Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbiota succession during aerobic stability of maize silage inoculated with Lentilactobacillus buchneri NCIMB 40788 and Lentilactobacillus hilgardii CNCM‐I‐4785

Aerobic deterioration of silage following feeding out is responsible for the deterioration of its quality. Inoculation of silage with lactic acid bacteria is one strategy to limit these effects. A trial was performed using whole‐plant corn ensiled in bag silo, and forage was inoculated with Lentilactobacillus buchneri NCIMB 40788 (Lactobacillus buchneri) and Lentilactobacillus hilgardii CNCM‐I‐4785 (Lactobacillus hilgardii) or not (Control silage). After 159 days of fermentation, the silos were opened and the silage was sampled at 24‐h intervals during a 10‐day aerobic stability assay to measure pH, the fermentation profile, mycotoxins, and microbial and fungal populations. In inoculated silage, lactic acid concentrations and pH remained stable during the aerobic phase and higher microorganism alpha‐diversity was observed. Treated silage was characterized by a high abundance of Saccharomycetes and maintenance of Lactobacillus throughout the aerobic stability assay. The high aerobic stability of the inoculated silage contrasted with the decrease in lactic acid contents and the increase in pH observed in the Control silage, concomitantly with an increase in lactate‐assimilating yeast (Pichia and Issatchenkia), and in Acetobacter and Paenibacillus OTUs. Remarkably, Penicillium and roquefortine C were detected in this silage by day 8 following exposure to air. Our study highlighted the fact that the use of L. buchneri with L. hilgardii modified the consequences of exposure to air by maintaining higher microbial diversity, avoiding the dominance of a few bacteria, and preventing fungi from having a detrimental effect on silage quality.
Ab initio determination of peptide structures by MicroED

Structural elucidation of small macromolecules such as peptides has recently been facilitated by a growing number of technological advances to existing crystallographic methods. The emergence of electron micro-diffraction (MicroED) of protein nanocrystals under cryogenic conditions has enabled the interrogation of crystalline peptide assemblies only hundreds of nanometers thick. Collection of atomic or near-atomic resolution data by these methods has permitted the ab initio determination of structures of various amyloid-forming peptides, including segments derived from prions and ice-nucleating proteins. This chapter focuses on the process of ab initio structural determination from nano-scale peptide assemblies and other similar molecules. of determination of the collection of high-resolution
Evaporation of Water from Structured Surfactant Solutions

Alkyl-propoxy-ethoxylate surfactant aqueous solution films are exposed to air of constant relative humidity, and the water loss from the film is monitored over time, until equilibrium is reached. The surfactants self-assemble into lyotropic liquid crystals with a structure that varies depending on the water concentration at a given time. The water loss data are analyzed to investigate the factors affecting the drying rate of the alkyl-propoxy-ethoxylate surfactants, such as the air relative humidity, microstructure in the surfactant film, and the surfactant degree of hydration. Analytical solutions of the diffusion equation are used to extract the water diffusion coefficient in the film. A diffusion model that accounts for varying film thickness and evaporation at the surface has been used to follow the water loss and thickness data over time, in order to assess the relative importance of diffusion and evaporation under various conditions.
Analysis of Pathogen Distribution and Its Antimicrobial Resistance in Bloodstream Infections in Hospitalized Children in East China, 2015–2018

Abstract This study analyzed the pathogen distribution in bloodstream-infected (BSI) children hospitalized in Shandong Province from 2015 to 2018, to identify prevention strategies and select empiric antimicrobial therapy for BSI in children. Blood sample data from 14 107 children from 162 hospitals of Shandong Province were obtained from the China Antimicrobial Resistance Surveillance System and analyzed with WHONET 5.6 software. The results of the blood culture test showed the growth of 70.6% Gram-positive and 29.4% Gram-negative bacteria. Of the 14 107 blood isolates, 59.3% were collected from males and 40.7% were from females. Coagulase-negative staphylococci (47.1%) were the most commonly distributed pathogens. The distribution of pathogens varied according to age group and season. All Staphylococcus isolates were susceptible to vancomycin, teicoplanin and linezolid. Clinically, significant declines in penicillin-resistant Streptococcus pneumonia and carbapenem-resistant Escherichia coli were observed during the study period; however, detection rates of carbapenem-resistant Klebsiella pneumoniae increased over time (p < 0.05). Empiric antimicrobial therapy should be prescribed according to corresponding regional pediatric antimicrobial-resistant data.
Stargardt misdiagnosis: How ocular genetics helps

Ocular Genetics at Wills Eye Hospital sees a wide range of rare disorders for accurate diagnosis. To demonstrate how focused consultation and genetic testing results in precise diagnoses, we investigated false diagnosis rates for patients referred with a diagnosis of Stargardt disease. This is a retrospective review of patients over a 3 year period referred to our Ocular Genetics clinic for possible Stargardt disease, or already holding a diagnosis of Stargardt disease. Results of diagnostic and genetic testing were compared to standard definition of Stargardt. Of 40 patients, 14 (35%) had been misdiagnosed. Four had non‐Stargardt phenotype of which three had ABCA4 pathogenic variants with phenotypes inconsistent with Stargardt disease. Two of those with pathogenic ABCA4 variants were related. Nine had pathogenic variants in other different genes with overlapping features of Stargardt disease. One had Thioridazine maculopathy. Our study highlights the essential role of the subspecialty field of ocular genetics in obtaining accurate diagnoses for the delivery of correct counseling and interventional trial eligibility assessment.
Understanding non-communicable diseases: combining health surveillance with local knowledge to improve rural primary health care in South Africa

ABSTRACT Background: NCDs are non-infectious, long-term conditions that account for 40 million deaths per annum. 87% of premature NCD mortality occurs in low- and middle-income countries. Objective: The aims were:develop methods to provide integrated biosocial accounts of NCD mortality; and explore the practical utility of extended mortality data for the primary health care system. Methods: We drew on data from research programmes in the study area. Data were analysed in three steps: [a]analysis of levels, causes and circumstances of NCD mortality [n = 4,166] from routine census updates including Verbal Autopsy and of qualitative data on lived experiences of NCDs in rural villages from participatory research; [b] identifying areas of convergence and divergence between the analyses; and [c]exploration of the practical relevance of the data drawing on engagements with health systems stakeholders. Results: NCDs constituted a significant proportion of mortality in this setting [36%]. VA data revealed multiple barriers to access in end-of-life care. Many deaths were attributed to problems with resources and health systems [21%;19% respectively]. The qualitative research provided rich complementary detail on the processes through which risk originates, accumulates and is expressed in access to end-of-life care, related to chronic poverty and perceptions of poor quality care in clinics. The exploration of practical relevance revealed chronic under-funding for NCD services, and an acute need for robust, timely data on the NCD burden. Conclusions: VA data allowed a significant burden of NCD mortality to be quantified and revealed barriers to access at and around the time of death. Qualitative research contextualised these barriers, providing explanations of how and why they exist and persist. Health systems analysis revealed shortages of resources allocated to NCDs and a need for robust research to provide locally relevant evidence to organise and deliver care. Pragmatic interdisciplinary and mixed method analysis provides relevant renditions of complex problems to inform more effective responses.
Effects of bisphosphonates on long-term kidney transplantation outcomes.

BACKGROUND Bisphosphonates are administered to post-transplantation patients with mineral and bone disorders; however, the association between bisphosphonate therapy and long-term renal graft survival remains unclear. METHODS This nested case-control study investigated the effects of bisphosphonates on long-term graft outcomes after kidney transplantation. We enrolled 3,836 kidney transplant recipients treated from April 1979 to June 2016 and matched patients with graft failure to those without (controls). Annual post-transplant bone mineral density assessments were performed, and recipients with osteopenia or osteoporosis received bisphosphonate therapy. The associations between bisphosphonate use, and long-term graft outcomes and graft survival were analyzed using conditional logistic regression and landmark analyses, respectively. RESULTS A landmark analysis demonstrated that the death-censored graft survival was significantly higher in bisphosphonate users than in non-users in the entire cohort (log-rank test, P < .001). In the nested case-control matched cohort, bisphosphonate users had a significantly reduced risk of graft failure than did non-users (odds ratio, 0.38; 95% confidence interval, 0.30-0.48). Bisphosphonate use, increased cumulative duration of bisphosphonate use over one year, and increased cumulative bisphosphonate dose above the first quartile were associated with a reduced risk of graft failure, after adjustments. CONCLUSIONS Bisphosphonates may improve long-term graft survival in kidney transplant recipients.
An ultrastructural connectomic analysis of a higher‐order thalamocortical circuit in the mouse

Many studies exist of thalamocortical synapses in primary sensory cortex, but much less in known about higher‐order thalamocortical projections to higher‐order cortical areas. We begin to address this gap using genetic labeling combined with large volume serial electron microscopy (i.e., “connectomics”) to study the projection from the thalamic posterior medial nucleus to the secondary somatosensory cortex in a mouse. We injected into this thalamic nucleus a cocktail combining a cre‐expressing virus and one expressing cre‐dependent ascorbate peroxidase that provides an electron dense cytoplasmic label. This “intersectional” viral approach specifically labeled thalamocortical axons and synapses, free of retrograde labeling, in all layers of cortex. Labeled thalamocortical synapses represented 14% of all synapses in the cortical volume, consistent with previous estimates of first‐order thalamocortical inputs. We found that labeled thalamocortical terminals, relative to unlabeled ones: were larger, were more likely to contain a mitochondrion, more frequently targeted spiny dendrites and avoided aspiny dendrites, and often innervated larger spines with spine apparatuses, among other differences. Furthermore, labeled terminals were more prevalent in layers 2/3 and synaptic differences between labeled and unlabeled terminals were greatest in layers 2/3. The laminar differences reported here contrast with reports of first‐order thalamocortical connections in primary sensory cortices where, for example, labeled terminals were larger in layer 4 than layers 2/3 (Viaene et al., 2011a). These data offer the first glimpse of higher‐order thalamocortical synaptic ultrastructure and point to the need for more analyses, as such connectivity likely represents a majority of thalamocortical circuitry.
Using area and volume measurement via weightbearing CT to detect Lisfranc instability

Weightbearing CT (WBCT) allows evaluation of the Lisfranc joint under physiologic load. We compared the diagnostic sensitivities of one‐dimensional (1D) distance, two‐dimensional (2D) area, and three‐dimensional (3D) volumetric measurement of the injured Lisfranc joint complex (tarsometatarsal, intertarsal, and intermetatarsal) on WBCT among patients with surgically‐confirmed Lisfranc instability. The experimental group comprised of 14 patients having unilateral Lisfranc instability requiring operative fixation who underwent preoperative bilateral foot and ankle WBCT. The control group included 36 patients without foot injury who underwent similar imaging. Measurements performed on WBCT images included: (1) Lisfranc joint (medial cuneiform‐base of second metatarsal) area, (2) C1‐C2 intercuneiform area, (3) C1‐M2 distance, (4) C1‐C2 distance, (5) M1‐M2 distance, (6) first tarsometatarsal (TMT1) angular alignment, (7) second tarsometatarsal (TMT2) angular alignment, (8) TMT1 dorsal step off distance, and (9) TMT2 dorsal step‐off distance. In addition, the volume of the Lisfranc joint in the coronal and axial plane were calculated. Among patients with unilateral Lisfranc instability, all WBCT measurements were increased on the injured side as compared to the contralateral uninjured side (p values: <.001–.008). Volumetric measurements in the coronal and axial plane had a higher sensitivity (92.3%; 91.6%, respectively) and specificity (97.7%; 96.5%, respectively) than 2D and 1D Lisfranc joint measurements, suggesting them to be the most accurate in diagnosing Lisfranc instability. The control group showed no difference in any of the measurements between the two sides. WBCT scan can effectively differentiate between stable and unstable Lisfranc injuries. Lisfranc joint volume measurements demonstrate high sensitivity and specificity, suggesting that this new assessment has high clinical implications for diagnosing subtle Lisfranc instability.
High rate of virological failure and HIV drug resistance in semi-rural Gabon and implications for dolutegravir-based regimen efficacy.

BACKGROUND The projected UNAIDS goal of ending AIDS by 2030 requires significant global efforts to improve current and future ART strategies. In this study, we assessed viral load (VL) suppression and acquired drug resistance, as well as future efficacy of dolutegravir-based combinations for patients living in semi-rural regions of Gabon. METHODS Eligible study participants were adults receiving ART and recruited between 2018 and 2019 in Franceville, Gabon. VL testing was conducted to assess VL suppression and HIV drug resistance (HIVDR) testing was performed to identify resistance mutations and assess their impact on ongoing and future ART regimens. RESULTS We recruited 219 participants overall. The median time on ART was 27 months and 216/219 participants were on first-line ART. VL suppression (VL < 1000 copies/mL) was 57.1% (95% CI 50.5-63.8) overall; 59.4% (51.4-67.5) and 52.2% (40.3-64.2) for women and men, respectively. The overall prevalence of HIVDR was 21.9% among the study population and 67.2% among those who failed ART. Presence of both NRTI and NNRTI mutations was found in 84.6% of sequences with drug resistance mutations, and full activity of a dolutegravir-based first-line regimen including tenofovir disoproxil fumarate/lamivudine/dolutegravir was expected only for 5/39 patients with a resistant virus. CONCLUSIONS This study shows a very low rate of VL suppression in a semi-rural context in Africa. Moreover, the high burden of HIVDR has affected both current and newly recommended ART strategies. Better management of ART in resource-limited settings is still a challenging ambition.
Metastable hydrogen atom trapping in hydrogenated amorphous silicon films : a microscopic model for metastable defect creation

Abstract In hydrogenated amorphous silicon (a-Si: H) films, the increase in the metastable defect density under high-intensity illumination is usually described by an empirical two-parameter stretched-exponential (SE) time dependence (characteristic time τSE and dispersion parameter β). In this study, a clearly different (one-parameter) analytic function is obtained from a microscopic model based on the formation and trapping of metastable hydrogen (MSH) atoms. In this microscopic model deduced from experimental observations, assuming that MSH atoms are the only mobile species, only three elemental chemical reactions are thus significant; MSH are produced from doubly hydrogenated (Si-H H-Si) configurations and trapped at either broken bonds or Si-H bonds, corresponding respectively to light-induced annealing and light-induced creation of defects. Competition between trapping sites results in a saturation of the defect density N(t) at a steady-state value N SS. An implicit analytic function is obtained for.
Upregulation of polycistronic microRNA-143 and microRNA-145 in colonocytes suppresses colitis and inflammation-associated colon cancer

ABSTRACT Because ADAM17 promotes colonic tumorigenesis, we investigated potential miRNAs regulating ADAM17; and examined effects of diet and tumorigenesis on these miRNAs. We also examined pre-miRNA processing and tumour suppressor roles of several of these miRNAs in experimental colon cancer. Using TargetScan, miR-145, miR-148a, and miR-152 were predicted to regulate ADAM17. miR-143 was also investigated as miR-143 and miR-145 are co-transcribed and associated with decreased tumour growth. HCT116 colon cancer cells (CCC) were co-transfected with predicted ADAM17-regulating miRNAs and luciferase reporters controlled by ADAM17-3’UTR. Separately, pre-miR-143 processing by colonic cells was measured. miRNAs were quantified by RT-PCR. Tumours were induced with AOM/DSS in WT and transgenic mice (Tg) expressing pre-miR-143/miR-145 under villin promoter. HCT116 transfection with miR-145, −148a or −152, but not scrambled miRNA inhibited ADAM17 expression and luciferase activity. The latter was suppressed by mutations in ADAM17-3’UTR. Lysates from colonocytes, but not CCC, processed pre-miR-143 and mixing experiments suggested CCC lacked a competency factor. Colonic miR-143, miR-145, miR-148a, and miR-152 were downregulated in tumours and more moderately by feeding mice a Western diet. Tg mice were resistant to DSS colitis and had significantly lower cancer incidence and tumour multiplicity. Tg expression blocked up-regulation of putative targets of miR-143 and miR-145, including ADAM17, K-Ras, XPO5, and SET. miR-145, miR-148a, and miR-152 directly suppress colonocyte ADAM17 and are down-regulated in colon cancer. This is the first direct demonstration of tumour suppressor roles for miR-143 and miR-145 in an in vivo model of colonic tumorigenesis.
Combination therapy with Treg and mesenchymal stromal cells enhances potency and attenuation of inflammation after traumatic brain injury compared to monotherapy

The inflammatory response after traumatic brain injury (TBI) can lead to significant secondary brain injury and chronic inflammation within the central nervous system. Cell therapies, including mesenchymal stromal cells (MSC), have led to improvements in animal models of TBI and are under investigation in human trials. One potential mechanism for the therapeutic potential of MSC is their ability to augment the endogenous response of immune suppressive regulatory T cells (Treg). We have recently shown that infusion of human cord blood Treg decreased chronic microgliosis after TBI and altered the systemic immune response in a rodent model. These cells likely use both overlapping and distinct mechanisms to modulate the immune system; therefore, combining Treg and MSC as a combination therapy may confer therapeutic benefit over either monotherapy. However, investigation of Treg + MSC combination therapy in TBI is lacking. In this study, we compared the ability MSC + Treg combination therapy, as well as MSC and Treg monotherapies, to inhibit the neuroinflammatory response to TBI in vivo and in vitro. Treg + MSC combination therapy demonstrated increased potency to reduce the neuro‐ and peripheral inflammatory response compared to monotherapy; furthermore, the timing of infusion proved to be a significant variable in the efficacy of both MSC monotherapy and Treg + MSC combination therapy in vivo and in vitro.
Short-Term Intake of Hesperetin-7-O-Glucoside Affects Fecal Microbiota and Host Metabolic Homeostasis in Mice.

Hesperetin-7-O-glucoside (Hes-7-G) is a typical flavonoid monoglucoside isolated from Citri Reticulatae Pericarpium (CRP), which is commonly used as a food adjuvant and exhibits potential biological activities. To explore the interaction between Hes-7-G ingestion and microbiome and host metabolism, here, 16S rRNA gene sequencing was first used to analyze the alteration of fecal microbiome in mice after Hes-7-G intake. Metabolic homeostasis in mice was subsequently investigated using untargeted 1H NMR-based metabolomics and targeted metabolite profiling. We found that dietary Hes-7-G significantly regulated fecal microbiota and its derived metabolites, including short-chain fatty acids (SCFAs) and tryptophan metabolites (indole and its derivatives), in feces of mice. Regulation of microbiota was further confirmed by the significantly changed urinary hippurate and trimethylamine N-oxide (TMAO), co-metabolites of the microbe and host. We also found that dietary Hes-7-G modulated the host tricarboxylic acid cycle (TCA) involved in energy metabolism. These findings suggested that Hes-7-G exhibits potential beneficial effects for human health.
Climate Change, Disinformation, and How to Combat It.

Climate change presents a challenge at multiple levels: It challenges our cognitive abilities because the effect of the accumulation of emissions is difficult to understand. Climate change also challenges many people's worldview because any climate mitigation regime will have economic and political implications that are incompatible with libertarian ideals of unregulated free markets. These political implications have created an environment of rhetorical adversity in which disinformation abounds, thus compounding the challenges for climate communicators. The existing literature on how to communicate climate change and dispel misinformation converges on several conclusions: First, providing information about climate change, in particular explanations of why it occurs, can enhance people's acceptance of science. Second, highlighting the scientific consensus can be an effective means to counter misinformation and raise public acceptance. Third, culturally aligned messages and messengers are more likely to be successful. Finally, climate misinformation is best defanged, through a process known as inoculation, before it is encountered, although debunking techniques can also be successful. Expected final online publication date for the Annual Review of Public Health, Volume 42 is April 2021. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.