Miracle-dz/UniFAR-FTUs huggingface dataset:
Is constructivist learning environment really effective on learning and long-term knowledge retention in mathematics? Example of the infinity concept

This study investigates the long-term effects of instructing Cantor set theory using constructivist learning approach on student knowledge retention. The participants included 60 first-year secondary mathematics pre-service teachers. Students were divided into two classes one of which was taught via traditional lecture (n = 30) and the other was taught using active learning approach (n = 30). A pre-test named “Minimum Requirements Identification Test” developed by the researcher was used in the determination of the groups. This test involves the concepts such as “set, relation, and function” which were required to be able to learn Cantor set theory. Student retention of Cantor set theory was measured by using a questionnaire which consists of open-ended questions about the topic. The test was administered to all of the students approximately 14 months after the first instruction. In addition, five students from each group were interviewed. Analyses of the data revealed that the students in the constructivist learning environment showed better retention of almost all of the concepts related to Cantor set theory than the students in the traditional class. Key words: Cantorian set theory, teacher education, infinity, retention, active learning.
Monolithically Integrated AlGaAs/InGaAs Laser Diode, p-n Photodetector and GaAs MESFET Grown on Si Substrate

We have demonstrated the first successful fabrication of the monolithically integrated AlGaAs/InGaAs laser diode, p-n photodetector and GaAs metal semiconductor field-effect transistor (MESFET) grown on a SiO2 back-coated p-Si substrate using selective regrowth by metalorganic chemical vapor deposition (MOCVD). The reliability of the laser diode on the Si substrate can be improved by utilization of the strain-relieved AlGaAs/InGaAs laser diode with the InGaAs intermediate layer. During the GaAs layer growth, the p-n photodetector is formed near the surface of the p-Si substrate by the diffusion of As atoms. The use of SiO2 back-coated Si substrate is effective in suppressing unintentional Si autodoping and in obtaining a good pinch-off GaAs MESFET.
Consensus Recovery from Intentional Attacks in Directed Nonlinear Multi-agent Systems

Abstract Resilience or recovery of multi-agent systems against attacks is believed to be one of the most important topics in control and management of complex systems. Previous studies have mainly focused on the random failure and intentional attack targeted on node degrees, whereas consensus recovery is much less investigated. In this paper, two kinds of targeted attacks are introduced and corresponding recovery strategies are proposed to address the consensus recovery of continuous-time nonlinear multi-agent systems under directed topologies against subsequent attacks. The cut-nodes and cut-edges are chosen as the targets of attack, and the multi-agent system becomes disconnected when they are deleted from the system. The neighbor nodes of the cut-node and end nodes of the cut-edge are used to recover the connectivity of the network. It is shown that our proposed strategies can significantly improve the convergence speed of reaching consensus of the resulting multi-agent systems. A cost function is also proposed to compare different recovery strategies.
Probing the effects of spectral overlap on quantum-dot-based FRET: Ensemble and single molecule studies

The photoluminescence spectrum of a quasi-monodisperse semiconductor quantum dot (QD) population is composed of a continuum of extremely narrow single QD spectra. This is due to inhomogeneities in nanocrystal size within a population and the color-size dependency imposed by effects of carrier quantum confinements. We take advantage of this population heterogeneity to gain a unique insight into the fluorescence resonant energy transfer (FRET) process between a QD donor and proximal dye-labeled protein acceptors. Our ensemble and single-QD studies demonstrate that the spectral dependency of the energy transfer rate matches the acceptor absorption spectrum as predicted by Forster formalism. This allows ratiometric FRET measurements based on the QD donor emission.
k-Nearest Neighbour method in functional nonparametric regression

The aim of this article is to study the k-nearest neighbour (kNN) method in nonparametric functional regression. We present asymptotic properties of the kNN kernel estimator: the almost-complete convergence and its rate. Then, we illustrate the effectiveness of this method by comparing it with the traditional kernel approach first on simulated datasets and then on a real chemometrical example. We also present in this article an important technical tool which could be useful in many other situations than ours.
Laparoscopic versus open appendicectomy in obese patients: a prospective randomized comparison

Background Obese patients who present with general surgical emergencies afford unique obstacles to emergency surgeons. Whereas there seems to be no absolute advantage to laparoscopy in acute appendicitis for the overall population, it has been postulated that among obese cases, the laparoscopic technique may provide more conclusive benefits. Objectives Because of limited data on this issue, the focus of this research was to compare the clinical outcomes of laparoscopic and open-appendicectomy techniques in obese population. Patients and methods A number of 64 cases of acute appendicitis with BMI more than or equal to 30 were randomly assigned to one of two groups: laparoscopic or open-appendicectomy groups. The outcomes evaluated include duration of hospital stay, operative times, postoperative complications comprising intra-abdominal abscesses and incision-site infections, time to start oral intake, and number of analgesic-dose requirements. Results In comparison with open appendicectomy, laparoscopic appendicectomy associated with shorter operative time P value of 0.042, shorter length of hospital stay (P=0.001), fewer doses of analgesia (P<0.001), and earlier toleration of oral intake (P=0.002). While there was nonsignificant difference between the groups for intraoperative complications (P=0.565) or postoperative complications (intra-abdominal or surgical-site complications) (P=0.708). Conclusion Laparoscopic appendectomy resulted in lower operative time, a shorter hospital stay, earlier oral intake, and a reduced need for analgesia with a complication rate that was comparable to its open counterpart, and it can be recommended as a standard procedure in obese patients with acute appendicitis.
Large-scale Gauss-Newton inversion of transient controlled-source electromagnetic measurement data using the model reduction framework

ABSTRACTTransient data controlled-source electromagnetic measurements are usually interpreted via extracting few frequencies and solving the corresponding inverse frequency-domain problem. Coarse frequency sampling may result in loss of information and affect the quality of interpretation; however, refined sampling increases computational cost. Fitting data directly in the time domain has similar drawbacks, i.e., its large computational cost, in particular, when the Gauss-Newton (GN) algorithm is used for the misfit minimization. That cost is mainly comprised of the multiple solutions of the forward problem and linear algebraic operations using the Jacobian matrix for calculating the GN step. For large-scale 2.5D and 3D problems with multiple sources and receivers, the corresponding cost grows enormously for inversion algorithms using conventional finite-difference time-domain (FDTD) algorithms. A fast 3D forward solver based on the rational Krylov subspace (RKS) reduction algorithm using an optimal subsp.
Minimax Lower Bound of k-Monotone Estimation in the Sup-norm

Belonging to the framework of shape constrained estimation, k-monotone estimation refers to the nonparametric estimation of univariate k-monotone functions, e.g., monotone and convex unctions. This paper develops minimax lower bounds for k-monotone regression problems under the sup-norm for general k by constructing a family of k-monotone piecewise polynomial functions (or hypotheses) belonging to suitable Hölder and Sobolev classes. After establishing that these hypotheses satisfy several properties, we employ results from general min-imax lower bound theory to obtain the desired k-monotone regression minimax lower bound. Implications and extensions are also discussed.
Detection of a very bright source close to the LMC supernova SN 1987A

High angular resolution observations of the supernova in the Large Magellanic Cloud, SN 1987A, have revealed a bright source separated from the SN by approximately 60 mas with a magnitude difference of 2.7 at 656 nm (H-alpha). Speckle imaging techniques were applied to data recorded with the CfA two-dimensional photon counting detector on the CTIO 4 m telescope on March 25 and April 2 to allow measurements in H-alpha on both nights and at 533 nm and 450 nm on the second night. The nature of this object is as yet unknown, though it is almost certainly a phenomenon related to the SN.
Rank-Reduction-Based Trace Interpolation

Summary In previous papers we described a family of multidimensional filters to suppress random noise based on matrix-rank reduction of constant-frequency slices. Here we extend these filters to perform multidimensional trace interpolation. This requires rank reduction when some, perhaps most, of the matrix elements are unknown, a procedure called matrix completion or matrix imputation. We show how this new interpolator improves the spatial resolution of 3D data when applied prior to prestack migration.
Arterial stiffness relates to executive dysfunction in later life

ABSTRACT Cardiovascular disease in older people is often linked with cognitive impairment, particularly in domains of executive function and processing speed. Our aims examined whether carotid-femoral pulse wave velocity (PWV) related to subtle changes of executive function and processing speed. Fifty-six individuals with subjective mood and/or cognitive concerns underwent PWV and neuropsychological assessments of processing speed (Trail Making Test Part A) and executive functioning (Delis Kaplan Executive Function System Stroop Task; Trail Making Test Part B, TMT-B). Individuals with high PWV (≥12.0m/s) had poorer performance on TMT-B, compared to low PWV (<12.0m/s), and a moderate negative correlation (r = −0.38, p = .004) between PWV and TMT-B performance. Our results confirm that in older adults at-risk for cognitive decline, early markers of CVD are associated with subtle decrements in rapid set-shifting (executive function), supporting efforts towards early detection of CVD as a secondary prevention strategy for older individuals with cognitive decline.
Bayesian multivariant fine mapping using the Laplace prior

Currently, the only effect size prior that is routinely implemented in a Bayesian fine‐mapping multi‐single‐nucleotide polymorphism (SNP) analysis is the Gaussian prior. Here, we show how the Laplace prior can be deployed in Bayesian multi‐SNP fine mapping studies. We compare the ranking performance of the posterior inclusion probability (PIP) using a Laplace prior with the ranking performance of the corresponding Gaussian prior and FINEMAP. Our results indicate that, for the simulation scenarios we consider here, the Laplace prior can lead to higher PIPs than either the Gaussian prior or FINEMAP, particularly for moderately sized fine‐mapping studies. The Laplace prior also appears to have better worst‐case scenario properties. We reanalyse the iCOGS case–control data from the CASP8 region on Chromosome 2. Even though this study has a total sample size of nearly 90,000 individuals, there are still some differences in the top few ranked SNPs if the Laplace prior is used rather than the Gaussian prior. R code to implement the Laplace (and Gaussian) prior is available at https://github.com/Kevin‐walters/lapmapr.
On the Linear Description of the k‐cycle Polytope

We study a linear description of $PC^k_n$ the convex hull of incidence vectors of all the cycles consisting of exactly $k$ edges ($k \ge 4$) in $K_n$, the complete undirected graph with $n$ vertices. First, we describe some properties of $PC^k_n$. Second, we discuss relations between $PC^k_n$ and $PC^{k'}_{n'}$ with $k' > k$ and $n' > n$. Then we give three lifting algorithms that transform a facet of $PC^k_n$ into facets of $PC^k_{n'}$ with $n' > n$. Finally, we provide an integer formulation and a partial linear description of $PC^k_n$.
Microbial sensitivity to temperature and sulfate deposition modulates greenhouse gas emissions from peat soils

Peatlands are among the largest natural sources of atmospheric methane (CH4) worldwide. Microbial processes play a key role in regulating CH4 emissions from peatland ecosystems, yet the complex interplay between soil substrates and microbial communities in controlling CH4 emissions as a function of global change remains unclear. Herein, we performed an integrated analysis of multi‐omics data sets to provide a comprehensive understanding of the molecular processes driving changes in greenhouse gas (GHG) emissions in peatland ecosystems with increasing temperature and sulfate deposition in a laboratory incubation study. We sought to first investigate how increasing temperatures (4, 21, and 35°C) impact soil microbiome–metabolome interactions; then explore the competition between methanogens and sulfate‐reducing bacteria (SRBs) with increasing sulfate concentrations at the optimum temperature for methanogenesis. Our results revealed that peat soil organic matter degradation, mediated by biotic and potentially abiotic processes, is the main driver of the increase in CO2 production with temperature. In contrast, the decrease in CH4 production at 35°C was linked to the absence of syntrophic communities and the potential inhibitory effect of phenols on methanogens. Elevated temperatures further induced the microbial communities to develop high growth yield and stress tolerator trait‐based strategies leading to a shift in their composition and function. On the other hand, SRBs were able to outcompete methanogens in the presence of non‐limiting sulfate concentrations at 21°C, thereby reducing CH4 emissions. At higher sulfate concentrations, however, the prevalence of communities capable of producing sufficient low‐molecular‐weight carbon substrates for the coexistence of SRBs and methanogens was translated into elevated CH4 emissions. The use of omics in this study enhanced our understanding of the structure and interactions among microbes with the abiotic components of the system that can be useful for mitigating GHG emissions from peatland ecosystems in the face of global change.
Comprehensive Analysis of Germline Drivers in Endometrial Cancer.

BACKGROUND We sought to determine the prevalence of germline pathogenic variants (gPVs) in unselected patients with endometrial cancer (EC), define biallelic gPVs within tumors, and describe their associations with clinicopathologic features. METHODS Germline assessment of ≥ 76 cancer predisposition genes was performed in patients with EC undergoing clinical tumor-normal MSK-IMPACT sequencing from 1/1/15-6/30/21. In patients with gPVs, biallelic alterations in ECs were identified through analysis of loss of heterozygosity and somatic PVs. Clinicopathologic variables were compared using non-parametric tests. RESULTS Of 1625 patients with EC, 216 (13%) had gPVs, and 15 patients had 2 gPVs. There were 231 gPVs in 35 genes (75 [32%] high-penetrance, 39 [17%] moderate-penetrance, and 117 [51%] low/recessive/uncertain-penetrance). Compared to those without gPVs, patients with gPVs were younger (P=.002), more often White (P=.009), less obese (P=.025) and had differences in distribution of tumor histology (P=.017) and molecular subtype (P<.001). Among 231 gPVs, 74 (32%) exhibited biallelic inactivation within tumors. For high-penetrance gPVs, 63% (47/75) of ECs had biallelic alterations, primarily affecting mismatch repair (MMR) and homologous recombination (HR) genes, including BRCA1/2, RAD51D, and PALB2. Biallelic inactivation varied across molecular subtypes with highest rates in microsatellite instability-high (MSI-H) or copy-number (CN)-high subtypes [3/12 (25%) POLE, 30/77 (39%) MSI-H, 27/60 (45%) CN-H, 9/57 (16%) CN-L, P<. 001]. CONCLUSIONS Thirteen percent of unselected patients with EC had gPVs, with 63% of gPVs in high-penetrance genes (MMR and HR) exhibiting biallelic inactivation, potentially driving cancer development. This supports germline assessment in EC given implications for treatment and cancer prevention.
Antiplasmodial activity of coumarins isolated from Polygala boliviensis: in vitro and in silico studies

Abstract Polygala boliviensis is found in the Brazilian semiarid region. This specie is little chemically and biologically studied. Polygala spp. have different metabolites, especially coumarins. Studies indicate that coumarins have antimalarial potential, denoting the importance of researching new active compounds from plants, since the resistance of Plasmodium strains to conventional therapy has increased. The present study aimed to evaluate the antiplasmodial activity of auraptene and poligalen against a chloroquine-resistant strain of Plasmodium falciparum. Coumarins were isolated from P. boliviensis by open column chromatography and identified by Nuclear Magnetic Resonance Spectroscopy. A cytotoxicity assay was carried out using MTT test, and the in vitro antiplasmodial activity was evaluated using the W2 strain. The antiplasmodial activity results found were IC50=0.171 ± 0.016 for auraptene and 0.164 ± 0.012 for poligalen; the selectivity indexes were 78.71 and 609.76, respectively. Inverse virtual screening in the BRAMMT database by OCTOPUS 1.2 was applied to coumarins to find potential P. falciparum targets and showed higher affinity energy of auraptene for purine nucleoside phosphorylase (PfPNP) and of poligalen for dihydroorotate dehydrogenase (PfDHODH). Molecular Dynamics studies (MD and MM-GBSA) approach were applied to calculate binding energies against selected P. falciparum targets and showed that all coumarins were stable at the binding site during simulations. Furthermore, energies were favorable for complexation. This is the first report of auraptene in P. boliviensis species and of in vitro antiplasmodial activity of auraptene and poligalen. In silico studies indicated that the mechanism of action of coumarins is the inhibition of PfPNP and PfDHODH. Communicated by Ramaswamy H. Sarma
Hereditary Diffuse Gastric Cancer.

Hereditary Diffuse Gastric Cancer (HDGC) is a dominantly-inherited cancer syndrome characterized by a high incidence of diffuse gastric cancer (DGC) and lobular breast cancer (LBC). HDGC is caused by germline mutations in two genes involved in the epithelial adherens junction complex, CDH1 and CTNNA1. Here, we discuss the genetics of HDGC and the variability of its clinical phenotype, in particular the variable penetrance of advanced DGC and LBC, both within and between families. We review the pathology of the disease, the mechanism of tumor initiation and its natural history. Finally, we describe current best practice for the clinical management of HDGC including emerging genetic testing criteria for the identification of new families, methods for endoscopic surveillance, the complications associated with prophylactic surgery, post-operative quality of life and the emerging field of HDGC chemoprevention.
Comparison of Biological Activities of BafA Family Autotransporters within Bartonella Species Derived from Cats and Rodents

Bartonella species are hemotropic, facultative intracellular bacteria, some of which cause zoonoses, that are widely disseminated among many mammals, including humans. During infection in humans, vascular endothelial cells play a crucial role as a replicative niche for Bartonella, and some are capable of promoting vascular proliferation. Along with well-studied pathogenic factors such as a trimeric autotransporter adhesin BadA or VirB/D4 type IV secretion system, bacteria-secreted protein BafA is also involved in Bartonella-induced vasoproliferation. ABSTRACT Bartonella species are hemotropic, facultative intracellular bacteria, some of which cause zoonoses, that are widely disseminated among many mammals, including humans. During infection in humans, vascular endothelial cells play a crucial role as a replicative niche for Bartonella, and some are capable of promoting vascular proliferation. Along with well-studied pathogenic factors such as a trimeric autotransporter adhesin BadA or VirB/D4 type IV secretion system, bacteria-secreted protein BafA is also involved in Bartonella-induced vasoproliferation. Genes encoding BafA orthologs have been found in the genomes of most Bartonella species, but their functionality remains unclear. In this study, we focused on three cat-derived zoonotic species (B. henselae, B. koehlerae, and B. clarridgeiae) and two rodent-derived species (B. grahamii and B. doshiae) and compared the activity of BafA derived from each species. Recombinant BafA proteins of B. henselae, B. koehlerae, B. clarridgeiae, and B. grahamii, species that also cause human disease, induced cell proliferation and tube formation in cultured endothelial cells, while BafA derived from B. doshiae, a species that is rarely found in humans, showed neither activity. Additionally, treatment of cells with these BafA proteins increased phosphorylation of both vascular endothelial growth factor receptor 2 and extracellular signal-regulated kinase 1/2, with the exception of B. doshiae BafA. Differential bafA mRNA expression and BafA secretion among the species likely contributed to the differences in the cell proliferation phenotype of the bacteria-infected cells. These findings suggest that the biological activity of BafA may be involved in the infectivity or pathogenicity of Bartonella species in humans.
Novel biomarkers and emerging tools to identify causal molecular pathways in hypertension and associated cardiovascular diseases.

Hypertension (HT) is a modifiable risk factor for life-threatening cardiovascular diseases (CVDs) including coronary artery disease, heart failure or stroke. Despite significant progress in understanding of the pathophysiological mechanisms of the disease, the molecular pathways targeted by HT treatment still remain largely unchanged. This warrants the necessity for searching novel biomarkers, which are causally related to persistent high blood pressure (BP) and may be pharmacologically targeted. Data from large-scale biobanks, containing high-throughput genetic and biochemical data, such as OLINK and SomaScan-based proteomics or Nuclear Magnetic Resonance-based metabolomics, as well as novel analytical tools including Mendelian randomisation (MR) approach enabling genetic casual inference, may create new treatment opportunities for HT and related CVDs. MR analysis may constitute an additional proof for observational studies and facilitate selection of druggable targets for clinical testing and have been already used to nominate potentially causal biomarkers for HT and CVDs such as circulating glycine, branched-chain amino acids, insulin-like growth factor 1 or fibronectin 1. Using MR framework, genetic proxies for targets of already known drugs, such as statins, PCSK9 and ACE inhibitors, may additionally inform about potential side effects and eventually contribute to a more personalized medicine. Finally, genetic causal inference may disentangle independent, direct effects of correlated traits such as lipid classes or markers of inflammation on cardiovascular clinical outcomes such as atherosclerosis and HT. While several novel HT-targeting drugs are currently under clinical investigation (e.g. brain renin-angiotensin-aldosterone system inhibitors or endothelin-1 receptor antagonists), analysis of high-throughput proteomic and metabolomic data from well-powered studies may deliver novel druggable molecular targets for HT and associated CVDs.