The effect of the da Vinci® Vessel Sealer on robot-assisted laparoscopic prostatectomy complications.

The da Vinci® Vessel Sealer is a major contributor to the total cost of robot-assisted laparoscopic prostatectomy (RALP). We aimed to assess whether the use of the Vessel Sealer is associated with better surgical outcomes in a population of patients that underwent RALP with lymphadenectomy. We tested whether the use of the Vessel Sealer is associated with the development of lymphocele and/or other surgical outcomes. Most surgeons used the Vessel Sealer in almost all or almost no patients. Thus, to avoid the potential confounding variable of surgeon skill, we performed the initial analyses using data from a single surgeon who changed practice over time, and then using the entire population. Overall, the Vessel Sealer was used in 500 (36%) RALPs. Surgeon 1 performed 492 surgeries, and used the Vessel Sealer in 191 (39%). The Vessel Sealer was not associated with better surgical outcomes in patients operated on by Surgeon 1. The odds ratio for development of lymphocele was 1.95 (95% confidence interval [CI] 0.57-6.75). In the entire population, use of the sealer was significantly associated with a very small reduction of blood loss (22 cc, CI 13-30) but with a 32-min increase in the operating room time (CI 26-37). Use of the Vessel Sealer will have, at best, a very small effect on RALP outcomes that is of highly questionable relevance given its cost. In light of these results, the Vessel Sealer will only be used at our institution in the context of clinical trials.

Within-subject changes in methylome profile identify individual signatures of early-life adversity, with a potential to predict neuropsychiatric outcome.

Background: Adverse early-life experiences (ELA), including poverty, trauma and neglect, affect a majority of the world's children. Whereas the impact of ELA on cognitive and emotional health throughout the lifespan is well-established, it is not clear how distinct types of ELA influence child development, and there are no tools to predict for an individual child their vulnerability or resilience to the consequences of ELAs. Epigenetic markers including DNA-methylation profiles of peripheral cells may encode ELA and provide a predictive outcome marker. However, the rapid dynamic changes in DNA methylation in childhood and the inter-individual variance of the human genome pose barriers to identifying profiles predicting outcomes of ELA exposure. Here, we examined the relation of several dimensions of ELA to changes of DNA methylation, using a longitudinal within-subject design and a high threshold for methylation changes in the hope of mitigating the above challenges. Methods: We analyzed DNA methylation in buccal swab samples collected twice for each of 110 infants: neonatally and at 12 months. We identified CpGs differentially methylated across time, calculated methylation changes for each child, and determined whether several indicators of ELA associated with changes of DNA methylation for individual infants. We then correlated select dimensions of ELA with methylation changes as well as with measures of executive function at age 5 years. We examined for sex differences, and derived a sex-dependent 'impact score' based on sites that most contributed to the methylation changes. Findings: Setting a high threshold for methylation changes, we discovered that changes in methylation between two samples of an individual child reflected age-related trends towards augmented methylation, and also correlated with executive function years later. Among the tested factors and ELA dimensions, including income to needs ratios, maternal sensitivity, body mass index and sex, unpredictability of parental and household signals was the strongest predictor of executive function. In girls, an interaction was observed between a measure of high early-life unpredictability and methylation changes, in presaging executive function. Interpretation: These findings establish longitudinal, within-subject changes in methylation profiles as a signature of some types of ELA in an individual child. Notably, such changes are detectable beyond the age-associated DNA methylation dynamics. Future studies are required to determine if the methylation profile changes identified here provide a predictive marker of vulnerabilities to poorer cognitive and emotional outcomes.

Role of ATP in the RNA Translocation Mechanism of SARS-CoV-2 NSP13 Helicase.

The COVID-19 pandemic has demonstrated the need to develop potent and transferable therapeutics to treat coronavirus infections. Numerous antiviral targets are being investigated, but nonstructural protein 13 (nsp13) stands out as a highly conserved and yet understudied target. Nsp13 is a superfamily 1 (SF1) helicase that translocates along and unwinds viral RNA in an ATP-dependent manner. Currently, there are no available structures of nsp13 from SARS-CoV-1 or SARS-CoV-2 with either ATP or RNA bound, which presents a significant hurdle to the rational design of therapeutics. To address this knowledge gap, we have built models of SARS-CoV-2 nsp13 in Apo, ATP, ssRNA and ssRNA+ATP substrate states. Using 30 µs of a Gaussian-accelerated molecular dynamics simulation (at least 6 µs per substrate state), these models were confirmed to maintain substrate binding poses that are similar to other SF1 helicases. A Gaussian mixture model and linear discriminant analysis structural clustering protocol was used to identify key structural states of the ATP-dependent RNA translocation mechanism. Namely, four RNA-nsp13 structures are identified that exhibit ATP-dependent populations and support the inchworm mechanism for translocation. These four states are characterized by different RNA-binding poses for motifs Ia, IV, and V and suggest a power stroke-like motion of domain 2A relative to domain 1A. This structural and mechanistic insight of nsp13 RNA translocation presents novel targets for the further development of antivirals.

Use of bot and content flags to limit the spread of misinformation among social networks: a behavior and attitude survey.

The COVID-19 infodemic is driven partially by Twitter bots. Flagging bot accounts and the misinformation they share could provide one strategy for preventing the spread of false information online. This article reports on an experiment (N = 299) conducted with participants in the USA to see whether flagging tweets as coming from bot accounts and as containing misinformation can lower participants' self-reported engagement and attitudes about the tweets. This experiment also showed participants tweets that aligned with their previously held beliefs to determine how flags affect their overall opinions. Results showed that flagging tweets lowered participants' attitudes about them, though this effect was less pronounced in participants who frequently used social media or consumed more news, especially from Facebook or Fox News. Some participants also changed their opinions after seeing the flagged tweets. The results suggest that social media companies can flag suspicious or inaccurate content as a way to fight misinformation. Flagging could be built into future automated fact-checking systems and other misinformation abatement strategies of the social network analysis and mining community.

The Role of Hydrophobicity in the Stability and pH-Switchability of (RXDX)4 and Coumarin-(RXDX)4 Conjugate ß-Sheets.

pH-Switchable, self-assembling materials are of interest in biological imaging and sensing applications. Here we propose that combining the pH-switchability of RXDX (X = Ala, Val, Leu, Ile, Phe) peptides and the optical properties of coumarin creates an ideal candidate for these materials. This suggestion is tested with a thorough set of all-atom molecular dynamics simulations. We first investigate the dependence of pH-switchabiliy on the identity of the hydrophobic residue, X, in the bare (RXDX)4 systems. Increasing the hydrophobicity stabilizes the fiber which, in turn, reduces the pH-switchabilty of the system. This behavior is found to be somewhat transferable to systems in which a single hydrophobic residue is replaced with a coumarin containing amino acid. In this case, conjugates with X = Ala are found to be unstable at both pHs, while conjugates with X = Val, Leu, Ile, and Phe are found to form stable ß-sheets at least at neutral pH. The coumarin-(RFDF)4 conjugate is found to have the largest relative entropy value of 0.884 ± 0.001 between neutral and acidic coumarin ordering distributions. Thus, we posit that coumarin-(RFDF)4 containing peptide sequences are ideal candidates for pH-sensing bioelectronic materials.

PBX-WNT-P63-IRF6 pathway in nonsyndromic cleft lip and palate.

Nonsyndromic cleft lip and palate (NSCLP) is one of the most common craniofacial anomalies in humans, affecting more than 135,000 newborns worldwide. NSCLP has a multifactorial etiology with more than 50 genes postulated to play an etiologic role. The genetic pathway comprised of Pbx-Wnt-p63-Irf6 genes was shown to control facial morphogenesis in mice and proposed as a regulatory pathway for NSCLP. Based on these findings, we investigated whether variation in PBX1, PBX2, and TP63, and their proposed interactions were associated with NSCLP. Fourteen single nucleotide variants (SNVs) in/nearby PBX1, PBX2, and TP63 were genotyped in 780 NSCLP families of nonHispanic white (NHW) and Hispanic ethnicities. Family-based association tests were performed for individual SNVs stratified by ethnicity and family history of NSCLP. Gene-gene interactions were also tested. A significant association was found for PBX2 rs3131300 and NSCLP in combined Hispanic families (p = .003) while nominal association was found for TP63 rs9332461 in multiplex Hispanic families (p = .005). Significant haplotype associations were observed for PBX2 in NHW (p = .0002) and Hispanic families (p = .003), and for TP63 in multiplex Hispanic families (.003). An independent case-control group was used to validate findings, and significant associations were found with PBX1 rs6426870 (p = .007) and TP63 rs9332461 (p = .03). Gene-gene interactions were detected between PBX1/PBX2/TP63 with IRF6 in NHW families, and between PBX1 with WNT9B in both NHW and Hispanic families (p < .0018). This study provides the first evidence for a role of PBX1 and PBX2, additional evidence for the role of TP63, and support for the proposed PBX-WNT-TP63-IRF6 regulatory pathway in the etiology of NSCLP.

Thiol-ene synthesis and characterization of lithium bis(malonato)borate single-ion conducting gel polymer electrolytes.

The development of high capacity anodes and high voltage cathodes for advanced lithium-ion batteries motivates the search for new polymer electrolytes that exhibit superior electrochemical stabilities and high ionic conductivities. We report a convenient, three-step synthesis of lithium bis(non-8-enyl-malonato)borate (LiBNMB) as a α,ω-diene monomer, which undergoes thermally initiated thiol-ene crosslinking polymerizations in propylene carbonate to yield gel polymer electrolytes with high lithium ion concentrations (∼0.9 M). By conducting these crosslinking polymerizations using mixtures of di- and tri-thiols and LiBNMB with [thiol] : [ene] = 1 : 1, we synthesized a series of gel networks with dynamic elastic moduli ranging from G' = 40-79 kPa that increase monotonically with trifunctional crosslinker content. While ionic conductivities for these polymer gels measured by electrochemical impedance spectroscopy at 22 °C are σ = 0.82-2.5 × 10-6 S cm-1, we show that the conductivity of propylene carbonate-solvated lithium ions though the bulk of these gel electrolytes is 8.5 × 10-5 S cm-1 independent of crosslinker density. However, the conductivities of the gel interfaces depend sensitively on crosslinker content, suggesting the importance of segmental rearrangement dynamics at the electrode interface in limiting the rate of ion motion. Thus, the design of highly conductive polymer electrolytes for advanced batteries demands careful design of both the internal and interfacial properties of these new materials.

Impact of self-reported data on the acquisition of multi-generational family history and lifestyle factors among women seen in a high-risk breast screening program: a focus on modifiable risk factors and genetic referral.

BACKGROUND: The phrase "high-risk for breast cancer" is used to identify various groups at elevated cancer risk, and the appropriate surveillance and risk-reducing strategies differ based on the etiology of risk. Here, we review the utility of patient-reported data to capture women with modifiable lifestyle risk factors and those suitable for genetic counseling referral. METHODS: Patient-reported data from a web-based survey were used to capture personal history, multi-generational family history, and lifestyle factors (body mass index, alcohol consumption, physical activity). Responses were tabulated, and percentage of patients who met criteria for possible intervention calculated. RESULTS: 1277 women completed the survey from October 2014 to December 2015. Women were considered high risk for a combination of the following: family history of breast and/or ovarian cancer (77%), history of atypical hyperplasia or lobular carcinoma in situ (35%), known breast cancer-related gene mutation (11%). Based on self-reported data, 65% qualified for genetic evaluation but 40% reporting no prior testing. Only half of the population met national physical activity recommendations, nearly 40% were overweight/obese, and 18% reported consuming ≥1 alcoholic beverage per day. CONCLUSIONS: Among women followed in a high-risk breast surveillance program, there is considerable opportunity for improved genetic referral and awareness of modifiable lifestyle factors based on self-reported data as 60% of respondents reported a possible area for intervention. While risk reduction associated with lifestyle changes is modest in comparison to chemoprevention or surgery, such changes are practically without risk, minimally expensive, and provide innumerable secondary health benefits.

A 10-Item Checklist Improves Reporting of Critical Procedural Elements during Transurethral Resection of Bladder Tumor.

PURPOSE: Previous studies have demonstrated significant variation in recurrence rates after transurethral resection of bladder tumor, likely due to differences in surgical quality. We sought to create a framework to define, measure and improve the quality of transurethral resection of bladder tumor using a surgical checklist. MATERIALS AND METHODS: We formed a multi-institutional group of urologists with expertise with bladder cancer and identified 10 critical items that should be performed during every high quality transurethral bladder tumor resection. We prospectively implemented a 10-item checklist into practice and reviewed the operative reports of such resections performed before and after implementation. Results at all institutions were combined in a meta-analysis to estimate the overall change in the mean number of items documented. RESULTS: The operative notes for 325 transurethral bladder tumor resections during checklist use were compared to those for 428 performed before checklist implementation. Checklist use increased the mean number of items reported from 4.8 to 8.0 per resection, resulting in a mean increase of 3.3 items (95% CI 1.9-4.7) on meta-analysis. With the checklist the percentage of reports that included all 10 items increased from 0.5% to 27% (p <0.0001). Surgeons who reported more checklist items tended to have a slightly higher proportion of biopsies containing muscle, although not at conventional significance (p = 0.062). CONCLUSIONS: The use of a 10-item checklist during transurethral resection of bladder tumor improved the reporting of critical procedural elements. Although there was no clear impact on the inclusion of muscle in the specimen, checklist use may enhance surgeon attention to important aspects of the procedure and be a lever for quality improvement.

Managing 'tail liability'.

To reduce and control their level of tail liability, hospitals should: Utilize a self-insurance vehicle; Consider combined limits between the hospital and physicians; Communicate any program changes to the actuary, underwriter, and auditor; Continue risk management and safety practices; Ensure credit is given to the organization's own medical malpractice program.

Azido push-pull fluorogens photoactivate to produce bright fluorescent labels.

Dark azido push-pull chromophores have the ability to be photoactivated to produce bright fluorescent labels suitable for single-molecule imaging. Upon illumination, the aryl azide functionality in the fluorogens participates in a photochemical conversion to an aryl amine, thus restoring charge-transfer absorption and fluorescence. Previously, we reported that one compound, DCDHF-V-P-azide, was photoactivatable. Here, we demonstrate that the azide-to-amine photoactivation process is generally applicable to a variety of push-pull chromophores, and we characterize the photophysical parameters including photoconversion quantum yield, photostability, and turn-on ratio. Azido push-pull fluorogens provide a new class of photoactivatable single-molecule probes for fluorescent labeling and super-resolution microscopy. Lastly, we demonstrate that photoactivated push-pull dyes can insert into bonds of nearby biomolecules, simultaneously forming a covalent bond and becoming fluorescent (fluorogenic photoaffinity labeling).

Cyclic guanidine organic catalysts: what is magic about triazabicyclodecene?

The bicyclic guanidine 1,5,7- triazabicyclo[4.4.0]dec-5-ene (TBD) is an effective organocatalyst for the formation of amides from esters and primary amines. Mechanistic and kinetic investigations support a nucleophilic mechanism where TBD reacts reversibly with esters to generate an acyl-TBD intermediate that acylates amines to generate the amides. Comparative investigations of the analogous bicyclic guanidine 1,4,6-triazabicyclo[3.3.0]oct-4-ene (TBO) reveal it to be a much less active acylation catalyst than TBD. Theoretical and mechanistic studies imply that the higher reactivity of TBD is a consequence of both its higher basicity and nucleophilicity than TBO as well as the high reactivity of the acyl-TBD intermediate, which is sterically prevented from adopting a planar amide structure.

DCDHF fluorophores for single-molecule imaging in cells.

There is a persistent need for small-molecule fluorescent labels optimized for single-molecule imaging in the cellular environment. Application of these labels comes with a set of strict requirements: strong absorption, efficient and stable emission, water solubility and membrane permeability, low background emission, and red-shifted absorption to avoid cell autofluorescence. We have designed and characterized several fluorophores, termed "DCDHF" fluorophores, for use in live-cell imaging based on the push-pull design: an amine donor group and a 2-dicyanomethylene-3-cyano-2,5-dihydrofuran (DCDHF) acceptor group, separated by a pi-rich conjugated network. In general, the DCDHF fluorophores are comparatively photostable, sensitive to local environment, and their chemistries and photophysics are tunable to optimize absorption wavelength, membrane affinity, and solubility. Especially valuable are fluorophores with sophisticated photophysics for applications requiring additional facets of control, such as photoactivation. For example, we have reengineered a red-emitting DCDHF fluorophore so that it is dark until photoactivated with a short burst of low-intensity violet light. This molecule and its relatives provide a new class of bright photoactivatable small-molecule fluorophores, which are needed for super-resolution imaging schemes that require active control (here turning-on) of single-molecule emission.

Improved synthesis of DCDHF fluorophores with maleimide functional groups.

A group of dicyanodihydrofuran (DCDHF) fluorophores with thiol-reactive maleimide functionality has been synthesized. One of the methods involves aromatic nucleophilic substitution reaction between an arylfluoride containing DCDHF and an amine containing protected maleimide. An alternative and generally useful method involves combination of the Mitsunobu reaction of a DCDHF-OH with a furan or 2-methylfuran protected maleimide and then subsequent retro Diels-Alder reaction.

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution.

Six measures of evolutionary change in the human genome were studied, three derived from the aligned human and mouse genomes in conjunction with the Mouse Genome Sequencing Consortium, consisting of (1) nucleotide substitution per fourfold degenerate site in coding regions, (2) nucleotide substitution per site in relics of transposable elements active only before the human-mouse speciation, and (3) the nonaligning fraction of human DNA that is nonrepetitive or in ancestral repeats; and three derived from human genome data alone, consisting of (4) SNP density, (5) frequency of insertion of transposable elements, and (6) rate of recombination. Features 1 and 2 are measures of nucleotide substitutions at two classes of "neutral" sites, whereas 4 is a measure of recent mutations. Feature 3 is a measure dominated by deletions in mouse, whereas 5 represents insertions in human. It was found that all six vary significantly in megabase-sized regions genome-wide, and many vary together. This indicates that some regions of a genome change slowly by all processes that alter DNA, and others change faster. Regional variation in all processes is correlated with, but not completely accounted for, by GC content in human and the difference between GC content in human and mouse.