanalysis of the origin recognition complex in the human fungal pathogenCandida albicans
Authors: Padmanabhan Sreedevi , Sanyal Kaustuv , Dubey Dharani Dhar
Published: September 2018

DNA replication in eukaryotes is initiated by the orchestrated assembly and association of initiator proteins (heterohexameric Origin Recognition Complex, ORC) on the replication origins. These functionally conserved proteins play significant roles in diverse cellular processes besides their central role in ignition of DNA replication at origins. WhileCandida albicans, a major human fungal pathogen, is an ascomycetous, asexual, diploid budding yeast but it is significantly diverged from a much better studied model organismSaccharomyces cerevisiae. The components of the DNA replication machinery inC. albicansremain largely uncharacterized. Identification of factors required for DNA replication is essential for understanding the evolution of the DNA replication machinery. We identified the putative ORC homologs inC. albicansand determined their relatedness with those of other eukaryotes including several yeast species. Our extensivein silicostudies demonstrate that the domain architecture of CaORC proteins share similarities with the ORC proteins ofS. cerevisiae. We dissect the domain organization of ORC (trans-acting factors) proteins that seem to associate with DNA replication origins inC. albicans. We present a model of the 3D structure of CaORC4 to gain further insights of this protein’s function.
In vivo CRISPRa decreases seizures and rescues cognitive deficits in a rodent model of epilepsy
Authors: Colasante Gaia , Qiu Yichen , Massimino Luca , Di Berardino Claudia , Cornford Jonathan H. , Snowball Albert , Weston Mikail , Jones Steffan P. , Giannelli Serena , Lieb Andreas , Schorge Stephanie , Kullmann Dimitri M. , Broccoli Vania , Lignani Gabriele
Published: September 2018

Epilepsy is a major health burden, calling for new mechanistic and therapeutic insights. CRISPR–mediated gene editing shows promise to cure genetic pathologies, although hitherto it has mostly been applied ex-vivo. Its translational potential for treating non-genetic pathologies is still unexplored. Furthermore, neurological diseases represent an important challenge for the application of CRISPR, because of the need in many cases to manipulate gene function of neurons in situ. A variant of CRISPR, CRISPRa, offers the possibility to modulate the expression of endogenous genes by directly targeting their promoters. We asked if this strategy can effectively treat acquired focal epilepsy, focusing on ion channels because their manipulation is known be effective in changing network hyperactivity and hypersynchronisation. We applied a doxycycline-inducible CRISPRa technology to increase the expression of the potassium channel gene Kcna1 (encoding Kv1.1) in mouse hippocampal excitatory neurons. CRISPRa-mediated Kv1.1 upregulation led to a substantial decrease in neuronal excitability. Continuous video-EEG telemetry showed that AAV9-mediated delivery of CRISPRa, upon doxycycline administration, decreased spontaneous generalized tonic-clonic seizures in a model of temporal lobe epilepsy, and rescued cognitive impairment and transcriptomic alterations associated with chronic epilepsy. The focal treatment minimizes concerns about off-target effects in other organs and brain areas. This study provides the proof of principle for a translational CRISPR-based approach to treat neurological diseases characterized by abnormal circuit excitability.
Crystal structures reveal that Lewis-x and fucose bind to secondary cholera toxin binding site – in contrast to fucosyl-GM1
Authors: Heim Joel B. , Hodnik Vesna , Heggelund Julie E. , Anderluh Gregor , Krengel Ute
Published: September 2018

Cholera is a life-threatening diarrhoeal disease caused by the human pathogenVibrio cholerae. Infection occurs after ingestion of the bacteria, which colonize the human small intestine and secrete their major virulence factor - the cholera toxin (CT). Recent studies suggest that the GM1 receptor may not be the only target of the CT, and that fucosylated receptors such as Lewisx(Lex) and histo-blood group antigens may also be important for cellular uptake and toxicity. However, where and how Lexbinds to the CT remains unclear. Here we report the high-resolution crystal structure (1.5 Å) of the receptor-binding B-subunit of the CT bound to the Lextrisaccharide, and present matching SPR data for CT holotoxins. Lex, and alsoL-fucose alone (at 500-fold molar excess), bind to the secondary binding site of the toxin, distinct from the GM1 binding site. In contrast, fucosyl-GM1 mainly binds to the primary binding site due to high-affinity interactions of its GM1 core. The two binding sites are likely connected by allosteric cross-talk, potentially affecting toxin uptake. We also discuss why secretors are protected from severe cholera.

Author summary

Cholera is a severe diarrhoeal disease that is still a major killer in many parts of the world, especially in regions struck by natural disasters and wars. However, some individuals experience milder cholera symptoms. These so-called ‘secretors’, who have blood group antigens also in their bodily fluids like their saliva and the slimy mucus layer covering their stomach and intestines, appear to be somewhat protected. Here we present detailed atomic structures of cholera toxin and quantitative binding data that give clues of the protective mechanisms. Interactions of the protein toxin with sugar molecules are of crucial importance both for toxicity and protection. In addition, we identify a new tool for biochemical studies, and lay the groundwork for the design of cholera drugs and vaccines that may save countless human lives.
Agent-based model of multicellular tumor spheroid evolution including cell metabolism
Authors: Cleri Fabrizio
Published: September 2018

Computational models aiming at the spatio-temporal description of cancer evolution are a suitable framework for testing biological hypotheses from experimental data, and generating new ones. Building on our recent work [J Theor Biol 389, 146-158 (2016)] we develop a 3D agent-based model, capable of tracking hundreds of thousands of interacting cells, over time scales ranging from seconds to years. Cell dynamics is driven by a Monte Carlo solver, incorporating partial differential equations to describe chemical pathways and the activation/repression of “genes”, leading to the up- or down-regulation of specific cell markers. Each cell-agent of different kind (stem, cancer, stromal etc.) runs through its cycle, undergoes division, can exit to a dormant, senescent, necrotic state, or apoptosis, according to the inputs from their systemic network. The basic network at this stage describes glucose/oxygen/ATP cycling, and can be readily extended to cancer-cell specific markers. Eventual accumulation of chemical/radiation damage to each cell’s DNA is described by a Markov chain of internal states, and by a damage-repair network, whose evolution is linked to the cell systemic network. Aimed at a direct comparison with experiments of tumorsphere growth from stem cells, the present model will allow to quantitatively study the role of transcription factors involved in the reprogramming and variable radio-resistance of simulated cancer-stem cells, evolving in a realistic computer simulation of a growing multicellular tumorsphere.
A conserved morphogenetic mechanism for epidermal ensheathment of nociceptive sensory neurites
Authors: Jiang Nan , Rasmussen Jeffrey P. , Clanton Joshua A. , Rosenberg Marci F. , Luedke Kory P. , Cronan Mark R. , Parker Ed , Kim Hyeon-Jin , Vaughan Joshua C. , Sagasti Alvaro , Parrish Jay Z.
Published: September 2018

Interactions between epithelial cells and neurons influence a range of sensory modalities including taste, touch, and smell. Vertebrate and invertebrate keratinocytes/keratinocyte-like epidermal cells ensheath peripheral arbors of somatosensory neurons, including nociceptors, yet the developmental origins and functional roles of this ensheathment are largely unknown. Here, we describe an evolutionarily conserved morphogenetic mechanism for epidermal ensheathment of somatosensory neurites. We found that somatosensory neurons inDrosophilaand zebrafish induce formation of epidermal sheaths, which wrap neurites of different types of neurons to different extents. Neurites induce formation of plasma membrane phosphatidylinositol 4,5-bisphosphate microdomains at nascent sheaths, followed by a filamentous actin network, and recruitment of junctional proteins that likely form autotypic junctions to seal sheaths. Finally, blocking epidermal sheath formation destabilized dendrite branches and reduced nociceptive sensitivity inDrosophila. Epidermal somatosensory neurite ensheathment is thus a deeply conserved cellular process that contributes to the morphogenesis and function of nociceptive sensory neurons.
Preventing S. aureus biofilm formation on titanium surfaces by the release of antimicrobial β-peptides from polyelectrolyte multilayers
Authors: de L. Rodríguez López Angélica , Lee Myung-Ryul , Whitehead Riley , Lynn David M. , Palecek Sean P.
Published: September 2018

Staphylococcus aureus infections represent the major cause of titanium based-orthopaedic implant failure. Current treatments for S. aureus infections involve the systemic delivery of antibiotics and additional surgeries, increasing health-care costs and affecting patient’s quality of life. As a step toward the development of new strategies that can prevent these infections, we build upon previous work demonstrating that the colonization of catheters by the fungal pathogen Candida albicans can be prevented by coating them with thin polymer multilayers composed of chitosan (CH) and hyaluronic acid (HA) designed to release a β-amino acid-based peptidomimetic of antimicrobial peptides (AMPs). We demonstrate here that this β-peptide is also potent against S. aureus (MIC = 4 µg/mL) and characterize its selectivity toward S. aureus biofilms. We demonstrate further that β-peptide-containing CH/HA thin-films can be fabricated on the surfaces of rough planar titanium substrates in ways that allow mammalian cell attachment and permit the long-term release of β-peptide. β-Peptide loading on CH/HA thin-films was then adjusted to achieve release of β-peptide quantities that selectively prevent S. aureus biofilms on titanium substrates in vitro for up to 24 days and remained antimicrobial after being challenged sequentially five times with S. aureus inocula, while causing no significant MC3T3-E1 preosteoblast cytotoxicity compared to uncoated and film-coated controls lacking β-peptide. We conclude that these β-peptide-containing films offer a novel and promising localized delivery approach for preventing orthopaedic implant infections. The facile fabrication and loading of β-peptide-containing films reported here provides opportunities for coating other medical devices prone to biofilm-associated infections.

STATEMENT OF SIGNIFICANCE

Titanium (Ti) and its alloys are used widely in internal fixation devices due to their mechanical strength and long-term biocompatibility. However, these devices are susceptible to bacterial colonization and the subsequent formation of biofilms. Here we report a chitosan and hyaluronic acid polyelectrolyte multilayer-based approach for the localized delivery of helical, cationic, globally amphiphilic β-peptide mimetics of antimicrobial peptides to inhibit S. aureus colonization and biofilm formation. Our results reveal that controlled release of this β-peptide can selectively kill S. aureus cells without exhibiting toxicity toward MC3T3-E1 preosteoblast cells. Further development of this polymer-based coating could result in new strategies for preventing orthopaedic implant-related infections, improving outcomes of these titanium implants.
Single-cell microRNA/mRNA co-sequencing reveals non-genetic heterogeneity and novel regulatory mechanisms
Authors: Wang Nayi , Zheng Ji , Chen Zhuo , Liu Yang , Dura Burak , Kwak Minsuk , Xavier-Ferrucio Juliana , Lu Yi-Chien , Zhang Miaomiao , Roden Christine , Cheng Jijun , Krause Diane , Ding Ye , Fan Rong , Lu Jun
Published: September 2018

Co-measurement of multiple omic profiles from the same single cells opens up the opportunity to decode molecular regulation that underlie intercellular heterogeneity in development and disease. Here, we present co-sequencing of microRNAs and mRNAs in the same single cells using a half-cell genomics approach. This method demonstrates good robustness (~95% success rate) and reproducibility (R2=0.93 for both miRNAs and mRNAs), and yields paired half-cell miRNA and mRNA profiles that could be independently validated. Linking the level of miRNAs to the expression of predicted target mRNAs across 19 single cells that are phenotypically identical, we observe that the predicted targets are significantly anti-correlated with the variation of abundantly expressed miRNAs, suggesting that miRNA expression variability alone may lead to non-genetic cell-to-cell heterogeneity. Genome-scale analysis of paired miRNA-mRNA co-profiles further allows us to derive and validate new regulatory relationships of cellular pathways controlling miRNA expression and variability.
Superresolved microparticle traction force microscopy reveals subcellular force patterns in immune cell-target interactions
Authors: Vorselen Daan , Wang Yifan , de Jesus Miguel M. , Shah Pavak K. , Footer Matthew J. , Huse Morgan , Cai Wei , Theriot Julie A.
Published: September 2018

Force exertion is an integral part of cellular behavior. Traction force microscopy (TFM) has been instrumental for studying such forces, providing both spatial and directional force measurements at subcellular resolution. However, the applications of classical TFM are restricted by the typical planar geometry. Here, we develop a particle-based force sensing strategy, specifically designed for studying ligand-dependent cellular interactions. We establish a straightforward batch approach for synthesizing highly uniform, deformable and tunable hydrogel particles, which can also be easily derivatized to trigger specific cellular behavior. The 3D shape of such particles can be resolved with superresolution (<50 nm) accuracy using conventional confocal microscopy. We introduce a computational method that allows inference of surface traction forces with high sensitivity (∼10 Pa) directly from the particle shape. We illustrate the potential and flexibility of this approach by revealing surprising subcellular force patterns throughout phagocytic engulfment and measuring dynamics of cytotoxic T cell force exertion in the immunological synapse. This strategy can readily be adapted for studying cellular forces in a wide range of applications.
The physiological butyrylcholinesterase tetramer is a dimer of dimers stabilized by a superhelical assembly
Authors: Leung Miguel Ricardo , van Bezouwen Laura S. , Schopfer Lawrence M. , Sussman Joel L. , Silman Israel , Lockridge Oksana , Zeev-Ben-Mordehai Tzviya
Published: September 2018

The quaternary structures of the cholinesterases, acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), are essential for their localisation and function. Of practical importance, BChE is a promising therapeutic candidate for intoxication by organophosphate nerve agents and insecticides, and for detoxification of addictive substances. Efficacy of the recombinant enzyme hinges on its having a long circulatory half-life; this, in turn, depends strongly on its ability to tetramerize. Here, we used cryo-electron microscopy (cryo-EM) to determine the structure of the highly glycosylated native BChE tetramer purified from human plasma at 5.7 Å. Our structure reveals that the BChE tetramer is organised as a staggered dimer of dimers. Tetramerization is mediated by assembly of the C-terminal tryptophan amphiphilic tetramerization (WAT) helices from each subunit as a superhelical assembly around a central anti-parallel polyproline II helix (PRAD). The catalytic domains within a dimer are asymmetrically linked to the WAT/PRAD. In the resulting arrangement, the tetramerization domain is largely shielded by the catalytic domains, which may contribute to the stability of the HuBChE tetramer. Our cryo-EM structure reveals the basis for assembly of the physiological tetramers, and has implications for the therapeutic applications of HuBChE. This mode of tetramerization is seen only in the cholinesterases, and may provide a promising template for designing other proteins with improved circulatory residence times.
LRIT3 is required for nyctalopin expression and normal ON and OFF pathway signaling in the retina
Authors: Hasan Nazarul , Pangeni Gobinda , Ray Thomas A. , Fransen Kathryn M. , Noel Jennifer , Borghuis Bart G. , McCall Maureen A. , Gregg Ronald G.
Published: September 2018

At its first synapse, the retina establishes two parallel channels that encode light increments (ON) or decrements (OFF). At the same synapse, changes in photoreceptor glutamate release are sensed by ON bipolar cells (BCs) via the metabotropic glutamate receptor 6 (mGluR6), and OFF BCs via ionotropic BCs, which differ in their synaptic configuration with the photoreceptor terminal. ON BCs form invaginating synapses that bring them in close proximity to presynaptic ribbons and the presumed sole source of glutamate release. OFF bipolar cells form flat contacts distal to the ribbon synapse. We investigated the role of LRIT3 in normal assembly and function of the mGlur6 signaling cascade present in ON BCs. We demonstrate that LRIT3 is required for nyctalopin expression and thus TRPM1 expression and function. Using glutamate imaging, whole-cell electrophysiology, and multi-electrode array extracellular recordings we demonstrate that the loss of LRIT3 impacts both the ON and OFF pathways at the level of the BCs. The effect on ON pathway signaling, a lack of ON BC response, is shared by mutants lacking mGluR6, TRPM1 GPR179 or nyctalopin. The effects on the OFF pathway are unique to LRIT3, and include a decrease in response amplitude of both OFF BC and GCs. Based on these results, we propose a working model where LRIT3 is required for either efficient glutamate release or reuptake from the first retinal synapse.

SIGNIFICANCE STATEMENT

At the first visual synapse, photoreceptor cells signal to two distinct bipolar cell (BC) populations, one characterized by a depolarizing response to light onset (ON or DBCs), the other by a hyperpolarizing response (OFF or HBCs). The DBC light response depends on a G protein-coupled receptor and associated protein complex, known as the signalplex. Mutations in signalplex proteins lead to DBC pathway-specific loss of visual function. Here we show how loss of LRIT3, a previously identified signalplex protein, prevents functional assembly of the DBC signalplex and alters visual function in both ON and OFF signaling pathways. Thus, our results indicate that the function of LRIT3 at this first synapse extends beyond assembly of the DBC signalplex.
VOLARE: Visual analysis of disease-associated microbiome-immune system interplay
Authors: Siebert Janet C. , Neff Charles Preston , Schneider Jennifer M. , Regner EmiLie H. , Ohri Neha , Kuhn Kristine A. , Palmer Brent E. , Lozupone Catherine A. , Görg Carsten
Published: September 2018

Background

Relationships between specific microbes and proper immune system development, composition, and function have been reported in a number of studies. However, researchers have discovered only a fraction of the likely relationships. High-dimensional “omic” methodologies such as 16S ribosomal RNA (rRNA) sequencing and Time-of-flight mass cytometry (CyTOF) immunophenotyping generate data that support generation of hypotheses, with the potential to identify additional relationships at a level of granularity ripe for further experimentation. Pairwise linear regressions between microbial and host immune features is one approach for quantifying relationships between “omes”, and the differences in these relationships across study cohorts or arms. This approach yields a top table of candidate results. However, the top table alone lacks the detail that domain experts need to vet candidate results for follow-up experiments.

Results

To support this vetting, we developed VOLARE (Visualization Of LineAr Regression Elements), a web application that integrates a searchable top table, small in-line graphs illustrating the fitted models, a network summarizing the top table, and on-demand detailed regression plots showing full sample-level detail. We applied VOLARE to three case studies—microbiome:cytokine data from fecal samples in HIV, microbiome:cytokine data in inflammatory bowel disease and spondyloarthritis, and microbiome:immune cell data from gut biopsies in HIV. We present both patient-specific phenomena and relationships that differ by disease state. We also analyzed interaction data from system logs to characterize usage scenarios. This log analysis revealed that, in using VOLARE, domain experts frequently generated detailed regression plots, suggesting that this detail aids the vetting of results.

Conclusions

Systematically integrating microbe:immune cell readouts through pairwise linear regressions and presenting the top table in an interactive environment supports the vetting of results for scientific relevance. VOLARE allows domain experts to control the analysis of their results, screening dozens of candidate relationships with ease. This interactive environment transcends the limitations of a static top table.
Heading direction with respect to a reference point modulates place-cell activity
Authors: Jercog P.E. , Ahmadian Y. , Woodruff C. , Deb-Sen R. , Abbott L.F. , Kandel E.R.
Published: October 2018

Utilizing electrophysiological recordings from CA1 pyramidal cells in freely moving mice, we find that a majority of neural responses are modulated by the heading-direction of the animal relative to a point within or outside their enclosure that we call a reference point. Our findings identify a novel representation in the neuronal responses in the dorsal hippocampus.
New ways to get policy into practice
Authors: Nugus Peter , Ranmuthugala Geetha , Lamothe Josianne , Greenfield David , Travaglia Joanne , Kolne Kendall , Kryluk Julia , Braithwaite Jeffrey
Published: October 2018

Purpose

Health service effectiveness continues to be limited by misaligned objectives between policy makers and frontline clinicians. While capturing the discretion workers inevitably exercise, the concept of “street-level bureaucracy” has tended to artificially separate policy makers and workers. The purpose of this paper is to understand the role of social-organizational context in aligning policy with practice.

Design/methodology/approach

This mixed-method participatory study focuses on a locally developed tool to implement an Australia-wide strategy to engage and respond to mental health services for parents with mental illness. Researchers: completed 69 client file audits; administered 64 staff surveys; conducted 24 interviews and focus groups (64 participants) with staff and a consumer representative; and observed eight staff meetings, in an acute and sub-acute mental health unit. Data were analyzed using content analysis, thematic analysis and descriptive statistics.

Findings

Based on successes and shortcomings of the implementation (assessment completed for only 30 percent of clients), a model of integration is presented, distinguishing “assimilist” from “externalist” positions. These depend on the degree to which, and how, the work environment affords clinicians the setting to coordinate efforts to take account of clients’ personal and social needs. This was particularly so for allied health clinicians and nurses undertaking sub-acute rehabilitative-transitional work.

Originality/value

A new conceptualization of street-level bureaucracy is offered. Rather than as disconnected, it is a process of mutual influence among interdependent actors. This positioning can serve as a framework to evaluate how and under what circumstances discretion is appropriate, and to be supported by managers and policy makers to optimize client-defined needs.
Estimation of grain elasticity properties from ultrasonic measurements on dry granular pack
Authors: Madadi Mahyar , Ahmed Zubair , Bona Andrej , Lebedev Maxim , Gurevich Boris
Published: September 2018

The elastic properties of crystalline rocks can be estimated from ultrasonic measurements on the powders of crushed rocks produced by the drilling process. To determine the elastic properties of grains from properties of powder packs, we study the dependence of their ultrasonic wave velocities on pressure. From this dependency, using the Hertz–Mindlin theory, we can calculate the effective ratio of the grain shear modulus to one minus the Poisson ratio. The Hertz–Mindlin theory requires the knowledge of grain coordination number as a function of pressure, which can be obtained using an empirical relation based on published numerical simulations. Previous work has shown that this approach gives an accurate prediction of the effective bulk modulus of glass beads but produces a significant discrepancy for sand. This discrepancy may be attributed to the angularity of sand grains. To overcome this problem, we introduce a shape factor into the empirical relation for the coordination number. This new shape factor allows us to reconcile the rock physics model with laboratory measurements. We show that the shape factor varies from 1 to 2.5 for different grain shape angularity and sorting (grain size distributions). The modified theory allows us to estimate a combination of elasticity parameters of the grains from the measured dependence of P‐wave velocity in the pack on the pressure.
Developing the global potential of citizen science: Assessing opportunities that benefit people, society and the environment in East Africa
Authors: Pocock Michael J. O. , Roy Helen E. , August Tom , Kuria Anthony , Barasa Fred , Bett John , Githiru Mwangi , Kairo James , Kimani Julius , Kinuthia Wanja , Kissui Bernard , Madindou Ireene , Mbogo Kamau , Mirembe Judith , Mugo Paul , Muniale Faith Milkah , Njoroge Peter , Njuguna Edwin Gichohi , Olendo Mike Izava , Opige Michael , Otieno Tobias O. , Ng'weno Caroline Chebet , Pallangyo Elisha , Thenya Thuita , Wanjiru Ann , Trevelyan Rosie
Published: September 2018

Citizen science is gaining increasing prominence as a tool for science and engagement. However, despite being a potentially valuable tool for sustainable development, citizen science has little visibility in many developing countries.

We undertook a collaborative prioritisation process with experts in conservation and the environment to assess the potential of environmental citizen science in East Africa, including its opportunities, benefits and barriers. This provided principles that are applicable across developing countries, particularly for large‐scale citizen science.

We found that there was great potential for citizen science to add to our scientific knowledge of natural resources and biodiversity trends. Many of the important benefits of citizen science were for people, as well as the environment directly. Major barriers to citizen science were mostly social and institutional, although projects should also consider access to suitable technology and language barriers.

Policy implications. Citizen science can provide data to support decision‐making and reporting against international targets. Participation can also provide societal benefits, informing and empowering people, thus supporting the United Nations’ Sustainable Development Goals. In developing countries, innovation is needed to further develop culturally relevant citizen science that benefits participants and end users. This should be supported through regional networks of stakeholders for sharing best practice.