In situ electrochemical regeneration of nanogap hotspots for continuously reusable ultrathin SERS sensors.

Surface-enhanced Raman spectroscopy (SERS) harnesses the confinement of light into metallic nanoscale hotspots to achieve highly sensitive label-free molecular detection that can be applied for a broad range of sensing applications. However, challenges related to irreversible analyte binding, substrate reproducibility, fouling, and degradation hinder its widespread adoption. Here we show how in-situ electrochemical regeneration can rapidly and precisely reform the nanogap hotspots to enable the continuous reuse of gold nanoparticle monolayers for SERS. Applying an oxidising potential of +1.5 V (vs Ag/AgCl) for 10 s strips a broad range of adsorbates from the nanogaps and forms a metastable oxide layer of few-monolayer thickness. Subsequent application of a reducing potential of -0.80 V for 5 s in the presence of a nanogap-stabilising molecular scaffold, cucurbit[5]uril, reproducibly regenerates the optimal plasmonic properties with SERS enhancement factors ≈106. The regeneration of the nanogap hotspots allows these SERS substrates to be reused over multiple cycles, demonstrating ≈5% relative standard deviation over at least 30 cycles of analyte detection and regeneration. Such continuous and reliable SERS-based flow analysis accesses diverse applications from environmental monitoring to medical diagnostics.

Controlling Atomic-Scale Restructuring and Cleaning of Gold Nanogap Multilayers for Surface-Enhanced Raman Scattering Sensing.

We demonstrate the reliable creation of multiple layers of Au nanoparticles in random close-packed arrays with sub-nm gaps as a sensitive surface-enhanced Raman scattering substrate. Using oxygen plasma etching, all the original molecules creating the nanogaps can be removed and replaced with scaffolding ligands that deliver extremely consistent gap sizes below 1 nm. This allows precision tailoring of the chemical environment of the nanogaps which is crucial for practical Raman sensing applications. Because the resulting aggregate layers are easily accessible from opposite sides by fluids and by light, high-performance fluidic sensing cells are enabled. The ability to cyclically clean off analytes and reuse these films is shown, exemplified by sensing of toluene, volatile organic compounds, and paracetamol, among others.

A low-tech method for monitoring survival and growth of coral transplants at a boutique restoration site.

Background: Coral reef restoration projects are becoming a popular corporate environmental responsibility activity at hotel resorts. Such involvement of private businesses offers the potential to expand restoration into a new socioeconomic sector. However, the scarcity of user-friendly monitoring methods for hotel staff, but robust enough to detect changes over time, hinders the ability to quantify the success or failure of the restoration activity. Here, we present a monitoring method of easy application by hotel staff, without scientific training, using the standard resources available at a hotel resort. Methods: Survival and growth of coral transplants were evaluated over 1 year at a boutique coral reef restoration site. The restoration was tailored to the needs of a hotel resort in Seychelles, Indian Ocean. A total of 2,015 nursery-grown corals of branching (four genera, 15 species), massive (16 genera, 23 species), and encrusting (seven genera, seven species) growth types were transplanted to a 1-3 m deep degraded patch reef. A unique cement mix was used to transplant corals onto the hard substrate. On the north side of each coral selected for monitoring, we attached an 8.2 cm × 8.2 cm reflective tile. We used reflective tiles instead of numbered tags due to the expected amount of biofouling growing on the tag surface. Every coral was recorded with top view photography (perpendicular to the plane of coral attachment), with the reflective square in the field of view. We drafted a map of the site to facilitate navigation and re-sighting of the monitored colonies. Then, we developed a simple monitoring protocol for hotel staff. Using the map, and the reflective tiles, the divers located the coral colonies, recorded status (alive, dead, bleaching), and took a photograph. We measured the two-dimensional coral planar area and the change in colony size over time using contour tissue measurements of photographs. Results: The monitoring method was robust enough to detect the expected survival of coral transplants, with encrusting and massive corals outperforming branching corals. Survival of encrusting and massive corals was higher (50%-100%) than branching corals (16.6%-83.3%). The change in colony size was 10.1 cm2 ± 8.8 (SE). Branching coral survivors grew faster than massive/encrusting corals. A comprehensive approach to the boutique restoration monitoring experiment would have included comparisons with a control patch reef with a similar species composition to the coral transplants. However, the ability to monitor such a control site, in addition to the restoration site, was beyond the logistic capabilities of the hotel staff, and we were limited to monitoring survival and growth within the restoration site. We conclude that science-based boutique coral reef restoration, tailored to the needs of a hotel resort, combined with a simple monitoring method, can provide a framework for involving hotels as partners in coral reef restoration worldwide.

Delays in Diagnosis and Treatment of Bacterial Meningitis in NYC: Retrospective Cohort Analysis.

Community-acquired bacterial meningitis (CABM) morbidity and mortality remains high in those infected. Rapid diagnosis and treatment is paramount to reducing mortality and improving outcome. This retrospective cohort study aims to assess the time from presentation to diagnosis and treatment of vaccine preventable CABM as well as identify possible factors associated with delays in diagnosis and antibiotic administration. A retrospective chart review was conducted of individuals who presented to Columbia University Irving Medical Center (CUIMC), Children's Hospital of New York (CHONY), Mount Sinai Medical Center, and Weill Cornell Medical Center with BM due to Haemophilus influenzae type B, Streptococcus pneumoniae, and Neisseria meningitidis between January 1, 2012 and December 31, 2017. Diagnosis was delayed by more than 8 hours in 13 patients (36.1%) and 5 individuals (13.9%) had a delay of 4 hours or more from presentation to the administration of antibiotics with appropriate CNS coverage. All of these patients were also initially misdiagnosed at an outpatient clinic, outside hospital, or emergency department. This retrospective study identified febrile and/or viral infections not otherwise specified and otitis media as the most common misdiagnoses underlying delays from presentation to diagnosis and to antibiotic treatment in those with BM.

Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance.

Corals from the northern Red Sea, in particular the Gulf of Aqaba (GoA), have exceptionally high bleaching thresholds approaching >5℃ above their maximum monthly mean (MMM) temperatures. These elevated thresholds are thought to be due to historical selection, as corals passed through the warmer Southern Red Sea during recolonization from the Arabian Sea. To test this hypothesis, we determined thermal tolerance thresholds of GoA versus central Red Sea (CRS) Stylophora pistillata corals using multi-temperature acute thermal stress assays to determine thermal thresholds. Relative thermal thresholds of GoA and CRS corals were indeed similar and exceptionally high (~7℃ above MMM). However, absolute thermal thresholds of CRS corals were on average 3℃ above those of GoA corals. To explore the molecular underpinnings, we determined gene expression and microbiome response of the coral holobiont. Transcriptomic responses differed markedly, with a strong response to the thermal stress in GoA corals and their symbiotic algae versus a remarkably muted response in CRS colonies. Concomitant to this, coral and algal genes showed temperature-induced expression in GoA corals, while exhibiting fixed high expression (front-loading) in CRS corals. Bacterial community composition of GoA corals changed dramatically under heat stress, whereas CRS corals displayed stable assemblages. We interpret the response of GoA corals as that of a resilient population approaching a tipping point in contrast to a pattern of consistently elevated thermal resistance in CRS corals that cannot further attune. Such response differences suggest distinct thermal tolerance mechanisms that may affect the response of coral populations to ocean warming.

Fully integrated 3D-printed electrochemical cell with a modified inkjet-printed Ag electrode for voltammetric nitrate analysis.

To address the need for low-cost analytical tools for on-site aquaculture water quality monitoring, miniaturized electrochemical sensor systems can be readily fabricated using additive manufacturing technologies such as 3D printing and inkjet printing. In this work, we report the design and fabrication of an additively manufactured electrochemical platform featuring a reusable 3D-printed electrochemical cell with integrated reference and counter electrodes, and a replaceable inkjet-printed Ag (IJP-Ag) working electrode. The electrochemical cell was 3D-printed with acrylonitrile butadiene styrene (ABS) filament and features a 3D-printed ABS-carbon counter electrode and a Ag|AgCl|gel-KCl reference electrode with a 3D-printed porous junction directly integrated along the sides of the sample compartment. The application of the integrated cell is demonstrated with the analysis of nitrate ions on the IJP-Ag electrode, which was modified with electrodeposited nanostructured Ag to enhance sensitivity to nitrate reduction. Linear sweep voltammetry (LSV) was successfully applied to detect nitrate with a LOD of 1.40 ppm and a sensitivity of 0.2086 µA ppm-1 in a background of artificial brackish aquaculture water (pH 8.0). The sensor response showed intra- and inter-electrode reproducibility and no significant interferences to most of the commonly encountered cations and anions in brackish water. The electrochemical sensor system was also applied to nitrate determination in real aquaculture water samples and demonstrated no significant differences with the results obtained using the standard spectrophotometric method at a 95% confidence level. Our results show how additive manufacturing is a promising approach to readily fabricate fit-for-purpose, low-cost miniaturized electrochemical sensor systems for point-of-use applications.

Clinical and electrographic features of persistent seizures and status epilepticus associated with anti-NMDA receptor encephalitis (anti-NMDARE).

Based on a multicenter cohort of people with anti-NMDA receptor encephalitis (anti-NMDARE), we describe seizure phenotypes, electroencephalographic (EEG) findings, and anti-seizure treatment strategies. We also investigated whether specific electrographic features are associated with persistent seizures or status epilepticus after acute presentation. In this retrospective cohort study, we reviewed records of children and adults with anti-NMDARE between 2010 and 2014 who were included in the Rare Epilepsy of New York City database, which included the text of physician notes from five academic medical centers. Clinical history (e.g., seizure semiology) and EEG features (e.g., background organization, slowing, epileptiform activity, seizures, sleep architecture, extreme delta brush) were abstracted. We compared clinical features associated with persistent seizures (ongoing seizures after one month from presentation) and status epilepticus, using bivariate and multivariable analyses. Among the 38 individuals with definite anti-NMDARE, 32 (84%) had seizures and 29 (76%) had seizures captured on EEG. Electrographic-only seizures were identified in five (13%) individuals. Seizures started at a median of four days after initial symptoms (IQR: 3-6 days). Frontal lobe-onset focal seizures were most common (n=12; 32%). Most individuals (31/38; 82%) were refractory to anti-seizure medications. Status epilepticus was associated with younger age (15 years [9-20] vs. 23 years [18-27]; p=0.04) and Hispanic ethnicity (30 [80%] vs. 8 [36%]; p=0.04). Persistent seizures (ongoing seizures after one month from presentation) were associated with younger age (nine years [3-14] vs. 22 years [15-28]; p<0.01). Measured electrographic features were not associated with persistent seizures. Seizures associated with anti-NMDARE are primarily focal seizures originating in the frontal lobes. Younger patients may be at increased risk of epileptogenesis and status epilepticus. Continuous EEG monitoring helps identify subclinical seizures, but specific EEG findings may not predict the severity or persistence of seizures during hospitalization.

Rapid Diagnosis of Meningococcal Meningitis in a Patient With Familial Mediterranean Fever by the FilmArray Meningitis/Encephalitis Panel: A Case Report.

Familial Mediterranean fever (FMF) is a rare autoinflammatory disorder of the innate immune system. Patients with innate immune system defects are at a high risk of meningococcal disease, although it is unclear if patients with FMF also have increased susceptibility to invasive infection. Herein, we present a diagnostically challenging case of a male adolescent with a past medical history of FMF stabilized on colchicine who presented with some of the early clinical features of community-acquired bacterial meningitis. To our knowledge, this is the first case of meningococcal meningitis in a patient with FMF diagnosed with the FilmArray Meningitis/Encephalitis (ME) Panel. This case report demonstrates that rapid detection of Neisseria meningitidis by the ME Panel can aid in the early diagnosis and prompt treatment of patients with suspected meningitis and may be the only positive test in patients with early presentation and/or prior antimicrobial therapy.

Coral reef restoration efforts in Latin American countries and territories.

Coral reefs worldwide are degrading due to climate change, overfishing, pollution, coastal development, coral bleaching, and diseases. In areas where the natural recovery of an ecosystem is negligible or protection through management interventions insufficient, active restoration becomes critical. The Reef Futures symposium in 2018 brought together over 400 reef restoration experts, businesses, and civil organizations, and galvanized them to save coral reefs through restoration or identify alternative solutions. The symposium highlighted that solutions and discoveries from long-term and ongoing coral reef restoration projects in Spanish-speaking countries in the Caribbean and Eastern Tropical Pacific were not well known internationally. Therefore, a meeting of scientists and practitioners working in these locations was held to compile the data on the extent of coral reef restoration efforts, advances and challenges. Here, we present unpublished data from 12 coral reef restoration case studies from five Latin American countries, describe their motivations and techniques used, and provide estimates on total annual project cost per unit area of reef intervened, spatial extent as well as project duration. We found that most projects used direct transplantation, the coral gardening method, micro-fragmentation or larval propagation, and aimed to optimize or scale-up restoration approaches (51%) or provide alternative, sustainable livelihood opportunities (15%) followed by promoting coral reef conservation stewardship and re-establishing a self-sustaining, functioning reef ecosystems (both 13%). Reasons for restoring coral reefs were mainly biotic and experimental (both 42%), followed by idealistic and pragmatic motivations (both 8%). The median annual total cost from all projects was $93,000 USD (range: $10,000 USD-$331,802 USD) (2018 dollars) and intervened a median spatial area of 1 ha (range: 0.06 ha-8.39 ha). The median project duration was 3 years; however, projects have lasted up to 17 years. Project feasibility was high with a median of 0.7 (range: 0.5-0.8). This study closes the knowledge gap between academia and practitioners and overcomes the language barrier by providing the first comprehensive compilation of data from ongoing coral reef restoration efforts in Latin America.

Central nervous system (CNS) enterovirus infections: A single center retrospective study on clinical features, diagnostic studies, and outcome.

Enteroviruses (EV) are responsible for a large number of meningoencephalitis cases, especially in children. The objective of this study was to identify modes of diagnosis including the significance of respiratory and cerebrospinal fluid samples, associated clinical characteristics, inpatient management, and outcome of individuals with EV infections of the central nervous system (CNS). Electronic medical records of individuals with enterovirus infections of the CNS who presented to the Columbia University Irving Medical Center and Children's Hospital of New York between January 1, 2012 and December 31, 2017 were reviewed retrospectively for demographic, epidemiological, and clinical data. The median age overall was 1.7 months (interquartile range 14 years) and most (62.4%) were male. The majority of CNS infections presented as meningitis (95.7%) and occurred in the summer (45.2%) and fall seasons (37.6%). Eighty-five cases (91.4%) demonstrated EV positivity in cerebrospinal fluid, thirty cases (32.3%) exhibited both cerebrospinal fluid and respiratory positivity, and eight cases (8.6%) exhibited respiratory positivity with coinciding neurological findings. Eighty-nine individuals overall (95.7%) received antibiotics and 37 (39.8%) received antiviral treatment. All surviving individuals had favorable Modified Rankin Scores (MRS) within the zero to two ranges upon discharge. Testing respiratory samples in addition to cerebrospinal fluid was found to be an important diagnostic tool in EV-associated cases. While clinical outcomes were favorable for an overwhelming majority of cases, etiological understanding of CNS infections is essential for identifying ongoing and changing epidemiological patterns and aid in improving the diagnosis and treatment.

Socioeconomic Disparities in Chronic Physiologic Stress Are Associated With Brain Structure in Children.

BACKGROUND: Socioeconomic factors have been consistently linked with the structure of children's hippocampus and anterior cingulate cortex (ACC). Chronic stress-as indexed by hair cortisol concentration-may represent an important mechanism underlying these associations. Here, we examined associations between hair cortisol and children's hippocampal and ACC structure, including across hippocampal subfields, and whether hair cortisol mediated associations between socioeconomic background (family income-to-needs ratio, parental education) and the structure of these brain regions. METHODS: Participants were 5- to 9-year-old children (N = 94; 61% female) from socioeconomically diverse families. Parents and children provided hair samples that were assayed for cortisol. High-resolution, T1-weighted magnetic resonance imaging scans were acquired, and FreeSurfer 6.0 was used to compute hippocampal volume and rostral and caudal ACC thickness and surface area (n = 37 with both child hair cortisol and magnetic resonance imaging data; n = 41 with both parent hair cortisol and magnetic resonance imaging data). RESULTS: Higher hair cortisol concentration was significantly associated with smaller CA3 and dentate gyrus hippocampal subfield volumes but not with CA1 or subiculum volume. Higher hair cortisol was also associated with greater caudal ACC thickness. Hair cortisol significantly mediated associations between parental education level and CA3 and dentate gyrus volumes; lower parental education level was associated with higher hair cortisol, which in turn was associated with smaller volume in these subfields. CONCLUSIONS: These findings point to chronic physiologic stress as a potential mechanism through which lower parental education level leads to reduced hippocampal volume. Hair cortisol concentration may be an informative biomarker leading to more effective prevention and intervention strategies aimed at childhood socioeconomic disadvantage.

Hepatoportoenterostomy surgery technique.

Biliary atresia (BA) is a pathology that causes jaundice in children because of an obstruction of the obliterated biliary tract. Despite being considered a rare disease, the incidence can reach 1/2400 live births in the Pacific region. The etiology is unknown. If untreated, it will lead to cirrhosis and death. Early operation (within 60 days after birth) is the most important prognostic factor. The objective of this article is to present the technical description step by step of a hepatoportoenterostomy operation in a female 61 days of age with BA.

Testing animal-assisted cleaning prior to transplantation in coral reef restoration.

Rearing coral fragments in nurseries and subsequent transplantation onto a degraded reef is a common approach for coral reef restoration. However, if barnacles and other biofouling organisms are not removed prior to transplantation, fish will dislodge newly cemented corals when feeding on biofouling organisms. This behavior can lead to an increase in diver time due to the need to reattach the corals. Thus, cleaning nurseries to remove biofouling organisms such as algae and invertebrates is necessary prior to transplantation, and this cleaning constitutes a significant time investment in a restoration project. We tested a novel biomimicry technique of animal-assisted cleaning on nursery corals prior to transplantation at a coral reef restoration site in Seychelles, Indian Ocean. To determine whether animal-assisted cleaning was possible, preliminary visual underwater surveys were performed to quantify the fish community at the study site. Then, cleaning stations consisting of nursery ropes carrying corals and biofouling organisms, set at 0.3 m, 2 m, 4 m, 6 m and 8 m from the seabed, were placed at both the transplantation (treatment) site and the nursery (control) site. Remote GoPro video cameras recorded fish feeding at the nursery ropes without human disturbance. A reef fish assemblage of 32 species from 4 trophic levels (18.8% herbivores, 18.8% omnivores, 59.3% secondary consumers and 3.1% carnivores) consumed 95% of the barnacles on the coral nursery ropes placed 0.3 m above the seabed. Using this cleaning station, we reduced coral dislodgement from 16% to zero. This cleaning station technique could be included as a step prior to coral transplantation worldwide on the basis of location-specific fish assemblages and during the early nursery phase of sexually produced juvenile corals.

Computational and serologic analysis of novel and known viruses in species human adenovirus D in which serology and genomics do not correlate.

In November of 2007 a human adenovirus (HAdV) was isolated from a bronchoalveolar lavage (BAL) sample recovered from a biopsy of an AIDS patient who presented with fever, cough, tachycardia, and expiratory wheezes. To better understand the isolated virus, the genome was sequenced and analyzed using bioinformatic and phylogenomic analysis. The results suggest that this novel virus, which is provisionally named HAdV-D59, may have been created from multiple recombination events. Specifically, the penton, hexon, and fiber genes have high nucleotide identity to HAdV-D19C, HAdV-D25, and HAdV-D56, respectively. Serological results demonstrated that HAdV-D59 has a neutralization profile that is similar yet not identical to that of HAdV-D25. Furthermore, we observed a two-fold difference between the ability of HAdV-D15 and HAdV-D25 to be neutralized by reciprocal antiserum indicating that the two hexon proteins may be more similar in epitopic conformation than previously assumed. In contrast, hexon loops 1 and 2 of HAdV-D15 and HAdV-D25 share 79.13 and 92.56 percent nucleotide identity, respectively. These data suggest that serology and genomics do not always correlate.

Five genome sequences of subspecies B1 human adenoviruses associated with acute respiratory disease.

Five genomes of human subspecies B1 adenoviruses isolated from cases of acute respiratory disease have been sequenced and archived for reference. These include representatives of two prevalent genomic variants of HAdV-7, i.e., HAdV-7h and HAdV-7d2. The other three are HAdV-3/16, HAdV-16 strain E26, and HAdV-3+7 strain Takeuchi. All are recombinant genomes. Genomics and bioinformatics provide detailed views into the genetic makeup of these pathogens and insight into their molecular evolution. Retrospective characterization of particularly problematic older pathogens such as HAdV-7h (1987) and intriguing isolates such as HAdV-3+7 strain Takeuchi (1958) may provide clues to their phenotypes and serology and may suggest protocols for prevention and treatment.

Genomic characterization of human adenovirus 36, a putative obesity agent.

Increased levels of serum antibody titers against human adenovirus 36 (HAdV-D36) are associated with human obesity and experimental obesity in laboratory animals. While HAdV-D36 has been studied as an infectious agent implicated in obesity for over a decade, the complete genome sequence and its analysis have yet to be reported. A detailed analysis of the genome sequence of HAdV-D36 may be important to understand its role in obesity. Genomic and bioinformatic comparisons with other HAdVs identified differences that suggested unique functions. Global pairwise genome alignment with all sequenced human adenovirus D (HAdV-D) genomes revealed areas of nonconserved sequences in the hexon, E3 CR1 beta, E3 CR1 gamma, and fiber genes. Phylogenetic analysis of all HAdV-D36 proteins confirmed that this virus belongs to species Human adenovirus D. This genomic analysis of HAdV-D36 provides an important tool for comprehending the role that this unique adenovirus may play in human obesity. Low amino acid sequence identity in the E3 CR1 beta and CR1 gamma genes may suggest distinctive roles for these proteins. Furthermore, the predicted molecular models of the HAdV-D36 fiber protein seem to implicate a unique tissue tropism for HAdV-D36.

The revolution in viral genomics as exemplified by the bioinformatic analysis of human adenoviruses.

Over the past 30 years, genomic and bioinformatic analysis of human adenoviruses has been achieved using a variety of DNA sequencing methods; initially with the use of restriction enzymes and more currently with the use of the GS FLX pyrosequencing technology. Following the conception of DNA sequencing in the 1970s, analysis of adenoviruses has evolved from 100 base pair mRNA fragments to entire genomes. Comparative genomics of adenoviruses made its debut in 1984 when nucleotides and amino acids of coding sequences within the hexon genes of two human adenoviruses (HAdV), HAdV-C2 and HAdV-C5, were compared and analyzed. It was determined that there were three different zones (1-393, 394-1410, 1411-2910) within the hexon gene, of which HAdV-C2 and HAdV-C5 shared zones 1 and 3 with 95% and 89.5% nucleotide identity, respectively. In 1992, HAdV-C5 became the first adenovirus genome to be fully sequenced using the Sanger method. Over the next seven years, whole genome analysis and characterization was completed using bioinformatic tools such as blastn, tblastx, ClustalV and FASTA, in order to determine key proteins in species HAdV-A through HAdV-F. The bioinformatic revolution was initiated with the introduction of a novel species, HAdV-G, that was typed and named by the use of whole genome sequencing and phylogenetics as opposed to traditional serology. HAdV bioinformatics will continue to advance as the latest sequencing technology enables scientists to add to and expand the resource databases. As a result of these advancements, how novel HAdVs are typed has changed. Bioinformatic analysis has become the revolutionary tool that has significantly accelerated the in-depth study of HAdV microevolution through comparative genomics.