bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome analysis of a thermophilic exopolysaccharide-producing bacterium - Geobacillus sp. WSUCF1
Authors: Wang Jia , Goh Kian Mau , Salem David R. , Sani Rajesh K.
Published: February 2019

Geobacillus sp. WSUCF1 is a Gram-positive, spore-forming, aerobic and thermophilic bacterium, isolated from a soil sample obtained from a compost facility. Strain WSUCF1 demonstrated EPS producing capability using different sugars as the carbon source. The whole-genome analysis of WSUCF1 was performed to disclose the essential genes correlated with nucleotide sugar precursor biosynthesis, assembly of monosaccharide units, export of the polysaccharide chain, and regulation of EPS production. Both the biosynthesis pathway and export mechanism of EPS were proposed based on functional annotation. Additionally, the genome description of strain WSUCF1 suggests sophisticated systems for its adaptation under thermophilic conditions. The presence of genes associated with CRISPR-Cas system, quorum quenching lactonase, polyketide synthesis and arsenic resistance makes this strain a potential candidate for various applications in biotechnology and biomedicine. The present study indicates that strain WSUCF1 has promise as a thermophilic EPS producer for a broad range of industrial applications. To the best of our knowledge, this is the first report on genome analysis of a thermophilic Geobacillus species focusing on its EPS biosynthesis and transportation, which will likely pave the way for both enhanced yield and tailor-made EPS production by thermophilic bacteria.
Spectral Weighting Underlies Perceived Sound Elevation
Authors: Zonooz Bahram , Arani Elahe , Körding Konrad P. , Aalbers P. A. T. Remco , Celikel Tansu , Van Opstal A. John
Published: February 2019

The brain estimates the two-dimensional direction of sounds from the pressure-induced displacements of the eardrums. Accurate localization along the horizontal plane (azimuth angle) is enabled by binaural difference cues in timing and intensity. Localization along the vertical plane (elevation angle), including frontal and rear directions, relies on spectral cues made possible by the elevation dependent filtering in the idiosyncratic pinna cavities. However, the problem of extracting elevation from the sensory input is ill-posed, since the spectrum results from a convolution between source spectrum and the particular head-related transfer function (HRTF) associated with the source elevation, which are both unknown to the system. It is not clear how the auditory system deals with this problem, or which implicit assumptions it makes about source spectra. By varying the spectral contrast of broadband sounds around the 6–9 kHz band, which falls within the human pinna’s most prominent elevation-related spectral notch, we here suggest that the auditory system performs a weighted spectral analysis across different frequency bands to estimate source elevation. We explain our results by a model, in which the auditory system weighs the different spectral bands, and compares the convolved weighted sensory spectrum with stored information about its own HRTFs, and spatial prior assumptions.
Searchers adjust their eye-movement dynamics to target characteristics in natural scenes
Authors: Rothkegel Lars O. M. , Schütt Heiko H. , Trukenbrod Hans A. , Wichmann Felix A. , Engbert Ralf
Published: February 2019

When searching a target in a natural scene, it has been shown that both the target’s visual properties and similarity to the background influence whether and how fast humans are able to find it. So far, it was unclear whether searchers adjust the dynamics of their eye movements (e.g., fixation durations, saccade amplitudes) to the target they search for. In our experiment, participants searched natural scenes for six artificial targets with different spatial frequency content throughout eight consecutive sessions. High-spatial frequency targets led to smaller saccade amplitudes and shorter fixation durations than low-spatial frequency targets if target identity was known. If a saccade was programmed in the same direction as the previous saccade, fixation durations and successive saccade amplitudes were not influenced by target type. Visual saliency and empirical fixation density at the endpoints of saccades which maintain direction were comparatively low, indicating that these saccades were less selective. Our results suggest that searchers adjust their eye movement dynamics to the search target efficiently, since previous research has shown that low-spatial frequencies are visible farther into the periphery than high-spatial frequencies. We interpret the saccade direction specificity of our effects as an underlying separation into a default scanning mechanism and a selective, target-dependent mechanism.
Perceived regularity of a texture is influenced by the regularity of a surrounding texture
Authors: Sun Hua-Chun , Kingdom Frederick A. A. , Baker Curtis L.
Published: February 2019

Previous studies have shown that texture regularity is adaptable, and have suggested that texture regularity might be coded by the peakedness of the underlying spatial frequency distribution. Here we demonstrate the related phenomenon of simultaneous regularity contrast (SRC), in which the perceived regularity of a central texture is influenced by the regularity of a surrounding texture. We presented center-surround arrangements of textures and measured the perceived regularity of the centre, using a centre-only comparison stimulus and a 2AFC procedure. From the resulting psychometric functions the SRC was measured as the difference between test and comparison regularity at the PSE (point of subjective equality). Observers generally exhibited asymmetric bidirectional SRC, in that more regular surrounds decreased the perceived regularity of the centre by between 20–40%, while less regular surrounds increased the perceived regularity of the centre by about 10%. Consistent with previous studies, a wavelet spatial frequency (SF) analysis of the stimuli revealed that their SF distributions became sharper with increased regularity, and therefore that distribution statistics such as kurtosis and SF bandwidth might be used to code regularity.
Three ancient documents solve the jigsaw of the parchment purple spot deterioration and validate the microbial succession model
Authors: Migliore Luciana , Perini Nicoletta , Mercuri Fulvio , Orlanducci Silvia , Rubechini Alessandro , Thaller Maria Cristina
Published: February 2019

The preservation of cultural heritage is one of the major challenges of today’s society. Parchments, a semi-solid matrix of collagen produced from animal skin, are a significant part of the cultural heritage, being used as writing material since ancient times. Due to their animal origin, parchments easily undergo biodeterioration: the most common biological damage is characterized by isolated or coalescent purple spots, that often lead to the detachment of the superficial layer and the consequent loss of written content. Although many parchments with purple spot biodegradative features were studied, no common causative agent had been identified so far. In a previous study a successional model has been proposed, basing on the multidisciplinary analysis of damaged versus undamaged samples from a moderately damaged document. Although no specific sequences were observed, the results pointed to Halobacterium salinarum as the starting actor of the succession. In this study, to further investigate this topic, three dramatically damaged parchments were analysed; belonging to a collection archived as Faldone Patrizi A 19, and dated back XVI-XVII century A.D. With the same multidisciplinary approach, the Next Generation Sequencing (NGS, Illumina platform) revealed DNA sequences belonging to Halobacterium salinarum; the RAMAN spectroscopy identified the pigment within the purple spots as haloarchaeal bacterioruberin and bacteriorhodopsine, and the LTA technique quantified the extremely damaged collagen structures through the entire parchments, due to the biological attack to the parchment frame structures. These results allowed to propose a model of the progressive degradation pattern of the parchment collagen. Overall, these data validate a multi-phase microbial succession model. This demonstration is pivotal to possible new restoration strategies, important for a huge number of ancient documents.
Increased biosynthesis and accumulation of cholesterol in maternal plasma, but not amniotic fluid in pre-eclampsia
Authors: Lee Seung Mi , Moon Ju-Yeon , Lim Byeong-Yun , Kim Sun Min , Park Chan-Wook , Kim Byoung Jae , Jun Jong Kwan , Norwitz Errol R. , Choi Man Ho , Park Joong Shin
Published: February 2019

Preeclampsia is one of the most serious complications during pregnancy, defined as development of hypertension during late pregnancy affecting other organ systems (proteinuria, thrombocytopenia, renal insufficiency, liver involvement, cerebral symptoms or pulmonary edema). Preeclampsia is known to be associated with significant dyslipidemia, but the cause or mechanism of this metabolic aberration is not clear. Quantitative analysis of cholesterol precursors and metabolites can reveal metabolic signatures of cholesterol, and provide insight into cholesterol biosynthetic and degradation pathways. We undertook this study to compare the metabolic signatures of cholesterol in serum and amniotic fluid collected from women who delivered in the late preterm period. Matching serum and amniotic fluid samples were collected from women who delivered in the late preterm period (34-0/7–36-6/7 weeks), had undergone amniocentesis within 3 days of delivery, had no evidence of rupture of membranes or intra-amniotic infection/inflammation, and who had not received antenatal corticosteroid prior to amniocentesis. Patients were classified into 3 groups according to the etiology of their preterm birth: Group 1, preeclampsia; Group 2, spontaneous preterm labor; Group 3, other maternal medical indications for iatrogenic preterm birth. Quantitative metabolite profiling of cholesterols was performed using gas chromatography-mass spectrometry. A total of 39 women were included in the analysis (n = 14 in Group 1, n = 16 in Group 2, n = 9 in Group 3). In maternal blood, patients in Group 1 had significantly higher ratios of cholesterol/desmosterol and cholesterol/7-dehydrocholesterol (which represent 24- and 7-reductase enzyme activity, respectively) than those in Group 3 (p < 0.05 for each), which suggests increased cholesterol biosynthesis. In contrast, patients in Group 1 had significantly decreased ratios of individual cholesterol esters/cholesterol and total cholesterol esters/cholesterol than those in Groups 3 (p < 0.01 for each), suggesting increased reverse cholesterol transport. No differences in cholesterol ratios were found in amniotic fluid among the 3 groups. In conclusion, the metabolic signatures of cholesterol suggest increased cholesterol biosynthesis and accumulation in the maternal blood (but not amniotic fluid) of women with preeclampsia.
Neuronal correlates of label facilitated tactile perception
Authors: Schmidt Timo Torsten , Miller Tally McCormick , Blankenburg Felix , Pulvermüller Friedemann
Published: February 2019

It is a long-standing question in neurolinguistics, to what extent language can have a causal effect on perception. A recent behavioural study reported that participants improved their discrimination ability of Braille-like tactile stimuli after one week of implicit association training with language stimuli being co-presented redundantly with the tactile stimuli. In that experiment subjects were exposed twice a day for 1 h to the joint presentation of tactile stimuli presented to the fingertip and auditorily presented pseudowords. Their discrimination ability improved only for those tactile stimuli that were consistently paired with pseudowords, but not for those that were discordantly paired with different pseudowords. Thereby, a causal effect of verbal labels on tactile perception has been demonstrated under controlled laboratory conditions. This raises the question as to what the neuronal mechanisms underlying this implicit learning effect are. Here, we present fMRI data collected before and after the aforementioned behavioral learning to test for changes in brain connectivity as the underlying mechanism of the observed behavioral effects. The comparison of pre- and post-training revealed a language-driven increase in connectivity strength between auditory and secondary somatosensory cortex and the hippocampus as an association-learning related region.
Evolutionary Approach of Intrinsically Disordered CIP/KIP Proteins
Authors: Fahmi Muhamad , Ito Masahiro
Published: February 2019

The mammalian CIP/KIP family proteins are intrinsically disordered proteins (IDPs) that can regulate various cellular processes. However, many reports have shown that IDPs generally evolve more rapidly than ordered proteins. Here, to elucidate the functional adaptability of CIP/KIP proteins in vertebrate, we analysed the rates of evolution in relation to their structural and sequence properties and predicted the post-translational modification based on the sequence data. The results showed that CIP/KIP proteins generally could maintain their function through evolution in the vertebrate. Basically, the disordered region that acts as a flexible linker or spacer has a conserved propensity for structural disorder and a persistent, fast rate of amino acid substitution, which could result in a significantly faster rate of evolution compared to the ordered proteins. Describing the pattern of structural order-disorder evolution, this study may give an insight into the well-known characteristics of IDPs in the evolution of CIP/KIP proteins.
Peroxidase-like activity of magnetic poly(glycidyl methacrylate-co-ethylene dimethacrylate) particles
Authors: Zasońska Beata A. , Šálek Petr , Procházková Jitka , Müllerová Sindy , Svoboda Jan , Petrovský Eduard , Proks Vladimír , Horák Daniel , Šafařík Ivo
Published: February 2019

Poly(glycidyl methacrylate) (PGMA) is prone to modifications with different functional groups, magnetic fluids or direct coupling with biological molecules. The purpose of this research was to synthesize new magnetically responsive particles with peroxidase-like activity. Poly(glycidyl methacrylate-co-ethylene dimethacrylate) [P(GMA-EDMA)] particles containing carboxyl groups were obtained by emulsifier-free emulsion polymerization and hydrolysis and oxidation of PGMA with KMnO4, resulting in poly(carboxymethyl methacrylate-co-ethylene dimethacrylate) [P(CMMA-EDMA)] particles. Thionine (Th) was also attached to the particles [(P(CMMA-EDMA)-Th] via EDC/NHS chemistry to observe its effect on electron transfer during the oxidation reaction. Finally, the particles were coated with a nitric acid-stabilized ferrofluid in methanol. The resulting magnetic particles were characterized by several methods, including scanning and transmission electron microscopy, X-ray photoelectron spectroscopy, and vibrating sample magnetometry. The effect of EDMA on the P(CMMA-EDMA) particle size and size distribution was investigated; the particle size changed from 300 to 340 nm, and the particles were monodispersed with a saturation magnetization of 11 Am2/kg. Finally, the effects of temperature and pH on the peroxidase-like activity of the magnetic P(CMMA-EDMA) and P(CMMA-EDMA)-Th particles were investigated. The particles, which exhibited a high activity at pH 4–6 and at ∼37 °C, represent a highly sensitive sensor component potentially useful in enzyme-based immunoassays.
Effects of electrostatic environment on the electrically triggered production of entangled photon pairs from droplet epitaxial quantum dots
Authors: Ramírez Hanz Y. , Chou Ying-Lin , Cheng Shun-Jen
Published: February 2019

Entangled photon pair generation is a crucial task for development of quantum information based technologies, and production of entangled pairs by biexciton cascade decays in semiconductor quantum dots is so far one of the most advanced techniques to achieve it. However, its scalability toward massive implementation requires further understanding and better tuning mechanisms to suppress the fine structure splitting between polarized exciton states, which persists as a major obstacle for entanglement generation from most quantum dot samples. In this work, the influence of electrostatic environment arising from electrically biased electrodes and/or charged impurities on the fine structure splitting of GaAs/AlGaAs droplet epitaxial quantum dots is studied, by means of numerical simulations considering a realistic quantum dot confining potential and electron-hole exchange interaction within a multiband k · p framework. We find that reduction of the fine structure splitting can be substantially optimized by tilting the field and seeding impurities along the droplet elongation axis. Furthermore, our results provide evidence of how the presence of charged impurities and in-plane bias components, may account for different degrees of splitting manipulation in dots with similar shape, size and growth conditions.
Risk assessment of personal exposure to polycyclic aromatic hydrocarbons and aldehydes in three commercial cooking workplaces
Authors: Wu Ming-Tsang , Lin Pei-Chen , Pan Chih-Hong , Peng Chiung-Yu
Published: February 2019

Cooking-related emissions are associated with environmental pollution and adverse health effects. Of the various chemical species emitted during cooking, polycyclic aromatic hydrocarbons (PAHs) and aldehydes are two chemical species with carcinogenic or tumor promoting characteristics. Although PAH exposure has been studied in commercial kitchen workers, few studies have investigated simultaneous exposure to PAHs and aldehydes in these workers. The aims of this study were to compare personal concentrations of PAH and aldehyde in three commercial cooking workplaces and to estimate their corresponding cancer risks. The three cooking workplaces included western fast food restaurant kitchens, Chinese cafeteria kitchens, and street food carts. Comparisons showed that workers in western fast food restaurant kitchens and Chinese cafeteria kitchens tended to have lower personal concentrations of these pollutants compared to workers in street food carts. The geometric mean (95% CI) cancer risks in the three workplaces were, from lowest to highest, 1.36 (1.12–1.67) × 10−5 for western fast food restaurant kitchens, 1.52 (1.01–2.28) × 10−5 for Chinese cafeteria kitchens, and 3.14 (2.45–4.01) × 10−5 for street food carts. The percentage contributions of aldehyde species to cancer risk were very high (74.9–99.7%). Street food cart workers had high personal exposure to aldehyde probably due to lack of effective exhaust systems. Thus, their cancer risk was significantly higher than those of workers in western fast food restaurant kitchens (p < 0.001) and Chinese cafeteria kitchens (p = 0.013).
miPIE: NGS-based Prediction of miRNA Using Integrated Evidence
Authors: Peace R. J. , Sheikh Hassani M. , Green J. R.
Published: February 2019

Methods for the de novo identification of microRNA (miRNA) have been developed using a range of sequence-based features. With the increasing availability of next generation sequencing (NGS) transcriptome data, there is a need for miRNA identification that integrates both NGS transcript expression-based patterns as well as advanced genomic sequence-based methods. While miRDeep2 does examine the predicted secondary structure of putative miRNA sequences, it does not leverage many of the sequence-based features used in state-of-the-art de novo methods. Meanwhile, other NGS-based methods, such as miRanalyzer, place an emphasis on sequence-based features without leveraging advanced expression-based features reflecting miRNA biosynthesis. This represents an opportunity to combine the strengths of NGS-based analysis with recent advances in de novo sequence-based miRNA prediction. We here develop a method, microRNA Prediction using Integrated Evidence (miPIE), which integrates both expression-based and sequence-based features to achieve significantly improved miRNA prediction performance. Feature selection identifies the 20 most discriminative features, 3 of which reflect strictly expression-based information. Evaluation using precision-recall curves, for six NGS data sets representing six diverse species, demonstrates substantial improvements in prediction performance compared to three methods: miRDeep2, miRanalyzer, and mirnovo. The individual contributions of expression-based and sequence-based features are also examined and we demonstrate that their combination is more effective than either alone.
From waste to surface modification of aluminum bronze using selective surface diffusion process
Authors: Singla Isha , Kumar Himanish , Pahlevani Farshid , Handoko Wilson , Cholake Sagar T. , Hossain Rumana , Sahajwalla Veena
Published: February 2019

When corrosion is the dominant failure factor in industrial application and at the same time high mechanical properties are required, aluminum bronze is one of the best candidates. Hence, there is a continuous quest for increasing the lifetime of aluminum bronze alloys through enhancing the abrasion and corrosion resistance. Existing methods are based on modifying the bulk properties of alloy or surface modification which required sophisticated equipment and process control. This approach has limited application for advanced components because of high price and difficulty to apply. In this research, we developed an innovative approach to enhance the corrosion and abrasion resistance of aluminum bronze through selective surface diffusion process. In this process, we have used waste materials as input and the modified surface has formed in a single and green process. New surface structure consists of finely dispersed kappa phase (χ ) in uniform alpha (α) solid solution matrix. Results have demonstrated that this uniform diffused modified surface layer has improved hardness of the base material and both corrosion and abrasion resistance has increased. This novel surface modification technique has opened a pathway for using waste materials as input for surface modification of aluminum bronze to meet the needs of industrial applications in a cost effective and environmentally friendly way.
New Thiol-Sensitive Dye Application for Measuring Oxidative Stress in Cell Cultures
Authors: Puente-Muñoz Virginia , Paredes José M. , Resa Sandra , Vílchez José Damaso , Zitnan Michal , Miguel Delia , Girón María Dolores , Cuerva Juan M. , Salto Rafael , Crovetto Luis
Published: February 2019

A xanthene derivative, Granada Green dinitrobenzene sulfonate (GGDNBS), has been synthesized to assay cellular oxidative stress based on changes in the concentration of biothiols. The dye is able to react with biological thiols by a thiolysis reaction that promotes a change in fluorescence intensity. To demonstrate the usefulness of GGDNBS for in vivo oxidative stress measurements, 661 W photoreceptor-derived cells were exposed to light to induce ROS generation, and changes in GGDNBS fluorescence were measured. In these cells, GGDNBS fluorescence was correlated with the biothiol levels measured by an enzymatic method. Therefore, GGDNBS allows us to monitor changes in the levels of biothiols associated with ROS generation via single-cell bioimaging.
Population connectivity of pelagic megafauna in the Cuba-Mexico-United States triangle
Authors: Rooker Jay R. , Dance Michael A. , Wells R. J. David , Ajemian Matthew J. , Block Barbara A. , Castleton Michael R. , Drymon J. Marcus , Falterman Brett J. , Franks James S. , Hammerschlag Neil , Hendon Jill M. , Hoffmayer Eric R. , Kraus Richard T. , McKinney Jennifer A. , Secor David H. , Stunz Gregory W. , Walter John F.
Published: February 2019

The timing and extent of international crossings by billfishes, tunas, and sharks in the Cuba-Mexico-United States (U.S.) triangle was investigated using electronic tagging data from eight species that resulted in >22,000 tracking days. Transnational movements of these highly mobile marine predators were pronounced with varying levels of bi- or tri-national population connectivity displayed by each species. Billfishes and tunas moved throughout the Gulf of Mexico and all species investigated (blue marlin, white marlin, Atlantic bluefin tuna, yellowfin tuna) frequently crossed international boundaries and entered the territorial waters of Cuba and/or Mexico. Certain sharks (tiger shark, scalloped hammerhead) displayed prolonged periods of residency in U.S. waters with more limited displacements, while whale sharks and to a lesser degree shortfin mako moved through multiple jurisdictions. The spatial extent of associated movements was generally associated with their differential use of coastal and open ocean pelagic ecosystems. Species with the majority of daily positions in oceanic waters off the continental shelf showed the greatest tendency for transnational movements and typically traveled farther from initial tagging locations. Several species converged on a common seasonal movement pattern between territorial waters of the U.S. (summer) and Mexico (winter).
High frequency of CHD7 mutations in congenital hypogonadotropic hypogonadism
Authors: Gonçalves Catarina Inês , Patriarca Filipa Marina , Aragüés José Maria , Carvalho Davide , Fonseca Fernando , Martins Sofia , Marques Olinda , Pereira Bernardo Dias , Martinez-de-Oliveira José , Lemos Manuel Carlos
Published: February 2019

Congenital hypogonadotropic hypogonadism (CHH) is characterized by lack of normal pubertal development due to deficient gonadotropin-releasing hormone (GnRH) secretion or action, and is caused by genetic defects in several genes. Mutations in the CHD7 gene cause CHARGE syndrome (Coloboma of the eye, Heart defects, Atresia of the choanae, Retardation of growth and development, Genital hypoplasia and Ear abnormalities), but have also been found in patients with isolated CHH. The aim of this study was to identify CHD7 mutations in patients with CHH. Fifty Portuguese patients with CHH were screened for mutations in the CHD7 gene by DNA sequencing. Eight (16%) patients had CHD7 rare sequence variants that consisted of six missense (p.Gly388Glu, p.His903Pro, p.Thr1082Ile, p.Val1452Leu, p.Asp1854Gly, and p.Arg2065His) and two synonymous (p.Ser559Ser, and p.Ala2785Ala) mutations. Five of these mutations have never been reported before. Three CHD7 mutations occurred in patients that had mutations in additional CHH-genes. This study uncovered novel genetic variants that expand the known spectrum of mutations associated with CHH. The frequency of CHD7 mutations in this cohort was higher than that of other major CHH-genes and confirms the importance of including CHD7 in the genetic testing of CHH, even in the absence of additional CHARGE features.
Role of selenium addition to CdZnTe matrix for room-temperature radiation detector applications
Authors: Roy U. N. , Camarda G. S. , Cui Y. , Gul R. , Hossain A. , Yang G. , Zazvorka J. , Dedic V. , Franc J. , James R. B.
Published: February 2019

Because of its ideal band gap, high density and high electron mobility-lifetime product, cadmium zinc telluride (CdZnTe or CZT) is currently the best room-temperature compound-semiconductor X- and gamma-ray detector material. However, because of its innate poor thermo-physical properties and above unity segregation coefficient for Zn, the wide spread deployment of this material in large-volume CZT detectors is still limited by the high production cost. The underlying reason for the low yield of high-quality material is that CZT suffers from three major detrimental defects: compositional inhomogeneity, high concentrations of dislocation walls/sub-grain boundary networks and high concentrations of Te inclusions/precipitates. To mitigate all these disadvantages, we report for the first time the effects of the addition of selenium to the CZT matrix. The addition of Se was found to be very effective in arresting the formation of sub-grain boundaries and its networks, significantly reducing Zn segregation, improving compositional homogeneity and resulting in much lower concentrations of Te inclusions/precipitates. Growth of the new quaternary crystal Cd1−xZnxTe1−ySey (CZTS) by the Traveling Heater Method (THM) is reported in this paper. We have demonstrated the production of much higher yield according to its compositional homogeneity, with substantially lower sub-grain boundaries and their network, and a lower concentration of Te inclusions/precipitates.
Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in rice
Authors: Tonnessen Bradley W. , Bossa-Castro Ana M. , Mauleon Ramil , Alexandrov Nickolai , Leach Jan E.
Published: February 2019

Plant disease resistance that is durable and effective against diverse pathogens (broad-spectrum) is essential to stabilize crop production. Such resistance is frequently controlled by Quantitative Trait Loci (QTL), and often involves differential regulation of Defense Response (DR) genes. In this study, we sought to understand how expression of DR genes is orchestrated, with the long-term goal of enabling genome-wide breeding for more effective and durable resistance. We identified short sequence motifs in rice promoters that are shared across Broad-Spectrum DR (BS-DR) genes co-expressed after challenge with three major rice pathogens (Magnaporthe oryzae,Rhizoctonia solani, andXanthomonas oryzaepv.oryzae) and several chemical elicitors. Specific groupings of these BS-DR-associated motifs, calledcis-Regulatory Modules (CRMs), are enriched in DR gene promoters, and the CRMs includecis-elements known to be involved in disease resistance. Polymorphisms in CRMs occur in promoters of genes in resistant relative to susceptible BS-DR haplotypes providing evidence that these CRMs have a predictive role in the contribution of other BS-DR genes to resistance. Therefore, we predict that a CRM signature within BS-DR gene promoters can be used as a marker for future breeding practices to enrich for the most responsive and effective BS-DR genes across the genome.
Beta diversity patterns reveal positive effects of farmland abandonment on moth communities
Authors: Dantas de Miranda Murilo , Pereira Henrique M. , Corley Martin F. V. , Merckx Thomas
Published: February 2019

Farmland abandonment and the accompanying natural succession are largely perceived as unwanted amongst many European conservationists due to alleged negative effects on biodiversity levels. Here, we test this assumption by analysing alpha, beta and gamma diversity patterns of macro-moth communities in habitats on an ecological succession gradient, from extensively managed meadows to scrub-encroached and wooded sites. Macro-moths were light-trapped at 84 fixed circular sampling sites arranged in a semi-nested design within the National Park of Peneda-Gerês, NW-Portugal. In total, we sampled 22825 individuals belonging to 378 species. Alpha, beta and gamma diversity patterns suggest that farmland abandonment is likely to positively affect both overall macro-moth diversity and forest macro-moth diversity, and to negatively affect species diversity of non-forest macro-moth species. Our results also show that spatial habitat heterogeneity is important to maintain gamma diversity of macro-moths, especially for rare non-forest species and habitat specialists.
Weight change is significantly associated with risk of thyroid cancer: A nationwide population-based cohort study
Authors: Kwon Hyemi , Han Kyung-Do , Park Cheol-Young
Published: February 2019

Obesity is a risk factor for many cancers including breast, esophageal, colon, and thyroid cancer. We aimed to evaluate the association of thyroid cancer with body mass index (BMI), waist circumference (WC), and weight change. This nationwide population-based cohort study included 11,323,006 adults who joined the national health screening program. Weight change was defined as the difference between the weight of the subjects measured during the study period and the weight at the time of four years ago. For evaluating the association between the weight change and the risk of thyroid cancer, subjects without weight change for four years were defined as the reference group. Mean age was 50.1 ± 13.7 years and 44% were female. In total, 50,464 subjects (0.4%) had newly-diagnosed thyroid cancer. After multivariable analyses, the incidence of thyroid cancer increased significantly in subjects with larger WC as well as higher BMI (P < 0.001 and P < 0.001, respectively). In subjects who were lean and became obese, the incidence of thyroid cancers increased significantly (hazard ratio [HR] 1.15 [1.11–1.19]). In subjects who were obese and became lean, the incidence of thyroid cancers decreased significantly (HR 0.89 [0.86–0.93]). These results demonstrated that higher BMI and larger WC were significantly associated with an increased risk of thyroid cancer. Weight gain in lean subjects was associated with an increased risk of thyroid cancer, and weight reduction in subjects with obesity was associated with a decreased risk of thyroid cancer.
Intraperitoneal delivery of a novel drug‐like compound improves disease severity in severe and intermediate mouse models of Spinal Muscular Atrophy
Authors: Osman E. Y. , Rietz A. , Kline R. A. , Cherry J. J. , Hodgetts K. J. , Lorson C. L. , Androphy E. J.
Published: February 2019

Spinal muscular atrophy (SMA) is an autosomal recessive neurodegenerative disorder that causes progressive muscle weakness and is the leading genetic cause of infant mortality worldwide. SMA is caused by the loss of survival motor neuron 1 (SMN1). In humans, a nearly identical copy gene is present, called SMN2. Although SMN2 maintains the same coding sequence, this gene cannot compensate for the loss of SMN1 because of a single silent nucleotide difference in SMN2 exon 7. SMN2 primarily produces an alternatively spliced isoform lacking exon 7, which is critical for protein function. SMN2 is an important disease modifier that makes for an excellent target for therapeutic intervention because all SMA patients retain SMN2. Therefore, compounds and small molecules that can increase SMN2 exon 7 inclusion, transcription and SMN protein stability have great potential for SMA therapeutics. Previously, we performed a high throughput screen and established a class of compounds that increase SMN protein in various cellular contexts. In this study, a novel compound was identified that increased SMN protein levels in vivo and ameliorated the disease phenotype in severe and intermediate mouse models of SMA.
Differentially expressed gene networks, biomarkers, long noncoding RNAs, and shared responses with cocaine identified in the midbrains of human opioid abusers
Authors: Saad Manal H. , Rumschlag Matthew , Guerra Michael H. , Savonen Candace L. , Jaster Alaina M. , Olson Philip D. , Alazizi Adnan , Luca Francesca , Pique-Regi Roger , Schmidt Carl J. , Bannon Michael J.
Published: February 2019

Opioid abuse is now the most common cause of accidental death in the US. Although opioids and most other drugs of abuse acutely increase signaling mediated by midbrain dopamine (DA)-synthesizing neurons, little is known about long-lasting changes in DA cells that may contribute to continued opioid abuse, craving, and relapse. A better understanding of the molecular and cellular bases of opioid abuse could lead to advancements in therapeutics. This study comprises, to our knowledge, the first unbiased examination of genome-wide changes in midbrain gene expression associated with human opioid abuse. Our analyses identified differentially expressed genes and distinct gene networks associated with opioid abuse, specific genes with predictive capability for subject assignment to the opioid abuse cohort, and genes most similarly affected in chronic opioid and cocaine abusers. We also identified differentially expressed long noncoding RNAs capable of regulating known drug-responsive protein-coding genes. Opioid-regulated genes identified in this study warrant further investigation as potential biomarkers and/or therapeutic targets for human substance abuse.
Depth-dependent hysteresis in adhesive elastic contacts at large surface roughness
Authors: Deng Weilin , Kesari Haneesh
Published: February 2019

Contact force–indentation depth measurements in contact experiments involving compliant materials, such as polymers and gels, show a hysteresis loop whose size depends on the maximum indentation depth. This depth-dependent hysteresis (DDH) is not explained by classical contact mechanics theories and was believed to be due to effects such as material viscoelasticity, plasticity, surface polymer interdigitation, and moisture. It has been observed that the DDH energy loss initially increases and then decreases with roughness. A mechanics model based on the occurrence of adhesion and roughness related small-scale instabilities was presented by one of the authors for explaining DDH. However, that model only applies in the regime of infinitesimally small surface roughness, and consequently it does not capture the decrease in energy loss with surface roughness at the large roughness regime. We present a new mechanics model that applies in the regime of large surface roughness based on the Maugis–Dugdale theory of adhesive elastic contacts and Nayak’s theory of rough surfaces. The model captures the trend of decreasing energy loss with increasing roughness. It also captures the experimentally observed dependencies of energy loss on the maximum indentation depth, and material and surface properties.
Association between decreased serum TBIL concentration and immediate memory impairment in schizophrenia patients
Authors: Yin Xiao Li , Jia Qiu Fang , Zhang Guang Ya , Zhang Jian Ping , Shirao Tomoaki , Jiang Cai Xia , Yin Xu Yuan , Liu Yan Song , Chen Peng , Gu Xiao Chu , Qian Zheng Kang , Yin Guang Zhong , Sen Xia Hai , Hui Li
Published: February 2019

Cognitive impairment is a core feature of schizophrenia (SCH). In addition to the toxic effect of Bilirubin (BIL), it has antioxidant properties that were associated with the psychopathology and cognitive impairment of psychiatric disorders. The aim of this study was to examine the correlation of serum total BIL (TBIL) concentration with cognitive impairment in SCH patients. We recruited 34 SCH patients and 119 healthy controls (HCs) in this case-control design. Cognition was assessed using the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS). Serum TBIL concentration was measured using the immunoturbidimetric method. Serum TBIL concentration was significantly decreased in SCH patients compared to HCs after adjusting for age, gender, and education. Serum TBIL concentration in SCH patients was also positively correlated with the RBANS immediate memory score. Further stepwise multiple regression analysis confirmed the positive association between serum TBIL concentration and immediate memory score in SCH patients. Our findings supported that the decline in serum TBIL concentration was associated with the immediate memory impairment and psychopathology of SCH.
Mechanism of hysteresis for composite multi-halide and its superior performance for low grade energy recovery
Authors: An Guoliang , Wang Liwei , Gao Jiao , Wang Ruzhu
Published: February 2019

Sorption hysteresis commonly exists for different sorbents and has a great impact on the performance, and recently it was found that the multi-halide sorbents could reduce the hysteresis phenomena. Here we report the mechanism of the sorption hysteresis for multi-halide under equilibrium/non-equilibrium conditions and its superior performance for low grade energy recovery. We find that the inner reaction among different halides does not happen and contribute to sorption hysteresis in sorption/desorption phases under equilibrium conditions. While under non-equilibrium conditions, multi-halide sorbents reduce the hysteresis significantly (the average hysteresis temperature difference decreases from 23.4 °C to 7.8 °C at 4.41 bar). The phenomena is studied, and results show that the continuous reaction within different halides under heterothermic condition leads to an operable multi-stage reaction property, which corresponds to better flexibility and faster response to heat source. The utilization of solar energy as heat source for a cloudy day is analyzed, and multi-halide sorbent has much larger average refrigeration power (improved by 43%) and could work efficiently most of the time. Such characteristics are also prospective for other thermochemical reaction technologies, such as de-NOx and energy storage because of lower energy input and higher energy output features.
Closed Loop Recycling of Electric Vehicle Batteries to Enable Ultra-high Quality Cathode Powder
Authors: Chen Mengyuan , Zheng Zhangfeng , Wang Qiang , Zhang Yubin , Ma Xiaotu , Shen Chao , Xu Dapeng , Liu Jin , Liu Yangtao , Gionet Paul , O’Connor Ian , Pinnell Leslie , Wang Jun , Gratz Eric , Arsenault Renata , Wang Yan
Published: February 2019

The lithium-ion battery (LIB) recycling market is becoming increasingly important because of the widespread use of LIBs in every aspect of our lives. Mobile devices and electric cars represent the largest application areas for LIBs. Vigorous innovation in these sectors is spurring continuous deployment of LIB powered devices, and consequently more and more LIBs will become waste as they approach end of life. Considering the significant economic and environmental impacts, recycling is not only necessary, but also urgent. The WPI group has successfully developed a closed-loop recycling process, and has previously demonstrated it on a relatively small scale 1 kg spent batteries per experiment. Here, we show that the closed-loop recycling process can be successfully scaled up to 30 kg of spent LIBs from electric vehicle recycling streams, and the recovered cathode powder shows similar (or better) performance to equivalent commercial powder when evaluated in both coin cells and single layer pouch cells. All of these results demonstrate the closed-loop recycling process has great adaptability and can be further developed into industrial scale.
Therapeutic potential of hepatocyte-like-cells converted from stem cells from human exfoliated deciduous teeth in fulminant Wilson’s disease
Authors: Fujiyoshi Junko , Yamaza Haruyoshi , Sonoda Soichiro , Yuniartha Ratih , Ihara Kenji , Nonaka Kazuaki , Taguchi Tomoaki , Ohga Shouichi , Yamaza Takayoshi
Published: February 2019

Wilson’s disease (WD) is an inherited metabolic disease arising from ATPase copper transporting beta gene (ATP7B) mutation. Orthotoropic liver transplantation is the only radical treatment of fulminant WD, although appropriate donors are lacking at the onset of emergency. Given the hepatogenic capacity and tissue-integration/reconstruction ability in the liver of stem cells from human exfoliated deciduous teeth (SHED), SHED have been proposed as a source for curing liver diseases. We hypothesized the therapeutic potential of SHED and SHED-converted hepatocyte-like- cells (SHED-Heps) for fulminant WD. SHED and SHED-Heps were transplanted into WD model Atp7b-mutated Long-Evans Cinnamon (LEC) rats received copper overloading to induce a lethal fulminant liver failure. Due to the superior copper tolerance via ATP7B, SHED-Hep transplantation gave more prolonged life-span of fulminant LEC rats than SHED transplantation. The integrated ATP7B-expressing SHED-Heps showed more therapeutic effects on to restoring the hepatic dysfunction and tissue damages in the recipient liver than the integrated naïve SHED without ATP7B expression. Moreover, SHED-Heps could reduce copper-induced oxidative stress via ATP7B- independent stanniocalcin 1 secretion in the fulminant LEC rats, suggesting a possible role for paracrine effect of the integrated SHED-Heps. Taken together, SHED-Heps offer a potential of functional restoring, bridging, and preventive approaches for treating fulminant WD.
Unusual Roles of Discharge, Slope and SOC in DOC Transport in Small Mountainous Rivers, Taiwan
Authors: Lee Li-Chin , Hsu Ting-Chang , Lee Tsung-Yu , Shih Yu-Ting , Lin Chuan-Yao , Jien Shih-Hao , Hein Thomas , Zehetner Franz , Shiah Fuh-Kwo , Huang Jr-Chuan
Published: February 2019

Riverine dissolved organic carbon (DOC), responsible for riverine productivity, is rarely documented in subtropical small mountainous rivers (SMRs) where high rainfall and steep slopes are the main features. This study investigated the DOC export at eight sites in three Taiwan SMRs to characterize the dynamics and controlling factors of DOC transport. Results showed that the mean DOC concentration of ~0.78 mg L−1 is much lower than the global average of ~5.29 mg L−1. However, the mean DOC yield, ~22.51 kg-C ha−1 yr−1, is higher than the global average of 14.4–19.3 kg-C ha−1 yr−1. Comparing with worldwide rivers from literature, the annual discharge, slope, and SOC (soil organic carbon) are controlling factors as expected, though they influence in different ways. SOC stock likely regulated by elevation-dependent biomes dominate the DOC supply, while slope restrains the DOC generation due to shallow soil depth and fast runoff velocity. However, the abundant discharge flushing this persistent low supply leads to a large DOC export in the SMRs. Furthermore, the DOC dynamics during typhoon periods showed a clockwise hysteresis, suggesting that the DOC is mainly from the riparian zone or downslope area during the rising limb of the hydrograph. This study elucidates the DOC transport in SMRs and provides an atypical yet significant piece of understanding on DOC transport in a global context.
Disclosure of complementary medicine use to medical providers: a systematic review and meta-analysis
Authors: Foley H. , Steel A. , Cramer H. , Wardle J. , Adams J.
Published: February 2019

Concomitant complementary medicine (CM) and conventional medicine use is frequent and carries potential risks. Yet, CM users frequently neglect to disclose CM use to medical providers. Our systematic review examines rates of and reasons for CM use disclosure to medical providers. Observational studies published 2003–2016 were searched (AMED, CINAHL, MEDLINE, PsycINFO). Eighty-six papers reporting disclosure rates and/or reasons for disclosure/non-disclosure of CM use to medical providers were reviewed. Fourteen were selected for meta-analysis of disclosure rates of biologically-based CM. Overall disclosure rates varied (7–80%). Meta-analysis revealed a 33% disclosure rate (95%CI: 24% to 43%) for biologically-based CM. Reasons for non-disclosure included lack of inquiry from medical providers, fear of provider disapproval, perception of disclosure as unimportant, belief providers lacked CM knowledge, lacking time, and belief CM was safe. Reasons for disclosure included inquiry from medical providers, belief providers would support CM use, belief disclosure was important for safety, and belief providers would give advice about CM. Disclosure appears to be influenced by the nature of patient-provider communication. However, inconsistent definitions of CM and lack of a standard measure for disclosure created substantial heterogeneity between studies. Disclosure of CM use to medical providers must be encouraged for safe, effective patient care.