Miracle-dz/UniFAR-FTUs huggingface dataset:
A Modeling Study of the Biogoechemical Cycling of Iron, Ligands, and Phytoplankton in the Ocean

Author(s): Sherman, Elliot | Advisor(s): Moore, Jefferson K | Abstract: Iron is a key micronutrient for marine biogeochemistry, limiting growth and nitrogen fixation in over a third of the ocean. However, the impacts of iron-binding ligands and iron source processes on dissolved iron distributions is not well known. The goal of this dissertation is to better understand the cycling of iron-binding ligands and the controls on their distributions and how that impacts dissolved iron. This dissertation also seeks to understand how individual iron sources influence iron distributions and biogeochemistry. To accomplish this, a new prognostic ligand tracer and iron-ligand speciation chemistry are incorporated into the Community Earth System Model (CESM). The CESM is now able to simulate realistic distributions of iron-binding ligands. The results show that with relatively few ligand sources and sinks the model was able to match observations of ligands, and that inclusion of a dynamic ligand tracer improves simulation of dissolved iron. To better understand the influence iron sources have on dissolved iron concentrations and biogeochemistry, sensitivity experiments for each source are conducted with the CESM. The results show that atmospheric dust and sedimentary iron inputs have the largest impact on dissolved iron concentrations and biogeochemistry. Hydrothermal vent inputs are important for deep ocean iron, and their inclusion in global biogeochemical ocean models would allow for more realistic iron simulation. This dissertation work also reevaluates the parameters governing the temperature influence on community phytoplankton growth rates. A dataset of in situ community phytoplankton growth rates was compiled and parameter values for the Q10 and Arrhenius models were optimized for use in global biogeochemical and ecosystem models. The results show and optimized Q10 value of 1.47 and an activation energy of 0.277 eV. Both the Q10 and Arrhenius models do equally well for estimating the temperature influence on community phytoplankton growth rates against the dataset. Evaluation of global biogeochemical and ecosystem models against our dataset will allow for further constraints on phytoplankton ecology and associated biogeochemitry.
South African Indians Show a High Prevalence of NIDDM and Bimodality in Plasma Glucose Distribution Patterns

OBJECTIVE To determine the prevalence of diabetes mellitus and impaired glucose tolerance (IGT) and to test for bimodality in the plasma glucose distribution in South African Indians. RESEARCH DESIGN AND METHODS Subjects were selected by systematic cluster sampling in various areas of Durban. They underwent a modified glucose tolerance test whereby fasting and 2-h postglucose (75 g) plasma glucose levels were measured. The program MIX was used to test for bimodality in the plasma glucose distribution. RESULTS We tested 2,479 subjects (1,441 women and 1,038 men). Based on the revised World Health Organization criteria, the crude prevalence of diabetes mellitus was 9.8%, and the crude prevalence of IGT was 5.8%; the age- and sex-adjusted prevalence was 13.0 and 6.9%, respectively. IGT was significantly more common in men (7.6%) than in women (4.4%). Obesity was a feature of both diabetes mellitus and IGT, particularly in women. Both fasting and 2-h plasma glucose values did not conform to a single normal distribution pattern in any age-group, whereas unequivocal evidence of bimodality was seen in the 55- to 74-year age-group of both sexes for fasting and 2-h glucose and also in the 2-h levels of men in the 25- to 34-year age-group. CONCLUSIONS This study has highlighted a high prevalence of non-insulindependent diabetes mellitus in South African Indians and bimodality in the plasma glucose distribution.
Ginger and its Health Claims: Molecular Aspects

Recent research has rejuvenated centuries-old traditional herbs to cure various ailments by using modern tools like diet-based therapy and other regimens. Ginger is one of the classic examples of an herb used for not only culinary preparations but also for unique therapeutic significance owing to its antioxidant, antimicrobial, and anti-inflammatory potential. The pungent fractions of ginger, namely gingerols, shogaols, paradols, and volatile constituents like sesquiterpenes and monoterpenes, are mainly attributed to the health-enhancing perspectives of ginger. This review elucidates the health claims of ginger and the molecular aspects and targets, with special reference to anticancer perspectives, immunonutrition, antioxidant potential, and cardiovascular cure. The molecular targets involved in chemoprevention like the inhibition of NF-κB activation via impairing nuclear translocation, suppresses cIAP1 expression, increases caspase-3/7 activation, arrests cell cycle in G2 + M phases, up-regulates Cytochrome-c, Apaf-1, activates PI3K/Akt/I kappaB kinases IKK, suppresses cell proliferation, and inducts apoptosis and chromatin condensation. Similarly, facts are presented regarding the anti-inflammatory response of ginger components and molecular targets including inhibition of prostaglandin and leukotriene biosynthesis and suppression of 5-lipoxygenase. Furthermore, inhibition of phosphorylation of three mitogen-activated protein kinases (MAPKs), extracellular signal-regulated kinases 1 and 2 (ERK1/2), and c-Jun N-terminal kinase (JNK) are also discussed. The role of ginger in reducing the extent of cardiovascular disorders, diabetes mellitus, and digestive problems has also been described in detail. Although, current review articles summarized the literature pertaining to ginger and its components. However, authors are still of the view that further research should be immediately carried out for meticulousness.
Mechanistically Identified Suitable Biomarkers of Exposure, Effect, and Susceptibility for Silicosis and Coal-Worker'S Pneumoconiosis: A Comprehensive Review

Clinical detection of silicosis is currently dependent on radiological and lung function abnormalities, both late manifestations of disease. Markers of prediction and early detection of pneumoconiosis are imperative for the implementation of timely intervention strategies. Understanding the underlying mechanisms of the etiology of coal workers pneumoconiosis (CWP) and silicosis was essential in proposing numerous biomarkers that have been evaluated to assess effects following exposure to crystalline silica and/or coal mine dust. Human validation studies have substantiated some of these proposed biomarkers and argued in favor of their use as biomarkers for crystalline silica- and CWP-induced pneumoconiosis. A number of “ideal” biological markers of effect were identified, namely, Clara cell protein-16 (CC16) (serum), tumor necrosis factor-α (TNF-α) (monocyte release), interleukin-8 (IL-8) (monocyte release), reactive oxygen species (ROS) measurement by chemiluminescence (neutrophil release), 8-isoprostanes (serum), total antioxidant levels measured by total equivalent antioxidant capacity (TEAC), glutathione, glutathione peroxidase activity, glutathione S-transferase activity, and platelet-derived growth factor (PDGF) (serum). TNF-α polymorphism (blood cellular DNA) was identified as a biomarker of susceptibility. Further studies are planned to test the validity and feasibility of these biomarkers to detect either high exposure to crystalline silica and early silicosis or susceptibility to silicosis in gold miners in South Africa.
Pathological amygdala activation during working memory performance: Evidence for a pathophysiological trait marker in bipolar affective disorder

Recent evidence suggests that deficits of working memory may be a promising neurocognitive endophenotype of bipolar affective disorder. However, little is known about the neurobiological correlates of these deficits. The aim of this study was to determine possible pathophysiological trait markers of bipolar disorder in neural circuits involved in working memory. Functional magnetic resonance imaging was performed in 18 euthymic bipolar patients and 18 matched healthy volunteers using two circuit‐specific experimental tasks established by prior systematic neuroimaging studies of working memory. Both euthymic bipolar patients and healthy controls showed working memory‐related brain activations that were highly consistent with findings from previous comparable neuroimaging studies in healthy subjects. While these patterns of brain activation were completely preserved in the bipolar patients, only the patients exhibited activation of the right amygdala during the articulatory rehearsal task. In the same task, functional activation in right frontal and intraparietal cortex and in the right cerebellum was significantly enhanced in the patients. These findings indicate that the right amygdala is pathologically activated in euthymic bipolar patients during performance of a circuit‐specific working memory task (articulatory rehearsal). This pathophysiological abnormality appears to be a trait marker in bipolar disorders that can be observed even in the euthymic state and that seems to be largely independent of task performance and medication. Hum Brain Mapp, 2010. © 2009 Wiley‐Liss, Inc.
Vitamin D and Autism Spectrum Disorder: A Literature Review

Low vitamin D status in early development has been hypothesised as an environmental risk factor for Autism Spectrum Disorder (ASD), given the concurrent increase in the prevalence of these two conditions, and the association of vitamin D with many ASD-associated medical conditions. Identification of vitamin D-ASD factors may provide indications for primary and secondary prevention interventions. We systematically reviewed the literature for studies on vitamin D-ASD relationship, including potential mechanistic pathways. We identified seven specific areas, including: latitude, season of conception/birth, maternal migration/ethnicity, vitamin D status of mothers and ASD patients, and vitamin D intervention to prevent and treat ASD. Due to differences in the methodological procedures and inconsistent results, drawing conclusions from the first three areas is difficult. Using a more direct measure of vitamin D status—that is, serum 25(OH)D level during pregnancy or childhood—we found growing evidence for a relationship between vitamin D and ASD. These findings are supported by convincing evidence from experimental studies investigating the mechanistic pathways. However, with few primary and secondary prevention intervention trials, this relationship cannot be determined, unless randomised placebo-controlled trials of vitamin D as a preventive or disease-modifying measure in ASD patients are available.
Comparison Between 2 Strategies of Fluid Management on Blood Loss and Transfusion Requirements During Liver Transplantation.

OBJECTIVE To compare the effects of low central venous pressure (LCVP) and transesophageal Doppler (TED)-guided fluid management on blood loss and blood transfusion during liver transplantation (LTx). DESIGN Retrospective study. SETTING Single institution, university hospital. PARTICIPANTS Adult recipients of LTx. INTERVENTIONS Two groups: control (LCVP G), n=45 with CVP maintained 40% lower than the preoperative value during the preanhepatic phase. The mean arterial pressure was kept >60 mmHg. This group was matched with the second group (TED G); n = 45, in which a TED protocol was followed maintaining the systemic vascular resistance (SVR) more than 750 dynes•s•cm-5. Coagulation defects were corrected following thromboelastometry. MEASUREMENTS AND MAIN RESULTS Intraoperative blood loss, blood products, perioperative creatinine, lactate, and postoperative patients' stratification according to the Acute Kidney Injury Network classification were compared. Prior to the anhepatic phase, CVP was significantly lower in LCVP G (p < 0.001). TED G tended to have less but nonsignificant, blood loss, packed red blood cells, fresh frozen plasma, and platelets and received significantly less colloid and higher norepinephrine. Lactate was significantly higher in LCVP G at the end of the anhepatic phase and end of surgery while urine output in the preanhepatic phase was significantly lower. Creatinine was significantly lower on postoperative days 1 and 3, and Acute Kidney Injury Network stages were better on postoperative day 1 in TED G. CONCLUSIONS During LTx, TED-guided fluid management, with norepinephrine used to maintain SVR, was similar to LCVP regarding blood loss and transfusion requirements and had better impacts on kidney function and lactate.
Modelling galaxy clustering: is new physics needed in galaxy formation models?

The clustering amplitude of galaxies depends on their intrinsic luminosity. We compare the properties of publicly available galaxy formation models with clustering measurements from the Two-degree Field Galaxy Redshift Survey. The model predictions show the same qualitative behaviour as the data but fail to match the observations at the level of accuracy at which current measurements can be made. We demonstrate that this is due to the model producing too many satellite galaxies in massive haloes. We implement simple models to describe two new processes: satellite–satellite mergers and the tidal dissolution of satellites to investigate their impact on the predicted clustering. We find that both processes need to be included in order to produce a model which matches the observations.
Real-Time Estimation of Pathological Tremor Parameters from Gyroscope Data

This paper presents a two stage algorithm for real-time estimation of instantaneous tremor parameters from gyroscope recordings. Gyroscopes possess the advantage of providing directly joint rotational speed, overcoming the limitations of traditional tremor recording based on accelerometers. The proposed algorithm first extracts tremor patterns from raw angular data, and afterwards estimates its instantaneous amplitude and frequency. Real-time separation of voluntary and tremorous motion relies on their different frequency contents, whereas tremor modelling is based on an adaptive LMS algorithm and a Kalman filter. Tremor parameters will be employed to drive a neuroprosthesis for tremor suppression based on biomechanical loading.
Delay effects in the human sensory system during balancing

Mechanical models of human self-balancing often use the Newtonian equations of inverted pendula. While these mathematical models are precise enough on the mechanical side, the ways humans balance themselves are still quite unexplored on the control side. Time delays in the sensory and motoric neural pathways give essential limitations to the stabilization of the human body as a multiple inverted pendulum. The sensory systems supporting each other provide the necessary signals for these control tasks; but the more complicated the system is, the larger delay is introduced. Human ageing as well as our actual physical and mental state affects the time delays in the neural system, and the mechanical structure of the human body also changes in a large range during our lives. The human balancing organ, the labyrinth, and the vision system essentially adapted to these relatively large time delays and parameter regions occurring during balancing. The analytical study of the simplified large-scale time-delayed models of balancing provides a Newtonian insight into the functioning of these organs that may also serve as a basis to support theories and hypotheses on balancing and vision.
Raman spectroscopic study of microcrystalline silica

Samples of microcrystalline silica have been examined with Raman spectroscopy to investigate the vibrational and structural characteristics ofthe component phases, including their spatial distribution. Using microspectroscopic techniques, we found variable amounts of a novel silica polymorph ("moganite") in samples of chalcedony, chert, and flint and have obtained the Raman spectrum of the pure phase. We identified 19 of the 27 Raman-active vibrational modes predicted by factor group analysis assuming the monoclinic structure previously reported for "moganite. " Notably, a strong band is found at 501 cm ', which may be correlated with the four-membered rings of SiO, tetrahedra in the refined structure. Comparison with Raman spectra of other tetrahedrally coordinated minerals confirmed that this new phase is a structurally distinct polymorph of silica.
Effect of Trilostane on Hormone and Serum Electrolyte Concentrations in Dogs with Pituitary‐Dependent Hyperadrenocorticism

Background The effects of trilostane on key hormones and electrolytes over 24 hours in dogs with pituitary‐dependent hyperadrenocorticism (PDH) are unknown. Objectives To determine the plasma concentration of cortisol, endogenous adrenocorticotropic hormone (ACTH), aldosterone, sodium, potassium, and ionized calcium concentrations, and plasma renin activity over a 24‐hour period after administration of trilostane to dogs with well‐controlled PDH. Animals Nine dogs (mean age 9.3 ± 0.67 years, mean weight 31.9 ± 6.4 kg) with confirmed PDH. Methods Prospective study. Thirty days after the first administration of trilostane, blood samples were taken at −30, 0 (baseline), 15, 30, 60, and 90 minutes, and 2, 3, 4, 6, 8, 12, 16, 20, and 24 hours after administration of trilostane and plasma concentration of cortisol, endogenous ACTH, aldosterone, sodium, potassium, ionized calcium, and renin activity were determined. Results Cortisol concentrations decreased significantly (P < .001) 2–4 hours after trilostane administration. From baseline, there was a significant (P < .001) increase in endogenous ACTH concentrations between hours 3–12, a significant increase (P < .001) in aldosterone concentration between hours 16–20, and a significant (P < .001) increase in renin activity between hours 6–20. Potassium concentration decreased significantly (P < .05) between hours 0.5–2. Conclusion and Clinical Importance Treatment with trilostane did not cause clinically relevant alterations in plasma aldosterone and potassium concentration. Results suggest that in dogs with PDH, the optimal time point for an ACTH‐stimulation test to be performed is 2–4 hours after trilostane dosing. Future studies are necessary to establish interpretation criteria for a 2‐ to 4‐hour postpill ACTH‐stimulation test.
Visio-lization: generating novel facial images

Our goal is to generate novel realistic images of faces using a model trained from real examples. This model consists of two components: First we consider face images as samples from a texture with spatially varying statistics and describe this texture with a local non-parametric model. Second, we learn a parametric global model of all of the pixel values. To generate realistic faces, we combine the strengths of both approaches and condition the local non-parametric model on the global parametric model. We demonstrate that with appropriate choice of local and global models it is possible to reliably generate new realistic face images that do not correspond to any individual in the training data. We extend the model to cope with considerable intra-class variation (pose and illumination). Finally, we apply our model to editing real facial images: we demonstrate image in-painting, interactive techniques for improving synthesized images and modifying facial expressions.
Natural image statistics and divisive normalization: Modeling nonlinearity and adaptation in cortical neurons

Understanding the functional role of neurons and neural systems is a primary goal of systems neuroscience. A longstanding hypothesis states that sensory systems are matched to the statistical properties of the signals to which they are exposed [e.g., 4, 6]. In particular, Barlow has proposed that the role of early sensory systems is to remove redundancy in the sensory input, resulting in a set of neural responses that are statistically independent. Variants of this hypothesis have been formulated by a number of other authors [e.g., 2, 52] (see [47] for a review). The basic version assumes a fixed environmental model, but Barlow and Foldiak later augmented the theory by suggesting that adaptation in neural systems might be thought of as an adjustment to remove redundancies in the responses to recently presented stimuli [8, 7]. There are two basic methodologies for testing such hypotheses. The most direct approach is to examine the statistical properties of neural responses under natural stimulation conditions [e.g., 25, 41, 17, 5, 40] or the statistical dependency of pairs (or groups) of neural responses. Due to their technical difficulty, such multi-cellular experiments are only recently becoming possible, and the earliest reports appear consistent with the hypothesis [e.g., 54]. An alternative approach is to " derive " a model for early sensory processing [e. statistical properties of environmental signals and shows that a transformation derived according to some statistical optimization criterion provides a good description of the response properties of a set of sensory neurons. We follow this latter approach in this chapter.
Scalable and versatile genome editing using linear DNAs with micro-homology to Cas9 sites in C. elegans

Homology-directed repair (HDR) of double-stranded DNA breaks is a promising method for genome editing, but is thought to be less efficient than error-prone non-homologous end joining (NHEJ) in most cell types. We have investigated HDR of double-strand breaks induced by CRISPR-associated protein 9 (Cas9) in C. elegans. We find that HDR is very robust in the C. elegans germline. Linear repair templates with short (~30-60 bases) homology arms support the integration of base and gene-sized edits with high efficiency, bypassing the need for selection. Based on these findings, we developed a systematic method to mutate, tag or delete any gene in the C. elegans genome, without the use of co-integrated markers or long homology arms. We generated 23 unique edits at 11 genes, including premature stops, whole-gene deletions, and protein fusions to antigenic peptides and GFP. The method is scalable for multi-gene editing projects and could be applied to other animals with an accessible germline. Highlights:-Short (30-60 bp) homology arms immediately flanking Cas9 cuts are sufficient to integrate both small and large edits in the C. elegans genome. -Scalable and versatile method for seamless editing of the C. elegans genome.
Food intake and serum levels of iron in children and adolescents with attention-deficit/hyperactivity disorder.

OBJECTIVE To investigate hematologic variables related to iron deficiency and food intake in attention-deficit/hyperactivity disorder. METHOD The sample comprised 62 children and adolescents (6-15 years old) divided into three groups: Group 1: 19 (30.6%) patients with attention-deficit/hyperactivity disorder using methylphenidate for 3 months; Group 2: 22 (35.5%) patients with attention-deficit/hyperactivity disorder who were methylphenidate naive and Group 3: 21 (33.9%) patients without attention-deficit/hyperactivity disorder. Serum iron, ferritin, transferrin, hemoglobin, mean corpuscular volume, red cell distribution width, mean corpuscular hemoglobin concentration, nutritional diagnostic parameters - Body Mass Index Coefficient, food surveys were evaluated among the groups. RESULTS The attention-deficit/hyperactivity disorder group drug naive for methylphenidate presented the highest red cell distribution width among the three groups (p = 0.03). For all other hematologic and food survey variables, no significant differences were found among the groups. No significant correlation between dimensional measures of attention-deficit/hyperactivity disorder symptoms and ferritin levels was found in any of the three groups. CONCLUSION Peripheral markers of iron status and food intake of iron do not seem to be modified in children with attention-deficit/hyperactivity disorder, but further studies assessing brain iron levels are needed to fully understand the role of iron in attention-deficit/hyperactivity disorder pathophysiology.