A survey of experimental stimulus presentation code sharing in major areas of psychology.

Computer code plays a vital role in modern science, from the conception and design of experiments through to final data analyses. Open sharing of code has been widely discussed as being advantageous to the scientific process, allowing experiments to be more easily replicated, helping with error detection, and reducing wasted effort and resources. In the case of psychology, the code used to present stimuli is a fundamental component of many experiments. It is not known, however, the degree to which researchers are sharing this type of code. To estimate this, we conducted a survey of 400 psychology papers published between 2016 and 2021, identifying those working with the open-source tools Psychtoolbox and PsychoPy that openly share stimulus presentation code. For those that did, we established if it would run following download and also appraised the code's usability in terms of style and documentation. It was found that only 8.4% of papers shared stimulus code, compared to 17.9% sharing analysis code and 31.7% sharing data. Of shared code, 70% ran directly or after minor corrections. For code that did not run, the main error was missing dependencies (66.7%). The usability of the code was moderate, with low levels of code annotation and minimal documentation provided. These results suggest that stimulus presentation code sharing lags behind other forms of code and data sharing, potentially due to less emphasis on such code in open-science discussions and in journal policies. The results also highlight a need for improved documentation to maximize code utility.

LocoBox: Modular Hardware and Open-Source Software for Circadian Entrainment and Behavioral Monitoring in Home Cages.

Day-night locomotor activities are the most readily observed outputs of the circadian (~24-h period) clock in many animals. Temporal patterns of the light-dark schedule serve as input to the clock. While circadian activity patterns under various lighting conditions have been observed and documented, the full extent of circadian locomotor activities by genotype and entrainment remains uncharacterized. To facilitate large-scale, parallel cataloging of circadian input-output patterns, we created the LocoBox, an easy-to-construct and easy-to-operate system that can control environmental light with flexible entrainment scenarios combined with the T-cycle and measure locomotor activities in individual home cages. The LocoBox is made using economical, common components, and normal breeding cages can be used for long-term recording. We provide details of the components and blueprints, along with software programs for Arduino and a Python-based graphical user interface (GUI), so that the system can be easily replicated in other laboratories.

Personality Traits and Aggressive Behavior in Vietnamese Adolescents.

Purpose: This study aims to reveal the relationship between personality characteristics and verbal or physical aggression in Vietnamese adolescents. Patients and Methods: We recruited 3003 participants [1498 boys (49.9%) and 1505 girls (50.1%); mean age ± SD = 13.50 ± 0.936] who we tested with the Eysenck Personality Questionnaire - Brief version (EPQ-BV), and Vietnamese Aggression Scale (VAS). A multivariate analysis of variance test, Pearson Correlation, and analyzing mediating variable interaction is used to analyze data. Results: The findings suggested a significant interaction between personality traits, specifically extraversion and neuroticism, and physical aggression, verbal aggression, and anger. Students with higher levels of personality had higher levels of verbal aggression, and students with higher levels of physical aggression and anger had stronger personality traits than others and lower levels of physical aggression and anger. Personality traits, specifically extraversion, and neuroticism, differed significantly by gender and school years in adolescence. Mediation analysis revealed a positive and statistically significant indirect correlation between personality traits and physically aggressive behavior, with anger as a mediator. Similarly, a positive and statistically significant indirect correlation between personality traits and verbally aggressive behavior through anger was found. The relationship between personality traits and physical aggression was also significant via verbal aggression and anger. Conclusion: This study improved our understanding of personality traits and verbal or physical aggression. Most crucially, physical and verbal aggression mediate personality traits and aggressive conduct. In secondary school, gender and school year affected extraversion and neuroticism. This discovery illuminates personality-based aggressiveness intervention.

Raphiocarpustaygiangensis (Gesneriaceae), a new species from central Vietnam.

Raphiocarpustaygiangensis, a new species of Gesneriaceae family discovered in Tay Giang District, Quang Nam Province, Central Vietnam, is here described and illustrated. The new species is diagnosed by the combination of its stem up to 2 m long, sericeous hairs on young stem, leaf petiole and adaxial mid-vein, sparsely and minutely serrate leaf margin, axillary inflorescence spreading along stem, sparsely long gland-tipped hairs on peduncle, pedicel, calyx, outside corolla and pistil, calyx 5-disparted from base, purplish white flower with purple stripes inside corolla tube, and dish-shaped stigma formed by 2 semi-orbicular lobes horizontally expanding. Distinct features of the new species and its morphologically closest congener, Rhaphiocarpusaxillaris, are compared and discussed. The conservation status of the described species is estimated as Vulnerable (VU D2) according to the IUCN Red List Criteria.

Contributions to the biodiversity of Vietnam - Results of VIETBIO inventory work and field training in Cuc Phuong National Park.

VIETBIO [Innovative approaches to biodiversity discovery and characterisation in Vietnam] is a bilateral German-Vietnamese research and capacity building project focusing on the development and transfer of new methods and technology towards an integrated biodiversity discovery and monitoring system for Vietnam. Dedicated field training and testing of innovative methodologies were undertaken in Cuc Phuong National Park as part and with support of the project, which led to the new biodiversity data and records made available in this article collection. VIETBIO is a collaboration between the Museum für Naturkunde Berlin - Leibniz Institute for Evolution and Biodiversity Science (MfN), the Botanic Garden and Botanical Museum, Freie Universität Berlin (BGBM) and the Vietnam National Museum of Nature (VNMN), the Institute of Ecology and Biological Resources (IEBR), the Southern Institute of Ecology (SIE), as well as the Institute of Tropical Biology (ITB); all Vietnamese institutions belong to the Vietnam Academy of Science and Technology (VAST). The article collection "VIETBIO" (https://doi.org/10.3897/bdj.coll.63) reports original results of recent biodiversity recording and survey work undertaken in Cuc Phuong National Park, northern Vietnam, under the framework of the VIETBIO project. The collection consist of this "main" cover paper - characterising the study area, the general project approaches and activities, while also giving an extensive overview on previous studies from this area - followed by individual papers for higher taxa as studied during the project. The main purpose is to make primary biodiversity records openly available, including several new and interesting findings for this biodiversity-rich conservation area. All individual data papers with their respective primary records are expected to provide useful baselines for further taxonomic, phylogenetic, ecological and conservation-related studies on the respective taxa and, thus, will be maintained as separate datasets, including separate GUIDs also for further updating.

Occipital gamma-aminobutyric acid and glutamate-glutamine alterations in major depressive disorder: An mrs study and meta-analysis.

The neurotransmitters GABA and glutamate have been suggested to play a role in Major Depressive Disorder (MDD) through an imbalance between cortical inhibition and excitation. This effect has been highlighted in higher brain areas, such as the prefrontal cortex, but has also been posited in basic sensory cortices. Based on this, magnetic resonance spectroscopy (MRS) was used to investigate potential changes to GABA+ and glutamate+glutamine (Glx) concentrations within the occipital cortex in MDD patients (n = 25) and healthy controls (n = 25). No difference in occipital GABA+ or Glx concentrations, nor in the GABA+/Glx ratio, was found between groups. An analysis of an extended MDD patient and unmatched control dataset (n = 90) found no correlation between metabolite concentrations and depressive symptoms. These results were integrated with prior studies through metabolite-specific meta-analyses, revealing no difference in occipital GABA and Glx concentrations between patients and controls. An effect of publication year on GABA group differences was found, suggesting that previously reported results may have been artifacts of measurement accuracy. Taken together, our results suggest that, contrary to some prior reports, MRS measurements of occipital GABA and Glx do not differ between MDD patients and controls.

Suggestions for improving the visualization of magnetic resonance spectroscopy voxels and spectra.

Magnetic resonance spectroscopy (MRS) has seen an increase in popularity as a method for studying the human brain. This approach is dependent on voxel localization and spectral quality, knowledge of which are essential for judging the validity and robustness of any analysis. As such, visualization plays a central role in appropriately communicating MRS studies. The quality of data visualization has been shown to be poor in a number of biomedical fields and so we sought to appraise this in MRS papers. To do this, we conducted a survey of the psychiatric single-voxel MRS literature. This revealed a generally low standard, with a significant proportion of papers not providing the voxel location and spectral quality information required to judge their validity or replicate the experiment. Based on this, we then present a series of suggestions for a minimal standard for MRS data visualization. The primary point of these is that both voxel location and MRS spectra be presented from all participants. Participant group membership should be indicated where more than one is included in the experiment (e.g. patients and controls). A set of suggested figure layouts that fulfil these requirements are presented with sample code provided to produce these (github.com/nwd2918/MRS-voxel-plot).

Design, synthesis, structure, in vitro cytotoxic activity evaluation and docking studies on target enzyme GSK-3ß of new indirubin-3'-oxime derivatives.

The addition of chalcone and amine components into indirubin-3'-oxime resulted in 15 new derivatives with high yields. Structures of new derivatives were also elucidated through 1D, 2D-NMR and HR-MS(ESI) spectra and X-ray crystallography. All designed compounds were screened for cytotoxic activity against four human cancer cell lines (HepG2, LU-1, SW480 and HL-60) and one human normal kidney cell line (HEK-293). Compound 6f exhibited the most marked cytotoxicity meanwhile cytotoxicity of compounds 6e, 6h and 6l was more profound toward cancer cell lines than toward normal cell. These new derivatives were further analyzed via molecular docking studies on GSK-3ß enzyme. Docking analysis shows that most of the derivatives exhibited potential inhibition activity against GSK-3ß with characteristic interacting residues in the binding site. The fast pulling of ligand scheme was then employed to refine the binding affinity and mechanism between ligands and GSK-3ß enzyme. The computational results are expected to contribute to predicting enzyme target of the trial inhibitors and their possible interaction, from which the design of new cytotoxic agents could be created in the future.

The Kidney Clock Contributes to Timekeeping by the Master Circadian Clock.

The kidney harbors one of the strongest circadian clocks in the body. Kidney failure has long been known to cause circadian sleep disturbances. Using an adenine-induced model of chronic kidney disease (CKD) in mice, we probe the possibility that such sleep disturbances originate from aberrant circadian rhythms in kidney. Under the CKD condition, mice developed unstable behavioral circadian rhythms. When observed in isolation in vitro, the pacing of the master clock, the suprachiasmatic nucleus (SCN), remained uncompromised, while the kidney clock became a less robust circadian oscillator with a longer period. We find this analogous to the silencing of a strong slave clock in the brain, the choroid plexus, which alters the pacing of the SCN. We propose that the kidney also contributes to overall circadian timekeeping at the whole-body level, through bottom-up feedback in the hierarchical structure of the mammalian circadian clocks.

Synthesis and anti-proliferative activity of novel azazerumbone conjugates with chalcones.

The conjugation of azazerumbone ((3E,7E,11E)-5,5,8,12-tetramethylazacyclododeca-3,7,11-trien-2-one (7)) and 2,4-dihydroxychalcones was carried out for the preparation of novel target compounds 9a-g with 1-ethylene-4-methylene-1,2,3-triazole linker and 10a-f with propylene linker between amide nitrogen of azazerumbone and 4-hydroxy group of chalcone. The anti-proliferative activity of these compounds against the LU-1, Hep-G2, MCF-7 and SW480 human cancer cell lines were significantly improved compared to those of azazerumbone or zerumbone. The anti-proliferative activities of (3E,7E,11E)-1-((1-(2-(3-hydroxy-4-((E)-3-(3-methoxyphenyl)acryloyl)phenoxy)ethyl)-1H-1,2,3-triazol-4-yl)methyl)-5,5,8,12-tetramethyl azacyclododeca-3,7,11-trien-2-one (9b) and (3E,7E,11E)-1-(3-(4-((E)-3-(3,4,5-trimethoxyphenyl)acryloyl)phenoxy)propyl)-5,5,8,12-tetramethylazacyclododeca-3,7,11-trien-2-one (10d) are nearly comparable to those of ellipticine.