Miracle-dz/UniFAR-FTUs huggingface dataset:
The methylation profiles of PRDM promoters in non–small cell lung cancer

Background Non–small cell lung cancer (NSCLC) is one of the leading malignant tumors worldwide. Aberrant gene promoter methylation contributes to NSCLC, and PRDM is a tumor suppressor gene family that possesses histone methyltransferase activity. This study aimed to investigate whether aberrant methylation of PRDM promoter is involved in NSCLC. Materials and methods Primary tumor tissues, adjacent nontumorous tissues, and distant lung tissues were collected from 75 NSCLC patients including 52 lung squamous cell carcinoma (LSCC) patients and 23 lung adenocarcinoma patients. The expression of PRDMs was detected by polymerase chain reaction (PCR), Western blot, and immunohistochemical analysis. The methylation of PRDM promoters was detected by methylation-specific PCR. The correlation of methylation and expression of PRDMs with clinicopathological characteristics of patients were analyzed. Results mRNA expression of PRDM2, PRDM5, and PRDM16 was low or absent in tumor tissues compared to distant lung tissues. The methylation frequencies of PRDM2, PRDM5, and PRDM16 in tumor tissues were significantly higher than those in distal lung tissues. In LSCC patients, methylation of PRDM2 and PRDM16 was correlated with smoking status and methylation of PRDM5 was correlated with tumor differentiation. Conclusion The expression of PRDM2, PRDM5, and PRDM16 is low or absent in NSCLC, and this is mainly due to gene promoter methylation. Smoking may be an important cause of PRDM2 and PRDM16 methylation in NSCLC.
Vitamin D3 Status and the Association with Human Cathelicidin Expression in Patients with Different Clinical Forms of Active Tuberculosis

Low vitamin D (vitD3) is one of the most common nutritional deficiencies in the world known to be associated with numerous medical conditions including infections such as tuberculosis (TB). In this study, vitD3 status and its association with the antimicrobial peptide, human cathelicidin (LL-37), was investigated in Ethiopian patients with different clinical forms of TB. Patients with active TB (n = 77) and non-TB controls (n = 78) were enrolled in Ethiopia, while another group of non-TB controls (n = 62) was from Sweden. Active TB included pulmonary TB (n = 32), pleural TB (n = 20), and lymph node TB (n = 25). Concentrations of 25-hydroxyvitamin D3 (25(OH)D3) were assessed in plasma, while LL-37 mRNA was measured in peripheral blood and in samples obtained from the site of infection. Median 25(OH)D3 plasma levels in active TB patients were similar to Ethiopian non-TB controls (38.5 versus 35.0 nmol/L) and vitD3 deficiency (<50 nmol/L) was common in both groups (73%). Ethiopians (low latitude) had significantly lower 25(OH)D3 levels compared with Swedish non-TB controls (51.0 nmol/L, high latitude), but vitD3 status was not affected by tuberculin-positivity or HIV infection. Patients with local lymph node TB had significantly higher 25(OH)D3 levels compared with pulmonary TB patients (48.0 versus 29.0 nmol/L). Moreover, plasma 25(OH)D3 levels correlated with local LL-37 expression in granulomatous lesions in TB infected lymph nodes. Instead, systemic LL-37 mRNA expression in blood cells was elevated compared with the site of infection in pulmonary and pleural TB. Low vitD3 status may be associated with an enhanced peripheral expression of LL-37 in patients with intrathoracic TB that could result from chronic inflammation.
The kinase activity of the channel-kinase protein TRPM7 regulates stability and localization of the TRPM7 channel in polarized epithelial cells

The channel-kinase transient receptor potential melastatin 7 (TRPM7) is a bifunctional protein with ion channel and kinase domains. The kinase activity of TRPM7 has been linked to the regulation of a broad range of cellular activities, but little is understood as to how the channel itself is regulated by its own kinase activity. Here, using several mammalian cell lines expressing WT TRPM7 or kinase-inactive variants, we discovered that compared with the cells expressing WT TRPM7, cells in which TRPM7's kinase activity was inactivated had faster degradation, elevated ubiquitination, and increased intracellular retention of the channel. Mutational analysis of TRPM7 autophosphorylation sites further revealed a role for Ser-1360 of TRPM7 as a key residue mediating both TRPM7 stability and intracellular trafficking. Additional trafficking roles were uncovered for Ser-1403 and Ser-1567, whose phosphorylation by TRPM7's kinase activity mediated the interaction of the channel with the signaling protein 14-3-3θ. In summary, our results point to a critical role for TRPM7's kinase activity in regulating proteasome-mediated turnover of the TRPM7 channel and controlling its cellular localization in polarized epithelial cells. Overall, these findings improve our understanding of the significance of TRPM7's kinase activity for functional regulation of its channel activity.
Shame as a self-conscious emotion and its role in identity formation

The aim of this paper is to discuss the possibility of using the category of shame, understood as one of the self-conscious emotions, in helping to explain human functioning, especially in regard to the process of identity formation. An analysis of different theoretical accounts of shame draws attention to the considerable differences that exist between them. These differences raise the fundamental question of whether shame can be treated as an adaptive emotion, playing a vital and constructive role in identity development, or as a destructive emotion, which disrupts the process of development including also the sphere of identity formation. In the article this problem is analyzed with reference to studies on the identity formation process conducted within the neo-eriksonian approach. The main thesis put forward in the present elaboration states that shame has significant importance for the identity formation processes, however, it does not influence these processes directly. An important mediator seem to be the mechanisms of emotion regulation. It has been assumed that the destructive and disrupting influence of shame is not an immanent feature of this emotion, but rather a consequence of malfunctioning mechanisms of emotion regulation that include the mechanisms of shame regulation.
Estimation of different data compositions for early-season crop type classification

Timely and accurate crop type distribution maps are an important inputs for crop yield estimation and production forecasting as multi-temporal images can observe phenological differences among crops. Therefore, time series remote sensing data are essential for crop type mapping, and image composition has commonly been used to improve the quality of the image time series. However, the optimal composition period is unclear as long composition periods (such as compositions lasting half a year) are less informative and short composition periods lead to information redundancy and missing pixels. In this study, we initially acquired daily 30 m Normalized Difference Vegetation Index (NDVI) time series by fusing MODIS, Landsat, Gaofen and Huanjing (HJ) NDVI, and then composited the NDVI time series using four strategies (daily, 8-day, 16-day, and 32-day). We used Random Forest to identify crop types and evaluated the classification performances of the NDVI time series generated from four composition strategies in two studies regions from Xinjiang, China. Results indicated that crop classification performance improved as crop separabilities and classification accuracies increased, and classification uncertainties dropped in the green-up stage of the crops. When using daily NDVI time series, overall accuracies saturated at 113-day and 116-day in Bole and Luntai, and the saturated overall accuracies (OAs) were 86.13% and 91.89%, respectively. Cotton could be identified 40∼60 days and 35∼45 days earlier than the harvest in Bole and Luntai when using daily, 8-day and 16-day composition NDVI time series since both producer’s accuracies (PAs) and user’s accuracies (UAs) were higher than 85%. Among the four compositions, the daily NDVI time series generated the highest classification accuracies. Although the 8-day, 16-day and 32-day compositions had similar saturated overall accuracies (around 85% in Bole and 83% in Luntai), the 8-day and 16-day compositions achieved these accuracies around 155-day in Bole and 133-day in Luntai, which were earlier than the 32-day composition (170-day in both Bole and Luntai). Therefore, when the daily NDVI time series cannot be acquired, the 16-day composition is recommended in this study.
Neuronal and non-neuronal signals regulate Caernorhabditis elegans avoidance of contaminated food

One way in which animals minimize the risk of infection is to reduce their contact with contaminated food. Here, we establish a model of pathogen-contaminated food avoidance using the nematode worm Caernorhabditis elegans. We find that avoidance of pathogen-contaminated food protects C. elegans from the deleterious effects of infection and, using genetic approaches, demonstrate that multiple sensory neurons are required for this avoidance behaviour. In addition, our results reveal that the avoidance of contaminated food requires bacterial adherence to non-neuronal cells in the tail of C. elegans that are also required for the cellular immune response. Previous studies in C. elegans have contributed significantly to our understanding of molecular and cellular basis of host–pathogen interactions and our model provides a unique opportunity to gain basic insights into how animals avoid contaminated food. This article is part of the Theo Murphy meeting issue ‘Evolution of pathogen and parasite avoidance behaviours’.
Rigging Research Results by Manipulating Top Websites Rankings

Researchers often use rankings of popular websites when measuring security practices, evaluating defenses or analyzing ecosystems. However, little is known about the data collection and processing methodologies of these rankings. In this paper, we uncover how both inherent properties and vulnerabilities to adversarial manipulation of these rankings may affect the conclusions of security studies. To that end, we compare four main rankings used in recent studies in terms of their agreement with each other, stability, representation bias and potential impact on research cases. Additionally, we introduce and illustrate novel ways for the adversary to manipulate the rankings and bend research results to their will. Overall, our study reveals significant shortcomings of current rankings and calls for a more cautious approach from the research community.
Oral shedding of human herpesviruses in patients undergoing radiotherapy/chemotherapy for head and neck squamous cell carcinoma is not affected by xerostomia

ABSTRACT Background: Xerostomia is a very relevant and frequent complication of radiotherapy, causing the irradiated oral mucosa to be affected by bacterial, fungal and viral infections. Objective: The objective of this study was to evaluate a possible relationship between oral shedding of human herpesviruses and xerostomia in patients with squamous cell carcinoma of head and neck submitted to radio/chemotherapy. Methods: In this study, oral rinse samples were collected weekly from 20 patients during radiotherapy. The samples were submitted to PCR and enzymatic digestion for detection of human herpesviruses. Xerostomia was evaluated according to the Seminars in Radiation Oncology criteria. Results: There was a higher frequency of grade 1 xerostomia (51.4%), observed first in the 1st week of radiotherapy. In the 4th week of radiotherapy, all patients presented some degree of xerostomia. Analysis of herpesviruses showed oral shedding of EBV, HHV-6 and HHV-7 in all weeks. Considering all the periods, the highest frequency was in patients with EBV excretion (55.0%), which was significantly higher than that of other viruses. Conclusion: We observed that oral shedding of herpesviruses was not affected by xerostomia as there was a progression in their excretion, even with the evolution of xerostomia. This suggested that there is a local replication in the oral cavity that is not completely dependent of salivary excretion.
Antihyperglycemic and anti-inflammatory effects of fermented food paste in high-fat diet and streptozotocin-challenged mice

Background Fermented food has been widely consumed as health food to ameliorate or prevent several chronic diseases including diabetes. Xeniji™, a fermented food paste (FFP), has been previously reported with various bioactivities, which may be caused by the presence of several metabolites including polyphenolic acids, flavonoids, and vitamins. In this study, the anti-hyperglycemic and anti-inflammatory effects of FFP were assessed. Methods In this study, type 2 diabetes model mice were induced by streptozotocin and high-fat diet (HFD) and used to evaluate the antihyperglycemic and anti-inflammatory effects of FFP. Mice were fed with HFD and challenged with 30 mg/kg body weight (BW) of streptozotocin for 1 month followed by 6 weeks of supplementation with 0.1 and 1.0 g/kg BW of FFP. Metformin was used as positive control treatment. Results Xeniji™-supplemented hyperglycemic mice were recorded with lower glucose level after 6 weeks of duration. This effect was contributed by the improvement of insulin sensitivity in the hyperglycemic mice indicated by the oral glucose tolerance test, insulin tolerance test, and end point insulin level. In addition, gene expression study has shown that the antihyperglycemic effect of FFP is related to the improvement of lipid and glucose metabolism in the mice. Furthermore, both 0.1 and 1 g/kg BW of FFP was able to reduce hyperglycemia-related inflammation indicated by the reduction of proinflammatory cytokines, NF-kB and iNOS gene expression and nitric oxide level. Conclusion FFP potentially demonstrated in vivo antihyperglycemic and anti-inflammatory effects on HFD and streptozotocin-induced diabetic mice.
The first signs of prospective memory

ABSTRACT We conducted a study to examine the impact of motivation and length of delay on performance on prospective memory (PM) tasks in 2-year of children. A total of 158 children aged exactly 24 months were asked to perform a naturalistic PM task. Length of delay (10 min; 35 min) and motivation (high; very high) were between-subjects factors. Two thirds of children had to be excluded from the analysis because of poor retrospective memory for the PM task instructions which were no longer remembered at the end of the session. For the children who did remember the instructions, both motivation and delay had significant effects on PM. Also, their PM performance was reliably above zero, even after the long delay. The findings indicate that when children as young as 24 months are able to remember the PM task instructions they can reliably succeed in PM tasks that are intrinsically motivating for them.
Activation , co – activation , and co – stimulation of resting human NK cells

NK cells possess potent perforin– and IFN-γ–dependent effector functions that are tightly regulated. Inhibitory receptors for MHC class I display variegated expression among NK cells, which confers specificity to individual NK cells. Specificity is also provided by engagement of an array of NK cell activation receptors. Target cells may express ligands for a multitude of activation receptors, many of which signal through different pathways. How inhibitory receptors intersect different signaling cascades is not fully understood. This review focuses on advances in understanding how activation receptors cooperate to induce cytotoxicity in resting NK cells. The role of activating receptors in determining specificity and providing redundancy of target cell recognition is discussed. Using Drosophila insect cells as targets, we have recently examined the contribution of individual receptors. Interestingly, the strength of activation is not determined simply by additive effects of parallel activation pathways. Combinations of signals from different receptors can have different outcomes: synergy, no enhancement over individual signals, or additive effects. Cytotoxicity requires combined signals for granule polarization and degranulation. The integrin LFA-1 contributes a signal for polarization, but not degranulation. Conversely, CD16 alone or synergistic combinations, such as NKG2D and 2B4, signal for PLC-γ and PI3K–dependent degranulation.
Effects of Mulberry Fruit (Morus alba L.) Consumption on Health Outcomes: A Mini-Review

Mulberry (Morus alba L.) belongs to the Moraceae family and is widely planted in Asia. Mulberry fruits are generally consumed as fresh fruits, jams and juices. They contain considerable amounts of biologically active ingredients that might be associated with some potential pharmacological activities that are beneficial for health. Therefore, they have been traditionally used in traditional medicine. Studies have reported that the presence of bioactive components in mulberry fruits, including alkaloids and flavonoid, are associated with bioactivities such as antioxidant. One of the most important compounds in mulberry fruits is anthocyanins which are water-soluble bioactive ingredients of the polyphenol class. Studies have shown that mulberry fruits possess several potential pharmacological health benefits including anti-cholesterol, anti-obesity and hepatoprotective effects which might be associated with the presence of some of these bioactive compounds. However, human intervention studies on the pharmacological activities of mulberry fruits are limited. Therefore, future studies should explore the effect of mulberry fruit consumption on human health and elucidate the detailed compounds. This paper provides an overview of the pharmacological activities of mulberry fruits.
Does the PillCam SB3 capsule endoscopy system improve image reading efficiency irrespective of experience? A pilot study

Abstract Background and study aims The aim of this study was tp compare the diagnostic efficiency of the PillCam SB3 capsule endoscopy (CE) system with the older system, PillCam SB2, taking into consideration the experience of the image reader. Patients and methods Small intestinal CE was conducted on 64 patients around May 2014 when the SB3 was introduced in our hospital. Data obtained from 20 patients (SB2: 10 and SB3: 10) based on transit time were assessed by junior (experience: 20 images), intermediate (> 50), and expert readers (> 600). Results Reading time with the CE down to the end of the small intestine was shorter in the SB3 group for each reader (SB2 vs. SB3: junior, 40.2 ± 10.1 vs. 23.7 ± 6.7 [P = 0.0009]; intermediate, 21.4 ± 4.9 vs. 10.3 ± 2.9 [P = 0.0003]; expert, 23.2 ± 5.6 vs. 11.1 ± 2.9 min [P = 0.0002]). Interpretation agreement rates between the findings by junior and intermediate readers and those by the expert reader were 84.6 % and 92.3 %, respectively. For the junior reader, rates of agreement using the SB2 and SB3 systems with those by the expert reader were 85.7 % and 83.3 %, respectively; no significant difference was noted between the two systems. Similarly, for the intermediate reader, the respective agreement rates using the SB2 and SB3 systems were 85.7 % and 100 %, respectively. Conclusions The PillCam SB3 reduces the time burden on readers irrespective of their experience.
Genotype × country interaction for weaning weight in the Angus populations of Brazil and Uruguay

It was analyzed the existence of genotype × environment interaction for weaning weight in populations of Angus from Brazil and Uruguay by using records of 73,205 animals (10,257 from Uruguay and 62,948 from Brazil) belonging to 33 and 161 farms and 13 and 34 regions in Uruguay and Brazil, respectively. It was used the one- and two-trait animal model analyses considering weight at weaning of each country as different characters. Coefficients of direct and maternal additive-genetic correlation estimated by two statistical models (including or not bull × country effect) Models included the fixed effects of contemporary group (herd-year and month of birth), sex of the calf, the covariates age of dam at calving (years) and age of calf at weaning (days), and the random effects genetic-additive maternal and direct, maternal permanent environment and residual. Herdabilidades (of direct effect) were similar in both countries and with moderate magnitude (0.35 and 0.15, respectively). Coeficients of correlation among maternal and direct genetic effects between Brazil and Uruguay were 0.77 and 0.13, respectively, and comparison among models (with and without bull × country effect) showed significant differences. Correlations among classifications (ranking of genetic values) of bulls with progenie in both countries ranged from 0.35 to 0.41 for estimations in one- and two-trait models, respectively. The results suggest the existence of genotype × environment interaction for weight at weaning of Angus populations between Brazil and Uruguay. There is a need of considering interaction in further international genetic evaluations of the breed.
iFair: Learning Individually Fair Data Representations for Algorithmic Decision Making

People are rated and ranked, towards algorithmic decision making in an increasing number of applications, typically based on machine learning. Research on how to incorporate fairness into such tasks has prevalently pursued the paradigm of group fairness: giving adequate success rates to specifically protected groups. In contrast, the alternative paradigm of individual fairness has received relatively little attention, and this paper advances this less explored direction. The paper introduces a method for probabilistically mapping user records into a lowrank representation that reconciles individual fairness and the utility of classifiers and rankings in downstream applications. Our notion of individual fairness requires that users who are similar in all task-relevant attributes such as job qualification, and disregarding all potentially discriminating attributes such as gender, should have similar outcomes. We demonstrate the versatility of our method by applying it to classification and learning-to-rank tasks on a variety of real-world datasets. Our experiments show substantial improvements over the best prior work for this setting.
ECRB-Based Optimal Parameter Encoding Under Secrecy Constraints

In this paper, optimal deterministic encoding of a scalar parameter is investigated in the presence of an eavesdropper. The aim is to minimize the expectation of the conditional Cramér–Rao bound at the intended receiver while keeping the mean-squared error (MSE) at the eavesdropper above a certain threshold. First, optimal encoding functions are derived in the absence of secrecy constraints for any given prior distribution on the parameter. Next, an optimization problem is formulated under a secrecy constraint and various solution approaches are proposed. Also, theoretical results on the form of the optimal encoding function are provided under the assumption that the eavesdropper employs a linear minimum mean-squared error (MMSE) estimator. Numerical examples are presented to illustrate the theoretical results and to investigate the performance of the proposed solution approaches.