Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis

Recent advances in mass spectrometry (MS)-based proteomics have enabled tremendous progress in the understanding of cellular mechanisms, disease progression, and the relationship between genotype and phenotype. Though many popular bioinformatics methods in proteomics are derived from other omics studies, novel analysis strategies are required to deal with the unique characteristics of proteomics data. In this review, we discuss the current developments in the bioinformatics methods used in proteomics and how they facilitate the mechanistic understanding of biological processes. We first introduce bioinformatics software and tools designed for mass spectrometry-based protein identification and quantification, and then we review the different statistical and machine learning methods that have been developed to perform comprehensive analysis in proteomics studies. We conclude with a discussion of how quantitative protein data can be used to reconstruct protein interactions and signaling networks.
Trustworthiness and a Zero Leakage OTMP-P2L Scheme Based on NP Problems for Edge Security Access †

Resource constraints have prevented comprehensive cryptography and multifactor authentication in numerous Internet of Things (IoT) connectivity scenarios. Existing IoT systems generally adopt lightweight security protocols that lead to compromise and privacy leakage. Edge computing enables better access control and privacy protection, furthermore, blockchain architecture has achieved a trusted store of value by open-source and distributed consensus mechanisms. To embrace these new paradigms, we propose a scheme that employs one-time association multitasking proofs for peer to local authentication (OTMP-P2L). The scheme chooses relevant nondeterministic polynomial (NP) problem tasks, and manages localized trust and anonymity by using smart devices such as phones and pads, thereby enabling IoT devices to autonomously perform consensus validation with an enhanced message authentication code. This nested code is a one-time zero-knowledge proof that comprises multiple logic verification arguments. To increase diversity and reduce the workload of each one, these arguments are chained by a method that establishes some of the inputs of the following task from the output of previous tasks. We implemented a smart lock system and confirmed that the scheme outperforms IoT authentication methods. The result demonstrates superior flexibility through dynamic difficulty strategies and succinct non-interactive peer-to-peer (P2P) verification.
The res (restored cell structure by salinity) tomato mutant reveals the role of the DEAD‐box RNA helicase SlDEAD39 in plant development and salt response

Abstract Increasing evidences highlight the importance of DEAD‐box RNA helicases in plant development and stress responses. In a previous study, we characterized the tomato res mutant (restored cell structure by salinity), showing chlorosis and development alterations that reverted under salt‐stress conditions. Map‐based cloning demonstrates that RES gene encodes SlDEAD39, a chloroplast‐targeted DEAD‐box RNA helicase. Constitutive expression of SlDEAD39 complements the res mutation, while the silencing lines had a similar phenotype than res mutant, which is also reverted under salinity. Functional analysis of res mutant proved SlDEAD39 is involved in the in vivo processing of the chloroplast, 23S rRNA, at the hidden break‐B site, a feature also supported by in vitro binding experiments of the protein. In addition, our results show that other genes coding for chloroplast‐targeted DEAD‐box proteins are induced by salt‐stress, which might explain the rescue of the res mutant phenotype. Interestingly, salinity restored the phenotype of res adult plants by increasing their sugar content and fruit yield. Together, these results propose an unprecedented role of a DEAD‐box RNA helicase in regulating plant development and stress response through the proper ribosome and chloroplast functioning, which, in turn, represents a potential target to improve salt tolerance in tomato crops.
Prevalence of overweight and obesity among school-age children in Jos, North Central, Nigeria.

Background: Overweight and obesity during childhood are gradually becoming a major public health problem in many developing countries in view of their increasing prevalence. This study determined the prevalence of overweight and obesity among school-age children in private and public schools in Jos, North Central, Nigeria. Methodology: A cross-sectional study of 600 school children aged 6-13 years recruited using the multistage sampling technique. Socio-demographic data of the children were obtained using a proforma. The weight and height were measured, from which body mass indexes were calculated. Overweight and obesity status was determined by the International Obesity Task Force cut-off points. Results: The overall prevalence of overweight and obesity was 10.3% and 1.7% respectively. More children in private schools (11%, 2%) than in public schools (9.7%, 1.3%) were overweight and obese respectively but the difference was not statistically significant (p>0.05). The prevalence of obesity was highest among girls in both private and public schools compared to the boys. Seventy percent of children from the upper socioeconomic class were obese compared with 30% from the middle class and none (0%) from the lower class (p<0.0001). Conclusion: There is a high prevalence of overweight and obesity among school- age children in Jos, North Central Nigeria but more among the children in private schools compare to those in public schools. Appropriate intervention programmes targeting school-age children in Northern Nigeria to combat this problem should be planned and implemented by the stakeholders.
Gender perspective in the analysis of the relationship between health and work cessation, and how to deal with it.

OBJECTIVES The main objective of this study is to examine the relationship between health and an early exit from paid employment in the Finnish, Polish, and Spanish populations. The authors have addressed the following 3 issues: who chooses not to work according to gender patterns, whether the health status is a determinant of being non-employed, and what diseases are associated with being non-employed. MATERIAL AND METHODS The studied material consists of data from the Collaborative Research on Ageing in Europe (COURAGE in Europe) project. The analysis was based on a sample of 5868 individuals, including 1214 from Finland, 2152 from Poland and 2532 from Spain. In the paper, these data were complemented with the results of the PArticipation To Healthy Workplaces And inclusive Strategies in the Work Sector (PATHWAYS) project. RESULTS The results of the study revealed that self-rated health was a strong predictor of being non-employed for different reasons. Chronic diseases, such as arthritis, angina, diabetes, chronic obstructive pulmonary disease, depression and hypertension, were typically associated with an increased risk of being non-employed due to health problems and early retirement. Women more frequently reported arthritis and depression, while a higher proportion of men suffered from angina and diabetes. CONCLUSIONS The results obtained by the authors highlight the importance of evaluating gender patterns in work cessation and, at the same time, the importance of gender-focused actions in terms of preventing withdrawal from the labor market. In principle, all chronic diseases have some impact on participation in the labor market. It is worth noting, however, that each of them affects workforce participation in a different manner, depending on the specific disease, country and gender. For this reason, tailored support to every individual's needs is highly recommended.
The effects of competition on pre- and post-metamorphic phenotypes in the common frog

Many species express different phenotypes when reared under different environmental conditions. However, few studies have considered the possible post-metamorphic effects associated with the induction of particular larval phenotypes in organisms which undergo metamorphosis. In this study, we manipulated both larval density and food availability to create the conditions likely to induce high and low competition morphs in the common frog Rana temporaria and examined the resulting pre- and post-metamorphic phenotypes. Tadpoles reared in a high competition environment took longer to reach metamorphosis, were smaller in terms of both mass and total length and possessed relatively narrow bodies and mouths and short, narrow tails compared to low competition tadpoles. Competition level also influenced swimming ability with high competition tadpoles swimming slower and less far than low competition tadpoles. The effects of high levels of larval competition persisted through metamorphosis; high competition froglets were initially shorter and lighter than those reared under a lower level of competition. In addition, froglets reared under a high level of competition as larvae developed relatively short femurs. However, differences in froglet morphology did not significantly affect performance. These results suggest that factors influencing the phenotype in the larval stage will also have post-metamorphic fitness consequences through influences on post-metamorphic morphology.
H2S, Polysulfides, and Enzymes: Physiological and Pathological Aspects

We have been studying the general aspects of the functions of H2S and polysulfides, and the enzymes involved in their biosynthesis, for more than 20 years. Our aim has been to elucidate novel physiological and pathological functions of H2S and polysulfides, and unravel the regulation of the enzymes involved in their biosynthesis, including cystathionine β-synthase (EC 4.2.1.22), cystathionine γ-lyase (EC 4.4.1.1), thiosulfate sulfurtransferase (rhodanese, EC 2.8.1.1), and 3-mercaptopyruvate sulfurtransferase (EC 2.8.1.2). Physiological and pathological functions, alternative biosynthetic processes, and additional functions of H2S and polysulfides have been reported. Further, the structure and reaction mechanisms of related enzymes have also been reported. We expect this issue to advance scientific knowledge regarding the detailed functions of H2S and polysulfides as well as the general properties and regulation of the enzymes involved in their metabolism. We would like to cover four topics: the physiological and pathological functions of H2S and polysulfides, the mechanisms of the biosynthesis of H2S and polysulfides, the properties of the biosynthetic enzymes, and the regulation of enzymatic activity. The knockout mouse technique is a useful tool to determine new physiological functions, especially those of H2S and polysulfides. In the future, we shall take a closer look at symptoms in the human congenital deficiency of each enzyme. Further studies on the regulation of enzymatic activity by in vivo substances may be the key to finding new functions of H2S and polysulfides.
PHYLUM DICYEMIDA IN AUSTRALIAN WATERS: FIRST RECORD AND DISTRIBUTION ACROSS DIVERSE CEPHALOPOD HOSTS

Dicyemid mesozoans are marine organisms that live exclusively in the excretory organs of cephalopod hosts. This study constitutes the first record of the Phylum Dicyemida from Australian waters and provides information on the degree of infections within and between shallow-water host species, and on the distribution of dicyemids across latitude. A total of 38 cephalopod species from 8 families were collected throughout southern, eastern and western Australia, and investigated for the presence of dicyemids. Individuals from 24 cephalopod species were found to be infected, generating new host records of dicyemids for 23 species, 5 genera (Euprymna, Grimpella, Hapalochlaena, Sepiadarium, Sepioloidea) and one family (Sepiadariidae). This investigation represents the first detailed cross-latitudinal survey of dicyemids. Findings of dicyemids in three tropical octopus species (Octopus alpheus, O. dierythraeus and O. ornatus) and multiple findings of uninfected adult benthic cephalopods in temperate regions allow us to re-evaluate and modify concepts of latitudinal trends proposed in previous studies on this group of parasites. Implications of our observations on the largely unknown dicyemid life cycle are discussed.
Comparison of Minimally Invasive versus Open Pancreatoduodenectomy for Pancreatic Ductal Adenocarcinoma: A Propensity Score Matching Analysis

Background: Few studies have compared perioperative and oncological outcomes between minimally invasive pancreatoduodenectomy (MIPD) and open pancreatoduodenectomy (OPD) for pancreatic ductal adenocarcinoma (PDAC). Methods: A retrospective review of patients undergoing MIPD and OPD for PDAC from January 2011 to December 2017 was performed. Perioperative, oncological, and survival outcomes were analyzed before and after propensity score matching (PSM). Results: Data from 1048 patients were evaluated (76 MIPD, 972 OPD). After PSM, 73 patients undergoing MIPD were matched with 219 patients undergoing OPD. Operation times were longer for MIPD than OPD (392 vs. 327 min, p < 0.001). Postoperative hospital stays were shorter for MIPD patients than OPD patients (12.4 vs. 14.2 days, p = 0.040). The rate of overall complications and postoperative pancreatic fistula did not differ between the two groups. Adjuvant treatment rates were higher following MIPD (80.8% vs. 59.8%, p = 0.002). With the exception of perineural invasion, no differences were seen between the two groups in pathological outcomes. The median overall survival and disease-free survival rates did not differ between the groups. Conclusions: MIPD showed shorter postoperative hospital stays and comparable perioperative and oncological outcomes to OPD for selected PDAC patients. Future randomized studies will be required to validate these findings.
Induction of neutrophil extracellular traps by Campylobacter jejuni

Campylobacter jejuni is the leading cause of bacterial‐derived gastroenteritis worldwide and can lead to several post‐infectious inflammatory disorders. Despite the prevalence and health impacts of the bacterium, interactions between the host innate immune system and C. jejuni remain poorly understood. To expand on earlier work demonstrating that neutrophils traffic to the site of infection in an animal model of campylobacteriosis, we identified significant increases in several predominantly neutrophil‐derived proteins in the faeces of C. jejuni‐infected patients, including lipocalin‐2, myeloperoxidase and neutrophil elastase. In addition to demonstrating that these proteins significantly inhibited C. jejuni growth, we determined they are released during formation of C. jejuni‐induced neutrophil extracellular traps (NETs). Using quantitative and qualitative methods, we found that purified human neutrophils are activated by C. jejuni and exhibit signatures of NET generation, including presence of protein arginine deiminase‐4, histone citrullination, myeloperoxidase, neutrophil elastase release and DNA extrusion. Production of NETs correlated with C. jejuni phagocytosis/endocytosis and invasion of neutrophils suggesting that host‐ and bacterial‐mediated activities are responsible for NET induction. Further, NET‐like structures were observed within intestinal tissue of C. jejuni‐infected ferrets. Finally, induction of NETs significantly increased human colonocyte cytotoxicity, indicating that NET formation during C. jejuni infection may contribute to observed tissue pathology. These findings provide further understanding of C. jejuni–neutrophil interactions and inflammatory responses during campylobacteriosis.
Early Restoration of Shank3 Expression in Shank3 Knock-Out Mice Prevents Core ASD-Like Behavioral Phenotypes

Abstract Several genes are associated with increased risk for autism spectrum disorder (ASD), neurodevelopmental disorders that present with repetitive movements and restricted interests along with deficits in social interaction/communication. While genetic alterations associated with ASD are present early in life, ASD-like behaviors are difficult to detect in early infancy. This raises the issue of whether reversal of an ASD-associated genetic alteration early in life can prevent the onset of ASD-like behaviors. Genetic alterations of SHANK3, a well-characterized gene encoding a postsynaptic scaffolding protein, are estimated to contribute to ∼0.5% of ASD and remain one of the more replicated and well-characterized genetic defects in ASD. Here, we investigate whether early genetic reversal of a Shank3 mutation can prevent the onset of ASD-like behaviors in a mouse model. Previously, we have demonstrated that mice deficient in Shank3 display a wide range of behavioral abnormalities such as repetitive grooming, social deficits, anxiety, and motor abnormalities. In this study, we replicate many of these behaviors in Shank3 mutant mice. With early genetic restoration of wild-type (WT) Shank3, we rescue behaviors including repetitive grooming and social, locomotor, and rearing deficits. Our findings support the idea that the underlying mechanisms involving ASD behaviors in mice deficient in Shank3 are susceptible to early genetic correction of Shank3 mutations.
Low-Risk Planned Out-of-Hospital Births: Characteristics and Perinatal Outcomes in Different Italian Birth Settings

Background: The present observational study aimed to describe women and delivery characteristics and early birth outcomes according to planned out-of-hospital delivery and to compare this information with comparable planned in-hospital deliveries. Methods: 1099 healthy low-risk women who delivered out-of-hospital between 2014 to 2018, with a gestational age of 37–42 completed weeks of pregnancy, with single, vertex babies whose birth was expected to be vaginal and spontaneous were enrolled. Moreover, a case-control study was designed comparing characteristics of these births to a matched 1:5 sample. Results: living in a medium city (RR 1.81, 95% CI 1.19–2.74), being multiparous (RR 1.66, CI 1.09–2.51), having the first child at ≥35 years old (RR 1.84, CI 1.02–3.33), not working (RR 1.77, CI 1.06–2.96), not being omnivorous (RR 1.80, CI 1.08–3.00), and not smoking (RR 2.53, CI 1.06–6.07) were all related to an increased chance of delivering at home compared to in a freestanding midwifery unit. The significant factors in choosing to give birth out-of-hospital instead of in-hospital were living in a large or medium city (OR 2.20; 1.75–2.77; OR 2.41; 1.93–3.02) and having a secondary or higher level of education (OR > 2 for both parents). Within the first week of delivery, 6 of 1099 mothers and 19 of 1099 neonates were hospitalized. Conclusions: out-of-hospital births in women with low-risk pregnancies is a possible option that needs to be planned, monitored, regulated, and evaluated according to healthcare control systems in order to work, as in hospitals, for the safest and most effective care to a mother and her neonate(s).
Trends in use of primary prophylactic colony stimulating factors and neutropenia-related hospitalization in commercially insured patients receiving myelosuppressive chemotherapy in the United States: 2005–2017

Purpose Describe temporal changes in use of myelosuppressive chemotherapy, primary prophylactic colony-stimulating factor, and neutropenia-related hospitalization, in commercially insured patients. Methods Using a large commercial administrative database, we identified annual cohorts of adult patients diagnosed with breast or lung cancer, or non-Hodgkin lymphoma and initiating myelosuppressive chemotherapy during 2005–2017. We described yearly changes in proportions of myelosuppressive chemotherapy by febrile neutropenia risk category (high, intermediate, unclassified) and proportion of prophylactic colony-stimulating factor use and unadjusted incidence of neutropenia-related hospitalization in the first cycle of myelosuppressive chemotherapy. Results Annual cohorts included 4383–5888 eligible patients during 2005–2017. The proportion of eligible patients aged ≥ 65 years increased from 26.0% in 2005 to 58.2% in 2017. Myelosuppressive chemotherapy use with regimens with high risk for febrile neutropenia increased from 15.1% in 2005 to 31.0% in 2017; and regimens with intermediate risk for febrile neutropenia decreased from 63.7% to 48.1% in 2017. Prophylactic colony-stimulating factor use increased from 41.6% in 2005 to 54.3% in 2017. Crude incidence of neutropenia-related hospitalization for all cancers increased from 2.0% to 3.1%, with a substantial increase in neutropenia-related hospitalization observed among non-Hodgkin lymphoma patients (2.8% to 8.5%) during 2005–2017. Conclusion Among adult patients with breast and lung cancer, and non-Hodgkin lymphoma receiving myelosuppressive chemotherapy, use of regimens with high risk for febrile neutropenia increased, as did the use of prophylactic colony-stimulating factors after 2005. Incidence of neutropenia-related hospitalization increased slightly, particularly among non-Hodgkin lymphoma patients. Further studies are required to understand this increasing trend of neutropenia-related hospitalization, changing patient-level risk factors, and febrile neutropenia management.
Early host–microbe interaction in a peri‐implant oral mucosa‐biofilm model

The host‐microbe relationship is pivotal for oral health as well as for peri‐implant diseases. Peri‐implant mucosa and commensal biofilm play important roles in the maintenance of host‐microbe homeostasis, but little is known about how they interact. We have therefore investigated the early host‐microbe interaction between commensal multispecies biofilm (Streptococcus oralis, Actinomyces naeslundii, Veillonella dispar, Porphyromonas gingivalis) and organotypic peri‐implant mucosa using our three‐dimensional model. After 24 hr, biofilms induced weak inflammatory reaction in the peri‐implant mucosa by upregulation of five genes related to immune response and increased secretion of IL‐6 and CCL20. Biofilm volume was reduced which might be explained by secretion of β‐Defensins‐1, ‐2, and CCL20. The specific tissue reaction without intrinsic overreaction might contribute to intact mucosa. Thus, a relationship similar to homeostasis and oral health was established within the first 24 hr. In contrast, the mucosa was damaged and the bacterial distribution was altered after 48 hr. These were accompanied by an enhanced immune response with upregulation of additional inflammatory‐related genes and increased cytokine secretion. Thus, the homeostasis‐like relationship was disrupted. Such profound knowledge of the host‐microbe interaction at the peri‐implant site may provide the basis to improve strategies for prevention and therapy of peri‐implant diseases.
Service Perceptions in Fitness Centers: IPA Approach by Gender and Age

Background: The number of fitness practitioners has increased in the last decades. A deeper understanding of user perceptions is required for better service design. Methods: An importance-performance analysis (IPA) and correlational analysis were performed on a sample of 414 members (173 women and 241 men) with a mean age of 32.33 years (SD = 11.50) and recruited from 25 fitness centers of Community of Madrid, Spain. Results: The results show that women’s levels of importance and performance are higher than men in most of the service attributes. Women also correlate with a higher priority than men in core elements of the service, such as the variety and number of activities, personal training and fitness service quality. Female members feel more attracted by services like swimming pools and other peripheral services, like a welcome pack and medical or physiotherapist service. According to age, older members feel less satisfied than young users with the cleanliness of activity spaces and with the safety of lockers. Conclusions: Differences in perceptions by age and gender were identified among members of fitness centers. These results should be considered by private and public organizations to provide the best practices and tailored services for engaging more people in physical activity.