Based on their unique properties, oligonucleotide aptamers have been named a gift of biological chemistry to life science. We report the development of DNA aptamers as the first high-affinity binding ...molecules available for fast and rapid labeling of the human gut bacterium Akkermansia muciniphila with a certain impact on Alzheimer´s disease. Fast and reliable analyses of the composition of microbiomes is an emerging field in microbiology. We describe the molecular evolution and biochemical characterization of a specific aptamer library by a FluCell-SELEX and the characterization of specific molecules from the library by bioinformatics. The aptamer AKK13.1 exerted universal applicability in different analysis techniques in modern microbiology, including fluorimetry, confocal laser scanning microscopy and flow cytometry. It was also functional as a specific binding entity hybridized to anchor primers chemically coupled via acrydite-modification to the surface of a polyacrylamide-hydrogel, which can be prototypically used for the construction of affinity surfaces in sensor chips. Together, the performance and methodological flexibility of the aptamers presented here may open new routes not only to develop novel Akkermansia-specific assays for clinical microbiology and the analyses of human stool samples but may also be an excellent starting point for the construction of novel electronic biosensors.
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Here we present for the first time a potential wound dressing material implementing aptamers as binding entities to remove pathogenic cells from newly contaminated surfaces of wound matrix-mimicking ...collagen gels. The model pathogen in this study was the Gram-negative opportunistic bacterium
, which represents a considerable health threat in hospital environments as a cause of severe infections of burn or post-surgery wounds. A two-layered hydrogel composite material was constructed based on an established eight-membered focused anti-
polyclonal aptamer library, which was chemically crosslinked to the material surface to form a trapping zone for efficient binding of the pathogen. A drug-loaded zone of the composite released the C14R antimicrobial peptide to deliver it directly to the bound pathogenic cells. We demonstrate that this material combining aptamer-mediated affinity and peptide-dependent pathogen eradication can quantitatively remove bacterial cells from the "wound" surface, and we show that the surface-trapped bacteria are completely killed. The drug delivery function of the composite thus represents an extra safeguarding property and thus probably one of the most important additional advances of a next-generation or smart wound dressing ensuring the complete removal and/or eradication of the pathogen of a freshly infected wound.
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A small fraction of cancer patients with advanced disease survive significantly longer than patients with clinically comparable tumors. Molecular mechanisms for exceptional responses to therapy have ...been identified by genomic analysis of tumor biopsies from individual patients. Here, we analyzed tumor biopsies from an unbiased cohort of 111 exceptional responder patients using multiple platforms to profile genetic and epigenetic aberrations as well as the tumor microenvironment. Integrative analysis uncovered plausible mechanisms for the therapeutic response in nearly a quarter of the patients. The mechanisms were assigned to four broad categories—DNA damage response, intracellular signaling, immune engagement, and genetic alterations characteristic of favorable prognosis—with many tumors falling into multiple categories. These analyses revealed synthetic lethal relationships that may be exploited therapeutically and rare genetic lesions that favor therapeutic success, while also providing a wealth of testable hypotheses regarding oncogenic mechanisms that may influence the response to cancer therapy.
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•Genomics of 110 patients with exceptional response to therapy profiled•Plausible molecular mechanisms related to therapy identified in ∼23% of cases•Proposed mechanisms involve DNA damage, signaling, and the immune response•Synthetic lethality with temozolomide in tumors with a defective DNA damage response
Profiling multi-platform genomics of 110 cancer patients with an exceptional therapeutic response, Wheeler et al. identify putative molecular mechanisms explaining this survival phenotype in ∼23% of cases. Therapeutic success is related to rare molecular features of responding tumors, exploiting synthetic lethality and oncogene addiction.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Antimicrobial peptides (AMPs) represent a promising class of therapeutic biomolecules that show antimicrobial activity against a broad range of microorganisms, including life-threatening pathogens. ...In contrast to classic AMPs with membrane-disrupting activities, new peptides with a specific anti-biofilm effect are gaining in importance since biofilms could be the most important way of life, especially for pathogens, as the interaction with host tissues is crucial for the full development of their virulence in the event of infection. Therefore, in a previous study, two synthetic dimeric derivatives (parallel Dimer 1 and antiparallel Dimer 2) of the AMP Cm-p5 showed specific inhibition of the formation of
biofilms. Here we show that these derivatives are also dose-dependently effective against de novo biofilms that are formed by the widespread pathogenic yeasts
and
. Moreover, the activity of the peptides was demonstrated even against two fluconazole-resistant strains of
.
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Abstract
Background
The proportion of tumors of various histologies that may respond to drugs targeted to molecular alterations is unknown. NCI-MATCH, a collaboration between ECOG-ACRIN Cancer ...Research Group and the National Cancer Institute, was initiated to find efficacy signals by matching patients with refractory malignancies to treatment targeted to potential tumor molecular drivers regardless of cancer histology.
Methods
Trial development required assumptions about molecular target prevalence, accrual rates, treatment eligibility, and enrollment rates as well as consideration of logistical requirements. Central tumor profiling was performed with an investigational next-generation DNA–targeted sequencing assay of alterations in 143 genes, and protein expression of protein expression of phosphatase and tensin homolog, mutL homolog 1, mutS homolog 2, and RB transcriptional corepressor 1. Treatments were allocated with a validated computational platform (MATCHBOX). A preplanned interim analysis evaluated assumptions and feasibility in this novel trial.
Results
At interim analysis, accrual was robust, tumor biopsies were safe (<1% severe events), and profiling success was 87.3%. Actionable molecular alteration frequency met expectations, but assignment and enrollment lagged due to histology exclusions and mismatch of resources to demand. To address this lag, we revised estimates of mutation frequencies, increased screening sample size, added treatments, and improved assay throughput and efficiency (93.9% completion and 14-day turnaround).
Conclusions
The experiences in the design and implementation of the NCI-MATCH trial suggest that profiling from fresh tumor biopsies and assigning treatment can be performed efficiently in a large national network trial. The success of such trials necessitates a broad screening approach and many treatment options easily accessible to patients.
The SEC's staff is considering requiring two rivals of Merck & Co.'s Medco Health unit to start using a Medco accounting technique that some critics have called aggressive, according to people ...familiar with the matter. If the SEC follows through, such a move would align the sector's accounting practices for billions of dollars of co-payments -- $5-to-$25 (4.65 euros-to-23.23 euros) fees paid by consumers to pharmacies when they fill prescriptions under many insurance plans -- and possibly give investors a misleading view of those companies' sales. Besides Medco, rival Caremark RX Inc. also books co-payments as revenue. Competitors Express Scripts Inc. and AdvancePCS don't. But that could change: In the past few weeks, the SEC sent so-called comment letters to AdvancePCS and Express Scripts. While the contents haven't been publicly disclosed, Express Scripts says the SEC raised as an issue "whether the company should include in revenue co-payments paid by individual members to retail pharmacies." Express Scripts has an opportunity to respond. A spokesman for the SEC declined to comment. In comments last June, Merck maintained that the accounting treatment is appropriate, because it has a residual legal liability that could require it under certain circumstances to cover additional costs under Medco's agreements with health-plan sponsors. Wednesday, Merck repeated that it "is confident that Medco Health's practice of recognizing retail co-payments as revenue is in accordance with generally accepted accounting principles. PricewaterhouseCoopers, Merck's independent public accountants, concurs with this accounting treatment." For Medco, retail co-payments amounted to $1.652 billion of its $8.44 billion in fourth-quarter revenue.
Merck disclosed the accounting treatment last year in a regulatory filing for an initial public offering of Medco, which it subsequently postponed. Before Merck shelved the IPO, the SEC's top ...accountants decided to accept Merck's approach, although some commission staff members disagreed with the decision. So did some accounting experts on the outside, who contended the SEC was going against more than 20 years of established accounting literature on the subject of revenue recognition. (The debate doesn't touch upon net income, because the same amount that is added to revenue also is added to costs, though profit margins shrink.) Besides Medco, rival Caremark RX Inc. also books co-payments as revenue. Competitors Express Scripts Inc. and AdvancePCS don't. But that could change: In the past few weeks, the SEC sent so-called comment letters to AdvancePCS and Express Scripts. While the contents haven't been publicly disclosed, Express Scripts says the SEC raised as an issue "whether the company should include in revenue co-payments paid by individual members to retail pharmacies." Express Scripts has an opportunity to respond. A spokesman for the SEC declined to comment. In releasing fourth-quarter earnings last week, Express Scripts disclosed receiving the SEC letter. The company didn't say if the SEC was leaning any particular way, only that the SEC raised the issue of recognizing co-payments in revenue.
Purpose
To develop and internally validate prediction models with machine learning for future potentially preventable healthcare utilization in patients with multiple long term conditions (MLTC). ...This study is the first step in investigating whether prediction models can help identify patients with MLTC that are most in need of integrated care.
Methods
A retrospective cohort study was performed with electronic health record data from adults with MLTC from an academic medical center in the Netherlands. Based on demographic and healthcare utilization characteristics in 2017, we predicted ≥ 12 outpatient visits, ≥ 1 emergency department (ED) visits, and ≥ 1 acute hospitalizations in 2018. Four machine learning models (elastic net regression, extreme gradient boosting (XGB), logistic regression, and random forest) were developed, optimized, and evaluated in a hold-out dataset for each outcome.
Results
A total of 14,486 patients with MLTC were included. Based on the area under the curve (AUC) and calibration curves, the XGB model was selected as final model for all three outcomes. The AUC was 0.82 for ≥ 12 outpatient visits, 0.76 for ≥ 1 ED visits and 0.73 for ≥ 1 acute hospitalizations. Despite adequate AUC and calibration, precision-recall curves showed suboptimal performance.
Conclusions
The final selected models per outcome can identify patients with future potentially preventable high healthcare utilization. However, identifying high-risk patients with MLTC and substantiating if they are most in need of integrated care remains challenging. Further research is warranted investigating whether patients with high healthcare utilization are indeed the most in need of integrated care and whether quantitively identified patients match the identification based on clinicians’ experience and judgment.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
In the context of investigating isostructural relationships between sulfates and monofluorophosphates, crystals of the double salts (NHsub.4 )sub.2 POsub.3 F·NHsub.4 NOsub.3 (AFP·AN) and (NHsub.4 ...)sub.2 XOsub.4 ·3NHsub.4 NOsub.3 (AX·3AN; X = Se, Cr) were grown from aqueous solutions and structurally characterized using X-ray diffraction and thermal analysis. Whereas the high-temperature forms of the two AX·3AN double salts are in fact isostructural with the sulfate analogue, AFP·AN crystallizes with a reduced amount of NHsub.4 NOsub.3 and thus has a unique crystal structure. Both AFP·AN and the two AX·3AN compounds exhibit reversible structural phase transitions. Upon cooling, the monofluorophosphate double salt transforms from the monoclinic room-temperature polymorph (I; P2sub.1 /n, Z = 4) to the intermediate triclinic polymorph (II; P1, Z = 4) that in turn transforms to the monoclinic low-temperature polymorph (III; P2sub.1 /n, Z = 4). The two phase transitions (I) → (II) and (II) → (III) are characterized by a significant increase of the unit cell volumes upon cooling. The two AX·3AN double salts transform upon cooling from a disordered monoclinic crystal structure (P2sub.1 , Z = 2) to a monoclinic polymorph with a doubled unit cell (P2sub.1 /c, Z = 4). Such a phase transition is not observed for the sulfate analogue. All molecular moieties are fully ordered at −93 °C for the selenate double salt, whereas one of the nitrate anions remains disordered for the chromate double salt even at −173 °C. In all AFP·AN and AX·3AN crystal structures, the nitrate anions play a crucial role during the phase transitions, and an extensive network of N–H···O hydrogen-bonding interactions is responsible for the cohesion of the crystal.
Prolonged exposure to HIV and anti-retroviral therapy (ART) has been linked with endothelial cell activation which subsequently predisposes people living with HIV (PLWH) to cardiovascular diseases. ...Serum biomarkers of endothelial cell activation such as E-Selectin and endothelial cell-specific molecule-1 (ESM-1) could aid in early detection of PLWH at a risk of cardiovascular diseases. However, there is a paucity of data on these biomarkers like E-selectin and endothelial cell-specific molecule-1 (ESM-1) among PLWH on long term ART (≥ 10 years) in Uganda. The aim of this study is to determine the serum levels of these biomarkers in this population.
This was a cross-sectional study where we randomly sampled 73 stored serum samples of PLWH who were enrolled in the Infectious Diseases Institute (IDI) ART long term (ALT cohort). We measured serum levels of E-selectin and ESM-1 by ELISA. Data was summarized using median and interquartile range. Inferential statistics were performed to determine predictors of elevated levels of E-selectin.
Of the 73 samples analyzed, 38 (52.1%) were from female participants. The mean age was 54 ± 9.0 years. Twenty participants (27.4%) had a history of smoking while 52 (71.2%) had a history of alcohol intake. Twenty-five (34.3%) of the participants were overweight whereas 4 (5.6%) were obese. Fifty-four (74%) had an undetectable viral load (≤ 0 copies/ml) and the mean duration of ART at the time of sampling (2014/2015) was 10.4 ± 0.4 years. While serum levels of ESM-1 were not detectable in any of our samples, the median E-selectin levels was 147.6 μm/L ranging from 8.44 μm/L and 1,979.36 μm/L. Sixty-seven participants (91.8%) had elevated levels of E-selectin (> 39 μm/L). CD4 count > 500 cells/µl compared to lower counts was a predictor of elevated levels of E-Selectin (adjusted Odd Ratio 12.5, 95% CI (1.03 - 149.95, p < 0.05).
The majority (91.8%) of PLWH on long term ART had elevated levels of E-selectin. Having high CD4 count (> 500 cells/µl) was predictive of elevated levels of E-Selectin. Future work should longitudinally assess the trend of levels of E-selectin and ESM-1 while assessing for cardiovascular diseases endpoint.
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