Miracle-dz/UniFAR-FTUs huggingface dataset:
Engineering conjugative CRISPR-Cas9 systems for the targeted control of enteric pathogens and antibiotic resistance

Pathogenic Escherichia coli and Salmonella enterica pose serious public health threats due to their ability to cause severe gastroenteritis and life-threatening sequela, particularly in young children. Moreover, the emergence and dissemination of antibiotic resistance in these bacteria have complicated control of infections. Alternative strategies that effectively target these enteric pathogens and negate or reduce the need of antibiotics are urgently needed. Such an alternative is the CRISPR-Cas9 system because it can generate sequence-specific lethal double stranded DNA breaks. In this study, two self-transmissible broad host range conjugative plasmids, pRK24 and pBP136, were engineered to deliver multiplexed CRSIPR-Cas9 systems that specifically target Enterohemorrhagic and Enteropathogenic strains of E. coli (EHEC and EPEC), S. enterica, and blaCMY-2 antibiotic resistance plasmids. Using in vitro mating assays, we show that the conjugative delivery of pRK24-CRISPR-Cas9 carrying guide RNAs to the EPEC/EHEC eae (intimin) gene can selectively kill enterohemorrhagic E. coli O157 eae+ cells (3 log kill at 6 h) but does not kill the isogenic Δeae mutant (P<0.001). Similar results were also obtained with a pBP136 derivative, pTF16, carrying multiplexed guide RNAs targeting E. coli eae and the S. enterica ssaN gene coding for the type III secretion ATPase. Another pBP136 derivative, TF18, carries guide RNAs targeting S. enterica ssaN and the antibiotic resistance gene, blaCMY-2, carried on the multi-drug resistant pAR06302. Introduction of pTF18 into bacteria harboring pAR06302 showed plasmids were cured at an efficiency of 53% (P<0.05). Using a murine neonate EPEC infection model, pTF16 was delivered by a murine derived E. coli strain to EPEC infected mice and showed significant reductions of intestinal EPEC (P<0.05). These results suggest that establishing conjugative CRISPR-Cas9 antimicrobials in the intestinal microbiome may provide protection from enteric pathogens and reduce antibiotic resistance without disrupting the normal microbiota.
Association of oxidized ApoB and oxidized ApoA-I with high-risk coronary plaque features in cardiovascular disease

BACKGROUND. Oxidized apolipoprotein B (oxLDL) and oxidized ApoA-I (oxHDL) are proatherogenic. Their prognostic value for assessing high-risk plaques by coronary computed tomography angiography (CCTA) is missing. METHODS. In a prospective, observational study, 306 participants with cardiovascular disease (CVD) had extensive lipoprotein profiling. Proteomics analysis was performed on isolated oxHDL, and atherosclerotic plaque assessment was accomplished by quantitative CCTA. RESULTS. Patients were predominantly White, overweight men (58.5%) on statin therapy (43.5%). Increase in LDL-C, ApoB, small dense LDL-C (P < 0.001 for all), triglycerides (P = 0.03), and lower HDL function were observed in the high oxLDL group. High oxLDL associated with necrotic burden (NB; β = 0.20; P < 0.0001) and fibrofatty burden (FFB; β = 0.15; P = 0.001) after multivariate adjustment. Low oxHDL had a significant reverse association with these plaque characteristics. Plasma oxHDL levels better predicted NB and FFB after adjustment (OR, 2.22; 95% CI, 1.27–3.88, and OR, 2.80; 95% CI, 1.71–4.58) compared with oxLDL and HDL-C. Interestingly, oxHDL associated with fibrous burden (FB) change over 3.3 years (β = 0.535; P = 0.033) when compared with oxLDL. Combined Met136 mono-oxidation and Trp132 dioxidation of HDL showed evident association with coronary artery calcium score (r = 0.786; P < 0.001) and FB (r = 0.539; P = 0.012) in high oxHDL, whereas Met136 mono-oxidation significantly associated with vulnerable plaque in low oxHDL. CONCLUSION. Our findings suggest that the investigated oxidized lipids are associated with high-risk coronary plaque features and progression over time in patients with CVD. TRIAL REGISTRATION. ClinicalTrials.gov NCT01621594. FUNDING. National Heart, Lung, and Blood Institute at the NIH Intramural Research Program.
Intra-and inter-laboratory reproducibility and predictivity of the HaCaSens assay : A skin sensitization test using human keratinocytes

Please cite this article as: Hyewon Chung, Hailian Quan, Daun Jung, Gautam Ravi, Ahrang Cho, Mijeong Kang, Eunju Kim, Jeonghwan Che, Eung-Seok Lee, Taecheon Jeong, Yong Heo, Seung Hyeok Seok , Intraand inter-laboratory reproducibility and predictivity of the HaCaSens assay: A skin sensitization test using human keratinocytes, HaCaT. The address for the corresponding author was captured as affiliation for all authors. Please check if appropriate. Tiv(2017), doi:10.1016/j.tiv. 2017.10. 018
An Experimental Design to Compare the Compatibility of Absorbable and Nonabsorbable Suture Materials in the Lateral Canthus Area

Polyglactin 910 (Vicryl) and polypropylene (Prolene) are common suture materials used in ophthalmic surgical procedures. However, there are limited studies assessing tissue reactions to different sutures in eyelid areas. In this study, these suture materials were used subcutaneously in 10 lateral canthi of 5 pigs. Clinical reactive score (CRS) was assessed 14 days and 60 days after surgery. On histology, subcutaneous tissue reactions were assessed by the presence of different inflammatory cells, and the aggregate tissue irritation score was calculated. CRS and the histology score did not differ between these sutures. None of the suture materials used were superior for use in the lateral canthi of pig eyes. Therefore, we recommend both of these sutures for use in the subcutaneous tissue of the eyelid area in animal experiments or clinical practice.
Severe (level 3) hypoglycaemia occurrence in a real-world cohort of adults with type 1 or 2 diabetes mellitus (iNPHORM, United States)

Among adults with insulin‐ and/or secretagogue‐treated diabetes in the United States, very little is known about the real‐world descriptive epidemiology of iatrogenic severe (level 3) hypoglycaemia. Addressing this gap, we collected primary, longitudinal data to quantify the absolute frequency of events as well as incidence rates and proportions.
Effect of Growth Regulator and Nutrients Spray on Control of Fruit Drop, Fruit Size and Quality of Ber under Sub-Montane Zone of Punjab

The effect of foliar spray of plant growth regulators and nutrients on fruit drop, fruit size and quality was studied in ber cv Sanuar-2 at Krishi Vigyan Kendra, Hoshiarpur, Punjab Agricultural University, Ludhiana, during 2005-2006. Plants were sprayed with NAA (20, 30 or 40 ppm), KNO3 (0.5, 1.0 or 1.5%) and ZnSO43333
Positive blood pressure response may predict the recovery of renal function after transcatheter aortic valve implantation

Objective Transcatheter aortic valve implantation (TAVI) may ameliorate renal function and increase blood pressure (BP). We aimed to investigate the association between increased BP and improved renal function (IRF) after TAVI. Methods A total of 176 patients who had undergone TAVI were evaluated retrospectively. BP records that were taken 24 h before and 72 h after TAVI were reviewed. Pre-procedural, post-procedural 48 h, and the first month estimated glomerular filtration rate (eGFR) levels were noted. IRF was accepted as a ≥ 10% increase in eGFR. The predictors of acute kidney injury (AKI) development at 48 h and IRF at 1 month were investigated. The association between mortality and BP response was assessed. Results A total of 157 patients were included in this study after exclusion as defined in the methodology. Mean age was 78.1 ± 7,1 and 51.6% were female. AKI occurred in 25.5% of patients and baseline eGFR and male gender were found as independent predictors for AKI development. IRF was observed in 16% at 48 h and 31.8% of patients at 1-month follow-up. Positive BP response was seen in 42% of patients. Pre-procedural chronic kidney disease, positive BP response, and an early increase in eGFR emerged as independent predictors of IRF at the first month. The patients with positive BP response were found to have decreased mortality at 710 days follow-up. Conclusion Positive BP response after TAVI is related to improved survival and renal functions. The beneficial effect of TAVI on renal function may be precisely evaluated at 1st month rather than 48 h.
Astrocytes in functional recovery following central nervous system injuries.

Astrocytes are increasingly recognised as partaking in complex homeostatic mechanisms critical for regulating neuronal plasticity following central nervous system (CNS) insults. Ischaemic stroke and traumatic brain injury are associated with high rates of disability and mortality. Depending on the context and type of injury, reactive astrocytes respond with diverse morphological, proliferative and functional changes collectively known as astrogliosis, which results in both pathogenic and protective effects. There is a large body of research on the negative consequences of astrogliosis following brain injuries. There is also growing interest in how astrogliosis might in some contexts be protective and help to limit the spread of the injury. However, little is known about how astrocytes contribute to the chronic functional recovery phase following traumatic and ischaemic brain insults. In this review, we explore the protective functions of astrocytes in various aspects of secondary brain injury such as oedema, inflammation and blood-brain barrier dysfunction. We also discuss the current knowledge on astrocyte contribution to tissue regeneration, including angiogenesis, neurogenesis, synaptogenesis, dendrogenesis and axogenesis. Finally, we discuss diverse astrocyte-related factors that, if selectively targeted, could form the basis of astrocyte-targeted therapeutic strategies to better address currently untreatable CNS disorders.
Extracapsular nodal extension and tumor deposits in head and neck squamous cell carcinoma

Tumor deposits (TDs) are an infrequently mentioned feature of head and neck squamous cell carcinoma (HNSCC) that are currently grouped under extranodal extension (ENE) in the AJCC 8th edition of HNSCC TNM staging. The prognostic implication of TDs in comparison to ENE remains uncertain.
Altered Oral Nitrate Reduction and Bacterial Profiles in Hypertensive Women Predict Blood Pressure Lowering Following Acute Dietary Nitrate Supplementation

BACKGROUND: The efficacy of dietary nitrate supplementation to lower blood pressure (BP) in pregnant women is highly variable. We aimed to investigate whether differences in oral microbiota profiles and oral nitrate-reducing capacity may explain interindividual differences in BP lowering following nitrate supplementation. METHODS: Participants recruited for this study were both pregnant and nonpregnant women, with or without hypertension (n=55). Following an overnight fast, plasma, saliva, and tongue scraping samples were collected for measurement of nitrate/nitrite concentrations, oral NaR (nitrate reductase) activity, and microbiota profiling using 16S rRNA gene sequencing. Baseline BP was measured, followed by the administration of a single dose of dietary nitrate (400 mg nitrate in 70 mL beetroot juice). Post-nitrate intervention, plasma and salivary nitrate/nitrite concentrations and BP were determined 2.5 hours later. RESULTS: Women with hypertension had significantly lower salivary nitrite concentrations (P=0.006) and reduced abundance of the nitrate-reducing taxa Veillonella(P=0.007) compared with normotensive women. Oral NaR activity was not significantly different in pregnant versus nonpregnant women (P=0.991) but tended to be lower in hypertensive compared with normotensive women (P=0.099). Oral NaR activity was associated with both baseline diastolic BP (P=0.050) and change in diastolic BP following acute nitrate intake (P=0.01, adjusted for baseline BP). CONCLUSIONS: The abundance and activity of oral nitrate-reducing bacteria impact both baseline BP as well as the ability of dietary nitrate supplementation to lower BP. Strategies to increase oral nitrate-reducing capacity could lower BP and enhance the efficacy of dietary nitrate supplementation, in pregnancy as well as in nonpregnant adults. REGISTRATION: URL: https://www.clinicaltrials. gov; Unique identifier: NCT03930693.
Dengue virus NS1 secretion is regulated via importin-subunit β1 controlling expression of the chaperone GRp78 and targeted by the clinical drug ivermectin

ABSTRACT Dengue virus (DENV) is a major human pathogen. An important pathogenicity factor is non-structural protein 1 (NS1) required for viral replication and secreted from infected cells. A clinical study indicated that the anti-parasitic drug ivermectin lowers NS1 blood levels without affecting viremia. Ivermectin targets nuclear transport by binding to importin-α, but how NS1 secretion in patients is suppressed by this drug is unknown. We show that ivermectin impairs folding and secretion of endoplasmic reticulum-luminal glycoproteins, including NS1. Proteomic analysis identified chaperones interacting with NS1, including GRp78 (78-kDa glucose-regulated protein, also known as HSPA5 or BIP). This chaperone increased in abundance on DENV infection via activation of the unfolded protein response (UPR). Ivermectin blocked the nuclear transport of transcription factors required for UPR, thus impairing GRp78 upregulation and NS1 secretion. Reduction of GRp78 and NS1 secretion was also observed in patients treated with ivermectin. These results link nuclear transport and its inhibition by ivermectin to folding and secretion of luminal glycoproteins, including DENV NS1. IMPORTANCE Dengue virus (DENV) is a major human pathogen that can cause hemorrhagic fever and shock syndrome. One important factor of DENV pathogenicity is non-structural protein 1 (NS1), a glycoprotein that is secreted from infected cells. Here we study the mode of action of the widely used drug ivermectin, used to treat parasitic infections and recently shown to lower NS1 blood levels in DENV-infected patients. We found that ivermectin blocks the nuclear transport of transcription factors required for the expression of chaperones that support the folding and secretion of glycoproteins, including NS1. Impairing nuclear transport of these transcription factors by ivermectin or depleting them from infected cells dampens NS1 folding and thus its secretion. These results reveal a novel mode of action of ivermectin that might apply to other flaviviruses as well. Dengue virus (DENV) is a major human pathogen that can cause hemorrhagic fever and shock syndrome. One important factor of DENV pathogenicity is non-structural protein 1 (NS1), a glycoprotein that is secreted from infected cells. Here we study the mode of action of the widely used drug ivermectin, used to treat parasitic infections and recently shown to lower NS1 blood levels in DENV-infected patients. We found that ivermectin blocks the nuclear transport of transcription factors required for the expression of chaperones that support the folding and secretion of glycoproteins, including NS1. Impairing nuclear transport of these transcription factors by ivermectin or depleting them from infected cells dampens NS1 folding and thus its secretion. These results reveal a novel mode of action of ivermectin that might apply to other flaviviruses as well.
Epigenetic architecture of Pseudotaxus chienii: Revealing the synergistic effects of climate and soil variables

Abstract Whether conifers can withstand environmental changes especially temperature fluctuations has been controversial. Epigenetic analysis may provide new perspectives for solving the issue. Pseudotaxus chienii is an endangered gymnosperm species endemic to China. In this study, we have examined the genetic and epigenetic variations in its natural populations aiming to disentangle the synergistic effects of climate and soil on its population (epi)genetic differentiation by using amplified fragment length polymorphism (AFLP) and methylation‐sensitive AFLP (MSAP) techniques. We identified 23 AFLP and 26, 7, and 5 MSAP outliers in P. chienii. Twenty‐one of the putative adaptive AFLP loci were found associated with climate and/or soil variables including precipitation, temperature, K, Fe, Zn, and Cu, whereas 21, 7, and 4 MSAP outliers were significantly related to precipitation of wettest month (Bio13), precipitation driest of month (Bio14), percent tree cover (PTC), and soil Fe, Mn, and Cu compositions. Total precipitation and precipitation in the driest seasons were the most influential factors for genetic and epigenetic variation, respectively. In addition, a high full‐methylation level and a strong correlation between genetic and epigenetic variation were detected in P. chienii. Climate is found of greater importance than soil in shaping adaptive (epi)genetic differentiation, and the synergistic effects of climate and climate–soil variables were also observed. The identified climate and soil variables should be considered when applying ex situ conservation.
Sustainable settlement in the Brazilian Amazon

This book is about small farmers in the Brazilian Amazon and how to raise their incomes while reducing resource degradation. The starting point of the book is the observation that whereas those farmers who deforested the Amazon during the 1970s and 1980s had migrated there from outside the basin, most of the small farmers deforesters of today have apparently come from within the region. Hence the greatest threat from small farmers to the Amazon forest is coming from intraregional migration. The issue is thus no longer how to prevent migration to the Amazon from the rest of the country but how to ensure that farmers already in the Amazon stay where they have already deforested, thus reducing migration and deforestation farther inland. The main argument in the book is that intraregional migration can be stemmed only by establishing sustainable farming in already deforested areas. Such sustainability would not likely attract intraregional migrants because of irreversible changes that occurred during the 1980s in Brazil's population and economy. Chapter 2 of this book reviews the population shifts in the Amazon during the 1980s and chapter 3 the economic shifts during the same period. Chapter 4 discusses land markets and sustainable frontier farming. Chapter 5 assesses the productive and speculative deforestation by frontier small farmers. Finally, chapter 6 addresses the policy implications, including the institutional improvements forsustainable settlement in the Amazon.
“It Makes You Feel Alive and Younger…but It’s Stressful …My Back and Legs Ache”: A Focus Group Study Encouraging Resistance Training Around Retirement

Muscle weakness is a key component of age-related conditions such as sarcopenia and frailty. Resistance training is highly effective at preventing and treating muscle weakness; however, few adults meet recommended levels. Retirement may be a key life-stage to promote resistance training. We carried out a virtual focus group study to explore motivators and barriers to resistance training around the time of retirement, with the aim of determining strategies and messages to increase its uptake. The five focus groups (n = 30) were recorded, transcribed and thematically analysed. We found that resistance training was positively viewed when associated with immediate and long-term health and wellbeing benefits and had a social dimension; but there was a lack of understanding as to what constitutes resistance training, the required intensity level for effects; the role of pain; and the consequences of muscle weakness.
Evaluation of the QIAstat-Dx Meningitis/Encephalitis Panel, a multiplex PCR platform for the detection of community-acquired meningoencephalitis

ABSTRACT Rapid identification of the causative pathogens of central nervous system infections is essential for providing appropriate management and improving patient outcomes. The performance of QIAstat-Dx Meningitis/Encephalitis (ME) Panel—a multiplex PCR testing platform—in detecting pathogens implicated in meningitis and/or encephalitis was evaluated using BioFire FilmArray ME Panel as a comparator method. This multicenter study analyzed 585 retrospective residual cerebrospinal fluid specimens and 367 contrived specimens. The QIAstat-Dx ME Panel showed positive percent agreement (PPA) values of 100% for Neisseria meningitidis, Streptococcus agalactiae, Escherichia coli K1, Listeria monocytogenes, and Cryptococcus gattii/neoformans on clinical samples compared to the BioFire FilmArray ME Panel. The PPA values observed for Haemophilus influenzae and Streptococcus pneumoniae were 80% and 88.24%, respectively. Negative percent agreement (NPA) values were >99.0% for each of the six bacterial targets and one fungal target tested with clinical samples. One viral target, herpes simplex virus 1, exhibited a PPA value of 100.0%, while the remaining viral targets—human parechovirus, herpes simplex virus 2, human herpes virus 6, and varicella zoster virus—were >90.0%, with the exception of enterovirus, which had a PPA value of 77.8%. The QIAstat-Dx ME Panel detected five true-positive and four true-negative cases compared to BioFire FilmArray ME Panel. The NPA values for all viral pathogens were >99.0%. Overall, the QIAstat-Dx ME Panel showed comparable performance to the BioFire FilmArray ME Panel as a rapid diagnostic tool for community-acquired meningitis and encephalitis.
Robotic-assisted Navigation Bronchoscopy

Background: Robotic-assisted navigation bronchoscopy (RANB) is a novel method to biopsy lung nodules, with initial reports demonstrating excellent accuracy. We aimed to evaluate pooled estimates of diagnostic yields and complication rates with RANB by performing a meta-analysis of the available literature. Methods: We searched 3 databases, including PubMed, EmBase, and Web of Science. The resulting abstracts were reviewed by 2 investigators. Analyses were performed using random effects models, and diagnostic yield and complication rates were estimated after the Freeman-Tukey transformation. Results: A total of 23 articles, comprising 1409 patients and 1541 nodules, were included in the final analysis. Mean ages ranged from 63.2 to 69.3 years. The average size of the nodules ranged between 5.9 and 25.0 mm. Most patients (54.0% to 92.0%) had a current or prior smoking history in studies that reported them (n=8). The pooled diagnostic yield was 81.9% (12 studies, 838 nodules, 95% CI: 83.4%-91.0%), and the pooled sensitivity for malignancy was 87.6% (8 studies, 699 nodules, 95% CI: 81.3%-89.5%). The pooled incidence of pneumothorax rates was 0.60% (95% CI: 0.11%-1.35%). The pooled incidence of major bleeding was <0.01%. Conclusion: Diagnostic yield for patients with pulmonary nodules undergoing RANB is high, though may be impacted by the prevalence of malignancy, participant selection, and publication bias. Complication rates, including pneumothoraces and bleeding rates, appear low across all studies. If RANB is available, clinicians should consider utilizing this platform to biopsy pulmonary nodules.