Miracle-dz/UniFAR-FTUs huggingface dataset:
Intestinal Proportion of Blautia sp. is Associated with Clinical Stage and Histoprognostic Grade in Patients with Early-Stage Breast Cancer

ABSTRACT Improving knowledge about breast cancer etiology is crucial in order to propose prevention strategies for this pathology. Gut microbiota is involved in numerous physiopathological situations including cancers. Although its potential involvement in breast cancer through the alteration of the enterohepatic circulation of estrogens and/or the metabolism of phytoestrogens has been discussed for some time, it remains to be demonstrated. The present study seeks to strengthen this hypothesis by identifying possible links between the fecal microbiota composition and clinical characteristics in breast cancer patients. Bacterial DNA was extracted from the feces of 31 patients with early-stage breast cancer and amplified by real-time polymerase chain reaction (qPCR), targeting 16S rRNA sequences specific to bacterial groups, and then analyzed in relation to clinical characteristics. The absolute numbers of total bacteria and of three bacterial groups (Firmicutes, Faecalibacterium prausnitzii, and Blautia) differed significantly according to the patient's body mass index. The percentage and the absolute numbers of certain bacterial groups, namely C. coccoides, F. prausnitzii, and Blautia, differed significantly according to the clinical stages and the histoprognostic grades. Our study highlighted that intestinal microbiota composition in these patients differs according to clinical characteristics and BMI. Further studies are required to clarify the link between breast cancer and intestinal microbiota.
A Method of Nonlinear Damage Analysis for Anisotropic Materials and Its Application to Thin Composite Laminates

A method of analysis describing the damage response of anisotropic brittle materials introduced earlier by the authors is generalized based on the concepts of damage surface and damage potential. The applicability and validity of the method is demonstrated by characterizing, for the first instance, the behavior of composite lamina, and then, the damage response of thin, continuous, and symmetric composite laminate subjected to in- plane loading. The global constitutive equation of the laminate with damage is derived from that of lamina and its interaction with other laminae. The method developed is finally applied to examine damage characteristics of angle-ply laminates subjected to in-plane loading, and a satisfactory agreement between the predicted and experimental results dem onstrates the viability of the proposed method.
Simultaneous magnetic resonance diffusion and pseudo‐diffusion tensor imaging

An emerging topic in diffusion magnetic resonance is imaging blood microcirculation alongside water diffusion using the intravoxel incoherent motion (IVIM) model. Recently, a combined IVIM diffusion tensor imaging (IVIM‐DTI) model was proposed, which accounts for both anisotropic pseudo‐diffusion due to blood microcirculation and anisotropic diffusion due to tissue microstructures. In this article, we propose a robust IVIM‐DTI approach for simultaneous diffusion and pseudo‐diffusion tensor imaging.
Neutralization of Clostridium difficile Toxin B Mediated by Engineered Lactobacilli That Produce Single-Domain Antibodies

ABSTRACT Clostridium difficile is the primary cause of nosocomial antibiotic-associated diarrhea in the Western world. The major virulence factors of C. difficile are two exotoxins, toxin A (TcdA) and toxin B (TcdB), which cause extensive colonic inflammation and epithelial damage manifested by episodes of diarrhea. In this study, we explored the basis for an oral antitoxin strategy based on engineered Lactobacillus strains expressing TcdB-neutralizing antibody fragments in the gastrointestinal tract. Variable domain of heavy chain-only (VHH) antibodies were raised in llamas by immunization with the complete TcdB toxin. Four unique VHH fragments neutralizing TcdB in vitro were isolated. When these VHH fragments were expressed in either secreted or cell wall-anchored form in Lactobacillus paracasei BL23, they were able to neutralize the cytotoxic effect of the toxin in an in vitro cell-based assay. Prophylactic treatment with a combination of two strains of engineered L. paracasei BL23 expressing two neutralizing anti-TcdB VHH fragments (VHH-B2 and VHH-G3) delayed killing in a hamster protection model where the animals were challenged with spores of a TcdA− TcdB+ strain of C. difficile (P < 0.05). Half of the hamsters in the treated group survived until the termination of the experiment at day 5 and showed either no damage or limited inflammation of the colonic mucosa despite having been colonized with C. difficile for up to 4 days. The protective effect in the hamster model suggests that the strategy could be explored as a supplement to existing therapies for patients.
COMPARISON-BASED APPLICATIONS FOR FULLY HOMOMORPHIC ENCRYPTED DATA

The cloud computing providers need to offer security warranties. As we all know, one of the critical points is the confidentiality and access to customer data which, these days, is migrated and managed in cloud environments. In this sense, one solution is based on encrypting data before its upload in cloud. But this approach sets a limit regarding data processing. In this article we present a practical application of the homomorphic encryption schemes, namely the problem of finding maximum/minimum from a collection of encrypted integers. First, we present our algorithm that can be run directly in cloud without the need for an intermediate data exchange with the client. Second, our experimental results show the time resources necessary to evaluate the proposed algorithm.
Graph fourier transform based descriptor for gesture classification

This paper proposes a method for gesture classification based on Graph Fourier transform (GFT) coefficients. GFT coefficients are the projection of image pixel block onto the eigenvectors of a Laplacian matrix. This Laplacian matrix is generated from undirected graph, representing a spatial connectedness between each pixel within an image block. This work proposes a method for generating an undirected graph by using edge information of the image. Edge information of the image is obtained by average sum of absolute difference between the current pixel and its neighboring pixels by using an appropriate threshold. The resulting GFT based feature vector is formed by concatenating GFT coefficients of each block. The resultant feature vector is applied to linear Support Vector Machine (SVM) classifier to predict the gesture class. For NTU and Massey hand gesture datasets, threshold value 30 gives maximum prediction accuracy. We compare the results of the proposed GFT based descriptor approach with Karhunen-Loeve transform (K-LT) and Discrete Cosine transform (DCT) based descriptors on three different gesture datasets: NTU, Cambridge and Massey. Simulation results show that the proposed GFT based descriptor gives a comparable results with Karhunen-Loeve transform (K-LT) and Discrete Cosine transform (DCT) based descriptors for gesture classification.
Motion magnification for endoscopic surgery

Endoscopic and laparoscopic surgeries are used for many minimally invasive procedures but limit the visual and haptic feedback available to the surgeon. This can make vessel sparing procedures particularly challenging to perform. Previous approaches have focused on hardware intensive intraoperative imaging or augmented reality systems that are difficult to integrate into the operating room. This paper presents a simple approach in which motion is visually enhanced in the endoscopic video to reveal pulsating arteries. This is accomplished by amplifying subtle, periodic changes in intensity coinciding with the patient’s pulse. This method is then applied to two procedures to illustrate its potential. The first, endoscopic third ventriculostomy, is a neurosurgical procedure where the floor of the third ventricle must be fenestrated without injury to the basilar artery. The second, nerve-sparing robotic prostatectomy, involves removing the prostate while limiting damage to the neurovascular bundles. In both procedures, motion magnification can enhance subtle pulsation in these structures to aid in identifying and avoiding them.
Type checking through unification

In this paper we describe how to leverage higher-order unification to type check a dependently typed language with meta-variables. The literature usually presents the unification algorithm as a standalone component, however the need to check definitional equality of terms while type checking gives rise to a tight interplay between type checking and unification. This interplay is a major source of complexity in the type-checking algorithm for existing dependently typed programming languages. We propose an algorithm that encodes a type-checking problem entirely in the form of unification constraints, reducing the complexity of the type-checking code by taking advantage of higher order unification, which is already part of the implementation of many dependently typed languages.
Respiratory outcomes after initial hospital discharge in children with ventricular shunts and bronchopulmonary dysplasia

Children born premature who require ventricular shunt placement for post hemorrhagic hydrocephalus are at increased risk for neurodevelopmental delay. We hypothesized that preterm infants with bronchopulmonary dysplasia (BPD) who require ventricular shunt (VS) placement are at additive risk for long‐term respiratory morbidities due to their higher likelihood of neurodevelopmental delay. We also hypothesized that children with BPD and ventricular shunts would require frequent shunt revisions during early childhood following initial shunt placement.
Anodes Stimulate Anaerobic Toluene Degradation via Sulfur Cycling in Marine Sediments

ABSTRACT Hydrocarbons released during oil spills are persistent in marine sediments due to the absence of suitable electron acceptors below the oxic zone. Here, we investigated an alternative bioremediation strategy to remove toluene, a model monoaromatic hydrocarbon, using a bioanode. Bioelectrochemical reactors were inoculated with sediment collected from a hydrocarbon-contaminated marine site, and anodes were polarized at 0 mV and +300 mV (versus an Ag/AgCl [3 M KCl] reference electrode). The degradation of toluene was directly linked to current generation of up to 301 mA m−2 and 431 mA m−2 for the bioanodes polarized at 0 mV and +300 mV, respectively. Peak currents decreased over time even after periodic spiking with toluene. The monitoring of sulfate concentrations during bioelectrochemical experiments suggested that sulfur metabolism was involved in toluene degradation at bioanodes. 16S rRNA gene-based Illumina sequencing of the bulk anolyte and anode samples revealed enrichment with electrocatalytically active microorganisms, toluene degraders, and sulfate-reducing microorganisms. Quantitative PCR targeting the α-subunit of the dissimilatory sulfite reductase (encoded by dsrA) and the α-subunit of the benzylsuccinate synthase (encoded by bssA) confirmed these findings. In particular, members of the family Desulfobulbaceae were enriched concomitantly with current production and toluene degradation. Based on these observations, we propose two mechanisms for bioelectrochemical toluene degradation: (i) direct electron transfer to the anode and/or (ii) sulfide-mediated electron transfer.
Subtractive Methods for Forming Microfluidic Gels of Extracellular Matrix Proteins

Microfluidic networks in extracellular matrix hydrogels hold great promise in tissue engineering. We have established two methods for forming microscale channels within collagen and fibrin gels. Both methods rely on molding gels around removable elements: stainless steel needles for creating single channels and gelatin meshes for forming networks of interconnected channels. These methods can form single channels 50 µm or more in diameter or networks 6 µm or more in width, at a rate of 5 to 10 samples per day. Potential applications include using microfluidic gels for engineering microvascular networks, perfusing cultured cells within native scaffolds, and controlling interstitial flows in cell culture models.
Thyroid follicular adenomas and carcinomas: molecular profiling provides evidence for a continuous evolution

Non-autonomous thyroid nodules are common in the general population with a proportion found to be cancerous. A current challenge in the field is to be able to distinguish benign adenoma (FA) from preoperatively malignant thyroid follicular carcinoma (FTC), which are very similar both histologically and genetically. One controversial issue, which is currently not understood, is whether both tumor types represent different molecular entities or rather a biological continuum. To gain a better insight into FA and FTC tumorigenesis, we defined their molecular profiles by mRNA and miRNA microarray. Expression data were analyzed, validated by qRT-PCR and compared with previously published data sets. The majority of deregulated mRNAs were common between FA and FTC and were downregulated, however FTC showed additional deregulated mRNA. Both types of tumors share deregulated pathways, molecular functions and biological processes. The additional deregulations in FTC include the lipid transport process that may be involved in tumor progression. The strongest candidate genes which may be able to discriminate follicular adenomas and carcinomas, CRABP1, FABP4 and HMGA2, were validated in independent samples by qRT-PCR and immunohistochemistry. However, they were not able to adequately classify FA or FTC, supporting the notion of continuous evolving tumors, whereby FA and FTC appear to show quantitative rather than qualitative changes. Conversely, miRNA expression profiles showed few dysregulations in FTC, and even fewer in FA, suggesting that miRNA play a minor, if any, role in tumor progression.
SlLAX1 is Required for Normal Leaf Development Mediated by Balanced Adaxial and Abaxial Pavement Cell Growth in Tomato

Leaves are the major plant organs with a primary function for photosynthesis. Auxin controls various aspects of plant growth and development, including leaf initiation, expansion and differentiation. Unique and intriguing auxin features include its polar transport, which is mainly controlled by the AUX1/LAX and PIN gene families as influx and efflux carriers, respectively. The role of AUX1/LAX genes in root development is well documented, but the role of these genes in leaf morphogenesis remains unclear. Moreover, most studies have been conducted in the plant model Arabidopsis thaliana, while studies in tomato are still scarce. In this study, we isolated six lines of the allelic curly leaf phenotype 'curl' mutants from a γ-ray and EMS (ethyl methanesulfonate) mutagenized population. Using a map-based cloning strategy combined with exome sequencing, we observed that a mutation occurred in the SlLAX1 gene (Solyc09g014380), which is homologous to an Arabidopsis auxin influx carrier gene, AUX1 (AtAUX1). Characterization of six alleles of single curl mutants revealed the pivotal role of SlLAX1 in controlling tomato leaf flatness by balancing adaxial and abaxial pavement cell growth, which has not been reported in tomato. Using TILLING (Targeting Induced Local Lesions IN Genome) technology, we isolated an additional mutant allele of the SlLAX1 gene and this mutant showed a curled leaf phenotype similar to other curl mutants, suggesting that Solyc09g014380 is responsible for the curl phenotype. These results showed that SlLAX1 is required for normal leaf development mediated by balanced adaxial and abaxial pavement cell growth in tomato.
A Remote Aerial Robot for Topographic Survey

In this paper a seminal system for the topographic survey with an unmanned aerial robot is presented. The proposed system has demonstrated the feasibility of acquiring initial 3D ground models using active laser range sensors on a low-flying helicopter platform. The robot system consists of a remote control helicopter with a laser sensor and a GPS (global positioning system) for collecting ground point data and a post-processing data sub-system for drawing a topographic map. This robot system has many potential applications, such as terrain modeling, structure inspection or climate and weather measurement, etc. The experiment results verify the proposal robot system for topographic survey
Molecular classification of autofluorescence excision margins in oral potentially malignant disorders.

OBJECTIVE To define molecular differences between autofluorescence and white light defined excision margins in oral potentially malignant disorders (OPMD) using transcriptome expression profiles. MATERIALS AND METHODS Excisional biopsy specimens were taken from 11 patients at three different sites for each lesion: centre, white light margin and autofluorescence margin. The lesions were diagnosed histopathologically as oral epithelial dysplasia, oral lichenoid dysplasia, oral lichen planus or other. Transcriptome analysis was performed by RNA sequencing, hierarchical clustering, differential expression and biological pathway analysis. RESULTS For hierarchical clustering, the samples broadly clustered according to histology rather than the margins with lichenoid samples clustering together. Differential expression analysis showed that independent of histology, there was greater molecular dysregulation between the lesion centre and autofluorescence margin compared to the lesion centre and white light margin. Furthermore, the autofluorescence and white light margins were molecularly distinct, indicating the white light margins harboured abnormality. CONCLUSION Our results indicate that the molecular profile of OPMD changes with divergence away from the centre of the lesion, and that autofluorescence determined margins are superior to the white light margin in achieving a clear molecular margin when excising an OPMD.
Nanomedicine for immunosuppressive therapy: achievements in pre-clinical and clinical research

ABSTRACT Introduction: Immunosuppression is the mainstay therapy in organ transplantation and autoimmune diseases. The effective clinical application of immunosuppressive agents has suffered from the emergence of systemic immunosuppression and/or individual drug side effects. Nanotechnology approaches may be used to modify the mentioned shortcomings by enhancing the delivery of immunosuppressants to target cells of the immune system, thus reducing the required dose for function, and/or reducing drug distribution to non-target tissues. Areas covered: We provide an overview on the development of nanotechnology products for the most commonly used immunosuppressive agents. At first, the rationale for the use of nanoparticles as means for immunosuppressive therapy is discussed. This is followed by a review of major accomplishments in this area, particularly in preclinical in vivo studies. Expert opinion: The results of research conducted in this area to date, points to a great promise for nano-medicine in increasing the bioavailability, reducing the toxicity, and/or potentiating the activity of immunosuppressive agents. It is, therefore, safe to speculate the more rapid translation of nanotechnologyin clinical immunosuppressive therapy in the near future providing to the overcoming of hurdles associated with nano-drug delivery such as high cost, inadequate reproducibility and potential safety concerns of the delivery systems themselves.
Preliminary study of genetic diversity and population structure of the Relict Gull Larus relictus (Charadriiformes Laridae) using mitochondrial and nuclear genes

Abstract The genetic diversity and the population history of the Relict Gull (Larus relictus) were studied based on the sequences of two mitochondrial genes (Cyt b and ND2) and one nuclear gene (the third intron of the Z-linked muscle-specific kinase gene [MUSK]) from 47 individuals. The results showed that the population expresses very low genetic diversity while lacking large geographical population. Demographic history analysis suggested that population expansion might have been recent and that the average estimated expansion time of L. relictus is from 0.09 to 0.23 Ma BP. Whether the other three breeding subpopulations are involved in the Ordos breeding subpopulation, require further study with more effective molecular markers. The species is threatened by habitat loss and fragmentation, and actions to protect it are suggested to improve the population fragmentation of breeding.
Trading Delay for Distortion in One-Way Video Communication Over the Internet

We study the problem of one-way video communication in a single-source, multiple-destination scenario over the lossy Internet. Forward error correction (FEC) coding is commonly adopted for data protection in implementing loss-resilient video transmission systems. However, the burst packet losses over the Internet frequently degrade FEC performance and induce video quality deteriorations. To address the challenging problem, we propose a novel transmission scheme dubbed trading delay for distortion (TELFORD) that includes three components: 1) adaptive multidestination status estimation; 2) delay-constrained transmission rate assignment; and 3) differentiated FEC packet spreading. We analytically formulate and solve the problem of FEC packet allocation and scheduling to minimize the end-to-end video distortion. The proposed TELFORD is able to cope with multiple-destination scheduling separately. We conduct performance evaluation through semiphysical emulations in Exata using real-time H.264 video streaming. Experimental results show that TELFORD outperforms existing error control transmission schemes in improving the video peak signal-to-noise ratio and mitigating packet transmission impairments.
Functional Mutation of Multiple Solvent-Exposed Loops in the Ecballium elaterium Trypsin Inhibitor-II Cystine Knot Miniprotein

Background The Ecballium elaterium trypsin inhibitor (EETI-II), a 28-amino acid member of the knottin family of peptides, contains three interwoven disulfide bonds that form multiple solvent-exposed loops. Previously, the trypsin binding loop of EETI-II has been engineered to confer binding to several alternative molecular targets. Here, EETI-II was further explored as a molecular scaffold for polypeptide engineering by evaluating the ability to mutate two of its structurally adjacent loops. Methodology/Principal Findings Yeast surface display was used to engineer an EETI-II mutant containing two separate integrin binding epitopes. The resulting knottin peptide was comprised of 38 amino acids, and contained 11- and 10-residue loops compared to wild-type EETI-II, which naturally contains 6- and 5-residue loops, respectively. This knottin peptide bound to αvβ3 and αvβ5 integrins with affinities in the low nanomolar range, but bound weakly to the related integrins α5β1 and αiibβ3. In addition, the engineered knottin peptide inhibited tumor cell adhesion to vitronectin, an extracellular matrix protein that binds to αvβ3 and αvβ5 integrins. A 64Cu radiolabeled version of this knottin peptide demonstrated moderate serum stability and excellent tumor-to-muscle and tumor-to-blood ratios by positron emission tomography imaging in human tumor xenograft models. Tumor uptake was ∼3–5% injected dose per gram (%ID/g) at one hour post injection, with rapid clearance of probe through the kidneys. Conclusions/Significance We demonstrated that multiple loops of EETI-II can be mutated to bind with high affinity to tumor-associated integrin receptors. The resulting knottin peptide contained 21 (>50%) non-native amino acids within two mutated loops, indicating that extended loop lengths and sequence diversity were well tolerated within the EETI-II scaffold. A radiolabeled version of this knottin peptide showed promise for non-invasive imaging of integrin expression in living subjects. However, reduced serum and metabolic stability were observed compared to an engineered integrin-binding EETI-II knottin peptide containing only one mutated loop.