Diversity and inclusion in digital scholarship and pedagogy: the case of The Programming Historian

This article presents several inclusion and diversity policies and strategies for digital scholarship and pedagogy, using The Programming Historian as a case study. By actively supporting and working towards gender diversity, as well as multilingualism, cultural inclusivity and open access, The Programming Historian aims to further enhance what is meant to be open in the context of access, diversity and inclusion in digital scholarship and pedagogy

Evaluation of the interactions between human serum albumin (HSA) and warfarin or diflunisal by using molecular fluorescence using two approaches

Serum albumin is the main drug transporter of the bloodstream and contains two main binding sites: Sudlow I or acidic drug binding site, and Sudlow II or benzodiazepine binding site. Warfarin, a well-known anticoagulant drug commonly used in the prevention of thrombosis and thromboembolism, binds to Sudlow I site, whereas non-steroidal antiinflammatory drugs (NSAIDs) such as diflunisal bind preferentially to Sudlow II site. Albumin is a fluorophore that modifies its fluorescence (quenching or enhancement effect) when it is bound to a drug. The application of the double logarithm Stern-Volmer equation allows the calculation of the stoichiometry and the binding constant of the process. This procedure does not consider the possible interferences coming from the fluorescence of the drug though. Another strategy to evaluate the binding constants is to consider the whole spectrum, taking into account all the possible species in equilibrium; in this case we have used an extended version of the STAR program, which can deal with 300 spectra, each containing up to 300 data points. The aim of this work is to compare both approaches to evaluate the interaction between warfarin (Sudlow I) and diflunisal (Sudlow II) and HSA: the double logarithm Stern-Volmer equation and the STAR program

Diferències morfomètriques i merístiques entre l'orada cultivada i salvatge

Gilthead seabream is of high commercíal interest and has become an important aquacultural resource in the Mediterranean countries. Now, the aim of improving the quality of reared products in order to meet markets preferences of conformity with wild standards is a new priority, The aim of this study is the use of morphometrics and meristics for the quantification of the differences in quality assessment and on their causative factors between and within sea bream reared in different fish farms and wild standards. Reared S.auratus show higher body depth, caudal peduncle depth, last dorsal spine, anal fin rays number and position of first anal spine respect to dorsal, and lower head depth, snout length, preorbital length, predorsal length, dorsal fin base, pectoral fin length, ventral fin length, caudal peduncle length, scales berween lateral line and dorsal, pectoral fin rays number and largest dorsal fin spine than wild sea bream. Apart of this measures, Cupimar hatchery facility has fish with lower head length, interorbital length and distance between pelvic and pectoral fins than wild sea bream; Maresa hatchery físhes have lower anal fin base and higher head length than wild standards, Blanes Peix sea cages show lower head length, orbital diameter and interorbital length than wild standards; and Aquadelt fishes show lower head length, orbital diameter, interorbital length, distance berween pelvic and pectoral fins and preanal length than wild sea bream and a non significant difference in last dorsal spine

The 4q25 variant rs13143308T links risk of atrial fibrillation to defective calcium homoeostasis

Aims: Single nucleotide polymorphisms on chromosome 4q25 have been associated with risk of atrial fibrillation (AF) but the exiguous knowledge of the mechanistic links between these risk variants and underlying electrophysiological alterations hampers their clinical utility. Here, we tested the hypothesis that 4q25 risk variants cause alterations in the intracellular calcium homoeostasis that predispose to spontaneous electrical activity. Methods and results: Western blotting, confocal calcium imaging, and patch-clamp techniques were used to identify mechanisms linking the 4q25 risk variants rs2200733T and rs13143308T to defects in the calcium homoeostasis in human atrial myocytes. Our findings revealed that the rs13143308T variant was more frequent in patients with AF and that myocytes from carriers of this variant had a significantly higher density of calcium sparks (14.1¿±¿4.5 vs. 3.1¿±¿1.3 events/min, P¿=¿0.02), frequency of transient inward currents (ITI) (1.33¿±¿0.24 vs. 0.26¿±¿0.09 events/min, P¿<¿0.001) and incidence of spontaneous membrane depolarizations (1.22¿±¿0.26 vs. 0.56¿±¿0.17 events/min, P¿=¿0.001) than myocytes from patients with the normal rs13143308G variant. These alterations were linked to higher sarcoplasmic reticulum calcium loading (10.2¿±¿1.4 vs. 7.3¿±¿0.5¿amol/pF, P¿=¿0.01), SERCA2 expression (1.37¿±¿0.13 fold, P¿=¿0.03), and RyR2 phosphorylation at ser2808 (0.67¿±¿0.08 vs. 0.47¿±¿0.03, P¿=¿0.01) but not at ser2814 (0.28¿±¿0.14 vs. 0.31¿±¿0.14, P¿=¿0.61) in patients carrying the rs13143308T risk variant. Furthermore, the presence of a risk variant or AF independently increased the ITI frequency and the increase in the ITI frequency observed in carriers of the risk variants was exacerbated in those with AF. By contrast, the presence of a risk variant did not affect the amplitude or properties of the L-type calcium current in patients with or without AF. Conclusions: Here, we identify the 4q25 variant rs13143308T as a genetic risk marker for AF, specifically associated with excessive calcium release and spontaneous electrical activity linked to increased SERCA2 expression and RyR2 phosphorylation.Peer ReviewedPostprint (author's final draft

Evaluation of the interactions between Human Serum Albumin (HSA) and Non‐Steroidal Anti‐Inflammatory (NSAIDs) drugs by multiwavelength molecular fluorescence, structural and computational analysis

The interaction between drugs and transport proteins, such as albumins, is a key factor in drug bioavailability. One of the techniques commonly used for the evaluation of the drug‐protein complex formation is fluorescence. This work studies the interaction of human serum albumin (HSA) with four non‐steroidal anti‐inflammatory drugs (NSAIDs) (ibuprofen, flurbiprofen, naproxen, and diflunisal) by monitoring the fluorescence quenching when the drug‐albumin complex is formed. Two approaches - the double logarithm Stern‐Volmer equation and the STAR program - are used to evaluate the binding parameters. The results are analyzed considering the bind‐ ing properties, determined by using other complementary techniques and the available structural information of albumin complexes with NSAID‐related compounds. Finally, this combined analysis has been synergistically used to interpret the binding of flurbiprofen to HSA

Cardiac electrical defects in progeroid mice and Hutchinson-Gilford progeria syndrome patients with nuclear lamina alterations

Hutchinson–Gilford progeria syndrome (HGPS) is a rare genetic disease caused by defective prelamin A processing, leading to nuclear lamina alterations, severe cardiovascular pathology, and premature death. Prelamin A alterations also occur in physiological aging. It remains unknown how defective prelamin A processing affects the cardiac rhythm. We show age-dependent cardiac repolarization abnormalities in HGPS patients that are also present in the Zmpste24-/- mouse model of HGPS. Challenge of Zmpste24-/- mice with the ß-adrenergic agonist isoproterenol did not trigger ventricular arrhythmia but caused bradycardia-related premature ventricular complexes and slow-rate polymorphic ventricular rhythms during recovery. Patch-clamping in Zmpste24-/- cardiomyocytes revealed prolonged calcium-transient duration and reduced sarcoplasmic reticulum calcium loading and release, consistent with the absence of isoproterenol-induced ventricular arrhythmia. Zmpste24-/- progeroid mice also developed severe fibrosis-unrelated bradycardia and PQ interval and QRS complex prolongation. These conduction defects were accompanied by overt mislocalization of the gap junction protein connexin43 (Cx43). Remarkably, Cx43 mislocalization was also evident in autopsied left ventricle tissue from HGPS patients, suggesting intercellular connectivity alterations at late stages of the disease. The similarities between HGPS patients and progeroid mice reported here strongly suggest that defective cardiac repolarization and cardiomyocyte connectivity are important abnormalities in the HGPS pathogenesis that increase the risk of arrhythmia and premature death.Peer ReviewedPostprint (published version

Clinical, Molecular and Genetic Characteristics of Early Onset Gastric Cancer: Analysis of a Large Multicenter Study

Gastric adenocarcinoma (GC) is a common tumor with high morbidity and mortality. Only 7% of patients with GC are diagnosed before age 50 (early onset gastric cancer (EOGC)), and their characteristics have been poorly described. We aimed to describe clinical, molecular, and genetic characteristics of EOGC. A total of 309 patients with EOGC were retrospectively studied in four Spanish centers. Personal information, family history, and tumor information were registered. Germinal genetic analysis was performed in patients who met current criteria of a hereditary syndrome at the time of diagnosis. The median age at diagnosis was 44 years. The majority (73.3%) of tumors were diffuse, and 78.3% were diagnosed in an advanced stage. Familial aggregation of GC was present in 18/117 (15.4%) cases, and 5/117 (4.3%) met criteria for familial GC. MMR-IHC was performed in 126/309 (40.7%) tumors: 4/126 (3.1%) had loss of expression in MLH1/PMS2, without an associated germline mutation. Sixteen germline genetic analyses were performed, detecting a pathogenic variant in four (25%) cases: one in BRCA2, one in TP53, and two in CDH1. Most EOGC are diffuse and diagnosed in an advanced stage. In these patients, DNA MMR system deficiency is uncommon. Although familial aggregation was observed in only 15% of cases, a germline mutation was found in 25% of patients tested with clinical criteria. This demonstrates that EOGC has a marked genetic heterogeneity, reinforcing the importance of an accurate genetic counseling and enhancing the emerging use of multigene panels

Hàbitat en cova i espai pels ramats ca.6200-6000 BP:La Cova Colomera (Prepirineu de Lleida) durant el Neolític Antic.

En aquest treball es presenten les dades referents a la Cova Colomera (Sant Esteve de la Sarga, Pallars Jussà) durant el Neolític cardial final. A partir de diferents sondejos duts a terme des de l'any 2005, s'ha pogut observar la varietat d'usos i funcionalitats del jaciment en moments potencialment sincrònics. Per una banda,una zona on predominen les estructures de caire domètic (fogars, fosses i forats de pal)que ens mostren les dades entorn a l'hàbitat al jaciment; i per altra banda, un gran sector de la cavitat dedicat a l'estabulació dels ramats amb sediments de tipus fumier i probablement també a l'emmagatzematge. Tot això succeix en unes datacions d'entre 6180 +/- 40 i 6020 +/- 510BP. Aquestes dades es contextualitzen amb les d'altres jaciments de la zona pirinenca, un àmbit que sempre ha estat definit en la bibliografia com un espai de pas entre diferents biòtops ecològics, de les plantes fèrtils a les pastures de l'estiu

ß2-adrenergic stimulation potentiates spontaneous calcium release by increasing signal mass and co-activation of ryanodine receptor clusters

Aims: It is unknown how ß-adrenergic stimulation affects calcium dynamics in individual RyR2 clusters and leads to the induction of spontaneous calcium waves. To address this, we analysed spontaneous calcium release events in green fluorescent protein (GFP)-tagged RyR2 clusters. Methods: Cardiomyocytes from mice with GFP-tagged RyR2 or human right atrial tissue were subjected to immunofluorescent labelling or confocal calcium imaging. Results: Spontaneous calcium release from single RyR2 clusters induced 91.4% ± 2.0% of all calcium sparks while 8.0% ± 1.6% were caused by release from two neighbouring clusters. Sparks with two RyR2 clusters had 40% bigger amplitude, were 26% wider, and lasted 35% longer at half maximum. Consequently, the spark mass was larger in two- than one-cluster sparks with a median and interquartile range for the cumulative distribution of 15.7 ± 20.1 vs 7.6 ± 5.7 a.u. (P < .01). ß2-adrenergic stimulation increased RyR2 phosphorylation at s2809 and s2815, tripled the fraction of two- and three-cluster sparks, and significantly increased the spark mass. Interestingly, the amplitude and mass of the calcium released from a RyR2 cluster were proportional to the SR calcium load, but the firing rate was not. The spark mass was also higher in 33 patients with atrial fibrillation than in 36 without (22.9 ± 23.4 a.u. vs 10.7 ± 10.9; P = .015). Conclusions: Most sparks are caused by activation of a single RyR2 cluster at baseline while ß-adrenergic stimulation doubles the mass and the number of clusters per spark. This mimics the shift in the cumulative spark mass distribution observed in myocytes from patients with atrial fibrillation. Keywords: calcium spark; cardiac myocyte; confocal imaging; ryanodine receptor; sarcoplasmic reticulum; ß-adrenergic.This work was supported by grants from the Spanish Ministry of Science and Innovation PID2020-116927RB-C21 and SAF2017-88019-C3-1R (to LHM) and SAF2017-88019-C3-3R (to RB); from Fundació Marató TV3, Marato-2015-2030 (to LHM); from Generalitat de Catalunya SGR2017-1769 (to LHM); from the Natural Sciences and Engineering Research Council of Canada (to SRWC); from the Canadian Institutes of Health Research (to SRWC); from the Heart and Stroke Foundation Chair in Cardiovascular Research (to SRWC), and from Spanish Ministry of Health and Consume CB16/11/00276 (to JC). SC was the recipient of a predoctoral grant (FPU18/01250) from the Spanish Ministry of Science and Innovation, and AL received a PERIS SALUT-16 grant from Generalitat de Catalunya

Pharmacological and optical activation of TrkB in Parvalbumin interneurons regulate intrinsic states to orchestrate cortical plasticity

Elevated states of brain plasticity typical for critical periods of early postnatal life can be reinstated in the adult brain through interventions, such as antidepressant treatment and environmental enrichment, and induced plasticity may be critical for the antidepressant action. Parvalbumin-positive (PV) interneurons regulate the closure of developmental critical periods and can alternate between high and low plasticity states in response to experience in adulthood. We now show that PV plasticity states and cortical networks are regulated through the activation of TrkB neurotrophin receptors. Visual cortical plasticity induced by fluoxetine, a widely prescribed selective serotonin reuptake inhibitor (SSRI) antidepressant, was lost in mice with reduced expression of TrkB in PV interneurons. Conversely, optogenetic gain-of-function studies revealed that activation of an optically activatable TrkB (optoTrkB) specifically in PV interneurons switches adult cortical networks into a state of elevated plasticity within minutes by decreasing the intrinsic excitability of PV interneurons, recapitulating the effects of fluoxetine. TrkB activation shifted cortical networks towards a low PV configuration, promoting oscillatory synchrony, increased excitatory-inhibitory balance, and ocular dominance plasticity. OptoTrkB activation promotes the phosphorylation of Kv3.1 channels and reduces the expression of Kv3.2 mRNA providing a mechanism for the lower excitability. In addition, decreased expression and puncta of Synaptotagmin2 (Syt2), a presynaptic marker of PV interneurons involved in Ca2+-dependent neurotransmitter release, suggests lower inputs onto pyramidal neurons suppressing feed-forward inhibition. Together, the results provide mechanistic insights into how TrkB activation in PV interneurons orchestrates the activity of cortical networks and mediating antidepressant responses in the adult brain.Peer reviewe