Miracle-dz/UniFAR-FTUs huggingface dataset:
Visual discrimination of optical material properties: A large-scale study

Complex visual processing involved in perceiving the object materials can be better elucidated by taking a variety of research approaches. Sharing stimulus and response data is an effective strategy to make the results of different studies directly comparable and can assist researchers with different backgrounds to jump into the field. Here, we constructed a database containing several sets of material images annotated with visual discrimination performance. We created the material images using physically-based computer graphics techniques and conducted psychophysical experiments with them in both laboratory and crowdsourcing settings. The observer’s task was to discriminate materials on one of six dimensions (gloss contrast, gloss distinctness-of-image, translucent vs. opaque, metal vs. plastic, metal vs. glass, and glossy vs. painted). The illumination consistency and object geometry were also varied. We used a non-verbal procedure (an oddity task) applicable for diverse use-cases such as cross-cultural, cross-species, clinical, or developmental studies. Results showed that the material discrimination depended on the illuminations and geometries and that the ability to discriminate the spatial consistency of specular highlights in glossiness perception showed larger individual differences than in other tasks. In addition, analysis of visual features showed that the parameters of higher-order color texture statistics can partially, but not completely, explain task performance. The results obtained through crowdsourcing were highly correlated with those obtained in the laboratory, suggesting that our database can be used even when the experimental conditions are not strictly controlled in the laboratory. Several projects using our dataset are underway.
The frailty of tropical restoration plantings

Conserving and restoring biodiversity are compelling challenges in the face of deforestation and fragmentation of tropical forests. Establishing restoration plantings that act as stepping‐stone corridors for animals and develop into forest islets is one way we can reconnect forest fragments split by active agricultural landscapes. However, this strategy's success is contingent on dispersal agents attracted from the forests that vary greatly in their dispersal services, diet, and mobility. Dispersal agents capable of traversing the agricultural matrix that also provide high‐quality and high‐quantity seed dispersal are often a small subset of the present fauna. They also tend to be large‐bodied birds with broad diets (e.g. toucans). This subset of dispersal agents (here termed “effective restoration agents”) plays a key role in driving succession in restoration plantings. Their absence or low numbers can compromise the strategy of using plantings to enhance connectivity in landscapes fragmented by crops, orchards, or extensive pastures. In this event, additional intervention may be required to attract other dispersal agents that would otherwise not disperse seeds at or play a significant role in restoration plantings.
High genetic differentiation of grapevine rootstock varieties determined by molecular markers and artificial neural networks

The genetic differentiation of grapevine rootstock varieties was inferred by the Artificial Neural Network approach based on the Self-Organizing Map algorithm. A combination of RAPD and SSR molecular markers, yielding polymorphic informative loci, was used to determine the genetic characterization among the rootstock varieties 420-A, Schwarzmann, IAC-766 Campinas, Traviú, Kober 5BB, and IAC-572 Jales. A neural network algorithm, based on allelic frequency, showed that the individual grapevine rootstocks (n = 64) were grouped into three genetically differentiated clusters. Cluster 1 included only the Kober 5BB rootstock, Cluster 2 included rootstocks of the varieties Traviú and IAC-572, and Cluster 3 included 420-A, Schwarzmann and IAC-766 plants. Evidence from the current study indicates that, despite the morphological similarities of the 420-A and Kober 5BB varieties, which share the same genetic origin, two new varieties were generated that are genetically divergent and show differences in performance.
Disruption of Nrxn1α within excitatory forebrain circuits drives value-based dysfunction

Goal-directed behaviors, complex action sequences that maximize reward, are essential for normal function and are significantly impaired across neuropsychiatric disorders. Despite extensive associations between genetic mutations and these brain disorders, the mechanisms by which candidate genes contribute to goal-directed dysfunction remains unclear, owing to challenges in (1) describing aspects of reward processing that drive goal-directed dysfunction, (2) localizing these deficits to specific brain circuits and (3) relating changes in physiology to behavioral alterations. Here we examined mice with mutations in Neurexin1α, a presynaptically-localized adhesion molecule with widespread neuropsychiatric dis ease association, in value-based decision-making paradigms. We found that Neurexin1α knockout animals exhibited blunted choice bias towards outcomes associated with greater benefits. Mutant mice were similarly impaired in avoiding costlier, benefit-neutral actions. Analysis of trial-by-trial choice data via reinforcement learning models suggested these behavioral patterns were driven largely by deficits in the updating and representation of choice values. Employing conditional gene ablation and region-specific Cre-recombinase strains, we revealed that Neurexin1α disruption within forebrain excitatory projection neurons, but not thalamic population s, recapitulated most aspects of the whole-brain knockout phenotype. Finally, utilizing in vivo recordings of direct pathway spiny neuron population calcium activity, we demonstrated that selective knockout of Neurexin1α within forebrain excitatory neurons disrupts reward-associated neural signals within striatum, a major site of feedback-based learning. By relating deficits in value-based decision-making to region-specific Nrxn1α disruption and changes in reward-associated neural activity, we reveal potential neural substrates for the pathophysiology of neuropsychiatric disease-associated cognitive dysfunction.
GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control

Ribosome-associated Quality Control (RQC) pathways protect cells from toxicity caused by incomplete protein products resulting from translation of damaged or problematic mRNAs. Extensive work in yeast has identified highly conserved mechanisms that lead to the degradation of the faulty mRNA and partially synthesized polypeptide. Here, we used CRISPR-Cas9-based screening to search for additional RQC strategies in mammals. We found that failed translation leads to specific silencing of translation initiation on that message. This negative feedback loop is mediated by two translation inhibitors, GIGYF2 and 4EHP, in part via the ribosome collision sensor ZNF598. Both model substrates and growth-based assays established that inhibition of additional rounds of translation acts in concert with known RQC pathways to prevent buildup of toxic proteins. Inability to block translation of faulty mRNAs, and subsequent accumulation of partially synthesized polypeptides, could explain the neurodevelopmental and neuropsychiatric disorders observed in mice and humans with compromised GIGYF2 function.
Temperature dependence of platelet metabolism

Temperature plays a fundamental role in biology, influencing cellular function, affecting chemical reaction rates, molecular structures, and interactions. While the temperature dependence of many biochemical reactions is well defined in vitro, the effect of temperature on metabolic function at the network level is not well understood but remains an important challenge in optimizing the storage of cells and tissues at lower temperatures. Here, we have used time-course metabolomics data and systems biology approaches to characterize the effects of storage temperature on human platelets (PLTs) in platelet additive solution. We observed that changes to the metabolome with storage time do not simply scale with temperature but instead display complex temperature dependence, with only a small subset of metabolites following an Arrhenius-type. Investigation of PLT energy metabolism through integration with computational modeling revealed that oxidative metabolism is more sensitive to temperature changes than is glycolysis. The increased contribution of glycolysis to ATP turnover at lower temperature indicates a stronger glycolytic phenotype with decreasing storage temperature. More broadly, these results demonstrate that the temperature dependence of the PLT metabolic network is not uniform, suggesting that efforts to improve the health of stored PLTs could be targeted at specific pathways. Statement of Significance The temperature dependence of cellular metabolism is difficult to study due to regulatory events that are activated upon deviation from the optimal temperature range. Platelets are blood components used in transfusion medicine but also serve as a model cell to study human energy metabolism in the absence of genetic regulation. We investigated changes in platelet metabolism at temperatures spanning from 4 °C-37 °C using a quantitative metabolic systems biology approach as opposed to assessing individual reactions. We found that energy producing metabolic pathways have different temperature sensitivities. The results define the metabolic response to temperature on the metabolic pathway level and are of importance for understanding the cryopreservation of human platelets and more complex human cells used in cellular therapy.
In pursuit of visual attention: SSVEP frequency-tagging moving targets

Previous research has shown that visual attention does not always exactly follow gaze direction, leading to the concepts of overt and covert attention. However, it is not yet clear how such covert shifts of visual attention to peripheral regions impact the processing of the targets we directly foveate as they move in our visual field. The current study utilised the co-registration of eye-position and EEG recordings while participants tracked moving targets that were embedded with a 30 Hz frequency tag in a steady-state evoked potentials paradigm. When the task required attention to be divided between the moving target (overt attention) and a peripheral region where a second target might appear (covert attention), the Steady State Visual Evoked Potentials elicited by the tracked car at the 30 Hz frequency band were significantly lower than when participants did not have to covertly monitor for a second target. Our findings suggest that neural responses of overt attention are reduced when attention is divided between covert and overt areas. This neural evidence is in line with theoretical accounts describing attention as a pool of finite resources, such as the perceptual load theory. Altogether, these results have practical implications for many real-world situations where covert shifts of attention may reduce visual processing of objects even when they are directly being tracked with the eyes.
Abundance, density, and social structure of African forest elephants (Loxodonta cyclotis) in a human-modified landscape in southwestern Gabon

The noninvasive monitoring of population size and demography is critical to effective conservation, but forest living taxa can be difficult to directly observe due to elusiveness and/or inaccessible habitat. This has been true of African forest elephants (Loxodonta cyclotis), for which we have limited information regarding population size and social behavior despite their threatened conservation status. In this study, we estimated demographic parameters focusing specifically on population size and density using genetic capture-recapture of forest elephants in the southern Industrial Corridor of the Gamba Complex of Protected Areas, which is considered a global stronghold for forest elephants in southwestern Gabon. Additionally, we examined forest elephant sociality through analysis of social networks, predicting that we would find matrilineal structure as exhibited by savanna elephants and other forest elephants. Given 95% confidence intervals, we estimate the size of the population in the sampled area to be between 754 and 1,502 individuals and our best density estimate ranges from 0.47 to 0.80 elephants per km2. When extrapolated across the entire Industrial Corridor, this estimate suggests an elephant population size of 3,033 to 6,043 in this area based on abundance or 1,684 to 2,832 based on density, which is 40 – 83% smaller than previously suggested. Furthermore, our social network analysis revealed approximately half of network components included females with different mitochondrial haplotypes; this suggests a wider range of variation in forest elephant sociality than has previously been reported. This study emphasizes the threatened status of forest elephants and demonstrates the need to further refine baseline estimates of population size and knowledge on social behavior in this taxon, both of which will aid in determining how population dynamics in this keystone species may be changing through time in relation to increasing conservation threats.
Evidence of character displacement in microhabitat use between two tropical sympatric Holcosus lizard species (Reptilia, Teiidae)

Interspecific competition between sympatric related species leading to character displacement is critical for species coexistence, especially in tropical habitats. We examined microhabitat use of two sympatric species of tropical lizards of the genus Holcosus in relationship to the microhabitats available in two ecosystems. The species H. festivus lives exclusively in the forest and uses microhabitats in proportion to their availability; while the other, H. quadrilineatus, lives both in forest and on the beach and selects microhabitats with specific characteristics. In the ecosystem where these two lizards live in sympatry (forest), we observed a differential microhabitat use between the two species. However, these differences indicated changes in habitat use by H. quadrilineatus (the smaller species) concerning its patterns of habitat selection in the ecosystem (beach) where only this species occurs. The age of the lizards did not affect the patterns of selection of microhabitats of either species. Shifts in microhabitat use may allow coexistence in sympatry of both species, which might result from the competitive exclusion of the smaller species by the larger species. Key words: Interspecific competition, Holcosus, Lizards, Microhabitat use, Tropical habitats
Mechanistic insight into crossing over during mouse meiosis

Characteristics of heteroduplex DNA illuminate how strands exchange during homologous recombination, but mismatch correction can obscure them. To investigate recombination mechanisms, meiotic crossover products were analyzed at two hotspots in Msh2–/– mice containing homologous chromosomes derived from inbred strains. Recombination frequencies were unchanged in the mutant, implying that MSH2-dependent recombination suppression does not occur at this level of diversity. However, a substantial fraction of crossover products retained heteroduplex DNA in the absence of MSH2, and some also had multiple switches between parental markers suggestive of MSH2-independent correction. Recombinants appeared to reflect a biased orientation of crossover resolution, possibly stemming from asymmetry at DNA ends established in earlier intermediates. Many crossover products showed no evidence of heteroduplex DNA, suggesting dismantling by D-loop migration. Unlike the complexity of crossovers in yeast, these two modifications of the original double-strand break repair model may be sufficient to explain most meiotic crossing over in mice.
Habilidade de permanência no rebanho (Stayability) de caprinos Saanen em condições tropicais, sob abordagem de análise de sobrevivência

Objetivou-se estudar o efeito de caracteristicas morfometricas, de tipo e producao leiteira sobre a habilidade de permanencia (stayability) e estimar os valores e tendencias geneticas de cabras Saanen em ambiente tropical nos diferentes rebanhos brasileiros. Para isso utilizou-se um modelo de regressao de Cox e o estimador Kaplan-Meier para as caracteristicas moformetricas e de tipo. Os efeitos das caracteristicas produtivas sobre a (stayability) foram analisados por meio do modelo animal de risco Weibull, sobre o risco relativo de descarte das cabras. Para estimar os componentes de variância e covariância foi utilizando o modelo de linear-limiar por analises bivariadas, por meio da abordagem bayesiana. Os efeitos considerados no modelo de Cox e estimador Kaplan-Meier foram o ano, estacao e rebanho de nascimento, as caracteristicas morfometricas e de tipo leiteiro. Para as caracteristicas de producao o grupo de contemporâneo foi um efeito independente do tempo e o efeito da idade ao parto e classes de producao como dependentes do tempo, no modelo animal de Weibull. O grupo de contemporâneo foi considerado efeito fixo; idade da cabra como covariavel (linear e quadratica), e os efeitos geneticos aditivos e residuais como aleatorios no modelo linear-limiar incluidos nas analises. Os resultados para analise de regressao de Cox indicaram que o acrescimo de um ano de nascimento, um centimetro no comprimento corporal e na largura da garupa proporcionam a diminuicao de 4, 2 e 5%, respectivamente, o risco de falha das cabras no rebanho. Os estimadores de Kaplan-Meier mostraram efeitos significativos das classes nas covariaveis. As cabras com pontuacoes superiores para caracteristicas relacionadas ao sistema mamario sao descartadas prematuramente do rebanho. A classe 4 de maior producao em volume e constituintes do leite foi a que apresentou diferenca significativa, reduzindo o risco de descarte e estando associada com a stayability (STAY28) das cabras, utilizando o modelo animal de Weibull. As herdabilidades para STAY28 tanto no modelo de Weibull (0,05-0,09), quanto no modelo de linear-limiar h² (0,07) foram baixas. Estimativas de correlacao genetica entre STAY28 e as caracteristicas de producao foram nulas no modelo de linear-limiar, porem a regressao dos valores geneticos demonstrou haver relacao significativa entre essas caracteristicas e STAY28. A caracteristica STAY28 e uma opcao viavel para selecao de animais com maiores valores geneticos para aumentar a vida produtiva em cabras leiteiras refletindo em animais com maiores producoes. Portanto, a melhora das caracteristicas produtivas e morfometricas das cabras trazem efeitos positivos na stayability dos animais no rebanho
Synthesis and biological activity of mimics of D-myo-inositol 1,4,5-trisphosphate and adenophostin A

The synthesis o f adenophostin A, a recently discovered exceptionally potent agonist at the lD-myo-inositol 1,4,5-trisphosphate [Ins(l,4,5)P3] receptor, and a series 2+ of adenophostin A analogues is described. Structure-activity correlations for Ca release at the hepatocyte Ins(l,4,5)P3 receptor are described. a-A nd /? -C-(hydroxymethyl)-1 -deoxy-D-glucopyranoside 3,4, 1'trisphosphates were designed and synthesised as monosaccharide analogues based on an originally described adenophostin A mimic (2-hydroxyethyl-cr-D-glucopyranoside2,3',4'-trisphosphate), but with a shorter and less flexible side chain. The a94trisphosphate was similar in potency for Ca release as Ins(l,4,5)P3 while the /? trisphosphate was considerably weaker. Simplification o f the adenophostin A structure led to the design and synthesis o f [(3S,4R)-3-hydroxytetrahydrofuran-4-yl] a-D-xylopyranoside 3,3',4-trisphosphate (xylofuranophostin), a disaccharide-derived analogue in which the adenine and both hydroxymethyl moieties have been deleted. In order to explore the effect o f stereochemical variations on the biological activity of xylofuranophostin, and in particular the positioning of the non-vicinal phosphate group for potent activity, the synthesis o f three o f its diastereoisomers was undertaken. Further simplification would inevitably result in a substantial decrease in potency, and xylofuranophostin is therefore likely to represent the simplest possible 94 structure for potent Ca -releasing activity in this type of carbohydrate-based analogue. To enable the synthesis of adenophostin A and base-modified adenophostin A analogues a disaccharide intermediate, l,2 ,3 ,,4,-tetra-tri-0-acetyl-2,,5,6'-0-benzyl-3O-a-D-glucopyranosyl-D-ribofuranose was synthesised. Vorbruggen condensation of this intermediate with 6-chloropurine/2,6-dichlorpurine led to the synthesis of a series of adenophostin A analogues elaborated at N-6 and C-2. Biological evaluation o f these compounds has shown N6-methyl adenophostin to be amongst the first totally synthetic compounds to approach the activity o f adenophostin A. By the introduction o f different sized molecules this study has revealed evidence o f a possible unoccupied and new receptor binding pocket for the Ins(l,4,5)P3R in complex with adenophostin A. These results further demonstrate that a base-modification approach represents a powerful strategy to develop high potency ligands.
Forty years of assisted reproduction research in non-domestic, wild and endangered mammals.

For nearly forty years, at three institutions, our team conducted studies to advance the use of ARTs for propagating threatened and endangered mammalian species. The initial studies began in 1978 in the Department of Obstetrics and Gynecology at the University of Alabama in Birmingham, moving in the mid-1980’s to The Center for Reproduction of Endangered Species (CREW) at the Cincinnati Zoo and lastly at the Audubon Center for Research in Endangered Species (ACRES) in New Orleans from 1996 to 2015. Our collaborative endeavors with more than two dozen zoological and academic institutions resulted in the births of ET offspring in two non-human primate species, four non-domestic bovid species and seven non-domestic felid species, six of which were interspecies transfers (Table 1). Origin of embryos that were successfully transferred ranged from those flushed from the uterus of mated females (baboon and bovids) to those generated by IVF, ICSI, and SCNT (gorilla and non-domestic felids). Additionally, embryos of five species underwent cryopreservation (baboon, common eland, African wildcat, caracal, black-footed cat) before successful transfer.
Short-term Follow-up Results of Medial Epicondylar Osteotomy for the Varus Knee in TKA

Purpose: We wanted to evaluate the results of medial epicondylar osteotomy for the varus knee when performing total knee arthroplasty. Materials and Methods: We reviewed 32 cases of medial epicondylar osteotomy for treating varus deformity, and these cases underwent operation from December 2004 to December 2007. The average age of the patients was 71.0-years-old and the average follow-up period was 23.5 months. The clinical outcomes were measured, including the Knee Society score (KSS), the function score (FS) and the range of the motion (ROM). The radiological outcomes were measured by anteroposterior simple radiographs for assessing the union state of the osteotomy site, and the valgus stress radiographs and the whole extremity radiographs were used for assessing the femorotibial angle, the mechanical axis angle and the alignment. Results: The KSS improved from 46.5±7.6 to 89.1±5.9 points (p＜0.001) and the FS increased from 39.5±9.2 to 84.2±8.5 points (p＜0.001). The range of motion increased from 101.5±28.2 o o