Miracle-dz/UniFAR-FTUs huggingface dataset:
Combination of digital signal processing and assembled predictive models facilitates the rational design of proteins

Predicting the effect of mutations in proteins is one of the most critical challenges in protein engineering; by knowing the effect a substitution of one (or several) residues in the protein's sequence has on its overall properties, could design a variant with a desirable function. New strategies and methodologies to create predictive models are continually being developed. However, those that claim to be general often do not reach adequate performance, and those that aim to a particular task improve their predictive performance at the cost of the method's generality. Moreover, these approaches typically require a particular decision to encode the amino acidic sequence, without an explicit methodological agreement in such endeavor. To address these issues, in this work, we applied clustering, embedding, and dimensionality reduction techniques to the AAIndex database to select meaningful combinations of physicochemical properties for the encoding stage. We then used the chosen set of properties to obtain several encodings of the same sequence, to subsequently apply the Fast Fourier Transform (FFT) on them. We perform an exploratory stage of Machine-Learning models in the frequency space, using different algorithms and hyperparameters. Finally, we select the best performing predictive models in each set of properties and create an assembled model. We extensively tested the proposed methodology on different datasets and demonstrated that the generated assembled model achieved notably better performance metrics than those models based on a single encoding and, in most cases, better than those previously reported. The proposed method is available as a Python library for non-commercial use under the GNU General Public License (GPLv3) license.
Fear in farmlands: how much does predator avoidance affect bird community structure?

The abundances of potential avian prey species may be lower in the vicinity of the nests of predatory birds than farther away. We predicted that, if this density depression is due to predation, the observed density pattern should develop gradually during the breeding season as raptors deplete the prey populations. In contrast, if the low abundance is a result of predator avoidance during breeding habitat selection, the observed pattern should be evident from the beginning of the breeding season. We tested these predictions by counting breeding birds along transect lines (length 700 m, width 100 m) radiating away from Kestrel Falco tinnunculus nests, and along control transect lines situated > 1000 m from Kestrel nests, five times in the course of the 1994 breeding season in western Finland. Breeding bird density was ca. 25% lower within 700 m of the Kestrel nests than on control sites. The positive relationship between bird densities and the distance from Kestrel nests was most evident in the early breeding season, which supports the predator avoidance hypothesis. The effect of predator presence on the distribution of breeding pairs seemed to be weak at species level but stronger at community level. At the beginning of the breeding season, distance from predator nests explained a larger proportion of the observed variation in the number of birds or species than any of the habitat variables used.
Spontaneous Mouse Behavior in Presence of Dissonance and Acoustic Roughness

According to a novel hypothesis (Arnal et al., 2015, Current Biology 25:2051–2056), auditory roughness, or temporal envelope modulations between 30 and 150 Hz, are present in both natural and artificial human alarm signals, which boosts the detection of these alarms in various tasks. These results also shed new light on the unpleasantness of dissonant sounds to humans, which builds upon the high level of roughness present in such sounds. However, it is not clear whether this hypothesis also applies to other species, such as rodents. In particular, whether consonant/dissonant chords, and particularly whether auditory roughness, can trigger unpleasant sensations in mice remains unknown. Using an autonomous behavioral system, which allows the monitoring of mouse behavior over a period of weeks, we observed that C57Bl6J mice did not show any preference for consonant chords. In addition, we found that mice showed a preference for rough sounds over sounds having amplitude modulations in their temporal envelope outside the “rough” range. These results suggest that some emotional features carried by the acoustic temporal envelope are likely to be species-specific.
Episodic Reinforcement Learning in Finite MDPs: Minimax Lower Bounds Revisited

In this paper, we propose new problem-independent lower bounds on the sample complexity and regret in episodic MDPs, with a particular focus on the non-stationary case in which the transition kernel is allowed to change in each stage of the episode. Our main contribution is a novel lower bound of $\Omega((H^3SA/\epsilon^2)\log(1/\delta))$ on the sample complexity of an $(\varepsilon,\delta)$-PAC algorithm for best policy identification in a non-stationary MDP. This lower bound relies on a construction of "hard MDPs" which is different from the ones previously used in the literature. Using this same class of MDPs, we also provide a rigorous proof of the $\Omega(\sqrt{H^3SAT})$ regret bound for non-stationary MDPs. Finally, we discuss connections to PAC-MDP lower bounds.
Further physicochemical characterization of anchomanes difformis starch

Anchomanes difformis (Blume) Engl. [family ARACEAE] is an herbaceous plant with prickly stem having huge divided leaf and spathe that arise from a horizontal tuber occurring in the forest of West Africa and presently untilized. The tuber of the plant was examined for its starch composition and physicochemical properties. The starch was isolated using 1 % w/v sodium metabisulphite and it gave a yield of about 21 % which is slightly off white in colour. The starch percentage solubility at 85 O C was 17.32 with a swelling power of 9.66 and gelatinization temperature of 72 O C. It has a browning temperature of 257.0 – 268.2 O C, charring temperature of 281.4 – 291.6 O C, water absorption capacity of 71 %, pH of 5.6, foam and emulsion capacities of 3.6 % and 9.17 % respectively. Phytochemical screening of the starch revealed the presence of carbohydrates, terpenoids, saponins and cardiac glycosides while the proximate analysis (in %) was found to be: fat – 1.0, ash – 0.75, crude fibre – 1.6, protein – 0.66, moisture – 6.0, and carbohydrates – 88.9. The paste clarity was determined at 580 nm as a function of the starch concentration. The photomicrograph indicates that the starch granule is generally small sized, not distinct but clustered with size ranging between 1 – 1.5 μm which is a reflection of the parent source. Generally, the values obtained from the physicochemical characterization of anchomanes difformis starch show that it has high potential for industrial applications especially in the food, textile and pharmaceutical industries.
Annual Under-vine Cover Crops Did Not Impact Vine Growth or Fruit Composition of Mature Cool-climate ‘Riesling’ Grapevines

In the cool and humid climate of the northeastern United States, vegetation is typically maintained between the rows of wine grape (Vitis vinifera) vineyards, but the area directly beneath vines is conventionally kept bare using herbicides or cultivation, to reduce competition for water and nutrients. Yet with rising concerns of herbicide resistance, environmental contamination, and soil erosion, alternatives to maintaining bare ground in vineyards should be considered. In warmer and more arid climates, using cover crops as an alternative to bare soil has sometimes resulted in reduced vine growth and yields. In more cool and humid climates, like in the northeastern United States, where conditions can promote excessive vine growth, replacing bare soil with under-vine cover crops was hypothesized to improve vine growth characteristics and fruit quality from reducing excessive vigor. This study compared three annual under-vine cover crops of resident vegetation (RES), buckwheat (BW) (Fagopyrum esculentum), and annual ryegrass (ARG) (Lolium multiflorum), planted in the 1-m-wide strip directly under vines at the start of each growing season, against the conventional weed-free under-vine row maintainedwith glyphosate. The experiment was established in 2011 and repeated in 2012 and 2013 in a 20-year-old block of ‘Riesling’ wine grapes (clone 198 on S04 rootstock) in a commercial vineyard in the Finger Lakes region of New York State. Harvested grapes were fermented in duplicate using standard white wine procedures. Among the four under-vine treatments, no significant differences were found in measures of vegetative growth, yield, petiole nutrient concentrations at veraison, or predawn andmidday stemwater potentials. Under-vine treatmentswere not found to significantly affect soil organic matter, aggregate stability, and nutrient concentrations. Juice characteristics were also not significantly different among treatments. In this study, the mature vines in this rain-fed ‘Riesling’ vineyard likely had a welldeveloped and extensive rooting system that was able to overcome any competition effects for water or nutrients from the comparatively shallow root systems of the annually established cover crops. Without any induced competition in the conditions of this study, under-vine cover crops had no effects on vine growth, yield, or juice characteristicswhen comparedwith conventional herbicide use in the under-vine row. When multidimensional scaling (MDS) analysis was used to determine differences in aroma among wine treatment replicates, treatments were found to significantly impact the perceived aromatic properties of the wines, even though no measures of growth or juice characteristics were affected. Using under-vine vegetation may be a viable alternative to conventional herbicide use for vineyard floor management in mature wine grape vineyards in cool and humid climates.
Who Deserves Compassion? The Moral and Emotional Dilemmas of Volunteering in the ‘Refugee Crisis’

Since the ‘refugee crisis’ in 2015, civil society across Europe has participated in an unprecedented wave of support towards migrants. This article focuses on the volunteers engaged in this movement and explores how they relate emotions of compassion and evaluations about the ‘deservingness’ of refugees. We do so by analysing the moral dilemmas British volunteers face in their interaction with refugees, and the strategies they develop to avoid the difficulties that emerge when judging who the ‘deserving’ refugees are. We illustrate how these coping strategies lead them to emphasise the practicality of their role and to move beyond logics of deservingness. We argue that these dilemmatic situations reshape the meaning of compassionate acts in ambivalent ways: while reinforcing a tendency to create an emotional distance, they also allow volunteers to challenge idealised representations of refugees and foreground the political nature of their vulnerability.
Metal chelation reduces skin epithelial inflammation and rescues epithelial cells from toxicity due to thermal injury in a rat model

Abstract Background One of the most pervasive complications of burn injury is wound progression, characterized by continuous tissue destruction in untreated wounds, which leads to wound infection, inflammation, oxidative stress and excessive scar formation. We determined whether additional tissue destruction could be attenuated with Livionex formulation (LF) lotion, which contains a metal-chelating agent and reduces inflammation in burn wounds. Methods We subjected male Sprague Dawley rats to a 2% total body surface area (TBSA) burn using a brass comb model and topically applied LF lotion (containing ethylenediaminetetraacetic acid and methyl sulfonyl methane) to the affected area every 8 hours over 3 days. Inflammatory cytokine levels, cell apoptosis and wound healing were compared in LF lotion-treated and untreated rats. Statistical analysis was performed using a one-way analysis of variance in conjunction with Tukey’s post-hoc test. Results Serum inflammatory cytokines were not detectable after 3 days, suggesting that small burn wounds induce only an immediate, localized inflammatory response. Microscopy revealed that LF lotion improved burn site pathology. Deoxynucleotidyl transferase biotin-d-UTP nick-end labeling staining showed reduced cell death in the LF-treated samples. LF lotion prevented the spread of tissue damage, as seen by increased amounts of Ki-67-positive nuclei in the adjacent epidermis and hair follicles. Tumor necrosis factor-alpha, interleukin-6 and inducible nitric oxide synthase levels in LF-treated skin sections from burned rats were comparable to the levels observed in unburned control sections, indicating that LF lotion reduces inflammation in and around the burn site. Conclusions These results establish LF lotion as a therapeutic agent for reducing inflammatory stress, cell death and tissue destruction when applied immediately after a burn injury. Further studies of LF lotion on large TBSA burns will determine its efficacy as an emergency treatment for reducing long-term morbidity and scarring.
Neurons and normativity: A critique of Greene’s notion of unfamiliarity

ABSTRACT In his article “Beyond Point-and-Shoot Morality,” Joshua Greene argues that the empirical findings of cognitive neuroscience have implications for ethics. Specifically, he contends that we ought to trust our manual conscious reasoning system more than our automatic emotional system when confronting unfamiliar problems; and because cognitive neuroscience has shown that consequentialist judgments are generated by the manual system and deontological judgments are generated by the automatic system, we ought to trust the former more than the latter when facing unfamiliar moral problems. In the present article, I analyze one of the premises of Greene’s argument. In particular, I ask what exactly an unfamiliar problem is, and whether moral problems can be classified as unfamiliar. After exploring several different possible interpretations of familiarity and unfamiliarity, I conclude that the concepts are too problematic to be philosophically compelling and, thus, should be abandoned.
Factor Structure and Gender Invariance of Chinese Version State-Trait Anxiety Inventory (Form Y) in University Students

Background Anxiety can be classified as state anxiety and trait anxiety which present the current level of anxiety and the generalized anxiety tendencies of individuals, respectively. The State-Trait Anxiety Inventory form Y (STAI-Y) is a reliable instrument used to test both the levels of state and trait anxiety across various countries. However, the optimal factor structure of STAI-Y in different populations is not consistent and is not clear in Chinese university students. In addition, the gender invariance is the premise for comparing the scores of STAI-Y between men and women which also need to be verified. Therefore, this study explored the optimal factor structure of STAI-Y and examined whether the optimal factor structure satisfied measurement invariance across gender in Chinese university students. Method A sample of 2117 Chinese university students participated in this study including 748 men and 1369 women. The optimal factor structure was decided by singer group confirmatory factor analysis (CFA) and exploratory structural equation modeling (ESEM). Furthermore, the configural invariance, metric invariance, scalar invariance, and strict invariance models were administrated in multigroup CFA to detect the measurement equivalence of STAI-Y across gender in Chinese university students. The reliability of STAI-Y was tested by Cronbach’s alpha coefficient and McDonald’s omega coefficients. Results The optimal factor structure of STAI-Y was four-factor model and reached strict gender invariance in Chinese university students. Moreover, the STAI-Y also had adequate reliability in Chinese university students. Conclusion This study explored the factor structure and gender invariance of STAI-Y in Chinese university students. In sum, the four-factor structure of STAI-Y obtained the best goodness-of-fit and satisfied gender invariance which deepened the understanding of STAI-Y in Chinese university students.
Rebooting the new evidence scholarship

The new evidence scholarship addresses three distinct approaches: legal probabilism, Bayesian decision theory and relative plausibility theory. Each has major insights to offer, but none seems satisfactory as it stands. This paper proposes that relative plausibility theory be modified in two substantial ways. The first is by defining its key concept of plausibility, hitherto treated as primitive, by generalising the standard axioms of probability. The second is by complementing the descriptive component of the theory with a normative decision theory adapted to legal process. Because this version of decision theory is based on plausibilities rather than probabilities, it generates plausibilistic expectations as outputs. Because these outputs are comparable, they function as relative plausibilities. Hence the resulting framework is an extension of relative plausibility theory, but it retains deep ties to legal probabilism, through the proposed definition of plausibility, and to Bayesian decision theory, through the normative use of decision theory.
The ESIF-HPC-2 benchmark suite

We describe the development of the ESIF-HPC-2 benchmark suite, a collection of kernel and application benchmark codes for measuring computational and I/O performance from single nodes to full HPC systems that was used for acceptance testing in our recent HPC procurement. The configurations of the benchmarks used for our system is presented. We also describe a set of "dimensions" that can be used to classify benchmarks and assess coverage of a suite systematically. The collection is offered cost-free as a GitHub repository for general usage and further development.
Grouping Mechanisms in Numerosity Perception

Enumeration of a dot array is faster and easier if the items form recognizable subgroups. This phenomenon, which has been termed “groupitizing,” appears in children after one year of formal education and correlates with arithmetic abilities. We formulated and tested the hypothesis that groupitizing reflects an ability to sidestep counting by using arithmetic shortcuts, for instance, using the grouping structure to add or multiply rather than just count. Three groups of students with different levels of familiarity with mathematics were asked to name the numerosity of sets of 1–15 dots in various arrangements, for instance, 9 represented as a single group of 9 items, three distinct groups of 2, 3, and 4 items (affording addition 2 + 3 + 4), or three identical groups of 3 items (affording multiplication 3 × 3). Grouping systematically improved enumeration performance, regardless of whether the items were grouped spatially or by color alone, but only when an array was divided into subgroups with the same number of items. Response times and error patterns supported the hypothesis of a multiplication process. Our results demonstrate that even a simple enumeration task involves mental arithmetic.
The Growth of Eimeria tenella: Characterization and Application of Quantitative Methods to Assess Sporozoite Invasion and Endogenous Development in Cell Culture

In vitro development of the complete life cycle of Eimeria species has been achieved in primary cultures of avian epithelial cells with low efficiency. The use of immortalized cell lines simplifies procedures but only allows partial development through one round of parasite invasion and intracellular replication. We have assessed the suitability of Madin-Darby Bovine Kidney (MDBK) cells to support qualitative and quantitative studies on sporozoite invasion and intracellular development of Eimeria tenella. Analysis of parasite ultrastructure by transmission electron microscopy and serial block face—scanning electron microscopy proved the suitability of the system to generate good quality schizonts and first-generation merozoites. Parasite protein expression profiles elucidated by mass spectrometry corroborated previous findings occurring during the development of the parasite such as the presence of alternative types of surface antigen at different stages and increased abundance of proteins from secretory organelles during invasion and endogenous development. Quantitative PCR (qPCR) allowed the tracking of development by detecting DNA division, whereas reverse transcription qPCR of sporozoite- and merozoite-specific genes could detect early changes before cell division and after merozoite formation, respectively. These results correlated with the analysis of development using ImageJ semi-automated image analysis of fluorescent parasites, demonstrating the suitability and reproducibility of the MDBK culture system. This systems also allowed the evaluation of the effects on invasion and development when sporozoites were pre-incubated with anticoccidial drugs, showing similar effects to those reported before. We have described through this study a series of methods and assays for the further application of this in vitro culture model to more complex studies of Eimeria including basic research on parasite cell biology and host-parasite interactions and for screening anticoccidial drugs.
Students’ Perceptions of Teachers’ Corrective Feedback, Basic Psychological Needs and Subjective Vitality: A Multilevel Approach

The way students perceive corrective feedback has repercussions on what they learn and think. Based on the self-determination theory, the aim of this study is to test a model of multilevel mediation that examines the relationships between the perception of corrective feedback with its degree of acceptance (perceived legitimacy) at the team level and the subjective vitality of students at the individual level, mediated by the satisfaction of the three psychological needs, in the context of physical education. The participants were 742 students aged between 10 and 13 years old (52.6% men, 47.4% women) in 29 physical education groups. The results of the multilevel structural equation modeling analysis found at the group (between) level a positive and significant relationship between corrective feedback and perceived legitimacy (Bbetween = 0.49, p < 0.01), as well as a positive and significant relationship between perceived legitimacy and the needs of competence (Bbetween = 0.66, p < 0.05) and relatedness (Bbetween = 0.95, p < 0.01). In addition, there was a positive and significant association between competence and subjective vitality (Bbetween = 2.06, p < 0.01), and a negative and significant association between relatedness and subjective vitality (Bbetween = −0.85, p < 0.01). Also, on an individual (within) level, the needs of autonomy (Bwithin = 0.09, p < 0.05), competence (Bwithin = 0.27, p < 0.01), and relatedness (Bwithin = 0.17, p < 0.01) were positively and significantly associated with subjective vitality. Finally, corrective feedback showed a positive indirect effect on subjective vitality through perceived legitimacy and competence, while the indirect effect was negative through perceived legitimacy and relatedness. In conclusion, on an individual level, students who perceive their basic psychological needs to be met in turn, increase their subjective vitality. At the group level, the results are discussed. These findings suggest that teachers might be best advised to ensure that their students accept corrective feedback, by having it couched in a manner that suggests that learning and improvement can follow, and communicated in an autonomy-supporting way.