Miracle-dz/UniFAR-FTUs huggingface dataset:
STATE TRANSITION7-Dependent Phosphorylation Is Modulated by Changing Environmental Conditions, and Its Absence Triggers Remodeling of Photosynthetic Protein Complexes1

The absence of a chloroplast protein kinase leads to remodeling of photosynthetic protein complexes, uncovering an intricate protein phosphorylation network. In plants and algae, the serine/threonine kinase STN7/STT7, orthologous protein kinases in Chlamydomonas reinhardtii and Arabidopsis (Arabidopsis thaliana), respectively, is an important regulator in acclimation to changing light environments. In this work, we assessed STT7-dependent protein phosphorylation under high light in C. reinhardtii, known to fully induce the expression of LIGHT-HARVESTING COMPLEX STRESS-RELATED PROTEIN3 (LHCSR3) and a nonphotochemical quenching mechanism, in relationship to anoxia where the activity of cyclic electron flow is stimulated. Our quantitative proteomics data revealed numerous unique STT7 protein substrates and STT7-dependent protein phosphorylation variations that were reliant on the environmental condition. These results indicate that STT7-dependent phosphorylation is modulated by the environment and point to an intricate chloroplast phosphorylation network responding in a highly sensitive and dynamic manner to environmental cues and alterations in kinase function. Functionally, the absence of the STT7 kinase triggered changes in protein expression and photoinhibition of photosystem I (PSI) and resulted in the remodeling of photosynthetic complexes. This remodeling initiated a pronounced association of LHCSR3 with PSI-LIGHT HARVESTING COMPLEX I (LHCI)-ferredoxin-NADPH oxidoreductase supercomplexes. Lack of STT7 kinase strongly diminished PSII-LHCII supercomplexes, while PSII core complex phosphorylation and accumulation were significantly enhanced. In conclusion, our study provides strong evidence that the regulation of protein phosphorylation is critical for driving successful acclimation to high light and anoxic growth environments and gives new insights into acclimation strategies to these environmental conditions.
Speed Regulation Technique of One Bearingless 8/6 Switched Reluctance Motor With Simpler Single Winding Structure

Some types of bearingless switched reluctance motors (BSRMs) have been developed up to now. Their differences mainly focus on different stator-rotor tooth number and winding structures: two layers of windings and single layer of windings for 12/8 or 8/6 BSRM. Their driving principles are just the same: driving current and radial force current are regulated to generate torque and radial force separately. The main difference is the loading of two currents on one single layer of windings or on two separate layers of windings. Further analysis proves that single layer winding structure has more advantages, for example simpler motor and winding structure. Based on the above researches, one 8/6 BSRM with simpler single layer of winding structure has been developed furthermore. Its main characteristic is that the total winding number of motor is decreased from eight to six, which is only two more than four windings of a normal 8/6 SRM. Only six converters are demanded to achieve levitation operation. Its special driving theory and speed regulation technique of the motor by applying three phase windings have been introduced. To testify the new idea, theoretical analysis and practical test have been finished for one test motor. One initial speed of 5000 r/min of levitation operation has been achieved.
The incidence of acute kidney injury in patients with traumatic brain injury

There is limited information on the incidence of acute kidney injury (AKI) in patients with traumatic brain injury (TBI) although AKI may contribute to morbidity and mortality. We investigated the incidence of AKI in patients with moderate and severe TBI and the association of AKI with risk factors and outcomes in these patients. We studied all TBI patients over 16 years of age admitted to the two designated trauma hospitals in the state of Victoria, Australia from 1 January to 31 December 2008. Patients were included if they had head trauma and presented with a Glasgow coma scale (GCS) <13. Prospectively collected data from the hospital trauma registries, ICUs, and pathology databases were analyzed retrospectively. Risk injury failure loss end (RIFLE) criteria were used to categorize renal function. The incidence of AKI was 9.2% (19/207). Patients who developed AKI were older, had higher severity of illness scores, and a lower GCS. Overall 42.1% of these patients died in hospital compared with 18.1% in patients without AKI. In univariable linear regression analysis, age, severity of illness, and admitting hospital were associated with AKI. After multivariable logistic regression, the occurrence of AKI was associated with age (p < 0.001) and higher APACHE III scores (p = 0.016). AKI is relatively common even in patients with TBI. Its association with age and APACHE III scores helps identify patients at higher risk of AKI.
Increased Affinity of c-Myb for CREB-binding Protein (CBP) after CBP-induced Acetylation*

The c-myb proto-oncogene product (c-Myb) is a sequence-specific DNA-binding protein that functions as a transcriptional activator. The transcriptional coactivator CREB-binding protein (CBP) binds via its KIX domain to the activation domain of c-Myb and mediates c-Myb-dependent transcriptional activation. CBP possesses intrinsic histone acetyltransferase activity, and can acetylate not only histones but also certain transcriptional factors such as GATA1 and p53. Here we demonstrate that the C/H2 domain of CBP, which is critical for the acetyltransferase activity, also directly interacts with the negative regulatory domain (NRD) of c-Myb. Consistent with this observation, CBP acetylated c-Myb in vitro at Lys438 and Lys441 within the NRD. In addition, CBP acetylated c-Myb in vivo not only at the sites found in this study but also at the p300-induced acetylation sites reported recently. Replacement of lysine by arginine at all of these sites dramatically decreased thetrans-activating capacity of c-Myb. The results of transcriptional activation assays with c-Myb acetylation site mutants suggested that acetylation of c-Myb at each of these five sites synergistically enhances c-Myb activity. Mutations of these acetylation sites reduced the strength of the interaction between c-Myb and CBP. Thus, acetylation of c-Myb by CBP increases thetrans-activating capacity of c-Myb by enhancing its association with CBP. These results demonstrate a novel molecular mechanism of regulation of c-Myb activity.
Spectral domain high-definition optical coherence tomography in patients undergoing epiretinal membrane surgery.

BACKGROUND AND OBJECTIVE To evaluate possible advantages of spectral domain optical coherence tomography (SD-OCT) in epiretinal membranes. PATIENTS AND METHODS Patients with idiopathic epiretinal membranes (ERMs) were examined before and after vitreoretinal surgery. Cirrus SD high-definition (HD)-OCT was compared with Stratus time domain OCT to find correlations with visual acuity (VA) and metamorphopsia. RESULTS Five consecutive patients were enrolled. With Cirrus HD-OCT, it was possible to differentiate between the ERM and the retinal surface in all patients. In areas where the ERM was adherent, this differentiation was severely limited with Stratus OCT. We found no significant correlations between Cirrus OCT and Stratus OCT for retinal thickness and VA. However, we found a relationship between metamorphopsia and topographic maps of the internal limiting membrane. CONCLUSION Cirrus HD-OCT improved the preoperative evaluation of ERMs, offered a topographic reconstruction of the vitreomacular interface, and improved identification of retinal structures.
Increased fibroblast growth factor 21 in obesity and nonalcoholic fatty liver disease.

BACKGROUND & AIMS Fibroblast growth factor 21 (FGF21) is an hepatic protein that plays a critical role in metabolism, stimulating fatty acid oxidation in liver and glucose uptake in fat. Systemic administration to obese rodents and diabetic monkeys leads to improved glucose homeostasis and weight loss. In rodents, FGF21 increases with fasting and consumption of a ketogenic diet (KD). In humans, FGF21 correlates with body mass index (BMI), but studies evaluating other parameters show inconsistent results. We examined FGF21 serum levels in lean and obese individuals and in response to dietary manipulation. We also evaluated FGF21 serum levels and liver messenger RNA (mRNA) expression in nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH). METHODS Serum FGF21 was measured after an overnight fast in individuals with BMI ranging from normal to obese. Volunteers fasted for 16 or 72 hours and then ate a standard meal. Another group consumed KD for 12 days. Serum FGF21 and hepatic mRNA expression were measured in obese individuals with NAFLD or NASH. RESULTS There was a positive correlation between BMI and FGF21. There was no change in FGF21 in response to a short fast or KD. A nonstatistically significant fall in FGF21 levels was seen after a 72-hour fast. Hepatic FGF21 mRNA expression was significantly elevated in NAFLD, which correlated with a substantial increase in serum FGF21. In NASH, serum FGF21 but not liver mRNA was increased. CONCLUSIONS FGF21 correlates with BMI and may be a novel biomarker for NAFLD, but is not nutritionally regulated in humans.
Fibrosis in chronic hepatitis C correlates significantly with body mass index and steatosis

Steatosis is a frequent histological finding in chronic hepatitis C infection; however, the pathophysiology of steatosis and its role in disease progression have not been established. We studied 148 consecutive patients with untreated chronic hepatitis C to assess the effect of body mass index, diabetes mellitus, alcohol consumption, hepatic iron content, and viral load on steatosis and hepatic fibrosis. Ninety‐one patients (61%) had steatosis: grade 1 (<30% hepatocytes involved) in 61 (41%), grade 2 (30%‐70% hepatocytes involved) in 17 (11%), and grade 3 (>70% hepatocytes involved) in 13 (9%). After adjusting for potential confounding variables, a highly significant relationship was found primarily between steatosis and body mass index (P < .0001). The mean (±SD) body mass index of patients with no steatosis was 23.9 ± 4.3 kg/m2, whereas for grade 1 steatosis it was 26.5 ± 5.1 kg/m2, and for grade 2 and 3 steatosis combined the body mass index was 28.4 ± 4.9 kg/m2. Hepatic fibrosis was significantly associated with age (P = .002). After adjusting for potential confounding variables, including age, hepatic fibrosis was also significantly associated with steatosis (P < .03). There was no significant association between hepatic iron content, alcohol intake, gender, and viral load and steatosis or fibrosis. These findings suggest that increasing body mass index has a role in the pathogenesis of steatosis in chronic hepatitis C and that steatosis may contribute to fibrosis. The association between body mass index and steatosis and fibrosis has important prognostic and therapeutic implications in the management of patients with chronic hepatitis C virus
Specificity of circulating antigen detection for schistosomiasis mansoni in Senegal and Burundi

The specificity of schistosome circulating antigen detection was determined in negative individuals from two S. mansoni‐ endemic countries, Senegal and Burundi, and compared with results from Dutch control individuals. A nearly absolute specificity was achieved for circulating anodic antigen (CAA) detection in serum, irrespective of the target population or sample pretreatment method. Circulating cathodic antigen (CCA) detection in serum and urine resulted in a lower specificity than serum CAA detection. Apparent large differences in specificity of CCA detection between countries were mainly due to pretreatment methods. Apparently, the alkaline/heating pretreatment method is not as effective as trichloroacetic acid (TCA) ‐pretreatment in removing (certain) interfering components, which may vary between populations. In view of the development of the urine CCA assay into a noninvasive screening test, a slightly lower specificity may still be acceptable. For precise epidemiological analyses the highly specific serum CAA assay remains the method of choice.
Low voltage IMD-TDDB lifetime model for advanced future logic technology nodes

Scaled advanced technologies with its narrow metal line spaces are prone to very wide variation. Therefore, having an accurate IMD-TDDB lifetime projection as the upcoming technologies shrink in dimensions is critical. It was reported previously that the Weibull shape parameter p is improved at low field stress (use condition) compared to higher fields (stress condition) in regard to field dependence model approach (E, a/E model) [1-2]. In this paper, we show that the P of IMD-TDDB improves as stress field or voltage is reduced through simulation by using the space data obtained from in-line SEM measurement This is further verified by the long-term (up to 8 months of package level) IMD-TDDB experimental data from various technology nodes with 80-100nm pitch. For the voltage projection, we also show that power-law shows better fit to the long term data. The study is highly useful for developing and qualifying the technology node beyond 14nm.
Regulation of monocyte chemoattractant protein-1 and macrophage colony-stimulating factor-1 by IFN-gamma, tumor necrosis factor-alpha, IgG aggregates, and cAMP in mouse mesangial cells.

The interaction of mesangial cells and monocyte-macrophages plays an important role in renal glomerular immune injury. We have, therefore, examined the regulation of two monocyte-specific cytokines, i.e., macrophage CSF-1 and monocyte chemoattractant protein (MCP-1), the product of the mouse JE gene, in mouse mesangial cells. TNF-alpha, IFN-gamma, and aggregates of IgG increased the synthesis of CSF-1 (determined by RIA) and of MCP-1 (determined by biolabeling and immunoprecipitation). Stimulation of cAMP generation by forskolin or PGE2 decreased basal CSF-1 synthesis and attenuated the responses to TNF-alpha, IFN-gamma, and IgG. Forskolin and PGE2 also decreased biolabeled MCP-1 generation after stimulation with IFN-gamma, TNF-alpha, or IgG. By Northern blot analysis steady state levels of mRNA for CSF-1 and JE/MCP-1 were increased after incubation with IFN-gamma, TNF-alpha, or IgG, and these effects were attenuated by forskolin. By using nuclear run-on assays the decrease in CSF-1 and JE/MCP-1 mRNA levels induced by stimulation of cAMP generation with forskolin was attributed to decreased transcription of these genes. Thus, agents stimulating cAMP generation, including PGE2, counterbalance the generation of CSF-1 and JE/MCP-1 in response to IFN-gamma, TNF-alpha, and IgG complexes. The locally produced CSF-1 and MCP-1 may in turn influence the interaction between mesangial cells and monocyte-macrophages in glomerular injury.
Perceived Uncertainty: Conceptual Frameworks and Research Instruments.

This paper attempts to provide a framework for future research on one of the central concepts of contingency theories―uncertainty. After reviewing earlier attempts at defining uncertainty, it offers explicit views of man and environments to guide the reader in the development of the conceptualization and definition of uncertainty as a psychological state of the individual. This concept of uncertainty is used to suggest four sources of variability in the perception of uncertainty by individuals: (1) the perception of stability and simplicity in an environment, (2) individual cognitive processes, (3) the variety of an individual's experience, and (4) social expectations of the perception of uncertainty. The paper makes suggestions, based on the concepts presented, for future research concerning uncertainty. These include strategies for methodological testing of uncertainty instruments and explorations of the role of individual characteristics in the perception of uncertainty.
On a Recognition Task in Which Some Distractors Were Half-Familiar

Models are suggested for the task of recognizing word-pairs, where the distractors may be pairs of new words, or may be a new word paired with a previously-seen word. These models are relevant to an experiment recently reported by Isingrini et al., and suggest rather different conclusions to theirs—namely, that the elderly differ from the young in both learning and response selection.
Exchange rate volatility, employment and macroeconomic dynamics in South Africa

This thesis focuses on the effects and causes of exchange rate volatility in South Africa. These issues are analysed in three stand-alone but related papers. The first paper (Chapter 2) investigates the impact of real exchange rate volatility on employment growth in the manufacturing sector. The study contributes to the literature on the employment effects of exchange rate volatility in emerging markets given limited studies. This is done by using the Autoregressive Distributed Lag (ARDL) counteraction approach which is able to estimate an error correction form of the model for the variables under investigation. This enables one to analyse the relationship between exchange rate volatility and employment growth. The advantage of this approach is that it performs better in small samples and works well even when the underlying variables are integrated of different orders. Employing quarterly time series data for the period 1995 . 2010, the analysis shows that real exchange rate volatility has a significant contractionary effect on manufacturing employment growth. The study also provides evidence that exchange rate level, output, wages and interest rates have significant effects on manufacturing employment growth. The results suggest that the government can reduce the adverse effects of exchange rate volatility on manufacturing by adopting macroeconomic policies that minimise exchange rate volatility and policies that promote employment creation, for instance, less restrictive policies given that the results show that an increase in interest rates leads to a decline in employment. Coming up with macroeconomic policies that minimise exchange rate volatility requires the knowledge of the causes of exchange rate volatility. As a result, the second paper (Chapter 3) investigates the determinants of exchange rate volatility in South Africa. Few studies investigate the determinants of rand volatility (Arezki, Dumitrescu, Freytag & Quintyn 2014, Farrell 2001). This study contributes to the literature by finding the sources of rand volatility using output volatility, money supply volatility, foreign reverses volatility, commodity price volatility, openness and a dummy for capital account liberalisation as explanatory variables. This is done using GARCH models for the period 1986- 2013 employing monthly time series data. The advantage of GARCH models is that they are able to model and forecast time-varying variance given that the exchange rate behaves similarly to other asset prices, for example, stock prices. The study tests the hypothesis that economic openness leads to a reduction in exchange rate volatility following Hau's (2002) modifications of the New Open Macroeconomics model of Obstfeld & Rogoff (1995, 1996). South Africa is a good case study following the liberalisation of the capital account in March 1995. The results show that switching to a coating exchange rate regime has a significant positive effect on exchange rate volatility. That is, it increases exchange rate volatility. The results also show that trade…
Statistical Model Building and Model Criticism for Human Circadian Data

Mathematical models have played an important role in the analysis of circadian systems. The models include simulation of differential equation systems to assess the dynamic properties of a circadian system and the use of statistical models, primarily harmonic regression methods, to assess the static properties of the system. The dynamical behaviors characterized by the simulation studies are the response of the circadian pacemaker to light, its rate of decay to its limit cycle, and its response to the rest-activity cycle. The static properties are phase, amplitude, and period of the intrinsic oscillator. Formal statistical methods are not routinely employed in simulation studies, and therefore the uncertainty in inferences based on the differential equation models and their sensitivity to model specification and parameter estimation error cannot be evaluated. The harmonic regression models allow formal statistical analysis of static but not dynamical features of the circadian pacemaker. The authors present a paradigm for analyzing circadian data based on the Box iterative scheme for statistical model building. The paradigm unifies the differential equation–based simulations (direct problem) and the model fitting approach using harmonic regression techniques (inverse problem) under a single schema. The framework is illustrated with the analysis of a core-temperature data series collected under a forced desynchrony protocol. The Box iterative paradigm provides a framework for systematically constructing and analyzing models of circadian data.
Sleep hygiene practices in two community dwelling samples of older adults.

STUDY OBJECTIVES Common sleep hygiene practices were examined in 2 community-based samples of older adults to determine which practices differentiated 4 sleep subgroups: noncomplainers without insomnia symptoms, complainers without insomnia symptoms, noncomplainers with insomnia symptoms, and complainers with insomnia symptoms. DESIGN Two weeks of sleep diaries provided napping and bed/out-of-bed time variability data. A retrospective questionnaire provided data on caffeine, cigarette, and alcohol usage. Recruitment involved random digit dialing (Sample 1) and advertisements (Sample 2). SETTING Memphis, TN area (Sample 1); Gainesville, FL area (Sample 2). PARTICIPANTS 310 individuals 60-96 years (Sample 1); 103 individuals 60-89 years (Sample 2). INVENTIONS N/A. MEASUREMENTS AND RESULTS Older individuals with sleep complaints did not report engaging in poorer sleep hygiene practices than those without complaints with the exception of frequency of napping. For Sample 1 only, complainers reported napping on 1.5-2.0 more days per week than noncomplainers. Sleep subgroups in both samples did not differ for the other sleep hygiene practices studied. CONCLUSIONS Overall, sleep hygiene behaviors did not differentiate the 4 sleep subgroups. The efficacy of sleep hygiene as a therapy for late life insomnia appears questionable in this context. Both complaining sleep subgroups napped more frequently than both noncomplaining subgroups in Sample 1. Additional research is needed to clarify the clinical implications of nap frequency as these results did not replicate in Sample 2, and the impact of napping on nighttime sleep remains unclear. Inconsistencies with previous research in younger samples support the need for more research specifically targeting older individuals' sleep patterns and behaviors.