Automatic Neuron Detection in Calcium Imaging Data Using Convolutional Networks

Calcium imaging is an important technique for monitoring the activity of thousands of neurons simultaneously. As calcium imaging datasets grow in size, automated detection of individual neurons is becoming important. Here we apply a supervised learning approach to this problem and show that convolutional networks can achieve near-human accuracy and superhuman speed. Accuracy is superior to the popular PCA/ICA method based on precision and recall relative to ground truth annotation by a human expert. These results suggest that convolutional networks are an efficient and flexible tool for the analysis of large-scale calcium imaging data.Comment: 9 pages, 5 figures, 2 ancillary files; minor changes for camera-ready version. appears in Advances in Neural Information Processing Systems 29 (NIPS 2016

Transformation of stimulus correlations by the retina

Redundancies and correlations in the responses of sensory neurons seem to waste neural resources but can carry cues about structured stimuli and may help the brain to correct for response errors. To assess how the retina negotiates this tradeoff, we measured simultaneous responses from populations of ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure. We found that pairwise correlations in the retinal output remained similar across stimuli with widely different spatio-temporal correlations including white noise and natural movies. Meanwhile, purely spatial correlations tended to increase correlations in the retinal response. Responding to more correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the similarity of pairwise correlations across stimuli where receptive field measurements were possible.Comment: author list corrected in metadat

Indigenous knowledges and development: a postcolonial caution

As a result of the failure of formal top-down development, there has recently been increased interest in the possibilities of drawing upon the indigenous knowledges of those in the communities involved, in an attempt to produce more effective development strategies. The concept of indigenous knowledge calls for the inclusion of local voices and priorities, and promises empowerment through ownership of the process. However, there has been little critical examination of the ways in which indigenous knowledges have been included in the development process. Drawing upon postcolonial theory, this article suggests that indigenous knowledges are often drawn into development by both theorists and development institutions in a very limited way, failing to engage with other ways of perceiving development, and thus missing the possibility of devising more challenging alternatives

Explicit kinetic heterogeneity: mechanistic models for interpretation of labeling data of heterogeneous cell populations

Estimation of division and death rates of lymphocytes in different conditions is vital for quantitative understanding of the immune system. Deuterium, in the form of deuterated glucose or heavy water, can be used to measure rates of proliferation and death of lymphocytes in vivo. Inferring these rates from labeling and delabeling curves has been subject to considerable debate with different groups suggesting different mathematical models for that purpose. We show that the three models that are most commonly used are in fact mathematically identical and differ only in their interpretation of the estimated parameters. By extending these previous models, we here propose a more mechanistic approach for the analysis of data from deuterium labeling experiments. We construct a model of "kinetic heterogeneity" in which the total cell population consists of many sub-populations with different rates of cell turnover. In this model, for a given distribution of the rates of turnover, the predicted fraction of labeled DNA accumulated and lost can be calculated. Our model reproduces several previously made experimental observations, such as a negative correlation between the length of the labeling period and the rate at which labeled DNA is lost after label cessation. We demonstrate the reliability of the new explicit kinetic heterogeneity model by applying it to artificially generated datasets, and illustrate its usefulness by fitting experimental data. In contrast to previous models, the explicit kinetic heterogeneity model 1) provides a mechanistic way of interpreting labeling data; 2) allows for a non-exponential loss of labeled cells during delabeling, and 3) can be used to describe data with variable labeling length

Small-scale solar magnetic fields

As we resolve ever smaller structures in the solar atmosphere, it has become clear that magnetism is an important component of those small structures. Small-scale magnetism holds the key to many poorly understood facets of solar magnetism on all scales, such as the existence of a local dynamo, chromospheric heating, and flux emergence, to name a few. Here, we review our knowledge of small-scale photospheric fields, with particular emphasis on quiet-sun field, and discuss the implications of several results obtained recently using new instruments, as well as future prospects in this field of research.Comment: 43 pages, 18 figure

Liposomes: a new non-pharmacological therapy concept for seasonal-allergic-rhinoconjunctivitis

Mucosal barrier disorders play an important role in the pathomechanism of the allergic disease. A new approach for their treatment uses liposomes, which consist of phospholipids that make up 75% of the protective nasal surfactant layer. Our aim was to investigate the efficacy of liposomal-based therapy, as a comprehensive treatment alternative to guideline cromoglycate-based therapy, in the treatment of seasonal allergic rhinoconjunctivitis (SAR). We compared nasal and conjunctival symptom reduction with LipoNasal n nasal spray used as monotherapy (LNM), or LipoNasal n nasal spray and Tears Again eye spray combination therapy (LTC), against standard cromoglycate combination therapy (CGC). This prospective, controlled, open observational study was conducted monocentrically. According to their symptoms and preferences 72 patients with SAR were distributed in three equal groups. The study comprised two visits at an interval of 7 days. The efficacy was examined by daily documenting nasal and conjunctival symptom scores. The Nasal-Spray-Sensory-Scale and the Eye-Drops/Spray-Sensory-Scale were used to investigate the tolerability. Quality of life (QoL) was evaluated, using the RHINASTHMA QoL German adapted version. LNM achieved significant improvement in nasal (p < 0.001) and conjunctival symptoms (p = 0.050). The symptom reduction using CGC was equally significant. LTC led to significant nasal symptom relief (p = 0.045). QoL did not improve significantly in all groups (p > 0.05). The tolerability of all treatments was good and no adverse reactions were observed. In all treatment groups the improvement of the nasal and conjunctival symptom scores exceeds the minimal clinically important difference (MCID). The results demonstrate good tolerability and efficacy of non-pharmaceutical liposomal-based treatment (LipoNasal n and Tears Again), given as monotherapy or combination therapy, for nasal and conjunctival symptoms caused by SAR. This study indicates that liposomal-based treatment for SAR may be a comparable alternative to cromoglycate therapy. Further studies are needed to verify these findings

Patient-specific RF safety assessment in MRI: Progress in creating surface-based human head and shoulder models

The interaction of electromagnetic (EM) fields with the human body during magnetic resonance imaging (MRI) is complex and subject specific. MRI radiofrequency (RF) coil performance and safety assessment typically includes numerical EM simulations with a set of human body models. The dimensions of mesh elements used for discretization of the EM simulation domain must be adequate for correct representation of the MRI coil elements, different types of human tissue, and wires and electrodes of additional devices. Examples of such devices include those used during electroencephalography, transcranial magnetic stimulation, and transcranial direct current stimulation, which record complementary information or manipulate brain states during MRI measurement. The electrical contact within and between tissues, as well as between an electrode and the skin, must also be preserved. These requirements can be fulfilled with anatomically correct surface-based human models and EM solvers based on unstructured meshes. Here, we report (i) our workflow used to generate the surface meshes of a head and torso model from the segmented AustinMan dataset, (ii) head and torso model mesh optimization for three-dimensional EM simulation in ANSYS HFSS, and (iii) several case studies of MRI RF coil performance and safety assessment

Aphrati and Kato Syme: Pottery, Continuity, and Cult in Late Archaic and Classical Crete

The analysis of ceramics from Aphrati sheds valuable new light on the history of this Cretan settlement and on its relationship with a nearby rural sanctuary at Kato Syme in the Late Archaic and Classical periods. It has long been held that Aphrati was deserted from ca. 600 to 400 B.C. A pottery deposit from the domestic quarter, however, now supports occupation of the city during this period. A ceramic classification system is presented and the morphological development and absolute chronology of several key shapes at Aphrati and Kato Syme are plotted. Historical implications of the ceramic evidence are also explored

Universal intermittent properties of particle trajectories in highly turbulent flows

We present a collection of eight data sets, from state-of-the-art experiments and numerical simulations on turbulent velocity statistics along particle trajectories obtained in different flows with Reynolds numbers in the range $R_\lambda \in [120:740]$. Lagrangian structure functions from all data sets are found to collapse onto each other on a wide range of time lags, revealing a universal statistics, and calling for a unified theoretical description. Parisi-Frisch Multifractal theory, suitable extended to the dissipative scales and to the Lagrangian domain, is found to capture intermittency of velocity statistics over the whole three decades of temporal scales here investigated.Comment: 5 pages, 1 figure; content changed, references update

Effect of Neoadjuvant Chemotherapy Followed by Surgical Resection on Survival in Patients With Limited Metastatic Gastric or Gastroesophageal Junction Cancer: The AIO-FLOT3 Trial

IMPORTANCE: Surgical resection has a potential benefit for patients with metastatic adenocarcinoma of the stomach and gastroesophageal junction. OBJECTIVE: To evaluate outcome in patients with limited metastatic disease who receive chemotherapy first and proceed to surgical resection. DESIGN, SETTING, AND PARTICIPANTS: The AIO-FLOT3 (Arbeitsgemeinschaft Internistische Onkologie-fluorouracil, leucovorin, oxaliplatin, and docetaxel) trial is a prospective, phase 2 trial of 252 patients with resectable or metastatic gastric or gastroesophageal junction adenocarcinoma. Patients were enrolled from 52 cancer care centers in Germany between February 1, 2009, and January 31, 2010, and stratified to 1 of 3 groups: resectable (arm A), limited metastatic (arm B), or extensive metastatic (arm C). Data cutoff was January 2012, and the analysis was performed in March 2013. INTERVENTIONS: Patients in arm A received 4 preoperative cycles of fluorouracil, leucovorin, oxaliplatin, and docetaxel (FLOT) followed by surgery and 4 postoperative cycles. Patients in arm B received at least 4 cycles of neoadjuvant FLOT and proceeded to surgical resection if restaging (using computed tomography and magnetic resonance imaging) showed a chance of margin-free (R0) resection of the primary tumor and at least a macroscopic complete resection of the metastatic lesions. Patients in arm C were offered FLOT chemotherapy and surgery only if required for palliation. Patients received a median (range) of 8 (1-15) cycles of FLOT. MAIN OUTCOMES AND MEASURES: The primary end point was overall survival. RESULTS: In total, 238 of 252 patients (94.4%) were eligible to participate. The median (range) age of participants was 66 (36-79) years in arm A (n = 51), 63 (28-79) years in arm B (n = 60), and 65 (23-83) years in arm C (n = 127). Patients in arm B (n = 60) had only retroperitoneal lymph node involvement (27 patients [45%]), liver involvement (11 [18.3%]), lung involvement (10 [16.7%]), localized peritoneal involvement (4 [6.7%]), or other (8 [13.3%]) incurable sites. Median overall survival was 22.9 months (95% CI, 16.5 to upper level not achieved) for arm B, compared with 10.7 months (95% CI, 9.1-12.8) for arm C (hazard ratio, 0.37; 95% CI, 0.25-0.55) (P < .001). The response rate for arm B was 60% (complete, 10%; partial, 50%), which is higher than the 43.3% for arm C. In arm B, 36 of 60 patients (60%) proceeded to surgery. The median overall survival was 31.3 months (95% CI, 18.9-upper level not achieved) for patients who proceeded to surgery and 15.9 months (95% CI, 7.1-22.9) for the other patients. CONCLUSIONS AND RELEVANCE: Patients with limited metastatic disease who received neoadjuvant chemotherapy and proceeded to surgery showed a favorable survival. The AIO-FLOT3 trial provides a rationale for further randomized clinical trials. TRIAL REGISTRATION: clinicaltrials.gov identifier: NCT00849615.info:eu-repo/semantics/publishedVersio