Miracle-dz/UniFAR-FTUs huggingface dataset:
Local Structural Differences in Homologous Proteins: Specificities in Different SCOP Classes

The constant increase in the number of solved protein structures is of great help in understanding the basic principles behind protein folding and evolution. 3-D structural knowledge is valuable in designing and developing methods for comparison, modelling and prediction of protein structures. These approaches for structure analysis can be directly implicated in studying protein function and for drug design. The backbone of a protein structure favours certain local conformations which include α-helices, β-strands and turns. Libraries of limited number of local conformations (Structural Alphabets) were developed in the past to obtain a useful categorization of backbone conformation. Protein Block (PB) is one such Structural Alphabet that gave a reasonable structure approximation of 0.42 Å. In this study, we use PB description of local structures to analyse conformations that are preferred sites for structural variations and insertions, among group of related folds. This knowledge can be utilized in improving tools for structure comparison that work by analysing local structure similarities. Conformational differences between homologous proteins are known to occur often in the regions comprising turns and loops. Interestingly, these differences are found to have specific preferences depending upon the structural classes of proteins. Such class-specific preferences are mainly seen in the all-β class with changes involving short helical conformations and hairpin turns. A test carried out on a benchmark dataset also indicates that the use of knowledge on the class specific variations can improve the performance of a PB based structure comparison approach. The preference for the indel sites also seem to be confined to a few backbone conformations involving β-turns and helix C-caps. These are mainly associated with short loops joining the regular secondary structures that mediate a reversal in the chain direction. Rare β-turns of type I’ and II’ are also identified as preferred sites for insertions.
BALB/Mtv-Null Mice Responding to Strong Mouse Mammary Tumor Virus Superantigens Restrict Mammary Tumorigenesis

ABSTRACT The absence of endogenous mouse mammary tumor viruses (MMTVs) in the congenic mouse strain, BALB/Mtv-null, restricts the early steps of exogenous C3H MMTV infection, preventing the superantigen (Sag) response and mammary tumorigenesis. Here we demonstrate that BALB/Mtv-null mice also resist tumor induction by FM MMTV, which encodes a stronger Sag compared to C3H MMTV. In contrast to infections with C3H MMTV, Mtv-null mice show FM-MMTV Sag-specific responses comparable to those observed in susceptible BALB/c mice. Neither virus shows significant replication in the spleen or mammary gland. Thus, Mtv-null mice restrict MMTV replication and mammary tumorigenesis even after a robust Sag response.
An Ontology-based Mapping Repository for Dynamic and Customized Data Integration ( CISE Technical Report )

There exist an increasing number of (semi-)structured info rmation sources over the Web. Data integration techniques are often applied to increase t he access efficiency of heterogeneous information sources. Data integration systems are bu ilt by combining a set of data sources for meeting specific user requirements. Due to vario us user needs, a growing trend of increasing variety of data integration system is noticeabl even for the same application. In the academic community, much effort has been devoted to buil ding a single data integration system. However, the existing approaches are impractical w hen the scale of data integration systems becomes large. This article proposes a key componen t f a total solution for holistically constructing a large number of customized data integr ation systems with the assistance of a considerable number of cooperative humans (a.k.a, a com munity). This component is an ontology-based mapping repository, called M-Ontology. Since each data integration system requires mappings for resolving semantic interoperabi lity among information sources, MOntology aims at the efficient storage, management and disco very f mappings. M-Ontology is shared by all the data integration systems in the same applic tion domain for mapping sharing and reuse. The internals of the mapping model are semanticsbased for easy understanding and management by (even non-technical) community members. Fol lowing this model, a “humanfriendly” mapping insertion algorithm is proposed for cons truction of a well-organized mapping ontology through incremental insertion of domain-spe cific mapping instances. Three types of human intervention strategies (i.e., validation, avoidance and prevention) are designed for improving the performance of construction algorithms. In addition, this article presents a mapping discovery algorithm to find the many-to-many comple x mappings by leveraging the mapping ontology. The discovered mappings are recycled to f ur her enrich the mapping ontology using the insertion algorithm. Finally, we conduct two s ets of experiments on real-world data integration over the Web, and the results show that the a ppro ch is feasible and effective.
Ready, Set, Go: Coalesced offloading from mobile devices to the cloud

With an abundance of computing resources, cloud computing systems have been widely used to elastically offload the execution of computation-intensive applications on mobile devices, leading to performance gains and better power efficiency. However, existing works have so far focused on one application only, and multiple applications are not coordinated when sending their offloading requests to the cloud. In this paper, we propose the new technique of coalesced offloading, which exploits the potential for multiple applications to coordinate their offloading requests with the objective of saving additional energy on mobile devices. The intuition is that, by sending these requests in “bundles,” the period of time that the network interface stays in the high-power state can be reduced. We present two online algorithms, collectively referred to as Ready, Set, Go (RSG), that make near-optimal decisions on how offloading requests from multiple applications are to be best coalesced. We show, both analytically and experimentally using actual smartphones, that RSG is able to achieve additional energy savings while maintaining satisfactory performance.
Tomographic reconstruction based on flexible geometric models

When dealing with ill-posed inverse problems in data analysis, the Bayesian approach allows one to use prior information to guide the result toward reasonable solutions. In this work the model consists of an object whose amplitude is constant inside a flexible boundary. The flexibility of the boundary is controlled by through a distortion energy. We present an example of reconstruction of the cross section of a blood vessel from just two projections. <<ETX>>
Edge preservation ratio for image sharpness assessment

Image sharpness is one of the most determining factors for image readability and scene understanding. How to accurately quantify it is a hot topic. This paper systematically validates a previously proposed index for full-reference image sharpness assessment (edge preservation ratio, EPR). Based on Gaussian blurring images in LIVE, CSIQ, TID2008 and TID2013 databases, we firstly evaluated EPR accuracy on five edge detectors on LIVE and selected an optimal one for further analysis. Then nine state-of-the-art image quality assessment metrics are compared, including full-reference, no-reference and dedicated image sharpness assessment categories. Experimental results demonstrate (1) Canny is an optimal edge detector for EPR implementation; (2) EPR is a top-ranking image sharpness assessment metric that outperforms PSNR and SSIM and rivals FSIM; and (3) EPR accords more closely with human subjective judgment than involved image sharpness assessment metrics. This study also indicates that image sharpness assessment is still full of challenges and utilizing deep learning architectures to learning the direct mapping from images to quality will be a trend in the near future.
Predictor and Moderator Effects of Ego Resilience and Mindfulness on the Relationship Between Academic Stress and Psychological Well-Being in a Sample of Ghanaian College Students

This study examined the predictor and moderator effects of ego resilience and mindfulness on the relationship between academic stress and psychological well-being in a sample of Ghanaian college students (N = 431). The results indicated that academic stress was positively associated with both anxiety and depression and that mindfulness and ego resilience were both negatively associated with anxiety and depression. Mindfulness buffered the positive relationship between academic stress and depression but not anxiety. In contrast, ego resilience buffered the positive relationship between academic stress and anxiety but not depression. Implications for the study’s findings are discussed and recommendations for future research are presented.
Conditions Affecting Perceived Coping for New Mothers: Analysis of a Pilot Study, Sydney, Australia

Much of the existing research on women’s mental health has not clarified the nature of the coping experience, nor taken a grounded theory approach using the participant's own words and meanings to describe the experience. Nine mothers (mean age = 34.2 years), working full-time at home with an average of two children (mean age = 21.5 months or 1¾ years), identifying themselves as well, participated in a series of two unstructured, in-depth interviews to help uncover their perceived coping experiences. For the mothers in this study, coping includes efforts to manage stressful, challenging or difficult events, and is affected by lifestyle changes experienced since the birth of a child, the general difficulty of the mothering role and social pressures to succeed in that role. The longer a woman has been a mother, the more persistence and lack of stressors encountered in the home setting (‘context’) were all nominated as conditions affecting perceptions of coping.
How peculiar is evaluative morphology?

Many languages possess morphological rules which serve to express diminution or augmentation, endearment or contempt; examples are the Breton rule relating potr ‘boy’ to potrig ‘little boy’, the Shona rule relating chibikiso ‘cooking tool’ to zichibikiso ‘huge cooking tool’ and the Italian rule relating poeta ‘poet’ to poetastro ‘bad poet’. Because of the possibility of interpreting diminution and augmentation in affective rather than purely objective terms (Wierzbicka, 1980: 53ff.; Szymanek, 1988: 106ff.), morphological expressions of diminution or augmentation are not always discrete from those of endearment or contempt; that is, diminutives and augmentatives are frequently used as expressions of endearment (such as Italian sorella ‘sister’ → sorellina ‘dear little sister’, donna ‘woman’ → donnotta ‘fine, stout woman’) or disdain (Italian uomo ‘man’ → uomicciuolo ‘contemptible little man’, donna → donnona ‘overgrown girl’).
TT virus (TTV) loads associated with different peripheral blood cell types and evidence for TTV replication in activated mononuclear cells

TT virus (TTV) loads associated with the peripheral blood cells of seven patients known to carry the virus in plasma were investigated by real‐time PCR. Whereas red cells/platelets were uniformly negative, six and four patients yielded positive peripheral blood mononuclear cells (PBMCs) and polymorphonuclear leukocytes, respectively, but viral titres were generally low. Fractionation of PBMCs into monocyte‐ and B, T4, and T8 lymphocyte‐enriched subpopulations showed no pattern in the viral loads that might suggest the preferential association of TTV to one or more specific cell types. TTV‐negative PBMCs absorbed measurable amounts of virus when incubated with infected plasma at 4°C. Furthermore, cultures of TTV‐negative phytohaemagglutinin‐stimulated PBMCs exposed in vitro to virus‐positive plasma and faecal extracts released considerable levels of infectious TTV into the supernatant fluid and the same was true for TTV‐positive stimulated PBMCs. These results indicate that, whereas freshly harvested resting PBMCs seem to produce little, if any TTV, stimulated PBMCs actively replicate the virus. J. Med. Virol. 64:190–194, 2001. © 2001 Wiley‐Liss, Inc.
Strategic responses decision model in developing a sustainable manufacturing strategy

This work presents a decision model that highlights the integration of manufacturing strategy and sustainability with strategic responses as a significant component. Due to the complexity and uncertainty of the decision components and elements derived from literature, a proposed hybrid MCDM approach in the form of an integrated probabilistic fuzzy analytic network process (PROFUZANP) is presented. In the proposed method, analytic network process (ANP) handles complexity of the decision model. Fuzzy set theory is used to describe vagueness in decision-making which is carried out by eliciting judgment in pairwise comparisons using linguistic variables with corresponding triangular fuzzy numbers (TFNs). Probability theory is used to handle randomness when aggregating experts' judgments. Results are reported in this paper. Insights were also discussed.
Efficient Posterior Inference and Prediction of Space-Time Processes Using Dynamic Process Convolutions

Bayesian dynamic process convolution models provide an appealing approach for modeling both univariate and multivariate spatial temporal data. Their structure can be exploited to significantly reduce the dimensionality of a complex spatial temporal process. This results in efficient Markov chain Monte Carlo (MCMC) algorithms required for full Bayesian inference. In addition, the dynamic process convolution framework readily handles both missing data and misaligned multivariate space-time data without the need for imputation. We review the dynamic process convolution framework and discuss these and other computational advantages of the approach. We present an application involving the modeling of air pollutants to demonstrate how this approach can be used to effectively model a space-time process and provide predictions along with corresponding uncertainty statements.
d -wave correlated critical Bose liquids in two dimensions

We develop a description of a quantum liquid phase of interacting bosons confined in two dimensions that possesses relative d-wave two-body correlations. We refer to this stable quantum phase as a d-wave Bose liquid (DBL). The DBL has no broken symmetries, supports gapless boson excitations that reside on “Bose surfaces” in momentum space, and exhibits power-law correlation functions characterized by a manifold of continuously variable exponents. While the DBL can be constructed for bosons moving in the two-dimensional continuum, the state only respects the point group symmetries of the square lattice. On the square lattice, the DBL respects all symmetries and does not require a particular lattice filling. However, lattice effects do allow for the possibility of a second distinct phase, a quasilocal variant we refer to as a d-wave local Bose liquid (DLBL). Remarkably, the DLBL has short-range boson correlations and hence no Bose surfaces, despite sharing gapless excitations and other critical signatures with the DBL. Moreover, both phases are metals with a resistance that vanishes as a power of the temperature. We establish these results by constructing a class of many-particle wave functions for the DBL, which are time reversal invariant analogs of Laughlin's quantum Hall wave function for bosons in a half-filled Landau level. A gauge theory formulation leads to a simple mean field theory, and a suitable N-flavor generalization enables incorporation of gauge field fluctuations to deduce the properties of the DBL/DLBL in a controlled and systematic fashion. Various equal-time correlation functions thereby obtained are in qualitative accord with the properties inferred from the variational wave functions. We also identify a promising microscopic Hamiltonian that might manifest the DBL or DLBL, and perform a variational energetics study comparing other competing phases, including the superfluid. We suggest how the d-wave Bose liquid wave function can be suitably generalized to describe an itinerant non-Fermi-liquid phase of electrons on the square lattice with a no-double-occupancy constraint, a d-wave metal phase.
Cloud Radio Access Networks With Coded Caching

A cloud radio access network (C-RAN) is considered as a candidate to meet the expectations of higher data rate de- mands in wireless networks. In C-RAN, low energy base stations (BSs) are deployed over a small geography and are allowed to connect to the cloud via finite capacity backhaul links where the information is processed. A conventional C-RAN, however, requires high capacity backhaul links, since the requested files need to be transferred first from the cloud to the BS before conveying them to the users. One approach to overcome the limitations of the backhaul links is to introduce local storage caches at the BSs, in which the popular files are stored locally in order to reduce the load of the backhaul links. Furthermore, we utilize coded caching with the goal to minimize the total network cost, i.e., the transmit power and the cost associated with the backhaul links. The initial formulation of the optimization problem for this model is non-convex. We first reformulate and then convexify the problem through some relaxation techniques. In comparison to the uncoded caching at the BSs, our results highlight the benefits associated with coded caching and show that it decreases the backhaul cost.
Congruence Subgroups of Lattices in Rank 2 Kac–Moody Groups over Finite Fields

Let G be a rank 2 complete affine or hyperbolic simply-connected Kac–Moody group over a finite field k. Then G is locally compact and totally disconnected. Let B− = HU− be the negative minimal parabolic subgroup of G, where H is the analog of a diagonal subgroup and U− is generated by all negative real root groups. Let w1 and w2 be the generators of the Weyl group. Let be the negative standard parabolic subgroup of G corresponding to w1. It is known that the subgroups U−, B− and , are nonuniform lattice subgroups of G. Here we construct an infinite sequence of congruence subgroups of as natural generalizations of the corresponding notions for lattices in Lie groups. We also show that the group U− contains analogous congruence subgroups. Our technique involves determining graphs of groups presentations for U−, B−, and with the fundamental apartment of the Bruhat–Tits tree X a quotient graph for U− and for B− on X. When k = 𝔽q and q = 2s, the graph of groups for has the the positive half of the fundamental apartment as quotient graph. We explicitly construct the graphs of groups for the principal (level 1) congruence subgroup of and the analogous subgroups of U− giving generalized amalgam presentations for them.
Special-Use IPv4 Addresses

This document obsoletes RFC 3330. It describes the global and other specialized IPv4 address blocks that have been assigned by the Internet Assigned Numbers Authority (IANA). It does not address IPv4 address space assigned to operators and users through the Regional Internet Registries, nor does it address IPv4 address space assigned directly by IANA prior to the creation of the Regional Internet Registries. It also does not address allocations or assignments of IPv6 addresses or autonomous system numbers. Information about the current status of this document, any errata, and how to provide feedback on it may be obtained at include Simplified BSD License text as described in Section 4.e of the Trust Legal Provisions and are provided without warranty as described in the Simplified BSD License.
GnRH agonist versus antagonist therapy.

I read with interest the article titled ‘Human ovarian steroid secretion in vivo: effects of GnRH agonist versus antagonist (cetrorelix)’ (Garcia-Velasco et al., 2001) and I got a little confused. The addition of four patients (two at the beginning of the study and two at the end) in order to have matching groups suggests that the study was a retrospective one. This is further supported by the fact that the subjects selected for this study were a subset of women enrolled in another phase III clinical study. There is no mention of this being a retrospective study, either in the Abstract or the text. Being retrospective can explain why two different regimens of FSH were used in both groups: step-down and fixed dose with gradual increments as needed. If it is really a retrospective study—using material obtained from subjects enrolled in another trial—then the conclusion reached by the authors would be markedly questionable (in view of the very limited sample size). Moreover, leuprolide acetate was given as 1 mg per day s.c. and the dose was adjusted according to the length of patient’s cycle in order to start the analogue 7 days prior to menstruation. In Table I it is confusing; the mean number of days of GnRH agonist was 12.2 while the mean total dose of GnRH agonist was 18.6 mg. The authors stated that, ‘If serum estradiol concentrations were beyond the cut-off point, the patient was excluded from the study’ and there is no mention of how many cases were excluded. Whether IVF was performed more than ICSI in the GnRH agonist-treated group is unclear from the data presented by the authors. Finally, the authors claimed a higher fertilization rate in the antagonist-treated group and this was the cornerstone of their conclusions. It is interesting that this was not the case in previous well designed, well conducted, randomized controlled trials comparing agonist versus antagonist (The European Orgalutran Study Group, 2000; the European Middle East Orgalutran Study Group, 2001).
Class and Family

This paper seeks to make a contribution to debates on ‘class analysis’, as well as exploring the role of the family in class reproduction. A broad distinction is drawn between primarily ‘economic’ and primarily ‘culturalist’ accounts of class reproduction. It is argued that despite their differences, these accounts also share many similarities. In particular, both approaches identify the role of the family as central to the reproduction of class. However, economic and cultural accounts cannot be integrated into a single ‘theory’, one reason being that the mechanisms whereby economic and cultural capital are transmitted are different. Nevertheless, economic and cultural approaches may be (and should be) used in combination with each other in order to develop a full account of the reproduction of class inequalities. In developing these arguments, a critique is offered of current theories of ‘individualisation’ in relation to class and the family. The argument is illustrated by two ‘worked examples’; teenage motherhood, and the patterning of mothers’ employment.
Identification of a Compound Origin of Replication at theHMR-E Locus in Saccharomyces cerevisiae *

Eukaryotic chromosomal origins of replication are best defined in Saccharomyces cerevisiae. Previous analysis of yeast origins suggests that they are relatively simple structures comprised of three or four small DNA sequence elements contained within approximately 100–200-base pair regions (Gilbert, D. M. (1998)Curr. Opin. Genet. Dev. 8, 194–199). In contrast, the sequence elements that may comprise origins in multicellular eukaryotes are largely unknown. The yeast HMR-E region is both a chromosomal origin of replication and a silencer that represses transcription of adjacent genes through a position effect. The analysis presented here indicated that HMR-E had a novel DNA structure that was more complex than defined for other yeast origins, and thus revealed that there is variation in the structural complexity of yeast origins. In contrast to “simple” yeast origins, the origin at HMR-E consisted of at least three independent subregions that had the capacity to initiate replication. We have termedHMR-E a compound origin to reflect its structural complexity. Furthermore, only one origin within the compound origin was a silencer.