Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial Colorants Production in Stirred-Tank Bioreactor and Their Incorporation in an Alternative Food Packaging Biomaterial

Natural colorants from microbial fermentation have gained significant attention in the market to replace the synthetic ones. Talaromyces spp. produce yellow-orange-red colorants, appearing as a potential microorganism to be used for this purpose. In this work, the production of natural colorants by T. amestolkiae in a stirred-tank bioreactor is studied, followed by its application as additives in bio-based films. The effect of the pH-shift control strategy from 4.5 to 8.0 after 96 h of cultivation is evaluated at 500 rpm, resulting in an improvement of natural colorant production, with this increase being more significant for the orange and red ones, both close to 4-fold. Next, the fermented broth containing the colorants is applied to the preparation of cassava starch-based films in order to incorporate functional activity in biodegradable films for food packaging. The presence of fermented broth did not affect the water activity and total solids of biodegradable films as compared with the standard one. In the end, the films are used to pack butter samples (for 45 days) showing excellent results regarding antioxidant activity. It is demonstrated that the presence of natural colorants is obtained by a biotechnology process, which can provide protection against oxidative action, as well as be a functional food additive in food packing biomaterials.
A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics

Dedication To the memory of Rossiter H. Crozier (1943-2009), an evolutionary biologist, who with his generosity and inquisitiveness inspired many students and scientists, in Australia and abroad. Molecular phylogenetics plays a key role in comparative genomics and has an increasingly-significant impact on science, industry, government, public health, and society. We report that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence the phylogenetic estimates. Based on the potential offered by well-established but under-used procedures (i.e., assessment of phylogenetic assumptions and test of goodness-of-fit), we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.
Metabolic determinants of cellular fitness dependent on mitochondrial reactive oxygen species

Mitochondrial complex I inhibition in the presence of a mito-antioxidant induces reductive stress, ISR, and cancer cell death. Mitochondria-derived reactive oxygen species (mROS) are required for the survival, proliferation, and metastasis of cancer cells. The mechanism by which mitochondrial metabolism regulates mROS levels to support cancer cells is not fully understood. To address this, we conducted a metabolism-focused CRISPR-Cas9 genetic screen and uncovered that loss of genes encoding subunits of mitochondrial complex I was deleterious in the presence of the mitochondria-targeted antioxidant mito-vitamin E (MVE). Genetic or pharmacologic inhibition of mitochondrial complex I in combination with the mitochondria-targeted antioxidants, MVE or MitoTEMPO, induced a robust integrated stress response (ISR) and markedly diminished cell survival and proliferation in vitro. This was not observed following inhibition of mitochondrial complex III. Administration of MitoTEMPO in combination with the mitochondrial complex I inhibitor phenformin decreased the leukemic burden in a mouse model of T cell acute lymphoblastic leukemia. Thus, mitochondrial complex I is a dominant metabolic determinant of mROS-dependent cellular fitness.
Associations between Household-Level Exposures and All-Cause Diarrhea and Pathogen-Specific Enteric Infections in Children Enrolled in Five Sentinel Surveillance Studies

Diarrheal disease remains a major cause of childhood mortality and morbidity causing poor health and economic outcomes. In low-resource settings, young children are exposed to numerous risk factors for enteric pathogen transmission within their dwellings, though the relative importance of different transmission pathways varies by pathogen species. The objective of this analysis was to model associations between five household-level risk factors—water, sanitation, flooring, caregiver education, and crowding—and infection status for endemic enteric pathogens in children in five surveillance studies. Data were combined from 22 sites in which a total of 58,000 stool samples were tested for 16 specific enteropathogens using qPCR. Risk ratios for pathogen- and taxon-specific infection status were modeled using generalized linear models along with hazard ratios for all-cause diarrhea in proportional hazard models, with the five household-level variables as primary exposures adjusting for covariates. Improved drinking water sources conferred a 17% reduction in diarrhea risk; however, the direction of its association with particular pathogens was inconsistent. Improved sanitation was associated with a 9% reduction in diarrhea risk with protective effects across pathogen species and taxa of around 10–20% risk reduction. A 9% reduction in diarrhea risk was observed in subjects with covered floors, which were also associated with decreases in risk for zoonotic enteropathogens. Caregiver education and household crowding showed more modest, inconclusive results. Combining data from diverse sites, this analysis quantified associations between five household-level exposures on risk of specific enteric infections, effects which differed by pathogen species but were broadly consistent with hypothesized transmission mechanisms. Such estimates may be used within expanded water, sanitation, and hygiene (WASH) programs to target interventions to the particular pathogen profiles of individual communities and prioritize resources.
Efficacy of Porcine Epidemic Diarrhea Vaccines: A Systematic Review and Meta-Analysis

Porcine epidemic diarrhea (PED) is a devastating disease that causes considerable economic damage to the global pig industry. Although the causative agent, the porcine epidemic diarrhea virus (PEDV), was identified about a half century ago, there is still much debate on the preventive measures against the disease, especially regarding the PED vaccine. Recent reports on PEDV variants make the vaccination for PEDV more confusing. Therefore, we systematically reviewed published articles on PED and vaccines against the disease and performed a meta-analysis of vaccine efficacy based on the clinical signs, fecal score and survival rates. A total of 299 articles on the efficacy of PED vaccines were found online, and 21 articles were selected that fulfilled all the criteria. A meta-analysis was performed on the 21 articles based on the fecal scores and survival rates. This analysis showed the efficacy of PED vaccines, and no significant differences in the efficacy depending on vaccine type (killed vs. live) or administration route (intramuscular vs. oral) were found. The results from our study suggest that any vaccination against PED is a useful strategy to control the disease regardless of the type of vaccine and administration route.
Acute pancreatitis and diabetes mellitus: a review

Diabetes following acute pancreatitis (AP) is becoming increasingly recognized. It is unclear what subtype of diabetes mellitus (DM) occurs; however, type 3c diabetes mellitus (T3cDM) is gaining increasing recognition. T3cDM has differing pathophysiology than other subtypes of DM and therefore differing disease course and treatment. Current studies have examined the incidence and prevalence of DM following AP, and meta-analyses have shown around 15% develop DM at 1 year with an increasing proportion developing DM at 5 years. It has been observed that some patients have transient hyperglycemia following AP episode with a subset developing persistent impaired glucose metabolism; however, the exact timeline is not well defined. The data on risk factors for developing DM after AP is limited and mixed; however, it is likely that severity of AP may impact the propensity to develop DM. Screening guidelines have not been established following AP; however, screening 1-year post-event will likely capture a sizable proportion of newly developed DM. The endocrine and exocrine pancreas are closely linked, and studies have found significant overlap in dysfunction of both after AP. Finally, there are some data to suggest that diabetes predisposes patients to structural changes in the pancreas and increased risk of developing AP.
Mutations of CNTNAP1 led to defects in neuronal development

Mutations of CNTNAP1 were associated with myelination disorders, suggesting the role of CNTNAP1 in myelination processes. Whether CNTNAP1 may have a role in early cortical neuronal development is largely unknown. In this study, we identified 4 compound heterozygous mutations of CNTNAP1 in 2 Chinese families. Using mouse models, we found that CNTNAP1 is highly expressed in neurons and is located predominantly in MAP2+ neurons during the early developmental stage. Importantly, Cntnap1 deficiency results in aberrant dendritic growth and spine development in vitro and in vivo, and it delayed migration of cortical neurons during early development. Finally, we found that the number of parvalbumin+ neurons in the cortex and hippocampus of Cntnap1–/– mice is strikingly increased by P15, suggesting that excitation/inhibition balance is impaired. Together, this evidence elucidates a critical function of CNTNAP1 in cortical development, providing insights underlying molecular and circuit mechanisms of CNTNAP1-related disease.
Cervical Screening Practices and Outcomes for Young Women in Response to Changed Guidelines in Calgary, Canada, 2007–2016

Supplemental digital content is available in the text. Objective The aim of the study was to describe temporal trends in screening and outcomes for women, after changes in guidelines in Alberta, Canada, that raised starting age to 21 years, then to 25 years of age, and reduced frequency to 3 yearly. Materials and Methods Calgary Laboratory Information System data were used to examine screening rates, follow-up procedures, and cancer among women 10–29 years from 2007 to 2016 in the whole population of Calgary. Interrupted time-series analyses were used to assess changes in screening and subsequent diagnostic procedures over the 10-year period. Results Annual screening rates dropped by approximately 10% at all ages older than 15 years after the 2009 Alberta cervical cancer screening guidelines, followed by a steady decrease. Further change continued subsequent to minimal apparent effect of the 2013 Canadian Task Force on Preventive Health Care guidelines. The rates of abnormal test results decreased in concert with decreased screening. No increases in cervical intraepithelial neoplasia 1, cervical intraepithelial neoplasia 2/3, or invasive cervical cancer rates were observed after reduced testing. Conclusions The largest decrease in screening and follow-up procedures occurred in the period immediately after implementation of 2009 Alberta screening guidelines. The number of consequent procedures also decreased in proportion to decreased screening, but there was no increase in cancer rates. Starting screening at the age of 25 years and reducing intervals seem to be safe.
Increasing Synaptic GluN2B levels within the Basal and Lateral Amygdala Enables the Modification of Strong Reconsolidation Resistant Fear Memories

Reconsolidation disruption has been proposed as a method to attenuate pathological memories in disorders such as PTSD. However, studies from our group and others indicate that strong memories are resistant to becoming destabilized following reactivation, rendering them impervious to agents that disrupt the re-stabilization phase of reconsolidation. Thus, therapies designed to attenuate maladaptive memories by disrupting reconsolidation updating have not been adequately developed. We previously determined that animals possessing strong auditory fear memories, compared to animals with weaker fear memories, are associated with an enduring increase in the synaptic GluN2A/GluN2B ratio in neurons of the mouse basal and lateral amygdala (BLA). In this study, we determined whether increasing GluN2B levels within BLA excitatory neuronal synapses is sufficient to enable modification of strong fear memories via reconsolidation. To accomplish this, we utilized a combinatorial genetic strategy to express GluN2B or GluN2B(E1479Q) in excitatory neurons of the mouse BLA before or after fear memory consolidation. GluN2B(E1479Q) contains a point mutation that increases synaptic expression of the subunit by interfering with phosphorylation-driven endocytosis. At the time of memory retrieval, increasing synaptic GluN2B levels by expression of GluN2B(E1479Q), but not GluN2B(WT), enhanced the induction of reconsolidation rendering the strong fear memory modifiable. GluN2B(WT) or GluN2B(E1479Q) expression did not influence fear memory maintenance or extinction. Fear memory consolidation, however, was enhanced when GluN2B(E1479Q) was expressed in the BLA at the time of training. These findings indicate that enhancing GluN2B synaptic trafficking may provide a novel therapeutic strategy to enhance modification of pathological memories.
The Effect of Surface Modification of Gold Nanotriangles for Surface-Enhanced Raman Scattering Performance

A surface modification of ultraflat gold nanotriangles (AuNTs) with different shaped nanoparticles is of special relevance for surface-enhanced Raman scattering (SERS) and the photo-catalytic activity of plasmonic substrates. Therefore, different approaches are used to verify the flat platelet morphology of the AuNTs by oriented overgrowth with metal nanoparticles. The most important part for the morphological transformation of the AuNTs is the coating layer, containing surfactants or polymers. By using well established AuNTs stabilized by a dioctyl sodium sulfosuccinate (AOT) bilayer, different strategies of surface modification with noble metal nanoparticles are possible. On the one hand undulated superstructures were synthesized by in situ growth of hemispherical gold nanoparticles in the polyethyleneimine (PEI)-coated AOT bilayer of the AuNTs. On the other hand spiked AuNTs were obtained by a direct reduction of Au3+ ions in the AOT double layer in presence of silver ions and ascorbic acid as reducing agent. Additionally, crumble topping of the smooth AuNTs can be realized after an exchange of the AOT bilayer by hyaluronic acid, followed by a silver-ion mediated reduction with ascorbic acid. Furthermore, a decoration with silver nanoparticles after coating the AOT bilayer with the cationic surfactant benzylhexadecyldimethylammonium chloride (BDAC) can be realized. In that case the ultraviolet (UV)-absorption of the undulated Au@Ag nanoplatelets can be tuned depending on the degree of decoration with silver nanoparticles. Comparing the Raman scattering data for the plasmon driven dimerization of 4-nitrothiophenol (4-NTP) to 4,4′-dimercaptoazobenzene (DMAB) one can conclude that the most important effect of surface modification with a 75 times higher enhancement factor in SERS experiments becomes available by decoration with gold spikes.
Group strength in safety performance: the effects of group characteristics on individual personality expression in high-speed railway operators

Objectives. In diverse working situations, the predictive effect of individual personality on job performance is not always the same. Thus, how to best understand and use personality in the workplace has been an important issue in recent years. Methods. Based on trait activation theory, the present study provides initial evidence from high-risk organizations (high-speed railway organizations) regarding interactionist effects of group-level characteristics on the relationship between individual personality (Big Five model) and safety performance (both safety compliance and safety participation). Data were obtained from a sample of high-speed rail operators from nine railway bureaus (N = 1012 from 86 working groups). Results. The results indicate that group conscientiousness, agreeableness and neuroticism enhance the relationship between individual personality and safety performance, while group openness weakens the relationship between individual personality and safety performance, and group extraversion has no effect on their relationship. Conclusion. These results suggest that high-risk organizations should focus not only on individual factors but also on the interactions between individual factors and group situations in individuals’ safety performance.
Many unreported crop pests and pathogens are probably already present

Biotic invasions threaten global biodiversity and ecosystem function, and present challenges to agriculture where invasive pest species require major economic investment in control and can cause significant production losses. Pest Risk Analysis (PRA) is key to prioritizing agricultural biosecurity efforts, but is hampered by incomplete knowledge of current crop pest and pathogen distributions. Here we develop predictive models of current pest distributions and test these models using new observations at sub-national resolution. We apply generalized linear models (GLM) to estimate presence probabilities for 1901 crop pests in the CABI pest distribution database. We test model predictions for 100 unobserved pests in the People’s Republic of China (PRC), against observations of these pests abstracted from the Chinese literature which has hitherto been omitted from databases on global pest distributions. Finally, we predict occurrences of all unobserved pests globally. Presence probability increases with host presence, presence in neighbouring regions, and global prevalence, and decreases with mean distance from coast, per capita GDP, and host number. The models are good predictors of pest presence in Provinces of the PRC, with AUC values of 0.76 – 0.80. Large numbers of currently unobserved, but probably present pests, are predicted in China, India, southern Brazil and some countries of the former USSR. GLMs can predict presences of pseudo-absent pests at sub-national resolution. Controlling for countries’ scientific capacity improves model fit. The Chinese scientific literature has been largely inaccessible to Western academia but contains important information that can support PRA. Prior studies have often assumed that unreported pests in a global distribution database is a true absence. Our analysis provides a method for quantifying pseudo-absences to enable improved PRA and species distribution modelling.
Computing hubs in the hippocampus and cortex

Neurons in an ensemble perform distinct information processing operations but dynamically switch their roles across states. Neural computation occurs within large neuron networks in the dynamic context of varying brain states. Whether functions are performed by specific subsets of neurons and whether they occur in specific dynamical regimes remain poorly understood. Using high-density recordings in the hippocampus, medial entorhinal, and medial prefrontal cortex of the rat, we identify computing substates where specific computing hub neurons perform well-defined storage and sharing operations in a brain state–dependent manner. We retrieve distinct computing substates within each global brain state, such as REM and nonREM sleep. Half of recorded neurons act as computing hubs in at least one substate, suggesting that functional roles are not hardwired but reassigned at the second time scale. We identify sequences of substates whose temporal organization is dynamic and stands between order and disorder. We propose that global brain states constrain the language of neuronal computations by regulating the syntactic complexity of substate sequences.
Impact of disease activity and treatments on ovarian reserve in patients with rheumatoid arthritis in the ESPOIR cohort.

OBJECTIVES Patients with RA have a higher prevalence of infertility than the general population. This study sought to examine the impact of RA disease activity and treatments on ovarian reserve measured by serum anti-Müllerian hormone (AMH) levels in the ESPOIR cohort. We sought to better define the indications for fertility preservation. METHODS Patients and serum analysis data were derived from the French national cohort ESPOIR. Enrolled patients (n = 102; 18-37-year-olds) fulfilled ACR/EULAR 2010 criteria for RA. Serum AMH levels were measured at T0, T6, T12, T24 and T36 months post-diagnosis. The impacts of RA activity (DAS28 and CRP level) and treatments (MTX only or with other medications) were evaluated at each study visit. RESULTS A gradual decrease in patients' serum AMH levels was observed over time, in line with the descending curve described for healthy women. Serum AMH levels of RA patients in comparison with the values considered normal for age did not reveal any significant differences (P > 0.05). We did not observe any impact of RA treatments. We demonstrated an inverse correlation between AMH variation and disease activity (DAS28: r = -0.27, P = 0.003; CRP: r = -0.16, P = 0.06). CONCLUSION This is the first study to determine serum AMH levels of a large cohort of RA patients over 36 months. Rapid disease activity control appears to be required to limit changes in the ovarian reserve. Fertility preservation is not likely to be necessary if inflammation is promptly controlled. ClinicalTrials.gov Identifier: NCT03666091.
A study of the reporting of patient and public involvement and engagement (PPIE) in orthodontic research

Introduction: Patient and public involvement and engagement (PPIE) in research is an essential component of high-quality research. Patients and the public can identify which research topics are most relevant to them, contribute to study design, and interpretation and dissemination of findings. While inclusion of PPIE is widely adopted in medical research, awareness within the dental research community is more limited. Aim: To examine patient and public involvement and engagement in orthodontic research activity. Design: Identification and appraisal of use of PPIE in orthodontic research reporting and funding applications using a systematic approach. Methods: Three sources of information were examined: (1) research articles published between September 2018 and September 2019 in four major orthodontic journals. Articles were examined for reported PPIE; (2) common funding bodies for orthodontic research were assessed to establish whether PPIE was mandated (National Institute for Health Research, Medical Research Council, Wellcome Trust, Chief Scientist Office (Scotland), Health and Care Research Wales, British Orthodontic Society Foundation, Royal College of Surgeons and CLEFT); and (3) publication guidance for authors in these journals was examined to identify whether reporting of PPIE was included. Results: Of the 363 research articles, 2 (0.6%) mention patient/public involvement. None of the 363 research articles mention patient/public engagement. Of nine funding bodies, 2 (22%) request evidence of patient/public involvement as a condition of receiving funding with one (11%) expecting evidence of public engagement to be provided as a condition of receiving funding. None of the four major orthodontic journals include patient/public involvement and/or engagement in their guidance for authors. Conclusion: There is currently: (1) a notable lack of reporting of PPIE in orthodontic research; (2) variability in the requirements of funding bodies for researchers to include PPIE in funding applications and throughout the research process; and (3) no stipulation in journals’ instructions for authors.