Miracle-dz/UniFAR-FTUs huggingface dataset:
Classification of microarray data with penalized logistic regression

Classification of microarray data needs a firm statistical basis. In principle, logistic regression can provide it, modeling the probability of membership of a class with (transforms of) linear combinations of explanatory variables. However, classical logistic regression does not work for microarrays, because generally there will be far more variables than observations. One problem is multicollinearity: estimating equations become singular and have no unique and stable solution. A second problem is over-fitting: a model may fit well into a data set, but perform badly when used to classify new data. We propose penalized likelihood as a solution to both problems. The values of the regression coefficients are constrained in a similar way as in ridge regression. All variables play an equal role, there is no ad-hoc selection of most relevant or most expressed genes. The dimension of the resulting systems of equations is equal to the number of variables, and generally will be too large for most computers, but it can dramatically be reduced with the singular value decomposition of some matrices. The penalty is optimized with AIC (Akaike's Information Criterion), which essentially is a measure of prediction performance. We find that penalized logistic regression performs well on a public data set (the MIT ALL/AML data).
Rare diseases of ectoderm: Translating discovery to therapy

Heritable conditions known as ectodermal dysplasias are rare and can be associated with marked morbidity, mortality, and a reduced quality of life. The diagnosis and care of individuals affected by one of the many ectodermal dysplasias presents myriad challenges due to their rarity and the diverse phenotypes. These conditions are caused by abnormalities in multiple genes and signaling pathways that are essential for the development and function of ectodermal derivatives. During a 2021 international conference focused on translating discovery to therapy, researchers and clinicians gathered with the goal of advancing the diagnosis and treatment of conditions affecting ectodermal tissues with an emphasis on skin, hair, tooth, and eye phenotypes. Conference participants presented a variety of promising treatment strategies including gene or protein replacement, gene editing, cell therapy, and the identification of druggable targets. Further, barriers that negatively influence the current development of novel therapeutics were identified. These barriers include a lack of accurate prevalence data for rare conditions, absence of an inclusive patient registry with deep phenotyping data, and insufficient animal models and cell lines. Overcoming these barriers will need to be prioritized in order to facilitate the development of novel treatments for genetic disorders of the ectoderm.
A Full View of EIT Waves

Early observations by the EUV Imaging Telescope (EIT) on the Solar and Heliospheric Observatory indicated that propagating diffuse wave fronts, now conventionally referred to as "EIT waves," can often be seen on the solar disk with a propagation velocity several times smaller than that of Hα Moreton waves. They are almost always associated with coronal mass ejections. We have previously confirmed the existence of such a wave phenomenon with numerical simulations, which indicate that there does exist a slower moving "wave" much behind the coronal counterpart of the Hα Moreton wave. Further observations have disclosed many new features of the EIT waves: the waves stop near the separatrix between active regions, sometimes they experience acceleration from the active region to the quiet region, and so on. Here we report on MHD simulations performed to demonstrate how the typical features of EIT waves can all be accounted for within our theoretical model, in which the EIT waves are thought to be formed by successive stretching or opening of closed field lines driven by an erupting flux rope. The relationship between EIT waves, Hα Moreton waves, and type II radio bursts is discussed, with an emphasis on reconciling the discrepancies among different views of the "EIT wave" phenomenon.
Dynamic fracture analysis using discrete cohesive crack method

Dynamic fracture is studied using a mesh‐ less discrete cohesive crack method. The method is based on partition of unity and cracks are represented by a set of crack segments. The crack segments are required to pass through the entire domain of influence of node. They are introduced when the maximum principal stress exceeds the uniaxial tensile strength. The crack segments are allowed to rotate in order to avoid too stiff system responses. The major advantage of our method is that it does not require algorithms to track the crack path. Copyright © 2009 John Wiley & Sons, Ltd.
Acute Toxicity Evaluation of Lindane-Waste Contaminated Soils Treated by Surfactant-Enhanced ISCO

The discharge of lindane wastes in unlined landfills causes groundwater and soil pollution worldwide. The liquid waste generated (a mixture of 28 chlorinated organic compounds, COCs) constitutes a dense non-aqueous phase liquid (DNAPL) that is highly persistent. Although in situ chemical oxidation (ISCO) is effective for degrading organic pollutants, the low COCs solubility requires high reaction times. Simultaneous injection of surfactants and oxidants (S-ISCO) is a promising technology to solve the limitation of ISCO treatment. The current work studies the remediation of highly polluted soil (COCs = 3682 mg/kg) obtained at the Sardas landfill (Sabiñáñigo, Spain) by ISCO and S-ISCO treatments. Special attention is paid to acute soil toxicity before and after the soil treatment. Microtox®, modified Basic Solid-Phase Test (mBSPT) and adapted Organic Solvent Sample Solubilization Test (aOSSST) were used for this scope. Persulfate (PS, 210 mM) activated by alkali (NaOH, 210 mM) was used in both ISCO and S-ISCO runs. A non-ionic and biodegradable surfactant selected in previous work, Emulse®3 (E3, 5, and 10 g/L), was applied in S-ISCO experiments. Runs were performed in soil columns filled with 50 g of polluted soil, with eight pore volumes (Pvs) of the reagents injected and 96 h between successive Pv injections. The total treatment time was 32 days. The results were compared with those corresponding without surfactant (ISCO). After remediation treatments, soils were water-washed, simulating the conditions of groundwater flux in the subsoil. The treatments applied highly reduced soil toxicity (final soil toxicity equivalent to that obtained for non-contaminated soil, mBSPT) and organic extract toxicity (reduction > 95%, aOSSST). Surfactant application did not cause an increase in the toxicity of the treated soil, highlighting its suitability for full-scale applications.
Enhancing Motor and Sensory Axon Regeneration after Peripheral Nerve Injury Using Bioluminescent Optogenetics

Introduction—Recovery from peripheral nerve injuries is poor even though injured peripheral axons can regenerate. Novel therapeutic approaches are needed. The most successful preclinical experimental treatments have relied on increasing the activity of the regenerating axons, but the approaches taken are not applicable to many nerve-injured patients. Bioluminescent optogenetics (BL-OG) is a novel method of increasing the excitation of neurons that might be similar to that found with activity-dependent experimental therapies. We investigated the use of BL-OG as an approach to promoting axon regeneration following peripheral nerve injury. Methods—BL-OG uses luminopsins, light-sensing ion channels (opsins) fused with a light-emitting luciferase. When exposed to a luciferase substrate, such as coelenterazine (CTZ), luminopsins expressed in neurons generate bioluminescence and produce excitation through their opsin component. Adeno-associated viral vectors encoding either an excitatory luminopsin (eLMO3) or a mutated form (R115A) that can generate bioluminescence but not excite neurons were injected into mouse sciatic nerves. After retrograde transport and viral transduction, nerves were cut and repaired by simple end-to-end anastomosis, and mice were treated with a single dose of CTZ. Results—Four weeks after nerve injury, compound muscle action potentials (M waves) recorded in response to sciatic nerve stimulation were more than fourfold larger in mice expressing the excitatory luminopsin than in controls expressing the mutant luminopsin. The number of motor and sensory neurons retrogradely labeled from reinnervated muscles in mice expressing eLMO3 was significantly greater than the number in mice expressing the R115A luminopsin and not significantly different from those in intact mice. When viral injection was delayed so that luminopsin expression was induced after nerve injury, a clinically relevant scenario, evoked M waves recorded from reinnervated muscles were significantly larger after injury in eLMO3-expressing mice. Conclusions—Treatment of peripheral nerve injuries using BL-OG has significant potential to enhance axon regeneration and promote functional recovery.
Pre-Existing Interstitial Lung Abnormalities Are Independent Risk Factors for Interstitial Lung Disease during Durvalumab Treatment after Chemoradiotherapy in Patients with Locally Advanced Non-Small-Cell Lung Cancer

Simple Summary Interstitial lung disease (ILD) is a life-threatening toxicity caused by chemoradiotherapy and durvalumab; however, the risk factors for ILD during durvalumab treatment after chemoradiotherapy have not been established in non-small-cell lung cancer patients. We examined whether interstitial lung abnormalities (ILAs) could be risk factors for ≥grade-two ILD during durvalumab treatment. The prevalence of ILAs in 148 patients before durvalumab treatment was 37.8%, and the multivariate analysis revealed ILAs as independent risk factors for ≥grade-two ILD. Attention should be paid to the development of ILD during durvalumab treatment in patients with ILAs. Abstract Introduction/Background: Chemoradiotherapy (CRT) followed by durvalumab, an immune checkpoint inhibitor, is the standard treatment for locally advanced non-small-cell lung cancer (NSCLC). Interstitial lung disease (ILD) is a life-threatening toxicity caused by these treatments; however, risk factors for the ILD have not yet been established. Interstitial lung abnormalities (ILAs) are computed tomography (CT) findings which manifest as minor interstitial shadows. We aimed to investigate whether ILAs could be risk factors for grade-two or higher ILD during durvalumab therapy. Patients and Methods: Patients with NSCLC who received durvalumab after CRT from July 2018 to June 2021 were retrospectively enrolled. We obtained patient characteristics, laboratory data, radiotherapeutic parameters, and chest CT findings before durvalumab therapy. Results: A total of 148 patients were enrolled. The prevalence of ILAs before durvalumab treatment was 37.8%. Among 148 patients, 63.5% developed ILD during durvalumab therapy. The proportion of patients with grade-two or higher ILD was 33.8%. The univariate logistic regression analysis revealed that older age, high dose-volume histogram parameters, and the presence of ILAs were significant risk factors for grade-two or higher ILD. The multivariate analysis showed that ILAs were independent risk factors for grade-two or higher ILD (odds ratio, 3.70; 95% confidence interval, 1.69–7.72; p < 0.001). Conclusions: We showed that pre-existing ILAs are risk factors for ILD during durvalumab treatment after CRT. We should pay attention to the development of grade-two or higher ILD during durvalumab treatment in patients with ILAs.
On-device High Accuracy Plant Classifier

In this paper, we present an on-device high accuracy plant classifier (HAPC) system, which classifies plant species from leaf images. The system generally uses a classic pre-trained ResNet variant called ResNet50-D as the backbone with several refinements. We use the EDA (Exploratory Data Analysis) approach to comprehend the dataset and explore the data structure to extract the dataset's main characteristics. Besides EDA, we also implement image augmentation for the dataset in order to improve model performance and generalize ability. The model, pre-trained with ImageNet, has 19 million parameters and 6 billion FLOPs. With 5-fold cross-validation at 50 epochs, we reached the accuracy of 98.522% on the validation set. Our baseline only has 85.681% accuracy, showing that a classic architecture with refinements can still gain a significant performance boost.
Analysis of Health Belief Model regarding Human Papillomavirus Vaccination among Female Employees at Sukabumi Regency Government

The high rate of cervical cancer case confirms it as the second most common cancer in Indonesia which required specific management and primary prevention efforts for everyone. The appeal issued by the Ministry of Health regarding HPV vaccination which will be mandatory as an effort to reduce cervical cancer rates in Indonesia. This study aims to analyze the health belief model as the influential factor for the willingness to get HPV vaccination as an effort to prevent cervical cancer among female employees in Sukabumi Regency government in 2022. This was a quantitative study with cross-sectional design. Data were collected among 213 respondents who were selected using purposive sampling technique. The results showed that 50.7% of respondents were willing to get HPV vaccination. Meanwhile, 49,3% of respondents were not willing to get HPV vaccination. There was a relationship between perceived susceptibility, benefit, obstacle, cues to action, and self-efficacy with the willingness to get HPV vaccination. Meanwhile, the perceived severity was not related to the willingness to get HPV vaccination. In the multivariate analysis, it was found that cues to action (POR=5,477; 95% CI=2,6-11,2) had the most significant effect on willingness to get HPV vaccination. It is expected that the current study can be used as an input for the government of Sukabumi Regency to plan for health promotion programs for every agency regarding cervical cancer, especially HPV vaccination.
Smoking Cessation after Cancer Diagnosis and Enhanced Therapy Response: Mechanisms and Significance

The adverse effects of smoking on human health have been recognized for several decades, especially in the context of cancer. The ability of tobacco smoke components, including tobacco-specific carcinogens and additive compounds such as nicotine, to initiate or promote tumor growth have been described in hundreds of studies. These investigations have revealed the tumor-promoting activities of nicotine and other tobacco smoke components and have also recognized the ability of these agents to suppress the efficacy of cancer therapy; it is now clear that smoking can reduce the efficacy of most of the widely used therapeutic modalities, including immunotherapy, radiation therapy, and chemotherapy. Several studies examined if continued smoking after cancer diagnosis affected therapy response; it was found that while never smokers or non-smokers had the best response to therapy, those who quit smoking at the time of diagnosis had higher overall survival and reduced side-effects than those who continued to smoke. These studies also revealed the multiple mechanisms via which smoking enhances the growth and survival of tumors while suppressing therapy-induced cell death. In conclusion, smoking cessation during the course of cancer therapy markedly increases the chances of survival and the quality of life.
Use of a Sprayable Sex Pheromone Formulation in Landscape-Level Control of Choristoneura fumiferana Populations

Simple Summary Mating disruption for insect pests can be an effective and environmentally sensible method. For landscape-level population management of forest insects, however, statistically rigorous experiments can be difficult to undertake. In 2021, we tested a new microencapsulated formulation (CONFOUNDSBW) that was designed specifically for low density spruce budworm populations in New Brunswick, Canada, in a fully replicated experiment. While adult trap catch was reduced by 90% in treatment blocks, larval density and apparent fecundity were not significantly affected when compared to those in untreated control blocks. Although mating disruption remains a potentially useful tool in landscape-level forest pest management, CONFOUNDSBW is not effective against spruce budworm at low population densities when applied in accordance to label rates and volumes. Abstract Choristoneura fumiferana (SBW) is a major defoliating pest of balsam fir and spruce in eastern North America. As part of an integrated management strategy for SBW, we evaluated the effectiveness of mating disruption as a landscape-level population control tactic. Using a sprayable formulation (CONFOUNDSBW) containing a synthetic sex pheromone blend, we treated five 300 ha blocks in Northern New Brunswick with an aerially applied microencapsulated mixture. There were significant reductions in adult trap catches in treated blocks compared to untreated control blocks. Branch sampling in treated blocks showed uniform distribution of CONFOUNDSBW deposition throughout the blocks. Population densities following treatment were not significantly affected when compared to densities in control blocks, or prior to treatment. Analysis of egg:adult ratios indicates that no immigration events occurred within treatment or control blocks. The lack of population reduction following treatment strongly suggests that widespread application of CONFOUNDSBW at a rate of 50 g of active ingredient per hectare is not an effective tool in controlling SBW populations.
Constructing pathological non-ideal active device models using mirror cells

The pathological modelling of active devices is very useful in performing symbolic analysis. To obtain more accurate symbolic equations rather than ideal approximations, the construction of non-ideal active device models using mirror cells is investigated in this article. Three popular active devices are illustrated, and an attempt is made to obtain more simplified versions to achieve higher analysed efficiency of symbolic analysis. Two practical circuit examples are given to demonstrate the feasibility of the presented models of non-ideal active devices.
Use of Antimicrobials by Class in Pigs in Germany—A Longitudinal Description Considering Different International Categorisation Systems

Antimicrobial usage in both human and veterinary medicine is considered one of the main drivers of antimicrobial resistance; its reduction poses a serious challenge. To analyse the associations between usage and resistance, data from monitoring systems and classification of all antimicrobial substances are crucial. In this analysis, we investigated longitudinal data collected between 2013 and 2020 within the Veterinary Consumption of Antibiotics project from pig farms in Germany, including all antimicrobial classes, but focusing on critically important antimicrobials: third- and fourth-generation cephalosporins, fluoroquinolones, macrolides, and polymyxins. Analysing the treatment frequency, we found that a reduction in antimicrobial use in all types of pig production has occurred over time, accompanied by a rising percentage of farms without any usage. The lists of the World Health Organisation, World Organisation for Animal Health, and European Medicine Agency classify different antimicrobial substances as critically important. The vast differences between the respective weighted treatment frequencies allocated to the antimicrobials of main interest reflect the huge impact of the three categorisation systems. We concluded that, with the aim of creating national treatment guidelines supporting veterinarians to make treatment decisions, the list of the European Medicine Agency is the most suitable.
Tree Growth in Epoxy Resin Under Unipolar and Bipolar Square-Wave Voltages

The influence of DC bias on electrical tree growth under 13 kV square-wave voltages at 50 Hz in epoxy resin is investigated. Tree growth is captured in a needle-plane configuration using a CCD camera and digital microscope. Tree growth is accelerated under positive unipolar square waves in comparison with a bipolar square waves and negative square waves. Tree growth under positive and negative unipolar square wave voltages can be described as a three-stage process, while under bipolar square wave voltages tree growth follows a five-stage process. Reverse tree growth is observed before breakdown only under bipolar square waves. No reverse tree growth was seen under unipolar square waves of either polarity. Damage was observed at the bottom of the plane surface of epoxy where the reverse tree channels initiated.
Growth Parameters of Various Green Microalgae Species in Effluent from Biogas Reactors: The Importance of Effluent Concentration

The use of liquid waste as a feedstock for cultivation of microalgae can reduce water and nutrient costs and can also be used to treat wastewater with simultaneous production of biomass and valuable products. This study applied strategies to treat diluted anaerobic digester effluent (ADE) as a residue of biogas reactors with moderate (87 ± 0.6 mg L−1; 10% ADE) and elevated NH4+-N levels (175 ± 1.1 mg L−1; 20% ADE). The effect of ADE dilution on the acclimatization of various microalgae was studied based on the analysis of the growth and productivity of the tested green algae. Two species of the genus Chlorella showed robust growth in the 10–20% ADE (with a maximum total weight of 3.26 ± 0.18 g L−1 for C. vulgaris and 2.81 ± 0.10 g L−1 for C. sorokiniana). The use of 10% ADE made it possible to cultivate the strains of the family Scenedesmaceae more effectively than the use of 20% ADE. The growth of Neochloris sp. in ADE was the lowest compared to other microalgal strains. The results of this study demonstrated the feasibility of introducing individual green microalgae into the processes of nutrient recovery from ADE to obtain biomass with a high protein content.
A characterization of conditional probability.

The conditional probability functions relative to a sub-σ-field g$ are shown to constitute a vector-valued measure on the σ-field of the probability space, and it is proved that the conditional expectation relative to ^ of an jgft random variable X is the integral of X with respect to this vector-valued measure. A complete characterization is given of those vector-valued measures which are conditional probabilities. This machinery is illustratively applied to give alternative deriva-tions of results of Moy and Rota on the characterization of conditional expectation operators.
Majorization-subordination theorems for locally univalent functions

A quantitative majorization-subordination result of Goluzin and Tao Shah for univalent functions is generalized to H„, the linear invariant family of locally univalent functions of finite order or. If f(z) is subordinate to F(z) in the open unit disc, /'(0) > 0, and F(z) is in U„ 1.65 < a < oo, then f'(z) is majorized by F'(z) in \z\ < (a + 1) - (a2 + 2a)vi. The result is sharp.