julilili42/papers huggingface dataset:
Impact of the antidepressant citalopram on the behaviour of two different life stages of brown trout
2020-03-12

Background Over the last two decades, there has been a constant increase in prescription rates of antidepressants. In parallel, neuroactive pharmaceuticals are making their way into aquatic environments at increasing concentrations. Among the antidepressants detected in the environment citalopram, a selective serotonin reuptake inhibitor, is one of the most commonly found. Given citalopram is specifically designed to alter mood and behaviour in humans, there is growing concern it can adversely affect the behaviour on non-target wildlife Methods In our study, brown trout were exposed to citalopram (nominal concentrations: 1, 10, 100, 1000 μg/L) in two different life stages. Larvae were exposed at 7 and 11 °C from the eyed ova stage until 8 weeks post yolk sac consumption, and juvenile brown trout were exposed for 4 weeks at 7 °C. At both stages we measured mortality, weight, length, tissue citalopram concentration, behaviour during exposure and behaviour in a stressfull environment. For brown trout larvae additionally hatching rate and heart rate, and for juvenile brown trout the tissue cortisol concentration were assessed. Results During the exposure, both larvae and juvenile fish exposed to the highest test concentration of citalopram (1 mg/L) had higher swimming activity and spent longer in the upper part of the aquaria compared to control fish, which is an indicator for decreased anxiety. Most probably due to the higher swimming activity during the exposure, the juveniles and larvae exposed to 1 mg/L citalopram showed decreased weight and length. Additionally, in a stressful artificial swimming measurement device, brown trout larvae displayed the anxiolytic effect of the antidepressant by reduced swimming activity during this stress situation, already at concentrations of 100 μg/L citalopram. Chemical analysis of the tissue revealed rising citalopram tissue concentrations with rising exposure concentrations. Tissue concentrations were 10 times higher in juvenile fish compared to brown trout larvae. Fish plasma concentrations were calculated, which exceeded human therapeutic levels for the highest exposure concentration, matching the behavioural results. Developmental parameters like hatching rate and heart rate, as well as mortality and tissue cortisol content were unaffected by the antidepressant. Overall, we could trace the pharmacological mode of action of the antidepressant citalopram in the non-target organism brown trout in two different life stages.
Eye contact during live social interaction in incarcerated psychopathic offenders.
2020-03-12

Psychopathy is characterized by a lack of empathy, callousness, and a range of severe antisocial behaviors. A deficit to accurately process social cues, which has been widely documented in psychopathic populations, is assumed to underlie their pathological development. Impaired attention to socially salient cues, such as the eyes of an interaction partner, is a possible mechanism compromising the development of social cognition. Preliminary evidence from static facial stimuli suggests that psychopathy is indeed linked to reduced eye gaze. However, no study to date has investigated whether these mechanisms apply to naturalistic interactions. This study is the first to examine patterns of visual attention during live social interactions and their association with symptom clusters of psychopathy. Eye contact was assessed in a sample of incarcerated offenders (<i>N</i> = 30) during semistructured face-to-face interactions with a mobile eye-tracking headset and analyzed using a novel automated areas of interest (e.g., eye region) labeling technique. The interactions included an exchange on neutral predetermined topics and included a condition in which the participants were active (talking) and passive (listening). The data reveal that across both listening and talking conditions higher affective psychopathy is a significant predictor of reduced eye contact (listening: <i>r</i> = -.39; talking: <i>r</i> = -.43). The present findings are in line with previous research suggesting impaired attention to social cues in psychopathy. This study is the first to document these deficits in naturalistic, live social interaction and therefore provides important evidence for their relevance to real-life behavior. (PsycInfo Database Record (c) 2020 APA, all rights reserved).
Elevational gradients of species richness, community structure, and niche occupation of tropical rove beetles (Coleoptera: Staphylinidae: Steninae) across mountain slopes in Northern Thailand
2020-03-12

Abstract We evaluated patterns of species richness, heterogeneity, niche occupation, and community structuring/similarity of staphylinid beetles of the subfamily Steninae across a 2500-m elevational gradient of a tropical mountain area in Northern Thailand. Predaceous Steninae were collected from a variety of habitat types. Increasing Sørensen dissimilarity with increasing elevation was explained by both species turnover (especially across the lower elevational zones) and declining numbers of species (especially across elevations &gt; 1400 m). Unlike the strong decline of the number of species with increasing elevation, species density (i.e., total number of species divided by the number of collection sites at the respective elevational zone) showed a much smoother decline suggesting that the negative gradient in the number of species was superimposed by a land-area effect inherent in mountain shape. In both the litter-inhabiting species and waterfall-associated species, the numbers of species showed a mid-elevational peak. Species frequency was positively correlated to both elevational (“ Dianous ” and Stenus ) and habitat niche width ( Stenus only). Stenus showed high interspecific variety of wide to narrow niche widths for both elevation and habitat. Numbers of Palearctic and Oriental species deviated from statistical expectation, suggesting that climate niche conservatism has played a role in their elevational distribution. The distributional patterns of “ Dianous ” beetles, with their strong hygrobiont preferences associated with rocks in running water and waterfalls, are potentially explained by source–sink dynamics along mountain streams.
Mapping the S1 and S1’ subsites of cysteine proteases with new dipeptidyl nitrile inhibitors as trypanocidal agents
2020-03-12

The cysteine protease cruzipain is considered to be a validated target for therapeutic intervention in the treatment of Chagas disease. A series of 26 new compounds were designed, synthesized, and tested against the recombinant cruzain (Cz) to map its S1/S1 ́ subsites. The same series was evaluated on a panel of four human cysteine proteases (CatB, CatK, CatL, CatS) and Leishmania mexicana CPB, which is a potential target for the treatment of cutaneous leishmaniasis. The synthesized compounds are dipeptidyl nitriles designed based on the most promising combinations of different moieties in P1 (ten), P2 (six), and P3 (four different building blocks). Eight compounds exhibited a Ki smaller than 20.0 nM for Cz, whereas three compounds met these criteria for LmCPB. Three inhibitors had an EC50 value of ca. 4.0 μM, thus being equipotent to benznidazole according to the antitrypanosomal effects. Our mapping approach and the respective structure-activity relationships provide insights into the specific ligand-target interactions for therapeutically relevant cysteine proteases.
Determination of skin penetration profiles by confocal Raman microspectroscopy: Evaluation of interindividual variability and interlab comparability
2020-03-12

Abstract Confocal Raman microspectroscopy is being increasingly used to investigate the skin penetration of actives and excipients. The aim of the present study was to compare results obtained with skin from different donors, acquired with two Raman systems: the RiverD gen2 Skin Composition Analyzer and the WiTec alpha 500 instrument. To elucidate the interindividual variability between the skin donors and to find out whether the two systems would give similar results in skin penetration analysis, we compared the penetration of the model drug procaine from hydrogel formulations with or without the penetration enhancer POE‐23‐lauryl ether. Penetration was investigated with both systems on skin from three different skin donors, each. Penetration plots were prepared by plotting the signal intensity of a typical peak of procaine against the skin depth. We then calculated the enhancement ratio from the areas under the curves of the penetration plots of procaine that had penetrated from the formulation with or without the enhancer. They ranged between 2.0 and 3.1 for the WiTec system and between 2.1 and 3.1 for the RiverD system. Thus, we found that both systems provide similar estimations of the skin penetration of procaine.
Privacy-preserving SVM on Outsourced Genomic Data via Secure Multi-party Computation
2020-03-12

Machine learning methods are employed in many areas, such as medical data research, for their efficient and powerful data mining ability. However, submitting unprotected data to a third party, which attempts to train a machine learning model, may suffer from data leakage and privacy violation when the third party is compromised by an adversary. Hence, designing a protocol to execute encrypted computation is inevitably indispensable. In order to address this problem, we propose protocols based on secure multi-party computation to train a support vector machine model privately. Utilizing the semi-honest adversary model and oblivious transfer, the proposed protocols enable the training of a non-linear support vector machine on the combined data from various sources without sacrificing the privacy of individuals. The protocols are applied to train a support vector machine model with the radial basis function kernel on HIV sequence data to predict the efficacy of a certain antiviral drug, which only works if the viruses can only use the human CCR5 coreceptor for cell entry. Benchmarked on synthesized data with 10 data sources that consist of randomly generated integers, containing 100 labeled samples each, the protocol has consumed online time 2991.386/166.912 ms on average in arithmetic/boolean circuits, respectively. The cross-validation has reached 0.5819 F1-score on average on training data with the optimized parameters, which have reached 0.7058 F1-score afterwards on testing data set, which consists of protein sequence of CCR5 and its subtypes. The complete training and testing process on the real data, which contains in total 766 samples having 924 features after encoding, has consumed 43.75/15.84 seconds on average using arithmetic/boolean circuits, respectively, which shows the effectiveness and efficiency of our protocols compared to some of the existing studies in the literature.
Extracellular Ca2+-sensitive fluorescent protein biosensor based on a collagen-binding domain
2020-03-12

Abstract The importance of extracellular gradients of biomolecules becomes increasingly appreciated in the processes of tissue development and regeneration, in health and disease. In particular, dynamics of extracellular calcium concentration is rarely studied. Here, we present low affinity Ca 2+ biosensor based on Twitch-2B fluorescent protein fused with the cellulose- and collagen-binding peptides. These recombinant chimeric proteins can bind cellulose and collagen scaffolds and enable for scaffold-based biosensing of Ca 2+ in proximity of live 3D tissue models. We found that the Twitch-2B mutant is compatible with intensity-based ratiometric and fluorescence lifetime imaging microscopy (FLIM) measurement formats, under one- and two-photon excitation modes. Furthermore, the donor fluorescence lifetime of ColBD-Twitch displays response to [Ca 2+ ] over a range of ∼2-2.5 ns, making it attractive biosensor for multiplexed FLIM microscopy assays. To evaluate performance of this biosensor in physiological measurements, we applied ColBD-Twitch to the live Lgr5-GFP mouse intestinal organoid culture and measured its responses to the changes in extracellular Ca 2+ upon chelation with EGTA. When we combined it with spectrally resolved FLIM of lipid droplets using Nile Red dye, we observed changes in cytoplasmic and basal membrane-associated lipid droplet composition in response to the extracellular Ca 2+ depletion, suggesting that intestinal epithelium can respond to and compensate such treatment. Altogether, our results demonstrate ColBD-Twitch as a prospective Ca 2+ sensor for multiplexed FLIM analysis in a complex 3D tissue environment.
Peer Review #2 of "Impact of the antidepressant citalopram on the behaviour of two different life stages of brown trout (v0.2)"
2020-03-12

Background.Over the last two decades, there has been a constant increase in prescription rates of antidepressants.In parallel, neuroactive pharmaceuticals are making their way into aquatic environments at increasing concentrations.Among the antidepressants detected in the environment citalopram, a selective serotonin reuptake inhibitor, is one of the most commonly found.Given citalopram is specifically designed to alter mood and behaviour in humans, there is growing concern it can adversely affect the behaviour on non-target wildlife Methods.In our study, brown trout were exposed to citalopram (nominal concentrations: 1, 10, 100, 1000 μg/L) in two different life stages.Larvae were exposed at 7 and 11 °C from the eyed ova stage until 8 weeks post yolk sac consumption, and juvenile brown trout were exposed for 4 weeks at 7°C.At both stages we measured mortality, weight, length, tissue citalopram concentration, behaviour during exposure and behaviour in a stressfull environment.For brown trout larvae additionally hatching rate and heart rate, and for juvenile brown trout the tissue cortisol concentration were assessed.Results.During the exposure, both larvae and juvenile fish exposed to the highest test concentration of citalopram (1 mg/L) had higher swimming activity and spent longer in the upper part of the aquaria compared to control fish, which is an indicator for decreased anxiety.Most probably due to the higher swimming activity during the exposure, the juveniles and larvae exposed to 1 mg/L citalopram showed decreased weight and length.Additionally, in a stressful artificial swimming measurement device, brown trout larvae displayed the anxiolytic effect of the antidepressant by reduced swimming activity during this stress situation, already at concentrations of 100 μg/L citalopram.Chemical analysis of the tissue revealed rising citalopram tissue concentrations with rising exposure concentrations.Tissue concentrations were 10 times higher in juvenile fish compared to brown trout larvae.Fish plasma concentrations were calculated, which exceeded human therapeutic levels for the highest exposure concentration, matching the behavioural results.Developmental parameters like hatching rate and heart rate, as well as mortality and tissue cortisol content were unaffected by the antidepressant.Overall, we could trace the pharmacological mode of action of the antidepressant citalopram in the non-target organism brown trout in two different life stages.
Peer Review #1 of "Impact of the antidepressant citalopram on the behaviour of two different life stages of brown trout (v0.1)"
2020-03-12

Background.Over the last two decades, there has been a constant increase in prescription rates of antidepressants.In parallel, neuroactive pharmaceuticals are making their way into aquatic environments at increasing concentrations.Among the antidepressants detected in the environment citalopram, a selective serotonin reuptake inhibitor, is one of the most commonly found.Given citalopram is specifically designed to alter mood and behaviour in humans, there is growing concern it can adversely affect the behaviour on non-target wildlife Methods.In our study, brown trout were exposed to citalopram (nominal concentrations: 1, 10, 100, 1000 μg/L) in two different life stages.Larvae were exposed at 7 and 11 °C from the eyed ova stage until 8 weeks post yolk sac consumption, and juvenile brown trout were exposed for 4 weeks at 7°C.At both stages we measured mortality, weight, length, tissue citalopram concentration, behaviour during exposure and behaviour in a stressfull environment.For brown trout larvae additionally hatching rate and heart rate, and for juvenile brown trout the tissue cortisol concentration were assessed.Results.During the exposure, both larvae and juvenile fish exposed to the highest test concentration of citalopram (1 mg/L) had higher swimming activity and spent longer in the upper part of the aquaria compared to control fish, which is an indicator for decreased anxiety.Most probably due to the higher swimming activity during the exposure, the juveniles and larvae exposed to 1 mg/L citalopram showed decreased weight and length.Additionally, in a stressful artificial swimming measurement device, brown trout larvae displayed the anxiolytic effect of the antidepressant by reduced swimming activity during this stress situation, already at concentrations of 100 μg/L citalopram.Chemical analysis of the tissue revealed rising citalopram tissue concentrations with rising exposure concentrations.Tissue concentrations were 10 times higher in juvenile fish compared to brown trout larvae.Fish plasma concentrations were calculated, which exceeded human therapeutic levels for the highest exposure concentration, matching the behavioural results.Developmental parameters like hatching rate and heart rate, as well as mortality and tissue cortisol content were unaffected by the antidepressant.Overall, we could trace the pharmacological mode of action of the antidepressant citalopram in the non-target organism brown trout in two different life stages.
Peer Review #2 of "Impact of the antidepressant citalopram on the behaviour of two different life stages of brown trout (v0.1)"
2020-03-12

Background.Over the last two decades, there has been a constant increase in prescription rates of antidepressants.In parallel, neuroactive pharmaceuticals are making their way into aquatic environments at increasing concentrations.Among the antidepressants detected in the environment citalopram, a selective serotonin reuptake inhibitor, is one of the most commonly found.Given citalopram is specifically designed to alter mood and behaviour in humans, there is growing concern it can adversely affect the behaviour on non-target wildlife Methods.In our study, brown trout were exposed to citalopram (nominal concentrations: 1, 10, 100, 1000 μg/L) in two different life stages.Larvae were exposed at 7 and 11 °C from the eyed ova stage until 8 weeks post yolk sac consumption, and juvenile brown trout were exposed for 4 weeks at 7°C.At both stages we measured mortality, weight, length, tissue citalopram concentration, behaviour during exposure and behaviour in a stressfull environment.For brown trout larvae additionally hatching rate and heart rate, and for juvenile brown trout the tissue cortisol concentration were assessed.Results.During the exposure, both larvae and juvenile fish exposed to the highest test concentration of citalopram (1 mg/L) had higher swimming activity and spent longer in the upper part of the aquaria compared to control fish, which is an indicator for decreased anxiety.Most probably due to the higher swimming activity during the exposure, the juveniles and larvae exposed to 1 mg/L citalopram showed decreased weight and length.Additionally, in a stressful artificial swimming measurement device, brown trout larvae displayed the anxiolytic effect of the antidepressant by reduced swimming activity during this stress situation, already at concentrations of 100 μg/L citalopram.Chemical analysis of the tissue revealed rising citalopram tissue concentrations with rising exposure concentrations.Tissue concentrations were 10 times higher in juvenile fish compared to brown trout larvae.Fish plasma concentrations were calculated, which exceeded human therapeutic levels for the highest exposure concentration, matching the behavioural results.Developmental parameters like hatching rate and heart rate, as well as mortality and tissue cortisol content were unaffected by the antidepressant.Overall, we could trace the pharmacological mode of action of the antidepressant citalopram in the non-target organism brown trout in two different life stages.
Peer Review #1 of "Impact of the antidepressant citalopram on the behaviour of two different life stages of brown trout (v0.2)"
2020-03-12

Background.Over the last two decades, there has been a constant increase in prescription rates of antidepressants.In parallel, neuroactive pharmaceuticals are making their way into aquatic environments at increasing concentrations.Among the antidepressants detected in the environment citalopram, a selective serotonin reuptake inhibitor, is one of the most commonly found.Given citalopram is specifically designed to alter mood and behaviour in humans, there is growing concern it can adversely affect the behaviour on non-target wildlife Methods.In our study, brown trout were exposed to citalopram (nominal concentrations: 1, 10, 100, 1000 μg/L) in two different life stages.Larvae were exposed at 7 and 11 °C from the eyed ova stage until 8 weeks post yolk sac consumption, and juvenile brown trout were exposed for 4 weeks at 7°C.At both stages we measured mortality, weight, length, tissue citalopram concentration, behaviour during exposure and behaviour in a stressfull environment.For brown trout larvae additionally hatching rate and heart rate, and for juvenile brown trout the tissue cortisol concentration were assessed.Results.During the exposure, both larvae and juvenile fish exposed to the highest test concentration of citalopram (1 mg/L) had higher swimming activity and spent longer in the upper part of the aquaria compared to control fish, which is an indicator for decreased anxiety.Most probably due to the higher swimming activity during the exposure, the juveniles and larvae exposed to 1 mg/L citalopram showed decreased weight and length.Additionally, in a stressful artificial swimming measurement device, brown trout larvae displayed the anxiolytic effect of the antidepressant by reduced swimming activity during this stress situation, already at concentrations of 100 μg/L citalopram.Chemical analysis of the tissue revealed rising citalopram tissue concentrations with rising exposure concentrations.Tissue concentrations were 10 times higher in juvenile fish compared to brown trout larvae.Fish plasma concentrations were calculated, which exceeded human therapeutic levels for the highest exposure concentration, matching the behavioural results.Developmental parameters like hatching rate and heart rate, as well as mortality and tissue cortisol content were unaffected by the antidepressant.Overall, we could trace the pharmacological mode of action of the antidepressant citalopram in the non-target organism brown trout in two different life stages.
Type-specific dendritic integration in mouse retinal ganglion cells
2020-03-12

Dataset for Ran et al (2020). These data can be read by Python (&gt;3.6) and Pandas (&gt;1.0.0): <pre><code class="language-python">import pickle data = pickle.load(open('./data_raw.pickle', 'rb')) </code></pre> Or use our custom scripts. For more details, see https://github.com/berenslab/rgc_dendrites.