Relative sarcolipin (SLN) and sarcoplasmic reticulum Ca2+ ATPase (SERCA1) transcripts levels in closely related endothermic and ectothermic scombrid fishes: Implications for molecular basis of futile calcium cycle non-shivering thermogenesis (NST).

Regional endothermy is the ability of an animal to elevate the temperature of specific regions of the body above that of the surrounding environment and has evolved independently among several fish lineages. Sarcolipin (SLN) is a small transmembrane protein that uncouples the sarcoplasmic reticulum calcium ATPase pump (SERCA1b) resulting in futile Ca2+ cycling and is thought to play a role in non-shivering thermogenesis (NST) in cold-challenged mammals and possibly some fishes. This study investigated the relative expression of sln and serca1 transcripts in three regionally-endothermic fishes (the skipjack, Katsuwonus pelamis, and yellowfin tuna, Thunnus albacares, both of which elevate the temperatures of their slow-twitch red skeletal muscle (RM) and extraocular muscles (EM), as well as the cranial endothermic swordfish, Xiphias gladius), and closely related ectothermic scombrids (the Eastern Pacific bonito, Sarda chiliensis, and Pacific chub mackerel, Scomber japonicus). Using Reverse Transcription quantitative PCR (RT-qPCR) and species-specific primers, relative sln expression trended higher in both the RM and EM for all four scombrid species compared to white muscle. In addition, relative serca1 expression was found to be higher in RM of skipjack and yellowfin tuna in comparison to white muscle. However, neither sln nor serca1 transcripts were higher in swordfish RM, EM or cranial heater tissue in comparison to white muscle. A key phosphorylation site in sarcolipin, threonine 5, is conserved in the swordfish, but is mutated to alanine or valine in tunas and the endothermic smalleye Pacific opah, Lampris incognitus, which should result in increased uncoupling of the SERCA pump. Our results support the role of potential SLN-NST in endothermic tunas and the lack thereof for swordfish.

Clonality, local population structure and gametophyte sex ratios in cryptic species of the Sphagnum magellanicum complex.

BACKGROUND AND AIMS: Sphagnum (peatmoss) comprises a moss (Bryophyta) clade with ~300-500 species. The genus has unparalleled ecological importance because Sphagnum-dominated peatlands store almost a third of the terrestrial carbon pool and peatmosses engineer the formation and microtopography of peatlands. Genomic resources for Sphagnum are being actively expanded, but many aspects of their biology are still poorly known. Among these are the degree to which Sphagnum species reproduce asexually, and the relative frequencies of male and female gametophytes in these haploid-dominant plants. We assess clonality and gametophyte sex ratios and test hypotheses about the local-scale distribution of clones and sexes in four North American species of the S. magellanicum complex. These four species are difficult to distinguish morphologically and are very closely related. We also assess microbial communities associated with Sphagnum host plant clones and sexes at two sites. METHODS: Four hundred and five samples of the four species, representing 57 populations, were subjected to restriction site-associated DNA sequencing (RADseq). Analyses of population structure and clonality based on the molecular data utilized both phylogenetic and phenetic approaches. Multi-locus genotypes (genets) were identified using the RADseq data. Sexes of sampled ramets were determined using a molecular approach that utilized coverage of loci on the sex chromosomes after the method was validated using a sample of plants that expressed sex phenotypically. Sex ratios were estimated for each species, and populations within species. Difference in fitness between genets was estimated as the numbers of ramets each genet comprised. Degrees of clonality [numbers of genets/numbers of ramets (samples)] within species, among sites, and between gametophyte sexes were estimated. Sex ratios were estimated for each species, and populations within species. Sphagnum-associated microbial communities were assessed at two sites in relation to Sphagnum clonality and sex. KEY RESULTS: All four species appear to engage in a mixture of sexual and asexual (clonal) reproduction. A single ramet represents most genets but two to eight ramets were dsumbers ansd text etected for some genets. Only one genet is represented by ramets in multiple populations; all other genets are restricted to a single population. Within populations ramets of individual genets are spatially clustered, suggesting limited dispersal even within peatlands. Sex ratios are male-biased in S. diabolicum but female-biased in the other three species, although significantly so only in S. divinum. Neither species nor males/females differ in levels of clonal propagation. At St Regis Lake (NY) and Franklin Bog (VT), microbial community composition is strongly differentiated between the sites, but differences between species, genets and sexes were not detected. Within S. divinum, however, female gametophytes harboured two to three times the number of microbial taxa as males. CONCLUSIONS: These four Sphagnum species all exhibit similar reproductive patterns that result from a mixture of sexual and asexual reproduction. The spatial patterns of clonally replicated ramets of genets suggest that these species fall between the so-called phalanx patterns, where genets abut one another but do not extensively mix because of limited ramet fragmentation, and the guerrilla patterns, where extensive genet fragmentation and dispersal result in greater mixing of different genets. Although sex ratios in bryophytes are most often female-biased, both male and female biases occur in this complex of closely related species. The association of far greater microbial diversity for female gametophytes in S. divinum, which has a female-biased sex ratio, suggests additional research to determine if levels of microbial diversity are consistently correlated with differing patterns of sex ratio biases.

PAs in the Republic of Ireland.

ABSTRACT: The physician associate/assistant (PA) profession was introduced into the Republic of Ireland following a 2-year pilot project with the Irish Department of Health between 2015 and 2017. Four PAs from North America were recruited into four designated surgical services at a large teaching hospital in Dublin. To date, the PA numbers are small in Ireland, with one university, in Dublin, running the program and 61 graduates working mostly in the hospital setting, with a small number in primary care. The cautious introduction of PAs partly is due to a delay in follow-up from the Department of Health after the pilot project and in the university's decision to increase the student intake slowly to ensure all graduates secure employment.

Prevalence of Musculoskeletal Symptoms in Interventional Radiologists.

PURPOSE: To investigate the prevalence of musculoskeletal symptoms, defined as aches, pains, discomfort, or numbness, by using a validated assessment tool among interventional radiologists. MATERIALS AND METHODS: A Web-based survey using the Nordic Musculoskeletal Questionnaire was disseminated to interventional radiologist members by email in November 2015. Musculoskeletal symptoms were evaluated in 9 body areas. Information regarding participant demographics, practice details, use of radio-protective equipment, and exercise routines was also gathered. Univariate and multivariate analyses were performed to determine risk factors associated with more severe symptoms. RESULTS: Of 4,096 SIR members at the time of the survey, 640 completed the questionnaire in its entirety (16% response rate). Respondents consisted of 69 females (11%) and 571 males (89%), with a mean age of 47.5 ± 10.2 years old, a mean body mass index of 25.5 ± 3.9 kg/m2, and a mean practice length of 17.1 ± 9.8 years. Prevalence of musculoskeletal symptoms was 88% in the 12 months preceding the survey. For those reporting musculoskeletal issues, 58% attributed the symptoms to work-related activities. Lower back (61%), neck (56%), and shoulder complaints (46%) were the most common. Symptoms prevented 21.2% of respondents from being able to work over the same time period. Multivariate analysis identified female gender, above-normal body mass index, and a practice length of 10 years or more as factors associated with a higher risk of moderate-to-severe symptoms. CONCLUSIONS: Musculoskeletal symptoms are prevalent among interventional radiologists, the majority of which are attributed to work-related causes.

Editorial Commentary: Intra-articular Injection for Osteoarthritis-Is It Hip or Not?

Intra-articular injections are commonly used in the treatment algorithm for osteoarthritis of the hip. A number of different adjuvants can be used, such as corticosteroids, hyaluronic acid, and platelet-rich plasma, but there is no consensus regarding indications for or anticipated outcomes of each of these interventions. Recent data suggest that corticosteroids provide the best relief in the short term whereas platelet-rich plasma may be more beneficial in the mid term, but the results are variable. Ultimately, more rigorous studies are needed to evaluate these adjuvants, in particular biologics, while remaining fastidious with our indications for injection therapy.

Orthopedic Injuries in Professional Surfers: A Retrospective Study at a Single Orthopedic Center.

BACKGROUND: Literature regarding surfing injuries is scarce and most studies report a high number of minor injuries. Recent literature suggests that musculoskeletal injuries are more common than previously reported. In the mid 2000s, competitive surfing has seen an increase in aerial maneuvers, as they have become more highly rewarded by the judging panel, which may be contributing to a change in injury patterns. Our goal was to evaluate orthopedic injuries in professional surfers. HYPOTHESIS: Orthopedic injuries in professional surfers are diverse and have evolved with skill and technology. STUDY DESIGN: Retrospective observational study. LEVEL OF EVIDENCE: Level 4 Case Series. METHODS: Medical records of professional surfers from a single orthopedic center between 1991 and 2016 were reviewed. Injuries sustained while surfing and chronic injuries related to surfing were included. Site of injury, diagnosis, and treatment were recorded along with demographic data. RESULTS: In total, 163 injuries in 86 athletes were recorded. The median injury age was 28.5 years (range 12-62 years) and 92.6% of patients were male. The most frequently injured body parts were the knee (28.2%), ankle (22.1%), and shoulder (19%). Most knee injuries were of the medial collateral ligament at 49%, with 75% of ankle injuries being sprains, and in shoulder, 48% had instability, 42% had a rotator cuff tear, and 35% had a superior anterior-posterior labral tear. Lower extremity injuries primarily affected the surfers' back leg (72.5%). In all, 34.6% of all injuries required surgical intervention and involved shoulder injuries most the time. CONCLUSIONS: The most common orthopedic injuries in professional surfers involve the knee, ankle, shoulder, hip, and back. Surfers' rear extremities were preferentially injured which is the extremity responsible for power and torque. Shoulder injuries increased the probability of an operative intervention. Last, overuse injuries (femoral-acetabular impingement, rotator cuffs) occurred in the older surf population compared with more acute injuries (ankle sprains/fractures, anterior cruciate ligament tears) which is also consistent with time to surgery.

Assessment of Cartilage Growth After Biopsy of Osteochondral Loose Bodies in Adolescent Knees for Use in Autologous Chondrocyte Implantation.

BACKGROUND: The goal of this study is to determine whether harvested cartilage from an osteochondral loose body maintains the same viability for implantation as cartilage harvested from the traditional locations within the adolescent knee for autologous chondrocyte implantation (ACI). METHODS: A retrospective study was performed on all ACI procedures performed from 2014 to 2017 at a single institution. Biopsies were derived from 2 groups: osteochondral loose body verses the intercondylar notch. The viability, yield, identity, potency, and density were obtained from each sample in addition to basic demographics and concomitant injuries. A total of 12 patients with osteochondral loose bodies 14.6 (SD=2.9) and 20 patients 13.6 (SD=3.3) with intercondylar notch biopsies were evaluated for the study. RESULTS: In the microscopic and histologic comparison, there was no significant difference in viability: 94% in the loose bodies and 93% in the intercondylar notch groups, identity: 7.4 d5L versus 6.3 d5L, or yield. Minimum yield is presented as different units in Carticel (1.2×10 cells/vial) and matrix-induced ACI (>8500 relative fluorescent units) products; however, there was no difference between groups and all samples were above the acceptable limit. Minimum identity value is recorded as d5L> -2.00 and all samples were above this limit. In addition, no sample had signs of contamination or endotoxin in either group. CONCLUSION: These results demonstrate an alternative method for obtaining cartilage biopsies in ACI procedures that may limit short-term and long-term donor site morbidity. LEVEL OF EVIDENCE: Level III.

Recognition of oral potentially malignant disorders and transformation to oral cancer.

Oral potentially malignant disorders refer to oral mucosal disorders with increased risk for malignant transformation, primarily to oral squamous cell carcinoma (SCC). Leukoplakia and erythroplakia are the most common of these disorders, but others have been identified. Transformation rates to oral cancer vary based on multiple factors. Healthcare providers should be aware of risk factors and clinical manifestations of these disorders and should intervene early to monitor and/or treat them to reduce the potential for malignant transformation.

Spatial quantification of the synaptic activity phenotype across large populations of neurons with Markov random fields.

Motivation: The collective and co-ordinated synaptic activity of large neuronal populations is relevant to neuronal development as well as a range of neurological diseases. Quantification of synaptically-mediated neuronal signalling permits further downstream analysis as well as potential application in target validation and in vitro screening assays. Our aim is to develop a phenotypic quantification for neuronal activity imaging data of large populations of neurons, in particular relating to the spatial component of the activity. Results: We extend the use of Markov random field (MRF) models to achieve this aim. In particular, we consider Bayesian posterior densities of model parameters in Gaussian MRFs to directly model changes in calcium fluorescence intensity rather than using spike trains. The basis of our model is defining neuron 'neighbours' by the relative spatial positions of the neuronal somata as obtained from the image data whereas previously this has been limited to defining an artificial square grid across the field of view and spike binning. We demonstrate that our spatial phenotypic quantification is applicable for both in vitro and in vivo data consisting of thousands of neurons over hundreds of time points. We show how our approach provides insight beyond that attained by conventional spike counting and discuss how it could be used to facilitate screening assays for modifiers of disease-associated defects of communication between cells. Availability and implementation: We supply the MATLAB code and data to obtain all of the results in the paper. Supplementary information: Supplementary data are available at Bioinformatics online.

Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields.

MOTIVATION: Incorporating gene interaction data into the identification of 'hit' genes in genomic experiments is a well-established approach leveraging the 'guilt by association' assumption to obtain a network based hit list of functionally related genes. We aim to develop a method to allow for multivariate gene scores and multiple hit labels in order to extend the analysis of genomic screening data within such an approach. RESULTS: We propose a Markov random field-based method to achieve our aim and show that the particular advantages of our method compared with those currently used lead to new insights in previously analysed data as well as for our own motivating data. Our method additionally achieves the best performance in an independent simulation experiment. The real data applications we consider comprise of a survival analysis and differential expression experiment and a cell-based RNA interference functional screen. AVAILABILITY AND IMPLEMENTATION: We provide all of the data and code related to the results in the paper. CONTACT: sean.j.robinson@utu.fi or laurent.guyon@cea.fr. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The mixed message behind "Medication-Assisted Treatment" for substance use disorder.

The gap between treatment utilization and treatment need for substance use disorders (SUDs) remains a significant concern in our field. While the growing call to bridge this gap often takes the form of more treatment services and/or better integration of existing services, this perspective proposes that more effective labels for and transparent descriptions of existing services would also have a meaningful impact. Adopting the perspective of a consumer-based health-care model (wherein treatments and services are products and patients are consumers) allows us to consider how labels like Addiction-focused Medical Management, Medication-Assisted Treatment, Medication-Assisted Therapy, and others may actually be contributing to the underutilization problem rather than alleviating it. In this perspective, "Medication-Assisted Therapy" for opioid-use disorder (OUD) is singled out and discussed as inherently confusing, providing the message that pharmacotherapy for this disorder is a secondary treatment to other services which are generally regarded, in practice, as ancillary. That this mixed message is occurring amidst a nationwide "opioid epidemic" is a potential cause for concern and may actually serve to reinforce the longstanding, documented stigma against OUD pharmacotherapy. We recommend that referring to pharmacotherapy for SUD as simply "medication," as we do for other chronic medical disorders, will bring both clarity and precision to this effective treatment approach.

"Alcoholic" or "Person with alcohol use disorder"? Applying person-first diagnostic terminology in the clinical domain.

A recent publication by Broyles et al. has recommended extending the use of diagnostically accurate, person-first language (e.g., "person with alcohol use disorder") as an alternative to non-diagnostic, idiosyncratic terms (e.g., "addict", "alcoholic") when describing individuals with substance use disorders (SUDs) in academic publications. Given the high levels of stigma towards individuals with SUDs in both the public and professional community alike, however, the present commentary advocates for extending the use of appropriate terminology in the description of individuals with SUDs beyond the academic arena- i.e., clinical charting. The use of potentially stigmatizing idiomatic terms and descriptions (e.g., "clean", "dirty") in clinical charting is discussed with respect to: a) the lingering problem of the treatment utilization gap, b) modern conceptualizations of stigma and labelling among individuals with SUDs, as well as c) the emerging concept of structural stigma and how institutional standards (or lack thereof) may inadvertently contribute to the perpetuation of providers' negative attitudes and beliefs. The negative implications of SUD-related stigma on quality of patient care are also discussed, and possible barriers to the successful adoption of the above approach are considered. A number of possible benefits from the successful adoption of person-first, patient-centered, diagnostically appropriate labelling standards within clinical notes are hypothesized, including improved alignment with patient-centered care models, institutional values, and professional ethics, as well as reductions in institutional stigma. A number of recommendations to facilitate adoption of are offered.

Preventing alcohol-exposed pregnancies among Hispanic women.

Project Healthy CHOICES, a self-administered, mail-based prevention intervention, was developed for women at risk of an alcohol-exposed pregnancy (AEP). Participants were sent their assessment and study materials through the United States Postal Service. This article uses data from a larger study (N = 354) and focuses on the 89 women who identified as Hispanic. Potential participants who called in response to English and Spanish ads and who said they could read and write Spanish were given a choice of receiving the intervention materials in English or Spanish. The main objective of the present study was to evaluate differences in outcomes as a function of (a) the language in which the intervention materials were received, and (b) the participants' acculturation levels. Prior to the study, all women were at risk of an AEP. At the 6-month follow-up, two thirds (66%) of all Hispanic women had reduced their overall risk of an AEP, primarily by practicing effective birth control. These outcomes are similar to those reported for previous Project CHOICES studies. Significantly more women who requested the intervention materials in English (75%) compared to Spanish (41%) reduced their overall risk of an AEP. Women with high English cultural domain scores were at significantly less risk of an AEP due to effective contraception and a reduced overall risk of an AEP. Compared to other Project CHOICES studies, Project Healthy CHOICES is less intensive; it is self-administered, freely available, and can be completed without visiting a health care practitioner or clinic.

Iodide Recognition and Sensing in Water by a Halogen-Bonding Ruthenium(II)-Based Rotaxane.

The synthesis and anion-recognition properties of the first halogen-bonding rotaxane host to sense anions in water is described. The rotaxane features a halogen-bonding axle component, which is stoppered with water-solubilizing permethylated ß-cyclodextrin motifs, and a luminescent tris(bipyridine)ruthenium(II)-based macrocycle component. (1) H NMR anion-binding titrations in D2 O reveal the halogen-bonding rotaxane to bind iodide with high affinity and with selectively over the smaller halide anions and sulfate. The binding affinity trend was explained through molecular dynamics simulations and free-energy calculations. Photo-physical investigations demonstrate the ability of the interlocked halogen-bonding host to sense iodide in water, through enhancement of the macrocycle component's Ru(II) metal-ligand charge transfer (MLCT) emission.

Halogen bonding rotaxanes for nitrate recognition in aqueous media.

Targeting the biologically and environmentally important nitrate anion, halogen bonding (XB) has been incorporated into three novel [2]rotaxane structural frameworks via an axle component containing covalently linked 3,5-bis-iodotriazole pyridine-pyridinium motifs. This has enabled the recognition of nitrate in aqueous media containing up to 90% water with equivalent binding affinity to chloride, illustrating the potency of XB for anion recognition in highly competitive aqueous solvent mixtures.

Alignment of time course gene expression data and the classification of developmentally driven genes with hidden Markov models.

BACKGROUND: We consider data from a time course microarray experiment that was conducted on grapevines over the development cycle of the grape berries at two different vineyards in South Australia. Although the underlying biological process of berry development is the same at both vineyards, there are differences in the timing of the development due to local conditions. We aim to align the data from the two vineyards to enable an integrated analysis of the gene expression and use the alignment of the expression profiles to classify likely developmental function. RESULTS: We present a novel alignment method based on hidden Markov models (HMMs) and use the method to align the motivating grapevine data. We show that our alignment method is robust against subsets of profiles that are not suitable for alignment, investigate alignment diagnostics under the model and demonstrate the classification of developmentally driven genes. CONCLUSIONS: The classification of developmentally driven genes both validates that the alignment we obtain is meaningful and also gives new evidence that can be used to identify the role of genes with unknown function. Using our alignment methodology, we find at least 1279 grapevine probe sets with no current annotated function that are likely to be controlled in a developmental manner.

Evidence for halogen bond covalency in acyclic and interlocked halogen-bonding receptor anion recognition.

The synthesis and anion binding properties of novel halogen-bonding (XB) bis-iodotriazole-pyridinium-containing acyclic and [2]catenane anion host systems are described. The XB acyclic receptor displays selectivity for acetate over halides with enhanced anion recognition properties compared to the analogous hydrogen-bonding (HB) acyclic receptor. A reversal in halide selectivity is observed in the XB [2]catenane, in comparison to the acyclic XB receptor, due to the interlocked host's unique three-dimensional binding cavity, and no binding is observed for oxoanions. Notable halide anion association constant values determined for the [2]catenane in competitive organic-aqueous solvent mixtures demonstrate considerable enhancement of anion recognition as compared to the HB catenane analogue. X-ray crystallographic analysis of a series of halide catenane complexes reveal strong XB interactions in the solid state. These interactions were studied using Cl and Br K-edge X-ray Absorption Spectroscopy (XAS) indicating intense pre-edge features characteristic of charge transfer from the halide to its bonding partner (σ(AX←X(-))(*) ← X1s), and providing a direct measure of the degree of covalency in the halogen bond(s). The data reveal that the degree of covalency is similar to that which is observed in transition metal coordinate covalent bonds. These results are supported by DFT results, which correlate well with the experimental data.

Downregulation of PIK3IP1/TrIP on T cells is controlled by TCR signal strength, PKC, and metalloprotease-mediated cleavage.

The protein known as PI3K-interacting protein (PIK3IP1), or transmembrane inhibitor of PI3K (TrIP), is highly expressed by T cells and can modulate PI3K activity in these cells. Several studies have also revealed that TrIP is rapidly downregulated following T cell activation. However, it is unclear as to how this downregulation is controlled. Using a novel monoclonal antibody that robustly stains cell-surface TrIP, we demonstrate that TrIP is lost from the surface of activated T cells in a manner dependent on the strength of signaling through the T cell receptor (TCR) and specific downstream signaling pathways. In addition, TrIP expression returns after 24 hours, suggesting that it may play a role in resetting TCR signaling at later time points. Finally, by expressing truncated forms of TrIP in cells, we identify the region in the extracellular stalk domain of TrIP that is targeted for proteolytic cleavage by metalloprotease ADAM17.

Simultaneous proteome localization and turnover analysis reveals spatiotemporal features of protein homeostasis disruptions.

The functions of proteins depend on their spatial and temporal distributions, which are not directly measured by static protein abundance. Under endoplasmic reticulum (ER) stress, the unfolded protein response (UPR) pathway remediates proteostasis in part by altering the turnover kinetics and spatial distribution of proteins. A global view of these spatiotemporal changes has yet to emerge and it is unknown how they affect different cellular compartments and pathways. Here we describe a mass spectrometry-based proteomics strategy and data analysis pipeline, termed Simultaneous Proteome Localization and Turnover (SPLAT), to measure concurrently the changes in protein turnover and subcellular distribution in the same experiment. Investigating two common UPR models of thapsigargin and tunicamycin challenge in human AC16 cells, we find that the changes in protein turnover kinetics during UPR varies across subcellular localizations, with overall slowdown but an acceleration in endoplasmic reticulum and Golgi proteins involved in stress response. In parallel, the spatial proteomics component of the experiment revealed an externalization of amino acid transporters and ion channels under UPR, as well as the migration of RNA-binding proteins toward an endosome co-sedimenting compartment. The SPLAT experimental design classifies heavy and light SILAC labeled proteins separately, allowing the observation of differential localization of new and old protein pools and capturing a partition of newly synthesized EGFR and ITGAV to the ER under stress that suggests protein trafficking disruptions. Finally, application of SPLAT toward human induced pluripotent stem cell derived cardiomyocytes (iPSC-CM) exposed to the cancer drug carfilzomib, identified a selective disruption of proteostasis in sarcomeric proteins as a potential mechanism of carfilzomib-mediated cardiotoxicity. Taken together, this study provides a global view into the spatiotemporal dynamics of human cardiac cells and demonstrates a method for inferring the coordinations between spatial and temporal proteome regulations in stress and drug response.

Imidazo[1,2-b]pyridazines as inhibitors of DYRK kinases.

Selective inhibitors of DYRK1A are of interest for the treatment of cancer, Type 2 diabetes and neurological disorders. Optimization of imidazo [1,2-b]pyridazine fragment 1 through structure-activity relationship exploration and in silico drug design efforts led to the discovery of compound 17 as a potent cellular inhibitor of DYRK1A with selectivity over much of the kinome. The binding mode of compound 17 was elucidated with X-ray crystallography, facilitating the rational design of compound 29, an imidazo [1,2-b]pyridazine with improved kinase selectivity with respect to closely related CLK kinases.