Miracle-dz/UniFAR-FTUs huggingface dataset:
Knowledge Generation with Rule Induction in Cancer Omics

The explosion of omics data availability in cancer research has boosted the knowledge of the molecular basis of cancer, although the strategies for its definitive resolution are still not well established. The complexity of cancer biology, given by the high heterogeneity of cancer cells, leads to the development of pharmacoresistance for many patients, hampering the efficacy of therapeutic approaches. Machine learning techniques have been implemented to extract knowledge from cancer omics data in order to address fundamental issues in cancer research, as well as the classification of clinically relevant sub-groups of patients and for the identification of biomarkers for disease risk and prognosis. Rule induction algorithms are a group of pattern discovery approaches that represents discovered relationships in the form of human readable associative rules. The application of such techniques to the modern plethora of collected cancer omics data can effectively boost our understanding of cancer-related mechanisms. In fact, the capability of these methods to extract a huge amount of human readable knowledge will eventually help to uncover unknown relationships between molecular attributes and the malignant phenotype. In this review, we describe applications and strategies for the usage of rule induction approaches in cancer omics data analysis. In particular, we explore the canonical applications and the future challenges and opportunities posed by multi-omics integration problems.
Genetic Diversity and Population Structure of Nutria (Myocastor coypus) in South Korea

Simple Summary Nutrias (Myocastor coypus) are large semiaquatic rodents native to subtropical and temperate South America. Nutrias have been introduced on all continents, except Oceania and Antarctica, and have become invasive in many countries. This study carried out a survey of nutrias in South Korea under the Nutria Eradication Project from January 2013 to August 2015. Out of 1509 habitat traces, 1497 tracks were observed in the Nakdong River basin. Based on the ecological field data, we identified concentrated areas of nutria populations. Tissue samples were collected from captured nutria for genetic analysis. According to the microsatellite marker analysis, the estimated genetic diversity of the nutria populations was low, which suggests that nutrias in South Korea originate from a single population. Abstract The nutria (Myocastor coypus) is an invasive alien species that have had major adverse effects on biodiversity and the agricultural economy in wetland habitats. Since 2014, the Ministry of Environment in South Korea has been carrying out the Nutria Eradication Project, and we investigated nutria distribution and genetic diversity of nutria populations in South Korea. We estimated that 99.2% of nutria habitats are in the mid-lower Nakdong River regions. To further analyze the genetic diversity in eight major nutria populations, we performed a genetic analysis using microsatellite markers. Genetic diversity levels of the eight nutria populations in South Korea were relatively lower than those in other countries. The probability of migration direction among nutria populations was predicted from genetic distance analysis. Genetic structure analysis showed little difference among the nutria populations in South Korea. These results suggest that nutrias in South Korea originated from a single population. Our results provide important data for establishing management strategies for the successful eradication of nutria populations in South Korea, as well as in other countries with alien invasive species.
Response to: ‘New 2019 SLE EULAR/ACR classification criteria are valid for identifying patients with SLE among patients admitted for pericardial effusion’ by Sacre et al

In their letter, Dr Sacre and colleagues1 describe an interesting retrospective study on 129 patients with pericardial effusion, of whom 17 were diagnosed with systemic lupus erythematosus (SLE). The authors arrive at a reassuring sensitivity of 100% for the new European League Against Rheumatism/American College of Rheumatology (EULAR/ACR) 2019 classification criteria.2 3 However, specificity was clearly lower at 84%, below the specificity of the ACR and the Systemic Lupus International Collaborating Clinics (SLICC) criteria. The latter is a somewhat unexpected result. Based on the …
Design and Preparation of Chitosan-Crosslinked Bismuth Ferrite/Biochar Coupled Magnetic Material for Methylene Blue Removal

Biochar obtained by pyrolysis of the fiber plant kenaf was mixed with bismuth ferrite (BiFeO3) in a chitosan-containing acetic acid solution, magnetized, and modified to prepare a chitosan-crosslinked BiFeO3/biochar coupled magnetic material. The adsorption properties of the composite were investigated using methylene blue dissolved in water, and the effects of external conditions, such as pH, methylene blue concentration, reaction time, and temperature, on the adsorption performance were studied. The adsorption data were fitted and analyzed with kinetic and isotherm models, and the results showed that the BiFeO3/biochar coupled magnetic material effectively adsorbed methylene blue. The amounts adsorbed onto this magnetic material increased with increasing initial methylene blue concentration, reaction time, and temperature, and the adsorption performance improved under neutral and alkaline conditions. The pseudo-first-order kinetic and Langmuir isotherm models satisfactorily fitted the adsorption data, showing that the adsorption of methylene blue involved both chemical and physical adsorption. The maximum adsorption capacity of methylene blue onto the BiFeO3/biochar coupled magnetic material reached 18.942 mg·g−1 at 25 °C, confirming the excellent dye binding activity of this material.
Dietary Compounds Influencing the Sensorial, Volatile and Phytochemical Properties of Bovine Milk

The main aim of this study was to evaluate the volatile profile, sensory perception, and phytochemical content of bovine milk produced from cows fed on three distinct feeding systems, namely grass (GRS), grass/clover (CLV), and total mixed ration (TMR). Previous studies have identified that feed type can influence the sensory perception of milk directly via the transfer of volatile aromatic compounds, or indirectly by the transfer of non-volatile substrates that act as precursors for volatile compounds. In the present study, significant differences were observed in the phytochemical profile of the different feed and milk samples. The isoflavone formonoetin was significantly higher in CLV feed samples, but higher in raw GRS milk, while other smaller isoflavones, such as daidzein, genistein, and apigenin were highly correlated to raw CLV milk. This suggests that changes in isoflavone content and concentration in milk relate to diet, but also to metabolism in the rumen. This study also found unique potential volatile biomarkers in milk (dimethyl sulfone) related to feeding systems, or significant differences in the concentration of others (toluene, p-cresol, ethyl and methyl esters) based on feeding systems. TMR milk scored significantly higher for hay-like flavor and white color, while GRS and CLV milk scored significantly higher for a creamy color. Milk samples were easily distinguishable by their volatile profile based on feeding system, storage time, and pasteurization.
Magnetic field induced vortices in graphene quantum dots

The energy spectrum and local current patterns in graphene quantum dots (QD) are investigated for different geometries in the presence of an external perpendicular magnetic field. Our results demonstrate that, for specific geometries and edge configurations, the QD exhibits vortex and anti-vortex patterns in the local current density, in close analogy to the vortex patterns observed in the probability density current of semiconductor QD, as well as in the order parameter of mesoscopic superconductors.
Intracholecystic Papillary Tubular Neoplasm of the Gallbladder With Microinvasive Carcinoma

For the intramucosal mass-forming preinvasive neoplasms (tumoral intraepithelial neoplasms) of the gallbladder, the term intracholecystic papillary tubular neoplasm (ICPN) has been proposed as a unifying category to embrace all the entities described in the World Health Organization 2010 classification as “adenoma,” “intracystic papillary neoplasm,” and “papillary adenocarcinoma. ” In essence, this category represents the gallbladder counterpart of the tumors known as intraductal papillary and intraductal tubulopapillary neoplasms in the pancreas and bile ducts. They are distinguished from nontumoral (“flat”) dysplasia by their exophytic tumor formation. They show a spectrum of dysplastic changes (adenoma-carcinoma sequence), various growth patterns, often in a mixture (papillary, tubular, and tubulopapillary), and a variety of cell lineages including biliary (MUC1), pyloric-mucinous (MUC6), complex-tubular (pyloric nonmucinous; MUC6; with morule formation and β-catenin nuclear positivity), gastric-foveolar, occasionally intestinal (MUC2/CDX2), and evenmore rarely oncocytic, often but not always with corresponding immunophenotypic changes. Invasive carcinoma is often encountered in association with these tumors (65% of the cases), and an estimated 6% to 8% of invasive carcinomas arise from ICPNs. Invasion is common in papillary examples and those with biliary or gastricfoveolar appearance, whereas it is very low, if at all, in complex tubularpyloric examples (although the latter often shows striking cytoarchitectural atypia as well). Extensive sampling is warranted to rule out invasive carcinoma. Carcinomas confined to above the tunica muscularis (early gallbladder carcinomas, which correspond to Tis/T1a/T1b cases) have a fairly good prognosis, especially if the possibility of T2 carcinoma (invasion through the muscularis) is ruled out by thorough sampling. More invasive examples have an aggressive behavior but still appear to be better behaving than ordinary adenocarcinomas without ICPNs, presumably partly due to early discovery of invasive carcinomas, but also partly due to differences in biologic behavior.
NPC1 Deficiency in Mice is Associated with Fetal Growth Restriction, Neonatal Lethality and Abnormal Lung Pathology

The rare lysosomal storage disorder Niemann-Pick disease type C1 (NPC1) arises from mutation of NPC1, which encodes a lysosomal transmembrane protein essential for normal transport and trafficking of cholesterol and sphingolipids. NPC1 is highly heterogeneous in both clinical phenotypes and age of onset. Previous studies have reported sub-Mendelian survival rates for mice homozygous for various Npc1 mutant alleles but have not studied the potential mechanisms underlying this phenotype. We performed the first developmental analysis of a Npc1 mouse model, Npc1em1Pav, and discovered significant fetal growth restriction in homozygous mutants beginning at E16.5. Npc1em1Pav/em1Pav mice also exhibited cyanosis, increased respiratory effort, and over 50% lethality at birth. Analysis of neonatal lung tissues revealed lipid accumulation, notable abnormalities in surfactant, and enlarged alveolar macrophages, suggesting that lung abnormalities may be associated with neonatal lethality in Npc1em1Pav/em1Pav mice. The phenotypic severity of the Npc1em1Pav model facilitated this first analysis of perinatal lethality and lung pathology in an NPC1 model organism, and this model may serve as a useful resource for developing treatments for respiratory complications seen in NPC1 patients.
Routing Schemes in FANETs: A Survey

Flying ad hoc network (FANET) is a self-organizing wireless network that enables inexpensive, flexible, and easy-to-deploy flying nodes, such as unmanned aerial vehicles (UAVs), to communicate among themselves in the absence of fixed network infrastructure. FANET is one of the emerging networks that has an extensive range of next-generation applications. Hence, FANET plays a significant role in achieving application-based goals. Routing enables the flying nodes to collaborate and coordinate among themselves and to establish routes to radio access infrastructure, particularly FANET base station (BS). With a longer route lifetime, the effects of link disconnections and network partitions reduce. Routing must cater to two main characteristics of FANETs that reduce the route lifetime. Firstly, the collaboration nature requires the flying nodes to exchange messages and to coordinate among themselves, causing high energy consumption. Secondly, the mobility pattern of the flying nodes is highly dynamic in a three-dimensional space and they may be spaced far apart, causing link disconnection. In this paper, we present a comprehensive survey of the limited research work of routing schemes in FANETs. Different aspects, including objectives, challenges, routing metrics, characteristics, and performance measures, are covered. Furthermore, we present open issues.
Novel Variants of Angiotensin Converting Enzyme-2 of Shorter Molecular Size to Target the Kidney Renin Angiotensin System

ACE2 is a monocarboxypeptidase which generates Angiotensin (1–7) from Angiotensin II (1–8). Attempts to target the kidney Renin Angiotensin System using native ACE2 to treat kidney disease are hampered by its large molecular size, 100 kDa, which precludes its glomerular filtration and subsequent tubular uptake. Here, we show that both urine and kidney lysates are capable of digesting native ACE2 into shorter proteins of ~60–75 kDa and then demonstrate that they are enzymatically very active. We then truncated the native ACE2 by design from the C-terminus to generate two short recombinant (r)ACE2 variants (1-605 and 1-619AA). These two truncates have a molecular size of ~70 kDa, as expected from the amino acid sequence and as shown by Western blot. ACE2 enzyme activity, measured using a specific substrate, was higher than that of the native rACE2 (1-740 AA). When infused to mice with genetic ACE2 deficiency, a single i.v. injection of 1-619 resulted in detectable ACE2 activity in urine, whereas infusion of the native ACE2 did not. Moreover, ACE2 activity was recovered in harvested kidneys from ACE2-deficient mice infused with 1-619, but not in controls (23.1 ± 4.3 RFU/µg creatinine/h and 1.96 ± 0.73 RFU/µg protein/hr, respectively). In addition, the kidneys of ACE2-null mice infused with 1-619 studied ex vivo formed more Ang (1–7) from exogenous Ang II than those infused with vehicle (AUC 8555 ± 1933 vs. 3439 ± 753 ng/mL, respectively, p < 0.05) further demonstrating the functional effect of increasing kidney ACE2 activity after the infusion of our short ACE2 1-619 variant. We conclude that our novel short recombinant ACE2 variants undergo glomerular filtration, which is associated with kidney uptake of enzymatically active proteins that can enhance the formation of Ang (1–7) from Ang II. These small ACE2 variants may offer a potentially useful approach to target kidney RAS overactivity to combat kidney injury.
Exogenous Melatonin and Abscisic Acid Expedite the Flavonoids Biosynthesis in Grape Berry of Vitis vinifera cv. Kyoho

Grape polyphenols contributing to more than half of the global polyphenol market were well studied; however, how melatonin (MLT), a potential plant hormone, and abscisic acid (ABA) affects polyphenols profile is still poorly understood. To explore whether these hormones are involved in polyphenolic biosynthesis, grape (Vitis vinifera cv. Kyoho) was exposed to MLT, ABA, and NDGA (nordihydroguaiaretic acid, an ABA biosynthesis inhibitor) treatments, and 16 polyphenols were identified from grape extracts by high performance liquid chromatography quadrupole time of flight mass spectrometry (HPLC-Q-TOF-MS). Both exogenous MLT and ABA significantly enhanced the biosynthesis of each flavonol and flavanol component, especially catechin, which was almost increased double by 200 µM of MLT treatment. Furthermore, the expression of genes involved in flavonoid biosynthesis, including 4-coumaroyl-CoA synthase, chalcone synthase, flavonoid 3′-hydroxylase, anthocyanin 3′-methyltransferase, flavonol synthase, flavonoid-3-O-glucosyltransferase, and flavonoid 3′,5′-methyltransferase were highly up-regulated as well but were down-regulated by NDGA. The present study provided new insights for improving flavonoids accumulation in agricultural production and its underlying mechanism.
Oral health of 12-year-old children in Jilin province, China

Abstract There is a lack of population-based surveys on oral health in Jilin province. Accordingly, this study aimed to understand the oral health status of 12-year-old children in Jilin province, China, to demonstrate the prevalence of oral health–related diseases, as well as to identify the associated risk factors. From February to April 2017, a cross-sectional investigation was conducted among 2324 children aged 12 years from 63 public schools of 9 regions in Jilin province, China. A questionnaire of World Health Organization (WHO) was conducted to ascertain the potential risk factors associated with oral diseases. The 3 examiners, who received theoretical and clinical training before the investigation, underwent clinical examinations to assess dental caries, dental fluorosis, presence of calculus, and gingival bleeding. Furthermore, the mean decayed-missing-filled tooth (DMFT), the rate of pit and fissure closure, education level of patients, brushing habits, and sugar consumption were also evaluated. All data analyses were conducted using SPSS version 19.0. A total of 2324 twelve-year-old children from 9 regions in Jilin-China were examined from February to April 2017. The prevalence of dental caries, dental fluorosis, calculus, and gingival bleeding reached 40.8%%, 21.8%, 47.93%, and 48.88%, respectively; the mean DMFT was 0.8787. The proportion of DMFT was 83.7% for decayed teeth, 0.2% for missing teeth, and 16.1% for filling teeth. The prevalence of pit and fissure closure was 10%. Educational level of parents was negatively correlated with the prevalence of oral diseases, whereas sugar consumption was positively associated with dental caries prevalent in children. We also found that there was no association between brushing habits and dental caries in children aged 12 years in Jilin Province.
Repeatability of Taste Recognition Threshold Measurements with QUEST and Quick Yes–No

Taste perception, although vital for nutrient sensing, has long been overlooked in sensory assessments. This can, at least in part, be attributed to challenges associated with the handling of liquid, perishable stimuli, but also with scarce efforts to optimize testing procedures to be more time-efficient. We have previously introduced an adaptive, QUEST-based procedure to measure taste sensitivity thresholds that was quicker than other existing approaches, yet similarly reliable. Despite its advantages, the QUEST procedure lacks experimental control of false alarms (i.e., response bias) and psychometric function slope. Variations of these parameters, however, may also influence the threshold estimate. This raises the question as to whether a procedure that simultaneously assesses threshold, false-alarm rate, and slope might be able to produce threshold estimates with higher repeatability, i.e., smaller variation between repeated measurements. Here, we compared the performance of QUEST with a method that allows measurement of false-alarm rates and slopes, quick Yes–No (qYN), in a test–retest design for citric acid, sodium chloride, quinine hydrochloride, and sucrose recognition thresholds. We used complementary measures of repeatability, namely test–retest correlations and coefficients of repeatability. Both threshold procedures yielded largely overlapping thresholds with good repeatability between measurements. Together the data suggest that participants used a conservative response criterion. Furthermore, we explored the link between taste sensitivity and taste liking or which we found, however, no clear association.
High Kanamycin Concentration as Another Stress Factor Additional to Temperature to Increase pDNA Production in E. coli DH5α Batch and Fed-Batch Cultures

Plasmid DNA (pDNA) vaccines require high supercoiled-pDNA doses (milligrams) to achieve an adequate immune response. Therefore, processes development to obtain high pDNA yields and productivity is crucial. pDNA production is affected by several factors including culture type, medium composition, and growth conditions. We evaluated the effect of kanamycin concentration and temperature on pDNA production, overflow metabolism (organic acids) and metabolic burden (neomycin phosphotransferase II) in batch and fed-batch cultures of Escherichia coli DH5α-pVAX1-NH36. Results indicated that high kanamycin concentration increases the volumetric productivity, volumetric and specific yields of pDNA when batch cultures were carried out at 42 °C, and overflow metabolism reduced but metabolic burden increased. Micrographs taken with a scanning electron microscope (SEM) were analyzed, showing important morphological changes. The high kanamycin concentration (300 mg/L) was evaluated in high cell density culture (50 gDCW/L), which was reached using a fed-batch culture with temperature increase by controlling heating and growth rates. The pDNA volumetric yield and productivity were 759 mg/L and 31.19 mg/L/h, respectively, two-fold greater than the control with a kanamycin concentration of 50 mg/L. A stress-based process simultaneously caused by temperature and high kanamycin concentration can be successfully applied to increase pDNA production.
Psychological Mediation of Dysfunction and Hyperfunction of Respiratory Regulation

This research investigates the continuum between the dysfunction and the hyperfunction of breath regulation and presents the psychological mediation that supports or disrupts this regulation. The pilot study compared breathing regulation in patients with hyperventilation syndrome (HVS), free divers, and healthy volunteers. To examine the ability of voluntary respiration regulation, breath holding involving “easy-going” and “struggling” phases was used. Psychological mediation was assessed through (a) respiratory experience interviews, (b) anxiety levels, and (c) psycho-semantic techniques. Free divers have a bigger “positive breathing vocabulary” and can endure the conflict between the physiological need to inhale and the voluntary motivation to hold their breath for longer. The connection between emotions and negative breathing experience in patients with HVS leads to less breathing control.
Anti-Symmetric Mode Vibration of Electrostatically Actuated Clamped–Clamped Microbeams for Mass Sensing

This paper details study of the anti-symmetric response to the symmetrical electrostatic excitation of a Micro-electro-mechanical-systems (MEMS) resonant mass sensor. Under higher order mode excitation, two nonlinear coupled flexural modes to describe MEMS mass sensors are obtained by using Hamilton’s principle and Galerkin method. Static analysis is introduced to investigate the effect of added mass on the natural frequency of the resonant sensor. Then, the perturbation method is applied to determine the response and stability of the system for small amplitude vibration. Through bifurcation analysis, the physical conditions of the anti-symmetric mode vibration are obtained. The corresponding stability analysis is carried out. Results show that the added mass can change the bifurcation behaviors of the anti-symmetric mode and affect the voltage and frequency of the bifurcation jump point. Typically, we propose a mass parameter identification method based on the dynamic jump motion of the anti-symmetric mode. Numerical studies are introduced to verify the validity of mass detection method. Finally, the influence of physical parameters on the sensitivity of mass sensor is analyzed. It is found that the DC voltage and mass adsorption position are critical to the sensitivity of the sensor. The results of this paper can be potentially useful in nonlinear mass sensors.