Miracle-dz/UniFAR-FTUs huggingface dataset:
How Biochemical Constraints of Cellular Growth Shape Evolutionary Adaptations in Metabolism

Evolutionary adaptations in metabolic networks are fundamental to evolution of microbial growth. Studies on unneeded-protein synthesis indicate reductions in fitness upon nonfunctional protein synthesis, showing that cell growth is limited by constraints acting on cellular protein content. Here, we present a theory for optimal metabolic enzyme activity when cells are selected for maximal growth rate given such growth-limiting biochemical constraints. We show how optimal enzyme levels can be understood to result from an enzyme benefit minus cost optimization. The constraints we consider originate from different biochemical aspects of microbial growth, such as competition for limiting amounts of ribosomes or RNA polymerases, or limitations in available energy. Enzyme benefit is related to its kinetics and its importance for fitness, while enzyme cost expresses to what extent resource consumption reduces fitness through constraint-induced reductions of other enzyme levels. A metabolic fitness landscape is introduced to define the fitness potential of an enzyme. This concept is related to the selection coefficient of the enzyme and can be expressed in terms of its fitness benefit and cost.
Clinical and Genetic Correlates of Circulating Angiopoietin-2 and Soluble Tie-2 in the Community

Background—Experimental studies suggest that endothelial growth factors play an important role in angiogenesis and vascular remodeling. The clinical and genetic correlates of circulating angiopoietin-2 (Ang-2) and its soluble receptor/regulator Tie-2 (sTie-2) have not been determined in a community-based sample. Methods and Results—Serum Ang-2 and sTie-2 were assayed in 3778 third-generation cohort participants of the Framingham Heart Study (mean age, 40±9 years; 53% women). Clinical correlates and heritability of both biomarkers were assessed using generalized estimating equations and variance-component analyses. Ang-2 levels were higher and sTie-2 levels were lower in women than in men. Ang-2 was positively related to age, smoking, systolic blood pressure, hypertension treatment, and diabetes (P<0.05 for all) but was inversely associated with total cholesterol and diastolic blood pressure (P<0.0001 for both), and sTie-2 was positively associated with body mass index, diabetes, and triglycerides but was inversely related to age, alcohol consumption, and glomerular filtration rate (P<0.05 for all). Both Ang-2 and sTie-2 were higher in participants with metabolic syndrome (P<0.005), with stronger associations of Ang-2 with blood pressure traits and of sTie-2 with obesity-dyslipidemia components. Heritability estimates for Ang-2 and sTie-2 were 27% and 56%, respectively (P<0.0001). A region on chromosome 9 was significantly linked to circulating sTie-2 levels (logarithm of the odds score, 8.31). Conclusion—Circulating levels of Ang-2 and sTie-2 are heritable traits associated with cardiovascular disease risk factors, including the metabolic syndrome. These observations are consistent with the notion that angiogenesis and vascular remodeling are determined in part by genetic influences and associated with metabolic risk factors.
I/O-efficiency of shortest path algorithms: an analysis

To establish the behavior of algorithms in a paging environment, the author analyzes the input/output (I/O) efficiency of several representative shortest path algorithms. These algorithms include single-course, multisource, and all pairs ones. The results are also applicable for other path problems such as longest paths, most reliable paths, and bill of materials. The author introduces the notation and a model of a paging environment. The I/O efficiencies of the selected single-source, all pairs, and multisource algorithms are analyzed and discussed. <<ETX>>
Gene identification for risk of relapse in stage I lung adenocarcinoma patients: a combined methodology of gene expression profiling and computational gene network analysis

Risk assessment and treatment choice remains a challenge in early non-smallcell lung cancer (NSCLC). The aim of this study was to identify novel genes involved in the risk of early relapse (ER) compared to no relapse (NR) in resected lung adenocarcinoma (AD) patients using a combination of high throughput technology and computational analysis. We identified 18 patients (n.13 NR and n.5 ER) with stage I AD. Frozen samples of patients in ER, NR and corresponding normal lung (NL) were subjected to Microarray technology and quantitative-PCR (Q-PCR). A gene network computational analysis was performed to select predictive genes. An independent set of 79 ADs stage I samples was used to validate selected genes by Q-PCR. From microarray analysis we selected 50 genes, using the fold change ratio of ER versus NR. They were validated both in pool and individually in patient samples (ER and NR) by Q-PCR. Fourteen increased and 25 decreased genes showed a concordance between two methods. They were used to perform a computational gene network analysis that identified 4 increased (HOXA10, CLCA2, AKR1B10, FABP3) and 6 decreased (SCGB1A1, PGC, TFF1, PSCA, SPRR1B and PRSS1) genes. Moreover, in an independent dataset of ADs samples, we showed that both high FABP3 expression and low SCGB1A1 expression was associated with a worse disease-free survival (DFS). Our results indicate that it is possible to define, through gene expression and computational analysis, a characteristic gene profiling of patients with an increased risk of relapse that may become a tool for patient selection for adjuvant therapy.
Periodontal Tissue Regeneration Using Fibroblast Growth Factor -2: Randomized Controlled Phase II Clinical Trial

Background The options for medical use of signaling molecules as stimulators of tissue regeneration are currently limited. Preclinical evidence suggests that fibroblast growth factor (FGF)-2 can promote periodontal regeneration. This study aimed to clarify the activity of FGF-2 in stimulating regeneration of periodontal tissue lost by periodontitis and to evaluate the safety of such stimulation. Methodology/Principal Findings We used recombinant human FGF-2 with 3% hydroxypropylcellulose (HPC) as vehicle and conducted a randomized double-blinded controlled trial involving 13 facilities. Subjects comprised 74 patients displaying a 2- or 3-walled vertical bone defect as measured ≥3 mm apical to the bone crest. Patients were randomly assigned to 4 groups: Group P, given HPC with no FGF-2; Group L, given HPC containing 0.03% FGF-2; Group M, given HPC containing 0.1% FGF-2; and Group H, given HPC containing 0.3% FGF-2. Each patient underwent flap operation during which we administered 200 µL of the appropriate investigational drug to the bone defect. Before and for 36 weeks following administration, patients underwent periodontal tissue inspections and standardized radiography of the region under investigation. As a result, a significant difference (p = 0.021) in rate of increase in alveolar bone height was identified between Group P (23.92%) and Group H (58.62%) at 36 weeks. The linear increase in alveolar bone height at 36 weeks in Group P and H was 0.95 mm and 1.85 mm, respectively (p = 0.132). No serious adverse events attributable to the investigational drug were identified. Conclusions Although no statistically significant differences were noted for gains in clinical attachment level and alveolar bone gain for FGF-2 groups versus Group P, the significant difference in rate of increase in alveolar bone height (p = 0.021) between Groups P and H at 36 weeks suggests that some efficacy could be expected from FGF-2 in stimulating regeneration of periodontal tissue in patients with periodontitis. Trial Registration ClinicalTrials.gov NCT00514657
Dislocations and their reduction in GaN

Abstract Gallium nitride (GaN) is a semiconductor used to make light emitting diodes, a technology that could decrease global energy demands significantly if used worldwide. Yet there are barriers to making high efficiency GaN based devices: defects, including threading dislocations (TDs), hamper the quality of the GaN crystalline film. The hypotheses proposed to explain the origin of TDs are critically reviewed. It has been suggested that TDs form upon GaN island coalescence during initial stages of crystalline film growth, yet some transmission electron microscopy and atomic force microscopy studies have shown few TDs at coalescence boundaries. Although harmful, TDs have a lesser effect on nitride based devices than on other compound semiconductors. Thus, GaN based devices are able to produce light despite high dislocation densities. This phenomenon has led to debate over the role of TDs in charge carrier recombination, which is reviewed. Some suggest that charge carriers arrive at TDs and recombine in a non-radiative manner, whereas others claim that they are repelled from the dislocations because the dislocation cores are electrically charged. The reduction of TDs in GaN films furthers the drive towards high efficiency devices. The final sections of this review address ways to effect reductions in TD density. Methods include changing growth conditions (including temperature and pressure), dosing the substrate with silane, and the exploitation of interlayers deposited during growth.
Mathematical Modeling of Transmission Dynamics and Optimal Control of Vaccination and Treatment for Hepatitis B Virus

Hepatitis B virus (HBV) infection is a worldwide public health problem. In this paper, we study the dynamics of hepatitis B virus (HBV) infection which can be controlled by vaccination as well as treatment. Initially we consider constant controls for both vaccination and treatment. In the constant controls case, by determining the basic reproduction number, we study the existence and stability of the disease-free and endemic steady-state solutions of the model. Next, we take the controls as time and formulate the appropriate optimal control problem and obtain the optimal control strategy to minimize both the number of infectious humans and the associated costs. Finally at the end numerical simulation results show that optimal combination of vaccination and treatment is the most effective way to control hepatitis B virus infection.
Family Satisfaction With End-of-Life Care in the Intensive Care Unit: A Systematic Review of the Literature

Background: Assessment of family satisfaction after the death of a loved one in the intensive care unit (ICU) provides a way to determine whether quality end-of-life care was received by the patient and family. The purpose of this systematic review was to explore the factors associated with family satisfaction with end-of-life care in the ICU. Methods: A systematic literature review was conducted using electronic databases CINAHL, MEDLINE, EMBASE, and PsychINFO. Databases were searched using a combination of search terms: “family satisfaction,” “end of life,” “intensive care unit,” and “family. ” Results were limited to English-language reports of empirical studies published from January 2000 to January 2016. Studies describing adult family members’ satisfaction with end-of-life care of patients admitted or transferred to an ICU were included in the review. Results: The search yielded 466 articles. Review of the titles and abstracts resulted in 122 articles that underwent full review; 30 articles met study inclusion and were included in the final analysis. Major themes identified from the literature reviewed included communication, decision making, nursing care, ICU environment, and spiritual care. Conclusions: Families can provide valuable insight and information on the quality of care provided in the ICU at end of life. Their perceptions of communication, decision making, nursing care, the ICU environment, and spiritual support strongly influence their satisfaction or dissatisfaction with end-of-life care in the ICU. Personalized and frequent communication; assistance in the decision-making process; compassionate nursing care; a warm, family-friendly environment; and spiritual support can help alleviate the sequelae and enhance family satisfaction with end-of-life care in the ICU.
Parkinson's Disease and Cryptogenic Epilepsy

Epilepsy is an uncommon comorbidity of Parkinson's disease (PD) and has been considered not directly associated with PD. We present five patients (3 men and 2 women; ages 49–85) who had concomitant PD and cryptogenic epilepsy. Although rare, epilepsy can coexist with PD and their coexistence may influence the progression of PD. While this may be a chance association, an evolving understanding of the neurophysiological basis of either disease may suggest a mechanistic association.
Bioavailability of the Polyphenols: Status and Controversies

The current interest in polyphenols has been driven primarily by epidemiological studies. However, to establish conclusive evidence for the effectiveness of dietary polyphenols in disease prevention, it is useful to better define the bioavailability of the polyphenols, so that their biological activity can be evaluated. The bioavailability appears to differ greatly among the various phenolic compounds, and the most abundant ones in our diet are not necessarily those that have the best bioavailability profile. In the present review, we focus on the factors influencing the bioavailability of the polyphenols. Moreover, a critical overview on the difficulties and the controversies of the studies on the bioavailability is discussed.
Laminin isoforms 8 and 10 are primary components of the subendothelial basement membrane promoting interaction with neoplastic lymphocytes.

To determine whether subendothelial laminins (LNs) could be implicated in the extravasation of neoplastic lymphocytes, we have examined the distribution of a number of LN isoforms in human vascular structures of adult individuals and have assayed the ability of the isolated LN molecules to promote adhesion of lymphoma and leukemic cells in vitro using a novel cell adhesion assay, CAFCA, Centrifugal Assay for Fluorescence-based Cell Adhesion (E. Giacomello et al., Biotechniques, 26: 758-762, 1999; P. Spessotto et al., Methods Mol. Biol., 139: 321-343, 2000). The use of previously characterized LN chain-specific antibodies showed that the vast majority of the smaller vascular compartments, known to correspond to sites of lymphocyte transmigration, expressed the subunits involved in the structuring of 9 of the 12 LN isoforms known to date. Eight LN isoforms (i.e., LN-1, -2, -4, -5, -8, -9, -10, and -11) and four naturally occurring LN complexes were isolated from various tissues and cultured cells by combined gel filtration, ion exchange, and immunoaffinity chromatographies, and the identity/composition of the isolated LNs/LN complexes was asserted by immunochemical means and amino-acid sequencing. Notwithstanding the widespread colocalization of LN isoforms, a panel of neoplastic B- and T-cell lines and lymphocytes isolated from patients affected by chronic lymphocytic B-cell leukemia attached preferentially and with high avidity to purified LN-8, purified LN-10, and LN-10-containing protein complexes, whereas lymphocytes derived from patients diagnosed with acute lymphocytic leukemia failed to bind to these LNs. All of the tested neoplastic lymphocytes failed to adhere to the isolated LN-1, LN-4, LN-9, and LN-11 and attached moderately well to purified LN-2 and LN-5. The interaction of transformed lymphocytes with LNs was cation-dependent and interchangeably mediated by the alpha3beta1 and alpha6beta1 integrins. The degree of engagement of the two LN receptors was dependent upon their relative levels of cell surface expression, whereas, irrespective of the phenotype, lymphocytes deprived of either of these receptors were incapable of LN binding. The findings suggest that LN-8 and LN-10 may act in an independent or complementary fashion as primary components of the endothelial basement membrane favoring the interaction of extravasating neoplastic lymphocytes. Thus, our results would demonstrate that different LN isoforms may evoke diverse cellular responses in different cell types and that this divergence may be the basis for the redundancy of LN distribution in a number of vascular structures.
Thermal sensitivity and phenotypic plasticity of cardiac mitochondrial metabolism in European perch, Perca fluviatilis

ABSTRACT Cellular and mitochondrial metabolic capacity of the heart has been suggested to limit performance of fish at warm temperatures. We investigated this hypothesis by studying the effects of acute temperature increases (16, 23, 30, 32.5 and 36°C) on the thermal sensitivity of 10 key enzymes governing cardiac oxidative and glycolytic metabolism in two populations of European perch (Perca fluviatilis) field-acclimated to 15.5 and 22.5°C, as well as the effects of acclimation on cardiac lipid composition. In both populations of perch, the activity of glycolytic (pyruvate kinase and lactate dehydrogenase) and tricarboxylic acid cycle (pyruvate dehydrogenase and citrate synthase) enzymes increased with acute warming. However, at temperatures exceeding 30°C, a drastic thermally induced decline in citrate synthase activity was observed in the cold- and warm-acclimated populations, respectively, indicating a bottleneck for producing the reducing equivalents required for oxidative phosphorylation. Yet, the increase in aspartate aminotransferase and malate dehydrogenase activities occurring in both populations at temperatures exceeding 30°C suggests that the malate–aspartate shuttle may help to maintain cardiac oxidative capacities at high temperatures. Warm acclimation resulted in a reorganization of the lipid profile, a general depression of enzymatic activity and an increased fatty acid metabolism and oxidative capacity. Although these compensatory mechanisms may help to maintain cardiac energy production at high temperatures, the activity of the electron transport system enzymes, such as complexes I and IV, declined at 36°C in both populations, indicating a thermal limit of oxidative phosphorylation capacity in the heart of European perch. Summary: Impaired myocardial energy production at high temperatures may set the thermal limit of the heart in European perch, despite the phenotypic plasticity and compensatory flexibility of its enzymatic components.
Photometric Repeatability of Scanned Imagery: UVIS

We provide the preliminary results of a study on the photometric repeatability of spatial scans of bright, isolated white dwarf stars with the UVIS channel of the Wide Field Camera 3 (WFC3) on the Hubble Space Telescope (HST). We analyze straight-line scans from the first pair of identical orbits of HST program 14878 to assess if sub 0.1% repeatability can be attained with WFC3/UVIS. This study is motivated by the desire to achieve better signal-tonoise in the UVIS contamination and stability monitor, in which observations of standard stars in staring mode have been taken from the installation of WFC3 in 2009 to the present to assess temporal photometric stability. Higher signal to noise in this program would greatly benefit the sensitivity to detect contamination, and to better characterize the observed small throughput drifts over time. We find excellent repeatability between identical visits of program 14878, with sub 0.1% repeatability achieved in most filters. These results support the initiative to transition the staring mode UVIS contamination and photometric stability monitor from staring mode images to spatial scans. Copyright c © 2017 The Association of Universities for Research in Astronomy, Inc. All Rights Reserved.
Exploring influencing factors of postoperative pain in school-age children undergoing elective surgery.

PURPOSE The purpose of this study was to examine the influencing factors of postoperative pain among children undergoing elective surgery. DESIGN AND METHODS A survey was conducted in 2011 with a convenience sample of 66 children, 6 to 14 years old, in a tertiary hospital in Singapore. RESULTS Children experienced moderate preoperative anxiety and postoperative pain. Gender, preoperative anxiety, and negative emotional behaviors were significant influencing factors for postoperative pain. Boys reported less postoperative pain than girls. PRACTICE IMPLICATIONS Effective strategies for assessing and managing children's preoperative anxiety are needed to achieve an optimal postoperative pain management outcome.
FURTHER EXPERIENCES WITH KIDNEY PRESERVATION FOR 24 HOURS USING CONTINUOUS HYPOTHERMIC PERFUSION

Preservation of pig kidneys for 24 hours at 8°C has been studied using continuous perfusion with cryoprecipitated, microfiltered, oxygenated ACD‐plasma. The perfusion pressure was about 65/30 mmHg and the flow from 1 to 2 ml/g kidney weight/min. Five consecutive experiments were performed. All the animals survived and were followed for three months. Measurements inulin, endogenous creatinine, urea and PAH clearances 10, 31 and 94 days after transplantation showed normal values as compared to a control group of autotransplanted, not long‐term preserved pig kidneys. The only permanent functional damage was a reduced maximal tubular excretion of PAH.
An experimental comparison of feature-based 3D retrieval methods

3D objects are an important type of multimedia data with many promising application possibilities. Defining the aspects that constitute the similarity among 3D objects, and designing algorithms that implement such similarity definitions is a difficult problem. Over the last few years, a strong interest in methods for feature-based 3D similarity search has arisen, and a growing number of competing algorithms for content-based retrieval of 3D objects have been proposed. We present an extensive experimental evaluation of the retrieval effectiveness and efficiency of a large part of the current state-of-the-art feature-based methods for 3D similarity search, giving a contrasting assessment of the different approaches.
The Etiological Role of Blood-Brain Barrier Dysfunction in Seizure Disorders

A wind of change characterizes epilepsy research efforts. The traditional approach, based on a neurocentric view of seizure generation, promoted understanding of the neuronal mechanisms of seizures; this resulted in the development of potent anti-epileptic drugs (AEDs). The fact that a significant number of individuals with epilepsy still fail to respond to available AEDs restates the need for an alternative approach. Blood-brain barrier (BBB) dysfunction is an important etiological player in seizure disorders, and combination therapies utilizing an AED in conjunction with a “cerebrovascular” drug could be used to control seizures more effectively than AED therapy alone. The fact that the BBB plays an etiologic role in other neurological diseases will be discussed in the context of a more “holistic” approach to the patient with epilepsy, where comorbidity variables are also encompassed by drug therapy.