Miracle-dz/UniFAR-FTUs huggingface dataset:
Altering Sphingolipid Metabolism in Saccharomyces cerevisiae Cells Lacking the Amphiphysin Ortholog Rvs161 Reinitiates Sugar Transporter Endocytosis

ABSTRACT Amphiphysins are proteins thought to be involved in synaptic vesicle endocytosis. Amphiphysins share a common BAR domain, which can sense and/or bend membranes, and this function is believed to be essential for endocytosis. Saccharomyces cerevisiae cells lacking the amphiphysin ortholog Rvs161 are inviable when starved for glucose. Altering sphingolipid levels in rvs161 cells remediates this defect, but how lipid changes suppress remains to be elucidated. Here, we show that the sugar starvation-induced death of rvs161 cells extends to other fermentable sugar carbon sources, and the loss of sphingolipid metabolism suppresses these defects. In all cases, rvs161 cells respond to the starvation signal, elicit the appropriate transcriptional response, and properly localize the requisite sugar transporter(s). However, Rvs161 is required for transporter endocytosis. rvs161 cells accumulate transporters at the plasma membrane under conditions normally resulting in their endocytosis and degradation. Transporter endocytosis requires the endocytosis (endo) domain of Rvs161. Altering sphingolipid metabolism by deleting the very-long-chain fatty acid elongase SUR4 reinitiates transporter endocytosis in rvs161 and rvs161 endo− cells. The sphingolipid-dependent reinitiation of endocytosis requires the ubiquitin-regulating factors Doa1, Doa4, and Rsp5. In the case of Doa1, the phospholipase A2 family ubiquitin binding motif is dispensable. Moreover, the conserved AAA-ATPase Cdc48 and its accessory proteins Shp1 and Ufd1 are required. Finally, rvs161 cells accumulate monoubiquitin, and this defect is remediated by the loss of SUR4. These results show that defects in sphingolipid metabolism result in the reinitiation of ubiquitin-dependent sugar transporter endocytosis and suggest that this event is necessary for suppressing the nutrient starvation-induced death of rvs161 cells.
Selection and validation of reference genes for functional studies in the Calliphoridae family

Abstract The genera Cochliomyia and Chrysomya contain both obligate and saprophagous flies, which allows the comparison of different feeding habits between closely related species. Among the different strategies for comparing these habits is the use of qPCR to investigate the expression levels of candidate genes involved in feeding behavior. To ensure an accurate measure of the levels of gene expression, it is necessary to normalize the amount of the target gene with the amount of a reference gene having a stable expression across the compared species. Since there is no universal gene that can be used as a reference in functional studies, candidate genes for qPCR data normalization were selected and validated in three Calliphoridae (Diptera) species, Cochliomyia hominivorax Coquerel, Cochliomyia macellaria Fabricius, and Chrysomya albiceps Wiedemann. The expression stability of six genes (Actin, Gapdh, Rp49, Rps17, α-tubulin, and GstD1) was evaluated among species within the same life stage and between life stages within each species. The expression levels of Actin, Gapdh, and Rp49 were the most stable among the selected genes. These genes can be used as reliable reference genes for functional studies in Calliphoridae using similar experimental settings.
and Nutrient-Nutrient Interactions Pyrroloquinoline Quinone Modulates Mitochondrial Quantity and Function in Mice 1

When pyrroloquinoline quinone (PQQ) is added to an amino acid-based, but otherwise nutritionally complete basal diet, it improves growth-related variables in young mice. We examined PQQ and mitochondrial function based on observations that PQQ deﬁciency results in elevated plasma glucose concentrations in young mice, and PQQ addition stimulates mitochondrial complex 1 activity in vitro. PQQ-deﬁcient weanling mice had a 20– 30% reduction in the relative amount of mitochondria in liver; lower respiratory control ratios, and lower respiratory quotients than PQQ-supplemented mice (2 mg PQQ/kg diet). In mice from dams fed a conventional laboratory diet, but switched at weaning to the basal diet, plasma glucose, Ala, Gly, and Ser concentrations were elevated at 4 wk (PQQ (cid:1) vs. PQQ 1 ), but not at 8 wk. The relative mitochondrial content (ratio of mtDNA to nuclear DNA) also tended ( P , 0.18) to be lower (PQQ (cid:1) vs. PQQ 1 ) at 4 wk, but not at 8 wk. PQQ also counters the mitochondrial complex 1 inhibitor, diphenylene iodonium (DPI). Mice were gavaged with 0, 0.4, or 4 m g PQQ/g body weight (BW) daily for 14 d. At each PQQ level, DPI was injected (i.p.) at 0, 0.4, 0.8, or 1.6 m g DPI/g BW. The PQQ-deﬁcient mice exposed to 0.4 or 4.0 m g DPI/g lost weight and had lower plasma glucose levels than PQQ-supplemented mice ( P , 0.05). In addition, ﬁbroblasts took up 3 H-PQQ added to cell cultures, and cultured hepatocytes maintained mitochondrial PQQ concentrations similar to those observed in vivo. Collectively, these results indicate that dietary PQQ can inﬂuence mitochondrial amount and function, particularly in perinatal and weanling mice. J. Nutr. 136: 390–396, 2006. fraction after isolation of the mitochondria was recentrifuged at 100,000 3 g for 60 min. The pellet was suspended with agitation, sonicated, and saved for determination of radioactivity by scintillation counting. In addition, normal mouse liver and mouse Hepa 1-6 cells were used as sources of tissue for PQQ quantitation. The Hepa 1-6 cells were cultured (at 37 8 C with 5–10% CO 2 , 24 h) in 90% DMEM (4.5 g/L glucose) plus 10% fetal calf serum to which 0, 15, or 30 m mol/L PQQ was added. The cells were harvested, washed twice with PBS and homogenized in isolation buffer (10 mmol/L Hepes pH 7.8, 0.2 mmol/L EGTA, and 0.25 mol/L sucrose). The cell homogenate was centrifuged at 1000 3 g for 10 min at 4 8 C. The resulting supernatant was then centrifuged at 12,000 3 g for 15 min at 4 8 C for separation of a mitochondrial enriched pellet and cytosol (supernatant) fractions. Values for PQQ obtained from the GDH assay were normalized per mg of protein (29). Statistical analysis. The Statview 5.0 statistical analysis program (SAS Institute) was used to analyze the results. Results were analyzed using a t test or ANOVA using a Bonferroni post hoc test. Results are presented as means 6 SEM or SD. Differences were considered signiﬁcant at P , 0.05.
Inflammation contributes to low plasma amino acid concentrations in patients with chronic kidney disease.

BACKGROUND Inflammation and malnutrition are common in chronic kidney disease (CKD) patients, and plasma concentrations of free amino acids (AAs) in these patients are often abnormal. Malnutrition contributes to alterations in AA concentrations. OBJECTIVE The objective was to study the effects of inflammation on plasma AA concentrations. DESIGN Concentrations of plasma AAs, serum albumin, and several inflammatory markers were analyzed in 200 fasting, nondiabetic CKD patients who were close to the start of renal replacement therapy. The nutritional status of these patients was assessed by a subjective global assessment. RESULTS The patients with inflammation [C-reactive protein (CRP) concentrations >10 mg/L] or malnutrition had lower AA concentrations than did the patients with no inflammation or malnutrition. The presence of both inflammation and malnutrition was associated with more marked reductions in AA concentrations than was malnutrition alone. Significant inverse correlations were observed between the plasma concentrations of most of the essential and nonessential AAs and inflammatory markers, whereas serum albumin concentrations were positively correlated with several AA concentrations. A stepwise multivariate regression analysis showed that serum CRP concentrations were independently associated with low concentrations of the sums of both nonessential AAs and all AAs. An analysis of all-cause mortality with a Kaplan-Meier test showed that the patients with higher AA concentrations had significantly better survival than did the patients with lower AA concentrations. CONCLUSIONS Plasma AA concentrations are low in CKD patients with inflammation and are inversely correlated with concentrations of inflammatory markers. Although inflammation and malnutrition are closely related, CRP concentrations were independently associated with low concentrations of the sums of both nonessential AAs and all AAs, which suggests an independent role of inflammation as a cause of low plasma AA concentrations in CKD patients.
Composition (lean and fat tissue) of weight changes in adult Danes.

BACKGROUND Weight loss may be associated with unfavorable changes in body composition not compensated for by subsequent weight gain. OBJECTIVE We examined the composition of weight change in relation to obesity, previous weight changes, weight-loss attempts, and physical activity. DESIGN Part of the Danish MONICA (Monitoring Trends in Cardiovascular Disease) project, this was a longitudinal population study of changes in weight and body composition, with examinations in 1982-1983, 1987-1988, and 1993-1994. A total of 1236 men and 1200 women aged 35, 45, 55, or 65 y in 1987-1988 participated. Changes in fat and fat-free mass were measured by bioelectrical impedance. RESULTS Before adjustment for age-related changes, fat-free mass made up 41% of weight lost and 24% of weight gained in men. In women, loss of fat-free mass (35%) was more than double that of gains (15%). After adjustment, the fractions of weight gained as fat-free mass were not significantly different from the fractions lost. These fractions were independent of age, obesity, and weight changes in the previous 5 y; successful weight-loss attempts; and physical activity. Independent of age and degree of obesity, weight changes were associated with greater changes in fat-free mass in men than in women. CONCLUSIONS These data do not support the theory that weight loss or weight cycling may lead to an unfavorable body composition, nor do they provide a biological explanation for why long-term weight loss is often unsuccessful. However, the metabolic and health consequences of weight change may differ in men and women.
Effect of long-chain polyunsaturated fatty acid supplementation of preterm infants on disease risk and neurodevelopment: a systematic review of randomized controlled trials.

BACKGROUND Supplementation of preterm formulas with long-chain polyunsaturated fatty acids (LCPUFAs) is based on their effectiveness to increase blood status and improve visual outcomes. Dispute remains over their efficacy on global development. OBJECTIVE The objective was to compare the effects of LCPUFA-supplemented with those of control formulas on neurodevelopment and diseases associated with prematurity. DESIGN We systematically reviewed randomized controlled trials involving preterm infants that tested LCPUFA-supplemented formulas. The weighted mean differences (WMDs) in neurodevelopmental scores and relative risk (RR) of disease were calculated to compare infants fed LCPUFA-supplemented formula with those fed control formula. RESULTS No clear differences in Bayley Scales of Infant Development (BSID) scores were observed between groups. Mental development of LCPUFA-supplemented infants was 3.4 points higher than that of control infants with BSID version II (WMD: 3.44; 95% CI: 0.56, 6.31; P = 0.02; n = 879), although it was driven by 2 trials with large effect sizes and wide CIs. Psychomotor development was lower in supplemented infants tested with BSID version I (WMD: -7.99; 95% CI: -14.00, -1.99; P = 0.009; n = 87); however, it was limited by small sample sizes. No differences in the RR of sepsis (1.08; 95% CI: 0.79, 1.46; P = 0.63; n = 1333) or in the RR of necrotizing enterocolitis (1.13; 95% CI: 0.62, 2.04; P = 0.69; n = 1333) were found. Similarly, the risks of retinopathy of prematurity, intraventricular hemorrhage, and bronchopulmonary dysplasia were not different between groups, but data were limited by small sample sizes and trials with an increased risk of bias. CONCLUSIONS LCPUFA-supplemented formula does not alter the risk of NEC or sepsis. Further work is needed to determine the extent of benefit of LCPUFA-supplemented formula on the mental development of preterm infants.
Soy sterol esters and beta-sitostanol ester as inhibitors of cholesterol absorption in human small bowel.

BACKGROUND Plant sterols are natural dietary components with serum cholesterol-lowering properties. The lowering of serum cholesterol by plant sterols is believed to be the result of an inhibition of cholesterol absorption in the small bowel, although increased bile acid excretion has also been suggested. The difference in effect of saturated and unsaturated plant sterols on cholesterol absorption needs to be elucidated further. OBJECTIVE The primary aim of this study was to measure small-bowel cholesterol absorption and sterol excretion in addition to hepatic cholesterol synthesis after intake of soy sterol esters and beta-sitostanol ester corresponding to 1.5 g plant sterols/d. DESIGN Seven ileostomy subjects were studied during a control period and 2 intervention periods when either soy sterol esters or beta-sitostanol ester was added to a basal diet. Ileostomy bags were collected every other hour and frozen immediately for analysis of nutrients and sterols. RESULTS Cholesterol absorption was 56% (43-65%) in the control period and decreased to 38% (32-46%) in the soy sterol ester period (P = 0.00) and to 39% (30-48%) in the beta-sitostanol ester period (P = 0.00). CONCLUSION Esterified soy sterols and beta-sitostanol inhibited cholesterol absorption equally, despite the different structures of the plant sterols.
Coalgebraic Trace Semantics via Forgetful Logics

We use modal logic as a framework for coalgebraic trace semantics, and show the flexibility of the approach with concrete examples such as the language semantics of weighted, alternating and tree automata. We provide a sufficient condition under which a logical semantics coincides with the trace semantics obtained via a given determinization construction. Finally, we consider a condition that guarantees the existence of a canonical determinization procedure that is correct with respect to a given logical semantics. That procedure is closely related to Brzozowski’s minimization algorithm.
Towards a Top-Domain Ontology for Linking Biomedical Ontologies

In this paper we present the ongoing development and extension work on BioTop--a top-domain ontology for linking biomedical domain ontologies. We start by making the case for the application of a common ontology to interface independent biomedical domain ontologies by introducing a set of more general classes. Then we briefly depict the relation of BioTop to the GENIA ontology as starting point of its initial developement. Afterwards we propose our distinction of ontologies into top, top-domain and domain ones and describe our approach to the integration of the top ontology BFO into BioTop. Then we present our plans to join the OBO and OBO Foundry repository of ontologies and list its admission principles in relation to our ontology. Some actual BioTop interface classes are shown subsequently. We conclude by detailing on some planned BioTop usages in the area of BioNLP and cancer research and show some further intended improvements.
Chemically reacting unsteady magnetohydrodynamic oscillatory Slip flow of a micropolar fluid in a planer channel with varying concentration

The study examines the problem of unsteady MHD mixed convection in a micropolar fluid with oscillatory flow of an electrically conducting optically thin fluid through a planer channel filled with saturated porous medium. The effect of buoyancy, heat source, thermal radiation and chemical reaction are taken into account embedded with slip boundary condition, varying temperature and concentration. The closed-form analytical solutions are obtained for the momentum, angular momentum, energy and concentration equations. The influence of the various parameters entering into the problem in the velocity, temperature and concentration fields are discussed with the help of graphs. Finally the effects of the pertinent parameters on the skin friction, couple stress and the rate of heat transfer coefficient at the plate are discussed.
Occurrence of long-term depression in the cerebellar flocculus during adaptation of optokinetic response

Long-term depression (LTD) at parallel fiber (PF) to Purkinje cell (PC) synapses has been considered as a main cellular mechanism for motor learning. However, the necessity of LTD for motor learning was challenged by demonstration of normal motor learning in the LTD-defective animals. Here, we addressed possible involvement of LTD in motor learning by examining whether LTD occurs during motor learning in the wild-type mice. As a model of motor learning, adaptation of optokinetic response (OKR) was used. OKR is a type of reflex eye movement to suppress blur of visual image during animal motion. OKR shows adaptive change during continuous optokinetic stimulation, which is regulated by the cerebellar flocculus. After OKR adaptation, amplitudes of quantal excitatory postsynaptic currents at PF-PC synapses were decreased, and induction of LTD was suppressed in the flocculus. These results suggest that LTD occurs at PF-PC synapses during OKR adaptation.
Yoga Is as Good as Stretching-Strengthening Exercises in Improving Functional Fitness Outcomes: Results From a Randomized Controlled Trial.

BACKGROUND Despite yoga's popularity, few clinical trials have employed rigorous methodology to systematically explore its functional benefits compared with more established forms of exercise. The objective of this study was to compare the functional benefits of yoga with the conventional stretching-strengthening exercises recommended for adults. METHODS Sedentary healthy adults (N = 118; M age = 62.0) participated in an 8-week (three times a week for 1 hour) randomized controlled trial, which consisted of a Hatha yoga group (n = 61) and a stretching-strengthening exercise group (n = 57). Standardized functional fitness tests assessing balance, strength, flexibility, and mobility were administered at baseline and postintervention. RESULTS A repeated measures multivariate analysis of variance showed a significant time effect for measures of balance [F(3,18) = 4.88, p < . 01, partial η(2) = . 45], strength [F(2,19) = 15.37, p < . 001, partial η(2) = . 62], flexibility [F(4,17) = 8.86, p < . 001, partial η(2) = . 68], and mobility [F(2,19) = 8.54, p < . 002, partial η(2) = . 47]. Both groups showed significant improvements on measures of balance (left-right leg and four square step); strength (chair stands and arm curls); flexibility (back scratch and sit-and-reach); and mobility (gait speed and 8-feet up and go), with partial η(2) ranging from . 05 to . 47. CONCLUSIONS These data suggest that regular yoga practice is just as effective as stretching-strengthening exercises in improving functional fitness. To our knowledge, this is the first study to examine functional benefits of yoga in comparison with stretching-strengthening exercises in sedentary, healthy, community-dwelling older adults. These findings have clinical implications as yoga is a more amenable form of exercise than strengthening exercises as it requires minimal equipment and can be adapted for individuals with lower levels of functioning or disabilities.
The GOD model

GOD (General Ontology Discovery) is an unsupervised system to extract semantic relations among domain specific entities and concepts from texts. Operationally, it acts as a search engine returning a set of true predicates regarding the query instead of the usual ranked list of relevant documents. Our approach relies on two basic assumptions: (i) paradigmatic relations can be established only among terms in the same Semantic Domain an (ii) they can be inferred from texts by analyzing the Subject-Verb-Object patterns where two domain specific terms co-occur. A qualitative analysis of the system output shows that GOD provide true, informative and meaningful relations in a very efficient way.
Microfluidic device for the formation of optically excitable, three-dimensional, compartmentalized motor units

Microfluidics and optogenetics enable the formation of light-excitable motor units in a compartmentalized and 3D environment. Motor units are the fundamental elements responsible for muscle movement. They are formed by lower motor neurons and their muscle targets, synapsed via neuromuscular junctions (NMJs). The loss of NMJs in neurodegenerative disorders (such as amyotrophic lateral sclerosis or spinal muscle atrophy) or as a result of traumatic injuries affects millions of lives each year. Developing in vitro assays that closely recapitulate the physiology of neuromuscular tissues is crucial to understand the formation and maturation of NMJs, as well as to help unravel the mechanisms leading to their degeneration and repair. We present a microfluidic platform designed to coculture myoblast-derived muscle strips and motor neurons differentiated from mouse embryonic stem cells (ESCs) within a three-dimensional (3D) hydrogel. The device geometry mimics the spinal cord–limb physical separation by compartmentalizing the two cell types, which also facilitates the observation of 3D neurite outgrowth and remote muscle innervation. Moreover, the use of compliant pillars as anchors for muscle strips provides a quantitative functional readout of force generation. Finally, photosensitizing the ESC provides a pool of source cells that can be differentiated into optically excitable motor neurons, allowing for spatiodynamic, versatile, and noninvasive in vitro control of the motor units.
Towards a Broad-Coverage Biomedical Ontology Based on Description Logics

We describe an ontology engineering methodology by which conceptual knowledge is extracted from an informal medical thesaurus (UMLS) and automatically converted into a formal description logics system (LOOM). Our approach consists of four steps: concept definitions are automatically generated from the UMLS, integrity checking of taxonomic and partonomic hierarchies is performed by LOOM's terminological classifier, cycles and inconsistencies are eliminated, as well as incremental refinement of the evolving knowledge base is performed by a domain expert. We report on experiments with a very large knowledge base composed of 164,000 concepts and 76,000 relations.
Revisiting Hammel et al. (1987): Does the shadowing property hold for modern computers?

Computational techniques are extensively applied in nonlinear science. However, while the use of computers for research has been expressive, the evaluation of numerical results does not grow in the same pace. Hammel et al. (Journal of Complexity, 1987, 3(2), 136--145) were pioneers in the numerical reliability field and have proved a theorem that a pseudo-orbit of a logistic map is shadowed by a true orbit within a distance of $10^{-8}$ for $10^{7}$ iterates. But the simulation of the logistic map with less than 100 iterates presents an error greater than $10^{-8}$ in a modern computer, performing a test based on the concept of multiple pseudo-orbits and symbolic computing.