Experimental design and power calculation in omics circadian rhythmicity detection using the cosinor model.

Circadian clocks are 24-h endogenous oscillators in physiological and behavioral processes. Though recent transcriptomic studies have been successful in revealing the circadian rhythmicity in gene expression, the power calculation for omics circadian analysis have not been fully explored. In this paper, we develop a statistical method, namely CircaPower, to perform power calculation for circadian pattern detection. Our theoretical framework is determined by three key factors in circadian gene detection: sample size, intrinsic effect size and sampling design. Via simulations, we systematically investigate the impact of these key factors on circadian power calculation. We not only demonstrate that CircaPower is fast and accurate, but also show its underlying cosinor model is robust against variety of violations of model assumptions. In real applications, we demonstrate the performance of CircaPower using mouse pan-tissue data and human post-mortem brain data, and illustrate how to perform circadian power calculation using mouse skeleton muscle RNA-Seq pilot as case study. Our method CircaPower has been implemented in an R package, which is made publicly available on GitHub ( https://github.com/circaPower/circaPower).

Preoperative measurement of the thickness of the center of the humeral head predicts screw cutout after locked plating of proximal humeral fractures.

HYPOTHESIS AND BACKGROUND: Preoperative computed tomography (CT) scans can be used to measure the thickness of the center of the humeral head to identify patients at a higher risk of screw cutout after open reduction-internal fixation. METHODS: At an academic medical center, we performed a retrospective review of all patients aged ≥ 18 years who had sustained a proximal humeral fracture that was treated with open reduction-internal fixation between January 1, 2005, and December 31, 2014, and who underwent preoperative shoulder CT. Ninety-four patients were included. Patient charts were reviewed to obtain demographic data, and radiographs were reviewed to assess screw cutout. A standardized method was devised to measure the thickness of the center of the humeral head. RESULTS: Screw cutout developed in 17 patients (17.7%). The mean humeral head thickness was significantly smaller on the axial (18 mm vs. 21 mm, P = .0031), coronal (18 mm vs. 21 mm, P = .0084), and sagittal (18 mm vs. 21 mm, P = .0033) sections in the patients who experienced screw cutout. When the smallest of the 3 measurements for each patient was analyzed, the risk of cutout was markedly greater when the humeral head thickness was <20 mm (25% vs. 6%). In addition, when the humeral head thickness was >25 mm, the risk of cutout was reduced to 0%. A low-energy injury was associated with a lower risk of cutout whereas age, sex, and fracture classification were not independent predictors of cutout on multivariate logistic regression. CONCLUSIONS: In a patient with a proximal humeral fracture in whom a preoperative CT scan is available, calculating the thickness of the center of the humeral head may provide valuable information to both the surgeon and the patient for preoperative planning and counseling. A smaller thickness of the center of the humeral head on preoperative CT is predictive of screw cutout following locked plating of proximal humeral fractures. A measurement of >25 mm in any one plane is highly protective against cutout; however, extreme caution and consideration of supplemental fixation methods should be taken when the measurements in all planes are <15 mm. This information may be helpful in counseling patients regarding the possibility of postoperative screw cutout.

Local neuropeptide signaling modulates serotonergic transmission to shape the temporal organization of C. elegans egg-laying behavior.

Animal behaviors are often composed of distinct alternating behavioral states. Neuromodulatory signals are thought to be critical for establishing stable behavioral states and for orchestrating transitions between them. However, we have only a limited understanding of how neuromodulatory systems act in vivo to alter circuit performance and shape behavior. To address these questions, we have investigated neuromodulatory signaling in the context of Caenorhabditis elegans egg-laying. Egg-laying activity cycles between discrete states-short bursts of egg deposition (active phases) that alternate with prolonged quiescent periods (inactive phases). Here using genetic, pharmacological and optogenetic approaches for cell-specific activation and inhibition, we show that a group of neurosecretory cells (uv1) located in close spatial proximity to the egg-laying neuromusculature direct the temporal organization of egg-laying by prolonging the duration of inactive phases. We demonstrate that the modulatory effects of the uv1 cells are mediated by peptides encoded by the nlp-7 and flp-11 genes that act locally to inhibit circuit activity, primarily by inhibiting vesicular release of serotonin from HSN motor neurons. This peptidergic inhibition is achieved, at least in part, by reducing synaptic vesicle abundance in the HSN motor neurons. By linking the in vivo actions of specific neuropeptide signaling systems with the generation of stable behavioral outcomes, our study reveals how cycles of neuromodulation emanating from non-neuronal cells can fundamentally shape the organization of a behavioral program.

A single pair of interneurons commands the Drosophila feeding motor program.

Many feeding behaviours are the result of stereotyped, organized sequences of motor patterns. These patterns have been the subject of neuroethological studies, such as electrophysiological characterization of neurons governing prey capture in toads. However, technical limitations have prevented detailed study of the functional role of these neurons, a common problem for vertebrate organisms. Complexities involved in studies of whole-animal behaviour can be resolved in Drosophila, in which remote activation of brain cells by genetic means enables us to examine the nervous system in freely moving animals to identify neurons that govern a specific behaviour, and then to repeatedly target and manipulate these neurons to characterize their function. Here we show neurons that generate the feeding motor program in Drosophila. We carried out an unbiased screen using remote neuronal activation and identified a critical pair of brain cells that induces the entire feeding sequence when activated. These 'feeding neurons' (here abbreviated to Fdg neurons for brevity) are also essential for normal feeding as their suppression or ablation eliminates sugar-induced feeding behaviour. Activation of a single Fdg neuron induces asymmetric feeding behaviour and ablation of a single Fdg neuron distorts the sugar-induced feeding behaviour to become asymmetric, indicating the direct role of these neurons in shaping motor-program execution. Furthermore, recording neuronal activity and calcium imaging simultaneously during feeding behaviour reveals that the Fdg neurons respond to food presentation, but only in starved flies. Our results demonstrate that Fdg neurons operate firmly within the sensorimotor watershed, downstream of sensory and metabolic cues and at the top of the feeding motor hierarchy, to execute the decision to feed.

Adaptively Integrative Association between Multivariate Phenotypes and Transcriptomic Data for Complex Diseases.

Phenotype-gene association studies can uncover disease mechanisms for translational research. Association with multiple phenotypes or clinical variables in complex diseases has the advantage of increasing statistical power and offering a holistic view. Existing multi-variate association methods mostly focus on SNP-based genetic associations. In this paper, we extend and evaluate two adaptive Fisher's methods, namely AFp and AFz, from the p-value combination perspective for phenotype-mRNA association analysis. The proposed method effectively aggregates heterogeneous phenotype-gene effects, allows association with different data types of phenotypes, and performs the selection of the associated phenotypes. Variability indices of the phenotype-gene effect selection are calculated by bootstrap analysis, and the resulting co-membership matrix identifies gene modules clustered by phenotype-gene effect. Extensive simulations demonstrate the superior performance of AFp compared to existing methods in terms of type I error control, statistical power and biological interpretation. Finally, the method is separately applied to three sets of transcriptomic and clinical datasets from lung disease, breast cancer, and brain aging and generates intriguing biological findings.

Rapid Eye Movement Sleep Engages Melanin-Concentrating Hormone Neurons to Reduce Cocaine Seeking.

BACKGROUND: Persistent sleep disruptions following withdrawal from abused drugs may hold keys to battle drug relapse. It is posited that there may be sleep signatures that predict relapse propensity, identifying which may open new avenues for treating substance use disorders. METHODS: We trained male rats (approximately postnatal day 56) to self-administer cocaine. After long-term drug withdrawal (approximately postnatal day 100), we examined the correlations between the intensity of cocaine seeking and key sleep features. To test for causal relationships, we then used behavioral, chemogenetic, or optogenetic methods to selectively increase rapid eye movement sleep (REMS) and measured behavioral and electrophysiological outcomes to probe for cellular and circuit mechanisms underlying REMS-mediated regulation of cocaine seeking. RESULTS: A selective set of REMS features was preferentially associated with the intensity of cue-induced cocaine seeking after drug withdrawal. Moreover, selectively increasing REMS time and continuity by environmental warming attenuated a withdrawal time-dependent intensification of cocaine seeking, or incubation of cocaine craving, suggesting that REMS may benefit withdrawal. Warming increased the activity of lateral hypothalamic melanin-concentrating hormone (MCH) neurons selectively during prolonged REMS episodes and counteracted cocaine-induced synaptic accumulation of calcium-permeable AMPA receptors in the nucleus accumbens-a critical substrate for incubation. Finally, the warming effects were partly mimicked by chemogenetic or optogenetic stimulations of MCH neurons during sleep, or intra-accumbens infusions of MCH peptide during the rat's inactive phase. CONCLUSIONS: REMS may encode individual vulnerability to relapse, and MCH neuron activities can be selectively targeted during REMS to reduce drug relapse.

Rethinking strategies for blood transfusion in hip fracture patients.

OBJECTIVES: Most patients can tolerate a hemoglobin (Hgb) > 8 g per deciliter. In some cases, however, transfusion will delay physical therapy and hospital discharge. This study aims to review Hgb and transfusion data for a large volume of recent hip fracture patients in order to identify new opportunities for decreasing the length of hospital stay. Our hypotheses are that in some cases, earlier transfusion of more blood will be associated with shorter hospital stays, and that Hgb levels consistently decrease for more than 3 days postoperatively. DESIGN: Retrospective chart review. SETTING: Two academic medical centers with Geriatric Fracture Programs. PATIENTS: Data was collected from patients 50 years and older with hip fractures April 2015 and October 2017. INTERVENTION: Operative stabilization of the hip fractures according to standard of care for the fracture type and patient characteristics. Transfusion according to established standards. MAIN OUTCOME MEASUREMENTS: Electronic records were retrospectively reviewed for demographic information, Hgb levels, and transfusion events. RESULTS: One thousand fifteen patients with femoral neck or intertrochanteric hip fractures were identified. Eight hundred sixty met the inclusion criteria. The average length of hospital stay was 6.7 days. The mean patient age was 82 years. The average American Society of Anesthesiologists score was 2.9. The average Hgb level consistently decreased for 5 days postoperatively before beginning to increase on day 6. There was poor consistency between intraoperative Hgb levels and preoperative or postoperative Hgb levels. Three hundred sixty-eight (42.8%) patients were transfused an average of 1.9 (range 1-6) units. One hundred five patients required a transfusion on postoperative day (POD) 1: 72 received only 1 unit of blood: 36 (50%) of the 72 required a second transfusion in the following days, compared to 9 of 33 (27%) who received 2 units on POD 1 (χ2 = 3.8898; P < .05). Patients who received transfusions on POD 3 or later had an average length of stay >2.5 days longer than those who received a transfusion earlier (P = 0.005). CONCLUSIONS: Our findings do not support earlier transfusion of more blood. Although in some cases, there is an association between earlier transfusion of more blood and shorter hospital stay, routine transfusion of more blood would incur higher transfusion risks in some patients who would not otherwise meet criteria for transfusion. After hip fracture surgery, the Hgb usually decreases for 5 days and does not begin to increase until POD 6. This information will provide utility in the population health management of hip fracture patients. LEVEL OF EVIDENCE: Level III, Retrospective Cohort Study.

The trauma severity model: An ensemble machine learning approach to risk prediction.

Statistical theory indicates that a flexible model can attain a lower generalization error than an inflexible model, provided that the setting is appropriate. This is highly relevant for mortality risk prediction with trauma patients, as researchers have focused exclusively on the use of generalized linear models for trauma risk prediction, and generalized linear models may be too inflexible to capture the potentially complex relationships in trauma data. To improve trauma risk prediction, we propose a machine learning model, the Trauma Severity Model (TSM). In order to validate TSM's performance, this study compares TSM to three established risk prediction models: the Bayesian Logistic Injury Severity Score, the Harborview Assessment for Risk of Mortality, and the Trauma Mortality Prediction Model. Our results indicate that TSM has superior predictive performance on National Trauma Data Bank data and on Nationwide Readmission Database data.

Recruitment of scribble to the synaptic scaffolding complex requires GUK-holder, a novel DLG binding protein.

BACKGROUND: Membrane-associated guanylate kinases (MAGUKs), such as Discs-Large (DLG), play critical roles in synapse maturation by regulating the assembly of synaptic multiprotein complexes. Previous studies have revealed a genetic interaction between DLG and another PDZ scaffolding protein, SCRIBBLE (SCRIB), during the establishment of cell polarity in developing epithelia. A possible interaction between DLG and SCRIB at synaptic junctions has not yet been addressed. Likewise, the biochemical nature of this interaction remains elusive, raising questions regarding the mechanisms by which the actions of both proteins are coordinated. RESULTS: Here we report the isolation of a new DLG-interacting protein, GUK-holder, that interacts with the GUK domain of DLG and which is dynamically expressed during synaptic bouton budding. We also show that at Drosophila synapses DLG colocalizes with SCRIB and that this colocalization is likely to be mediated by direct interactions between GUKH and the PDZ2 domain of SCRIB. We show that DLG, GUKH, and SCRIB form a tripartite complex at synapses, in which DLG and GUKH are required for the proper synaptic localization of SCRIB. CONCLUSIONS: Our results provide a mechanism by which developmentally important PDZ-mediated complexes are associated at the synapse.

The Ras1-mitogen-activated protein kinase signal transduction pathway regulates synaptic plasticity through fasciclin II-mediated cell adhesion.

Ras proteins are small GTPases with well known functions in cell proliferation and differentiation. In these processes, they play key roles as molecular switches that can trigger distinct signal transduction pathways, such as the mitogen-activated protein kinase (MAPK) pathway, the phosphoinositide-3 kinase pathway, and the Ral-guanine nucleotide dissociation stimulator pathway. Several studies have implicated Ras proteins in the development and function of synapses, but the molecular mechanisms for this regulation are poorly understood. Here, we demonstrate that the Ras-MAPK pathway is involved in synaptic plasticity at the Drosophila larval neuromuscular junction. Both Ras1 and MAPK are expressed at the neuromuscular junction, and modification of their activity levels results in an altered number of synaptic boutons. Gain- or loss-of-function mutations in Ras1 and MAPK reveal that regulation of synapse structure by this signal transduction pathway is dependent on fasciclin II localization at synaptic boutons. These results provide evidence for a Ras-dependent signaling cascade that regulates fasciclin II-mediated cell adhesion at synaptic terminals during synapse growth.

A large-scale behavioral screen to identify neurons controlling motor programs in the Drosophila brain.

Drosophila is increasingly used for understanding the neural basis of behavior through genetically targeted manipulation of specific neurons. The primary approach in this regard has relied on the suppression of neuronal activity. Here, we report the results of a novel approach to find and characterize neural circuits by expressing neuronal activators to stimulate subsets of neurons to induce behavior. Classical electrophysiological studies demonstrated that stimulation of command neurons could activate neural circuits to trigger fixed action patterns. Our method was designed to find such command neurons for diverse behaviors by screening flies in which random subsets of brain cells were activated. We took advantage of the large collection of Gal4 lines from the NP project and crossed 835 Gal4 strains with relatively limited Gal4 expression in the brain to flies carrying a UAS transgene encoding TRPM8, a cold-sensitive ion channel. Low temperatures opened the TRPM8 channel in Gal4-expressing cells, leading to their excitation, and in many cases induced overt behavioral changes in adult flies. Paralysis was reproducibly observed in the progeny of crosses with 84 lines, whereas more specific behaviors were induced with 24 other lines. Stimulation performed using the heat-activated channel, TrpA1, resulted in clearer and more robust behaviors, including flight, feeding, and egg-laying. Through follow-up studies starting from this screen, we expect to find key components of the neural circuits underlying specific behaviors, thus providing a new avenue for their functional analysis.

Rapid activity-dependent modifications in synaptic structure and function require bidirectional Wnt signaling.

Activity-dependent modifications in synapse structure play a key role in synaptic development and plasticity, but the signaling mechanisms involved are poorly understood. We demonstrate that glutamatergic Drosophila neuromuscular junctions undergo rapid changes in synaptic structure and function in response to patterned stimulation. These changes, which depend on transcription and translation, include formation of motile presynaptic filopodia, elaboration of undifferentiated varicosities, and potentiation of spontaneous release frequency. Experiments indicate that a bidirectional Wnt/Wg signaling pathway underlies these changes. Evoked activity induces Wnt1/Wg release from synaptic boutons, which stimulates both a postsynaptic DFz2 nuclear import pathway as well as a presynaptic pathway involving GSK-3beta/Shaggy. Our findings suggest that bidirectional Wg signaling operates downstream of synaptic activity to induce modifications in synaptic structure and function. We propose that activation of the postsynaptic Wg pathway is required for the assembly of the postsynaptic apparatus, while activation of the presynaptic Wg pathway regulates cytoskeletal dynamics.

Nuclear trafficking of Drosophila Frizzled-2 during synapse development requires the PDZ protein dGRIP.

The Wingless pathway plays an essential role during synapse development. Recent studies at Drosophila glutamatergic synapses suggest that Wingless is secreted by motor neuron terminals and binds to postsynaptic Drosophila Frizzled-2 (DFz2) receptors. DFz2 is, in turn, endocytosed and transported to the muscle perinuclear area, where it is cleaved, and the C-terminal fragment is imported into the nucleus, presumably to regulate transcription during synapse growth. Alterations in this pathway interfere with the formation of new synaptic boutons and lead to aberrant synaptic structures. Here, we show that the 7 PDZ protein dGRIP is necessary for the trafficking of DFz2 to the nucleus. dGRIP is localized to Golgi and trafficking vesicles, and dgrip mutants mimic the synaptic phenotypes observed in wg and dfz2 mutants. DFz2 and dGRIP colocalize in trafficking vesicles, and a severe decrease in dGRIP levels prevents the transport of endocytosed DFz2 receptors to the nucleus. Moreover, coimmunoprecipitation experiments in transfected cells and yeast two-hybrid assays suggest that the C terminus of DFz2 interacts directly with the PDZ domains 4 and 5. These results provide a mechanism by which DFz2 is transported from the postsynaptic membrane to the postsynaptic nucleus during synapse formation and implicate dGRIP as an essential molecule in the transport of this signal.

The Drosophila Wnt, wingless, provides an essential signal for pre- and postsynaptic differentiation.

At vertebrate neuromuscular junctions (NMJs), Agrin plays pivotal roles in synapse development, but molecules that activate synapse formation at central synapses are largely unknown. Members of the Wnt family are well established as morphogens, yet recently they have also been implicated in synapse maturation. Here we demonstrate that the Drosophila Wnt, Wingless (Wg), is essential for synapse development. We show that Wg and its receptor are expressed at glutamatergic NMJs, and that Wg is secreted by synaptic boutons. Loss of Wg leads to dramatic reductions in target-dependent synapse formation, and new boutons either fail to develop active zones and postsynaptic specializations or these are strikingly aberrant. We suggest that Wg signals the coordinated development of pre- and postsynaptic compartments.