Miracle-dz/UniFAR-FTUs huggingface dataset:
Objective Versus Subjective Effort in Schizophrenia

Background and Objectives Performance on cognitive tasks is often impaired in individuals with schizophrenia (SCZ), possibly resulting from either cognitive deficits (e.g., limited working memory capacity) or diminished mental effort or both. Investment of mental effort itself can be affected by cognitive resources, task load, and motivational factors and has thus proven difficult to measure. Pupil dilation during task performance has been proposed as an objective measure, but it remains unclear to what extent this converges with self-reports of perceived task demands, motivation, and invested effort. The current study tried to elucidate this question. Methods A visual version of the digit span task was administered in a sample of 29 individuals with a diagnosis from the SCZ spectrum and 30 individuals without any psychiatric disorder. Pupil size was recorded during the task, whereas self-reported invested effort and task demand were measured afterward. Results No group difference was found for working memory capacity, but individuals with SCZ showed diminished trial-by-trial recall accuracy, showed reduced pupil dilation across all task load conditions, and reported higher perceived task demands. Conclusion Results indicate reduced effort investment in patients with SCZ, but it remains unclear to what extent this alone could explain the lower recall performance. The lack of a direct link between objective and subjective measures of effort further suggests that both may assess different facets of effort. This has important implications for clinical and research settings that rely on the reliability of neuropsychological test results when assessing cognitive capacity in this patient group.
Evaluating Variants of Firefly Algorithm for Ligand Pose Prediction in Protein-ligand Docking Program

Protein-ligand docking is an important and effective structure-based drug design method widely used for large-scale screening of drug candidates. The core of a protein-ligand docking program consists of a sampling algorithm and a scoring function, which produce different poses of a ligand and estimate a score for the pose with respect to how good it reproduces the native conformation of the ligand at the protein binding site, respectively. Nature-inspired algorithms such as particle swarm optimization (PSO) and firefly algorithm (FA) are emerging optimization techniques for simulating social behavior of creatures and the nature-based law of the survival of the fittest. In this study, we investigated the application of FA in ligand pose prediction using a protein-ligand docking program PSOVina. Importantly, we tested four strategies on the classical FA to enhance the protein-ligand docking performance, namely application of the logistic map to diversify the search, Mantegna's method for simulating Lévy flight to generate random walk, elite selection to inherit better solutions across iteration, and k-mean clustering to find more than one optimum solutions. We performed parametric analysis of FA and benchmark tests using two datasets, PDBbind database (version 2014) and Astex Diverse set. The results show that although the average relative mean standard deviation (RMSD) of predicted poses is not always the best, our FA variants are better than those of PSOVina in average success rate, suggesting that FA has potential usefulness for performing robust searches in the ligand conformational space.
Enhancement of Copper Dissolution from a Sulfide Ore by Using Thiobacillus thiooxidans

Copper dissolution from a sulfide ore (with covellite as the main copper phase) was investigated in cultures of Thiobacillus ferrooxidans or Thiobacillus thiooxidans and in abiotic controls. In unsupplemented media, T. ferrooxidans was more efficient than T. thiooxidans. In the presence of ferric iron, the dissolution of covellite was not significantly different in cultures inoculated with T. ferrooxidans or T. thiooxidans. However, the most extraction was found in T. thiooxidans cultures supplemented with ferrous sulfate. The first results were explained by the mechanism proposed by Schippers and Sand (Appl Envir Microbiol 65:319-321, 1999), which involves polysulfides and sulfur as intermediates. This mechanism was extended to explain the behavior of T. thiooxidans culture supplemented with ferrous iron.
Cache-Efficient Parallel-Partition Algorithms using Exclusive-Read-and-Write Memory

We present an in-place algorithm for the parallel-partition problem with linear work and polylogarithmic span. The algorithm uses only exclusive read/write shared variables and can be implemented using parallel-for-loops without any additional concurrency considerations (i.e., the algorithm is EREW). A key feature of the algorithm is that it exhibits provably optimal cache behavior up to small-order factors. We also present a second in-place EREW algorithm with work O(n) and span O(log n · log log n), which is within an O(log log n) factor of the optimal span. By using this low-span algorithm as a subroutine within the cache-friendly algorithm, we obtain a single EREW algorithm that combines their theoretical guarantees: the algorithm achieves span O(log n · log log n) and exhibits optimal cache behavior. As an immediate consequence, we also get an in-place EREW Quicksort algorithm with work O(n log n) and span O(log2 n · log log n). Whereas the standard EREW algorithm for parallel-partition is memory-bandwidth bound on large numbers of cores, our cache-friendly algorithm is able to achieve near-ideal scaling in practice by avoiding the memory-bandwidth bottleneck. Our algorithm's performance is comparable to that of the Blocked Strided Algorithm of Francis, Pannan, Frias, and Petit, which is the previous state-of-the-art for parallel EREW sorting algorithms, but which lacks theoretical guarantees on its span and cache behavior.
Taxonomic Richness and Diversity of Larval Fish Assemblages in the Oceanic Gulf of Mexico: Links to Oceanographic Conditions

Biodiversity enhances the productivity and stability of marine ecosystems and provides important ecosystem services. The aim of this study was to characterize larval fish assemblages in pelagic waters of the northern Gulf of Mexico (NGoM) and identify oceanographic conditions associated with areas of increased taxonomic richness (TF) and Shannon diversity (H’). Summer ichthyoplankton surveys were conducted in the NGoM in 2015 and 2016 using neuston net (surface layer; upper 1 m) and oblique bongo net (mixed layer; 0–100 m) tows. Over 17,000 fish larvae were collected over the two-year study, and 99 families of fish larvae were present. Catch composition in the surface layer was relatively similar to the mixed-layer catch, with carangids (jacks), scombrids (mackerels, tunas), and exocoetids (flyingfishes) being numerically dominant, while deep-pelagic species, including myctophids (lanternfishes), gonostomatids (bristlemouths), and sternoptychids (marine hatchetfishes), were present almost exclusively in the mixed layer samples. Generalized additive models were used to evaluate the effect of oceanographic conditions on ichthyoplankton abundance and biodiversity. Salinity and sea surface height (SSH) were the most influential oceanographic conditions, with higher occurrence, higher TF, and higher H’ all present in areas of lower salinity, and lower SSH. This study highlights the ecological importance of cyclonic mesoscale features and areas of upwelling as areas of increased biodiversity for larval fishes, and also indicates that the mixed layer in the NGoM is essential habitat for deep-pelagic fishes during the early life interval.
Investigation on the Evolution of Shiga Toxin-Converting Phages Based on Whole Genome Sequencing

Bacteriophages are pivotal elements in the dissemination of virulence genes. The main virulence determinants of Shiga Toxin producing E. coli, Shiga Toxins (Stx), are encoded by genes localized in the genome of lambdoid bacteriophages. Stx comprise two antigenically different types, Stx1 and Stx2, further divided into subtypes. Among these, certain Stx2 subtypes appear to be more commonly occurring in the most severe forms of the STEC disease, haemorrhagic colitis and haemolytic uremic syndrome (HUS). This study aimed at obtaining insights on the evolution of Stx2 bacteriophages, due to their relevance in public health, and we report here on the analysis of the genomic structure of Stx2 converting phages in relation with the known reservoir of the E. coli strains harboring them. Stx2-converting phages conveying the genes encoding different stx2 subtypes have been isolated from STEC strains and their whole genomes have been sequenced, analyzed and compared to those of other Stx2 phages available in the public domain. The phages’ regions containing the stx2 genes have been analyzed in depth allowing to make inference on the possible mechanisms of selection and maintenance of certain Stx2 phages in the reservoir. The “stx regions” of different stx2 gene subtypes grouped into three different evolutionary lines in the comparative analysis, reflecting the frequency with which these subtypes are found in different animal niches, suggesting that the colonization of specific reservoir by STEC strains could be influenced by the Stx phage that they carry. Noteworthy, we could identify the presence of nanS-p gene exclusively in the “stx regions” of the phages identified in STEC strains commonly found in cattle. As a matter of fact, this gene encodes an esterase capable of metabolizing sialic acids produced by submaxillary glands of bovines and present in great quantities in their gastrointestinal tract.
Robots as Malevolent Moral Agents: Harmful Behavior Results in Dehumanization, Not Anthropomorphism

A robot's decision to harm a person is sometimes considered to be the ultimate proof of it gaining a human-like mind. Here, we contrasted predictions about attribution of mental capacities from moral typecasting theory, with the denial of agency from dehumanization literature. Experiments 1 and 2 investigated mind perception for intentionally and accidentally harmful robotic agents based on text and image vignettes. Experiment 3 disambiguated agent intention (malevolent and benevolent), and additionally varied the type of agent (robotic and human) using short computer-generated animations. Harmful robotic agents were consistently imbued with mental states to a lower degree than benevolent agents, supporting the dehumanization account. Further results revealed that a human moral patient appeared to suffer less when depicted with a robotic agent than with another human. The findings suggest that future robots may become subject to human-like dehumanization mechanisms, which challenges the established beliefs about anthropomorphism in the domain of moral interactions.
Review Essay : Heuristics as Plausible Models of Rationality?

sociology that argues that models of ’aggregations’ of individual actions (like the ’selffulfilling prophecy’, the ’hog cycle’ or the ’Concordet paradox’) are independent of assumptions as to how these actions are ’chosen’ by the individual. An aggregation model is regarded as simply concatenable to a decision model, and the individual decision is to serve as an interface that links the output of one model to the input of another. The tragedy of this view is certainly that due to its conceptual point of departure it is condemned to overlook that it could be adequate only insofar as actions are in fact reducible to decisions. Sociologists with an interest in the psychology of cognition and problem-solving will agree, however, that
NRF2, a Transcription Factor for Stress Response and Beyond

Nuclear factor erythroid 2-related factor 2 (NRF2) is a transcription factor that regulates the cellular defense against toxic and oxidative insults through the expression of genes involved in oxidative stress response and drug detoxification. NRF2 activation renders cells resistant to chemical carcinogens and inflammatory challenges. In addition to antioxidant responses, NRF2 is involved in many other cellular processes, including metabolism and inflammation, and its functions are beyond the originally envisioned. NRF2 activity is tightly regulated through a complex transcriptional and post-translational network that enables it to orchestrate the cell’s response and adaptation to various pathological stressors for the homeostasis maintenance. Elevated or decreased NRF2 activity by pharmacological and genetic manipulations of NRF2 activation is associated with many metabolism- or inflammation-related diseases. Emerging evidence shows that NRF2 lies at the center of a complex regulatory network and establishes NRF2 as a truly pleiotropic transcription factor. Here we summarize the complex regulatory network of NRF2 activity and its roles in metabolic reprogramming, unfolded protein response, proteostasis, autophagy, mitochondrial biogenesis, inflammation, and immunity.
STXBP1 encephalopathies: Clinical spectrum, disease mechanisms, and therapeutic strategies

Mutations in Munc18‐1/STXBP1 (syntaxin‐binding protein 1) are linked to various severe early epileptic encephalopathies and neurodevelopmental disorders. Heterozygous mutations in the STXBP1 gene include missense, nonsense, frameshift, and splice site mutations, as well as intragenic deletions and duplications and whole‐gene deletions. No genotype–phenotype correlation has been identified so far, and patients are treated by anti‐epileptic drugs because of the lack of a specific disease‐modifying therapy. The molecular disease mechanisms underlying STXBP1‐linked disorders are yet to be fully understood, but both haploinsufficiency and dominant‐negative mechanisms have been proposed. This review focuses on the current understanding of the phenotypic spectrum of STXBP1‐linked disorders, as well as discusses disease mechanisms in the context of the numerous pathways in which STXBP1 functions in the brain. We additionally evaluate the available animal models to study these disorders and highlight potential therapeutic approaches for treating these devastating diseases.
Deep brain stimulation and eye movements

Deep brain stimulation (DBS) has been most widely used in the management of movement disorders, but more recently to treat a growing number of neurological and psychiatric conditions. It is know to have a variety of effects upon oculomotor function, depending not only on the location of the stimulation, but also the underlying pathology being treated. Understanding how DBS affects eye movements is important, given the widespread nature of eye movement control and its inevitable overlap with many of the networks targeted by the stimulation. Moreover, it can also offer additional mechanistic insights into neural circuits involved in complex eye movement control. Here, we discuss the application of DBS treatment across different diseases and explore how distinct stimulation locations interfere with known eye movement circuits and the ensuing oculomotor and visual effects it can produce. We also discuss more experimental DBS targets and its effects on ocular motility, as well as discussing unilateral versus bilateral deep brain stimulation and possible hemispheric asymmetry in relation to eye movement control. Contradictory findings across studies reporting DBS effects on eye movements likely relate to differences in the methodological approaches used, levodopa medication status, as well as possible variability in DBS electrode placement. We highlight the need for further research with less common DBS targets on the possible effects upon eye movements.
Chronic fluoxetine or ketamine treatment differentially affects brain energy homeostasis which is not exacerbated in mice with trait suboptimal mitochondrial function

Antidepressants have been shown to influence mitochondrial function directly, and suboptimal mitochondrial function (SMF) has been implicated in complex psychiatric disorders. In the current study, we used a mouse model for trait SMF to test the hypothesis that chronic fluoxetine treatment in mice subjected to chronic stress would negatively impact brain bioenergetics, a response that would be more pronounced in mice with trait SMF. In contrast, we hypothesized that chronic ketamine treatment would positively impact mitochondrial function in both WT and mice with SMF. We used an animal model for trait SMF, the Ndufs4GT/GT mice, which exhibit 25% lower mitochondrial complex I activity. In addition to antidepressant treatment, mice were subjected to chronic unpredictable stress (CUS). This paradigm is widely used to model complex behaviours expressed in various psychiatric disorders. We assayed several physiological indices as proxies for the impact of chronic stress and antidepressant treatment. Furthermore, we measured brain mitochondrial complex activities using clinically validated assays as well as established metabolic signatures using targeted metabolomics. As hypothesized, we found evidence that chronic fluoxetine treatment negatively impacted brain bioenergetics. This phenotype was, however, not further exacerbated in mice with trait SMF. Ketamine did not have a significant influence on brain mitochondrial function in either genotype. Here we report that trait SMF could be a moderator for an individual's response to antidepressant treatment. Based on these results, we propose that in individuals with SMF and comorbid psychopathology, fluoxetine should be avoided, whereas ketamine could be a safer choice of treatment.
The a-Dystroglycan-b-Dystroglycan Complex

Aberrant expression of the dystrophin-associated protein complex is thought to underlie the pathogenesis of Duchenne dystrophy, Becker muscular dystrophy, and severe childhood autosomal recessive muscular dystrophy. Recently, our laboratory identified an agrin receptor from Torpedo electric organ postsynaptic membranes. It is a heteromer of 190- and 50-kDa subunits with similarity to two components of the dystrophinassociated protein complex of a- and b-dystroglycan. We now confirm the relationship between theTorpedoagrin receptor and mammalian dystroglycans and provide further information about the structure of the a-dystroglycan-b-dystroglycan complex. The sequences of three peptides from each Torpedo subunit were 69% identical to mammalian dystroglycans. An antiserum to mammalian b-dystroglycan recognizes the Torpedo 50-kDa polypeptide. Additionally, like a-dystroglycan, the 190kDa agrin receptor subunit binds laminin. Previous studies have indicated that a- and b-dystroglycan arise by cleavage of a precursor protein. Tryptic peptide mapping of both subunits and amino-terminal sequencing of Torpedo b-dystroglycan indicate a single cleavage site, corresponding to serine 654 of the mammalian dystroglycan precursor. Gel electrophoresis analysis indicates there is at least one intrachain disulfide bond in b-dystroglycan. These results provide precise primary structures for a- and b-dystroglycan.
Age and Size of Hybrid Water Frogs: The Role of Genotype and Ecology

Abstract: Where fecundity, mortality, immigration, or emigration differ among species, genotypes, environments, sexes, or age and size classes, we must expect differences in the composition and dynamics of populations and communities. However, as shown in this study on all-hybrid populations of the hemiclonal waterfrog Pelophylax esculentus, the reverse conclusion is not necessarily true: Population differences in genotype composition were not paralleled by differences in genotype-specific age and size distributions. We investigated 12 ponds with different ratios of diploid (LR) and triploid (LLR and LRR) hybrids and tested whether the pond-to-pond ratio differences result from differential survival of the three genotypes under different ecological conditions (selection hypothesis). This should then be reflected in the age and size distribution of the frogs. Age (determined through skeletochronology) and size (measured as snout–vent length) were related to eight ecological variables that in previous studies had been found to affect genotype ratios: temperature, dissolved oxygen, pH, pond size, amounts of submerged and floating pond vegetation, and proportions of forest and wetland area within 20 m of the pond. Only two of these eight variables had a significant effect on growth and survival: frogs in larger ponds were, on average, older and larger than frogs in smaller ponds, and body size also increased with water temperature. Since these relationships did not differ between genotypes and sexes, we conclude that ecological conditions are unlikely to exert their influence on population structure via differential individual performance. The conclusion is supported by our finding that across the 12 study ponds there was no significant relationship between the proportion of a particular genotype × sex category and the average age and size of the individuals belonging to that category. An alternative to the selection hypothesis is offered by the recently proposed gamete pattern hypothesis. It states that pond-to-pond differences in genotype ratios arise from different gamete production patterns of LLR, LR, and LRR males and females. But, so far, support for this hypothesis is also weak.
Hyperaspidius venustulus (Mulsant) (Coleoptera: Coccinellidae): A Rarely Collected Lady Beetle Associated with the Mealybug Dysmicoccus dennoi Kosztarab on Big Cordgrass, Spartina cynosuroides (Poaceae)

Abstract Since its description from North America (America boreali) in 1850, Hyperaspidius venustulus (Mulsant) has been recorded only from an adult at a locale in Georgia and from Miami–Dade County, Florida (number of adults unspecified). Its habits and habitats have remained unknown. This scymnine coccinellid is newly reported from South Carolina on the basis of 43 adults from grasses, mainly big cordgrass (Spartina cynosuroides (L.) Roth; Poaceae), in or near brackish marshes and along tidal waterways. Its probable prey on big cordgrass is the mealybug Dysmicoccus dennoi Kosztarab. Near stands of S. cynosuroides, the coccinellid was collected occasionally from marshhay cordgrass (S. patens (Ait.) Muhl. ) and from a beardgrass, Andropogon tenuispatheus (Nash) Nash (sensu Weakley 2007), that was infested by the mealybug Trionymus clandestinus McConnell and the eriococcid or felt scale Eriococcus dubius Cockerell. A diagnosis of H. venustulus and color photograph of the adult habitus are provided to facilitate recognition of this little-known lady beetle.
Effects of irrigation water salinity and leaching fraction on the growth of six halophyte species

A pot experiment was carried out at Nahshala Farm, about 50 km from Al-Ain, UAE, during the 1998/99 growing seasons, using six halophytes: Spartina sp. , Distichlis palmeri, Paspalum vaginatum, Juncus roemerianus, Salicornia bigelovii and Batis maritima, under two levels of leaching fraction, 0·25 and 0·50 and three levels of irrigation salinity, 10, 20 and 40 g/l. The objectives of the experiment were twofold: (1) to find out the optimum and threshold of saline water irrigation to keep salinity level down as much as possible in the soil using the leaching fraction technique; and (2) to study the response (growth and biomass production) of some halophytes to different levels of salinity. The experiment was conducted in triplicate with a split-plot design arranged in a randomized complete block. Results indicate that these halophyte species can be grown productively at a leaching fraction between 0·25 and 0·50 when salinity of the irrigation water is less than 20 g/l. At higher salinities, Salicornia bigelovii can grow and yield satisfactorily under these conditions, while the other species may require more frequent irrigation at higher leaching fractions. Some of these tested halophytes may be able to revegetate the salt-affected lands and be a potential source of forage in these harsh habitats. This study supports the idea of seawater agriculture by demonstrating the possibility of using some high salt-tolerant halophytes at relatively higher leaching fraction in order to maintain satisfactory yield production of such halophytes.