Large-scale genomic data reveal the phylogeny and evolution of owlet moths (Noctuoidea).

The owlet moths (Noctuoidea; ~43-45K described species) are one of the most ecologically diverse and speciose superfamilies of animals. Moreover, they comprise some of the world's most notorious pests of agriculture and forestry. Despite their contributions to terrestrial biodiversity and impacts on ecosystems and economies, the evolutionary history of Noctuoidea remains unclear because the superfamily lacks a statistically robust phylogenetic and temporal framework. We reconstructed the phylogeny of Noctuoidea using data from 1234 genes (946.4 kb nucleotides) obtained from the genome and transcriptome sequences of 76 species. The relationships among the six families of Noctuoidea were well resolved and consistently recovered based on both concatenation and gene coalescence approaches, supporting the following relationships: Oenosandridae + (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))). A Yule tree prior with three unlinked molecular clocks was identified as the preferred BEAST analysis using marginal-likelihood estimations. The crown age of Noctuoidea was estimated at 74.5 Ma, with most families originating before the end of the Paleogene (23 Ma). Our study provides the first statistically robust phylogenetic and temporal framework for Noctuoidea, including all families of owlet moths, based on large-scale genomic data.

Reconstituted Extracellular Vesicles from Human Platelets Decrease Viral Myocarditis in Mice.

Patients with viral myocarditis are at risk of sudden death and may progress to dilated cardiomyopathy (DCM). Currently, no disease-specific therapies exist to treat viral myocarditis. Here it is examined whether reconstituted, lyophilized extracellular vesicles (EVs) from platelets from healthy men and women reduce acute or chronic myocarditis in male mice. Human-platelet-derived EVs (PEV) do not cause toxicity, damage, or inflammation in naïve mice. PEV administered during the innate immune response significantly reduces myocarditis with fewer epidermal growth factor (EGF)-like module-containing mucin-like hormone receptor-like 1 (F4/80) macrophages, T cells (cluster of differentiation molecules 4 and 8, CD4 and CD8), and mast cells, and improved cardiac function. Innate immune mediators known to increase myocarditis are decreased by innate PEV treatment including Toll-like receptor (TLR)4 and complement. PEV also significantly reduces perivascular fibrosis and remodeling including interleukin 1 beta (IL-1ß), transforming growth factor-beta 1, matrix metalloproteinase, collagen genes, and mast cell degranulation. PEV given at days 7-9 after infection reduces myocarditis and improves cardiac function. MicroRNA (miR) sequencing reveals that PEV contains miRs that decrease viral replication, TLR4 signaling, and T-cell activation. These data show that EVs from the platelets of healthy individuals can significantly reduce myocarditis and improve cardiac function.

Phase I evaluation of CycloSam® (Sm-153-DOTMP) bone seeking radiopharmaceutical in dogs with spontaneous appendicular osteosarcoma.

153 Sm-DOTMP (CycloSam® ) is a newly-patented radiopharmaceutical for bone tumor treatment. DOTMP (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetramethylene-phosphonate) is a macrocyclic chelating agent with superior binding properties to 153 Sm when compared with EDTMP (Quadramet™, used for palliative treatment of bone cancer). CycloSam® was administered at 1 mCi/kg (37 MBq/kg) in a prospective pilot study to seven dogs with bone cancer resulting in no myelosuppression. Then, 13 dogs were enrolled in a prospective clinical trial study using traditional 3+3 dose escalation and starting at 1.5 mCi/kg. Baseline evaluation included hematologic and biochemical testing, diagnosis confirmation, thoracic and limb radiographs, technetium-99 m-HDP bone scintigraphy, and 18 F-FDG PET scan (SUVmax). Toxicity (primary endpoint) was assessed through weekly blood counts and adverse events. Dogs received 1.5 mCi/kg (n = 4), 1.75 mCi/kg (n = 6), and 2 mCi/kg (n = 3) of 153 Sm-DOTMP. Dose-limiting neutropenia and thrombocytopenia were seen at 2 mCi/kg. No dose-limiting nonhematologic toxicities occurred. Efficacy (secondary endpoint) was assessed by objective lameness measurement (body-mounted inertial sensors), owner quality-of-life (QoL) questionnaire, and repeat PET scan. Objective lameness measurement improved in four dogs (53%-60% decrease) was equivocal in three dogs, and worsened in four dogs (66%-115% increase); two dogs were not evaluable. Repeat 18 F-FDG PET scan results varied and change in lameness did not consistently correlate with SUVmax changes. QoL score worsened (n = 5) or was improved/stable (n = 7). Carboplatin chemotherapy (300 mg/m2 IV every 3 weeks ×4) started 4 weeks after 153 Sm-DOTMP injection. No dog died of chemotherapy-related complications. All dogs completed study monitoring. The recommended dose for CycloSam® in dogs is 1.75 mCi/kg, which resulted in some pain control with minimal toxicity and was safely combined with chemotherapy.

The MG-RAST metagenomics database and portal in 2015.

MG-RAST (http://metagenomics.anl.gov) is an open-submission data portal for processing, analyzing, sharing and disseminating metagenomic datasets. The system currently hosts over 200,000 datasets and is continuously updated. The volume of submissions has increased 4-fold over the past 24 months, now averaging 4 terabasepairs per month. In addition to several new features, we report changes to the analysis workflow and the technologies used to scale the pipeline up to the required throughput levels. To show possible uses for the data from MG-RAST, we present several examples integrating data and analyses from MG-RAST into popular third-party analysis tools or sequence alignment tools.

Vertical pelvic movement asymmetry and lameness location in ipsilateral combined forelimb and hindlimb lameness cases.

BACKGROUND: Compensatory vertical head and pelvis movement asymmetry may occur in trotting horses with a primary cause of lameness in one end of the body due to the weight shifting between limbs, leading to apparent combined forelimb and hindlimb lameness (CFHL). Little is known about CFHL patterns observed with body-mounted inertial sensors (BMIS) and regardless of their underlying mechanisms, compensatory and secondary lameness may complicate the definitive identification of the primary causes of lameness. OBJECTIVE: Determine associations between vertical pelvic movement asymmetry and location of primary lameness in ipsilateral CFHL cases where hindlimb lameness is solely impact or push-off type. STUDY DESIGN: Retrospective cohort. METHODS: From a body-mounted inertial sensor (BMIS) evaluated equine lameness database, we identified cases with a consistent, low-variability ipsilateral impact (IpI) or ipsilateral pushoff (IpP) hindlimb lameness in a straight-line trot and that had definitive diagnoses. Cases were categorised by lameness location to the limb(s), diagnosis, and ratio of the amplitude of forelimb to hindlimb lameness (Forea/Hinda). Differences in the numbers of IpI and IpP cases in these categories were analysed with chi-square tests, effect sizes, and odds ratios. RESULTS: Among the 2375 total lameness cases screened, 49 IpI and 36 IpP cases met the criteria for consistency, low variability, and definitive diagnosis. IpI cases were more likely than IpP cases to have forelimb-only lameness causes when Forea/Hinda >1 (OR = 43, 95% CI = 2.3-798). IpP cases were more likely than IpI cases to have hindlimb-only causes at both Forea/Hinda >1.0 (OR = 20, 95% CI = 2.2-200) and <1.0 (OR = 14, 95% CI = 2.9-66.7). Compared with IpI, IpP cases were more frequently diagnosed with tendon, suspensory ligament, or high-motion joint disorders in hindlimbs (OR = 3.6, 95% CI = 1.1-12.3) and less with unknown causes (OR = 13.2, 95% CI = 3.2-75.2). In IpI cases, positive forelimb regional anaesthesia often reduced hindlimb lameness, whereas in IpP cases, positive hindlimb regional anaesthesia typically lessened forelimb lameness. MAIN LIMITATIONS: Most cases were Quarter Horses. The likelihood of location and cause of lameness may be different for other breeds. CONCLUSIONS: The type of pelvic movement asymmetry observed in IpI and IpP cases is linked to the location and underlying cause of the primary lameness.

A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE.

We provide a novel method, DRISEE (duplicate read inferred sequencing error estimation), to assess sequencing quality (alternatively referred to as "noise" or "error") within and/or between sequencing samples. DRISEE provides positional error estimates that can be used to inform read trimming within a sample. It also provides global (whole sample) error estimates that can be used to identify samples with high or varying levels of sequencing error that may confound downstream analyses, particularly in the case of studies that utilize data from multiple sequencing samples. For shotgun metagenomic data, we believe that DRISEE provides estimates of sequencing error that are more accurate and less constrained by technical limitations than existing methods that rely on reference genomes or the use of scores (e.g. Phred). Here, DRISEE is applied to (non amplicon) data sets from both the 454 and Illumina platforms. The DRISEE error estimate is obtained by analyzing sets of artifactual duplicate reads (ADRs), a known by-product of both sequencing platforms. We present DRISEE as an open-source, platform-independent method to assess sequencing error in shotgun metagenomic data, and utilize it to discover previously uncharacterized error in de novo sequence data from the 454 and Illumina sequencing platforms.

Chemical genetics identifies Rab geranylgeranyl transferase as an apoptotic target of farnesyl transferase inhibitors.

A chemical genetics approach identified a cellular target of several proapoptotic farnesyl transferase inhibitors (FTIs). Treatment with these FTIs caused p53-independent apoptosis in Caenorhabditis elegans, which was mimicked by knockdown of endosomal trafficking proteins, including Rab5, Rab7, the HOPS complex, and notably the enzyme Rab geranylgeranyl transferase (RabGGT). These FTIs were found to inhibit mammalian RabGGT with potencies that correlated with their proapoptotic activity. Knockdown of RabGGT induced apoptosis in mammalian cancer cell lines, and both RabGGT subunits were overexpressed in several tumor tissues. These findings validate RabGGT, and by extension endosomal function, as a therapeutically relevant target for modulation of apoptosis, and enhance our understanding of the mechanism of action of FTIs.

Prevalence and clinical significance of increasing head height asymmetry as a measure of forelimb lameness in horses when trotting in a straight line after palmar digital nerve block.

BACKGROUND: Some horses increase in forelimb lameness, measured as vertical head height asymmetry, or differences in maximums and minimums of head heights (HDmax, HDmin), after a palmar digital nerve (PDN) block. The prevalence of this finding, or what it means clinically, has not been reported in peer-reviewed literature. OBJECTIVES: To estimate the prevalence of increasing head height asymmetry after a PDN block and determine if this is associated with cause of forelimb lameness. STUDY DESIGN: Retrospective case series. METHODS: Head height asymmetry, normalised to expected vertical head displacement, from inertial-sensor data collections of all horses evaluated for forelimb lameness while trotting in a straight line at two different clinics were screened for cases that had an initial PDN block and then another more proximal block in the same limb during the same lameness evaluation. Medical records of the screened cases (n = 213) were evaluated to determine the cause of lameness. Prevalence of increasing head height asymmetry was calculated. Differences in lameness amplitude between groups of cases that remained unchanged (Group 1), that increased (Group 2), and that decreased (Group 3) in head height asymmetry before and after the initial PDN block were compared (Kruskal-Wallis). Determination of the location of the cause of lameness and final diagnoses of cases were compared between Group 1 and Group 2 (chi-squared tests of independence). RESULTS: The PDN block increased head height asymmetry at a prevalence of 32.5% (95% CI = 24.5%-41.5%) and 13.8% (95% CI = 7.3%-22.9%), in clinic 1 and 2, respectively. Increasing head height asymmetry after an initial PDN block did not predict localization of the cause of forelimb lameness or specific diagnosis (p = 0.1), other than indicating that it is unlikely to be in the foot (p = 0.02). MAIN LIMITATIONS: Study samples consisted primarily of Warmbloods (clinic 1) and Quarter Horses (clinic 2). Analysis of blocking induced changes was limited to straight line trot only. CONCLUSIONS: Increasing head height asymmetry after PDN block is common during forelimb lameness evaluations. Other than indicating that the cause of lameness is more proximal in the blocked forelimb, this does not help determine the final diagnosis.

Short-read reading-frame predictors are not created equal: sequence error causes loss of signal.

BACKGROUND: Gene prediction algorithms (or gene callers) are an essential tool for analyzing shotgun nucleic acid sequence data. Gene prediction is a ubiquitous step in sequence analysis pipelines; it reduces the volume of data by identifying the most likely reading frame for a fragment, permitting the out-of-frame translations to be ignored. In this study we evaluate five widely used ab initio gene-calling algorithms-FragGeneScan, MetaGeneAnnotator, MetaGeneMark, Orphelia, and Prodigal-for accuracy on short (75-1000 bp) fragments containing sequence error from previously published artificial data and "real" metagenomic datasets. RESULTS: While gene prediction tools have similar accuracies predicting genes on error-free fragments, in the presence of sequencing errors considerable differences between tools become evident. For error-containing short reads, FragGeneScan finds more prokaryotic coding regions than does MetaGeneAnnotator, MetaGeneMark, Orphelia, or Prodigal. This improved detection of genes in error-containing fragments, however, comes at the cost of much lower (50%) specificity and overprediction of genes in noncoding regions. CONCLUSIONS: Ab initio gene callers offer a significant reduction in the computational burden of annotating individual nucleic acid reads and are used in many metagenomic annotation systems. For predicting reading frames on raw reads, we find the hidden Markov model approach in FragGeneScan is more sensitive than other gene prediction tools, while Prodigal, MGA, and MGM are better suited for higher-quality sequences such as assembled contigs.

Connecting genotype to phenotype in the era of high-throughput sequencing.

BACKGROUND: The development of next generation sequencing technology is rapidly changing the face of the genome annotation and analysis field. One of the primary uses for genome sequence data is to improve our understanding and prediction of phenotypes for microbes and microbial communities, but the technologies for predicting phenotypes must keep pace with the new sequences emerging. SCOPE OF REVIEW: This review presents an integrated view of the methods and technologies used in the inference of phenotypes for microbes and microbial communities based on genomic and metagenomic data. Given the breadth of this topic, we place special focus on the resources available within the SEED Project. We discuss the two steps involved in connecting genotype to phenotype: sequence annotation, and phenotype inference, and we highlight the challenges in each of these steps when dealing with both single genome and metagenome data. MAJOR CONCLUSIONS: This integrated view of the genotype-to-phenotype problem highlights the importance of a controlled ontology in the annotation of genomic data, as this benefits subsequent phenotype inference and metagenome annotation. We also note the importance of expanding the set of reference genomes to improve the annotation of all sequence data, and we highlight metagenome assembly as a potential new source for complete genomes. Finally, we find that phenotype inference, particularly from metabolic models, generates predictions that can be validated and reconciled to improve annotations. GENERAL SIGNIFICANCE: This review presents the first look at the challenges and opportunities associated with the inference of phenotype from genotype during the next generation sequencing revolution. This article is part of a Special Issue entitled: Systems Biology of Microorganisms.

A dynamic role for the mushroom bodies in promoting sleep in Drosophila.

The fruitfly, Drosophila melanogaster, exhibits many of the cardinal features of sleep, yet little is known about the neural circuits governing its sleep. Here we have performed a screen of GAL4 lines expressing a temperature-sensitive synaptic blocker shibire(ts1) (ref. 2) in a range of discrete neural circuits, and assayed the amount of sleep at different temperatures. We identified three short-sleep lines at the restrictive temperature with shared expression in the mushroom bodies, a neural locus central to learning and memory. Chemical ablation of the mushroom bodies also resulted in reduced sleep. These studies highlight a central role for the mushroom bodies in sleep regulation.

Anti-nociceptive efficacy of the soluble epoxide hydrolase inhibitor t-TUCB in horses with mechanically induced lameness.

INTRODUCTION: Soluble epoxide hydrolase (sEH) inhibitors are novel anti-inflammatory and analgesic agents that could improve pain management in horses. The objective of the present study was to evaluate the anti-nociceptive effect of a single-dose intravenous administration of the sEH inhibitor trans-4-{4-[3-(4-trifluro-methoxy-phenyl)-ureido]-cyclohexyloxy}-benzoic acid (t-TUCB) using an adjustable heart bar shoe (a-HBS) model of lameness. We hypothesized that t-TUCB would improve objective and subjective lameness measures compared to the control. MATERIALS AND METHODS: Reversible lameness was induced in 8 horses for 24 h using an a-HBS in a randomized, crossover design. A vehicle-control placebo (DMSO) or t-TUCB (1 mg/kg) was intravenously administered at time 0 following a baseline induced lameness evaluation. Blood was collected and lameness was objectively measured with an inertial sensor system at 0-, 1-, 3-, 6-, 12-, and 24-h time points. Front-facing videos were obtained at each time point for subjective evaluation by three blinded evaluators using a visual analog scale (VAS). RESULTS: Treatment with t-TUCB significantly decreased (i.e. improved) lameness compared to placebo at 1-h and compared to baseline at 1-, 3-, and 6-h following administration. Lameness significantly increased (i.e. worsened) from baseline in placebo-treated horses 12 h after administration. All horses returned to baseline soundness within 24 h of reversing lameness. CONCLUSION: Treatment with single-dose IV administration of t-TUCB improved lameness induced by the a-HSB, suggesting that t-TUCB has anti-nociceptive effects in horses. CLINICAL RELEVANCE: The soluble epoxide hydrolase inhibitor, t-TUCB, is a promising novel analgesic for horses.

The Scope and Impact of the COVID-19 Pandemic on Neuroemergent Patient Transfers, Clinical Care and Patient Outcomes.

Introduction: The SARS-CoV-2 (COVID-19) pandemic continues to substantially alter previously established clinical practice patterns and has transformed patient care in American healthcare. However, studies to evaluate the impact of COVID-19 on neuroemergent patient care and associated clinical outcomes are limited. Herein, we describe the impact of COVID-19 on the Neuroemergency Transfer Program (NTP) - a novel, urban, high volume interhospital patient transfer program. Objective: To evaluate and describe the clinical impact of the COVID-19 pandemic on the NTP. Study Design: A single-center retrospective study of prospectively collected consecutive neuroemergent patient transfer data between 2018-2021 was analyzed. Adult patients were divided based upon transfer date into a Pre-COVID (PCOV) or COVID cohort. Patient demographics, transfer characteristics and clinical data and outcomes were analyzed. Results: 3,096 patients were included for analysis. Mean age at transfer in the PCOV and COVID cohorts were 62.4 ± 0.36 and 61.1 ± 0.6 years. A significant decrease in mean transfers per month was observed between cohorts (PCOV = 97.8 vs. COV = 68.2 transfers/month, p < 0.01). Total transfer time in the PCOV cohort was 155.1 ± 3.4 min which increased to 169.3 ± 12.8 min in the COVID cohort (p = 0.13). Overall mean transfer distance was significantly longer in the PCOV cohort at 22.0 ± 0.4 miles vs. 20.3 ± 0.67 miles in the COV cohort (p = 0.03). The relative frequency of transfer diagnoses was unchanged between cohorts. A significant increase in mean inpatient length of stay was noted, 7.9 ± 0.15 days to 9.6 ± 0.33 days in the PCOV vs. COVID cohorts (p < 0.01). Ultimately, no difference in the frequency of good vs. poor clinical outcome were noted between the PCOV (79.8% and 19.4%) vs. COV (78.8% and 20.4%) cohorts. Conclusion: The impact of COVID-19 on current healthcare dynamics are far reaching. Here, we show a significant decrease in interhospital patient transfers and increased length of stay between a Pre-COVID and COVID cohort. Further work to better elucidate the specific interplay of clinical contributors to account for these changes is indicated.

A retrospective comparison of radiographic and clinical outcomes in single-level degenerative lumbar disease undergoing anterior versus transforaminal lumbar interbody fusion.

BACKGROUND: Single-level lumbar degenerative disc disease (DDD) remains a significant cause of morbidity in adulthood. Anterior lumbar interbody fusion (ALIF) and Transforaminal lumbar interbody fusion (TLIF) are surgical techniques developed to treat this condition. With limited studies on intermediate term outcomes in a single cohort, we compare radiographic and clinical outcomes in patients undergoing ALIF and TLIF. METHODS: A retrospective chart review was performed on 164 patients (111 TLIF; 53 ALIF) over a 60-month period. X-ray radiographs obtained pre-operatively, prior to discharge, and at one year were utilized for radiographic assessment. Segmental lordosis, lumbar lordosis and HRQOL scores were measured preoperatively and at one-year timepoints. RESULTS: Changes in lumbar lordosis and segmental lordosis were significantly greater after ALIF (4.6° vs. -0.6°, P=0.05; 4.7° vs. -0.7°, P<0.05) at one year (mean time, 366±20 days). At one year or greater, there was a greater reduction in mean VAS-leg score in TLIF patients (3.4 vs. 0.6, P<0.05) and ODI score (16.2 vs. 5.4, P<0.05). Similar outcomes were seen for VAS-back, SF-12 Physical Health, and SRS-30 Function/Activity. SF-12 Mental Health scores were found to be lower in patients undergoing TLIF (-3.5 vs. 2.7, P<0.05). CONCLUSIONS: ALIF demonstrated a superior method of increasing lumbar and segmental lordosis. TLIF was utilized more in patients with higher pre-operative VAS-leg pain scores and therefore, showed a greater magnitude of VAS-leg pain improvement. TLIF also demonstrated a greater improvement in ODI scores despite similar baseline scores, suggesting a possible enhanced functional outcome.

Transforaminal lumbar interbody fusion using a novel minimally invasive expandable interbody cage: patient-reported outcomes and radiographic parameters.

OBJECTIVE: The goal of this study was to evaluate the clinical and radiographic outcomes of a novel multidirectional in situ expandable minimally invasive surgery (MIS) transforaminal lumbar interbody fusion (TLIF) cage. METHODS: A retrospective analysis of 69 consecutive patients undergoing a 1- or 2-level MIS TLIF using an expandable cage was performed over a 2-year period. Standard MIS techniques with pedicle screw fixation were used in all cases. Upright lateral dynamic flexion/extension radiographs were reviewed prior to and at 1 year after surgery. Clinical metrics included numeric rating scale for back and leg pain, Oswestry Disability Index, and the SF-12 and VR-12 physical and mental health surveys. Radiographic parameters included anterior and posterior disc height, neuroforaminal height, spondylolisthesis, segmental lordosis, lumbar lordosis, and fusion rate. RESULTS: A total of 69 patients representing 75 operative levels met study inclusion criteria. The mean patient age at surgery was 63.4 ± 1.2 years, with a female predominance of 51%. The average radiographic and clinical follow-ups were 372 and 368 days, respectively. A total of 63 patients (91%) underwent 1-level surgery and 6 patients (9%) underwent 2-level surgery. Significant reductions of numeric rating scale scores for back and leg pain were observed-from 6.1 ± 0.7 to 2.5 ± 0.3 (p < 0.0001) and 4.9 ± 0.6 to 1.9 ± 0.2 (p < 0.0001), respectively. A similar reduction in Oswestry Disability Index from 38.0 ± 4.6 to 20.0 ± 2.3 (p < 0.0001) was noted. Likewise, SF-12 and VR-12 scores all showed statistically significant improvement from baseline (p < 0.001). The mean anterior and posterior disc heights improved from 8.7 ± 1.0 mm to 13.4 ± 1.5 mm (p = 0.0001) and 6.5 ± 0.8 mm to 9.6 ± 1.1 mm (p = 0.0001), respectively. Neuroforaminal height improved from 17.6 ± 2.0 mm to 21.9 ± 2.5 mm (p = 0.0001). When present, spondylolisthesis was, on average, reduced from 4.3 ± 0.5 mm to 1.9 ± 0.2 mm (p = 0.0001). Lumbar lordosis improved from 47.8° ± 5.5° to 58.5° ± 6.8° (p = 0.2687), and no significant change in segmental lordosis was observed. The overall rate of radiographic fusion was 93.3% at 1 year. No perioperative complications requiring operative revision were encountered. CONCLUSIONS: In this series of MIS TLIFs, use of this novel interbody cage was shown to be safe and effective. Significant improvements in pain and disability were observed. Effective and durable restoration of disc height and neuroforaminal height and reduction of spondylolisthesis were obtained, with concurrent gains in lumbar lordosis. Taken together, this device offers excellent clinical and radiographic outcomes via an MIS approach.

Clockwork orange encodes a transcriptional repressor important for circadian-clock amplitude in Drosophila.

Gene transcription is a central timekeeping process in animal clocks. In Drosophila, the basic helix-loop helix (bHLH)-PAS transcription-factor heterodimer, CLOCK/CYCLE (CLK/CYC), transcriptionally activates the clock components period (per), timeless (tim), Par domain protein 1 (Pdp1), and vrille (vri), which feed back and regulate distinct features of CLK/CYC function. Microarray studies have identified numerous rhythmically expressed transcripts, some of which are potential direct CLK targets. Here we demonstrate a circadian function for one such target, a bHLH-Orange repressor, CG17100/CLOCKWORK ORANGE (CWO). cwo is rhythmically expressed, and levels are reduced in Clk mutants, suggesting that cwo is CLK activated in vivo. cwo mutants display reduced-amplitude molecular and behavioral rhythms with lengthened periods. Molecular analysis suggests that CWO acts, in part, by repressing CLK target genes. We propose that CWO acts as a transcriptional and behavioral rhythm amplifier.

Effect of induced hindlimb length difference on body-mounted inertial sensor measures used to evaluate hindlimb lameness in horses.

This study has investigated the immediate effect of induced hindlimb length difference on hindlimb lameness measured as differences in minimum (Pmin) and maximum (Pmax) pelvic heights in 16 horses trotting in a straight line and lungeing on both hard and soft surfaces with body-mounted inertial sensors. Hindlimb length differences were induced by applying an Easyboot Glue-on shoe to one hindlimb. Changes in Pmin and Pmax with induced hindlimb length difference were assessed with a two-way repeated-measures ANOVA with trial (straight, lunge with inside limb elevation, lunge with outside limb elevation) and surface (hard, soft) as within-subject factors. Change in Pmin, indicating an impact-type lameness, in the hind limb with the elevation, was significant in both the straight line and while lunging on both hard and soft surfaces. Change in Pmax, indicating pushoff-type lameness, in the opposite, non-elevated hind limb, was significant when trotting in a straight line but not while lunging.

Comparison of results for body-mounted inertial sensor assessment with final lameness determination in 1,224 equids.

OBJECTIVE: To compare results for initial body-mounted inertial sensor (BMIS) measurement of lameness in equids trotting in a straight line with definitive findings after full lameness evaluation. ANIMALS: 1,224 equids. PROCEDURES: Lameness measured with BMIS equipment while trotting in a straight line was classified into categories of none, forelimb only, hind limb only, and 8 patterns of combined forelimb and hind limb lameness (CFHL). Definitive findings after full lameness evaluation were established in most horses and classified into types (no lameness, forelimb- or hind limb-only lameness, CFHL, or lameness not localized to the limbs). Observed proportions of lameness type in equids with definitive findings for each initial BMIS-assessed category were compared with hypothetical expected proportions through χ2 goodness-of-fit analysis. RESULTS: The most common initial BMIS-assessed lameness category was CFHL (693/1,224 [56.6%]), but this was the least common definitive finding (94/ 862 [10.9%]). The observed frequency of no lameness after full lameness evaluation was greater than expected only when initial BMIS measurements indicated no lameness. The observed frequency of forelimb-only lameness was greater than expected when initially measured as forelimb-only lameness and for CFHL categories consistent with the diagonal movement principle of compensatory lameness. Observed frequency of hind limb-only lameness was greater than expected when initially measured as hind limb-only lameness and for CFHL categories consistent with the sagittal movement principle of compensatory lameness. Equids initially assessed as having no lameness had the highest (103/112 [92%]) and those assessed as CFHL pattern 7 (forelimb with contralateral hind limb impact-only lameness) had the lowest (36/66 [55%]) rates of definitive findings. CONCLUSIONS AND CLINICAL RELEVANCE: In equids, results of initial straight-line trotting evaluations with a BMIS system did not necessarily match definitive findings but may be useful in planning the remaining lameness evaluation.

Evaluation of intraoperative culture results as a predictor for short-term incisional complications in 49 horses undergoing abdominal surgery.

This study evaluated bacterial isolates obtained during abdominal surgery and their relationship to short-term incisional complications. Samples of peritoneal fluid and from resection and/or enterotomy sites from 49 horses were cultured, with 96% having at least one positive culture result. The most common isolates were Escherichia coli, Streptococcus spp, and Enterococcus spp. Horses with small intestinal resections were more likely to grow obligate anaerobes and enteric organisms. Horses with small intestinal lesions (+/- resection) were more likely to grow enteric organisms and less likely to grow non-enteric organisms. Horses without enterotomy or resection procedures were more likely to grow 3 isolates and did not grow obligate anaerobes. The continued incisional drainage rate was 10%. Horses with preoperative peripheral leukocyte counts >8,500 cells/ul were more likely to develop incisional drainage. Many horses undergoing abdominal surgery may have positive intraoperative culture results. Our results did not provide evidence for the routine use of intraoperative culture to predict short-term incisional complications. Further studies are needed to evaluate the value of intraoperative culture in horses at high risk for incisional complications.

Meta-analysis of Drosophila circadian microarray studies identifies a novel set of rhythmically expressed genes.

Five independent groups have reported microarray studies that identify dozens of rhythmically expressed genes in the fruit fly Drosophila melanogaster. Limited overlap among the lists of discovered genes makes it difficult to determine which, if any, exhibit truly rhythmic patterns of expression. We reanalyzed data from all five reports and found two sources for the observed discrepancies, the use of different expression pattern detection algorithms and underlying variation among the datasets. To improve upon the methods originally employed, we developed a new analysis that involves compilation of all existing data, application of identical transformation and standardization procedures followed by ANOVA-based statistical prescreening, and three separate classes of post hoc analysis: cross-correlation to various cycling waveforms, autocorrelation, and a previously described fast Fourier transform-based technique. Permutation-based statistical tests were used to derive significance measures for all post hoc tests. We find application of our method, most significantly the ANOVA prescreening procedure, significantly reduces the false discovery rate relative to that observed among the results of the original five reports while maintaining desirable statistical power. We identify a set of 81 cycling transcripts previously found in one or more of the original reports as well as a novel set of 133 transcripts not found in any of the original studies. We introduce a novel analysis method that compensates for variability observed among the original five Drosophila circadian array reports. Based on the statistical fidelity of our meta-analysis results, and the results of our initial validation experiments (quantitative RT-PCR), we predict many of our newly found genes to be bona fide cyclers, and suggest that they may lead to new insights into the pathways through which clock mechanisms regulate behavioral rhythms.