Miracle-dz/UniFAR-FTUs huggingface dataset:
The nature and role of patient expectations in exercise in osteoarthritis

The purpose of this thesis was to explore the area of expectations and examine their role in exercise behaviour in individuals with knee ostcoarthritis (OA). In a systematic review on the role of expectations in interventions for chronic musculoskeletal joint pain, positive expectations were consistently related to positive outcomes. However, only three studies were suitable and a number of methodological problems with measuring expectations were identified. A cross-sectional qualitative study explored outcome and treatment expectations and findings were used to develop a questionnaire to measure OA-related beliefs. In a second qualitative study a small number of participants were re-interviewed a year later to examine how the condition and perceptions of the condition had changed. Findings suggest expectations are malleable and respond to new information. The Knee Pain Beliefs Questionnaire (KPBQ) was developed from the qualitative data and consisted of four factors, including two on expectations (future state/illness expectations and defensive optimism). The measure showed satisfactory internal reliability, test-retest reliability and discriminant validity. The KPBQ was used to measure expectations in a sample of primary care OA patients. Questionnaires were completed at baseline (time 1), time 2 (approximately 8 weeks after baseline) and time 3 (approximately 8 months after baseline). In the cross-sectional analyses of these data (N=80), illness expectations and defensive optimism were more strongly related to activity levels than outcome or self-efficacy expectations, with higher illness expectations and lower defensive optimism scores related to higher activity levels. In the longitudinal analyses (N=57), more positive illness expectations predicted lower activity levels at time 3, but expectations were not significant at time 2. Recommendations for future work include examining the different effects of expectations and hopes, clarifying the role of uncertainty, testing an extended version of the Self-Regulatory Model that incorporates dispositional optimism, and developing novel interventions.
Effects of Consuming Almonds on Insulin Sensitivity and Other Cardiometabolic Health Markers in Adults With Prediabetes

Abstract Objective: This study was designed to assess the effects of replacing high-carbohydrate (CHO) foods with raw almonds on insulin sensitivity and cardiometabolic health markers in overweight or obese adults with prediabetes. Method: This randomized crossover study consisted of two 6-week dietary intervention periods, separated by a ≥ 4-week washout. Subjects incorporated 1.5 oz of raw almonds twice daily or isocaloric CHO-based foods into their diets, with instructions to maintain body weight. Dietary intakes as well as insulin sensitivity, CHO metabolism indices, lipoprotein lipids and particles, and inflammatory markers were assessed. Results: Thirty-three subjects (17 male, 16 female), mean age 48.3 ± 2.2 years and body mass index 30.5 ± 0.7 kg/m2, provided evaluable data. Compared to CHO, almonds resulted in significantly (p < 0.01) higher intakes of protein, fat (unsaturated fatty acids), fiber, and magnesium and significantly (p < 0.001) lower intakes of CHO and sugars. No differences were observed between diet conditions for changes from baseline in the insulin sensitivity index from a short intravenous glucose tolerance test or other indices of glucose homeostasis. No significant differences were observed in biomarkers of cardiovascular risk except that the CHO intervention led to a shift toward a higher concentration of cholesterol in small, dense low-density lipoprotein subfraction 3+4 (LDL3 + 4) particles (p = 0.024 vs almonds). Conclusions: Intake of 3.0 oz/d raw almonds, vs energy-matched CHO foods, improved the dietary nutrient profile, but did not significantly affect insulin sensitivity and most markers of cardiometabolic health in overweight and obese men and women with prediabetes.
Structural characteristics of lipocalin allergens: Crystal structure of the immunogenic dog allergen Can f 6

Lipocalins represent the most important protein family of the mammalian respiratory allergens. Four of the seven named dog allergens are lipocalins: Can f 1, Can f 2, Can f 4, and Can f 6. We present the structure of Can f 6 along with data on the biophysical and biological activity of this protein in comparison with other animal lipocalins. The Can f 6 structure displays the classic lipocalin calyx-shaped ligand binding cavity within a central β-barrel similar to other lipocalins. Despite low sequence identity between the different dog lipocalin proteins, there is a high degree of structural similarity. On the other hand, Can f 6 has a similar primary sequence to cat, horse, mouse lipocalins as well as a structure that may underlie their cross reactivity. Interestingly, the entrance to the ligand binding pocket is capped by a His instead of the usually seen Tyr that may help select its natural ligand binding partner. Our highly pure recombinant Can f 6 is able to bind to human IgE (hIgE) demonstrating biological antigenicity.
Regression of Epileptogenesis by Inhibiting Tropomyosin Kinase B Signaling following a Seizure

Temporal lobe epilepsy (TLE) is a devastating disease in which seizures persist in 35% of patients despite optimal use of antiseizure drugs. Clinical and preclinical evidence implicates seizures themselves as one factor promoting epilepsy progression. What is the molecular consequence of a seizure that promotes progression? Evidence from preclinical studies led us to hypothesize that activation of tropomyosin kinase B (TrkB)–phospholipase‐C‐gamma‐1 (PLCγ1) signaling induced by a seizure promotes epileptogenesis.
Scenes Modulate Object Processing Before Interacting With Memory Templates

When searching for relevant objects in our environment (say, an apple), we create a memory template (a red sphere), which causes our visual system to favor template-matching visual input (applelike objects) at the expense of template-mismatching visual input (e.g., leaves). Although this principle seems straightforward in a lab setting, it poses a problem in naturalistic viewing: Two objects that have the same size on the retina will differ in real-world size if one is nearby and the other is far away. Using the Ponzo illusion to manipulate perceived size while keeping retinal size constant, we demonstrated across 71 participants that visual objects attract attention when their perceived size matches a memory template, compared with mismatching objects that have the same size on the retina. This shows that memory templates affect visual selection after object representations are modulated by scene context, thus providing a working mechanism for template-based search in naturalistic vision.
Graph convolutional network approach applied to predict hourly bike-sharing demands considering spatial, temporal, and global effects

Solving the supply–demand imbalance is the most crucial issue for stable implementation of a public bike-sharing system. This gap can be reduced by increasing the accuracy of demand prediction by considering spatial and temporal properties of bike demand. However, only a few attempts have been made to account for both features simultaneously. Therefore, we propose a prediction framework based on graph convolutional networks. Our framework reflects not only spatial dependencies among stations, but also various temporal patterns over different periods. Additionally, we consider the influence of global variables, such as weather and weekday/weekend to reflect non-station-level changes. We compare our framework to other baseline models using the data from Seoul’s bike-sharing system. Results show that our approach has better performance than existing prediction models.
DNA barcoding of southern African crustaceans reveals a mix of invasive species and potential cryptic diversity

Globally, crustaceans represent one of the most taxonomically diverse and economically important invertebrate group. Notwithstanding, the diversity within this group is poorly known because most crustaceans are often associated with varied habits, forms, sizes and habitats; making species identification by conventional methods extremely challenging. In addition, progress towards understanding the diversity within this group especially in southern Africa has been severely hampered by the declining number of trained taxonomists, the presence of invasive alien species, over exploitation, etc. However, the advent of molecular techniques such as “DNA barcoding and Metabarcoding” can accelerate species identification and the discovery of new species. To contribute to the growing body of knowledge on crustacean diversity, we collected data from five southern African countries and used a DNA barcoding approach to build the first DNA barcode reference library for southern African crustaceans. We tested the reliability of this DNA barcode reference library to facilitate species identification using two approaches. We recovered high efficacy of specimen identification/discrimination; supported by both barcode gap and tree-base species identification methods. In addition, we identified alien invasive species and specimens with ‘no ID” in our DNA barcode reference library. The later; highlighting specimens requiring (i) further investigation and/or (ii) the potential presence of cryptic diversity or (iii) misidentifications. This unique data set although with some sampling gaps presents many opportunities for exploring the effect and extent of invasive alien species, the role of the pet trade as a pathway for crustacean species introduction into novel environments, sea food authentication, phylogenetic relationships within the larger crustacean groupings and the discovery of new species.
Seizure initiation in infantile spasms vs. focal seizures: proposed common cellular mechanisms

Abstract Infantile spasms (IS) and seizures with focal onset have different clinical expressions, even when electroencephalography (EEG) associated with IS has some degree of focality. Oddly, identical pathology (with, however, age-dependent expression) can lead to IS in one patient vs. focal seizures in another or even in the same, albeit older, patient. We therefore investigated whether the cellular mechanisms underlying seizure initiation are similar in the two instances: spasms vs. focal. We noted that in-common EEG features can include (i) a background of waves at alpha to delta frequencies; (ii) a period of flattening, lasting about a second or more – the electrodecrement (ED); and (iii) often an interval of very fast oscillations (VFO; ~70 Hz or faster) preceding, or at the beginning of, the ED. With IS, VFO temporally coincides with the motor spasm. What is different between the two conditions is this: with IS, the ED reverts to recurring slow waves, as occurring before the ED, whereas with focal seizures the ED instead evolves into an electrographic seizure, containing high-amplitude synchronized bursts, having superimposed VFO. We used in vitro data to help understand these patterns, as such data suggest cellular mechanisms for delta waves, for VFO, for seizure-related burst complexes containing VFO, and, more recently, for the ED. We propose a unifying mechanistic hypothesis – emphasizing the importance of brain pH – to explain the commonalities and differences of EEG signals in IS versus focal seizures.
The monothiol glutaredoxin GrxD is essential for sensing iron starvation in Aspergillus fumigatus

Efficient adaptation to iron starvation is an essential virulence determinant of the most common human mold pathogen, Aspergillus fumigatus. Here, we demonstrate that the cytosolic monothiol glutaredoxin GrxD plays an essential role in iron sensing in this fungus. Our studies revealed that (i) GrxD is essential for growth; (ii) expression of the encoding gene, grxD, is repressed by the transcription factor SreA in iron replete conditions and upregulated during iron starvation; (iii) during iron starvation but not iron sufficiency, GrxD displays predominant nuclear localization; (iv) downregulation of grxD expression results in de-repression of genes involved in iron-dependent pathways and repression of genes involved in iron acquisition during iron starvation, but did not significantly affect these genes during iron sufficiency; (v) GrxD displays protein-protein interaction with components of the cytosolic iron-sulfur cluster biosynthetic machinery, indicating a role in this process, and with the transcription factors SreA and HapX, which mediate iron regulation of iron acquisition and iron-dependent pathways; (vi) UV-Vis spectra of recombinant HapX or the complex of HapX and GrxD indicate coordination of iron-sulfur clusters; (vii) the cysteine required for iron-sulfur cluster coordination in GrxD is in vitro dispensable for interaction with HapX; and (viii) there is a GrxD-independent mechanism for sensing iron sufficiency by HapX; (ix) inactivation of SreA suppresses the lethal effect caused by GrxD inactivation. Taken together, this study demonstrates that GrxD is crucial for iron homeostasis in A. fumigatus.
Large-Scale Antitumor Screening Based on Heterotypic 3D Tumors Using an Integrated Microfluidic Platform.

Chemotherapy screening plays a crucial role in cancer drug discovery and clinical medicine. While conventional methods have contributed greatly to macromanipulation of cell populations, a profounder insight related to tumor microenvironment requires approaches for completing integrated cell/3D tumor micromanipulation, massive tumor simulation and production, dynamic and high-throughput tumor analysis. In this study, we introduced an integrated microfluidic platform with multi-parallel components for heterotypic 3D tumor reconstruction and antitumor screening. Sequential microfluidic manipulations including sample loading, precise localization, 3D tumor formation, chemical stimulation, on-chip analysis, and tumor recovery for off-chip assessment were permitted and experimentally confirmed in the device based on facile and efficient pneumatic control. Heterotypic 3D tumors with tissue-biomimetic phenotypes can be produced in massive and size-uniform manners. Notably, we accomplished screening-like chemotherapy assessment involving different heterotypic 3D tumors and antitumor drugs, and demonstrated the versatility of the platform in large-scale tumor manipulation and analysis. This advancement in microfluidics has potential applications in the fields of oncology, pharmacology, and tissue engineering, and provides insight into the construction of high-performance microsystems for drug development and cancer research.
Community exercise for individuals with spinal cord injury with inspiratory muscle training: A pilot study

Context/Objective: Respiratory disorders are a common cause of rehospitalization, and premature death in individuals with spinal cord injuries (SCI). Respiratory training combined with community exercise programs may be a method to reduce secondary complications in this population. Objective: The present study explores the inclusion of inspiratory muscle training (IMT) in an existing community exercise program. Design: Case series. Setting: Community. Participants: Participants (N = 6) completed the exercise program. Five were male and one was female; four reported incomplete injuries, and two reported complete injuries; four had cervical injuries, and two had thoracic injuries. The average age was 33 years (SD = 18.6) and time since injury was 7 years (SD = 4.0). Interventions: Participants completed an 8-week program, once-per-week for 4 h that included a circuit of resistance training, aerobic exercise, trunk stability, and education. IMT was completed as a home exercise program. Outcome Measures: Transfer test, T-shirt test, four-directional reach, four-directional trunk strength, weekly training diaries, and a subjective interview. Results: Twenty-eight training logs were collected. All measures improved: transfer test (mean = −14.62, SD = 7.00 s), T-shirt test (mean = −7.83, SD = 13.88 s), four-directional reach (mean = 3.75, SD = 8.06 in) and hand-held dynamometer (mean = 6.73, SD = 8.02 kg). Individuals reported a positive impact of the program. Conclusions: This pilot study demonstrated community exercise with IMT use may have positive impact on functional measures for people with SCI who are vulnerable to respiratory compromise. Continued education may increase successful health outcomes. Trial Registration: NCT03743077.
Body Composition in Early Alzheimer's Disease

Abstract Background: Alzheimer’s disease (AD) is associated with unintended weight loss. We examined body composition in early AD and nondemented aging and its relation to brain volume and cognition. Methods: Brain magnetic resonance imaging (MRI) and neuropsychological testing were performed on nondemented (CDR 0, n=70) and early-stage AD (CDR 0.5 or 1, n=70) subjects. Dual energy x-ray absorptiometry (DEXA) determined whole-body fat mass and lean mass. Body mass index (BMI) was determined from height and weight. Linear regression analyses controlling for age and sex assessed the relationship between body composition, cognition, and brain volume. Results: Lean mass was reduced in early AD compared to nondemented controls (F=7.73, p=0.006) after controlling for sex. Lean mass was associated with whole-brain volume (beta=0.20, p<0.001) and white matter volume (beta=0.19, p<0.001) when controlling for age and sex. Lean mass was also associated with global cognitive performance (beta=0.12, p=0.007) when controlling for age and sex. Total body fat and percent body fat were not different across groups or related to cognition and brain volume.
Genetic diversity and population structure of four Chinese rabbit breeds

There are a few well-known indigenous breeds of Chinese rabbits in Sichuan and Fujian provinces, for which the genetic diversity and population structure have been poorly investigated. In the present study, we successfully employed the restriction-site-associated DNA sequencing (RAD-seq) approach to comprehensively discover genome-wide SNPs of 104 rabbits from four Chinese indigenous breeds: 30 Sichuan White, 34 Tianfu Black, 32 Fujian Yellow and eight Fujian Black. A total of 7,055,440 SNPs were initially obtained, from which 113,973 high-confidence SNPs (read depth ≥ 3, calling rate = 100% and biallelic SNPs) were selected to study the genetic diversity and population structure. The mean polymorphism information content (PIC) and nucleotide diversity (π) of each breed slightly varied with ranging from 0.2000 to 0.2281 and from 0.2678 to 0.2902, respectively. On the whole, Fujian Yellow rabbits showed the highest genetic diversity, which was followed by Tianfu Black and Sichuan White rabbits. The principal component analysis (PCA) revealed that the four breeds were clearly distinguishable. Our results first reveal the genetic differences among these four rabbit breeds in the Sichuan and Fujian provinces and also provide a high-confidence set of genome-wide SNPs for Chinese indigenous rabbits that could be employed for gene linkage and association analyses in the future.
Feeling the heat: Elevated temperature affects male display activity of a lekking grassland bird

Most species-climate models relate range margins to long-term mean climate but lack mechanistic understanding of the ecological or demographic processes underlying the climate response. We examined the case of a climatically limited edge-of-range population of a medium-sized grassland bird, for which climate responses may involve a behavioural trade-off between temperature stress and reproduction. We hypothesised that temperature will be a limiting factor for the conspicuous, male snort-call display behaviour, and high temperatures would reduce the display activity of male birds. Using remote tracking technology with tri-axial accelerometers we classified and studied the display behaviour of 17 free-ranging male little bustards, Tetrax tetrax, at 5 sites in the Iberian Peninsula. Display behaviour was related to temperature using two classes of Generalized Additive Mixed Models (GAMMs) at different temporal resolutions. GAMMs showed that temperature, time of the day and Julian date explained variation in display behaviour within the day, with birds snort-calling significantly less during higher temperatures. We also showed that variation in daily snort-call activity was related to average daytime temperatures, with our model predicting an average decrease in daytime snort-call display activity of up to 10.4% for the temperature increases projected by 2100 in this region due to global warming. For lekking birds and mammals undertaking energetically-costly displays in a warming climate, reduced display behaviour could impact inter- and intra-sex mating behaviour interactions through sexual selection and mate choice mechanisms, with possible consequences on mating and reproductive success. The study provides a reproducible example for how accelerometer data can be used to answer research questions with important conservation inferences related to the impacts of climate change on a range of taxonomic groups.
Identification and Analysis of Differentially Expressed Genes in Human Saphenous Vein Endothelial Cells Overexpressing Domain-Containing mTOR-Interacting Protein (DEPTOR) by RNA-Seq

Background Autologous saphenous vein is the most common choice for coronary artery bypass grafting. This study was conducted to identify and characterize differentially expressed genes (DEGs) induced by overexpressing DEPTOR in human saphenous vein endothelial cells (hsVECs) that might play roles in restenosis. Material/Methods hsVECs isolated from the saphenous veins were transfected with DEPTOR overexpression vector and analyzed for mTOR expression. RNA was prepared from the cells and sequenced using high-throughput sequencing technology (RNA-Seq). The DEGs were analyzed based on enrichment scores in GO terms and KEGG pathways. Results The cells had typical hsVEC morphology and characteristics based on the HE staining and immunohistochemical and immunofluorescence assays. The expression of mTOR increased, and 102 genes were upregulated, and 409 genes were downregulated after DEPTOR overexpression. KEGG analysis showed that the DEGs were mainly enriched in 20 signal pathways, such as Focal adhesion and ECM-receptor interaction pathways. The DEGs were enriched in GO terms such as integrin binding and glycosaminoglycan binding. For cellular components, GO analysis revealed that the DEGs were enriched in main axon, plasma membrane part, cell junction, and proteinaceous extracellular matrix. DEGs included many cytokines, such as bone morphogenetic protein-7, interleukin-8, interleukin-1β, and inhibin, which have important effects on vascular growth and inflammation. Conclusions The overexpression of DEPTOR in hsVECs results in DEGs that are involved in cell proliferation and differentiation, intercellular junction, and extracellular matrix receptor. These findings may provide valuable molecular information for improving venous permeability through manipulation of DEPTOR and related mTOR pathways.