Miracle-dz/UniFAR-FTUs huggingface dataset:
Refinement of Protein Tertiary Structure by Using Spin-Spin Coupling Constants from Nuclear Magnetic Resonance Measurements

Modelling protein structure seems a challenging enterprise because the number of structure parameters required ordinarily exceeds the amount of independent data points available from experimental observations. Expressing the predominant conformation of a protein in terms of a geometry model, a polypeptide chain consisting of N atoms would command 3N – 6 Cartesian coordinates be fixed. Even for small proteins, this becomes a daunting number. Fortunately, so-called holonomic constraints limit the number of variables, leaving substantially fewer, truly relevant parameters for folding the polypeptide chain into its native tertiary structure. For example, adjusting bond lengths and the many angles between the covalent bonds connecting the atoms is of little concern and appropriate standard values can be inserted from tableworks (Pople & Gordon, 1967; Engh & Huber, 1991, 2006). Table 1 exemplifies for the 147-residue protein Desulfovibrio vulgaris flavodoxin how the number of truly independent internal rotational degrees of freedom amounts to less than one-tenth of the Cartesian coordinate set size.
A Place to Call Home: An Analysis of the Bacterial Communities in Two Tethya rubra Samaai and Gibbons 2005 Populations in Algoa Bay, South Africa

Sponges are important sources of bioactive secondary metabolites. These compounds are frequently synthesized by bacterial symbionts, which may be recruited from the surrounding seawater or transferred to the sponge progeny by the parent. In this study, we investigated the bacterial communities associated with the sponge Tethya rubra Samaai and Gibbons 2005. Sponge specimens were collected from Evans Peak and RIY Banks reefs in Algoa Bay, South Africa and taxonomically identified by spicule analysis and molecular barcoding. Crude chemical extracts generated from individual sponges were profiled by ultraviolet high performance liquid chromatography (UV-HPLC) and subjected to bioactivity assays in mammalian cells. Next-generation sequencing analysis of 16S rRNA gene sequences was used to characterize sponge-associated bacterial communities. T. rubra sponges collected from the two locations were morphologically and genetically indistinguishable. Chemical extracts from sponges collected at RIY banks showed mild inhibition of the metabolic activity of mammalian cells and their UV-HPLC profiles were distinct from those of sponges collected at Evans Peak. Similarly, the bacterial communities associated with sponges from the two locations were distinct with evidence of vertical transmission of symbionts from the sponge parent to its embryos. We conclude that these distinct bacterial communities may be responsible for the differences observed in the chemical profiles of the two Algoa Bay T. rubra Samaai and Gibbons 2005 populations.
Engaging Children in Family Therapy: Creative Approaches to Integrating Theory and Research in Clinical Practice

About the Editor. Contributors.Series Editor's Foreword. Preface. Acknowledgments. Part I: Issues Related to Working with Children. Sori, On Counseling Children and Families: Recommendations From the Experts. Sori, Reflections on Children in Family Therapy: An Interview with Salvador Minuchin. Dermer, Olund, Sori, Integrating Play in Family Therapy Theories. Part II: Models for Working with Children and Families: Interviews with the Experts. Sori, Family Play Therapy: An Interview with Eliana Gil. Sori, Filial Therapy: An Interview with Rise VanFleet. Sori, A Playful Postmodern Approach to Counseling Children and Families: An Interview with Lee Shilts. Part III: Conceptual, Practical and Ethical Issues in Counseling Children and Families. Sori, Dermer, Wesolowski, Involving Children in Family Counseling and Involving Parents in Children's Counseling: Theoretical and Practical Guidelines. Sori, Hecker, Ethical and Legal Considerations When Counseling Children and Families. Part IV: Children and Family Counseling with Specific Child Issues. Hecker, Sori, Divorce and Stepfamily Issues. C. Everett, S. Everett, Treating Children and Families with ADHD. Sori, Biank, Treating Children and Families Experiencing Serious Illness. Biank, Sori, Helping Children Cope with the Death of a Family Member.
Kinect and 3 D GIS in archaeology

This paper explores the potential of using Microsoft’s Kinect to create a low-cost and portable system to virtually navigate, through a prototype 3D GIS, the digitally reconstructed ancient Maya city and UNESCO World Heritage Site of Copan in Honduras. The 3D GIS, named QueryArch3D, was developed as part of the MayaArch3D project (http://mayaarch3d.unm.edu), which explores the possibilities of integrating databases and 3D digital tools for research and teaching on ancient architectures and landscapes. The developed system, based on the Flexible Action and Articulated Skeleton Toolkit (FAAST), controls in a remote and touchless mode the movements in the 3D environment in order to create a sense of spatial awareness and embodiment. A user can thus use gestures to interact with information stored in the spatial database, calling up photos, videos, textual descriptions as he/she moves through the virtual space of the ancient Maya city. Keywords3D Modeling, Virtual Reality, 3D GIS, Kinect, Archaeology
Transition Path Theory for Markov Jump Processes

The framework of transition path theory (TPT) is developed in the context of continuous-time Markov chains on discrete state-spaces. Under assumption of ergodicity, TPT singles out any two subsets in the state-space and analyzes the statistical properties of the associated reactive trajectories, i.e., those trajectories by which the random walker transits from one subset to another. TPT gives properties such as the probability distribution of the reactive trajectories, their probability current and flux, and their rate of occurrence and the dominant reaction pathways. In this paper the framework of TPT for Markov chains is developed in detail, and the relation of the theory to electric resistor network theory and data analysis tools such as Laplacian eigenmaps and diffusion maps is discussed as well. Various algorithms for the numerical calculation of the various objects in TPT are also introduced. Finally, the theory and the algorithms are illustrated in several examples.
A Fingerprinting System for Musical Content

Driven by the recent advances in digital entertainment technologies, digital multimedia content (such as music and movies) is becoming a major part of the average computer user experience. Through daily interaction with digital multimedia content, large digital collections of music, audio and sound effects have emerged. Furthermore, these collections are produced/consumed by different groups of users such as the entertainment, music, movie and animation industries. Therefore, the need for identification and management of such content grows proportionally to the increasing widespread availability of such media virtually "any time and any where" over the internet. In this paper, we propose a novel algorithm for robust perceptual hashing of musical content using balanced multiwavelets (BMW). The procedure for generating robust perceptual hash values (or fingerprints) is described in details. The generated hash values are used for identifying, searching, and retrieving musical content from large musical databases. Furthermore, we illustrate, through extensive computer simulation, the robustness of the proposed framework to efficiently represent audio content and withstand several signal processing attacks and manipulations
Investigating active learning techniques for document level sentiment classification of tweets

Active Learning is a technique to automatically select the useful instances from the unlabelled data in such a way that, when these are augmented to the training data, overall classification performance improves. The creation of training examples otherwise involves significant amount of costs and efforts and hence, is a major constraint in the supervised algorithms. In this paper, we investigate the effectiveness of active learning for sentiment classification of Tweets. The algorithm selects the informative unlabelled data based on the concept of uncertainty sampling which dictates that only those Tweets be added to the training set for which the classifier can quickly refine its decision boundary. Our experiments on a benchmark dataset of Tweets show an overall accuracy of 83.95%, which is an increment of 6.75% over the baseline model, constructed by training a Support Vector Machine (SVM) with all the available set of features. The approach, being very general, is scalable, domain-adaptable and easy to implement for a wide variety of problems.
Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts

DNA microarrays and RNA sequencing (RNA-seq) are major technologies for performing high-throughput analysis of transcript abundance. Recently, concerns have been raised regarding the concordance of data derived from the two techniques. Using cDNA libraries derived from normal human foreskin fibroblasts, we measured changes in transcript abundance as cells transitioned from proliferative growth to quiescence using both DNA microarrays and RNA-seq. The internal reproducibility of the RNA-seq data was greater than that of the microarray data. Correlations between the RNA-seq data and the individual microarrays were low, but correlations between the RNA-seq values and the geometric mean of the microarray values were moderate. The two technologies had good agreement when considering probes with the largest (both positive and negative) fold change (FC) values. An independent technique, quantitative reverse-transcription PCR (qRT-PCR), was used to measure the FC of 76 genes between proliferative and quiescent samples, and a higher correlation was observed between the qRT-PCR data and the RNA-seq data than between the qRT-PCR data and the microarray data.
Observed and Simulated Multidecadal Variability in the Northern Hemisphere

Analyses of proxy based reconstructions of surface temperatures during the past 330 years show the existence of a distinct oscillatory mode of variability with an approximate time scale of 70 years. This variability is also seen in instrumental records, although the oscillatory nature of the variability is dicult to assess due to the short length of the instrumental record. The spatial pattern of this variability is hemispheric or perhaps even global in scale, but with particular emphasis on the Atlantic region. Independent analyses of multi-century integrations of two versions of the GFDL coupled atmosphere-ocean model also show the existence of distinct multidecadal variability in the North Atlantic region which resembles the observed pattern. The model variability involves ¯uctuations in the intensity of the thermohaline circulation in the North Atlantic. It is our intent here to provide a direct comparison of the observed variability to that simulated in a coupled ocean-atmosphere model, making use of both existing instrumental analyses and newly available proxy based multi-century surface temperature estimates. The analyses demonstrate a substantial agreement between the simulated and observed patterns of multidecadal variability in sea surface temperature (SST) over the North Atlantic. There is much less agreement between the model and observations for sea level pressure. Seasonal analyses of the variability demonstrate that for both the model and observations SST appears to be the primary carrier of the multidecadal signal.
Toward a British Taxonomy of Perceived Managerial and Leadership Effectiveness

A long-standing problem in management research has been the lack of agreement about the specific managerial behaviors that are most closely associated with effective management practice and leadership practice. The study reports the results of a qualitative multiple cross-case and cross-sector exploration of what managers and nonmanagerial employees within British public-, private-, and third-sector organizations perceive as effective and least effective/ineffective managerial behavior. Based on empirical findings obtained from nine prior emic replication studies, our derived etic comparative analysis has led to a deduced taxonomy of perceived managerial and leadership effectiveness comprised of eight positive (effective) and six negative (least effective/ineffective) generic behavioral criteria. Comparisons against extant U.S.-derived taxonomies have revealed many similarities but also significant differences. The findings go against the grain of predominant discourse, and challenge long-held, taken-for-granted assumptions about the “contingent” nature of management and leadership. Implications for HRD research and practice are discussed.
Validation of Reference Genes for Robust qRT-PCR Gene Expression Analysis in the Rice Blast Fungus Magnaporthe oryzae

The rice blast fungus causes significant annual harvest losses. It also serves as a genetically-tractable model to study fungal ingress. Whilst pathogenicity determinants have been unmasked and changes in global gene expression described, we know little about Magnaporthe oryzae cell wall remodelling. Our interests, in wall remodelling genes expressed during infection, vegetative growth and under exogenous wall stress, demand robust choice of reference genes for quantitative Real Time-PCR (qRT-PCR) data normalisation. We describe the expression stability of nine candidate reference genes profiled by qRT-PCR with cDNAs derived during asexual germling development, from sexual stage perithecia and from vegetative mycelium grown under various exogenous stressors. Our Minimum Information for Publication of qRT-PCR Experiments (MIQE) compliant analysis reveals a set of robust reference genes used to track changes in the expression of the cell wall remodelling gene MGG_Crh2 (MGG_00592). We ranked nine candidate reference genes by their expression stability (M) and report the best gene combination needed for reliable gene expression normalisation, when assayed in three tissue groups (Infective, Vegetative, and Global) frequently used in M. oryzae expression studies. We found that MGG_Actin (MGG_03982) and the 40S 27a ribosomal subunit MGG_40s (MGG_02872) proved to be robust reference genes for the Infection group and MGG_40s and MGG_Ef1 (Elongation Factor1-α) for both Vegetative and Global groups. Using the above validated reference genes, M. oryzae MGG_Crh2 expression was found to be significantly (p<0.05) elevated three-fold during vegetative growth as compared with dormant spores and two fold higher under cell wall stress (Congo Red) compared to growth under optimal conditions. We recommend the combinatorial use of two reference genes, belonging to the cytoskeleton and ribosomal synthesis functional groups, MGG_Actin, MGG_40s, MGG_S8 (Ribosomal subunit 40S S8) or MGG_Ef1, which demonstrated low M values across heterogeneous tissues. By contrast, metabolic pathway genes MGG_Fad (FAD binding domain-containing protein) and MGG_Gapdh (Glyceraldehyde-3-phosphate dehydrogenase) performed poorly, due to their lack of expression stability across samples.
Temporal changes in hepatic antioxidant enzyme activities after ischemia and reperfusion in a rat liver ischemia model

This study investigated the hypothesis that administration of tilapia fish oil diet would attenuate warm liver ischemia/reperfusion injury (IRI) and whether fish oil modulates prooxidant/antioxidant status. Male Wistar rats were subjected to 30 min of approximately 70% hepatic ischemia followed by 1, 12, and 24 h reperfusion. Rats were randomly divided into three groups: sham-operated group (SO), control–warm hepatic ischemia (WI) group, and Oil–WI group given tilapia oil for 3 weeks followed by liver IRI. Aspartate aminotransferase (AST) and alanine aminotransferase (ALT) levels were measured in the plasma. Levels of thiobarbituric acid reactive substances (TBARS) and antioxidant enzymes as superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) activities were measured in liver fractions. In the sham group, there was no enzymatic or histological change. I/R caused significant increase in serum AST, ALT, and tissue TBARS levels. As compared to the control group, animals treated with tilapia oil experienced a significant decrease (p < 0.05) in AST and ALT levels in reperfusion periods. Tissue TBARS levels in Oil–WI group were significantly (p < 0.05) reduced as compared to control group at 60 min after reperfusion. After ischemia, 1, 12, and 24 h of reperfusion, CAT, SOD, and GPx values were the lowest in the Oil–WI group and highest in the control group and were statistically significant (p < 0.05). Histological analysis also revealed that fish oil provided some protection compared with the control group. Tilapia oil exerts a protective effect during the early phase of reperfusion, and it modulates prooxidant/antioxidant status of rat liver subjected to warm IRI.
A novel mitotic spindle pole component that originates from the cytoplasm during prophase

Several unique aspects of mitotic spindle formation have been revealed by investigation of an autoantibody present in the serum of a patient with the CREST (calcinosis, Raynaud's phenomenon, esophageal dysmotility, schlerodacytyly, and telangiectasias) syndrome. This antibody was previously shown to label at the spindle poles of metaphase and anaphase cells and to be absent from interphase cells. We show here that the serum stained discrete cytoplasmic foci in early prophase cells and only later localized to the spindle poles. The cytoplasmic distribution of the antigen was also seen in nocodazole- arrested cells and prophase cells in populations treated with taxol. In normal and taxol-treated cells, the microtubules appeared to emanate from the cytoplasmic foci and polar stain, and in cells released from nocodazole block, microtubules regrew from antigen-containing centers. This characteristic distribution suggests that the antigen is part of a microtubule organizing center. Thus, we propose that a prophase originating polar antigen functions in spindle pole organization as a coalescing microtubule organizing center that is present only during mitosis. Characterization of the serum showed reactions with multiple proteins at 115, 110, 50, 36, 30, and 28 kD. However, affinity-eluted antibody from the 115/110-kD bands was shown to specifically label the spindle pole and cytosolic foci in prophase cells.
Lung Function Classification of Smartphone Recordings - Comparison of Signal Processing and Machine Learning Combination Sets

Worldwide, over 250 million people are affected by chronic lung conditions such as Asthma and COPD. These can cause breathlessness, a harsh decrease in quality of life and, if not detected and duly managed, even death. In this paper, we aim to find the best and most efficient combination of signal processing and machine learning approaches to produce a smartphone application that could accurately classify lung function, using microphone recordings as the only input. A total of 61 patients performed the forced expiration maneuver providing a dataset of 101 recordings. The signal processing comparison experiments were conducted in a backward selection approach, reducing from 54 to 12 final envelopes, per recording. The classification experiments focused first on differentiating Normal from Abnormal lung function, and second in multiple lung function patterns. The results from this project encourage further development of the system.
Relative Lefschetz action and BPS state counting

In this paper, we propose a mathematical definition of a new ``numerical invariants" of Calabi--Yau 3-folds from stable sheaves of dimension one, which is motivated by the Gopakumar-Vafa conjecture in M-theory. Moreover, we show that for any projective morphism $f:X -> Y$ of normal projective varieties, there exists a natural $sl_2 \times sl_2$ action on the intersection cohomology group $IH(X, \Q)$ which fits into the perverse Leray spectral sequence.
Tsunami risk assessment in the Marquesas Islands (French Polynesia) through numerical modeling of generic far-field events

Abstract. Earthquakes occurring at the Pacific Rim can trigger tsunamis that propagate across the ocean and can produce significant damages far away from the source. In French Polynesia, the Marquesas Islands are the most exposed to the far-field tsunami hazards, since they are not protected by any outer coral reef and since submarine slopes are less steep than in other islands. Between 1994 and 1996, four tsunamis have reached the bays of the archipelago, among them, the tsunami initiated by the Chilean Mw 8.1 earthquake, produced up to 3 m high waves in Tahauku Bay. Numerical modeling of these recent events has already allowed us to validate our method of resolution of hydrodynamics laws through a finite-difference scheme that simulates the propagation of the tsunamis across the ocean and computes the inundation heights (run-up) in remote bays. We present in this paper the simulations carried out to study potentially threatening areas located at the Pacific Rim, on the seismogenic Aleutian and Tonga subduction zones. We use a constant seismic moment source (that of the M w 8.1 Chile 1995 earthquake, M 0 = 1.2 10 21 N.m) located at several potential epicenters, with the fault strike adapted from the regional seismotectonics pattern. Our results show that the sources chosen in the Aleutian trench do not produce large inundations in the Marquesas bays, except for the easternmost source (longitude 194° E). Sources located in the Tonga trench do not produce high amplifications either, except for the northernmost one (latitude 16° S). We also discuss the behaviour of the tsunami waves within the archipelago, and evidence contrasting responses depending on the arrival azimuths. These results show that, for a given initial seismic energy, the tsunami amplification in remote bays is highly dependent on the source location and fault strike.
Formation of adherens junctions leads to the emergence of a tissue-level tension in epithelial monolayers

ABSTRACT Adherens junctions and desmosomes integrate the cytoskeletons of adjacent cells into a mechanical syncitium. In doing so, intercellular junctions endow tissues with the strength needed to withstand the mechanical stresses encountered in normal physiology and to coordinate tension during morphogenesis. Though much is known about the biological mechanisms underlying junction formation, little is known about how tissue-scale mechanical properties are established. Here, we use deep atomic force microscopy (AFM) indentation to measure the apparent stiffness of epithelial monolayers reforming from dissociated cells and examine which cellular processes give rise to tissue-scale mechanics. We show that the formation of intercellular junctions coincided with an increase in the apparent stiffness of reforming monolayers that reflected the generation of a tissue-level tension. Tension rapidly increased, reaching a maximum after 150 min, before settling to a lower level over the next 3 h as monolayers established homeostasis. The emergence of tissue tension correlated with the formation of adherens junctions but not desmosomes. As a consequence, inhibition of any of the molecular mechanisms participating in adherens junction initiation, remodelling and maturation significantly impeded the emergence of tissue-level tension in monolayers.