Miracle-dz/UniFAR-FTUs huggingface dataset:
Detailing regulatory networks through large scale data integration

MOTIVATION Much of a cell's regulatory response to changing environments occurs at the transcriptional level. Particularly in higher organisms, transcription factors (TFs), microRNAs and epigenetic modifications can combine to form a complex regulatory network. Part of this system can be modeled as a collection of regulatory modules: co-regulated genes, the conditions under which they are co-regulated and sequence-level regulatory motifs. RESULTS We present the Combinatorial Algorithm for Expression and Sequence-based Cluster Extraction (COALESCE) system for regulatory module prediction. The algorithm is efficient enough to discover expression biclusters and putative regulatory motifs in metazoan genomes (>20,000 genes) and very large microarray compendia (>10,000 conditions). Using Bayesian data integration, it can also include diverse supporting data types such as evolutionary conservation or nucleosome placement. We validate its performance using a functional evaluation of co-clustered genes, known yeast and Escherichea coli TF targets, synthetic data and various metazoan data compendia. In all cases, COALESCE performs as well or better than current biclustering and motif prediction tools, with high accuracy in functional and TF/target assignments and zero false positives on synthetic data. COALESCE provides an efficient and flexible platform within which large, diverse data collections can be integrated to predict metazoan regulatory networks. AVAILABILITY Source code (C++) is available at http://function.princeton.edu/sleipnir, and supporting data and a web interface are provided at http://function.princeton.edu/coalesce. CONTACT ogt@cs.princeton.edu; hcoller@princeton.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Reliability of clinical nurse specialists in the staging of dementia.

We studied the reliability of master's-prepared clinical nurse specialists for the identification and staging of dementia, using videotapes of physician assessments of both healthy older persons and those with senile dementia of the Alzheimer type. The Washington University (St Louis, Mo) Clinical Dementia Rating system was the staging instrument. The results from three nurses, each reviewing 25 videotaped assessments, indicate that agreement is high between clinical nurse specialists and physicians for the presence and severity of dementia (kappa = .75). This study suggests that clinical nurse specialists can use the Clinical Dementia Rating scale effectively, and thus reliably identify and stage dementia.
Issues in the addition of ISO standard annotations to the Switchboard corpus

This paper analyzes the issues that arise when trying to add annotations to the dialogues in the Switchboard corpus according to ISO standard 24617-2, exploiting the existing SWBD-DAMSL annotations. These issues relate to differences between the two tag sets; to the highly multidimensional view that underlies the ISO standard; to differences in segmenting the dialogues into functional units; to the use of in-line markups for certain phenomena in Switchboard, and to the use of intra-dialogue dependence relations as defined in the ISO standard. The analysis is supplemented by a discussion of how the existing annotations may be helpful to semi-automatically create a fullyfledged ISO standard annotation alongside the existing SWBD-DAMSL annotation.
Conference on ‘ Over-and undernutrition : challenges and approaches ’ Postgraduate Symposium Long-chain n-3 PUFA : intakes in the UK and the potential of a chicken meat prototype to increase them

With the wide acceptance of the long-chain (LC) n-3 PUFA EPA and DHA as important nutrients playing a role in the amelioration of certain diseases, efforts to understand factors affecting intakes of these fatty acids along with potential strategies to increase them are vital. Widespread aversion to oil-rich fish, the richest natural source of EPA and DHA, highlights both the highly suboptimal current intakes in males and females across all age-groups and the critical need for an alternative supply of EPA and DHA. Poultry meat is a popular and versatile food eaten in large quantities relative to other meats and is open to increased LC n-3 PUFA content through manipulation of the chicken’s diet to modify fatty acid deposition and therefore lipid composition of the edible tissues. It is therefore seen as a favourable prototype food for increasing human dietary supply of LC n-3 PUFA. Enrichment of chicken breast and leg tissue is well established using fish oil or fishmeal, but concerns about sustainability have led to recent consideration of algal biomass as an alternative source of LC n-3 PUFA. Further advances have also been made in the quality of the resulting meat, including achieving acceptable flavour and storage properties as well as understanding the impact of cooking on the retention of fatty acids. Based on these considerations it may be concluded that EPAand DHA-enriched poultry meat has a very positive potential future in the food chain.
Phox homology band 4.1/ezrin/radixin/moesin-like proteins function as molecular scaffolds that interact with cargo receptors and Ras GTPases

Following endocytosis, the fates of receptors, channels, and other transmembrane proteins are decided via specific endosomal sorting pathways, including recycling to the cell surface for continued activity. Two distinct phox-homology (PX)-domain-containing proteins, sorting nexin (SNX) 17 and SNX27, are critical regulators of recycling from endosomes to the cell surface. In this study we demonstrate that SNX17, SNX27, and SNX31 all possess a novel 4.1/ezrin/radixin/moesin (FERM)-like domain. SNX17 has been shown to bind to Asn-Pro-Xaa-Tyr (NPxY) sequences in the cytoplasmic tails of cargo such as LDL receptors and the amyloid precursor protein, and we find that both SNX17 and SNX27 display similar affinities for NPxY sorting motifs, suggesting conserved functions in endosomal recycling. Furthermore, we show for the first time that all three proteins are able to bind the Ras GTPase through their FERM-like domains. These interactions place the PX-FERM-like proteins at a hub of endosomal sorting and signaling processes. Studies of the SNX17 PX domain coupled with cellular localization experiments reveal the mechanistic basis for endosomal localization of the PX-FERM-like proteins, and structures of SNX17 and SNX27 determined by small angle X-ray scattering show that they adopt non-self-assembling, modular structures in solution. In summary, this work defines a novel family of proteins that participate in a network of interactions that will impact on both endosomal protein trafficking and compartment specific Ras signaling cascades.
Tabu Search for Multiprocessor Scheduling: Application to High Level Synthesis

This paper describes a tabu search approach for a multiprocessor scheduling problem, where a list of jobs has to be scheduled on identical parallel processors. Each job in the list has a release date, a due date, a processing time and a set of predecessors. The objective is to minimize the number of processors used while respecting the constraints imposed by release dates, due dates and precedences. Two versions of this problem are considered here, in the first one precedence constraints are relaxed, they are taken into account in the second one. The proposed method is used to solve High Level Synthesis problem instances. The results show the effectiveness of our approach for both versions of the problem. A comparison with an exact method is also conducted.
Deterministic Parsing of Languages with Dynamic Operators

Allowing the programmer to dene operators in a language makes for more readable code but also complicates the job of parsing; standard parsing techniques cannot accommodate dynamic grammars. We present an LR parsing methodology, called deferred decision parsing, that handles dynamic operator declarations, that is, operators that are declared at run time, are applicable only within a program or context, and are not in the underlying language or grammar. It uses a parser generator that takes production rules as input, and generates a table-driven LR parser, much like yacc. Shift/reduce conicts that involve dynamic operators are resolved at parse time rather than at table construction time. For an operator-rich language, this technique reduces the size of the grammar needed and parse table produced. The added cost to the parser is minimal. Ambiguous operator constructs can either be detected by the parser as input is being read or avoided altogether by enforcing reasonable restrictions on operator declarations. We have been able to describe the syntax of Prolog, a language known for its liberal use of operators, and Standard ML, which supports local declarations of operators. Denite clause grammars (DCGs), a novel parsing feature of Prolog, can be translated into ecien t code by our parser generator. The implementation has the advantage that the Originally appeared in \Logic Programming | Proceedings of the 1993 International Symposium (ILPS93)"
Effect of heat treatment on H2O2/HCl etched pure titanium dental implant: An in vitro study

Summary Background Surface chemistry of dental implant plays an important role in osseointegration. Heat treatment might alter surface chemistry and result in different biological response. The aim of this study was to investigate the roles of heat treatment of H2O2/HCl-treated Ti implants in cell attachment, proliferation and osteoblastic differentiation. Material/Methods Sandblasted, dual acid-etched and H2O2/HCl heat-treated discs were set as the control group and sandblasted, dual acid-etched H2O2/HCl-treated discs were the test group. Both groups’ discs were sent for surface characterization. MC3T3-E1 cells were seeded on these 2 groups’ discs for 3 hours to 14 days, and then cell attachment, cell proliferation and cell differentiation were evaluated. Results Scanning electron microscope analysis revealed that the titanium discs in the 2 groups shared the same surface topography, while x-ray diffraction examination showed an anatase layer in the control group and titanium hydride diffractions in the test group. The cell attachment of the test group was equivalent to that of the control group. Cell proliferation was slightly stimulated at all time points in the control group, but the alkaline phosphatase (ALP) activity and osteocalcin (OC) production increased significantly in the test group compared with those in the control group at every time point investigated (p<0.05 or p<0.01). Moreover, the osteoblastic differentiation-related genes AKP-2, osteopontin (OPN) and OC were greatly up-regulated in the test group (p<0.05 or p<0.01). Conclusions The results implied that surface chemistry played an important role in cell response, and H2O2/HCl etched titanium surface without subsequent heat treatment might improve osseointegration response.
Probabilistic Inference in General Graphical Models through Sampling in Stochastic Networks of Spiking Neurons

An important open problem of computational neuroscience is the generic organization of computations in networks of neurons in the brain. We show here through rigorous theoretical analysis that inherent stochastic features of spiking neurons, in combination with simple nonlinear computational operations in specific network motifs and dendritic arbors, enable networks of spiking neurons to carry out probabilistic inference through sampling in general graphical models. In particular, it enables them to carry out probabilistic inference in Bayesian networks with converging arrows (“explaining away”) and with undirected loops, that occur in many real-world tasks. Ubiquitous stochastic features of networks of spiking neurons, such as trial-to-trial variability and spontaneous activity, are necessary ingredients of the underlying computational organization. We demonstrate through computer simulations that this approach can be scaled up to neural emulations of probabilistic inference in fairly large graphical models, yielding some of the most complex computations that have been carried out so far in networks of spiking neurons.
Isolation and Characterization of Fractions of Mycoplasma pneumoniae I. Chemical and Chromatographic Separation

Prescott, B. (National Institute of Allergy and Infectious Diseases, Bethesda, Md.), O. Sobeslavsky, G. Caldes, and R. M. Chanock. Isolation and characterization of fractions of Mycoplasma pneumoniae. I. Chemical and chromatographic separation. J. Bacteriol. 91:2117–2125. 1966. —Fractionation of Mycoplasma pneumoniae, cultured on a beef heart infusion-horse serum-yeast extract medium, was carried out by chemical and chromatographic procedures. The chemical method yielded eight fractions consisting of lipid, carbohydrates, and proteins. Four protein-rich fractions were isolated by chromatographing a supernatant fluid of sonically treated organisms on Sephadex G-25. The 12 fractions were tested for serological and antigenic activity in vitro and in vivo. The lipid fraction was serologically active and the relative order of activity of the protein fractions appeared to depend on the amount of lipid present in the molecule. The highly serologically active Sephadex G-25 protein fraction 1 prepared chromatographically contained 15% lipid in the molecule, whereas the less serologically active protein fraction 2 prepared by chemical means contained 2% lipid. The acetone-extracted lipid fraction was chromatographed on thin-layer chromatography plates and found to consist of nine fractions. Serological activity was associated with only the first three spots above the origin. Lipid extracted from the protein fractions seemed to be similar to the acetone-extracted lipid from the sediment of the sonically treated organisms.
Exactly realizable desired trajectories

Trajectory tracking of nonlinear dynamical systems with affine open-loop controls is investigated. The control task is to enforce the system state to follow a prescribed desired trajectory as closely as possible. We introduce exactly realizable desired trajectories as these trajectories which can be tracked exactly by an appropriate control. Exactly realizable trajectories are characterized mathematically by means of Moore-Penrose projectors constructed from the input matrix. The approach leads to differential-algebraic systems of equations and is considerably simpler than the related concept of system inversion. Furthermore, we identify a particularly simple class of nonlinear affine control systems. Systems in this class satisfy the so-called linearizing assumption and share many properties with linear control systems. For example, conditions for controllability can be formulated in terms of a rank condition for a controllability matrix analogously to the Kalman rank condition for linear time-invariant systems.
Detection and Characterization of Influenza A Virus PA-PB2 Interaction through a Bimolecular Fluorescence Complementation Assay

ABSTRACT The influenza virus polymerase complex, consisting of the PA, PB1, and PB2 subunits, is required for the transcription and replication of the influenza A viral genome. Previous studies have shown that PB1 serves as a core subunit to incorporate PA and PB2 into the polymerase complex by directly interacting with PA and PB2. Despite numerous attempts, largely involving biochemical approaches, a specific interaction between PA and PB2 subunits has yet to be detected. In the current study, we developed and utilized bimolecular fluorescence complementation (BiFC) to study protein-protein interactions in the assembly of the influenza A virus polymerase complex. Proof-of-concept experiments demonstrated that BiFC can specifically detect PA-PB1 interactions in living cells. Strikingly, BiFC demonstrated an interaction between PA and PB2 that has not been reported previously. Deletion-based BiFC experiments indicated that the N-terminal 100 amino acid residues of PA are responsible for the PA-PB2 interaction observed in BiFC. Furthermore, a detailed analysis of subcellular localization patterns and temporal nuclear import of PA-PB2 binary complexes suggested that PA and PB2 subunits interacted in the cytoplasm initially and were subsequently transported as a dimer into the nucleus. Taken together, results of our studies reveal a previously unknown PA-PB2 interaction and provide a framework for further investigation of the biological relevance of the PA-PB2 interaction in the polymerase activity and viral replication of influenza A virus.
The frontopolar cortex mediates event knowledge complexity: a parametric functional MRI study

Event knowledge is organized on the basis of goals that enable the selection of specific event sequences to organize everyday life activities. Although the medial prefrontal cortex represents event knowledge, little is known about its role in mediating event knowledge complexity. We used functional MRI to investigate the patterns of brain activation while healthy volunteers were engaged in the task of evaluating the complexity (i.e. numbers of events) of daily life activities selected on the basis of normative data. Within a left frontoparietal network, we isolated the medial frontopolar cortex as the only region that showed a linear relationship between changes in the blood oxygen level-dependent signal and changes in event knowledge complexity. Our results specify the importance of the medial frontopolar cortex in subserving event knowledge that is required to build and execute complex behavior.
Racism as Policy: A Critical Race Analysis of Education Reforms in the United States and England

Abstract Critical race theory (CRT) views education as one of the principal means by which white supremacy is maintained and presented as normal in society. The article applies CRT to two real-world case studies: changes to education statutes in the state of Arizona (USA) and the introduction of a new measure of educational success in England, the English baccalaureate. The analysis highlights the globalized nature of neoliberal education reform and its fundamentally raced and racist character.
Computer-based working memory training in children with mild intellectual disability

We designed a working memory (WM) training programme in game framework for mild intellectually disabled students. Twenty-four students participated as test and control groups. The auditory and visual–spatial WM were assessed by primary test, which included computerised Wechsler numerical forward and backward sub-tests and secondary tests, which contained three parts: dual visual–spatial test, auditory test and a one-syllable word recalling test. The results showed significant difference between WM capacity in the intellectually disabled children and normal ones (p-value < 0.00001). Visual–spatial WM, auditory WM and speaking were improved in the trained group. Four tests showed significant differences between pre-test and post-tests. The trained group showed more improvements in forward tasks. The trained participant's processing speed increased with training. We found that school is the best place for training. More comprehensive human–computer interfaces could be suitable for intellectually disabled students with visual and auditory impairments and problems in motor skills.
A Legitimate Concern for Environmental Accounting

This essay adapts John Rawls' A Theory of Justice to justify environmental accounting. The essay encourages accountants to report on the sustainable use of resources for present and future human generations and other life-forms. In this way, corporations would satisfy accountability relationship as part of an administrative solution to the environmental crisis. The essay supports the middle-of-the-road position of Gray et al. (1988, 1991), adding a notion of justice to society's background institutions. The approach to the environmental crisis is a theoretical one and responds to the charges of pluralism, relativism and quietism raised by Tinker et al. (1991). By adding fairness to the lexicon of accountability it justifies the publication of environmental information in accounting reports.
New approaches to genome sequence analysis based on digital signal processing

In this paper, two tools based on typical digital signal processing approaches are presented for analyzing long range correlations in DNA sequences. In order to illustrate the evolution of a DNA sequence, a three-dimensional DNA walk has been introduced and a Gauss-wavelet-based analysis has been performed to reveal the fractal behavior of the walk sequence. The second tool is devoted to exploring characteristics of the data using a lossless, Huffmanbased encoding technique. This technique compresses the DNA sequences and it allows analysis to be performed in the encoded domain. Experimental results show the effectiveness of the proposed approaches and their efficacy for future work.
Polynomial/Rational Approximation of Minkowski Sum Boundary Curves

Given two planar curves, their convolution curve is defined as the set of all vector sums generated by all pairs of curve points which have the same curve normal direction. The Minkowski sum of two planar objects is closely related to the convolution curve of the two object boundary curves. That is, the convolution curve is a superset of the Minkowski sum boundary. By eliminating all redundant parts in the convolution curve, one can generate the Minkowski sum boundary. The Minkowski sum can be used in various important geometric computations, especially for collision detection among planar curved objects. Unfortunately, the convolution curve of two rational curves is not rational, in general. Therefore, in practice, one needs to approximate the convolution curves with polynomial/rational curves. Conventional approximation methods of convolution curves typically use piecewise linear approximations, which is not acceptable in many CAD systems due to data proliferation. In this paper, we generalize conventional approximation techniques of offset curves and develop several new methods for approximating convolution curves. Moreover, we introduce efficient methods to estimate the error in convolution curve approximation. This paper also discusses various other important issues in the boundary construction of the Minkowski sum.
Oxidative stabilization of iso‐1‐cytochrome c by redox‐inspired protein engineering

Iso‐1‐cytochrome c, as any other hemeprotein, is able to react with hydrogen peroxide and to engage in the peroxidase cycle. However, peroxidases are irreversibly inactivated by their substrate, hydrogen peroxide. The oxidative inactivation of hemeproteins is mechanism based and arises as the consequence of unproductive electron abstraction reactions. Protein elements, such as the porphyrin ring or the protein backbone, act as simultaneous and competing electron sources even in the presence of exogenous reducing substrates, leading to a decline in activity. It is hypothetically possible to alter the intramolecular electron transfer pathways by direct replacement of low redox potential residues around the active site; as a consequence, the inactivation process would be delayed or even suppressed. To demonstrate this hypothesis, a redox‐inspired strategy was implemented until an iso‐1‐cytochrome c variant fully stable at catalytic concentrations of hydrogen peroxide was obtained. This variant, harboring the N52I,W59F,Y67F,K79A,F82G substitutions, preserved the catalytic performance of the parental protein but achieved a 15‐fold higher total‐turnover number. The phenotype of this variant was reflected in the stability of its electronic components, allowing identification of a protein‐based radical intermediate mechanistically similar to Compound I of classical peroxidases. The results presented here clearly demonstrate that redox‐inspired protein engineering is a useful tool for the rational modulation of intramolecular electron transfer networks. —Valderrama, B. , García‐Arellano, H. , Giansanti, S. , Baratto, M. C. , Pogni, R. , Vazquez‐Duhalt, R. Oxidative stabilization of iso‐1‐cytochrome c by redox‐inspired protein engineering. FASEB J. 20, E472–E481 (2006)