Miracle-dz/UniFAR-FTUs huggingface dataset:
Cost reduction in bottom‐up hierarchical‐based VLSI floorplanning designs

From the industrial perspective, floorplanning is a crucial step in the VLSI physical design process as its efficiency determines the quality and the time‐to‐market of the product. A new perturbation method, called Cull‐and‐Aggregate Bottom‐up Floorplanner (CABF), which consists of culling and aggregating stages, is developed to perform variable‐order automated floorplanning for VLSI. CABF will generate VLSI floorplan layout by calculating the modules' dimensions' differences (hard module floorplanning problems) and the modules' areas' differences (soft module floorplanning problems). Through mathematical derivation, the hard modules floorplanning area minimization cost function (two‐dimensional) during culling stage is proven that a dimensional reduction can be carried out to be the difference‐based cost function (one‐dimensional) which simplifies the computation. During the culling stage, CABF employs linear ordering method to select and determine the order of modules where this linear runtime complexity property allows CABF to cull the modules faster. The aggregating stage of CABF will reduce the subsequent search space of this floorplanner, and the variable order aggregation enables CABF to search for the best near‐optimal solution. Based on Gigascale Systems Research Center and Microelectronics Center of North Carolina circuit benchmarks, CABF gives better optimal solutions and faster runtimes for floorplanning problems involving 9 to 600 modules. This has established that CABF is performing well in respect of reliability and scalability. Besides, CABF shows its potential to be implemented in VLSI physical design as the runtime of CABF is faster with a near‐optimal outcome as compared to the other existing algorithms. Copyright © 2013 John Wiley & Sons, Ltd.
Households, The Homeless and Slums Towards a Standard for Representing City Shelter Open Data

In order to compare and analyse open data across cities, standard representations or ontologies have to be created. This paper defines a shelter ontology that includes concepts of shelters, slums, households and homelessness. The design of the ontology is based upon the data requirements of ISO 37120. ISO 37120 defines 100 indicators to measure and compare city performance. There are three shelter-themed indicators defined, namely 15.1 Percentage of city population living in slums, 15.2 Number of homeless per 100 000 population, and 15.3 Percentage of households that exist without registered legal titles. This ontology enables both the representation of the ISO 37120 Shelter theme indicators' definitions, and a city's indicator values and supporting data. This enables the analysis of city indicators by intelligent agents.
Modified images reflecting effects of age‐related macular degeneration on perception of everyday scenes

Depictions of vision with age‐related macular degeneration (AMD) in public information material typically show a central region of absolute vision loss. Patients with early and moderate disease frequently do not report this. We aimed to measure how a group of people with AMD perceive everyday scenes in order to produce accurate depictions.
The association between Dietary Approaches to Stop Hypertension and incidence of chronic kidney disease in adults: the Tehran Lipid and Glucose Study: Clinical Epidemiology in Nephrology

Background This study was conducted to examine the association of adherence to the Dietary Approaches to Stop Hypertension (DASH)‐style diet with incident chronic kidney disease (CKD) among an Iranian population. Methods We followed‐up 1630 participants (50.5% women, mean age: 42.8 years) of the Tehran Lipid and Glucose Study for 6.1 years, who were initially free of CKD. Baseline diet was assessed using a valid and reliable 168‐item food frequency questionnaire. A DASH‐style diet, based on scoring eight components (fruits, vegetables, whole grains, nuts and legumes, low‐fat dairy, red and processed meats, sweetened beverages and sodium) was used. Estimated glomerular filtration rate (eGFR) was calculated using the Modification of Diet in Renal Disease Study equation and CKD was defined as eGFR <60 mL/min/1.73 m2. Odds ratio (OR) using multivariable logistic regression was reported for the association of incident CKD with DASH‐style diet score. Results The incidence of CKD among those in the top quintile of the DASH‐style diet was 30%, 18% lower than those in the bottom quintile. After controlling for age, sex, smoking, total energy intake, body mass index, eGFR, triglycerides, physical activity, hypertension and diabetes, adherence to the DASH‐style diet was found to be inversely associated with incident CKD (OR: 0.41; 95% confidence interval: 0.24‐0.70). In addition, higher scores of fruits, whole grains, nuts and legumes, sweetened beverages and sodium were inversely associated with incidence of CKD. Conclusion Results revealed that after 6.1 years of follow‐up, adherence to the DASH‐style diet was associated with a lower risk of incident CKD among adults.
MS2 Lysis of Escherichia coli Depends on Host Chaperone DnaJ

ABSTRACT The L protein of the single-stranded RNA phage MS2 causes lysis of Escherichia coli without inducing bacteriolytic activity or inhibiting net peptidoglycan (PG) synthesis. To find host genes required for L-mediated lysis, spontaneous Ill (insensitivity to Llysis) mutants were selected as survivors of L expression and shown to have a missense change of the highly conserved proline (P330Q) in the C-terminal domain of DnaJ. In the dnaJP330Q mutant host, L-mediated lysis is completely blocked at 30°C without affecting the intracellular levels of L. At higher temperatures (37°C and 42°C), both lysis and L accumulation are delayed. The lysis block at 30°C in the dnaJP330Q mutant was recessive and could be suppressed by Lovercomes dnaJ (Lodj) alleles selected for restoration of lysis. All three Lodj alleles lack the highly basic N-terminal half of the lysis protein and cause lysis ∼20 min earlier than full-length L. DnaJ was found to form a complex with full-length L. This complex was abrogated by the P330Q mutation and was absent with the Lodj truncations. These results suggest that, in the absence of interaction with DnaJ, the N-terminal domain of L interferes with its ability to bind to its unknown target. The lysis retardation and DnaJ chaperone dependency conferred by the nonessential, highly basic N-terminal domain of L resembles the SlyD chaperone dependency conferred by the highly basic C-terminal domain of the E lysis protein of ϕX174, suggesting a common theme where single-gene lysis can be modulated by host factors influenced by physiological conditions. IMPORTANCE Small single-stranded nucleic acid lytic phages (Microviridae and Leviviridae) lyse their host by expressing a single “protein antibiotic. ” The protein antibiotics from two out of three prototypic small lytic viruses have been shown to inhibit two different steps in the conserved PG biosynthesis pathway. However, the molecular basis of lysis caused by L, the lysis protein of the third prototypic virus, MS2, is unknown. The significance of our research lies in the identification of DnaJ as a chaperone in the MS2 L lysis pathway and the identification of the minimal lytic domain of MS2 L. Additionally, our research highlights the importance of the highly conserved P330 residue in the C-terminal domain of DnaJ for specific protein interactions.
Use of Negative Pressure Wound Therapy for Lower Limb Bypass Incisions

Objective: The use of negative pressure wound therapy (NPWT) for post-surgical cardiothoracic, orthopedic, plastic, and obstetric and gynecologic procedures has been described. However, there are no data regarding its use for lower limb bypass incisions. We aimed to investigate the outcomes of NPWT in preventing surgical site infection (SSI) in patients with lower limb arterial bypass incisions. Materials and Methods: We retrospectively used data of 42 patients who underwent lower limb arterial bypass with reversed great saphenous vein between March 2014 and June 2016 and compared conventional wound therapy and NPWT with regard to preventing SSI. Results: Twenty-eight (67%) patients underwent conventional wound therapy and 14 (33%) underwent NPWT. There were no statistical differences regarding patient characteristics and mean SSI risk scores between the two patient groups (13.7% for conventional wound therapy vs. 13.4% for NPWT; P=0.831). In the conventional group, nine instances of SSI (32%) and three (11%) of these required subsequent surgical wound debridement, whereas in the NPWT group, there was no SSI incidence (P=0.019). Secondary outcomes such as the length of hospital stay, 30-day readmission rate, and need for secondary vascular procedures were not statistically different between the two groups. Conclusion: The use of NPWT for lower limb arterial bypass incisions is superior to that of conventional wound therapy because it may prevent SSIs.
Backside-surface imprinting as a new strategy to generate specific plastic antibody materials.

A backside protein-surface imprinting process is presented herein as a novel way to generate specific synthetic antibody materials. The template is covalently bonded to a carboxylated-PVC supporting film previously cast on gold, let to interact with charged monomers and surrounded next by another thick polymer. This polymer is then covalently attached to a transducing element and the backside of this structure (supporting film plus template) is removed as a regular "tape". The new sensing layer is exposed after the full template removal, showing a high density of re-binding positions, as evidenced by SEM. To ensure that the templates have been efficiently removed, this re-binding layer was cleaned further with a proteolytic enzyme and solution washout. The final material was named MAPS, as in the back-side reading of SPAM, because it acts as a back-side imprinting of this recent approach. It was able to generate, for the first time, a specific response to a complex biomolecule from a synthetic material. Non-imprinted materials (NIMs) were also produced as blank and were used as a control of the imprinting process. All chemical modifications were followed by electrochemical techniques. This was done on a supporting film and transducing element of both MAPS and NIM. Only the MAPS-based device responded to oxLDL and the sensing layer was insensitive to other serum proteins, such as myoglobin and haemoglobin. Linear behaviour between log(C, μg mL-1) versus charged tranfer resistance (RCT, Ω) was observed by electrochemical impedance spectroscopy (EIS). Calibrations made in Fetal Calf Serum (FCS) were linear from 2.5 to 12.5 μg mL-1 (RCT = 946.12 × log C + 1590.7) with an R-squared of 0.9966. Overall, these were promising results towards the design of materials acting close to the natural antibodies and applied to practical use of clinical interest.
Evolution of Ecological Diversity in Biofilms of Pseudomonas aeruginosa by Altered Cyclic Diguanylate Signaling

ABSTRACT The ecological and evolutionary forces that promote and maintain diversity in biofilms are not well understood. To quantify these forces, three Pseudomonas aeruginosa populations were experimentally evolved from strain PA14 in a daily cycle of attachment, assembly, and dispersal for 600 generations. Each biofilm population evolved diverse colony morphologies and mutator genotypes defective in DNA mismatch repair. This diversity enhanced population fitness and biofilm output, owing partly to rare, early colonizing mutants that enhanced attachment of others. Evolved mutants exhibited various levels of the intracellular signal cyclic-di-GMP, which associated with their timing of adherence. Manipulating cyclic-di-GMP levels within individual mutants revealed a network of interactions in the population that depended on various attachment strategies related to this signal. Diversification in biofilms may therefore arise and be reinforced by initial colonists that enable community assembly. IMPORTANCE How biofilm diversity assembles, evolves, and contributes to community function is largely unknown. This presents a major challenge for understanding evolution during chronic infections and during the growth of all surface-associated microbes. We used experimental evolution to probe these dynamics and found that diversity, partly related to altered cyclic-di-GMP levels, arose and persisted due to the emergence of ecological interdependencies related to attachment patterns. Clonal isolates failed to capture population attributes, which points to the need to account for diversity in infections. More broadly, this study offers an experimental framework for linking phenotypic variation to distinct ecological strategies in biofilms and for studying eco-evolutionary interactions.
Endocitose e tráfego intracelular de nanomateriais Endocytosis and intracellular trafficking of nanomaterials

Recent advances in nanotechnology have increased the use of nanomaterials and nanodevices for diagnostic, therapeutic and other technological applications. The knowledge about the interaction between nanomaterials and biological media allows the development of more rational applications, as well understand and anticipate adverse and toxic effects resulting from this interaction. Endocytosis is an energy-dependent biological process responsible for internalization of nanoparticles, which depends on orchestrated events that require lipids and plasma membrane proteins functioning. Studies that aim to investigate in detail the endocytosis and intracellular trafficking of nanoparticles are essential for understanding cellular mechanisms, which in turn help to select its biomedical applications. In this context, this review aims to conceptualize the main routes of endocytosis used to study the internalization of nanomaterials in eukaryotic cells. In addition, we discuss some intracellular trafficking of nanomaterials to aid in studies of the cellular processing and development of new therapeutic tools.
Measles — United States, January 4–April 2, 2015

Measles is a highly contagious, acute viral illness that can lead to complications such as pneumonia, encephalitis, and death. As a result of high 2-dose measles vaccination coverage in the United States and improved control of measles in the World Health Organization's Region of the Americas, the United States declared measles elimination (defined as interruption of year-round endemic transmission) in 2000. Importations from other countries where measles remains endemic continue to occur, however, which can lead to clusters of measles cases in the United States. To update surveillance data on current measles outbreaks, CDC analyzed cases reported during January 4-April 2, 2015. A total of 159 cases were reported during this period. Over 80% of the cases occurred among persons who were unvaccinated or had unknown vaccination status. Four outbreaks have occurred, with one accounting for 70% of all measles cases this year. The continued risk for importation of measles into the United States and occurrence of measles cases and outbreaks in communities with high proportions of unvaccinated persons highlight the need for sustained, high vaccination coverage across the country.
Dietary inflammatory index, bone health and body composition in a population of young adults: a cross-sectional study

Abstract Diet quality has been postulated as a relevant factor in disorders like obesity and osteoporosis as it modulates inflammatory biomarkers. The aim of this study was to investigate whether the dietary inflammatory index (DII) is associated with bone health status and body composition parameters in a population of young adults. The study population consisted of 599 young adults (aged 20.41 ± 2.72). Linear regression analysis revealed that weight and fat-free mass (FFM) were significantly associated with the DII after adjustments for age, sex and total energy (β = −0.91, 95% CI −1.782, −0.213, p = .013 and β = −0.059, 95% CI −0.842, −0.107, p = .011, respectively). Our results suggest that the inflammatory potential of diet, measured using the DII, is associated with obesity-related parameters such as FFM and weight, although it may not contribute to osteoporosis in early adulthood.
MBROLE 2.0—functional enrichment of chemical compounds

Metabolites Biological Role (MBROLE) is a server that performs functional enrichment analysis of a list of chemical compounds derived from a metabolomics experiment, which allows this list to be interpreted in biological terms. Since its release in 2011, MBROLE has been used by different groups worldwide to analyse metabolomics experiments from a variety of organisms. Here we present the latest version of the system, MBROLE2, accessible at http://csbg.cnb. csic.es/mbrole2. MBROLE2 has been supplemented with 10 databases not available in the previous version, which allow analysis over a larger, richer set of vocabularies including metabolite–protein and drug–protein interactions. This new version performs automatic conversion of compound identifiers from different databases, thus simplifying usage. In addition, the user interface has been redesigned to generate an interactive, more intuitive representation of the results.
Ionic conduction and relaxation processes in melt compounded poly(ethylene oxide)-lithium perchlorate trihydrate-montmorillonite nanocomposite electrolyte

Polymer nanocomposite electrolyte (PNCE) films comprising complexes of poly(ethylene oxide) (PEO) and lithium perchlorate trihydrate (LiClO 4�3H 2O) filled with nano thickness platelets of montmorillonite (MMT) clay up to 20 wt% concentration of PEO are synthesized by melt compounding hot-pressed technique at 70 o C and 105 o C. Complex dielectric function, electric modulus, alternating current electrical conductivity and impedance behaviour of these PNCE films have been investigated in the frequency range 20 Hz to 1 MHz at ambient temperature. The direct current ionic conductivity of the PNCE films initially increases up to 2 wt% MMT loading and vary anomalously at higher concentrations. The PNCE films synthesized at 105 o C have ionic conductivity nearly one order of magnitude higher than that of synthesized at 70 o C. Relaxation times corresponding to electrode polarization and ionic conduction relaxation processes in the PNCE films are determined from the values of peak frequencies of the dielectric loss tangent and electric modulus loss spectra, respectively. Results confirm that the ionic conductivity of the PNCE films are governed by the PEO chain dynamics, electrode polarization and ionic conduction relaxation times, and also the structures of dispersed exfoliated/intercalated MMT nano platelets in PEO matrix and the material melt compounding temperature.
Change in groundwater chemistry as a consequence of suppression of floods : the case of the Rhine floodplain

Spatio-temporal variations of nitrogen, phosphorus and base cation concentrations in groundwater were related to the drastic change in hydrological conditions of the Rhine alluvial floodplain (Eastern France), which has been disconnected from the river by canalisation. The Groundwater chemistry was studied in two alluvial forests with contrasting hydrological conditions: one in a sector unflooded for 30 years, the second one in a sector still subject to flooding. Nutrient concentrations were measured at two levels, in the root zone (1.5 m depth) and in the gravel below the root layer (4.5 m depth). In the unflooded sector, the average nitrate concentration was significantly lower in the shallow groundwater (2.06 mg l NO3 ) than in the deeper layer (5.84 mg lNO3 ). In contrast, in the flooded sector the nitrate concentrations in the shallow groundwater (5.02 mg l NO3 ) were not significantly different from those in the deep groundwater (3.98 mg l NO3 ). The concentration of phosphate was similar in shallow and deep groundwater in the unflooded sector (46 and 35 mg l, respectively) but significantly lower in the deep groundwater of the flooded sector (47 mg l), than in the shallow groundwater (58 mg l). The major elements (cations: Ca2þ, Mg2þ, Naþ and associated anions: HCO3 , SO4 , Cl) concentrations were significantly higher in the groundwaters than in the surface water. The results are discussed in terms of changes that accompanied suppression of floods, and processes that take place during the transfer of nutrients through the groundwater–soil–plant compartments. The reduction of groundwater fluctuations in the unflooded sector modified the transfer of nitrate by reducing the resolubilisation of locally produced nitrate, and/or denitrification. The transfer of phosphate was affected to a lesser extent, because of precipitation and adsorption. Base cation concentrations reflect exchange between groundwater and the calcareous gravel.
Point-of-care paediatric gastric sonography: can antral cut-off values be used to diagnose an empty stomach?

Background Gastric sonography is emerging as a valuable clinical point-of-care tool to assess aspiration risk. A recent study proposed that a single cut-off cross-sectional area (CSA) in the supine position could diagnose an empty stomach in the parturient. This study establishes the sensitivity and specificity of a single CSA cut-off measurement in both supine and right lateral decubitus (RLD) positions in the diagnosis of an empty antrum in paediatric patients. Methods Following induction of anaesthesia, antral sonography was performed in supine and RLD positions in 100 fasted paediatric patients prior to upper endoscopic evaluation. Following upper endoscopy, any residual stomach content was suctioned under direct visualization and antral sonography was immediately performed. Antral CSA values were compared using Wilcoxon signed rank test. Receiver operator characteristic (ROC) curves were plotted to estimate the discriminating power of antral sonography position in the diagnosis of an empty antrum. Results Significant differences were found between pre-suctioned and post-suctioned CSA values in the RLD position. The cut-off CSAs of the empty antrum in the supine and RLD positions were 2.19 cm2 (sensitivity 75%, specificity 36%) and 3.07 cm2 (sensitivity 76%, specificity 67%), respectively. Conclusions The RLD position produces the most sensitive and specific CSA cut-off value where an antral CSA of ≤ 3.07 cm2 in the RLD position presents with acceptable performance in the ability to discriminate an empty antrum in paediatric patients over 1 yr of age. As age increases, the sensitivity and specificity of this test increases in the RLD position.