Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence-Based Annotation of Transcripts and Proteins in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough

ABSTRACT We used high-resolution tiling microarrays and 5′ RNA sequencing to identify transcripts in Desulfovibrio vulgaris Hildenborough, a model sulfate-reducing bacterium. We identified the first nucleotide position for 1,124 transcripts, including 54 proteins with leaderless transcripts and another 72 genes for which a major transcript initiates within the upstream protein-coding gene, which confounds measurements of the upstream gene's expression. Sequence analysis of these promoters showed that D. vulgaris prefers −10 and −35 boxes different from those preferred by Escherichia coli. A total of 549 transcripts ended at intrinsic (rho-independent) terminators, but most of the other transcripts seemed to have variable ends. We found low-level antisense expression of most genes, and the 5′ ends of these transcripts mapped to promoter-like sequences. Because antisense expression was reduced for highly expressed genes, we suspect that elongation of nonspecific antisense transcripts is suppressed by transcription of the sense strand. Finally, we combined the transcript results with comparative analysis and proteomics data to make 505 revisions to the original annotation of 3,531 proteins: we removed 255 (7.5%) proteins, changed 123 (3.6%) start codons, and added 127 (3.7%) proteins that had been missed. Tiling data had higher coverage than shotgun proteomics and hence led to most of the corrections, but many errors probably remain. Our data are available at http://genomics.lbl. gov/supplemental/DvHtranscripts2011/.
The Macromolecular Polymers for the Preparation of Hydrodynamically Balanced Systems—Methods of Evaluation

Evaluation of macromolecular polymers used as excipients for the preparation of hydrodynamically balanced systems (HBS) was carried out. Hard gelatine capsules were filled with polymeric substances belonging to various chemical groups (chitosan, sodium alginate, hydroxypropylmethycellulose—HPMC). The following properties of the HBS were investigated: density, hydration, erosion and floating force. The solvent penetration process into the HBS was visualized using magnetic resonance imaging (MRI) technique. Densities of the HBS in hydrochloric acid (0.1 M) ranged from 0.37 g/cm3 to 0.71 g/cm3. Each polymer demonstrated different hydration/erosion abilities and floating properties. The maximum floating force (Ffloat max) for capsules size 0, ranged from 26.7 mN (sodium alginate) to 64.7 mN (chitosan). HBS formulations also varied in time to reach maximum floating force (Tfloat max). HPMC and sodium alginate formulation reached Ffloat max within half an hour after immersion, while in the case of chitosan formulations (deacetylation degree (d.d.) 66% and d.d. 93%), the time was 184 minutes and 218 minutes respectively. The floating properties of the dosage forms were reliant on type of the polymer and the medium—fasted state simulated gastric fluid (FaSSGF) or fed state simulated gastric fluid (FeSSGF). The size of the HBS influenced the floating force value. The mechanisms of erosion and swelling of the polymeric matrices play a dominant role in flotation of the dosage forms.
Charting Sociotechnical Dimensions of Values for Design Research

The relationship of values to technology is an important topic in the fields of information studies, human–computer interaction, media studies, and science and technology studies, but definitions and attributes of values differ within and among these fields. We suggest that researchers currently conflate multiple categories when they discuss values. Some of these categories are attributes of the source of values (i.e., people, systems, and hybrid assemblages), and others are attributes of the values themselves. This article disambiguates values in sociotechnical systems by providing a framework to describe where and how values are negotiated and enacted by people, institutions, and technology. The framework includes three dimensions that pertain to the source of values (agency, unit, and assemblage) and three dimensions that pertain to attributes of values (salience, intention, and enactment) to enable precision and comparison across this research trajectory. We illustrate each dimension with examples from the values and design literature.
Potencialidad evolutiva del tesauro: hacia una base de conocimineto experto

Traditional thesauri in new information systems are used as a lexical resource and as a tool for searching by suggesting either a more generic, a more specific or a wider search. The evolution of the traditional thesaurus towards a structure with a high capacity for concept representation and for conceptual relations identification points to the possibility for the thesaurus to become a knowledge base for intelligent information retrieval in specialized domains
Using Web Archives to Enrich the Live Web Experience Through Storytelling

The web has become an integral part of our lives, shaping how we get news, shop, and communicate. When critical events occur, social media and news websites cover the stories as they break and continually revise them as the story evolves. Unfortunately, much of the content around these stories is vulnerable and prone to loss. Thus, web archives have become a significant repository of our recent history and cultural heritage. Content from web archives can be used to fill in the gaps in the live web about the evolution of the story of an important event. Every story is made up of a sequence of events. In this research, events are exemplified through corresponding web pages from the live web and web archives, (semi-)automatically discovered, arranged in a narrative structure ordered by time, and replayed through an appropriate visualization interface.
Invariance of wearing location of Omron-BI pedometers: a validation study.

BACKGROUND The purpose of this study was to investigate the validity and reliability evidences of the Omron BI pedometer, which could count steps taken even when worn at different locations on the body. METHODS Forty (20 males and 20 females) adults were recruited to walk wearing 5 sets, 1 set at a time, of 10 BI pedometers during testing, 1 each at 10 different locations. For comparison, they also wore 2 Yamax Digi-Walker SW-200 pedometers and a Dynastream AMP 331 activity monitor. The subjects walked in 3 free-living conditions: a flat sidewalk, stairs, and mixed conditions. RESULTS Except for a slight decrease in accuracy in the pant pocket locations, Omron BI pedometers counted steps accurately across other locations when subjects walked on the flat sidewalk, and the performance was consistent across devices and trials. When the subjects climbed up stairs, however, the absolute error % of the pant pocket locations increased significantly (P < .05) and similar or higher error rates were found in the AMP 331 and SW-200s. CONCLUSIONS The Omron BI pedometer can accurately count steps when worn at various locations on the body in free-living conditions except for front pant pocket locations, especially when climbing stairs.
Early disease control by low‐dose prednisone comedication may affect the quality of remission in patients with early rheumatoid arthritis

In order to identify rate and stability of remission induced by low‐dose prednisone comedication in early rheumatoid arthritis (RA), we evaluated patients with early RA (<1 year) who were randomized to receive (P) or not (non‐P) low‐dose prednisone in association with step‐up disease‐modifying antirheumatic drug therapy over 2 years. Prevalence and duration of clinical remission were evaluated in the first and second year. Each treatment group included 105 patients; no significant differences were found at baseline. During the first year, P patients achieved higher rates of clinical remission with a time‐averaged odds ratio (OR) of 1.965 (CI 95% 1.214–3.182, P= 0.006). Moreover, they showed a higher probability of sustained remission during the second year (OR 4.480, CI 95% 1.354–14.817, P= 0.014). In conclusion, we found as in early RA low‐dose prednisone comedication is associated with higher rate of clinical remission, earlier disease activity control and more stable remission over time.
Mobile robot navigation using PSO-optimized fuzzy artificial potential field with fuzzy control

The objective of this paper is to develop a path planning algorithm that is able to plan the trajectory of mobile robots from its start point to target point in static and dynamic unknown environments. The classical artificial potential field (APF) method is not sufficient and ineffective for that purpose since it has the problem of local minima. To enhance the performance of the classical APF algorithm and to produce a more efficient and effective path planning for mobile robots, a new method based on combination of a modified APF algorithm with fuzzy logic (i.e. FAPF) is proposed. The proposed algorithm is designed to overcome the problems of the classical APF especially the local minima and enhances the navigation in complex environments. The fuzzy logic controller (FLC) is also used for motion control of the mobile robot. The membership functions of the FLC are optimized with particle swarm optimization (PSO) algorithm for optimality. Simulation models for the proposed path planning and motion control methods are built with MATLAB. Simulation results are obtained and proved that the robot with FAPF navigates with smoother path, react much faster in static and dynamic environments, and avoid obstacles efficiently. The work is compared with other implementations that used conventional PID controllers. All the system is then implemented practically to prove the proposed algorithms and tested in complex and unknown environment.
Apparent and real recombination frequencies in multicopy plasmids: the need for a novel approach in frequency determination

Recombination studies of bacteria are often carried out with multicopy plasmids, and recombination frequencies are often deduced from the proportion of cells in the population that express a recombinant phenotype. These frequencies should however be called apparent frequencies, since detection of the recombinant cells requires not only the formation of a rearranged plasmid but also its establishment in the cell. The establishment of the recombinant plasmid can possibly be affected by its interaction with the parental plasmids. To test this hypothesis, we have used a plasmid system enabling the study of deletion formation between short direct repeats (18 bp) in Bacillus subtilis and developed a method by which deletion frequencies are measured under conditions under which interaction is abolished. Real deletion frequencies were thus determined and compared with apparent deletion frequencies. Real frequencies were underestimated by a factor ranging from 4- to 500-fold, depending upon the plasmid under study. This implies that a large majority of the recombinant molecules that are formed are generally not detected. We show that apparent deletion frequencies strongly depend upon (i) the parental plasmid copy number, (ii) the ability of the recombinant molecules to form heterodimeric plasmids, and (iii) the fitness of the recombinant molecules relative to that of parental molecules. Finally, we show that under conditions under which all recombinant molecules are scored, transcription can inhibit the deletion process 10-fold.
Challenges and opportunities in understanding and utilisation of African insect diversity

Approximately 100 000 species of insects have been described from sub-Saharan Africa. Largely as a result of Africa’s colonial history, the region’s insect fauna is probably better known than that of other tropical regions, but information is often more difficult to locate. Few centres of expertise on insect diversity and systematics exist in tropical Africa, while most large insect collections are housed in South Africa, Europe and the United States. Recent surveys of in-country resources show that human resources are also thinly distributed in tropical Africa. Yet, there is urgent need for basic information on insect diversity for pest management related to plant, livestock and human health, as well as conservation and environmental management. Invasive (alien) species represent a newly recognised threat that cuts across traditional sectors. Recent work shows the potential of different approaches to these challenges, including compilation and synthesis of pre-existing data and research targeted at strategic needs. Information can also be applied in novel ways to promote ‘environmentally friendly’ income-generating schemes such as silk and honey production, ecotourism, butterfly farming and bioprospecting. The Global Taxonomy Initiative of the Convention on Biological Diversity provides an opportunity to expand these experiments to better meet the needs. 197
Epidemiology of Blood Pressure in Relation to Certain Quantitative Traits among Urban Punjabi Adolescents

The objective of the present work was to study the blood pressure with respect to some anthropometric characteristics in adolescent’s age groups. The study comprised 1225 subjects (634 males and 591 females) aged 10-18 years. The range of average blood pressure (systolic/diastolic) was 116.33-134.52/ 78.23-92.62 mmHg in males and 117.71-128.75/ 77.97-88.85 mm Hg in females of 10 to 18 years of age respectively. It was observed that 11 and 12 years of age groups were more susceptible for pre-hypertension (4.49% and 4.24% respectively). Whereas, 10 years and 14 years age groups were more susceptible for hypertension (6.12% and 4.40% respectively). According to multivariate regression analysis, systolic and diastolic blood pressure was significantly associated with weight, BMI and waist circumference. The results of the present analysis support the hypothesis that BMI is a significant predictor of blood pressure in adolescent age groups.
Identification of novel putative adipomyokines by a cross-species annotation of secretomes and expression profiles

Abstract Adipose tissue and skeletal muscle are organs that respond strongly to obesity and physical activity exhibiting high secretory activity. To identify novel putative adipomyokines, comparative expression studies of skeletal muscle and adipose tissue of lean (C57BL/6J) and obese (C57BL/6J on a high-fat diet and NZO) mice, of sedentary and endurance trained C57BL/6J mice and of cattle characterized by different amounts of intramuscular fat were combined with human secretome data and scored. In highly regulated transcripts, we identified 119 myokines, 79 adipokines and 22 adipomyokines. Network analysis of these candidates revealed remodelling of extracellular matrix and tissue fibrosis as relevant functions of several of these candidates. Given the pathophysiogical relevance of fibrosis for adipose-muscle-cross-talk in obesity and type 2 diabetes and its physiological role in exercise adaptation and meat quality of farm animals, they represent interesting candidates for further investigations in different research areas and species.
Human Cancer Biology Role and Relevance of TrkB Mutations and Expression in Non – Small Cell Lung Cancer

Purpose: TrkB has been involved in poor cancer outcome. TrkB mutations have been reported in non– small cell lung cancer. In this study, we aimed at characterizing the role of three potentially sensitizing TrkB mutations previously reported in lung cancer. Experimental Design: We characterized three activation loop mutants of TrkB (M713I, R715G, and R734C) in terms of pathway activation/phosphorylation, migration, anchorage-independent growth, and sensitivity to a Trk inhibitor, using NIH3T3 cells and Baf3 cells. We also sequenced the tyrosine kinase domain of TrkB in a large number of lung cancer samples of East-Asian origin and cell lines. Results:None of themutants were constitutively active in NIH3T3 transformation andmigration assays. M713I and R734Cmutants showed low levels of autophosphorylation in comparison with wild-type TrkB. Although R715G showed similar level of autophosphorylation to wild-type TrkB on brain-derived neurotrophic factor stimulation, the mutant was not as competent as wild-type TrkB in supporting interleukin-3–independent growth of Baf3 cells. In addition, the Trk inhibitor AZD6918 inhibited wild-type TrkB-induced cell migration and cell growth, whereas the mutants were relatively resistant to the Trk inhibitor compared with wild-type TrkB. We could not confirm the presence of nonsynonymous mutation in 78 lung cancer samples and 29 cell lines. Conclusions: Wild-type, but not mutant, TrkB enhances cell migration and transformation. Our study suggests that TrkB mutations should not be used for selection of patients with lung cancer treated with Trk inhibitors. High expression of wild-type TrkB might be beneficial for studies of Trk inhibitors. Clin Cancer Res; 17(9); 2638–45. 2011 AACR.
Tyrosine 251 at the C‐terminus of neuronal glycoprotein M6a is critical for neurite outgrowth

Neuronal glycoprotein M6a is involved in neuronal plasticity, promoting neurite and filopodia outgrowth and, likely, synaptogenesis. Polymorphisms in the human M6a gene GPM6A have recently been associated with mental illnesses such as schizophrenia, bipolar disorders, and claustrophobia. Nevertheless, the molecular bases underlying these observations remain unknown. We have previously documented that, to induce filopodia formation, M6a depends on the association of membrane lipid microdomains and the activation of Src and mitogen‐activated protein kinase kinases. Here, in silico analysis of the phosphorylation of tyrosine 251 (Y251) at the C‐terminus of M6a showed that it could be a target of Src kinases. We examined whether phosphorylation of M6a at Y251 affects neurite and filopodia outgrowth and the targets involved in its signal propagation. This work provides evidence that the Src kinase family and the phosphatidylinositide 3‐kinase (PI3K), but not Ras, participate in M6a signal cascade leading to neurite/filopodia outgrowth in hippocampal neurons and murine neuroblastoma N2a cells. Phosphorylation of M6a at Y251 is essential only for neurite outgrowth by the PI3K/AKT‐mediated pathway and, moreover, rescues the inhibition caused by selective Src inhibitor and external M6a monoclonal antibody treatment. Thus, we suggest that phosphorylation of M6a at Y251 is critical for a specific stage of neuronal development and triggers redundant signaling pathways leading to neurite extension. © 2014 Wiley Periodicals, Inc.
A Re‐Appraisal of the Fertility Response to the Australian Baby Bonus

The Australian baby bonus offering parents $3,000 on the birth of a new child was announced on 11 May 2004. The availability of five years of birth data following the introduction of the baby bonus allows for a more comprehensive analysis of the policy implications than is current in the literature. The focus of this paper is to identify if there is a positive fertility choice response to the introduction of the Australian baby bonus policy and if this response is sustained over time. To do this, 19 years of birth and macroeconomic data, beginning in 1990, is analysed using an unobservable components model. The results indicate a significant increase in birth numbers ten months following the announcement of the baby bonus, and this overall increase was sustained up to the end of the observed period. A cumulative growth in birth numbers which commenced in January 2006 slows in 2008 and 2009. It is suggested that the initial increase in births, identified in March 2005, is a direct fertility response to the introduction of the policy, and that the subsequent change in the growth of birth numbers may be the result of a delayed effect working through a number of channels. We estimate that approximately 108,000 births are attributable to the baby bonus over the period, at an approximate cost of $43,000 per extra child.
Applying the RMMAC methodology to an unstable plant

In this paper we revisit previous work on Robust Multiple Models Adaptive Control (RMMAC) of uncertain plants [1]. RMMAC was originally developed to control open-loop stable plants. We formulate and study the problem of robust adaptive control of open-loop unstable plants with structured and unstructured uncertainty in the presence of external disturbances and measurement noises, an issue that poses considerable theoretical and practical challenges. In particular, we show, with the help of an example, how a slight modification of the technique introduced in previous work on the RMMAC for stable plants yields a methodology that has the potential to deal with unstable plants. A design example and several nontrivial computer simulations are presented and discussed.
Patterns of tree species composition at watershed-scale in the Amazon ‘arc of deforestation’: implications for conservation

SUMMARY The loss of biodiversity in transitional forests between the Cerrado and Amazonia, the two largest neotropical phytogeographic domains, is an issue of great concern. This extensive region is located within the ‘arc of deforestation’ zone where tropical forests are being lost at the fastest rate on the planet, but floristic diversity and variation among forests here is still poorly understood. We aimed to characterize the floristic composition of forests in this zone and explored the degree and drivers of differentiation within and across Araguaia and Xingu watersheds. In 10 sites we identified all trees with diameter ≥10 cm; these totaled 4944 individuals in 257 species, 107 genera and 52 families. We evaluated the data for multivariate variation using TWINSPAN and DCA to understand the species distribution among sites. There was a larger contribution from the Amazonian flora (169 species) than that of the Cerrado (109) to the transitional forests. Remarkably, 142 species (55%) were restricted to only one sampling site, while 29 species (>16%) are endemic to Brazil, suggesting potentially large loss of species and unique forest communities with the loss and fragmentation of large areas. Our results also suggest that watersheds may be a critical factor driving species distribution among forests in the Amazonian–Cerrado transition zone, and quantifying their role can provide powerful insight into devising better conservation strategies for the remaining forests.
AFTER-EFFECTS OF YOUTH UNEMPLOYMENT 1 The after-effects of youth unemployment : More vulnerable persons are less likely to succeed in Youth Guarantee programs

This article investigates unemployed adolescents’ success in reemployment programs. We propose that not being in employment, education, or training indicates a setback in the achievement of important life-goals, which affects mental health and success in reemployment programs. Adolescents who are more affected by the experience of unemployment will be even less likely to succeed. An analysis of longitudinal archival records of 300 adolescents in a Youth Guarantee apprenticeship scheme confirms the expectations. Adolescents who were more vulnerable during unemployment and who had a worse relationship with their parents when starting the apprenticeship were more likely to drop out within the first year. The effect of age was moderated by relationship quality. The results show that taking the prior experience of not being in employment, education and training into account can offer a new understanding for the success of reemployment programs. Theoretical and practical implications of the findings are discussed.