Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic surveillance of antimicrobial resistance shows cattle and poultry are a moderate source of multi-drug resistant non-typhoidal Salmonella in Mexico

Multi-drug resistant (MDR) non-typhoidal Salmonella (NTS) is a public health concern globally. This study reports the phenotypic and genotypic antimicrobial resistance (AMR) profiles of NTS isolates from bovine lymph nodes (n = 48) and ground beef (n = 29). Furthermore, we compared genotypic AMR data of our isolates with those of publicly available NTS genomes from Mexico (n = 2400). The probability of finding MDR isolates was higher in ground beef than in lymph nodes:χ2 = 12.0, P = 0.0005. The most common resistant phenotypes involved tetracycline (40.3%), carbenicillin (26.0%), amoxicillin-clavulanic acid (20.8%), chloramphenicol (19.5%) and trimethoprim-sulfamethoxazole (16.9%), while more than 55% of the isolates showed decreased susceptibility to ciprofloxacin and 26% were MDR. Conversely, resistance to cephalosporins and carbapenems was infrequent (0–9%). MDR phenotypes were strongly associated with NTS serovar (χ2 = 24.5, P<0.0001), with Typhimurium accounting for 40% of MDR strains. Most of these (9/10), carried Salmonella genomic island 1, which harbors a class-1 integron with multiple AMR genes (aadA2, blaCARB-2, floR, sul1, tetG) that confer a penta-resistant phenotype. MDR phenotypes were also associated with mutations in the ramR gene (χ2 = 17.7, P<0.0001). Among public NTS isolates from Mexico, those from cattle and poultry had the highest proportion of MDR genotypes. Our results suggest that attaining significant improvements in AMR meat safety requires the identification and removal (or treatment) of product harboring MDR NTS, instead of screening for Salmonella spp. or for isolates showing resistance to individual antibiotics. In that sense, massive integration of whole genome sequencing (WGS) technologies in AMR surveillance provides the shortest path to accomplish these goals.
Treatment strategies and predicting lymph node metastasis in elderly patients with papillary thyroid microcarcinoma

Abstract This study aims to explore the prognostic variables for elderly papillary thyroid microcarcinoma (PTMC) patients as well as create a nomogram that could predict the occurrence of cervical lymph node metastasis (CLNM) on the basis of a large population database with high quality. A total of 5165 PTMC patients from Surveillance, Epidemiology, and End Results database database were enrolled in the study. In the meantime, we retrospectively collected 205 PTMC patients who underwent thyroidectomy in our medical center as an external control to test the accuracy of the model. The independent predictors of survival were identified by multivariate Cox regression analysis. Risk factors were selected as nomogram parameters to develop a model to predict CLNM. The C-index and calibration plots were used to evaluate CLNM model discrimination. The predictive nomogram was further validated in the external validation set. 76.8% of the enrolled patients underwent thyroidectomy. Overall survival and cancer-specific survival were significantly better in patients who underwent surgery than in those who did not (P < .001). Sex, tumor size, and extent of tumor were included in a multivariable logistic regression model to predict lymph node metastasis. The nomogram had good discrimination with a C-index of 0.71. The calibration curves showed perfect agreement between nomogram predictions and actual observations. Elderly PTMC patients who received a surgical approach without radiotherapy showed survival advantage than those with other treatment strategies. Moreover, a nomogram model was established to predict the risk of CLNM, which will help clinicians in making treatment decisions.
Weight loss with bariatric surgery or behaviour modification and the impact on female obesity‐related urine incontinence: A comprehensive systematic review and meta‐analysis

Women with obesity are at risk of pelvic floor dysfunction with a 3‐fold increased incidence of urge urinary incontinence (UUI) and double the risk of stress urinary incontinence (SUI). The National Institute for Health and Care Excellence (NICE) and European Association of Urology (EAU) recommend that women with a body mass index ≥30 kg/m2 should consider weight loss prior to consideration for incontinence surgery. This systematic review and meta‐analysis will assess this recommendation to aid in the counselling of women with obesity‐related urinary incontinence (UI). Medical Literature Analysis and Retrieval System online (MEDLINE), EMBASE, Cochrane, ClinicalTrials.gov, and SCOPUS were systematically and critically appraised for all peer reviewed manuscripts that suitably fulfilled the inclusion criteria established a priori and presented original, empirical data relevant to weight loss intervention in the management of urinary incontinence. Thirty‐three studies and their outcomes were meta‐analysed. Weight loss interventions were associated in a decreased prevalence in UI (OR 0.222, 95% CI [0.147, 0.336]), SUI (OR 0.354, 95% CI [0.256, 0.489]), UUI (OR 0.437, 95% CI [0.295, 0.649]) and improved quality of life (PFDI‐20, SMD ‐0.774 (95% CI [−1.236, −0.312]). This systematic review and meta‐analysis provide evidence that weight loss interventions are effective in reducing the prevalence of obesity‐related UI symptoms in women. Bariatric surgery in particular shows greater sustained weight loss and improvements in UI prevalence. Further large scale, randomized control trials assessing the effect of bariatric surgery on women with obesity‐related UI are needed to confirm this study's findings.
Patients’ Perception of Vitiligo Severity

Identifying which factors contribute to vitiligo severity and determining their individual weight are important in the management of vitiligo. The aim of this study is to investigate the predictive variables concerning vitiligo severity as perceived by the patients. Based on a questionnaire, several factors that may contribute to the Patient Global Assessment (PtGA) of severity were investigated within a Belgian vitiligo population (n = 291). In addition, possible factors influencing vitiligo severity were scored and ranked. The strongest correlations with the PtGA of severity were found for impact, Dermatology Life Quality Index and disease extent. Based on multivariable regression analyses, 64.7% of PtGA of severity could be predicted by subjective and objective variables, while 32% could be explained by objective clinical features only. Patients considered lesion location, extent and disease activity as the most important contributing factors to severity. Vitiligo severity is determined by objective clinical features, but also, for a significant part, by the perceived impact of the disease.
Network interdigitations of Tau and amyloid‐beta deposits define cognitive levels in aging

Amyloid‐beta (Aβ) plaques and tau neurofibrillary tangles are pathological hallmarks of Alzheimer's disease (AD); their contribution to neurodegeneration and clinical manifestations are critical in understanding preclinical AD. At present, the mechanisms related to Aβ and tau pathogenesis leading to cognitive decline in older adults remain largely unknown. Here, we examined graph theory‐based positron emission tomography (PET) analytical approaches, within and between tau and Aβ PET modalities, and tested the effects on cognitive changes in cognitively normal older adults (CN). Particularly, we focused on the network interdigitations of Aβ and tau deposits, along with cognitive test scores in CN at both baseline and 2‐year follow‐up (FU). We found highly significant Aβ‐tau network integrations in AD vulnerable areas, as well as significant associations between those Aβ‐tau interdigitations and general cognitive impairment in CN at baseline and FU. Our findings suggest a distinctive contribution of interlinking network relationships between Aβ and tau deposits in heteromodal areas of the human brain. They support a network‐based interaction between Aβ and tau accumulations as a key factor for cognitive deterioration in CN prior to dementia.
Factors associated with psychological distress for couples facing head and neck cancer: A systematic literature review

Cancer patients in supportive relationships display improved health and survival outcomes. Identifying factors that might respond to intervention for Head and Neck Cancer (HNC) dyads is important as HNC patients and their partners experience heightened distress. This article systematically reviewed and evaluated the research findings and methodological quality of studies which identified factors influencing psychological distress for couples facing HNC.
Drug Release from Thermo‐Responsive Polymer Brush Coatings to Control Bacterial Colonization and Biofilm Growth on Titanium Implants

Despite decades of biomedical advances, the colonization of implant devices with bacterial biofilms is still a leading cause of implant failure. Clearly, new strategies and materials that suppress both initial and later stage bacterial colonization are required in this context. Ideal would be the implementation of a bactericidal functionality in the implants that is temporally and spatially triggered in an autonomous fashion at the infection site. Herein, the fabrication and validation of functional titanium‐based implants with triggered antibiotic release function afforded via an intelligent polymer coating is reported. In particular, thermo‐responsive poly(di(ethylene glycol) methyl ether methacrylate) (PDEGMA) brushes on titanium implants synthesized via a surface‐initiated atom transfer radical polymerization with activators regenerated through the electron transfer technique (ARGET ATRP) allows for a controlled and thermally triggered release of the antibiotic levofloxacin at the wound site. Antibiotic loaded brushes are investigated as a function of thickness, loading capacity for antibiotics, and temperature. At temperatures of the infection site >37 °C the lower critical solution temperature behavior of the brushes afforded the triggered release. Hence, in addition to the known antifouling effects, the PDEGMA coating ensured enhanced bactericidal effects, as demonstrated in initial in vivo tests with rodents infected with Staphylococcus aureus.
Hypoxia-inducible factor-dependent ADAM12 expression mediates breast cancer invasion and metastasis

Significance Hypoxia (reduced oxygen availability) is a common finding in the tumor microenvironment and plays a critical role in stimulating the metastasis of breast cancer cells from the primary tumor to distant organs, which is closely related to patient mortality. Critical transcriptional responses to reduced O2 availability are mediated by hypoxia-inducible factors (HIFs). In this study, we demonstrate that hypoxia induces HIF-dependent expression of a disintegrin and metalloproteinase 12 (ADAM12), which clips off the extracellular domain of the membrane-bound heparin-binding epidermal growth factor-like growth factor (HB-EGF). The liberated extracellular domain of HB-EGF binds to the epidermal growth factor receptor, triggering a signal transduction pathway that endows breast cancer cells with increased capability for cell migration and invasion, leading to distant metastasis. Breast cancer patients with increased expression of hypoxia-inducible factors (HIFs) in primary tumor biopsies are at increased risk of metastasis, which is the major cause of breast cancer-related mortality. The mechanisms by which intratumoral hypoxia and HIFs regulate metastasis are not fully elucidated. In this paper, we report that exposure of human breast cancer cells to hypoxia activates epidermal growth factor receptor (EGFR) signaling that is mediated by the HIF-dependent expression of a disintegrin and metalloprotease 12 (ADAM12), which mediates increased ectodomain shedding of heparin-binding EGF-like growth factor, an EGFR ligand, leading to EGFR-dependent phosphorylation of focal adhesion kinase. Inhibition of ADAM12 expression or activity decreased hypoxia-induced breast cancer cell migration and invasion in vitro, and dramatically impaired lung metastasis after orthotopic implantation of MDA-MB-231 human breast cancer cells into the mammary fat pad of immunodeficient mice.
Pulse Wave Imaging Coupled With Vector Flow Mapping: A Phantom, Simulation, and In Vivo Study

Pulse wave imaging (PWI) is an ultrasound imaging modality that estimates the wall stiffness of an imaged arterial segment by tracking the pulse wave propagation. The aim of the present study is to integrate PWI with vector flow imaging, enabling simultaneous and co-localized mapping of vessel wall mechanical properties and 2-D flow patterns. Two vector flow imaging techniques were implemented using the PWI acquisition sequence: 1) multiangle vector Doppler and 2) a cross-correlation-based vector flow imaging (CC VFI) method. The two vector flow imaging techniques were evaluated <italic>in vitro</italic> using a vessel phantom with an embedded plaque, along with spatially registered fluid structure interaction (FSI) simulations with the same geometry and inlet flow as the phantom setup. The flow magnitude and vector direction obtained through simulations and phantom experiments were compared in a prestenotic and stenotic segment of the phantom and at five different time frames. In most comparisons, CC VFI provided significantly lower bias or precision than the vector Doppler method (<inline-formula> <tex-math notation="LaTeX">${p} < {0.05}$ </tex-math></inline-formula>) indicating better performance. In addition, the proposed technique was applied to the carotid arteries of nonatherosclerotic subjects of different ages to investigate the relationship between PWI-derived compliance of the arterial wall and flow velocity <italic>in vivo</italic>. Spearman’s rank-order test revealed positive correlation between compliance and peak flow velocity magnitude (<inline-formula> <tex-math notation="LaTeX">${r}_{s} = {0.90}$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">${p} < {0.001}$ </tex-math></inline-formula>), while significantly lower compliance (<inline-formula> <tex-math notation="LaTeX">${p} < {0.01}$ </tex-math></inline-formula>) and lower peak flow velocity magnitude (<inline-formula> <tex-math notation="LaTeX">${p} < {0.001}$ </tex-math></inline-formula>) were determined in older (54–73 y.o.) compared with young (24–32 y.o.) subjects. Finally, initial feasibility was shown in an atherosclerotic common carotid artery <italic>in vivo</italic>. The proposed imaging modality successfully provided information on blood flow patterns and arterial wall stiffness and is expected to provide additional insight in studying carotid artery biomechanics, as well as aid in carotid artery disease diagnosis and monitoring.
Carbonate chemistry seasonality in a tropical mangrove lagoon in La Parguera, Puerto Rico

We investigated the seasonal carbonate chemistry variability within a semi-enclosed tropical mangrove lagoon in southwestern Puerto Rico. Biweekly measurements of seawater temperature, salinity, total alkalinity (TA), and dissolved inorganic carbon (DIC) were conducted from 2014 to 2018. We describe the possible mechanisms driving the observed variability by correlating the DIC/TA ratio with pH and Ωarg, suggesting that the mean pH (7.87 ± 0.09) and aragonite saturation state (Ωarg, 2.96 ± 0.47) of the mangrove lagoon negatively affected calcification. The measured pCO2 and DIC/TA ratios indicate that heterotrophic activity was the primary driver for persistent acidification, which reached its maximum expression during the wet season. We conclude that mangrove lagoons with limited seawater exchange and high carbon input will not mitigate ocean acidification.
Chromosome-Scale Assembly of the Bread Wheat Genome Reveals Thousands of Additional Gene Copies.

Bread wheat (Triticum aestivum) is a major food crop and an important plant system for agricultural genetics research. However, due to the complexity and size of its allohexaploid genome, genomic resources are limited compared to other major crops. The IWGSC recently published a reference genome and associated annotation (IWGSC CS v1.0, Chinese Spring) that has been widely adopted and utilized by the wheat community. Although this reference assembly represents all three wheat subgenomes at chromosome-scale, it was derived from short reads, and thus is missing a substantial portion of the expected 16 Gbp of genomic sequence. We earlier published an independent wheat assembly (Triticum_aestivum_3.1, Chinese Spring) that came much closer in length to the expected genome size, although it was only a contig-level assembly lacking gene annotations. Here, we describe a reference-guided effort to scaffold those contigs into chromosome-length pseudomolecules, add in any missing sequence that was unique to the IWGSC CS v1.0 assembly, and annotate the resulting pseudomolecules with genes. Our updated assembly, Triticum_aestivum_4. 0, contains 15.07 Gbp of nongap sequence anchored to chromosomes, which is 1.2 Gbps more than the previous reference assembly. It includes 108,639 genes unambiguously localized to chromosomes, including over 2000 genes that were previously unplaced. We also discovered >5700 additional gene copies, facilitating the accurate annotation of functional gene duplications including at the Ppd-B1 photoperiod response locus.
Extract of neem (Azadirachta indica) leaf exhibits bactericidal effect against multidrug resistant pathogenic bacteria of poultry

Abstract The aim of the study was to determine the efficacy of neem leaf extract against multidrug resistant (MDR) pathogenic bacteria. Laboratory stock culture of Pasteurella multocida, Salmonella pullorum, Salmonella gallinarum and Escherichia coli was revived. Antibiogram profiles of these bacteria were determined by disc diffusion method. Ethanolic extract of neem leaf was prepared. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of neem leaf extract (112.5, 100, 50, 25, 12.5, 6.25 and 3.12 mg/ml) against MDR pathogenic bacteria of poultry were determined by double dilution method. The MIC and MBC of the neem leaf extract were 12.5 and 25 mg/ml, respectively for P. multocida, 50 and 100 mg/ml for S. pullorum and S. gallinarum, 100 and 112.5 mg/ml for E. coli. Neem leaf extracts exhibited bactericidal effect against MDR pathogenic bacteria of poultry.
Structure, DFT studies and evaluation of catechol oxidase (CO) mimic activity of mononuclear Co(II) complexes derived from aminoalcohols: an experimental and theoretical approach

Abstract The impetus to modeling of enzyme mimics comes from their potential to provide insight to the alternate mechanistic pathways of the native enzymes. The present study demonstrates the syntheses and characterization of two different cobalt(II) complexes, [Co(pdm)(Phen)Cl]Cl·H2O (1) and [Co(pmmH)2(SCN)2] (2) with the aminoalcohol ligands such as pyridine-2,6-dimethanol (pdmH2) or 2-pyridinemonomethanol (pmmH) and their assessment as catechol oxidase (CO) enzyme mimic. Single Crystal X-ray diffraction and powder X-ray diffraction data suggest the octahedral environment around the Co(II) ion and the complexes form extensive 1D or 2D propagating network as a result of non-covalent interactions (O···H and C-H···π). TD-DFT calculations were used to explain the spectral bands obtained during the UV-Vis absorption studies and it is ascertained that the transitions were mainly of the intra-ligand charge transfer (ILCT) type. The catecholase biomimetic catalytic activity of the synthesized complexes has been investigated in detail and the kinetics is also performed. The results obtained show that both the complexes catalyze the aerobic oxidation of catechol to the corresponding o-quinone. The K cat value for 1 is 106.99 h‒1 and for 2 is 90.32 h‒1 in methanol. It may be mentioned here that 1 and 2 are effective catalysts, with the order of activity being 1 > 2. The order of enzymatic activity is well justified by CV and DFT studies. Communicated by Ramaswamy H. Sarma
Die-off of plant pathogenic bacteria in tile drainage and anoxic water from a managed aquifer recharge site

Managed aquifer recharge (MAR) can provide irrigation water and overcome water scarcity in agriculture. Removal of potentially present plant pathogens during MAR is essential to prevent crop diseases. We studied the die-off of three plant pathogenic bacteria in water microcosms with natural or filtered tile drainage water (TDW) at 10 and 25°C and with natural anoxic aquifer water (AW) at 10°C from a MAR site. These bacteria were: Ralstonia solanacearum (bacterial wilt), and the soft rot Pectobacteriaceae (SRP) Dickeya solani and Pectobacterium carotovorum sp. carotovorum (soft rot, blackleg). They are present in surface waters and cause destructive crop diseases worldwide which have been linked to contaminated irrigation water. Nevertheless, little is known about the survival of the SRP in aqueous environments and no study has investigated the persistence of R. solanacearum under natural anoxic conditions. We found that all bacteria were undetectable in 0.1 mL samples within 19 days under oxic conditions in natural TDW at 10°C, using viable cell counting, corresponding to 3-log10 reduction by die-off. The SRP were no longer detected within 6 days at 25°C, whereas R. solanacearum was detectable for 25 days. Whereas in anoxic natural aquifer water at 10°C, the bacterial concentrations declined slower and the detection limit was reached within 56 days. Finally, we modelled the inactivation curves with a modified Weibull model that can simulate different curve shapes such as shoulder phenomena in the beginning and long tails reflecting persistent bacterial populations. The non-linear model was shown to be a reliable tool to predict the die-off of the analysed plant pathogenic bacteria, suggesting its further application to other pathogenic microorganisms in the context of microbial risk assessment.
Electroacupuncture at GV20-GB7 regulates mitophagy to protect against neurological deficits following intracerebral hemorrhage via inhibition of apoptosis

The acupuncture penetrating line of Baihui (GV20) to Qubin (GB7) spans the parietal, frontal and temporal lobes. The present study aimed to elucidate the mechanism by which electroacupuncture (EA) at GV20-GB7 regulates mitophagy in intracerebral hemorrhage (ICH) and whether it serves a neuroprotective role. A whole blood-induced ICH model was used. Mitophagy-regulating proteins, including BCL/adenovirus E1B 19 kDa-interacting protein 3 (BNIP3), PTEN-induced putative kinase 1 (PINK1), Parkin and apoptosis-associated proteins were detected by western blotting; autophagy following ICH was evaluated by immunofluorescent techniques; morphological characteristics of mitophagy were observed using transmission electron microscopy; and TUNEL assay was performed to determine the number of apoptotic cells. Immunohistochemistry was used to detect p53 expression. The protective role of EA (GV20-GB7) via enhanced mitophagy and suppressed apoptosis in ICH was further confirmed by decreased modified neurological severity score. The results showed that EA (GV20-GB7) treatment upregulated mitochondrial autophagy following ICH and inhibited apoptotic cell death. The mechanism underlying EA (GV20-GB7) treatment may involve inhibition of p53, an overlapping protein of autophagy and apoptosis. EA (GV20-GB7) treatment decreased neurobehavioral deficits following ICH but pretreatment with 3-methyladenine counteracted the beneficial effects of EA (GV20-GB7) treatment. In conclusion, EA (GV20-GB7) improved recovery from ICH by regulating the balance between mitophagy and apoptosis.