Novel evaluation of upper-limb motor performance after stroke based on normal reaching movement model.

BACKGROUND: Upper-limb rehabilitation robots provide repetitive reaching movement training to post-stroke patients. Beyond a pre-determined set of movements, a robot-aided training protocol requires optimization to account for the individuals' unique motor characteristics. Therefore, an objective evaluation method should consider the pre-stroke motor performance of the affected arm to compare one's performance relative to normalcy. However, no study has attempted to evaluate performance based on an individual's normal performance. Herein, we present a novel method for evaluating upper limb motor performance after a stroke based on a normal reaching movement model. METHODS: To represent the normal reaching performance of individuals, we opted for three candidate models: (1) Fitts' law for the speed-accuracy relationship, (2) the Almanji model for the mouse-pointing task of cerebral palsy, and (3) our proposed model. We first obtained the kinematic data of healthy (n = 12) and post-stroke (n = 7) subjects with a robot to validate the model and evaluation method and conducted a pilot study with a group of post-stroke patients (n = 12) in a clinical setting. Using the models obtained from the reaching performance of the less-affected arm, we predicted the patients' normal reaching performance to set the standard for evaluating the affected arm. RESULTS: We verified that the proposed normal reaching model identifies the reaching of all healthy (n = 12) and less-affected arm (n = 19; 16 of them showed an R2 > 0.7) but did not identify erroneous reaching of the affected arm. Furthermore, our evaluation method intuitively and visually demonstrated the unique motor characteristics of the affected arms. CONCLUSIONS: The proposed method can be used to evaluate an individual's reaching characteristics based on an individuals normal reaching model. It has the potential to provide individualized training by prioritizing a set of reaching movements.

De novo assembly and phasing of a Korean human genome.

Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing, next-generation mapping, microfluidics-based linked reads, and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17.9 Mb and a scaffold N50 size of 44.8 Mb, resolving 8 chromosomal arms into single scaffolds. The de novo assembly, along with local assemblies and spanning long reads, closes 105 and extends into 72 out of 190 euchromatic gaps in the reference genome, adding 1.03 Mb of previously intractable sequence. High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides strong support for the robustness of the assembly. We identify 18,210 structural variants by direct comparison of the assembly with the human reference, identifying thousands of breakpoints that, to our knowledge, have not been reported before. Many of the insertions are reflected in the transcriptome and are shared across the Asian population. We performed haplotype phasing of the assembly with short reads, long reads and linked reads from whole-genome sequencing and with short reads from 31,719 BAC clones, thereby achieving phased blocks with an N50 size of 11.6 Mb. Haplotigs assembled from single-molecule real-time reads assigned to haplotypes on phased blocks covered 89% of genes. The haplotigs accurately characterized the hypervariable major histocompatability complex region as well as demonstrating allele configuration in clinically relevant genes such as CYP2D6. This work presents the most contiguous diploid human genome assembly so far, with extensive investigation of unreported and Asian-specific structural variants, and high-quality haplotyping of clinically relevant alleles for precision medicine.

Dynamic Control of Nanocavities with Tunable Metal Oxides.

Fabry-Pérot metal-insulator-metal (MIM) nanocavities are widely used in nanophotonic applications due to their extraordinary electromagnetic properties and deeply subwavelength dimensions. However, the spectral response of nanocavities is usually controlled by the spatial separation between the two reflecting mirrors and the spacer's refractive index. Here, we demonstrate static and dynamic control of Fabry-Pérot nanocavities by inserting a plasmonic metasurface, as a passive element, and a gallium doped-zinc oxide (Ga:ZnO) layer as a dynamically tunable component within the nanocavities' spacer. Specifically, by changing the design of the silver (Ag) metasurface one can "statically" tailor the nanocavity response, tuning the resonance up to 200 nm. To achieve the dynamic tuning, we utilize the large nonlinear response of the Ga:ZnO layer near the epsilon near zero wavelength to enable effective subpicosecond (<400 fs) optical modulation (80%) at reasonably low pump fluence levels (9 mJ/cm2). We demonstrate a 15 nm red shift of a near-infrared Fabry-Pérot resonance (λ ≅ 1.16 µm) by using a degenerate pump probe technique. We also study the carrier dynamics of Ga:ZnO under intraband photoexcitation via the electronic band structure calculated from first-principles density functional method. This work provides a versatile approach to design metal nanocavities by utilizing both the phase variation with plasmonic metasurfaces and the strong nonlinear response of metal oxides. Tailorable and dynamically controlled nanocavities could pave the way to the development of the next generation of ultrafast nanophotonic devices.

Generation of Nanoparticles from Friction between Railway Brake Disks and Pads.

In this study, we measured the size distribution of particles ranging in size from 5.6 to 560 nm that were emitted between brake disks and pads under various braking conditions to observe and analyze changes to the resulting particle size distribution over braking time. A peak of 178-275 nm (200 nm peak) was observed in all braking conditions. However, the generation of spherical particles of a 10 nm range was observed only when the disk speed and brake force were above certain levels and intensified only when speed and brake force further increased. The total number concentration of ultrafine particles (no larger than 0.1 µm; PM0.1) generated was found to correlate with disk speed and brake force. Thus, the generation of nanoparticles resulting from disk speed and brake force was attributable primarily to increases in the contact surface temperature. The critical temperature for the generation of nanoparticles of a 10 nm range was found to be about 70 °C, which is the average temperature between the surface and the inside of the disk. If the speed or brake force was higher, that is, the temperature of the contact surface reached a certain level, evaporation and condensation took place. Vapor then left the friction surface, met with the air, and quickly cooled to form nanoparticles through nucleation. When the newly generated particles became highly concentrated, they grew through coagulation to form agglomerates or the vapor condensed directly onto the surface of existing particles of about 200 nm (formed by mechanical friction).

Functional identification of oleate 12-desaturase and ω-3 fatty acid desaturase genes from Perilla frutescens var. frutescens.

KEY MESSAGE: We described identification, expression, subcellular localization, and functions of genes that encode fatty acid desaturase enzymes in Perilla frutescens var. frutescens. Perilla (Perilla frutescens var. frutescens) seeds contain approximately 40 % of oil, of which α-linolenic acid (18:3) comprise more than 60 % in seed oil and 56 % of total fatty acids (FAs) in leaf, respectively. In perilla, endoplasmic reticulum (ER)-localized and chloroplast-localized ω-3 FA desaturase genes (PfrFAD3 and PfrFAD7, respectively) have already been reported, however, microsomal oleate 12-desaturase gene (PfrFAD2) has not yet. Here, four perilla FA desaturase genes, PfrFAD2-1, PfrFAD2-2, PfrFAD3-2 and PfrFAD7-2, were newly identified and characterized using random amplification of complementary DNA ends and sequence data from RNAseq analysis, respectively. According to the data of transcriptome and gene cloning, perilla expresses two PfrFAD2 and PfrFAD3 genes, respectively, coding for proteins that possess three histidine boxes, transmembrane domains, and an ER retrieval motif at its C-terminal, and two chloroplast-localized ω-3 FA desaturase genes, PfrFAD7-1 and PfrFAD7-2. Arabidopsis protoplasts transformed with perilla genes fused to green fluorescence protein gene demonstrated that PfrFAD2-1 and PfrFAD3-2 were localized in the ER, and PfrFAD7-1 and PfrFAD7-2 were localized in the chloroplasts. PfrFAD2 and perilla ω-3 FA desaturases were functional in budding yeast (Saccharomyces cerevisiae) indicated by the presence of 18:2 and 16:2 in yeast harboring the PfrFAD2 gene. 18:2 supplementation of yeast harboring ω-3 FA desaturase gene led to the production of 18:3. Therefore, perilla expresses two functional FAD2 and FAD3 genes, and two chloroplast-localized ω-3 FA desaturase genes, which support an evidence that P. frutescens cultivar is allotetraploid plant.

Coexpression of multiple genes reconstitutes two pathways of very long-chain polyunsaturated fatty acid biosynthesis in Pichia pastoris.

The introduction of novel traits to cells often requires the stable coexpression of multiple genes within the same cell. Herein, we report that C22 very long-chain polyunsaturated fatty acids (VLC-PUFAs) were synthesized from C18 precursors by reactions catalyzed by delta 6-desaturase, an ELOVL5 involved in VLC-PUFA elongation, and delta 5-desaturase. The coexpression of McD6DES, AsELOVL5, and PtD5DES encoding the corresponding enzymes, produced docosatetraenoic acid (C22:4 n-6) and docosapentaenoic acid (C22:5 n-3), as well as arachidonic acid (C20:4 n-6) and eicosapentaenoic acid (C20:5 n-3) in the methylotrophic yeast Pichia pastoris. The expression of each gene increased within 24 h, with high transcript levels after induction with 0.5 or 1 % methanol. High levels of the newly expressed VLC-PUFAs occurred after 144 h. This expression system exemplifies the recent progress and future possibilities of the metabolic engineering of VLC-PUFAs in oilseed crops.

Identification and functional characterization of polyunsaturated fatty acid elongase (McELOVL5) gene from pike eel (Muraenesox cinereus).

The cDNA coding for a polyunsaturated fatty acid elongase (McELOVL5) was isolated from the brain of the pike eel (Muraenesox cinereus) being based on available sequences in 23 types of fish. Four sequence variants were identified with different amino acid substitutions as compared with two clones of McELOVL5 gene (McELOVL5 11.7 and McELOVL5 12.4). When the two variants of McELOVL5 were expressed in Saccharomyces cerevisiae, the two recombinant yeasts elongated γ-linolenic acid (GLA, 18:3n-6) to di-homo-γ-linolenic acid (DGLA, 20:3n-6) but differed in the rate of GLA conversion to DGLA. Cells transformed with McELOVL5 12.4 also converted arachidonic acid (20:4n-6) and eicosapentaenoic acid (20:5n-3) to docosatetraenoic acid (22:4n-6) and docosapentaenoic acid (22:5n-3), respectively. However McELOVL5 11.7 lost its function for the elongation of C20 fatty acids. The four sequence variants have changed substrate specificities. Three-dimensional models of the McELOVL5 proteins are suggested.

Perovskite Lanthanum-Doped Barium Stannate: A Refractory Near-Zero-Index Material for High-Temperature Energy Harvesting Systems.

The recent interests in bridging intriguing optical phenomena and thermal energy management has led to the demonstration of controlling thermal radiation with epsilon-near-zero (ENZ) and the related near-zero-index (NZI) optical media. In particular, the manipulation of thermal emission using phononic ENZ and NZI materials has shown promise in mid-infrared radiative cooling systems operating under low-temperature environments (below 100 °C). However, the absence of NZI materials capable of withstanding high temperatures has limited the spectral extension of these advanced technologies to the near-infrared (NIR) regime. Herein, a perovskite conducting oxide, lanthanum-doped barium stannate (La:BaSnO3 [LBSO]), as a refractory NZI material well suited for engineering NIR thermal emission is proposed. This work focuses on the experimental demonstration of superior high-temperature stability (of at least 1000 °C) of LBSO films in air and its durability under intense UV-pulsed laser irradiation below peak power of 9 MW cm-2 . Based on the low optical-loss in LBSO, a selective narrow-band thermal emission utilizing a metal-insulator-metal (MIM) Fabry-Pérot nanocavity consisting of LBSO films as metallic component is demonstrated. This study shows that LBSO is an ideal candidate as a refractory NZI component for thermal energy conversion operating at high temperatures in air and under strong light irradiations.

A robotic treadmill system to mimic overground walking training with body weight support.

Introduction: Body weight support overground walking training (BWSOWT) is widely used in gait rehabilitation. However, existing systems require large workspace, complex structure, and substantial installation cost for the actuator, which make those systems inappropriate for the clinical environment. For wide clinical use, the proposed system is based on a self-paced treadmill, and uses an optimized body weight support with frame-based two-wire mechanism. Method: The Interactive treadmill was used to mimic overground walking. We opted the conventional DC motors to partially unload the body weight and modified pelvic type harness to allow natural pelvic motion. The performance of the proposed system on the measurement of anterior/posterior position, force control, and pelvic motion was evaluated with 8 healthy subjects during walking training. Results: We verified that the proposed system was the cost/space-effective and showed the more accurate anterior/posterior position than motion sensor, comparable force control performance, and natural pelvic motion. Discussion: The proposed system is cost/space effective, and able to mimic overground walking training with body weight support. In future work, we will improve the force control performance and optimize the training protocol for wide clinical use.

ZIF-L to ZIF-8 Transformation: Morphology and Structure Controls.

The control of the structure, shape, and components of metal-organic frameworks, in which metal ions and organic ligands coordinate to form crystalline nanopore structures, plays an important role in the use of many electrochemical applications, such as energy storage, high-performance photovoltaic devices, and supercapacitors. In this study, systematic controls of synthesis variables were performed to control the morphology of ZIF-8 during the ZIF-L-to-ZIF-8 transformation of ZIF-L, which has the same building block as ZIF-8 but forms a two-dimensional structure. Furthermore, additional precursors or surfactants (Zn2+, 2mIm, and CTAB) were introduced during the transition to determine whether the alteration could be regulated. Lastly, the partial substitution insertion of a new organic precursor, 2abIm, during the ZIF-L-to-ZIF-8 transformation of ZIF-L was achieved, and modulation of the adsorption and pore characteristics (suppression of gate-opening properties of ZIF-8) has been confirmed.

An EEG-based asynchronous MI-BCI system to reduce false positives with a small number of channels for neurorehabilitation: A pilot study.

Many studies have used motor imagery-based brain-computer interface (MI-BCI) systems for stroke rehabilitation to induce brain plasticity. However, they mainly focused on detecting motor imagery but did not consider the effect of false positive (FP) detection. The FP could be a threat to patients with stroke as it can induce wrong-directed brain plasticity that would result in adverse effects. In this study, we proposed a rehabilitative MI-BCI system that focuses on rejecting the FP. To this end, we first identified numerous electroencephalogram (EEG) signals as the causes of the FP, and based on the characteristics of the signals, we designed a novel two-phase classifier using a small number of EEG channels, including the source of the FP. Through experiments with eight healthy participants and nine patients with stroke, our proposed MI-BCI system showed 71.76% selectivity and 13.70% FP rate by using only four EEG channels in the patient group with stroke. Moreover, our system can compensate for day-to-day variations for prolonged session intervals by recalibration. The results suggest that our proposed system, a practical approach for the clinical setting, could improve the therapeutic effect of MI-BCI by reducing the adverse effect of the FP.

Facile Fabrication of α-Alumina Hollow Fiber-Supported ZIF-8 Membrane Module and Impurity Effects on Propylene Separation Performance.

The separation of C3 olefin and paraffin, which is essential for the production of propylene, can be facilitated by the ZIF-8 membrane. However, the commercial application of the membrane has not yet been achieved because the fabrication process does not meet industrial regulatory criteria. In this work, we provide a straightforward and cost-effective membrane fabrication technique that permits the rapid synthesis of ZIF-8 hollow fiber membranes. The scalability of the technology was confirmed by the incorporation of three ZIF-8 hollow fiber membranes into a single module using an introduced fiber mounting methodology. The molecular sieving characteristics of the ZIF-8 membrane module on a binary combination of C3 olefin and paraffin (C3H6/C3H8 selectivity of 110 and a C3H6 permeance of 13 GPU) were examined at atmospheric conditions. In addition, the high-pressure performance of these membranes was demonstrated at a 5 bar of equimolar binary feed pressure with a C3H6/C3H8 selectivity of 55 and a C3H6 permeance of 9 GPU due to propylene adsorption site saturation. To further accurately portray the separation performance of the membrane on an actual industrial feed, the effect of impurities (ethylene, ethane, butylene, i-butane, and n-butane), which can be found in C3 splitters, was investigated and a considerable decrement (~15%) in the propylene permeance upon an interaction with C4 hydrocarbons was confirmed. Finally, the long-term stability of the ZIF-8 membrane was confirmed by continuous operation for almost a month without any loss of its initial performance (C3H6/C3H8 separation factor of 110 and a C3H6 permeance of 13 GPU). From an industrial point of view, this straightforward technique could offer a number of merits such as a short synthesis time, minimal chemical requirements, and excellent reproductivity.

Controlling of lattice strains for crack-free and strong ferroelectric barium titanate films by post-thermal treatment.

In this study, we experimentally demonstrate fabrication of ultra-smooth and crystalline barium titanate (BTO) films on magnesium oxide (MgO) substrates by engineering lattice strain and crystal structure via thermal treatment. We observe that oxygen-depleted deposition allows growth of highly strained BTO films on MgO substrates with crack-free surface. In addition, post-thermal treatment relaxes strain, resulting in an enhancement of ferroelectricity. Surface roughening of the BTO films caused by recrystallization during post-thermal treatment is controlled by chemical-mechanical polishing (CMP) to retain their initial ultra-smooth surfaces. From Raman spectroscopy, reciprocal space map (RSM), and capacitance-voltage (C-V) curve measurements, we confirm that the ferroelectricity of BTO films strongly depend on the relaxation of lattice strain and the phase transition from a-axis to c-axis oriented crystal structure.

Genome sequencing in microfabricated high-density picolitre reactors.

The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, in one four-hour run. To achieve an approximately 100-fold increase in throughput over current Sanger sequencing technology, we have developed an emulsion method for DNA amplification and an instrument for sequencing by synthesis using a pyrosequencing protocol optimized for solid support and picolitre-scale volumes. Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine.

Toward Comparison of Cortical Activation with Different Motor Learning Methods Using Event-Related Design: EEG-fNIRS Study.

Recently, motor imagery brain-computer interface (MI-BCI) has been studied as a motor learning method and evaluated by comparing with conventional passive and active training. Most functional near-infrared spectroscopy (fNIRS) studies adopted block design for comparing those motor learning methods, including MI-BCI. Compared to the block design, event-related design would be more appropriate for estimating cortical activation in MI-BCI which provides feedback for each trial. This paper is a preliminary study to check the feasibility whether event-related design can be applicable for MI-BCI. To this end, three different motor learning methods involving MI-BCI were compared. In hemodynamic response, MI-BCI showed significantly stronger cortical activation than passive training (PT), and weaker than active training (AT), which conforms most existing studies. The results demonstrate that event-related design could be applied to investigate cortical effects of MI-BCI and comparing hemodynamic responses of different motor learning methods.

A two-wire body weight support system for interactive treadmill.

Body weight support (BWS) system is widely used for patients to help their gait training. However, that existing systems require large workspace and elastic component in actuation makes the systems inappropriate for wide clinical use. The interactive treadmill was reported to be cost/space effectively simulate overground walking, but there was no suitable BWS system for the treadmill. We proposed a new concept of body weight support system for interactive treadmill. For wide clinical use, we applied a two-wire driven mechanism with simple actuator and a custom pelvic-type harness. With three healthy subjects, the performance of the proposed BWS system on unloading force control was evaluated, and the result showed that the feasibility of the proposed BWS system.

Interfacial Defect-Mediated Near-Infrared Silicon Photodetection with Metal Oxides.

Due to recent breakthroughs in silicon photonics, sub-band-gap photodetection in silicon (Si) has become vital to the development of next-generation integrated photonic devices for telecommunication systems. In particular, photodetection in Si using complementary metal-oxide semiconductor (CMOS) compatible materials is in high demand for cost-effective integration. Here, we achieve broad-band near-infrared photodetection in Si/metal-oxide Schottky junctions where the photocurrent is generated from interface defects induced by aluminum-doped zinc oxide (AZO) films deposited on a Si substrate. The combination of photoexcited carrier generation from both interface defect states and intrinsic Si bulk defect states contributes to a photoresponse of 1 mA/W at 1325 nm and 0.22 mA/W at 1550 nm with zero-biasing. From a fit to the Fowler equation for photoemission, we quantitatively determine the individual contributions from these effects. Finally, using this analysis, we demonstrate a gold-nanoparticle-coated photodiode that has three distinct photocurrent responses resulting from hot carriers in the gold, interface defects from the AZO, and bulk defects within the Si. The hot carrier response is found to dominate near the band gap of Si, while the interface defects dominate for longer wavelengths.

P-TEFb Regulates Transcriptional Activation in Non-coding RNA Genes.

Many non-coding RNAs (ncRNAs) serve as regulatory molecules in various physiological pathways, including gene expression in mammalian cells. Distinct from protein-coding RNA expression, ncRNA expression is regulated solely by transcription and RNA processing/stability. It is thus important to understand transcriptional regulation in ncRNA genes but is yet to be known completely. Previously, we identified that a subset of mammalian ncRNA genes is transcriptionally regulated by RNA polymerase II (Pol II) promoter-proximal pausing and in a tissue-specific manner. In this study, human ncRNA genes that are expressed in the early G1 phase, termed immediate early ncRNA genes, were monitored to assess the function of positive transcription elongation factor b (P-TEFb), a master Pol II pausing regulator for protein-coding genes, in ncRNA transcription. Our findings indicate that the expression of many ncRNA genes is induced in the G0-G1 transition and regulated by P-TEFb. Interestingly, a biphasic characteristic of P-TEFb-dependent transcription of serum responsive ncRNA genes was observed: Pol II carboxyl-terminal domain phosphorylated at serine 2 (S2) was largely increased in the transcription start site (TSS, -300 to +300) whereas overall, it was decreased in the gene body (GB, > +350) upon chemical inhibition of P-TEFb. In addition, the three representative, immediate early ncRNAs, whose expression is dependent on P-TEFb, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), nuclear enriched abundant transcript 1 (NEAT1), and X-inactive specific transcript (XIST), were further analyzed for determining P-TEFb association. Taken together, our data suggest that transcriptional activation of many human ncRNAs utilizes the pausing and releasing of Pol II, and that the regulatory mechanism of transcriptional elongation in these genes requires the function of P-TEFb. Furthermore, we propose that ncRNA and mRNA transcription are regulated by similar mechanisms while P-TEFb inhibition unexpectedly increases S2 Pol II phosphorylation in the TSSs in many ncRNA genes. One Sentence Summary: P-TEFb regulates Pol II phosphorylation for transcriptional activation in many stimulus-inducible ncRNA genes.

Phylogenetic relationships and biogeography of the Japanese clawed salamander, Onychodactylus japonicus (Amphibia: Caudata: Hynobiidae), and its congener inferred from the mitochondrial cytochrome b gene.

Using the mitochondrial cytochrome b gene, we investigated phylogenetic relationships between and within the Japanese clawed salamander, Onychodactylus japonicus, and its close continental relative O. fischeri. Monophyly of O. japonicus was well supported, and O. japonicus was clearly distinguished from O. fischeri. However, O. fischeri comprises genetically distinct populations from Russia, NE China, and Korea that do not form a monophyletic group. Within O. japonicus, four major clades were clearly recognized: Clade I from northern Tohoku district, Clade II from southern Tohoku district and the Tsukuba Mountains, Clade III from southwestern Honshu, and Clade IV from Kinki and Chugoku districts in Honshu and from Shikoku. Although genetic distances among these clades were large (5.5-9.6%), relationships among the clades were unresolved. All clades except Clade I contained two or three distinct subclades. In several localities in Kinki and Chugoku, Clades III and IV were sympatric. The estimated divergence times and available geohistorical data suggest that O. japonicus began to differentiate in the Upper Late Miocene and that the pattern of genetic differentiation of this species has been affected strongly by climate changes and geohistorical events such as volcanic activity and mountain formation. Our results suggest that both O. fischeri and O. japonicus comprise multiple cryptic species.

A risk-informed decision framework for setting environmental windows for dredging projects.

Sediment dredging is necessary to sustain navigation infrastructure in ports and harbor areas. In the United States alone between 250 and 300 million cubic yards of sediment are dredged annually. Dredging activities may cause stress on aquatic biota by locally increasing turbidity and suspended sediment concentrations, physically disturbing habitat by elevated sedimentation rates, interfering in migratory behaviors, and hydraulically entraining bottom dwelling organisms. Environmental windows are a management practice used to alleviate such stresses on resident and transient biota by placing temporal restrictions on the conduct of dredging operations. Adherence to environmental windows can significantly inflate costs for project sponsors and local stakeholders. Since their inception following passage of NEPA in 1969 the process for setting environmental windows has not followed structured procedures and represents an example of the difficulty inherent in achieving a balance between biological resource protection and cost-effective construction and maintenance of navigation infrastructure. Recent developments in the fields of risk assessment for non-chemical stressors as well as experience in implementing structured risk-informed decision-making tools for sediment and natural resource management are summarized in this paper in relation to setting environmental windows. Combining risk assessment and multi-criteria decision analysis allows development of a framework for an objective process consistent with recommendations by the National Academy of Sciences for setting environmental windows. A hypothetical application of the framework for protection of Pacific herring (Clupea pallasii) in San Francisco Bay is discussed.