Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural basis for the substrate specificity of the feruloyl esterase domain of the cellulosomal xylanase Z from Clostridium thermocellum.

Feruloyl esterases function in the cleavage of ferulic acid's bonds to arabinoxylan and pectin where the ferulic acid moieties cross-link the layers of polysaccharide chains within hemicellulose. This work presents the crystal structure of FAE_XynZ, the domain of Clostridium thermocellum's cellulosomal xylanase Z that displays feruloyl esterase activity. The structure was obtained via multiple isomorphous replacement with anomalous scattering (MIRAS) using three heavy atom derivatives and refined against X-ray diffraction data of up to 1.75 A resolution. The R-value of the final model was 0.187 (R(free) = 0.21). FAE_XynZ displays an eight-stranded alpha/beta-fold with the characteristic "catalytic triad" at the heart of the active site. To define the substrate specificity determinants of the enzyme, the crystal structures of FAE_XynZ and the inactive FAE_XynZ(S172A) mutant were determined in complexes with the feruloyl-arabinoxylans FAXX and FAX(3), respectively. In the complex crystals, the ferulic acid moieties are clearly recognizable and allowed identification of the hydrophobic binding pocket. The carbohydrate part of both substrates is not visible in either structure. The location of the putative carbohydrate binding-pocket was inferred based on the location and orientation of the adjacent ferulic acid molecule. Five of the six residues lining the pocket were found to be conserved in FAE A from Orpinomyces sp. , which further supports the proposed role of these amino acids.
Green gentrification: Urban sustainability and the struggle for environmental justice, by Kenneth A. Gould and Tammy L. Lewis

Clark, D. (2003). Urban world/global city (2nd ed.). London, UK: Routledge. Grossman, J. R. , Keating, A. D. , & Reiff, J. L. (Eds.) (2004). The Encyclopedia of Chicago. Chicago, IL: University of Chicago Press. Harvey, D. (2005). A brief history of neoliberalism. Oxford, UK: Oxford University Press. Locke, J. (1993). Two treatises of government: An essay concerning the true original extent and end of civil government. Cambridge, UK: Everyman Press. (Original work published 1669) Perry, D. C. , & Villamizar-Duarte, N. (2016). The social contract: A political and economic overview. InM.A. Pagano (Ed.), Remaking the urban social contract: Health, energy, and the environment (pp. 3–32). Chicago, IL: University of Illinois Press. Rawls, J. (1999). A theory of justice (2nd ed.). Cambridge, MA: Harvard University Press. Sassen, S. (1991). The global city: New York, London, Tokyo. Princeton, NJ: Princeton University Press. Skidelesky, R. (2015). The essential Keynes. New York, NY: Penguin.
The study of Salmonellaenteritidis growth kinetics using Rapid Automated Bacterial Impedance Technique

In order to study strain‐specific differences in their growth behaviour at different, and particularly lower, temperatures, generation times for 45 strains of Salmonella enteritidis isolated from food were determined impedimetrically over a temperature range from 7 to 42 °C. In practical terms, 7 °C is the minimum requirement for Salm. enteritidis growth, and generation time variability increases markedly as this temperature is reached. Reports in the literature describing psychrotrophic behaviour and multiplication at lower temperatures cannot be confirmed. Generation time variability increased as temperature moved away from the optimal range with variation coefficients tending to rise as temperature fell. The great variability of multiplication parameters near the growth limit found in Salm. enteritidis may also be a characteristic of other bacterial species. It is therefore imperative to commence studies on larger numbers of strains to allow prediction of their behaviour at lower temperatures.
Assessment of side effects induced by injection of different adjuvant/antigen combinations in rabbits and mice

We evaluated the side effects induced by injection of Freund's adjuvant (FA) and alternative adjuvants combined with different antigens. Rabbits and mice were injected subcutaneously, intramuscularly (rabbits) and intraperitoneally (mice) with different adjuvants (FA, Specol, RIBI, TiterMax, Montanide ISA50) in combination with several types of antigens (synthetic peptides, autoantigen, glycolipid, protein, mycoplasma or virusesl. The effects of treatment on the animals' well-being were assessed by clinical and behavioural changes (POT and LABORAS assays) and gross and histopathological changes. In rabbits, treatment did not appear to induce acute or prolonged pain and distress. Mice showed behavioural changes immediately after (predominantly secondary) immunization. Injection of several adjuvant/antigen mixtures resulted in severe pathological changes, depending on adjuvant, type of antigen, animal species used and route of injection. Both rabbits and mice showed pathological changes ranging from marked to severe after injection of FA, and ranging from minimal to marked after Specol and Montanide injections. Pathological changes after RIBI injections were severe in rabbits, though slight in mice. After TiterMax injections, pathological changes were moderate in rabbits, though severe in mice. In conclusion, injection of FA according to present guidelines resulted mostly in severe pathological changes, whereas only very few clinical and behavioural signs indicated prolonged severe pain. Our findings indicate that Montanide ISA50 and Specol induce acceptable antibody titres, and cause fewer pathological changes than FA. Thus they are effective alternatives to FA.
Affects and autonomic cardiac reactivity during experimentally induced stress as related to precursors of insulin resistance syndrome

This study examined the association of insulin resistance syndrome (IRS) precursors with state affects and autonomic reactivity in randomly selected healthy young adults. It was asked whether IRS precursors are able to predict a person’s mental and physiological coping with acute stress over an 11-year follow-up period. IRS parameters were serum insulin, high-density lipoprotein cholesterol, triglycerides, systolic blood pressure, body-mass index, and subscapular skinfold thickness. In the psychophysiological experiment, state affects and cardiac responses (heart rate, respiratory sinus arrhythmia, and pre-ejection period) were measured during different challenges. The main result was that IRS precursors predicted high levels of negative emotions during the challenges; IRS accounted for 19% of the variance in tiredness. IRS was unrelated to cardiac reactivity. Mechanisms underlying the associations found are discussed.
Inositol hexakisphosphate kinase-2 acts as an effector of the vertebrate Hedgehog pathway

Inositol phosphate (IP) kinases constitute an emerging class of cellular kinases linked to multiple cellular activities. Here, we report a previously uncharacterized cellular function in Hedgehog (Hh) signaling for the IP kinase designated inositol hexakisphosphate kinase-2 (IP6K2) that produces diphosphoryl inositol phosphates (PP-IPs). In zebrafish embryos, IP6K2 activity was required for normal development of craniofacial structures, somites, and neural crest cells. ip6k2 depletion in both zebrafish and mammalian cells also inhibited Hh target gene expression. Inhibiting IP6 kinase activity using N(2)-(m-(trifluoromethy)lbenzyl) N(6)-(p-nitrobenzyl)purine (TNP) resulted in altered Hh signal transduction. In zebrafish, restoring IP6K2 levels with exogenous ip6k2 mRNA reversed the effects of IP6K2 depletion. Furthermore, overexpression of ip6k2 in mammalian cells enhanced the Hh pathway response, suggesting IP6K2 is a positive regulator of Hh signaling. Perturbations from IP6K2 depletion or TNP were reversed by overexpressing smoM2, gli1, or ip6k2. Moreover, the inhibitory effect of cyclopamine was reversed by overexpressing ip6k2. This identified roles for the inositol kinase pathway in early vertebrate development and tissue morphogenesis, and in Hh signaling. We propose that IP6K2 activity is required at the level or downstream of Smoothened but upstream of the transcription activator Gli1.
[The effects of intestinal parasites on anemia of children].

OBJECTIVE In this case-control epidemiological study, we aimed to investigate the effects of intestinal parasites on the anemia of children and show the association between intestinal parasites and anemia. METHODS A total of 50 healthy and 50 malnourished children aged 0-72 months who went to physicians of Tilfindir Primary Health Care Center were enrolled in this study. The stool specimens were examined by using native-lugol, concentration, cellophane tape, and acid fast and trichrome staining methods. The complete blood count was measured by an automatic blood device. RESULTS A total of 58% of the children were infected with intestinal parasites; 55.2% of these were infected with only one parasite, and 44.8% of them were infected with polyparasites. Also, 50.0% of the children with parasitic infection and 19.0% of children without parasitic infection were anemic. There was a positive association between intestinal parasites and anemia statistically (p<0.05). The mean hemoglobin level of the children with parasitic infection was 11.15±1.30, and the mean hemoglobin level of the children without parasitic infection was 12.13±1.47. There was a significant difference between mean hemoglobin levels of the two groups statistically (p<0.001). CONCLUSION Consequently, this study emphasized that intestinal parasites can affect the anemia of children adversely, and there was a positive association between intestinal parasites and anemia of children.
Novel VCO Architecture Using Series Above-IC FBAR and Parallel LC Resonance

A quasi-monolithic voltage-tunable film bulk acoustic resonator (FBAR) enhanced oscillator for 2.1 GHz in 0.25-mum SiGe BiCMOS technology is designed, fabricated, and evaluated. The narrow-band FBAR was built above the SiGe circuit through later Si post-processing steps. The oscillator is based on a two-transistor loop structure and uses two resonators, namely a parallel LC tank and an above-IC FBAR in its series-resonant mode. The improvement in phase noise performance is significant compared to a similar reference LC voltage-controlled oscillator (VCO), with the best phase noise being -144.1 dBc/Hz at an offset of 1 MHz and -149.6 dBc/Hz at 3 MHz. The architecture offers advantages in overcoming frequency tuning difficulties usually present when using high-Q resonators. Although the width of the tuning range comes at some cost on phase noise, the measured performance satisfies contemporary wireless standards such as GPS
Overlapping divergent transcripts mapping to the HindIII F region of the Autographa californica nuclear polyhedrosis virus.

We have mapped a set of transcripts that cross the XhoI site in the HindIII F fragment of the genome of the Autographa californica nuclear polyhedrosis virus. These transcripts overlap at their 5' ends by about 550 bases and run in opposite directions. We have tentatively identified two open reading frames corresponding to the leftward transcript. The rightward transcript is present from 8 h post-infection (p.i.) to 24 h p.i. ; the leftward transcripts are present from 2 h p.i. to 24 h p.i. The early (2 h) transcript is about 2.1 kb in size and its 5' end maps about 504 bp to the right of the XhoI site. Beginning at about 8 h p.i. a new transcription start site is used, about 80 bp downstream (to the left) of the first. The late (rightward) transcript is about 1.2 kb in size; its 5' end seems to be heterogeneous and maps about 44 to 60 bp to the left of the XhoI site. Late in infection transcription proceeds in both directions at the same time through the overlapping region of the DNA encoding these transcripts.
Dynamic Product‐Level Analysis of In‐Use Aluminum Stocks in the United States

This study estimates product‐level in‐use stocks of aluminum in the United States for the period 1960–2009 (or longer in some cases) and explores patterns of the historical evolution of in‐use aluminum stocks at both product and sector levels. The principal findings are the following: (1) results estimated by the product‐level methods in this study match reasonably well with those estimated by the sector‐level method for five sectors (except the Machinery and Equipment sector), meaning that the methods verify the robustness and reliability of each other; (2) after early period(s) of increase since aluminum‐containing products were introduced into the market, in‐use aluminum stocks at the product level, based on either absolute, per capita, or per household terms, follow one of four different patterns (Increase, Decrease, Saturation, and Fluctuation), determined by the historical evolution of product stocks and flows and aluminum contents in products; and (3) when aggregated, in‐use aluminum stocks at the product level can be used to compare with and explain the historical evolution of the in‐use aluminum stocks at the sector level that are estimated by the top‐down method, with only a few products dominating or significantly influencing the historical evolution pattern for a whole sector. These results may enable manufacturers, metal suppliers, recyclers, and governments to plan their material‐related policies and actions with increased precision compared to previous top‐down results that are only available at the sector level.
Changes in positive affect and mindfulness predict changes in cortisol response and psychiatric symptoms: A latent change score modelling approach

Objective: This study examined whether and how changes in positive affect and mindfulness predicted changes in cortisol secretion and psychological distress in adaptation to examination stress. Design: A sample of 105 college students completed a questionnaire set and provided salivary samples before (T1), during (T2) and after (T3) an examination period. Results: Latent change score modelling revealed that T1–T2 and T2–T3 increases in mindfulness were associated with larger T2–T3 decrease in area-under-the-curve ground of cortisol awakening response (CARg), whereas T2–T3 increases in both positive affect and mindfulness were associated with larger T2–T3 decrease in anxiety symptoms (comparative fit index = .96; Tucker-Lewis index = .93–.95; root-mean-square error of approximation = .04–.08; standardised root-mean-square residual = .08–.10). T1–T2 and T2–T3 increases in positive affect were not associated T2–T3 decrease in CARg, whereas T1–T2 increases in positive affect and mindfulness were not associated with T2–T3 decrease in anxiety symptoms. Conclusion: The levels of post-stress recovery from anxiety symptoms could depend on concurrent increases in positive affect and mindfulness, whereas the levels of post-stress decline in cortisol secretion could depend on increases in mindfulness both during and after stress. Directions for translating the present findings into stress management programmes in college settings are discussed.
Characterization of MTHFR, GSTM1, GSTT1, GSTP1, and CYP1A1 genotypes in childhood acute leukemia

The role of methylenetetrahydrofolate reductase (MTHFR C677T), glutathione S‐transferases (GSTM1 and GSTT1 null, GSTP1 Ile105Val), and cytochromes p450 (CYP1A1*2A) genotypes in the etiology of childhood leukemia was simultaneously investigated. 144 Turkish children with acute lymphoblastic leukemia (ALL) and 33 with acute nonlymphoblastic leukemia (ANLL) were studied and compared with 185 healthy pediatric controls. The frequency of MTHFR genotype was insignificantly higher in ALL (7.7%) and ANLL (6.3%) than in controls (4.4%). Equal distribution of the GSTM1 null genotype was detected between ALL patients and controls (55%), while its incidence was slightly higher in ANLL patients (61.3%). Although GSTT1 null genotype was insignificantly lower in ALL patients (20.9%) than controls (22.7%), it was significantly underrepresented in ANLL patients (6.5%) (P = 0.05, OR 0.24, 95% CI 0.05–1.03). The homozygous frequency of GSTP1 genotype did not differ significantly between groups of ALL (3.7%), ANLL patients (9.1%) and controls (4.9%). Homozygous CYP1A1*2A genotype was underrepresented in ALL patients (1%) as compared to control (4.8%) but the differences did not reach to statistical significance (OR 0.21; 95% CI 0.03–1.72). Homozygosity for this genotype was not detected in ANLL patients. No particular association was noted between different combinations of combined genotypes and risk of development of childhood ALL and ANLL. These results suggested that there are no significant associations between the studied genotypes and the risk of developing either form of acute leukemia except GSTT1 null and homozygosity for CYP1A1 genotypes that may play protective roles in the development of ANLL in Turkish children. Am. J. Hematol. 73:154–160, 2003. © 2003 Wiley‐Liss, Inc.
Collaborative Practice and Patient Satisfaction

The Collaborative Practice Project was a demonstration project sponsored by the Hartford Hospital Administration, and the Departments of Medicine and Nursing. A prospective evaluative study was established to measure the impact of collaborative practice on increased patient and family satisfaction with health care, as well as the impact on selected outcome variables. A specific 27-bed medical unit and a comparison unit with identical structural characteristics were chosen for study from March 31, 1982, to March 31, 1983. Results of the study indicate that significant differences in patients' perceptions of care existed between the Collaborative Practice Unit (CPU) and the comparison unit under a traditional team nursing system. More positive ratings from patients on the CPU were found for all selected dimensions: patient-provider interaction; quality of care; health education; knowledge of practitioners; and the environment. In order to assess the impact of collaborative practice on outcome variables, a retrospective audit of randomly selected patient records was done. No significant differences for selected variables were found except for the number of health teaching plans. More documented health teaching was recorded on the Team Nursing Unit.
DNA Barcoding Distinguishes Pest Species of the Black Fly Genus Cnephia (Diptera: Simuliidae)

ABSTRACT Accurate species identification is essential for cost-effective pest control strategies. We tested the utility of COI barcodes for identifying members of the black fly genus Cnephia Enderlein (Diptera: Simuliidae). Our efforts focus on four Nearctic Cnephia species—Cnephia dacotensis (Dyar & Shannon), Cnephia eremities Shewell, Cnephia ornithophilia (Davies, Peterson & Wood), and Cnephia pecuarum (Riley)—the latter two being current or potential targets of biological control programs. We also analyzed one Palearctic species, Cnephia pallipes (Fries). Although Cnephia adults can be identified anatomically to species, control programs target the larval stage, which is difficult or impossible to distinguish morphologically. By using neighborjoining, maximum parsimony, and Bayesian methods, we found that COI barcodes successfully identified three Nearctic Cnephia species, but not C. pecuarum. The Palearctic C. pallipes was also successfully identified. Despite nonmonophyly of C. pecuarum, we show that data from COI barcoding, in combination with geographical and ecological information, can be used to distinguish all four Nearctic species. Finally, we discussed 1) possible reasons for paraphyly in C. pecuarum, 2) topological concordance to previously reported chromosomal dendrograms, and 3) evolution of diverse feeding strategies within the genus Cnephia.
Characterization of chromosome aberrations in salivary gland tumors by FISH, including multicolor COBRA‐FISH

Fluorescence in situ hybridization (FISH), including COBRA‐FISH, was used to characterize 11 salivary gland tumors that had been investigated by banding analysis. Five cases were pleomorphic adenoma (PA), three were adenoid cystic carcinoma, and one case each was mucoepidermoid carcinoma, carcinoma ex‐pleomorphic adenoma (CaPA), and adenocarcinoma. All 11 cases were selected on the basis that they had shown rearrangement of 6q or 9p or had unresolved aberrations after karyotyping. The COBRA‐FISH and FISH analyses led to a revised karyotype in all informative cases and made it possible to clarify almost all chromosomal rearrangements occurring in the tumors. Of particular note were the confirmation of the existence of 6q deletions, a common change in salivary gland carcinomas, and the demonstration that a seemingly balanced t(6;9) resulted in del(6q). Other rearrangements that were revealed by FISH included amplification of 12q sequences (MDM2 and CDK4) in one PA. We also investigated the status of the PLAG1 gene in four cases (one PA, one CaPA, one adenoid cystic carcinoma, and one mucoepidermoid carcinoma) with 8q12 rearrangements. Only in the former two cases were the FISH results compatible with intragenic rearrangements. Overall, the results of the study show that, even with good banding quality and in karyotypes of modest complexity, much new information will be gained by supplementing the banding analysis with a multicolor FISH approach, such as COBRA‐FISH. © 2000 Wiley‐Liss, Inc.
The Tragedy of Forestland Sustainability in Postcolonial Africa: Land Development, Cocoa, and Politics in Côte d’Ivoire

Tropical countries are often blamed for not managing their natural resources sustainably. But what if overexploitation is inherent in political structures and policies—rooted in foreign colonial order—and is consistently detrimental in the contemporary use of forestlands? This article argues that post-colonial land development policies and related political interests seriously impede the sustainability of forest ecosystems in Côte d’Ivoire. Methodologically, the study builds on a historic contextualisation of forestland use policies in Sub-Saharan Africa, with Côte d’Ivoire serving as a case study. The results indicate that the increasing development of so-called rent crops clearly follows the historical dynamics of ‘land grabbing’ and a post-colonial agrarian model. This situation benefits agribusiness entrepreneurs and, more recently, sustainability standards. The study discusses the findings based on recent literature and empirical evidence. In conclusion, the post-colonial heritage and the manipulation of the related patterns by elites and policy-makers largely explains the present-day unsustainable forestland conversions in Côte d’Ivoire.
Seasonality of dizziness and vertigo in a tropical region

Vertigo and dizziness are among the most common medical complaints in the emergency room, and are associated with a considerable personal and health care burden. Scarce and conflicting reports indicate those symptoms may present a seasonal distribution. This study aimed at investigating the existence of a seasonal distribution of vertigo/dizziness in a tropical region, and the correlations of these findings with climatic variables. The charts of all patients consecutively admitted between 2009 and 2012 in the emergency room of a Brazilian general hospital were reviewed. A total of 4920 cases containing these terms were sorted from a sample of 276 076 emergency records. Seasonality was assessed using Cosinor Analysis. Pearson's correlations were performed between the incidence of consultations, considering separately dizziness and vertigo and each of the predictor climatic variables of that index month. Significant seasonal patterns were observed for dizziness and vertigo in the emergency room. Vertigo was more frequent in late winter–spring, negatively correlating to humidity (r = −0.374; p = 0.013) and rainfall (r = −0.334; p = 0.020). Dizziness peaked on summer months, and positively correlated to average temperatures (r = 0.520; p < 0.001) and rainfall (r = 0.297; p = 0.040), but negatively to atmospheric pressure (r = −0.424; p = 0.003). The different seasonal patterns evidenced for dizziness and vertigo indicate possible distinct underlying mechanisms of how seasons may influence the occurrence of those symptoms.