Miracle-dz/UniFAR-FTUs huggingface dataset:
Widespread domain-like perturbations of DNA methylation in whole blood of Down syndrome neonates

Introduction Down syndrome (DS) is the most frequent genetic cause of intellectual disability. Despite the fact that more than 50 years have passed since the discovery of its genetic aberrations, the exact pathogenesis of the DS phenotype has remained largely unexplained. It was recently hypothesized that the DS pathogenesis involves complex (epi)genetic, molecular and cellular determinants. To date, many reports have addressed epigenetic aberrations associated with DS at different developmental stages/ages and tissue types, but to our best knowledge not in DS newborns. This study aimed to investigate genome-wide methylation patterns in DS newborns compared to non-trisomic newborns. Method We analyzed blood samples obtained from ten newborns with DS and five age-matched non-trisomic newborns. Epigenetic profiles were obtained from extracted DNA using the Illumina Infinium 450K array. Since aberrant blood cell distribution is known to be present in DS, we applied two distinct models: with and without correction for estimated blood cell distribution. Results Differentially methylated position (DMP) analysis of the uncorrected model detected 19525 significant hits (51,2% hypomethylated). In the corrected model, we found 121953 significant DMPs (49,8% hypomethylated). Independent of the used model we observed a chromosome 21 dosage effect. Moreover, we detected 46 and 145 differentially methylated regions in the uncorrected and corrected model respectively, both showing hypomethylation overrepresentation. Replication analyses of DMPs and DMRs found by Bacalini et al. (2015) showed a large overlap. Conclusion In this study, we found methylation profile differences between DS newborns and controls reflecting a systematically affected epigenetic profile. The observed chromosome 21 dosage effect suggests the involvement of affected essential regulatory factors/regions or altered expression of chromatin modeling enzymes located on chromosome 21. Additional research is necessary to substantiate these hypotheses.
Water Uptake along the Length of Grapevine Fine Roots: Developmental Anatomy, Tissue-Specific Aquaporin Expression, and Pathways of Water Transport1[W][OPEN]

Peak aquaporin expression/activity and hydraulic conductivity occurred in root tips and interior tissues; contrary to theoretical predictions, low aquaporin expression and activity in suberized secondary growth portions of fine roots suggests a limited role in controlling water uptake in this region of the root. To better understand water uptake patterns in root systems of woody perennial crops, we detailed the developmental anatomy and hydraulic physiology along the length of grapevine (Vitis berlandieri × Vitis rupestris) fine roots from the tip to secondary growth zones. Our characterization included the localization of suberized structures and aquaporin gene expression and the determination of hydraulic conductivity (Lpr) and aquaporin protein activity (via chemical inhibition) in different root zones under both osmotic and hydrostatic pressure gradients. Tissue-specific messenger RNA levels of the plasma membrane aquaporin isogenes (VvPIPs) were quantified using laser-capture microdissection and quantitative polymerase chain reaction. Our results highlight dramatic changes in structure and function along the length of grapevine fine roots. Although the root tip lacked suberization altogether, a suberized exodermis and endodermis developed in the maturation zone, which gave way to the secondary growth zone containing a multilayer suberized periderm. Longitudinally, VvPIP isogenes exhibited strong peaks of expression in the root tip that decreased precipitously along the root length in a pattern similar to Arabidopsis (Arabidopsis thaliana) roots. In the radial orientation, expression was always greatest in interior tissues (i.e. stele, endodermis, and/or vascular tissues) for all root zones. High Lpr and aquaporin protein activity were associated with peak VvPIP expression levels in the root tip. This suggests that aquaporins play a limited role in controlling water uptake in secondary growth zones, which contradicts existing theoretical predictions. Despite having significantly lower Lpr, woody roots can constitute the vast majority of the root system surface area in mature vines and thus provide for significant water uptake potential.
Comparison of reactor configurations for biogas production from rapeseed straw.

To investigate the effects of reactor configurations on the anaerobic digestion performance of agricultural residue rapeseed straw, semi-continuous, one-stage, continuously stirred tank reactors (CSTR) and batch, two-stage, leach bed-upﬂow anaerobic sludge blanket (UASB) reactors were operated at the same hydraulic retention time (HRT) (30 days) and target organic loading rate (OLR) (3.0 gVS/L.d). In the continuously loaded CSTR, the specific methane yields did not substantially change as the OLR increased from 1.5 gVS/L.d to 3.0 gVS/L.d during the four periods. Conversely, the specific methane yields in the batch-fed leach bed-UASB increased considerably with the increase in OLR. The leach bed reactor contributed 75% of the total yield, while the UASB reactor contributed only 25% of the total yield. The total specific methane yields were 108 mL/gVS and 160 mL/gVS for the leach bed-UASB and CSTR, respectively, while the volatile solid (VS) reductions of the rapeseed straw were 27.1% and 36.6%, respectively. The results indicated that the process performance was more efficient in the CSTR than in the leach bed-UASB for the digestion of rapeseed straw. Biogas production was clearly affected by the reactor configurations.
Soy and phytoestrogens: possible side effects

Phytoestrogens are present in certain edible plants being most abundant in soy; they are structurally and functionally analogous to the estrogens. Phytoestrogens have been applied for compensation of hormone deficiency in the menopause. At the same time, soy products are used in infant food and other foodstuffs. Furthermore, soy is applied as animal fodder, so that residual phytoestrogens and their active metabolites such as equol can remain in meat and influence the hormonal balance of the consumers. There have been only singular reports on modified gender-related behavior or feminization in humans in consequence of soy consumption. In animals, the intake of phytoestrogens was reported to impact fertility, sexual development and behavior. Feminizing effects in humans can be subtle and identifiable only statistically in large populations.
Top-Down and Bottom-Up Attention to Memory Are Dissociated in Posterior Parietal Cortex: Neuroimaging and Neuropsychological Evidence

Posterior parietal cortex is active during episodic memory retrieval, yet its role remains unclear. According to a recent proposal, dorsal parietal cortex (DPC) allocates top-down attention to memory retrieval, whereas ventral parietal cortex (VPC) mediates the bottom-up attentional capture by retrieved contents, i.e., the Attention-to-Memory (AtoM) hypothesis. Here, for the first time, functional magnetic resonance imaging (fMRI) and lesion techniques were combined in a single study to test the role of parietal cortex in episodic retrieval. Participants studied word pairs and then detected studied (target) words among new words. In some conditions, a studied word cued the upcoming target word, facilitating recognition performance. In line with the AtoM hypothesis, left DPC was engaged when participants searched for/anticipated memory targets upon presentation of relevant memory cues and predicted the ensuing behavioral advantage. In contrast, left VPC predicted efficacy and speed of target detection on noncued trials and was largest for memory targets that were invalidly cued. Consistent with fMRI evidence, patients with lesions in DPC did not benefit from memory cueing, whereas patients with lesions in VPC had problems recognizing unexpected memory targets. These results support the AtoM hypothesis that DPC and VPC mediate top-down and bottom-up attention to memory retrieval, respectively.
HEVC inverse transform architecture utilizing coefficient sparsity

The inverse transform function of the HEVC Decoder has grown greatly in complexity with the addition of larger transform sizes and recent works have focused on efficient architectures that can achieve the required throughput. In this work we make the observation that a majority of the coefficients in a typical transform operation is zero, and therefore has no impact on the final outcome. We propose an architecture that can efficiently operate on such sparse matrices and introduce a scheduling strategy which completes a 2D IDCT with bare minimum iterations, with the added advantage of being able to integrate seamlessly with the entropy decoder without a coefficient reordering buffer. Experiments show that although the performance of this approach is scalable with the bit rate, a 120 MHz operating frequency is sufficient to handle QHD @ 48 Mbps, which is less than one third of the frequency requirement of prior work.
Effectiveness of behavioral activation group therapy on attributional styles, depression, and quality of life in women with breast cancer

Introduction: Breast cancer is the most common type of cancer in women. This study has been conducted with the aim of investigating the effectiveness of behavioral activation group therapy on attributional styles, depression, and quality of life in women with breast cancer. Materials and Methods: This clinical trial carried out using a pretest-posttest control â��group design. Of all the women suffering from breast cancer who referred to Mashhad Omid Hospital in 2015, 30 individuals were selected through convenience sampling method and were randomly assigned into experimental and control groups. The experimental group received 8 weeks of behavioral activation group therapy while the control group was put on the waiting list to get treated. Peterson and Seligman Attributional Style Questionnaire (ASQ), Short Form Health Survey (SF-36), and Beck Depression Inventory II (BDI-II) were applied in the pretest and posttest. Data were analyzed using multivariate analysis of covariance (MANCOVA) by SPSS-22 software. Results: The results demonstrated that behavioral activation group therapy leads to a change in attributional styles (P<0.001), a significant increase in quality of life (P<0.001), and reduced depression (P<0.001) compared to the control group. Conclusion: It seems that behavioral activation group therapy can improve the attributional styles, depression, and quality of life in women with breast cancer.
Crude extract of bacterially expressed, infectious bursal disease virus VPX/VP2 proteins induces protective immune response to the virus in chickens

Infectious bursal disease virus (IBDV) infects young chickens and causes serious lose to the poultry industry, worldwide. Previous attempts using purified bacterially expressed IBDV VP2 failed to elicit a protective immune response to the virus. This study was designed to investigate if the initial expressed protein contained neutralizing epitopes but became nonfunctional during purification steps. The full length IBDV VP2 and its precursor VPX genes from the highly virulent IBDV (hvIBDV) SDH1 isolate were cloned and expressed in BL21 bacterial cells. Specific pathogen-free (SPF) chickens were inoculated subcutaneously with 0.3 ml crude extract with/without adjuvant at week 0, 2, and 4. At week 2 post-immunization, IBDV antibody was detected in the vaccinated chickens and increased to its highest titre at week 4. Virus challenge using the SDH1 isolate did not result in IBDV specific clinical signs when chickens were vaccinated with adjuvant-extract preparation (100% protection) while mock-inoculated chickens died 3-4 days post-inoculation. The above results, taken together, demonstrated that bacterially expressed IBDV VP2 harbors neutralizing epitopes required for induction of protective response, and suggest less detrimental purification procedures for vaccine preparation.
Solar Torrefaction of Solid Olive Mill Residue

Torrefaction is a thermochemical pretreatment method for improving fuel characteristics of biomass. The process is conducted between 200 and 300 °C under inert atmosphere. The relatively low process temperature of torrefaction makes the use of solar energy suitable with low costs. In this study, solid olive mill residue (SOMR) was used to test the feasibility of using solar energy in the torrefaction process. SOMR is an agricultural waste obtained from olive oil extraction, and it is mainly produced in the Mediterranean region, which has high solar energy potential. In this study, the torrefaction of SOMR was conducted by concentrating solar energy with a parabolic dish concentrator, at 250 °C for 10 min. The fuel properties of solar torrefaction products were compared with raw SOMR. Solar torrefaction yielded a deoxygenated solid fuel with increased carbon content and higher heating value (HHV), similar to torrefaction.
Stature and Its Estimation Utilizing Arm Span Measurements in Male Adolescents from Federation of Bosnia and Herzegovina Entity in Bosnia and Herzegovina

Th e purpose of this study was to evaluate stature in males from the Federation of Bosnia and Herzegovina Entity in Bosnia and Herzegovina (hereinaft er BH) as well as the relationship between arm span as an alternative to estimating stature, which varies in diff erent ethnic and racial groups. Th e nature and scope of this study analyse 193 male students (aged 20.84±2.08) from the University of Sarajevo and University of Mostar. Anthropometric measurements were used in accordance with the protocol of the ISAK. Means and standard deviations were obtained. Statures and arm spans were compared using a t-test. Th e relation between arm span and stature were determined using simple correlation coeffi cients and a confi dence interval of them of 95%. A linear regression analysis was then executed to examine the extent to which stature can be reliably predicted by arm span. Th e results have shown that males from the Federation of Bosnia and Herzegovina Entity are 183.84±6.41 cm tall and have an arm span of 185.65±7.55 cm. In comparison to other studies, the results of this one show the BH population to be one of the tallest nations in the world, perhaps the tallest one. Moreover, arm span surely predicts stature in males (61.6%). However, the estimation equations, which were obtained in Bosnian Herzegovinians from mentioned entity, are substantially diff erent alike in the population from other entities, since arm span was not close to statures (1.81±1.14 cm more than the stature). Th is confi rms the need for developing individual height models for this population.
Fertility regulation as identity maintenance: Understanding the social aspects of birth control

We take a dialogical approach to exploring fertility regulation practices and show how they can maintain or express social identity. We identify three themes in educated Ghanaian women’s accounts of how they navigate conflicting social demands on their identity when trying to regulate fertility: secrecy and silence – hiding contraception use and avoiding talking about it; tolerating uncertainty – such as using unreliable but more socially acceptable contraception; and wanting to be fertile and protecting menses. Family planning programmes that fail to tackle such social-psychological obstacles to regulating fertility will risk reproducing social spaces where women struggle to claim their reproductive rights.
The spiritual meaning of pre-loss music therapy to bereaved caregivers of advanced cancer patients

ABSTRACT Objective: The aim of this study was to learn how music therapy sessions, held prior to the death of a loved one, impact spirituality in surviving caregivers of advanced cancer patients. Method: The method of naturalistic inquiry was used to investigate the spiritual meaning of pre-loss music therapy sessions. Bereaved caregivers of seven different patients, who had been receiving music therapy through a home-based hospice program, participated in individual open-ended interviews. Interviews were recorded, transcribed, and coded. Themes were organized as they emerged. Results: As caregivers reflected on their experiences in music therapy, they reported autonomous joy (music therapy affected the caregiver directly) and empathic joy (caregivers' joy was based in remembering seeing the patient happy in music therapy). They also noted feelings of empowerment due to the ways they felt they had contributed in the care of the patients through music therapy. The caregivers were found to engage in processes of reflection that inspired these spiritual themes: reflection on the present (connectedness), reflection on the past (remembrance), and reflection on the future (hope). They referred to the ways that the music therapy sessions helped them find connection with self, others (through bringing their loved ones “back to life” and have a “renewal of self”), and the “beyond”; and that times in music therapy brought them happy memories and sentiments of hope. Meaning through transcendence was found to be the overarching trend in this study, as caregivers were lifted from remorse into heightened sense of meaning and gained “airplane views” of their lives. Significance of results: Pre-loss music therapy can potentially assist caregivers during times of bereavement, as they retain memories of joy and empowerment, rather than memories of pain and distress, and find meaning through transcendence.
Side population cell level in human breast cancer and factors related to disease-free survival.

UNLABELLED Side population (SP) cells have stem cell-like properties with a capacity for self-renewal and are resistant to chemotherapy and radiotherapy. Therefore the presence of SP cells in human breast cancer probably has prognostic value. OBJECTIVE To investigate the characteristics of SP cells and identify the relationship between the SP cells levels and clinico-pathological parameters of the breast tumor and disease-free survival (DFS) in breast cancer patients. MATERIALS AND METHODS A total of 122 eligible breast cancer patients were consecutively recruited from January 1, 2006 to December 31, 2007 at Yunnan Tumor Hospital. All eligible subjects received conventional treatment and were followed up for seven years. Predictors of recurrence and/or metastasis and DFS were analyzed using Cox regression analysis. Human breast cancer cells were also obtained from fresh human breast cancer tissue and cultured by the nucleic acid dye Hoechst33342 with Verapami. Flow cytometry (FCM) was employed to isolate the cells of SP and non-SP types. RESULTS In this study, SP cells were identified using flow cytometric analysis with Hoechst 33342 dye efflux. Adjusted for age, tumor size, lymph nodal status, histological grade, the Cox model showed a higher risk of recurrence and/or metastasis positively associated with the SP cell level (1.75, 1.02-2.98), as well as with axillary lymph node metastasis (2.99, 1.76-5.09), pathology invasiveness type (1.7, 1.14-2.55), and tumor volume doubling time (TVDT) (1.54, 1.01-2.36). CONCLUSIONS The SP cell level is independently associated with tumor progression and clinical outcome after controlling for other pathological factors. The axillary lymph node status, TVDT and the status of non-invasive or invasive tumor independently predict the prognosis of breast cancer.
Immunization practices in low birth weight infants from rural Haryana, India: Findings from secondary data analysis

Background Low birth weight (LBW) infants constitute a vulnerable subset of infants with impaired immunity in early life. In India, there is scarcity of studies that focus on immunization practices in such infants. This analysis aimed to examine immunization practices in LBW infants with the intention to identify areas requiring intervention. Methods Data on immunization status of LBW infants enrolled in an individually randomized, double–masked, placebo–controlled trial of neonatal vitamin A supplementation were analysed. Study outcomes were full immunization by one year of age and delayed vaccination with DPT1 and DPT3. Multivariable logistic regression was performed to identify factors associated with the outcome(s). Findings Out of 10 644 LBW infants enrolled in trial, immunization data were available for 10 517 (98.8%). Less than one–third (29.7%) were fully immunized by one year of age. Lowest wealth quintile (adjusted odds ratio (AOR) 0.39, 95% confidence interval (CI) 0.32–0.47), Muslim religion (AOR 0.41, 95% CI 0.35–0.48) and age of mother <20 years (AOR 0.62, 95% CI 0.52–0.73) were associated with decreased odds of full immunization. Proportion of infants with delayed vaccination for DPT1 and DPT3 were 52% and 81% respectively. Lowest wealth quintiles (AOR 1.51, 95% CI 1.25–1.82), Muslim religion (AOR 1.41, 95% CI 1.21–1.65), mother aged <20 years (AOR 1.31, 95% CI 1.11–1.53) and birth weight <2000 g (AOR 1.20, 95% CI 1.03–1.40) were associated with higher odds of delayed vaccination for DPT–1. Maternal education (≥12 years of schooling) was associated with high odds of full immunization (AOR 2.39, 95% CI 1.97–2.91) and low odds of delayed vaccination for both DPT–1 (AOR 0.59, 95% CI 0.49–0.73) and DPT–3 (AOR 0.57, 95% CI 0.43–0.76) Conclusion In this population, LBW infants are at a risk of delayed and incomplete immunization and therefore need attention. The risks are even higher in identified subgroups that should specifically be targeted
EEG Connectivity Patterns in Childhood Sexual Abuse: A Multivariate Application Considering Curvature of Brain Space

ABSTRACT Introduction. A limitation of the bivariate electroencephalogram (EEG) coherence measure is low precision in location specification in anatomical space and functional connectivity. A more powerful use of functional connectivity of distributed brain systems maybe evaluation of patterns of correlations obtained through the functional connectivity matrix of Principal Component Analysis. The eigenimages that result from such analysis represent a descriptive characterization of anatomically distributed changes in the brain. There is little research exploring the relationship between childhood sexual abuse (CSA) and connectivity patterns in the brain. This study explored the connectivity patterns between 24 high-functioning, unmedicated adults with a history of CSA and age, gender, and handedness matched high-functioning adults with no history of CSA. Method. Resting eyes closed quantitative EEG (QEEG) was recorded from 19 scalp locations with a linked ears reference from 60 unmedicated adult research .