Miracle-dz/UniFAR-FTUs huggingface dataset:
Pyocyanin Restricts Social Cheating in Pseudomonas aeruginosa

Quorum sensing (QS) in Pseudomonas aeruginosa coordinates the expression of virulence factors, such as exoproteases and siderophores, that are public goods utilized by the whole population of bacteria, regardless of whether they invested or not in their production. These public goods can be used by QS defective mutants for growth, and since these mutants do not contribute to public goods production, they are considered social cheaters. Pyocyanin is a phenazine that is a toxic, QS-controlled metabolite produced by P. aeruginosa. It is a redox-active compound and promotes the generation of reactive oxygen species; it also possesses antibacterial properties and increases fitness in competition with other bacterial species. Since QS-deficient individuals are less able to tolerate oxidative stress, we hypothesized that the pyocyanin produced by the wild-type population could promote selection of functional QS systems in this bacterium. Here, we demonstrate, using competition experiments and mathematical models, that, indeed, pyocyanin increases the fitness of the cooperative QS-proficient individuals and restricts the appearance of social cheaters. In addition, we also show that pyocyanin is able to select QS in other bacteria such as Acinetobacter baumannii.
Multi-Modal Image Processing Based on Coupled Dictionary Learning

In real-world scenarios, many data processing problems often involve heterogeneous images associated with different imaging modalities. Since these multimodal images originate from the same phenomenon, it is realistic to assume that they share common attributes or characteristics. In this paper, we propose a multi-modal image processing framework based on coupled dictionary learning to capture similaries and disparities between different image modalities. In particular, our framework can capture favorable structure similarities across different image modalities such as edges, corners, and other elementary primitives in a learned sparse transform domain, instead of the original pixel domain, that can be used to improve a number of image processing tasks such as denoising, inpainting, or super-resolution. Practical experiments demonstrate that incorporating multimodal information using our framework brings notable benefits.
Postsurgical Cataract Prophylaxis With Intravitreal “Triamcinolone-Moxifloxacin” May Not Be Optimal For Preventing Endophthalmitis

Purpose: Intravitreal injections of antibiotics and anti-inflammatories are used by some cataract surgeons for surgical prophylaxis. To support this prophylaxis, intravitreal triamcinolone–moxifloxacin (TM) and triamcinolone–moxifloxacin–vancomycin (TMV) were tested for preventing Staphylococcus aureus (SA) endophthalmitis in rabbits. Methods: Trademark formulations of TM (15/1 mg/mL) and TMV (15/1/10 mg/mL) were intravitreally injected into seven groups of eight rabbits each (A–G). Before intravitreal injection, the vitreous was first challenged with clinical SA endophthalmitis isolates (5,000 colony-forming unit) with varying minimum inhibitory concentrations (MICs in &mgr;g/mL) to moxifloxacin (denoted by the MIC at the end of each group listed): A) TMV-10, B) TM-10, C) Saline-10, D) TM-2, E) Saline-2, F) TM-0.032, and G) Saline-0.032. After 24 hr, the rabbit eyes were graded for clinical endophthalmitis and cultured for viable SA. Results: Rabbits treated with TMV and challenged by SA with a moxifloxacin MIC of 10 &mgr;g/mL did not present with endophthalmitis (0/8, no eyes with endophthalmitis). For SA with moxifloxacin MICs of 10.0 and 2.0 &mgr;g/mL, TM did not prevent endophthalmitis (16/16, 100% of eyes with endophthalmitis). For SA with a moxifloxacin MIC of 0.032 &mgr;g/mL, endophthalmitis was prevented with TM (0/8, no eyes with endophthalmitis). All saline-treated eyes developed endophthalmitis (23/23, 100% of eyes with endophthalmitis). Conclusions: Intravitreal monotherapy with TM did not provide consistent prevention of SA endophthalmitis, whereas intravitreal TMV successfully prevented endophthalmitis because of SA with elevated MIC values to moxifloxacin. Cataract surgeons need to be aware that vancomycin seems to be essential for intravitreal prophylaxis to cover moxifloxacin resistance.
Global time trends in the incidence of esophageal squamous cell carcinoma

Background and aims Esophageal squamous cell carcinoma (ESCC) is the dominant histological type of esophageal cancer worldwide (90%). We aimed to provide an update of the global temporal trends in the incidence of ESCC. Methods Incidence data for ESCC were collected from 30 well-established cancer registries from 20 countries in Europe, Northern America, Australia, or Asia for 1970–2015. Time trends in annual age-standardized incidence rates of ESCC were assessed using joinpoint analysis and log-linear regression. Age–period–cohort analysis was used to estimate the influence of age, calendar-period, and birth-cohort on the observed time trends in incidence. Results The age-standardized incidence rates of ESCC varied more than eightfold in men and sevenfold in women across populations. In 2012, the highest rate of ESCC in men was observed in Nagasaki, Japan (9.7/100,000 person-years) and in women in Scotland (2.7/100,000 person-years). In men, the incidence decreased globally during the study period, as well as during the last few years. In women, the incidence increased in Japan (three regions), the Netherlands, New Zealand, Norway, and Switzerland, whereas it stabilized or decreased in other populations. Among ethnic groups in the United States, black men and women had more pronounced decreases in incidence than other groups. Generally, birth-cohort effects were stronger determinants of incidence trends than calendar-period effects. Conclusion In men, the global ESCC incidence has decreased over time. In women, the incidence trends vary across populations, and the rates have increased in some countries. Changes in the prevalence of tobacco smoking and alcohol consumption may have contributed to these time trends.
Antibiotics in early life: dysbiosis and the damage done

Antibiotics are the most common type of medication prescribed to children, including infants, in the Western world. While use of antibiotics has transformed previously lethal infections into relatively minor diseases, antibiotic treatments can have adverse effects as well. It has been shown in children, adults and animal models that antibiotics dramatically alter the gut microbial composition. Since the gut microbiota plays crucial roles in immunity, metabolism and endocrinology, the effects of antibiotics on the microbiota may lead to further health complications. In this review, we present an overview of the effects of antibiotics on the microbiome in children, and correlate them to long-lasting complications of obesity, behavior, allergies, autoimmunity and other diseases.
Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

ABSTRACT In situ hybridization based on the mechanism of the hybridization chain reaction (HCR) has addressed multi-decade challenges that impeded imaging of mRNA expression in diverse organisms, offering a unique combination of multiplexing, quantitation, sensitivity, resolution and versatility. Here, with third-generation in situ HCR, we augment these capabilities using probes and amplifiers that combine to provide automatic background suppression throughout the protocol, ensuring that reagents will not generate amplified background even if they bind non-specifically within the sample. Automatic background suppression dramatically enhances performance and robustness, combining the benefits of a higher signal-to-background ratio with the convenience of using unoptimized probe sets for new targets and organisms. In situ HCR v3.0 enables three multiplexed quantitative analysis modes: (1) qHCR imaging – analog mRNA relative quantitation with subcellular resolution in the anatomical context of whole-mount vertebrate embryos; (2) qHCR flow cytometry – analog mRNA relative quantitation for high-throughput expression profiling of mammalian and bacterial cells; and (3) dHCR imaging – digital mRNA absolute quantitation via single-molecule imaging in thick autofluorescent samples. Highlighted Article: In situ hybridization chain reaction (HCR) v3.0 exploits automatic background suppression to enable multiplexed quantitative mRNA imaging and flow cytometry with dramatically enhanced performance and ease of use.
Risk of Cardiovascular Events in Patients with Primary Biliary Cholangitis - Systematic Review

Abstract Background and Aims: Hypercholesterolemia is a common finding in patients with primary biliary cholangitis (PBC) and is a well-defined risk factor for cardiovascular disease. However, studies have been mixed on whether PBC patients do, in fact, have higher cardiovascular risk. The aim of this study is to review the current literature and provide an evidence-based assessment of cardiovascular risk in PBC patients. Methods: We performed a systematic literature search on PubMed regarding patients with PBC and cardiovascular events from the database inception to July 1, 2017. A total of 33 articles fulfilling our inclusion criteria were found. Results: The majority of the studies evaluated yielded no statistically significant difference in cardiovascular disease in the PBC population compared to the general public. However, some reports found a statistically significantly increase in coronary artery disease. Several studies have looked at the specific lipid profile of patients with PBC with hypocholesteremia. While these lipid abnormalities differ by stage of disease, there is evidence to suggest that the specific lipid profile in PBC may have lower atherogenicity than in patients with hypercholesterolemia without PBC. Studies looking at patients with PBC with other risk factors for cardiovascular disease, such as hypertension and metabolic syndrome, have consistently found a higher risk for cardiovascular disease in these patients. Statin treatment is effective in reducing lipid levels and possibly improving endothelial inflammation in patients with PBC with hypercholesterolemia. Conclusions: There is not enough evidence to suggest an increased risk of cardiovascular disease in patients with PBC with hypercholesterolemia, except for those individuals with concomitant features of metabolic syndrome. In patients with PBC with no additional cardiovascular risk factors, individual risk/benefit discussion on lipid-lowering treatment should be considered.
Maturational trajectories of local and long‐range functional connectivity in autism during face processing

Autism spectrum disorder (ASD) is characterized neurophysiologically by, among other things, functional connectivity abnormalities in the brain. Recent evidence suggests that the nature of these functional connectivity abnormalities might not be uniform throughout maturation. Comparing between adolescents and young adults (ages 14–21) with ASD and age‐ and IQ‐matched typically developing (TD) individuals, we previously documented, using magnetoencephalography (MEG) data, that local functional connectivity in the fusiform face areas (FFA) and long‐range functional connectivity between FFA and three higher order cortical areas were all reduced in ASD. Given the findings on abnormal maturation trajectories in ASD, we tested whether these results extend to preadolescent children (ages 7–13). We found that both local and long‐range functional connectivity were in fact normal in this younger age group in ASD. Combining the two age groups, we found that local and long‐range functional connectivity measures were positively correlated with age in TD, but negatively correlated with age in ASD. Last, we showed that local functional connectivity was the primary feature in predicting age in ASD group, but not in the TD group. Furthermore, local functional connectivity was only correlated with ASD severity in the older group. These results suggest that the direction of maturation of functional connectivity for processing of faces from childhood to young adulthood is itself abnormal in ASD, and that during the processing of faces, these trajectory abnormalities are more pronounced for local functional connectivity measures than they are for long‐range functional connectivity measures.
Life Course Transitions and Changes in Alcohol Consumption Among Older Irish Adults: Results From The Irish Longitudinal Study on Ageing (TILDA)

Objective: The objective of this study was to determine whether trajectories of older adults’ alcohol consumption are influenced by the following life course transitions, relationship status, employment status, and self-rated health. Method: Volume and frequency of drinking were harmonized across first three waves of The Irish Longitudinal Study on Ageing (TILDA; N = 4,295). Multilevel regression models were used to model frequency, average weekly consumption, and heavy episodic drinking. Results: Men and women drank more frequently over time, with frequency decreasing with age for women. Average weekly consumption decreased over time and with increasing age. Transitions in self-rated health, particularly those reflecting poorer health, were associated with lower frequency and weekly consumption. Heavy episodic drinking decreased with age. Men who were retired across all waves were more likely to engage in heavy episodic drinking at baseline. Discussion: Despite the decline in average weekly consumption and heavy episodic drinking, the observed quantities consumed and the increase in frequency of consumption suggest that older Irish adults remain vulnerable to alcohol-related harms.
Improvements in clinical characteristics of patients with non-alcoholic fatty liver disease, after an intervention based on the Mediterranean lifestyle: a randomised controlled clinical trial

Abstract Lifestyle interventions remain the cornerstone therapy for non-alcoholic fatty liver disease (NAFLD). This randomised controlled single-blind clinical trial investigated the effect of Mediterranean diet (MD) or Mediterranean lifestyle, along with weight loss, in NAFLD patients. In all, sixty-three overweight/obese patients (50 (sd 11) years, BMI=31·8 (sd 4·5) kg/m2, 68 % men) with ultrasonography-proven NAFLD (and elevated alanine aminotransferase (ALT) and/or γ-glutamyl transpeptidase (GGT) levels) were randomised to the following groups: (A) control group (CG), (B) Mediterranean diet group (MDG) or (C) Mediterranean lifestyle group (MLG). Participants of MDG and MLG attended seven 60-min group sessions for 6 months, aiming at weight loss and increasing adherence to MD. In the MLG, additional guidance for increasing physical activity and improving sleep habits were given. Patients in CG received only written information for a healthy lifestyle. At the end of 6 months, 88·8 % of participants completed the study. On the basis of intention-to-treat analysis, both MDG and MLG showed greater weight reduction and higher adherence to MD compared with the CG (all P<0·05) at the end of intervention. In addition, MLG increased vigorous exercise compared with the other two study groups (P<0·001) and mid-day rest/naps compared with CG (P=0·04). MLG showed significant improvements in ALT levels (i.e. ALT<40 U/l (P=0·03) and 50 % reduction of ALT levels (P=0·009)) and liver stiffness (P=0·004) compared with CG after adjusting for % weight loss and baseline values. MDG improved only liver stiffness compared with CG (P<0·001) after adjusting for the aforementioned variables. Small changes towards the Mediterranean lifestyle, along with weight loss, can be a treatment option for patients with NAFLD.
Anaeromyces contortus, sp. nov., a new anaerobic gut fungal species (Neocallimastigomycota) isolated from the feces of cow and goat

ABSTRACT Ten different anaerobic gut fungal strains were isolated from fecal samples of cow and goat in Oklahoma, USA. The isolates displayed polycentric thalli, uniflagellated zoospores, and sausage-shaped hyphal constrictions, all characteristic of the genus Anaeromyces, and lobed or appressorium-like structures on the hyphae, previously reported in Anaeromyces elegans but not in A. mucronatus or A. robustus. Further, the strains exhibited highly coiled and entangled hyphae previously unreported in the Neocallimastigomycota, but resembling fungal traps previously observed in multiple nematophagous fungi. Scanning electron micrographs of isolates grown on switchgrass showed entrapment of plant material by the hyphal coils and the penetration of plant fibers at various sites by the appressorium-like structures. Molecular analysis based on sequences of both partial nuc rDNA ITS1 spacer region and the D1–D2 domains of the nuc28S rDNA confirmed the classification of all isolates in Anaeromyces and confirmed their phylogenetic distance from the available A. mucronatus and A. robustus sequences. On the basis of morphological and phylogenetic distinctions, we conclude that these strains represent a new Anaeromyces species, for which A. contortus is proposed.
Exploring construct validity of clinical staging in schizophrenia spectrum disorders in an acute psychiatric ward.

OBJECTIVE clinical staging and profiling of schizophrenia spectrum disorders has been proposed to describe and define the heterogenous course of disease. We examined the construct validity of clinical staging in schizophrenia spectrum disorders by measuring differences in distribution and severity of relevant clinical profilers and therapeutic improvement (HoNOS) across clinical stages. METHODS we performed a prospective cross-sectional study with 258 inpatiënts who met DSM-IV criteria for schizophrenia spectrum disorders, recruited in an acute ward of a psychiatric hospital from 1-1-2015 until 31-12-2016. All patients (N=258) were assigned to a clinical stage, according to the criteria described by McGorry and clinical profilers were determined. Therapeutic improvement was assessed by measuring change in differences in HoNOS score during admission. RESULTS significant higher severity scores of clinical profilers were found in more advanced stages compared to earlier stages. This pattern was apparent in the clinical profilers negative symptoms (F=4.56, P<0.01), number of psychotic episodes last year (F=13.65, P<0.01), compliance (F=2.76, P<0.05), work and daily activities (F=9.85, P<0.001), living situation (F=3.71, P<0.05), support of close relatives (F=9.38, P<0.001) and pre-morbid functioning (F=7.33, P<0.001). Judicial background was less prevalent in earlier stages compared to more advanced disease stages. No differences in therapeutic improvement (HoNOS) were found between clinical stages. CONCLUSION this study demonstrates that clinical staging in schizophrenia spectrum disorders has an acceptable construct validity between earlier and more chronic stages of disease. Several clinical profilers increase in more advanced stages compared to earlier clinical stages, which supports construct validity.
The plant cell wall integrity maintenance and immune signaling systems cooperate to control stress responses in Arabidopsis thaliana

Cell wall integrity and immune signaling systems cooperatively mediate responses to cell wall damage in the model plant Arabidopsis. Responding to plant cell wall damage When plant cell walls are damaged by mechanical or biochemical means, the cells initiate adaptive responses to repair the walls and prevent infection. Whereas the cell wall integrity (CWI) maintenance mechanism monitors the status of the cell wall and initiates adaptive cellular responses to damage, pattern-triggered immunity (PTI) induces both cellular and systemic responses that limit infection. Engelsdorf et al. found that osmosensitive alterations in the mechanical properties of the cell wall were important for inducing the adaptive responses to cell wall damage. The receptor-like kinases THE1 and FEI2 and the ion channel MCA1 were required for stimulating CWI-dependent responses to damage. Cell wall damage also induced the expression of host defense peptides that promoted PTI and dampened CWI-dependent processes. The CWI mechanism still elicited damage responses even when PTI was impaired, suggesting that it serves as a failsafe to protect plants even if the immune response is compromised. Cell walls surround all plant cells, and their composition and structure are modified in a tightly controlled, adaptive manner to meet sometimes opposing functional requirements during growth and development. The plant cell wall integrity (CWI) maintenance mechanism controls these functional modifications, as well as responses to cell wall damage (CWD). We investigated how the CWI system mediates responses to CWD in Arabidopsis thaliana. CWD induced by cell wall–degrading enzymes or an inhibitor of cellulose biosynthesis elicited similar, turgor-sensitive stress responses. Phenotypic clustering with 27 genotypes identified a core group of receptor-like kinases (RLKs) and ion channels required for the activation of CWD responses. A genetic analysis showed that the RLK FEI2 and the plasma membrane–localized mechanosensitive Ca2+ channel MCA1 functioned downstream of the RLK THE1 in CWD perception. In contrast, pattern-triggered immunity (PTI) signaling components, including the receptors for plant elicitor peptides (AtPeps) PEPR1 and PEPR2, repressed responses to CWD. CWD induced the expression of PROPEP1 and PROPEP3, which encode the precursors of AtPep1 and AtPep3, and the release of PROPEP3 into the growth medium. Application of AtPep1 and AtPep3 repressed CWD-induced phytohormone accumulation in a concentration-dependent manner. These results suggest that AtPep-mediated signaling suppresses CWD-induced defense responses controlled by the CWI mechanism. This suppression was alleviated when PTI signaling downstream of PEPR1 and PEPR2 was impaired. Defense responses controlled by the CWI maintenance mechanism might thus compensate to some extent for the loss of PTI signaling elements.
Genetically Epilepsy-Prone Rats Display Anxiety-Like Behaviors and Neuropsychiatric Comorbidities of Epilepsy

Epilepsy is associated with a variety of neuropsychiatric comorbidities, including both anxiety and depression. Despite high occurrences of depression and anxiety seen in human epilepsy populations, little is known about the etiology of these comorbidities. Experimental models of epilepsy provide a platform to disentangle the contribution of acute seizures, genetic predisposition, and underlying circuit pathologies to anxious and depressive phenotypes. Most studies to date have focused on comorbidities in acquired epilepsies; genetic models, however, allow for the assessment of affective phenotypes that occur prior to onset of recurrent seizures. Here, we tested male and female genetically epilepsy-prone rats (GEPR-3s) and Sprague-Dawley controls in a battery of tests sensitive to anxiety-like and depressive-like phenotypes. GEPR-3s showed increased anxiety-like behavior in the open field test, elevated plus maze, light-dark transition test, and looming threat test. Moreover, GEPR-3s showed impaired prepulse inhibition of the acoustic startle reflex, decreased sucrose preference index, and impaired novel object recognition memory. We also characterized defense behaviors in response to stimulation thresholds of deep and intermediate layers of the superior colliculus (DLSC), but found no difference between strains. In sum, GEPR-3s showed inherited anxiety, an effect that did not differ significantly between sexes. The anxiety phenotype in adult GEPR-3s suggests strong genetic influences that may underlie both the seizure disorder and the comorbidities seen in epilepsy.