Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation of miRNAs as Breast Cancer Biomarkers with a Machine Learning Approach

Certain small noncoding microRNAs (miRNAs) are differentially expressed in normal tissues and cancers, which makes them great candidates for biomarkers for cancer. Previously, a selected subset of miRNAs has been experimentally verified to be linked to breast cancer. In this paper, we validated the importance of these miRNAs using a machine learning approach on miRNA expression data. We performed feature selection, using Information Gain (IG), Chi-Squared (CHI2) and Least Absolute Shrinkage and Selection Operation (LASSO), on the set of these relevant miRNAs to rank them by importance. We then performed cancer classification using these miRNAs as features using Random Forest (RF) and Support Vector Machine (SVM) classifiers. Our results demonstrated that the miRNAs ranked higher by our analysis had higher classifier performance. Performance becomes lower as the rank of the miRNA decreases, confirming that these miRNAs had different degrees of importance as biomarkers. Furthermore, we discovered that using a minimum of three miRNAs as biomarkers for breast cancers can be as effective as using the entire set of 1800 miRNAs. This work suggests that machine learning is a useful tool for functional studies of miRNAs for cancer detection and diagnosis.
Optimizing pegylated asparaginase use: An institutional guideline for dosing, monitoring, and management

The incorporation of L-asparaginase and pegylated asparaginase into pediatric-inspired regimens has conferred a survival advantage in treatment of adults with acute lymphoblastic leukemia. Use of asparaginase products requires careful prevention, monitoring, and management of adverse effects including hypersensitivity, hepatotoxicity, pancreatitis, coagulopathy, and thrombosis. Currently, there is limited published literature to offer guidance on management of these toxicities. At the University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, a standard of practice guideline was created to prevent and manage asparaginase-related adverse events. By sharing our long-term experience with asparaginase products and clinical management of asparaginase-induced toxicities, this article aims to improve patient safety and optimize treatment outcomes.
Modeled Impacts of Sea Ice Exchange Processes on Arctic Ocean Carbon Uptake and Acidification (1980–2015)

A regional Arctic ice ocean model incorporating biogeochemical processes occurring inside the sea ice and water column is used to assess changes to the Arctic Ocean's carbon system, including oceanic carbon uptake and ocean acidification, over the recent period of Arctic sea ice decline (1980–2015). Two novel modifications are the following: (1) incorporation of carbon uptake by sea ice algae and (2) modification of the sea ice carbon pump to allow for vertical transport by brine plumes with high concentrations of dissolved inorganic carbon (DIC) and total alkalinity (TA) to the bottom of the mixed layer. The simulated carbon uptake north of 66.5°N increases by 20%, from 110 to 135 Tg C yr−1 from 1980–2015, and the mean pan‐Arctic sea surface pH decreases from 8.1 to 8.0. There is substantial regional and seasonal variability, highlighting potential problems with interpolating sparse measurements. Two sensitivity studies assess the effects of modifications to the near‐surface carbonate system. First, excluding the sea ice carbon pump results in a marked decrease in seasonal variability of pan‐Arctic‐mean sea surface DIC (∼25% less than the standard run) and TA (∼10% less), suggesting that neglecting the ice carbon pump results in models overestimating the saturation state in summer. Second, neglecting the sea ice algae results in an underestimation of the Arctic Ocean's annual carbon uptake (∼3% per year), indicating that the accumulating year‐on‐year underestimation of annual carbon uptake, as a result of neglecting sea ice algae, would lead to increasing error over multidecadal runs of polar ocean models.
Crime, Different Taxation, Police Spending and Embodied Human Capital

We develop a model with crime, embodied human capital, police spending and three different taxation. Based on propositions examined analytically, numerically and empirically using a cross‐country panel data on crime, we contribute to the literature by identifying a positive crime‐labor income tax nexus and a negative crime‐capital income tax nexus. The opposite effect between labor and capital income taxation on crime is novel in the literature. We also document positive association between crime and consumption tax, which suggests that apprehension probability (a proxy for the effectiveness of criminal justice system) is endogenous to fiscal mechanism. These findings have potential policy implications in that, there is a potential role for dedicated tax instruments to be used in supporting conventional crime prevention and deterrence policies.
The landscape of enteric pathogen exposure of young children in public domains of low-income, urban Kenya: The influence of exposure pathway and spatial range of play on multi-pathogen exposure risks

Background Young children are infected by a diverse variety of enteric pathogens in low-income, high-burden countries. Little is known about which conditions pose the greatest risk for enteric pathogen exposure and infection. Young children frequently play in residential public areas around their household, including areas contaminated by human and animal feces, suggesting these exposures are particularly hazardous. Objectives The objective of this study was to examine how the dose of six types of common enteric pathogens, and the probability of exposure to one or multiple enteric pathogens for young children playing at public play areas in Kisumu, Kenya is influenced by the type and frequency of child play behaviors that result in ingestion of soil or surface water, as well as by spatial variability in the number of public areas children are exposed to in their neighborhood. Methods A Bayesian framework was employed to obtain the posterior distribution of pathogen doses for a certain number of contacts. First, a multivariate random effects tobit model was used to obtain the posterior distribution of pathogen concentrations, and their interdependencies, in soil and surface water, based upon empirical data of enteric pathogen contamination in three neighborhoods of Kisumu. Then, exposure doses were estimated using behavioral contact parameters from previous studies, and contrasted under different exposure conditions. Results Multi-pathogen exposure of children at public play areas was common. Pathogen doses and the probability of multi-pathogen ingestion increased with: higher frequency of environmental contact, especially for surface water; larger volume of soil or water ingested; and with play at multiple sites in the neighborhood versus single site play. Discussion Child contact with surface water and soil at public play areas in their neighborhood is an important cause of exposure to enteric pathogens in Kisumu, and behavioral, environmental, and spatial conditions are determinants of exposure.
In Vitro Antioxidant and Antimicrobial Properties of Flower, Leaf, and Stem Extracts of Korean Mint

Traditionally, Agastache rugosa (Korean mint) has been widely used to treat various infectious diseases. The aims of this study were to: (i) determine the phenylpropanoid content of the plant using high-performance liquid chromatography; (ii) undertake total anthocyanin, flavonoid, and phenolic assays; (iii) and evaluate the antioxidant and antibacterial properties of the methanol extracts from the stem, leaves, and flowers of Korean mint. The total anthocyanin, flavonoid, and phenolic content assays showed that the flowers had higher phenolic levels than the stem and leaves. The reducing power, the 2,2-diphenyl-1-picrylhydrazyl superoxide radical scavenging abilities, and the hydrogen peroxide radical scavenging activities were also evaluated so that the antioxidant activities of the extracts from the different plant parts could be evaluated. The flower extracts revealed higher antioxidant properties than the other parts. The antibacterial properties of the methanol extracts from A. rugosa were analyzed by the disc diffusion method, and the flower extracts had higher antibacterial activities against the six bacterial strains used in the study than the other parts. This study provides information on the synergistic antioxidant and antibacterial properties of phenolics derived from the different parts of Korean mint.
Lysyl oxidase induces epithelial‐mesenchymal transition and predicts intrahepatic metastasis of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) has high recurrence rates even after curative hepatectomy. Drug therapy for recurrence of HCC is still limited; therefore, identifying new therapeutic targets is urgently needed. We searched for genes that would predict HCC recurrence from intrahepatic metastasis in an exhaustive DNA microarray database by searching genes associated with high early recurrence rate and having higher expression in the tumor area compared to background liver. We detected lysyl oxidase (LOX) and validated the clinical significance of LOX in 358 patients who underwent hepatectomy. Expression of LOX was evaluated by qRT‐ PCR, and immunohistochemical (IHC) staining. High LOX expression group had a significantly higher recurrence rate than the low LOX expression group (2‐year recurrence rate was 64.0% vs 24.2%, P < .0001 for IHC) and poorer survival rate (5‐year rate was 60.1% vs 86.2%, P < .0001 for IHC). Multivariate analysis showed that high LOX expression was an independent risk factor for early recurrence (IHC: HR, 2.52; P < .0001). Bioinformatic analysis showed that LOX expression was associated with hypoxia‐inducible factor‐1α (HIF‐1α) and the hypoxia cascade, suggesting that HIF‐1α or hypoxia regulates LOX expression and induces epithelial‐mesenchymal transition (EMT). In vitro, LOX and HIF‐1α were involved in migration and invasion capability. High LOX expression is associated with EMT markers and predicts early recurrence and poor survival in patients with HCC. These findings indicate that lysyl oxidase could be a potential therapeutic target for early recurrence of HCC.
Testing Measurement Invariance Across Unobserved Groups: The Role of Covariates in Factor Mixture Modeling

Factor mixture modeling (FMM) has been increasingly used to investigate unobserved population heterogeneity. This study examined the issue of covariate effects with FMM in the context of measurement invariance testing. Specifically, the impact of excluding and misspecifying covariate effects on measurement invariance testing and class enumeration was investigated via Monte Carlo simulations. Data were generated based on FMM models with (1) a zero covariate effect, (2) a covariate effect on the latent class variable, and (3) covariate effects on both the latent class variable and the factor. For each population model, different analysis models that excluded or misspecified covariate effects were fitted. Results highlighted the importance of including proper covariates in measurement invariance testing and evidenced the utility of a model comparison approach in searching for the correct specification of covariate effects and the level of measurement invariance. This approach was demonstrated using an empirical data set. Implications for methodological and applied research are discussed.
Sublingual endothelial glycocalyx and atherosclerosis. A cross-sectional study

Background Damage to endothelial glycocalyx is thought to be an early marker of atherosclerosis and measuring reduced glycocalyx size clinically via the Perfused Boundary Region (PBR) may allow early detection of cardiovascular disease. However, the true value of the glycocalyx in estimating cardiovascular risk or detecting cardiovascular disease is uncertain. We therefore investigated whether small glycocalyx size is associated with cardiovascular risk or disease in a large multi-ethnic cohort. Methods In a multi-ethnic community-based sample (N = 6169, 42.4% male, mean age 43.6 ±13) we applied multiple imputation for missing data and used logistic regression and odds ratios to cross-sectionally investigate the relationship of small glycocalyx size as estimated by highest quartile of PBR with, on the one hand, classical risk factors for atherosclerosis including age, sex, diastolic and systolic blood pressure, LDL, HDL, triglycerides, BMI, diabetes, smoking status, and antihypertensive and lipid-lowering medication; on the other hand, prevalent cardiovascular disease. Analyses were additionally adjusted for ethnicity. Results With PBR divided in quartiles, the highest PBR quartile (smallest glycocalyx size) as dependent variable was independently associated with female sex (OR for male versus female: 0.61, 95% CI: 0.53, 0.70) and diabetes (OR: 1.28, 95% CI: 1.03–1.59) in a model adjusted for all classical risk factors of atherosclerosis and for ethnicity. With regard to cardiovascular disease, no association was found between the smallest glycocalyx size as independent variable and overall cardiovascular disease, coronary heart disease and revascularization procedures, or stroke. Conclusions Small glycocalyx size as estimated by highest PBR is associated with female sex and diabetes, which do not completely reflect a high cardiovascular risk profile. At the same time, glycocalyx size is not associated with prevalent cardiovascular disease.
Cache-Version Selection and Content Placement for Adaptive Video Streaming in Wireless Edge Networks

Wireless edge networks are promising to provide better video streaming services to mobile users by provisioning computing and storage resources at the edge of wireless network. However, due to the diversity of user interests, user devices, video versions or resolutions, cache sizes, network conditions, etc., it is challenging to decide where to place the video contents, and which cache and video version a mobile user device should select. In this paper, we study the joint optimization of cache-version selection and content placement for adaptive video streaming in wireless edge networks. We propose practical distributed algorithms that operate at each user device and each network cache to maximize the overall network utility. In addition to proving the optimality of our algorithms, we implement our algorithms as well as several baseline algorithms on ndnSIM, an ns-3 based Named Data Networking simulator. Simulation evaluations demonstrate that our algorithms significantly outperform conventional heuristic solutions.
Assessing the Pathogenicity of Two Bacteria Isolated from the Entomopathogenic Nematode Heterorhabditis indica against Galleria mellonella and Some Pest Insects

The entomopathogenic nematodes Heterorhabditis are parasites of insects and are associated with mutualist symbiosis enterobacteria of the genus Photorhabdus; these bacteria are lethal to their host insects. Heterorhabditis indica MOR03 was isolated from sugarcane soil in Morelos state, Mexico. The molecular identification of the nematode was confirmed using sequences of the ITS1-5.8S-ITS2 region and the D2/D3 expansion segment of the 28S rRNA gene. In addition, two bacteria HIM3 and NA04 strains were isolated from the entomopathogenic nematode. The genomes of both bacteria were sequenced and assembled de novo. Phylogenetic analysis was confirmed by concatenated gene sequence datasets as Photorhabdus luminescens HIM3 (16S rRNA, 23S rRNA, dnaN, gyrA, and gyrB genes) and Pseudomonas aeruginosa NA04 (16S rRNA, 23S rRNA and gyrB genes). H. indica MOR03 infects Galleria mellonella, Tenebrio molitor, Heliothis subflexa, and Diatraea magnifactella larvae with LC50 values of 1.4, 23.5, 13.7, and 21.7 IJs/cm2, respectively, at 48 h. These bacteria are pathogenic to various insects and have high injectable insecticide activity at 24 h.
Risk Factors Associated with Infusion Reactions to Infliximab in Chinese Patients with Inflammatory Bowel Disease: A Large Single-Center Study

Background This study investigated the risk factors of infliximab (IFX)-related infusion reactions (IR) in Chinese patients with inflammatory bowel disease (IBD). Material/Methods The medical records of 330 consecutive IBD patients treated with IFX between 2009 and 2017 were reviewed. The incidence of IR and adverse effects were recorded in detail, and the potential risk factors related to IR were analyzed by univariate and logistic regression analysis. Results The 330 patients received a total of 2108 IFX infusions, with a median follow-up of 29 months. Eighteen patients (5.5%) experienced IR: 15 were immediate (2 severe) and 3 were late (0 severe). The patients who were treated with episodic IFX without concomitant IM therapy and at the 2nd IFX series (all P<0.001) had higher incidence of IR. Logistic regression revealed the 2nd IFX treatment series (OR=0.017, P<0.001) and episodic use of IFX (OR=0.113, P<0.001) as the significant predictors. Antibodies against infliximab (ATI) were highly positive in 10 of 14 patients (71%) with IR. Sixty-seven percent of patients finished infusions after IR through appropriate management. Conclusions IFX infusions were accompanied by IR in about 5% of Chinese IBD patients. Severe IR was rare. The patients with the 2nd series or episodic use of IFX should be monitored closely during infusion.
Latent Trait, Latent-Trait State, and a Network Approach to Mental Problems and Their Mechanisms of Change

In this theoretical study, we examined whether and how a latent trait, a latent-trait state, and a network conceptualization of mental problems account for their descriptive features and causal mechanisms. The latent-trait approach is restricted to between-persons relations and thus provides no direct tests of mechanisms, which involve within-persons relations. The latent-trait-state approach can address within-persons relations, but the assumption of independence between latent constructs is often violated. Moreover, the focus on latent states results only in global clinical recommendations. In the network approach, clinical disorders are viewed as causal networks of observable mental problems and symptoms. The network approach has so far not addressed the episodic clusters of reactions surrounding every symptom. We propose an extended network approach, which identifies mechanistic relationships with the causal interactions among the reactions of these clusters. This approach is associated with differentiated clinical models and leads to specific clinical recommendations.
Prognostic Factors of Malignant Pheochromocytoma and Paraganglioma: A Combined SEER and TCGA Databases Review

Abstract Pheochromocytoma (PCC) and paraganglioma (PGL) are rare malignancies while pathogenesis is strongly influenced by genetics. The prognostic factors of these patients remain poorly defined. We aim to study the epidemiology and survival pattern by analyzing the combination of SEER and Cancer Genome Atlas (TCGA) database. Primary outcome was overall survival (OS) and disease specific survival (DSS). Between 1973 and 2013, a total of 1014 patients with PGL or PCC were analyzed. Younger age and female were associated with better outcomes. The incidence of second primary malignancy in PGL/PCC patients was about 14.6%. This population had a significant longer DSS. Other factors, including surgical resection and origin from of aortic/carotid bodies, conferred remarkable survival advantage. In contrast, distant spread portended worse prognosis. Laterality, race, positive serum catecholamine marker did not demonstrate a significant association with OS and DSS. By analyzing TCGA database with total 184 patients were identified. Eighty out of 184 patients (43.5%) had at least one pathogenic mutation. Female had higher ratio of pathogenic mutations than male (58.7% vs. 41.3%) and NF1 mutation was associated with elderly population. SHDB mutation had higher percentage in male. Twenty-nine patients (15.8%) had 2 or more primary. ATRX was the most common oncogenic mutations in metastatic cohort. In conclusion, younger age, female sex, origin from aortic/carotid bodies, complete surgical resection, regional disease, as well as concomitant second primary malignancies were associated with better prognosis. The prognostic value of radiotherapy and oncogenomics warrants further investigation.
Do the Calls of a Bird, the Noisy Miner (Manorina melanocephala), Need Adjustment for Efficient Communication in Urban Anthropogenic Noise?

Simple Summary A common feature of urban environments is constant, low frequency, anthropogenic noise. To communicate effectively acoustically in this environment requires avoidance of sound masking by this background noise. Research suggests that some animals can adjust their vocalizations so that they lie outside the main frequency range of urban anthropogenic noise, whilst others may produce sound signals that naturally avoid masking and therefore do not require adjustment. To date, research in this area has tended to focus on adjustment to complex songs, rather than simpler calls. The Noisy miner, Manorina melanocephala, is a very successful avian urban colonizer that uses calls in its acoustic communication. We compared the calls of this species in both urban and rural populations. Of all calls compared, only those that lay within the main frequency range of anthropogenic noise (1–2 kHz) showed shifts in minimum sound frequency in urban individuals, but these frequency shifts were notably small and insufficient to entirely preclude masking by urban noise. However, several Noisy miner calls had frequencies of more than 2 kHz that lay outside the main frequency range of urban anthropogenic noise (>2 kHz), suggesting intriguingly that this species may be inherently well-suited to communicating vocally in urban settings, which may be one of the keys to its success as an urban colonizer. Abstract Urban environments are characteristically noisy and this can pose a challenge for animals that communicate acoustically. Although evidence suggests that some birds can make acoustic adjustments that preclude masking of their signals in high-disturbance environments such as cities, studies to date have tended to focus on acoustic signals important in mate attraction (e.g., songs). Far less attention has been given to the impact of urban noise on other kinds of calls. To redress this, we compared a range of different vocalizations (encompassing alarm calls, begging calls and parent response calls) among urban and rural individuals of a successful Australian ‘urban adapter’, the Noisy miner, Manorina melanocephala. We found that urban miners had significantly higher minimum sound frequencies for calls with low base-frequencies (<2 kHz); however, calls with base-frequencies ‘naturally’ above the main frequency range of urban noise (>2 kHz) had the same minimum frequency in urban and rural birds. Dominant frequency and call duration did not differ between urban and rural individuals. Although urban Noisy miners exhibited differences from rural individuals in the minimum frequency of calls, this shift was not large enough to avoid masking from low-frequency, anthropogenic noise. Nevertheless, our findings suggest that the calls of Noisy miners may be naturally well suited to being heard in noisy urban environments by having (a) dominant frequencies higher than low-level, anthropogenic noise and (b) several important call-types with frequencies above the main frequency range associated with urban noise.