Miracle-dz/UniFAR-FTUs huggingface dataset:
High Dimensional Bayesian Optimization with Elastic Gaussian Process

Bayesian optimization is an efﬁcient way to optimize expensive black-box functions such as designing a new product with highest quality or tuning hyperparameter of a machine learning al-gorithm. However, it has a serious limitation when the parameter space is high-dimensional as Bayesian optimization crucially depends on solving a global optimization of a surrogate utility function in the same sized dimensions. The surrogate utility function, known commonly as acquisition function is a continuous function but can be extremely sharp at high dimension - having only a few peaks marooned in a large terrain of almost ﬂat surface. Global optimization algorithms such as DIRECT are infeasible at higher dimensions and gradient-dependent meth-ods cannot move if initialized in the ﬂat terrain. We propose an algorithm that enables local gradient-dependent algorithms to move through the ﬂat terrain by using a sequence of gross-to-ﬁner Gaussian process priors on the objective function as we leverage two underlying facts - a) there exists a large enough length-scales for which the acquisition function can be made to have a signiﬁcant gradient at any location in the parameter space, and b) the extrema of the consecutive acquisition functions are close although they are different only due to a small difference in the length-scales. Theoretical guarantees are provided and experiments clearly demonstrate the utility of the proposed method on both benchmark test functions and real-world case studies.
Asp–Tyr–Leu–Lys tetrapeptide inhibits airway inflammation in toluene‐2,4‐diisocyanate‐induced asthma mice

Background Airway inflammation and remodelling contribute to chronic airway obstruction of asthma. Currently, no medication effectively controls airway remodelling and related vascular changes. Therefore, new strategies need to be developed. The kringle 5 domain has anti‐angiogenic activity resulting from the tetrapeptide Lys–Leu–Tyr–Asp (KLYD).
Endometrial Adenocarcinoma Associated With Intrauterine Pregnancy A Report of Five Cases and a Review of the Literature

SummaryEndometrial adenocarcinoma associated with pregnancy is a rare lesion; only 14 acceptable examples have been reported in the literature. This study describes five additional examples with a critical review of the previously published cases. Four of the five women were nulliparous and three had sought medical intervention for infertility. The tumors were all well-differentiated endometrioid adenocarcinomas; three had a focal to extensive papillary pattern and three had focal to extensive squamous differentiation. Four were diagnosed at the time of dilatation and curettage and one at the time of cesarean section for a 28-week, live infant. Follow-up was available for four of the five women. Two women underwent hysterectomy with bilateral oophorectomy and were alive and well 12 and 48 months after diagnosis. The woman who had the live birth and the remaining woman were treated by repeat curettage with or without progesterone therapy, and each woman has had two subsequent full-term pregnancies with live births. These women are alive and well 57 and 58 months after diagnosis. Women with focal, well-differentiated carcinomas can successfully maintain their fertility if followed by repeat curettage with or without progesterone therapy.
Contribution of 111In-pentetreotide SPECT/CT imaging to conventional somatostatin receptor scintigraphy in the detection of neuroendocrine tumours

AimThe aim of the study was to assess the contribution of 111In-pentetreotide single-photon emission computed tomography/computed tomography (SPECT/CT) imaging to conventional somatostatin receptor scintigraphy (SRS) in terms of lesion characterization and localization in the detection of neuroendocrine tumours (NETs). Materials and methodsA total of 107 patients with suspected or confirmed NET underwent SRS and SPECT/CT after the injection of 148–222 MBq of 111In-pentetreotide. SRS and SPECT/CT images were interpreted independently. Each site of abnormal tracer uptake was recorded according to the anatomical localization, and as being consistent or not with NET. The findings were confirmed with pathological and/or clinical/imaging follow-up data. ResultsA final diagnosis of NET was achieved in 49/107 patients (45.8%). No evidence of NET was found in the rest. SPECT/CT resulted in a significant reduction of indeterminate cases [14/107 (13.1%) vs. 1/107 (0.9%); P<0.001] and correctly reclassified one patient as negative for NET and another as positive for NET. SPECT/CT had 87.8% sensitivity and 96.6% specificity on a patient-based analysis, statistically higher than SRS (P<0.001). A total of 160 foci were detected (108 NETs and 52 physiological/benign tumours). SRS correctly classified 105/160 foci (65.6%) and remained inaccurate for 55 lesions. These 55 included 31 indeterminate lesions, 12 lesions detected only by SPECT/CT and 12 false-positive lesions. The number of foci correctly classified on the SPECT/CT images was 151/160 (94.4%), whereas two remained indeterminate and seven were false-positive findings. ConclusionSPECT/CT provides incremental diagnostic value over SRS, mainly because of a precise anatomical localization that helps discriminate between tumour lesions and physiological uptake. SPECT/CT may detect unsuspected lesions in a small proportion of patients.
A novel horn radiator with high aperture efficiency and low cross-polarization and applications in arrays and multibeam reflector antennas

A step horn structure is presented that yields about 90% aperture efficiency with low cross-polar radiation. It is found that for obtaining high aperture efficiency, the horn aperture should consist of only the TE/sub z/ type of modes in appropriate amplitudes and phases. The desired TE/sub z/ modes are produced using multiple steps in the horn walls. The distances between the steps are critical to suppress the undesired TM/sub z/ modes. Radiation characteristics of high efficiency circular and square horns are presented and potential applications of such high efficiency horns are discussed.
Lessons learnt from the Named Entity rEcognition and Linking (NEEL) challenge series

This work was supported by the H2020 FREME project (GA no. 644771), by the research grant from Science Foundation Ireland (SFI) under Grant Number SFI/12/RC/2289, and by the CLARIAH-CORE project financed by the Netherlands Organisation for Scientific Research (NWO).
Nonlinear Controller Designs for Thermal Management in PCR Amplification

We have developed a theoretical model for a cascade two-stage Peltier device based on the electrothermal dynamics of Peltier modules and the heat balance equations of the interfacing materials. Both open- and closed-loop data are used to tune the scaling factors of the nonlinear model. The effectiveness of the model is validated over a large temperature range with the experimental data from a thermal cycling application of the Peltier device used to perform the polymerase chain reaction (PCR), a genetic amplification technique having important medical diagnostic applications. Based on the theoretical model, two novel nonlinear controllers are designed for a PCR cycling temperature profile. The first controller is an extension of conventional input-to-state feedback linearization design to a class of nonlinear systems that is not only affine on the control but also affine on the square of control inputs. The desired performance is achieved by tuning the parameters to control the convergent rates of the tracking errors. The second one is a switching controller design, which switches between a nonlinear pseudo-proportional-integral-differential (PID)/state feedback controller and a linear time-invariant proportional-integral (PI)/state feedback controller. A Lyapunov function method is used to develop the algorithm for the nonlinear controller, whose parameter values at the switching time are used in the linear controller. Such a combination of linear and nonlinear controllers could reduce the calculation burden and minimize the steady-state errors. Both controllers are tested with our simulation model and implemented in a microcontroller. We verified the designs with improved temperature tracking performances compared to our earlier linear switching design on reduced overshoots (<; 0.5 °C) and settling time (8-10 s faster). The modeling methodology and the feedback linearization-based controller design are scalable and both nonlinear designs can avoid future local model identifications when applied to different references, therefore, are easily extended to other thermal applications.
Reflective multi-agent model using semantic similarity measure and negotiation protocol for solving heterogeneity

Semantic similarity measures play important role in communication in an open and heterogeneous multi-agent system (MAS). A survey on similarity measures between concepts is afforded in this paper. We present these techniques, provide evaluations of their result performances, and discuss their shortcomings. We propose a measure by combining a psychological knowledge of the relevance, the resemblance and the non-symmetry of similarity. The proposed measure leads us to suggest a novel reflective agent model allowing agents to autonomously communicate between each other through semantic heterogeneity. The agent can enrich its own ontology by using semantic negotiation approach in several steps. We develop firstly, a model using an alignment ontology framework. Then, we improve a similarity measure to select the most similar pairs. Then, we suggest a protocol for supporting semantic negotiation. At the end, we present our experiments on many benchmark datasets proving that our results are more reasonable, we provide evaluations of some result performances of the existing semantic similarity metrics, and discuss their advantages and drawbacks.
Quantitative Real-Time PCR Detection of Rift Valley Fever Virus and Its Application to Evaluation of Antiviral Compounds

ABSTRACT The Rift Valley fever virus (RVFV), a member of the genusPhlebovirus (family Bunyaviridae) is an enveloped negative-strand RNA virus with a tripartite genome. Until 2000, RVFV circulation was limited to the African continent, but the recent deadly outbreak in the Arabian Peninsula dramatically illustrated the need for rapid diagnostic methods, effective treatments, and prophylaxis. A method for quantifying the small RNA segment by a real-time detection reverse transcription (RT)-PCR using TaqMan technology and targeting the nonstructural protein-coding region was developed, and primers and a probe were designed. After optimization of the amplification reaction and establishment of a calibration curve with synthetic RNA transcribed in vitro from a plasmid containing the gene of interest, real-time RT-PCR was assessed with samples consisting of RVFV from infected Vero cells. The method was found to be specific for RVFV, and it was successfully applied to the detection of the RVFV genome in animal sera infected with RVFV as well as to the assessment of the efficiency of various drugs (ribavirin, alpha interferon, 6-azauridine, and glycyrrhizin) for antiviral activity. Altogether, the results indicated a strong correlation between the infectious virus titer and the amount of viral genome assayed by real time RT-PCR. This novel method could be of great interest for the rapid diagnosis and screening of new antiviral compounds, as it is sensitive and time saving and does not require manipulation of infectious material.
Membrane-Associated Maturation of the Heterotetrameric Nitrate Reductase of Thermus thermophilus

ABSTRACT The nar operon, coding for the respiratory nitrate reductase of Thermus thermophilus (NRT), encodes a di-heme b-type (NarJ) and a di-heme c-type (NarC) cytochrome. The role of both cytochromes and that of a putative chaperone (NarJ) in the synthesis and maturation of NRT was studied. Mutants of T. thermophilus lacking either NarI or NarC synthesized a soluble form of NarG, suggesting that a putative NarCI complex constitutes the attachment site for the enzyme. Interestingly, the NarG protein synthesized by both mutants was inactive in nitrate reduction and misfolded, showing that membrane attachment was required for enzyme maturation. Consistent with its putative role as a specific chaperone, inactive and misfolded NarG was synthesized by narJ mutants, but in contrast to its Escherichia coli homologue, NarJ was also required for the attachment of the thermophilic enzyme to the membrane. A bacterial two-hybrid system was used to demonstrate the putative interactions between the NRT proteins suggested by the analysis of the mutants. Strong interactions were detected between NarC and NarI and between NarG and NarJ. Weaker interaction signals were detected between NarI, but not NarC, and both NarG and NarH. These results lead us to conclude that the NRT is a heterotetrameric (NarC/NarI/NarG/NarH) enzyme, and we propose a model for its synthesis and maturation that is distinct from that of E. coli. In the synthesis of NRT, a NarCI membrane complex and a soluble NarGJH complex are synthesized in a first step. In a second step, both complexes interact at the cytoplasmic face of the membrane, where the enzyme is subsequently activated with the concomitant conformational change and release of the NarJ chaperone from the mature enzyme.
Adaptive NN controller design for an autonomous underwater vehicle

In this paper, we present a nonlinear adaptive neural network controller design for free-pitch-angle diving behavior of an autonomous underwater vehicle (AUV). The dynamics of the AUV is simplified as a non-affine pure-feedback system with only one assumption. By applying adaptive neural network controller design with implicit function theorem, the difficulty in diving control of the AUV is overcome. Advantages of the proposed approach over previous methods include: the simplified dynamics has only one assumption; the output of the system is proven to converge to a small neighborhood of the desired trajectories and the control performance of the closed-loop system is also guaranteed by appropriately choosing the design parameters. Simulation studies are included to illustrate the proposed approach.
Identification of a Bile-Induced Exopolysaccharide Required for Salmonella Biofilm Formation on Gallstone Surfaces

ABSTRACT Salmonella enterica serovar Typhi can establish a chronic, asymptomatic infection of the human gallbladder, suggesting that this bacterium utilizes novel mechanisms to mediate enhanced colonization and persistence in a bile-rich environment. Gallstones are one of the most important risk factors for developing carriage, and we have previously demonstrated that salmonellae form biofilms on human gallstones in vitro. Thus, we hypothesize that bile-induced biofilms on gallstone surfaces promote gallbladder colonization and maintenance of the carrier state. A colanic acid/cellulose S. enterica serovar Typhimurium double mutant formed a mature biofilm on gallstones in a test tube assay and in a new, gallstone-independent assay using cholesterol-coated Eppendorf tubes. These data suggest the presence of an unidentified exopolysaccharide necessary for mature biofilm development and demonstrate specific binding affinity between salmonellae and cholesterol. Our experiments indicate that the Salmonella O-antigen capsule (yihU-yshA and yihV-yihW) is a crucial determinant in gallstone and cholesterol biofilms but that expression of this exopolysaccharide is not necessary for binding to glass or plastic. Real-time PCR revealed that growth in bile resulted in upregulation of the O-antigen capsule-encoding operon in an agfD-independent manner. Thus, the O-antigen capsule genes are bile induced, and the capsule produced by the enzymes of this operon is specifically required for biofilm formation on cholesterol gallstones. These studies provide new therapeutic targets for preventing asymptomatic serovar Typhi gallbladder carriage.
Rapid non‐genomic inhibition of ATP‐induced Cl− secretion by dexamethasone in human bronchial epithelium

A non‐genomic antisecretory role for dexamethasone at low concentrations (0.1 nm to1 μm) is described in monolayers of human bronchial epithelial cells in primary culture and in a continuous cell line (16HBE14o‐ cells). Dexamethasone produced a rapid decrease of [Ca2+]i (measured with fura‐2 spectrofluorescence) to a new steady‐state concentration. After 15 min exposure to dexamethasone (1 nm), [Ca2+]i was reduced by 32 ± 11 nm (n= 7, P < 0.0001) from a basal value of 213 ± 36 nm (n= 7). We have shown previously that aldosterone (1 nm) also produces a rapid fall in [Ca2+]i; however, after the decrease in [Ca2+]i induced by dexamethasone, subsequent addition of aldosterone did not produced any further lowering of [Ca2+]i. The rapid response to dexamethasone was insensitive to pretreatment with cycloheximide and unaffected by the glucocorticoid type II and mineralocorticoid receptor antagonists RU486 and spironolactone, respectively. The rapid [Ca2+]i decrease induced by dexamethasone was inhibited by the Ca2+‐ATPase pump inhibitor thapsigargin (1 μm), the adenylate cyclase inhibitor MDL hydrochloride (500 μm) and the protein kinase A inhibitor Rp‐adenosine 3′,5′‐cyclic monophosphorothioate (200 μm), but was not affected by the protein kinase C inhibitor, chelerythrine chloride (0.1 μm). Treatment of 16HBE14o‐ cell monolayers with dexamethasone (1 nm) inhibited the large and transient [Ca2+]i increase induced by apical exposure to ATP (10−4m). Dexamethasone (1 nm) also reduced by 30 % the Ca2+‐dependant Cl− secretion induced by apical exposure to ATP (measured as the Cl−‐sensitive short‐circuit current across monolayers mounted in Ussing chambers). Our results demonstrate, for the first time, that dexamethasone at low concentrations inhibits Cl− secretion in human bronchial epithelial cells. The rapid inhibition of Cl− secretion induced by the synthetic glucocorticoid is associated with a rapid decrease in [Ca2+]i via a non‐genomic mechanism that does not involve the classical glucocorticoid or mineralocorticoid receptor. Rather, it is a result of rapid non‐genomic stimulation of thapsigargin‐sensitive Ca2+‐ATPase, via adenylate cyclase and protein kinase A signalling.
Orbital Reconstruction After Eyelid- and Conjunctiva-Sparing Orbital Exenteration

Purpose: To describe the technique and results of eyelid- and conjunctiva-sparing orbital exenteration with temporalis transfer and dermis-fat graft. Methods: Five patients who underwent this procedure were studied, based on retrospective chart review. Schematic drawings were produced to illustrate the surgical technique. Results: The study included three female and two male patients with an age range of 7 to 76 years. Two patients required surgery for invasive optic nerve sheath meningioma, one for hemangiopericytoma, and the fourth for mesenchymal chondrosarcoma. The last patient had eyelid-sparing exenteration performed more than 20 years earlier for retinoblastoma and underwent a similar reconstruction. One case was complicated by infection and graft atrophy. The remaining four cases retained orbital volume and eyelid structures with a reasonable cosmetic outcome. Average follow-up period was 21 months, during which one patient had development of intracranial meningioma at the proximal end of the optic canal. Conclusions: Eyelid- and conjunctiva-sparing orbital exenteration with temporalis transfer and dermis-fat graft is a useful technique that minimizes the usual deformity and achieves good results. Case selection is emphasized, as this technique is mainly reserved for histopathologically benign orbital lesions that exhibit local aggressive behavior and for malignant lesions only if there is no eyelid, lacrimal gland, or orbital fissure involvement nor significant conjunctival or deep extension of an intraocular tumor.
The perception of risk messages regarding electromagnetic fields: extending the extended parallel process model to an unknown risk.

The Extended Parallel Process Model (EPPM) was developed as a model to assist in the development of effective risk communication messages, specifically messages that elicit adaptive behavioral responses. It has shown to be effective in several settings invoking clearly delineated dangers (e.g., safety belt usage, condom usage). Unfortunately, communicating risk messages is not always so straightforward. One increasing concern in the risk communication field is the controversy over electromagnetic fields (EMFs) and the uncertain hazards they present to individuals. The purpose of this study is to test the EPPM with this unknown risk and to explore which type of risk message may motivate adaptive behavioral responses. In accordance with the EPPM model, 251 participants received either a low- or high-threat risk message and a list of control measures they could use to reduce their exposure to EMFs. Results suggest that the EPPM model can be extended to an unknown risk.
Linked Open Data for content-based recommender systems

The World Wide Web is moving from a Web of hyper-linked Documents to a Web of linked Data. Thanks to the Semantic Web spread and to the more recent Linked Open Data (LOD) initiative, a vast amount of RDF data have been published in freely accessible datasets. These datasets are connected with each other to form the so called Linked Open Data cloud. The aim of LOD is to make available rich datasets to be used as the knowledge background of complex applications. As of today, there are tons of RDF data available in the Web of Data but only few applications really exploit their potential power. In this paper we show how these data can successfully be used to develop a recommender system (RS) that relies exclusively on the information encoded in the Web of Data. We implemented a content-based RS that leverages on the data available within Linked Open Data datasets (in particular DBpedia and LinkedMDB) in order to recommend movies to the end users. We extensively evaluated the approach and validated the effectiveness of the algorithms with precision and recall tests.
The reliability and predictive accuracy of the falls risk for older people in the community assessment (FROP-Com) tool.

BACKGROUND the Falls Risk for Older People in the Community assessment (FROP-Com) tool was designed for use in targeted multi-factorial falls prevention programmes. It fills the gap between the short screening tools and the longer assessment tools, e.g. the physiological profile assessment (PPA). The aim of this study was to determine the reliability and predictive accuracy of the FROP-Com. METHODS the intra-rater and inter-rater reliability studies were performed with 20 participants each. The prospective study was performed with 344 community-dwelling older people presenting to an emergency department after a fall and being discharged directly home. Following a home-based assessment, including the FROP-Com, Timed Up and Go (TUG) and functional Reach (FR), participants were monitored for falls for 12 months. RESULTS the intra-class correlation coefficient (ICC) for intra-rater reliability and inter-rater reliability for the FROP-Com was 0.93 (95% CI 0.84-0.97) and 0.81 (95% CI 0.59-0.92) respectively. The AUC for the FROP-Com was 0.68 (95% CI 0.63-0.74). At the cut-off 18/19, sensitivity was 71.3% (95% CI 64.4-78.3) and specificity was 56.1% (95% CI 48.9-63.4). The AUC for the TUG was 0.63 (95% CI 0.57-0.69) and for the FR was 0.60 (95% CI 0.54-0.66). CONCLUSION the FROP-Com demonstrated good reliability and a moderate capacity to predict falls.