Miracle-dz/UniFAR-FTUs huggingface dataset:
High prevalence of plasmid-mediated quinolone resistance determinants in commensal members of the Enterobacteriaceae in Ho Chi Minh City, Vietnam

Antimicrobial-resistant pathogenic members of the Enterobacteriaceae are a well-defined global problem. We hypothesized that one of the main reservoirs of dissemination of antimicrobial resistance genes in Vietnam is non-pathogenic intestinal flora, and sought to isolate antimicrobial-resistant organisms from hospitalized patients and non-hospitalized healthy individuals in Ho Chi Minh City. The results identified substantial faecal carriage of gentamicin-, ceftazidime- and nalidixic acid-resistant members of the Enterobacteriaceae in both hospitalized patients and non-hospitalized healthy individuals. A high prevalence of quinolone resistance determinants was identified, particularly the qnrS gene, in both community- and hospital-associated strains. Furthermore, the results demonstrated that a combination of quinolone resistance determinants can confer resistance to nalidixic acid and ciprofloxacin, even in the apparent absence of additional chromosomal resistance mutations in wild-type strains and laboratory strains with transferred plasmids. These data suggest that intestinal commensal organisms are a significant reservoir for the dissemination of plasmid-mediated quinolone resistance in Ho Chi Minh City.
Composite luminosity function of cluster galaxies

We constructed the composite Luminosity Function (LF) of cluster galaxies in the g,r and i bands from the photometry of a mixed (Abell and X-ray selected) sample of the cores of 65 clusters, ranging in redshift from 0.05 to 0.25. The composite LF has been obtained from complete samples of ~2200 galaxies in the magnitude range -23<M<-17.5 (-18 in i). Cluster membership has been determined on the basis of color-color plots for each cluster and the resulting outlier counts have been checked against field counts in the same bands. We find that the galaxy density of the environment determines the shape of the LF, in the sense that bright galaxies are more abundant in dense clusters.
Imaging Ladar for 3-D Surveying and CAD Modeling of Real-World Environments

To establish mobile robot operations and to realize survey and inspection tasks, robust and precise measurements of the geometry of the 3-D environment is a required basic sensor technology. For visual inspection, surface classification, and documentation purposes, however, additional information concerning reflectance of measured objects is necessary. High-speed acquisition of both geometric and visual information is achieved by the described active ladar, developed by Zoller and Fröhlich (Z+F). In contrast to other range-sensing devices, the Z+F system is designed for high-speed and high-performance operation in real indoor and outdoor environments, emitting a minimum of near-infrared laser energy. It integrates a single-point laser measurement system and a mechanical deflection system for 3-D environmental measurements. Experimental results are reported from surface inspections in tunnels, the generation of 3-D CAD models of a work cell in an automotive manufacturing plant, the modeling of free-form surfaces such as historic sculptures, and applications in mobile robot navigation.
Interactive visualization of assembly instruction for stone tools restoration

3D exploded views have been widely used for assembly instructions in many fields but have seldom been used in archaeology. For studying stone tools, relics are repeatedly assembled using indistinct traditional illustrations. We apply this powerful presentation technique on the stone tool models, and study algorithms for point cloud data. In addition to presenting principles for the restoration of stone tools, we designed our system based on archaeological rules. In this paper, we propose an interactive visualization method of assembly instruction using 3D visualization technology to assist in the efficient restoration of stone tools.
k-Nearest Neighbors on Road Networks: A Journey in Experimentation and In-Memory Implementation

A k nearest neighbor (kNN) query on road networks retrieves the k closest points of interest (POIs) by their network distances from a given location. Today, in the era of ubiquitous mobile computing, this is a highly pertinent query. While Euclidean distance has been used as a heuristic to search for the closest POIs by their road network distance, its efficacy has not been thoroughly investigated. The most recent methods have shown significant improvement in query performance. Earlier studies, which proposed disk-based indexes, were compared to the current state-of-the-art in main memory. However, recent studies have shown that main memory comparisons can be challenging and require careful adaptation. This paper presents an extensive experimental investigation in main memory to settle these and several other issues. We use efficient and fair memory-resident implementations of each method to reproduce past experiments and conduct additional comparisons for several overlooked evaluations. Notably we revisit a previously discarded technique (IER) showing that, through a simple improvement, it is often the best performing technique.
Genetic polymorphisms of CYP2D6*10 and CYP2C19*2, *3 are not associated with prognosis, endometrial thickness, or bone mineral density in Japanese breast cancer patients treated with adjuvant tamoxifen

BACKGROUND: The authors investigated the impact of the genetic polymorphisms cytochrome P450 (CYP) family 2, subfamily D, polypeptide 6, allele *10 (CYP2D6*10) and CYP family 2, subfamily C, polypeptide 19, allele *2,*3 (CYP2C19*2,*3) on disease recurrence in patients with breast cancer who received adjuvant tamoxifen and evaluated the impact of those polymorphisms on endometrial thickness, bone mineral density (BMD), and serum total cholesterol levels. METHODS: Patients with primary breast cancer (n=173) who had hormone receptor-positive tumors and who also received adjuvant tamoxifen were included in the current study. Genetic polymorphisms of CYP2D6*10 and CYP2C19*2,*3 were analyzed. RESULTS: Recurrence-free survival (RFS) rates did not differ significantly between patients with the CYP2D6 *10/*10 genotype (n=40) and patients with the CYP2D6 wild-type (wt)/wt or wt/*10 genotype (n=133) or between patients with the CYP2C19 *2/*2, *2/*3, or *3/*3 genotypes (n=41) and patients with the CYP2C19 wt/wt, wt/*2, or wt/*3 genotype (n=132). Multivariate analysis indicated that, even after adjustment for well established prognostic factors, these CYP2D6 or CYP2C19 genotypes were not associated significantly with the RFS rate. Moreover, these genotypes did not affect endometrial thickness, BMD, or total cholesterol levels 1 year after the start of tamoxifen treatment. CONCLUSIONS: Neither the CYP2D6 *10/*10 genotype nor the CYP2C19 genotype is likely to have a clinically significant impact on prognosis, endometrial thickness, BMD, or total cholesterol levels in Japanese patients with breast cancer who are treated with adjuvant tamoxifen. Cancer 2009. © 2009 American Cancer Society.
Molecular Recognition of the Catalytic Zinc(II) Ion in MMP-13: Structure-Based Evolution of an Allosteric Inhibitor to Dual Binding Mode Inhibitors with Improved Lipophilic Ligand Efficiencies

Matrix metalloproteinases (MMPs) are a class of zinc dependent endopeptidases which play a crucial role in a multitude of severe diseases such as cancer and osteoarthritis. We employed MMP-13 as the target enzyme for the structure-based design and synthesis of inhibitors able to recognize the catalytic zinc ion in addition to an allosteric binding site in order to increase the affinity of the ligand. Guided by molecular modeling, we optimized an initial allosteric inhibitor by addition of linker fragments and weak zinc binders for recognition of the catalytic center. Furthermore we improved the lipophilic ligand efficiency (LLE) of the initial inhibitor by adding appropriate zinc binding fragments to lower the clogP values of the inhibitors, while maintaining their potency. All synthesized inhibitors showed elevated affinity compared to the initial hit, also most of the novel inhibitors displayed better LLE. Derivatives with carboxylic acids as the zinc binding fragments turned out to be the most potent inhibitors (compound 3 (ZHAWOC5077): IC50 = 134 nM) whereas acyl sulfonamides showed the best lipophilic ligand efficiencies (compound 18 (ZHAWOC5135): LLE = 2.91).
Functional limitations in the phase of clinically suspect arthralgia are as serious as in early clinical arthritis; a longitudinal study

Introduction A phase of arthralgia may precede the emergence of rheumatoid arthritis (RA). Although several studies have focused on biomarkers, the relevance of this phase for patients is less studied. It is unknown if patients already have functional limitations and if this is correlated to the extent of subclinical inflammation. Therefore, we assessed functional disability in patients with clinically suspect arthralgia (CSA), its association with MRI-detected subclinical inflammation and its course during progression to clinical arthritis. Methods From April 2012 to March 2015, 241 patients had arthralgia for <1 year and were, based on clinical presentation, considered at risk for RA by their rheumatologists. At baseline, Health Assessment Questionnaire (HAQ) scores were determined and unilateral 1.5 T MRI of metacarpophalangeal, wrist and metatarsophalangeal joints were made. Presence of MRI-detected subclinical inflammation was assessed by summing synovitis, tenosynovitis and bone marrow oedema scores (range 0–189). Patients were followed on arthritis development and HAQ scores were repeated when clinical arthritis had developed. Results The median HAQ score at presentation with CSA was 0.50. Higher MRI-inflammation scores were associated with higher HAQ scores (β=0.017, 95% CI=0.004 to 0.030). During median 103 weeks follow-up, 44 patients progressed to clinical arthritis. HAQ scores ≥1.0 were associated with arthritis development (HR=2.50, 95% CI=1.03 to 6.10). Within converters, median HAQ scores did not increase from presentation with CSA to arthritis development (0.88 and 0.75, p=0.36). Conclusions HAQ scores ≥1.0 at presentation were associated with the development of clinical arthritis. Functional limitations in the prearthritis phase of CSA were as serious as in the early clinical phase, demonstrating the relevance of CSA from patients’ perspectives.
Experimental evidence that women's mate preferences are directly influenced by cues of pathogen prevalence and resource scarcity

When choosing a mate, women are thought to face a trade-off between genetic and parental quality. Recent research suggests that this trade-off is influenced by environmental factors such as pathogen prevalence and resource scarcity, which affect the relative value of genetic and parental quality to offspring fitness. To further investigate these findings, the current study primed 60 women with pathogen prevalence, resource scarcity or an irrelevant threat, before administering a forced trade-off task that assessed mate preferences for traits thought to be indicative of genetic or parental quality. Women primed with pathogen prevalence revealed greater preferences for traits indicative of genetic quality at the expense of traits indicative of parental quality. The reverse was found for women primed with resource scarcity. These findings suggest that environmental factors may directly influence women's mate preferences owing to evolved plasticity, such that mate preferences are flexible in response to environmental factors.
Changing partners in an obligate symbiosis: a facultative endosymbiont can compensate for loss of the essential endosymbiont Buchnera in an aphid

Almost all aphids harbour an endosymbiotic bacterium, Buchnera aphidicola, in bacteriocytes. Buchnera synthesizes essential nutrients and supports growth and reproduction of the host. Over the long history of endosymbiosis, many essential genes have been lost from the Buchnera genome, resulting in drastic genome reduction and the inability to live outside the host cells. In turn, when deprived of Buchnera, the host aphid suffers retarded growth and sterility. Buchnera and the host aphid are often referred to as highly integrated almost inseparable mutualistic partners. However, we discovered that, even after complete elimination of Buchnera, infection with a facultative endosymbiotic γ-proteobacterium called pea aphid secondary symbiont (PASS) enabled survival and reproduction of the pea aphid. In the Buchnera-free aphid, PASS infected the cytoplasms of bacteriocytes that normally harbour Buchnera, establishing a novel endosymbiotic system. These results indicate that PASS can compensate for the essential role of Buchnera by physiologically and cytologically taking over the symbiotic niche. By contrast, PASS negatively affected the growth and reproduction of normal host aphids by suppressing the essential symbiont Buchnera. These findings illuminate complex symbiont-symbiont and host-symbiont interactions in an endosymbiotic system, and suggest a possible evolutionary route to novel obligate endosymbiosis by way of facultative endosymbiotic associations.
A prospective study of the parent–baby bond in men and women 15 months after birth

Objective: To prospectively examine the impact of parental mental health (PTSD, depression and anxiety), the couple’s relationship quality and the infant temperament on the parent–baby bond in first-time mothers and fathers. Background: Evidence suggests that poor parental mental health, difficult infant temperament and/or lower quality of the couple’s relationship may impede the parent–baby bond. However, little research has included both parents or followed these measures across time. Methods: 75 women and 66 men completed questionnaire measures during pregnancy, 3 and 15 months postpartum, assessing mental health symptoms, the parent–baby bond, the couple’s relationship and infant characteristics. The response rates at different time-points were 90%, 77% and 70%. Results: The parent–baby bond was associated with parental mental health, the couple’s relationship and infant characteristics. The most important predictors of the parent–baby bond three months postpartum for both men and women were the couple’s relationship during pregnancy and their baby’s temperament at three months. At 15 months postpartum, after accounting for the parent–baby bond at 3 months, only concurrent infant temperament remained a significant predictor for women. However, men’s bond with their baby at 15 months was predicted by their relationship with their partner in pregnancy and concurrent affective symptoms. Few significant gender differences were found, apart from women reporting more mental health symptoms than men. Conclusion: This study highlights the significance of the couple’s relationship in pregnancy and the infant’s temperament on the development of the parent–baby bond. Future research is needed to examine this in larger more representative samples.
A method for head related impulse response simplification

We present a method to extract a common subsystem from a HRIR dataset to allow for easier real-time convolution in interactive audio environments and more efficient HRIR interpolation. An iterative least squares method is described for this deconvolution operation, and the relation of this method to that of finding the approximate greatest common divisor of polynomial systems is discussed.
Direct nose-brain transport of benzoylecgonine following intranasal administration in rats.

In our previous research, cocaine applied intranasally in rats diffused or was transported directly from the nasal cavity to the brain. However, the direct nose-brain cocaine transport only contributes to an initial increase in the relative cocaine brain exposure. In this study, we have determined the nose-brain transport of a polar metabolite of cocaine, benzoylecgonine, to help understand factors affecting drug transport via this novel pathway. The nasal cavity of male Sprague-Dawley rats was isolated to prevent drainage of nasally applied dosing solution to non-nasal regions. Benzoylecgonine was then administered, either by intranasal administration or by intravenous (iv) injection. At different times postdose, blood and tissues from different regions of the brain were collected from groups of rats (n = 4 for each collection time) and benzoylecgonine concentrations in these samples were analyzed by high-performance liquid chromatography. Benzoylecgonine concentrations in plasma were at maximal levels immediately after iv dosing and declined as a function of time. Following intranasal administration, benzoylecgonine concentrations in plasma reached maximal levels between 15 and 30 min after dosing and declined as a function of time. To allow comparison of brain benzoylecgonine content after iv and intranasal administration, brain benzoylecgonine contents were normalized by plasma benzoylecgonine concentrations. The ratios of the area under the benzoylecgonine concentration-time curve (AUC) between the olfactory bulb and plasma following intranasal administration were 10-100 times higher than those obtained after iv dosing. The olfactory tract-to-plasma benzoylecgonine AUC ratios after intranasal administration were significantly higher than those after iv dosing up to 120 min following dosing. The brain tissue-to-plasma AUC ratios in cerebellum, brain stem, and cerebral cortex after intranasal administration were significantly higher than the corresponding ratios after iv administration up to 30 min following dosing. We conclude than nasally administered benzoylecgonine was transported directly from the nasal cavity to the brain and that the significant increase in brain levels was sustained for a prolonged period of time. Factors contributing to the observed differences in the nose-brain transport of cocaine and benzoylecgonine are discussed.
Automatic object segmentation from large scale 3D urban point clouds through manifold embedded mode seeking

This paper presents a system that can automatically segment objects in large scale 3D point clouds obtained from urban ranging images. The system consists of three steps: The first one involves a ground detection process that can detect relatively complex terrain and separate it from other objects. The second step superpixelizes the remaining objects to speed up the segmentation process. In the final step, a manifold embedded mode seeking method is adopted to segment the point clouds. Even though the segmentation of urban objects is a challenging problem in terms of accuracy and problem scale, our system can efficiently generate very good segmentation results. The proposed manifold learning effectively improves the segmentation performance due to the fact that continuous artificial objects often have manifold-like structures.
Investigation of corrosion resistance of electrodeposited Ni–W/SiC composite coatings

In this research, Ni–W/SiC composite coatings were electrodeposited from a plating bath containing suspension of SiC particles. The influences of SiC particle concentration in the plating bath on the composition of composite coatings were investigated. The surface morphology and composition of the composite coatings were characterised by scanning electron microscopy, energy dispersive X-ray measurements and X-ray diffraction analysis. The corrosion characteristics of Ni–W/SiC composite coatings were investigated by mass loss and electrochemical measurements, including open circuit potential, electrochemical impedance spectroscopy and potentiodynamic polarisation in a 3·5 wt-%NaCl solution. The results showed that the addition of SiC particle to the deposition bath of Ni–W significantly increased the corrosion resistance. The significant improvement in corrosion resistance observed for Ni–W/SiC composite coatings (17100 Ω cm2) compared to Ni–W (5619 Ω cm2) could have resulted from the microstructural differences.
An improved tuned mass damper (SMA-TMD) assisted by a shape memory alloy spring

The tuned mass damper (TMD) is a well acclaimed passive control device for vibration control of structures. However, the requirement of a higher mass ratio restricts its applicability for seismic vibration control of civil engineering structures. Improving the performance of TMDs has been attempted by supplementing them with nonlinear restoring devices. In this regard, the ability of shape memory alloy (SMA) in dissipating energy through a hysteretic phase transformation of its microstructure triggered by cyclic loading is notable. An improved version of TMD assisted by a nonlinear shape memory alloy (SMA) spring, referred as SMA-TMD, is studied here for seismic vibration mitigation. Extensive numerical simulations are conducted based on nonlinear random vibration analysis via stochastic linearization of the nonlinear force–deformation hysteresis of the SMA. A design optimization based on minimizing the root mean square displacement of the main structure is also carried out to postulate the optimal design parameters for the proposed system. The viability of the optimal design is verified with respect to its performance under recorded earthquake motions. Significant improvements of the control efficiency and a reduction of the TMD displacement at a much reduced mass ratio are shown to be achieved in the proposed SMA-TMD over those in the linear TMD.
Bending characteristics of SU-8

This study characterises SU-8's material properties under large deformations in out-of-plane bending. A novel test setup is presented to deform the SU-8 to high levels, and a mathematical model presented that accurately predicts the results. This test shows that hard-baked SU-8, with a Young's modulus tested at 1.9 GPa, is capable of undergoing stresses of up to 120 MPa before failure and in some cases will undergo plastic deformation.
Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics

The concept of pathogenesis has evolved considerably over recent years, and the scenario “a microbe + virulence factors = disease” is probably far from reality in a number of cases. Actual pathogens have extremely broad biological diversity and are found in all major groups of microorganisms (viruses, bacteria, fungi, protozoa…). Their pathogenicity results from strong and often highly specific interactions they have with either their microbial environment, hosts and/or arthropod vectors. In this review, we explore the contribution of metagenomic approaches toward understanding pathogens within the context of microbial communities. With this broader view, we discussed the concept of “pathobiome” and the research questions that this raises.