Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Barcoding, species delineation and taxonomy: a historical perspective

: DNA barcoding is a system designed to provide species identification by using standardized gene regions as internal species tag. Foreseen since its earlier development as a solution to speed up the pace of species discovery, DNA barcoding has established as a mature field of biodiversity sciences filing the conceptual gap between traditional taxonomy and different fields of molecular systematics. Initially proposed as a tool for species identification, DNA barcoding has also been applied in taxonomy routines for automated species delineation. Species identification and species delineation, however, should be considered as distinct activities relying on different theoretical and methodological backgrounds. The aim of the present review is to provide an overview of the use of DNA sequences in taxonomy, since the earliest development of molecular taxonomy until the development of DNA barcoding. We further present the differences between procedures of species identification and species delineation and highlight how DNA barcoding proposed a new paradigm that helps promote more sustainable practices in taxonomy.
Vitamin C and Doxycycline: A synthetic lethal combination therapy targeting metabolic flexibility in cancer stem cells (CSCs)

Here, we developed a new synthetic lethal strategy for further optimizing the eradication of cancer stem cells (CSCs). Briefly, we show that chronic treatment with the FDA-approved antibiotic Doxycycline effectively reduces cellular respiration, by targeting mitochondrial protein translation. The expression of four mitochondrial DNA encoded proteins (MT-ND3, MT-CO2, MT-ATP6 and MT-ATP8) is suppressed, by up to 35-fold. This high selection pressure metabolically synchronizes the surviving cancer cell sub-population towards a predominantly glycolytic phenotype, resulting in metabolic inflexibility. We directly validated this Doxycycline-induced glycolytic phenotype, by using metabolic flux analysis and label-free unbiased proteomics. Next, we identified two natural products (Vitamin C and Berberine) and six clinically-approved drugs, for metabolically targeting the Doxycycline-resistant CSC population (Atovaquone, Irinotecan, Sorafenib, Niclosamide, Chloroquine, and Stiripentol). This new combination strategy allows for the more efficacious eradication of CSCs with Doxycycline, and provides a simple pragmatic solution to the possible development of Doxycycline-resistance in cancer cells. In summary, we propose the combined use of i) Doxycycline (Hit-1: targeting mitochondria) and ii) Vitamin C (Hit-2: targeting glycolysis), which represents a new synthetic-lethal metabolic strategy for eradicating CSCs. This type of metabolic Achilles’ heel will allow us and others to more effectively “starve” the CSC population.
Anti‐cooperativity and cooperativity in hydrophobic interactions: Three‐body free energy landscapes and comparison with implicit‐solvent potential functions for proteins

Potentials of mean force (PMFs) of three‐body hydrophobic association are investigated to gain insight into similar processes in protein folding. Free energy landscapes obtained from explicit simulations of three methanes in water are compared with that predicted by popular implicit‐solvent effective potentials for the study of proteins. Explicit‐water simulations show that for an extended range of three‐methane configurations, hydrophobic association at 25°C under atmospheric pressure is mostly anti‐cooperative, that is, less favorable than if the interaction free energies were pairwise additive. Effects of free energy nonadditivity on the kinetic path of association and the temperature dependence of additivity are explored by using a three‐methane system and simplified chain models. The prevalence of anti‐cooperativity under ambient conditions suggests that driving forces other than hydrophobicity also play critical roles in protein thermodynamic cooperativity. We evaluate the effectiveness of several implicit‐solvent potentials in mimicking explicit water simulated three‐body PMFs. The favorability of the contact free energy minimum is found to be drastically overestimated by solvent accessible surface area (SASA). Both the SASA and a volume‐based Gaussian solvent exclusion model fail to predict the desolvation barrier. However, this barrier is qualitatively captured by the molecular surface area model and a recent “hydrophobic force field. ” None of the implicit‐solvent models tested are accurate for the entire range of three‐methane configurations and several other thermodynamic signatures considered. Proteins 2002;48:15–30. © 2002 Wiley‐Liss, Inc.
Proc . SPIN 2015 , ( c ) Springer Refinement Selection

Counterexample-guided abstraction refinement (CEGAR) is a property-directed approach for the automatic construction of an abstract model for a given system. The approach learns information from infeasible error paths in order to refine the abstract model. We address the problem of selecting which information to learn from a given infeasible error path. In previous work, we presented a method that enables refinement selection by extracting a set of sliced prefixes from a given infeasible error path, each of which represents a different reason for infeasibility of the error path and thus, a possible way to refine the abstract model. In this work, we (1) define and investigate several promising heuristics for selecting an appropriate precision for refinement, and (2) propose a new combination of a value analysis and a predicate analysis that does not only find out which information to learn from an infeasible error path, but automatically decides which analysis should be preferred for a refinement. These contributions allow a more systematic refinement strategy for CEGAR-based analyses. We evaluated the idea on software verification. We provide an implementation of the new concepts in the verification framework CPAchecker and make it publicly available. In a thorough experimental study, we show that refinement selection often avoids state-space explosion where existing approaches diverge, and that it can be even more powerful if applied on a higher level, where it decides which analysis of a combination should be favored for a refinement.
“Waiting for Better Times”

Swedish fathers are largely involved in their infant’s care, and Sweden has a generous parental leave, with 2 months especially assigned for fathers. The prevalence of depressive symptoms postpartum for fathers appears to be similar as for mothers in Sweden. This study aimed to describe fathers’ experiences of the first year postpartum, when they showed depressive symptoms 3 to 6 months postpartum. Semistructured interviews with 19 fathers were conducted and analyzed with content analysis. The fathers experienced loss of control and powerlessness due to discrepancies between their expectations and the reality they met after birth. They found the everyday-life turbulent, with much stress and worries for the infant, conflicts between family and work, and lack of support in everyday life. In addition, the fathers struggled with impaired partner-relationship, losses, and contradictory messages from both the society and their partners. These findings indicate that the fathers had difficulties to balance the competing demands of family, work, and their own needs. Thus, it is important to identify fathers with depressive symptoms at the Child Health Care Centers and attend to fathers’ needs of support and acknowledge them as parents equal to mothers.
How do slender mineral crystals resist buckling in biological materials?

Mineral crystals in biological materials such as bone, tooth, and sea shell are susceptible to buckling under compressive loading due to their slender geometry with large aspect ratios. How does nature deal with this problem? This question is especially interesting in view of the three orders of magnitude difference in elastic modulus between protein and mineral. As a first analysis of this question, we study the stability of a single mineral platelet confined in an otherwise perfect protein–mineral nanostructure. We find that there exists a transition of buckling strength from an aspect ratio-dependent regime to a lower threshold value, independent of the crystal geometry. Typical values of the aspect ratio of mineral crystals of bone and nacre fall in this transition region. The existence of a buckling strength independent of the detailed geometrical parameters of mineral may be critically important from the point of view of structure robustness as the composite behaviour of biomaterials should not depend sensitively on small variations in crystal size and shape.
Adaptive Neural Output Feedback Control for Nonstrict-Feedback Stochastic Nonlinear Systems With Unknown Backlash-Like Hysteresis and Unknown Control Directions

This paper investigates the problem of output feedback adaptive stabilization for a class of nonstrict-feedback stochastic nonlinear systems with both unknown backlashlike hysteresis and unknown control directions. A new linear state transformation is applied to the original system, and then, control design for the new system becomes feasible. By combining the neural network’s (NN’s) parameterization, variable separation technique, and Nussbaum gain function method, an input-driven observer-based adaptive NN control scheme, which involves only one parameter to be updated, is developed for such systems. All closed-loop signals are bounded in probability and the error signals remain semiglobally bounded in the fourth moment (or mean square). Finally, the effectiveness and the applicability of the proposed control design are verified by two simulation examples.
Study of initial damage and damage development of concrete by compression test

Quantitation of initial damage in concrete due to holes and small cracks resulting from concrete pouring is a difficult thing.In this paper, initial damage is simulated through mixing different quantities of initiator into five test samples of the same concrete. Axial compression tests are carried out,and the value of initial damage and nondestructive elastic modulus of the concrete are obtained. The regularity of damage development of the samples under limit strength is analyzed.It is found that the damage did not develop until the load was more than 40%～50% of the limit load.
Recombinant human HSP 60 produced in ClearColi TM BL 21 ( DE 3 ) does not activate the NF j B pathway

http://dx.doi. org/10.1016/j.cyto. 2015.01. 028 1043-4666/ 2015 Elsevier Ltd. All rights reserved. Abbreviations: APC, antigen presenting cells; CD14, cluster of differentiation 14; DAMP, damage-associated molecular pattern; exHSP60, extracellular 60 kDa-heat shock protein; GST, glutathion-S-transferase; HSP, heat shock proteins; HSP60, 60 kDa-heat shock protein; hTNF-a, human tumor necrosis factor a; LPS, lipopolysaccharide; MD2, myeloid differentiation 2; NFjB, nuclear factor kappa B; PMA, phorbol 12-myristate 13-acetate; PMB, polymixin B; rhHSP60, recombinant human 60 kDa-heat shock protein; RPMI medium, Roswell Park Memorial Institute medium; SEAP, secreted alkaline phosphatase; TLR2, toll-like receptor 2; TLR4, toll-like receptor 4. ⇑ Corresponding author at: Laboratoire GRI, Université de La Réunion and plateforme CYROI, 15, Avenue René Cassin, BP 7151, 97715 Saint Denis Messag. Cedex 9, Reunion. Tel. : +262 262 93 88 29. E-mail address: wildriss.viranaicken@univ-reunion.fr (W. Viranaïcken). 1 These two authors contribute equally to this work. 2 Co-authors seniorship. Cynthia Planesse , Brice Nativel , Thomas Iwema , Philippe Gasque , Christine Robert-Da Silva , Wildriss Viranaïcken b,2,⇑
New model order selection in large dimension regime for complex elliptically symmetric noise

This paper presents a new model order selection technique for signal processing applications related to source localization or subspace orthogonal projection techniques in large dimensional regime (Random Matrix Theory) when the noise environment is Complex Elliptically Symmetric (CES) distributed, with unknown scatter matrix. The proposed method consists first in estimating the Toeplitz structure of the background covariance matrix. In a second step, after a whitening process, the eigenvalues distribution of any Maronna's M-estimators is exploited, leading to the order selection. Simulations made on different kinds of CES noise as well as analysis of real hyperspectral images demonstrate the superiority of the proposed technique compared to those of Akaike Information Criterion and the Minimum Description Length.
Effect of Intravitreal Anti-Vascular Endothelial Growth Factor Therapy on the Risk of Arterial Thromboembolic Events: A Meta-Analysis

Background Intravitreal anti-vascular endothelial growth factor (VEGF) monoclonal antibodies are used in ocular neovascular diseases. A consensus has emerged that intravenous anti-VEGF can increase the risk of arterial thromboembolic events. However, the role of intravitreal anti-VEGF in arterial thromboembolism is controversial. Therefore, we did a systematic review and meta-analysis to investigate the effects of intravitreal anti-VEGF on the risk of arterial thromboembolic events. Methods Electronic databases were searched to identify relevant randomized clinical trials comparing intravitreal anti-VEGF with controls. Criteria for inclusion in our meta-analysis included a study duration of no less than 12 months, the use of a randomized control group not receiving any intravitreal active agent, and the availability of outcome data for arterial thromboembolic events, myocardial infarction, cerebrovascular accidents, and vascular death. The risk ratios and 95% CIs were calculated using a fixed-effects or random-effects model, depending on the heterogeneity of the included studies. Results A total of 4942 patients with a variety of ocular neovascular diseases from 13 randomized controlled trials were identified and included for analysis. There was no significant difference between intravitreal anti-VEGF and control in the risk of all events, with risk ratios of 0.87 (95% CI, 0.64 to 1.19) for arterial thromboembolic events, 0.96 (95% CI, 0.55–1.68) for cerebrovascular accidents, 0.69 (95% CI 0.40–1.21) for myocardial infarctions, and 0.68 (95% CI, 0.37–1.27) for vascular death. Conclusions The strength evidence suggests that the intravitreal use of anti-VEGF antibodies is not associated with an increased risk of arterial thromboembolic events.
A two-stage allocation scheme for delay-sensitive services in dense vehicular networks

Driven by the rapid development of wireless communication system, more and more vehicular services can be efficiently supported via vehicle-to-everything (V2X) communications. In order to allocate radio resource with the reasonable implementation complexity in dense urban intersection, a two-stage allocation algorithm is proposed in this paper, whose main objective is to minimize delay and ensure reliability. In particular, as for the first stage, the allocation policy is based on traffic density information (TDI), which is different from utilizing channel state information (CSI) and queue state information (QSI) in the second stage. Moreover, in order to reflect the influence of TDI on delay, a macroscopic vehicular mobility model is employed in this paper. Simulation results show that the proposed algorithm can acquire an asymptotically optimal performance with the acceptable complexity.
Perturbation-induced droplets for manipulating droplet structure and configuration in microfluidics

In this work, we mechanically perturb a liquid-in-liquid jet to manipulate the size and structure of the droplets formed from break-up of the jet. The induced break-up is relatively insensitive to fluctuations in the surrounding fluid flow. When the amplitude of perturbations is large and the interfacial tension of the liquid–liquid system is low, the size of the droplets can be precisely tuned by controlling the rate at which the liquid exits the tip of the dispensing nozzle through the frequency of perturbation. When applied to microfluidic devices with the appropriate geometry, our perturbation-induced droplet approach offers a strategy to manipulating droplet structures. We demonstrate that by varying the imposed perturbation frequency and phase lag, the structure of the multi-compartmental drops and the configuration of the resultant drops in the same flow condition can be manipulated. Moreover, after careful treatment of the wettability of the devices, we show that the structure of the droplets can be precisely controlled to change from single emulsion to double emulsion within the same device. The perturbation-induced droplet generation represents a new paradigm in the engineering of droplets, enhancing current droplet-based technologies for applications ranging from particle fabrication to confined micro-reactions.
Expanded Genomic Profiling of Circulating Tumor Cells in Metastatic Breast Cancer Patients to Assess Biomarker Status and Biology Over Time (CALGB 40502 and CALGB 40503, Alliance)

Purpose: We profiled circulating tumor cells (CTCs) to study the biology of blood-borne metastasis and to monitor biomarker status in metastatic breast cancer (MBC). Methods: CTCs were isolated from 105 patients with MBC using EPCAM-based immunomagnetic enrichment and fluorescence-activated cells sorting (IE/FACS), 28 of whom had serial CTC analysis (74 samples, 2–5 time points). CTCs were subjected to microfluidic-based multiplex QPCR array of 64 cancer-related genes (n = 151) and genome-wide copy-number analysis by array comparative genomic hybridization (aCGH; n = 49). Results: Combined transcriptional and genomic profiling showed that CTCs were 26% ESR1−ERBB2−, 48% ESR1+ERBB2−, and 27% ERBB2+. Serial testing showed that ERBB2 status was more stable over time compared with ESR1 and proliferation (MKI67) status. While cell-to-cell heterogeneity was observed at the single-cell level, with increasingly stable expression in larger pools, patient-specific CTC expression “fingerprints” were also observed. CTC copy-number profiles clustered into three groups based on the extent of genomic aberrations and the presence of large chromosomal imbalances. Comparative analysis showed discordance in ESR1/ER (27%) and ERBB2/HER2 (23%) status between CTCs and matched primary tumors. CTCs in 65% of the patients were considered to have low proliferation potential. Patients who harbored CTCs with high proliferation (MKI67) status had significantly reduced progression-free survival (P = 0.0011) and overall survival (P = 0.0095) compared with patients with low proliferative CTCs. Conclusions: We demonstrate an approach for complete isolation of EPCAM-positive CTCs and downstream comprehensive transcriptional/genomic characterization to examine the biology and assess breast cancer biomarkers in these cells over time. Clin Cancer Res; 24(6); 1486–99. ©2018 AACR.
Why do people pirate? A neuroimaging investigation

ABSTRACT It is not uncommon for people to openly admit to pirating information from the internet despite the known legal consequences. Those same people are often less inclined to steal the same physical item from a shop. This raises the question, why do people have fewer reservations with stealing intangible items compared to tangible? Using questionnaires and fMRI we provide evidence across three studies as to the differences between tangible and intangible theft. In a questionnaire (Study 1), participants revealed that across different conditions they were more willing to steal intangible compared to tangible goods. Study 2a used fMRI to reveal that a network involved in imagining objects was more active when participants were representing intangible versus tangible objects, suggesting people have greater difficulty representing intangible items. Study 2b used fMRI to show that when stealing tangible objects versus intangible, participants had increased activation in left lateral orbitofrontal cortex, an area typically activated in response to morally laden situations. The findings from the current investigation provide novel insights into the higher prevalence of intangible theft and suggest that differential neural representation of tangible and intangible items may, in part, explain why people are more willing to steal intangible items.
A Fast Framework for the Constrained Mean Trajectory Segment Model by Avoidance of Redundant Computation on Segment

The segment model (SM) is a family of methods that use the segmental distribution rather than frame-based density (e.g. HMM) to represent the underlying characteristics of the observation sequence. It has been proved to be more precise than HMM. However, their high level of complexity prevents these models from being used in practical systems. In this paper, we propose a framework that can reduce the computational complexity of the Constrained Mean Trajectory Segment Model (CMTSM), one type of SM, by fixing the number of regions in a segment so as to share the intermediate computation results. Our work is twofold. First, we compare the complexity of SM with that of HMM and point out the source of the complexity in SM. Secondly, a fast CMTSM framework is proposed, and two examples are used to illustrate this framework. The fast CMTSM achieves a 95.0% string accurate rate in the speaker-independent test on our mandarin digit string data corpus, which is much higher than the performance obtained with HMM-based system. At the mean time, we successfully keep the computation complexity of SM at the same level as that of HMM.
Structure generation and performance comparison of elliptic Gm‐C filters

Starting from a set of matrices describing a general Gm‐C filter topology, a procedure is developed for generating structures of lowpass filters. As the matrices and the filter topologies have a one‐to‐one correspondence, an algebraic method is used to identify filter topologies with desired properties, here, transfer functions with finite jω‐axis transmission zeros, specifically elliptic filters. Sensitivity expressions for these structures are derived and a performance comparison based on a set of chosen criteria is made. For a specified elliptic transfer function, filters with only grounded capacitors and those containing also floating capacitors emerge as alternative realizations, as are filters with a single input and those with distributed inputs. For third‐order functions, a detailed comparison is performed of leapfrog (LF) and inverse follow‐the‐leader‐feedback (IFLF), the most popular special cases, and of topologies that have also floating capacitors (LFf, IFLFf), as well as of a novel configuration that uses also distributed inputs (DIf) and leads to a reduced element count. Design guidelines and restrictions are given, which follow from the derived results with focus on the circuits' sensitivity performance and other properties important for IC implementation. Copyright © 2004 John Wiley & Sons, Ltd.
TraIL: Pinpoint Trajectory for Indoor Localization

Indoor localization on smartphones is an enabler for a number of ubiquitous and mobile computing applications attracting worldwide attentions. Many location-based services rely on WiFi fingerprinting approaches to achieve a reasonable accuracy. However, there is still room for improvement due to the prevalent-existing errors (e.g., 8∼12 m). In this study, we devise and implement a high-accuracy indoor localization solution leveraging the WiFi-based method and pedestrian mobility provided by smartphones. Our basic idea is that WiFi-only localization can generate rough but absolute positions, while user motion is able to bring accurate but relative locations. Taking both sides into account simultaneously, we design techniques to refine the raw WiFi positions in the process of laying the precise local trajectory appropriately down to the absolute coordinate using a novel least median of squares (LMS) fit algorithm. We develop a prototype system, named TraIL, and conduct comprehensive experiments in a building along different shaped routes. The evaluation results show that TraIL can achieve 80% improvement on average error with respect to WiFi-only indoor localization.