Miracle-dz/UniFAR-FTUs huggingface dataset:
Redirection of CMV Specific CTL towards B-CLL Via CD20 Targeted HLA/CMV Complexes.

Because B cell chronic lymphocytic leukemia (B-CLL) can not be cured with current therapies, but in general has a slow progression and rather long median survival, it is considered an attractive candidate for active T cell mediated immunotherapy. However B-CLL cells have poor antigen presenting capacity because they express low levels of co-stimulatory molecules. Moreover, most immunotherapeutic strategies require knowledge of the eliciting tumor antigen and/or ex vivo manipulation of patient cells. To circumvent these drawbacks we aim to redirect existing viral immunity towards B-CLL. Previously, we have shown that in patients with B-CLL considerably expanded numbers of cytomegalovirus (CMV)-specific CD45RA + CD27 CD8 + cytotoxic T cells are present (W. Mackus et al. Blood2003; 102:1057). These cells are potent cytotoxic effector cells when directed against B-CLL cells loaded with CMV peptide (A.Kater et al. Br.J. Haematol.2004; 126:512). In the current study, we apply a novel bridging reagent to redirect CMV-specific CTL to specifically target B-CLL. The targeting complex is composed of a streptavidin fused anti-CD20 single chain variable fragment (scFv) in combination with biotinylated MHC class I molecules containing CMV pp65 peptide (HLA/CMV). We demonstrate that this complex is stable on the cell surface for ≥24 hours, and that B-CLL cells coated with this CD20-HLA/CMV complex can be lysed by autologous CMV-specific CD8 + CTL with similar efficiency as B-CLL cells directly loaded with CMV-peptide. Killing occurs at scFv CD20 concentrations of ≥100 ng ml −1 and HLA/CMV concentrations of ≥20 ng ml −1 . Lysis of CD20-HLA/CMV complex coated CLL cells could not be blocked by anti-LFA1 antibodies, in contrast to B-CLL cells directly loaded with CMV-peptide, indicating a different immunological synapse. HLA- A2 positive B-CLL cells coated with HLA- B7 /CMV complexes were only lysed by HLA- B7 positive CMV-specific CTL, whereas HLA- A2 /CMV complex targeted HLA- A2 positive B-CLL cells were unaffected by HLA- B7 positive CMV specific CTL, proving HLA restriction of the killing. Furthermore, CD20-HLA/CMV complex coated B-CLL cells induce both proliferation and cytokine production (interferon γ, tumor necrosis factor α, and macrophage inflammatory protein-1 β) in CMV-specific CD8+ T cells. Thus, CD20-HLA/CMV complexes elicit both immune activation and direct cytotoxicity towards B-CLL cells. The findings of our study constitute a necessary step towards possible application of CD20-HLA/CMV complexes for immunotherapy of B cell malignancies. It is obvious that this recently recognized capacity to redirect existing antiviral immunity towards tumor cells has a utility in cancer immunotherapy far beyond CMV and B-CLL.
Neural tube defects prevalence

Objectives: to determine neural tube closing defects in newborns delivered in the maternity ward of the Women Care Center of the Instituto Materno Infantil Prof. Fernando Figueira (IMIP). Methods: a descriptive cross-sectional cohort study, with data collected from a Born Alive Information System from which all records of newborns with fetal malformation were selected. From these records the ones pertaining to newborns between 2000 and 2004 with the neural tube closing defect were considered. Results: of 24.964 births, 709 newborns with some type of malformation were r egistered. When narrowing this to the newborns with the neural tube closing defect the number disclosed was 124, with a prevalence of 0.5% of the births within the period. Newborns with the neural tube closing defect, in general, had similar characteristics to newborns with other malformations. The majority (68.5%) of these newborns was delivered through C-Section and 37.7% had low birthweight.
Evaluation of MI-BCI Performance in Ten Spinal Cord Injured End Users

Highly paralyzed people have only a few residual motor functions that can be used for control of conventional assistive devices (ADs). These devices can be extended to accept input from a Motor-Imagery-Brain-Computer Interface (MI-BCI) to make them accessible for such individuals. However, it is still unclear to what extend disabled individuals are able to control an MI-BCI. In this study, the outcomes of MI-BCI training sessions with ten high spinal cord injured (SCI) subjects are presented. Only one subject achieved a performance greater than 70%, three subjects were around 70%. The average performance of all subjects was 70.5%, which is significantly lower than in healthy subjects.
Tension wood and opposite wood in 21 tropical rain forest species : occurence and efficiency of the G.-Layer

Wood samples were taken from the upper and lower sides of 21 naturally tilted trees from 18 families of angiosperms in the tropical rain forest in French Guyana. The measurement of growth stresses ensured that the two samples were taken from wood tissues in a different mechanical state: highly tensile stressed wood on the upper side, called tension wood, and lower tensile stressed wood on the lower side, called opposite wood. Eight species had tension wood fibres with a distinct gelatinous layer (G-layer). The distribution of gelatinous fibres varied from species to species. One of the species, Casearia javitensis (Flacourtiaceae), showed a peculiar multilayered secondary wall in its reaction wood. Comparison between the stress level and the occurrence of the G-layer indicates that the G-layer is not a key factor in the production of high tensile stressed wood.
EVALUATION OF RELATIONSHIP BETWEEN SERUM LEVELS OF TUMOR MARKERS (CEA, CA19-9) WITH DIAGNOSIS, PATHOLOGICAL FINDING AND STAGING IN COLORECTAL CARCINOMA

Background and Objectives: The diagnosis of colorectal cancer in early stage increases the survival rate and quality of life in patients with colorectal cancer. The aim of the present study was to evaluate the relationship between the tumor markers of CEA and CA19-9 with diagnosis, staging and pathological finding in patients with colorectal cancer. Materials and Methods: One hundred confirmed colorectal cancer patients who were candidates for surgery were included in the study group. Demographical, clinical and pathological information were collected. Peripheral blood samples were obtained from patients preoperatively for serum assay of the tumor marker (CEA and CA19-9). Results: The mean age of the patients was 56.95±15.16 years. The mean serum levels of CEA and CA19-9 tumor markers were 101.63±18.9ìg/L and 83.53±39.55 KU/L, respectively. More than one third of the patients had abnormal range of tumor markers (CEA, 36% and CA19-9, 35%). Simultaneous increase in both tumor markers was observed in 17.5% of the patients. An increase in the serum level of CA19-9 was correlated with the number of the involved lymph nodes (P=0.03). Moreover, an increase in the serum level of CEA was correlated with the depth of invasion (P=0.05), number of metastatic lymph nodes (P=0.001) and stage of the disease (P=0.01). Simultaneous increase in both tumor markers was correlated with the number of metastatic lymph nodes (P=0.01). Conclusion: According to the results of this study, the elevated preoperative serum levels of CEA and CA19-9 may be indicative of the disease progression, but not diagnosis of the disease in early stages.
Periodic Pólya Urns, the Density Method, and Asymptotics of Young Tableaux

P\'olya urns are urns where at each unit of time a ball is drawn and replaced with some other balls according to its colour. We introduce a more general model: the replacement rule depends on the colour of the drawn ball and the value of the time ($\operatorname{mod} p$). We extend the work of Flajolet et al. on P\'olya urns: the generating function encoding the evolution of the urn is studied by methods of analytic combinatorics. We show that the initial partial differential equations lead to ordinary linear differential equations which are related to hypergeometric functions (giving the exact state of the urns at time n). When the time goes to infinity, we prove that these periodic P\'olya urns have asymptotic fluctuations which are described by a product of generalized gamma distributions. With the additional help of what we call the density method (a method which offers access to enumeration and random generation of poset structures), we prove that the law of the south-east corner of a triangular Young tableau follows asymptotically a product of generalized gamma distributions. This allows us to tackle some questions related to the continuous limit of large random Young tableaux and links with random surfaces.
Development of surface pattern during division in Paramecium. I. Mapping of duplication and reorganization of cortical cytoskeletal structures in the wild type

The shape of a Paramecium is determined by the organization of its cortex which constitutes most of the cell cytoskeleton. These structures and networks are organized in relation to the approx. 4000 ciliary basal bodies present at the surface. Each basal body is the centre of a polarized and asymmetrical cortical unit. At the whole-cell level, all units are tandemly arranged in parallel rows and form a defined asymmetrical pattern with dorsoventral and anteroposterior polarities. During division, the cortex is the site of the major morphogenetic processes. In order to analyse how the surface pattern and the shape of the cell are reconstructed at each division, we have used specific immunological and cytological probes to map, in space and time, the reorganization of each of the major cytoskeletal cortical components: basal bodies and microtubules, kinetodesmal fibres, epiplasm and outer lattice. This cytological dissection demonstrates that the surface of the dividing cell is progressively invaded by morphogenetic waves which successively and individually trigger the duplication, assembly or reorganization of each structure and which all spread from the same epicentre (oral apparatus and fission furrow) with the same shape. Furthermore, the response of units to the morphogenetic waves depends on their position on the cell. It thus appears that despite the structural local constraints within units, the development of surface pattern is controlled in an integrated manner by transcellular signals.
Evaluación del estado nutricional en escolares de bajos recursos socioeconómicos en el contexto de la transición nutricional

Fil: Orden, Alicia Bibiana. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Centro de Investigaciones en Genetica Basica y Aplicada; Argentina
Room Detection for Topological Maps

Mapping is an important part of many robotic applications. In order to measure the performance of the mapping process we have to measure the quality of its result: the map. The map is essential for robotic algorithms like localization and path planning. Previously it was shown how matched Topology Graphs can be used for map evaluation by comparing the topology of the robot generated map to the topology of a ground truth map. In this paper we are extending the previous work by detecting open areas, for example rooms, in the 2D grid map and adding those to the topological representation. This way we can avoid the unreliable generation of paths in open areas, thus making the Topology Graph generation, and through that also the Topology Graph matching, more stable and robust. The detection applies the alpha shape algorithm for room detection.
Drug Bank: An Update-Resource for in Silico Drug Discovery

Drug Bank plays a vital role in the research of bioinformatics/chemo informatics. Drug bank is a richly annotated resource that combines detailed drug data with comprehensive drug target and drug action information. Since its first release in the 2006, Drug Bank has been widely used to facilitate, in silico drug target discovery, drug design, drug docking or screening, drug metabolism prediction, drug interaction prediction and general pharmacological education. First drug bank was released in 2006 with version 1.0. Now it is successfully updated by the releasing of 2.0, 2.5 and 3.0 version. First released in 2006, Drug Bank has become widely used by pharmacists, medicinal chemists, pharmaceutical researchers, clinicians, educators and the general public. The database contains 6707 drug entries including 1436 FDA-approved small molecule drugs, 134 FDA-approved biotech (protein/peptide) drugs, 83 nutraceuticals and 5086 experimental drugs. Additionally, 4228 non-redundant protein (i.e. drug target/enzyme/transporter/carrier) sequences are linked to these drug entries. Each DrugCard entry contains more than 150 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data. Since its last update in 2008, DrugBank has been greatly expanded through the addition of new drugs, new targets and the inclusion of more than 40 new data fields per drug entry (a 40% increase in data ‘depth ’). These data field additions include illustrated drug-action pathways, drug transporter data, drug metabolite data, pharmacogenomic data, adverse drug response data, ADMET data, pharmacokinetic data, computed property data and chemical classification data. Drug Bank 3.0 also offers expanded database links, improved search tools for drug –drug and food –drug interaction, new resources for querying and viewing drug pathways and hundreds of new drug entries with detailed patent, pricing and manufacturer data. These additions have been complemented by enhancements to the quality and quantity of existing data, particularly with regard to drug target, drug description and drug action data. Drug Bank 3.0 represents the result of 2 years of manual annotation work aimed at making the database much more useful for a wide range of ‘Omics ’ (i.e. pharmacogenomic, pharmacoproteomic, pharmacometabolomic and even pharmacoeconomic) applications.
Computing the small-scale galaxy power spectrum and bispectrum in configuration space

We present a new class of estimators for computing small-scale power spectra and bispectra in configuration space via weighted pair and triple counts, with no explicit use of Fourier transforms. Particle counts are truncated at $R_0\sim 100\, h^{-1}\, \mathrm{Mpc}$ via a continuous window function, which has negligible effect on the measured power spectrum multipoles at small scales. This gives a power spectrum algorithm with complexity $\mathcal {O}(NnR_0^3)$ (or $\mathcal {O}(Nn^2R_0^6)$ for the bispectrum), measuring N galaxies with number density n. Our estimators are corrected for the survey geometry and have neither self-count contributions nor discretization artefacts, making them ideal for high-k analysis. Unlike conventional Fourier-transform-based approaches, our algorithm becomes more efficient on small scales (since a smaller R0 may be used), thus we may efficiently estimate spectra across k-space by coupling this method with standard techniques. We demonstrate the utility of the publicly available power spectrum algorithm by applying it to BOSS DR12 simulations to compute the high-k power spectrum and its covariance. In addition, we derive a theoretical rescaled-Gaussian covariance matrix, which incorporates the survey geometry and is found to be in good agreement with that from mocks. Computing configuration- and Fourier-space statistics in the same manner allows us to consider joint analyses, which can place stronger bounds on cosmological parameters; to this end we also discuss the cross-covariance between the two-point correlation function and the small-scale power spectrum.
APLICAÇÃO DA PRESSÃO POSITIVA EXPIRATÓRIA NAS VIAS AÉREAS (EPAP): existe um consenso?

INTRODUCAO: a pressao positiva expiratoria (PEEP) e uma alternativa terapeutica utilizada com muita frequencia pelo fisioterapeuta em varias condicoes clinicas. OBJETIVO: o objetivo deste estudo foi realizar uma revisao da literatura sobre como a pressao positiva expiratoria nas vias aereas (EPAP) tem sido utilizada de forma terapeutica, bem como seus efeitos fisiologicos, nas diversas situacoes clinicas. METODO: foram realizadas buscas nas bases de dados: MEDLINE, LILACS e SciELO, nas linguas portuguesa e inglesa com temas relacionados ao EPAP. Foram excluidos os trabalhos cujo objetivo principal era a aplicacao da PEEP durante a ventilacao mecânica invasiva ou nao invasiva e no uso do RPPI (respiracao com pressao positiva intermitente). RESULTADOS: foram encontrados 257 artigos, sendo selecionados 18 artigos. Resultados: A maioria dos estudos foram randomizados, utilizaram resistores a fluxo e PEEP acima de 10 cmH2O. O EPAP mostrou ser mais eficaz que outras tecnicas comparadas na melhora da funcao pulmonar, troca gasosa e desobstrucao bronquica. Fisioter Mov. 2009 abr/jun; 22(2): 281-292 ISSN 0103-5150 Fisioter. Mov. , Curitiba, v. 22, n. 2, p. 281-292, jan./mar. 2009 Licenciado sob uma Licenca Creative Commons 282 Freitas FS de, Silva LCR, Tavares LD, Barroso EF, Silva MC, Godoi RL. Fisioter Mov. 2009 abr/jun; 22(2): 281-292 CONCLUSAO: A literatura suporta resultados satisfatorios com o uso do EPAP, contudo nao ha um consenso quanto a melhor forma de aplicacao desta tecnica, sendo, portanto, essencial a busca da padronizacao dos metodos de utilizacao deste recurso.
Application of optomechanical frequency conversion on gravitational wave detection.

Optomechanical interaction can be a platform for converting quantum optical sates at different frequencies. In this work, we propose to combine the idea of optomechanical frequency conversion and the dual-use of laser interferometer, for the purpose of improving the broadband sensitivity of laser interferometer gravitational wave detectors by filtering the light field. We found that compare to the previous schemes of implementing the optomechanical devices in gravitational wave detectors, this frequency converter scheme will have less stringent requirement on the thermal noise dilution.
Training Robust Tree Ensembles for Security

Tree ensemble models including random forests and gradient boosted decision trees, are widely used as security classifiers to detect malware, phishing, scam, social engineering, etc. However, the robustness of tree ensembles has not been thoroughly studied. Existing approaches mainly focus on adding more robust features and conducting feature ablation study, which do not provide robustness guarantee against strong adversaries. In this paper, we propose a new algorithm to train robust tree ensembles. Robust training maximizes the defender's gain as if the adversary is trying to minimize that. We design a general algorithm based on greedy heuristic to find better solutions to the minimization problem than previous work. We implement the algorithm for gradient boosted decision trees in xgboost and random forests in scikit-learn. Our evaluation over benchmark datasets show that, we can train more robust models than the start-of-the-art robust training algorithm in gradient boosted decision trees, with a 1.26X increase in the $L_\infty$ evasion distance required for the strongest whitebox attacker. In addition, our algorithm is general across different gain metrics and types of tree ensembles. We achieve 3.32X increase in $L_\infty$ robustness distance compared to the baseline random forest training method. Furthermore, to make the robustness increase meaningful in security applications, we propose attack-cost-driven constraints for the robust training process. Our training algorithm maximizes attacker's evasion cost by integrating domain knowledge about feature manipulation costs. We use twitter spam detection as a case study to analyze attacker's cost increase to evade our robust model. Our technique can train robust model to rank robust features as most important ones, and our robust model requires about 8.4X increase in attacker's economic cost to be evaded compared to the baseline.
Evaluation of Smartphone IMUs for Small Mobile Search and Rescue Robots

Small mobile robots are an important class of Search and Rescue Robots. Integrating all required components into such small robots is a difficult engineering task. Smartphones have already been made small, lightweight and cheap by the industry and are thus an excellent candidate as main controller for such robots. In this paper we outline how ROS can be used on Android devices and then evaluate one sensor which is very important for mobile robots: the Inertial Measurement Unit (IMU). Experiments are performed under static and dynamic conditions to measure the error of the IMUs of three smartphones and three professional IMUs. In the experiments we make use of a tracking system and an autonomous mobile robot.
Robust Morph-Detection at Automated Border Control Gate Using Deep Decomposed 3D Shape & Diffuse Reflectance

Face recognition is widely employed in Automated Border Control (ABC) gates, which verify the face image on passport or electronic Machine Readable Travel Document (eMTRD) against the captured image to confirm the identity of the passport holder. In this paper, we present a robust morph detection algorithm that is based on differential morph detection. The proposed method decomposes the bona fide image captured from the ABC gate and the digital face image extracted from the eMRTD into the diffuse reconstructed image and a quantized normal map. The extracted features are further used to learn a linear classifier (SVM) to detect a morphing attack based on the assessment of differences between the bona fide image from the ABC gate and the digital face image extracted from the passport. Owing to the availability of multiple cameras within an ABC gate, we extend the proposed method to fuse the classification scores to generate the final decision on morph-attack-detection. To validate our proposed algorithm, we create a morph attack database with overall 588 images, where bona fide are captured in an indoor lighting environment with a Canon DSLR Camera with one sample per subject and correspondingly images from ABC gates. We benchmark our proposed method with the existing state-of-the-art and can state that the new approach significantly outperforms previous approaches in the ABC gate scenario.
Current Trends in Trauma Education and Thoughts about Emergency Surgery in Turkey

The number of trauma victims in Turkey is expected to increase as a consequence of the increasing vehicular traffic, potential for earthquakes, and risk of terrorist attacks. To improve prehospital trauma care, the Ministry of Health has issued new guidelines to staff ambulances with specially trained paramedics and to obligate all general practitioners to attend internationally recognized courses in life support, trauma and resuscitation. The Turkish Association for Trauma and Emergency Surgery monitors trauma cases, publishes a quarterly journal, organizes seminars, and offers educational courses in trauma to various health personnel. It is also extending efforts to improve in-hospital care by establishing trauma and emergency surgery fellowships and trauma and emergency surgery centers nationwide. Turkey faces the same dilemma as the rest of the developed world regarding the future of trauma surgeons in the current era of nonoperative trauma management. We suggest that the field of trauma and emergency surgery be redefined to include emergency general surgery, vascular surgery, and noncoronary urgent thoracic procedures in order to increase the operative potential of trauma surgeons without compromising patient care.