Miracle-dz/UniFAR-FTUs huggingface dataset:
Environmental complexity: A buffer against stress in the domestic chick

Birds kept in commercial production systems can be exposed to multiple stressors from early life and this alters the development of different morphological, immunological and behavioural indicators. We explore the hypothesis that provision of a complex environment during early life, better prepares birds to cope with stressful events as well as buffers them against future unpredictable stressful episodes. In this study, 96 one day old pullets were randomly distributed in eight pens (12 birds/pen). Half of the chicks (N = 48) were assigned to a Complex Environment (CENV: with perches, a dark brooder etc.) the others to a Simple Environment (SENV: without enrichment features). Half of the birds from each of these treatments were assigned to a No Stress (NSTR, 33°C) or to an acute Cold Stress (CSTR, 18–20°C) treatment during six hours on their second day of life. At four weeks of age, chicks with these four different backgrounds were exposed to an Intermittent Stressful Challenges Protocol (ISCP). In an immunological test indicative of pro-inflammatory status Phytohemagglutinin-P (PHA-P), the response of CSTR birds was ameliorated by rearing chicks in a CENV as they had a similar response to NSTR chicks and a significantly better pro-inflammatory response than those CSTR birds reared in a SENV (five days after the CSTR treatment was applied). A similar better response when coping with new challenges (the ISCP) was observed in birds reared in a CENV compared to those from a SENV. Birds reared in the CENV had a lower heterophil/lymphocyte ratio after the ISCP than birds reared in SENV, independently of whether or not they had been exposed to CSTR early in life. No effects of stress on general behaviour were detected, however, the provision of a CENV increased resting behaviour, which may have favoured stress recover. Additionally, we found that exposure to cold stress at an early age might have rendered birds more vulnerable to future stressful events. CSTR birds had lower humoral immune responses (sheep red blood cells induced antibodies) after the ISCP and started using elevated structures in the CENV later compared to their NSTR conspecifics. Our study reflects the importance of the early provision of a CENV in commercial conditions to reduce negative stress-related effects. Within the context of the theory of adaptive plasticity, our results suggest that the early experience of the birds had long lasting effects on the modulation of their phenotypes.
Magnetic Resonance Imaging of Cerebral Small Vessel Disease in Men Living with HIV and HIV-Negative Men Aged 50 and Above.

We assessed whether HIV status was associated with white matter hyperintensities (WMH), a neuroimaging correlate of cerebral small vessel disease (CSVD), in men aged ≥50 years. A cross-sectional substudy was nested within a larger cohort study. Virologically suppressed men living with HIV (MLWH) and demographically matched HIV-negative men aged ≥50 underwent magnetic resonance imaging (MRI) at 3 Tesla. Sequences included volumetric three-dimensional (3D) T1-weighted, fluid-attenuated inversion recovery and pseudocontinuous arterial spin labeling. Regional segmentation by automated image processing algorithms was used to extract WMH volume (WMHV) and resting cerebral blood flow (CBF). The association between HIV status and WMHV as a proportion of intracranial volume (ICV; log-transformed) was estimated using a multivariable linear regression model. Thirty-eight MLWH [median age 59 years (interquartile range, IQR 55-64)] and 37 HIV-negative [median 58 years (54-63)] men were analyzed. MLWH had median CD4+ count 570 (470-700) cells/μL and a median time since diagnosis of 20 (14-24) years. Framingham 10-year risk of cardiovascular disease was 6.5% in MLWH and 7.4% in controls. Two (5%) MLWH reported a history of stroke or transient ischemic attack and five (13%) reported coronary heart disease compared with none of the controls. The total WMHV in MLWH was 1,696 μL (IQR 1,229-3,268 μL) or 0.10% of ICV compared with 1,627 μL (IQR 1,032-3,077 μL), also 0.10% of ICV in the HIV-negative group (p = .43). In the multivariable model, WMHV/ICV was not associated with HIV status (p = .86). There was an age-dependent decline in cortical CBF [-3.9 mL/100 mL/min per decade of life (95% confidence interval 1.1-6.7 mL)] but no association between CBF and HIV status (p > .2 in all brain regions analyzed). In conclusion, we found no quantitative MRI evidence of an increased burden of CSVD in MLWH aged 50 years and older.
Maximum Likelihood Methods for Hierarchical Structure from Motion of Uncalibrated Video

HEINRICH, STUART BENJAMIN. Maximum Likelihood Methods for Hierarchical Structure from Motion of Uncalibrated Video. (Under the direction of Wesley Snyder.) This dissertation addresses the general problem of reconstructing static 3D scene structure and camera parameters from an uncalibrated video or image series using structure from motion. Using these techniques, reconstructions can be made from video or still images taken with any hand held camera. We make no prior assumptions about the camera except that it takes images that are not stretched or skewed, which is true for all modern cameras, and require no additional information beyond the images. The advancements proposed in this dissertation include a novel overall system architecture that is designed to maximize robustness to noise and outliers, analysis of the theoretical instabilities of traditional methods of autocalibration along with a maximum likelihood approach that overcomes these limitations, a maximum likelihood method of merging projective reconstructions that is invariant to the uncertainty in structure points, a parallel decomposition for bundle adjustment, a derivation of new internal constraints of the trifocal tensor, and several other contributions. Many of these advancements are useful not only to uncalibrated video reconstruction but also reconstructions from arbitrary photo collections as well as visual odometry systems for robot navigation. c © Copyright 2011 by Stuart Benjamin Heinrich
Diverse genotypes of the amphibian‐killing fungus produce distinct phenotypes through plastic responses to temperature

Phenotypes are the target of selection and affect the ability of organisms to persist in variable environments. Phenotypes can be influenced directly by genes and/or by phenotypic plasticity. The amphibian‐killing fungus Batrachochytrium dendrobatidis (Bd) has a global distribution, unusually broad host range, and high genetic diversity. Phenotypic plasticity may be an important process that allows this pathogen to infect hundreds of species in diverse environments. We quantified phenotypic variation of nine Bd genotypes from two Bd lineages (Global Pandemic Lineage [GPL] and Brazil) and a hybrid (GPL‐Brazil) grown at three temperatures (12, 18 and 24°C). We measured five functional traits including two morphological traits (zoospore and zoosporangium sizes) and three life history traits (carrying capacity, time to fastest growth and exponential growth rate) in a phylogenetic framework. Temperature caused highly plastic responses within each genotype, with all Bd genotypes showing phenotypic plasticity in at least three traits. Among genotypes, Bd generally showed the same direction of plastic response to temperature: larger zoosporangia, higher carrying capacity, longer time to fastest growth and slower exponential growth at lower temperatures. The exception was zoospore size, which was highly variable. Our findings indicate that Bd genotypes have evolved novel phenotypes through plastic responses to temperature over very short timescales. High phenotypic variability likely extends to other traits and may facilitate the large host range and rapid spread of Bd.
The effect of interactive computer play on balance and functional abilities in children with moderate cerebral palsy: a pilot randomized study

Objectives: To investigate the feasibility and potential efficacy of a six-week interactive computer play training on balance and gross motor function in children with moderate cerebral palsy. Design: A pilot single-blinded matched randomized controlled study. Setting: Community. Participants: In total, 18 children with moderate cerebral palsy were recruited, paired according to age and severity of cerebral palsy and randomized into intervention group or control group. Intervention: The intervention group received additional trunk control training using the interactive computer play in sitting four times per week, 20 minutes per session for six weeks. All study children continued their usual physiotherapy programme. Measurements: All study children were assessed at baseline, week 3, week 6 (completion of intervention) and week 12 using the Pediatric Reach Test, Gross Motor Function Measure–66-Item Set and 2-Minute Walk Test. Results: All intervention children completed and enjoyed the training with no reported adverse event. All children were assessed at all time points. No significant difference was found between the two groups in all assessments. In both groups of children, significant improvements were found in the Gross Motor Function Measure–66-Item Set between week 3 (intervention group: mean 53.41, SD 5.34; control group: mean 52.86, SD 8.33) and week 6 (intervention group: mean 55.00, SD 6.32; control group: mean 54.20, SD 8.35). Conclusion: The intervention protocol of a six-week interactive computer play training was feasible and safe for children with moderate cerebral palsy in special school settings. Future studies with larger sample sizes or using single-subject designs are recommended.
The Synergistic Effects of APOE Genotype and Obesity on Alzheimer’s Disease Risk

The APOE gene has three common alleles—E2, E3, and E4, with APOE4 being the strongest genetic risk factor for developing Alzheimer’s Disease (AD). Obesity is a global epidemic and contributes to multiple metabolic problems. Obesity is also a risk factor for cognitive decline. Here, we review the effects of APOE4 and obesity on cognition and AD development, independently and together. We describe studies that have associated APOE4 with cognitive deficits and AD, as well as studies that have associated obesity to cognitive deficits and AD. We then describe studies that have examined the effects of obesity and APOE genotypes together, with a focus on APOE4 and high fat diets. Both human studies and rodent models have contributed to understanding the effects of obesity on the different APOE genotypes, and we outline possible underlying mechanisms associated with these effects. Data across approaches support a model in which APOE4 and obesity combine for greater detrimental effects on metabolism and cognition, in ways that are influenced by both age and sex.
A qualitative study about the experiences of ethnic minority pregnant women with gestational diabetes.

BACKGROUND Gestational diabetes mellitus demands rapid health behaviour changes for the pregnant woman to obtain stable blood glucose levels. In Denmark, the general incidence of gestational diabetes mellitus is about 3%, but more than 4.5% among non-Western immigrants and descendants. Women belonging to ethnic minorities may be particularly challenged by health behaviour changes due to educational, language and cultural barriers. AIM To explore how non-Western ethnic minority pregnant women in Denmark experience the hospital-based information about gestational diabetes mellitus and how they integrate this information into their everyday life. A secondary aim was to investigate how health literacy and distributed health literacy affect this process. METHODS Semistructured, qualitative interviews with 11 women. Thematic analysis was conducted with a special focus on health literacy as analytical approach. RESULTS Three themes were identified: Reaction to the diagnosis, Everyday life and Information needs. All women felt sad and worried by the diagnosis. Some struggled to implement the recommended behaviour changes, and many lacked supports from their spouse. The hospital-based information was positively evaluated, but in some cases, the information was misunderstood. Social networks, language skills, and the ability to seek and assess information were important factors influencing the degree to which the women experienced gestational diabetes mellitus to be a challenge. CONCLUSION Women were generally satisfied with the hospital-based information. Women with low health literacy/poor Danish language skills seem to be most challenged by the diagnosis. Future research should examine ways to organise patient-centred health care while simultaneously supporting women's opportunity to increase health literacy through, for example social network and the Internet.
HOMA‐IR: An independent predictor of advanced liver fibrosis in nondiabetic non‐alcoholic fatty liver disease

Although non‐alcoholic fatty liver disease (NAFLD) is common in the general population, identifying patients with advanced fibrosis remains a challenge. We investigated whether the homeostasis model assessment parameter of insulin resistance (HOMA‐IR), an index of IR and one of the most important metabolic factors, is an independent predictive factor for advanced fibrosis in nondiabetic patients with NAFLD.
Time for change: using implementation intentions to promote physical activity in a randomised pilot trial

Abstract Objective: A common barrier to exercise is a perceived lack of time. The current pilot study examined the effects of an implementation intention intervention to enhance exercise self-efficacy, increase confidence to exercise when facing time constraints, and increase physical activity in middle-aged adults (n = 63, aged 35–69). Design: Participants received a pedometer (Fitbit) to objectively measure activity and were randomly assigned to either a control or intervention condition. After a 1-week baseline, the intervention condition received instructions to plan how, where, and when they would add steps to their daily routine to meet their step goal, using personalised schedules and maps. Both groups were contacted nightly via email. Main Outcome Measures: Physical activity (steps and time spent in moderate-to-vigorous activity), goal achievement, exercise self-efficacy, time-relevant exercise self-efficacy and affect. Results: Compared to the control, the intervention condition significantly increased in steps, time spent in moderate-to-vigorous activity, and time-relevant exercise self-efficacy. Goal achievement was related to greater time-relevant exercise self-efficacy and more positive affect at the daily level. Conclusion: Findings suggest that the personalised planning intervention increased physical activity and confidence in achieving physical activity goals under time constraints. Avenues for future directions, especially for producing more sustained effects, are discussed.
Targeted exome sequencing of unselected heavy‐ion beam‐irradiated populations reveals less‐biased mutation characteristics in the rice genome

Summary Heavy‐ion beams have been widely utilized as a novel and effective mutagen for mutation breeding in diverse plant species, but the induced mutation spectrum is not fully understood at the genome scale. We describe the development of a multiplexed and cost‐efficient whole‐exome sequencing procedure in rice, and its application to characterize an unselected population of heavy‐ion beam‐induced mutations. The bioinformatics pipeline identified single‐nucleotide mutations as well as small and large (>63 kb) insertions and deletions, and showed good agreement with the results obtained with conventional polymerase chain reaction (PCR) and sequencing analyses. We applied the procedure to analyze the mutation spectrum induced by heavy‐ion beams at the population level. In total, 165 individual M2 lines derived from six irradiation conditions as well as eight pools from non‐irradiated ‘Nipponbare’ controls were sequenced using the newly established target exome sequencing procedure. The characteristics and distribution of carbon‐ion beam‐induced mutations were analyzed in the absence of bias introduced by visual mutant selections. The average (±SE) number of mutations within the target exon regions was 9.06 ± 0.37 induced by 150 Gy irradiation of dry seeds. The mutation frequency changed in parallel to the irradiation dose when dry seeds were irradiated. The total number of mutations detected by sequencing unselected M2 lines was correlated with the conventional mutation frequency determined by the occurrence of morphological mutants. Therefore, mutation frequency may be a good indicator for sequencing‐based determination of the optimal irradiation condition for induction of mutations.
Diagnostic Utility of Exome Sequencing for Kidney Disease

BACKGROUND Exome sequencing is emerging as a first‐line diagnostic method in some clinical disciplines, but its usefulness has yet to be examined for most constitutional disorders in adults, including chronic kidney disease, which affects more than 1 in 10 persons globally. METHODS We conducted exome sequencing and diagnostic analysis in two cohorts totaling 3315 patients with chronic kidney disease. We assessed the diagnostic yield and, among the patients for whom detailed clinical data were available, the clinical implications of diagnostic and other medically relevant findings. RESULTS In all, 3037 patients (91.6%) were over 21 years of age, and 1179 (35.6%) were of self‐identified non‐European ancestry. We detected diagnostic variants in 307 of the 3315 patients (9.3%), encompassing 66 different monogenic disorders. Of the disorders detected, 39 (59%) were found in only a single patient. Diagnostic variants were detected across all clinically defined categories, including congenital or cystic renal disease (127 of 531 patients [23.9%]) and nephropathy of unknown origin (48 of 281 patients [17.1%]). Of the 2187 patients assessed, 34 (1.6%) had genetic findings for medically actionable disorders that, although unrelated to their nephropathy, would also lead to subspecialty referral and inform renal management. CONCLUSIONS Exome sequencing in a combined cohort of more than 3000 patients with chronic kidney disease yielded a genetic diagnosis in just under 10% of cases. (Funded by the National Institutes of Health and others.)
Nonlinear model for the carotid artery disease 10‐year risk prediction by fusing conventional cardiovascular factors to carotid ultrasound image phenotypes: A Japanese diabetes cohort study

This study presents a novel nonlinear model which can predict 10‐year carotid ultrasound image‐based phenotypes by fusing nine traditional cardiovascular risk factors (ethnicity, gender, age, artery type, body mass index, hemoglobin A1c, hypertension, low‐density lipoprotein, and smoking) with five types of carotid automated image phenotypes (three types of carotid intima‐media thickness (IMT), wall variability, and total plaque area).
Normal Speech Should be the Expected Outcome in the Adopted Cleft Child

Significantly worse speech outcomes and higher complication rates are reported among internationally adopted cleft patients. We evaluated our cohort to provide more accurate counseling to adoptive parents. Methods We reviewed internationally adopted children with unrepaired cleft palate who had 2-flap palatoplasty with radical intravelarveloplasty from 2003 to 2015 in a single-surgeon, consecutive series. Results Seventy-two children adopted with unrepaired cleft palate were identified, 2 with syndromic association. The average age at palatoplasty was 28.1 months. Meaningful speech assessment was available in 58 patients. Successful speech was defined by a competent or borderline-competent velopharyngeal mechanism (Pittsburgh Weighted Speech Score <2). Twenty-five patients (43%) had successful speech outcomes. Twenty-nine patients (50%) were recommended secondary operation for nasality. Nonfistula repair secondary operation was performed using the following: fat grafting (9 patients, 43%), intravelarveloplasty (8 patients, 38%), and sphincter pharyngoplasty (4 patients, 19%). The average Pittsburgh Weighted Speech Score improved 5.8 to 1.3 (P = 1.3E-6); 4.8 to 1.0 (P = 0.0009) with fat grafting alone. After all interventions, normal speech was achieved in 43 (74%) of 58 patients. Palatal fistula (9.2% vs 0.9%, P = 0.001) and velopharyngeal insufficiency (50% vs 6.7%, P = 0.0004) rates were both significantly higher in the internationally adopted cohort than our nonadopted population data. The need for secondary surgery was independent of cleft type (P = 0.89), age (P = 0.78), or presence of a “wide” cleft (P = 1). Conclusions Our results demonstrate higher fistula and secondary surgery rates. Successful speech outcomes were achieved in most patients with minimally invasive secondary procedures.
Yeast-model-based study identified myosin- and calcium-dependent calmodulin signalling as a potential target for drug intervention in chorea-acanthocytosis

ABSTRACT Chorea-acanthocytosis (ChAc) is a rare neurodegenerative disease associated with mutations in the human VPS13A gene. The mechanism of ChAc pathogenesis is unclear. A simple yeast model was used to investigate the function of the single yeast VSP13 orthologue, Vps13. Vps13, like human VPS13A, is involved in vesicular protein transport, actin cytoskeleton organisation and phospholipid metabolism. A newly identified phenotype of the vps13Δ mutant, sodium dodecyl sulphate (SDS) hypersensitivity, was used to screen a yeast genomic library for multicopy suppressors. A fragment of the MYO3 gene, encoding Myo3-N (the N-terminal part of myosin, a protein involved in the actin cytoskeleton and in endocytosis), was isolated. Myo3-N protein contains a motor head domain and a linker. The linker contains IQ motifs that mediate the binding of calmodulin, a negative regulator of myosin function. Amino acid substitutions that disrupt the interaction of Myo3-N with calmodulin resulted in the loss of vps13Δ suppression. Production of Myo3-N downregulated the activity of calcineurin, a protein phosphatase regulated by calmodulin, and alleviated some defects in early endocytosis events. Importantly, ethylene glycol tetraacetic acid (EGTA), which sequesters calcium and thus downregulates calmodulin and calcineurin, was a potent suppressor of vps13Δ. We propose that Myo3-N acts by sequestering calmodulin, downregulating calcineurin and increasing activity of Myo3, which is involved in endocytosis and, together with Osh2/3 proteins, functions in endoplasmic reticulum-plasma membrane contact sites. These results show that defects associated with vps13Δ could be overcome, and point to a functional connection between Vps13 and calcium signalling as a possible target for chemical intervention in ChAc. Yeast ChAc models may uncover the underlying pathological mechanisms, and may also serve as a platform for drug testing. This article has an associated First Person interview with the first author of the paper. Summary: Using the vps13Δ strain, a yeast model of the neurodegenerative disorder chorea-acanthocytosis, we found that its defects can be overcome by reduction of calcineurin activity and/or type-I-myosin activation.