Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic convergence of phase separation and mitotic function in the disordered protein BuGZ

Intrinsically disordered proteins (IDPs) effect biological function despite their sequence‐encoded lack of preference for stable three‐dimensional structure. Among their many functions, IDPs form membraneless cellular compartments through liquid–liquid phase separation (LLPS), also termed biomolecular condensation. The extent to which LLPS has been evolutionarily selected remains largely unknown, as the complexities of IDP evolution hamper progress. Unlike structured proteins, rapid sequence divergence typical of IDPs confounds inference of their biophysical or biological functions from comparative sequence analyses. Here, we leverage mitosis as a universal eukaryotic feature to interrogate condensate evolutionary history. We observe that evolution has conserved the ability for six homologs of the mitotic IDP BuGZ to undergo LLPS and to serve the same mitotic function, despite low sequence conservation. We also observe that cellular context may tune LLPS. The phylogenetic correlation of LLPS and mitotic function in one protein raises the possibility of an ancient evolutionary interplay between LLPS and biological function, dating back at least 1.6 billion years to the last common ancestor of plants and animals.
Simultaneous control of natural and extra degrees of freedom by isometric force and electromyographic activity in the muscle-to-force null space

Objective. Muscle activation patterns in the muscle-to-force null space, i.e. patterns that do not generate task-relevant forces, may provide an opportunity for motor augmentation by allowing to control additional end-effectors simultaneously to natural limbs. Here we tested the feasibility of muscular null space control for augmentation by assessing simultaneous control of natural and extra degrees of freedom. Approach. We instructed eight participants to control translation and rotation of a virtual 3D end-effector by simultaneous generation of isometric force at the hand and null space activity extracted in real-time from the electromyographic signals recorded from 15 shoulder and arm muscles. First, we identified the null space components that each participant could control more naturally by voluntary co-contraction. Then, participants performed several blocks of a reaching and holding task. They displaced an ellipsoidal cursor to reach one of nine targets by generating force, and simultaneously rotated the cursor to match the target orientation by activating null space components. We developed an information-theoretic metric, an index of difficulty defined as the sum of a spatial and a temporal term, to assess individual null space control ability for both reaching and holding. Main results. On average, participants could reach the targets in most trials already in the first block (72%) and they improved with practice (maximum 93%) but holding performance remained lower (maximum 43%). As there was a high inter-individual variability in performance, we performed a simulation with different spatial and temporal task conditions to estimate those for which each individual participants would have performed best. Significance. Muscular null space control is feasible and may be used to control additional virtual or robotics end-effectors. However, decoding of motor commands must be optimized according to individual null space control ability.
An Interactive Voice Response System to Increase Physical Activity and Prevent Cancer in the Rural Alabama Black Belt: Design and Usability Study

Background Increased physical activity (PA) levels are associated with reduced risk and improved survival for several cancers; however, most Americans engage in less than the recommended levels of PA. Using interactive voice response (IVR) systems to provide personalized health education and counseling may represent a high-reach, low-cost strategy for addressing physical inactivity and cancer disparities in disproportionately burdened rural regions. However, there has been a paucity of research conducted in this area to date. Objective The aim of this study is to design, develop, and test the usability of an IVR system aimed at increasing PA levels in the rural Alabama Black Belt. Methods A pilot version of the IVR system was used to assess initial feasibility and acceptability. Detailed exit interviews were conducted to elicit participant feedback, which helped inform the development of a substantially upgraded in-house IVR system. This refined IVR system was then subjected to a sequential explanatory mixed methods evaluation. Participating rural county coordinators and research staff (N=10) tested the usability of the IVR system features for 2 weeks and then completed the System Usability Scale and qualitative semistructured interviews. Results The study sample comprised mostly African American people, women, rural county coordinators, and research staff (N=10). Participants rated the IVR system with a mean score of 81 (SD 5) on the System Usability Scale, implying excellent usability. In total, 5 overarching themes emerged from the qualitative interviews: likes or dislikes of the intervention, barriers to or facilitators of PA, technical difficulties, quality of calls, and suggestions for intervention improvement. Message framing on step feedback, call completion incentives, and incremental goal-setting challenges were areas identified for improvement. The positive areas highlighted in the interviews included the personalized call schedules, flexibility to call in or receive a call, ability to make up for missed calls, narration, and PA tips. Conclusions The usability testing and feedback received from the rural county coordinators and research staff helped inform a final round of refinement to the IVR system before use in a large randomized controlled trial. This study stresses the importance of usability testing of all digital health interventions and the benefits it can offer to the intervention.
Self-Esteem Moderates the Relationship Between Secure Attachment and Internalizing and Externalizing Problems in Preadolescence

This longitudinal study examined the interactive effects of secure attachment and self-esteem on change in internalizing and externalizing problems in a sample of preadolescents. 407 youth (Mage = 11.1 years) completed measures of self-esteem, secure attachment style, and peer nomination inventories tapping internalizing and externalizing problems at the beginning of the fourth and fifth grades. Results suggest that internalizing and externalizing problems may be reduced for securely attached youth with high self-esteem. Implications for future research are examined, along with a discussion on clinical applications of studies involving interaction effects.
State estimation of probabilistic hybrid systems with particle filters

Robotic and embedded systems have become increasingly pervasive in every-day applications, ranging from space probes and life support systems to autonomous rovers. In order to act robustly in the physical world, robotic systems must handle the uncertainty and partial observability inherent in most real-world situations. A convenient modeling tool for many applications, including fault diagnosis and visual tracking, are probabilistic hybrid models. In probabilistic hybrid models, the hidden state is represented with discrete and continuous state variables that evolve probabilistically. The hidden state is observed indirectly, through noisy observations. A challenge is that real-world systems are non-linear, consist of a large collection of concurrently operating components, and exhibit autonomous mode transitions, that is, discrete state transitions that depend on the continuous dynamics. In this thesis, we introduce an efficient algorithm for hybrid state estimation that combines Rao-Blackwellised particle filtering with a Gaussian representation. Conceptually, our algorithm samples trajectories traced by the discrete variables over time and, for each trajectory, estimates the continuous state with a Kalman Filter. A key insight to handling the autonomous transitions is to reuse the continuous estimates in the importance sampling step. We extended the class of autonomous transitions that can be efficiently handled by Gaussian techniques and provide a detailed empirical evaluation of the algorithm on a dynamical system with four continuous state variables. Our results indicate that our algorithm is substantially more efficient than non-RaoBlackwellised approaches. Though not as good as a k-best filter in nominal scenarios, our algorithm outperforms a k-best filter when the correct diagnosis has too low a probability to be included in the leading set of trajectories. Through these accomplishments, the thesis lays ground work for a unifying stochastic search algorithm that shares the benefits of both methods. Thesis Supervisor: Brian C. Williams Title: Associate Professor
Contrasting Effects of Local Environmental and Biogeographic Factors on the Composition and Structure of Bacterial Communities in Arid Monospecific Mangrove Soils

Mangrove ecosystems are increasingly being recognized for their potential to sequester atmospheric carbon, thereby mitigating the effects of anthropogenically driven greenhouse gas emissions. The bacterial community in the soils plays an important role in the breakdown and recycling of carbon and other nutrients. ABSTRACT Mangrove forests are important biotic sinks of atmospheric CO2 and play an integral role in nutrient-cycling and decontamination of coastal waters, thereby mitigating climatic and anthropogenic stressors. These services are primarily regulated by the activity of the soil microbiome. To understand how environmental changes may affect this vital part of the ecosystem, it is key to understand the patterns that drive microbial community assembly in mangrove forest soils. High-throughput amplicon sequencing (16S rRNA) was applied on samples from arid Avicennia marina forests across different spatial scales from local to regional. Alongside conventional analyses of community ecology, microbial co-occurrence networks were assessed to investigate differences in composition and structure of the bacterial community. The bacterial community composition varied more strongly along an intertidal gradient within each mangrove forest, than between forests in different geographic regions (Australia/Saudi Arabia). In contrast, co-occurrence networks differed primarily between geographic regions, illustrating that the structure of the bacterial community is not necessarily linked to its composition. The local diversity in mangrove forest soils may have important implications for the quantification of biogeochemical processes and is important to consider when planning restoration activities. IMPORTANCE Mangrove ecosystems are increasingly being recognized for their potential to sequester atmospheric carbon, thereby mitigating the effects of anthropogenically driven greenhouse gas emissions. The bacterial community in the soils plays an important role in the breakdown and recycling of carbon and other nutrients. To assess and predict changes in carbon storage, it is important to understand how the bacterial community is shaped by its environment. Here, we compared the bacterial communities of mangrove forests on different spatial scales, from local within-forest to biogeographic comparisons. The bacterial community composition differed more between distinct intertidal zones of the same forest than between forests in distant geographic regions. The calculated network structure of theoretically interacting bacteria, however, differed most between the geographic regions. Our findings highlight the importance of local environmental factors in shaping the microbial soil community in mangroves and highlight a disconnect between community composition and structure in microbial soil assemblages.
Basketball ball tracking: towards an automatic detection of infractions

Technology is being widely used in basketball courts. The best improvement in this field is Instant Replay: a crucial tool used by referees to review, in real time, certain controversial actions of a match handling a screen placed in the officials’ table. The aim of this project is to create a software that could be helpful while using Instant Replay to detect infractions automatically. The project basis is an accurate automatic tracking of a basketball ball: first, the foreground is extracted, then, a color filter is applied, and finally, an optical flow algorithm tracks the ball. Having detected the ball, two algorithms have been created in order to detect two common infractions: goaltending and shots out of possession. By recording some homemade videos with three cameras in a professional basketball court, algorithms could be tested, obtaining successful results. Resum La tecnologia és una eina cada vegada més utilitzada en les pistes de bàsquet. La millora més substancial en aquest camp ha estat l’Instant Replay: una eina crucial per als àrbitres que els serveix per revisar accions polèmiques d’un partit a temps real, utilitzant una pantalla situada a la taula d’anotadors. L’objectiu d’aquest projecte és crear un programa que pugui ser útil mentre s’usi l’Instant Replay , capaç de detectar infraccions automàticament. La base del projecte és un seguiment de la pilota de bàsquet: primer, s’extreu el primer pla de l’escena, després, s’aplica un filtre de color, i finalment, un algoritme de flux òptic segueix la pilota. Un cop detectada, s’han creat dos algoritmes per identificar dues infraccions tı́piques: els taps il·legals i els llançaments fora de temps. S’han grabat vı́deos amb un sistema de tres càmeres en una pista de bàsquet professional, amb els quals s’han testejat els algoritmes i s’han obtingut resultats satisfactoris.
Understanding Whole Grain Consumption among Low-Income Older Adults Using the Theory of Planned Behavior

Abstract Older adults have low whole grain (WG) intake. This qualitative study used the Theory of Planned Behavior (TPB) to identify low-income older adults’ WG beliefs. A convenience sample of 25 low-income adults 60 years and older were interviewed using questions developed based on TPB constructs: behavioral, normative, and control beliefs. Interviews were audio-recorded, transcribed verbatim, cross-checked for consistency, and analyzed using content analysis. Study results revealed that regarding behavioral beliefs, health benefits, taste, and nutrition were WG advantages and sensory qualities, higher cost, and longer cooking time were disadvantages. Regarding normative beliefs, healthcare professionals and family members approved WG intake and those less informed about WGs disapproved. Regarding control beliefs, availability/accessibility, knowledge of WG benefits, and WG cooking skills facilitated WG intake and age-related changes, WG cost, decreased motivation to cook, and low knowledge (label reading) were barriers. Results provide insights for developing programs to increase older adults’ WG intake.
Association between 17q21 variants and asthma predisposition in Pashtun population from Pakistan

Abstract Objective Asthma is a heterogeneous and genetically complex respiratory disease, and more than 300 million people are affected worldwide. In this study, frequencies of four SNPs (rs3816470, rs7216389, rs8067378, rs12603332) in chromosome 17q21 region were analyzed and their relationship with the asthma susceptibility, in the Pashtun population of Khyber Pakhtunkhwa province (KPK) of Pakistan were investigated. Methods DNA samples from 500 subjects (asthma cases/controls) were genotyped by Sanger sequencing. Chi-square tests, logistic regression analysis, linkage disequilibrium, and haplotype analysis techniques were applied to study the association of the SNPs with asthma. Results Genetic models, including recessive, dominant, co-dominant, over-dominant, and additive, were tested. The frequencies of alleles T/T at rs3816470 (OR = 1.91; 95%CI = 1.15–3.18; p = .011*) and rs7216389 (OR = 2.14; 95%CI = 1.21–3.79; p = .0076*), A/A at rs 8067378 (OR = 1.89; 95%CI = 1.17–3.06; p = .0081*), C/C at rs12603332 (OR = 1.97; 95%CI = 1.18–3.27; p = .008*), under recessive models, respectively, were significantly (p-values < .0125) associated with asthma susceptibility. The frequencies of T/T genotype in rs3816470 (OR = 6.01; 95%CI = 2.48–14.60; p = .000147*), and rs7216389 (OR = 5.05; 95%CI = 1.79–14.21; p = .003296*), and C/C at rs12603332 (OR = 2.64; 95%CI = 1.11–6.32; p = .019063*), were significantly (p-values < .0125) associated with asthma susceptibility in Pashtun women by stratified analysis based on age and gender. Similarly, three unique haplotypes were found associated with disease development and protective effect in female and male subjects. Linkage disequilibrium analysis presented a strong linkage (≥80%) between SNP variants and predicted their co-inheritance in the studied population. Conclusion The 17q21 variants (rs3816470, rs7216389, rs12603332) were found significantly (p-values < .0125) associated with asthma predisposition in the Pashtun population of KPK exclusively in the female asthmatic cases. Supplemental data for this article can be accessed
Cardiovascular Burden Is High in Pediatric Lung Transplant Recipients

Background. Cardiovascular morbidity is common in adults after lung transplantation (LTx) but has not been described for pediatric LTx recipients. Early subclinical cardiovascular damage is reflected by increases in pulse wave velocity (PWV; indicating arteriosclerosis), intima–media thickness (IMT; indicating atherosclerosis), and left ventricular mass index (LVMI; indicating left ventricular hypertrophy). Methods. We annually assessed 47 pediatric LTx recipients in a prospective longitudinal study (144 observations, mean 3.1 visits/patient, range of 1–4 visits, mean follow-up 2.2 y). Results. At inclusion, increased PWV and IMT were detected in 13% and 30%, respectively, and elevated LVMI was detected in 33%. Higher PWV was associated with male sex, longer time since LTx, higher diastolic blood pressure, and lower glomerular filtration rate. Male sex and lower hemoglobin levels were associated with higher IMT, and the presence of diabetes was associated with higher LVMI. Conclusions. Pediatric LTx recipients suffer from a high and sustained burden of subclinical cardiovascular damage. In light of improving long-term outcomes, cardiovascular morbidity needs to be addressed. Our analysis identified classical and nonclassical risk factors to be associated with the measures for cardiovascular damage, which could serve as targets for intervention.
Submicron drops from flapping bursting bubbles

Significance Bubble bursting aerosols play a critical role in forming clouds, scattering sunlight, and transporting pathogens from water to the air. Most of them are produced from the fragmentation of bubble cap film. They usually have a diameter below 1 μm. However, their physical production mechanism has remained unknown. In this work, we discovered that these drops are probably generated from flapping bubble cap film (like a flapping flag). It explains the mysterious relation between bubble size and number of drops produced per bubble, providing a fundamental framework for understanding the production flux of bubble bursting aerosols, such as sea spray aerosol, and substance transfer through the air–water interface during drop ejection. Tiny water drops produced from bubble bursting play a critical role in forming clouds, scattering sunlight, and transporting pathogens from water to the air. Bubbles burst by nucleating a hole at their cap foot and may produce jets or film drops. The latter originate from the fragmentation of liquid ligaments formed by the centripetal destabilization of the opening hole rim. They constitute a major fraction of the aerosols produced from bubbles with cap radius of curvature (R) > ∼0.4 × capillary length (a). However, our present understanding of the corresponding mechanisms does not explain the production of most submicron film drops, which represent the main number fraction of sea spray aerosols. In this study, we report observations showing that bursting bubbles with R < ∼0.4a are actually mainly responsible for submicron film drop production, through a mechanism involving the flapping shear instability of the cap with the outer environment. With this proposed pathway, the complex relations between bubble size and number of drops produced per bubble can be better explained, providing a fundamental framework for understanding the production flux of aerosols and the transfer of substances mediated by bubble bursting through the air–water interface and the sensitivity of the process to the nature of the environment.
Protein disulfide-isomerase A3 knockdown attenuates oxidized low-density lipoprotein-induced oxidative stress, inflammation and endothelial dysfunction in human umbilical vein endothelial cells by downregulating activating transcription factor 2

ABSTRACT Atherosclerosis is a chronic inflammatory disease implicated in oxidative stress and endothelial dysfunction. Protein disulfide-isomerase A3 (PDIA3) has been reported to regulate oxidative stress and suppress inflammation. This study aimed to explore the function of PDIA3 in atherosclerosis and the underlying mechanisms. PDIA3 expression in oxidized low-density lipoprotein (ox-LDL)-induced human umbilical vein endothelial cells (HUVECs) was detected using RT-qPCR and Western blotting. Following PDIA3 knockdown through transfection with small interfering RNA targeting PDIA3, cell viability, oxidative stress and inflammation in ox-LDL-induced HUVECs was examined using a Cell Counting Kit-8, corresponding kits and ELISA, respectively. The levels of CD31, α-smooth muscle, iNOS, p-eNOS, eNOS and NO were assessed using RT-qPCR, Western blotting and an NO kit to reflect endothelial dysfunction in ox-LDL-induced HUVECs. The relationship between PDIA3 and the activating transcription factor 2 (ATF2) was confirmed using co-immunoprecipitation. In addition, ATF2 expression was examined following PDIA3 silencing. The results indicated that PDIA3 was highly expressed in ox-LDL-induced HUVECs. PDIA3 silencing increased cell viability, and reduced oxidative stress and inflammation, as evidenced by the decreased levels of reactive oxygen species, malondialdehyde, TNF-α, IL-1β and IL-6, and increased superoxide dismutase and glutathione peroxidase activity. In addition, PDIA3 deletion improved endothelial dysfunction. PDIA3 interacted with ATF2, and PDIA3 deletion downregulated ATF2 expression. Furthermore, ATF2 overexpression reversed the effects of PDIA3 knockdown on ox-LDL-induced damage of HUVECs. Collectively, PDIA3 knockdown was found to attenuate ox-LDL-induced oxidative stress, inflammation and endothelial dysfunction in HUVECs by downregulating ATF2 expression, showing promise for the future treatment of atherosclerosis.