Miracle-dz/UniFAR-FTUs huggingface dataset:
Flagellum-Mediated Mechanosensing and RflP Control Motility State of Pathogenic Escherichia coli

Flagella and motility are widespread virulence factors among pathogenic bacteria. Motility enhances the initial host colonization, but the flagellum is a major antigen targeted by the host immune system. Here, we demonstrate that pathogenic E. coli strains employ a mechanosensory function of the flagellar motor to activate flagellar expression under high loads, while repressing it in liquid culture. We hypothesize that this mechanism allows pathogenic E. coli to regulate its motility dependent on the stage of infection, activating flagellar expression upon initial contact with the host epithelium, when motility is beneficial, but reducing it within the host to delay the immune response. ABSTRACT Bacterial flagellar motility plays an important role in many processes that occur at surfaces or in hydrogels, including adhesion, biofilm formation, and bacterium-host interactions. Consequently, expression of flagellar genes, as well as genes involved in biofilm formation and virulence, can be regulated by the surface contact. In a few bacterial species, flagella themselves are known to serve as mechanosensors, where an increased load on flagella experienced during surface contact or swimming in viscous media controls gene expression. In this study, we show that gene regulation by motility-dependent mechanosensing is common among pathogenic Escherichia coli strains. This regulatory mechanism requires flagellar rotation, and it enables pathogenic E. coli to repress flagellar genes at low loads in liquid culture, while activating motility in porous medium (soft agar) or upon surface contact. It also controls several other cellular functions, including metabolism and signaling. The mechanosensing response in pathogenic E. coli depends on the negative regulator of motility, RflP (YdiV), which inhibits basal expression of flagellar genes in liquid. While no conditional inhibition of flagellar gene expression in liquid and therefore no upregulation in porous medium was observed in the wild-type commensal or laboratory strains of E. coli, mechanosensitive regulation could be recovered by overexpression of RflP in the laboratory strain. We hypothesize that this conditional activation of flagellar genes in pathogenic E. coli reflects adaptation to the dual role played by flagella and motility during infection. IMPORTANCE Flagella and motility are widespread virulence factors among pathogenic bacteria. Motility enhances the initial host colonization, but the flagellum is a major antigen targeted by the host immune system. Here, we demonstrate that pathogenic E. coli strains employ a mechanosensory function of the flagellar motor to activate flagellar expression under high loads, while repressing it in liquid culture. We hypothesize that this mechanism allows pathogenic E. coli to regulate its motility dependent on the stage of infection, activating flagellar expression upon initial contact with the host epithelium, when motility is beneficial, but reducing it within the host to delay the immune response.
Associations of inflammatory markers with impaired left ventricular diastolic and systolic function in collagen-induced arthritis

Background High-grade inflammation may play a pivotal role in the pathogenesis of left ventricular (LV) dysfunction. Evidence to support a role of systemic inflammation in mediating impaired LV function in experimental models of rheumatoid arthritis (RA) remains limited. The aim of the present study was to determine the effects of high-grade systemic inflammation on LV diastolic and systolic function in collagen-induced arthritis (CIA). Methods To induce CIA, bovine type-II collagen emulsified in incomplete Freund’s adjuvant was injected at the base of the tail into 21 three-month old Sprague Dawley rats. Nine-weeks after the first immunisation, LV function was assessed by pulsed Doppler, tissue Doppler imaging and Speckle tracking echocardiography. Cardiac collagen content was determined by picrosirius red staining; circulating inflammatory markers were measured using ELISA. Results Compared to controls (n = 12), CIA rats had reduced myocardial relaxation as indexed by lateral e’ (early diastolic mitral annular velocity) and e’/a’ (early-to-late diastolic mitral annular velocity) and increased filling pressures as indexed by E/e’. No differences in ejection fraction and LV endocardial fractional shortening between the groups were recorded. LV global radial and circumferential strain and strain rate were reduced in CIA rats compared to controls. Higher concentrations of circulating inflammatory markers were associated with reduced lateral e’, e’/a’, radial and circumferential strain and strain rate. Greater collagen content was associated with increased concentrations of circulating inflammatory markers and E/e’. Conclusion High-grade inflammation is associated with impaired LV diastolic function and greater myocardial deformation independent of haemodynamic load in CIA rats.
Action potentials in Xenopus oocytes triggered by blue light

Channelrhodopsin-2 is the key ion channel in optogenetics. Walther et al. demonstrate that coupling channelrhodopsin-2 to the β1 subunit of voltage-gated sodium channels allows action potentials to be triggered by blue-light illumination of Xenopus laevis oocytes coexpressing different types of sodium channel α subunits.
Global Research on Quality of Life of Patients with HIV/AIDS: Is It Socio-Culturally Addressed? (GAPRESEARCH)

Quality of life (QOL) has been considered as an important outcome indicator in holistic care for HIV-infected people, especially as HIV/AIDS transforms from a fatal illness to a chronic condition. This study aimed to identify trends and emerging topics among research concerning the QOL of people living with HIV/AIDS (PLWHA). The analyzed data were English papers published from 1996 to 2017, searched and extracted from the Web of Science Core Collection. Collaborations between countries and the correlation between the keywords were visualized by VOSviewer while the abstracts’ content was analyzed using exploratory factor analysis and Jaccard’s’ similarity index. There has been an increase in both the number of publications and citations. The United Nations of America leads in terms of paper volume. The cross-nation collaborations are mainly regional. Despite a rather comprehensive coverage of topics relating to QOL in PLWHA, there has evidently been a lack of studies focusing on socio-cultural factors and their impacts on the QOL of those who are HIV-infected. Further studies should consider investigating the role of socio-cultural factors, especially where long-term treatment is involved. Policy-level decisions are recommended to be made based on the consideration of cultural factors, while collaborations between developed and developing nations, in particular in HIV/AIDS-ridden countries, are strongly recommended.
Experimental Evolution of Legume Symbionts: What Have We Learnt?

Rhizobia, the nitrogen-fixing symbionts of legumes, are polyphyletic bacteria distributed in many alpha- and beta-proteobacterial genera. They likely emerged and diversified through independent horizontal transfers of key symbiotic genes. To replay the evolution of a new rhizobium genus under laboratory conditions, the symbiotic plasmid of Cupriavidus taiwanensis was introduced in the plant pathogen Ralstonia solanacearum, and the generated proto-rhizobium was submitted to repeated inoculations to the C. taiwanensis host, Mimosa pudica L. This experiment validated a two-step evolutionary scenario of key symbiotic gene acquisition followed by genome remodeling under plant selection. Nodulation and nodule cell infection were obtained and optimized mainly via the rewiring of regulatory circuits of the recipient bacterium. Symbiotic adaptation was shown to be accelerated by the activity of a mutagenesis cassette conserved in most rhizobia. Investigating mutated genes led us to identify new components of R. solanacearum virulence and C. taiwanensis symbiosis. Nitrogen fixation was not acquired in our short experiment. However, we showed that post-infection sanctions allowed the increase in frequency of nitrogen-fixing variants among a non-fixing population in the M. pudica–C. taiwanensis system and likely allowed the spread of this trait in natura. Experimental evolution thus provided new insights into rhizobium biology and evolution.
Overcoming Shellfish Allergy: How Far Have We Come? †

Shellfish allergy caused by undesirable immunological responses upon ingestion of crustaceans and mollusks is a common cause of food allergy, especially in the Asia-Pacific region. While the prevalence of shellfish allergy is increasing, the mainstay of clinical diagnosis for these patients includes extract-based skin prick test and specific IgE measurement while clinical management consists of food avoidance and as-needed use of adrenaline autoinjector should they develop severe allergic reactions. Such a standard of care is unsatisfactory to both patients and healthcare practitioners. There is a pressing need to introduce more specific diagnostic methods, as well as effective and safe therapies for patients with shellfish allergy. Knowledge gained on the identifications and defining the immuno-molecular features of different shellfish allergens over the past two decades have gradually translated into the design of new diagnostic and treatment options for shellfish allergy. In this review, we will discuss the epidemiology, the molecular identification of shellfish allergens, recent progress in various diagnostic methods, as well as current development in immunotherapeutic approaches including the use of unmodified allergens, hypoallergens, immunoregulatory peptides and DNA vaccines for the prevention and treatment of shellfish allergy. The prospect of a “cure “for shellfish allergy is within reach.
The Initial Factors with Strong Predictive Value in Relation to Six-Month Outcome among Patients Operated due to Extra-Axial Hematomas

Introduction: Traumatic brain injuries (TBI) are a real social problem, with an upward trend worldwide. The most frequent consequence of a traumatic brain injury is extra-axial hemorrhage, i.e., an acute subdural (SDH) and epidural hematoma (EDH). Most of the factors affecting the prognosis have been analyzed on a wide group of traumatic brain injuries. Nonetheless, there are few studies analyzing factors influencing the prognosis regarding patients undergoing surgery due to acute subdural and epidural hematoma. The aim of this study was to identify the factors which have the strongest prognostic value in relation to the 6-month outcome of the patients undergoing surgery for SDH and EDH. Patients and methods: The study included a group of 128 patients with isolated craniocerebral injuries. Twenty eight patients were operated upon due to EDH, and a group of 100 patients were operated upon due to SDH. The following factors from the groups were analyzed: demographic data, physiological factors, laboratory factors, computed tomography scan characteristics, and time between the trauma and the surgery. All of these factors were correlated in a multivariate analysis with the six-month outcome in the Glasgow outcome scale. Results: The factors with the strongest prognostic value are GCS score, respiration rate, saturation, glycaemia and systolic blood pressure. Conclusion: Initial GCS score, respiratory rate, saturation, glycaemia and systolic blood pressure were the factors with the strongest prognostic value.
Help to Overcome Problems Effectively for Cancer Survivors: Development and Evaluation of a Digital Self-Management Program

Background People living with cancer face numerous psychosocial challenges, including cancer-related fatigue, fear of recurrence, and depression. There is a lack of digital interventions tailored to the needs of people living with all types of cancer. We developed a 6-week, digital, peer-delivered, self-management program: iHOPE (Help to Overcome Problems Effectively; where ‘i’ indicates the digital version of the program). The program is underpinned by positive psychology and cognitive behavioral therapy to meet these psychosocial challenges. Objective This study aimed to assess the feasibility of the iHOPE program among people living with cancer. Program adherence and satisfaction along with changes in psychological distress and positive well-being were measured. Methods A pre-post, acceptability, and feasibility design was used. People living with cancer (N=114) were recruited via a national cancer charity in the United Kingdom and were given access to the iHOPE program. Demographic and other participant characteristics were recorded. Participants completed digital measures at baseline and the end of the 6-week program for depression, anxiety, cancer-related fatigue, cancer worry or fear of cancer recurrence, positive mental well-being, hope, gratitude, and health status. The website’s system recorded data on the usage of the program. Satisfaction with the program was also measured. Results A total of 114 participants completed the baseline questionnaires. Of these, 70 people (61.4%) participated in all 6 sessions. The mean number of sessions undertaken was 5.0 (SD 1.5). Moreover, 44.7% (51/114) of participants completed at least three sessions and end-of-program outcome measures. A total of 59 participants completed the satisfaction questionnaire, where ≥90% (54/58) of participants reported that the program was easy to navigate and was well managed by the peer facilitators, and that they found the social networking tools useful. Preliminary efficacy testing among the 51 participants who completed baseline and postprogram outcome measures showed that postprogram scores decreased for depression, anxiety, cancer-related fatigue, and fear of recurrence (all P<.001) and increased for positive mental well-being (P<.001), hope (both P<.001), and gratitude (P=.02). Conclusions The feasibility evidence is promising, showing that the peer-delivered digital iHOPE program is acceptable and practical. Implementation of the iHOPE program on a wider scale will incorporate further research and development to maximize the completion rates of the measures. Initial effectiveness data suggest positive impacts on important cancer-related quality of life and mental well-being outcomes. A randomized controlled trial design with a longer follow-up is needed to confirm the potential of the iHOPE program for improving mental and physical health outcomes for cancer survivors.
Efficacy and safety of Saccharomyces boulardii in the treatment of acute gastroenteritis in the paediatric population: a systematic review

Context: Gastroenteritis (GE) remains the second major cause of death in the most vulnerable of the world’s populations. Potential treatments include the use of probiotics, with the yeast Saccharomyces boulardii being one such option. Objectives: The primary objective was to assess the efficacy and safety of Saccharomyces boulardii in the treatment of acute GE in the paediatric population. Method: Major electronic databases were searched from April 2014 to January 2015. Additional literature was obtained through hand-searching and reviewing of reference lists of articles and other systematic reviews. Randomised controlled trials (RCTs) in a hospital setting, involving participants < 16 years were used as the data source. Two reviewers independently screened studies for eligibility, assessed study quality and performed data extraction. Review Manager 5 was used to analyse data and a random-effects model of meta-analysis was applied owing to heterogeneity. Results: Ten of 190 articles were selected for final inclusion. A meta-analysis of five of the included studies showed that Saccharomyces boulardii compared with the control significantly shortened the duration of diarrhoea (in days) (MD –0.57, 95% CI –0.83 to –0.30, p < 0.0001), but there was no difference between groups regarding time to achieving formed stools. No adverse effects were reported. The GRADE tool assessed overall methodological quality as moderate. Conclusion: Saccharomyces boulardii showed a potential benefit in treating acute GE in the paediatric patient. A dose of 250 mg 1–2 times per day for up to 5 days showed some benefit and appears safe. Larger, rigorous RCTs are needed to investigate the efficacy and safety of Saccharomyces boulardii in order to offer specific treatment guidelines. Trial registration: CRD42014009913.
When a Palearctic bacterium meets a Nearctic insect vector: Genetic and ecological insights into the emergence of the grapevine Flavescence dorée epidemics in Europe

Flavescence dorée (FD) is a European quarantine grapevine disease transmitted by the Deltocephalinae leafhopper Scaphoideus titanus. Whereas this vector had been introduced from North America, the possible European origin of FD phytoplasma needed to be challenged and correlated with ecological and genetic drivers of FD emergence. For that purpose, a survey of genetic diversity of these phytoplasmas in grapevines, S. titanus, black alders, alder leafhoppers and clematis were conducted in five European countries. Out of 132 map genotypes, only 11 were associated to FD outbreaks, three were detected in clematis, whereas 127 were detected in alder trees, alder leafhoppers or in grapevines out of FD outbreaks. Most of the alder trees were found infected, including 8% with FD genotypes M6, M38 and M50, also present in alders neighboring FD-free vineyards and vineyard-free areas. The Macropsinae Oncopsis alni could transmit genotypes unable to achieve transmission by S. titanus, while the Deltocephalinae Allygus spp. and Orientus ishidae transmitted M38 and M50 that proved to be compatible with S. titanus. Variability of vmpA and vmpB adhesin-like genes clearly discriminated 3 genetic clusters. Cluster Vmp-I grouped genotypes only transmitted by O. alni, while clusters Vmp-II and -III grouped genotypes transmitted by Deltocephalinae leafhoppers. Interestingly, adhesin repeated domains evolved independently in cluster Vmp-I, whereas in clusters Vmp-II and–III showed recent duplications. Latex beads coated with various ratio of VmpA of clusters II and I, showed that cluster II VmpA promoted enhanced adhesion to the Deltocephalinae Euscelidius variegatus epithelial cells and were better retained in both E. variegatus and S. titanus midguts. Our data demonstrate that most FD phytoplasmas are endemic to European alders. Their emergence as grapevine epidemic pathogens appeared restricted to some genetic variants pre-existing in alders, whose compatibility to S. titanus correlates with different vmp gene sequences and VmpA binding properties.
Renin-Angiotensin System Blockers and the COVID-19 Pandemic

During the spread of the severe acute respiratory syndrome coronavirus-2, some reports of data still emerging and in need of full analysis indicate that certain groups of patients are at risk of COVID-19. This includes patients with hypertension, heart disease, diabetes mellitus, and clearly the elderly. Many of those patients are treated with renin-angiotensin system blockers. Because the ACE2 (angiotensin-converting enzyme 2) protein is the receptor that facilitates coronavirus entry into cells, the notion has been popularized that treatment with renin-angiotensin system blockers might increase the risk of developing a severe and fatal severe acute respiratory syndrome coronavirus-2 infection. The present article discusses this concept. ACE2 in its full-length form is a membrane-bound enzyme, whereas its shorter (soluble) form circulates in blood at very low levels. As a mono-carboxypeptidase, ACE2 contributes to the degradation of several substrates including angiotensins I and II. ACE (angiotensin-converting enzyme) inhibitors do not inhibit ACE2 because ACE and ACE2 are different enzymes. Although angiotensin II type 1 receptor blockers have been shown to upregulate ACE2 in experimental animals, the evidence is not always consistent and differs among the diverse angiotensin II type 1 receptor blockers and differing organs. Moreover, there are no data to support the notion that ACE inhibitor or angiotensin II type 1 receptor blocker administration facilitates coronavirus entry by increasing ACE2 expression in either animals or humans. Indeed, animal data support elevated ACE2 expression as conferring potential protective pulmonary and cardiovascular effects. In summary, based on the currently available evidence, treatment with renin-angiotensin system blockers should not be discontinued because of concerns with coronavirus infection.
Feature selection based on differentially correlated gene pairs reveals the mechanism of IFN-β therapy for multiple sclerosis

Multiple sclerosis (MS) is one of the most common neurological disabilities of the central nervous system. Immune-modulatory therapy with Interferon-β (IFN-β) is a commonly used first-line treatment to prevent MS patients from relapses. Nevertheless, a large proportion of MS patients on IFN-β therapy experience their first relapse within 2 years of treatment initiation. Feature selection, a machine learning strategy, is routinely used in the fields of bioinformatics and computational biology to determine which subset of genes is most relevant to an outcome of interest. The majority of feature selection methods focus on alterations in gene expression levels. In this study, we sought to determine which genes are most relevant to relapse of MS patients on IFN-β therapy. Rather than the usual focus on alterations in gene expression levels, we devised a feature selection method based on alterations in gene-to-gene interactions. In this study, we applied the proposed method to a longitudinal microarray dataset and evaluated the IFN-β effect on MS patients to identify gene pairs with differentially correlated edges that are consistent over time in the responder group compared to the non-responder group. The resulting gene list had a good predictive ability on an independent validation set and explicit biological implications related to MS. To conclude, it is anticipated that the proposed method will gain widespread interest and application in personalized treatment research to facilitate prediction of which patients may respond to a specific regimen.
Impairment of myocardial perfusion correlates with heart failure severity in patients with non‐compaction cardiomyopathy

Non‐compaction cardiomyopathy (NCM) is a congenital heart disease characterized by an arrest of the myocardial compaction process. Although NCM patients have impaired formation of microvasculature, the functional impact of these changes remains undefined. We sought to analyse a potential correlation between myocardial ischemia and heart failure severity in NCM patients.
Heart Connexin43 cDNA

The carboxyl terminal cytoplasmic domain of distinct gap junction proteins may play an important role in assembly of functional channels as well as differential responsiveness to pH, voltage, and intracellular second messengers. Oligonucleotide-directed site-specific mutagenesis in a paired Xenopus laevis oocyte expression system was used to examine the expression of mRNAs encoding wild-type and carboxyl terminal mutant connexin43 (Cx43) proteins. Oocytes were stripped, injected with mRNA or distilled water (dH2O), preincubated for 16-20 hours, and then paired for 5-10 hours; this process was followed by electrophysiological recording using the dual voltage-clamp technique. Initial experiments compared the relative junctional conductances (Gjs) in oocyte pairs expressing Cx43 (382 amino acid residues) and two truncated mutants lacking most or a portion of the cytoplasmic carboxyl terminal. The shortest mutant (M241) contained 240 amino acid residues and was devoid of all phosphorylatable serine residues in the cytoplasmic tail; its length approximated the length of liver connexin26. The longest mutant (M257) tested contained 256 amino acid residues, including two serine residues. Oocyte pairs expressing M241 yielded a Gj similar to that of oocytes injected with dH2O, whereas M257 yielded a Gj similar to that of oocytes injected with Cx43. Immunoprecipitation studies showed that Cx43, M257, and M241 proteins