Miracle-dz/UniFAR-FTUs huggingface dataset:
Large Scale Comparative Proteomics of a Chloroplast Clp Protease Mutant Reveals Folding Stress, Altered Protein Homeostasis, and Feedback Regulation of Metabolism*

The clpr2-1 mutant is delayed in development due to reduction of the chloroplast ClpPR protease complex. To understand the role of Clp proteases in plastid biogenesis and homeostasis, leaf proteomes of young seedlings of clpr2-1 and wild type were compared using large scale mass spectrometry-based quantification using an LTQ-Orbitrap and spectral counting with significance determined by G-tests. Virtually only chloroplast-localized proteins were significantly affected, indicating that the molecular phenotype was confined to the chloroplast. A comparative chloroplast stromal proteome analysis of fully developed plants was used to complement the data set. Chloroplast unfoldase ClpB3 was strongly up-regulated in both young and mature leaves, suggesting widespread and persistent protein folding stress. The importance of ClpB3 in the clp2-1 mutant was demonstrated by the observation that a CLPR2 and CLPB3 double mutant was seedling-lethal. The observed up-regulation of chloroplast chaperones and protein sorting components further illustrated destabilization of protein homeostasis. Delayed rRNA processing and up-regulation of a chloroplast DEAD box RNA helicase and polynucleotide phosphorylase, but no significant change in accumulation of ribosomal subunits, suggested a bottleneck in ribosome assembly or RNA metabolism. Strong up-regulation of a chloroplast translational regulator TypA/BipA GTPase suggested a specific response in plastid gene expression to the distorted homeostasis. The stromal proteases PreP1,2 were up-regulated, likely constituting compensation for reduced Clp protease activity and possibly shared substrates between the ClpP and PreP protease systems. The thylakoid photosynthetic apparatus was decreased in the seedlings, whereas several structural thylakoid-associated plastoglobular proteins were strongly up-regulated. Two thylakoid-associated reductases involved in isoprenoid and chlorophyll synthesis were up-regulated reflecting feedback from rate-limiting photosynthetic electron transport. We discuss the quantitative proteomics data and the role of Clp proteolysis using a “systems view” of chloroplast homeostasis and metabolism and provide testable hypotheses and putative substrates to further determine the significance of Clp-driven proteolysis.
TIF‐IC, a factor involved in both transcription initiation and elongation of RNA polymerase I.

We have characterized a transcription factor from Ehrlich ascites cells that is required for ribosomal gene transcription by RNA polymerase I (Pol I). This factor, termed TIF‐IC, has a native molecular mass of 65 kDa, associates with Pol I, and is required both for the assembly of Sarkosyl‐resistant initiation complexes and for the formation of the first internucleotide bonds. In addition to its function in transcription initiation, TIF‐IC also plays a role in elongation of nascent RNA chains. At suboptimal levels of TIF‐IC, transcripts with heterogeneous 3′ ends are formed which are chased into full‐length transcripts by the addition of more TIF‐IC. Moreover, on a tailed template, which allows initiation in the absence of auxiliary factors, TIF‐IC was found to stimulate the overall rate of transcription elongation and suppress pausing of Pol I. Thus TIF‐IC appears to serve a function similar to the Pol II‐specific factor TFIIF which is required for Pol II transcription initiation and elongation.
Traction control of wheeled vehicles using dynamic feedback approach

A dynamic traction control scheme for mobile robots/vehicles with two steerable and drivable wheels is presented. The kinematic modeling and position/orientation control of such a mobile robot/vehicle was studied previously by the authors (1996). In this paper, a dynamic feedback control algorithm is developed based on the dynamics of the vehicle, which not only enables the vehicle to move from any initial configuration (position and orientation) to any final configuration, but also strives to optimally distribute the tractive efforts between the two wheels for better performance. It is also shown that the same cannot be achieved by any static feedback controller. Such a control algorithm will be useful where surface conditions vary, and tractive torques between the wheels need to be dynamically allocated to maintain the required dynamic performance.
Evaluation of a Computer Program for Caries Risk Assessment in Schoolchildren

The ‘Cariogram’ is an interactive PC program for caries risk evaluation. It takes into account the interactions between caries-related factors and expresses a graphic assessment of the risk. The aim of this study was to assess the caries risk in schoolchildren using the Cariogram and to evaluate the program by comparing the caries risk assessments with the actual change in DMF. A 2-year prospective study on 446 schoolchildren, 10–11 years old, was conducted. At baseline, data on general health, diet, oral hygiene and use of fluoride were obtained. Saliva analyses included mutans streptococci and lactobacilli counts, buffer capacity and secretion rate. DMFT and DMFS were calculated from records and bitewing radiographs. Scores were entered and caries risk was assessed. Re-examination for caries was done after 2 years. The children were divided into 5 groups according to the assessed caries risk at baseline. Where the Cariogram predicted a 0–20% (high risk), 21–40%, 41–60%, 61–80% and 81–100% (low risk) chance of avoiding new lesions, 8, 35, 42, 73 and 83%, respectively, had no new lesions 2 years later. Logistic regression analyses were carried out. When the Cariogram was included, only two factors, the Cariogram (p < 0.001) and the DMFS at baseline, i.e. past caries experience (p = 0.001), turned out to be significantly associated with caries increment. The Cariogram was the most powerful explanatory variable. When the Cariogram was excluded, lactobacillus count, mutans streptococci, diet intake frequency and DMFS at baseline were significantly associated with caries increment. The Cariogram predicted caries increment more accurately than any included single-factor model. How this finding can be translated into daily practice in the best and most practical way is a matter for future research.
Cognitive development in childhood and drinking behaviour over two decades in adulthood

Background/aims: Childhood cognition predicts adult morbidity and mortality, potentially working through health behaviours. This study investigates if childhood cognition influences life course (i) non-drinking and (ii) binge drinking and pathways through which this might act—namely, childhood behaviour problems, adult social position and educational qualifications. Methods: Prospective cohort of British births in March 1958, with information on cognition at 7, 11 and 16 years and alcohol use at 23, 33 and 42 years. Non-drinkers drank “infrequently/on special occasions” or “never”. Binge drinkers consumed ⩾10 units/occasion (men) and ⩾7 units/occasion (women). Results: Lower cognitive ability increased the odds of non-drinking at each adult survey (for example, for men at 42 years OR 1.52 (95% CI 1.34 to 1.72) per SD decrease in 7-year maths). Associations remained after adjustment for pathway factors (i) behaviour problems, (ii) adult social position and (iii) educational qualifications. Decreased ability rank across childhood (7–16 years) also increased odds of non-drinking at 42 years, but the association operated via pathway factors. Lower 7-year ability elevated the odds of 42-year binge drinking, operating via pathway factors. Declining ability rank across childhood also increased the odds of adult binge drinking; associations operated through behavioural problems, adult social position and qualifications. In women, the decline in risk of binge drinking from an age 23-year peak to 42 years was associated with higher 7-year score. Conclusions: Poorer childhood cognition was associated with non-drinking and binge drinking up to the early 40s. Associations between childhood cognition and drinking status may mediate between childhood cognition and adult health.
Dementia care in nursing homes: a golden opportunity

The paper by Kleijer and colleagues (2014) in this issue of International Psychogeriatrics describes factors that may influence antipsychotic drug (APD) prescribing rates in nursing homes in several countries. The authors conclude that the large variability is only partly explained by differences in resident characteristics, and that it is associated with certain facility characteristics such as bed size and urban/rural location. They also identify the likelihood that differences in physician prescribing patterns or facility prescribing culture may influence APD prescribing rates, as has been found in previous studies (Briesacher et al., 2005; Chen et al., 2010).
Aryl Hydrocarbon Receptor–Dependent Pathways in Immune Regulation

The idea of possible involvement of the aryl hydrocarbon receptor (AhR) in transplant tolerance can be traced back >30 years, when very low doses of dioxin—the most potent AhR ligand—were found to markedly reduce the generation of cytotoxic T lymphocytes in response to alloantigen challenge in vivo. AhR is a ligand‐activated transcription factor that is activated by dioxins and other environmental pollutants. We now know that AhR can bind a broad variety of activating ligands that are disparate in nature, including endogenous molecules and those formed in the gut from food and bacterial products. Consequently, in addition to its classical role as a toxicological signal mediator, AhR is emerging as a transcription factor involved in the regulation of both innate and adaptive immune responses in various immune cell types, including lymphocytes and antigen‐presenting cells (APCs). Allograft rejection is mostly a T cell–mediated alloimmune response initiated by the recognition of alloantigens presented by donor and recipient APCs to recipient CD4+ and CD8+ T cells. Based on those findings, AhR may function as a critical sensor of outside and inside environments, leading to changes in the immune system that may have relevance in transplantation.
The roles of polyphenols in cancer chemoprevention

Oxidative stress imposed by reactive oxygen species (ROS) plays a crucial role in the pathophysiology associated with neoplasia, atherosclerosis, and neurodegenerative diseases. The ROS‐induced development of cancer involves malignant transformation due to altered gene expression through epigenetic mechanisms as well as DNA mutations. Considerable attention has been focused on identifying naturally occurring antioxidative phenolic phytochemicals that are able to decrease ROS levels, but the efficacies of antioxidant therapies have been equivocal at best. Several studies have shown that some antioxidants exhibit prooxidant activity under certain conditions and potential carcinogenicity under others, and that dietary supplementation with large amounts of a single antioxidant may be deleterious to human health. This article reviews the intracellular signaling pathways that respond to oxidative stress and how they are modulated by naturally occurring polyphenols. The possible toxicity and carcinogenicity of polyphenols is also discussed.
Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families

MOTIVATION Annotation of the biological function of different protein sequences is a time-consuming process currently performed by human experts. Genome analysis tools encounter great difficulty in performing this task. Database curators, developers of genome analysis tools and biologists in general could benefit from access to tools able to suggest functional annotations and facilitate access to functional information. APPROACH We present here the first prototype of a system for the automatic annotation of protein function. The system is triggered by collections of s related to a given protein, and it is able to extract biological information directly from scientific literature, i.e. MEDLINE abstracts. Relevant keywords are selected by their relative accumulation in comparison with a domain-specific background distribution. Simultaneously, the most representative sentences and MEDLINE abstracts are selected and presented to the end-user. Evolutionary information is considered as a predominant characteristic in the domain of protein function. Our system consequently extracts domain-specific information from the analysis of a set of protein families. RESULTS The system has been tested with different protein families, of which three examples are discussed in detail here: 'ataxia-telangiectasia associated protein', 'ran GTPase' and 'carbonic anhydrase'. We found generally good correlation between the amount of information provided to the system and the quality of the annotations. Finally, the current limitations and future developments of the system are discussed. AVAILABILITY The current system can be considered as a prototype system. As such, it can be accessed as a server at http://columba.ebi. ac. uk:8765/andrade/abx. The system accepts text related to the protein or proteins to be evaluated (optimally, the result of a MEDLINE search by keyword) and the results are returned in the form of Web pages for keywords, sentences and s. SUPPLEMENTARY INFORMATION Web pages containing full information on the examples mentioned in the text are available at: http://www.cnb.uam.es/ approximately cnbprot/keywords/ CONTACT valencia@cnb.uam.es
Nutrient Retention, Nutrient Limitation, and Sediment-Nutrient Interactions in a Pasture-Dominated Stream

Even though agricultural land use is a principal source of nonpoint-source pollution, the in-stream movement and transport of nutrients and their interaction with benthic sediments are not well understood. The objectives of this study were to: (1) assess if nutrients were limiting algal growth, (2) assess equilibrium between sediments and water column phosphorus (P), (3) evaluate spatial and temporal variability in P buffering capacity and easily exchangeable P, and (4) evaluate variations in stream nutrient retention efficiency in Moore's Creek, a pasture-dominated watershed in northwest Arkansas. This study used nutrient limitation bioassays, sediment nutrient extractions, and short-term nutrient injections to accomplish the study objectives. Results suggested that light, not nutrients, was limiting algal growth in Moore's Creek. Sediment equilibrium P concentration measurements suggested that sediments may be releasing dissolved inorganic P during winter and spring; however, sediments were a potential temporary sink of dissolved inorganic P during summer and fall. Exchangeable P concentrations varied between 0.4 and 1.0 mg kg-1 of dry sediments, and P sorption index varied between 3.2 and 5. Concentrations of ammonia nitrogen (NH4-N) and ortho P (PO4-P) generally decreased between sampling stations during nutrient injections at all three sites; however, nitrate N (NO3-N) concentrations increased downstream. A significant retention of NO3-N was not observed in any of the experiments, indicating that agricultural headwater streams may be a source of downstream NO3-N transport. The results indicated that a riparian cover should be maintained in nutrient-rich headwater streams in order to minimize algal production in the streams. Even nutrient-rich streams may continue to assimilate, to some extent, increased loads of P, altering the timing and magnitude of downstream transport of P.
Techno-Economic Modeling of a Corn Based Ethanol Plant in 2011

As studies continue to examine new value added uses for ethanol coproducts, it is important to have means to easily determine the feasibility of the processing steps involved. Many industries widely use computer simulation programs for this purpose, and for planning the use of resources and equipment capacities, and to determine processing costs. The objective of this project was to determine the sensitivity of 40 million gal/y corn-based ethanol plant model to changes in input material prices, product market prices, and various coproduct processing scenarios (i.e., oil extraction and drying of DDGS). The techno-economics of the base case ethanol plant were examined by factorially adjusting material and market costs, as well as adjusting the quantities of distillers wet grains (DWG), distillers dried grains with solubles (DDGS), and corn oil produced. The simulations verified that corn price has the greatest impact on the overall annual operating costs for the ethanol plant, and that the market price of ethanol has the greatest impact on annual revenues. The effect of coproduct processing on utility usage was also observed; oil extraction and drying of DDGS consumed substantially more energy and had higher capital costs than production of DWG alone. It was apparent that coproducts are an essential component to the sustainability of an ethanol plant in that: 1) they have continued marketability to the livestock industry, and 2) processing is not overly-expensive. This study has provided a basis for further exploration of the feasibility of new coproduct processing options, and illustrates the use of the model for determination of processing costs and revenues, as well as mass and energy balances.
Environmental toxins

This review comprehensively summarizes the effects of more than 15 mostly used pesticides on male reproductive physiology, as recent experimental and epidemiological research have indicated their alarming impact on overall human health. Mechanisms have described that pesticide exposure damages spermatozoa, alter Sertoli or Leydig cell function, both in vitro and in vivo and thus affects semen quality. But, the literature suggests a need for more intricate research in those pesticides that are defined as mutagens or carcinogens and directly affect the hypothalamic–pituitary–gonadal axis. This literature review also proposes specific solutions to overcome these health effects.
The invisible addiction: Cell-phone activities and addiction among male and female college students

Background and aims: The primary objective of the present study was to investigate which cell-phone activities are associated with cell-phone addiction. No research to date has studied the full-range of cell-phone activities, and their relationship to cell-phone addiction, across male and female cell-phone users. Methods: College undergraduates (N = 164) participated in an online survey. Participants completed the questionnaire as part of their class requirements. The questionnaire took 10 and 15 minutes to complete and contained a measure of cell-phone addiction and questions that asked how much time participants spent daily on 24 cell-phone activities. Results: Findings revealed cell-phone activities that are associated significantly with cell-phone addiction (e.g., Instagram, Pinterest), as well as activities that one might logically assume would be associated with this form of addiction but are not (e.g., Internet use and Gaming). Cell-phone activities that drive cell-phone addiction (CPA) were found to vary considerably across male and female cell-phone users. Although a strong social component drove CPA for both males and females, the specific activities associated with CPA differed markedly. Conclusions: CPA amongst the total sample is largely driven by a desire to connect socially. The activities found to be associated with CPA, however, differed across the sexes. As the functionality of cell-phones continues to expand, addiction to this seemingly indispensable piece of technology becomes an increasingly realistic possibility. Future research must identify the activities that push cell-phone use beyond its “;tipping point” where it crosses the line from a helpful tool to one that undermines our personal well-being and that of others.
Substance Use Among Young Adolescents in HIV-Affected Families: Resiliency, Peer Deviance, and Family Functioning

This study examines the association of risk and protective factors with substance use among 77 early adolescents (11–15 years old) with an HIV-infected parent who were interviewed in 2000–2001 in the South Bronx, a HIV high-prevalence area of New York City. The subjects were 49% female, 53% African American, and 30% Hispanic; mean age was 13 years old. A face-to-face interview was used to administer a battery of instruments representing community, family, peer, and resiliency factors. Forty percent reported ever using tobacco, alcohol or drugs; 71% were aware of their parent's HIV seropositivity. An age-adjusted path analytic model was constructed which showed : 1) family functioning predicted resiliency (a composite measure of psychological adjustment and personal competencies); 2) positive community factors and resiliency predicted less affiliation with deviant peers; and 3) poorer family functioning and affiliation with deviant peers predicted substance use. These results underscore the need for interventions that address social influence factors among vulnerable early adolescents with HIV-positive parents.
Transforming growth factor β2, but not β1 and β3, is critical for early rat lung branching

Mesenchymal‐epithelial tissue interactions are critical for lung branching morphogenesis, and polypeptide growth factors are likely involved in these tissue interactions. Transforming growth factorβs (TGFβs) have been implicated in lung development, but their involvement in early lung branching morphogenesis is unclear. In the present study, we investigated the role of the three mammalian TGFβ subtypes (β1, β2, and β3) and their receptors (type III (TβR‐III), type II (TβR‐II), and two types I (TβR‐I), ALK‐1 and ALK‐5) in early rat lung organogenesis by using an embryonic rat lung explant culture. Transcripts and proteins for all three TGFβs and their receptors were detected during the embryonic period of fetal rat lung development. Inhibition of TGFβ2, but not β1 and β3, with antisense oligonucleotides and neutralizing antibodies resulted in significant inhibition of early lung branching in culture. Addition of minute amounts (≤1 ng/ml) of exogenous TGFβ2, but not β1 and β3, restored the branching of TGFβ2 antisense‐treated explants. Higher concentrations of TGFβ2 were inhibitory. BrdU labeling of lung explants was not altered by antisense TGFβ2 treatment, but low concentrations of TGFβ2 increased thymidine uptake by isolated epithelial cells. Fibronectin and metallogelatinase activities of embryonic lung cells were not affected by any TGFβ isoform but TGFβ2 specifically decreased mesenchymal hyaluronan synthesis. Antisense inhibition of ALK‐5 and TβR‐II showed a similar reduction in early lung branching as observed with antisense TGFβ2. Incubation of lung explants with soluble TβR‐II receptors also abrogated lung branching. ALK‐1 antisense treatment did not affect early branching. Administration of neither activin A, which can act via ALK‐1, nor follistatin, the natural inhibitor of activin, to the explants cultures had any significant effect on lung branching. Antisense inhibition of the activin receptor‐II (Act‐RII) also did not affect lung branching. These results are consistent with TGFβ2, but not β1 and β3, regulating pattern formation during early rat lung organogenesis. This TGFβ signaling in rat lung branching in vitro appears to be predominantly mediated via the TβR‐I(ALK‐5)/TβR‐II heteromeric complex. Dev Den;217:343–360. © 2000 Wiley‐Liss, Inc.