Miracle-dz/UniFAR-FTUs huggingface dataset:
Critical Structural and Functional Roles for the N-Terminal Insertion Sequence in Surfactant Protein B Analogs

Background Surfactant protein B (SP-B; 79 residues) belongs to the saposin protein superfamily, and plays functional roles in lung surfactant. The disulfide cross-linked, N- and C-terminal domains of SP-B have been theoretically predicted to fold as charged, amphipathic helices, suggesting their participation in surfactant activities. Earlier structural studies with Mini-B, a disulfide-linked construct based on the N- and C-terminal regions of SP-B (i.e., ∼residues 8–25 and 63–78), confirmed that these neighboring domains are helical; moreover, Mini-B retains critical in vitro and in vivo surfactant functions of the native protein. Here, we perform similar analyses on a Super Mini-B construct that has native SP-B residues (1–7) attached to the N-terminus of Mini-B, to test whether the N-terminal sequence is also involved in surfactant activity. Methodology/Results FTIR spectra of Mini-B and Super Mini-B in either lipids or lipid-mimics indicated that these peptides share similar conformations, with primary α-helix and secondary β-sheet and loop-turns. Gel electrophoresis demonstrated that Super Mini-B was dimeric in SDS detergent-polyacrylamide, while Mini-B was monomeric. Surface plasmon resonance (SPR), predictive aggregation algorithms, and molecular dynamics (MD) and docking simulations further suggested a preliminary model for dimeric Super Mini-B, in which monomers self-associate to form a dimer peptide with a “saposin-like” fold. Similar to native SP-B, both Mini-B and Super Mini-B exhibit in vitro activity with spread films showing near-zero minimum surface tension during cycling using captive bubble surfactometry. In vivo, Super Mini-B demonstrates oxygenation and dynamic compliance that are greater than Mini-B and compare favorably to full-length SP-B. Conclusion Super Mini-B shows enhanced surfactant activity, probably due to the self-assembly of monomer peptide into dimer Super Mini-B that mimics the functions and putative structure of native SP-B.
Semantically-Enhanced Recommenders

Recommendation models based on collaborative filtering have good prediction accuracy; however, they have very poor performance in cold-start scenarios, when no or few rating data are associated to certain items or users. An approach for dealing with cold-start problem is to build hybrid models that include content-based filtering. This paper focuses on knowledge-based hybrids that exploit semantic relations among item attributes to enhance traditional models. We investigate novel methods for exploiting this semantics during the recommendation process, in domains where explicit semantic relations among attributes in the form of ontologies are not available. We carry out an extensive performance comparison in which the proposed semantically-enhanced models are evaluated in normal and cold-start scenarios. The experimental results with a publicly available dataset demonstrate superior better performance of the proposed semantically-enhanced models, above all in cold-start scenarios, with respect to a state-of-the-art collaborative-filtering model based on matrix factorization. The proposed models, additionally, provide for interpretable recommendations, in contrast to black-box models.
Stress and earthquakes in southern California

We compute the stress tensor in the upper crust of southern California as a function of time and compare observed seismicity with the estimated stress at the time of each earthquake Several recent developments make it possible to do this much more realistically than before a wealth of new geodetic and geologic data for southern California and a catalog of moment tensors for all earthquakes with magnitudes larger than since and larger than since We model crustal deformation using both updated geodetic data and geologically determined fault slip rates We sub divide the crust into elastic blocks delineated by faults which move freely at a constant rate below a locking depth with a rate determined by the rel ative block motion We compute normal and shear stresses on nodal planes for each earthquake in the catalog We consider stress increments from pre vious earthquakes seismic stress and aseismic tectonic stress both sep arately and in combination The locations and mechanisms of earthquakes are best correlated with the aseismic shear stress Including the cumulative coseismic e ects from past earthquakes does not signi cantly improve the correlation Correlations between normal stress and earthquakes are always very sensitive to the start date of the catalog whether we exclude earthquakes very close to others and whether we evaluate stress at the hypocenter or through out the rupture surface of an earthquake Although the correlation of tec tonic stress with earthquake triggering is robust other results are unstable apparently because the catalog has so few earthquakes Index terms Seismology ESE Earthquake parameters Earth quake dynamics and mechanics Seismicity and seismotectonics Seismicity and seismotectonics
Association of the I264T Variant in the Sulfide Quinone Reductase-Like (SQRDL) Gene with Osteoporosis in Korean Postmenopausal Women

To identify novel susceptibility variants for osteoporosis in Korean postmenopausal women, we performed a genome-wide association analysis of 1180 nonsynonymous single nucleotide polymorphisms (nsSNPs) in 405 individuals with osteoporosis and 722 normal controls of the Korean Association Resource cohort. A logistic regression analysis revealed 72 nsSNPs that showed a significant association with osteoporosis (p<0.05). The top 10 nsSNPs showing the lowest p-values (p = 5.2×10-4–8.5×10-3) were further studied to investigate their effects at the protein level. Based on the results of an in silico prediction of the protein’s functional effect based on amino acid alterations and a sequence conservation evaluation of the amino acid residues at the positions of the nsSNPs among orthologues, we selected one nsSNP in the SQRDL gene (rs1044032, SQRDL I264T) as a meaningful genetic variant associated with postmenopausal osteoporosis. To assess whether the SQRDL I264T variant played a functional role in the pathogenesis of osteoporosis, we examined the in vitro effect of the nsSNP on bone remodeling. Overexpression of the SQRDL I264T variant in the preosteoblast MC3T3-E1 cells significantly increased alkaline phosphatase activity, mineralization, and the mRNA expression of osteoblastogenesis markers, Runx2, Sp7, and Bglap genes, whereas the SQRDL wild type had no effect or a negative effect on osteoblast differentiation. Overexpression of the SQRDL I264T variant did not affect osteoclast differentiation of the primary-cultured monocytes. The known effects of hydrogen sulfide (H2S) on bone remodeling may explain the findings of the current study, which demonstrated the functional role of the H2S-catalyzing enzyme SQRDL I264T variant in osteoblast differentiation. In conclusion, the results of the statistical and experimental analyses indicate that the SQRDL I264T nsSNP may be a significant susceptibility variant for osteoporosis in Korean postmenopausal women that is involved in osteoblast differentiation.
Heuristic approaches to Double Vehicle Routing Problem with Multiple Stacks

The Double Routing Vehicle Problem with Multiple Stacks (DVRPMS) consists in a Double Traveling Salesman Problem with Multiple Stacks (DTSPMS) with multiple vehicles. Both problems appeared for the urgent need of optimizing intermodal transportation in the european context. Consolidated economies call for logistics studies, particularly on intermodal transportation, which consists of using different transport modes between a start point and an end point. In DVRPMS, the collecting region is usually connected to the delivery region by sea, and the cities that make up each of these regions are interconnected by land routes. In this paper, we propose three heuristics for the DVRPMS based on the Iterated Local Search (ILS), Simulated Annealing (SA) and Variable Neighborhood Descent (VND). The objective is to provide a route with near optimum cost in a timeframe that complies with the customer's needs. The heuristics were applied in known instances and compared to the exact method. Both ILS and SA algorithms showed to be satisfactory for small instances and open to improvement for large instances. The SA algorithm managed to find solutions better than the best known upperbound. The VND algorithm served more as a guide to the quality of the initial solution than as a provider of a good final solution.
Influence of noise on the equivalence of word-lists in a phonemically balanced word test: comparison in young and older adults

Abstract Purpose: The main purpose of the study was to determine the influence of noise on the equivalency of word-lists in a speech-in-noise test. Additionally, the performance of young and older adults was compared. Method: Thirty-four young adults with normal hearing, aged 18–36 years, were compared with 49 older adults, aged 55–75 years having hearing sensitivity ≤20 dB HL till 2000 Hz. The young adults were evaluated using a speech-in-noise test having four word-lists that were equivalent in quiet, with half being tested in the right ear and half in the left ear. The older adults were tested with two of the lists, one in each ear. Results: In the presence of speech-babble, the younger adults obtained no significant difference between the two ears as well as between gender. Their scores on all four lists of the test were equivalent. In contrast, in the older adults the females performed significantly better than the males on one of the two lists that they were evaluated on, but no ear difference was observed. There was a significant difference between the lists in the older adults. Additionally, the older adults performed significantly poorer when compared to the younger group. Conclusions: In the presence of noise, the lists were found to be equivalent in the young adults but was not in the older adults. A gender difference was absent in the younger adults but was present in the older listeners. The performance of the older listeners was consistently poorer compared to that of the younger listeners.
Probabilistic Query Expansion method using recommended past user queries

A plenty of Query Expansion techniques have been proposed to solve the problems of information retrieval systems, but new challenges has been introduced for these methods of expansion of user queries because of the rapid growth of the size of the Web collection. In this paper we have focused our attention on the improvement of the precision of the user query by a Probabilistic Query Expansion Method. Our approach consists on the use of information contained in query logs, which includes past user queries and their clicked documents, for providing high-level recommendations. The experiment results shows that the precision of the short queries increases even if we add a few terms, but the same number of terms added don't affect the long queries precision as much as for the short queries.
A Combinatorial Fusion Method for Feature Construction

This paper demonstrates how methods borrowed from information fusion can improve the performance of a classifier by constructing (i.e., fusing) new features that are combinations of existing numeric features. The new features are constructed by mapping the numeric values for each feature to a rank and then averaging these ranks. The quality of the fused features is measured with respect to how well they classify minority-class examples, which makes this method especially effective for dealing with data sets that exhibit class imbalance. This paper evaluates our combinatorial feature fusion method on ten data sets, using three learning methods. The results indicate that our method can be quite effective in improving classifier performance.
Reducing Power Consumption in Backbone Networks

According to several studies, the power consumption of the Internet accounts for up to 10% of the worldwide energy consumption, and several initiatives are being put into place to reduce the power consumption of the ICT sector in general. To this goal, we propose a novel approach to switch off network nodes and links while still guaranteeing full connectivity and maximum link utilization. After showing that the problem falls in the class of capacitated multi-commodity flow problems, and therefore it is NP-complete, we propose some heuristic algorithms to solve it. Simulation results in a realistic scenario show that it is possible to reduce the number of links and nodes currently used by up to 30% and 50% respectively during off-peak hours, while offering the same service quality.
The chiral effective pion-nucleon Lagrangian of order $p^{4}$

Abstract We construct the minimal effective chiral pion-nucleon SU(2) Lagrangian at fourth order in the chiral expansion. The Lagrangian contains 118 in principle measurable terms. We develop both the relativistic as well as the heavy baryon formulation of the effective field theory. For the latter, we also work out explicitly all 1/m corrections at fourth order. We display all relevant relations needed to find the linearly independent terms.
Institutional Investors and Securities Markets: Which Comes First?

Institutional investors comprise pension funds, insurance companies, and mutual funds. Should a country promote their creation if it lacks well-developed securities markets? The answer to this question, says the author, varies by type of investor. He argues that private pension funds and insurance companies are promoted for their own sake and for their potential economic, fiscal, and financial benefits, whether or not a country already has well-developed securities markets. Mutual funds, by contrast, are unlikely to thrive without strong and well-regulated securities markets. A limited supply of financial instruments should not be a major obstacle to the creation of pension funds and insurance companies. Such institutions build up their financial resources gradually but steadily, giving reforming governments ample time to develop securities markets. More important than the prior development of securities markets is a strong and lasting political commitment to holistic reform: macroeconomic, fiscal, banking, and capital market reform, as well as pension and insurance reform. Institutional investors need to attain critical mass and to be supported by conducive regulations. The author reviews Anglo-American experience since the 1940s. This shows that institutional investors can serve as a countervailing force to commercial and investment banks, helping to stimulate financial innovation, modernize capital markets, enhance transparency and disclosure, strengthen corporate governance, and improve financial regulation.
An extended core‐based framework for delay‐constrained group communication

Multipoint communications is the simultaneous transmission of data streams from a number of sources to a set of receivers in a group according to predetermined metrics. The core‐based approach in multipoint communication enhances potential solutions in terms of quality‐of‐service (QoS)‐efficiency and feasibility of the results in inter and intra‐domain routing. In this paper, we first analyse the solution space for constrained multipoint communication problems under the core‐based approach. We show that the range of solutions examined by the models proposed to date is restricted to a subset of the entire solution space, which restricts the potential efficiency of the results. We propose SPAN, a core‐based framework processing on our identified extended solution space for constrained multi‐source group applications. SPAN consists of core selection and tree construction as two modular components complimenting one another to achieve more efficient solutions in distributed processing. SPAN is also asymmetric, hence potentially operates in domains in which link weights are not necessarily equal in both directions. We analyse the computational and message complexity of our framework and show its feasibility for distributed deployment. Our performance results show that SPAN consistently outperforms its counterparts in the literature in terms of cost and QoS‐efficiency. Copyright © 2007 John Wiley & Sons, Ltd.
Return migration, entrepreneurship and development: Contrasting the economic growth perspective of Senegal’s diaspora policy through a migrant-centred approach

ABSTRACT In recent years, the prominence of ‘migration’ as a policy domain in many African countries has shifted from labour-export policies to so-called ‘diaspora policies’. In these policies, migration is emphasised as a key instrument to stimulate development, particularly through return to the homeland and migrant entrepreneurship. Despite much attention accorded to migrants’ agency and affiliated cultural aspects in the ‘migration and development nexus’ debate, practices of return migration policy suffer from an inconsistency problem. The intention to promote national development is restricted by conceptual boundaries that define ‘return migration’ as a uni-directional flow from countries of immigration to countries of origin, and that reduce ‘development’ to its economic dimension. Acknowledging that migration and development have been long recognised in the scholarly literature as multi-faceted phenomena, this article exposes this inconsistency problem through ethnographic research among return businessmen in Senegal, whose experiences are advocated in diaspora policy as ideal returnees. I show how their practices are rooted in transnational relationships with the former country of immigration and, by implication, are built on bi-directional rather than uni-directional flows. Their motivations to return and invest depend on the sustainability of such relationships. I further illustrate that, by cultivating transnational linkages, initiating innovation and setting new examples, return businessmen bring implications for development well beyond economic growth as the core interest of diaspora policy. I conclude that the framing of development as a goal of diaspora policy in economic terms neglects what return migrants themselves value as important development objectives and outcomes.
A Multiscale Model of First and Second Order Phase Transformations with Application to SMA Single Crystals

This work aims to connect an atomistic model with continuum theory of phase transformations in shape memory alloys (SMAs). A formulation of the Helmholtz free energy potential based on Einstein potential has been developed. The atomic potential was used to describe the interatomic interactions in a biatomic crystal of NiTi. The microscopic expressions of the instantaneous mechanical (continuum) variables of mass, momentum, internal energy, and temperature have been derived in terms of the atomic variables. The developed Helmholtz thermodynamic potential is used in the context of the sharp phase front-based continuum framework proposed by Stoilov and Bhattacharyya [Acta Mater. , 50 (2002), pp. 4939–4952] to study the micro-macro transition during the thermomechanical response of NiTi crystals. The developed model has been successfully used to predict the response of a one-dimensional single crystal system.
Characterizing programmers' information-seeking during software evolution

This paper proposes an empirical approach, called content analysis, to identify the information sought and obtained by programmers as they maintain software systems. Using this information, researchers have the potential to determine the information bottlenecks that programmers encounter as they view representations of their software systems. As such, this work promises both direction and an evaluation framework for those involved in creating software visualization tools
Modelling techniques for enhanced realism in an open surgery simulation

This paper is a continuation of work originating from the simulation of Inguinal Hernia Repair. Whilst the majority of research in the medical simulation field is for minimally invasive techniques, the objective of our research is to develop a general framework for open surgery simulation. We focus here on the finer details of implementing such a simulator using advanced rendering techniques, collision detection and haptic feedback.
Density functional calculations of nuclear quadrupole coupling constants in the zero-order regular approximation for relativistic effects

The zeroth-order regular approximation (ZORA) is used for the evaluation of the electric field gradient, and hence nuclear quadrupole coupling constants, in some closed shell molecules. It is shown that for valence orbitals the ZORA-4 electron density, which includes a small component density (“picture-change correction”), very accurately agrees with the Dirac electron density. For hydrogen-like atoms exact relations between the ZORA-4 and Dirac formalism are given for the calculation of the electric field gradient. Density functional (DFT) calculations of the electric field gradients for a number of diatomic halides at the halogen nuclei Cl, Br, and I and at the metallic nuclei Al, Ga, In, Th, Cu, and Ag are presented. Scalar relativistic effects, spin–orbit effects, and the effects of picture-change correction, which introduces the small component density, are discussed. The results for the thallium halides show a large effect of spin–orbit coupling. Our ZORA-4 DFT calculations suggest adjustment of som.
On the finite element analysis of shells and their full interaction with Navier-stokes fluid flows

Our objective is to present an overview of some of our latest research and developments in the finite element analysis of shells, Navier-Stokes fluid flows and the full interactions of these flows with general shell structures. In the area of shell analysis, we have studied some generic physical behaviours of shells with specific emphasis on boundary and internal layers as the thickness of the shell decreases. Furthermore, we have studied how best to evaluate general finite element discretization schemes when considering the variety of shell behaviours. We review in this paper some of the results obtained. In the area of fluid flow analysis, we are developing a new solution approach (a flow-condition-based interpolation, FCBI, finite element scheme) to solve high Reynolds number incompressible fluid flows. This scheme has a number of advantages as discussed and demonstrated in the paper. In particular, the procedure is useful for the solution of fluid flows fully coupled to shells and other structures.
3D measurements for tumours malignancies early diagnosis

Several medical studies have shown that tumor malignancy can be evaluated by two different measurements concerning to the volumetric growth of tumors and the irregularities of their surfaces. Today Doubling Time (DT) is widely used for quantification of tumor growth rate, but may not be appropriate for some tumors, because it does not concern to the fact that benign tumors are expansive, while malignant ones are infiltrative. This work is then focused on: 3D rendering of tumor, reconstruction of a synthetic model that approximates its shape, and extraction of geometric features that can attest malignancy both in terms of volumes and of a proposal of new irregularity indexes. In particular, we refer to colorectal and lung cancers and then present the description and the implementation of a new software. This paper is organized as follows: description of tumor segmentation from a dataset of Computer Tomography (CT) axial slices, 3D tumor reconstruction, Genetic Algorithm synthetic model implementation and evaluation of regularity of tumor shape.