Miracle-dz/UniFAR-FTUs huggingface dataset:
Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli

Recent insights suggest that non-specific and/or promiscuous enzymes are common and active across life. Understanding the role of such enzymes is an important open question in biology. Here we develop a genome-wide method, PROPER, that uses a permissive PSI-BLAST approach to predict promiscuous activities of metabolic genes. Enzyme promiscuity is typically studied experimentally using multicopy suppression, in which over-expression of a promiscuous ‘replacer’ gene rescues lethality caused by inactivation of a ‘target’ gene. We use PROPER to predict multicopy suppression in Escherichia coli, achieving highly significant overlap with published cases (hypergeometric p = 4.4e-13). We then validate three novel predicted target-replacer gene pairs in new multicopy suppression experiments. We next go beyond PROPER and develop a network-based approach, GEM-PROPER, that integrates PROPER with genome-scale metabolic modeling to predict promiscuous replacements via alternative metabolic pathways. GEM-PROPER predicts a new indirect replacer (thiG) for an essential enzyme (pdxB) in production of pyridoxal 5’-phosphate (the active form of Vitamin B6), which we validate experimentally via multicopy suppression. We perform a structural analysis of thiG to determine its potential promiscuous active site, which we validate experimentally by inactivating the pertaining residues and showing a loss of replacer activity. Thus, this study is a successful example where a computational investigation leads to a network-based identification of an indirect promiscuous replacement of a key metabolic enzyme, which would have been extremely difficult to identify directly.
Cross Domain Mathematical Concept Formation

Many interesting concepts in mathematics are essentially ‘cross-domain’ in nature, relating objects from more than one area of mathematics, e.g. prime order groups. These concepts are often vital to the formation of a mathematical theory. Often, the introduction of cross-domain concepts to an investigation seems to exercise a mathematician’s creative ability. The HR program, (Colton et al., 1999), proposes new concepts in mathematics. Its original implementation was limited to working in one mathematical domain at a time, so it was unable to create cross-domain concepts. Here, we describe an extension of HR to multiple domains. Cross-domain concept formation is facilitated by generalisation of the data structures and heuristic measures employed by the program, and the implementation of a new production rule. Results achieved include generation of the concepts of prime order groups, graph nodes of maximal degree and an interesting
MC3T3-E1 Cellular Response and Protein Detection on Surface Potential-Controlled TiO2 Scale in Serum-Containing Medium

MC3T3-E1 cell differentiation and related surface potentials of rutile-type TiO2 scales formed on Ti are controlled by varying the Ti heat treatment conditions in a N2 atmosphere containing a trace amount of O2. The zeta potentials of the samples heated at 873 and 973 K for 1 h show large negative and positive values, respectively, while cell differentiation on the surface is enhanced in both cases (14 days incubation). In the case of untreated Ti, the cell differentiation diminishes and the zeta potential becomes more neutral. Protein detection by an immunogold-labeling technique and Ca and P detection by time-of-flight secondary ion mass spectrometry reveal that Ca and P, rather than an adhesive protein such as fibronectin, predominantly adsorbed on the scales formed in 1 h at 873 and 973 K, respectively. In the case of untreated Ti, both fibronectin and a non-adhesive protein such as albumin adsorbed, but no Ca and P were detected. The present findings illuminate the relationship between charged surfaces and MC3T3-E1 cellular response.
The Contribution of Single Synapses to Sensory Representation in Vivo

The extent to which synaptic activity can signal a sensory stimulus limits the information available to a neuron. We determined the contribution of individual synapses to sensory representation by recording excitatory postsynaptic currents (EPSCs) in cerebellar granule cells during a time-varying, quantifiable vestibular stimulus. Vestibular-sensitive synapses faithfully reported direction and velocity, rather than position or acceleration of whole-body motion, via bidirectional modulation of EPSC frequency. The lack of short-term synaptic dynamics ensured a highly linear relationship between velocity and charge transfer, and as few as 100 synapses provided resolution approaching psychophysical limits. This indicates that highly accurate stimulus representation can be achieved by small networks and even within single neurons.
Energy Optimized Subthreshold VLSI Logic Family With Unbalanced Pull-Up/Down Network and Inverse Narrow-Width Techniques

Ultralow-energy biomedical applications have urged the development of a subthreshold VLSI logic family in standard CMOS. This brief proposes an unbalanced pull-up/down network, together with an inverse narrow-width technique, to improve the operating speed of the individual logic cell. Effective logical efforts save both power and die area in the process of device sizing and topology optimization. Three experimental 14-tap 8-bit finite impulse response filters optimized for ultralow-voltage operation were fabricated in 0.18-μm CMOS. Measurements show that the optimized 0.45 and 0.6 V libraries achieve minimum energy operations at 100 kHz, with a figure-of-merit of 0.365 (at 0.31 V) and 0.4632 (at 0.39 V), respectively. They correspond to 35.96% and 18.74% improvements, and the overall performances are well comparable with the state of the art.
The Membrane-Anchored BOTRYTIS-INDUCED KINASE1 Plays Distinct Roles in Arabidopsis Resistance to Necrotrophic and Biotrophic Pathogens[W]

Plant resistance to disease is controlled by the combination of defense response pathways that are activated depending on the nature of the pathogen. We identified the Arabidopsis thaliana BOTRYTIS-INDUCED KINASE1 (BIK1) gene that is transcriptionally regulated by Botrytis cinerea infection. Inactivation of BIK1 causes severe susceptibility to necrotrophic fungal pathogens but enhances resistance to a virulent strain of the bacterial pathogen Pseudomonas syringae pv tomato. The response to an avirulent bacterial strain is unchanged, limiting the role of BIK1 to basal defense rather than race-specific resistance. The jasmonate- and ethylene-regulated defense response, generally associated with resistance to necrotrophic fungi, is attenuated in the bik1 mutant based on the expression of the plant defensin PDF1.2 gene. bik1 mutants show altered root growth, producing more and longer root hairs, demonstrating that BIK1 is also required for normal plant growth and development. Whereas the pathogen responses of bik1 are mostly dependent on salicylic acid (SA) levels, the nondefense responses are independent of SA. BIK1 is membrane-localized, suggesting possible involvement in early stages of the recognition or transduction of pathogen response. Our data suggest that BIK1 modulates the signaling of cellular factors required for defense responses to pathogen infection and normal root hair growth, linking defense response regulation with that of growth and development.
Clinical Relevance of KRAS in Human Cancers

The KRAS gene (Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) is an oncogene that encodes a small GTPase transductor protein called KRAS. KRAS is involved in the regulation of cell division as a result of its ability to relay external signals to the cell nucleus. Activating mutations in the KRAS gene impair the ability of the KRAS protein to switch between active and inactive states, leading to cell transformation and increased resistance to chemotherapy and biological therapies targeting epidermal growth factor receptors. This review highlights some of the features of the KRAS gene and the KRAS protein and summarizes current knowledge of the mechanism of KRAS gene regulation. It also underlines the importance of activating mutations in the KRAS gene in relation to carcinogenesis and their importance as diagnostic biomarkers, providing clues regarding human cancer patients' prognosis and indicating potential therapeutic approaches.
Full- and reduced-order filter design for discrete-time T-S fuzzy systems with time-varying delay

This paper is focused on the problem of ℋ∞ filtering for a class of discrete-time T-S fuzzy time-varying delay systems. Our interest is how to design full- and reduced-order filters that guarantee the filtering error system to be asymptotically stable with a prescribed ℋ∞ performance. Sufficient conditions for the obtained filtering error system are proposed by applying an input-output approach and a two-term approximation method, which is employed to approximate the time-varying delay. The corresponding full and reduced-order filter design is cast into a convex optimization problem, which can be efficiently solved by standard numerical algorithms.
The Daily Relation between Parental Rejection and Emotional Eating in Youngsters: A Diary Study

KEY POINTS Cross-sectional survey studies have demonstrated significant associations between parental rejection and peer rejection on the one hand and disturbed eating in youngsters, like emotional eating, on the other hand. In this study, we wanted to expand our knowledge on these relationships by investigating the daily fluctuations in these variables. Youngsters completed a 7-day diary to assess daily parental rejection, peer rejection and emotional eating. Using multilevel analyses, our results showed that daily variations in parental rejection were related to daily variations in emotional eating of the youngsters. This highlights the importance of addressing the parent-child relationship in interventions for emotional eating in youngsters. Background: This study investigated the daily relation between parental rejection and peer rejection on the one hand and emotional eating in youngsters on the other hand. Methods: Participants (N = 55) between the ages of 11 and 15 years completed a 7-day diary. A multilevel design was used to examine day-to-day within-person relationships between parental and peer rejection (measured by CHS) and emotional eating (measured by DEBQ-C) of youngsters. Results: The results showed that daily variations in parental rejection were related to daily variations in emotional eating of the youngsters. Daily peer rejection was only marginally significantly related to the emotional eating of the youngsters. Conclusions: These results indicate that especially parental rejection, and to a lesser extent peer rejection, are associated with the emotional eating of youngsters. The findings highlight the importance of addressing the parent-child relationship in interventions for emotional eating in youngsters.
Identification of Developmentally Regulated PCP-Responsive Non-Coding RNA, prt6, in the Rat Thalamus

Schizophrenia and similar psychoses induced by NMDA-type glutamate receptor antagonists, such as phencyclidine (PCP) and ketamine, usually develop after adolescence. Moreover, adult-type behavioral disturbance following NMDA receptor antagonist application in rodents is observed after a critical period at around 3 postnatal weeks. These observations suggest that the schizophrenic symptoms caused by and psychotomimetic effects of NMDA antagonists require the maturation of certain brain neuron circuits and molecular networks, which differentially respond to NMDA receptor antagonists across adolescence and the critical period. From this viewpoint, we have identified a novel developmentally regulated phencyclidine-responsive transcript from the rat thalamus, designated as prt6, as a candidate molecule involved in the above schizophrenia-related systems using a DNA microarray technique. The transcript is a non-coding RNA that includes sequences of at least two microRNAs, miR132 and miR212, and is expressed strongly in the brain and testis, with trace or non-detectable levels in the spleen, heart, liver, kidney, lung and skeletal muscle, as revealed by Northern blot analysis. The systemic administration of PCP (7.5 mg/kg, subcutaneously (s.c.)) significantly elevated the expression of prt6 mRNA in the thalamus at postnatal days (PD) 32 and 50, but not at PD 8, 13, 20, or 24 as compared to saline-treated controls. At PD 50, another NMDA receptor antagonist, dizocilpine (0.5 mg/kg, s.c.), and a schizophrenomimetic dopamine agonist, methamphetamine (4.8 mg/kg, s.c.), mimicked a significant increase in the levels of thalamic prt6 mRNAs, while a D2 dopmamine receptor antagonist, haloperidol, partly inhibited the increasing influence of PCP on thalamic prt6 expression without its own effects. These data indicate that prt6 may be involved in the pathophysiology of the onset of drug-induced schizophrenia-like symptoms and schizophrenia through the possible dysregulation of target genes of the long non-coding RNA or microRNAs in the transcript.
E-Business Triggers: Further Insights into Barriers and Facilitators amongst Ghanaian Non-Traditional Exporters (NTEs)

AbstrAct E-business is key to export development for developing economy firms. There are however key barriers and facilitators to e-business adoption for small and large internationalizing firms the world over. This chapter sets to find out, by means of the testing of key hypothesis, the main barriers and facilitators of e-business adoption by Ghanaian export firms. We adopt a quantitative approach to this study and draw our study sample from a directory of active non-traditional exporters (NTEs) in Ghana. We find that an export firm's international orientation, owner/management idiosyncrasies, e-sophistication of partners, export firm's characteristics (age, number of employees and location) and weak government regulation have no significant influence on e-business adoption by Ghanaian NTE firms. On the other hand, competitive pressure (as measured by competition from Ghanaian export firms and growth in size of export operations) significantly facilitates e-business adoption. Internal resource constraints (measured by technological and financial resources for e-business adoption and business culture) and environmental bottlenecks (measured by lack of support from export sector regulators and export associations and high internet access fees carged by ISPs) also reduce the likelihood of e-business adoption by Ghanaian NTE firms. We find interestingly that Export facilitation (measured by pressures from GEPC and FAGE) and digitalization (measured by perceived importance of e-business in digitalizing export operations and improving export competitiveness) perceived to facilitate e-business adoption however exhibit significant negative relationships with adoption. We proffer some explanations for this unusual finding and provide general management implications for improving e-business practices amongst the various players in Ghana's non-traditional export sector.
Language Use and Coalition Formation in Multiparty Negotiations

The alignment of bargaining positions is crucial to a successful negotiation. Prior research has shown that similarity in language use is indicative of the conceptual alignment of interlocutors. We use latent semantic analysis to explore how the similarity of language use between negotiating parties develops over the course of a three-party negotiation. Results show that parties that reach an agreement show a gradual increase in language similarity over the course of the negotiation. Furthermore, reaching the most financially efficient outcome is dependent on similarity in language use between the parties that have the most to gain from such an outcome.
Scheme of thinking quantum systems

A general approach describing quantum decision procedures is developed. The approach can be applied to quantum information processing, quantum computing, creation of artificial quantum intelligence, as well as to analyzing decision processes of human decision makers. Our basic point is to consider an active quantum system possessing its own strategic state. Processing information by such a system is analogous to the cognitive processes associated to decision making by humans. The algebra of probability operators, associated with the possible options available to the decision maker, plays the role of the algebra of observables in quantum theory of measurements. A scheme is advanced for a practical realization of decision procedures by thinking quantum systems. Such thinking quantum systems can be realized by using spin lattices, systems of magnetic molecules, cold atoms trapped in optical lattices, ensembles of quantum dots, or multilevel atomic systems interacting with electromagnetic field.
An Al-inducible expansin gene, OsEXPA10 is involved in root cell elongation of rice.

Expansins are cell wall loosening proteins, which are encoded by multigene families. However, the physiological role of most expansin genes is still poorly understood. Here, we functionally characterized an Al-inducible expansin gene, OsEXPA10, which is regulated by a C2H2-type zinc-finger transcription factor, ART1 in rice. A detailed expression analysis showed that OsEXPA10 was expressed in both the roots and shoots at a similar level, but only the expression in the roots was rapidly upregulated in response to Al. Furthermore, spatial expression analysis showed that the Al-induced expression was only found in the root tips (0-3 mm), but not in the mature root zones. The expression was neither induced by other metals including Cd and La nor by low pH. Immunostaining showed that OsEXPA10 was localized at all cells of the root tips. Knockout of OsEXPA10 resulted in a significant decrease in the cell elongation of the roots in the absence of Al. In the presence of Al, knockout of OsEXPA10 did not alter the Al sensitivity evaluated by relative root elongation, but the root cell wall of knockout lines accumulated less Al compared to those of the wild-type rice. Collectively, our results indicate that OsEXPA10 expressed in the root tips is required for the root cell elongation, but that the contribution of this gene to high Al tolerance in rice is small.
Elevated Serum C-Reactive Protein Levels and Advanced Atherosclerosis in Youth

Objective—To determine the associations among serum C-reactive protein (CRP) concentration, age, sex, risk factors for coronary heart disease (CHD), and atherosclerosis in young people. Methods and Results—In 1244 subjects 15 to 34 years of age, we measured gross atherosclerotic lesions in the right coronary artery (RCA) and abdominal aorta (AA) and American Heart Association (AHA) lesion grade in the left anterior descending (LAD) coronary artery; serum CRP, lipoprotein cholesterol, and thiocyanate (for smoking) concentrations; intimal thickness of renal arteries (for hypertension); glycohemoglobin (for hyperglycemia); and body mass index (for obesity). Serum CRP levels increased with age, were higher in women than in men, and were positively related to obesity and hyperglycemia. Serum CRP ≥10 mg/L was associated with more extensive gross raised lesions in the RCA after age 25 and in the AA after age 30. Serum CRP ≥3 was associated with a greater prevalence of AHA grade 5 lesions in the proximal LAD coronary artery after age 25. The associations of CRP with lesions were independent of the traditional CHD risk factors. Conclusion—Serum CRP level is independently associated with advanced atherosclerosis in young persons.
Confidence mapping in diffusion tensor magnetic resonance imaging tractography using a bootstrap approach

The bootstrap technique is an extremely powerful nonparametric statistical procedure for determining the uncertainty in a given statistic. However, its use in diffusion tensor MRI tractography remains virtually unexplored. This work shows how the bootstrap can be used to assign confidence to results obtained with deterministic tracking algorithms. By invoking the concept of a “tract‐propagator,” it also underlines the important effect of local fiber architecture or architectural milieu on tracking reproducibility. Finally, the practical advantages and limitations of the technique are discussed. Not only does the bootstrap allow any deterministic tractography algorithm to be used in a probabilistic fashion, but also its model‐free inclusion of all sources of variability (including those that cannot be modeled) means that it provides the most realistic approach to probabilistic tractography. Magn Reson Med 53:1143–1149, 2005. Published 2005 Wiley‐Liss, Inc.
Resource quality effects on life histories of Daphnia

We investigated the changes in life histories imposed on the water flea, Daphnia magna, due to biochemical and mineral limitations. Phosphorus‐deficient Scenedesmus obliquus were incubated with or without a single essential fatty acid, eicosapentaenoic acid (EPA). Additionally, the algae were spiked with dissolved phosphorus to create a range of C: P ratios from 600 to 200. This procedure created the possibility to study the importance of different essential resources. We found that somatic growth is retarded until a C: P ratio (molar) ~350 is reached. Adding more phosphorus did not further increase growth. At the same time, at high C: P ratios the addition of EPA did not make a difference in growth, whereas below the nutrient threshold (C : P = 350), the fatty acid had a strong positive impact on growth. In a second experiment we studied how the food conditions (with regard to EPA) affected the growth and investment in reproduction and whether this effect was passed on to the next generation. We found that animals fed EPA made an earlier and larger investment in reproduction. Also, the EPA‐enriched animals had a higher mortality. The juveniles from mothers fed EPA‐enriched algae had a higher growth rate than neonates from control mothers.
Supporting Design Enhancement by Pattern-Based Transformation

In general, a design pattern is usually documented in the form of an essay, with descriptions and rough design such as intent, motivation, structure, behavior, applicability and consequence, etc. Even though there are tools supporting pattern application, developers still may misuse patterns since misunderstanding. It may result failures of systems because of inconsistencies or design errors. In fact, the refinement process by applying a design pattern is merely the addition or removal of model elements in structure view. The refinement process for each design pattern is almost constant whenever the same pattern is applied. In this paper, we propose an approach for design pattern application and assisting the design enhancement by model transformation. Furthermore, we demonstrate our approach by a case study on a real-world multi-core embedded system PVE (Parallel Video Encoder), where a design pattern Command Pipeline is designed for the design enhancement.
Transfinite induction and bar induction of types zero and one, and the role of continuity in intuitionistic analysis

The following is a self-contained proof theoretic treatment of two of the principal axiom schemata of current intuitionistic analysis: the axiom of bar induction (Brouwer's bar theorem) and the axiom of continuity. The results are formulated in terms of formal derivability in elementary intuitionistic analysis H(§ 1), so the positive (i.e., derivability) results also apply to elementary classical analysis Z1 (Appendix 1). Both schemata contain the combination of quantifiers νfΛn, where f, g, … are intended to range over free choice sequences of suitable kinds of objects x, y, …; for example, natural numbers or sequences of natural numbers, and n, m, p, r, … over natural numbers (non-negative integers).