Miracle-dz/UniFAR-FTUs huggingface dataset:
Linkage of biochemical responses to population‐level effects: A case study with vitellogenin in the fathead minnow (Pimephales promelas)

A challenge in the field of ecotoxicology is the linkage of alterations at molecular and biochemical levels of organization to adverse outcomes in individuals and populations. In the present study, a predictive relationship between plasma vitellogenin (VTG) concentration and fecundity in female fathead minnows (Pimephales promelas) was derived from 21‐d laboratory toxicity tests with five chemicals (17β‐trenbolone, 17α‐trenbolone, prochloraz, fenarimol, and fadrozole) that inhibit VTG production through different mechanisms. Because VTG is key to egg production in female oviparous animals, changes in the lipoprotein could, theoretically, serve as an indicator of reproductive success. Regression of fecundity versus VTG concentration from the various studies yielded a highly significant linear model (fecundity = −0.042 + 0.95‐VTG, p < 0.01, r2 = 0.88). This relationship was integrated into a population model to translate changes in VTG concentrations of female fathead minnows to alterations in population growth. The model predicted relatively profound effects on population size offish experiencing moderate decreases in vitellogenesis. For example, a fathead minnow population at a carrying capacity exposed to a chemical stressor that causes a 25% decrease in VTG concentration in females from baseline values would exhibit a 34.6% projected decrease in size after two years of exposure and reach an equilibrium population size that was only 30.2% of the preexposed population. Overall, the current study provides an example of how changes in a biomarker (VTG concentration) can be quantitatively translated into adverse effects at the individual and population levels.
Natural Language Database Interface for the Community Based Monitoring System

In most information systems, databases are accessed and manipulated typically through systems developed to tailor-fit the company's needs. The usual problem in these cases is the limitation on data accessibility because the users are constrained to the forms created for the system. Another way of accessing the database is through Structured Query Language (SQL), a language that is not familiar to end users, thus still limiting the access to the data. Natural Language Database Interfaces were developed to address limited database accessibility for end users. This paper presents AlLaDIn, a web-based natural language interface to the Community-Based Monitoring System of a city in the Philippines.
Robust Satisfiability for CSPs: Hardness and Algorithmic Results

An algorithm for a constraint satisfaction problem is called robust if it outputs an assignment satisfying at least a (1 − <i>f</i>(<i>ε</i>))-fraction of constraints for each (1 − <i>ε</i>)-satisfiable instance (i.e., such that at most a <i>ε</i>-fraction of constraints needs to be removed to make the instance satisfiable), where <i>f</i>(<i>ε</i>) → 0 as <i>ε</i> → 0. We establish an algebraic framework for analyzing constraint satisfaction problems admitting an efficient robust algorithm with functions <i>f</i> of a given growth rate. We use this framework to derive hardness results. We also describe three classes of problems admitting an efficient robust algorithm such that <i>f</i> is <i>O</i>(1/log (1/<i>ε</i>)), <i>O</i>(<i>ε</i><sup>1/k</sup>) for some <i>k</i> > 1, and <i>O</i>(<i>ε</i>), respectively. Finally, we give a complete classification of robust satisfiability with a given <i>f</i> for the Boolean case.
First complete mitochondrial genome from the brown lacewings (Neuroptera: Hemerobiidae)

Abstract The first complete mitochondrial genome of the family Hemerobiidae (Neuronema laminatum Tjeder, 1936) is sequenced in this study. The complete mitochondrial genome is a typical double-stranded circular molecule of 17,164 bp (GenBank accession number: KR078257) containing 37 typical animal mitochondrial gene and an A + T-rich region. The gene order is identical to that of the putative ancestral arrangement of insects and other lacewings. Thirteen protein-coding genes (PCGs) possessed common triplet initiation codons ATN and mostly terminate with TAN codons except for ND5 with a single T residue adjacent to a downstream tRNA gene. All the 22 tRNAs, ranging from 63 to 72 bp, can be folded into classic clover-leaf secondary structure except for tRNASer(AGN), in which the dihydrouridine (DHU) arm did not form a stable stem-loop structure. The control region is 2131 bp long with an A + T content of 87.4%. In the sampled families of Neuroptera, Osmylidae + the remaining families, Hemerobiidae + Mantispidae, Polystoechotidae + Rapismatidae, are recovered in phylogenetic analyses with high supports.
Automating the Discovery of Recommendation Knowledge

In case-based reasoning (CBR) systems for product recommendation, the retrieval of acceptable products based on limited information is an important and challenging problem. As we show in this paper, basic retrieval strategies such as nearest neighbor are potentially unreliable when applied to incomplete queries. To address this issue, we present techniques for automating the discovery of recommendation rules that are provably reliable and non-conflicting while requiring minimal information for their application in a rule-based approach to the retrieval of recommended cases.
Predictive validity of the ACC/AHA pooled cohort equations in predicting cancer‐specific mortality in a National Prospective Cohort Study of Adults in the United States

The American College of Cardiology/American Heart Association Task Force on Practice Guidelines recently developed the Pooled Cohort Risk (PCR) equations to predict 10‐years risk for a first atherosclerotic cardiovascular disease (ASCVD) event. The predictive validity of these PCR equations on cancer‐specific mortality among a national sample of US adults has yet to be evaluated, which was this study's purpose.
Development of a simulation model for a community microgrid system

Research on Community based Microgrid (C-μGrid) systems is attracting considerable research interest as a transitional solution in countries where policies for microgeneration (μGen) is present but Microgrid (μGrid) policies do not exist. This paper presents a model of a simulation-based grid connected C-μGrid system where multiple wind-based μGen systems are connected to the grid through a central converter. Dublin, Ireland has been chosen as the geographical location for this simulation study. In the C-μGrid system, the communication system is very important to facilitate calculation of the import/export energy from the grid/DG sources. Therefore, based on the μGen system capacity, an algorithm for the central C-μGrid controller (C-μGCC) is proposed to manage the power sharing between the prosumers (combined producer and consumer). The system architecture with the power sharing algorithm has been developed in MATLAB. The simulation results verify the effectiveness of the method in proper sharing of power amongst the prosumers.
Revista Latinoamericana y del Caribe de la Asociación de Sistemas de Información

alinhamento associadas estratégias ABSTRACT This research aims at analyzing the relationship between the Information Technology (IT) outsourcing and IT strategic alignment in organizations. The research method used was a multiple case study. This is an exploratory study and comprises two large companies that operate in different industries, with business and operations in the Brazilian market. Data were collected between 2010 and 2011 through interviews. It was possible to analyze the data collected using strategic alignment models and outsourcing models. The results showed that different perspectives of IT strategic alignment may be associated with different outsourcing strategies.
Prevention of diabetes in women with a history of gestational diabetes: effects of metformin and lifestyle interventions.

CONTEXT A past history of gestational diabetes mellitus (GDM) confers a very high risk of postpartum development of diabetes, particularly type 2 diabetes. OBJECTIVE The Diabetes Prevention Program (DPP) sought to identify individuals with impaired glucose tolerance (IGT) and intervene in an effort to prevent or delay their progression to diabetes. This analysis examined the differences between women enrolled in DPP with and without a reported history of GDM. DESIGN The DPP was a randomized, controlled clinical trial. SETTING The study was a multicenter, National Institutes of Health-sponsored trial carried out at 27 centers including academic and Indian Health Services sites. PATIENTS A total of 2190 women were randomized into the DPP and provided information for past history of GDM. This analysis addressed the differences between those 350 women providing a past history of GDM and those 1416 women with a previous live birth but no history of GDM. INTERVENTIONS Subjects were randomized to either standard lifestyle and placebo or metformin therapy or to an intensive lifestyle intervention. MAIN OUTCOMES The primary outcome was the time to development of diabetes ascertained by semiannual fasting plasma glucose and annual oral glucose tolerance testing. Assessments of insulin secretion and insulin sensitivity were also performed. RESULTS Whereas entering the study with similar glucose levels, women with a history of GDM randomized to placebo had a crude incidence rate of diabetes 71% higher than that of women without such a history. Among women reporting a history of GDM, both intensive lifestyle and metformin therapy reduced the incidence of diabetes by approximately 50% compared with the placebo group, whereas this reduction was 49 and 14%, respectively in parous women without GDM. These data suggest that metformin may be more effective in women with a GDM history as compared with those without. CONCLUSIONS Progression to diabetes is more common in women with a history of GDM compared with those without GDM history despite equivalent degrees of IGT at baseline. Both intensive lifestyle and metformin are highly effective in delaying or preventing diabetes in women with IGT and a history of GDM.
An Inexpensive, Fast and Sensitive Quantitative Lateral Flow Magneto-Immunoassay for Total Prostate Specific Antigen

We describe the detection characteristics of a device the Resonant Coil Magnetometer (RCM) to quantify paramagnetic particles (PMPs) in immunochromatographic (lateral flow) assays. Lateral flow assays were developed using PMPs for the measurement of total prostate specific antigen (PSA) in serum samples. A detection limit of 0.8 ng/mL was achieved for total PSA using the RCM and is at clinically significant concentrations. Comparison of data obtained in a pilot study from the analysis of serum samples with commercially available immunoassays shows good agreement. The development of a quantitative magneto-immunoassay in lateral flow format for total PSA suggests the potential of the RCM to operate with many immunoassay formats. The RCM has the potential to be modified to quantify multiple analytes in this format. This research shows promise for the development of an inexpensive device capable of quantifying multiple analytes at the point-of-care using a magneto-immunoassay in lateral flow format.
A Quality Measure for Multi-Level Community Structure

Mining relational data often boils down to computing clusters, that is finding sub-communities of data elements forming cohesive sub-units, while being well separated from one another. The clusters themselves are sometimes terms "communities" and the way clusters relate to one another is often referred to as a "community structure". We study a modularity criterion MQ introduced by Mancoridis et al. in order to infer community structure on relational data. We prove a fundamental and useful property of the modularity measure MQ, showing that it can be approximated by a Gaussian distribution, making it a prevalent choice over less focused optimization criterion for graph clustering. This makes it possible to compare two different clusterings of a same graph as well as asserting the overall quality of a given clustering relying on the fact that MQ is Gaussian. Moreover, we introduce a generalization extending MQ to hierarchical clusterings of graphs which reduces to the original MQ when the hierarchy becomes flat
Influence of surfactants on the structure of titanium oxide gels: Experiments and simulations.

We report here on experimental and numerical studies of the influence of surfactants on mineral gel synthesis. The modification of the gel structure when the ratios water-precursor and water-surfactant vary is brought to the fore by fractal dimension measures. A property of {\em polydispersity of the initial hydrolysis} is proposed to explain these results, and is successfuly tested through numerical experiments of three dimensional chemically limited aggregation.
A Survey of the Processing and Chemical Composition of Gariss Produced by Nomadic Camel Women Herders in Al Gaderif State , Sudan

Gariss is the most popular stable food for the camel herders who depend on Gariss for the sustainability of their livestock. The objective of the current study is to assess the traditional fermented camel milk (Gariss) prepared by nomadic camel woman herders in AlGadarif State in Butana. It is also meant to improve the quality of camel milk products through sharing knowledge. The samples (n= 19) were collected during rainy and dry seasons. The nomad’s housekeepers were interviewed in the study area. The effect of different types of containers and the additives used during Gariss preparation and the compositional quality were all estimated. The survey reported the different types of spoilage and the variations in the shelf life of Gariss. When compared with the mean values of the Gariss samples collected during dry season, the result indicated that the values of the total solids and the pH of the samples collected during the rainy season were significantly higher (p<0.05), whereas the values of the fat, protein and ash were significantly lower (p<0.05). The container types had a significant (p<0.05) effect on the total solids, fat and ash content only. The Gariss prepared in Bukhsa showed the highest total solids content (13.15±0.54%) and that prepared in stainless steel showed the highest fat (4.65± 0.34%) content. However, when Gariss was prepared in plastic containers it showed the lowest pH value (3.59±0.16%), whereas samples from ‘‘Siin’’ (goat leather) was significantly lower (p<0.05) in the ash content (0.35± 0.09%). The present study concludes that the chemical composition of Gariss from the nomadic camel women herders is affected by seasons, types of additives and containers used. Hence more studies are needed to be done on the effect of the additive and containers on Gariss quality.
Incorporating a New Relational Feature in Arabic Online Handwritten Character Recognition

Artificial neural networks have shown good performance in classification tasks. However, models used for learning in pattern classification are challenged when the differences between the patterns of the training set are small. Therefore, the choice of effective features is mandatory for obtaining good performance. Statistical and geometrical features alone are not suitable for recognition of hand printed characters due to variations in writing styles that may result in deformations of character shapes. We address this problem by using a relational context feature combined with a local descriptor for training a neural network-based recognition system in a user-independent online character recognition application. Our feature extraction approach provides a rich representation of the global shape characteristics, in a considerably compact form. This new relational feature provides a higher distinctiveness and increases robustness with respect to character deformations. While enhancing the recognition accuracy, the feature extraction is computationally simple. We show that the ability to discriminate in Arabic handwriting characters is increased by adopting this mechanism in feed forward neural network architecture. Our experiments on Arabic character recognition show comparable results with the state-of-the-art methods for online recognition of these characters.
RNA interference for treating haematological malignancies

RNA interference (RNAi) is a method for silencing gene expression. It is relatively gene-specific, potent, and minimally toxic. For these reasons, RNAi holds great promise for the treatment of haematological malignancies. Much has already been learned about RNAi in the laboratory, although many fundamental questions about its mechanisms remain to be elucidated. For human trials, major hurdles to be overcome include the induction of a nonspecific immune response to RNAi, the selection of the most appropriate targets, the design of more specific molecules, and the assurance of efficient delivery and safety in patients. Translational research efforts are currently well on their way to solving these problems, and will be reviewed here.
Drug binding and resistance mechanism of KIT tyrosine kinase revealed by hydrogen/deuterium exchange FTICR mass spectrometry

Mutations of the receptor tyrosine kinase KIT are linked to certain cancers such as gastrointestinal stromal tumors (GISTs). Biophysical, biochemical, and structural studies have provided insight into the molecular basis of resistance to the KIT inhibitors, imatinib and sunitinib. Here, solution‐phase hydrogen/deuterium exchange (HDX) and direct binding mass spectrometry experiments provide a link between static structure models and the dynamic equilibrium of the multiple states of KIT, supporting that sunitinib targets the autoinhibited conformation of WT‐KIT. The D816H mutation shifts the KIT conformational equilibrium toward the activated state. The V560D mutant exhibits two low energy conformations: one is more flexible and resembles the D816H mutant shifted toward the activated conformation, and the other is less flexible and resembles the wild‐type KIT in the autoinhibited conformation. This result correlates with the V560D mutant exhibiting a sensitivity to sunitinib that is less than for WT KIT but greater than for KIT D816H. These findings support the elucidation of the resistance mechanism for the KIT mutants.
Targeting the Mevalonate Pathway Inhibits the Function of the Epidermal Growth Factor Receptor

Purpose: The epidermal growth factor receptor (EGFR) is a key regulator of growth, differentiation, and survival of epithelial cancers. In a small subset of tumors, the presence of activating mutations within the ATP binding site confers increased susceptibility to gefitinib, a potent tyrosine kinase inhibitor of EGFR. Agents that can inhibit EGFR function through different mechanisms may enhance gefitinib activity in patients lacking these mutations. Mevalonate metabolites play significant roles in the function of the EGFR; therefore, mevalonate pathway inhibitors may potentiate EGFR-targeted therapies. Experimental Design: In this study, we evaluated the effect of lovastatin on EGFR function and on gefitinib activity. Effects on EGFR function were analyzed by Western blot analysis using phosphospecific antibodies to EGFR, AKT, and extracellular signal-regulated kinase. Cytotoxic effects of lovastatin and/or gefitinib were evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay and flow cytometry. Results: Lovastatin treatment inhibited EGF-induced EGFR autophosphorylation by 24 hours that was reversed by the coadministration of mevalonate. Combining lovastatin and gefitinib treatments showed enhanced inhibition of AKT activation by EGF in SCC9 cells. The combination of 10 μmol/L lovastatin and 10 μmol/L gefitinib treatments showed cooperative cytotoxicity in all 8 squamous cell carcinomas, 4 of 4 non–small cell lung carcinoma and 4 of 4 colon carcinoma cell lines tested. Isobologram and flow cytometric analyses of three representative cell lines with wild-type EGFR ATP binding sites confirmed that this combination was synergistic inducing a potent apoptotic response. Conclusions: Taken together, these results show that targeting the mevalonate pathway can inhibit EGFR function. They also suggest the potential utility of combining these clinically relevant therapeutic approaches.
Identification of protein coding regions in RNA transcripts

Massive parallel sequencing of RNA transcripts by the next generation technology (RNA-Seq) is a powerful method of generating critically important data for discovery of structure and function of eukaryotic genes. The transcripts may or may not carry protein-coding regions. If protein coding region is present, it should be a continuous (spliced) open reading frame. Gene finding in transcripts can be done by statistical (alignment-free) as well as by alignment based methods. We describe a new tool, GeneMarkS-T, for ab initio identification of protein-coding regions, complete or incomplete, in RNA transcripts assembled from RNA-Seq reads. Important feature of GeneMarkS-T is unsupervised estimation of parameters of the algorithm that makes unnecessary several conventional steps used in the gene prediction protocols, most importantly the manually curated preparation of training sets. We demonstrate that i/the GeneMarkS-T self-training is robust with respect to the presence of errors in assembled transcripts and ii/accuracy of GeneMarkS-T in identification of protein-coding regions and, particularly, in prediction of gene starts compares favorably to other existing methods.
Resting heart rate and its change induced by physical training in patients with ischemic heart disease at various ages treated with beta-blockers.

BACKGROUND The present study was aimed at possible modifications of resting HR induced by systematic physical training in patients of different age populations with ischemic heart disease (IHD) subjected to chronic therapeutic beta-blockade. METHODS The goal was the assessment of initial resting heart rate (HR) and its change after 6 months of physical training in two groups of patients with IHD at various ages (A: 55.5 +/- +/- 4.6 years; B: 72.5 +/- 4.37 years) treated with beta-blockers, the dosage of which was not modified during the observation. RESULTS Comparison between the groups A and B concerned the initial rHR (min-1): 79.3 +/- +/- 8.3 vs. 73.6 +/- 8.3 (p < 0.01), the after-training rHR: 70.9 +/- 7.9 vs. 67.7 +/- 8.4 (NS), and the delta of rHR: -8.4 +/- 4.8 vs. -5.9 +/- 2.8 (p < 0.01). Statistically significant correlation coefficients both between the patients' ages and the initial rHR (r = -0.377) and the delta of rHR (r = 0.347) were noted. CONCLUSIONS The reduction of rHR after 6-months of training was less in the older IHD patients because of their lower initial rHR compared with the younger patients, which was probably determined more by physiological vagotonia than therapeutic beta-blockade. (Cardiol J 2007; 14: 493-496).
Late Onset Preeclampsia is not an Innocuous Condition

Objective: To describe the profile and outcome of late-onset preeclampsia (LOPE). Methods. Retrospective study of 264 singleton pregnancies presenting before delivery at two referral centres in South Africa. Results: Primigravid patients constituted 56.8% of the group, while 57.6% were graded as severe. Median gestational age at diagnosis was 37 (34–43) weeks. 30.7% of patients experienced ≥1 major maternal complication including 34 (12.9%) cases of eclampsia. There were no maternal or early neonatal deaths. Five intrauterine deaths occurred, all due to placental abruption. The perinatal mortality rate was 18.9 per thousand births. Conclusions: Late-onset preeclampsia often presents as severe disease.