Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate

Oscillations in patterns of expression of a large fraction of yeast genes are associated with the “metabolic cycle,” usually seen only in prestarved, continuous cultures of yeast. We used FISH of mRNA in individual cells to test the hypothesis that these oscillations happen in single cells drawn from unsynchronized cultures growing exponentially in chemostats. Gene-expression data from synchronized cultures were used to predict coincident appearance of mRNAs from pairs of genes in the unsynchronized cells. Quantitative analysis of the FISH results shows that individual unsynchronized cells growing slowly because of glucose limitation or phosphate limitation show the predicted oscillations. We conclude that the yeast metabolic cycle is an intrinsic property of yeast metabolism and does not depend on either synchronization or external limitation of growth by the carbon source.
The Dilemma of Defining International Human Resource Development

From the beginning of the use of the term human resource development (HRD) to describe our field, there have been struggles over the meaning of the term and, even more broadly, of the field itself. In recent years, there has been increased attention to the question of the field’s definition, in general, as well as attention to the emerging field of national HRD. This article moves this exploration one more step toward an exploration of the dilemma of defining international and cross-national HRD. A beginning definition is offered, not as a definitive answer but to facilitate ongoing discussion in the dialogue on HRD definitions.
Structural analysis for glycolipid recognition by the C-type lectins Mincle and MCL

Significance Here we report the crystal structures of human C-type lectin receptors Mincle (macrophage inducible C-type “calcium-dependent” lectin; CLEC4E) and MCL (macrophage C-type lectin; CLEC4D), both of which are receptors for mycobacterial glycolipid adjuvant cord factor (also called trehalose-6,6′-dimycolate; TDM). Our structural and functional studies clearly reveal the simultaneous recognition of sugar and lipid moieties by Mincle and MCL, distinct from other C-type lectin receptors. Because better adjuvants are desired for enhancing vaccination effects of medical treatments for infectious diseases, cancer, and so forth, these structures provide a framework for the rational design of more effective adjuvants than TDM. Mincle [macrophage inducible Ca2+-dependent (C-type) lectin; CLEC4E] and MCL (macrophage C-type lectin; CLEC4D) are receptors for the cord factor TDM (trehalose-6,6′-dimycolate), a unique glycolipid of mycobacterial cell-surface components, and activate immune cells to confer adjuvant activity. Although it is known that receptor–TDM interactions require both sugar and lipid moieties of TDM, the mechanisms of glycolipid recognition by Mincle and MCL remain unclear. We here report the crystal structures of Mincle, MCL, and the Mincle–citric acid complex. The structures revealed that these receptors are capable of interacting with sugar in a Ca2+-dependent manner, as observed in other C-type lectins. However, Mincle and MCL uniquely possess shallow hydrophobic regions found adjacent to their putative sugar binding sites, which reasonably locate for recognition of fatty acid moieties of glycolipids. Functional studies using mutant receptors as well as glycolipid ligands support this deduced binding mode. These results give insight into the molecular mechanism of glycolipid recognition through C-type lectin receptors, which may provide clues to rational design for effective adjuvants.
Novel Methodology to Evaluate Renal Cysts in Polycystic Kidney Disease

Aim: To develop and assess a semiautomated method for segmenting and counting individual renal cysts from mid-slice MR images in patients with autosomal dominant polycystic kidney disease (ADPKD). Methods: A semiautomated method was developed to segment and count individual renal cysts from mid-slice MR images in 241 subjects with ADPKD from the Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease. For each subject, a mid-slice MR image was selected from each set of coronal T2-weighted MR images covering the entire kidney. The selected mid-slice image was processed with the semiautomated method to segment and count individual renal cysts. The number of cysts from the mid-slice image of each kidney was also measured by manual counting. The level of agreement between the semiautomated and manual cyst counts was compared using intraclass correlation (ICC) and a Bland-Altman plot. Results: Individual renal cysts were successfully segmented using the semiautomated method in all 241 cases. The number of cysts in each kidney measured with the semiautomated and manual counting methods correlated well (ICC = 0.96 for the right or left kidney), with a small average difference (-0.52, with higher semiautomated counts, for the right kidney, and 0.13, with higher manual counts, for the left kidney) in the semiautomated method. However, there was substantial variation in a small number of subjects; 6 of 241 participants (2.5%) had a difference in the total cyst count of more than 15. Conclusion: We have developed a semiautomated method to segment individual renal cysts from mid-slice MR images in ADPKD kidneys as a quantitative indicator of characterization and disease progression of ADPKD.
H3K4 monomethylation dictates nucleosome dynamics and chromatin remodeling at stress-responsive genes

Chromatin remodeling is essential for proper adaptation to extracellular stimuli. The p38-related Hog1 SAPK is an important regulator of transcription that mediates chromatin remodeling upon stress. Hog1 targets the RSC chromatin remodeling complex to stress-responsive genes and rsc deficient cells display reduced induction of gene expression. Here we show that the absence of H3K4 methylation, either achieved by deletion of the SET1 methyltransferase or by amino acid substitution of H3K4, bypasses the requirement of RSC for stress-responsive gene expression. Monomethylation of H3K4 is specifically inhibiting RSC-independent chromatin remodeling and thus, it prevents osmostress-induced gene expression. The absence of H3K4 monomethylation permits that the association of alternative remodelers with stress-responsive genes and the Swr1 complex (SWR-C) is instrumental in the induction of gene expression upon stress. Accordingly, the absence of SWR-C or histone H2A.Z results in compromised chromatin remodeling and impaired gene expression in the absence of RSC and H3K4 methylation. These results indicate that expression of stress-responsive genes is controlled by two remodeling mechanisms: RSC in the presence of monomethylated H3K4, and SWR-C in the absence of H3K4 monomethylation. Our findings point to a novel role for H3K4 monomethylation in dictating the specificity of chromatin remodeling, adding an extra layer of regulation to the transcriptional stress response.
Human Capital Accumulation, Economic Growth and Social Harmony in Rural China

This paper analyzes the relation among the accumulation of human capital, economic growth and social harmony in rural China based on a cointegration analysis and Granger causality test model. The analysis demonstrates equilibrium among them in the long periods. In the short periods economic growth and social harmony will change 0.48 and 2.38 separately if human capital accumulation in rural China changes every other unit, as the cause of the recent increase in inequality in China. In the long periods imbalance among the three variables will disappear by adjustment for 29 years by about 6.9% biennially. Our findings suggest that economic growth is developmental cause of human capital accumulation in rural areas both in the long term and in the short term. On the contrary, human capital accumulation in rural China just impulses economic growth in the long term since its lagged development makes itself not to release pulling role effectively. Study also shows human capital accumulation does not cause income gap between urban and rural areas. Reversely, the latter will affect the former in the long term, which maybe plays referenced roles for plans and policies. The results of VECM analysis suggest that the goal of quadrupling the farmers' per capita net income of the year 2008 by 2020 put forward by the CPC has its scientific reasons.
Altered inflammation, paraoxonase-1 activity and HDL physicochemical properties in obese humans with and without Prader-Willi syndrome

SUMMARY Prader-Willi syndrome (PWS) represents the most common form of genetic obesity. Several studies confirm that obesity is associated with inflammation, oxidative stress and impairment of antioxidant systems; however, no data are available concerning PWS subjects. We compared levels of plasma lipids and C-reactive protein (CRP) in 30 subjects of ‘normal’ weight (18.5–25 kg/m2), 15 PWS obese (>30 kg/m2) subjects and 13 body mass index (BMI)-matched obese subjects not affected by PWS. In all subjects, we evaluated the levels of lipid hydroperoxides and the activity of paraoxonase-1 (PON1), an enzyme involved in the antioxidant and anti-inflammatory properties exerted by high-density lipoproteins (HDLs). Furthermore, using the fluorescent molecule of Laurdan, we investigated the physicochemical properties of HDLs isolated from normal weight and obese individuals. Altogether, our results demonstrated, for the first time, higher levels of lipid hydroperoxides and a lower PON1 activity in plasma of obese individuals with PWS with respect to normal-weight controls. These alterations are related to CRP levels, with a lower PON1:CRP ratio in PWS compared with non-PWS obese subjects. The study of Laurdan fluorescence parameters showed significant modifications of physicochemical properties in HDLs from PWS individuals. Whatever the cause of obesity, the increase of adiposity is associated with inflammation, oxidative stress and alterations in HDL compositional and functional properties.
An Adaptive Approach to P2P Resource Discovery in Distributed Scientific Research Communities

Resource discovery in a distributed environment is always a challenging issue. It is even more difficult to provide an efficient query routing mechanism while still able to support complex query processing in a decentralised P2P environment. This paper presents an adaptive approach to P2P resource discovery. It separates the routing of queries from query matching mechanism so that an effective combination could be explored. Three properties of scientific research communities provide the grounding for the method: the existence of common interest groups, the willingness to share resources of common interests and the transitive relationship in the sharing behaviour. By exploiting these properties, search queries can be efficiently forwarded to those who are more likely to have the answers to improve the quality of search results and to reduce the network traffic. Experimental results have provided some evidence to confirm the efficiency of this adaptive approach
Genetic Modification of Plant Cell Walls for Enhanced Biomass Production and Utilization Investigators

Introduction In 2002, The US Department of Energy released a document entitled “The Vision for Bioenergy and Biobased Products in the US” that envisioned 5% of energy, 20% of transportation fuel and 25% of chemicals being derived from biomass by 2030. A crucial factor in reaching these goals will be the net productivity of the plants used. It is generally accepted that the current practice of converting excess starch production to ethanol does not represent a significant long-term opportunity. By contrast harvesting the “cellulosic biomass” that comprises the body of plants represents an attractive target. A recent study by DOE and USDA estimated that there is approximately 1.4 billion dry tons per year of renewable excess biomass capacity in the US. This is roughly equivalent to the energy content of all imported petroleum.
2 Componentwise Ordering and an Application in Intensity Modulated Radiation Therapy

This manuscript is on the theory and numerical procedures of vector optimization w.r. t. various ordering structures, on recent developments in this area and, most important, on their application to medical engineering. In vector optimization one considers optimization problems with a vectorvalued objective map and thus one has to compare elements in a linear space. If the linear space is the finite dimensional space R this can be done componentwise. That corresponds to the notion of an Edgeworth-Pareto-optimal solution of a multiobjective optimization problem. Among the multitude of applications which can be modeled by such a multiobjective optimization problem, we present an application in intensity modulated radiation therapy and its solution by a numerical procedure. In case the linear space is arbitrary, maybe infinite dimensional, one may introduce a partial ordering which defines how elements are compared. Such problems arise for instance in magnetic resonance tomography where the number of Hermitian matrices which have to be considered for a control of the maximum local specific absorption rate can be reduced by applying procedures from vector optimization. In addition to a short introduction and the application problem, we present a numerical solution method for solving such vector optimization problems. A partial ordering can be represented by a convex cone which describes the set of directions in which one assumes that the current values are deteriorated. If one assumes that this set may vary dependently on the actually considered element in the linear space, one may replace the partial ordering by a variable ordering structure. This was for instance done in an application in medical image registration. We present a possibility of how to model such variable ordering structures mathematically and how optimality can be defined in such a case. We also give a numerical solution method for the case of a finite set of alternatives.
Optical Biosensors: A Revolution Towards Quantum Nanoscale Electronics Device Fabrication

The dimension of biomolecules is of few nanometers, so the biomolecular devices ought to be of that range so a better understanding about the performance of the electronic biomolecular devices can be obtained at nanoscale. Development of optical biomolecular device is a new move towards revolution of nano-bioelectronics. Optical biosensor is one of such nano-biomolecular devices that has a potential to pave a new dimension of research and device fabrication in the field of optical and biomedical fields. This paper is a very small report about optical biosensor and its development and importance in various fields.
Practical delay monitoring for ISPs

Point-to-point delay is an important network performance measure as well as a key parameter in SLAs. We study how to measure and report delay in a concise and meaningful way for an ISP, and how to monitor it efficiently. We analyze various measurement intervals and potential metric definitions. We find that reporting high quantiles (between 0.95 and 0.99)every 10-30 minutes as the most effective way to summarize the delay in an ISP. We then propose an active probing scheme to estimate a high quantile with bounded error. We show that only a small number of probes are sufficient to provide an accurate estimate. We validate the proposed delay monitoring technique on real data collected on the Sprint IP backbone network.
Automated Calculation of Term Relatedness Weights for Semantic Searches

Information retrieval - finding and retrieving relevant sources of data, such as documents or geospatially located records - is a bottleneck in the process of accessing online data. Metadata describing data sources is variable in quality and quantity, textual descriptions are defined by data providers and the terminology they use will not always match search terms, particularly in fields with specialised terminology, such as health. Augmenting the original query with related terms increases the likelihood of matching to relevant metadata. Related terms can be extracted from thesaurus and term definition resources or from the Semantic Web, which defines resources and relationships between them. However, relationships between terms are complicated by multiple interpretations, often dependent upon context (for example, 'sign' may mean a 'road sign' or a 'medical sign', such as fever). Including the strength and/or context of a relationship in a semantic link could help narrow down extra terms to those most relevant to the query. In this paper, methods for automatically calculating the relative strength of relationships between terms were investigated and compared for general and domain-specific terms. Calculations were based on a variety of textual resources including public, crowd-sourced online sources Wikipedia and Google search engine. Measures for term relatedness in a specialist domain were tested using health as a case study. Results show promise for automatic calculation of weights between terms, which can be used to develop weighted graphs for use in semantic searches.
Risk of Recurrent Cardiac Events After Onset of Menopause in Women With Congenital Long-QT Syndrome Types 1 and 2

Background— Women with congenital long-QT syndrome experience an increased risk for cardiac events after the onset of adolescence that is more pronounced among carriers of the LQT2 genotype. We hypothesized that the hormonal changes associated with menopause may affect clinical risk in this population. Methods and Results— We used a repeated-events analysis to evaluate the risk for recurrent syncope during the menopause transition and postmenopausal periods (5 years before and after the age at onset of menopause, respectively) among 282 LQT1 (n=151) and LQT2 (n=131) women enrolled in the Long-QT Syndrome Registry. Multivariate analysis showed that the risk for recurrent syncope (n=150) among LQT2 women was significantly increased during both menopause transition (hazard ratio, 3.38; P=0.005) and the postmenopausal period (hazard ratio, 8.10; P<0.001) compared with the reproductive period. The risk increase was evident among women who did or did not receive estrogen therapy. In contrast, among LQT1 women, the onset of menopause was associated with a reduction in the risk for recurrent syncope (hazard ratio, 0.19; P=0.05; P=0.02 for genotype-by-menopause interaction). Only 22 women (8%) experienced aborted cardiac arrest or sudden cardiac death during follow-up. The frequency of aborted cardiac arrest/sudden cardiac death showed a similar genotype-specific association with the onset of menopause. Conclusions— The onset of menopause is associated with a significant increase in the risk of cardiac events (dominated by recurrent episodes of syncope) in LQT2 women, suggesting that careful follow-up and continued long-term therapy are warranted in this population.
Subgrouping of Patients With Rheumatoid Arthritis Based on Pain, Fatigue, Inflammation, and Psychosocial Factors

Among patients with rheumatoid arthritis (RA), pain may be attributed to peripheral inflammation or other causes, such as central pain mechanisms. The aim of this study was to use self‐report measures and physical examination findings to identify clusters of RA patients who may have different causes of pain as well as different prognoses and treatment options.
The Walkability Premium in Commercial Real Estate Investments

This article examines the effects of walkability on property values and investment returns. Walkability is the degree to which an area within walking distance of a property encourages walking for recreational or functional purposes. We use data from the National Council of Real Estate Investment Fiduciaries and Walk Score to examine the effects of walkability on the market value and investment returns of more than 4,200 office, apartment, retail and industrial properties from 2001 to 2008 in the United States. We found that, all else being equal, the benefits of greater walkability were capitalized into higher office, retail and apartment values. We found no effect on industrial properties. On a 100‐point scale, a 10‐point increase in walkability increased values by 1–9%, depending on property type. We also found that walkability was associated with lower cap rates and higher incomes, suggesting it has been favored in both the capital asset and building space markets. Walkability had no significant effect on historical total investment returns. All walkable property types have the potential to generate returns as good as or better than less walkable properties, as long as they are priced correctly. Developers should be willing to develop more walkable properties as long as any additional cost for more walkable locations and related development expenses do not exhaust the walkability premium.
Localism and the Logic of Nationalistic Folklore: Cretan Reflections

The object of this article is to explore a familiar paradox of folklore studies: the promotion of powerfully localist readings in the service of an inclusive national entity. In the logic of European nationalism, this might seem an irresolvable paradox. The object of the nation-state is to unify all potentially divergent cultural and social entities within a single framework, so that localist sentiment ceases to represent the threat of political separatism. In some nation-states, the most harmonious symbiosis of localism with nationalism appears in those regions that are stereotypically regarded as culturally and politically marginal and are consequently subjected to the double-edged opprobrium of being both “simple” and yet also corrupted by a vast range of allegedly foreign elements both culturally and “racially. ” A study of these tension-laden matters must dodge among several levels in order to go beyond the limitations both of purely local ethnography and of national-level historiography. If the former too easily occludes the effects of larger events on local perceptions, the latter can, and often does, fail to account for the success of nationalist ideologies in securing loyalty unto death even—or perhaps especially? —from populations that are notoriously unwilling to accept state rule in more mundane matters of law and order.
Tumorigenesis and Neoplastic Progression Snail Family Transcription Factors Are Implicated in Thyroid Carcinogenesis

E-Cadherin (CDH1) expression is reduced in thyroid carcinomas by primarily unknown mechanisms. In several tissues, SNAIL (SNAI1) and SLUG (SNAI2) induce epithelial-mesenchymal transition by altering target gene transcription, including CDH1 repression, but these transcription factors have not been studied in thyroid carcinoma. Recently, our group has provided direct evidence that ectopic SNAI1 expression induces epithelial and mesenchymal mouse tumors. SNAI1, SNAI2, and CDH1 expression were analyzed in thyroid-derived cell lines and samples of human follicular and papillary thyroid carcinoma by reverse transcriptase-polymerase chain reaction, Western blotting, and immunohistochemistry. The effect of SNAI1 expression on CDH1 transcription was analyzed by reverse transcrip-tase-polymerase chain reaction and Western blotting in ori-3 cells. Thyroid carcinoma development was analyzed in CombitTA-Snail mice, in which SNAI1 levels are up-regulated. SNAI1 and SNAI2 were not expressed in cells derived from normal thyroid tissue, or in normal human thyroid samples, but were highly expressed in cell