Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving population health in US cities.

Interest in population health and the promotion of greater collaboration between medical, public health, and social service institutions has surged in recent months. (1) This approach adopts a comprehensive notion of health determinants that are spread across domains of behavioral risk, social and economic circumstances, environmental exposures, and medical care. The balance and effects of many of these determinants, eg, availability of healthy foods, parks and other safe places to play and exercise, exposure to environmental irritants, and safe housing, are specific to geographic locale. (2) Although there is general enthusiasm for efforts to advance population health, strategies for tailoring approaches to specific locales are not well established. Of particular strategic interest is the need for developing population health approaches for the 80% of US residents who live in urban environments. While the diversity and fragmentation of services within cities pose formidable organizational challenges, there are several key attributes of urban settings, if harnessed strategically, that offer opportunities for potentially effective population health strategies.
The Type II Transforming Growth Factor (TGF)-β Receptor-interacting Protein TRIP-1 Acts as a Modulator of the TGF-β Response*

The transforming growth factor-β (TGF-β) receptor interacting protein TRIP-1 was originally identified as a WD40 repeat-containing protein that has the ability to associate with the TGF-β type II receptor and is phosphorylated by it (1). However, its function was not known. We now show that TRIP-1 expression represses the ability of TGF-β to induce transcription from the plasminogen activator inhibitor-1 promoter, a common reporter of the TGF-β-induced gene expression response, but does not affect the ability of TGF-β to inhibit cyclin A transcription. TRIP-1 can also inhibit the plasminogen activator inhibitor-1 expression induced by Smads as well as activated TGF-β type I receptors. Its inhibitory effect is exerted by a combination of receptor-dependent and receptor-independent mechanisms. Deletion mutational analysis revealed that two distinct regions, which do not contain recognizable WD40 repeats, are required for the ability of TRIP-1 to inhibit the gene expression response. Expression of other segments of TRIP-1 increased the TGF-β-induced gene expression response and therefore may exert a dominant negative phenotype. We conclude that TRIP-1 acts as a modulator of the TGF-β response.
Characterization of in vitro and in vivo hypomethylating effects of decitabine in acute myeloid leukemia by a rapid, specific and sensitive LC-MS/MS method

DNA hypermethylation is a common finding in malignant cells and has been explored as a therapeutic target for hypomethylating agents (e.g., decitabine). Detection of changes in DNA methylation might serve as a pharmacodynamic endpoint to establish the biological activity of these agents and predict clinical response. We developed and validated a rapid, sensitive and specific LC-MS/MS method for determination of global DNA methylation (GDM) in vitro and in vivo. Ratios of 5-methyl-2′-deoxycytidine (5mdC) to the internal standard 2-deoxyguanosine (2dG) in mass signal were used to quantify GDM levels. The assay was validated in a linear range from 40 fmol to 200 pmol 5mdC. The intra-day precision values ranged from 2.8 to 9.9% and the inter-day values from 1.1 to 15.0%. The accuracy of the assay varied between 96.7 and 109.5%. This method was initially applied for characterization of decitabine-induced GDM changes in in-vitro-treated leukemia cells. Following exposure to 2.5 μM decitabine, GDM decreased to ∼50% of the baseline value. The clinical applicability of this method was then demonstrated in bone marrow samples from patients with acute myeloid leukemia treated with decitabine. Our data support the use of our LC-MS/MS method for clinical pharmacodynamic determination of changes in GDM in vivo.
Reconceptualizing Anxiety as a Continuum That Ranges From High Calmness to High Anxiety: The Joint Importance of Reducing Distress and Increasing Well-Being

We first replicate a study by Vautier and Pohl (2009), who used the State–Trait Anxiety Inventory (STAI) to reexamine the structure of anxiety. Using two large samples (N = 4,138 and 1,824), we also find that state and trait anxiety measure continua that range from high calmness to high anxiety. We then significantly extend previous findings and make the clinical importance of this topic more explicit by characterizing the (linear or nonlinear) form of the relationship between the calmness–anxiety continuum and other psychiatric variables for the first time. This form is critical to understanding anxiety problems, as discontinuities in relationships with other psychological conditions could be used to define a natural boundary of problematic anxiety. Baseline levels on the calmness–anxiety continuum are found to have a near linear relationship with changes in depression, aggression, and substance misuse over time. Taken together, these results indicate the joint importance and usefulness of treating anxiety problems and promoting calmness, as doing so may promote resilience from developing other psychiatric conditions. Psychiatric and psychological interventions that are grounded in this continuum conceptualization would logically be stopped when an individual reports experiencing high levels of calmness. Our results point to the usefulness of early intervention and prevention (when people begin to move away from high calmness) and instilling resilience (by providing interventions to move people toward high calmness).
Extensible distributed coordination

Most services inside a data center are distributed systems requiring coordination and synchronization in the form of primitives like distributed locks and message queues. We argue that extensibility is a crucial feature of the coordination infrastructures used in these systems. Without the ability to extend the functionality of coordination services, applications might end up using sub-optimal coordination algorithms, possibly leading to low performance. Adding extensibility, however, requires mechanisms that constrain extensions to be able to make reasonable security and performance guarantees. We propose a scheme that enables extensions to be introduced and removed dynamically in a secure way. To avoid performance overheads due to poorly designed extensions, it constrains the access of extensions to resources. Evaluation results for extensible versions of ZooKeeper and DepSpace show that it is possible to increase the throughput of a distributed queue by more than an order of magnitude (17x for ZooKeeper, 24x for DepSpace) while keeping the underlying coordination kernel small.
Improving the description of metabolic networks: the TCA cycle as example

To collect the ever‐increasing yet scattered knowledge on metabolism, multiple pathway databases like the Kyoto Encyclopedia of Genes and Genomes have been created. A complete and accurate description of the metabolic network for human and other organisms is essential to foster new biological discoveries. Previous research has shown, however, that the level of agreement among pathway databases is surprisingly low. We investigated whether the lack of consensus among databases can be explained by an inaccurate representation of the knowledge described in scientific literature. As an example, we focus on the well‐known tricarboxylic acid (TCA) cycle and evaluated the description of this pathway as found in a comprehensive selection of 10 human metabolic pathway databases. Remarkably, none of the descriptions given by these databases is entirely correct. Moreover, consensus exists on only 3 reactions. Mistakes in pathway databases might lead to the propagation of incorrect knowledge, misinterpretation of high‐throughput molecular data, and poorly designed follow‐up experiments. We provide an improved description of the TCA cycle via the community‐curated database WikiPathways. We review various initiatives that aim to improve the description of the human metabolic network and discuss the importance of the active involvement of biological experts in these. —Stobbe, M. D. , Houten, S. M. , van Kampen, A. H. C. , Wanders, R. J. A. , Moerland, P. D. Improving the description of metabolic networks: the TCA cycle as example. FASEB J. 26, 3625–3636 (2012). www.fasebj. org
Systematic engineering of phytochelatin synthesis and arsenic transport for enhanced arsenic accumulation in E. coli

Phytochelatin (PC) is a naturally occurring peptide with high affinity towards arsenic (As). In this article, we demonstrated the systematic engineering of PC‐producing E. coli for As accumulation by addressing different bottlenecks in PC synthesis as well as As transport. Phytochelatin synthase from Schizosaccharomyces pombe (SpPCS) was expressed in E. coli resulting in 18 times higher As accumulation. PC production was further increased by co‐expressing a feedback desensitized γ‐glutamylcysteine synthetase (GshI*), resulting in 30‐fold higher PC levels and additional 2‐fold higher As accumulation. The significantly increased PC levels were exploited further by co‐expressing an arsenic transporter GlpF, leading to an additional 1.5‐fold higher As accumulation. These engineering steps were finally combined in an arsenic efflux deletion E. coli strain to achieve an arsenic accumulation level of 16.8 µmol/g DCW, a 80‐fold improvement when compared to a control strain not producing phytochelatins. Biotechnol. Bioeng. 2010. 105: 780–785. © 2009 Wiley Periodicals, Inc.
Chill coma temperatures appear similar along a latitudinal gradient, in contrast to divergent chill coma recovery times, in two widespread ant species

Populations of widely distributed ectotherms demonstrate different cold resistance corresponding to the local climate. However, efficiently thermoregulating ectotherms could avoid divergence in cold resistance. Two species of ants, previously shown to even out latitudinal differences of mean summer temperatures in their nests, were used to test this hypothesis by comparing the temperature dependence of cold resistance in three distant populations (from 50°, 60° and 67°N). The species differ in habitat preferences, one (Myrmica rubra) being less stenotopic than the other (M. ruginodis). Therefore, three different predictions were made about their cold resistance: along the latitudinal gradient, it might be similar within the two species (because of thermoregulation within nests/habitats) or similar only in M. rubra (as a result of thermoregulation among habitats), or divergent at least in M. rubra (no effect of thermoregulation). Among populations of both species, neither differences nor latitudinal trends in chill coma temperature were statistically significant after 11 months of standard conditions, with or without cold hardening. In contrast, recovery time significantly differed among populations in both species, although its latitudinal trends were strongly curvilinear: in M. rubra, the intermediate population tended towards the slowest recovery, and in M. ruginodis, it tended towards the fastest. After 22 months, the patterns remained the same, except that M. ruginodis showed a significant linear latitudinal trend in chill coma temperature (with no significant populational differences). Hence, thermoregulation, both within and among habitats, apparently does keep chill coma temperatures similar. Recovery rate demonstrates divergence, but its curvilinear trends suggest a connection with climates experienced by ancestral populations.
A R T I C L E I N T R O D U C T I O N

Mutations in bestrophin-1 are responsible for several retinopathies, including Best vitelliform macular dys-trophy (Marquardt et al., 1998 ; Petrukhin et al., 1998), adult-onset macular dystrophy (Seddon et al., 2001), autosomal-dominant vitreochoidopathy (Yardley et al., 2004), autosomal-recessive bestrophinopathy (Burgess et al., 2008), and canine multifocal retinopathy (Guziewicz et al., 2007). There is considerable evidence that bestro-phins are Cl Ϫ channels (for review see Hartzell et al., 2008). Expression of a variety of different bestrophins in HEK293 cells induces novel Cl
Exploring Fifth-Grade Turkish Children's Solutions and Future Plans for Environmental Pollution through Their Drawings.

The pollution of land, water, air, noise, light etc. threatens people, plants, animals and ecosystems. Environmental literacy is at the heart of environmental education, and environmentally literate people are expected to be aware of how to help solve environmental problems such as pollution. The purpose of the present study is to explore 5th grade Turkish children’s solutions and future plans for environmental pollution, as revealed through their Asia-Pacific Forum on Science Learning and Teaching, 17(2), Article 17, p.2 (Dec., 2016) Murat SAGLAM Exploring fifth–grade Turkish children’s solutions and future plans for environmental pollution through their drawings Copyright (C) 2016 EdUHK APFSLT. Volume 17, Issue 2, Article 17 (Dec., 2016). All Rights Reserved. drawings. A total of 40 5th graders (25 girls and 15 boys, aged 10-11 years) completed drawings of their solutions and future plans for environmental pollution. The three themes used to analyse their work were physical action, persuasion and political action. The most recurring solutions in the drawings were collecting litter, putting litter in a bin or recycling bin, planting saplings and public persuasion. Many children in the study knew that littering was an environmental problem, which needs more than one strategy to be dealt with. The children in this study found it difficult to visually express their thoughts related to the themes of persuasion and political action. It therefore appears that it is better to explore children’s ideas about persuasion and political action verbally and/or in writing. An instruction based on socio-scientific issues may help children learn about pollutants and their impacts on the environment as they produce solutions and plans for an open-ended problem.
Twenty years on.

One of the problems of moving to the USA to practise medicine is taking "finals" again. I don't mean the exam for an Educational Council for Foreign Medical Graduates (ECFMG) certificate, which is a one-day affair taken in the familiar surroundings of London or Edinburgh. Without the ECFMG, of course, one's chances of getting a visa to live in the USA are next to nil. But actually to practise as an independent and fully functioning doctor something more extensive is demanded. One can sit these further tests only after burning one's boats, migrating to the USA, and risking all on the three-day "trial. " Each State has its own regulations but all, except Alaska and Florida, take a satisfactory performance in the Federation Licensing Examination (FLEX) held only in the USA as evidence of competence. Unlike Britain, where the MB ChB degrees or royal college diplomas are themselves registerable as evidence of competence, the MD degree in the USA does not give automatic entry into the ranks of practising doctors. In addition to having the MD a newly graduated doctor has to be successful in a three-part National Board of Medical Examiners (NBME) examination or FLEX, the latter having strong clinical emphasis in each of its three parts. Usually the NBME is taken by native US graduates and FLEX is favoured by the many foreign medical graduates who come to the USA to find fortune if not fame. The FLEX is extremely thorough and lasts three days, starting at 0830 and ending at 1730 with an hour for lunch and one 15-minute break during the morning and afternoon sessions. I took the exam at the beginning of December 1975 at the McCormick Place Centre in Chicago, which is a huge, draughty, hanger-like exhibition hall overlooking Lake Michigan and Meigs Field aerodrome. The 500-odd candidates were a colourfully international crowd with only a few from Britain. The place was so cold that most people sat in their overcoats and the proctors refreshed themselves at frequent intervals from hot vacuum flasks.
African origin of Bradyrhizobium populations nodulating Bambara groundnut (Vigna subterranea L. Verdc) in Ghanaian and South African soils

Flavonoids secreted by legumes play a major role as signal molecules for attracting compatible rhizobia. The aim of this study was to assess and understand the diversity of microsymbionts nodulating Bambara groundnut (Vigna subterranea L. Verdc.) landraces of different seedcoat colours using restriction fragment length polymorphism and phylogenetic analysis. Seedcoat pigmentation of landraces had effect on the diversity of microsymbionts of Bambara groundnut. Even when planted together in one hole, nodulating bradyrhizobia clustered differently. For example, 16S rDNA-RFLP typing of rhizobial samples TUTVSBLM.I, TUTVSCRM.I and TUTVSRDM.I originating respectively from Black, Cream and Red landraces that were co-planted in the same hole at Manga in the Sudano-sahelian savanna, as well as TUTVSCRK.I and TUTVSRDK.I respectively from Cream and Red landraces co-planted at Kpalisogu in the Guinea savanna, revealed different 16S rDNA- RFLP types. Phylogenetic analysis of 16S rDNA, glnII, recA and atpD sequences showed that Vigna subterranea was nodulated specifically by a diverse group of Bradyrhizobium species (e.g. Bradyrhizobium vignae, and a novel group of Bradyrhizobium spp.) in soils from Ghana and South Africa. The recA gene phylogeny showed incongruency with the other housekeeping genes, indicating the possibility of lateral gene transfer and/or recombination events. The grouping of isolates according to symbiotic gene (nifH and nodD) phylogenies revealed inter- and intra-specific symbiotic plasmid transfer and different evolutionary history. The results also showed that a cropping history and physico-chemical environment of soils increased bradyrhizobial diversity in Ghana and South Africa.
Prevalence and associations of epiretinal membrane in an elderly urban Chinese population in China: the Jiangning Eye Study

Aims To describe the prevalence and associations of epiretinal membrane (ERM) in an elderly urban Chinese population in China. Methods A population-based cross-sectional study was conducted using a cluster random sample of residents aged 50 years or older living in the Jiangning Road Sub-district, Shanghai, China. All participants underwent a standardised interview and comprehensive eye examinations, including digital retinal photography and spectral domain optical coherence tomography (SD-OCT) examinations of both eyes between November 2012 and February 2013. ERM was identified and classified as either cellophane macular reflex (CMR) or preretinal macular fibrosis (PMF) based on the fundus photography and OCT features. Results Of the 2044 subjects who participated (82.5% response rate), 2005 had fundus photographs and OCT results of sufficient quality for grading of ERM signs. ERM was present in 8.4% of participants, including 5.0% with CMR and 3.4% with PMF. After age and gender standardisation to the 2010 Chinese census population, the prevalence rate of ERM in mainland Chinese individuals of 50 years of age or older was estimated to be 7.3%. After adjusting for age and/or gender, idiopathic ERM was positively associated with age (OR, 1.06; 95% CI 1.04 to 1.08), female gender (OR 1.67, 95% CI 1.16 to 2.40), myopia (OR 2.21, 95% CI 1.51 to 3.22) and hyperlipaemia (OR 1.80, 95% CI 1.04 to 3.12). Conclusions The prevalence of ERM in elderly urban Chinese was similar to that in Caucasians. Risk factors for idiopathic ERM were older age, female gender, myopia and hyperlipaemia.
Potential Use of Turkish Medicinal Plants in the Treatment of Various Diseases

Medicinal plants are sources of health-promoting substances, including phytochemicals and phytoalexins that comprise polyphenols, flavonoids, carotenoids, vitamins A, C, E and several other constituents. Many studies have indicated that medicinal plants have been used to treat human diseases for thousands of years owing to their antimicrobial and antioxidant activities. Medicinal plants reduce the oxidative stress in cells and prevent cancer, cardiovascular and inflammatory diseases, neurodegenerative and digestive system disorders. These potential beneficial effects have been attributed to the presence of bioactive compounds that show antioxidant properties by acting as free radical scavengers or metal chelators, reducing the reactions that produce reactive oxygen and nitrogen species (ROS/RNS). Considering the importance of medicinal plants in terms of their beneficial health effects, some of the medicinally important plants grown in Turkey are covered in this review with respect to their antioxidant potential and phytochemical profile.
Presence of Tissue Transglutaminase in Granular Endoplasmic Reticulum is Characteristic of Melanized Neurons in Parkinson's Disease Brain

Parkinson's disease (PD) is characterized by the accumulation of α‐synuclein aggregates and degeneration of melanized neurons. The tissue transglutaminase (tTG) enzyme catalyzes molecular protein cross‐linking. In PD brain, tTG‐induced cross‐links have been identified in α‐synuclein monomers, oligomers and α‐synuclein aggregates. However, whether tTG and α‐synuclein occur together in PD affected neurons remains to be established. Interestingly, using immunohistochemistry, we observed a granular distribution pattern of tTG, characteristic of melanized neurons in PD brain. Apart from tTG, these granules were also positive for typical endoplasmic reticulum (ER)‐resident chaperones, that is, protein disulphide isomerase, ERp57 and calreticulin, suggesting a direct link to the ER. Additionally, we observed the presence of phosphorylated pancreatic ER kinase (pPERK), a classical ER stress marker, in tTG granule positive neurons in PD brain, although no subcellular colocalization of tTG and pPERK was found. Our data therefore suggest that tTG localization to granular ER compartments is specific for stressed melanized neurons in PD brain. Moreover, as also α‐synuclein aggregates were observed in tTG granule positive neurons, these results provide a clue to the cellular site of interaction between α‐synuclein and tTG.