Miracle-dz/UniFAR-FTUs huggingface dataset:
GeoPacker: A novel deep learning framework for protein side‐chain modeling

Atomic interactions play essential roles in protein folding, structure stabilization, and function performance. Recent advances in deep learning‐based methods have achieved impressive success not only in protein structure prediction, but also in protein sequence design. However, highly efficient and accurate protein side‐chain prediction methods that can give detailed atomic interactions are still lacking. In the present study, we developed a deep learning based method, GeoPacker, that uses geometric deep learning coupled ResNet for protein side‐chain modeling. GeoPacker explicitly represents atomic interactions with rotational and translational invariance for information extraction of relative locations. GeoPacker outperformed the state‐of‐the‐art energy function‐based methods in side‐chain structure prediction accuracy and runs about 10 and 700 times faster than the deep learning‐based method DLPacker and OPUS‐rota4 with comparable prediction accuracy, respectively. The performance of GeoPacker does not depend on the secondary structures that the residues belong to. GeoPacker gives highly accurate predictions for buried residues in the protein core as well as protein–protein interface, making it a useful tool for protein structure modeling, protein, and interaction design.
Identity and pregnancy in conflict?: an examination of sexual minority women using qualitative description

Abstract While there is growing documentation of pregnancy among sexual minority women, little research has focused on their perceptions and experiences of conflict between sexual minority identity and pregnancy. Because of this, this study used Social Identity Theory and qualitative descriptive analysis to explore the following questions: do sexual minority women perceive sexual minority identity and pregnancy as in conflict; and if so, from where does this conflict arise and how do sexual minority women experience it? Participants included 21 lesbian, gay, bisexual, queer and other non-heterosexual cisgender women, a third of whom had previously been pregnant. Themes captured internally located conflict, including participants who saw pregnancy as irrelevant and those who experienced pregnancy as acceptable for sexual minority women; imposed conflict from healthcare contexts, including both health provider assumptions and imposed conflict on reproductive autonomy; and ambivalence. Overall, few participants noted internalised conflict between their sexual minority identity and pregnancy. Instead, sexual minority women experienced ambivalence or imposed conflict between their sexual minority identities and pregnancy from their health providers, although this imposed conflict was not limited to sexual orientation.
Chicken β -defensin-1 peptide as a candidate anticoccidial agent in broiler chickens

Abstract The current study aimed to investigate the potentiality of using avian β-defensin-1 peptide as a candidate agent against coccidiosis infection in broiler chicken.We employed an in-silico analysis to study the primary structure of β-defensin-1 peptide as well as its 3-D and molecular dynamic structures. This will also enable obtaining adequate information about the mode of action of these peptides and the intra-cellular transduction pathways. The results revealed no significant difference among groups of broiler chicken in terms of body weight before the Eimeria challenge.The results of our study indicated a significant reduction in oocyst count in birds administered β-defensin-1 peptide treatment, vis-a-vis healthy birds. The treated group showed a 2–3 times reduction in oocyst count, compared to the positive control group. The Eimeria oocysts count evaluated for birds administered with β-defensin-1 after the Eimeria challenge showed a significant difference. The study indicated significant reduction and down-regulation in the level of expression of β-defensin 1 and 4 in the control and treatment groups.This electrostatic profile and hydrophobicity regulate the functioning of this peptide. The results may help in the development of novel approaches that could be used as alternatives or adjunct to the existing means of coccidiosis control in broilers.
Haplotype study of the mitochondrial control region of broiler breeds with different growth rates

Abstract This study discussed the haplotype characteristics of mitochondrial control region (D-loop region) of broiler breeds with different growth rates as well as the relationships between different haplotypes and growth performance. The D-loop region’s sequence size of the 974 individuals from 20 broiler breeds ranged from 1,231 to 1,232bp, as a C base deletion at 859 bp. A total of 52 mutation sites and 72 haplotypes were detected, which were divided into four haplogroups, A, B, C and E. Of these, haplogroup E was the dominant haplogroup among 817 broilers and all medium/fast-growing broiler breeds. While its proportion was not exceed 40.00% among others types breeds. Correlation analysis showed that there was a significant negative correlation between birth weight and haplogroup A and a significant positive correlation between birth weight and haplogroup E. Age in days and feed conversion ratios were positively correlated with haplogroup B but negatively correlated with haplogroup E when the average body weight was approximately 1.8 kg. The cluster analysis showed that haplogroups A and B with Gallus gallus spadiceus and E with Gallus gallus murgha, respectively clustered into one branch. This study provided a theoretical basis for broiler breeding and genetic resource protection, development and utilization.
“No‐one knows how to care for LGBT community like LGBT do”: LGBTQIA+ experiences of COVID‐19 in the UK and Brazil

The coronavirus pandemic and responses have had uneven impacts on different segments of societies. We analysed experiences of LGBTQIA+ people during COVID‐19, based on interviews in the UK and Brazil in 2020. The UK and Brazil are instructive cases, with the same crisis impacting these two different social, cultural, economic, and political contexts. Pre‐existing marginalisation shaped COVID‐19 experiences in both contexts, influencing challenges faced, such as isolation or disruption to transgender healthcare, and coping strategies, including the important role of LGBTQIA+ volunteer and mutual‐aid groups. We argue that despite commonalities, there is no single LGBTQIA+ experience, and that disaster strategies will be ineffective until they recognise intersectionality and support the diversity of LGBTQIA+ populations. We conclude with a call to action for more inclusive disaster research, policy, and practice, which requires scrutinising dominant cisgender‐heteronormative structures that produce and reproduce LGBTQIA+ marginalisation.
Branes and Geometry in String and M-Theory

This thesis is based on two papers by the author and consists of two parts. We review the recent developments in the theory of multiple M2-branes and 3-algebras leading to multiple D2-brane theories. The inclusion of flux terms for the supersymmetric BLG and ABJM theories of closed M2-branes is discussed and then generalised to open M2-branes. Here the boundary condition is derived and different BPS configurations are examined where we find a mass deformed Basu-Harvey equation for the M2-M5 system. The Lorentzian 3-algebra is then employed for obtaining a theory of D2-branes in a flux background, we then obtain the new fuzzy funnel solution of the system of D2-D4 branes in a flux. Matrix theories and their compactifications as well as noncommutative geometry and noncommutative gauge theories are reviewed with a discussion of their generalisations to three dimensions to be used to describe the M-theory three form potential. A new feature of string theory is then obtained called the quantum Nambu geometry (QNG). It is found by considering the action for D1-strings in a RR flux background and we demonstrate that there is a large flux double scaling limit where the action is dominated by a Chern-Simons-Myers coupling term. A classical solution to this is the quantised spacetime known as the quantum Nambu geometry. Various matrix models are obtained from this action, these are the large flux dominated terms of the full actions for the corresponding matrix models. The QNG gives rise to an expansion of D1-strings to D4-branes in the IIA theory, so we obtain an action for the large flux terms for this action which is verified by a dimensional reduction of the PST action describing M5-branes. We make a generalisation of the D4-brane action to describe M5-branes using a duality. We are describing the 3-form self-dual field strength of a non-abelian generalisation of the PST action.
Covid-19-stress associated with worse sleep quality, particularly with increasing age

Abstract Objectives Based on SST, one might predict that older adults’ well-being would be less negatively impacted by Covid-19-stress, as with other stressors, than younger people. However, whether sleep quality, which is negatively affected by aging, is similarly protected from the negative consequences of Covid-19-stress with age is unknown. Here, we examined the association between Covid-19-stress, above and beyond general-stress, and sleep quality and how it varies by age. Method From December 2020 to April 2021, 386 adults reported their Covid-19-stress, sleep quality, and resilience in an online study. Results While older age was related to lower Covid-19-stress, Covid-19-stress was associated with worse sleep quality with greater age. Discussion These results suggest that at least some aspects of one’s well-being may be more susceptible to the negative consequences of stress with increasing age. Our results might be better understood via SAVI model, which posits that older adults have increased susceptibility to prolonged and unavoidable stress.
Service Coordination in HUD Housing During the COVID-19 Pandemic: Bridging the Gap

ABSTRACT During the COVID-19 pandemic, service coordinators increased the capacity of a large and diffuse inter-organizational network to support lower-income older adults. Researchers conducted two surveys of service coordinators who worked with older residents of US Department of Housing and Urban Development (HUD) multifamily properties in mid-2020 and late-2021. These residents experienced many pandemic-related disruptions to their support systems, and findings revealed ways that service coordinators assessed resident need, linked them to public benefits programs, improved their access to technology, translated public health responses, and facilitated access to partner organizations and professional supports. Through assessment and communication, and decision-management and problem solving, service coordinator work increased the efficiency and effectiveness of external supports available to help meet residents’ needs for food, medicine, supplies, personal care, and mental and physical healthcare. With an aging population and an increasing rate of unpredictable weather events, service coordination, which is inconsistently funded and is not mandated for HUD properties, may offer an opportunity to improve the adaptability and resilience of older supported housing residents.
Anchored in the present: preschoolers more accurately infer their futures when confronted with their pasts

People often speculate about what the future holds. They wonder what will happen tomorrow, and what the world will be like in the distant future. Nonetheless, people's ability to consider future possibilities may be restricted when they consider their own futures. Adults show the ‘end of history’ illusion, believing they have changed more in the past than they will in the future. Further, preschoolers are even more limited in anticipating future change, as 3-year-olds insist their current desires will persist later in life. These findings suggest a deficit in children's and adults' abilities to simulate alternative possibilities that pertain to themselves. However, we report four experiments (n = 233) suggesting otherwise, at least for children. We find that 3-year-olds accurately infer their futures when prompted to consider their past rather than present preferences. Children also succeed at inferring their past preferences when not shown items they currently prefer. This shows that children can reason about their pasts and futures, though this ability is hindered when they are shown items that anchor them to the present. Our findings suggest that children's difficulties with mental time travel reflect a failure to shift away from the present rather than an inability to simulate alternative possibilities. This article is part of the theme issue ‘Thinking about possibilities: mechanisms, ontogeny, functions and phylogeny’.
The pupillometry of the possible: an investigation of infants' representation of alternative possibilities

Contrasting possibilities has a fundamental adaptive value for prediction and learning. Developmental research, however, has yielded controversial findings. Some data suggest that preschoolers might have trouble in planning actions that take into account mutually exclusive possibilities, while other studies revealed an early understanding of alternative future outcomes based on infants' looking behaviour. To better understand the origin of such abilities, here we use pupil dilation as a potential indicator of infants' representation of possibilities. Ten- and 14-month-olds were engaged in an object-identification task by watching video animations where three different objects with identical top parts moved behind two screens. Importantly, a target object emerged from one of the screens but remained in partial occlusion, revealing only its top part, which was compatible with a varying number of possible identities. Just as adults' pupil diameter grows monotonically with the amount of information held in memory, we expected that infants' pupil size would increase with the number of alternatives sustained in memory as candidate identities for the partially occluded object. We found that pupil diameter increased with the object's potential identities in 14- but not in 10-month-olds. We discuss the implications of these results for the foundation of humans' capacities to represent alternatives. This article is part of the theme issue ‘Thinking about possibilities: mechanisms, ontogeny, functions and phylogeny’.
Alternate day fasting on subjective feelings of appetite and body weight for adults with overweight or obesity: a systematic review

Abstract Alternate day fasting (ADF) with consumption of calories up to 25 % of the daily energy intake on fast days is one of the most used intermittent fasting regimens and promoted as a promising, alternative approach for treating obesity. Feelings of appetite are critical for adherence to dietary approaches, and therefore the success of dietary interventions. This systematic review aimed to assess the effects of a minimum of 8 weeks of ADF on subjective feelings of appetite and body weight for adults with overweight and obesity. We conducted the review in accordance with the Cochrane guidelines, including systematic searches in four databases. Because of the high level of clinical and methodological heterogeneity, a narrative approach was used to synthesise the results. Eight studies with a total of 456 participants met the eligibility criteria: three randomised controlled trials and five uncontrolled before-after studies. Seven of the studies had high risk of bias. Feelings of appetite were assessed by hunger in eight studies, fullness in seven studies, satisfaction in four studies and desire to eat in one study. All the studies assessed weight loss. The certainty of the evidence was rated low or very low for all outcomes, thus no firm conclusions can be drawn about the potential benefits of ADF on subjective feelings of appetite and body weight. Despite the high interest in ADF, good quality evidence is still needed to determine its effectiveness and if offered in clinical practice, ADF should be offered cautiously while concomitantly evaluated.
Intertemporal choice reflects value comparison rather than self-control: insights from confidence judgements

Intertemporal decision-making has long been assumed to measure self-control, with prominent theories treating choices of smaller, sooner rewards as failed attempts to override immediate temptation. If this view is correct, people should be more confident in their intertemporal decisions when they ‘successfully’ delay gratification than when they do not. In two pre-registered experiments with built-in replication, adult participants (n = 117) made monetary intertemporal choices and rated their confidence in having made the right decisions. Contrary to assumptions of the self-control account, confidence was not higher when participants chose delayed rewards. Rather, participants were more confident in their decisions when possible rewards were further apart in time-discounted subjective value, closer to the present, and larger in magnitude. Demonstrating metacognitive insight, participants were more confident in decisions that better aligned with their separate valuation of possible rewards. Decisions made with less confidence were more prone to changes-of-mind and more susceptible to a patience-enhancing manipulation. Together, our results establish that confidence in intertemporal choice tracks uncertainty in estimating and comparing the value of possible rewards—just as it does in decisions unrelated to self-control. Our findings challenge self-control views and instead cast intertemporal choice as a form of value-based decision-making about future possibilities. This article is part of the theme issue ‘Thinking about possibilities: mechanisms, ontogeny, functions and phylogeny’.
Causal learning, counterfactual reasoning and pretend play: a cross-cultural comparison of Peruvian, mixed- and low-socioeconomic status U.S. children

Pretend play universally emerges during early childhood and may support the development of causal inference and counterfactual reasoning. However, the amount of time spent pretending, the value that adults place on pretence and the scaffolding adults provide vary by both culture and socioeconomic status (SES). In middle class U.S. preschoolers, accuracy on a pretence-based causal reasoning task predicted performance on a similar causal counterfactual task. We explore the relationship between cultural environment, pretence and counterfactual reasoning in low-income Peruvian (N = 62) and low-income U.S. (N = 57) 3- to 4-year olds, and contrast findings against previous findings in an age-matched, mixed-SES U.S. sample (N = 60). Children learned a novel causal relationship, then answered comparable counterfactual and pretence-based questions about the relationship. Children's responses for counterfactual and pretence measures differed across populations, with Peruvian and lower-income U.S. children providing fewer causally consistent responses when compared with middle class U.S. children. Nevertheless, correlations between the two measures emerged in all populations. Across cohorts, children also provided more causally consistent answers during pretence than counterfactually. Our findings strengthen the hypothesis that causal pretend play is related to causal counterfactual reasoning across cultural contexts, while also suggesting a role for systematic environmental differences. This article is part of the theme issue ‘Thinking about possibilities: mechanisms, ontogeny, functions and phylogeny’.
Study of plume dynamics and plasma density during its expansion

The electron density is one of the crucial parameters in plasma plume, which plays a major role in producing the key reactive species required for biological and industrial applications. In this work, experiments are performed to estimate the spatial variation of plasma density in a steady plume. The time-resolved images obtained from the ICCD camera, plume current measurements are utilized for estimating the plasma density. We observed the plasma density increases from the glass nozzle to the plume tip. This increase in plasma density is due to the combined effect of reduction of drift velocity, charge, and area confinement of plume. Further, the intensity plots of the ICCD camera images obtained with larger exposure time validate the increased density at the plume tip. The plasma density along the plume gives information about the approximation to the plume exposure time desired and the impact it creates on the very sensitive targets. The spatial variation of plasma density in a plume is a futuristic requirement for several biological and industrial applications considering a single plasma device.
Emerging Technologies in K–12 Education: A Future HCI Research Agenda

This systematic mapping review sheds light on how emerging technologies have been introduced and taught in various K–12 learning settings, particularly with regard to artificial intelligence (AI), machine learning (ML), the internet of things (IoT), augmented reality (AR), and virtual reality (VR). These technologies are rapidly being integrated into children's everyday lives, but their functions and implications are rarely understood due to their complex and distributed nature. The review provides a rigorous overview of the state of the art based on 107 records published across the fields of human-computer interaction, learning sciences, computing education, and child–computer interaction between 2010 and 2020. The findings show the urgent need on a global scale for inter- and transdisciplinary research that can integrate these dispersed contributions into a more coherent field of research and practice. The article presents nine discussion points for developing a shared agenda to mature the field. Based on the HCI community's expertise in human-centred approaches to technology and aspects of learning, we argue that the community is ideally positioned to take a leading role in the realisation of this future research agenda.
Super Resolution DOA Based on Virtual Sparse Extension Array for FMCW Automotive Radar

Automotive radar has been emerging as a key technology enabling intelligent and autonomous features in modern vehicles. However, its great weakness is the poor angular resolution compared with its competitors, such as LiDAR or camera. Thus, one of the most challenging problems automotive radars faced is how to achieve high angular resolution, especially with the restriction of limited array aperture and in high dynamic environment. In this paper, a novel approach for high angular resolution DOA is proposed to separate two targets in the same range and Doppler cell by introducing one completely new concept of virtual sparse extension array. Based on the radar returns from the physical array, an extremely large virtual sparse aperture can be formed in a unique way. The simulation results demonstrate that, for a typical time division modulation (TDM) multiple-input multiple-output (MIMO) automotive radar with 3 transmitters and 4 receivers, the angular resolution can reach 0.01°, which is far better than other algorithms. In addition, the proposed method only needs single snapshot, and this is especially valuable to deal with the practical high dynamic environment.
Obstacle-recognition Method for Soccer Robot Based on Human Selective Attention

In the Robocup soccer competition, all participating robots must operate completely autonomously by using their own sensors to recognize information about their environment and determine what to do next to win the match. Therefore, real-time recognition of obstacles in constant motion is important. Considering the processing resources of the robot, it is difficult to achieve real-time recognition by using conventional computational methods. Therefore, inspired by the mechanism of selective attention in the human visual system, we developed an obstacle-recognition method. With this method, multiple obstacles can be recognized, and successful real-time recognition of multiple obstacles is possible by significantly reducing the required processing resources.