Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-attractor gene reordering for graph bisection

We propose a new gene reordering scheme for the graph bisection problem. Our gene reordering starts with two or more vertices to capture the clustering structure of graphs effectively. We devised a chromosome repairing method for hybrid genetic search, which helps exploit clusters when combined with gene reordering. Experimental tests showed that the suggested reordering scheme significantly improves the performance of genetic algorithms over previous reordering methods.
Surface properties estimation of sandy land based on multi-angle polarized image information

In this paper a method to estimate surface roughness of sand land from multi-angle and multi-waveband polarized detections is presented. Firstly, the polarized bidirectional reflectance distribution function (pBRDF) of the sand land’s surface based on the microfacet theory was established. Then three sand samples with particle sizes of 0.5 mm, 0.7 mm and 1 mm were obtained by a series of sieves. And the polarization information was acquired by full-polarized multispectral imaging system based on Liquid Crystal Variable Retarder (LCVR). We used the nonlinear least squares method to estimate the surface roughness of from the measured data. Lastly, the analysis results show that the accuracy of sand roughness estimation is improved as the number of the angles (i.e., source incident angles and detection angles) and wavebands increase until the estimation accuracy saturates. It is indicated that the method based on polarization imaging detection to estimate sandy land surface roughness is effective.
Light- and Carbon-Signaling Pathways. Modeling Circuits of Interactions1

Here, we report the systematic exploration and modeling of interactions between light and sugar signaling. The data set analyzed explores the interactions of sugar (sucrose) with distinct light qualities (white, blue, red, and far-red) used at different fluence rates (low or high) in etiolated seedlings and mature green plants. Boolean logic was used to model the effect of these carbon/light interactions on three target genes involved in nitrogen assimilation: asparagine synthetase (ASN1 and ASN2) and glutamine synthetase (GLN2). This analysis enabled us to assess the effects of carbon on light-induced genes (GLN2/ASN2) versus light-repressed genes (ASN1) in this pathway. New interactions between carbon and blue-light signaling were discovered, and further connections between red/far-red light and carbon were modeled. Overall, light was able to override carbon as a major regulator of ASN1 and GLN2 in etiolated seedlings. By contrast, carbon overrides light as the major regulator of GLN2 and ASN2 in light-grown plants. Specific examples include the following: Carbon attenuated the blue-light induction of GLN2 in etiolated seedlings and also attenuated the white-, blue-, and red-light induction of GLN2 and ASN2 in light-grown plants. By contrast, carbon potentiated far-red-light induction of GLN2 and ASN2 in light-grown plants. Depending on the fluence rate of far-red light, carbon either attenuated or potentiated light repression of ASN1 in light-grown plants. These studies indicate the interaction of carbon with blue, red, and far-red-light signaling and set the stage for further investigation into modeling this complex web of interacting pathways using systems biology approaches.
High-resolution image analysis of laminae (organic-rich with calcareous nannofossils) in a black shale sequence: probability of orbital and suborbital climate cycles in the latest Cenomanian

We conducted a high-resolution image analysis of the lamination present in a core interval of black shale from Hole 1260B (ODP Leg 207) on the Demerara Rise in the western tropical Atlantic. Gray scale digital image analysis results revealed environmental cyclic patterns that could be related to orbital and suborbital changes during the latest Cenomanian (94 Ma). High-resolution nannofossil biostratigraphy provided the detailed chronological information needed to constrain the time intervals of each cyclic event. A study of thin sections showed that the basic pattern of the millimeter-scale laminae was couplets of alternating dark organic-rich layers and white biogenic test layers. The composition of the dark organic-rich layer appeared to include the remains from microbial organisms with a chain-like structure. From the combination of the gray scale and thin section analyses, three well-expressed cyclic patterns could be recognized in the black shale interval, namely (1) meter-scale cyclic events (average interval of approximately 413 mm), (2) centimeter-scale cyclic events (approximately 10 – 30 mm intervals), and (3) millimeter-scale cycles (average interval of approximately 5 mm). These cyclic events could imply approximately 40 ky, 1 – 3 ky, and 300 – 700 yr time spans, respectively, on the basis of biostratigraphy. In addition, two other cyclic patterns indicating approximately 20 ky and 60 – 150 yr time intervals were weakly expressed.
Rapid detection and identification of clinically important bacteria by high-resolution melting analysis after broad-range ribosomal RNA real-time PCR.

BACKGROUND Broad-range PCR provides valuable information for detecting bacterial infections. This study assesses the combined use of broad-range real-time PCR and high-resolution melting analysis for rapid detection and identification of clinically important bacteria. METHODS We subjected 46 bacterial culture colonies representing 25 clinically important bacterial species to LightCycler real-time PCR amplification of the 16S rRNA gene in the presence of LCGreen I fluorescent dye. We performed high-resolution melting analysis of the PCR products with the HR-1 instrument and used melting profiles as molecular fingerprints for bacterial species identification. We validated this method via assessment of 54 consecutive bacteria culture colonies obtained from a clinical microbiology laboratory. RESULTS The 16S rRNA gene of all 25 bacterial species was amplifiable by this method, with PCR product lengths of 216 or 217 bp. Of the 25 bacterial species, we identified 11 via a 1-step post-PCR high-resolution melting analysis. The remaining bacterial species were identified via the high-resolution melting plots obtained by heteroduplex formation between the PCR products of the tested and reference bacterial species or by a 2nd real-time PCR targeting a different region of the 16S rRNA gene. A high-resolution melting database and a working protocol were established for identifying these 25 bacterial species. In the validation assay, a 94% accuracy rate was achieved when the bacterial species were in the high-resolution melting database. CONCLUSIONS This assay requires no multiplexing or hybridization probes and provides a new approach for bacterial species identification in a molecular diagnostic laboratory.
Solar Differential Rotation and Meridional Flow: The Role of a Subadiabatic Tachocline for the Taylor-Proudman Balance

We present a simple model for the solar differential rotation and meridional circulation based on a mean field parameterization of the Reynolds stresses that drive the differential rotation. We include the subadiabatic part of the tachocline and show that this, in conjunction with turbulent heat conductivity within the convection zone and overshoot region, provides the key physics to break the Taylor-Proudman constraint, which dictates differential rotation with contour lines parallel to the axis of rotation in case of an isentropic stratification. We show that differential rotation with contour lines inclined by 10°-30° with respect to the axis of rotation is a robust result of the model, which does not depend on the details of the Reynolds stress and the assumed viscosity, as long as the Reynolds stress transports angular momentum toward the equator. The meridional flow is more sensitive with respect to the details of the assumed Reynolds stress, but a flow cell, equatorward at the base of the convection zone and poleward in the upper half of the convection zone, is the preferred flow pattern.
Collaborative monocular SLAM with multiple Micro Aerial Vehicles

This paper presents a framework for collaborative localization and mapping with multiple Micro Aerial Vehicles (MAVs) in unknown environments. Each MAV estimates its motion individually using an onboard, monocular visual odometry algorithm. The system of MAVs acts as a distributed preprocessor that streams only features of selected keyframes and relative-pose estimates to a centralized ground station. The ground station creates an individual map for each MAV and merges them together whenever it detects overlaps. This allows the MAVs to express their position in a common, global coordinate frame. The key to real-time performance is the design of data-structures and processes that allow multiple threads to concurrently read and modify the same map. The presented framework is tested in both indoor and outdoor environments with up to three MAVs. To the best of our knowledge, this is the first work on real-time collaborative monocular SLAM, which has also been applied to MAVs.
Treatment of Real-World HCV Genotype 2-Infected Japanese Patients with Sofosbuvir plus Ribavirin

The aim of this study was to characterize the treatment response and tolerability of sofosbuvir plus ribavirin therapies in Japanese patients infected with hepatitis C virus (HCV) genotype (GT)-2. This retrospective study analyzed 114 Japanese HCV GT-2 patients treated for 12 weeks with 400 mg of sofosbuvir plus weight-based ribavirin daily. This treatment led to higher sustained virologic response at 12-weeks post-treatment (SVR12) rates in both treatment-naïve and treatment-experienced patients. The efficacy of this treatment in compensated cirrhotics was the same as that in patients with chronic hepatitis. HCV GT-2a infection and lower estimated glomerular filtration rates (eGFR) tended to be associated with SVR12. Of 114 patients, 113 completed the combination of sofosbuvir plus ribavirin for 12 weeks. Seven patients without SVR12 did not have HCV NS5B-S282 mutations. The overall SVR12 rate was 90.4% (103 of 114). More effective therapeutic options with less adverse events are desired to achieve higher SVR rates in HCV GT-2 Japanese patients.
Audio Content-Based Music Retrieval

The rapidly growing corpus of digital audio material requires novel retrieval strategies for exploring large music collections. Traditional retrieval strategies rely on metadata that describe the actual audio content in words. In the case that such textual descriptions are not available, one requires content-based retrieval strategies which only utilize the raw audio material. In this contribution, we discuss content-based retrieval strategies that follow the query-by-example paradigm: given an audio query, the task is to retrieve all documents that are somehow similar or related to the query from a music collection. Such strategies can be loosely classified according to their "specificity", which refers to the degree of similarity between the query and the database documents. Here, high specificity refers to a strict notion of similarity, whereas low specificity to a rather vague one. Furthermore, we introduce a second classification principle based on "granularity", where one distinguishes between fragment-level and document-level retrieval. Using a classification scheme based on specificity and granularity, we identify various classes of retrieval scenarios, which comprise "audio identification", "audio matching", and "version identification". For these three important classes, we give an overview of representative state-of-the-art approaches, which also illustrate the sometimes subtle but crucial differences between the retrieval scenarios. Finally, we give an outlook on a user-oriented retrieval system, which combines the various retrieval strategies in a unified framework.
In vitro and in silico biopotentials of phytochemical compositions and antistaphylococcal and antipseudomonal activities of volatile compounds of Argania spinosa (L.) seed oil

Active components in medicinal plants provide unlimited useful and traditional medicines. Antimicrobial activities are found in secondary metabolites in plant extracts such as argan oil. This experimental investigation aims to determine argan oil’s volatile compounds and examine their in vitro antimicrobial properties. In silico simulations, molecular docking, pharmacokinetics, and drug-likeness prediction revealed the processes underlying the in vitro biological possessions. Gas chromatography–mass spectrometry (GC/MS) was used to screen argan oil’s primary components. In silico molecular docking studies were used to investigate the ability of the selected bioactive constituents of argan oil to act effectively against Pseudomonas aeruginosa and Staphylococcus aureus (S. aureus) isolated from infections. The goal was to study their ability to interact with both bacteria’s essential therapeutic target protein. The 21 chemicals in argan oil were identified by GC/MS. Docking results for all compounds with S. aureus and P. aeruginosa protease proteins ranged from −5 to −9.4 kcal/mol and −5.7 to −9.7 kcal/mol, respectively, compared to reference ligands. Our docking result indicates that the 10-octadecenoic acid, methyl ester was the most significant compound with affinity scores of −9.4 and −9.7 kcal/mol for S. aureus and P. aeruginosa proteins, respectively. The minimal bactericidal concentration (MBC) and minimal inhibitory concentration (MIC) of argan oil were 0.7 ± 0.03 and 0.5 ± 0.01 for S. aureus and 0.4 ± 0.01 and 0.3 ± 0.02 for P. aeruginosa, respectively. We confirmed the antimicrobial properties of argan oil that showed significant growth inhibition for S. aureus and P. aeruginosa.
Kinetics of antibody response of calves immunized with Schistosoma mansoni glutathione-S-transferase

Six calves were immunized with Schistosoma mansoni glutathione-S-transferase (GST) antigen vaccine, expressed in E. coli (GST-coli) or yeast (GST-yeast). Six calves were injected with extracts of E. coli or yeast and kept as controls. Two experimentally infected calves were kept as source of infection and to provide positive antiserum to Schistosoma bovis. Kinetics of antibody response of the immunized calves was monitored by Western blots and enzyme-linked immunosorbent assay (ELISA). Using Western blots, the immunized calves produced specific IgG antibodies, which recognized S. mansoni GST (S.mGST) antigen, whereas the control calves did not. Using ELISA, antibodies to S.mGST antigen were detected in sera from S.mGSTcoli and GST-yeast vaccinated calves, but not in sera from control calves or S. bovis experimentally infected calves. In addition, the ELISA failed to detect S.mGST specific antibodies in sera from immunized calves or their controls when S. bovis adult worm extract was used as an antigen. The results of this study indicated that S.mGST antigen has no diagnostic potential for detection of bovine schistosomosis, caused by S. bovis infection, in susceptible ruminants.
The Benefits of Workforce Well-Being on Profitability in Listed Companies: A Comparative Analysis between Europe and Mexico from an ESG Investor Perspective

This paper evaluates the relationship between investing in workforce well-being and profitability of listed companies in Mexico compared to European companies from an Environmental, Social, and Governance (ESG) investor perspective. In this case, the Refinitiv workforce score or High-Performance Work Policies (HPWP) is used as an indicator of the quality of workforce well-being by including the industry effects (economic and business sectors) and the behavioral (sentiment) factors as control variables. Specifically, this article examines the relationships between HPWP, stock price changes (measured as a percentage), profitability (ROE), and market risk (betas). We used a sample of companies from the Refinitiv Mexico and European stock indices for this purpose. In the Mexican case, the results show that a higher level of well-being promotion relates to better company profits. The opposite happens in European companies. Regarding market prices, European companies show higher prices when they have higher HPWP and Mexican companies confirm the opposite. Regarding market risk, only European basic materials with high HPWP show less risk. Finally, in almost all Mexican business sectors, the relationship between market risk and workforce well-being is negative.
Retraining-based timing error mitigation for hardware neural networks

Recently, neural network (NN) accelerators are gaining popularity as part of future heterogeneous multi-core architectures due to their broad application scope and excellent energy efficiency. Additionally, since neural networks can be retrained, they are inherently resillient to errors and noises. Prior work has utilized the error tolerance feature to design approximate neural network circuits or tolerate logical faults. However, besides high-level faults or noises, timing errors induced by delay faults, process variations, aging, etc. are dominating the reliability of NN accelerator under nanoscale manufacturing process. In this paper, we leverage the error resiliency of neural network to mitigate timing errors in NN accelerators. Specifically, when timing errors significantly affect the output results, we propose to retrain the accelerators to update their weights, thus circumventing critical timing errors. Experimental results show that timing errors in NN accelerators can be well tamed for different applications.
Mortality prediction model is preferable to APACHE

EDITOR—In their article on scoring systems in intensive care, Gunning and Rowan provide a detailed description of the APACHE II mortality prediction model.1 This model was developed with data collected between 1979 and 1982 and was replaced by APACHE III in 1991.2 Unfortunately, there is a substantial charge for using APACHE III;thus many intensive care units continue using the outdated APACHE II, but do you really want to compare your standard of care with that delivered by North American units 20 years ago? There …
Analytical Design Framework for Torque and Back-EMF Optimization, and Inductance Calculation in Double-Rotor Radial-Flux Air-Cored Permanent-Magnet Synchronous Machines

Analytical models have been demonstrated to be effective tools in the analysis of electromagnetic devices by providing fast, yet accurate solutions. In this paper, a comprehensive analytical framework for double-rotor radial-flux air-cored permanent-magnet (PM) machines is developed whereby the average as well as the torque ripples, back-electromotive force (EMF) waveforms, air-gap flux density distribution, and a number of other characteristics regarding the design of the machine are predicted. Also, closed-form expressions for inductances of the stator coils are analytically derived. All machine parameters and material properties including iron saturation are considered in the model. Moreover, an algorithm in order to optimally design the thicknesses of the rotor yokes based on the utilized steel is presented. Finally, genetic optimizations regarding the enhancement of the produced torque and back-EMF are performed. It is also shown that the results obtained from the proposed model match well with those issued from finite element method.
Kinetic Modeling of ABCG2 Transporter Heterogeneity: A Quantitative, Single-Cell Analysis of the Side Population Assay

The side population (SP) assay, a technique used in cancer and stem cell research, assesses the activity of ABC transporters on Hoechst staining in the presence and absence of transporter inhibition, identifying SP and non-SP cell (NSP) subpopulations by differential staining intensity. The interpretation of the assay is complicated because the transporter-mediated mechanisms fail to account for cell-to-cell variability within a population or adequately control the direct role of transporter activity on staining intensity. We hypothesized that differences in dye kinetics at the single-cell level, such as ABCG2 transporter-mediated efflux and DNA binding, are responsible for the differential cell staining that demarcates SP/NSP identity. We report changes in A549 phenotype during time in culture and with TGFβ treatment that correlate with SP size. Clonal expansion of individually sorted cells re-established both SP and NSPs, indicating that SP membership is dynamic. To assess the validity of a purely kinetics-based interpretation of SP/NSP identity, we developed a computational approach that simulated cell staining within a heterogeneous cell population; this exercise allowed for the direct inference of the role of transporter activity and inhibition on cell staining. Our simulated SP assay yielded appropriate SP responses for kinetic scenarios in which high transporter activity existed in a portion of the cells and little differential staining occurred in the majority of the population. With our approach for single-cell analysis, we observed SP and NSP cells at both ends of a transporter activity continuum, demonstrating that features of transporter activity as well as DNA content are determinants of SP/NSP identity.
Mapping of Myxococcus xanthus Social Motility dsp Mutations to the dif Genes

ABSTRACT Myxococcus xanthus dsp and dif mutants have similar phenotypes in that they are deficient in social motility and fruiting body development. We compared the two loci by genetic mapping, complementation with a cosmid clone, DNA sequencing, and gene disruption and found that 16 of the 18 dsp alleles map to the dif genes. Another dsp allele contains a mutation in the sglK gene. About 36.6 kb around the dsp-dif locus was sequenced and annotated, and 50% of the genes are novel.
Case 3736 — Garypus latus Hansen, 1884 (currently Larca lata; Arachnida, Pseudoscorpiones): proposed precedence over Garypus hungaricus Tömösváry, 1882

Abstract. The purpose of this application, under Article 23.9. 3 of the Code, is to conserve the widely used specific name Larca lata (Hansen, 1884) for a species of pseudoscorpion from northern and central Europe. The name is threatened by the senior subjective synonym Garypus hungaricus Tömösváry, 1882, which has seldom been used since its first publication. Therefore, precedence of the name Larca lata (Hansen, 1884) is proposed.
Gait Extraction and Description by Evidence-Gathering

Using gait as a biometric is of increasing interest, yet there are few model-based, parametric, approaches to extract and describe moving articulated objects. One new approach can detect moving parametric objects by evidence gathering, hence accruing known performance advantages in terms of performance and occlusion. Here we show how that the new technique can be extended not only to extract a moving person, but also to extract and concurrently provide a gait signature for use as a biometric. We show the natural relationaship between the bases of these approaches, and the results they can provide. As such, these techniques allow for gait extraction and description for recognition purposes, and with known performance advantages of a well-established vision technique.