Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparing and evaluating terminology services application programming interfaces: RxNav, UMLSKS and LexBIG

To facilitate the integration of terminologies into applications, various terminology services application programming interfaces (API) have been developed in the recent past. In this study, three publicly available terminology services API, RxNav, UMLSKS and LexBIG, are compared and functionally evaluated with respect to the retrieval of information from one biomedical terminology, RxNorm, to which all three services provide access. A list of queries is established covering a wide spectrum of terminology services functionalities such as finding RxNorm concepts by their name, or navigating different types of relationships. Test data were generated from the RxNorm dataset to evaluate the implementation of the functionalities in the three API. The results revealed issues with various aspects of the API implementation (eg, handling of obsolete terms by LexBIG) and documentation (eg, navigational paths used in RxNav) that were subsequently addressed by the development teams of the three API investigated. Knowledge about such discrepancies helps inform the choice of an API for a given use case.
Risk management and contingency sum of construction projects

Purpose Most organisations do not have established guidelines for the estimation and management of contingency funds. The purpose of this paper is to identify the risk factors at the construction phase causing project cost overruns, and a reliable method for the estimation of contingency sum is established. Design/methodology/approach Combined qualitative–quantitative exploratory methods were used. Qualitative interviews were conducted with five expert practitioners working in a Public Works Department in Zambia to determine how contingency sum is estimated and to explore what risk factors should be considered. Quantitative regression used cost and risk data collected from 30 recently completed building and refurbishment projects. Findings The qualitative study indicated that the project budget overruns constitute a major issue. This finding is in line with the paired-samples t-test results which show that the difference between the total variations and the initial contingency sum tends to be significant. The regression analysis proved that the contingency sum was positively correlated to the estimated contract sum. The qualitative interview results and Pearson correlation analysis also showed that contingency sum and project complexity tend to have a significant correlation. The research also demonstrates that the type of works is not a direct significant factor. Research limitations/implications Because the projects used for the study were relatively short, duration of the project and economic factor of tax rate, exchange rate and inflation rate were not examined in the multiple regression analysis. Further studies should be conducted on longer projects to test out whether these risk factors are significant in influencing the project contingency. Practical implications The results demonstrate that the multiple regression method can be applied as a reliable tool to predict contingency sums. Accurate contingency sums and project budget estimates benefit construction clients and their project managers. Individual project conditions should be carefully examined when assessing the contingency. Originality/value This research establishes a reliable regression method for the assessment of the contingency for the pre-tender estimate which has significant impact on the project feasibility and cost control, using related risk factors involved in construction contingency and client’s contingency.
Food restriction markedly increases dopamine D2 receptor (D2R) in a rat model of obesity as assessed with in‐vivo μPET imaging ([11C] raclopride) and in‐vitro ([3H] spiperone) autoradiography

Introduction: Dopamine (DA) regulates food intake by modulating food reward and motivation but its involvement in obesity is much less understood. Recent evidence points to the involvement of leptin in the DA‐related modulation of food intake. Here we assess DA D2 receptors (D2R) in a genetic rodent obesity model characterized by leptin‐receptor deficiency and assess the influence of food restriction on these receptors. Methods: We compared D2R levels between Zucker Obese (fa/fa) and Lean (Fa/Fa) rats at 1 and 4 months of age and in two different feeding conditions (restricted and unrestricted food access) using in‐vivo μPET imaging ([11C] raclopride, which is a method sensitive to competition with endogenous DA) and in‐vitro ([3H] spiperone washed to ensure no competition with endogenous DA) autoradiography (ARG). Results: Both ARG and μPET showed that D2R were higher at 1 month than at 4 months of age and that food restricted animals had higher D2R than unrestricted animals. However there were significant differences in the results obtained at 4 months between ARG and μPET. ARG showed that at 1 month and at 4 months unrestricted lean rats (Le U) had significantly higher D2R binding than obese unrestricted rats (Ob U) but showed no differences between restricted obese (Ob R) and restricted lean rats (Le R). It also showed that D2R decline between 1 and 4 months of age was significantly attenuated in food restricted rats [both obese and lean]. In contrast, μPET showed that at 4 months of age, Ob U showed greater D2R availability than Le U rats but like ARG showed no differences between Ob R and Le R rats. Conclusion: The lower D2R binding in Ob U than Le U rats observed with ARG most likely reflects decreases in striatal D2 receptors levels whereas the increased availability observed with μPET is likely to reflect reduced DA release (resulting in decreased competition with endogenous DA). Lack of a significant difference between Ob R and Le R suggests that the differences in dopamine activity and D2R levels between Ob and Le Zucker rats are modulated by access to food. The ARG finding of an attenuation of the age‐related loss of D2R binding corroborates previous studies of the salutary effects of food restriction in the aging process. Because [11C] raclopride is sensitive to competition with endogenous DA, the higher D2R binding in obese rats with raclopride despite the lower D2R levels shown with spiperone could reflect lower extracellular DA in the Ob rats and merits further investigation. Synapse 62:50–61, 2008. Published 2007 Wiley‐Liss, Inc.
Air embolism of the brain in rabbits pretreated with mechlorethamine.

Infusion of 400 microliters air into the left internal carotid artery of five anesthetized rabbits caused transient pial arteriole air embolism, an immediate 41.9 +/- 0.8% dilatation of the embolized vessels, suppression of the cortical somatosensory evoked response to 29.4 +/- 2.7% of baseline, and a progressive decline in ipsilateral cerebral blood flow (measured by hydrogen clearance) to 46 +/- 4.1% of baseline after 2 hours. These values were significantly different from those at baseline and from the responses of 10 control rabbits given equivalent intracarotid saline infusions. Twelve other rabbits were made leukopenic by treatment with 1.5 mg/kg i.v. mechlorethamine 72 hours prior to study. Mean +/- SEM leukocyte count decreased from 6,320 +/- 73/mm3 to 1,890 +/- 66/mm3 without any change in the leukocyte differential or erythrocyte and platelet counts. Intracarotid infusion of saline into seven of the leukopenic rabbits caused no changes. In the other five leukopenic rabbits, infusion of 400 microliters air caused air embolism but did not produce the anticipated declines in cerebral blood flow or the cortical somatosensory evoked response, both of which remained indistinguishable from baseline values and responses in the seven saline-treated leukopenic controls. Similarly, air-embolized arterioles showed nonsignificant dilatation in leukopenic rabbits. Our data suggest that the decreases in both cerebral blood flow and brain function seen after air embolism require the presence of leukocytes.
Noncognitive Symptoms and Long-Term Treatment Expectations for Alzheimer Disease

Alzheimer disease (AD) is characterized by both cognitive and noncognitive symptoms that can lead to functional impairment, increased caregiver burden, and institutionalization. Pharmacologic therapies traditionally used to treat cognitive symptoms of AD may prevent and/or control many noncognitive symptoms as well. The acetylcholinesterase inhibitors (AChEIs) galantamine, rivastigmine, and donepezil have been shown to maintain or improve function for at least 1 year. They also have been shown to improve or delay the onset of neuropsychiatric and behavioral symptoms. These noncognitive benefits can impact greatly the lives of patients with AD as well as the persons who care for them.
Latest treatment options for Alzheimer’s disease, Parkinson’s disease dementia and dementia with Lewy bodies

Introduction: Alzheimer’s disease (AD), Parkinson’s disease dementia (PDD) and dementia with Lewy bodies (DLB) together account for the vast majority of individuals with dementia. Approximately 35 million people worldwide are affected with this condition, and despite decades of research, effective therapies that slow or reverse disease progression have not yet been developed. The recent failure of several large-scale clinical trials is beginning to challenge the magnitude of focus on amyloid-related therapies for AD, and newer drug targets that have shown promise in the laboratory are being investigated in clinical trials. Areas covered: This review summarises the current understanding of the underlying biology of AD, PDD and DLB and outlines the most recent drug candidates in advanced clinical trials. Expert opinion: The lack of success in drug discovery for disease-modifying therapies for AD, PDD and DLB can be attributed to limitations in the design of clinical trials and the narrow focus of molecular targets for treatment. New avenues for drug discovery including repositioning and novel target identification may now provide opportunities for success, provided a critical mass of clinical trials is achieved through increased investment.
Performance of rain-fed Aman rice yield in Bangladesh in the presence of climate change

Abstract This paper uses the framework of the Just–Pope production function to evaluate the impacts of climate change on yields of the rainfed Aman rice crop in Bangladesh. It analyses disaggregated district-level data on climate variables and Aman rice yield over a 48 year time horizon. The results reveal that changes in maximum temperatures have had positive and negative effects on yield in the linear and quadratic functional forms, respectively. However, the elasticity values in the variance function confirm that maximum temperature is risk-increasing for Aman rice while minimum temperature is likely to decrease yield variability. Rainfall has become risk-increasing for Aman rice. Based on three climate change scenarios, this paper also reveals that future climate change is expected to increase the variability of Aman rice yields. Finally, statistically significant dummies for different in-country climate zones require zone-specific adaptation policies to reduce the adverse impacts of climate change.
Functional Characteristics of Heteromeric Cx40-Cx43 Gap Junction Channel Formation

Cx40:Cx43 expression ratio in A7r5 cells is augmented in growth stimulated vs. growth arrested conditions. To determine the impact of changing Cx40:Cx43 expression ratio on gap junction function, we have developed A7r5 cell lines that display Cx40:Cx43 ratios of 1:1 (6B5n) and 10:1 (A7r540C3). When Rin43 cells were paired with these coexpressing cells, there was an increasing asymmetry of voltage dependent gating as the Cx40:Cx43 ratio increased in the coexpressing cell. This asymmetry was opposite to that which is predicted by Cx40/Cx43 heterotypic channels. In addition, when Rin43 cells were paired with coexpressing cells there was a shift toward smaller single channel event amplitudes with increasing Cx40:Cx43 ratio in the coexpressing cell. Again, this is opposite to that which is predicted by Cx40/Cx43 heterotypic channels. In dye coupling experiments, 6B5N, A7r5, and A7r540C3 cells displayed charge and size selectivity that increased with increasing Cx40:Cx43 expression ratio. These data indicate that although the electrophysiological properties of heteromeric/heterotypic channels are not directly related to the proportions of Cx constituents that comprise the channel, the dye permeability data fit what would be predicted by an increase in Cx40:Cx43 ratio.
Hepatic protein kinase B (Akt)–target of rapamycin (TOR)-signalling pathways and intermediary metabolism in rainbow trout (Oncorhynchus mykiss) are not significantly affected by feeding plant-based diets

The aim of the present study was to analyse the effects of partial or total replacement of fish meal (FM) and fish oil (FO) by a mixture of plant protein (PP) and a mixture of vegetable oils (VO) on the hepatic insulin–nutrient-signalling pathway and intermediary metabolism-related gene expression in rainbow trout (Oncorhynchus mykiss). Triplicate groups of fish were fed four practical diets containing graded levels of replacement of FM and FO by PP and VO for 12 weeks: diet 0/0 (100 % FM, 100 % FO); diet 50/50 (50 % FM and 50 % PP, 50 % FO and 50 % VO); diet 50/100 (50 % FM and 50 % PP, 100 % VO); diet 100/100 (100 % PP, 100 % VO). Samplings were performed on trout starved for 5 d then refed with their allocated diet. In contrast to partial substitution (diet 50/50), total substitution of FM and FO (diet 100/100) led to significantly lower growth compared with diet 0/0. The insulin–nutrient-signalling pathway (protein kinase B (Akt), target of rapamycin (TOR), S6 protein kinase 1 (S6K1) and S6) was characterised in trout liver and found to be activated by refeeding. However, changes in diet compositions did not differentially affect the Akt–TOR-signalling pathway. Moreover, expression of genes encoding fructose-1,6-biphosphatase, mitochondrial phosphoenolpyruvate carboxykinase, glucokinase, pyruvate kinase and carnitine palmitoyl transferase 1 were not affected by refeeding or by dietary changes. Refeeding down- and up-regulated the expression of gluconeogenic glucose-6-phosphatase isoform 1 and lipogenic fatty acid synthase genes, respectively. Expression of both genes was also increased with partial replacement of FM and total replacement of FO (diet 50/100). These findings indicate that plant-based diets barely affect glucose and lipid metabolism in trout.
Immunophenotypic and ultrastructural study in peripheral blood neutrophil granulocytes following bone marrow transplantation

Neutrophil studies after bone marrow transplantation (BMT) describe chemotactic and phagocytotic alterations and dyshaemopoiesis. Neutrophil granulocytes (NG) in peripheral blood after BMT were analysed in 28 patients. 14 patients (six receiving GM‐CSF) underwent autologous BMT and 14 underwent allogeneic BMT. Immunophenotypic and electron microscopic studies were performed during post‐BMT granulopoietic regeneration. Results were compared with NG from 15 healthy bone marrow donors (control group A) and from six patients receiving intensive chemotherapy before autologous BMT (control group B).
Structure of the cel-3 gene from Fibrobacter succinogenes S85 and characteristics of the encoded gene product, endoglucanase 3

The cel-3 gene cloned from Fibrobacter succinogenes into Escherichia coli coded for the enzyme EG3, which exhibited both endoglucanase and cellobiosidase activities. The gene had an open reading frame of 1,974 base pairs, coding for a protein of 73.4 kilodaltons (kDa). However, the enzyme purified from the osmotic shock fluid of E. coli was 43 kDa. The amino terminus of the 43-kDa protein matched amino acid residue 266 of the protein coded for by the open reading frame, indicating proteolysis in E. coli. In addition to the 43-kDa protein, Western immunoblotting revealed a 94-kDa membranous form of the enzyme in E. coli and a single protein of 118 kDa in F. succinogenes. Thus, the purified protein appears to be a proteolytic degradation product of a native protein which was 94 kDa in E. coli and 118 kDa in F. succinogenes. The discrepancy between the molecular weight expected on the basis of the DNA sequence and the in vivo form may be due to anomalous migration during electrophoresis, to glycosylation of the native enzyme, or to fatty acyl substitution at the N terminus. One of two putative signal peptide cleavage sites bore a strong resemblance to known lipoprotein leader sequences. The purified 43-kDa peptide exhibited a high Km (53 mg/ml) for carboxymethyl cellulose but a low Km (3 to 4 mg/ml) for lichenan and barley beta-glucan. The enzyme hydrolyzed amorphous cellulose, and cellobiose and cellotriose were the major products of hydrolysis. Cellotriose, but not cellobiose, was cleaved by the enzyme. EG3 exhibited significant amino acid sequence homology with endoglucanase CelC from Clostridium thermocellum, and as with both CelA and CelC of C. thermocellum, it had a putative active site which could be aligned with the active site of hen egg white lysozyme at the highly conserved amino acid residues Asn-44 and Asp-52.
Ten years of AFLP in ecology and evolution: why so few animals?

Researchers in the field of molecular ecology and evolution require versatile and low‐cost genetic typing methods. The AFLP (amplified fragment length polymorphism) method was introduced 10 years ago and shows many features that fulfil these requirements. With good quality genomic DNA at hand, it is relatively easy to generate anonymous multilocus DNA profiles in most species and the start‐up time before data can be generated is often less than a week. Built‐in dynamic, yet simple modifications make it possible to find a protocol suitable to the genome size of the species and to screen thousands of loci in hundreds of individuals for a relatively low cost. Until now, the method has primarily been applied in studies of plants, bacteria and fungi, with a strong bias towards economically important cultivated species and their pests. In this review we identify a number of research areas in the study of wild species of animals where the AFLP method, presently very much underused, should be a very valuable tool. These aspects include classical problems such as studies of population genetic structure and phylogenetic reconstructions, and also new challenges such as finding markers for genes governing adaptations in wild populations and modifications of the protocol that makes it possible to measure expression variation of multiple genes (cDNA‐AFLP) and the distribution of DNA methylation. We hope this review will help molecular ecologists to identify when AFLP is likely to be superior to other more established methods, such as microsatellites, SNP (single nucleotide polymorphism) analyses and multigene DNA sequencing.
Proposal of a cognitive based MAC protocol for M2M environments

The radio resource shortage is one of the most important issues to be taken into account when deploying modern wireless communication systems. A novel communication paradigm named cognitive radio, has been introduced in the last years for a more efficient exploitation of the limited available spectrum and cope with the inefficiency in the spectrum usage. Its main aim is to allow the co-existence of different wireless systems on the same spectral resources by limiting the mutual interference. The aim of this paper is to design a cognitive networking environment where the primary network is based on the OFDMA principle. The proposed Medium Access Control (MAC) technique for the secondary network, named Data Aided Cognitive Technique (DACT), aims to exploit the framing information broadcast by the primary network in order to setup transparently an independent network with a particular focus on Machine to Machine (M2M) communications.
HIV-1 Nef impairs MHC class II antigen presentation and surface expression

HIV-1-infected cells can avoid cytotoxic T lymphocyte killing by Nef-mediated down-regulation of surface MHC I. Here, we show that HIV-1 Nef inhibits MHC II restricted peptide presentation to specific T cells and thus may affect the induction of antiviral immune responses. Nef mediates this effect by reducing the surface level of mature (i.e., peptide-loaded) MHC II while increasing levels of immature MHC II, which are functionally incompetent because of their association with the invariant chain. Nef was the only HIV-1 gene product to possess this capacity, which was also observed in the context of the whole HIV-1 genome. Other proteins of the endocytic pathway were not affected by Nef expression, suggesting that Nef effects on MHC II did not result from a general alteration of the endocytic pathway. Response patterns to previously characterized mutations of Nef differed for Nef-induced modulation of mature and immature MHC II. Furthermore, the doses of Nef required to observe each of the two effects were clearly different, suggesting that Nef could affect MHC II peptide presentation through distinct mechanisms. Cooperation between those mechanisms may enable Nef to efficiently inhibit MHC II function.
Circular Economy: Measuring Innovation in the Product Chain

An important question is how to measure the progress of the transition towards a circular economy (CE transition). Together PBL and Utrecht University have developed a framework about the role of innovation in CE-transitions in product chains, and applied this framework to a number of cases. This enabled us to identify the relevant information types for measuring the progress of CE transitions in product chains.
System Maintenance Scheduling With Prognostics Information Using Genetic Algorithm

Condition based maintenance (CBM) aims to balance two extreme sides (i.e., corrective maintenance (CM), and preventive maintenance (PM)) by observing and forecasting the real time health of machines. Recent developments in CBM revealed promising technologies for advanced fault detection, and forecasting. Traditional maintenance scheduling in CBM is based on the threshold setting on forecasted failure probability, or remaining useful life (RUL) for individual components. However, this approach may not give the best result for the system, because individual components are inter-related, and mutually dependent. It is not uncommon in systems that turning off a machine due to failure or maintenance causes other machinery or components to be turned off. Designing a comprehensive tool that optimizes availability & cost of the whole system incorporating prognostics information is crucial to fully benefit from CBM. The goal of this paper is to emphasize this need by demonstrating scenarios in CM, PM, and CBM; and to present a solution that optimizes system availability, and cost with system-maintenance constraints using genetic algorithms. The proposed tool acquires the forecasted failure probability of individual components from the prognostics module, and their reliability expectations after maintenance. The tradeoff between maintenance & failure is quantified in risk as the objective function to be minimized. The risk is minimized utilizing genetic algorithms for the whole system rather than individual components. The results of the proposed tool are compared with PM, CM, and CBM in which prognostics information of components are analyzed individually.