Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution.

The gap between the amount of genome information released by genome sequencing projects and our knowledge about the proteins' functions is rapidly increasing. To fill this gap, various 'genomic-context' methods have been proposed that exploit sequenced genomes to predict the functions of the encoded proteins. One class of methods, phylogenetic profiling, predicts protein function by correlating the phylogenetic distribution of genes with that of other genes or phenotypic characteristics. The functions of a number of proteins, including ones of medical relevance, have thus been predicted and subsequently confirmed experimentally. Additionally, various approaches to measure the similarity of phylogenetic profiles and to account for the phylogenetic bias in the data have been proposed. We review the successful applications of phylogenetic profiling and analyse the performance of various profile similarity measures with a set of one microsporidial and 25 fungal genomes. In the fungi, phylogenetic profiling yields high-confidence predictions for the highest and only the highest scoring gene pairs illustrating both the power and the limitations of the approach. Both practical examples and theoretical considerations suggest that in order to get a reliable and specific picture of a protein's function, results from phylogenetic profiling have to be combined with other sources of evidence.     

Synergetic nanowire growth

Interest in nanowires continues to grow because they hold the promise of monolithic integration of high-performance semiconductors with new functionality into existing silicon technology. Most nanowires are grown using vapour-liquid-solid growth, and despite many years of study this growth mechanism remains under lively debate. In particular, the role of the metal particle is unclear. For instance, contradictory results have been reported on the effect of particle size on nanowire growth rate. Additionally, nanowire growth from a patterned array of catalysts has shown that small wire-to-wire spacing leads to materials competition and a reduction in growth rates. Here, we report on a counterintuitive synergetic effect resulting in an increase of the growth rate for decreasing wire-to-wire distance. We show that the growth rate is proportional to the catalyst area fraction. The effect has its origin in the catalytic decomposition of precursors and is applicable to a variety of nanowire materials and growth techniques.     

Simultaneous quantitative analysis of metabolites using ion-pair liquid chromatography-electrospray ionization mass spectrometry

We have developed an analytical method, consisting of ion-pair liquid chromatography coupled to electrospray ionization mass spectrometry (IP-LC-ESI-MS), for the simultaneous quantitative analysis of several key classes of polar metabolites, like nucleotides, coenzyme A esters, sugar nucleotides, and sugar bisphosphates. The use of the ion-pair agent hexylamine and optimization of the pH of the mobile phases were critical parameters in obtaining good retention and peak shapes of many of the above-mentioned polar and acidic metabolites that are impossible to analyze using standard reversed-phase LC/MS. Optimum conditions were found when using a gradient from 5 mM hexylamine in water (pH 6.3) to 90% methanol/10% 10 mM ammonium acetate (pH 8.5). The IP-LC-ESI-MS method was extensively validated by determining the linearity (R2 > 0.995), sensitivity (limit of detection 0.1-1 ng), repeatability, and reproducibility (relative standard deviation <10%). The IP-LC-ESI-MS method was shown to be a useful tool for microbial metabolomics, i.e., the comprehensive quantitative analysis of metabolites in extracts of microorganisms, and for the determination of the energy charge, i.e., the cellular energy status, as an overall quality measure for the sample workup and analytical protocols.     

A global model for residential energy use: Uncertainty in calibration to regional data

Uncertainties in energy demand modelling allow for the development of different models, but also leave room for different calibrations of a single model. We apply an automated model calibration procedure to analyse calibration uncertainty of residential sector energy use modelling in the TIMER 2.0 global energy model. This model simulates energy use on the basis of changes in useful energy intensity, technology development (AEEI) and price responses (PIEEI). We find that different implementations of these factors yield behavioural model results. Model calibration uncertainty is identified as influential source for variation in future projections: amounting 30% to 100% around the best estimate. Energy modellers should systematically account for this and communicate calibration uncertainty ranges.     

Concentration of phenolic compounds from apple pomace extracts by nanofiltration at lab and pilot scale with a techno‐economic assessment

Apple pomace can be used as resource for the extraction of phenolic compounds with antioxidant properties. Pressing of apple in juice and pomace at lab scale in open air (aerobic) and under N₂ atmosphere (anaerobic) showed a recovery of phenolic compounds of 85% in juice and pomace after anaerobic pressing, compared to 43% after aerobic pressing, indicating loss of phenolic compounds by oxidation and the advantage of anaerobic over aerobic pressing. After a membrane screening and concentration test at lab scale, the commercial nanofiltration membrane NFX was selected to concentrate phenolic compounds in an ethanol : water extract of apple pomace. At pilot scale, the concencentration of 10 selected phenolic compounds and quinic acid increased from 59.5 mg/L in the ethanol : water extract to 1256.1 mg/L in the final retentate, that is, by a factor 21.1. The volume of the crude extract was reduced by a factor of 28.5 during the filtration, indicating some loss of phenolic compounds during pilot testing due to membrane fouling or oxidation of polyphenols. The pilot concentration test using a spiral‐wound membrane module showed good flux and concentration of phenolic compounds, indicating the technical feasibility of membrane technology for efficient concentration of polyphenols in an ethanol : water extraction solvent. Unfortunately, the extraction and concentration process was not economically feasible under the assumptions made.

Practical applications

The valorization of food waste for the production of high‐added value products is an increasingly hot topic. Phytochemicals are present in relatively low concentration in the fruit matrix, and concentration in the extraction solvent is necessary to develop an industrially relevant process. In this study, membrane filtration was selected for concentration due to its low energy consumption and mild processing conditions compared to other technologies. Membrane screening and testing at lab and pilot scale with techno‐economic assessment can be used by food and nutraceutical industries to evaluate membrane technology for concentration of phytochemicals extracted from agroindustrial by‐products.     

临时博物馆

精选理由这是一个单层的临时博物馆建筑。其柔和、细腻的流线形外观,抽象自湖水水流形成的轮廓。设计师让博物馆置于大面积的绿地当中,其略显瘦小的体量巧妙地融入到周围环境之中。建筑采用了未经处理的木材,其质地和色彩更赋予了建筑一种柔美和温婉。     

Effect of intrauterine dextrose or antibiotic therapy on reproductive performance of lactating dairy cows diagnosed with clinical endometritis

The objectives of this study were to assess the responses to treatments (clinical cure and cow survival 14 d posttherapy) of cows with clinical endometritis (CE) that received intrauterine infusion of a hypertonic solution of 50% dextrose (DEX) or subcutaneous ceftiofur crystalline free acid (CCFA) and subsequent pregnancy per artificial insemination (P/AI) in cows with CE compared with cows without CE. Cows (n=760) from 2 dairy herds were screened for CE using vaginoscopy and measurement of cervix diameters [exam 1; 26±3 d in milk (DIM)]. Cows with vaginal discharge scores of 2 or 3 (scale 0-3) were stratified by parity and randomly allocated into 1 of 3 treatment groups: (1) intrauterine infusion (～200 mL) of 50% DEX solution (n=79); (2) 6.6 mg/kg single-dose of subcutaneous administration of CCFA (n=75); or (3) untreated control animals (CON, n=83). Fourteen days posttherapy (at 40±3 DIM), cows with CE were re-examined (exam 2; 40±3 DIM) to assess the response to treatments. All cows were presynchronized with 2 injections of PGF(2α) given 14 d apart (starting at 26±3 DIM) followed by Ovsynch (OV; GnRH-7 d-PGF-56 h-GnRH 16 h-timed-AI) 12 to 14 d later. Cows displaying signs of standing estrus any time during the protocol were inseminated, whereas the remaining cows were subjected to timed AI 16 h after the second GnRH of OV. Pregnancy diagnosis was performed via transrectal ultrasonography at 39±3d post-AI followed by pregnancy reconfirmation 30 d after the first pregnancy diagnosis. Uterine swabs revealed that Arcanobacterium pyogenes and Escherichia coli were the most predominant bacteria isolated at the time of treatments. Mortality within 14 d posttherapy was not different among treatment groups. Cows with CE had greater cervical diameter at exam 1 and decreased P/AI compared with cows without CE. Treatment with CCFA or DEX increased the proportion of cows with clear vaginal discharge (score 0; clinical cure) 14 d posttherapy compared with CON cows. Pregnancy per AI from DEX (29.8±4%) cows tended to differ from that of CON (21.1±4%) or CCFA cows (19.7±4%), but it resulted in similar P/AI as those cows without CE (39.1±2%). The use of intrauterine DEX alone or as an adjunct of antibiotic therapy for the treatment of CE needs further investigation.     

Complementary integrated circuits on plastic foil using inkjet printed n- and p-type organic semiconductors: Fabrication,characterization, and circuit analysis

Complementary thin-film transistor circuits composed of 6,13-bis(triisopropyl-silylethynyl) pentacene (TIPS–PEN) and a rylene carboxylic diimide derivative for p- and n-channel thin-film transistors (TFTs) were fabricated on flexible foils. The so-called staggered TFT configuration is used, meaning that the semiconductors layers are deposited last. The work-function of the injecting gold electrodes were modified using several self-assembled monolayers (SAMs). For optimized contacts the mobility of the n- and p-channel TFTs was 0.5 cm²/Vs and 0.2 cm²/Vs, respectively. Strongly degraded performance is obtained when the n-channel material was printed on contacts optimized for the p-channel TFT, and vice versa. This illustrates that for CMOS circuits we need careful work-function engineering to allow proper injection for both electrons and holes. We show for the first time that by using a bimolecular mixture for the SAM we can systematically vary the work function, and demonstrate how this affects the performance of discrete n-type and p-type transistors, as well as CMOS inverters and ring oscillators. Under optimal processing conditions we realized complementary 19-stage ring oscillators with 10 μs stage delay operating at 20 V.