Miracle-dz/UniFAR-FTUs huggingface dataset:
The Molecular Composition of Dissolved Organic Matter in Forest Soils as a Function of pH and Temperature

We examined the molecular composition of forest soil water during three different seasons at three different sites, using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS). We examined oxic soils and tested the hypothesis that pH and season correlate with the molecular composition of dissolved organic matter (DOM). We used molecular formulae and their relative intensity from ESI-FT-ICR-MS for statistical analysis. Applying unconstrained and constrained ordination methods, we observed that pH, dissolved organic carbon (DOC) concentration and season were the main factors correlating with DOM molecular composition. This result is consistent with a previous study where pH was a main driver of the molecular differences between DOM from oxic rivers and anoxic bog systems in the Yenisei River catchment. At a higher pH, the molecular formulae had a lower degree of unsaturation and oxygenation, lower molecular size and a higher abundance of nitrogen-containing compounds. These characteristics suggest a higher abundance of tannin connected to lower pH that possibly inhibited biological decomposition. Higher biological activity at a higher pH might also be related to the higher abundance of nitrogen-containing compounds. Comparing the seasons, we observed a decrease in unsaturation, molecular diversity and the number of nitrogen-containing compounds in the course of the year from March to November. Temperature possibly inhibited biological degradation during winter, which could cause the accumulation of a more diverse compound spectrum until the temperature increased again. Our findings suggest that the molecular composition of DOM in soil pore waters is dynamic and a function of ecosystem activity, pH and temperature.
Reply to Piperno et al.: It is too soon to argue for localized, short-term human impacts in interfluvial Amazonia

We welcome the debate opened by Piperno et al. (1) in response to our recent article (2), and thank the editors of PNAS for the opportunity to reply. Although acknowledging that we detected localized human impacts in our study area, Piperno et al. (1) downplay the increases in palms observed at the geoglyph sites, stating it’s “unclear” whether humans actively managed the forest in these locations. Independent of one’s opinion about intentionality, we argue that the rapid decline of palms after geoglyph abandonment suggests that their previously high levels were because of much more regular, longer-term human influences than Piperno et al. suggest. We also reemphasize that … [↵][1]1To whom correspondence should be addressed. Email: jenny.g. watling{at}gmail.com. [1]: #xref-corresp-1-1
Prosocial Conformity

Generosity is contagious: People imitate others’ prosocial behaviors. However, research on such prosocial conformity focuses on cases in which people merely reproduce others’ positive actions. Hence, we know little about the breadth of prosocial conformity. Can prosocial conformity cross behavior types or even jump from behavior to affect? Five studies address these questions. In Studies 1 to 3, participants decided how much to donate to charities before learning that others donated generously or stingily. Participants who observed generous donations donated more than those who observed stingy donations (Studies 1 and 2). Crucially, this generalized across behaviors: Participants who observed generous donations later wrote more supportive notes to another participant (Study 3). In Studies 4 and 5, participants observed empathic or non-empathic group responses to vignettes. Group empathy ratings not only shifted participants’ own empathic feelings (Study 4), but they also influenced participants’ donations to a homeless shelter (Study 5). These findings reveal the remarkable breadth of prosocial conformity.
The infectious intracellular lifestyle of Salmonella enterica relies on the adaptation to nutritional conditions within the Salmonella-containing vacuole

ABSTRACT Salmonella enterica serovar Typhimurium (S. Typhimurium) is a Gram-negative pathogen that causes various host-specific diseases. During their life cycle, Salmonellae survive frequent exposures to a variety of environmental stresses, e.g. carbon-source starvation. The virulence of this pathogen relies on its ability to establish a replicative niche, named Salmonella-containing vacuole, inside host cells. However, the microenvironment of the SCV and the bacterial metabolic pathways required during infection are largely undefined. In this work we developed different biological probes whose expression is modulated by the environment and the physiological state of the bacterium. We constructed transcriptional reporters by fusing promoter regions to the gfpmut3a gene to monitor the expression profile of genes involved in glucose utilization and lipid catabolism. The induction of these probes by a specific metabolic change was first tested in vitro, and then during different conditions of infection in macrophages. We were able to determine that Entner-Doudoroff is the main metabolic pathway utilized by Salmonella during infection in mouse macrophages. Furthermore, we found sub-populations of bacteria expressing genes involved in pathways for the utilization of different sources of carbon. These populations are modified in presence of different metabolizable substrates, suggesting the coexistence of Salmonella with diverse metabolic states during the infection.
Stochastic gradient algorithms for design of minimum error-rate linear dispersion codes in MIMO wireless systems

Linear dispersion (LD) codes are a good candidate for high-data-rate multiple-input multiple-ouput (MIMO) signaling. Traditionally LD codes were designed by maximizing the average mutual information, which cannot guarantee good error performance. This paper presents a new design scheme for LD codes that directly minimizes the block error rate (BLER) in MIMO channels with arbitrary fading statistics and various detection algorithms. For MIMO systems employing LD codes, the error rate does not admit an explicit form. Therefore, we cannot use deterministic optimization methods to design the minimum-error-rate LD codes. In this paper, we propose a simulation-based optimization methodology for the design of LD codes through stochastic approximation and simulation-based gradient estimation. The gradient estimation is done using the score function method originally developed in the discrete-event-system community. The proposed method can be applied to design the minimum-error-rate LD codes for a variety of detector structures including the maximum-likelihood (ML) detector and several suboptimal detectors. It can also design optimal codes under arbitrary fading channel statistics; in particular, it can take into account the knowledge of spatial fading correlation at the transmitter and receiver ends. Simulation results show that codes generated by the proposed new design paradigm generally outperform the codes designed based on algebraic number theory.
Prevalence of Myopia and Its Risk Factors in Urban School Children in Delhi: The North India Myopia Study (NIM Study)

Purpose Assess prevalence of myopia and identify associated risk factors in urban school children. Methods This was a cross-sectional study screening children for sub-normal vision and refractive errors in Delhi. Vision was tested by trained health workers using ETDRS charts. Risk factor questionnaire was filled for children with vision <6/9.5, wearing spectacles and for a subset (10%) of randomly selected children with normal vision. All children with vision <6/9.5 underwent cycloplegic refraction. The prevalence of myopia <-0.5 diopters was assessed. Association of risk factors and prevalence of myopia was analyzed for children with myopia and randomly selected non myopic children and adjusted odds ratio values for all risk factors were estimated. Results A total number of 9884 children were screened with mean age of 11.6 + 2.2 years and 66.8% boys. Prevalence of myopia was 13.1% with only 320 children (24.7%) wearing appropriate spectacles. Mean myopic spherical error was -1.86 + 1.4 diopters. Prevalence of myopia was higher in private schools compared to government schools (p<0.001), in girls vs. boys (p = 0.004) and among older (> 11 years) children (p<0.001). There was a positive association of myopia with studying in private schools vs. government schools (p<0.001), positive family history (p< 0.001) and higher socio-economic status (p = 0.037). Positive association of presence of myopia was observed with children studying/reading > 5 hours per day (p < 0.001), watching television > 2 hours / day (p < 0.001) and with playing computer/video/mobile games (p < 0.001). An inverse association with outdoor activities/playing was observed with children playing > 2 hours in a day. Conclusion Myopia is a major health problem in Indian school children. It is important to identify modifiable risk factors associated with its development and try to develop cost effective intervention strategies.
Factors Affecting Sand Solidification Using MICP with Pararhodobacter sp.

Biomineralization is an environmentally friendly technology for improving soil-engineering properties. One of the most common biomineralization processes is microbially induced calcite precipitation (MICP). In this study, sand solidi cation tests were conducted using Pararhodobacter sp. , which is a local ureolytic bacteria obtained from the sand near beach rock in Okinawa, Japan. The goal of this study was to solidify a specimen having an estimated uncon ned compressive strength (UCS) of more than several MPa to improve soil properties and investigate the in uence of various factors on the engineering properties of treated soil catalyzed by ureolytic bacteria (curing temperature, injection interval of cementation solution, Ca2+ concentration, curing time, bacterial population, re-injection of bacteria and particle size of sand). Model test specimens were cemented up to an estimated UCS of 10 MPa after 14 days under the following conditions: a curing temperature of 30°C, an injection interval of 1 day, and a Ca2+ concentrations in cementation solution of 0.5 M. Multiple regression analysis showed that the relevant conditions for estimating UCS were test period, D (days), and Ca2+ concentration of the cementation solution, Cca (M). The formula for predicting the estimated UCS (qeu (MPa)) was qeu = 13.99 Cca + 0.37 D − 0.09. Overall, the results of this study will contribute to the application of a new technique to sand improvement and bio-stimulation. [doi:10.2320/matertrans.M-M2017849]
Analysis of Causal Relationships by Structural Equation Modeling to Determine the Factors Influencing Cognitive Function in Elderly People in Japan

The purpose of this study is to identify a potentiality factor that is a preventive factor for decline in cognitive function. Additionally, this study pursues to clarify the causal relationship between the each potential factor and its influence on cognitive function. Subjects were 366 elderly community residents (mean age 73.7 ± 6.4, male 51, female 315) who participated in the Taketoyo Project from 2007 to 2011. Factor analysis was conducted to identify groupings within mental, social, life, physical and cognitive functions. In order to detect clusters of 14 variables, the item scores were subjected to confirmatory factor analysis. We performed Structural Equation Modeling analysis to calculate the standardization coefficient and correlation coefficient for every factor. The cause and effect hypothesis model was used to gather two intervention theory hypotheses for dementia prevention (direct effect, indirect effect) in one system. Finally, we performed another Structural Equation Modeling analysis to calculate the standardization of the cause and effect hypothesis model. Social participation was found to be activated by the improvement of four factors, and in turn, activated “Social participation” acted on cognitive function.
A Mouse Model of L-2-Hydroxyglutaric Aciduria, a Disorder of Metabolite Repair

The purpose of the present work was to progress in our understanding of the pathophysiology of L-2-hydroxyglutaric aciduria, due to a defect in L-2-hydroxyglutarate dehydrogenase, by creating and studying a mouse model of this disease. L-2-hydroxyglutarate dehydrogenase-deficient mice (l2hgdh -/-) accumulated L-2-hydroxyglutarate in tissues, most particularly in brain and testis, where the concentration reached ≈ 3.5 μmol/g. Male mice showed a 30% higher excretion of L-2-hydroxyglutarate compared to female mice, supporting that this dicarboxylic acid is partially made in males by lactate dehydrogenase C, a poorly specific form of this enzyme exclusively expressed in testes. Involvement of mitochondrial malate dehydrogenase in the formation of L-2-hydroxyglutarate was supported by the commensurate decrease in the formation of this dicarboxylic acid when down-regulating this enzyme in mouse l2hgdh -/- embryonic fibroblasts. The concentration of lysine and arginine was markedly increased in the brain of l2hgdh -/- adult mice. Saccharopine was depleted and glutamine was decreased by ≈ 40%. Lysine-α-ketoglutarate reductase, which converts lysine to saccharopine, was inhibited by L-2-hydroxyglutarate with a Ki of ≈ 0.8 mM. As low but significant activities of the bifunctional enzyme lysine-α-ketoglutarate reductase/saccharopine dehydrogenase were found in brain, these findings suggest that the classical lysine degradation pathway also operates in brain and is inhibited by the high concentrations of L-2-hydroxyglutarate found in l2hgdh -/- mice. Pathological analysis of the brain showed significant spongiosis. The vacuolar lesions mostly affected oligodendrocytes and myelin sheats, as in other dicarboxylic acidurias, suggesting that the pathophysiology of this model of leukodystrophy may involve irreversible pumping of a dicarboxylate in oligodendrocytes. Neurobehavioral testing indicated that the mice mostly suffered from a deficit in learning capacity. In conclusion, the findings support the concept that L-2-hydroxyglutaric aciduria is a disorder of metabolite repair. The accumulation of L-2-hydroxyglutarate exerts toxic effects through various means including enzyme inhibition and glial cell swelling.
Pigeonpea Biological Seed Coating: Combined Inoculation of Biofertilizers and Bioprotectants

Pigeonpea [Cajanus cajan (L.)] is an important staple food pulse crop rich in protein content of 22%, which is almost three times that of cereals. Throughout the world pigeon pea is cultivated in an area of 6.23 Mha with a production of 4.68 Mt and productivity of 751 kg ha -1 (India stat, 2014-2015). In India, pigeon pea is cultivated in an area of 3.90 mha with a production of 3.17 Mt and productivity of 813 kg ha -1 (IIPR, 2014 and FAO, 2016). The main constraints in obtaining potential yield of the pigeon pea are incidence of diseases, insects and other physiological stresses in the field. Early stages of plant growth (4-6 week old plant) period are mostly susceptible which essentially affects yield. The present investigation is carried out to study the viability and shelf life of Rhizobium and Phosphorus Solubilizing Bacteria in the combined inoculations with either Trichoderma viride or Pseudomonas fluorescens on the biologically coated Pigeonpea seed. The effect of combined inoculation on the viability and shelf life of biofertilizers and seed quality parameters were studied at monthly intervals during storage period of six months. The results indicated that among adjuvants, seed inoculated with biofriendly polymer recorded more colony units and long shelf life than farmer practiced sugar syrup. At the end of six months storage period, both Rhizobium and Phosphorus Solubilizing Bacteria with biofriendly polymer recorded sufficient number of colony units on the surface of biologically coated pigeonpea seed. Both Rhizobium and PSB showed high colony counts with Trichoderma than with Pseudomonas and same trend was recorded throughout the storage period of six months. At the end of storage period, good seed germination and seedling vigour was recorded in the seeds that are co-inoculated with PSB and Pseudomonas than with Trichoderma and Rhizobium. This study reveals that the farmers can be supplied biologically coated seed in advance and the general practice of treating the seed a day prior to sowing can be avoided. K e y w o r d s
Influence of Weave Design and Yarn Types on Mechanical and Surface Properties of Woven Fabric

The purpose of this study was to examine the effect of spinning technologies and weave design on fabric mechanical and surface properties. For this purpose, ring spun (combed, carded) and open-end (OE) techniques were used to manufacture yarns of polyester cotton (50:50) which were used in the weft, and 100% cotton yarn in the warp. Plain, twill, and satin weave designs were selected to construct woven samples on a projectile loom. The variation in fabric tensile strength is obvious with respect to weave designs. Higher interlacing of yarn produces more crimp in the load bearing, which may cause lower breaking strength and fewer broad floats. The mechanical and surface properties of these fabric samples were investigated and statistical analysis was performed, which showed a significant effect of the spinning technique and weave design on these properties.
When It’s Bad to Be Friendly and Smart

Morality, sociability, and competence are distinct dimensions in person perception. We argue that a person’s morality informs us about their likely intentions, whereas their competence and sociability inform us about the likelihood that they will fulfill those intentions. Accordingly, we hypothesized that whereas morality would be considered unconditionally positive, sociability and competence would be highly positive only in moral others, and would be less positive in immoral others. Using exploratory factor analyses, Studies 1a and 1b distinguished evaluations of morality and sociability. Studies 2 to 5 then showed that sociability and competence are evaluated positively contingent on morality—Study 2 demonstrated this phenomenon, while the remaining studies explained it (Study 3), generalized it (Studies 3-5), and ruled out an alternative explanation for it (Study 5). Study 6 showed that the positivity of morality traits is independent of other morality traits. These results support a functionalist account of these dimensions of person perception.
Overcoming Limitations in Semiconductor Alloy Design

Inorganic semiconductors provide an astonishingly versatile, robust, and efficient platform for optoelectronic energy conversion devices. However, conventional alloys and growth regimes face materials challenges that restrict the full potential of these devices. Novel alloy designs based on isoelectronic co-doping, metamorphic growth and controllable atomic ordering offer new pathways to practical and ultra-high-efficiency optoelectronic devices including solar cells and light-emitting diodes. Abnormal isoelectronic alloys of GaP1-xBix, GaP1-x-yBixNy, and GaAs1-xBix with unprecedented bismuth incorporation fractions and crystalline quality are explored in this thesis research. Comparative studies of several GaP1-xBix and GaP1-x-yBixNy alloys demonstrate that the site-specific incorporation of bismuth during epitaxial growth is sensitive to growth temperature and has dramatic effects on carrier transfer processes in these alloys. Additionally, distinctive bismuth-related localized states are spectrally identified for the first time in samples of GaAs1-xBix grown by laser-assisted epitaxial growth. These results address fundamental questions about the nature of bismuth-bismuth inter-impurity interactions.
Tumor Necrosis Factor Disrupts Claudin-5 Endothelial Tight Junction Barriers in Two Distinct NF-κB-Dependent Phases

Capillary leak in severe sepsis involves disruption of endothelial cell tight junctions. We modeled this process by TNF treatment of cultured human dermal microvascular endothelial cell (HDMEC) monolayers, which unlike human umbilical vein endothelial cells form claudin-5-dependent tight junctions and a high-resistance permeability barrier. Continuous monitoring with electrical cell-substrate impedance sensing revealed that TNF disrupts tight junction-dependent HDMEC barriers in discrete steps: an ~5% increase in transendothelial electrical resistance over 40 minutes; a decrease to ~10% below basal levels over 2 hours (phase 1 leak); an interphase plateau of 1 hour; and a major fall in transendothelial electrical resistance to < 70% of basal levels by 8–10 hours (phase 2 leak), with EC50 values of TNF for phase 1 and 2 leak of ~30 and ~150 pg/ml, respectively. TNF leak is reversible and independent of cell death. Leak correlates with disruption of continuous claudin-5 immunofluorescence staining, myosin light chain phosphorylation and loss of claudin-5 co-localization with cortical actin. All these responses require NF-κB signaling, shown by inhibition with Bay 11 or overexpression of IκB super-repressor, and are blocked by H-1152 or Y-27632, selective inhibitors of Rho-associated kinase that do not block other NF-κB-dependent responses. siRNA combined knockdown of Rho-associated kinase-1 and -2 also prevents myosin light chain phosphorylation, loss of claudin-5/actin co-localization, claudin-5 reorganization and reduces phase 1 leak. However, unlike H-1152 and Y-27632, combined Rho-associated kinase-1/2 siRNA knockdown does not reduce the magnitude of phase 2 leak, suggesting that H-1152 and Y-27632 have targets beyond Rho-associated kinases that regulate endothelial barrier function. We conclude that TNF disrupts TJs in HDMECs in two distinct NF-κB-dependent steps, the first involving Rho-associated kinase and the second likely to involve an as yet unidentified but structurally related protein kinase(s).
Time Trends of Period Prevalence Rates of Patients with Inhaled Long-Acting Beta-2-Agonists-Containing Prescriptions: A European Comparative Database Study

Background Inhaled, long-acting beta-2-adrenoceptor agonists (LABA) have well-established roles in asthma and/or COPD treatment. Drug utilisation patterns for LABA have been described, but few studies have directly compared LABA use in different countries. We aimed to compare the prevalence of LABA-containing prescriptions in five European countries using a standardised methodology. Methods A common study protocol was applied to seven European healthcare record databases (Denmark, Germany, Spain, the Netherlands (2), and the UK (2)) to calculate crude and age- and sex-standardised annual period prevalence rates (PPRs) of LABA-containing prescriptions from 2002–2009. Annual PPRs were stratified by sex, age, and indication (asthma, COPD, asthma and COPD). Results From 2002–2009, age- and sex-standardised PPRs of patients with LABA-containing medications increased in all databases (58.2%–185.1%). Highest PPRs were found in men ≥ 80 years old and women 70–79 years old. Regarding the three indications, the highest age- and sex-standardised PPRs in all databases were found in patients with “asthma and COPD” but with large inter-country variation. In those with asthma or COPD, lower PPRs and smaller inter-country variations were found. For all three indications, PPRs for LABA-containing prescriptions increased with age. Conclusions Using a standardised protocol that allowed direct inter-country comparisons, we found highest rates of LABA-containing prescriptions in elderly patients and distinct differences in the increased utilisation of LABA-containing prescriptions within the study period throughout the five European countries.