Miracle-dz/UniFAR-FTUs huggingface dataset:
B-spline Nonparametric Regression Models and Information Criteria

We consider the use of B-spline nonparametric regression models to analyze data with complex structure. The essential points of model construction in B-splines are the choice of the smoothing parameter and the number of basis functions. We investigate this problem from an information theoretic point of view and introduce a criterion as an estimator of Kullback-Leibler information. We also introduce B-spline nonlinear regression model with discontinuities or with heterogeneous error variances, and apply it to estimate the change points. Real data examples and numerical comparisons are used to examine the properties of the proposed method.
Bad luck in attempts to make scientific discoveries

WHEN THE Committee for the Fifth Fritz London Award asked me to give my recipient's address a somewhat personal nature, I hesitated about how to combine the modest review that I could give of certain recent advances made in the Kamerlingh Onnes Laboratory with this request. Not finding a satisfactory solution, I remembered that from time to time I am asked why I have just missed making certain discoveries. Since I have received a favorable reaction from the committee chairman, Dean Boorse, to my enquiry about whether it would be admissible to drop all discussion of recent work and to speak only on apparent bad luck in my attempts to make certain scientific discoveries, I shall do so in the hope of satisfying once and for all those who have asked or would like to ask me about these matters. I shall talk mainly on attempts to observe nuclear and electron magnetic resonances, gamma anisotropy after orienting atomic nuclei, anisotropy of beta emission, and flux quantization in superconductors.
Circ_0007429/miR‐637/TRIM71/Ago2 axis participates in the regulation of proliferation, migration, invasion, apoptosis, and aerobic glycolysis of HCC

CircRNAs play an important role in the progression of hepatocellular carcinoma (HCC), however, the role of circ_0007429 in HCC remains unknown. Using bioinformatics tools, we selected circ_0007429 that was most highly expressed in HCC tissues and investigated its role in HCC progression. Immunohistochemistry, plasmid transfection, real‐time quantitative PCR, and western blot analysis were used to identify the relationship between circ_0007429 and its potential target, miR‐637, and TRIM71. The regulatory effect of circ_0007429 on miR‐637/TRIM71/Ago2 signaling and its key role in HCC progression were studied in vitro. A nude mouse xenograft model was used to examine tumor growth in vivo. Circ_0007429 and TRIM71 expression were upregulated, while miR‐637 expression was downregulated in HCC tissues and cells compared with their expression in control groups. Knockdown of circ_0007429 enhanced apoptosis in HCC cells, while impeded proliferation, migration, invasion, and aerobic glycolysis, which were reversed by miR‐637 inhibitor. High levels of circ_0007429 correlated with a poor survival rate of HCC patients. Additionally, circ_0007429 interfering inhibited tumor growth in vivo. TRIM71 directly bound to miR‐637 and inhibited Ago2 expression. Moreover, circ_0007429 promotes aerobic glycolysis in HCC cells through the miR/TRIM71/Ago2 axis. Circ_0007429 promotes HCC progression by promoting cell proliferation, migration, invasion, and aerobic glycolysis and by inhibiting cell apoptosis through the miR/TRIM71/Ago2 axis. These results provide molecular insights into the mechanism of HCC and suggest that circ_0007429 could be a therapeutic target for HCC.
Large-eddy simulation of curved-geometry flows using contravariant components of velocity

The current large-eddy simulation (LES) research makes use of the contravariant components as the dependent variables on a staggered grid system for the discretisation of the governing equations in curvilinear coordinates. This technology provides a possibility to investigate efficiently turbulent flows in complex geometries. To test and validate the recently developed in-house LES code, LESSGA (Large-Eddy Simulation on a Staggered Grid Arrangement), numerical simulations were performed for turbulent flows in a concentric annular pipe and transitional flows past an airfoil. In this article, the computed results of flows in a concentric annular pipe with a radius ratio of a = R inner/Router = 0.5 at and flows past an SD7003 airfoil at Rec = 60,000 and angle of attack α = 4° are compared with available experimental and DNS data. Technical difficulties experienced are also discussed.
In-vitro accuracy of casts for orthodontic purposes obtained by a conventional and by a printer workflow

This in-vitro study was designed to investigate whether conventionally produced casts and printed casts for orthodontic purposes show comparable full-arch accuracy. To produce casts, either a conventional impression or a digital data set is needed. A fully dentate all ceramic master cast was digitized with an industrial scanner to obtain a digital reference cast [REF]. Intraoral scans [IOS] and alginate impressions were taken from the master cast so that ten printed and ten gypsum casts were obtained. The printed casts [DLP] were digitized by an industrial scanner and as well as the gypsum casts [GYPSUM]. The following absolute mean trueness evaluations by superimposition were accomplished: [REF vs. GYPSUM]; [REF vs. DLP]; [REF vs. IOS]; [IOS vs. DLP]. For precision analysis the data sets of [GYPSUM], [IOS] and [DLP] were available. The absolute mean trueness values were 68 μm ± 15 μm for [REF vs. GYPSUM], 46 μm ± 4 μm for [REF vs. DLP], 20 μm ± 2 μm for [REF vs. IOS] and 41 μm ± 4 μm for [IOS vs. DLP]. [REF vs. GYPSUM] and [REF vs. DLP], [REF vs. IOS], [REF vs. DLP] and [IOS vs. DLP] showed statistically significant differences. The precision values were 56 μm ± 17 μm for [GYPSUM], 25 μm ± 9 μm for [DLP] and 12 μm ± 2 μm for [IOS] and differed significantly among each other. In the present study the print workflow revealed superior results in comparison to the conventional workflow. Due to contrary deviations in the [REF vs. IOS] and the [IOS vs. DLP] data sets the overall trueness deviations was enhanced.
Application of the network scale‐up method to estimate the sizes of key populations for HIV in Singapore using online surveys

Singapore lacks robust data on the sizes of the key populations that are most at risk for HIV. Using the network scale‐up method for hidden or hard‐to‐reach populations, we estimate the sizes of five key populations—male clients of female sex workers (MCFSW), men who have sex with men (MSM), female sex workers (FSW), people who inject drugs (PWID) and transgender people—and profile the ages and ethnicities of respondents with the high‐risk contacts they report knowing.
Molecular insights into Escherichia coli Cpx envelope stress response activation by the sensor lipoprotein NlpE

Bacterial two‐component signal transduction systems provide sensory inputs for appropriately adapting gene expression. These systems rely on a histidine kinase that phosphorylates a response regulator which alters gene expression. Several two‐component systems include additional sensory components that can activate the histidine kinase. In Escherichia coli, the lipoprotein NlpE was identified as a sensor for the Cpx cell envelope stress response. It has remained unclear how NlpE signals to Cpx in the periplasm. In this study, we used a combination of genetics, biochemistry, and AlphaFold2 complex modeling to uncover the molecular details of how NlpE triggers the Cpx response through an interaction with the CpxA histidine kinase. Remarkably, only a short loop of NlpE is required to activate the Cpx response. A single substitution in this loop inactivates NlpE signaling to Cpx and abolishes an in vivo biochemical NlpE:CpxA interaction. An independent AlphaFold multimer prediction supported a role for the loop and predicted an interaction interface at CpxA. Mutations in this CpxA region specifically blind the histidine kinase to NlpE activation but preserve the ability to respond to other cell envelope stressors. Hence, our work additionally reveals a previously unrecognized complexity in signal integration by the CpxA periplasmic sensor domain.
Probiotic Lactobacillus Species and Their Biosurfactants Eliminate Acinetobacter baumannii Biofilm in Various Manners

A. baumannii biofilm is a significant virulence factor that causes the biofilm colonization of invasive illnesses. Rising bacterial resistance to synthetic antimicrobials has prompted researchers to look at natural alternatives, such as probiotics and their derivatives. ABSTRACT Acinetobacter baumannii is a critical biofilm-forming pathogen that has presented great challenges in the clinic due to multidrug resistance. Thus, new methods of intervention are needed to control biofilm-associated infections. In this study, among three tested Lactobacillus species, Lactobacillus rhamnosus showed significant antimaturation and antiadherence effects against A. baumannii biofilm. Lactic acid (LA) and acetic acid (AA) were the most effective antibiofilm biosurfactants (BSs) produced by L. rhamnosus. This antibiofilm phenomenon produced by LA and AA was due to the strong bactericidal effect, which worked from very early time points, as determined by colony enumeration and confocal laser scanning microscope. The cell destruction of A. baumannii appeared in both the cell envelope and cytoplasm. A discontinuous cell envelope, the leakage of cell contents, and the increased extracellular activity of ATPase demonstrated the disruption of the cell membrane by LA and AA. These effects also demonstrated the occurrence of protein lysis. In addition, bacterial DNA interacted with and was damaged by LA and AA, resulting in significantly reduced expression of biofilm and DNA repair genes. The results highlight the possibility and importance of using probiotics in clinical prevention. Probiotics can be utilized as novel biocides to block and decrease biofilm formation and microbial contamination in medical equipment and during the treatment of infections. IMPORTANCE A. baumannii biofilm is a significant virulence factor that causes the biofilm colonization of invasive illnesses. Rising bacterial resistance to synthetic antimicrobials has prompted researchers to look at natural alternatives, such as probiotics and their derivatives. In this study, L. rhamnosus and its BSs (LA and AA) demonstrated remarkable antibiofilm and antimicrobial characteristics, with a significant inhibitory effect on A. baumannii. These effects were achieved by several mechanisms, including the disruption of the cell envelope membrane, protein lysis, reduced expression of biofilm-related genes, and destruction of bacterial DNA. The results provide support for the possibility of using probiotics and their derivatives in the clinical prevention and therapy of A. baumannii infections.
Distinct Aurora B pools at the inner centromere and kinetochore have different contributions to meiotic and mitotic chromosome segregation

Proper chromosome segregation depends on the establishment of bioriented kinetochore–microtubule attachments, which often requires multiple rounds of release and reattachment. Aurora B and C kinases phosphorylate kinetochore proteins to release tensionless attachments. Multiple pathways recruit Aurora B/C to the centromere and kinetochore. We studied how these pathways contribute to anaphase onset timing and correction of kinetochore–microtubule attachments in budding yeast meiosis and mitosis. We find that the pool localized by the Bub1/Bub3 pathway sets the normal duration of meiosis and mitosis, in differing ways. Our meiosis data suggests a model that disruption of this pathway leads to PP1 kinetochore localization, which dephosphorylates Cdc20 for premature anaphase onset. For error correction, the Bub1/Bub3 and COMA pathways are individually important in meiosis but compensatory in mitosis. Finally, we find that the haspin and Bub1/3 pathways function together to ensure error correction in mouse oogenesis. Our results suggest that each recruitment pathway localizes spatially distinct kinetochore-localized Aurora B/C pools that function differently between meiosis and mitosis.
Experimental evidence for the functional importance and adaptive advantage of A-to-I RNA editing in fungi

Significance RNA editing is hypothesized to facilitate adaptive evolution via flexibly diversifying the proteome temporally or spatially. However, direct experimental evidence is lacking. This study unveils the functional importance of conserved missense adenosine-to-inosine (A-to-I) RNA editing (CME) sites in Fusarium graminearum and provides convincing experimental evidence for the adaptive advantages of two CME sites. The first CME site drives the CME5 gene gaining a new important function in ascus and ascospore formation during evolution. Having an editable A at this site is fitter than an uneditable A or a genomically encoded G. The second CME site in the CME11 gene confers a “heterozygote advantage” during ascosporogenesis, meaning that concurrently expressing both edited and unedited versions is more advantageous than either.
Validation of Nickel Bioavailability Models for Algae, Invertebrates, and Fish in Chinese Surface Waters

Nickel (Ni) is used primarily in the production of alloys like stainless steel and is increasingly being used in the production of batteries for the electric vehicle market. Exposure of Ni to ecosystems is of concern because Ni can be toxic to aquatic organisms. The influence of water chemistry constituents (e.g., hardness, pH, dissolved organic carbon) on the toxicity of Ni has prompted the development and use of bioavailability models, such as biotic ligand models (BLMs), which have been demonstrated to accurately predict Ni toxicity in broadly different ecosystems, including Europe, North America, and Australia. China, a leading producer of Ni, is considering bioavailability‐based approaches for regulating Ni emissions. Adoption of bioavailability‐based approaches in China requires information to demonstrate the validity of bioavailability models for the local water chemistry conditions. The present study investigates the toxicity of Ni to three standard test species (Daphnia magna, Pseudokirchneriella subcapitata, and Danio rerio) in field‐collected natural waters that are broadly representative of the range of water chemistries and bioavailabilities encountered in Chinese lakes and rivers. All experimental data are within a factor of 3 of the BLM predicted values for all tests with all species. For D. magna, six of seven waters were predicted within a factor of 2 of the experimental result. Comparison of experimental data against BLM predictions shows that the existing Ni bioavailability models are able to explain the differences in toxicity that result from water chemistry conditions in China. Validation of bioavailability models to water chemistries and bioavailability ranges within China provides technical support for the derivation of site‐specific Ni water quality criteria in China. Environ Toxicol Chem 2023;42:1257–1265. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
Whole-Genome Sequence of Endophytic Bacteria Associated with Poison Ivy Vine (Toxicodendron radicans)

Here, we report the genome assemblies of 11 endophytic bacteria, isolated from poison ivy vine (Toxicodendron radicans). Five species belonging to the genus Pseudomonas, two species of Curtobacterium, one strain of Pantoea agglomerans, and one species from the Bacillus, Cellulomonas, and Enterobacter genera were isolated from the interior tissue of poison ivy. ABSTRACT Here, we report the genome assemblies of 11 endophytic bacteria, isolated from poison ivy vine (Toxicodendron radicans). Five species belonging to the genus Pseudomonas, two species of Curtobacterium, one strain of Pantoea agglomerans, and one species from the Bacillus, Cellulomonas, and Enterobacter genera were isolated from the interior tissue of poison ivy.
Maternal characteristics associated with referral to obstetrician-led care in low-risk pregnant women in the Netherlands: A retrospective cohort study

Background In the Netherlands, maternity care is divided into midwife-led care (for low-risk women) and obstetrician-led care (for high-risk women). Referrals from midwife-led to obstetrician-led care have increased over the past decade. The majority of women are referred during their pregnancy or labour. Referrals are based on a continuous risk assessment of the health and characteristics of mother and child, yet referral for non-medical factors and characteristics remain unclear. This study investigated which maternal characteristics are associated with women’s referral from midwife-led to obstetrician-led care. Materials and methods A retrospective cohort study in one midwife-led care practice in the Netherlands included 1096 low-risk women during January 2015–17. The primary outcomes were referral from midwife-led to obstetrician-led care in (1) the antepartum period and (2) the intrapartum period. In total, 11 maternal characteristics were identified. Logistic regression models of referral in each period were fitted and stratified by parity. Results In the antepartum period, referral among nulliparous women was associated with an older maternal age (aOR, 1.07; 95%CI, 1.05–1.09), being underweight (0.45; 0.31–0.64), overweight (2.29; 1.91–2.74), or obese (2.65; 2.06–3.42), a preconception period >1 year (1.34; 1.07–1.66), medium education level (0.76; 0.58–1.00), deprivation (1.87; 1.54–2.26), and sexual abuse (1.44; 1.14–1.82). Among multiparous women, a referral was associated with being underweight (0.40; 0.26–0.60), obese (1.61; 1.30–1.98), a preconception period >1 year (1.71; 1.27–2.28), employment (1.38; 1.19–1.61), deprivation (1.23; 1.03–1.46), highest education level (0.63; 0.51–0.80), psychological problems (1.24; 1.06–1.44), and one or multiple consultations with an obstetrician (0.68; 0.58–0.80 and 0.64; 0.54–0.76, respectively). In the intrapartum period, referral among nulliparous women was associated with an older maternal age (1.02; 1.00–1.05), being underweight (1.67; 1.15–2.42), a preconception period >1 year (0.42; 0.31–0.57), medium or high level of education (2.09; 1.49–2.91 or 1.56; 1.10–2.22, respectively), sexual abuse (0.46; 0.33–0.63), and multiple consultations with an obstetrician (1.49; 1.15–1.94). Among multiparous women, referral was associated with an older maternal age (1.02; 1.00–1.04), being overweight (0.65; 0.51–0.83), a preconception period >1 year (0.33; 0.17–0.65), non-Dutch ethnicity (1.98; 1.61–2.45), smoking (0.75; 0.57–0.97), sexual abuse (1.49; 1.09–2.02), and one or multiple consultations with an obstetrician (1.34; 1.06–1.70 and 2.09; 1.63–2.69, respectively). Conclusions This exploratory study showed that several non-medical maternal characteristics of low-risk pregnant women are associated with referral from midwife-led to obstetrician-led care, and how these differ by parity and partum period.
Deterministic sampling and range counting in geometric data streams

We present memory-efficient deterministic algorithms for constructing ε-nets and ε-approximations of streams of geometric data. Unlike probabilistic approaches, these deterministic samples provide guaranteed bounds on their approximation factors. We show how our deterministic samples can be used to answer approximate online iceberg geometric queries on data streams. We use these techniques to approximate several robust statistics of geometric data streams, including Tukey depth, simplicial depth, regression depth, the Thiel-Sen estimator, and the least median of squares. Our algorithms use only a polylogarithmic amount of memory, provided the desired approximation factors are at least inverse-polylogarithmic. We also include a lower bound for noniceberg geometric queries.
The Enduring Effects of COVID for Cancer Care: Learning from Real-Life Clinical Practice

Abstract For three years, COVID-19 has circulated among our communities and around the world, fundamentally changing social interactions, health care systems, and service delivery. For people living with (and receiving treatment for) cancer, pandemic conditions presented significant additional hurdles in an already unstable and shifting environment, including disrupted personal contact with care providers, interrupted access to clinical trials, distanced therapeutic encounters, multiple immune vulnerabilities, and new forms of financial precarity. In a 2020 perspective in this journal, we examined how COVID-19 was reshaping cancer care in the early stages of the pandemic and how these changes might endure into the future. Three years later, and in light of a series of interviews with patients and their caregivers from the United States and Australia conducted during the pandemic, we return to consider the potential legacy effects of the pandemic on cancer care. While some challenges to care provision and survivorship were unforeseen, others accentuated and amplified existing problems experienced by patients, caregivers, and health care providers. Both are likely to have enduring effects in the “post-pandemic” world, raising the importance of focusing on lessons that can be learned for the future.
Objective Prediction of Next-Day’s Affect Using Multimodal Physiological and Behavioral Data: Algorithm Development and Validation Study

Background Affective states are important aspects of healthy functioning; as such, monitoring and understanding affect is necessary for the assessment and treatment of mood-based disorders. Recent advancements in wearable technologies have increased the use of such tools in detecting and accurately estimating mental states (eg, affect, mood, and stress), offering comprehensive and continuous monitoring of individuals over time. Objective Previous attempts to model an individual’s mental state relied on subjective measurements or the inclusion of only a few objective monitoring modalities (eg, smartphones). This study aims to investigate the capacity of monitoring affect using fully objective measurements. We conducted a comparatively long-term (12-month) study with a holistic sampling of participants’ moods, including 20 affective states. Methods Longitudinal physiological data (eg, sleep and heart rate), as well as daily assessments of affect, were collected using 3 modalities (ie, smartphone, watch, and ring) from 20 college students over a year. We examined the difference between the distributions of data collected from each modality along with the differences between their rates of missingness. Out of the 20 participants, 7 provided us with 200 or more days’ worth of data, and we used this for our predictive modeling setup. Distributions of positive affect (PA) and negative affect (NA) among the 7 selected participants were observed. For predictive modeling, we assessed the performance of different machine learning models, including random forests (RFs), support vector machines (SVMs), multilayer perceptron (MLP), and K-nearest neighbor (KNN). We also investigated the capability of each modality in predicting mood and the most important features of PA and NA RF models. Results RF was the best-performing model in our analysis and performed mood and stress (nervousness) prediction with ~81% and ~72% accuracy, respectively. PA models resulted in better performance compared to NA. The order of the most important modalities in predicting PA and NA was the smart ring, phone, and watch, respectively. SHAP (Shapley Additive Explanations) analysis showed that sleep and activity-related features were the most impactful in predicting PA and NA. Conclusions Generic machine learning–based affect prediction models, trained with population data, outperform existing methods, which use the individual’s historical information. Our findings indicated that our mood prediction method outperformed the existing methods. Additionally, we found that sleep and activity level were the most important features for predicting next-day PA and NA, respectively.