Miracle-dz/UniFAR-FTUs huggingface dataset:
Dietary choline requirements of women: effects of estrogen and genetic variation.

BACKGROUND Choline is obtained from the diet and from the biosynthesis of phosphatidylcholine. Phosphatidylcholine is catalyzed by the enzyme phosphatidylethanolamine-N-methyltransferase (PEMT), which is induced by estrogen. Because they have lower estrogen concentrations, postmenopausal women are more susceptible to the risk of organ dysfunction in response to a low-choline diet. A common genetic polymorphism (rs12325817) in the PEMT gene can also increase this risk. OBJECTIVE The objective was to determine whether the risk of low choline-related organ dysfunction increases with the number of alleles of rs12325817 in premenopausal women and whether postmenopausal women (with or without rs12325817) treated with estrogen are more resistant to developing such symptoms. DESIGN Premenopausal women (n = 27) consumed a choline-sufficient diet followed by a very-low-choline diet until they developed organ dysfunction (or for 42 d), which was followed by a high-choline diet. Postmenopausal women (n = 22) were placed on the same diets but were first randomly assigned to receive estrogen or a placebo. The women were monitored for organ dysfunction and plasma choline metabolites and were genotyped for rs12325817. RESULTS A dose-response effect of rs12325817 on the risk of choline-related organ dysfunction was observed in premenopausal women: 80%, 43%, and 13% of women with 2, 1, or 0 alleles, respectively, developed organ dysfunction. Among postmenopausal women, 73% who received placebo but only 18% who received estrogen developed organ dysfunction during the low-choline diet. CONCLUSIONS Because of their lower estrogen concentrations, postmenopausal women have a higher dietary requirement for choline than do premenopausal women. Choline requirements for both groups of women are further increased by rs12325817. This trial was registered at clinicaltrials.gov as NCT00065546.
Insights from Ion Binding Site Network Analysis into Evolution and Functions of Proteins

Many biological phenomena can be represented as complex networks. Using a protein binding site comparison approach, we generated a network of ion binding sites on the scale of all known protein structures from the Protein Data Bank. We found that this ion binding site similarity network is scale‐free, indicating a network in which a few ion binding site scaffolds are the network hubs, and these are connected to hundreds of nodes, whereas the vast majority of nodes have only a few neighbors. Enrichment and statistical analysis of the network components and communities yielded insights into underlying processes from the functional and the structural perspective. Largest components and communities were observed to be closely related to basic metabolic processes and some of the most common structural folds, which, from the evolutionary point of view, indicates that they may be the oldest ones. Further, we derived the first comprehensive map of ion interchangeability, based on binding site similarity. Several highly interchangeable protein‐ion binding site pairs emerged (e.g., Ca2+ and Mg2+), as well as structurally distinct ones. The constructed network of ion binding site similarities will aid in understanding the general principles of protein‐ion binding sites structure, function and evolution. We demonstrate potential uses of the network on proteins involved in cancer development and immune response, where individual ions play prominent roles in disease development.
Nucleotide and Amino Acid Complexity of Hepatitis C Virus Quasispecies in Serum and Liver

ABSTRACT The quasispecies nature of the hepatitis C virus (HCV) is thought to play a central role in maintaining and modulating viral replication. Several studies have tried to unravel, through the parameters that characterize HCV circulating quasispecies, prognostic markers of the disease. In a previous work we demonstrated that the parameters of circulating viral quasispecies do not always reflect those of the intrahepatic virus. Here, we have analyzed paired serum and liver quasispecies from 39 genotype 1b-infected patients with different degrees of liver damage, ranging from minimal changes to cirrhosis. Viral level was quantified by real-time reverse transcription-PCR, and viral heterogeneity was characterized through the cloning and sequencing of 540 HCV variants of a genomic fragment encompassing the E2-NS2 junction. Although in 95% of patients, serum and liver consensus HCV amino acid sequences were identical, quasispecies complexity varied considerably between the viruses isolated from each compartment. Patients with HCV quasispecies in serum more complex (26%) than, less complex (28%) than, or similarly complex (41%) to those in liver were found. Among the last, a significant correlation between fibrosis and all the parameters that measure the viral amino acid complexity was found. Correlation between fibrosis and serum viral load was found as well (R = 0.7). With regard to the origin of the differences in quasispecies complexity between serum and liver populations, sequence analysis argued against extrahepatic replication as a quantitatively important contributing factor and supported the idea of a differential effect or different selective forces on the virus depending on whether it is circulating in serum or replicating in the liver.
Uptake of depression treatment recommendations among Latino primary care patients.

BACKGROUND Primary care providers (PCP) are the entry point for public sector depression treatment for many Latino patients. However, many Latino patients do not initiate their PCPs' recommended treatment, which likely contributes to ethnic disparities in depression treatment. This study examined factors related to Latino patients' uptake of their PCPs' recommendations for depression treatment. METHOD Ninety Latino primary care patients who received a depression treatment recommendation from their PCP participated in a telephone interview. Patients rated their working alliance with their PCP and their PCP's cultural competence. They also reported their treatment preference, the type of recommendation, and their intended and actual uptake of the recommendation. Patients were contacted at two time points (Time 1: M = 14 days after PCP appointment; Time 2: M = 84 days after PCP appointment) to report their uptake status. RESULTS At Time 1, 23% of patients had initiated uptake of the treatment recommendation, increasing to 53% at Time 2. Patients who received a medication recommendation were more likely to have followed though on the recommendation, compared with patients who received a psychotherapy recommendation. The working alliance was positively associated with intention to follow up on a treatment recommendation, and also mediated the relationship between cultural competence and intention of following up on the recommendation. CONCLUSION PCP's treatment recommendation and the PCP-patient alliance play a role in Latino primary care patients intention to follow a treatment recommendation for depression. An improved understanding of this role could enhance efforts to improve depression treatment uptake.
The Pharmacological Therapy of Chronic Neuropathic Pain.

BACKGROUND Chronic neuropathic pain, including painful peripheral polyneuropathy and post-herpetic neuralgia, affects 6.9-10% of the general population. METHODS In this article, we present current treatment recommendations on the basis of a selective review of the literature. RESULTS Neuropathic pain does not respond consistently to classic non-opioid analgesic drugs and is better treated with co-analgesic, antidepressant, and anticonvulsant drugs and topical agents. Under certain conditions, however, neuropathic pain can be treated with opioids, even chronically. It was concluded in a large-scale m eta- analysis that tricyclic antidepressants, selective serotonin- norepinephrine reuptake inhibitors, and calcium-channel anticonvulsants are the drugs of first choice, with a number needed to treat (NNT) of 3.5-7.7 for a 50% reduction of pain. An analysis of all studies yielded an estimated publication bias of 10%. Treatment planning must include adequate consideration of the patient's age and comorbidities, concomitant medication, and potential side effects. CONCLUSION Drugs are now chosen to treat neuropathic pain independently of the cause and symptoms of the pain. Topical agents are used only to treat peripheral neuropathy. The utility of a treatment approach based on the patient's symptoms and pathological mechanisms was recently demonstrated for the first time in a randomized trial. The goal of current research is to facilitate treatment planning on the basis of the clinical phenotype.
On the accuracy of Federal Reserve forecasts of the saving rate

This study investigates the unbiasedness and efficiency of the Federal Reserve forecasts of the saving rate for two distinct periods. For 1984–1997, when the saving rate was relatively stable, the forecasts are generally unbiased and efficient. For 1998–2007, when the saving rate experienced significant declines, the forecasts are generally biased (over-predicting) but still efficient. Evidence of efficiency or ‘weakly’ rationality implies that the Federal Reserve forecasts were generated under symmetric (asymmetric) loss for 1984–1997 (1998–2007). Under asymmetric loss where the forecast errors of the same magnitude but of different signs possess different costs, biased forecasts may still be optimal if the bias is strictly due to asymmetric loss. As such, for 1998–2007, the Federal Reserve staff may have assigned high cost (loss) to under-predictions but little or no cost to over-predictions due to, perhaps, perceiving the unusual declines in the saving rate as temporary.
Making sense of stakeholder values emergence

Relatively little is known about how the concept of sensemaking is triggered by knowledge of human values during the multi-stakeholder decision-making process of construction projects. The emergent, complex and dynamic nature of a cultural value and values system is modelled on a longitudinal case study to demonstrate stakeholders' unique perceptions. Empirical data were gathered through action research and the 'value in design' method were used to structure stakeholder dialogues at three interventions in the briefing and design stages of a new primary school project over a two-year period. A universal theory of human values was subsequently used to theoretically triangulate and postulate on the emergence of unique stakeholder values. The findings contribute new insights into the complex and emerging interrelationship between stakeholder value and values systems. It provides a dynamic perspective of a project culture and illustrates the role of universal values in supporting sensemaking.
White Matter Changes Related to Subconcussive Impact Frequency during a Single Season of High School Football

Seventeen male athletes (mean age, 16 years) underwent MR imaging before and after the football season. Changes in fractional anisotropy across the white matter skeleton were assessed with Tract-Based Spatial Statistics and ROI analysis. The mean number of impacts over a 10-g threshold sustained was 414. Voxelwise analysis failed to show significant changes in fractional anisotropy across the season or a correlation with impact frequency, after correcting for multiple comparisons. ROI analysis showed significant decreases in fractional anisotropy in the fornix-stria terminalis and cingulum hippocampus, which were related to impact frequency. The authors conclude that subclinical neurotrauma related to participation in American football may result in white matter injury and that alterations in white matter tracts within the limbic system may be detectable after only 1 season of play at the high school level. BACKGROUND AND PURPOSE: The effect of exposing the developing brain of a high school football player to subconcussive impacts during a single season is unknown. The purpose of this pilot study was to use diffusion tensor imaging to assess white matter changes during a single high school football season, and to correlate these changes with impacts measured by helmet accelerometer data and neurocognitive test scores collected during the same period. MATERIALS AND METHODS: Seventeen male athletes (mean age, 16 ± 0.73 years) underwent MR imaging before and after the season. Changes in fractional anisotropy across the white matter skeleton were assessed with Tract-Based Spatial Statistics and ROI analysis. RESULTS: The mean number of impacts over a 10-g threshold sustained was 414 ± 291. Voxelwise analysis failed to show significant changes in fractional anisotropy across the season or a correlation with impact frequency, after correcting for multiple comparisons. ROI analysis showed significant (P < .05, corrected) decreases in fractional anisotropy in the fornix-stria terminalis and cingulum hippocampus, which were related to impact frequency. The effects were strongest in the fornix-stria terminalis, where decreases in fractional anisotropy correlated with worsening visual memory. CONCLUSIONS: Our findings suggest that subclinical neurotrauma related to participation in American football may result in white matter injury and that alterations in white matter tracts within the limbic system may be detectable after only 1 season of play at the high school level.
Formal experiments in casual attire: case studies in information exploration

Abstract This paper addresses the issue of how research methodology can be developed for the specific needs of research into information exploration behaviour, based on a four year program of research on individual strategies in information exploration. We propose a meta-experimental framework where research is carried out through a dynamic interaction between what and why questions, and between confirmatory and exploratory analyses. This approach preserves many of the advantages of formal experimentation, while permitting a more holistic examination of phenomena that is characteristic of ethnography. The application of the meta-theoretical framework is illustrated in three case studies that examined new information exploration functionalities and interfaces and their relationship to expertise and exploration strategy
The Measurement of Relationships between Regional Structure and its Evolution

Using a regional case study, the paper investigates some methodological problems concerning the measure of the relationships between two sets of variables. Canonical analysis seems a good tool, but discussion of its advantages and drawbacks shows it is not fully satisfactory. Other methods are tested and their efficiency discussed: Regression, joint-set component analysis, canonical-subspace interpretation by communalities, component-based redundancy. In conclusion, simultaneous use of canonical analysis and other methods is recommended since their results appear complementary.
NFκB decoy oligodeoxynucleotides reduce monocyte infiltration in renal allografts

Monocyte influx secondary to ischemia‐reperfusion conditions the renal allograft to rejection by presentation of antigens and production of cytokines. Monocyte influx depends on NFicB‐dependent transcription of genes encoding adhesion molecules and chemokines. Here we demonstrate that cationic liposomes containing phosphorothioated oligodeoxynucleotides (ODN) with the kB binding site serving as competitive binding decoy, can prevent TNF‐α‐induced NFκB activity in endothelial cells in vitro. In an allogenic rat kidney transplantation model (BN to LEW), we show that perfusing the renal allograft with this decoy prior to transplantation abolishes nuclear NFκB activity in vivo and inhibits VCAM‐1 expression in the donor endothelium (P<0.05). At 24 h postreperfusion, periarterial infiltration of mono‐cytes/macrophages was significantly reduced in decoy ODN‐treated allografts compared to control allografts (3.7±0.7 vs. 9.2±1.2 macrophages/ves‐sel; P<0.01). At 72 h, there was a reduction of tubulointerstitial macrophage infiltration in decoy ODN‐treated kidneys compared to controls (75.6±13.9 vs. 120.0±11.2 macrophages/tubuloin‐terstitial area; P<0.05). In conclusion, perfusion of the renal allograft with NFκB decoy ODN prior to transplantation decreases the initial inflammatory response in a stringent, nonimmunosup‐pressed allogenic transplantation model. Therefore, the NFκB decoy approach may be useful to explore the role of endothelium and macrophages in graft rejection and may be developed into a graft‐specific immunosuppressive strategy allowing reduction of systemic immunosuppression on organ transplantation. —Vos, I. , Govers, R. , Groöne, H. ‐J., Kleij, L. , Schurink, M. , de Weger, R. , Goldschmeding, R. , Rabelink, T. J. NFκB decoy oligodeoxynucleotides reduce monocyte infiltration in renal allografts FASEB J. 14, 815–822 (2000)
The evolutionary nature of the firm within industrial districts

Abstract The Italian industrial district phenomenon has been widely analyzed and admired. It demonstrates that small firm collaboration is globally competitive. But the conditions for competitiveness changed in the 1980s. The question some authors posed was: can the districts survive? Using an evolutionary economic analysis, this article analyzes the challenges faced by the district paradigm of development, with special attention being paid to their capacities to improve efficiency and innovation. It concludes that strategic adaptation will be slow but that the flexibility inherent in the district model will sustain those firms that link to global networks.
Results account as a source of economic information / Rachunek wyników jako źródło informacji ekonomicznych

Summary Financial result is one of the fundamental economic categories subject to measurement within the accounting system. Financial result is a complex economic category, since its fluctuations are determined by expenses and revenues. The volume of financial results is related to activities in each of the individual areas of business operation and to selected external factors. Information on company results is of interest to all stakeholders, both internal and external, but the information requirements of each group are dissimilar. One common denominator here is the use of financial information in economic decision-making processes. This paper presents the role of results account as an important source of information used for decision-making purposes by company stakeholders, both external and internal. Streszczenie Wynik finansowy jest jedną z podstawowych kategorii ekonomicznych podlegających pomiarowi w systemie rachunkowości. Przy tym wynik ten jest złożoną kategorią ekonomiczną, gdyż kształtuje się pod wpływem ponoszonych kosztów i osiąganych przychodów. Wielkość wyniku finansowego zależy od działań podejmowanych w różnych obszarach aktywności biznesowej przedsiębiorstwa a także od czynników zewnętrznych. Wynikami osiągniętymi przez przedsiębiorstwo interesują się różni interesariusze: zewnętrzni i wewnętrzni, przy czym ich potrzeby są odmienne. Wspólną ich cechą jest wykorzystanie informacji finansowych przy podejmowaniu decyzji ekonomicznych. Artykuł niniejszy ukazuje rolę rachunku wyników jako ważnego źródła informacji na potrzeby podejmowania decyzji przez różnych interesariuszy przedsiębiorstwa: zewnętrznych i wewnętrznych
Gene-set profiles: visualizing dissimilarity within gene co-expression networks for biomarker identification

We present a method to visualize gene co-expression from microarray data by plotting profiles of dissimilarity within gene-sets of biological pathways. A gene co-expression network is created by computing the correlation between each gene pair in a gene-set. We transform the networks into scale-free networks in order to calculate the dissimilarity weights that are used to create our profiles. Our approach further distinguishes between gene pairs consisting of both, one, or no statistically significant genes. We find that the shapes and density of the profiles provide useful information for identification of disease gene biomarkers. Our results provide a means of visualizing the overall distribution of gene dissimilarity for each gene-set, as well as how gene dissimilarity is linked to the mutual significance of gene pairs within a gene-set.
Impact of biodiesel demand on the Malaysian palm oil industry: A simultaneous equations approach

The European Union (EU) Renewable Energy Directive set a target of 20 % share of energy from the renewable sources and 10% share of renewable energy specifically in the transport sector.This has resulted in some countries looking for bio-based alternative energies which lead to the increase in demand for bio-based feedstocks such as palm and rapeseed oil (for biodiesel) and sugar cane and corn (for ethanol). One of the new elements in the palm oil market is the growing demand for this commodity as a feedstock to biodiesel production.This will also put Malaysia in a better light on the international front for taking the effort to reduce carbon emissions.In line with this, the palm oil sector in Malaysia will be able to match the New Economic Model’s (NEM) major goals of high income, sustainability and inclusiveness.This new development is affecting the dynamics of the market, in particular, the supply and demand sectors of this commodity.This paper seeks to examine the impact of biodiesel demand on the Malaysian palm oil industry.This paper proposes a structural econometric model consisting of nine structural equations and four identities.The model has been estimated by the two stage least squares method using annual data for the period 1976–2010.The specification of the structural model is based on a series of assumptions about general economic conditions, agricultural policies and technological change.The study indicates that counterfactual simulation of a sustained 30% increase in biodiesel demand predicts a positive increase (2.48%) in palm oil exports for non-biodiesel, 13% increase in the domestic price of palm oil and a marginal increase in production.An increase in export demand would make Malaysia more competitive regionally and globally with benefits accruing to all Malaysians.Apart from this, the biodiesel demand income is also sustainable and will position the nation on the right path towards a high income country by 2020
Effect of Simulation on the Development of Critical Thinking in Associate Degree Nursing Students

Aim. The purpose of this study was to explore the development of critical thinking for students who received instruction using high‐fidelity patient simulation (HFPS) versus low‐fidelity simulation (instructor‐written case studies). Background. Simulated patient care environments have become increasingly more sophisticated in nursing labs, with HFPS fast becoming the standard for laboratory teaching/learning. Method. A convenience sample of first‐semester associate degree nursing students participated in this quasi‐experimental study. One group of students received weekly HFPS patient simulations and the other group received weekly case studies. Both groups took a pre‐ and posttest using the Health Studies Reasoning Test. Results. Both groups showed an increase in critical thinking skills; however, there was no statistically significant difference between the HFPS and case study groups. Conclusion. Results suggest that high‐ and low‐fidelity simulations are both associated with increases in critical thinking scores.
Comparison of algorithms for patent documents clusterization

Ever increasing number of patents makes impossible to find and analyze relevant documents manually. Various software tools have been developed in the patent field. They could analyze individual patents as well as patent portfolios; retrieve patents and make basic statistics as well as visualize, map and landscape the same data. The essential function any tool should provide is patent clustering. There have been many different clustering approaches. In this paper we compare performances of k-means, the neural-gas, fuzzy c-means and ronn clustering technique when used on patent data set that was also clustered by the experts.