An Artificial Neural Network to Eliminate the Detrimental Spectral Shift on Mid-Infrared Gas Spectroscopy.

We demonstrate the successful implementation of an artificial neural network (ANN) to eliminate detrimental spectral shifts imposed in the measurement of laser absorption spectrometers (LASs). Since LASs rely on the analysis of the spectral characteristics of biological and chemical molecules, their accuracy and precision is especially prone to the presence of unwanted spectral shift in the measured molecular absorption spectrum over the reference spectrum. In this paper, an ANN was applied to a scanning grating-based mid-infrared trace gas sensing system, which suffers from temperature-induced spectral shifts. Using the HITRAN database, we generated synthetic gas absorbance spectra with random spectral shifts for training and validation. The ANN was trained with these synthetic spectra to identify the occurrence of spectral shifts. Our experimental verification unambiguously proves that such an ANN can be an excellent tool to accurately retrieve the gas concentration from imprecise or distorted spectra of gas absorption. Due to the global shift of the measured gas absorption spectrum, the accuracy of the retrieved gas concentration using a typical least-mean-squares fitting algorithm was considerably degraded by 40.3%. However, when the gas concentration of the same measurement dataset was predicted by the proposed multilayer perceptron network, the sensing accuracy significantly improved by reducing the error to less than ±1% while preserving the sensing sensitivity.

Suspended Graphene Membranes with Attached Silicon Proof Masses as Piezoresistive Nanoelectromechanical Systems Accelerometers.

Graphene is an atomically thin material that features unique electrical and mechanical properties, which makes it an extremely promising material for future nanoelectromechanical systems (NEMS). Recently, basic NEMS accelerometer functionality has been demonstrated by utilizing piezoresistive graphene ribbons with suspended silicon proof masses. However, the proposed graphene ribbons have limitations regarding mechanical robustness, manufacturing yield, and the maximum measurement current that can be applied across the ribbons. Here, we report on suspended graphene membranes that are fully clamped at their circumference and have attached silicon proof masses. We demonstrate their utility as piezoresistive NEMS accelerometers, and they are found to be more robust, have longer life span and higher manufacturing yield, can withstand higher measurement currents, and are able to suspend larger silicon proof masses, as compared to the previous graphene ribbon devices. These findings are an important step toward bringing ultraminiaturized piezoresistive graphene NEMS closer toward deployment in emerging applications such as in wearable electronics, biomedical implants, and internet of things (IoT) devices.

UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study.

BACKGROUND: Research on orphan crops is often hindered by a lack of genomic resources. With the advent of affordable sequencing technologies, genotyping an entire genome or, for large-genome species, a representative fraction of the genome has become feasible for any crop. Nevertheless, most genotyping-by-sequencing (GBS) methods are geared towards obtaining large numbers of markers at low sequence depth, which excludes their application in heterozygous individuals. Furthermore, bioinformatics pipelines often lack the flexibility to deal with paired-end reads or to be applied in polyploid species. RESULTS: UGbS-Flex combines publicly available software with in-house python and perl scripts to efficiently call SNPs from genotyping-by-sequencing reads irrespective of the species' ploidy level, breeding system and availability of a reference genome. Noteworthy features of the UGbS-Flex pipeline are an ability to use paired-end reads as input, an effective approach to cluster reads across samples with enhanced outputs, and maximization of SNP calling. We demonstrate use of the pipeline for the identification of several thousand high-confidence SNPs with high representation across samples in an F3-derived F2 population in the allotetraploid finger millet. Robust high-density genetic maps were constructed using the time-tested mapping program MAPMAKER which we upgraded to run efficiently and in a semi-automated manner in a Windows Command Prompt Environment. We exploited comparative GBS with one of the diploid ancestors of finger millet to assign linkage groups to subgenomes and demonstrate the presence of chromosomal rearrangements. CONCLUSIONS: The paper combines GBS protocol modifications, a novel flexible GBS analysis pipeline, UGbS-Flex, recommendations to maximize SNP identification, updated genetic mapping software, and the first high-density maps of finger millet. The modules used in the UGbS-Flex pipeline and for genetic mapping were applied to finger millet, an allotetraploid selfing species without a reference genome, as a case study. The UGbS-Flex modules, which can be run independently, are easily transferable to species with other breeding systems or ploidy levels.

Population genetics of Setaria viridis, a new model system.

An extensive survey of the standing genetic variation in natural populations is among the priority steps in developing a species into a model system. In recent years, green foxtail (Setaria viridis), along with its domesticated form foxtail millet (S. italica), has rapidly become a promising new model system for C4 grasses and bioenergy crops, due to its rapid life cycle, large amount of seed production and small diploid genome, among other characters. However, remarkably little is known about the genetic diversity in natural populations of this species. In this study, we survey the genetic diversity of a worldwide sample of more than 200 S. viridis accessions, using the genotyping-by-sequencing technique. Two distinct genetic groups in S. viridis and a third group resembling S. italica were identified, with considerable admixture among the three groups. We find the genetic variation of North American S. viridis correlates with both geography and climate and is representative of the total genetic diversity in this species. This pattern may reflect several introduction/dispersal events of S. viridis into North America. We also modelled demographic history and show signal of recent population decline in one subgroup. Finally, we show linkage disequilibrium decay is rapid (<45 kb) in our total sample and slow in genetic subgroups. These results together provide an in-depth understanding of the pattern of genetic diversity of this new model species on a broad geographic scale. They also provide key guidelines for on-going and future work including germplasm preservation, local adaptation, crossing designs and genomewide association studies.

New genomic regions associated with white mold resistance in dry bean using a MAGIC population.

Dry bean (Phaseolus vulgaris L.) production in many regions is threatened by white mold (WM) [Sclerotinia sclerotiorum (Lib.) de Bary]. Seed yield losses can be up to 100% under conditions favorable for the pathogen. The low heritability, polygenic inheritance, and cumbersome screening protocols make it difficult to breed for improved genetic resistance. Some progress in understanding genetic resistance and germplasm improvement has been accomplished, but cultivars with high levels of resistance are yet to be released. A WM multiparent advanced generation inter-cross (MAGIC) population (n = 1060) was developed to facilitate mapping and breeding efforts. A seedling straw test screening method provided a quick assay to phenotype the population for response to WM isolate 1980. Nineteen MAGIC lines were identified with improved resistance. For genome-wide association studies (GWAS), the data was transformed into three phenotypic distributions-quantitative, polynomial, and binomial-and coupled with ∼52,000 single-nucleotide polymorphisms (SNPs). The three phenotypic distributions identified 30 significant genomic intervals [-log10 (P value) ≥ 3.0]. However, across distributions, four new genomic regions as well as two regions previously reported were found to be associated with resistance. Cumulative R2 values were 57% for binomial distribution using 13 genomic intervals, 41% for polynomial using eight intervals, and 40% for quantitative using 11 intervals. New resistant germplasm as well as new genomic regions associated with resistance are now available for further investigation.

Modified screening method of middle american dry bean genotypes reveals new genomic regions on Pv10 associated with anthracnose resistance.

Anthracnose, caused by the fungal pathogen Colletotrichum lindemuthianum (Sacc. & Magnus) Lams.-Scrib., is one of the most devastating diseases in dry bean (Phaseolus vulgaris L.) with seed yield losses up to 100%. Most anthracnose resistance genes thus far identified behave in a dominant manner and were identified by seedling screening. The Middle American Diversity Panel (MDP; n=266) was screened with a modified greenhouse screening method to evaluate the response to anthracnose race 73. Thirty MDP genotypes exhibited resistance to the race of which 16 genotypes were not known to contain anthracnose resistance genes to race 73. GWAS with ~93,000 SNP markers identified four genomic regions, two each on Pv01 and Pv10, associated race 73 resistance. A likelihood-ratio-based R2 analysis indicated the peak four SNP markers are responsible for 26% of the observed phenotypic variation, where one SNP, S10_072250, explains 23% of the total variation. SNP S10_072250 is associated with a new region of anthracnose resistance and is in an intron of a ZPR1-like gene. Further greenhouse testing of the 16 resistant lines without previously known resistance to race 73 revealed various levels of resistance under various levels of disease pressure. Disease resistance was further characterized in the field using four representative genotypes. GTS-900 and Remington exhibited field resistance while Merlot and Maverick were susceptible. Field testing with two different fungicide regimes revealed the resistant genotypes had no significant disease differences. The results suggest resistance to anthracnose may differ at various growth stages and that breeders have been selecting for major genes at early seedling stages while ignoring the effect of alternative genes that may be active at later stages. The newly identified resistant lines may be related to Age Related Resistance (ARR) and could be exploited as parental sources of anthracnose resistance in addition to already known major genes. The physical localization of the multiple regions of resistance confirms the presence of two clusters of disease resistance genes on Pv01 and identifies two new regions of anthracnose resistance on Pv10 possibly associated with ARR. Future research should look at the mode of inheritance of this resistance and its effect when combined with other anthracnose resistance loci.

A large-area single-filament infrared emitter and its application in a spectroscopic ethanol gas sensing system.

Nondispersive infrared (NDIR) spectroscopy is an important technology for highly accurate and maintenance-free sensing of gases, such as ethanol and carbon dioxide. However, NDIR spectroscopy systems are currently too expensive, e.g., for consumer and automotive applications, as the infrared (IR) emitter is a critical but costly component of these systems. Here, we report on a low-cost large-area IR emitter featuring a broadband emission spectrum suitable for small NDIR gas spectroscopy systems. The infrared emitter utilizes Joule heating of a Kanthal (FeCrAl) filament that is integrated in the base substrate using an automated high-speed wire bonding process, enabling simple and rapid formation of a long meander-shaped filament. We describe the critical infrared emitter characteristics, including the effective infrared emission spectrum, thermal frequency response, and power consumption. Finally, we integrate the emitter into a handheld breath alcohol analyzer and show its operation in both laboratory and real-world settings, thereby demonstrating the potential of the emitter for future low-cost optical gas sensor applications.

Site-specific analysis of N-linked oligosaccharides of recombinant lysosomal arylsulfatase A produced in different cell lines.

Metachromatic leukodystrophy (MLD) is a lysosomal storage disease caused by a deficiency of the lysosomal enzyme arylsulfatase A (ASA). Enzyme replacement therapy (ERT) is a therapeutic option for MLD and other lysosomal disorders. This therapy depends on N-linked oligosaccharide-mediated delivery of intravenously injected recombinant enzyme to the lysosomes of patient cells. Because of the importance of N-linked oligosaccharide side chains in ERT, we examined the composition of the three N-linked glycans of four different recombinant ASAs in a site-specific manner. Depending on the culture conditions and the cell line expressing the enzyme, we detected a high variability of the high-mannose-type N-glycans which prevail at all glycosylation sites. Our data show that the composition of the glycans is largely determined by substantial trimming in the medium. The susceptibility for trimming is different for the glycans at the three N-glycosylation sites. Interestingly, which of the glycans is most susceptible to trimming also depends on production conditions. CHO cells cultured under bioreactor conditions yielded recombinant ASA with the most preserved N-glycan structures, the highest mannose-6-phosphate content and the highest similarity to non-recombinant enzyme. Notably, roughly one-third of the N-glycans released from the three glycosylation sites were fucosylated. In the last years, numerous recombinant lysosomal enzymes were used for preclinical ERT trials. Our data show that the oligosaccharide structures were very different in these trials making it difficult to draw common conclusions from the various investigations.

Manufacture and characterization of graphene membranes with suspended silicon proof masses for MEMS and NEMS applications.

Graphene's unparalleled strength, chemical stability, ultimate surface-to-volume ratio and excellent electronic properties make it an ideal candidate as a material for membranes in micro- and nanoelectromechanical systems (MEMS and NEMS). However, the integration of graphene into MEMS or NEMS devices and suspended structures such as proof masses on graphene membranes raises several technological challenges, including collapse and rupture of the graphene. We have developed a robust route for realizing membranes made of double-layer CVD graphene and suspending large silicon proof masses on membranes with high yields. We have demonstrated the manufacture of square graphene membranes with side lengths from 7 µm to 110 µm, and suspended proof masses consisting of solid silicon cubes that are from 5 µm × 5 µm × 16.4 µm to 100 µm × 100 µm × 16.4 µm in size. Our approach is compatible with wafer-scale MEMS and semiconductor manufacturing technologies, and the manufacturing yields of the graphene membranes with suspended proof masses were >90%, with >70% of the graphene membranes having >90% graphene area without visible defects. The measured resonance frequencies of the realized structures ranged from tens to hundreds of kHz, with quality factors ranging from 63 to 148. The graphene membranes with suspended proof masses were extremely robust, and were able to withstand indentation forces from an atomic force microscope (AFM) tip of up to ~7000 nN. The proposed approach for the reliable and large-scale manufacture of graphene membranes with suspended proof masses will enable the development and study of innovative NEMS devices with new functionalities and improved performances.

Genetic Architecture of Flooding Tolerance in the Dry Bean Middle-American Diversity Panel.

Flooding is a devastating abiotic stress that endangers crop production in the twenty-first century. Because of the severe susceptibility of common bean (Phaseolus vulgaris L.) to flooding, an understanding of the genetic architecture and physiological responses of this crop will set the stage for further improvement. However, challenging phenotyping methods hinder a large-scale genetic study of flooding tolerance in common bean and other economically important crops. A greenhouse phenotyping protocol was developed to evaluate the flooding conditions at early stages. The Middle-American diversity panel (n = 272) of common bean was developed to capture most of the diversity exits in North American germplasm. This panel was evaluated for seven traits under both flooded and non-flooded conditions at two early developmental stages. A subset of contrasting genotypes was further evaluated in the field to assess the relationship between greenhouse and field data under flooding condition. A genome-wide association study using ~150 K SNPs was performed to discover genomic regions associated with multiple physiological responses. The results indicate a significant strong correlation (r > 0.77) between greenhouse and field data, highlighting the reliability of greenhouse phenotyping method. Black and small red beans were the least affected by excess water at germination stage. At the seedling stage, pinto and great northern genotypes were the most tolerant. Root weight reduction due to flooding was greatest in pink and small red cultivars. Flooding reduced the chlorophyll content to the greatest extent in the navy bean cultivars compared with other market classes. Races of Durango/Jalisco and Mesoamerica were separated by both genotypic and phenotypic data indicating the potential effect of eco-geographical variations. Furthermore, several loci were identified that potentially represent the antagonistic pleiotropy. The GWAS analysis revealed peaks at Pv08/1.6 Mb and Pv02/41 Mb that are associated with root weight and germination rate, respectively. These regions are syntenic with two QTL reported in soybean (Glycine max L.) that contribute to flooding tolerance, suggesting a conserved evolutionary pathway involved in flooding tolerance for these related legumes.

Piezoresistive Properties of Suspended Graphene Membranes under Uniaxial and Biaxial Strain in Nanoelectromechanical Pressure Sensors.

Graphene membranes act as highly sensitive transducers in nanoelectromechanical devices due to their ultimate thinness. Previously, the piezoresistive effect has been experimentally verified in graphene using uniaxial strain in graphene. Here, we report experimental and theoretical data on the uni- and biaxial piezoresistive properties of suspended graphene membranes applied to piezoresistive pressure sensors. A detailed model that utilizes a linearized Boltzman transport equation describes accurately the charge-carrier density and mobility in strained graphene and, hence, the gauge factor. The gauge factor is found to be practically independent of the doping concentration and crystallographic orientation of the graphene films. These investigations provide deeper insight into the piezoresistive behavior of graphene membranes.

Resistive graphene humidity sensors with rapid and direct electrical readout.

We demonstrate humidity sensing using a change of the electrical resistance of single-layer chemical vapor deposited (CVD) graphene that is placed on top of a SiO2 layer on a Si wafer. To investigate the selectivity of the sensor towards the most common constituents in air, its signal response was characterized individually for water vapor (H2O), nitrogen (N2), oxygen (O2), and argon (Ar). In order to assess the humidity sensing effect for a range from 1% relative humidity (RH) to 96% RH, the devices were characterized both in a vacuum chamber and in a humidity chamber at atmospheric pressure. The measured response and recovery times of the graphene humidity sensors are on the order of several hundred milliseconds. Density functional theory simulations are employed to further investigate the sensitivity of the graphene devices towards water vapor. The interaction between the electrostatic dipole moment of the water and the impurity bands in the SiO2 substrate leads to electrostatic doping of the graphene layer. The proposed graphene sensor provides rapid response direct electrical readout and is compatible with back end of the line (BEOL) integration on top of CMOS-based integrated circuits.

Contactless operating table control based on 3D image processing.

Interaction with mobile consumer devices leads to a higher acceptance and affinity of persons to natural user interfaces and perceptional interaction possibilities. New interaction modalities become accessible and are capable to improve human machine interaction even in complex and high risk environments, like the operation room. Here, manifold medical disciplines cause a great variety of procedures and thus staff and equipment. One universal challenge is to meet the sterility requirements, for which common contact-afflicted remote interfaces always pose a potential risk causing a hazard for the process. The proposed operating table control system overcomes this process risk and thus improves the system usability significantly. The 3D sensor system, the Microsoft Kinect, captures the motion of the user, allowing a touchless manipulation of an operating table. Three gestures enable the user to select, activate and manipulate all segments of the motorised system in a safe and intuitive way. The gesture dynamics are synchronised with the table movement. In a usability study, 15 participants evaluated the system with a system usability score by Broke of 79. This states a high potential for implementation and acceptance in interventional environments. In the near future, even processes with higher risks could be controlled with the proposed interface, while interfaces become safer and more direct.

Molecular phylogeny of the genus Vitis (Vitaceae) based on plastid markers.

PREMISE OF THE STUDY: This work represents the first molecular phylogeny of the economically important genus Vitis, an important genetic resource for breeding in grapevine, Vitis vinifera. • METHODS: A molecular phylogeny of Vitis using a combined data set of three noncoding regions of the plastid DNA genome was constructed from 47 accessions covering 30 species of Vitis. The data for the trnL-F marker were combined with previously published data across the Vitaceae. • KEY RESULTS: The molecular phylogeny demonstrated monophyly of the genus Vitis. Based on the combined analysis of three genes, Vitis is split into three clades that mirror the continental distribution of these accessions. The diversity is highest in the Asian clade, but the general genetic distances across taxa from different continents are relatively small. • CONCLUSIONS: The findings support a relatively recent and intense gene flow between East Asia and North America and the possible impact of hybridization on the evolution of the genus Vitis. Taxon identity in important stock collections should be screened carefully because roughly 10% of the accessions analyzed in the present study had been misidentified.

Enzyme replacement improves nervous system pathology and function in a mouse model for metachromatic leukodystrophy.

A deficiency of arylsulfatase A (ASA) causes the lysosomal storage disease metachromatic leukodystrophy, which is characterized by accumulation of the sphingolipid 3-O-sulfogalactosylceramide (sulfatide). Sphingolipid storage results in progressive demyelination and severe neurologic symptoms. The disease is lethal, and curative therapy is not available. To assess the therapeutic potential of enzyme replacement therapy (ERT), ASA knockout mice were treated by intravenous injection of recombinant human ASA. Plasma levels of ASA declined with a half-time of approximately 40 min, and enzyme was detectable in tissues within minutes after injection. The uptake of injected enzyme was high into liver, moderate into peripheral nervous system (PNS) and kidney and very low into brain. The apparent half-life of endocytosed enzyme was approximately 4 days. A single injection led to a time- and dose-dependent decline of the excess sulfatide in PNS and kidney by up to 70%, but no reduction was seen in brain. Four weekly injections with 20 mg/kg body weight not only reduced storage in peripheral tissues progressively, but also were surprisingly effective in reducing sulfatide storage in brain and spinal cord. The histopathology of kidney and central nervous system was ameliorated. Improved neuromotor coordination capabilities and normalized peripheral compound motor action potential demonstrate the benefits of ERT on the nervous system function. Enzyme replacement may therefore be a promising therapeutic option in this devastating disease.

Derivatization of phosphorylated peptides with S- and N-nucleophiles for enhanced ionization efficiency in matrix-assisted laser desorption/ionization mass spectrometry.

The identification of phosphorylation sites is essential for a full understanding of the cellular functions of proteins. However, mass spectrometric analysis is often hampered by the low abundance of phosphoproteins, the difficulty of obtaining full sequence coverage by specific proteolysis reactions, and the low ionization efficiency of phosphopeptides compared with their non-phosphorylated analogs. In the present work a beta-elimination/Michael addition was used to replace the phosphate groups of pSer or pThr by a group which gives rise to an enhanced ionization efficiency. In order to find optimum reaction conditions, beta-elimination/Michael addition was examined using phosphorylated model peptides. Whereas complete elimination of phosphate could be achieved by treatment with barium hydroxide in organic solvents such as ethanol or acetonitrile, the yield of the Michael adduct strongly depended on the nucleophile and the peptide sequence. Reaction with 2-phenylethanethiol, p-bromophenethylamine and ethylenediamine clearly resulted in products showing higher matrix-assisted laser desorption/ionization (MALDI) signal intensities compared with those of the corresponding phosphorylated precursors. The method was successfully used to identify phosphorylated sequences of ovalbumin and human Stat1 by in-gel derivatization with 2-phenylethanethiol and subsequent peptide mass fingerprint analysis of the trypsin digests.