Miracle-dz/UniFAR-FTUs huggingface dataset:
The evidence for the benefits from breast milk in the neurodevelopment of premature babies – a review of the recent literature

Introduction. The brain in preterm babies is usually not fully developed and therefore early post-term events can have long-lasting neurodevelopment and cognitive outcomes. It is known that cerebral white matter connectivity is important for later intact cognitive functioning amongst children born very preterm and that breast milk imparts neurotrophic factors. The relationship between breastfeeding and child development is a long and well-studied area, and the evidence in support of breast milk is already substantial. Here we review the recent literature on the topic to establish whether additional evidence is available to strengthen the view that breast milk is superior in maximizing neurological development in premature infants. Materials and Methods. A search was undertaken of PubMed, limited to the last 10 years and humans. No language restrictions were imposed. Results. The search yielded 45 articles, of which 12 included all three elements of breast milk, neurological/cognitive development and preterm babies; 10 were reviewed. The gestation period and birth weight (either or both were reported) ranged from 23 to 36 weeks and from 580g to <1500g. Studies were heterogeneous in methodology. In addition to two systematic reviews and a review of the literature, other studies focused particularly on the effects of certain key components within breast milk on neurological development. They generally found evidence to support the beneficial effects of breast milk on brain, visual, and cognitive development in Preterm infants. Studies focusing on how breast milk intake affects the preterm infant brain are limited. We found only two studies published in the last 2 years in relation to brain volume in breast fed preterm infants. Both used magnetic resonance imaging (MRI) to examine the brains of breast-fed babies born prematurely. These studies found that preterm infants fed more breast milk had larger brain volumes (cortical surface) compared to those fed little/no breast milk. The timing of the nutritional intervention and the dose of the nutrient/supplement have been found to be relevant factors. However, not all studies have been conclusively positive. Conclusions. Although the profile of preterm infants is a wide one, from the limited but recent evidence, it is reasonable to conclude that breast milk contributes positively to neurological development.
GENOMIC AND TRANSCRIPTOMIC LANDSCAPE OF COLORECTAL PREMALIGNANCY

Colorectal cancer (CRC) is the third most commonly diagnosed cancer among men and women in the United States, with 3 to 5 percent of the cases diagnosed in the background of a hereditary form of the disease. Biologically, CRC is divided into two groups: microsatellite instable (MSI) and chromosomally unstable (CIN). Genomic and transcriptomic characterization of CRC has emerged from large -scale studies in recent years due to the advancement of next -generation sequencing technologies. These studies have identified key genes and pathways altered in CRC and provided insights to the discovery of therapeutic targets. Despite the wealth of knowledge acquired in the carcinoma stage, there have been insufficient efforts to systematically characterize premalignant lesions at the molecular level, which could lead to a better understanding of neoplastic initiation, risk prediction, and the development of targeted chemoprevention strategies. The challenge in characterizing premalignancy has always been the limited availability of sample material. This challenge is tackled by getting more samples, integrating public datasets, deploying better technology that use less amount of nucleic acids and in silico tools to extract multi-layer information from the same experiment. My genomic study consisted of whole exome sequencing (WES) and highdepth targeted sequencing on 80 premalignant lesions bulk tissue and crypts to assess clonality and mutational heterogeneity. WES results showed the presence of multiple clone in premalignancy based on clustering somatic mutation allele vi frequency. In addition, I determined that multiple clones originate from independent crypts harboring distinct APC and KRAS alterations. In my second study, I performed immune expression profiling and assessment of mutation and neoantigen rate of 28 premalignant lesions with DNA mismatch repair (MMR) deficient and proficient background using RNAseq. My results showed an activated immune profile despite low mutational and neoantigen rate, which challenges the canonical view in MMRdeficient carcinoma stage that immune activation is largely due to high mutation and neoantigen rate. In the last study, I performed transcriptomic sub-classifications of 398 premalignant lesions that associate them with different carc inomas subtypes, and clinical and histopathological features. My results revealed two major findings: prominent immune activation and WNT and MYC activation in premalignancy. In summary, my large-scale genomic and transcriptomic analyses of colorectal adenomas have identified key molecular characteristics in early colorectal tumorigenesis and provide a foundation for discovering novel preventive strategies .
Does global niche construction lead to environmental regulation

Ecological models often ignore the interaction between the biota and the environment. For example, Lotka-Volterra population models (Lotka, 1925; Volterra, 1926) and replicator equation models (Hofbauer and Sigmund, 1998) typically look only at the interaction between species. The external environment, where it is modelled at all, is usually taken only as a source of food; other aspects that may affect the growth and reproductive success of organisms are ignored. However, it is increasingly recognised that there is a constant and significant interaction between living things and the abiotic environment that extends beyond food web dynamics. Ideas of niche construction (Laland et al., 1996; Laland et al., 1999) and the extended phenotype (Dawkins, 1982) highlight the importance of the environment in evolutionary dynamics, while the increasingly accepted Gaia theory (Lovelock, 1979) suggests that that not only do organisms affect their environment, they do so in a way that regulates the biosphere to conditions that are suitable for life. Proposed Gaian phenomena include the regulation of local climate by marine algae that influence the formation of clouds over the oceans (Charlson et al., 1987; Lovelock, 1997; Liss et al., 1997; Andreae and Crutzen, 1997), global temperature regulation by biotic enhancement of rock weathering (Schwartzman and Volk, 1989; Schwartman and Volk, 1991), and the maintenance of constant marine salinity and N:P ratios by the aquatic biota (Redfield, 1958; Lenton and Watson, 2000; Volk, 1998).
Proliferosphaera, a new genus from India

Proliferosphaera , anamorph gen. nov. and Proliferosphaera capsici anamorph sp. nov. are proposed to accommodate a eustromatic fungus collected from the fruits of Capsicum annuum L. (Solanaceae) from Gujarat state of India causing die-back and fruit rot disease. The genus is characterized by the presence of dense conidiomata (pycnidia) with distinct zonation and were globose, with one or two ostioles when young, became irregular in shape with successive development of a number of broad and long beaks; attachment of dense mycelium with the matured conidiomata; production of many hyaline, aseptate, thin walled, ellipsoidal to sub-globose conidia with 10 x 2.5-7.5 μm in size having two conspicuous guttules one at each end. Proliferosphaera is recognized as a new genus distinct from the closed genera viz. , Capitorostrum, Corniculariella, Cryptosporiopsis, Cytonema, Dinemasporium, Dwiroopa, Endothiella, Monochaetia, Phoma, Phomopsis, Phyllosticta and Seimatosporium in the order Sphaeropsidales both at morphological and molecular (Internal Transcribed Spacer; ITS) analyses. In this article, the type genus Proliferosphaera with type species Proliferosphaera capsici, is described and illustrated.
Modeling Personas for Older Adults with Heart Failure

In the early stages of the design process, designers often benefit from the use of personas, or archetypes of target users presented in a vivid way to highlight design-relevant characteristics. In the growing efforts to create health information technology (HIT) for older adults, empirically derived personas could help orchestrate more user-centered design activities. However, there is a lack of ready-to-use personas for older adult HIT users and more so for those designing in specific domains such as heart failure self-care. This paper presents personas of older adults derived from qualitative analysis of interviews with 24 older patients with heart failure. Analyses unearthed key dimensions distinguishing patients based on their dispositions towards the self-management of their chronic condition, including locus of control, relationship with the health/support system, information needs, and activities of self-care. Two personas are presented: Direction Follower and Researcher, with subtypes for the latter codified as Investigator and Explorer. Our work contributes to future design of systems including HIT to support chronically ill older adults.
Survival, Mortality, and Life Expectancy

Cerebral palsy (CP) is a heterogenous condition, with level of disability ranging from immaterial to profound. In concert with the continuum of level of severity of disability/ independent functioning, health care needs, therapies, medications, surgical interven- tions, costs of care, daily demands on parents and other family members, and expectations for the future in terms of education, employment, and other milestones of life all vary widely. Similarly, life expectancy in CP follows a continuum, from far lower than to potentially as high as general population life expectancy, that parallels the continuum of levels of disability. Here we review the literature documenting this, and examine the specific factors that are known to be strongly associated with mortality and longevity in CP. We also examine the evidence regarding causes of death in CP, and present some new findings related to this. Finally, we outline important methodological considerations for future research in this area.
Reliability and Validity of the 6‐Minute Walk Test in Hypophosphatasia

This investigation evaluated the reliability and validity of the 6‐Minute Walk Test (6MWT) in patients with pediatric hypophosphatasia (HPP). Children (aged 6 to 12 years; n = 11), adolescents (13 to 17 years; n = 4), and adults (18 to 65 years; n = 9) completed the 6MWT at screening and baseline in two clinical studies of asfotase alfa. Test‐retest reliability of the 6MWT, evaluated with Pearson's correlation coefficients (r) for screening versus baseline, was high for children (r = 0.95; p < 0.0001), adolescents (r = 0.81; p = 0.125), and adults (r = 0.94; p = 0.0001). The most conservative minimal clinically important differences, estimated using distribution‐based methods, were 31 m (children and adults) and 43 m (adolescents). In children, the 6MWT correlated significantly with scores on measures of skeletal disease, which included the Radiographic Global Impression of Change scale (r = 0.50; p < 0.0001) and the Rickets Severity Scale (r = −0.78; p < 0.0001), such that distance walked increased as the severity of skeletal disease decreased. Significant (p < 0.0001) correlations with the 6MWT distance walked were also observed for children with scores on parent‐reported measures of disability (r = −0.67), ability to function in activities of daily living (r = 0.71 to 0.77), and parent‐reported measures of pain (r = −0.39). In adolescents and adults, 6MWT distance walked correlated significantly (p < 0.05) with measures of lower extremity function (r = 0.83 and 0.60, respectively), total pain severity (r = −0.41 and −0.36, respectively), and total pain interference (r = −0.41 and −0.49, respectively). Collectively, these data indicate that the 6MWT is a reliable, valid measure of physical functioning in patients with pediatric HPP. © 2018 The Authors. JBMR Plus Published by Wiley Periodicals, Inc. on behalf of the American Society for Bone and Mineral Research.
Enduring neurobehavioural effects induced by early-life microbiota-gut-brain axis alterations

XVIII Chapter 1. General Introduction 1 1.1 The Gut Microbiota as a Key Regulator of the Gut-Brain Axis . 1 1.1.1 The Gut-Brain Axis . 1 1.2 The Gut Microbiota . 3 1.2. 1 Microbial Distribution across the Gut . 4 1.2. 2 The Establishment of the Microbiome in Early-life . 5 1.2. 3 Targeting the Microbiota with Pre and Probiotics in Early-Life . 12 1.2. 4 Tools for Investigating the Impact of the Gut Microbiota on Gut-Brain Function . 15 1.3 The Microbiota-gut Brain Axis . 21 1.3. 2 Microbiota-gut Brain Axis Routes of Communication . 24 1.3. 3 The Intestinal Barrier . 30 1.4 Microbiota-gut Brain Axis and Stress . 33 1.4. 1 Stress . 33 1.4. 2 HPA Axis, Stress and Stress-related Disorders . 34 1.5 Microbiota-gut Brain Axis and Neurodevelopment . 47 1.5. 1 Neurodevelopment . 47 1.5. 2 Interactions During Critical Developmental Windows . 48
SCREENING AND CHARACTERIZATION OF ARABIDOPSIS THALIANA MUTANTS WITH ALTERED CAROTENOID PROFILE

II ACKNOWLEDGEMENT . IV LIST OF TABLES . IX LIST OF FIGURES . X LIST OF ABBREVIATIONS . XV 1 GENERAL INTRODUCTION . 1 1.1 CAROTENOID BIOSYNTHESIS IN PLANTS. 2 1.2 FUNCTIONS OF CAROTENOIDS . 5 1.3 REGULATION OF CAROTENOID BIOSYNTHESIS IN PLANTS. 9 1.4 NORFLURAZON AFFECTS CAROTENOID BIOSYNTHESIS . 12 1.5 FATTY ACIDS AND CAROTENOIDS . 13 1.6 RNA BINDING PROTEINS IN ARABIDOPSIS . 14 1.7 ACTIVATION TAGGING IN ARABIDOPSIS . 15 2 SCREENING AND CHARACTERIZATION OF RED SEED COAT ARABIDOPSIS MUTANTS . 19 2.
Translocation d'acides nucleiques au travers d'une bicouche lipidique : du nanopore au bacteriophage

Ce travail porte sur l'etude experimentale de deux mecanismes de translocations d'acides nucleiques au travers d'une membrane lipidique : la translocation, forcee electrophoretiquement, d'oligomeres au travers d'un pore d'alpha-hemolysine et la translocation passive d'un ADN genomique hors de la capside du bacteriophage T5. La premiere partie de la these porte sur l'ouverture de molecules d'ADN double brin a travers le nanopore d'alpha hemolysine. Les temps de passage individuels de molecules d'ADN a travers le pore sont mesures experimentalement en fonction de la sequence, de la longueur et de la force appliquee sur l'ADN. Les distributions obtenues sont confrontees a un modele decrivant le passage de l'ADN par la diffusion d'une fourche d'ouverture dans un paysage energetique unidimensionnel, determine par la sequence de la molecule. La deuxieme partie porte sur un systeme in vitro reconstituant les etapes initiales d'infection du bacteriophage T5. L'interaction de T5 avec son recepteur membranaire FhuA purifie en detergent, genere une sequence d'evenements qui conduit a l'ejection du genome viral hors de la capside : (i) fixation du recepteur ; (ii) activation conduisant a l'ouverture d'un canal d'ADN ; (iii) ejection de l'ADN. La dynamique des trois etapes est mesuree a l'aide d'experiences en population et en virus unique. La derniere etape est comparee a un modele physique qui revele une dynamique fortement hors d'equilibre a l'initiation de l'ejection. Enfin, FhuA est reconstitue dans des vesicules lipidiques geantes afin de suivre l'ejection par microscopie de fluorescence et par electrophysiologie a travers une membrane lipidique.
The role of mevalonate pathway intermediates in erythropoietin receptor signal transduction and surface expression: Studies in hematopoietic and non-hematopoietic cancers

Approved: ____________________________________ Thesis Supervisor ____________________________________ Title and Department ____________________________________ Date THE ROLE OF MEVALONATE PATHWAY INTERMEDIATES IN ERYTHROPOIETIN RECEPTOR SIGNAL TRANSDUCTION AND SURFACE EXPRESSION: STUDIES IN HEMATOPOIETIC AND NON-HEMATOPOIETIC CANCERS by Sumaya Nizar Hamadmad A thesis submitted in partial fulfillment of the requirements for the Doctor of Philosophy degree in Pharmacology in the Graduate College of The University of Iowa
International consensus statement on the management of hypotension with vasopressors during caesarean section under spinal anaesthesia

1 Consultant, Department of Anaesthesia, St Michael’s Hospital, Bristol, UK 2 Professor, Department of Anesthesiology, Stanford University School of Medicine, Stanford, CA, USA 3 Professor Emeritus, Department of Anaesthesia and Peri-operative Medicine, University of Cape Town, Cape Town, South Africa 4 Senior Consultant, Department of Anaesthesia, Hamad Women’s Hospital, Doha, Qatar 5 Clinical Associate Professor, Department of Anaesthesia and Pain Medicine, King Edward Memorial Hospital for Women, Subiaco, Australia 6 Professor, D epartement d’Anesth esie-R eanimation, Hôpital Antoine B ecl ere, Clamart, France 7 Assistant Professor, Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, USA 8 Professor and Senior Consultant, Department of Women’s Anaesthesia, KKWomen’s and Children’s Hospital, Singapore 9 Chair, Department of Anesthesiology, UZ Leuven, Leuven, Belgium 10 Professor of Anesthesiology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium 11 Consultant, Department of Anaesthesia and Intensive Care Medicine, King’s College Hospital NHS Foundation Trust, London, UK
Exercise for dementia and Mild Cognitive Impairment: methodological considerations

1. Faculty of Education, University of Alicante, Spain. 2. IES La Creueta, Spain. __________________________________________________________________________________________________________________ ABSTRACT The exponential worldwide increase in the number of older adults is causing a parallel rise in the number of cases of neurodegenerative diseases, such as mild cognitive impairment (MCI) and dementia. Exercise is a promising strategy for improving physical and cognitive function in healthy older adults, reducing the risk of developing MCI and dementia, and improving physical and cognitive function as well as decreasing neuropsychiatric symptoms in people with MCI and dementia. However, there are still some inconsistencies in the literature, especially in regards to the cognitive benefits, and there are currently no guidelines for prescribing exercise for older adults with cognitive impairment. In this article, a narrative review on the benefits of exercise for people with MCI and dementia was conducted, establishing some preliminary guidelines for prescribing exercise efficiently and safely in this population.
Cuckoo Cycle : a graph-theoretic proof-of-work system

We introduce the first graph-theoretic proof-of-work system, based on finding cycles in large random graphs. Such problems are arbitrarily scalable and trivially verifiable. Our implementation uses 1 bit per edge, and up to 1 bit per node. We hypothesize that using significantly less causes superlinear slowdown.
Molecular and functional characterization of breast cancer through a combination of MR imaging, transcriptomics and metabolomics

Tumor cells have increased glycolytic activity, and glucose is mainly used to form lactate and alanine, even when high concentrations of oxygen are present (Warburg effect). The purpose of the present study was to investigate glucose metabolism in two xenograft models representing basal-like and luminal-like breast cancer using (13) C high-resolution-magic angle spinning (HR-MAS) MRS and gene expression analysis. Tumor tissue was collected from two groups for each model: untreated mice (n=19) and a group of mice (n=16) that received an injection of [1-(13) C]-glucose 10 or 15 min before harvesting the tissue. (13) C HR-MAS MRS was performed on the tumor samples and differences in the glucose/alanine (Glc/Ala), glucose/lactate (Glc/Lac) and alanine/lactate (Ala/Lac) ratios between the models were studied. The expression of glycolytic genes was studied using tumor tissue from the same models. In the natural abundance MR spectra, a significantly lower Glc/Ala and Glc/Lac ratio (p<0.001) was observed in the luminal-like model compared with the basal-like model. In the labeled samples, the predominant glucose metabolites were lactate and alanine. Significantly lower Glc/Ala and Glc/Lac ratios were observed in the luminal-like model (p<0.05). Most genes contributing to glycolysis were expressed at higher levels in the luminal-like model (fdr<0.001). The lower Glc/Ala and Glc/Lac ratios and higher glycolytic gene expression observed in the luminal-like model indicates that the transformation of glucose to lactate and alanine occurred faster in this model than in the basal-like model, which has a growth rate several times faster than that of the luminal-like model. The results from the present study suggest that the tumor growth rate is not necessarily a determinant of glycolytic activity.
Assessing Spatial Variability in an Agricultural Experiment Station Field: Opportunities Arising from Spatial Dependence

Spatio-temporal field soil and crop processes are important for site-specific farming. The objectives of this study were to spatially evaluate selected soil physical and chemical properties and their relationship to wheat (Triticum aestivum L.) yield, and to discuss stochastic approaches to help identify processes underlying yield variability in heterogeneous field sites. Modified grid sampling included 330 sites including a primary transect. Soil properties measured for the Ap, E if present, and upper B horizons at each site included pH, P, Zn, Cu, exchangeable cations, percentage base saturation, cation exchange capacity, bulk density, soil water contents at -10, -33, and -1500 kPa, texture, and humic matter content. Wheat grain and straw were hand-harvested on 1- by 2-m plots centered on each site. Soil water content on the primary transect was determined by neutron attenuation on nine dates. Field and primary transect means and semivariograms for a given soil or plant parameter were similar. The range of spatial dependence or autocorrelation of soil parameters ranged from 10 m for Ap horizon depth to 100 m for -1500 kPa water content of the Ap. Base saturation and available water storage capacity were cross-correlated with grain yield to a distance of ±15 and 12.5 m, respectively. State-space analysis was used to develop a grain yield model using these two variables. Spearman rank correlation of the soil water content data suggests that the temporal stability of soil water storage is less for shallow than for deeper soil layers.
Systematics and phylogeny of cattle.

The mammalian tribe Bovini (subfamily Bovinae, family Bovidae) contains all the most important of the world’s larger domestic species. The domestications of these cattle and cattle-like taxa were among the most significant advances of the neolithic transition. With their specialized digestive system, these species can utilize cellulose as an energy source, generating the benefits of dairy, meat and hide production. In addition, cattle provided, for several millennia, the animal draught power that underpinned agriculture in the Old World and have assumed a cultural and even religious importance, which is preserved to the present day in some societies. In this chapter we describe the wild and domestic cattle species and their systematics, and we review the phylogenetic analyses that have been performed on this closely related and poorly resolved group.