Miracle-dz/UniFAR-FTUs huggingface dataset:
The rat albumin promoter: cooperation with upstream elements is required when binding of APF/HNF1 to the proximal element is partially impaired by mutation or bacterial methylation

We have characterized in the accompanying paper (P. Herbomel, A. Rollier, F. Tronche, M.-O. Ott, M. Yaniv, and M. C. Weiss, Mol. Cell. Biol. 9:4750-4758, 1989) six different elements in the albumin promoter. One of them, the proximal element (PE), is the binding site for a strictly liver specific factor, APF/HNF1. This binding site contains a bacterial DAM DNA methylase methylation target sequence which, when methylated, decreases the affinity of the protein for this element. When the different albumin promoter constructions were prepared in an Escherichia coli deoxyadenosine methylase-negative strain, the respective contributions of the elements to the overall promoter activity were strikingly different. An intact proximal element plus the TATA box gave almost full transcriptional activity in transient transfection experiments and only in differentiated hepatoma cells of line H4II, whereas the distal elements (distal element III [DEIII], the NF1-binding site DEII, and the E/CBP-binding site DEI) had become essentially dispensable. Mutations affecting the CCAAT box showed only a two- to threefold decrease. When PE was methylated, mutated, or replaced by the homologous element from the alpha-fetoprotein gene, activity in the context of the short promoter (PE plus the TATA box) was abolished. However, activity was restored in the presence of the upstream elements, showing that cooperation with factors binding to the CCAAT box and distal elements favors the functional interaction of the liver-specific APF/HNF1 factor with lower-affinity binding sites.
Effects of Host Plant Phenology on Oviposition Preference of Crocidolomia pavonana (Lepidoptera: Pyralidae)

Abstract Field studies have demonstrated mixed success in trap cropping to manage Crocidolomia pavonana (=binotalis) [F. ], a major pest of cruciferous crops in Asia. A possible explanation for this is an influence of host plant phenology on oviposition preference. We tested this in simultaneous two-choice oviposition bioassays under laboratory conditions. In cylindrical cardboard experimental arenas, with 5-cm2 leaf windows, individual C. pavonana females were offered eight sequential phenological stages of cabbage (Brassica oleracea L., Capitata group, cultivar Gloria) with a constant stage of preflowering Indian mustard (Brassica juncea, variety rugosa, cultivar Green Wave). Results showed a significant effect of cabbage developmental stage on oviposition preference. We continued with two-choice bioassays, using whole leaves, in screen cage experimental arenas. Females were offered the three most preferred phenological stages of cabbage and differing stages of four potential trap crop alternatives: preflowering Indian mustard; preflowering Chinese cabbage (B. rapa L., variety pekinensis [Lour.] Olsson); preflowering, flowering, and “with silique” sawi manis (B. rapa, variety parachinensis [Bailey] Tsen and Lee); and preflowering and flowering sayur pahit (B. rapa, variety parachinensis [Bailey] Tsen and Lee). Results indicated that the phenological stages of both plants had a significant effect on relative oviposition preference. However, patterns of preference changed in the context of the different plant species combinations. In addition, implicit hierarchical preference order was frequently contradicted. These results have implications for the improvement of trap cropping strategies to manage C. pavonana and for the potential success of biological control of Plutella xylostella [L. ], where these pests occur in complex.
Formulation development and investigation of domperidone transdermal patches

Aim and Background: Domperidone is a dopamine antagonist with antiemetic properties having a plasma half life of 7-9 h with 15% oral bioavailability. In the present work transdermal patches of domperidone were prepared with the objective to improve its therapeutic efficacy, patient compliance and to reduce the frequency of dosing and side effects, as well as to avoid its extensive first pass metabolism of the drug. Materials and Methods: The patches were prepared using ethyl cellulose (EC): Poly vinyl pyrrolidone (PVP), poly vinyl alcohol (PVA): Poly vinyl pyrrolidone (PVP) and hydroxypropylmethylcellulose (HPMC): Sodium (carboxy methyl cellulose) CMC as polymers in combination. The physicochemical parameters like thickness, drug content, weight variation, moisture absorption and drug permeation studies were evaluated for the prepared patches. No significant difference in thickness, average weight and in the drug content among the patches. Results: It was observed that from hydrophilic polymers the drug release was found to be faster compared to (F5 and F6 & F3 and F4) combination of hydrophilic and lipophilic polymers used in the study. Patches containing HPMC and Sodium CMC (F5 and F6) showed faster release as the patches showed maximum percentage amount moisture absorption. The in vitro release data was treated with kinetic equations and it followed Higuchi's diffusion mechanism. The in vivo bioavailability study was performed in rats and observed that, drug reached to the peak in approximately 60 min (16%) after oral route of administration. However, approximately same amount of drug was found in the serum from transdermal formulation in 6 h and further increase in the amount of drug in the serum, indicated that the drug 5 bioavailability could be better and hence the hepatic metabolism can be avoided, as it is evident from the data. Further, the decrease in the amount of drug present in the serum 45 min after oral administration also indicated that major amount of drug might have got metabolized and the bioavailability is reduced. However, the transdermal patch released further amount of drug (33%) at the end of 24 h. Conclusion: The present study can be concluded that transdermal patch can extend the release of drug for many hours with better bioavailability and also can avoid the first pass effect.
Initial Public Offering Prospectus Forecast Errors and Mandatory Explanations: Evidence from New Zealand

This paper examines management forecast errors in initial public offering (IPO) prospectuses of New Zealand firms and subsequent management explanations for earnings forecast errors in recent years. New Zealand has several unique features and recent changes that are worthy of research, including the requirement for management to make forecasts; a requirement to explain differences between forecast and actual; and a recent change that provides the voluntary opportunity to obtain a negative assurance opinion on forecasts. Using hand‐collected IPO data between 1998 and 2014, we find that firms that include a negative assurance opinion on the prospective financial information in the prospectus have more accurate earnings and cash flow forecasts. We investigate the subsequent explanations for forecast errors, which are mandated by a financial reporting standard. We show that management tends to attribute negative and large forecast errors to external causes rather than their own actions. Our findings have implications for regulators and investors in New Zealand and other settings.
Lactose Malabsorption, Calcium Intake, and Bone Mass in Children and Adolescents

Objectives: The objective of the present study was to evaluate the calcium intake and bone mass in children and early adolescents in accordance with their absorption capacity to lactose. Patients and Methods: A transversal study was conducted on a sample composed of 76 individuals. Lactose malabsorption status was determined with hydrogen breath test. The hydrogen breath test was applied using 2 g of lactose per kilogram of weight up to a maximum of 50 g. A hydrogen increment ≥20 ppm in relation to fasting was used to characterize lactose malabsorption. Two 24-hour recalls were applied for the evaluation of food consumption. Bone mineral content and bone mineral density were evaluated in the lumbar spine by dual-energy x-ray absorptiometry. Results: The prevalence of lactose malabsorption was 61.8%. The participants were divided into 2 groups: lactose malabsorbers (n = 47) and lactose absorbers (n = 29). There was no statistically significant difference (P > 0.05) between the groups with respect to the intake of total calcium, milk calcium, milk, cheese, yogurt, ice cream, and calcium density of the diet. Additionally, there was no difference with respect to the bone mineral content and the bone mineral density of the lumbar spine. Independent from lactose absorption capacity, it was observed that the majority of the children and early adolescents showed calcium intake lower than the recommended value. Conclusions: There was no relation among lactose malabsorption and bone densities, bone mineral content, or calcium intake within the present study.
Study of dynamic pressure-induced refractive index change using derivative total reflection method

Abstract. We report the dynamic refractive index (RI) change of tissue under a stepped compression load using a custom-built pressure apparatus. Angle-dependent reflectance profiles of biotissue samples are recorded, and the RI values are resolved using the derivative total reflection method. These results are relevant for understanding the mechanism of mechanical optical clearing, for investigating tissue dynamics under mechanical stimuli, and for other biomedical applications.
Determinants of Judgments of Explanatory Power: Credibility, Generality, and Statistical Relevance

Explanation is a central concept in human psychology. Drawing upon philosophical theories of explanation, psychologists have recently begun to examine the relationship between explanation, probability and causality. Our study advances this growing literature at the intersection of psychology and philosophy of science by systematically investigating how judgments of explanatory power are affected by (i) the prior credibility of an explanatory hypothesis, (ii) the causal framing of the hypothesis, (iii) the perceived generalizability of the explanation, and (iv) the relation of statistical relevance between hypothesis and evidence. Collectively, the results of our five experiments support the hypothesis that the prior credibility of a causal explanation plays a central role in explanatory reasoning: first, because of the presence of strong main effects on judgments of explanatory power, and second, because of the gate-keeping role it has for other factors. Highly credible explanations are not susceptible to causal framing effects, but they are sensitive to the effects of normatively relevant factors: the generalizability of an explanation, and its statistical relevance for the evidence. These results advance current literature in the philosophy and psychology of explanation in three ways. First, they yield a more nuanced understanding of the determinants of judgments of explanatory power, and the interaction between these factors. Second, they show the close relationship between prior beliefs and explanatory power. Third, they elucidate the nature of abductive reasoning.
Changes in Regional Cerebral Oxidative Metabolism Induced by Tactile Learning and Recognition in Man

We measured the regional cerebral oxidative metabolism (rCMRO2) with positron emission tomography in normal healthy volunteers in three different stages: rest, tactile learning, and tactile recognition of complicated geometrical objects. The frequency of manipulatory movements during tactile recognition was twice that of tactile learning. Tactile recognition with the right hand increased rCMRO2 in six prefrontal cortical areas, bilaterally in the supplementary motor areas, the premotor areas and supplementary sensory areas, in the left primary motor and primary sensory area, in the left anterior superior parietal lobule, bilaterally in the secondary somatosensory area, the anterior insula, lingual gyri, hippocampus, basal ganglia, anterior parasagittal cerebellum, and lobus posterior cerebelli. These structures have in other studies been found to participate in manipulatory movements and analysis of somatosensory information. Tactile learning increased rCMRO2 in the same structures as did tactile recognition. Thus we found no differences in the anatomical structures participating in storage and retrieval. However the rCMRO2 increases in the left premotor cortex, supplementary motor area, and left somatosensory hand area were larger during tactile recognition in accordance with the higher frequency of manipulatory movements and higher flux of somatosensory information from the periphery during recognition. Despite this the rCMRO2 was significantly higher in the neocerebellar cortex during tactile learning. Since there were no learning effects on the manipulatory movements, this extra metabolic activity in the lateral cerebellum was attributed to energy demanding processes associated with climbing fibre activity during storage of somatosensory information.
BELIEF-TWISTING SHOCKS AND THE MACROECONOMY

I study the role of shocks to beliefs combined with Bayesian learning in a standard equilibrium business cycle framework. In particular, I examine how a prior belief arising from the Great Depression may have influenced the macroeconomy during the last 75 years. In the model, households hold twisted beliefs concerning the likelihood and persistence of recession and boom states that are affected by the Great Depression. These initial beliefs are substantially different from the true data generating process and are only gradually unwound during subsequent years. Even though the driving stochastic process for technology is unchanged over the entire period, the nature of macroeconomic performance is altered considerably for many decades before eventually converging to the rational expectations equilibrium. This provides some evidence of the lingering effects of beliefs-twisting events on the behavior of macroeconomic variables.
Bank credit and money creation in a DSGE model of a small open economy

ABSTRACT By the act of lending banks do not actually intermediate pre-accumulated real resources but rather create new financial resources in the form of deposits. Therefore, bank credit needs to be modelled as a monetary phenomenon, which directly fuels domestic demand and inflationary pressures. So far, there have been just a few attempts to model banks as monetary institutions in the DSGE model. In this paper we propose a simple DSGE model, which nevertheless accommodates banks as genuinely monetary institutions and captures banks' institutional ability to create money. Our model features a small open economy with nominal prices, savers and borrowers and a banking sector. Following an exogenously induced shock to banker's willingness to lend, the bank does not have to raise deposit rates or significantly increase borrowing from abroad as deposit dynamics closely resembles that of credit, which allows us to analyse real and nominal consequences of bank credit (and money) creation.
The Relationships among Constructs in the Health Belief Model and the Transtheoretical Model among African-American College Women for Physical Activity

Purpose. Health Belief Model (HBM) and Transtheoretical Model concepts were used to investigate possible differences in perceptions of physical activity among African-American college women categorized by their stage of physical activity behavior. Methods. A survey was administered to 233 participants to assess their stage of physical activity behavior and HBM perceptions. Analysis of variance was used to investigate possible differences among HBM constructs for each behavior stage. Results. Perceived barriers were significantly higher (p < .05), and perceived severity, cues to action, and self-efficacy were significantly lower in the inactive group than in the active group. For example, perceived barriers were significantly higher in the inactive (mean = 2.3) stage than in the preparation (mean = 2.1), action (mean = 1.9), and maintenance (mean = 1.7) stages of physical activity behavior. Discussion. The results suggest that many perceptions of physical activity differ significantly among stages of behavior in this sample of African-American college women. A limitation was that some scales were modified specifically for this population and were not validated.
PKC‐dependent regulation of the receptor locus dominates functional consequences of cysteinyl leukotriene type 1 receptor activation

Leukotrienes are important lipid mediators of asthma that contribute to airway inflammation and bronchoconstriction. Critical mechanisms for physiological regulation of the main G protein‐coupled receptor (GPCR) mediating the leukotriene responses in asthma, cysteinyl leukotriene type 1 receptor (CysLT1R), have not been delineated. Although desen‐sitization of GPCRs is a well‐established phenomenon, studies demonstrating its physiological relevance are lacking. Here, we demonstrate that relief of PKC‐mediated desensitization of endogenous CysLT1Rs augments multiple LTD4‐stimulated cellular functions, with associated increases in intracellular signaling events. In analyses of airway smooth muscle contraction ex vivo, PKC inhibition augmented LTD4‐stimulated contraction, and increased phosphoinositide hydrolysis and calcium flux in both murine and human airway smooth muscle cells. Similarly, for human monocytes, PKC inhibition augmented LTD4‐stimulated calcium flux and cell migration assessed in transwell chamber experiments and also augmented LTD4‐induced production of monocyte chemotactic protein assessed by ELISA. In contrast, PKC inhibition had no effect or slightly attenuated these cell functions and signaling events promoted by other receptor agonists, suggesting that despite antithetical effects on downstream events, desensitization of the CysLT1R is the principal mechanism by which PKC regulates the functional consequences of CysLTIR activation. —Deshpande, D. A. , Pascual, R. M. , Wang, S. ‐W. , Eckman, D. M. , Riemer, E. C. , Funk, C. D. , Penn, R. B. PKC‐dependent regulation of the receptor locus dominates functional consequences of cysteinyl leukotriene type 1 receptor activation. FASEB J. 21, 2335–2342 (2007)
Common patterns and unique features of P-type ATPases: a comparative view on the KdpFABC complex from Escherichia coli (Review)

P-type ATPases are ubiquitously abundant primary ion pumps, which are capable of transporting cations across the cell membrane at the expense of ATP. Since these ions comprise a large variety of vital biochemical functions, nature has developed rather sophisticated transport machineries in all kingdoms of life. Due to the importance of these enzymes, representatives of both eu- and prokaryotic as well as archaeal P-type ATPases have been studied intensively, resulting in detailed structural and functional information on their mode of action. During catalysis, P-type ATPases cycle between the so-called E1 and E2 states, each of which comprising different structural properties together with different binding affinities for both ATP and the transport substrate. Crucial for catalysis is the reversible phosphorylation of a conserved aspartate, which is the main trigger for the conformational changes within the protein. In contrast to the well-studied and closely related eukaryotic P-type ATPases, much less is known about their homologues in Bacteria. Whereas in Eukarya there is predominantly only one subunit, which builds up the transport system, in Bacteria there are multiple polypeptides involved in the formation of the active enzyme. Such a rather unusal prokaryotic P-type ATPase is the KdpFABC complex of the enterobacterium Escherichia coli, which serves as a highly specific K+ transporter. A unique feature of this member of P-type ATPases is that catalytic activity and substrate transport are located on two different polypeptides. This review compares generic features of P-type ATPases with the rather unique KdpFABC complex and gives a comprehensive overview of common principles of catalysis as well as of special aspects connected to distinct enzyme functions.
Oral health condition in southern Chinese after radiotherapy for nasopharyngeal carcinoma: extent and nature of the problem.

OBJECTIVE To measure the oral health status of southern Chinese nasopharyngeal carcinoma (NPC) survivors 1-4 years after radiotherapy. SUBJECTS AND METHODS A total of 109 subjects participated in this cross-sectional study. Thirty-eight subjects were NPC survivors, 40 subjects were patients newly diagnosed with NPC and 31 were healthy subjects. Verified clinical examination techniques were used to assess limitation of jaw opening, the presence of mucositis, candidiasis, dental caries, periodontal disease [community periodontal index (CPI)] including attachment loss (ALoss) and prosthetic status/need. Differences among three groups were tested by chi-squared and Kruskal-Wallis tests. Relationships between selected clinical variables and radiation parameters were analysed using Spearman's rank correlation coefficients. RESULTS The NPC survivors attended for dental treatment more frequently than the other groups (P < 0.01). NPC survivors had significant xerostomia (92%, P < 0.01), trismus (29%, P < 0.01), a higher prevalence of clinical candidiasis (24%, P < 0.01), a greater DMFT (16.4 +/- 7.0, P < 0.01), more decay/filled roots (2.1 +/- 2.9, P = 0.01) compared with new NPC patients and controls. No difference was found in CPI, ALoss, prosthetic status and need between groups. Dry mouth and tooth hypersensitivity were the most common oral problems perceived by the NPC survivors. CONCLUSION Despite having regular dental follow-ups, oral health was compromised in NPC survivors 1-4 years postradiotherapy.
Identification of novel phosphorylation modification sites in human proteins that originated after the human-chimpanzee divergence

MOTIVATION Phosphorylation modifications of specific protein residues are involved in a wide range of biological processes such as modulation of intracellular signal networks. Here, we present the development and application of a bioinformatics procedure for systematic identification of human-specific phosphorylation sites in proteins that may have occurred after the human-chimpanzee divergence. RESULTS We collected annotated human phosphorylation sites and compared each site to orthologous mammalian proteins across taxa including chimpanzee, orangutan, rhesus macaque, marmoset, mouse, dog, cow, elephant, opossum and platypus. We identified 37 human-specific gains of annotated phosphorylation sites in 35 proteins: 22 serines, 12 threonines and 3 tyrosines. The novel phosphorylation sites are situated in highly conserved segments of the protein. Proteins with novel phosphorylation sites are involved in crucial biological processes such as cell division (AURKB, CASC5, MKI67 and PDCD4) and chromatin remodeling (HIRA, HIRIP3, HIST1H1T, NAP1L4 and LRWD1). Modified phosphorylatable residues produce novel target sites for protein kinases such as cyclin-dependent kinases and casein kinases, possibly resulting in rewiring and fine-tuning of phosphorylation regulatory networks. The potential human-specific phosphorylation sites identified in this study are useful as candidates for functional analysis to identify novel phenotypes in humans. CONTACT hahny@cau.ac. kr SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.