Miracle-dz/UniFAR-FTUs huggingface dataset:
Ion channel crystallisation for structural studies

Ion channels control the movement of ions allowing specific ions to pass across biological membranes. This apparently simple process is used to control many essential physiological processes including the generation and propagation of neuronal excitation, regulation of insulin secretion, heartbeat and cell volume. Ion channels are able to do this by having multiple means of controlling the opening and closing of the ion conduction pathway. Several recent ion channel structures have shed light on the important process of ion selectivity as well as providing clues on channel gating. However, it is not yet completely clear how ion channels control the passage of ions across the membrane. My work is centred on understanding the gating process through structural analysis mostly using X-ray crystallography. In order to get to this point, crystals of the target ion channels need to be grown. This thesis presents four projects that were aimed at developing the techniques for over-expression, purification and crystallisation of ion channels or transporters making them amenable for structural studies. One of the difficult steps in the structure determination pathway is obtaining well-ordered crystals of the target membrane protein. Crystals of the EcCLC channel (now found to be a transporter) from E. coli were initially unacceptable for structure determination. It was shown that the process of dehydration improved the quality and diffraction limit of the EcCLC crystals. This simple method provides a possible procedure for improving the resolution limit of soluble and membrane protein crystals. Inward rectifier potassium channels (Kir channels) are a distinct subfamily that preferentially allows K + ions to move into the cell. Two bacterial homologues of Kir channels, KirBac1.1 and KirBac3.1, were crystallised in 3-D and 2-D forms, respectively. As the crystal structure revealed the full-length model provided an excellent starting point for understanding the gating process in these channels. The 3-D structure of KirBac1.1 was captured in the closed state. This K + channel prevents ion movement by using hydrophobic residues to occlude the ion conduction pathway, altering the conformation of selectivity filter, misaligning the pore helices and decreasing the volume of the cavity. The 2-D projection maps of KirBac3.1 were obtained in both closed and a potentially open conformations. These two maps provided evidence as to how the structural elements of the inner, outer, slide helices and the C-terminal domains change relative to one another as the channel moves between these two gating states. These motions were modelled as rigid body movements. They included bending of the inner helices, a rotation of the outer helices as they straighten in the membrane, translocation of the slide helices and C-terminal domain rotations. It is hoped that the information gained from these projects, the plasmids construction, the expression systems and the protocols that were established for crystallisation of the ion channels and transporter will provide guidelines for future structural studies of membrane proteins.
Animated triangles: An eye tracking investigation

We presented three types of animations on an eye tracking monitor to 31 adult participants. In line with previous work, verbal descriptions of these animations indicate that one type (theory of mind or ToM) evokes mental state attributions, while another type (random) does not, with an intermediate category (goal-directed) evoking a moderate amount of mental state attributions. We expected longer fixations with greater depth of processing, which we assume is required for mental state attributions. In line with this expectation we found that the ToM animations invited long fixations; the random animations invited short fixations, while the goal-directed animations invited an intermediate amount of fixations, with some clips inviting shorter and others longer fixations. These findings demonstrate that it is possible to capture systematic differences in behaviour while viewing animations not only by means of a verbal measure, but also in terms of a simple measure of eye movements.
Biomaterials in endoprosthetics

Drago Dolinar1, Matev` Goren{ek2, Monika Jenko3, Matja` Godec3, Barbara [etina Bati~3, ^rtomir Donik3, Aleksandra Kocijan3, Mojca Debeljak4, Bo{tjan Kocjan~i~1 1Department of Orthopaedic Surgery, University Medical Centre Ljubljana, Zalo{ka 9, 1000 Ljubljana, Slovenia, 2MD-Medicine, Sanatorium Ljubljana, Bohori~eva 8, 1000 Ljubljana, Slovenia, 3Institute of Metals and Technology, Lepi pot 11, 1000 Ljubljana, Slovenia 4University Rehabilitation Institute, Republic of Slovenia, Linhartova 51, 1000 Ljubljana, Slovenia monika.jenko@imt.si
HLA DPA1, DPB1 Alleles and Haplotypes Contribute to the Risk Associated With Type 1 Diabetes

OBJECTIVE To determine the relative risk associated with DPA1 and DPB1 alleles and haplotypes in type 1 diabetes. RESEARCH DESIGN AND METHODS The frequency of DPA1 and DPB1 alleles and haplotypes in type 1 diabetic patients was compared to the family based control frequency in 1,771 families directly and conditional on HLA (B)-DRB1-DQA1-DQB1 linkage disequilibrium. A relative predispositional analysis (RPA) was performed in the presence or absence of the primary HLA DR-DQ associations and the contribution of DP haplotype to individual DR-DQ haplotype risks examined. RESULTS Eight DPA1 and thirty-eight DPB1 alleles forming seventy-four DPA1-DPB1 haplotypes were observed; nineteen DPB1 alleles were associated with multiple DPA1 alleles. Following both analyses, type 1 diabetes susceptibility was significantly associated with DPB1*0301 (DPA1*0103-DPB1*0301) and protection with DPB1*0402 (DPA1*0103-DPB1*0402) and DPA1*0103-DPB1*0101 but not DPA1*0201-DPB1*0101. In addition, DPB1*0202 (DPA1*0103-DPB1*0202) and DPB1*0201 (DPA1*0103-DPB1*0201) were significantly associated with susceptibility in the presence of the high risk and protective DR-DQ haplotypes. Three associations (DPB1*0301, *0402, and *0202) remained statistically significant when only the extended HLA-A1-B8-DR3 haplotype was considered, suggesting that DPB1 alone may delineate the risk associated with this otherwise conserved haplotype. CONCLUSIONS HLA DP allelic and haplotypic diversity contributes significantly to the risk for type 1 diabetes; DPB1*0301 (DPA1*0103-DPB1*0301) is associated with susceptibility and DPB1*0402 (DPA1*0103-DPB1*0402) and DPA1*0103-DPB1*0101 with protection. Additional evidence is presented for the susceptibility association of DPB1*0202 (DPA1*0103-DPB1*0202) and for a contributory role of individual amino acids and DPA1 or a gene in linkage disequilibrium in DR3-DPB1*0101 positive haplotypes.
Immunological Features of the Non-Structural Proteins of Porcine Reproductive and Respiratory Syndrome Virus

Porcine reproductive and respiratory syndrome virus (PRRSV) is currently one of the most important viruses affecting the swine industry worldwide. Despite the large number of papers published each year, the participation of non-structural proteins (nsps) in the immune response is not completely clear. nsps have been involved in the host innate immune response, specifically, nsp1α/β, nsp2, nsp4 and nsp11 have been associated with the immunomodulation capability of the virus. To date, only participation by nsp1, nsp2, nsp4 and nsp7 in the humoral immune response has been reported, with the role of other nsps being overlooked. Furthermore, nsp1, nsp2, nsp5, nsp7 nsp9, nsp10, nsp11 have been implicated in the induction of IFN-γ and probably in the development of the cell-mediated immune response. This review discusses recent reports involving the participation of nsps in the modulation of the innate immune response and their role in the induction of both the humoral and cellular immune responses.
The baubellum is more developmentally and evolutionarily labile than the baculum

Abstract Understanding the evolutionary forces that influence sexual dimorphism is a fundamental goal in biology. Here, we focus on one particularly extreme example of sexual dimorphism. Many mammal species possess a bone in their penis called a baculum. The female equivalent of this bone is called the baubellum and occurs in the clitoris, which is developmentally homologous to the male penis. To understand the potential linkage between these two structures, we scored baculum/baubellum presence/absence across 163 species and analyzed their distribution in a phylogenetic framework. The majority of species (N = 134) shared the same state in males and females (both baculum and baubellum present or absent). However, the baubellum has experienced significantly more transitions, and more recent transitions, so that the remaining 29 species have a baculum but not a well‐developed baubellum. Even in species where both bones are present, the baubellum shows more ontogenetic variability and harbors more morphological variation than the baculum. Our study demonstrates that the baculum and baubellum are generally correlated across mammals, but that the baubellum is more evolutionarily and developmentally labile than the baculum. The accumulation of more evolutionary transitions, especially losses in the baubellum, as well as noisier developmental patterns, suggests that the baubellum may be nonfunctional, and lost over time.
FunnelCloud: a cloud-based system for exploring tornado events

ABSTRACT Recent research has shown an increase in the number of extreme tornado outbreaks per year. The characterization of the spatio-temporal pattern of tornado events is therefore a critical task in the analysis of meteorological data. Currently, there are a large number of available meteorological datasets that can be used for such analysis. However, much of these data are distributed across multiple websites and are not accessible in a central location. This poses a significant challenge for a scientist who is interested in exploring meteorological patterns associated with tornado events. This paper presents a novel system which uses cloud-based technology for integrating, storing, exploring, analyzing, and visualizing meteorological data associated with tornado outbreaks. The system employs a novel NoSQL database schema and web services architecture for data integration and provides a user friendly interface that allows scientists to explore the spatio-temporal pattern of tornado events. Furthermore, scientists can use this interface to analyze the relationship between different meteorological variables and properties of tornado outbreaks using a number of spatio-temporal statistical and data mining methods. The efficacy of the system is demonstrated on a use case centered on the analysis of climatic indicators of large spatio-temporally clustered tornado outbreaks.
Identifying insecticide resistance genes in mosquito by combining AFLP genome scans and 454 pyrosequencing

AFLP‐based genome scans are widely used to study the genetics of adaptation and to identify genomic regions potentially under selection. However, this approach usually fails to detect the actual genes or mutations targeted by selection owing to the difficulties of obtaining DNA sequences from AFLP fragments. Here, we combine classical AFLP outlier detection with 454 sequencing of AFLP fragments to obtain sequences from outlier loci. We applied this approach to the study of resistance to Bacillus thuringiensis israelensis (Bti) toxins in the dengue vector Aedes aegypti. A genome scan of Bti‐resistant and Bti‐susceptible A. aegypti laboratory strains was performed based on 432 AFLP markers. Fourteen outliers were detected using two different population genetic algorithms. Out of these, 11 were successfully sequenced. Three contained transposable elements (TEs) sequences, and the 10 outliers that could be mapped at a unique location in the reference genome were located on different supercontigs. One outlier was in the vicinity of a gene coding for an aminopeptidase potentially involved in Bti toxin‐binding. Patterns of sequence variability of this gene showed significant deviation from neutrality in the resistant strain but not in the susceptible strain, even after taking into account the known demographic history of the selected strain. This gene is a promising candidate for future functional analysis.
2-Phenoxyethyl benzoate

In the title compound, C15H14O3, the dihedral angle between the benzene rings is 75.85 (7)°. In the crystal, centrosymmetrically related molecules are weakly associated through pairs of interactions between a benzene ring and an O atom of the ester group [ring centroid⋯O = 3.952 (7) Å], and through pairs of interactions between the other benzene ring and an O atom of the phenoxy group [ring centroid⋯O = 3.912 (7) Å], giving chains extending along [110].
Fast Generalized Cross-Validation Algorithm for Sparse Model Learning

We propose a fast, incremental algorithm for designing linear regression models. The proposed algorithm generates a sparse model by optimizing multiple smoothing parameters using the generalized cross-validation approach. The performances on synthetic and real-world data sets are compared with other incremental algorithms such as Tipping and Faul's fast relevance vector machine, Chen et al.'s orthogonal least squares, and Orr's regularized forward selection. The results demonstrate that the proposed algorithm is competitive.
Breast Cancer Vaccines: New Insights

Breast cancer (BC) is a persistent global challenge for its high frequency in women (although it seldom occurs in men), due to the large diffusion of risk factors and gene mutations, and for its peculiar biology and microenvironment. To date, BC can benefit from different therapeutic strategies involving surgery, ablation, chemotherapy, radiotherapy, and more specific approaches such as hormone therapy and the administration of various substances impairing cancer growth, aggressivity, and recurrence with different modalities. Despite these relatively wide chances, also used in combinatory protocols, relevant mortality and relapse rates, often associated with resistant phenotypes, stress the need for a personalized-medicine based on prompting the patient’s immune system (IS) against cancer cells. BC immunogenicity was latterly proven, so the whole immunotherapy field for BC is still at a very early stage. This immunotherapeutic approach exploits both the high specificity of adaptive immune response and the immunological memory. This review is focused on some of the majorly relevant BC vaccines available (NeuVax, AVX901, and INO-1400), providing a description of the more promising clinical trials. The efficacy of cancer vaccines highly depends on the patient’s IS, and a wide optimization is needed in terms of targets’ selection, drug design and combinations, dose finding, protocol structuring, and patients’ recruitment; moreover, new standards are being discussed for the outcome evaluation. However, early-phases excellent results suggest that the manipulation of the IS via specific vaccines is a highly attractive approach for BC.
Multilevel early packet filtering technique based on traffic statistics and splay trees for firewall performance improvement

This paper presents a mechanism to improve firewall packet filtering time through optimizing the order of security policy filtering fields for early packet rejection. The proposed mechanism is based on the optimization of the filtering fields order according to traffic statistics. Furthermore, the mechanism uses multilevel packet filtering, and in each level unwanted packets are rejected as early as possible. So, the proposed mechanism can be considered also as a device protection mechanism against denial of service (DoS) attacks targeting the default policy rule. In addition, early packet acceptance is done through using the splay tree data structure which changes dynamically according to traffic flows. So, repeated packets will have less memory accesses and therefore reducing the overall packets matching time. The proposed technique aims to overcome some of the performance limitations of the previous technique, named Self Adjusting Binary Search on Prefix Length (SA-BSPL). The numerical results obtained by simulations demonstrate that the proposed mechanism is able to significantly improve the firewall performance in terms of cumulative packet processing time compared to SA-BSPL technique.
Local Algorithms for Block Models with Side Information

There has been a recent interest in understanding the power of local algorithms for optimization and inference problems on sparse graphs. Gamarnik and Sudan (2014) showed that local algorithms are weaker than global algorithms for finding large independent sets in sparse random regular graphs thus refuting a conjecture by Hatami, Lovász, and Szegedy (2012). Montanari (2015) showed that local algorithms are suboptimal for finding a community with high connectivityin the sparse Erdös-Rényi random graphs. For the symmetric planted partition problem (also named community detection for the block models) on sparse graphs, a simple observation is that local algorithms cannot have non-trivial performance. In this work we consider the effect of side information on local algorithms for community detection under the binary symmetric stochastic block model. In the block model with side information each of the n vertices is labeled + or - independently and uniformly at random; each pair of vertices is connected independently with probability a/n if both of them have the same label or b/n otherwise. The goal is to estimate the underlying vertex labeling given 1) the graph structure and 2) side information in the form of a vertex labeling positively correlated with the true one. Assuming that the ratio between in and out degree a/b is θ(1) and the average degree (a+b) / 2 = n{o(1), we show that a local algorithm, namely, belief propagation run on the local neighborhoods, maximizes the expected fraction of vertices labeled correctly in the following three regimes: |a--b|<2 and all 0 < α < 1/2 (a--b)2 > C (a+b) for some constant C and all 0 < α < 1/2 For all a,b if the probability that each given vertex label is incorrect is at most α* for some constant α* ∈ (0,1/2). Thus, in contrast to the case of independent sets or a single community in random graphs and to the case of symmetric block models without side information, we show that local algorithms achieve optimal performance in the above three regimes for the block model with side information. To complement our results, in the large degree limit α → ∞, we give a formula of the expected fraction of vertices labeled correctly by the local belief propagation, in terms of a fixed point of a recursion derived from the density evolution analysis with Gaussian approximations.
Cost-Effectiveness of New Cardiac and Vascular Rehabilitation Strategies for Patients with Coronary Artery Disease

Objective Peripheral arterial disease (PAD) often hinders the cardiac rehabilitation program. The aim of this study was evaluating the relative cost-effectiveness of new rehabilitation strategies which include the diagnosis and treatment of PAD in patients with coronary artery disease (CAD) undergoing cardiac rehabilitation. Data Sources Best-available evidence was retrieved from literature and combined with primary data from 231 patients. Methods We developed a Markov decision model to compare the following treatment strategies: 1. cardiac rehabilitation only; 2. ankle-brachial index (ABI) if cardiac rehabilitation fails followed by diagnostic work-up and revascularization for PAD if needed; 3. ABI prior to cardiac rehabilitation followed by diagnostic work-up and revascularization for PAD if needed. Quality-adjusted-life years (QALYs), life-time costs (US $), incremental cost-effectiveness ratios (ICER), and gain in net health benefits (NHB) in QALY equivalents were calculated. A threshold willingness-to-pay of $75 000 was used. Results ABI if cardiac rehabilitation fails was the most favorable strategy with an ICER of $44 251 per QALY gained and an incremental NHB compared to cardiac rehabilitation only of 0.03 QALYs (95% CI: −0.17, 0.29) at a threshold willingness-to-pay of $75 000/QALY. After sensitivity analysis, a combined cardiac and vascular rehabilitation program increased the success rate and would dominate the other two strategies with total lifetime costs of $30 246 a quality-adjusted life expectancy of 3.84 years, and an incremental NHB of 0.06 QALYs (95%CI:−0.24, 0.46) compared to current practice. The results were robust for other different input parameters. Conclusion ABI measurement if cardiac rehabilitation fails followed by a diagnostic work-up and revascularization for PAD if needed are potentially cost-effective compared to cardiac rehabilitation only.
Subunits fold at position-dependent rates during maturation of a eukaryotic RNA virus

Effective antiviral agents are difficult to develop because of the close relationship between the cell biology of the virus and host. However, viral capsid maturation, the in vivo process where the particle transitions from a noninfectious provirion to an infectious virion, is an ideal process to interrupt because the provirion is usually fragile and the conversion to the virion often involves large conformational changes and autocatalytic chemistry that can be hampered by small molecules. The Nudaurelia capensis ω virus (NωV) is one of the few eukaryotic viruses where this process can be investigated in vitro with a variety of biophysical methods, allowing fundamental chemical and structural principles of the maturation to be established. It has a T = 4 quasi-equivalent capsid with a dramatic maturation pathway that includes a particle size reduction of 100 Å and an autocatalytic cleavage. Here we use cryo-EM and difference maps, computed at three time points following maturation initiation, to show that regions of NωV subunit folding are maturation dependent and occur at rates determined by their quasi-equivalent position in the capsid, explaining the unusual kinetics of the maturation cleavage. This study shows that folding is rapid and peptide chain self-cleavage occurs early for subunits adjacent to 3-fold and 5-fold icosahedral symmetry elements and that folding is slower in regions where molecular switches are required for the formation of the proper interfacial contacts. The results connect viral maturation to the well-studied assembly-dependent folding that occurs in the formation of cellular complexes.
Human cell‐based artificial antigen‐presenting cells for cancer immunotherapy

Adoptive T‐cell therapy, where anti‐tumor T cells are first prepared in vitro, is attractive since it facilitates the delivery of essential signals to selected subsets of anti‐tumor T cells without unfavorable immunoregulatory issues that exist in tumor‐bearing hosts. Recent clinical trials have demonstrated that anti‐tumor adoptive T‐cell therapy, i.e. infusion of tumor‐specific T cells, can induce clinically relevant and sustained responses in patients with advanced cancer. The goal of adoptive cell therapy is to establish anti‐tumor immunologic memory, which can result in life‐long rejection of tumor cells in patients. To achieve this goal, during the process of in vitro expansion, T‐cell grafts used in adoptive T‐cell therapy must be appropriately educated and equipped with the capacity to accomplish multiple, essential tasks. Adoptively transferred T cells must be endowed, prior to infusion, with the ability to efficiently engraft, expand, persist, and traffic to tumor in vivo. As a strategy to consistently generate T‐cell grafts with these capabilities, artificial antigen‐presenting cells have been developed to deliver the proper signals necessary to T cells to enable optimal adoptive cell therapy.