Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple Model-Informed Open-Loop Control of Uncertain Intracellular Signaling Dynamics

Computational approaches to tune the activation of intracellular signal transduction pathways both predictably and selectively will enable researchers to explore and interrogate cell biology with unprecedented precision. Techniques to control complex nonlinear systems typically involve the application of control theory to a descriptive mathematical model. For cellular processes, however, measurement assays tend to be too time consuming for real-time feedback control and models offer rough approximations of the biological reality, thus limiting their utility when considered in isolation. We overcome these problems by combining nonlinear model predictive control with a novel adaptive weighting algorithm that blends predictions from multiple models to derive a compromise open-loop control sequence. The proposed strategy uses weight maps to inform the controller of the tendency for models to differ in their ability to accurately reproduce the system dynamics under different experimental perturbations (i.e. control inputs). These maps, which characterize the changing model likelihoods over the admissible control input space, are constructed using preexisting experimental data and used to produce a model-based open-loop control framework. In effect, the proposed method designs a sequence of control inputs that force the signaling dynamics along a predefined temporal response without measurement feedback while mitigating the effects of model uncertainty. We demonstrate this technique on the well-known Erk/MAPK signaling pathway in T cells. In silico assessment demonstrates that this approach successfully reduces target tracking error by 52% or better when compared with single model-based controllers and non-adaptive multiple model-based controllers. In vitro implementation of the proposed approach in Jurkat cells confirms a 63% reduction in tracking error when compared with the best of the single-model controllers. This study provides an experimentally-corroborated control methodology that utilizes the knowledge encoded within multiple mathematical models of intracellular signaling to design control inputs that effectively direct cell behavior in open-loop.
Purification, Cloning, Characterization and Essential Amino Acid Residues Analysis of a New ι-Carrageenase from Cellulophaga sp. QY3

ι-Carrageenases belong to family 82 of glycoside hydrolases that degrade sulfated galactans in the red algae known as ι-carrageenans. The catalytic mechanism and some substrate-binding residues of family GH82 have been studied but the substrate recognition and binding mechanism of this family have not been fully elucidated. We report here the purification, cloning and characterization of a new ι-carrageenase CgiA_Ce from the marine bacterium Cellulophaga sp. QY3. CgiA_Ce was the most thermostable carrageenase described so far. It was most active at 50°C and pH 7.0 and retained more than 70% of the original activity after incubation at 50°C for 1 h at pH 7.0 or at pH 5.0–10.6 for 24 h. CgiA_Ce was an endo-type ι-carrageenase; it cleaved ι-carrageenan yielding neo-ι-carrabiose and neo-ι-carratetraose as the main end products, and neo-ι-carrahexaose was the minimum substrate. Sequence analysis and structure modeling showed that CgiA_Ce is indeed a new member of family GH82. Moreover, sequence analysis of ι-carrageenases revealed that the amino acid residues at subsites −1 and +1 were more conserved than those at other subsites. Site-directed mutagenesis followed by kinetic analysis identified three strictly conserved residues at subsites −1 and +1 of ι-carrageenases, G228, Y229 and R254 in CgiA_Ce, which played important roles for substrate binding. Furthermore, our results suggested that Y229 and R254 in CgiA_Ce interacted specifically with the sulfate groups of the sugar moieties located at subsites −1 and +1, shedding light on the mechanism of ι-carrageenan recognition in the family GH82.
Communicable Disease and Young Children in Group Settings

transdisciplinary play-based assessment effectively. The suggested structure of transdisciplinary play-based assessment and the information provided will enable developmental assessors to develop rich descriptions of a child's developmental abilities, identify developmental strengths and weaknesses in an environmental context, integrate information and perspectives from families, and determine approximate developmental ages. Under provides pertinent examples to illustrate points throughout the book, as well as an immensely helpful case study example of transdisciplinary play-based assessment. The case study includes a complete description for one child: social history; areas of developmental concern; assessment activities and observations; conversations among team members, including the child's father; implications for intervention; and a complete assessment report. This integrated example helps the reader to understand the coordination of the various principles and activities of transdisciplinary play-based assessment. The book concludes with a chapter on parent involvement in transdisciplinary playbased assessment. Although this chapter lacks the detail of the rest of the book, the chapter and the comments concerning parents throughout the book reflect the author's view of parents and their importance in the assessment process. The practices of transdisciplinary play-based assessment encourage the level and scope of parent involvement that is appropriate to development of Individual Family Service Plans. Transdisciplinary Play-Based Assessment offers a well-written, comprehensive, and extremely useful resource for early intervention. The relevant and practical content is enhanced by well-designed headings and formatting within the text. Teachers, therapists, psychologists, and all who participate in developmental assessments with young chil-
Charting the Landscape of Children's Rights

This issue of the Journal of Social Issues presents current theory, research, and methodological considerations pertaining to “Young People's Perspectives on the Rights of the Child. ” The following brief introduction charts the landscape of children's rights by outlining the purpose and goals of the issue, provides a short historical overview on the topic, sets the context for the individual articles, and highlights the recurring themes making up this issue of JSI. The authors of the articles in this issue extend current knowledge and thinking on the topic of children rights and also set the foundation for future empirical work, practice, and policy pertaining to children's rights and rights-focused research.
Improving Water-Quality through Real-Time , Continuous Monitoring An innovative research tool with extensive application potential

Overview An approach is described for monitoring water-quality continuously, and for developing surrogate regression equations to predict concentrations of other water-quality constituents. Although the approach described below is for estimating suspended sediment concentrations using turbidity as a surrogate, turbidity can theoretically be used to predict any particulate or sediment-associated water-quality constituent (such as bacteria, total phosphorus, and mercury).
Lipid Accumulation in Smooth Muscle Cells Under LDL Loading Is Independent of LDL Receptor Pathway and Enhanced by Hypoxic Conditions

Objective—The effect of a variety of hypoxic conditions on lipid accumulation in smooth muscle cells (SMCs) was studied in an arterial wall coculture and monocultivation model. Methods and Results—Low density lipoprotein (LDL) was loaded under various levels of oxygen tension. Oil red O staining of rabbit and human SMCs revealed that lipid accumulation was greater under lower oxygen tension. Cholesterol esters were shown to accumulate in an oxygen tension–dependent manner by high-performance liquid chromatographic analysis. Autoradiograms using radiolabeled LDL indicated that LDL uptake was more pronounced under hypoxia. This result holds in the case of LDL receptor–deficient rabbit SMCs. However, cholesterol biosynthesis and cellular cholesterol release were unaffected by oxygen tension. Conclusions—Hypoxia significantly increases LDL uptake and enhances lipid accumulation in arterial SMCs, exclusive of LDL receptor activity. Although the molecular mechanism is not clear, the model is useful for studying lipid accumulation in arterial wall cells and the difficult-to-elucidate events in the initial stage of atherogenesis.
A Test Collection for Email Entity Linking

Most prior work on entity linking has focused on linking name mentions found in third-person communication (e.g., news) to broad-coverage knowledge bases (e.g., Wikipedia). A restricted form of domain-specific entity linking has, however, been tried with email, linking mentions of people to specific email addresses. This paper introduces a new test collection for the task of linking mentions of people, organizations, and locations to Wikipedia. Annotation of 200 randomly selected entities of each type from the Enron email collection indicates that domainspecific knowledge bases are indeed required to get good coverage of people and organizations, but that Wikipedia provides good (93%) coverage for the named mentions of locations in the Enron collection. Furthermore, experiments with an existing entity linking system indicate that the absence of a suitable referent in Wikipedia can easily be recognized by automated systems, with NIL precision (i.e., correct detection of the absence of a suitable referent) above 90% for all three entity types.
Estimated and Measured BMI and Self-Perceived Body Image of Adolescents in Germany: Part 1 – General Implications for Correcting Prevalence Estimations of Overweight and Obesity

Objective: This study examines the degree of divergence between BMI calculated from subjective assessments and BMI calculated from measured height and weight as a function of gender and body image. Methods: In the German National Health Interview and Examination Survey for Children and Adolescents (KiGGS) the height and weight of 17,641 children and adolescents aged 0–18 years were measured. Participants were also questioned about their subjective body image (whether they considered themselves much too thin, a bit too thin, exactly the right weight, too fat or much too fat). A representative subsample of adolescents between 11 and 17 years old (N = 3,436: 1,663 boys and 1,773 girls) was asked additionally to self-report their body weight and height before being measured. Results: The bias in the self-reported BMI yielded an underestimation of overweight and obesity prevalence. Girls who considered themselves much too fat or too fat and boys who considered themselves as much too fat underestimated their BMI. This was taken into account using a correction procedure for prevalence estimates of overweight and obesity based on the concept of conditional probabilities. Conclusion: The proposed correction formula using data from the KiGGS study can be applied to other German studies of adolescents in which weight, height and body image are only determined by self-report. Furthermore the correction procedure in principle can be transferred to other studies in other countries as long as a parallel validation study has been conducted to assess both subjective and objective BMI and body image.
The Theory and Applications of Multiple Description Coding

Loss of descriptions of stochastic processes transmitted over unreliable channels is typical in communication network. An intuitive approach to address this problem is to send more than one descriptions of the same sources and hope that at least one description can survive. Each description is supposed to be good enough to meet some decoder requirement if it get through itself. So these descriptions carry a lot of similar information and are dependent. However, if all these descriptions are received, we also hope the combined results to be as good as possible. This requires that the descriptions are far apart and thus can not be individually good. The multiple description problem refers to ”if an information source is described by two or more separate descriptions, what are the concurrent limitations on qualities of these descriptions taken separately and jointly? ”[1]. In other words, the fundamental problem is how can we achieve tradeoff between making descriptions individually good and sufficiently different. A multiple description coding(MDC) model with two channels and three receivers is shown in figure 1. An encoder is given a symbol sequence yielded by a stochastic process {Xk}, where Xk’s are independent identically distributed (i.i.d.) according to some known distribution p(x). Two descriptions of the same sequence, of rate R1 and R2, are sent to decoder 1 and 2 through two channels, respectively. The central decoder 0 receives information over both two channels while the other two only receive information over their respective channels. All decoders have their own specific quality requirement in terms of distortion, denoted by D0, D1 and D2. One key theoretical problem in MDC was answered by El Gamal and T. Cover in [2]. Their proof gave a general bound, in usual Shannon sense ,for the achievable set of values of the quintuple (R1, R2,D0,D1,D2), thus determine what are the achievable rates R1 and R2 given distortions D0, D1 and D2. Ozarow further showed a tight bound for memoryless Gaussian source with with mean-square error(MSE). Unfortunately, these bound can only be achieved by coding arbitrarily long sequences, which are not applicable in real network.
Seasonal Changes in an Alpine Soil Bacterial Community in the Colorado Rocky Mountains

ABSTRACT The period when the snowpack melts in late spring is a dynamic time for alpine ecosystems. The large winter microbial community begins to turn over rapidly, releasing nutrients to plants. Past studies have shown that the soil microbial community in alpine dry meadows of the Colorado Rocky Mountains changes in biomass, function, broad-level structure, and fungal diversity between winter and early summer. However, little specific information exists on the diversity of the alpine bacterial community or how it changes during this ecologically important period. We constructed clone libraries of 16S ribosomal DNA from alpine soil collected in winter, spring, and summer. We also cultivated bacteria from the alpine soil and measured the seasonal abundance of selected cultured isolates in hybridization experiments. The uncultured bacterial communities changed between seasons in diversity and abundance within taxa. The Acidobacterium division was most abundant in the spring. The winter community had the highest proportion of Actinobacteria and members of the Cytophaga/Flexibacter/Bacteroides (CFB) division. The summer community had the highest proportion of the Verrucomicrobium division and of β-Proteobacteria. As a whole,α -Proteobacteria were equally abundant in all seasons, although seasonal changes may have occurred within this group. A number of sequences from currently uncultivated divisions were found, including two novel candidate divisions. The cultured isolates belonged to the α-, β-, and γ-Proteobacteria, the Actinobacteria, and the CFB groups. The only uncultured sequences that were closely related to the isolates were from winter and spring libraries. Hybridization experiments showed that actinobacterial and β-proteobacterial isolates were most abundant during winter, while the α- andγ -proteobacterial isolates tested did not vary significantly. While the cultures and clone libraries produced generally distinct groups of organisms, the two approaches gave consistent accounts of seasonal changes in microbial diversity.
Student switchers and the regulation of residency: the interface of the individual and Australia's immigration regime

Since 1998, policy changes to Australia's skilled migration program have favoured international students as potential skilled migrants. This has included legislation allowing holders of an Australian tertiary qualifi cation to apply for permanent residency (PR) onshore within 6 months of completing their study. This process, dubbed 'student switching' (McLaughlan and Salt, 2002) has created a distinct migration process through which increasing numbers of international students use their study in Australia as a pathway to residency. In this paper, I will address how individuals experience the bureaucratic processes of application for PR, in that the granting or denying of visas involves the interface between government and individual. I will explore how individuals' interactions with the power of the state as gatekeeper impact on their experiences as transnational subjects, and their social positioning within the new society.
What have scholars retrieved from Walsh and Ungson (1991)? A citation context study

Organizational memory is fundamentally important to organizational learning. The seminal work on organizational memory is Walsh and Ungson’s article published in the Academy of Management Review in 1991. More than 300 articles have cited this classic work, but a simple citation count reveals nothing about the nature of what has been retrieved. We examine this issue through a citation context analysis (i.e. content analysis) of the citations that citing authors have made to this classic article. Our analysis provides a richer understanding of which knowledge claims made by Walsh and Ungson have been retrieved and have had the greatest impact on later work in the area of organizational memory, and also what criticisms have been leveled against their claims. Through this analysis and a review of the citing articles that contain the largest number of citations to Walsh and Ungson, we identify several important directions for future research.
Theoretical Considerations for Single-Phase Interleaved Converters Operated With SHE-PWM

This letter defines selective harmonic elimination pulse width modulation (SHE-PWM) formulations for single-phase, interleaved converters. Through precalculated solutions, interleaved converters work at the same operating point while eliminating multiple low-order harmonics. It is shown that multiple continuous solutions can be acquired for three-level interleaved waveforms. Extending the method to multiple levels further complicates the problem and reduces both the number and continuity of the solutions. Searching for solutions when the maximum possible number of harmonics, that can be minimized using this PWM method, is reduced confirms that such compromise can provide additional solutions with a minimal effect on the waveform's harmonic distortion. The SHE-PWM considerations are verified with simulations and experimental results.
Proactive fault‐tolerant model predictive control

Fault-tolerant control methods have been extensively researched over the last 10 years in the context of chemical process control applications, and provide a natural framework for integrating process monitoring and control aspects in a way that not only fault detection and isolation but also control system reconfiguration is achieved in the event of a process or actuator fault. But almost all the efforts are focused on the reactive fault-tolerant control. As another way for fault-tolerant control, proactive fault-tolerant control has been a popular topic in the communication systems and aerospace control systems communities for the last 10 years. At this point, no work has been done on proactive fault-tolerant control within the context of chemical process control. Motivated by this, a proactive fault-tolerant Lyapunov-based model predictive controller (LMPC) that can effectively deal with an incipient control actuator fault is proposed. This approach to proactive fault-tolerant control combines the unique stability and robustness properties of LMPC as well as explicitly accounting for incipient control actuator faults in the formulation of the MPC. Our theoretical results are applied to a chemical process example, and different scenaria were simulated to demonstrate that the proposed proactive fault-tolerant model predictive control method can achieve practical stability and efficiently deal with a control actuator fault. © 2013 American Institute of Chemical Engineers AIChE J, 59: 2810–2820, 2013
Long‐Term Memory for an Emotional Interpersonal Interaction Occurring at 5 Months of Age

We examined infants' long-term retention of a single unique emotional experience into early childhood. Twenty-month-olds who had participated in a still-face procedure at 5 months (experience group) fixated the face of the person who had instigated the still face significantly less than the faces of 2 other novel persons. Control 20-month-olds (no-experience group) looked longer overall and fixated the target person equally or more than the 2 novel persons. In short, children who interacted with a stranger in the laboratory under both natural and anomalous social conditions just once when they were infants apparently retained a specific memory of that person and the experience into toddlerhood.
Sampling from the Multivariate Gaussian Distribution using Reconfigurable Hardware

The multivariate Gaussian distribution models random processes as vectors of Gaussian samples with a fixed correlation matrix. Such distributions are useful for modelling real-world multivariate time-series such as equity returns, where the returns for businesses in the same sector are likely to be correlated. Generating random samples from such a distribution presents a computational challenge due to the dense matrix-vector multiplication needed to introduce the required correlations. This paper proposes a hardware architecture for generating random vectors, utilising the embedded block RAMs and multipliers found in contemporary FPGAs. The approach generates a new n dimensional random vector every n clock cycles, and has a raw generation rate over 200 times that of a single Opteron 2.2GHz using an optimised BLAS package for linear algebra computation. The generation architecture is an ideal source for both software simulations connected via high bandwidth connection, and for completely FPGA based simulations. Practical performance is explored in a case study in Delta-Gamma Value-at-Risk, where a standalone Virtex-4 xc4vsx55 solution at 400 MHz is 33 times faster than a quad Opteron 2.2GHz SMP. The FPGA solution also scales well for larger problem sizes, allowing larger portfolios to be simulation.