Biogeosciences Perspectives on Integrated, Coordinated, Open, Networked (ICON) Science.

This article is composed of three independent commentaries about the state of Integrated, Coordinated, Open, Networked (ICON) principles in the American Geophysical Union Biogeosciences section, and discussion on the opportunities and challenges of adopting them. Each commentary focuses on a different topic: (a) Global collaboration, technology transfer, and application (Section 2), (b) Community engagement, community science, education, and stakeholder involvement (Section 3), and (c) Field, experimental, remote sensing, and real-time data research and application (Section 4). We discuss needs and strategies for implementing ICON and outline short- and long-term goals. The inclusion of global data and international community engagement are key to tackling grand challenges in biogeosciences. Although recent technological advances and growing open-access information across the world have enabled global collaborations to some extent, several barriers, ranging from technical to organizational to cultural, have remained in advancing interoperability and tangible scientific progress in biogeosciences. Overcoming these hurdles is necessary to address pressing large-scale research questions and applications in the biogeosciences, where ICON principles are essential. Here, we list several opportunities for ICON, including coordinated experimentation and field observations across global sites, that are ripe for implementation in biogeosciences as a means to scientific advancements and social progress.

A wafer-scale fabrication method for three-dimensional plasmonic hollow nanopillars.

Access to nanofabrication strategies for crafting three-dimensional plasmonic structures is limited. In this work, a fabrication strategy to produce 3D plasmonic hollow nanopillars (HNPs) using Talbot lithography and I-line photolithography is introduced. This method is named subtractive hybrid lithography (SHL), and permits intermixed usage of nano-and-macroscale patterns. Sputter-redeposition of gold (Au) on the SHL resist pattern yields large areas of dense periodic Au-HNPs. These Au-HNPs are arranged in a square unit cell with a 250 nm pitch. The carefully controlled fabrication process resulted in Au-HNPs with nanoscale dimensions over the Au-HNP dimensions such as an 80 ± 2 nm thick solid base with a 133 ± 4 nm diameter, and a 170 ± 10 nm high nano-rim with a 14 ± 3 nm sidewall rim-thickness. The plasmonic optical response is assessed with FDTD-modeling and reveals that the highest field enhancement is at the top of the hollow nanopillar rim. The modeled field enhancement factor (EF) is compared to the experimental analytical field enhancement factor, which shows to pair up with ca. 103 < EF < 104 and ca. 103 < EF < 105 for excitation wavelengths of 633 and 785 nm. From a broader perspective, our results can stimulate the use of Au-HNPs in the fields of plasmonic sensors and spectroscopy.

The effect of coronavirus disease 2019 on the hearing system.

OBJECTIVE: This study aimed to evaluate different auditory regions with audiological tests, based on the presumption that there may be damage to the structures in the hearing system after coronavirus disease 2019. METHODS: Twenty individuals with no history of coronavirus disease 2019 and 27 individuals diagnosed with coronavirus disease 2019 were compared. Pure tone, speech and extended high-frequency audiometry, acoustic immitansmetry, transient evoked and distortion product otoacoustic emissions testing, and auditory brainstem response testing were conducted. RESULTS: The pure tone audiometry and extended high-frequency mean threshold values were higher in the coronavirus disease 2019 group. The transient evoked otoacoustic emissions signal-to-noise ratios were bilaterally lower at 4 kHz in individuals with a coronavirus disease 2019 history. In the auditory brainstem response test, only the interpeak latencies of waves III-V were significantly different between groups. CONCLUSION: Coronavirus disease 2019 may cause damage to the hearing system. Patients should be followed up in the long term with advanced audiological evaluation methods in order to determine the extent and level of damage.

Acute acetaminophene-induced hepatotoxicity and nephrotoxicity; therapeutic effect of dexmedetomidine.

OBJECTIVE AND BACKGROUND: Acute acetaminophen (APAP) overdose has been shown to cause toxicity and the primary treatment medication is N-acetylcysteine (NAC). Dexmedetomidine (DEX) is a sedative drug with known antioxidant properties. We researched whether DEX has an injury-reducing effect on toxicity. METHODS: Rats were divided into: Group I (control), Group II (APAP) Group III (NAC) Group IV (DEX) and Group V (NAC+DEX). Histopathologic investigations of tissues were performed and glutathione peroxidase (GSH-Px), catalase (CAT), malondialdehyde (MDA), myeloperoxidase (MPO) and beta trace protein (PGD2S) levels were studied in blood samples. RESULTS: DEX administration for hepatotoxicity and nephrotoxicity induced with APAP, caused a significant reduction in oxidative injury markers like MDA and MPO, a significant increase in GSH-Px level and a significant degree of amelioration in liver histopathologic scores. CONCLUSION: DEX administration for APAP toxicity causes a reduction in oxidative injury biomarkers, increased antioxidant biomarker levels and significant reduction in liver histopathologic scores. The beneficial effect of DEX use for detection of toxicity induced by acute APAP overdose, was shown in this study for the first time (Tab. 5, Fig. 2, Ref. 41).

Preoperative Vitamin D levels and respiratory complications of general anesthesia.

AIMS: This research aims to investigate whether there is a correlation between the respiratory complications occurring in patients under general anesthesia and preoperative Vitamin D levels. SETTINGS AND DESIGN: The study was a prospective observational study. MATERIALS AND METHODS: This study included 95 adult cases. The cases had total 25-hydroxyvitamin D (25OHD) levels identified in blood samples before the operation. Patients given routine general anesthesia and were assessed in terms of respiratory complications during anesthesia induction, extubation, anesthesia recovery, and the first 24-h postoperative. STATISTICAL ANALYSIS USED: The Shapiro-Wilk test, Student's-t-test, one-way ANOVA test, Pearson correlation coefficient, and Chi-square tests were used. RESULTS: The mean 25OHD vitamin level identified in the preoperative period was 13.00 ± 6.57 ng/mL, with 25OHD vitamin levels found to be significantly low in female cases compared to male cases (P < 0.05). There was a statistically significant negative relationship between age and 25OHD vitamin levels identified (P = 0.045). When assessed in terms of surgery types, there was no significant difference found in Vitamin D levels in terms of surgery type. When examined for complications in the induction, extubation period, and postoperative recovery period, there was a significant difference identified between 25OHD vitamin levels and these complications (P < 0.01). CONCLUSIONS: This research observed that patients with low preoperative 25OHD vitamin levels encountered respiratory complications related to general anesthesia more often. Especially, in the early postoperative period, there is a very significant difference between complications and low 25OHD vitamin levels.

Microbial dynamics in anaerobic digestion reactors for treating organic urban residues during the start-up process.

Anaerobic digestion of organic residues offers economic benefits via biogas production, still methane (CH4 ) yield relies on the development of a robust microbial consortia for adequate substrate degradation, among other factors. In this study, we monitor biogas production and changes in the microbial community composition in two semi-continuous stirred tank reactors during the setting process under mesophilic conditions (35°C) using a 16S rDNA high-throughput sequencing method. Reactors were initially inoculated with anaerobic granular sludge from a brewery wastewater treatment plant, and gradually fed organic urban residues (4·0 kg VS m-3  day-1 ) . The inocula and biomass samples showed changes related to adaptations of the community to urban organic wastes including a higher relative proportion of Clostridiales, with Ruminococcus spp. and Syntrophomonas spp. as recurrent species. Candidatus Cloacamonas spp. (Spirochaetes) also increased from ~2·2% in the inoculum to >10% in the reactor biomass. The new community consolidated the cellulose degradation and the propionate and amino acids fermentation processes. Acetoclastic methanogens were more abundant in the reactor, where Methanosaeta spp. was found as a key player. This study demonstrates a successful use of brewery treatment plant granular sludge to obtain a robust consortium for methane production from urban organic solid waste in Mexico. SIGNIFICANCE AND IMPACT OF THE STUDY: This study describes the selection of relevant bacteria and archaea in anaerobic digesters inoculated with anaerobic granular sludge from a brewery wastewater treatment plant. Generally, these sludge granules are used to inoculate reactors digesting organic urban wastes. Though, it is still not clearly understood how micro-organisms respond to substrate variations during the reactor start-up process. After feeding two reactors with organic urban residues, it was found that a broader potential for cellulose degradation was developed including Bacteroidetes, Firmicutes and Spirochaetes. These results clarify the bacterial processes behind new reactors establishment for treating organic wastes in urban areas.

Filling of charged cylindrical capillaries.

We provide an analytical model to describe the filling dynamics of horizontal cylindrical capillaries having charged walls. The presence of surface charge leads to two distinct effects: It leads to a retarding electrical force on the liquid column and also causes a reduced viscous drag force because of decreased velocity gradients at the wall. Both these effects essentially stem from the spontaneous formation of an electric double layer (EDL) and the resulting streaming potential caused by the net capillary-flow-driven advection of ionic species within the EDL. Our results demonstrate that filling of charged capillaries also exhibits the well-known linear and Washburn regimes witnessed for uncharged capillaries, although the filling rate is always lower than that of the uncharged capillary. We attribute this to a competitive success of the lowering of the driving forces (because of electroviscous effects), in comparison to the effect of weaker drag forces. We further reveal that the time at which the transition between the linear and the Washburn regime occurs may become significantly altered with the introduction of surface charges, thereby altering the resultant capillary dynamics in a rather intricate manner.

Translation and validation of the Turkish version of the Ankylosing Spondylitis Quality of Life (ASQOL) questionnaire.

The Ankylosing Spondylitis Quality of Life (ASQoL) questionnaire is a disease-specific measure of needs-based quality of life developed in the UK and the Netherlands. This study describes translation, validation, and reliability of the scale into Turkish population. The ASQoL was translated into Turkish using the dual-panel process. Content validity was assessed via cognitive debriefing interviews with ankylosing spondylitis (AS) patients. Patients with AS according to modified New York criteria were recruited into the study from 12 hospitals of all part of Turkey. Psychometric and scaling properties were assessed via a two administration survey involving the ASQoL, the Nottingham Health Profile (NHP), Bath AS Functional Index (BASFI), and Bath AS Disease Activity Index (BASDAI). Classical psychometrics assessed reliability, convergent validity (correlation of ASQoL with NHP, BASFI, and BASDAI) and discriminative validity (correlation of ASQoL with perceived AS-severity and general health). Cognitive debriefing showed the new Turkish ASQoL to be clear, relevant, and comprehensive. Completed survey questionnaires were received from 277 AS patients (80% Male, mean age 42.2/SD 11.6, mean AS duration 9.4 years/SD 9.4). Test-retest reliability was excellent (0.96), indicating low random measurement error for the scale. Correlations of ASQoL with NHP sections were low to moderate (NHP Sleep 0.34; NHP Emotional Reactions 0.83) suggesting the measures assess related but distinct constructs. The measure was able to discriminate between patients based on their perceived disease severity (p < 0.0001) and self-reported general health (p < 0.0001). The Turkish version of ASQoL has good reliability and validity properties. It is practical and useful scale to assess the quality of life in AS patients in Turkish population.

Wafer-scale thin encapsulated two-dimensional nanochannels and its application toward visualization of single molecules.

We present a new and simple approach to fabricate wafer-scale, thin encapsulated, two-dimensional nanochannels by using conventional surface-micromachining technology and thin-film evaporation. The key steps to the realization of two-dimensional nanochannels are a fine etching of a sacrificial layer to create underetching spaces at the nanometer regime, and an accurate thin-film evaporation for encapsulation. Well-defined cross-sectional, encapsulated nanochannel arrays with dimensions as small as 20 nm in both width and height have been realized at the wafer-scale. The fabricated nanochannels with a channel length of 10mm have been used as a suitable fluidic platform for confining a solution containing nanomolar concentrations of Alexa fluorescent molecules. Initial results toward visualization of single Alexa molecules in the confined solution are reported.

Analysis of single quantum-dot mobility inside 1D nanochannel devices.

We visualized individual quantum dots using a combination of a confining nanochannel and an ultra-sensitive microscope system, equipped with a high numerical aperture lens and a highly sensitive camera. The diffusion coefficients of the confined quantum dots were determined from the experimentally recorded trajectories according to the classical diffusion theory for Brownian motion in two dimensions. The calculated diffusion coefficients were three times smaller than those in bulk solution. These observations confirm and extend the results of Eichmann et al (2008 Langmuir 24 714-21) to smaller particle diameters and more narrow confinement. A detailed analysis shows that the observed reduction in mobility cannot be explained by conventional hydrodynamic theory.

Chemically anisotropic single-crystalline silicon nanotetrahedra.

We describe a method based on silicon micromachining to machine single-crystalline silicon nanoparticles bounded by (111) faces in the form of tetrahedra. The technology allows the fabrication of tetrahedra in a size range from 20 to 1000 nm side length, and gives the possibility to chemically modify sites (faces, edges and/or tips) within certain limits. The chemical modification is anticipated to facilitate the self-assembly into new supermaterials such as photonic crystals in the diamond lattice.

Transition flow through an ultra-thin nanosieve.

The fabrication and gas flow characterization of an ultra-thin inorganic nanosieve structured by interference lithography and a bond-micromachining approach are reported. The nanosieve has been observed to exhibit transition gas flow behaviour around atmospheric pressure and ambient temperature. The small lip thickness (45 nm) of the nanopores with respect to their diameter (120 nm) helps in understanding pure transition flow by minimizing interactions between the molecule and inner pore wall. Due to the absence of these collisions, the transition flux is the superimposition of viscous and molecular fluxes without the need for higher-order slip correction. The nanosieve shows a flow selectivity of 3.1 between helium and argon at 20 mbar.

Formation of liquid menisci in flexible nanochannels.

In this paper we analyze the characteristic shape of the liquid meniscus at the fluid air interface in nanochannels of less than 80 nm height capped by a flexible membrane. Because of the induced negative pressure difference between the liquid pressure and the pressure outside, the 0.18 microm thin membrane on top of the channels bends downward. This elastocapillary equilibrium between the surface tension of the wetting liquid and the mechanical forces in the capillary results in a very peculiar shape of the interfacial meniscus, visible from the top through the transparent membrane. For increasing deflection of the membrane, the meniscus is seen to protrude along the channel and its curvature changes from concave to convex in the center. We present an analytical model to describe the meniscus shape in the deformed channel for small membrane deflections. We also show that the protrusion length of the meniscus, which can be measured easily, is an accurate and useful indicator for the membrane deflection. Experimental results on nanochannels filled with ethanol and water are presented and the observed menisci are seen to be in good agreement with the proposed model.

Investigation of variations in microbial diversity in anaerobic reactors treating landfill leachate.

A young landfill leachate containing elevated total ammonia concentrations frequently as high as 2,700 mg/l was anaerobically treated for 1,015 days in two different laboratory-scale anaerobic reactors configured as sludge blanket and hybrid bed. In this paper, the last 265 days of this long-term anaerobic treatability study are presented. Effects of high ammonia concentrations on reactor performances were correlated to the variations in microbial diversity by identifying the dominant microorganisms with FISH (fluorescent in-situ hybridization), cloning, DGGE (denaturing gradient gel electrophoresis) and morphological analysis. The results have indicated that the high ammonia landfill leachate can be treated successfully by using either an UASB or a hybrid bed reactor if temporary pH adjustments in the reactor influents are made when high ammonia concentrations are experienced. Consequently, COD removal efficiency is independent of microbial diversity and reactor configuration and it depends on the biodegradable portion of the leachate. Under this circumstance, stability of the reactors with low levels of acetate was supported by the abundance of Methanosaeta population. In both of the reactors, some populations of Methanobacteriaceae were also detected while other methanogenic species were virtually absent. However, after the termination of pH adjustment at Day 860, reactors immediately became unstable due to the sudden increase in free ammonia concentration up to 400 mg/l. COD removal efficiency decreased to 42% in the hybrid bed and to 48% in the UASB reactor. The durations of inhibitions were not long enough to severely deteriorate the massive Methanosaeta cells; therefore, many of them were again identified after two free ammonia inhibitions. However, subsequently, long filamentous morphologies of Methanosaeta cells shifted to shorter filaments and they lost their aggregating property.

Nanofluidic bubble pump using surface tension directed gas injection.

A new concept for liquid manipulation has been developed and implemented in surface-micromachined fluid channels. It is based on the surface tension directed injection of a gas into the liquid flow through micrometer-sized holes in the microchannel wall. The injected gas is directed to an exhaust by a cross-sectional asymmetry of the microchannel and thereby moves minute liquid volumes. Successful pumping experiments were performed with single stroke volumes of tens of picoliters at frequencies around 1 Hz. The minimum actuation pressure is 0.6 bar for a 2-microm channel height, in accordance with theoretical predictions.

Hand orthosis as a writing aid in writer's cramp.

Writer's cramp is a focal, task-specific dystonia of the hand and wrist. It primarily affects people who do a significant amount of writing, and causes difficulties in writing. We present five cases with writer's cramp who showed improvement in their writing ability with an applied hand orthosis.

Effects of electrode geometry and combination on nerve fibre selectivity in spinal cord stimulation.

The differential effects of the geometry of a rostrocaudal array of electrode contacts on dorsal column fibre and dorsal root fibre activation in spinal cord stimulation are analysed theoretically. 3-D models of the mid-cervical and mid-thoracic vertebral areas are used for the computation of stimulation induced field potentials, whereas a cable model of myelinated nerve fibre is used for the calculation of the excitation thresholds of large dorsal column and dorsal root fibres. The size and spacing of 2-D rectangular electrode contacts are varied while mono-, bi- and tripolar stimulation are applied. The model predicts that the highest preferential stimulation of dorsal root fibres is obtained in monopolar stimulation with a large cathode, whereas dorsal column fibre preference is highest in tripolar stimulation with small contacts and small contact spacings. Fibre type preference is most sensitive to variations of rostrocaudal contact size and least sensitive to variations of lateral contact size. Dorsal root fibre preference is increased and sensitivity to lead geometry is reduced as the distance from contacts to spinal cord is increased.