Miracle-dz/UniFAR-FTUs huggingface dataset:
Serotypes in the ciliate Dileptus anser: epigenetic phenomena

Summary This review presents some data obtained by the authors in their study of the serotype system in the lower ciliate Dileptus anser, a species that has not been explored previously in this aspect. These data show many features similar to those described in serotype systems of higher ciliates, Paramecium and Tetrahymena. At the same time, some of the results do not agree with conventional patterns generally accepted for these classical objects. The authors discuss the data obtained in dilepti in terms of epigenetic variation and inheritance.
Integrative analyses of biomarkers and pathways for adipose tissue after bariatric surgery

ABSTRACT We explored potential biomarkers and molecular mechanisms regarding multiple benefits after bariatric surgery. Differentially expressed genes (DEGs) for subcutaneous adipose tissue (AT) after bariatric surgery were identified by analyzing two expression profiles from the GEO. Subsequently, enrichment analysis, GSEA, PPI network, and gene-microRNAs and gene-TFs networks were interrogated to identify hub genes and associated pathways. Co-expressed DEGs included one that was up-regulated and 22 that were down-regulated genes. The enrichment analyses indicated that down-regulated DEGs were significantly involved in inflammatory responses. GSEA provided comprehensive evidence that most genes enriched in pro-inflammation pathways, while gene-sets after surgery enriched in metabolism. We identified nine hub genes in the PPI network, most of which were validated as highly expressed and hypomethylated in obesity by Attie Lab Diabetes and DiseaseMeth databases, respectively. DGIdb was also applied to predict potential therapeutic agents that might reverse abnormally high hub gene expression. Bariatric surgery induces a significant shift from an obese pro-inflammatory state to an anti-inflammatory state, with improvement in adipocyte metabolic function – representing key mechanisms whereby AT function improves after bariatric surgery. Our study deepens a mechanistic understanding of the benefits of bariatric surgery and provides potential biomarkers or treatment targets for further research.
Introduction to Kalman Filter and Its Applications

We provide a tutorial-like description of Kalman filter and extended Kalman filter. This chapter aims for those who need to teach Kalman filters to others, or for those who do not have a strong background in estimation theory. Following a problem definition of state estimation, filtering algorithms will be presented with supporting examples to help readers easily grasp how the Kalman filters work. Implementations on INS/GNSS navigation, target tracking, and terrain-referenced navigation (TRN) are given. In each example, we discuss how to choose, implement, tune, and modify the algorithms for real world practices. Source codes for implementing the examples are also provided. In conclusion, this chapter will become a prerequisite for other contents in the book.
β-Alanine N-Methyltransferase of Limonium latifolium. cDNA Cloning and Functional Expression of a Novel N-Methyltransferase Implicated in the Synthesis of the Osmoprotectant β-Alanine Betaine1

β-alanine (Ala) betaine, an osmoprotectant suitable under saline and hypoxic environments, is found in most members of the halophytic plant family Plumbaginaceae. In Limonium latifolium (Plumbaginaceae), it is synthesized via methylation of β-Ala by the action of a trifunctional S-adenosyl l-methionine (Ado-Met): β-Ala N-methyltransferase (NMTase). Peptide sequences from purified β-Ala NMTase were used to design primers for reverse transcriptase-PCR, and several cDNA clones were isolated. The 5′ end of the cDNA was cloned using a 5′-rapid amplification of cDNA ends protocol. A 500-bp cDNA was used as a probe to screen a λ-gt10 L. latifolium leaf cDNA library. Partial cDNA clones represented two groups, NMTase A and NMTase B, differing only in their 3′-untranslated regions. The full-length NMTase A cDNA was 1,414 bp and included a 1128-bp open reading frame and a 119-bp 5′-untranslated region. The deduced amino acid sequence of 375 residues had motifs known to be involved in the binding of Ado-Met. The NMTase mRNA was expressed in L. latifolium leaves but was absent in Limonium sinuatum, a member of the genus that lacks the synthetic pathway for β-Ala betaine. NMTase mRNA expression was high in young and mature leaves and was enhanced by light. NMTase cDNA was expressed in yeast (Saccharomyces cerevisiae) under the control of a galactose-inducible promoter. Protein extracts of galactose-induced recombinant yeast had Ado-Met-specific NMTase activities that were highly specific to β-Ala, N-methyl β-Ala, and N,N-dimethyl β-Ala as methyl acceptors. NMTase activities were not detectable in comparable protein extracts of yeast, transformed with vector control. The NMTase protein sequence shared homology with plant caffeic acid O-methyltransferases and related enzymes. Phylogenetic analyses suggested that β-Ala NMTase represents a novel family of N-methyltransferases that are evolutionarily related to O-methyltransferases.
Associations of physical and psychiatric conditions with chronic fatigue syndrome in Germany: an exploratory case-control study

Abstract Background Only a few studies have analyzed the effects of physical and psychiatric conditions on the risk of chronic fatigue syndrome (CFS). Therefore, the goal of this exploratory case-control study was to investigate the associations of physical and psychiatric conditions with CFS in almost 19 800 adults from Germany. Methods This study included patients diagnosed for the first time with CFS in one of 1238 general practices in Germany between 2010 and 2017 (index date). Controls without CFS were matched (1:1) to cases with CFS by sex, age, index year, and practice. Physical and psychiatric conditions diagnosed in the year prior to the index date were included if they were present in at least 3% of patients with CFS. Associations between physical and psychiatric conditions (33 potential independent variables) and CFS (dependent variable) were analyzed in an adjusted conditional logistic regression model, and physical and psychiatric disorders were included in the model using forward stepwise selection. Results This study included 9896 cases with CFS and 9896 controls without CFS [65.1% women; mean (standard deviation) age 49.5 (18.3) years]. Seven conditions were associated with CFS in the adjusted regression model. The disorders displaying the strongest relationship with CFS were cancer [odds ratio (OR) = 2.57, 95% confidence interval (CI) = 2.24–2.95], sleep disorders (OR = 1.88, 95% CI = 1.66–2.12) and depression (OR = 1.77, 95% CI = 1.61–1.95). Conclusions Cancer, sleep disorders, and depression were strongly and positively associated with CFS. Additional studies are needed to gain a better understanding of the mechanisms underlying these relationships.
A systematic review of the prevalence of depression, anxiety, and apathy in frontotemporal dementia, atypical and young-onset Alzheimer’s disease, and inherited dementia

ABSTRACT Objectives: Depression, anxiety, and apathy are the most commonly reported neuropsychiatric symptoms (NPS) in Alzheimer’s disease (AD). Understanding their prevalence in rarer dementias such as frontotemporal dementia (FTD), primary progressive aphasia (PPA), posterior cortical atrophy (PCA), young-onset AD (YOAD), and inherited dementias has implications for both clinical practice and research. In this study, we aimed to examine the current state of knowledge of the prevalence of these three NPS in less prevalent dementias. Design: We conducted a systematic review based on searches of EMBASE, PsycINFO, and PubMed up to September 2019. Results: 47 articles meeting inclusion criteria were identified. Depression, anxiety, and apathy were commonly reported across the phenotypes studied but their prevalence showed large variation between studies. Apathy showed the highest reported frequency in FTD (50–100% across studies), behavioral variant frontotemporal dementia (bvFTD) (73–100%), and YOAD (44–100%). Anxiety was frequently reported in FTD (0–100%) and bvFTD (19–63%). Depression showed the highest prevalence in FTD (7–69%) and YOAD (11–55%). Among the three variants of PPA, sv-PPA is the one most investigated (seven articles). Three or fewer articles were identified examining NPS in the remaining PPA variants, PCA, familial AD, and familial FTD. Inconsistency in the tools used to measure symptoms and small sample sizes were common methodological limitations. Conclusions: Future studies should consider the inclusion of larger sample sizes (e.g. through multicenter collaborations) and the use of harmonized protocols that include the combination of caregiver and patient-derived measures and symptom-specific questionnaires. More research is needed on the phenotype-specific barriers and facilitators for people living with dementia to successfully engage in self-reports of NPS.
Australian blattidae (Blattodea). 3. Revision of the genera Zonioploca Stal and Eppertia Shaw

Nine species of Zonioploca are known, three of them being new, namely Z. fullerae, sp. nov., Z. occidentalis, sp, nov., and Z. tepperi, sp. nov. Four species of Eppertia are known, one of them being new. It is not described owing to lack of suitable material.
Mentalising and conversation-following in autism

Some people with autism spectrum disorders have been observed to experience difficulties with making correct inferences in conversations in social situations. However, the nature and origin of their problem is rarely investigated. This study used manipulations of video stimuli to investigate two questions. The first question was whether it is the number of people involved in social situations, that is, the source of problems in following conversations, or whether it is the increased mentalising demands required to comprehend interactions between several people. The second question asked was whether the nature and pattern of the errors that autism spectrum disorder participants show are the same as typically developing people make when they make an error. In total, 43 typically developed adults and 30 adults diagnosed with autism spectrum disorder were studied. We found that it was the amount of mentalising required, rather than the number of people involved, which caused problems for people with autism spectrum disorder in following conversations. Furthermore, the autism spectrum disorder participants showed a more heterogeneous pattern of errors, showing less agreement among themselves than the typically developed group as to which test items were hardest. So, fully understanding the observed behaviour consequent upon weakness in mentalising ability in people with autism spectrum disorders requires consideration of factors other than mentalising.
Potential for Pharmacology of Ryanadine Receptor/Calcium Release Channelsa

ABSTRACT: Calcium release channels, known also as ryanodine receptors (RyRs), play an important role in Ca2+ signaling in muscle and nonmuscle cells by releasing Ca2+ from intracellular stores. Mammalian tissues express three different RyR isoforms comprising four 560‐kDa (RyR polypeptide) and four 12‐kDa (FK506 binding protein) subunits. The large protein complexes conduct monovalent and divalent cations and are capable of multiple interactions with other molecules. The latter include small diffusible endogenous effector molecules including Ca2+, Mg2+, adenine nucleotides, sufhydryl modifying reagents (glutathione, NO, and NO adducts) and lipid intermediates, and proteins such as protein kinases and phosphatases, calmodulin, immunophilins (FK506 binding proteins), and in skeletal muscle the dihydropyridine receptor. Because of their role in regulating intracellular Ca2+ levels and their multiple ligand interactions, RyRs constitute an important, potentially rich pharmacological target for controlling cellular functions. Exogenous effectors found to affect RyR function include ryanoids, toxins, xanthines, anthraquinones, phenol derivatives, adenosine and purinergic agonists and antagonists, NO donors, oxidizing reagents, dantrolene, local anesthetics, and polycationic reagents.
What Makes Opportunistic GP Interventions Effective? An Analysis of Behavior Change Techniques Used in 237 GP-Delivered Brief Interventions for Weight Loss.

BACKGROUND Evidence shows that clinician-delivered brief opportunistic interventions are effective in obesity, and guidelines promote their use. However, there is no evidence on how clinicians should do this, and guidelines are not based on clinical evidence. PURPOSE A trial (Brief Interventions for Weight Loss [BWeL]) showed that brief opportunistic interventions on obesity that endorsed, offered, and facilitated referral to community weight management service (CWMS) led to 77% agreeing to attend, and 40% attending CWMS, as well as significantly greater weight loss than control at 12 months. We assessed which behavior change techniques (BCTs) doctors used that were associated with CWMS attendance. METHODS We coded 237 recorded BWeL interventions using the behavioral change techniques version one taxonomy. We also coded the BWeL training video to examine delivery of recommended BCTs. Mixed effects logistic regression assessed the association between each BCT, the total number of BCTs, and delivery of recommended BCTs, with patient's agreement to attend and actual CWMS attendance. RESULTS Of 237 patients, 133 (56%) agreed to attend and 109 (46%) attended. Thirteen BCTs were used more than eight times but none of the 13 were associated with increased attendance. One, "practical social support," was significantly associated with increased patient agreement (odds ratio [OR] = 4.80, 95% confidence interval [CI] = 1.15, 20.13). Delivery of recommended BCTs and the total number of BCTs used were both associated with increased agreement (OR = 1.56, 95% CI = 1.09, 2.23 and OR = 1.34, 95% CI = 1.03, 1.75, respectively), but not attendance at CWMS (OR = 1.20, 95% CI = 0.98-1.47 and OR = 1.08, 95% CI = 0.94-1.24, respectively). CONCLUSIONS There is no evidence that particular BCT can increase the effectiveness of brief opportunistic interventions for obesity in adults. However, using more BCTs and delivery of recommended BCTs may increase agreement to attend community weight management services.
Residue interaction dynamics in Vaucheria aureochrome1 light‐oxygen‐voltage: Bridging theory and experiments

Allosteric communication is the basis of signaling and information transfer. Collective interactions between amino acid residues, which are spatially distributed in the three dimensional structure of a protein molecule, form the basis of allosteric network. While the construction of residue interaction graphs (RIG) is based on static crystal structures of proteins, it is important to extract information on protein dynamics to understand allostery. Therefore, quantitative analysis of RIG based on the framework of differential network (DN), is immensely helpful in identifying key amino acid residue interactions within such communication pathways. While the simultaneous availability of protein structures from two different states is essential for DN, there are additional challenges. Crystallographic artifacts like nonbiological dimeric arrangements within the crystal lattice automatically influence the construction and eventually the interpretation of RIG. Therefore, experimental validation of predictions from the analyses of RIG is naturally scarce in the literature. Herein, we study the photo sensor domain of the signaling photoreceptor transcription factor, aureochrome1, to understand light‐driven signaling. We perform direct experiments to verify the predictions from RIG using the machinery of DN. However, the agreement leaves scope for improvement. We then discuss the notion of quaternary structure alignment to obtain a biologically meaningful dimer. Thence, we reconstruct the RIG and reanalyze the modified structure. Results of these reanalyses render far superior agreement with experiments. Therefore, this notion of addressing crystallographic biases provides a fresh yet general approach for reconciliation of theory and experiments. It is applicable beyond the present case to all signaling proteins in general.
Predictive Value of Fibrinogen-to-Albumin Ratio for Post-Contrast Acute Kidney Injury in Patients Undergoing Elective Percutaneous Coronary Intervention

Background Post-contrast acute kidney injury (PC-AKI) is a contributor to adverse outcomes after percutaneous coronary intervention (PCI). This study aimed to investigate whether fibrinogen-to-albumin ratio (FAR), a novel inflammation-based risk index, can predict the occurrence of PC-AKI in patients undergoing elective PCI. Material/Methods We retrospectively enrolled 291 patients who underwent elective PCI from June 2017 to June 2019. PC-AKI was defined as an increase in serum creatinine ≥0.3 mg/dL (≥26.5 μmol/L), or ≥1.5 times baseline within 48 to 72 hours after PCI. The area under the receiver-operating characteristic curve (AUC), continuous net reclassification improvement (NRI), and integrated discrimination improvement (IDI) were calculated to make comparison for PC-AKI prediction. Results PC-AKI occurred in 43 patients (14.8%). FAR showed an AUC of 0.691 (95% confidence interval: 0.64–0.74; P<0.001) in predicting PC-AKI. In stepwise multivariable logistic regression, FAR was independently associated with the occurrence of PC-AKI along with hypertension, diabetes, hemoglobin, estimated glomerular filtration rate, and left ventricular ejection fraction. FAR significantly improved PC-AKI prediction over Mehran risk score in the continuous NRI and IDI, but not AUC. Conclusions FAR is independently associated with the occurrence of PC-AKI, and can significantly improve PC-AKI prediction over Mehran risk score in patients undergoing elective PCI.
A pilot study for early detection of oral premalignant diseases using oral cytology and Raman micro‐spectroscopy: Assessment of confounding factors

This study demonstrates the efficacy of Raman micro‐spectroscopy of oral cytological samples for differentiating dysplastic, potentially malignant lesions from those of normal, healthy donors. Cells were collected using brush biopsy from healthy donors (n = 20) and patients attending a Dysplasia Clinic (n = 20). Donors were sampled at four different sites (buccal mucosa, tongue, alveolus, gingiva), to ensure matched normal sites for all lesions, while patient samples were taken from clinically evident, histologically verified dysplastic lesions. Spectra were acquired from the nucleus and cytoplasm of individual cells of all samples and subjected to partial least squares‐discriminant analysis. Discriminative sensitivities of 94% and 86% and specificity of 85% were achieved for the cytoplasm and nucleus, respectively, largely based on lipidic contributions of dysplastic cells. Alveolar/gingival samples were differentiated from tongue/buccal samples, indicating that anatomical site is potentially a confounding factor, while age, gender, smoking and alcohol consumption were confirmed not to be.
Gone with the Wind

Objective: If the narrative of “coronavirus” has an underlying theme, it may perhaps for some be one of survival, whilst for others, the theme might be suffering. The recurring motif of survival has continued throughout history, yet for the first time the sum of all fears has amounted to a run on the bare essentials. This paper seeks to offer an alternative formulation of “panic buying,” with references to literature, philosophy, and contemporary neurobiology. Conclusion: The bare essentials disappeared perhaps as part of some self-fulfilling prophecy: the supermarkets became bare because others inadvertently lead us to believe they would become bare. The contagion model of emotional propagation provides a psychological model of how “panic buying” by an individual might lead to the replication of panic in an observer. The Polyvagal Theory further informs us of how the threat posed by the pandemic primes our limbic system to perceive danger, and explains how witnessing others engaging in fight-flight responses might evoke a fearful affect in an observer. In the end, it is perhaps through Nietzsche’s study of classical tragedy that we may find some meaning to the pandemic, allowing our collective lived experience to serve as a template for growth.
Selection of wheat mutant genotypes carrying HMW glutenin alleles related to baking quality by using PCR (STS method).

This study was performed in the Agriculture, Medicine and Industry Research School, Nuclear Science and Technology Research Institute of Iran in 2005-2006, through Polymerase Chain Reaction by using Sequence Tagged Site (STS) method, to characterize in terms of bread quality of some wheat mutant genotypes (Roshan, Omid, Tabasi, Azar and Azadi), their parents and other cultivars such as Chamran, Enia, Bezostaya, Tajan, Pishtaz and Chinese spring. Twelve pairs of primers were used in this study; seven of them were extracted from the literature and the others were designed from the D genome subunites sequences of wheat. Some studies on drought resistance, salt resistance, etc., have been done for these mutant genotypes, some of them showing good results. However, their baking quality has not been studied before. The alleles Dx2+Dy12 (with negative effect on bread quality) and Dx2*, Dx5+Dy10 (with positive effect on bread quality) had the main effect on wheat bread quality. Special primers of these subunits were used to amplify these alleles. Except for the cultivars that had Dx5+Dx10, six mutant genotypes whose parents did not have these alleles (T-66-58-60, Ro-5, Ro-4, Ro-3, Ro-1 and O-64-1-10), showed Dx5+Dx10. SDS-PAGE analyses showed no contradictory results with molecular experiments. Significant differences were seen on protein percentage for polymorphic mutant genotypes, Ro-1 , Ro-3 and Ro-5 with Roshan (their parent), at 1% probability level.
Data availibility for the fisheries impact assessment of the FIMPAS project

The project Fisheries Measures in Protected Areas (FIMPAS) aims to introduce fisheries measures in the marine Natura 2000 sites within the Exclusive Economic Zone of the Dutch part of the North Sea by the end of 2011. The FIMPAS project covers three such areas, the Dogger Bank and the Cleaver Bank (both to be designated for protection under the Habitats Directive) and the Frisian Front (to be designated for protection under the Birds Directive). These sites are beyond the Dutch 12 nm zone and several EU Member States fish within these areas. Therefore fisheries measures must be implemented through the Common Fisheries Policy. These marine protected areas, as well as the potential fisheries measures, are a consequence of the implementation of the European Birds and Habitats Directives and will be proposed to the European Commission by the Dutch government. The Dutch Ministry for Agriculture, Nature and Food Quality (LNV), together with Dutch environmental NGOs and the Dutch fishing industry, are cooperating within the FIMPAS project to develop the necessary fisheries measures to achieve the conservation objectives for the Dutch Natura 2000 sites of the North Sea. LNV has asked the International Council for the Exploration of the Sea (ICES) to organize the necessary scientific processes and give advice on the desired fisheries measures involving the relevant stakeholders in this process.