An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics

The development of new imaging and optogenetics techniques to study the dynamics of large neuronal circuits is generating datasets of unprecedented volume and complexity, demanding the development of appropriate analysis tools. We present a comprehensive computational workflow for the analysis of neuronal population calcium dynamics. The toolbox includes newly developed algorithms and interactive tools for image pre-processing and segmentation, estimation of significant single-neuron single-trial signals, mapping event-related neuronal responses, detection of activity-correlated neuronal clusters, exploration of population dynamics, and analysis of clusters' features against surrogate control datasets. The modules are integrated in a modular and versatile processing pipeline, adaptable to different needs. The clustering module is capable of detecting flexible, dynamically activated neuronal assemblies, consistent with the distributed population coding of the brain. We demonstrate the suitability of the toolbox for a variety of calcium imaging datasets. The toolbox open-source code, a step-by-step tutorial and a case study dataset are available at https://github.com/zebrain-lab/Toolbox-Romano-et-al

Arqueología del genocidio en Tucumán: Biografías, inhumaciones, espacios concentracionarios y cartografías

Los trabajos forenses realizados por el Colectivo de Arqueología, Memoria e Identidad de Tucumán (CAMIT), en el marco de causas judiciales, posibilitaron tanto recuperar e identificar nominalmente a 113 personas en el denominado “Pozo de Vargas” como así también contribuir con pruebas referidas a la dinámica del Centro de Exterminio que funcionó en el predio militar Compañía de Arsenales Miguel de Azcuénaga. Estas investigaciones pusieron en manifiesto las estrechas relaciones entre una diversidad de lugares que fueron integrados a la política de exterminio diseñada por las fuerzas de seguridad y armadas durante el período comprendido entre los años 1975 y 1983. En efecto, no es posible dimensionar las características que asumió el genocidio a escala provincial si no se vinculan materialidades y testimonios y que viabilizan -conjuntamente- dar cuenta de la complejidad de la persecución, represión y exterminio de una importante fracción social. Durante los últimos años desde el equipo nos abocamos a determinar las biografías de cada uno/a de los/las hombres y mujeres recuperados/as en el Pozo de Vargas, para ello centramos la atención en: la información disponible en cada caso (ampliándola con nuevas indagaciones –entrevistas, relevamiento en distintos archivos, etc.–, reevaluación de la información disponible, etc.); definir grupos hacia el interior del universo de identificados hasta el momento en dicha inhumación clandestina (los grupos fueron delimitados considerando distintas variables tales como: militancias sociales y políticas; trabajo y ocupación; etc.); y, evaluando la información disponible sobre los lugares donde atravesaron sus experiencias concentracionarias (en Tucumán y en otras provincias). Como resultado preliminar –en esta primera etapa del trabajo prestamos mayor atención a la capital tucumana y al período comprendido entre 1975 y 1978- contamos actualmente con mayor información referida a las trayectorias de las personas: desde sus secuestros -y los distintos espacios de reclusión clandestinos por los que transitaron- hasta sus asesinatos y ocultamiento de los cuerpos en el Pozo de Vargas. Asimismo, tales itinerarios fueron incorporados a cartografías personales y colectivas que posibilitan evaluar, por ejemplo, aquellos aspectos de logística y diseño de circuitos a los fines de efectivizar el exterminio. Tales cartografías, además, destacan una diversidad de espacios –entre privados y públicos– involucrados a los fines de llevar a cabo una matanza como la perpetrada en la provincia de Tucumán. Toda esta información posibilita dimensionar las características que asumió el genocidio a una escala local.Fil: Ataliva, Víctor Hugo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto Superior de Estudios Sociales. Universidad Nacional de Tucumán. Instituto Superior de Estudios Sociales; Argentina. Colectivo de Arqueología Memoria E Identidad de Tucumán; ArgentinaFil: Gerónimo, A.. Colectivo de Arqueología, Memoria e Identidad de Tucumán; ArgentinaFil: Huetagoyena Gutiérrez, G.. Colectivo de Arqueología, Memoria e Identidad de Tucumán; ArgentinaFil: Zurita, R. D.. Colectivo de Arqueología, Memoria e Identidad de Tucumán; ArgentinaFil: Cano, S.. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo. Instituto Interdisciplinario de Estudios Andinos; Argentina. Colectivo de Arqueología, Memoria e Identidad de Tucumán; ArgentinaFil: Molina, L. R.. Colectivo de Arqueología, Memoria e Identidad de Tucumán; ArgentinaFil: Romano, Andres Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto Superior de Estudios Sociales. Universidad Nacional de Tucumán. Instituto Superior de Estudios Sociales; Argentina. Colectivo de Arqueología, Memoria e Identidad de Tucumán; ArgentinaFil: Srur, Florencia Rocío. Colectivo de Arqueología, Memoria e Identidad de Tucumán; ArgentinaFil: Lund, Julia. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo. Instituto de Arqueología y Museo; Argentina. Colectivo de Arqueología, Memoria e Identidad de Tucumán; ArgentinaFil: Leiva, A.. Colectivo de Arqueología, Memoria e Identidad de Tucumán; ArgentinaXIV Jornadas Internas de Comunicaciones en Investigación, Docencia y ExtensiónSan Miguel de TucumánArgentinaUniversidad Nacional de Tucumán. Facultad de Ciencias Naturales. Instituto Miguel Lill

Barred Galaxies in the Abell 901/2 Supercluster with STAGES

We present a study of bar and host disk evolution in a dense cluster environment, based on a sample of ~800 bright (MV <= -18) galaxies in the Abell 901/2 supercluster at z~0.165. We use HST ACS F606W imaging from the STAGES survey, and data from Spitzer, XMM-Newton, and COMBO-17. We identify and characterize bars through ellipse-fitting, and other morphological features through visual classification. (1) We explore three commonly used methods for selecting disk galaxies. We find 625, 485, and 353 disk galaxies, respectively, via visual classification, a single component S'ersic cut (n <= 2.5), and a blue-cloud cut. In cluster environments, the latter two methods miss 31% and 51%, respectively, of visually-identified disks. (2) For moderately inclined disks, the three methods of disk selection yield a similar global optical bar fraction (f_bar-opt) of 34% +10%/-3%, 31% +10%/-3%, and 30% +10%/-3%, respectively. (3) f_bar-opt rises in brighter galaxies and those which appear to have no significant bulge component. Within a given absolute magnitude bin, f_bar-opt is higher in visually-selected disk galaxies that have no bulge as opposed to those with bulges. For a given morphological class, f_bar-opt rises at higher luminosities. (4) For bright early-types, as well as faint late-type systems with no evident bulge, the optical bar fraction in the Abell 901/2 clusters is comparable within a factor of 1.1 to 1.4 to that of field galaxies at lower redshifts (5) Between the core and the virial radius of the cluster at intermediate environmental densities, the optical bar fraction does not appear to depend strongly on the local environment density and varies at most by a factor of ~1.3. We discuss the implications of our results for the evolution of bars and disks in dense environments.Comment: accepted for publication in ApJ, abstract abridged, for high resolution figures see http://www.as.utexas.edu/~marinova/STAGES/STAGES_bars.pd

Molecular control of sucrose utilization in Escherichia coli W, an efficient sucrose-utilizing strain

Sucrose is an industrially important carbon source for microbial fermentation. Sucrose utilization in Escherichia coli, however, is poorly understood, and most industrial strains cannot utilize sucrose. The roles of the chromosomally encoded sucrose catabolism (csc) genes in E. coli W were examined by knockout and overexpression experiments. At low sucrose concentrations, the csc genes are repressed and cells cannot grow. Removal of either the repressor protein (cscR) or the fructokinase (cscK) gene facilitated derepression. Furthermore, combinatorial knockout of cscR and cscK conferred an improved growth rate on low sucrose. The invertase (cscA) and sucrose transporter (cscB) genes are essential for sucrose catabolism in E. coli W, demonstrating that no other genes can provide sucrose transport or inversion activities. However, cscK is not essential for sucrose utilization. Fructose is excreted into the medium by the cscK-knockout strain in the presence of high sucrose, whereas at low sucrose (when carbon availability is limiting), fructose is utilized by the cell. Overexpression of cscA, cscAK, or cscAB could complement the W Delta cscRKAB knockout mutant or confer growth on a K-12 strain which could not naturally utilize sucrose. However, phenotypic stability and relatively good growth rates were observed in the K-12 strain only when overexpressing cscAB, and full growth rate complementation in W Delta cscRKA Balso required cscAB. Our understanding of sucrose utilization can be used to improve E. coli Wand engineer sucrose utilization in strains which do not naturally utilize sucrose, allowing substitution of sucrose for other, less desirable carbon sources in industrial fermentations

Efficient Construction of an Inverted Minimal H1 Promoter Driven siRNA Expression Cassette: Facilitation of Promoter and siRNA Sequence Exchange

RNA interference (RNAi), mediated by small interfering RNA (siRNA), is an effective method used to silence gene expression at the post-transcriptional level. Upon introduction into target cells, siRNAs incorporate into the RNA-induced silencing complex (RISC). The antisense strand of the siRNA duplex then "guides" the RISC to the homologous mRNA, leading to target degradation and gene silencing. In recent years, various vector-based siRNA expression systems have been developed which utilize opposing polymerase III promoters to independently drive expression of the sense and antisense strands of the siRNA duplex from the same template.We show here the use of a ligase chain reaction (LCR) to develop a new vector system called pInv-H1 in which a DNA sequence encoding a specific siRNA is placed between two inverted minimal human H1 promoters (approximately 100 bp each). Expression of functional siRNAs from this construct has led to efficient silencing of both reporter and endogenous genes. Furthermore, the inverted H1 promoter-siRNA expression cassette was used to generate a retrovirus vector capable of transducing and silencing expression of the targeted protein by>80% in target cells.The unique design of this construct allows for the efficient exchange of siRNA sequences by the directional cloning of short oligonucleotides via asymmetric restriction sites. This provides a convenient way to test the functionality of different siRNA sequences. Delivery of the siRNA cassette by retroviral transduction suggests that a single copy of the siRNA expression cassette efficiently knocks down gene expression at the protein level. We note that this vector system can potentially be used to generate a random siRNA library. The flexibility of the ligase chain reaction suggests that additional control elements can easily be introduced into this siRNA expression cassette

Changes in Drug Utilization during a Gap in Insurance Coverage: An Examination of the Medicare Part D Coverage Gap

Jennifer Polinski and colleagues estimated the effect of the "coverage gap" during which US Medicare beneficiaries are fully responsible for drug costs and found that the gap was associated with a doubling in discontinuing essential medications

Effects of hospital facilities on patient outcomes after cancer surgery: an international, prospective, observational study

Background Early death after cancer surgery is higher in low-income and middle-income countries (LMICs) compared with in high-income countries, yet the impact of facility characteristics on early postoperative outcomes is unknown. The aim of this study was to examine the association between hospital infrastructure, resource availability, and processes on early outcomes after cancer surgery worldwide.Methods A multimethods analysis was performed as part of the GlobalSurg 3 study-a multicentre, international, prospective cohort study of patients who had surgery for breast, colorectal, or gastric cancer. The primary outcomes were 30-day mortality and 30-day major complication rates. Potentially beneficial hospital facilities were identified by variable selection to select those associated with 30-day mortality. Adjusted outcomes were determined using generalised estimating equations to account for patient characteristics and country-income group, with population stratification by hospital.Findings Between April 1, 2018, and April 23, 2019, facility-level data were collected for 9685 patients across 238 hospitals in 66 countries (91 hospitals in 20 high-income countries; 57 hospitals in 19 upper-middle-income countries; and 90 hospitals in 27 low-income to lower-middle-income countries). The availability of five hospital facilities was inversely associated with mortality: ultrasound, CT scanner, critical care unit, opioid analgesia, and oncologist. After adjustment for case-mix and country income group, hospitals with three or fewer of these facilities (62 hospitals, 1294 patients) had higher mortality compared with those with four or five (adjusted odds ratio [OR] 3.85 [95% CI 2.58-5.75]; p&lt;0.0001), with excess mortality predominantly explained by a limited capacity to rescue following the development of major complications (63.0% vs 82.7%; OR 0.35 [0.23-0.53]; p&lt;0.0001). Across LMICs, improvements in hospital facilities would prevent one to three deaths for every 100 patients undergoing surgery for cancer.Interpretation Hospitals with higher levels of infrastructure and resources have better outcomes after cancer surgery, independent of country income. Without urgent strengthening of hospital infrastructure and resources, the reductions in cancer-associated mortality associated with improved access will not be realised