Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of Aliphatic n-Alkynes To Discriminate Soil Nitrification Activities of Ammonia-Oxidizing Thaumarchaea and Bacteria

ABSTRACT Ammonia (NH3)-oxidizing bacteria (AOB) and thaumarchaea (AOA) co-occupy most soils, yet no short-term growth-independent method exists to determine their relative contributions to nitrification in situ. Microbial monooxygenases differ in their vulnerability to inactivation by aliphatic n-alkynes, and we found that NH3 oxidation by the marine thaumarchaeon Nitrosopumilus maritimus was unaffected during a 24-h exposure to ≤20 μM concentrations of 1-alkynes C8 and C9. In contrast, NH3 oxidation by two AOB (Nitrosomonas europaea and Nitrosospira multiformis) was quickly and irreversibly inactivated by 1 μM C8 (octyne). Evidence that nitrification carried out by soilborne AOA was also insensitive to octyne was obtained. In incubations (21 or 28 days) of two different whole soils, both acetylene and octyne effectively prevented NH4 +-stimulated increases in AOB population densities, but octyne did not prevent increases in AOA population densities that were prevented by acetylene. Furthermore, octyne-resistant, NH4 +-stimulated net nitrification rates of 2 and 7 μg N/g soil/day persisted throughout the incubation of the two soils. Other evidence that octyne-resistant nitrification was due to AOA included (i) a positive correlation of octyne-resistant nitrification in soil slurries of cropped and noncropped soils with allylthiourea-resistant activity (100 μM) and (ii) the finding that the fraction of octyne-resistant nitrification in soil slurries correlated with the fraction of nitrification that recovered from irreversible acetylene inactivation in the presence of bacterial protein synthesis inhibitors and with the octyne-resistant fraction of NH4 +-saturated net nitrification measured in whole soils. Octyne can be useful in short-term assays to discriminate AOA and AOB contributions to soil nitrification.
Calcitriol Imparts Neuroprotection In Vitro to Midbrain Dopaminergic Neurons by Upregulating GDNF Expression

During development a tightly controlled signaling cascade dictates the differentiation, maturation and survival of developing neurons. Understanding this signaling mechanism is important for developing therapies for neurodegenerative illnesses. In previous work we have sought to understand the complex signaling pathways responsible for the development of midbrain dopamine neurons using a proteomic approach. One protein we have identified as being expressed in developing midbrain tissue is the vitamin D receptor. Therefore we investigated the effect of the biologically active vitamin D3 metabolite, calcitriol, on primary fetal ventral mesencephalic cultures of dopamine neurons. We observed a dose responsive increase in numbers of rat primary dopamine neurons when calcitriol was added to culture media. Western blot data showed that calcitriol upregulated the expression of glial derived neurotrophic factor (GDNF). Blocking GDNF signaling could prevent calcitriol’s ability to increase numbers of dopamine neurons. An apoptosis assay and cell birth dating experiment revealed that calcitriol increases the number of dopamine neurons through neuroprotection and not increased differentiation. This could have implications for future neuroprotective PD therapies.
Dietary Glucosinolate Intake, Polymorphisms in Selected Biotransformation Enzymes, and Risk of Prostate Cancer

A protective role of glucosinolates in prostate cancer development might be mediated by the induction of biotransformation enzymes. These enzymes, enhancing the elimination of carcinogens from the body, are known to be polymorphic. Therefore, we evaluated whether a possible association between glucosinolate intake and prostate cancer risk is modified by polymorphisms in GSTT1, GSTM1, GSTA1, GSTP1, or NOQ1 genes. A case-control study including 248 prostate cancer cases and 492 matched controls was nested in the prospective European Prospective Investigation into Cancer and Nutrition-Heidelberg cohort. At baseline, participants provided dietary and lifestyle data and blood samples, which were used for genotyping and measurement of serum glutathione S-transferase-α concentration. Odds ratios and 95% confidence intervals were calculated by conditional logistic regression. We found an inverse association of glucosinolate intake with prostate cancer risk (adjusted odds ratio, 0.72 per 10 mg/d increment; 95% confidence interval, 0.53-0.96). Stratification by genotype showed significantly reduced risks for subjects with wild-type of NQO1 (C609T) compared with CT or TT carriers (Pinteraction = 0.04). Those with deletions in both GSTM1 and GSTT1 genes combined had a significantly reduced risk with increasing glucosinolate intake (Pinteraction = 0.01). There was no effect modification of glucosinolate intake and cancer risk by GSTA1 (G-52A) or GSTP1 (A313G) genotype, but serum glutathione S-transferase-α concentrations were inversely associated with prostate cancer. This study showed that the inverse association between glucosinolate intake and prostate cancer risk was modified by NQO1 (C609T) and GSTM1 and GSTT1 deletion polymorphisms. This information will help to further elucidate the mechanism of action of potentially protective substances in vivo. Cancer Epidemiol Biomarkers Prev; 19(1); 135–43
Role of TolR N-Terminal, Central, and C-Terminal Domains in Dimerization and Interaction with TolA and TolQ

ABSTRACT The Tol-PAL system of Escherichia coli is a multiprotein system involved in maintaining the cell envelope integrity and is necessary for the import of some colicins and phage DNA into the bacterium. It is organized into two complexes, one near the outer membrane between TolB and PAL and one in the cytoplasmic membrane between TolA, TolQ, and TolR. In the cytoplasmic membrane, all of the Tol proteins have been shown to interact with each other. Cross-linking experiments have shown that the TolA transmembrane domain interacts with TolQ and TolR. Suppressor mutant analyses have localized the TolQ-TolA interaction to the first transmembrane domain of TolQ and have shown that the third transmembrane domain of TolQ interacts with the transmembrane domain of TolR. To get insights on the composition of the cytoplasmic membrane complex and its possible contacts with the outer membrane complex, we focused our attention on TolR. Cross-linking and immunoprecipitation experiments allowed the identification of Tol proteins interacting with TolR. The interactions of TolR with TolA and TolQ were confirmed, TolR was shown to dimerize, and the resulting dimer was shown to interact with TolQ. Deletion mutants of TolR were constructed, and they allowed us to determine the TolR domains involved in each interaction. The TolR transmembrane domain was shown to be involved in the TolA-TolR and TolQ-TolR interactions, while TolR central and C-terminal domains appeared to be involved in TolR dimerization. The role of the TolR C-terminal domain in the TolA-TolR interaction and its association with the membranes was also demonstrated. Furthermore, phenotypic studies clearly showed that the three TolR domains (N terminal, central, and C terminal) and the level of TolR production are important for colicin A import and for the maintenance of cell envelope integrity.
Why People Want to Continuously Use Mobile IM Service: The Moderating Role of Perceived Value

As the fast development and wide adoption of mobile instant messaging (IM) service, to find out which factors will significantly impact on user's continuance intention is very important for mobile IM practitioners. In this study, we integrated the constructs of interaction and network externalities as independent variables. Interaction includes interface interaction and social interaction; meanwhile, Network externalities includes referent network size and perceived complementarity. The results of this study reveal that both interaction and network externalities have significant influences on the generation of user's satisfaction. Furthermore, from the perspective of network externalities, perceived complementarity is the only available antecedent to generating user's perceived value. Finally, the moderating effect of perceived value on the relationship between satisfaction and continuance intention is verified in this study. When perceived value is high, even for low satisfied users are more likely to continue using mobile IM service than high satisfied users, who have low perceived value.
Clinical and Genetic Factors Associated With Thiazide-Induced Hyponatremia

AbstractThiazide diuretics are associated with an increased risk of hyponatremia. The aim of this study was to investigate possible predictors of thiazide-induced hyponatremia.A total of 48 patients admitted to the ward or to the emergency department due to severe thiazide-induced hyponatremia (Na < 125 mmol/L) were enrolled in our study as the case group. Another 211 hypertensive patients with normal sodium levels after treatment with thiazide diuretics were selected as the control group. Twelve tag single nucleotide polymorphism markers were selected from the Potassium Channel, Inwardly Rectifying Subfamily J, Member 1 (KCNJ1) gene: rs1231254, rs2238009, rs1148058, rs675482, rs673614, rs12795437, rs2855800, rs2509585, rs3016774, rs881333, rs4529890, and rs7116606. Clinical and genetic parameters between patients with thiazide-induced hyponatremia and the control group were compared. Logistic regression was used to analyze data.The patients with thiazide-induced hyponatremia were older (P < 0.001), predominantly female (P = 0.008), had a lower mean body mass index (BMI) (P < 0.001), and more commonly used angiotensin II receptor antagonist (P < 0.001) and spironolactone (P = 0.007) compared with the control groups. Analysis with multivariate logistic regression revealed that age (odds ratio [OR], 1.13; 95% confidence interval [CI], 1.08–1.19, P < 0.001), female gender (OR, 4.49; 95% CI, 1.54–13.11, P = 0.006), BMI (OR, 0.80; 95% CI, 0.69–0.93, P = 0.003), and KCNJ1 rs2509585 C/T or T/T polymorphisms (OR, 5.75; 95% CI, 1.25–26.45, P = 0.03) were independent predictors for thiazide-induced hyponatremia.Older female patients with lower BMIs and KCNJ1 rs2509585 C/T or T/T polymorphisms were more likely to develop thiazide-induced hyponatremia.
Nanoscale Morphological and Chemical Changes of High Voltage Lithium–Manganese Rich NMC Composite Cathodes with Cycling

Understanding the evolution of chemical composition and morphology of battery materials during electrochemical cycling is fundamental to extending battery cycle life and ensuring safety. This is particularly true for the much debated high energy density (high voltage) lithium–manganese rich cathode material of composition Li1 + xM1 – xO2 (M = Mn, Co, Ni). In this study we combine full-field transmission X-ray microscopy (TXM) with X-ray absorption near edge structure (XANES) to spatially resolve changes in chemical phase, oxidation state, and morphology within a high voltage cathode having nominal composition Li1.2Mn0. 525Ni0.175Co0. 1O2. Nanoscale microscopy with chemical/elemental sensitivity provides direct quantitative visualization of the cathode, and insights into failure. Single-pixel (∼30 nm) TXM XANES revealed changes in Mn chemistry with cycling, possibly to a spinel conformation and likely including some Mn(II), starting at the particle surface and proceeding inward. Morphological analysis of the particles revealed, with high resolution and statistical sampling, that the majority of particles adopted nonspherical shapes after 200 cycles. Multiple-energy tomography showed a more homogeneous association of transition metals in the pristine particle, which segregate significantly with cycling. Depletion of transition metals at the cathode surface occurs after just one cycle, likely driven by electrochemical reactions at the surface.
Comparison of orange oil and chloroform as gutta- percha solvents in endodontic retreatment.

OBJECTIVE To compare the efficacy of gutta-percha removal achieved with simple mechanical technique using two different solvents. MATERIALS AND METHODS It was an in vitro experimental study conducted at the Aga Khan University Hospital, Karachi, Pakistan on 27 extracted human molars divided into two groups by alternate sampling technique. The teeth were prepared by manual filing and obturated with gutta-percha and calcium hydroxide sealer. Two drops of the assigned solvent were placed on the orifice of the obturated canal and Gates Glidden drills #1, 2 and 3 were used for removal of coronal gutta-percha. Manual filing was done for removal of remaining gutta-percha and the solvent was used in drops until needed. Postoperative periapical radiographs were taken to visualize the remaining gutta-percha left in the canals. Descriptive statistics (mean and SD) of the variables such as tooth type, obturation length and canal curvatures were determined. Chi-square and independent sample t-tests were applied and level of significance was set at 0.05. RESULTS There was 5.19 (3.8) mm of remaining gutta-percha in the orange oil group and 5.37 (4.2) mm in the chloroform group (p=0.90). CONCLUSION There is no statistically significant difference between the orange oil and chloroform when used as solvent for removing gutta-percha.
Relationship between school professional climate and teachers' satisfaction with the evaluation process

This study examined the relationship between teachers’ perceptions of school professional climate and their satisfaction with the process for evaluating their performance. It used the responses of a nationally representative sample of teachers to examine whether teachers’ satisfaction with the evaluation process was associated with two measures of school professional climate (principal leadership and teacher influence), teacher and school characteristics, and the inclusion of student test scores in the evaluation system. Teachers’ perceptions of their principal’s leadership was positively associated with their satisfaction with the evaluation system. Teachers’ evaluation rating was also associated with their satisfaction, with those rated satisfactory or higher more likely to be satisfied. Teachers’ whose evaluations included student test scores were less likely to be satisfied.
Testing a nested skills model of the relations among invented spelling, accurate spelling, and word reading, from kindergarten to grade 1

ABSTRACT The goal was to assess the role of invented spelling to subsequent reading and spelling as proposed by the Nested Skills Model of Early Literacy Acquisition. 107 English-speaking children were tested at the beginning of kindergarten and grade 1, and at the end of grade 1. The findings provided support for the proposed model. First, the role played by phoneme awareness and letter knowledge to early reading was mediated, at least in part, by the sophistication of their invented spelling. Second, all children who spelled words accurately at the beginning of grade 1 could read words, but not all children who could read spelled accurately. Third, word reading, and, to a smaller extent, invented spelling in kindergarten predicted unique variance in spelling accuracy in grade 1. Fourth, invented spelling (not accurate spelling) predicted growth in word reading during the first year of reading instruction. Implications for education are discussed.
PENGARUH STRUKTUR KEPEMILIKAN, UKURAN PERUSAHAAN, DAN UMUR PERUSAHAAN TERHADAP PENGUNGKAPAN CORPORATE SOCIAL RESPONSIBILITY (CSR) (Studi Empiris pada Perusahaan Manufaktur yang Terdaftar dalam Bursa Efek Indonesia periode 2011-2014)

Pertumbuhan industri manufaktur di Indonesia pada tahun 2014 melampaui tingkat pertumbuhan ekonomi. Sedangkan pengungkapan Corporate Social Responsibility bagi perusahaan belum maksimal sampai tahun 2014. Pertumbuhan perusahaan yang seharusnya memiliki keseimbangan dengan pelaksanaan tanggung jawab sosial perusahaan, namun pada prakteknya belum terjadi keseimbangan yang diharapkan. Dalam perusahaan manufaktur yang terdaftar dalam BEI, pengungkapan Corporate Social Responsibility dinilai penting dalam laporan tahunan yang dikeluarkan oleh perusahaan. Yang mana kegunaan laporan tahunan ini bagi investor, internal perusahaan dan juga masyarakat luas. Penelitian ini bertujuan untuk mengetahui perkembangan dari pengungkapan Corporate Social Responsibility, struktur kepemilikan saham, ukuran perusahaan, dan umur perusahaan. Serta mencari tahu pengaruh antara kepemilikan saham, ukuran perusahaan, dan umur perusahaan terhadap pengungkapan corporate social responsibility baik secara simultan maupun parsial. Melalui penelitian ini akan dilakukan pengukuran pengungkapan Corporate Social Responsibility dengan variabel struktur kepemilikan saham, ukuran perusahaan, dan umur perusahaan pada 18 sampel perusahaan manufaktur yang terdaftar di Bursa Efek Indonesia selama tahun 2011-2014. Dimana pemilihan sampel menggunakan metode purposive sampling. Metode pengumpulan data dilakukan dengan menganalisis laporan tahunan perusahaan manufaktur yag menjadi sampel dalam penelitian ini pada tahun 2011-2014. Dengan melihat item-item pengungkapan CSR, total kepemilikan saham, total asset, dan lama tidaknya perusahaan listing di BEI. Pengolahan data penelitian menggunakan Eviews 8. Dilihat dari rata-rata keseluruhan nilai pervariabel dengan total data sebanyak 72 dari tahun 2011-2014 menunjukkan bahwa nilai pervariabel yang variatif juga fluktuatif tiap tahunnya. Nilai rata-rata tertinggi pada variabel ukuran perusahaan dengan nilai 28.36283. Nilai standard deviasi paling tinggi pada variabel umur perusahaan yang mencapai 5.641618. Dari penelitian ini dapat dipeoleh beberapa kesimpulan, berdasarkan evaluasi pengaruh dari variabel-variabel secara simultan memiliki pengaruh yang signifikan terhadap pengungkapan Corporate Social Responsibility dengan tingkat signifikan yang dapat dijelaskan oleh variabel-variabel x sebesar 93%. Secara parsial, hanya umur perusahaan yang mempunyai pengaruh secara signifikan, terhadap pengungkapan Corporate Social Responsibility sedang variabel struktur kepemilikan institusional, asing dan ukuran perusahaan tidak memiliki pengaruh terhadap pengungkapan Corporate Social Responsibility. Keywords: Pengungkapan Corporate Social Responsibility, Struktur Kepemilikan, Ukuran perusahaan dan Umur Perusahaan
Reflective Agile Iterative Design

In Sacks’ account of new technology adoption, new technologies do not transform the world, but rather they are “made at home in the world that has whatever organization it already has”. In this process of being made at home, use emerges and design understandings arise. A Reflective Agile Iterative Design (RAID) framework was employed to iteratively design a mobile social group communication technology which harnessed existing mundane technology such as instant messaging and SMS, and study its emergent use. The technology was “made at home” in peoples’ lives over time and led to small shifts in their communication and coordination patterns. RAID-style approaches are often glimpsed behind Web 2.0 sites and academia, although the style itself has received little direct attention in the academic literature. The approach is summed up as ‘learning about technology through living with it’ and is well suited to understanding and designing mundane technology with its fusion of the action research and agile development philosophies. The characteristics and challenges of designing using this approach are described.
Pods : Issues in the Design of Practical Ad-Hoc Wireless Sensor Networks

The Pods ad-hoc wireless sensor network has been designed to study the environment of endangered species of plants. This paper presents the overall design of this network, focusing on the design of the network nodes and of the algorithms we use. In designing and building the Pods network, several issues have become apparent that are more widely applicable to sensor networks in general. Of these issues, the two most fundamental are scaling and energy efficiency. In the foreseeable future large sensor networks can and will be built, and any algorithms used must scale to many thousands of nodes and to networks with diameters of hundreds or thousands of hops. As such networks are built, energy efficiency becomes an essential element of both the overall cost and the ease of deployment. These two elements can therefore significantly affect the viability of a wireless sensor network design. Algorithms developed as part of the Pods project, particularly the MOR routing protocol, provide good performance on both of these measures.
Putative Sugar Transporters of the Mustard Leaf Beetle Phaedon cochleariae: Their Phylogeny and Role for Nutrient Supply in Larval Defensive Glands

Background Phytophagous insects have emerged successfully on the planet also because of the development of diverse and often astonishing defensive strategies against their enemies. The larvae of the mustard leaf beetle Phaedon cochleariae, for example, secrete deterrents from specialized defensive glands on their back. The secretion process involves ATP-binding cassette transporters. Therefore, sugar as one of the major energy sources to fuel the ATP synthesis for the cellular metabolism and transport processes, has to be present in the defensive glands. However, the role of sugar transporters for the production of defensive secretions was not addressed until now. Results To identify sugar transporters in P. cochleariae, a transcript catalogue was created by Illumina sequencing of cDNA libraries. A total of 68,667 transcripts were identified and 68 proteins were annotated as either members of the solute carrier 2 (SLC2) family or trehalose transporters. Phylogenetic analyses revealed an extension of the mammalian GLUT6/8 class in insects as well as one group of transporters exhibiting distinctive conserved motifs only present in the insect order Coleoptera. RNA-seq data of samples derived from the defensive glands revealed six transcripts encoding sugar transporters with more than 3,000 counts. Two of them are exclusively expressed in the glandular tissue. Reduction in secretions production was accomplished by silencing two of four selected transporters. RNA-seq experiments of transporter-silenced larvae showed the down-regulation of the silenced transporter but concurrently the up-regulation of other SLC2 transporters suggesting an adaptive system to maintain sugar homeostasis in the defensive glands. Conclusion We provide the first comprehensive phylogenetic study of the SLC2 family in a phytophagous beetle species. RNAi and RNA-seq experiments underline the importance of SLC2 transporters in defensive glands to achieve a chemical defense for successful competitive interaction in natural ecosystems.