Miracle-dz/UniFAR-FTUs huggingface dataset:
Viral etiology of severe pneumonia among Kenyan infants and children.

CONTEXT Pneumonia is the leading cause of childhood death in sub-Saharan Africa. Comparative estimates of the contribution of causative pathogens to the burden of disease are essential for targeted vaccine development. OBJECTIVE To determine the viral etiology of severe pneumonia among infants and children at a rural Kenyan hospital using comprehensive and sensitive molecular diagnostic techniques. DESIGN, SETTING, AND PARTICIPANTS Prospective observational and case-control study during 2007 in a rural Kenyan district hospital. Participants were children aged 1 day to 12 years, residing in a systematically enumerated catchment area, and who either were admitted to Kilifi District Hospital meeting World Health Organization clinical criteria for severe pneumonia or very severe pneumonia; (2) presented with mild upper respiratory tract infection but were not admitted; or (3) were well infants and children attending for immunization. MAIN OUTCOME MEASURES The presence of respiratory viruses and the odds ratio for admission with severe disease. RESULTS Of 922 eligible admitted patients, 759 were sampled (82% [median age, 9 months]). One or more respiratory viruses were detected in 425 of the 759 sampled (56% [95% confidence interval {CI}, 52%-60%]). Respiratory syncytial virus (RSV) was detected in 260 participants (34% [95% CI, 31%-38%]) and other respiratory viruses were detected in 219 participants (29%; 95% CI, 26%-32%), the most common being Human coronavirus 229E (n = 51 [6.7%]), influenza type A (n = 44 [5.8%]), Parainfluenza type 3 (n = 29 [3.8%]), Human adenovirus (n = 29 [3.8%]), and Human metapneumovirus (n = 23 [3.0%]). Compared with well control participants, detection of RSV was associated with severe disease (5% [corrected] in control participants; adjusted odds ratio, 6.11 [95% CI, 1.65-22.6]) while collectively, other respiratory viruses were not associated with severe disease (23% in control participants; adjusted odds ratio, 1.27 [95% CI, 0.64-2.52]). CONCLUSION In a sample of Kenyan infants and children admitted with severe pneumonia to a rural hospital, RSV was the predominant viral pathogen.
An examination of self-determination, student participation in extracurricular activities and psychological well-being among juniors in one Massachusetts (U.S.) public high school

This quantitative research project examined self-determination and student participation in extracurricular activities (ECAs) as predictors of psychological well-being. The intent of the project is to provide educators and policymakers information on the value of providing opportunities for students to participate in ECAs in support of student well-being. The sample was 149 juniors attending one suburban public high school in Massachusetts. A single confidential questionnaire comprised of four sections was employed: (a) demographic questions (age, race), (b) ECA participation questions (what activity, time devoted), (c) Self-determination Scale (SDS) (Sheldon & Deci, 1996), and (d) Ryff Scale of Psychological Well-Being (Ryff & Singer, 2006). The study utilized descriptive statistics and inferential statistics utilizing the General Linear Model (GLM) including the t-test for differences between groups, t-tests for independent samples, correlation analyses, regression analysis and Levene’s Test for Equality of Variances. Findings suggest that statistically significant relationships exist between selfdetermination and well-being and between self-determination, ECA participation and well-being. Findings also revealed that the relationships between ECA participation and well-being and between self-determination and ECA participation were positive but not statistically significant. The study considered level of participation in ECAs serving as a dichotomous variable for which the subgroups were participants and nonparticipants. ECAs included in the study were schoolbased. Two study recommendations are that researchers extend the definition of level of participation and that outcomes derived from activities outside of schools be considered and studied together to consider positive or negative outcomes including well-being.
Post-Operative Benefits of Animal-Assisted Therapy in Pediatric Surgery: A Randomised Study

Background Interest in animal-assisted therapy has been fuelled by studies supporting the many health benefits. The purpose of this study was to better understand the impact of an animal-assisted therapy program on children response to stress and pain in the immediate post-surgical period. Patients and Methods Forty children (3–17 years) were enrolled in the randomised open-label, controlled, pilot study. Patients were randomly assigned to the animal-assisted therapy-group (n = 20, who underwent a 20 min session with an animal-assisted therapy dog, after surgery) or the standard-group (n = 20, standard postoperative care). The study variables were determined in each patient, independently of the assigned group, by a researcher unblinded to the patient’s group. The outcomes of the study were to define the neurological, cardiovascular and endocrinological impact of animal-assisted therapy in response to stress and pain. Electroencephalogram activity, heart rate, blood pressure, oxygen saturation, cerebral prefrontal oxygenation, salivary cortisol levels and the faces pain scale were considered as outcome measures. Results After entrance of the dog faster electroencephalogram diffuse beta-activity (> 14 Hz) was reported in all children of the animal-assisted therapy group; in the standard-group no beta-activity was recorded (100% vs 0%, p<0.001). During observation, some differences in the time profile between groups were observed for heart rate (test for interaction p = 0.018), oxygen saturation (test for interaction p = 0.06) and cerebral oxygenation (test for interaction p = 0.09). Systolic and diastolic blood pressure were influenced by animal-assisted therapy, though a higher variability in diastolic pressure was observed. Salivary cortisol levels did not show different behaviours over time between groups (p=0.70). Lower pain perception was noted in the animal-assisted group in comparison with the standard-group (p = 0.01). Conclusion Animal-assisted therapy facilitated rapid recovery in vigilance and activity after anaesthesia, modified pain perception and induced emotional prefrontal responses. An adaptative cardiovascular response was also present. Trial Registration ClinicalTrials.gov NCT02284100
Bringing the state back in: Understanding and validating measures of governments' political commitment to HIV

Analysis of the politics of HIV programme scale-up requires critical attention to the role of the state, since the state formulates HIV policies, provides resources for the HIV response and negotiates donor involvement in HIV programmes. However, conceptual and methodological approaches to analysing states' responses to HIV remain underdeveloped. Research suggests that differences in states' successes in HIV programme scale-up reflect their levels of ‘political commitment’ to responding to HIV. Few empirical measures of political commitment exist, and those that do, notably the AIDS Program Effort Index (API), employ ad hoc scoring approaches to combine information from different variables into an index of commitment. The indices are thus difficult to interpret and may not have empirically useful meaning. In this paper, we apply exploratory factor analysis to examine whether, and how, selected variables that comprise the API score reflect previously theorised dimensions of political commitment. We investigate how variables associated with each of the factors identified in the analyses correspond to these theorised dimensions as well as to API categories. Finally, we discuss potential uses – such as political benchmarking and accountability – and challenges of factor analysis as a means to identify and measure states' political commitment to respond to HIV.
Normal bone and soft tissue distribution of fluorine-18-sodium fluoride and artifacts on 18F-NaF PET/CT bone scan: a pictorial review

Fluorine-18-sodium fluoride (18F-NaF) PET/CT is a relatively new and high-resolution bone imaging modality. Since the use of 18F-NaF PET/CT has been increasing, it is important to accurately assess the images and be aware of normal distribution and major artifacts. In this pictorial review article, we will describe the normal uptake patterns of 18F-NaF in the bone tissues, particularly in complex structures, as well as its physiologic soft tissue distribution and certain artifacts seen on 18F-NaF PET/CT images.
Superior mitochondrial adaptations in human skeletal muscle after interval compared to continuous single‐leg cycling matched for total work

A classic unresolved issue in human integrative physiology involves the role of exercise intensity, duration and volume in regulating skeletal muscle adaptations to training. We employed counterweighted single‐leg cycling as a unique within‐subject model to investigate the role of exercise intensity in promoting training‐induced increases in skeletal muscle mitochondrial content. Six sessions of high‐intensity interval training performed over 2 weeks elicited greater increases in citrate synthase maximal activity and mitochondrial respiration compared to moderate‐intensity continuous training matched for total work and session duration. These data suggest that exercise intensity, and/or the pattern of contraction, is an important determinant of exercise‐induced skeletal muscle remodelling in humans.
Cancer Risk After Pediatric Solid Organ Transplantation

In a study of 17 958 pediatric solid organ transplant recipients, highly elevated cancer risk was identified for numerous cancer types. BACKGROUND: The effects of pediatric solid organ transplantation on cancer risk may differ from those observed in adult recipients. We described cancers in pediatric recipients and compared incidence to the general population. METHODS: The US transplant registry was linked to 16 cancer registries to identify cancer diagnoses among recipients <18 years old at transplant. Standardized incidence ratios (SIRs) were estimated by dividing observed cancer counts among recipients by expected counts based on the general population rates. Cox regression was used to estimate the associations between recipient characteristics and non-Hodgkin’s lymphoma (NHL) risk. RESULTS: Among 17 958 pediatric recipients, 392 cancers were diagnosed, of which 279 (71%) were NHL. Compared with the general population, incidence was significantly increased for NHL (SIR = 212, 95% confidence interval [CI] = 188–238), Hodgkin’s lymphoma (SIR = 19, 95% CI = 13–26), leukemia (SIR = 4, 95% CI = 2–7), myeloma (SIR = 229, 95% CI = 47–671), and cancers of the liver, soft tissue, ovary, vulva, testis, bladder, kidney, and thyroid. NHL risk was highest during the first year after transplantation among recipients <5 years old at transplant (SIR = 313), among recipients seronegative for Epstein-Barr virus (EBV) at transplant (SIR = 446), and among intestine transplant recipients (SIR = 1280). In multivariable analyses, seronegative EBV status, the first year after transplantation, intestine transplantation, and induction immunosuppression were independently associated with higher NHL incidence. CONCLUSIONS: Pediatric recipients have a markedly increased risk for many cancers. NHL constitutes the majority of diagnosed cancers, with the highest risk occurring in the first year after transplantation. NHL risk was high in recipients susceptible to primary EBV infection after transplant and in intestine transplant recipients, perhaps due to EBV transmission in the donor organ.
Flexible Multiple Description Lattice Vector Quantizer with L &amp;ge; 3 Descriptions

In previous work on multiple description lattice vector quantizers (MDLVQ) with L ≥ 3 descriptions, once the central and side lattice codebooks are fixed, the decoding quality is determined for all numbers k of received descriptions. Therefore, it is not possible to achieve tradeoffs between the quality of reconstruction for different values of k, 1 ≤ k ≤ L - 1. This work proposes a flexible MDLVQ capable of overcoming the above drawback. For this, a different reconstruction method is employed and a heuristic index assignment algorithm, which uses L - 2 parameters to control the distortions for 2 ≤ k ≤ L - 1, is developed. The second contribution of this work is a structured index assignment for the case L = 3 and the derivation of asymptotical expressions of the distortions at high resolution. The proposed index assignment has a simple mechanism for controlling the tradeoff between the reconstruction quality when k = 1 and when k = 2, and is able to achieve a wide range of distortion values.
Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils

Bioremediation is a cost-effective and sustainable approach for treating polluted soils, but our ability to improve on current bioremediation strategies depends on our ability to isolate microorganisms from these soils. Although culturing is widely used in bioremediation research and applications, it is unknown whether the composition of cultured isolates closely mirrors the indigenous microbial community from contaminated soils. To assess this, we paired culture-independent (454-pyrosequencing of total soil DNA) with culture-dependent (isolation using seven different growth media) techniques to analyse the bacterial and fungal communities from hydrocarbon-contaminated soils. Although bacterial and fungal rarefaction curves were saturated for both methods, only 2.4% and 8.2% of the bacterial and fungal OTUs, respectively, were shared between datasets. Isolated taxa increased the total recovered species richness by only 2% for bacteria and 5% for fungi. Interestingly, none of the bacteria that we isolated were representative of the major bacterial OTUs recovered by 454-pyrosequencing. Isolation of fungi was moderately more effective at capturing the dominant OTUs observed by culture-independent analysis, as 3 of 31 cultured fungal strains ranked among the 20 most abundant fungal OTUs in the 454-pyrosequencing dataset. This study is one of the most comprehensive comparisons of microbial communities from hydrocarbon-contaminated soils using both isolation and high-throughput sequencing methods.
Predictors of HIV Serodiscordance among Couples in Southwestern Ethiopia

Background: With transmission of HIV occurring mainly through heterosexual contact, it is paramount to identify serodiscordant couples and implement preventive strategies that will protect the negative partner. The burden of serodiscordance and its predictors in Ethiopia is not clearly understood due to the dearth of data. Objective: To assess the prevalence and predictors of HIV serodiscordance among couples tested in Jimma University Specialized Hospital (JUSH) Voluntary Counseling and Testing (VCT) center. Methods: The study employed a case–control study design conducted at VCT center of JUSH in all registered serodiscordant couples and seroconcordant couples that were selected from the registered clients in the period from 2003 to 2010. A pretested structured questionnaire was used for data collection using medical chart abstraction. Data were entered, cleaned, and coded using Statistical Package of Social Sciences (SPSS) version 16. Results: The prevalence of serodiscordance in the study population was found to be 8.4%. Male and female discordants accounted for 5.8% (137) and 2.6% (62), respectively. Rare use of condom (adjusted odds ratio [AOR] = 7.2; 95% confidence interval [CI] = 1.59-32.54) and active tuberculosis (TB) at enrollment (AOR= 17.7; 95% CI = 2.3-139.2) were significantly found to be the predictors of serodiscordance. Conclusion: The prevalence of serodiscordance in the study area was found to be low, but it contributes to a clinically significant population that mandates implementation of preventive strategy. Sero-positive individuals who use condoms rarely should be encouraged to have their partners tested, and the association between active TB and serodiscordance underscores the need for further study.
Elevated Homocysteine Level and Folate Deficiency Associated with Increased Overall Risk of Carcinogenesis: Meta-Analysis of 83 Case-Control Studies Involving 35,758 Individuals

Background Results of the association of folate metabolism and carcinogenesis are conflicting. We performed a meta-analysis to examine the effect of the interaction of serum concentration of homocysteine (Hcy), folate, and vitamin B12 and 5,10-methylenetetrahydrofolate reductase (MTHFR) polymorphism on risk of cancer overall. Method Two reviewers independently searched for all published studies of Hcy and cancer in PubMed, EMBASE-MEDLINE and Chinese databases. Pooled results were reported as odds ratios (ORs) and mean differences and presented with 95% confidence intervals (95% CIs) and 2-sided probability values. Results We identified 83 eligible studies of 15,046 cases and 20,712 controls. High level of Hcy but low level of folate was associated with risk of cancer overall, with little effect by type of cancer or ethnicity. Vitamin B12 level was inversely associated with only urinary-system and gastrointestinal carcinomas and for Asian and Middle Eastern patients. As well, MTHFR C677T, A1298C and G1793A polymorphisms were related to elevated serum level of Hcy, and folate and vitamin B12 deficiency. However, only MTHFR C677T homogeneity/wild-type (TT/CC) polymorphism was positively associated with overall risk of cancer. Conclusion Elevated serum Hcy level and folate deficiency are associated with increased overall risk of cancer.
Reflectance Photoplethysmography as Noninvasive Monitoring of Tissue Blood Perfusion

In the last decades, photoplethysmography (PPG) has been used as a noninvasive technique for monitoring arterial oxygen saturation by pulse oximetry (PO), whereas near-infrared spectroscopy (NIRS) has been employed for monitoring tissue blood perfusion. While NIRS offers more parameters to evaluate oxygen delivery and consumption in deep tissues, PO only assesses the state of oxygen delivery. For a broader assessment of blood perfusion, this paper explores the utilization of dual-wavelength PPG by using the pulsatile (ac) and continuous (dc) PPG for the estimation of arterial oxygen saturation (SpO2) by conventional PO. Additionally, the Beer-Lambert law is applied to the dc components only for the estimation of changes in deoxyhemoglobin (HHb), oxyhemoglobin (HbO2), and total hemoglobin (tHb) as in NIRS. The system was evaluated on the forearm of 21 healthy volunteers during induction of venous occlusion (VO) and total occlusion (TO). A reflectance PPG probe and NIRS sensor were applied above the brachioradialis, PO sensors were applied on the fingers, and all the signals were acquired simultaneously. While NIRS and forearm SpO2 indicated VO, SpO2 from the finger did not exhibit any significant drop from baseline. During TO, all the indexes indicated the change in blood perfusion. HHb, HbO2, and tHb changes estimated by PPG presented high correlation with the same parameters obtained by NIRS during VO (r2 = 0.960, r2 = 0.821, and r2 = 0.974, respectively) and during TO (r2 = 0.988, r2 = 0.940, and r2 = 0.938, respectively). The system demonstrated the ability to extract valuable information from PPG signals for a broader assessment of tissue blood perfusion.
Accelerations of Water Masers in NGC 4258

The water masers in NGC 4258 delineate the structure and dynamics of a subparsec-diameter accretion disk around a supermassive black hole. Very Long Baseline Array (VLBA) observations provide precise information about the positions in the plane of the sky and the three-dimensional velocity vectors for the maser emission, but the positions along the line of sight must be inferred from models. Previous measurements placed an upper limit on the accelerations of the high-velocity spectral features of 1 km s-1 yr-1, suggesting that they are located near the midline (the diameter perpendicular to the line of sight), where they would have exactly zero acceleration. From similar measurements, the accelerations of the systemic velocity spectral features have been estimated to be about 9 km s-1 yr-1, indicating that they lie toward the front of the disk where the acceleration vector points directly away from the line of sight. We report acceleration measurements for 12 systemic velocity spectral features and 19 high-velocity spectral features using a total of 25 epochs of observations from Effelsberg (five epochs), the Very Large Array (15 epochs), and the VLBA (five epochs) spanning the years 1994-1997. The measured accelerations of the systemic velocity features are between 7.5 and 10.4 km s-1 yr-1, and there is no evidence for a dip in the spectrum at the systemic velocity. Such a dip has been attributed in the past to an absorbing layer of noninverted H2O. The accelerations of the high-velocity features, measured here for the first time, range from -0.77 to 0.38 km s-1 yr-1. From the line-of-sight accelerations and velocities, we infer the positions of these high-velocity masers with a simple edge-on disk model. The resulting positions fall between -13. °6 and 9. °3 in azimuth (measured from the midline). A model that suggests a spiral shock origin of the masers, in which changes in maser velocity are due to the outward motion of the shock wave, predicts apparent accelerations of -0.05(θp/2.°5) km s-1 yr-1, where θp is the pitch angle of the spiral arms. Our data are not consistent with these predictions. We also discuss the physical properties of the high-velocity masers. Most notably, the strongest high-velocity masers lie near the midline, where the velocity gradient is smallest, thereby providing the longest amplification path lengths.
Continuous polo-like kinase 1 activity regulates diffusion to maintain centrosome self-organization during mitosis

Whether mitotic structures like the centrosome can self-organize from the regulated mobility of their dynamic protein components remains unclear. Here, we combine fluorescence spectroscopy and chemical genetics to study in living cells the diffusion of polo-like kinase 1 (PLK1), an enzyme critical for centrosome maturation at the onset of mitosis. The cytoplasmic diffusion of a functional EGFP-PLK1 fusion correlates inversely with known changes in its enzymatic activity during the cell cycle. Specific EGFP-PLK1 inhibition using chemical genetics enhances mobility, as do point mutations inactivating the polo-box or kinase domains responsible for substrate recognition and catalysis. Spatial mapping of EGFP-PLK1 diffusion across living cells, using raster image correlation spectroscopy and line scanning, detects regions of low mobility in centrosomes. These regions exhibit characteristics of increased transient recursive EGFP-PLK1 binding, distinct from the diffusion of stable EGFP-PLK1–containing complexes in the cytoplasm. Chemical genetic suppression of mitotic EGFP-PLK1 activity, even after centrosome maturation, causes defects in centrosome structure, which recover when activity is restored. Our findings imply that continuous PLK1 activity during mitosis maintains centrosome self-organization by a mechanism dependent on its reaction and diffusion, suggesting a model for the formation of stable mitotic structures using dynamic protein kinases.