Miracle-dz/UniFAR-FTUs huggingface dataset:
Generation and characterization of inhibitory nanobodies towards thrombin activatable fibrinolysis inhibitor

Summary. Background and objective: As activated thrombin‐activatable fibrinolysis inhibitor (TAFIa) is a potent antifibrinolytic enzyme, the development of TAFI inhibitors is a new promising approach in the development of profibrinolytic drugs. We, therefore, aimed to generate nanobodies, camelid‐derived single‐domain antibodies towards TAFI. Methods and results: This study reports the generation and characterization of a panel of 22 inhibitory nanobodies. This panel represents a wide diversity in mechanisms for interference with the functional properties of TAFI as the nanobodies interfere with various modes of TAFI activation, TAFIa activity and/or TAFI zymogen activity. Nanobodies inhibiting TAFIa activity and thrombin/thrombomodulin‐mediated TAFI activation revealed profibrinolytic properties in a clot lysis experiment with exogenously added thrombomodulin (TM), whereas nanobodies inhibiting plasmin‐mediated TAFI activation only revealed profibrinolytic properties in a clot lysis experiment without TM. The results of in vitro clot lysis experiments provided evidence that inhibitory nanobodies penetrate the clot better compared with inhibitory monoclonal antibodies. Conclusions: These data suggest that the generated nanobodies are potent TAFI inhibitors and are a step forward in the development of a profibrinolytic drug. They might also be an excellent tool to unravel the role of the physiological activators of TAFI in various pathophysiological processes.
Title : Sorting things out-assessing effects of unequal specimen biomass on DNA 1 metabarcoding 2 3 Running Title : Influence of specimen biomass in metabarcoding 4

14 Environmental bulk samples often contain many taxa that vary several orders of magnitude in biomass. This can be 15 problematic in DNA metabarcoding and metagenomic high-throughput sequencing approaches, as large specimens 16 contribute disproportionately high amounts of DNA template. Thus, a few specimens of high biomass will dominate the 17 dataset, potentially leading to smaller specimens remaining undetected. Sorting of samples by specimen size and balancing 18 the amounts of tissue used per size fraction should improve detection rates, but this approach has not been systematically 19 tested. 20 Here we explored the effects of size sorting on taxa detection using two freshwater macroinvertebrate monitoring samples, 21 collected from a low-mountain stream in Germany. Specimens were morphologically identified and sorted into three size 22 classes (body size < 2.5x5, 5x10 and up to 10x20 mm). Tissue from each size category was extracted individually, and 23 pooled to simulate samples that were not sorted by biomass ("Unsorted"). Additionally, size fractions were pooled so that 24 each specimen contributed approximately equal amounts of biomass ("Sorted"). Mock samples were amplified using four 25 different DNA metabarcoding primer sets targeting the Cytochrome c oxidase I (COI) gene. 26 Sorting taxa by size and pooling them proportionately according to their abundance lead to a more equal amplification of 27 taxa compared to the processing of complete samples without sorting. The sorted samples recovered 30% more taxa than the 28 PeerJ Preprints | https://doi.org/10.7287/peerj.preprints. 2561v3 | CC BY 4.0 Open Access | rec: 29 May 2017, publ: 29 May 2017 2 unsorted samples, at the same sequencing depth. Our results imply that sequencing depth can be decreased approximately 29 five-fold when sorting the samples into three size classes and pooling by specimen abundance. 30 Our study demonstrates that even a coarse size sorting can substantially improve taxa detection using DNA metabarcoding. 31 While high throughput sequencing will become more accessible and cheaper within the next years, sorting bulk samples by 32 specimen biomass is a simple yet efficient method to reduce current sequencing costs. 33 34
Discovering drugs combination pattern using FP-growth algorithm

A drug can be used to deal more than one diseases and to deal an illness often need a combination of more than one drugs. This paper present how to discover a pattern of a combination of medicines related to a diagnosis of diseases using FP-Growth one of frequent pattern mining algorithm. We use FP-Growth because it has better performance than Apriori and Eclat. Data is collected from outpatients pharmacy of Sukoharjo state hospital, Central Java, Indonesia during January 2015 to June 2016 and obtain 526,195 records of prescription data and use a diagnosis of diseases base on the ICD-10 standard. This studies just apply on the top ten of the most frequently occurred illness in the outpatient's services of Sukoharjo state hospital. Then the pattern of association between diseases and combination of drugs was reviewed by pharmacist committed to being validated. These studies result in some combination of medicines for to top ten of the most frequent diseases. We also found 21 similar combinations of drugs for various diseases. In the future, this finding can be used to provide suggestions to physicians to select an appropriate mix of the drug to deal some diseases.
Long-Term Multiepitopic Cytotoxic-T-Lymphocyte Responses Induced in Chimpanzees by Combinations of Plasmodium falciparum Liver-Stage Peptides and Lipopeptides

ABSTRACT Preclinical immunogenicity studies of 12 malaria peptides, selected from four Plasmodium falciparum antigens (Ags), namely, LSA1, LSA3, SALSA, and STARP, that are expressed at the pre-erythrocytic (sporozoite and liver) stages of the human parasite were carried out in chimpanzees. To strengthen their immunogenicity, six of these synthetic peptides were modified by the C-terminal addition of a single palmitoyl chain (lipopeptides) and delivered without adjuvant, whereas the remaining six unmodified peptides were emulsified and delivered by using Montanide ISA51 adjuvant. We have previously reported that these peptides and lipopeptides induce high B-cell and CD4+-T-helper responses in chimpanzees. In this report, we show their ability to induce multiepitopic and long-lasting antigen-specific CD8+ cytotoxic-T-lymphocyte (CTL) responses. The magnitude, consistency, and memory of CTL responses generated by LSA3 peptides point to the strong immunogenicity of this liver-stage Ag. These findings support the screening strategy used to select the four P. falciparum pre-erythrocytic Ags and emphasize their valuable immunogenic properties. The successful immunization of nonhuman primates with combinations of corresponding peptides in a mineral oil emulsion (ISA51) and lipopeptides in saline provide a vaccine formulation that can be tested in humans.
Sociosexuality, Commitment, Sexual Infidelity, and Perceptions of Infidelity: Data From the Second Love Web Site

This study explored the association between sociosexuality (behavior, attitudes, and desire) and commitment to understand sexual infidelity in current relationships. We also explored how these variables were associated with attitudes toward infidelity. Participants were romantically involved heterosexuals (N = 252; 51 women, 201 men; Mage = 41.13, SD = 9.82) registered on a dating Web site directed at romantically involved individuals. Results showed that sociosexuality, alongside commitment, was associated with sexual infidelity. Individuals who had (versus had not) previously engaged in infidelity reported more unrestricted sociosexuality, while reporting less commitment. For individuals reporting prior sexual infidelity, unrestricted sociosexual desire and lesser commitment were associated with more permissive perceptions of infidelity. For individuals reporting no prior sexual infidelity, greater commitment was always associated with more strict perceptions of infidelity. No gender differences emerged in the analyses. Also, no differences were found according to individual motivations (i.e., looking to know other people versus seeking casual sex) or relational motivations (i.e., individual registration versus registration as a couple) underlying individuals’ registration on the Web site. These results are an important addition to the literature on infidelity by analyzing a specific sample motivated to engage in infidelity. Implications for future research are discussed.
Investigation into Different Polarimetric Features for Sea Ice Classification Using X-Band Synthetic Aperture Radar

Satellite-borne synthetic aperture radar has proven to be a valuable tool for sea ice monitoring for more than two decades. In this study, we examine the performance of an automated sea ice classification algorithm based on polarimetric TerraSAR-X images. In the first step of our approach, we extract 12 polarimetric features from HH-VV dualpol StripMap images. In a second step, we train an artificial neural network, and then, feed the feature vectors into the trained neural network to classify each pixel into an ice type. The first part of our analysis addresses the predictive value of different subsets of features for our classification process (by means of measuring mutual information). Some polarimetric features such as polarimetric span and geometric intensity are proven to be more useful than eigenvalue decomposition based features. The classification is based on and validated by in situ data acquired during the N-ICE2015 field campaign. The results on a TerraSAR-X dataset indicate a high reliability of a neural network classifier based on polarimetric features. Performance speed and accuracy promise applicability for near real-time operational use.
Real-time framework for tensor-based image enhancement for object classification

In many practical situations visual pattern recognition is vastly burdened by low quality of input images due to noise, geometrical distortions, as well as low quality of the acquisition hardware. However, although there are techniques of image quality improvements, such as nonlinear filtering, there are only few attempts reported in the literature that try to build these enhancement methods into a complete chain for multi-dimensional object recognition such as color video or hyperspectral images. In this work we propose a joint multilinear signal filtering and classification system built upon the multi-dimensional (tensor) approach. Tensor filtering is performed by the multi-dimensional input signal projection into the tensor subspace spanned by the best-rank tensor decomposition method. On the other hand, object classification is done by construction of the tensor sub-space constructed based on the Higher-Order Singular Value Decomposition method applied to the prototype patters. In the experiments we show that the proposed chain allows high object recognition accuracy in the real-time even from the poor quality prototypes. Even more importantly, the proposed framework allows unified classification of signals of any dimensions, such as color images or video sequences which are exemplars of 3D and 4D tensors, respectively. The paper discussed also some practical issues related to implementation of the key components of the proposed system.
A constrained optimization based torque control approach for inverter-fed induction motors

In this paper, a constrained optimization based approach is proposed for the control of inverter-fed induction motors. This approach has many distinguished features: the measurements are motor velocity and currents, the tracking of torque command is optimized, the switching signal of inverter is determined directly from the feedback signals. This approach may be viewed as an improved SVM (space vector modulation) method, but instead of the tracking of a voltage command we track the current and flux commands directly which is equivalent to the tracking of torque and flux commands. This method greatly simplifies the control structure and computation complexity, and the optimality is guaranteed even in the overmodulation region.
Distinguishing computer graphics from photographic images using a multiresolution approach based on local binary patterns

With the ongoing development of rendering technology, computer graphics CG are sometimes so photorealistic that to distinguish them from photographic PG images by human eyes has become difficult. To this end, many methods have been developed for automatic CG and PG classification. In this paper, we present a simple, yet efficient, multiresolution approach to distinguish CG from PG based on uniform gray-scale invariant local binary patterns LBPs with the help of support vector machines SVM. We select YCbCr as the color model. The original Joint Photographic Experts Group JPEG coefficients of Y, Cb, and Cr components and their prediction errors are used for two LBP operators. From each 2D array and each LBP operator, we obtain 59 uniform LBP features. In total, 12 groups of 59 features are obtained from each image. But after multiresolution analysis, we select six groups of 59 features for CG and PG classification. The proposed features have been tested with thousands of CG and PG. Classification accuracy reaches 95.1% with support vector machines and outperforms the state-of-the-art works. Copyright © 2013 John Wiley & Sons, Ltd.
Combining optimal performance with cost-efficiency in adaptive wireless broadcast-based systems

Research on push-based systems has introduced several outstanding theoretical analyses and algorithms, aiming to optimize the clients' mean waiting time under several conditions. However, the computational and memory requirements aspect has been neglected to a great extend, thusly undermining the primary advantage of push systems over pull-based ones, i.e. their minimal cost. In this paper influential and top performing, well-known algorithms are evaluated from a cost aspect. It is shown that radical improvements are required for them to be realizable. Moreover, a new cost-efficient broadcast scheduling algorithm is introduced, achieving nearly top performance with minimal CPU and memory requirements. The new algorithm also promotes the adaptivity of push systems to the clients' changing needs, another factor that has not been taken into account by traditional approaches.
Retrograde viral transduction of cortical pyramidal neurons from the spinal cord.

PURPOSE The primary motor pathway, the corticospinal tract, is a major target for spinal cord regeneration studies. One way of improving the regeneration of corticospinal axons is to introduce regeneration-associated genes into cortical motor neurons using viral vector delivery. METHODS We used an engineered Herpes Simplex virus (HSV1) with the EF1alpha promoter encoding either LacZ or GFP to transduce cortical neurons through retrograde transport following the injection of vector into adult rat striatum or spinal cord. After three-days to one-month post-injection, sections of brain and spinal cord were viewed with fluorescence microscopy or processed for LacZ histochemistry. RESULTS Many layer V motor cortical neurons were transduced following striatal injections. These were not corticospinal neurons as they were not fluorogold-labelled following tracer injection into spinal cord. Corticospinal neurons in both hemispheres were, however, transduced following direct vector injections into the dorsal column of spinal cord, yielding 250-400 transduced corticospinal neurons per animal. No non-pyramidal neurons or thalamic neurons were transduced by spinal injections. CONCLUSIONS Therefore, this HSV1.EF1alpha vector is highly effective for the transduction of corticospinal neurons without direct injection into the brain and could be used to introduce regeneration-relevant genes into these neurons with the aim of regenerating the corticospinal tract.
NMR Solution Structure and Biophysical Characterization of Vibrio harveyi Acyl Carrier Protein A75H

Bacterial acyl carrier protein (ACP) is a highly anionic, 9 kDa protein that functions as a cofactor protein in fatty acid biosynthesis. Escherichia coli ACP is folded at neutral pH and in the absence of divalent cations, while Vibrio harveyi ACP, which is very similar at 86% sequence identity, is unfolded under the same conditions. V. harveyi ACP adopts a folded conformation upon the addition of divalent cations such as Ca2+ and Mg2+ and a mutant, A75H, was previously identified that restores the folded conformation at pH 7 in the absence of divalent cations. In this study we sought to understand the unique folding behavior of V. harveyi ACP using NMR spectroscopy and biophysical methods. The NMR solution structure of V. harveyi ACP A75H displays the canonical ACP structure with four helices surrounding a hydrophobic core, with a narrow pocket closed off from the solvent to house the acyl chain. His-75, which is charged at neutral pH, participates in a stacking interaction with Tyr-71 in the far C-terminal end of helix IV. pH titrations and the electrostatic profile of ACP suggest that V. harveyi ACP is destabilized by anionic charge repulsion around helix II that can be partially neutralized by His-75 and is further reduced by divalent cation binding. This is supported by differential scanning calorimetry data which indicate that calcium binding further increases the melting temperature of V. harveyi ACP A75H by ∼20 °C. Divalent cation binding does not alter ACP dynamics on the ps-ns timescale as determined by 15N NMR relaxation experiments, however, it clearly stabilizes the protein fold as observed by hydrogen-deuterium exchange studies. Finally, we demonstrate that the E. coli ACP H75A mutant is similarly unfolded as wild-type V. harveyi ACP, further stressing the importance of this particular residue for proper protein folding.
Medication use in normal weight and overweight children in a nationally representative sample of Canadian children

Background As overweight and obese children are more likely to develop serious medical conditions, they incur higher doctor and hospital costs compared to their normal weight counterparts. Consequently, the differential healthcare costs between obese and normal weight children may be even greater if medication use is considered. Objective To compare medication use between normal weight and overweight children in a nationally representative sample from Canada. Methods Data from the Canadian Health Measures Survey 2007/2009, a cross-sectional survey assessing indicators of health and wellness in Canadians, was used in the current study. The analysis included 2087 children and adolescents between 6–19 years of age with valid measures of body mass index (BMI). Poisson/negative binomial regression was used to examine the association between weight status and the number of medications taken in the last month. Result For 6–11 year olds, the frequency of prescription, over-the-counter and natural health product (NHP) medication use did not differ between normal weight and overweight/obese children. For 12–19 year olds, overweight/obese children used prescription medication significantly more often than their normal weight peers (adjusted incidence rate ratio (IRR), 1.59; 95% CI 1.19 to 2.14), whereas for NHP the opposite was the case (adjusted IRR, 0.52; 95% CI 0.32 to 0.82). These children also used nervous system and respiratory medications more frequently than their normal weight peers. Conclusion The findings of the present study suggest that the differential usage of prescription drugs among overweight/obese children underline the need to develop effective obesity prevention programmes and policies that may reduce the health and economic burden of childhood obesity.
A Test Facility for Cable in Conduit Conductors

An 11 T superconducting magnet has been manufactured for a 45 T hybrid magnet, the superconducting magnet has a large room temperature bore of 800 mm, so it can provide an 11 T background field for performance test of cable in conduit conductors (CICC). A test facility for superconducting CICCs has been designed as an insert combined with the superconducting magnet, wherein an 80 kA superconducting transformer has been designed to provide high operating current for the CICC samples. The CICC sample was designed to be a bifilar non-inductive solenoid coil. This paper will describe the principle design of the test facility and the overview of the 80 kA superconducting transformer.
Genomic structure of the human p47-phox (NCF1) gene.

The cytosolic factor p47-phox, encoded by the NCF1 gene, is an essential component of the phagocyte NADPH-oxidase system. Upon activation of this multicomponent system, p47-phox translocates to the membrane and participates in the electron transfer from NADPH to molecular oxygen. A deficiency or absence of p47-phox is the most common autosomal form of chronic granulomatous disease (CGD). We have cloned and characterized the NCF1 gene from four bacteriophage clones, a P1 clone and genomic DNA from normal individuals. The gene is 15,236 base pairs long and includes 11 exons. It is 98.6% homologous in sequence to at least one pseudogene that maps to the same region of chromosome 7q11.23. Slightly more than half (50.37%) of the wild-type NCF1 gene consists of repetitive elements. In particular, the density of Alu sequences is high (1.4 Alu/kb); there are 21 Alu repeats interspersed through 10 introns. These findings are consistent with the observation that recombination events between the wild-type gene and its highly homologous pseudogenes account for the majority of potentially lethal mutations in p47-phox-deficient chronic granulomatous disease. Analysis of 1.96 kb of sequence 5' of the start of translation revealed a high homology (99.6%) between wild-type and pseudogene clones. Characterization of NCF1 establishes a foundation for detailed molecular analysis of p47-phox-deficient CGD patients as well as for the study of the regulation of the NCF1 gene and pseudogenes, both of which are present as full-length transcripts in normal individuals.
Information Model for IP Flow Information Export

This memo defines an information model for the IP Flow Information eXport (IPFIX) protocol. It is used by the IPFIX protocol for encoding measured traffic information and information related to the traffic Observation Point, the traffic Metering Process, and the Exporting Process. Although developed for the IPFIX protocol, the model is defined in an open way that easily allows using it in other protocols, interfaces, and applications. [STANDARDS-TRACK]
Perspective security procedures for femtocell backbone

Femtocells provide a relatively new approach, how the mobile operator can extend the cellular network, using the IP based Internet connection as the backbone link, into places where it is hard to cover the area using traditional methods. Femtocells offer also a new scope of commercial services for the customer, attractive for both the customer and the mobile operator. Currently, the security, in the untrustworthy public environment, is accomplished via IPsec tunnel between the femtocell access point and femto security gateway. This approach is not an advantage in case where an appliance using network address translation is used. Moreover, IPsec was proposed for data transport not voice packet traffic, so that can cause an involuntary data overhead, increase end-to-end delay and decrease the quality of service. In this paper we have introduced alternative femtocell IP backbone security mechanisms using other higher level security protocols (TLS, DTLS, SRTP).